|
| Status |
Public on Jul 03, 2017 |
| Title |
DTP_TSA_ChIP_Input |
| Sample type |
SRA |
| |
|
| Source name |
NSCLC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC9
chip antibody: none
treatment: 8 day 1 μM erlotinib + 5 hour 50 nM TSA
|
| Treatment protocol |
To generate DTPs, PC9 cells were treated with 1 μM erlotinib for 8 days. Media was replaced with fresh media supplemented with erlotinib every 3 days. Cells that survive the 8 day-treatment were considered DTPs. DTP_TSA samples were generated by treating DTPs on day 8 of erlotinib treatment with 50 nM TSA for 5 hours.
|
| Growth protocol |
PC9 cells were cultured at 37 °C with 5% CO2 in RPMI-1640 (Invitrogen) supplemented with 10% FBS (HyClone).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
Illumina sequencing libraries were prepared from the ChIP and input DNAs following standard enzymatic steps consisting of end-polishing, dA-addition, and adaptor ligation. The resulting DNA libraries were quantified and sequenced as 150 bp paired-end reads using Illumina’s HiSeq 2500. The average size of the sequenced fragments were around 380 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were aligned to human genome build hg19 with BWA using default parameters (Li 2013).
Alignments were filtered to extract only reads that belonged to matching pairs; pairs of reads that spanned on the average ~350-400 nt and were in the correct orientation. Read pairs with mapping quality 0 (high quality mappings to multiple locations) were not used for further analysis; in addition, presumptive PCR duplicates and reads that did not pass Illumina’s purity filter were removed.
Total number of reads was normalized according to the total number of reads that map to the Drosophila dm3 genome from each sample.
H3K9me3 ChIPseq peaks were called with SICER using input files as control (Zang et al., 2009).
Genome_build: hg19
Supplementary_files_format_and_content: Coverage files in bigWig format were generated by extending reads to 380 nt in silico and counting tags for 50-nt bins over the genome. Tab delimited text files report the genomic location along with the average number of tags for each H3K9me3-enriched regions (ChIPseq peaks).
|
| |
|
| Submission date |
Oct 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Suchit Jhunjhunwala |
| E-mail(s) |
suchitj@gene.com
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way, MS-444A
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE74179 |
Drug-tolerant cancer cell persisters survive lethal exposures by silencing transposable elements [ChIP-Seq] |
| GSE74180 |
Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures |
|
| Relations |
| BioSample |
SAMN04254242 |
| SRA |
SRX1425834 |
