|
| Status |
Public on Nov 28, 2024 |
| Title |
E12.5_CDX2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Intestine
cell type: Epithelial
genotype: Wild Type
treatment: NA
antibody: CDX2(Cell Signalling: Catalogue # D11D10)
|
| Treatment protocol |
Mouse small intestine was disected from Fetus at E12.5 and E16.5. Intestine was cut into pieces. Single cell suspension was generated by 10mM Trypsin. Epithelial cells were isolated using EasySep Release beads and Antibody againt EpCAM.
Adult Villi Cells: Fetus Intestine Epithelial: 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.
HCT116: Cells were treated with DMSO or 10uM GSK-3484862 for 6 days. After 6 days cells were grwon without any DMSO or GSK-3484862 for 3 days.
|
| Growth protocol |
Mouse intestinal epithelial cell.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using EpiCypher CUTANA kit according to manufacturer protocol with the following changes. Cells were resuspended in the permeabilization buffer (CUTANA Wash Buffer, 0.01% Digitonin, and 1X protease inhibitor) directly after isolation. Cells were incubated on ice for 5 minutes and bound to Concanavalin A Beads at room temperature for 10 minutes. Bead-bound cells were resuspended in 180ul of antibody buffer (permeabilization buffer, 2mM EDTA) with 0.5 ug antibody of interest, and incubated overnight. Digestion was done at 4C for 30minutes on a nutator. Fragment release postdigestion was done at 4C for 30 minutes and purified using SeraMag beads with 30% PEG-8000.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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, GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN
|
| |
|
| 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 |
GPL24247 |
| Series (1) |
| GSE253736 |
Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis |
|
| Relations |
| BioSample |
SAMN39510847 |
| SRA |
SRX23343469 |
