Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Kidney
Cell type
Kidney
MeSH Description
Body organ that filters blood for the secretion of URINE and that regulates ion concentrations.

Attributes by original data submitter

Sample

ENA first public
2013-03-21
ENA last update
2018-03-08
External Id
SAMEA1710308
INSDC center alias
Cancer Research UK
INSDC center name
Cancer Research UK
INSDC first public
2013-03-21T17:02:36Z
INSDC last update
2018-03-08T16:19:32Z
INSDC status
public
Submitter Id
E-MTAB-1104:tc1_122.1_b
age
2-6 month
broker name
ArrayExpress
common name
house mouse
developmental stage
adult
genotype
Tc1_with_hschr21
individual
tc1_122.1
organism part
kidney
sample name
E-MTAB-1104:tc1_122.1_b
sex
male

Sequenced DNA Library

library_name
tc1_122.1_b
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
doi:10.1016/j.ymeth.2009.03.001; Crosslinked animal livers were dounce homogenized into a single cell suspension and rinsed with ice cold PBS. Each pellet of cross-linked material was resuspended in 10 ml of LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100) and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4???_???C. Pellets were then rinsed in 10 ml of LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA) and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4???_???C. The nuclei preparation was resuspended in 3 ml LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin in the nuclei fraction was fragmented to an average length of 300 bp by sonication. After sonication 300 ???_???l of 10% Triton X-100 was added to the 3 ml of sonicated lysate and debris was removed by centrifugation at 20,000 x rcf for 10 minutes at 4???_???C.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
30953596
Reads aligned (%)
94.9
Duplicates removed (%)
7.3
Number of peaks
333 (qval < 1E-05)

mm9

Number of total reads
30953596
Reads aligned (%)
94.8
Duplicates removed (%)
7.8
Number of peaks
313 (qval < 1E-05)

Base call quality data from DBCLS SRA