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Sample GSM2495702 Query DataSets for GSM2495702
Status Public on Oct 25, 2017
Title LIN-35 ChIP-seq in wild-type late embryos, rep 1a
Sample type SRA
 
Source name LIN-35 ChIP-seq in wild-type late embryos
Organism Caenorhabditis elegans
Characteristics genotype: wild-type
tissue: late embryo
chip-antibody: SDIX/Novus Biologicals Q2003
input control: wild-type extract rep 1a
Treatment protocol Frozen late embryos were ground using a mortar and pestle and crosslinked for 10 minutes in 1% formaldehyde.
Growth protocol Synchronized N2 or lin-35(n745) L1s were grown in standard S-basal media liquid culture for 72 or 96 hours, respectively. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated for up to 3.5 hours then frozen in liquid nitrogen
Extracted molecule genomic DNA
Extraction protocol Crosslinked samples were resuspended in FA buffer, and sonicated in a Diagenode Bioruptor (60 pulses of 30 seconds at full power with 1 minute rest in between). Extracts were clarified, protein concentrations determined using a Qubit fluorometer, and precleared with Protein A Dynabeads before proceeding to ChIP. DRM subunits were individually IPed using 1-5 μg appropriate antibodies on prepared lysates. ChIPs were performed with 1-2 mg of extract, and 2% of the extract was set aside for an input reference control. ChIPs were incubated overnight at 4°C with 1% sarkosyl. Protein A Dynabeads equilibrated in 20 μL FA buffer were added and incubated for 2 hours at 4°C. ChIPs were washed with the following buffers: once with FA buffer containing 1 M NaCl, once with FA buffer containing 0.5 M NaCl, once with TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). 2 elutions of 50 μL elution buffer containing TE plus 1% SDS and 250 mM NaCl were incubated at 55°C. Eluted ChIP and input samples were incubated with proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified by phenol-chloroform extraction and ethanol precipitation using glycogen as a carrier.
Libraries from wild-type late embryos, extracts rep 1a, 1b, 2a, and 2b: Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature. Libaries from wild-type late embryo extract rep 3 and lin-35(n745) late embryo extracts rep 1-3 were prepared using the TruSeq ChIP Sample Prep Kit (Illumina). Amplifed libraries were size selected to obtain 200-500 base pair fragments using Agencourt AMPure XP beads (Beckman Coulter).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description processed data file:
LIN-35.SDQ2003.N2.rep0.vsInputRep0.SES.bw
LIN-35.SDQ2003.N2.IDR.0.01.narrowPeak
Data processing bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10
SPP v1.10.1 peak caller (from phantompeakqualtools) was run on the bowtie output for each subunit for each replicate (rep 1-3), pseudoreplicates (rep1.pr1,rep1.pr2,etc), pooled replicates (rep 0), and pooled psuedoreplicates (rep0.pr1,rep0.pr2) against pooled input with the following parameters: -npeak=40000, -savn, -savp, -rf
IDR v2.0.2 was run on SPP peak outputs for each subunit on replicates (rep1v2, rep1v3, rep2v3) defining N1-2, N1-3, and N2-3 (threshold IDR < 0.01), selfPseudoReplicates (rep1.pr1vpr2) defining N1, N2, and N3 (threshold IDR < 0.02), and pooledPseudoReplicates (rep0.pr1vpr2) defining Np (threshold IDR < 0.005). N1-2, N1-3, and N2-3 were averaged to define Nt for each factor, which was selected as the final number of peaks passing the 1% IDR threshold. The Rescue Ratio (Np/Nt) and Self-consistency ratio (Max(N1,N2,N3)/Min(N1,N2,N3)) were calculated to check for low consistency between replicates (low consistency is defined as ratio >> 2).
The deepTools v2.0 tool bamCompare was used to normalize to input and create bigwig signal track files for visualization. Pooled replicates were normalized to pooled input using the Signal Extraction Scaling (SES) method using the following parameters: --scaleFactorsMethod SES--numberOfSamples=100000 --ratio ratio --binSize 10 --pseudocount=1 --extendReads x (x was calculated from SPP analysis for each factor)
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bigwig signal track files of combined replicates (rep0) for each ChIP normalized to pooled input using the SES method (Diaz et al. 2012) and narrowPeak files containing peak regions for each ChIP (IDR < 0.01)
 
Submission date Feb 19, 2017
Last update date May 15, 2019
Contact name Paul Goetsch
Organization name UCSC
Department MCD Biology
Lab Strome lab
Street address 1156 High Street
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
 
Platform ID GPL9269
Series (1)
GSE95071 Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB’s innate function as the repressor of DREAM target genes
Relations
BioSample SAMN06348014
SRA SRX2576632

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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