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Sample GSM4870634 Query DataSets for GSM4870634
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 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
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)
BioSample SAMN16580363
SRA SRX9386570

Supplementary file Size Download File type/resource 174.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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