|
| Status |
Public on May 13, 2015 |
| Title |
ChIP-seq_IgG_H3_hMSC |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal stem cell
genotype/variation: WT
chip antibody: IgG (Santa Cruz, sc-2027, rabbit)
|
| Treatment protocol |
We sought to generate an isogenic human embryonic stem cell (hESC) line by knocking out the conserved 15th and 16th exons of WRN gene encoding for the DNA helicase domain of the WRN protein by helper-dependent adenoviral vector (HDAdV).
|
| Growth protocol |
H9 hESCs (WiCell Research) and their WRN mutant derivatives were maintained on Mitomycin C treated mouse embryonic fibroblasts (MEFs) in hESC medium or on Matrigel (BD Biosciences) coated plates in mTeSR medium (STEMCELL Technology). Human bone marrow-derived MSCs were maintained in Minimum Essential Medium (MEM) Alpha Medium supplemented with 10% FBS, and 0.1 mM NEAA with or without 1ng/ml bFGF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were constructed by TruSeq DNA Sample Preparation Kit (Illumina, #FC-121-2001) according to the manufacturer’s manuals.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against IgG
|
| Data processing |
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to gynab refference genome (hg19) using BWA software
Unique mapping reads were used to call peaks by MACS(v1.4) software
The abundance measurements were determined by RPKM with the fomula: RPKM=TR/(MR(million)*EL(KB)), TR is the total reads that mapped to the reference, MR is total number of the reads that mapped to one of the transcripts of the gene, EL is the length of the longest transcript of a gene.
Genome_build: hg19
Supplementary_files_format_and_content: bed files whilch include the peaks called by MACS(v1.4)
Supplementary_files_format_and_content: bedgraph files which depict the reads distribution among the genome
Supplementary_files_format_and_content: .txt files which include abundance measurements (RPKM)
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingyi Li |
| E-mail(s) |
lijy201@gmail.com
|
| Organization name |
Peking University
|
| Street address |
Yiheyuan Road, No.5, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE52285 |
A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging |
|
| Relations |
| BioSample |
SAMN02401731 |
| SRA |
SRX376724 |
