|
| Status |
Public on Jul 25, 2022 |
| Title |
Liver_scRNASeq_LSL_7d_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver_scRNASeq_LSL_7d
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: ROSA26-rtTA-IRES-EGFP; tetYAP
treatment: doxycycline food for 7 days
tissue: Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver cells from collagenease treated whole livers were processed with the GemCode Single Cell Platform loaded into Chromium microfluidic chips.
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries were prepared with Chromium Single Cell v2 and v3 reagent kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads alignment and the gene-barcode matrices were obtained using cellranger 10X v. 2.1.1 and mm10 genome assembly
Replicates aggregation and downstream analyses were carried out using Seurat v.2 R package
Cell type identification was carried out using scMCA (single-cell mouse cell atlas) R package
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts_scRNASeq
|
| |
|
| Submission date |
Sep 30, 2019 |
| Last update date |
Jul 25, 2022 |
| Contact name |
stefano campaner |
| E-mail(s) |
stefano.campaner@iit.it
|
| Organization name |
fondazione Istituto italiano di tecnologia
|
| Department |
Center for Genomic Science
|
| Lab |
Cancer Biology
|
| Street address |
via adamello 16
|
| City |
milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE138189 |
Single cell transcripional analysis of adult liver cells following YAP induction [Liver_scRNAseq_allTissue] |
| GSE138191 |
Genome-wide chromatin analyses and RNA-seq of liver cells upon YAP induction |
|
| Relations |
| BioSample |
SAMN12875217 |
| SRA |
SRX6924524 |
