|
| Status |
Public on Oct 27, 2021 |
| Title |
HNF6-KO_ESC_Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
HUES8
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: embryonic stem cells, HUES8
genotype: HNF6-Knockout
Stage: undifferentiated
|
| Growth protocol |
HUES8 control and HNF6 KO hESC were subjected to in vitro pancreatic differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at definitve endoderm (DE), pancreatic endoderm (PE) and pancreatic progenitor (PP) stage. Total RNA from ESC-derived pancreatic cells was isolated using GeneJET RNA Purification Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.
After quality check with samples reaching RNA integrity values RIN>8, up to 1µg of total RNA was used for poly-A enrichment and subsequent library preparation with the TrueSeq stranded mRNA Kit from Illumina (HUES8 n=6)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
HiSeq 3000/4000 System (Illumina®) with single-end reads of 50bp
Reads were aligned with STAR aligner (Dobin, 2013; Version 2.5.2b) on human genome hg38 and using Ensembl Transcriptome Annotation e87 as transcriptome reference.
DESeq2 (version 1.22.1) was used for normalization and differential expression analysis (Love, 2014). Only genes with at least 10 reads, an adjusted p-value < 0.05 and abs(FC) > 1.5 were considered
SAMtools and deepTools were used for further processing
Genome_build: hg38
Supplementary_files_format_and_content: We provide bigwig, VST(Variance Stabilizing Transformation) model count and FPKM(Fragments Per Kilobase Million)
|
| |
|
| Submission date |
Aug 05, 2019 |
| Last update date |
Oct 27, 2021 |
| Contact name |
Ivan Costa |
| E-mail(s) |
ivan.costa@rwth-aachen.de
|
| Organization name |
Unikilink RWTH Aachen
|
| Lab |
Computational Biology
|
| Street address |
Pauwelsstraße 19
|
| City |
Aachen |
| ZIP/Postal code |
52074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE131817 |
Role of transcription factor ONECUT1 during in vitro pancreatic differentiation of human pluripotent stem cells |
| GSE135416 |
Role of transcription factor ONECUT1 (HNF6) during in vitro pancreatic differentiation of human pluripotent stem cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN12498909 |
| SRA |
SRX6658378 |
