Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human neuron progenitors
cell type
hESC-derived neuron progenitors
passages
30-45
chip-antibody
None
genotype/variation
WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-Seq, total RNA was extracted by TRIzol and subjected to quality control and quantification; For ChIP-Seq, cross-linked cells were lysed in lysis buffer, and the samples were sheared for 14 cycles (30s on/off) in a Bioruptor Pico (Diagenode, Belgium) to achieve an average fragment size of 200-300 bp. Solubilized fragmented chromatin was immunoprecipitated with Anti-FLAG® M2 Magnetic Beads (M8823, Sigma-Aldrich). Antibody-chromatin complexes were pulled down using a magnetic separation rack, washed several times, and then eluted from the magnetic beads. Reverse crosslink was performed subsequently under 65℃ for at least 4 hours. ChIP-DNA was treated with RNase A and Proteinase K, precipitated with ethanol. ChIP-DNA was finally solved in nuclease-free water and quantified using Qubit (Thermo). For RNA-Seq, cDNA libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370S, NEB). High-throughput sequencing was performed on a HiSeq2500 instrument at the Berry Genomics Co, Ltd, using a 125 bp paired-end-reads setting; For ChIP-Seq, sequencing libraries were generated by using the NEBNext Ultra DNA library preparation kit (E7370, NEB). Libraries were quality-controlled and quantified using a Qubit 2.0 Fluorometer (Life Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies). High-throughput sequencing was performed on a Illumina HiSeq instrument at the Berry Genomics Co, Ltd.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
100078279
Reads aligned (%)
70.2
Duplicates removed (%)
25.6
Number of peaks
2164 (qval < 1E-05)

hg19

Number of total reads
100078279
Reads aligned (%)
69.6
Duplicates removed (%)
26.1
Number of peaks
535 (qval < 1E-05)

Base call quality data from DBCLS SRA