|
| Status |
Public on Mar 29, 2023 |
| Title |
iBeta-like rep5 |
| Sample type |
SRA |
| |
|
| Source name |
Foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Foreskin
cell line: HFF10.3
cell type: fibroblast
treatment: Overexpression Ngn3, Pdx1,Mafa,Pax4, Nkx2-2
|
| Treatment protocol |
When fibroblasts reached 80% confluence, they were infected with a polycystronic adenovirus expressing Ngn3+Pdx1+Mafa (day 1). At days 4 and 7, cells were treated with adenoviruses encoding Pax4 and Nkx2-2 respectively.
|
| Growth protocol |
Parental fibroblasts and reprogrammed cells were maintained in RPMI-1640 with 6% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using NucleoSpin RNA XS (Mackerey Nagel).
Total RNA (200ng) was used to construct mRNA strand-specific RNA libraries using the Illumina® Stranded mRNA Prep Ligation kit (Ref.20040532) and IDT for Illumina RNA UD Indexes (Ref.20040553).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
We generated a custom transcriptome by adding the Gencode M10 mouse transcripts from the transgenes Pdx1, Pax4, Neurog3 and Mafa to the human GENCODE release 39 human transcripts.
We assigned reads to this custom transcriptome using Salmon v.1.3.0 with parameters “-l A --validateMappings”.
Assembly: Custom hg38 with some transcripts from mm10
Supplementary files format and content: Tab-delimited quant.sf files outputed by Salmon
|
| |
|
| Submission date |
Jul 29, 2022 |
| Last update date |
Mar 29, 2023 |
| Contact name |
Rosa Gasa |
| E-mail(s) |
rgasa@recerca.clinic.cat
|
| Phone |
+34 661649269
|
| Organization name |
IDIBAPS
|
| Street address |
C/Rosselló 149-153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE210075 |
Direct reprogramming of human fibroblasts towards beta-like cells |
|
| Relations |
| BioSample |
SAMN30051703 |
| SRA |
SRX16731489 |
