|
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
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|
|
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
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|
|
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 |