|
| Status |
Public on Jan 01, 2021 |
| Title |
X-PSR-YB1 |
| Sample type |
SRA |
| |
|
| Source name |
A10 cell (ATCC CRL-1476)
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: aorta, thoracic/medial layer
passages: 10-15
chip antibody: YBX1 (abcam ab12481, CST D299, MBL RN015P)
|
| Treatment protocol |
Lipofactamine 3000 was used for plasmid transfection.
|
| Growth protocol |
Rat thoracic aortic vascular smooth muscle A10 cells was purchased from ATCC (CRL-1476), and cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% FBS, 100U/mL penicillin and 100g/mL streptomycin at 37 °C in a 95% air-5% CO2 atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext ChIP-seq library prep master mix set for Illumina was used to prepare the sequencing library with custom-synthesized primers (Wang et al., 2019). 50 nt single end reads (Arteridin ChIP-Seq) were generated on Illumina Hiseq 2500 platform and 150bp pair end reads (YBX1 ChIP-Seq) were generated on Illumina HiSeq X Ten.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Fastqs were qualified by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and they were mapped to UCSC reference genome Rnor.6.0 using Bowtie2
SAMtools was used to manipulate SAM files into sorted BAM files
To capture ChIP signals, MACS2 was applied with the option qvalue cutoff = 0.05
Peaks were annotated by annotatePeaks.pl in Homer using Rat gtf files from ENSEMBL.
Genome_build: Rnor6
|
| |
|
| Submission date |
Feb 26, 2020 |
| Last update date |
Jan 02, 2021 |
| Contact name |
Junyi Yu |
| E-mail(s) |
junyiyuamu@gmail.com
|
| Phone |
(+86)13032388928
|
| Organization name |
Daping Hospital, The Third Military Medical University, Chongqing, P.R. China.
|
| Department |
Department of Cardiology
|
| Lab |
Chongqing Institute of Cardiology
|
| Street address |
10th Changjiangzhilu Road, Yuzhong District
|
| City |
Chongqing |
| ZIP/Postal code |
400042 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE145965 |
Coordinated Regulation of Smooth Muscle Cell Remodeling by Non-coding and Coding products of Phenotype Switching Regulator Gene. |
|
| Relations |
| BioSample |
SAMN14212314 |
| SRA |
SRX7805903 |
