|
| Status |
Public on Apr 24, 2024 |
| Title |
F1-AGVT hPGCLC_2 |
| Sample type |
SRA |
| |
|
| Source name |
NCLCN(XX) AGVT261
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCLCN-261
cell type: human PGCLC
transgene: TFAP2C-EGFP, DDX4-tdTomato knock-in
genotype: WT
time point: culture day 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Gemomic DNA extraction was integrated in "library construction protocol" process.
EM-seq libraries were generated as described previously (Gyobu-Motani, 2023).
EM-seq, (Vaisvila, 2021)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
F1-AGVT (NCLCN-261), hPGCLC day6, replicate 2
|
| Data processing |
Paired-end reads were processed with Trim_Galore! V0.6.3 and mapped on the GRCh38.p12 genome using Bismark v0.22.1 and Bowtie2 v2.3.4.1 with the “-X 2000” option. BAM files were, then, processed with deduplicate_bismark script to remove PCR duplicates, and bismark_methylation_extractor to count methyl- and unmehyl-Cytosine per at CpG or CpA sequences.
Assembly: GRCh38.p12
Supplementary files format and content: bismark report file
Library strategy: EM-seq
|
| |
|
| Submission date |
May 05, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Yukihiro Yabuta |
| E-mail(s) |
yabyab@anat2.med.kyoto-u.ac.jp
|
| Organization name |
Kyoto University, Graduate school of medicine
|
| Department |
Anatomy and Cell Biology
|
| Street address |
Yoshida-Konoe-cho, Sakyo-ku
|
| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE231813 |
In vitro reconstitution of epigenetic reprogramming in the human germ line [EM-Seq] |
| GSE232078 |
In vitro reconstitution of epigenetic reprogramming in the human germ line |
|
| Relations |
| BioSample |
SAMN34721810 |
| SRA |
SRX20238395 |
