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Sample GSM4008468 Query DataSets for GSM4008468
Status Public on Oct 27, 2021
Title HNF6-KO_PE_Rep2
Sample type SRA
 
Source name HUES8
Organism Homo sapiens
Characteristics tissue: embryonic stem cells, HUES8
genotype: HNF6-Knockout
Stage: pancreatic endoderm
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 SAMN12498840
SRA SRX6658388

Supplementary file Size Download File type/resource
GSM4008468_HNF6-KO_PE_Rep2_Forward.bw 8.8 Mb (ftp)(http) BW
GSM4008468_HNF6-KO_PE_Rep2_Reverse.bw 9.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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