|
| Status |
Public on Feb 12, 2018 |
| Title |
HeLa (p77-infected) γ-H2AX ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: γH2AX
antibody catalog number: 05-636
antibody vendor: Millipore
infection: p77
|
| Treatment protocol |
HeLa cells were transduced with EGFP-p77 virus or control pLL3.7 virus in the presence of 8 μg/ml polybrene. 72hr after transduction, cells were subjected to ChIP analysis.
|
| Growth protocol |
HeLa cells were culture in DMEM medium supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 250 and 350bp (representing shear fragments between 150 and 250nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
raw data with 4-nucleotide barcodes TGCT
|
| Data processing |
Barcode splitter: All our libraries had 4nt barcodes at the 5 prime of each reads (ACGT for P77 RNA polymerase II chip-seq, GTAT for PL3.7 RNA polymerase II chip-seq, TGCT for P77 γH2AX chip-seq and CATT for PL3.7 γH2AX chip-seq). We splitted data according to the barcodes. Both P77 RNA polymerase II and γH2AX chip-seq had two replicates. We merged those two replicates into a single file and analyzed them together.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata" Total reads used to map was 27.7M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 18.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 35.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 16M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample. After alignment 21.2M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 15.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 22.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 12.3M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample maped to the genome
Peak calling: Peak calling was performed by MACS and SICER by default parameter except for band width: 200 bps for MACS and Windowsize: 50 bps, Fragment size: 200 bps, Gap size: 150 bps and Evalue for identification of significant islands: 100 for SICER
Wiggle file: The number of ChIP-Seq reads across the genome, in 50 bp non-overlapping bins was summarized and performed rank quantile normalization for P77 and PLL3.7.
Genome Build:
TGCT.HeLa (p77-infected) +-H2AX ChIP-seq.bed: hg18
TGCT.HeLa (p77-infected) +-H2AX ChIP-seq.wig: hg18
|
| |
|
| Submission date |
Feb 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
XiaLu Li |
| E-mail(s) |
6239@cnu.edu.cn
|
| Organization name |
Capital Normal University
|
| Street address |
105 Xisanhuan Beilu
|
| City |
beijing |
| ZIP/Postal code |
100037 |
| Country |
China |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE35964 |
Tumor suppressor REST/NRSF controls genome stability by preventing R-loop formation |
|
| Relations |
| SRA |
SRX121181 |
| BioSample |
SAMN00791479 |
