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Status |
Public on Jun 05, 2020 |
Title |
H3K4me3_Input_Sperm +geminin 3 |
Sample type |
SRA |
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Source name |
input
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Organism |
Xenopus laevis |
Characteristics |
cell type: sperm chip antibody: input
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Growth protocol |
no growth protocol
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 1500 |
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Description |
ChIP, single-ended H3K4me3_sperm_EggTr_GMN_2rep_strict.bed
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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
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Submission date |
Jan 31, 2019 |
Last update date |
Jun 05, 2020 |
Contact name |
Angela Simeone |
E-mail(s) |
angela.simeone@gmail.com
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Organization name |
Genomic Services QIAGEN
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Street address |
200 Hathersage Rd
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City |
Manchester |
ZIP/Postal code |
M13 0BH |
Country |
United Kingdom |
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Platform ID |
GPL21046 |
Series (1) |
GSE125982 |
Epigenetic homogeneity underlies sperm programming for embryonic transcription |
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Relations |
BioSample |
SAMN10855156 |
SRA |
SRX5318624 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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