|
| Status |
Public on May 05, 2024 |
| Title |
bulk RNA-Seq Sox9-derived organoids 1 |
| Sample type |
SRA |
| |
|
| Source name |
primary liver cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: liver
|
| Treatment protocol |
none
|
| Growth protocol |
primary liver cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell suspension are obtained by enzymatic digestion of liver or macroscopic lesions. YFP+ cells (indicative of efficient Cre-mediated recombination of floxed alleles) are isolated by Flow cytometry for further processing.
standard protocol for the analysis of bulk RNA-Seq data were performed by the Penn Genomic Core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Sox9-derived organoids 1
|
| Data processing |
the raw reads were mapped to the mm9 genome assembly using the RNA-seq aligner STAR version 2.5.4b. The algorithm was given known gene models provided by GENCODE (release_27_hg19) (https://www.gencodegenes.org/) to achieve higher mapping accuracy. Quantification was also performed by STAR using the quantMode Genecounts flag. These raw counts were normalized (TMM normalization implemented in edgeR, followed by the voom transformation). Lastly, the Bioconductor package Limma was used to assess differential expression using linear models. Genes were considered for further analysis if the FDR<0.05 and the fold change>1.5 between replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Spreadsheet includes raw gene counts for each sample as obtained with featureCounts (part of the subread package) using ensembl_mus_musculus_87/Mus _musculus.GRCm38.87.chr.gtf
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
May 05, 2024 |
| Contact name |
Patrick Viatour |
| E-mail(s) |
viatourp@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3501 Civic Center Blvd
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE173949 |
Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model (Bulk RNA-Seq) |
| GSE173952 |
Expression data from early and macroscopic HCC lesions isolated from the Rb family Triple Knock Out model |
|
| Relations |
| BioSample |
SAMN19025618 |
| SRA |
SRX10786634 |
