|
| Status |
Public on Feb 18, 2019 |
| Title |
ATAC-seq mouse E16.5 Cdx2-KO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse midgut epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E16.5
strain: C57BL6; mixed background
cell type: Embryonic epithelial cells from the midgut
genotype: Cdx2-KO(Shh-cre; Cdx2f/f)
treatment: NO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
midguts were dissected and treated in 0.25% Trypsin for 7-10 mins on a vortex station, neutralized with FBS; Epcam+ cells were enriched using magnetic antibody.
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
E16_ATAC_Cdx2KO_rep1_NK46
Cdx2-KO midgut epithelial cell chromatin accessibility by ATAC at E16.5 biological rep1
|
| Data processing |
Alignment: ChIP-seq:bowtie2 version 2.2.6. RNA-seq: Tophat, version 2.1.0
peak calling: macs 1.4.1
RNA-seq cxb files: cuffquant v2.2.1
Bigwig: bamCoverage 2.4.2
Genome_build: mm9, hg19
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: cxb file for expression profile and cuffnorm table with normalized gene expression values
|
| |
|
| Submission date |
Jun 04, 2018 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Michael P Verzi |
| Organization name |
Rutgers, the State University of New Jersey
|
| Department |
Genetics
|
| Lab |
Verzi
|
| Street address |
145 Bevier Road
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE115314 |
The lineage-specific transcriptional regulator, CDX2, navigates a dynamic chromatin landscape to control distinct stages of intestinal development |
|
| Relations |
| BioSample |
SAMN09345350 |
| SRA |
SRX4161605 |
