|
| Status |
Public on Jan 12, 2018 |
| Title |
BS003 CDI_astrocytes |
| Sample type |
SRA |
| |
|
| Source name |
CDI_astrocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: iPSC derived astrocytes
parental cell type: CDI - Caucasian ethnicity
treatment & infection status: MOCK
|
| Treatment protocol |
ZIKV 1MOI, 72h
|
| Growth protocol |
organoids were grown for 16 weeks, dissociated and grown as two-dimensional culture for 1 week
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with phenol-chloroform and subsequent NaCl/ethanol precipitation. 200 ng of genomic DNA were fragmented with a Covaris S2 for 6 min using the following program: duty cycle 5%; intensity 5; cycle per burst 200. The sheared DNA was purified with the DNA Clean & Concentrator kit from Zymo Research according to the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted with the EZ DNA Methylation-Gold kit (Zymo Research) following the manufacturer's protocol and eluted in 15 µl low TE buffer.
WGBS libraries were generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) following the manufacturer’s protocol. RRBS library construction was performed as described before by Boyle et al., 2012
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RRBS
bisulfite converted DNA
|
| Data processing |
Raw sequencing reads were trimmed by 10 bp at each end and aligned to the human genome build hg19/GRCh37 using BSMAP (Xi and Li, 2009).
Methylation levels at CpGs were determined with the mCall package from MOABS (Sun et al., 2014). Only CpGs covered by 5 or more reads were used for analysis.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bed files containing chromosomal positions and methylation scores of CpGs
|
| |
|
| Submission date |
Jan 11, 2018 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Sylvie Janssens |
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Department for Developmental and Regenerative Biology
|
| Lab |
Zwaka lab
|
| Street address |
1452 Madison Avenue
|
| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE109104 |
DNA methylation in hESC derived brain organoids and iPSC derived neurons, astrocytes and neural progenitors |
|
| Relations |
| BioSample |
SAMN08354894 |
| SRA |
SRX3554440 |
