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Sample GSM2689432 Query DataSets for GSM2689432
Status Public on Jun 05, 2018
Title Endocrine progenitors at e16.5_ATAC-seq_2
Sample type SRA
 
Source name Ngn3-eGFP+ e16.5 cells
Organism Mus musculus
Characteristics developmental stage: e16.5
tissue: pancreas
cell type: Ngn3-eGFP+ cells
strain: Ngn3-eGFP
Extracted molecule genomic DNA
Extraction protocol Cells resuspended in transposase-containing reaction mixture with 0.05% digitonin before tagmentation at 37 degrees C for 30 minutes with 300rpm agitation. DNA was then purified with a Qiagen MinElute reaction cleanup kit.
As described in Buenrostro JD et al., 2013 Nature Methods
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Reads mapped to mm9 genome using Bowtie2 with default paired-end settings
Non-nuclear and unmapped reads discarded
picard MarkDuplicates to remove duplicate reads
Peak calling using Homer (findPeaks -style factor) on the merged BAM file of all e14.5 and e16.5 replicates
Blacklisted regions from mm9 were removed from comprehensive peak file
Reads were counted for each condition from the comprehensive peak file using bedtools (mulicov module)
DEseq2 was used for differential accessibility analysis with the multicov file as input
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph.gz of processed bam file, generated using homer makeUCSC
 
Submission date Jun 28, 2017
Last update date May 15, 2019
Contact name Malgorzata Borowiak
E-mail(s) borowiak@bcm.edu
Organization name Baylor College of Medicine
Street address 1 Baylor Plaza
City Houston
ZIP/Postal code 77030
Country USA
 
Platform ID GPL19057
Series (2)
GSE100621 High-Resolution temporal profiling of developing pancreas uncovers the mechanisms of endocrine cell fate determination [ATAC-Seq]
GSE100622 High-Resolution temporal profiling of developing pancreas uncovers the mechanisms of endocrine cell fate determination
Relations
BioSample SAMN07290546
SRA SRX2965694

Supplementary file Size Download File type/resource
GSM2689432_E16_Ngn3_rep2.ucsc.bedGraph.gz 352.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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