Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K16ac

Cell type

Cell type Class
Larvae
Cell type
L3
NA
NA

Attributes by original data submitter

Sample

source_name
L3 larvae, H4K16ac ChIP
strain/background
N2
genotype/variation
wild-type
tissue
whole body
developmental stage
L3
Sex
mixed, male, and hermaphrodite
chip antibody
anti-H4K16ac
chip antibody supplier
Millipore

Sequenced DNA Library

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 (normally 500ug-1mg extract with 2-3ug antibody). 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 ul 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 Illumina TruSeq DNA Sample Prep Kit. Prepared samples are sequenced using Illumina GAII or HiSeq 2000 at the High-Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce10

Number of total reads
5096702
Reads aligned (%)
75.4
Duplicates removed (%)
7.5
Number of peaks
402 (qval < 1E-05)

ce11

Number of total reads
5096702
Reads aligned (%)
75.4
Duplicates removed (%)
7.5
Number of peaks
401 (qval < 1E-05)

Base call quality data from DBCLS SRA