|
| Status |
Public on Jan 30, 2023 |
| Title |
HPD00_Rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
HPD00 primed-iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primed induced pluripotent stem cells
|
| Treatment protocol |
None
|
| Growth protocol |
Cells were cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (CORNING 356231) (in PBS with MgCl2/CaCl2, Sigma-Aldrich D8662) in E8 medium (made in-house according to12) at 37°C, 5% CO2, 5% O2. Cells were passaged every 3-4 days at a split ratio of 1:8 following dissociation with 0.5 mM EDTA (Invitrogen AM99260G) in PBS without MgCl2/CaCl2 (Sigma-Aldrich D8662), pH8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) is used for library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
trimming was performed using BBDuk from BBTools v38.87
alignment was performed with STAR 2.7.6a
quantification was performed with featureCounts 2.0.1
Genome_build: Human GRCh38.p13 Ensembl release 100
Supplementary_files_format_and_content: raw_counts_matrix.txt is a TSV containing EnsemblID, official gene symbols and raw counts for each condition
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Graziano Martello |
| E-mail(s) |
graziano.martello@unipd.it
|
| Organization name |
University of Padua
|
| Department |
Department of Molecular Medicine
|
| Street address |
viale Colombo 3
|
| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE184562 |
Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells following transient naive genes activation. |
|
| Relations |
| BioSample |
SAMN21542100 |
| SRA |
SRX12287125 |
