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Sample GSM640433 Query DataSets for GSM640433
Status Public on Dec 21, 2010
Title BFU-E_CD71_4h_Dexnegative_RNA-Seq
Sample type SRA
 
Source name Fetal liver E13.5-14.5
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: E13.5-14.5
cell population: BFU-E
agent: CD71_4h_Dexnegative
tissue: Fetal liver
Treatment protocol In experiments labelled " BFU-E (CD71) 4 h..." BFU-E cells were cultured 4 hours in serum free erythroid liquid expansion medium (SFELE), which consists of 100ng/mL rmSCF, 40ng/mL rmIGF-1 and 2U /mL rhEPO, in StemSpan® SFEM. After 4 hours 100nM Dexamethasone was added to half the cells and water to the other half. Total RNA was isolated after 4 additional hours of culture. In experimetns labelled " BFU-E (CD71, CD24a) 4 h..." BFU-E cells were cultured 4 hours in serum free erythroid liquid expansion medium (SFELE), which consists of 100ng/mL rmSCF, 40ng/mL rmIGF-1 and 2U /mL rhEPO, in StemSpan® SFEM. After 4 hours 100nM Dexamethasone and 333uM DMOG was added to 25% of the cells, 100nM Dexamethasone was added to 25% of the cells, 333uM DMOG was added to 25% of the cells and water to the other 25%. Total RNA was isolated after 4 additional hours of culture.
Growth protocol Fresh BFU-E, CFU-E and Ter119+ erythroblasts were purified from E 13.5-14.5 fetal liver by flow cytometry cell sorting. "Ter119+ erythroblasts" are positive for Ter119 and negative for kit. "CFU-E" cells are the 20% with highest expression of CD71 of cells that are negative for Ter119, B220, Mac-1, CD3, Gr-1, CD16/32 (FcgR), CD41 and CD34; and positive for kit. "BFU-E" cells are the 10% with lowest expression of CD71 of cells that are negative for Ter119, B220, Mac-1, CD3, Gr-1, CD16/32 (FcgR), CD41 and CD34; and positive for kit. In the experimetns labelled "BFU-E (CD71,CD24a)" BFU-E cells were purified from E 13.5-14.5 fetal liver by flow cytometry cell sorting."BFU-E" cells are the 10% with lowest expression of CD71 AND CD24a of cells that are negative for Ter119, B220, Mac-1, CD3, Gr-1, CD16/32 (FcgR), CD41 and CD34; and positive for kit.
Extracted molecule total RNA
Extraction protocol Samples for Paired-End mRNA-Seq were prepared using the Illumina kit according to the manufacturer’s instructions with the exception that we extracted 300bp bands, before and after the PCR step (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Hematopoietic
Paired End
Data processing Images acquired from the Solexa sequencer were processed through the bundled Solexa image extraction pipeline version 1.4. mRNA-Seq reads were aligned to mouse NCBI build 37 (mm9) using ELAND, Briefly, the first 32 bases of a read were used as a seed. Each matched seed was then extended up to 36 bases and scored to break any ties between multi-matches. All reads mapping to unique positions in the known transcriptome were counted to asign a count for each gene which where further normalized to gene length to get Reads Per Kb per Million (RPKM)
 
Submission date Dec 15, 2010
Last update date May 15, 2019
Contact name Whitehead Institute
E-mail(s) sgupta@wi.mit.edu
Phone 617-324-0339
Organization name Whitehead Institute
Department Genome Technology Core
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02141
Country USA
 
Platform ID GPL9250
Series (1)
GSE26086 HIF-1synergizes with glucocorticoids to promote BFU-E progenitor self-renewal
Relations
SRA SRX036988
BioSample SAMN00189322

Supplementary file Size Download File type/resource
GSM640433_BFU-E_CD71_4h_Dexnegative_RPKM_mm9.txt.gz 151.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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