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| Status |
Public on Dec 21, 2010 |
| Title |
BFU-E_RNA-Seq |
| Sample type |
SRA |
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| Source name |
Fetal liver E13.5-14.5
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: E13.5-14.5
cell population: BFU-E
tissue: Fetal liver
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| 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.
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Hematopoietic
Paired End
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| 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)
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| Submission date |
Dec 15, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Whitehead Institute |
| E-mail(s) |
sgupta@wi.mit.edu
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| Phone |
617-324-0339
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| Organization name |
Whitehead Institute
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| Department |
Genome Technology Core
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| Street address |
9 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE26086 |
HIF-1synergizes with glucocorticoids to promote BFU-E progenitor self-renewal |
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| Relations |
| SRA |
SRX036984 |
| BioSample |
SAMN00189318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM640429_BFU-E_RPKM_mm9.txt.gz |
159.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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