GSM2833202: TE_embryo2_14; Homo sapiens; Bisulfite-Seq - SRA

SRX3337195: GSM2833202: TE_embryo2_14; Homo sapiens; Bisulfite-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 28.4M spots, 8.5G bases, 4Gb downloads

Submitted by: NCBI (GEO)

Study: Single-cell multi-omics sequencing of human early embryos

PRJNA391189 • SRP109843 • All experiments • All runs

show Abstracthide Abstract

DNA methylation, chromatin states, and their interrelationships represent critical epigenetic information, but those are largely unknown in human early embryos. Here, we apply scCOOL-seq (Chromatin Overall Omic-scale Landscape Sequencing) to generate a genome-wide map of DNA methylation and chromatin accessibility at single-cell resolution during human preimplantation development. Unlike in mice, the chromatin of paternal genome is already more open than that of maternal genome at the mid-zygote stage in humans, and this state is maintained until the 4-cell stage. After fertilization, genes with high variations in DNA methylation and those with high variations in chromatin accessibility tend to be two different sets. Furthermore, 1,797 (35%) out of 5,155 widely open chromatin regions in promoters closed when transcription activity was inhibited, indicating a feedback mechanism between transcription and open chromatin maintenance. Our work paves the way for dissecting the complex, yet highly coordinated, epigenetic reprogramming during human preimplantation development. Overall design: In total, we analyzed 265 single cells (13 sperm, 9 oocytes, 10 zygotes, 14 2-cell blastomeres, 26 4-cell blastomeres, 48 8-cell blastomeres, 25 morulae blastomeres, 50 ICM, 48 TE and 22 hESCs) as well as 23 alpha-Amanitin treated 8-cell blastomeres.

Sample: TE_embryo2_14

SAMN07840330 • SRS2639357 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: Illumina HiSeq 4000

Strategy: Bisulfite-Seq

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Construction protocol: The single cell of early embryos were picked into PCR tube containing lysis buffer (10 mM Tris-HCl pH 7.4, 0.25 mM EDTA, 0.25 mM PMSF, 0.5% NP-40, 10 mM DDT, 50 mM NaCl and 1 pg unmethylated lambda DNA) by mouth pipette, in order to release genomic DNA. After pick a single cell into lysis buffer, the tube was vortexed violently for 30 s to lyse efficiently. After spinning down, the lysate was incubated in 5 U GpC MTase (NEB, M0227L) and 160 μM S-adenosylmethionine at 37 ℃ for 45 min and 65 ℃ for 25 min. To release the genomic DNA, 0.5 μl 20 mg/ul protease (QIAGEN) was added and the sample was incubated at 50 ℃ for 3 hrs, 20 ℃ for 20 min. The scCOOL-seq libraries were constructed with slight modification. Briefly, the bisulfite conversion was performed using EZ-96 DNA Methylation-DirectTMMagPrep (Zymo, D5044) according to the user guide. After purification, 10 rounds of amplification were completed in the presence of Klenow exo- (Enzymics) and scBS-seq-P5-N6-oligo1 (CTACACGACGCTCTTCCGATCTNNNNNN). The amplification product was purified by 0.8x Agencourt AMPure XP beads (Beckman). The second strand was synthesied using scBS-seq-P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNN), followed by 0.8x Agencourt AMPure XP beads (Beckman). 13 cycles of PCR were performed to amplify the library using index primer and universal primer (NEB). The libraries were sequenced on Illumina Hiseq 4000 platform on pair-end 150 bp mode.

Experiment attributes:

GEO Accession: GSM2833202

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 28.4M spots, 8.5G bases, 4Gb

Run	# of Spots	# of Bases	Size	Published
SRR6228599	28,413,902	8.5G	4Gb	2018-04-30

ID:: 4666324

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