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Sample GSM2417504 Query DataSets for GSM2417504
Status Public on Aug 01, 2017
Title Normoxia control KD ATAC-seq rep2
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.
 
Library strategy ATAC-seq
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description shGFP_nor2
S6-TCCTGAGC
technical replicate of sample "S5-AGGCAGAA"
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 SAMN06111892
SRA SRX2396717

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

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