Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Adult
Cell type
Whole body
NA
NA

Attributes by original data submitter

Sample

source_name
whole worms
genotype/variation
BAT1753 [hmg-3(bar24[hmg-3::3xHA]) I]
tissue
whole worms
passages/stage
L4

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worms were frozen in liquid nitrogen prior to pulverization using a hammer as well as mortar and pestle. The resulting powder was fixed in 1,1 % formaldehyde. The sample was sonicated twice using a Bioruptor (Diagenode) for 15 times 30 sec ON, 30 sec OFF on high settings at 4°C. 5% of the supernatant was taken off as input and the protein concentration was determined using Bradford assay. The input was digested with 1 µl RNase A for 1 h at 37°C, the crosslink was reversed as described for the ChIP sample. 2-4 mg of extract was used for ChIPs. Library preparation was done following standard Bioo Scientific protocol and NEXTflex® qRNA-Seq™ Kit v2 (Bioo Scientific). Libraries were sequnced using single end sequencing length of a 75 nucleotides on a HiSeq400 machine (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

ce11

Number of total reads
27766032
Reads aligned (%)
89.8
Duplicates removed (%)
30.1
Number of peaks
3357 (qval < 1E-05)

ce10

Number of total reads
27766032
Reads aligned (%)
89.7
Duplicates removed (%)
30.1
Number of peaks
3357 (qval < 1E-05)

Base call quality data from DBCLS SRA