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| Status |
Public on May 10, 2016 |
| Title |
L4-B [ATAC-seq] |
| Sample type |
SRA |
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| Source name |
liver metastasis
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| Organism |
Mus musculus |
| Characteristics |
strain background: mixed; C57BL/6N, 129S1/SvImJ, 129X1/129Ola, and with some FVB/Ntac
tissue/cell type: liver
genotype/variation: Trp53-/-;Rb1-/-;p130-/-;R26mG
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| 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.
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| 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.
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| 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).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, L4.from140625and140115.rmdup.new.s20.w150sw.bw !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.
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| 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.
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| Submission date |
May 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
William Greenleaf |
| E-mail(s) |
wjg@stanford.edu
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| Organization name |
Stanford University
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| Street address |
279 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| 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 |
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| Relations |
| Reanalyzed by |
GSM3273011 |
| BioSample |
SAMN04965834 |
| SRA |
SRX1753510 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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