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Sample GSM4476735 Query DataSets for GSM4476735
Status Public on Oct 05, 2021
Title WT Colon rep 1 (ATAC-seq)
Sample type SRA
 
Source name Intestine epithelium
Organism Mus musculus
Characteristics genotype: wild type
tissue: Colon
Treatment protocol 50K intestinal epithelial cells were purified by FACS . Genotypes include Vil-CreER;Satb2f/f and Satb2f/f control mice
Extracted molecule genomic DNA
Extraction protocol Nuclei were exacted in ATAC-Resuspension Buffer (RSB, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. DNA was fragmented by Netera Tn5 Transposase (Illumina)
NEBNext 2x MasterMix to pre-Amplify for 5 cycles and determined the required number of additional cycles by qPCR amplification. The final libraries were size selected (200bp to 800bp, including index) with AMpure beads
Sequencing strategy was on Illumina HiSeq-2000 Pair-end 150 (PE150)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Data processing Alignment BAM files for the ATAC-seq were generated with the mm10 reference genome using nf-core pipelines
Narrow peaks were called using standard MACS2.
ATAC-seq peak files had regions of less than 1kb from TSS removed using bedtool.
Biological replicates were concatenated and sorted, and peaks merged within a maximum distance of 500 bp.
Six optimum clusters were determined for k-means clustering using the elbow method. The top 3 clusters were not unique across samples and, therefore, merged into one, according to signal pattern similarity. Cluster 6 was excluded due to very low non-distinct signal.
The three resulting clusters were then annotated in R 3.6.0 using the annotatePeak function from the ChIPseeker package using known mm10 genes.
Genome_build: mm10 reference genome
Supplementary_files_format_and_content: called peaks .bed files
 
Submission date Apr 15, 2020
Last update date Oct 05, 2021
Contact name Wei Gu
E-mail(s) wei.gu@beigene.com
Phone 13776921246
Organization name Beigene
Department Beigene Institute
Lab Gu Lab
Street address 51 Rijing Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200135
Country China
 
Platform ID GPL21103
Series (2)
GSE148690 ATAC-seq of Intestine Epithelia (Ileum and Colon) from Satb2-deficient and WT mice
GSE148695 SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling
Relations
BioSample SAMN14600363
SRA SRX8118326

Supplementary file Size Download File type/resource
GSM4476735_Atac5_summits.bed.gz 1.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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