JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Stem Cell Hub, California Institute for Regenerative Medicine CESCG at UC Santa Cruz

Return to all data sets

Analysis of erythroid maturation by RNAseq: collaboration between IGI (Berkeley) and CIRM-sponsored CESCG

Lab information [ Lab website | CIRM grants ]

Experimental design

Flowchart

Summary

A key goal of our participation in CESCG is to define genetic and epigenetic contributions to fetal globin expression in maturing red blood cells (erythrocytes). For this project, we are collaborating with David Martin and Dario Boffelli at Children’s Hospital Oakland Research Institute (CHORI).Over the past year and a half, our groups have pursued two primary lines of inquiry: first, characterization of isogenic clonal cell lines bearing mutations that cause disease (hemoglobinopathies: beta thalassemia major and sickle cell disease) and second generation of novel genotypes believed to alter globin expression based on observation of naturally occurring mutations associated with hereditary persistence of fetal hemoglobin. All cell lines were generated from an immortalized erythroblast cell line, HUDEP-2 cells, using CRISPR/Cas9, and a ssDNA HDR donor, for precise incorporation of disease mutations. These cell lines serve as a platform to explore cellular phenotypes of both healthy and diseased cells using RNAseq.

To perform RNAseq, we engaged with the team at CESCG to prepare libraries from these cell lines, and sequence them at high throughput. We are currently working with the bioinformatics team to analyze the data from these cells. From our collaborators, we already have some preliminary RNAseq data from the panel of disease-associated cell lines, and are validating hits using CRISPR-interference and siRNA knockdown. In the coming months, we will seek to merge and curate these datasets, which should provide a nice resource for researchers studying erythroid maturation in both healthy and diseased backgrounds. Surprisingly, curated databases of this sort do not exist yet.

Publications

Primary files

Lab analysis

Biomarkers, protocols, clustering or other supplementary files supplied by the lab

Secondary analysis

Expression Matrix (lab-generated) | Expression matrix (UCSC) | QC Metrics

CESCG Center Standard Analysis

FastQC | Picard | RSEM | STAR | bigWig

Tertiary analysis

Cell Browser

Sample Psychic

SCIMITAR

RIGGLE

SurfacePlots

JCVI BioMarkers


Return to all data sets