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Sample GSM7791181 Query DataSets for GSM7791181
Status Public on Feb 06, 2024
Title PC9EV, osimertinib, rep1
Sample type SRA
Source name PC9
Organism Homo sapiens
Characteristics cell line: PC9
cell type: human NSCLC cell line
transfection: empty vector transfected
treatment: osimertinib for 3 days
Treatment protocol vehicle or 100nM osimertinib
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.
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).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
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
Submission date Sep 19, 2023
Last update date Feb 06, 2024
Contact name Bomiao Hu
Organization name Yale University
Street address 310 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06519
Country USA
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
BioSample SAMN37460489
SRA SRX21827423

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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