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Sample GSM2147608 Query DataSets for GSM2147608
Status Public on May 10, 2016
Title KP22-empty-2d_B [ATAC-seq]
Sample type SRA
 
Source name cell line
Organism Mus musculus
Characteristics cell line: KP22
tissue/cell type: tumor-derived cell line
genotype/variation: Trp53-/-;Rb1-/-
genotype/variation: containing empty vector with Dox-inducible promoter
induced for: 2 days
Treatment protocol Stable Nfib knockdown cell lines were generated using lentiviral pLKO/PuroR vectors. Inducible and constitutive Nfib expressing human and mouse cells were generated using lentiviral vectors.
Growth protocol All murine and human SCLC cell lines used in this study grow as floating spheres and were cultured in RPMI with 10% FBS. Primary tumors and metastases were dissected and dissociated using collagenase IV, dispase, and trypsin at 37oC for 30 minutes. After dissociation the samples are continually on ice, in contact with ice-cold solutions, and in the presence of 2mM EDTA and 1U/ml DNase to prevent aggregation, and were FACS sorted for purity.
Extracted molecule genomic DNA
Extraction protocol Cells were lysed, incubated with Tn5 transposase, and purified with Qiagen MinElute kit.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter, but no downstream gene. under induction for 2days before ATAC-seq
Data processing library strategy: ATAC-seq
Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag. Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30
peak calling was done on the merged ex vivo data (samples 1-27) for the mouse data, or on the merged human cell lines (60-67) with MACS2 with the --nomodel, --broad flags
counts per sample were found within peaks, and differential accessibility was called within each group of samples (ex vivo, cell lines, modified cell lines, and human modified cell lines)
Genome_build: mm9 for mus musculus, hg19 for homo sapiens
Supplementary_files_format_and_content: peak_calls_mm9.nheader.up.bed are the peaks used for all mouse data. Four columns indicate chromosome, start, and end of accessible regions, plus a fourth column giving a unique identifier per peak
Supplementary_files_format_and_content: all_merged.H14_H29_H52_H69_H82_H88_peaks.broadPeak are the peaks used for human data. Standard broadpeak output is given.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)
Supplementary_files_format_and_content: *.bw are bigwig files containing the insertions per base pair, smoothed over 150 bp windows (20bp step size). Sample replicates are merged.
 
Submission date May 09, 2016
Last update date May 15, 2019
Contact name William Greenleaf
E-mail(s) wjg@stanford.edu
Organization name Stanford University
Street address 279 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL17021
Series (2)
GSE81255 Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility [ATAC-seq]
GSE81258 Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility
Relations
BioSample SAMN04965874
SRA SRX1753546

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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