Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

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

Attributes by original data submitter

Sample

source_name
46C mES cells
cell type
embryonic stem cells
treatment
none
strain
129/Ola
chip antibody
RNAPII Ser2P (Cell Signaling Technology, 13499)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃. Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer. ChIP was done following previously protocol (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 2 μg antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃. DNA Libraries were prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer. RNA-seq libraries for TT-seq were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq X Ten

mm10

Number of total reads
9221631
Reads aligned (%)
0.0
Duplicates removed (%)
12.1
Number of peaks
290 (qval < 1E-05)

mm9

Number of total reads
9221631
Reads aligned (%)
0.0
Duplicates removed (%)
11.9
Number of peaks
262 (qval < 1E-05)

Base call quality data from DBCLS SRA