|
| Status |
Public on Sep 26, 2019 |
| Title |
Stag2KO_RM2_LinNeg |
| Sample type |
SRA |
| |
|
| Source name |
Stag2KO_LinNeg
|
| Organism |
Mus musculus |
| Characteristics |
cell type: lineage depleted bone marrow (LinNegBM)
genotype/variation: Stag2KO
|
| Growth protocol |
Whole BM was negatively selected for lineage markers using antibodies conjugated to magnetic beads and separated using EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by TRIzol extraction
RNA-sequencing libraries were generated by 3' sequencing and SMART-Seq2 amplification for GMP and CFU-E populations and by SMARTer amplification of full transcripts for LSK cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Stag2KO_RM2_LinNeg_IGO_07848_4_S62
|
| Data processing |
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.
|
| |
|
| Submission date |
Sep 25, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Richard Koche |
| E-mail(s) |
kocher@mskcc.org
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
417 E. 68th St.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE135031 |
Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control |
| GSE138007 |
Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [RNA_LinNegBM] |
|
| Relations |
| BioSample |
SAMN12842199 |
| SRA |
SRX6903150 |
