Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
mre-11

Cell type

Cell type Class
Adult
Cell type
Germline containing young adult
NA
NA

Attributes by original data submitter

Sample

source_name
seq-SDQ2366_MRE11_FEM2_AD_ChIP_Rep1
strain
fem-2(b245)
developmental stage
Germline containing young adult
genotype
fem-2(b245)III
Sex
hermaphrodite

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (1 hour 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 extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA. Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay. Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection . 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.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

ce11

Number of total reads
25639516
Reads aligned (%)
91.1
Duplicates removed (%)
38.0
Number of peaks
1721 (qval < 1E-05)

ce10

Number of total reads
25639516
Reads aligned (%)
91.1
Duplicates removed (%)
38.0
Number of peaks
1740 (qval < 1E-05)

Base call quality data from DBCLS SRA