GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3273005 Query DataSets for GSM3273005
Status Public on Jul 17, 2018
Title 1_V1L1_B (re-analysis of GSM2147563)
Sample type SRA
Source name liver metastasis
Organism Mus musculus
Characteristics tissue: liver metastasis
genotype: Trp53-/-;Rb1-/-;p130-/-;R26mG
expression vector: Ad-CMV-Cre
not included for low atac-seq enrichment: FALSE
nfib amplification: TRUE
cmv model (v), nfib amplifiied (1) vs not (0): V_1
sequencing batch: 1
sample prep batch: 1
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 ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description liver metastasis from CMV TKO line with hyperaccessible chromatin state
Data processing Sequencing data processing: 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
Determining peak summits: Peak calling was done on merged data for each sequencing batch, with peak calling done using MACS2 ( --nomodel --call-summits) resulting in the bed files merged_bams_X_summits.bed.
Peak filtering: Peak summits were expanded by 250 bps to either side of the summit to form a region of 500 bp. Peaks were filtered to not include blacklist regions or regions that appeared to have copy number amplification.
Peak filtering2: Each peak was assessed for having at least one read in all samples, or at least one sample with large number of normalized reads (>1 std. deviation above the mean). If it did not meet either of these criterion, it was filtered out.
Merging peaks: The three peak sets (one for each sequencing batch) were concatenated. Overlapping peaks were resolved by taking the peak with the highest numbers of reads.
Determining differential accessibility: counts per sample were found within peaks, and differential accessibility was called with different contrasts using DESeq2
Genome_build: mm9 for mus musculus
Supplementary_files_format_and_content: merged_peaks_filtered_subset.bed are the set of accessible regions, after fltering and merging. Five columns indicate chromosome, start, and end of accessible regions, a unique name, and the peak score from the MACs2 data.
Supplementary_files_format_and_content: res_G_LvsT_comb.csv gives the differential accessibility across accessible regions between CGRP liver metastasis and tumor samples (i.e. comparing samples with the label G_L vs G_T in column "CGRP model (G): tumors (T) versus mets (L)"). The output is directly from DEseq2. Columns appended by '_GA.5' assess signficance of abs value of log2fold change being greater than 0.5
Supplementary_files_format_and_content: res_V_1vs0_comb.csv gives the differential accessibility across accessible regions between CMV model with Nfib amplification versus not (i.e. comparing samples with the label V_1 vs V_0 in column "CMV model (V), Nfib amplifiied (1) vs not (0)"). Output is formatted exactly as for res_G_LvstT_comb.csv
Submission date Jul 16, 2018
Last update date Jul 17, 2018
Contact name William Greenleaf
Phone 6507253672
Organization name Stanford University
Department Genetics
Street address 279 Campus Drive, Beckman Center B257
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL17021
Series (1)
GSE117177 Inter-tumoral heterogeneity in SCLC is influenced by the cell-type of origin
Reanalysis of GSM2147563
BioSample SAMN09665993
SRA SRX4394810

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap