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Sample GSM6416148 Query DataSets for GSM6416148
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

Supplementary file Size Download File type/resource
GSM6416148_REPR05.quant.sf.gz 3.2 Mb (ftp)(http) SF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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