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Sample GSM3587280 Query DataSets for GSM3587280
Status Public on Jun 05, 2020
Title Input_Sperm2 paired-end
Sample type SRA
 
Source name input
Organism Xenopus laevis
Characteristics cell type: sperm
chip antibody: input
Growth protocol no growth protocol
Extracted molecule genomic DNA
Extraction protocol Preparation sperm and egg extract treated sperm chromatin for ChIP-seq: Chromatin fractionation and chromatin immunoprecipitation (ChIP) were performed as described before (Hisano et al., 2013 and Teperek et al., 2016) with slight modifications. Xenopus sperm were purified from their testes and permeabilised before ChIP. Sperm or egg extract treated sperm chromatin was resuspended in 50 l of Buffer 1 (0.3 M Sucrose, 15 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM DTT) and added 50 l of Buffer 1 with detergent (Buffer 1 including 0.5% NP40 and 1% NaDOC). Samples were incubated for 10 min on ice. 100 l of MNase buffer (0.3 M Sucrose, 85 mM Tris, 3 mM MgCl2, 2 mM CaCl2, 2.5U of micrococcal nuclease: Roche 10107921001) was added in to each tube (0.5 million of cells per tube). Tubes were incubated at 37C for 30 min in pre-warmed water bath. Reaction was stopped by adding 2 l of 0.5 M EDTA pH8.0 in the same order as started. Tubes were vortexed and placed on ice for at least 5 min. Supernatant and pellet were separated by centrifugation at 13,000 rpm for 10 min at room temperature. Supernatant was transferred to new tube and stored on ice. For ICeChIP, semi-synthetic nucleosomes were spiked in as described (Grzybowski et al., 2015) before MNase digestion. Preparation Chromatin for embryo ChIP-seq: ChIP was performed as described previously (Gentsch and Smith, 2014) with the following modifications. Blastula (stage 7) embryos were generated by in vitro fertilization. For each ChIP experiment, 50 embryos were fixed in 2 mL of 1% Formaldehyde in 1x MMR for 25 min at room temperature, followed by 4 washes with 1 ml of 1xMMR and equilibration in 500 μl HEG solution (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 20% Glycerol) at 4°C, then excess buffer was removed and samples were frozen at −80°C. To extract chromatin, the samples were transferred to 2 ml tube or 15 ml Falcon tube and homogenized in 200-250 μl of sonication buffer (20 mM Tris-HCl pH 8.0, 70 mM KCl, 1 mM EDTA pH 8.0, 10% Glycerol, 5 mM DTT, 0.125% NP40, 1x complete protease inhibitors), by pipetting up and down in a 1 ml pipette tip. 250 μl of diagenode beads were transferred to diagenode falcon tube (Diagenode, C1020031). 750 μl of embryo lysates were added and diagnode falcons were transferred to the sonicator bath (diagnode bioruptor). Sonication is carried out in 30 cycles (with 30 s on/off cycles). Sonicated embryo extract was transferred into eppendorf tubes. Chromatin was collected by centrifugation for 5 min at top speed in tabletop centrifuge at 4°C. Chromatin extract was transferred to new tube and stored on ice.
ChIP-seq library preparation was performed using the TruSeq DNA kit (Illumina, FC-121-2001) according to the manufacturer’s protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description ICeChIP, paired-ended
Data processing Adatpert trimming (cutadapt)
duplicate marked with Picard(2.14 - markDupicates) and removed; removal of reads with quality below 20 (samtools view -q20)
BAM files sorted, unmapped reads and secondary alignment removed; properly paired reads were joined to have fragments information and stored as BEDPE
BED files extracted from BEDPE
Given the length of fragments, BED for each fragment group have been created (150 - 110 - 70)
Peak calling with MACS2 (-q 0.01) with default options for H3K4me3 in frog ,and H3K4me3 H3K27me3 in Human, with broad option in H3K27me3 frog.
HMD was estimated as reported in paper considering coverages in windows 50-bp wide across the genome.
Genome_build: Xenopus laevis 6.1
Genome_build: HG38
Supplementary_files_format_and_content: BED files for peaks, bigwig files for tracks
 
Submission date Jan 31, 2019
Last update date Jun 05, 2020
Contact name Angela Simeone
E-mail(s) angela.simeone@gmail.com
Organization name University of Cambridge
Department Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL21046
Series (1)
GSE125982 Epigenetic homogeneity underlies sperm programming for embryonic transcription
Relations
BioSample SAMN10855163
SRA SRX5318617

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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