|
| Status |
Public on May 07, 2020 |
| Title |
pooled TCF21 ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
human coronary artery smooth muscle cells
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: TCF21 (HPA013189)
cell type: smooth muscle cells
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysis by 0.5% SDS and the lysates were clarified from sonicated cells and protein-DNA complexes were isolated with TCF21 antibody (HPA013189).
Libraries were prepared with KAPA Hyper Prep kit (KK8502) per standrad instruction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
1238 1278 1346 1347 1369 1386 1401 1448 1483 1497 1508 1522 1559 1576 1587 1596 1795 1848 1858 1923 2102 2105 2109 2115 2139 2228 2282 2305 2135 2356 2435 2510 2989 2999 3141 10705 20805 112201 177089 200212 289727 313605 317155 1020301 1042702 1060602 1062201.3 2030801 2040401 3100203 3101801 61646600 7103002 8072501 8100901 9052004 9070202 9071501 9092401 9102101 59386145 59885590 397Z030 399Z015 400Z012
4-7
|
| Data processing |
Quality control of ChIP-seq data was performed using Fastqc v0.11.5, and then low-quality bases and adaptor contamination were trimmed by cutadapt 1.15 with default configuration
ChIP-seq reads were aligned to the hg19 genome assembly using BWA mem version 0.7.17-r1188 with the default configuration
Duplicate reads were marked by Picard MarkDuplicates 2.18.0
Duplicate reads and unmapped reads were removed by samtools view -f 2 -F 1804 (1.7)
BAM files were loaded into MCAS2.1.1 for peaks calling with --broad parameters and input as control.
Genome_build: hg19
Supplementary_files_format_and_content: BED6+4. 1st: chromosome, 2nd: start position of peak, 3rd: end position of peak, 4th: peak name, 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
May 07, 2020 |
| Contact name |
Thomas Quertermous |
| E-mail(s) |
tomq1@stanford.edu
|
| Phone |
650-723-5012
|
| Organization name |
Stanford University
|
| Department |
Medicine Cardiology
|
| Lab |
Quertermous
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE141751 |
Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (ChIP-Seq) |
| GSE141752 |
Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci |
|
| Relations |
| BioSample |
SAMN13523051 |
| SRA |
SRX7299332 |
