Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Adult
Cell type
Young adult
NA
NA

Attributes by original data submitter

Sample

source_name
Whole animal, young adult
strain
met-1(xk4)
replicate
2
generation
F5
barcode
GTGCTT
antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
40 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-H3K36me3 (300-95289, WAKO) was added to 400 μl of the lysate (containing approximately 10 μg DNA). The IP mix was rotated overnight at 4°C. 50 μl of Protein A(for H3K9me3) or protein G (for H3K36me3) Dynabeads (Life Technology) was added and rotated for another 2 hours. The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate). To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 80 μg of proteinase K) at 65 °C for 4 hours with continuous agitation (IP input lysate was treated similarly to reverse crosslink). DNA was extracted by phenolchloroform and dissolved in TE buffer. ChIP-seq libraries were made using NuGen Ovation Ultralow Library Systems v2 according to manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce11

Number of total reads
19070323
Reads aligned (%)
87.6
Duplicates removed (%)
8.7
Number of peaks
0 (qval < 1E-05)

ce10

Number of total reads
19070323
Reads aligned (%)
87.5
Duplicates removed (%)
8.7
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA