|
| Status |
Public on May 01, 2023 |
| Title |
E2_c_R1.fastq.gz |
| Sample type |
SRA |
| |
|
| Source name |
hbdTSC#2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human bastocyst-derived trophoblast stem cells - line #2
|
| 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 |
SAMN12655358 |
| SRA |
SRX6773195 |
