|
| Status |
Public on Apr 09, 2019 |
| Title |
shStag2_2_HPC_Rad21_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
shStag2 inducible shRNA in HPC
|
| Organism |
Mus musculus |
| Characteristics |
cell line: HPC-7
cell type: Hematopoietic stem and progenitors
genotype: HPC_shStag2
|
| Treatment protocol |
72 hours knock-down induction with Doxycycline
|
| Growth protocol |
Cells were grown in standard media with addition of 100 ng/ul murine recombinant SCF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
x-linking was performed with 1% Formaldehyde. Lysates were clarified from sonicated nuclei and chromatin proteins were isolated with antibodies.
ChIP-Seq libraries were prepared for sequencing using a TruSeq ChIP Sample Prep Kit (Illumina) and standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ChIP antibody: Rad21 (Abcam, ab992)
|
| Data processing |
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped, deduplicated reads were retained and peaks were called using MACS2.
bedGraph files for ChIP Seq
Genome_build: mm10
|
| |
|
| Submission date |
Apr 08, 2019 |
| Last update date |
Jan 17, 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 |
SAMN11359372 |
| SRA |
SRX5654340 |
