Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Adult
Cell type
Whole worm
NA
NA

Attributes by original data submitter

Sample

source_name
C. elegans whole worm lysate
age
mixed stage
genotype
cebp-1(tm2807); juIs418 [Pcebp-1::FLAG::CEBP-1::cebp-1 3'UTR]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
FLAG::CEBP-1-DNA complexes were isolated with anti-FLAG antibody. Both ChIPed DNA and input genomic DNA were ligated to specific adaptors and amplified by barcode primers. 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 (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with primers for 12 (1st) or 18 (2nd) cycles with DNA polymerase (KAPA) and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was quantified using Qubit. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce11

Number of total reads
44152645
Reads aligned (%)
74.5
Duplicates removed (%)
57.6
Number of peaks
0 (qval < 1E-05)

ce10

Number of total reads
44152645
Reads aligned (%)
74.5
Duplicates removed (%)
57.6
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA