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| Status |
Public on Jul 03, 2017 |
| Title |
2a: DTP_OCSA ATAC-seq |
| Sample type |
SRA |
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| Source name |
NSCLC
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| Organism |
Homo sapiens |
| Characteristics |
cell line: PC9
treatment: 8 day 1 μM erlotinib
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| 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. ALDH_High and ALDH_Low samples were obtained from PC9 cells treated with DMSO or 1 μM erlotinib erlotinib for 12 hours as indicated prior to aldefluor sorting by FACS.
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| Growth protocol |
PC9 cells were cultured at 37 °C with 5% CO2 in RPMI-1640 (Invitrogen) supplemented with 10% FBS (HyClone).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Prior to the assay, cells were cryopreserved in culture media containing 5% DMSO. The cells were then thawed in a 37C water bath, pelleted at 500g for 5 min at 4C, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013) with some modifications.
Cell pellets were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), pelleted at 500g for 10 min at 4C, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure XP beads (Beckman Coulter).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequencing reads were aligned to human genome build hg19 using BWA with the MEM mode. Aligned reads mapped to mitochondria genome, aligned reads with no proper pairs, low mapping quality and duplicates, supplementary alignments were further removed for downstream analysis.
For comparative analysis, the number of usable reads for each sample were normalized to the smallest number of usable reads among all samples under comparison.
Usable reads of all triplicates were combined for each experimental condition after normalization of read counts for downstream analysis.
All peaks were detected using MACS 1.4.2 with p-value 1e-7 and nomodel option. Peak filtering was performed by removing false peaks in the ENCODE blacklist.
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks
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| Submission date |
Jul 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Suchit Jhunjhunwala |
| E-mail(s) |
suchitj@gene.com
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| Organization name |
Genentech
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| Street address |
1 DNA Way, MS-444A
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE74180 |
Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures |
| GSE100750 |
Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures [ATAC-Seq] |
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| Relations |
| BioSample |
SAMN07312230 |
| SRA |
SRX2980127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2692562_2a_DTP_OCSA.bw |
58.8 Mb |
(ftp)(http) |
BW |
| GSM2692562_2a_DTP_OCSA_peaks.bed.gz |
610.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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