|
| Status |
Public on Apr 24, 2024 |
| Title |
F1-AGVT_c107_VT (MS356_057) |
| Sample type |
SRA |
| |
|
| Source name |
NCLCN AGVT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCLCN-261
transgene: TFAP2C-EGFP, DDX4-tdTomato knock-in
cell type: differentiated hPGCLC
genotype: WT
time: culture day 107
treatment: Expansion culture with BMP signalling
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from cells by NucleoSpin RNA XS (MACHEREY-NAGEL, U0902A) according to the manufacturer’s instructions.
1 ng of extracted RNA was used for the reverse transcription and the cDNA amplification described in the previous report (Nakamura, 2015). Sequencing libraries were generated from amplified cDNA as described previously (Murase, 2020).
SC3-seq (Nakamura, 2015)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c107 BMP2(+) AG(+) VT(+)
|
| Data processing |
All reads were processed with cutadapt v1.18 for trimming adaptor and poly-A, then mapped onto GRCh38.p12 transcript references using Tophat v2.1.1.
Resulting BAM files were processed with HTseq v0.9.1 to calculate read counts per gene.
Read counts per gene were divided by total read counts in all chromosomal genes to estimate RPM values for genes.
Resulting BAM files were separately processed with SNPsplit v0.3.2 to split into alleles. Resulting bam files were processed with Htseq v0.9.1 to calculate read counts per gene.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
May 09, 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 |
GPL18573 |
| Series (2) |
| GSE232076 |
In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] |
| GSE232078 |
In vitro reconstitution of epigenetic reprogramming in the human germ line |
|
| Relations |
| BioSample |
SAMN35012144 |
| SRA |
SRX20272183 |
