|
| Status |
Public on Feb 05, 2024 |
| Title |
ROSA26 rep 2, RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse ApcDHep hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: liver
cell type: hepatocytes
genotype: ApcDHep
condition: ROSA26
treatment: tamoxifen 2mg 7 days
|
| Treatment protocol |
RNA profiles from hepatocytes isolated from ApcDHep livers by perfusion with collagenase in three-month old mice injected with AAV8 containing SaCas9 constructs for 1 month and treated with tamoxifen for 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted by Trizol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Normalized-matrix.tsv
R194_r770
|
| Data processing |
STAR version 2.7.6a: STAR --genomeDir $reference_dir --sjdbGTFfile $reference_GTF --runThreadN 20 --readFilesIn $fq1 $fq2 --outFileNamePrefix $echantillon --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
RSEM version 1.3.1: rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_RSEM $resultats_RSEM
R version 3.6.3: DESeq2_1.26.0
Assembly: Ensembl release 96: Mus_musculus.GRCm38
Supplementary files format and content: RSEM count file: count file from the rsem-calculate-expression program
Design DESeq2: tabulated file with the name of the sample file, the sample name, and each factor integrated in the deseq2 design
Normalized matrix: matrix with normalized values from DESeq2
Raw UMI matrix: matrix with raw count value from the QIAGEN pipeline
|
| |
|
| Submission date |
Jun 16, 2022 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Angelique Gougelet |
| E-mail(s) |
angelique.gougelet@inserm.fr
|
| Organization name |
INSERM U1138
|
| Street address |
15 rue de l'école de médecine
|
| City |
Paris |
| ZIP/Postal code |
75006 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE206262 |
RNA and miRNA profiles in mouse hepatocytes ApcdeltaHep ROSA or DLK1DeltaWRE |
|
| Relations |
| BioSample |
SAMN29145335 |
| SRA |
SRX15763803 |
