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Sample GSM2931707 Query DataSets for GSM2931707
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
BioSample SAMN08354894
SRA SRX3554440

Supplementary file Size Download File type/resource
GSM2931707_BS003_Astrocytes_MOCK_RRBS.bam.G.bed.gz 40.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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