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Sample GSM5731239 Query DataSets for GSM5731239
Status Public on Aug 13, 2022
Title FOXA2 KO, Mature Hepatocytes, Samp10
Sample type SRA
 
Source name FOXA2 KO, Mature Hepatocytes
Organism Homo sapiens
Characteristics cell type: Mature hepatocytes
genotype: FOXA2 knock out
Treatment protocol No chemical treatment was carried out. CRISPR-CAS9 was used to create deletion in FOXA2 gene in iPSC generated from two healthy controls.
Growth protocol iPSC were grown on matrigel coated plates and allowed to undergo differentiation using a previously published protocol (Ang et al., Cell Reports 2018)
Extracted molecule total RNA
Extraction protocol Cells were collected using TRIzol reagent (Cat Number.15596026) and RNA was extracted using Norgen rna extraction kit (Cat Number. 47700)
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library(Cat # 20020594, for Hepatic Progenitors) and NEBNext Ultra Directional Library Prep Kit (NEB, E7420L, for Mature Hepatocytes) following the manufacturer’s protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina sequencing and conventional base calling
Sequenced reads were quality-controlled by FASTQC and trimmed by Trimmomatic v.0.36 for adaptor sequence (if present).
Clean sequences were mapped to the GRCh38 whole genome using STAR v2.7.2b
The uniquely-mapped reads aligned to exons were counted with HTSeq v.0.9.1 , then tested for the presence of differentially expressed genes (DEGs) by the DESeq2 R package v.1.26.0
Genome_build: Homo Sapiens GRCh38
Supplementary_files_format_and_content: tab-delimited files with the raw counts for each sample
 
Submission date Dec 13, 2021
Last update date Aug 13, 2022
Contact name Ramy Elgendy
E-mail(s) [email protected]
Organization name AstraZeneca
Street address Pepparedsleden 1
City Mölndal
State/province Göteborg
ZIP/Postal code 43153
Country Sweden
 
Platform ID GPL20301
Series (1)
GSE190763 Effect of FOXA2 knockout (KO) on transcriptome wide gene expression in hepatic progenitors (HP) and mature hepatocytes (MH)
Relations
BioSample SAMN23971336
SRA SRX13396870

Supplementary file Size Download File type/resource
GSM5731239_FOXA2_KO_Mature_Hepatocytes_sample_10_S30.txt.gz 205.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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