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Sample GSM4052482 Query DataSets for GSM4052482
Status Public on May 01, 2023
Title KEN_a2_R1.fastq.gz
Sample type SRA
 
Source name HFF (KEN)
Organism Homo sapiens
Characteristics tissue: Human foreskin fibroblasts - KEN line
Growth protocol hiTSC and hbdTSC cells were grown on a layer of Mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells and cultured in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin. hiTSC and hbdTSC cells were passaged twice on matrigel in order to minimize the presence of MEF feeder cells. hESCs and hiPSCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from samples and incubated in lysis buffer (25mM Tris-HCl at pH8, 2mM EDTA, 0.2%SDS, 200mM NaCl) supplemented with 300μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. hiTSC colonies and hbdTSC colonies were passaged twice on matrigel in order to eliminate the presence of MEF feeder cells.
Libraries were prepared as previously described in Boyle et al., 2012.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
Data processing Raw reads were quality-trimmed and adapters removed.
BSMAP V 2.9 was used to align the paired-end reads to the human genome (hg19)
The methylation ratio of CpGs with sequencing depth of at least 10 reads were computed based on 100bp tiles.
 
Submission date Aug 29, 2019
Last update date May 01, 2023
Contact name Yosef Buganim
E-mail(s) yossib@ekmd.huji.ac.il
Organization name HUJI
Department Developmental Biology and Cancer Research
Lab Yosef Buganim
Street address Jerusalem, IMRIC-Hadassah Medical School
City Jerusalem
ZIP/Postal code 91120
Country Israel
 
Platform ID GPL16791
Series (2)
GSE136599 Direct Induction of Trophoblast Stem Cells from Human Fibroblasts (RRBS)
GSE136600 Direct Induction of Trophoblast Stem Cells from Human Fibroblasts
Relations
BioSample SAMN12655363
SRA SRX6773190

Supplementary file Size Download File type/resource
GSM4052482_KEN_a2_CpG.bed.gz 29.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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