Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Larvae
Cell type
L2-L3
NA
NA

Attributes by original data submitter

Sample

source_name
ssup-72(0) worms
Stage
L2-L3
strain
ssup-72(0)
chip antibody
4H8

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Larvae were cross-linked at RT for 30 min in 2% formaldehyde (Fisher). Crosslinking was quenched with 0.25 M glycine for another 30 min at RT. For each immunoprecipitation, 10 mg 4H8 antibody was coupled to 50 ml Dynabeads (Invitrogen) coated with protein A and G (25 ml protein A plus 25 ml protein G). After sonication and centrifugation, 1.5 ml supernatant (around 30 mg protein) was pre-cleared by rotating for 2 hrs with 30 ml empty Dynabeads (15 ml protein A plus 15 ml protein G) before incubating with 4H8-coupled Dynabeads at 4°C overnight. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce11

Number of total reads
37064023
Reads aligned (%)
73.1
Duplicates removed (%)
21.9
Number of peaks
11433 (qval < 1E-05)

ce10

Number of total reads
37064023
Reads aligned (%)
73.1
Duplicates removed (%)
21.9
Number of peaks
11320 (qval < 1E-05)

Base call quality data from DBCLS SRA