Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ama-1

Cell type

Cell type Class
Larvae
Cell type
L2
NA
NA

Attributes by original data submitter

Sample

source_name
L2 larvae
developmental stage
L2 larvae
tissue
whole animal
strain
AM1061
genotype
unc-119(ed9)III, rmSi1[hsf-1p(4kb)::hsf-1(minigene)::gfp::3'UTR(hsf-1)+Cbrunc-119(+)] II; hsf-1(ok600)I
chip antibody
anti-AMA-1 (Novus, #38520002)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worms were collected and washed in cold M9 buffer, crosslinked with 2% formaldehyde at room temperature for 15 min., re-suspended in FA buffer, lysed by douncing in a Kontes 2 ml glass dounce and sonicated in Bioruptor to yield 200 bp–800 bp size DNA fragments. Extracts corresponding to 200 μg of protein from L2 Larvae or 400 μg of protein from young adults was used for each pull-down. For ChIP-seq analysis of HSF-1 and Pol II, 5 μl of antibody against GFP (clontech, polyclonal) or 2.5 μl of antibody against Pol II (Novus) was used in each immunoprecipitation. DNA was pooled from 6 immunoprecipitations for each ChIP-seq experiment. Libraries were prepared following PrepX DNA library protocol with Appollo 324 system.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce10

Number of total reads
6113677
Reads aligned (%)
60.3
Duplicates removed (%)
34.1
Number of peaks
3890 (qval < 1E-05)

ce11

Number of total reads
6113677
Reads aligned (%)
60.3
Duplicates removed (%)
34.1
Number of peaks
3889 (qval < 1E-05)

Base call quality data from DBCLS SRA