Curated Sample Data


Genome
ce10
Antigen Class
Histone
Antigen
H3K4me3
Cell type Class
Larvae
Cell type
L2

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
L2 larvae
strain
N2
antibody
H3K4me3
antibody id
ab8580
antibody manufacturer
Abcam

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen worm pellets were ground, fixed for 10 minutes in 1% formaldehyde, fixative was quenched with 125 mM glycine and cross-linked tissue washed 2X with PBS + protease inhibitors, then resuspended in FA buffer and subjected to sonication in a Bioruptor or Bioruptor pico to an average DNA size of 200bp. Extracts were spun down and the soluble fraction used for ChIP. For ChIPs of protein factors, 1mg of ChIP extract was incubated with 5ug antibody; for histone modifications, 500ug ChIP extract was incubated with 2ug of antibody. After overnight incubation with rotation at 4C, 40ul of equilibrated magnetic beads (coupled to protein A or G, depending on antibody) were added and incubated for 2 hrs at room temperature with rotation. Washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer were performed and DNA was eluted in elution buffer (1% SDS in TE with 250 mM NaCl) two times with 57 ul volume each, at 65°C. Samples were treated with RNAse, proteinase K and then crosslinks were reversed overnight at 65°C. DNA was purified on Qiagen PCR purification columns and used for ChIP library preparation. ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used. Samples were sequenced on a HiSeq1500

Platform Information


instrument_model
Illumina HiSeq 1500

External Database Query

Logs in read processing pipeline


Number of total reads
14310994
Reads aligned (%)
89.1
Duplicates removed (%)
23.7
Number of peaks
7201 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA