Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GLYR1

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa Clone KO1.2, anti-NDF 7
cell type
HeLa S3
genotype/variation
NDF knockout 1.2
chip antibodies
NDF7, home-made

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For human ChIP-seq, ~15 million wild-type HeLa S3 cells or the indicated hNDF knockout cells were collected and crosslinked with 1% formaldehyde. After cell lysis and genome fragmentation by sonication, samples were incubated with 20 μL of Dynabeads Protein A that were pre-bound with 1 μL of NDF antiserum. [Note that 1 μL of hNDF antiserum was optimal for hNDF antiserum #7. For hNDF antiserum #6, 2 μL was the optimal volume.] Bound DNA were isolated with MinElute columns (Qiagen). For human RNA-seq, total RNA was purified by using the PureLink RNA Mini RNA Kit (Thermo Fisher Invitrogen). Mouse BMDM ChIP-seq and RNA-seq were performed as described in Kaikkonen, M. U. et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51, 310-325. Human ChIP-seq libraries were prepared by end-repair, A-tailing, and ligation of Illumina TruSeq adaptors, which was then followed by PCR amplification and size selection with AMPure beads (Beckman Coulter). Human RNA-seq libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Mouse ChIP-seq libraries were prepared from ChIP DNA and inputs by blunting, A-tailing, and adapter ligations were performed by using NextFlex barcode adapters. Mouse RNA-seq libraries were prepared from poly(A)-enriched mRNA, as described in Kaikkonen, M. U. et al. Mol. Cell 51, 310-325.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
41121082
Reads aligned (%)
81.8
Duplicates removed (%)
14.6
Number of peaks
1239 (qval < 1E-05)

hg38

Number of total reads
41121082
Reads aligned (%)
84.0
Duplicates removed (%)
13.2
Number of peaks
1267 (qval < 1E-05)

Base call quality data from DBCLS SRA