|
| Status |
Public on Jun 16, 2020 |
| Title |
CT3 hTSC |
| Sample type |
SRA |
| |
|
| Source name |
Human trophoblast stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: trophoblast stem cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was collected using Qiagen Blood and Tissue kit. An RNase A treatment step was included according to manufacturer’s protocol. DNA concentration was measured using Nanodrop.
500ng of DNA was fragment using Covaris M202 instrument and 250ng was processed with a Zymogen Bisulfite conversion kit. The equivalent of 50ng-100ng of starting DNA used for library prep, which was conducted using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) and Unique Dual Index adaptors according to manufacturer protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
WGBS library for CT3 human trophoblast stem cells
|
| Data processing |
The adaptor sequences of paired end 150bp WGBS raw reads were first trimmed based on the FastQC(v0.11.8)(Andrews, 2010) report using Cutadapt(v1.9.1)(Martin, 2011).
Then the last 15 bp of read1 and first 15 bp of read2 were cut according to Swift kits manual using Cutadapt(v1.9.1)(Martin, 2011).
Trimmed paired end reads were then aligned to human reference genome (GRCh38) using BSMAP (v2.7.4)(Xi and Li, 2009) allowing 2 mismatches.
Methylation level over each cytosine were then calculated using BSMAP (v2.7.4) methratio.py scripts.
Potential unconverted reads were removed as described before with customized function incorporated in the methratio.py script(Cokus et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: Fomat: txt; Content: CG methratio
|
| |
|
| Submission date |
May 08, 2020 |
| Last update date |
Jun 17, 2020 |
| Contact name |
Yixin Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
Zhejiang University
|
| Street address |
718 East Haizhou Rd.
|
| City |
Haining |
| ZIP/Postal code |
314400 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE150168 |
Naïve human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome [Bisulfite-Seq] |
| GSE152104 |
Naïve human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome |
|
| Relations |
| BioSample |
SAMN14858751 |
| SRA |
SRX8295673 |
