Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HMGA1

Cell type

Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HMGA1.vector
cell line
IMR90
cell type
human diploid fibroblasts
infected with
vector
chip antibody
anti-HMGA1 antibody (Abcam, Cat. No. 129153, lot GR211599-2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNAs were extracted for ChIP-seq using 5 ug of anti-HMGA1 antibody (Abcam, Cat. No. 129153, lot GR211599-2). Preparation of the ChIP-seq libraries for next-generation sequencing was performed using the NEB Next Ultra DNA Library Prep kit for Illumina (New England Biolabs) from 10 nanograms of ChIP DNA. Q5 high-fidelity DNA polymerase (New England Biolabs) was used to amplify the ChIP-seq libraries (12 cycles)

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
41669827
Reads aligned (%)
93.6
Duplicates removed (%)
4.0
Number of peaks
1343 (qval < 1E-05)

hg38

Number of total reads
41669827
Reads aligned (%)
95.2
Duplicates removed (%)
3.1
Number of peaks
1170 (qval < 1E-05)

Base call quality data from DBCLS SRA