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
ChIP_Input
cell type
E14 embryonic stem cell (ESC)
genotype/variation
TET3
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
(RNA-Seq)Prior to RNA isolation cell lines carrying different Tet3 constructs were enriched for cells with TET3 expression by flow sorting for GFP fluorescence using a BD Influx High-speed Cell Sorter. RNA was isolated using Qiagen RNeasy Micro columns and treated with DNaseI (Ambion). (ChIP-Seq)Chromatin immunoprecipitation was performed as described in (Schmidt et al. 2009). ES cell lines expressing different TET3 isoforms were cross-linked and harvested. 10 ug of a TET3 antibody developed with Millipore (ABE290) was used per precipitation, and cross-linked, sonicated nuclear material was used as input control. (ATAC-Seq)ATAC-seq was performed according to the original protocol (Buenrostro et al., 2015) with the following modifications. 10,000 cells were treated with 0.5μl Tn5 transposase in a total volume of 20 μl for 30 minutes at 37 degrees. (RNA-Seq)Indexed RNA-Seq libraries were constructed from 500 ng total RNA using theTruSeq Stranded Total RNA Library Prep Kit for Illumina with Ribo-Zero Gold. (ChIP-Seq)Sequencing libraries from precipitated DNA were prepared using the Diagenode MicroPlex Library Preparation Kit. (ATAC-Seq)Sequencing libraries were prepared according to the original protocol (Buenrostro et al., 2015). A total of 15 PCR cycles and two rounds of Ampure Bead clean-up were performed.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
27785621
Reads aligned (%)
98.3
Duplicates removed (%)
4.3
Number of peaks
258 (qval < 1E-05)

mm9

Number of total reads
27785621
Reads aligned (%)
98.2
Duplicates removed (%)
4.4
Number of peaks
247 (qval < 1E-05)

Base call quality data from DBCLS SRA