|
Status |
Public on Aug 01, 2017 |
Title |
Normoxia control KD ATAC-seq rep1 |
Sample type |
SRA |
|
|
Source name |
Normoxia control KD
|
Organism |
Mus musculus |
Characteristics |
strain background: B6/129 mixed genotype/variation: KPCT (Kras-LSL-G12D;p53-LSL-R172H;Pdx1-cre;R26-LSL-Tomato) mouse id: SC0688 cell line: 688M cell type: PDAC liver metastasis cell line cell line genotype: control cultured under: 20% O2 for 24 h
|
Extracted molecule |
total RNA |
Extraction protocol |
ATACSeq libraries were prepared for sequencing using standard protocols described in Buenrostro et al. 2013. Nat Methods 12:1213-8. ATACSeq libraries were prepared for sequencing using standard protocols described in Buenrostro et al. 2013. Nat Methods 12:1213-8.
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|
|
Library strategy |
ATAC-seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
shGFP_nor1 S5-AGGCAGAA technical replicate of sample "S6-TCCTGAGC"
|
Data processing |
Reads were trimmed using cutadapt and aligned to the mouse genome (mm9) using Bowtie2. Subsequently, peaks were called using MACS2 after being filtered using a custom blacklist, as previously described in Buenrostro et al. 2013. Nat Methods 12:1213-8. Genome_build: mm9 Supplementary_files_format_and_content: tab-delimited text files include peaks and insert count for each Sample
|
|
|
Submission date |
Dec 05, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Shin-Heng Chiou |
E-mail(s) |
shinheng@stanford.edu
|
Organization name |
Stanford University
|
Department |
Genetics
|
Street address |
450 Serra Mall
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE90825 |
Blimp1 induces transient metastatic heterogeneity in pancreatic cancer |
GSE90918 |
Blimp1 induces transient metastatic heterogeneity in pancreatic cancer [688M_ATAC-seq] |
|
Relations |
BioSample |
SAMN06111893 |
SRA |
SRX2396716 |