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| Status |
Public on Jun 27, 2016 |
| Title |
HSPC_rep3 |
| Sample type |
SRA |
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| Source name |
Human Stem and Progenitor Cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HSPC
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| Growth protocol |
To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668. Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured in StemSpan SF expansion medium (StemSpan 09650) with estradiol (100 ng/ml), dexamethasone (10 ng/ml), human transferrin (200 ng/ml), insulin (10 ng/ml), Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml) for 9 to 14 days. FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Qiagen RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.
Single end RNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Center for Genome Analysis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 genome using TopHat Version 2.0.4 software with default parameters
Reads in every gene were counted using htseq-count (http://www.ncbi.nlm.nih.gov/pubmed/25260700). Read counts per gene and log2 reads per kilobase per million reads were obtained using the edgeR package.
Genome_build: hg19
Supplementary_files_format_and_content: Counts per gene and log2 RPKM
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| Submission date |
Apr 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Vince Schulz |
| E-mail(s) |
vincent.schulz@yale.edu
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| Organization name |
Yale University
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| Department |
Department of Pediatrics
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| Lab |
Gallagher
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| Street address |
333 Cedar St. LMP 4085
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE67892 |
CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells [RNA-Seq] |
| GSE67893 |
CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells |
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| Relations |
| BioSample |
SAMN03483164 |
| SRA |
SRX995506 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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