|
| Status |
Public on Aug 13, 2022 |
| Title |
FOXA2 KO, Hepatic Progenitor, HP3 |
| Sample type |
SRA |
| |
|
| Source name |
FOXA2 KO, Hepatic Progenitor
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hepatic progenitors
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) |
ramy.elgendy@astrazeneca.com
|
| 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 |
SAMN23971339 |
| SRA |
SRX13396873 |
