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| Status |
Public on Nov 16, 2019 |
| Title |
AdultBlood-Rep1 (RNA-Seq) |
| Sample type |
SRA |
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| Source name |
CD34+ hematopoetic cells differentiated
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| Organism |
Homo sapiens |
| Characteristics |
developmental stage: adult
cell type: hematopoetic cells
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| Treatment protocol |
NA
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| Growth protocol |
CD34+ HSPCs from various stages were cultured in a three-stage erythroid differentiation culture system that we have previously described30. Briefly, the cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Life Technologies) containing 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 200 μg/mL human holo-transferrin, 3 U/mL heparin, and 10 μg/mL insulin (base medium). In Phase I (day 0-7), the cultures were supplemented with erythropoietin (EPO) (3 U/mL), stem cell factor (SCF) (10 ng/mL), and interleukin 3 (IL-3) (1 ng/mL), and in Phase II (day 7-12), they were supplemented with EPO and SCF alone. In Phase III (day 12 onwards), primary cell cultures contained 1mg/mL human holo-transferrin and were supplemented with EPO. Cell counts were measured either using a Beckman Coulter automated cell counter or manually with a hemocytometer. Cells were maintained between 105-106 cells per mL in Phases I and II, and at 106 cells per mL in Phase III. Cells were split into fresh culture medium every 3 days in this culture.
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| Extracted molecule |
total RNA |
| Extraction protocol |
NA
Illumina Truseq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ad1
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| Data processing |
Adapter sequences were trimmed from FASTQs using trimmomatic
Transcript pseudocounts were estimated using kallisto v0.4.4 for a 31-mer index built on hg19
TPM counts at the gene level were estimated using sleuth
Genome_build: hg19
Supplementary_files_format_and_content: TPM count estimates are assembled in a matrix
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| Submission date |
Aug 09, 2018 |
| Last update date |
Nov 16, 2019 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
[email protected]
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| Organization name |
Memorial Sloan Kettering
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| Street address |
417 E 68th St, Zuckerman - ZRC 1132
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE118358 |
Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation [RNA-Seq] |
| GSE118359 |
Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation |
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| Relations |
| BioSample |
SAMN09787617 |
| SRA |
SRX4524919 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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