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10 files match

access	all
accession	sc007RTW
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.481622
biosample_ancestry_population	asian
biosample_cell_type	alpha cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTW.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	34.4802
fastq_qual_type	sanger
file_id	136504
file_name	sc007RTW.fastq.gz
file_size	34862073
format	fastq
geo_sample	GSM2174425
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1007489
lab	quake
map_ratio	0.877812
map_to_ecoli	0.00003
map_to_fly	0.0372
map_to_mouse	0.53244
map_to_rat	0.57336
map_to_repeat	0.627648
map_to_ribosome	0.624512
map_to_worm	0.00102
map_to_yeast	0.03611
md5	007f0e0374f2237b3a3f8dc9a0ede049
meta	SRR3564753
ncbi_bio_sample	SAMN05161710
organ_anatomical_name	pancreas
output	reads
paired_end	2
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	172.614
paired_end_distance_min	65
paired_end_distance_std	45.2512
paired_end_mate	sc007RTV
pmid	28965763
read_size_max	65
read_size_mean	64.2566
read_size_min	30
read_size_std	1.83431
sample_label	22yr_male_cell2544
seq_depth	0.0183463
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564753.sra_2.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTV
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.480373
biosample_ancestry_population	asian
biosample_cell_type	alpha cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTV.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	35.155
fastq_qual_type	sanger
file_id	136503
file_name	sc007RTV.fastq.gz
file_size	32085088
format	fastq
geo_sample	GSM2174425
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1007489
lab	quake
map_ratio	0.904224
map_to_ecoli	0.00005
map_to_fly	0.03526
map_to_mouse	0.54678
map_to_rat	0.59173
map_to_repeat	0.637044
map_to_ribosome	0.633856
map_to_worm	0.00079
map_to_yeast	0.03367
md5	d81d61379b74c0c3cb40b60a78dc3f73
meta	SRR3564753
ncbi_bio_sample	SAMN05161710
organ_anatomical_name	pancreas
output	reads
paired_end	1
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	172.614
paired_end_distance_min	65
paired_end_distance_std	45.2512
paired_end_mate	sc007RTW
pmid	28965763
read_size_max	65
read_size_mean	64.3539
read_size_min	30
read_size_std	1.75596
sample_label	22yr_male_cell2544
seq_depth	0.0189195
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564753.sra_1.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTU
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.494883
biosample_ancestry_population	asian
biosample_cell_type	alpha cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTU.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	34.4738
fastq_qual_type	sanger
file_id	136502
file_name	sc007RTU.fastq.gz
file_size	52227452
format	fastq
geo_sample	GSM2174424
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1377153
lab	quake
map_ratio	0.81918
map_to_ecoli	0.00022
map_to_fly	0.02489
map_to_mouse	0.37684
map_to_rat	0.40448
map_to_repeat	0.443712
map_to_ribosome	0.439312
map_to_worm	0.0008
map_to_yeast	0.02429
md5	c829c87f81934c52d9b5a76990ead971
meta	SRR3564752
ncbi_bio_sample	SAMN05161709
organ_anatomical_name	pancreas
output	reads
paired_end	2
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	172.391
paired_end_distance_min	65
paired_end_distance_std	45.3672
paired_end_mate	sc007RTT
pmid	28965763
read_size_max	65
read_size_mean	64.2422
read_size_min	30
read_size_std	1.80617
sample_label	22yr_male_cell2543
seq_depth	0.0233998
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564752.sra_2.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTT
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.493456
biosample_ancestry_population	asian
biosample_cell_type	alpha cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTT.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	35.1484
fastq_qual_type	sanger
file_id	136501
file_name	sc007RTT.fastq.gz
file_size	48451437
format	fastq
geo_sample	GSM2174424
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1377153
lab	quake
map_ratio	0.845676
map_to_ecoli	0.0002
map_to_fly	0.02363
map_to_mouse	0.38931
map_to_rat	0.4189
map_to_repeat	0.451084
map_to_ribosome	0.446576
map_to_worm	0.00049
map_to_yeast	0.02358
md5	55ee9c522871101f3f10eef7ad5b9e65
meta	SRR3564752
ncbi_bio_sample	SAMN05161709
organ_anatomical_name	pancreas
output	reads
paired_end	1
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	172.391
paired_end_distance_min	65
paired_end_distance_std	45.3672
paired_end_mate	sc007RTU
pmid	28965763
read_size_max	65
read_size_mean	64.3366
read_size_min	30
read_size_std	1.73943
sample_label	22yr_male_cell2543
seq_depth	0.0241857
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564752.sra_1.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTS
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.477417
biosample_ancestry_population	asian
biosample_cell_type	mesenchymal cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTS.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	34.3206
fastq_qual_type	sanger
file_id	136500
file_name	sc007RTS.fastq.gz
file_size	47658800
format	fastq
geo_sample	GSM2174423
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1310145
lab	quake
map_ratio	0.84826
map_to_ecoli	0.00019
map_to_fly	0.02999
map_to_mouse	0.47974
map_to_rat	0.51672
map_to_repeat	0.565804
map_to_ribosome	0.5641
map_to_worm	0.00101
map_to_yeast	0.03093
md5	58f635d1ce521a96d5a235e7f27d4a4b
meta	SRR3564751
ncbi_bio_sample	SAMN05161708
organ_anatomical_name	pancreas
output	reads
paired_end	2
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	174.97
paired_end_distance_min	67
paired_end_distance_std	44.7513
paired_end_mate	sc007RTR
pmid	28965763
read_size_max	65
read_size_mean	64.2468
read_size_min	30
read_size_std	1.76215
sample_label	22yr_male_cell2542
seq_depth	0.0230524
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564751.sra_2.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTR
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.47643
biosample_ancestry_population	asian
biosample_cell_type	mesenchymal cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTR.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	35.1549
fastq_qual_type	sanger
file_id	136499
file_name	sc007RTR.fastq.gz
file_size	43420915
format	fastq
geo_sample	GSM2174423
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1310145
lab	quake
map_ratio	0.875832
map_to_ecoli	0.00021
map_to_fly	0.02912
map_to_mouse	0.49932
map_to_rat	0.53913
map_to_repeat	0.57578
map_to_ribosome	0.573968
map_to_worm	0.00063
map_to_yeast	0.03029
md5	dc38012920acd45e505b7ae10ef64ed3
meta	SRR3564751
ncbi_bio_sample	SAMN05161708
organ_anatomical_name	pancreas
output	reads
paired_end	1
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	174.97
paired_end_distance_min	67
paired_end_distance_std	44.7513
paired_end_mate	sc007RTS
pmid	28965763
read_size_max	65
read_size_mean	64.3602
read_size_min	30
read_size_std	1.67143
sample_label	22yr_male_cell2542
seq_depth	0.023833
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564751.sra_1.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTQ
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.533286
biosample_ancestry_population	asian
biosample_cell_type	beta cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTQ.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	34.5189
fastq_qual_type	sanger
file_id	136498
file_name	sc007RTQ.fastq.gz
file_size	49503587
format	fastq
geo_sample	GSM2174422
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1209846
lab	quake
map_ratio	0.774284
map_to_ecoli	0.00078
map_to_fly	0.00452
map_to_mouse	0.07198
map_to_rat	0.07639
map_to_repeat	0.083444
map_to_ribosome	0.078968
map_to_worm	0.00016
map_to_yeast	0.00394
md5	5290ab86dc03e6d3ba81a51598d32f11
meta	SRR3564750
ncbi_bio_sample	SAMN05161707
organ_anatomical_name	pancreas
output	reads
paired_end	2
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	167.413
paired_end_distance_min	65
paired_end_distance_std	46.1439
paired_end_mate	sc007RTP
pmid	28965763
read_size_max	65
read_size_mean	64.2062
read_size_min	30
read_size_std	1.98767
sample_label	22yr_male_cell2541
seq_depth	0.0194232
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564750.sra_2.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTP
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.532672
biosample_ancestry_population	asian
biosample_cell_type	beta cell
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTP.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	35.1976
fastq_qual_type	sanger
file_id	136497
file_name	sc007RTP.fastq.gz
file_size	46018787
format	fastq
geo_sample	GSM2174422
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1209846
lab	quake
map_ratio	0.796236
map_to_ecoli	0.00082
map_to_fly	0.00427
map_to_mouse	0.07383
map_to_rat	0.0785
map_to_repeat	0.084772
map_to_ribosome	0.08032
map_to_worm	0.00028
map_to_yeast	0.00429
md5	4300a5ea64f7cc184e842dac82a8d600
meta	SRR3564750
ncbi_bio_sample	SAMN05161707
organ_anatomical_name	pancreas
output	reads
paired_end	1
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	167.413
paired_end_distance_min	65
paired_end_distance_std	46.1439
paired_end_mate	sc007RTQ
pmid	28965763
read_size_max	65
read_size_mean	64.2983
read_size_min	30
read_size_std	1.91657
sample_label	22yr_male_cell2541
seq_depth	0.0199984
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564750.sra_1.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTO
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.501447
biosample_ancestry_population	asian
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTO.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	34.3575
fastq_qual_type	sanger
file_id	136496
file_name	sc007RTO.fastq.gz
file_size	59406268
format	fastq
geo_sample	GSM2174421
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1511137
lab	quake
map_ratio	0.62236
map_to_ecoli	0.00263
map_to_fly	0.01754
map_to_mouse	0.28116
map_to_rat	0.30374
map_to_repeat	0.32974
map_to_ribosome	0.329036
map_to_worm	0.00044
map_to_yeast	0.01805
md5	e2980cba245fb869c00a588828758020
meta	SRR3564749
ncbi_bio_sample	SAMN05161706
organ_anatomical_name	pancreas
output	reads
paired_end	2
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	171.145
paired_end_distance_min	65
paired_end_distance_std	44.6857
paired_end_mate	sc007RTN
pmid	28965763
read_size_max	65
read_size_mean	64.2038
read_size_min	30
read_size_std	1.91771
sample_label	22yr_male_cell2540
seq_depth	0.0195089
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564749.sra_2.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38

access	all
accession	sc007RTN
assay	sc-RNA-seq
assay_platform	Illumina NextSeq 500
at_ratio	0.498938
biosample_ancestry_population	asian
biosample_source_age_unit	year
biosample_source_age_value	22
biosample_source_gender	male
biosample_source_life_stage	postpartum
biosample_tissue_type	pancreatic islet
cdw_file_name	/data/cirm/cdw/2018/9/6/sc007RTN.fastq.gz
data_set_id	quakeAdultAgingPancreas1
enriched_in	exon
fastq_qual_mean	35.0291
fastq_qual_type	sanger
file_id	136495
file_name	sc007RTN.fastq.gz
file_size	55223673
format	fastq
geo_sample	GSM2174421
geo_series	GSE81547
GEO_Series_summary	As organisms biosample_source_age_value, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific biosample_source_age_value-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial biosample_source_age_value-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes.
item_count	1511137
lab	quake
map_ratio	0.642232
map_to_ecoli	0.00269
map_to_fly	0.01727
map_to_mouse	0.29137
map_to_rat	0.31517
map_to_repeat	0.335736
map_to_ribosome	0.334988
map_to_worm	0.00035
map_to_yeast	0.01774
md5	bb1d51f246c30034f4116decf63f8941
meta	SRR3564749
ncbi_bio_sample	SAMN05161706
organ_anatomical_name	pancreas
output	reads
paired_end	1
paired_end_concordance	1
paired_end_distance_max	250
paired_end_distance_mean	171.145
paired_end_distance_min	65
paired_end_distance_std	44.6857
paired_end_mate	sc007RTO
pmid	28965763
read_size_max	65
read_size_mean	64.263
read_size_min	30
read_size_std	1.97364
sample_label	22yr_male_cell2540
seq_depth	0.0201557
seq_library_prep	Smart-Seq2
single_cell	yes
species	Homo sapiens
submit_dir	/data/cirm/wrangle/quakeAdultAgingPancreas1
submit_file_name	raw/PRJNA322355/fastq/SRR3564749.sra_1.fastq.gz
submitter	martin enge
title	Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
ucsc_db	hg38