Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
C3H10T1/2 cells & S2 cells
cell type
C3H10T1/2: C3H embryo-derived mesenchymal progenitor cells; S2: derived from a primary culture of late stage (20-24 hours old) Drosophila melanogaster embryos
genotype
C3H10T1/2: Stably expressing FLAG-HA-tagged wildtype H3.1; S2: None
passage
C3H10T1/2: Passage 10-15; S2: unknown

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
~2x10^7 C3H10T1/2 cells were lysed using digesting buffer (50 mM Tris-HCl pH 7.6, 1 mM CaCl2 and 0.2% Triton X-100) and digested with micrococcal nuclease to obtain mono-nucleosomes. The chromatin were then dialyzed into RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100) for 2 h at 4°C. After centrifugation, soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5% of the mouse cell chromatin. The mixed soluble chromatin was incubated with αH3K36me3 (Active Motif, 61101), αH3K36me2 (Millipore, 07-369) or αH3K27me3 (Cell Signaling Tech, 9733) antibody bound to 75 μl protein A or protein G Dynal magnetic beads (Invitrogen) and incubated overnight at 4°C, with 5% kept as input DNA. Magnetic beads were washed with RIPA buffer and LiCl buffer (0.25 M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate) and chromatin was eluted. ChIP DNA was treated with Proteinase K (Roche) and recovered using Qiagen PCR purification kit. libraries were prepared according to the Illumina TruSeq protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm6

Number of total reads
44417472
Reads aligned (%)
0.6
Duplicates removed (%)
79.9
Number of peaks
999 (qval < 1E-05)

dm3

Number of total reads
44417472
Reads aligned (%)
0.6
Duplicates removed (%)
64.3
Number of peaks
1646 (qval < 1E-05)

Base call quality data from DBCLS SRA