Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Neural
Cell type
Thalamus
MeSH Description
Paired bodies containing mostly GRAY MATTER and forming part of the lateral wall of the THIRD VENTRICLE of the brain.

Attributes by original data submitter

Sample

ENA first public
2020-07-24
ENA last update
2020-07-22
ENA-CHECKLIST
ERC000011
External Id
SAMEA7086106
INSDC center alias
Laboratory of Molecular Neurobiology Centre of New Technologies University of Warsaw
INSDC center name
Laboratory of Molecular Neurobiology Centre of New Technologies University of Warsaw
INSDC first public
2020-07-24T04:03:48Z
INSDC last update
2020-07-22T18:34:52Z
INSDC status
public
Submitter Id
E-MTAB-9384:WT TCF7L2 2
age
60
broker name
ArrayExpress
common name
house mouse
developmental stage
adult
genotype
wild type genotype
individual
8-14
organism part
thalamus
replicate
2
sample name
E-MTAB-9384:WT TCF7L2 2
sex
male
strain
C57BL/6

Sequenced DNA Library

library_name
WT TCF7L2 2_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fresh thalami isolated from adult mice were cut briefly and fixed with 1% formaldehyde for 10 minutes, chromatin isolated according to Cotney and Noonan, 2015 was sonicated into 200-500 bp fragments with Covaris S220 DNA was purified with Monarch PCR & DNA Cleanup Kit (T1030, NEB) Library preparation was conducted by NGS Core Facility, Centre of New Technologies, University of Warsaw. Libraries were prepared with KAPA HyperPrep Kit and KAPA Dual-Indexed adapters (Cat. no. 7962363001, KK8722 Kapa Biosciences). Enrichment by 15 cycles of amplification was applied and final library was size-selected using Kapa Pure Beads to obtain avarage size of 350 bp. Libraries were tested for quality with High Sensitivity DNA kit (Cat. no. 5067-4626, Agilent)

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

mm10

Number of total reads
54416571
Reads aligned (%)
68.7
Duplicates removed (%)
37.4
Number of peaks
12346 (qval < 1E-05)

mm9

Number of total reads
54416571
Reads aligned (%)
68.6
Duplicates removed (%)
37.4
Number of peaks
12282 (qval < 1E-05)

Base call quality data from DBCLS SRA