|
| Status |
Public on Apr 09, 2019 |
| Title |
shStag2_1_Ery_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
shStag2 inducible shRNA in erythroid cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: HPC-7
cell type: Hematopoietic stem and progenitors
genotype: Ery_shStag2
|
| Treatment protocol |
72 hours knock-down induction with Doxycycline, followed by EPO-mediated differentiation (4 U/l EPO, 20 ng/ul SCF) for 48 hours
|
| Growth protocol |
Cells were grown in standard media with addition of 100 ng/ul murine recombinant SCF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per manufacturer’s protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA Seq pipeline: Rads were trimmed for adaptor sequence. Paired end reads were aligned to mm10 genome STAR version 2.4.0. To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated count files using HTSeq.
HTSeq count files for RNA Seq
Genome_build: mm10
|
| |
|
| Submission date |
Apr 08, 2019 |
| Last update date |
Jan 16, 2021 |
| Contact name |
Daniel Sasca |
| E-mail(s) |
danielsasca@gmail.com
|
| Organization name |
University Medical Center Mainz
|
| Department |
Department of Hematology and Oncology
|
| Street address |
Langenbeckstr 1
|
| City |
Mainz |
| ZIP/Postal code |
55131 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE129478 |
Cohesin-dependent regulation of dynamic gene expression during differentiation is lost in Cohesin-mutated myeloid malignancies |
|
| Relations |
| BioSample |
SAMN11359321 |
| SRA |
SRX5654327 |
