Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
lin-35

Cell type

Cell type Class
Larvae
Cell type
L1
NA
NA

Attributes by original data submitter

Sample

source_name
LIN35.lin36.whole worm
strain
lin-36 (we36)
developmental stage
starved L1
growth temperature
25°C
tissue
whole worm
chip antibody
LIN35
sample id
AA899

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen starved L1 worms were ground to a powder, which was incubated in 1.5 mM EGS (Pierce 21565) in PBS for 8 minutes, followed by the addition of formaldehyde to a final concentration of 1%, and incubated for a further 8 minutes. The fixation was quenched for 5 minutes by the addition of 0.125 M glycine. Fixed tissue was washed 2X with PBS with protease inhibitors (Roche EDTA-free protease inhibitor cocktail tablets 05056489001) and once in FA buffer (50 mM Hepes pH7.5, 1 mM EDTA, 1% TritonX-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with protease inhibitors (FA+), then resuspended in 1 ml FA+ buffer per 1 ml of ground worm powder. The extract was sonicated to an average size of ~250 base pairs using a Bioruptor Pico (Diagenode), and 10-20 ug of DNA was used per ChIP reaction. ChIP 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.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

ce11

Number of total reads
20187825
Reads aligned (%)
84.4
Duplicates removed (%)
47.1
Number of peaks
8939 (qval < 1E-05)

ce10

Number of total reads
20187825
Reads aligned (%)
84.4
Duplicates removed (%)
47.1
Number of peaks
8939 (qval < 1E-05)

Base call quality data from DBCLS SRA