Curated Sample Data


Genome
ce10
Antigen Class
TFs and others
Antigen
zfp-1
Cell type Class
Larvae
Cell type
L3

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
seq-JL00006_ZFP1_N2_L3_ChIP_Rep2
strain
N2
developmental stage
L3 Larva
genotype
wild type
sex type
mixed Male and Hermaphrodite population

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worm_L3_extraction_vKI1.doc Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac. Solexa_Library_Prep_vKI3 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
13613870
Reads aligned (%)
94.2
Duplicates removed (%)
32.9
Number of peaks
8710 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA