GSM1677802: Brain 5W embryo1 HiSeq2500; Homo sapiens; Bisulfite-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Bisulfite-Seq
Antigen
Bisulfite-Seq
Cell type
Cell type Class
Neural
Cell type
Adult brains
NA
NA
Attributes by original data submitter
Sample
source_name
Brain
developmental stage
5 week gestation
gender
male
Sequenced DNA Library
library_strategy
Bisulfite-Seq
library_source
GENOMIC
library_selection
RANDOM
library_construction_protocol
For single cell transcriptome analysis, the protocol for single-cell RNA-Seq has been published previously (Tang et al., 2010; Tang et al., 2009). Briefly, after a MACS or FACS procedure, a single PGC or somatic cell was randomly picked by using a mouth pipette and transferred into lysate buffer. And for DNA methylome analysis, the KIT-positive PGCs that were obtained by FACS were further washed with DPBS, and then DNA was isolated from the cell pellets using DNeasy Blood & Tissue Kits (Qiagen). For single cell RNA-seq library construction, a total of 20–100 ng of cDNA was sheared into 150 bp to 350 bp by Covaris S2 after the generation of cDNA from a single cell, and the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, Inc.) was used to prepare the sequencing library following the manufacturer’s protocol. Briefly, the fragmented cDNA was end-repaired, dA tailed, adapter ligated and then subjected to 10–12 cycles of PCR amplification. Libraries were pooled and sequenced on Illumina HiSeq2500 sequencers for 100-bp paired-end sequencing. And for whole genome bisulfite sequencing (WGBS) library construction, samples of 5–100 ng of genomic DNA were used to construct the PBAT library, as previously described with minor modifications (Miura et al., 2012; Smallwood et al., 2014). Briefly, the isolated genomic DNAs, together with 1% unmethylated lambda DNA (Thermo Scientific), were subjected to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions. The bisulfite-converted templates were then annealed using random nonamer primers with a 5’ biotin tag and a truncated Illumina P5 adapter (5’-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) supplemented with 50 units of klenow polymerase (3’ to 5’ exo-, NEB). The excess primers were removed using 40 U exonuclease I (NEB) before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter). Then, the newly synthesized DNA strands were immobilized using the Dynabeads M280 Streptavidin (Invitrogen) and the original bisulfite-treated DNA templates were removed via two rounds of 0.1 N NaOH washes. The second strands were synthesized using 50 units klenow polymerase (3’ to 5’ exo-, NEB) with random nonamer primers containing a truncated P7 Illumina adapter (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads were further collected and were washed several times, and the library was finally amplified with 4–6 cycles of PCR using 1 U Kapa HiFi HS DNA Polymerase (Kapa Biosystems) together with 0.4 µM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 µM pre-indexed Illumina Reversed primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates index sequences). Amplified libraries were purified with 0.8× Agencourt Ampure XP beads twice and were assessed on the Agilent Bioanalyzer 2100 platform and quantified with a standard curve-based qPCR assay (Kapa Biosystems). The final quality-ensured libraries were pooled and sequenced on the Illumina HiSeq2000/2500 sequencer for 100 bp or 150 bp paired-end sequencing.