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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 08, 2023 |
| Title |
Mouse Lung tumor_KrasLA1_641_rep2 |
| Sample type |
SRA |
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| Source name |
Lung tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung tumor
strain: C57B6J
Sex: Male
genotype: KrasLA1/+
age in_weeks: 55w
assay: Atac-sequencing
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| 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
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Apr 04, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Raisa Reyes-Castro |
| E-mail(s) |
RAReyes2@mdanderson.org
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| Organization name |
UT Health MD Anderson Cancer Center
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| Department |
Genetics
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| Lab |
Swathi Arur
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| Street address |
6767 Bertner Ave
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN34071635 |
| SRA |
SRX19868353 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7146569_2_0CMY_01VKMDA_Control-641_ATAC_mm10_i212_uniqnorm_signal.bw |
121.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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