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| Status |
Public on Feb 06, 2024 |
| Title |
PC9EV, osimertinib, rep1 |
| Sample type |
SRA |
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| Source name |
PC9
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| Organism |
Homo sapiens |
| Characteristics |
cell line: PC9
cell type: human NSCLC cell line
transfection: empty vector transfected
treatment: osimertinib for 3 days
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| Treatment protocol |
vehicle or 100nM osimertinib
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| Growth protocol |
RPMI 1640 supplemented with 10% tet system-certified FBS, 1μg/ml doxycycline, 1mM sodium pyruvate, 10mM HEPES, 100U/ml penicillin and 100μg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell nuclei were extracted with resuspension buffer containing 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin, followed by tagmentation with transposase (illumina, 20034197). The tagmented DNA was purified with DNA cleanup kit (Zymo, D4014).
The tagmented DNA was amplified using NEBNext Master Mix (NEB, M0541S) to construct illumina sequencer-compatible libraries. ATAC-seq DNA libraries was purified with AMPure XP magnetic beads (Beckman Coulter, A63880) and quantified with KAPA Library Quantification Kit (KAPA, KK4854).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
PC9EO.merge.merge.RPKM.bw
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| Data processing |
Quality control of the reads with FastQC; trimming and adapter removal of the reads with Trimmomatic; alignment to human genome build 37 (GRCh37/hg19) reference genome with Bowtie2; marking and removal of duplicates with Picard. Samtools was used to manage SAM & BAM files.
Coverage of BAM files was obtained using deepTools bamCoverage. Kent tools from UCSC were used to generate the visualization of bigwig files, which were managed in Integrative Genomics Viewer (IGV).
The heatmaps of differentially accessible regions were made with deepTools. BAM files from replicates were merged using Samtools and the peaks were called using Macs2. Peaks were counted using featureCounts.
Annotation of peaks was performed with HOMER.
Assembly: hg19
Supplementary files format and content: bigWig files including peak information in each experimental group
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| Submission date |
Sep 19, 2023 |
| Last update date |
Feb 06, 2024 |
| Contact name |
Bomiao Hu |
| E-mail(s) |
bomiao.hu@yale.edu
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| Organization name |
Yale University
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| Street address |
310 Cedar Street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE243568 |
ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [Cell Line ATAC-seq] |
| GSE243569 |
ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts |
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| Relations |
| BioSample |
SAMN37460489 |
| SRA |
SRX21827423 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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