Curated Sample Data


Genome
ce10
Antigen Class
TFs and others
Antigen
cec-3
Cell type Class
Adult
Cell type
Germline containing young adult

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
seq-SDQ4501_T09A5.8_FEM2_AD_ChIP_Rep2
strain
fem-2(b245)
developmental stage
Germline containing young adult
genotype
fem-2(b245)III
Sex
hermaphrodite

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worm extract was made from adult worms. Frozen worm popcorn was ground up in a mixer mill. Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use. Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA. Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay. Libraries were prepared according to Illumina's instructions for ?Preparing Samples for ChIP Sequencing of DNA?, with some variation. DNA was end-repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 DNA polymerase. A?s were then added to the 3? ends of the fragments using Kelow fragment (3? ? 5? exo minus). Paired-end adapters were then ligated onto the ends of the fragments. DNA library was size selected by gel purification, fragments of 250-500 bp were band isolated from an agarose gel. DNA was PCR amplified for 18 cycles. The Bioanalyzer was used to verify fragment purification and quantify DNA. Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

Platform Information


instrument_model
Illumina Genome Analyzer

External Database Query

Logs in read processing pipeline


Number of total reads
13002342
Reads aligned (%)
75.3
Duplicates removed (%)
14.6
Number of peaks
3186 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA