Curated Sample Data


Genome
ce10
Antigen Class
Histone
Antigen
H3K9me3
Cell type Class
Larvae
Cell type
L3

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
seq-HK00009_H3K9me3:2F3_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_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP. Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications. ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. The protocol uses the Illuimina TruSeq DNA Sample Prep Kit. 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
11803024
Reads aligned (%)
97.0
Duplicates removed (%)
21.0
Number of peaks
878 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA