Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PAX8

Cell type

Cell type Class
Kidney
Cell type
786-O
Primary Tissue
Kidney
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

Alias
E-MTAB-7812:786o_pax8
Broker name
ArrayExpress
Description
Protocols: Chromatin immunoprecipitation was performed as previously described (Galli et al., 2015). Briefly, 8*15 cm dishes of cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes. The cross-linking was quenched by fresh glycine at a final concentration of 0.125 M. The cells were then harvested and lysed in SDS lysis buffer to collect the nuclei. Nuclei suspension was sonicated using a Diagenode Bioruptor (14 cycles 30\ ON and 30\ OFF using setting High) to obtain fragments of 250bp average size. Appropriate amount of chromatin (100ug for PAX8 or 10ug for histone modification) was incubated with the indicated antibodies overnight and complexes retrieved using Protein G coupled Dynabeads. After extensive washes, DNA was reverse crosslinked and purified using AmpPure XP beads. ChIP-seq libraries were constructed using Nugen Ovation® Ultralow System V2 according to manufacturer's instructions.
ENA checklist
ERC000011
INSDC center alias
Novartis Institutes for Biomedical Research
INSDC center name
Novartis Institutes for Biomedical Research
INSDC first public
2019-06-28T04:03:10Z
INSDC last update
2019-03-22T12:23:55Z
INSDC status
public
SRA accession
ERS3331152
Sample Name
ERS3331152
Title
786o_pax8
cell_line
786-0
cell_type
kidney cell
developmental stage
adult
disease
clear cell renal carcinoma
genotype
PAX8 doxycycline inducible KD
organism
Homo sapiens
organism part
kidney

Sequenced DNA Library

library_name
786o_pax8_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed as previously described (Galli et al., 2015). Briefly, 8*15 cm dishes of cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes. The cross-linking was quenched by fresh glycine at a final concentration of 0.125 M. The cells were then harvested and lysed in SDS lysis buffer to collect the nuclei. Nuclei suspension was sonicated using a Diagenode Bioruptor (14 cycles 30\" ON and 30\" OFF using setting High) to obtain fragments of 250bp average size. Appropriate amount of chromatin (100ug for PAX8 or 10ug for histone modification) was incubated with the indicated antibodies overnight and complexes retrieved using Protein G coupled Dynabeads. After extensive washes, DNA was reverse crosslinked and purified using AmpPure XP beads. ChIP-seq libraries were constructed using Nugen Ovation® Ultralow System V2 according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
54969252
Reads aligned (%)
173.9
Duplicates removed (%)
10.7
Number of peaks
3037 (qval < 1E-05)

hg38

Number of total reads
54969252
Reads aligned (%)
175.1
Duplicates removed (%)
10.5
Number of peaks
3539 (qval < 1E-05)

Base call quality data from DBCLS SRA