 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 14, 2022 |
| Title |
msc_cardio_bio2_input |
| Sample type |
SRA |
| |
|
| Source name |
biopsy2_MSC from heart
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Heart
cell type: Heart derived mesenchymal stromal cells
antibody: None
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Cardiac mesenchymal stromal cells were obtained from the right ventricular free wall of cadaveric donors within 24 hours of death (accidental death, healthy subjects) by collagenase solution (collagenase NB4 mix in IMDM medium to obtain a final solution with a concentration of 3 mg/mL) treatment. The tissue was incubated for 1.5 h at 37 °C under continuous rotating agitation and centrifuged at 400 x g for 10 min at RT. Then the supernatant was removed and the pellet resuspended and propagated in 1 mL of TMES medium (Iscove's Modified Dulbecco's Medium (IMDM), supplemented with 20% Fetal Bovine Serum (FBS), 10 ng/mL basic fibroblast growth factor, 10,000 U/mL Penicillin, 10,000 µg/mL Streptomycin, and 0.02 M L-Glutamine).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CHIP followed by de-crosslinking and purification with Qiaquick PCR Purification kit (Qiagen)
TruSeq ChIP Sample Prep Kit, Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
ChIP-seq analysis on untreated growing mesenchymal stromal cells derived from heart. Immunoprecipitation was performed using anti-PREP1 antibody (SCBT). Replicate 2.
|
| Data processing |
Reads were aligned to the hg19 genome using bowtie2 v.2.2.9 with default parameters.
Duplicate reads were removed using Samtools rmdup v1.9.
Peaks were called using MACS version 2.1.1.20160309 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Mar 14, 2022 |
| Contact name |
Francesco Blasi |
| E-mail(s) |
francesco.blasi@ifom.eu
|
| Organization name |
IFOM
|
| Street address |
Via Adamello 16
|
| City |
Milan |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE160286 |
Transcriptional regulation of cellular mechanosignaling by PREP1 (PKNOX1) |
|
| Relations |
| BioSample |
SAMN16580363 |
| SRA |
SRX9386570 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4870634_182R_012.bw |
174.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
