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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
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv

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

E-mail(s)

wjg@stanford.edu

Phone

6507253672

Organization name

Stanford University