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Sample GSM6639970 Query DataSets for GSM6639970
Status Public on Mar 15, 2023
Title PRKAR2A knock-out human hepatocyte organoid, clone 2
Sample type SRA
 
Source name Liver
Organism Homo sapiens
Characteristics tissue: Liver
cell line: Human hepatocyte organoid
cell type: Hepatocyte
genotype: PRKAR2A mutant
treatment: Hepatocyte medium
Growth protocol Organoids were cultured in a humidified atmosphere with 5% CO2 at 37C
Extracted molecule total RNA
Extraction protocol total RNA was isolated using TRIzol Reagent (Thermo Fisher)
RNA libraries were prepared using TruSeq Stranded mRNA polyA kit (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description PRKAR2A_2
Data processing Quality control on the sequence reads from the raw FASTQ files was done with FastQC.
TrimGalore was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA after which the resulting reads were aligned to the reference genome fasta (genome.fa) using the STAR aligner.
Followup QC on the mapped (bam) files was done using Sambamba, RSeQC and PreSeq.
Read counts were then generated using the Subread FeatureCounts module with the Homo_sapiens.GRCh37.74.gtf file as annotation
Assembly: hg19
Supplementary files format and content: csv file including feature raw counts for all samples
 
Submission date Oct 14, 2022
Last update date Mar 15, 2023
Contact name Delilah Hendriks
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platform ID GPL30173
Series (1)
GSE215785 Transcriptomic characterization of FLC-mutant engineered human hepatocyte organoids
Relations
BioSample SAMN31282925
SRA SRX17890271

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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