|
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)
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|
|
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 |