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
2016-11-16
ENA last update
2016-08-11
ENA-CHECKLIST
ERC000011
External Id
SAMEA4378457
INSDC center alias
Cancer Research UK Cambridge Institute University of Cambridge
INSDC center name
Cancer Research UK Cambridge Institute University of Cambridge
INSDC first public
2016-11-16T17:02:46Z
INSDC last update
2016-08-11T16:38:46Z
INSDC status
public
Submitter Id
E-MTAB-4913_2:do8375
broker name
ArrayExpress
common name
house mouse
genotype
Tc1x[129S8xB6]F1
individual
26244
organism part
kidney
phenotype
Female Germline
sample name
E-MTAB-4913_2:do8375
sex
male
strain
Tc1

Sequenced DNA Library

library_name
do8375_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The Tc1 mouse line was obtained from Dr. E. Fisher and Dr. V. Tybulewizc and housed in the Biological Resources Unit (BRU) in the Cancer Research UK – Cambridge Institute under the Home Office Licence (PPL 70/7535). For maintenance of the transgenic line, the human chromosome 21 (HsChr21) was transmitted through the female germline by breeding female Tc1 mice to male (129S8 x C57BL/6J) F1 mice (conventional breeding setup). For male germline transmission, female (129S8 x C57BL/6J) F1 mice were crossed with male Tc1 mice. Samples were harvested after direct perfusion of the liver with buffered salt solution and cross-linked in 1% formaldehyde for 20 minutes, followed by quenching with 1/20 volume of 2.5M glycine to neutralise formaldehyde. Cross-linked tissues were homogenised in dounce tissue grinder and lysed according to published protocols (10.1016/j.ymeth.2009.03.001). Sonication was performed on a Misonix sonicator 3000 with a 418 tip to fragment chromatin to an average length of 300bp. 50 ul of cell lysate after sanitation were removed as input control DNA and processed alongside ChIP samples. The following antibodies were used for immuno-precipitation: H3K4me3 (Millipore 05-1339 CMA304, Lot numbers 236661 and 2504863), H3K27ac (abcam ab4729, Lot numbers GR150367 and GR200563), CEBPA (Santa Cruz sc-9314, Lot L1113), HNF4A (ARP31946, Lot numbers QC22894 and QC1455(R1)100317), RNA polymerase II (abcam, ab5408, Lot number GR106949). Up to 50ng of immuno-precipitated DNA or input DNA was used for library preparation following the ThruPLEX DNA-Seq library preparation protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
35370295
Reads aligned (%)
97.4
Duplicates removed (%)
13.9
Number of peaks
614 (qval < 1E-05)

mm9

Number of total reads
35370295
Reads aligned (%)
97.2
Duplicates removed (%)
13.9
Number of peaks
686 (qval < 1E-05)

Base call quality data from DBCLS SRA