Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878 cell line
biomaterial_provider
GM12878
cell line
GM12878

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The mouse line C57Bl/6 was bred and maintained in groups of 3-4 per cage with food ad libitum. 8-10 week old mice were anesthetized with isoflurane and decapitated. The cerebellum was rapidly dissected and frozen on dry ice and stored at -80 ℃ until used for nuclei isolation. Cerebellum was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl 100 mM PMSF and 5 μl 1 M DTT. In addition, 7.5 μl 40 U/μl RNase inhibitor (N2611, Promega) was also added when RNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was transferred into an ultracentrifugation tube (355631, Beckman Coulter) and underlayered with 9.5 ml sucrose cushion (1.8 M sucrose, 3 mM Mg(Ac)2 and 10 mM Tris-HCl). The homogenate was centrifuged at 32,300 rpm (107,164g) for 2.5 h at 4 ℃ with 70 Ti rotor (Optima L-90K Ultracentrifuge, Beckman Counter). The spinning was slowly braked to avoid disturbing the nuclei pellet. All the supernatant was removed and the nuclei was gently resuspended in 0.4 ml 10% normal goat serum (50062Z, Life Technologies) and 1.6 ml Dulbecco's phosphate-buffered saline (14190144, Life Technologies). For RNA-seq, 3 μl 40 U/μl RNase inhibitor was added into nuclei suspension. The integrity and the number of nuclei were checked under the microscope. 32 μl 2 ng/μl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was incubated with the nuclei suspension (2 ml) for 1 h at 4 ℃ on an end-to-end rotator. The stained samples were sorted using a FACS (BD FACSAria, BD Biosciences) with 50,000 to 100,000 unlabeled nuclei used as non-staining control. Human genomic DNA was purified from GM 12878 cells using QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s protocol and suspended in 50 µl EB buffer. Mouse genomic DNA was purified using QIAamp DNA Blood Midi Kit (Qiagen) from nuclei and suspended in 200 µl AE buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0). The eluate was reloaded on the column membrane and spun to maximize DNA yield. Mouse DNA was concentrated by ethanol precipitation to 20 µl EB buffer. RNA was extracted from ~10,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment step was included following kit instructions to remove gDNA contamination. SurfaceChIP-seq library construction. The sequencing libraries were constructed using TruePLEX DNA-seq kit (Rubicon Genomics) or Accel-NGS 2S plus DNA library kit (Swift bioscience). GM12878 samples starting with ≥ 100 cells using DNA oligo linker were prepared using TruePLEX kit. The other samples are prepared using Accel-NGS 2S plus kit following instructions. mRNA-seq library construction. RNA was extracted from ~100,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment was included following manufacturer instructions to remove gDNA contamination. mRNA-seq libraries were prepared using SMART-seq v4 Ultra Low Input RNA kit (Clontech) and Nextera XT DNA library prep kit (Illumina) following instructions. ChIP-seq and mRNA-seq

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
32535610
Reads aligned (%)
91.8
Duplicates removed (%)
83.0
Number of peaks
161 (qval < 1E-05)

hg19

Number of total reads
32535610
Reads aligned (%)
91.1
Duplicates removed (%)
84.4
Number of peaks
139 (qval < 1E-05)

Base call quality data from DBCLS SRA