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Sample GSM5448680 Query DataSets for GSM5448680
Status Public on Oct 05, 2021
Title Postnatal_day1_hindgut
Sample type SRA
 
Source name Intestine epithelium
Organism Mus musculus
Characteristics time point: P1
genotyping: wild type
Treatment protocol Embryonic hindgut (distal to the cecum) was digested in 0.25% Trypsin-EDTA at 37°C for 30 minutes followed by neutralization with 5%FBS. Cells were incubated with APC-conjugated EpCAM antibody (BioLegend) and FACS-purified on an Aria II SORP flow cytometer (Becton-Dickinson).
Growth protocol As described in Banerjee et al, Genes & Dev. 2018. 32: 1430-1442
Extracted molecule total RNA
Extraction protocol Five to Thiry thousand cells were lysed and nuclei extracted 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 transposed by Nextera Tn5 Transposase (Illumina) for 30min at 37C and purified with QIAquick column (Qiagen)
NEBNext 2x MasterMix was used to pre-Amplify transposed DNA for 5 cycles and determine the required number of additional cycles by qPCR amplification. The final libraries were size selected (200bp to 800bp, including index) with AMpure beads
Libraries were sequenced on a NextSeq500 instrument (Ilumina)
 
Library strategy ATAC-seq
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description P1_hindgut
Data processing Adapter removal and trimming: Cutadapt 1.42 with Python 2.7.12. Trimming with Trim Galore version: 0.4.4_dev, trimming mode: single-ended.
75-bp single-end reads were aligned to mouse reference genome Mm10 using Bowtie2 v2.3.4.3
Nonunique and duplicate reads were removed using SAMtools version 1.9
Bigwig files were generated using the bamCoverage module in deepTools v3.0.2 and normalized for 1x coverage using 10bp bins, smoothened over 30bp.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files
 
Submission date Jul 13, 2021
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 GPL19057
Series (2)
GSE148695 SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling
GSE180037 ATAC-seq of Embronic Hindgut Epithelia from WT mice
Relations
BioSample SAMN20202623
SRA SRX11432468

Supplementary file Size Download File type/resource
GSM5448680_P1_hindgut.10x30.bw 134.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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