SRX5862978
GSM3780706: Sox9 Negative atac Rep C; Mus musculus; ATAC-seq

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Digestive tract
Cell type
Intestinal epithelium
NA
NA

Attributes by original data submitter

Sample

source_name
Intestinal epithelial cells
strain
C57BL/6
cell type
Intestinal epithelial cells
cell population
Sox9 Negative

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
12,000 cells per Sox9EGFP population were collected directly into 250uL 1X sort media, pelleted by centrifugation at 2,000g for 5min, and subjected to Omni-ATAC as previously described in (Corces et al., 2017). Paired end omni-atac protocol

Sequencing Platform

instrument_model
NextSeq 500

Where can I get the processing logs?

Read processing pipeline log

mm10

Number of total reads
67249045
Reads aligned (%)
62.5
Duplicates removed (%)
34.9
Number of peaks
38250 (qval < 1E-05)

mm9

Number of total reads
67249045
Reads aligned (%)
62.4
Duplicates removed (%)
35.0
Number of peaks
38197 (qval < 1E-05)

Base call quality data from DBCLS SRA