Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
mrg-1

Cell type

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

Attributes by original data submitter

Sample

source_name
seq-SDQ4068_MRG1_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
Worm extract was made from adult worms. Frozen worm popcorn was ground up in a mixer mill. Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use. 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

ce10

Number of total reads
36072847
Reads aligned (%)
60.4
Duplicates removed (%)
37.3
Number of peaks
6456 (qval < 1E-05)

ce11

Number of total reads
36072847
Reads aligned (%)
60.4
Duplicates removed (%)
37.3
Number of peaks
6455 (qval < 1E-05)

Base call quality data from DBCLS SRA