|
| Status |
Public on Feb 23, 2023 |
| Title |
FASi treated APOB-/- organoids from donor 1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
individual: donor 1
tissue: Liver
cell line: Human hepatocyte organoid
cell type: Hepatocyte
genotype: APOB-mutant
treatment: FASi 7 days
|
| Treatment protocol |
Organoids were treated for 7 days with the indicated drug or vehicle
|
| 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 |
FASi_donor1
|
| 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 |
Dec 23, 2022 |
| Last update date |
Feb 23, 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) |
| GSE221705 |
Transcriptomic characterization of control and drug-treated APOB-mutant organoids to study steatosis-resolving drug effects |
|
| Relations |
| BioSample |
SAMN32389086 |
| SRA |
SRX18840742 |
