Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse Embryonic Stem Cells (mESCs)
strain/background
V6.5
cell type
Embryonic stem cells
mll2 status
catalytic dead Mll2 (Y2602A mutant) embryonic stem cells (generated in A. Shilatifard Lab)
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al, Cell Stem Cell 2013). PROseq: We followed the protocol as described previously (Mahat et al, Nat Protoc., 2016) with some modifications. After 4-hydroxytamoxifen treatment for 96 h, nuclei were isolated by Dounce homogenizer with loose pestle. ~10^7 nuclei were subjected to nuclear run-on (30 °C, 3 min) in the presence of 25 µM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer) and 6x10^5 Drosophila S2 spike-in nuclei. Total RNA were extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). Biotinylated nascent RNA were purified by Dynabeads M-280 streptavidin (Invitrogen). After 3' VRA3 adapter ligation and the 2nd purification by Dynabeads, 5' cap and 5' hydroxyl RNA were converted to 5' monophosphorylated RNA by RppH (NEB) and PNK (NEB), respectively. After 5' VRA5 adapter ligation and the 3rd purification by Dynabeads, cDNA were generated by reverse transcription with SuperScript III (Invitrogen) and RP1 primer. PCR by Phusion Hot Start (Thermo) and RP1/RPIx primer sets in 10 cycles amplified indexed DNA libraries. 140–350 bp DNA libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science) and then sequenced by NextSeq 500 system (illumina) with single-read runs. Libraries were prepared according to Illumina instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
50555341
Reads aligned (%)
98.2
Duplicates removed (%)
14.9
Number of peaks
588 (qval < 1E-05)

mm9

Number of total reads
50555341
Reads aligned (%)
97.9
Duplicates removed (%)
14.8
Number of peaks
659 (qval < 1E-05)

Base call quality data from DBCLS SRA