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Sample GSM6597211 Query DataSets for GSM6597211
Status Public on Jan 19, 2023
Title beta_biological_replicate_3
Sample type SRA
 
Source name FACS-sorted beta cells
Organism Mus musculus
Characteristics cell type: beta
strain: mouse
status: healthy
Extracted molecule genomic DNA
Extraction protocol mIns1-H2b-mCherry [1] x Rosa-LSL-YFP crossed to either Sst-Cre [44] or Gcg-Cre [45] triple transgenic mice were pooled by sex, each sample yielding a median of 20,000 cells, with islet isolation and FACS-sorting as previously described (Supplemental Fig. 1) [1, 46-48].
Single-end 50 bp reads were generated after library size selection yielded an average of 450 bp fragments and sequenced as previously described using NexteraDNA library protocol [30].
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description chromatin accessibility
Data processing FastQC
Trimmomatic
Bowtie2
Picard Tools
MACS2
Assembly: mm10
Supplementary files format and content: Aligned BAM Files
 
Submission date Sep 22, 2022
Last update date Jan 19, 2023
Contact name Mark O. Huising
E-mail(s) mhuising@ucdavis.edu
Organization name University of California, Davis
Department Neurobiology, Physiology and Behavior
Lab Huising Lab
Street address One Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL19057
Series (1)
GSE213970 Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers
Relations
BioSample SAMN30964218
SRA SRX17676049

Supplementary file Size Download File type/resource
GSM6597211_delta5_S24_L007_R1_001.SE.tagAlign.gz_peaks.narrowPeak.gz 1.9 Mb (ftp)(http) NARROWPEAK
GSM6597211_delta5_S24_L007_R1_001.bam 495.2 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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