|
| Status |
Public on Nov 28, 2024 |
| Title |
EedKO_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Intestine
cell type: Epithelial
genotype: Eed fl/fl Villin-CreER-T2
treatment: Tamoxifen
|
| Treatment protocol |
Mouse intestine was dissected and cut into 1cm pieces and treated with 5mM EDTA for 30 minutes with vigurous shaking. Villi were isolated by using 70um filter. Villi were treated by 4X TrypLE to generate single cell suspension.
|
| Growth protocol |
Mouse intestinal epithelial cell.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were lysed in 50 µl cold ATAC lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) followed by centrifugation at 500 g at 4°C to isolate nuclei. Nuclei were resuspended in 50 µl transposition reaction mix with Nextera Tn5 Transposase (Illumina, FC-121-1030) and incubated for 30 min at 37°C. Transposed DNA was purified using columns (Qiagen, 28004) and amplified using high-fidelity 2X PCR Master Mix
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Samtools version 1.17
Tracks for libraries were generated by converting bam files to to BigWig by deeptools for display on the UCSC browser.
Assembly: GRCm38
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Jan 19, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Unmesh Jadhav |
| E-mail(s) |
[email protected]
|
| Phone |
323-442-2563
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell and Regenerative Medicine
|
| Lab |
Jadhav Lab
|
| Street address |
1425 San Pablo Street
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE253736 |
Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis |
|
| Relations |
| BioSample |
SAMN39510701 |
| SRA |
SRX23331490 |
