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Sample GSM7146567 Query DataSets for GSM7146567
Status Public on Aug 08, 2023
Title Mouse Lung tumor_KrasLA1_695_rep1
Sample type SRA
Source name Lung tumor
Organism Mus musculus
Characteristics tissue: Lung tumor
strain: C57B6J
Sex: Female
genotype: KrasLA1/+
age in_weeks: 55w
assay: Atac-sequencing
Extracted molecule genomic DNA
Extraction protocol A total of 40-50 mg of lung tumors were dissected from euthanized mice, snap frozen in liquid nitrogen and submitted for ATAC-sequencing
Samples were send to Active Motif for library prep, sequencing and analysis
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Reads were mapped to mouse mm10 reference genome using BWA (v0.7.12) algorithm and saved as BAM files.
Reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome were used for further analysis. In addition, duplicate reads (“PCR duplicates”) were removed.
Genomic regions with a high level of transposition/tagging events were determined using the MACS3 (v3.0.0) peak calling algorithm with a cut off of p-value 1e-7
For comparative analysis, normalization was achieved by reducing the number of alignments per sample to match the number of alignments in the sample with fewer number of alignments. Reduction was done through random sampling
To identify the density of transposition events along the genome, the genome was divided into 32 bp bins and the number of fragments in each bin was determined
The histograms showing the density of each signal (peaks) was stored in a bigWig file and visualized using the USCC Genome browser
BigWig files were generated using deeptools (v3.5.1)
A FRIP (fraction of reads in peaks) value of 10% or higher was used to define good data quality and false peaks were defined within the ENCODE blacklist (Consortium, 2012) and removed from analysis
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Submission date Apr 04, 2023
Last update date Aug 08, 2023
Contact name Raisa Reyes-Castro
Organization name UT Health MD Anderson Cancer Center
Department Genetics
Lab Swathi Arur
Street address 6767 Bertner Ave
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
Platform ID GPL19057
Series (2)
GSE228964 Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas [ATAC-seq]
GSE228968 Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas
BioSample SAMN34071636
SRA SRX19868352

Supplementary file Size Download File type/resource 123.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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