|
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 |