Curated Sample Data


Genome
mm9
Antigen Class
DNase-seq
Antigen
DNase-Seq
Cell type Class
Digestive tract
Cell type
Ileum

Cell type information


MeSH Description
The distal and narrowest portion of the SMALL INTESTINE, between the JEJUNUM and the ILEOCECAL VALVE of the LARGE INTESTINE.

Attributes by Original Data Submitter


source_name
Intestinal Epithelial Cells
strain
C57BL/6
tissue
Ileum
condition
conventionally-raised (CR)

Metadata from Sequence Read Archive

Library Description


library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
IECs were isolated from the duodenum (anterior 5 cm of midgut), ileum (posterior 6 cm of midgut), and colon (6 cm of terminal hindgut) of 8 to 12-week old mice ; Nuclei were isolated by 0.1% NP-40 lysis for DNase digestions ; Total RNA extracted by cell lysis in TRIzol reagent (Invitrogen) and further purified using Qiagen RNeasy kit according to manufacturer's protocol DNase-seq libraries were prepared as described (Song and Crawford 2010; PMID:20150147) with 5 µg of DNA pooled from nuclei digested for 2 min, 4 min, and 8 min at 37°C with no exogenous DNase I added ; RNA-seq libraries were prepared with 2 micrograms total RNA used for standard TruSeq library preparation (Illumina) with polyA selection and sequenced with 2 x 50bp paired-end reads

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
231429528
Reads aligned (%)
0.0
Duplicates removed (%)
9.2
Number of peaks
22 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA