 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 05, 2021 |
| Title |
WT Colon rep 2 (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 |
SAMN14600362 |
| SRA |
SRX8118327 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4476736_Atac6_summits.bed.gz |
991.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
