|
| Status |
Public on Jul 01, 2021 |
| Title |
Nizatidine-treated immune cells |
| Sample type |
SRA |
| |
|
| Source name |
Liver immune cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver tissues from patients with advanced liver disease and HCC
cell type: CD45+ immune cells
treatment: Nizatidine
|
| Treatment protocol |
Cells were treated for 48h with Nizatidine or DMSO (vehicle). Single cells were sorted into 384 well cell capture plates (Single Cell Discovery, https://www.scdiscoveries.com) using SH800 cell sorter (Sony).
|
| Growth protocol |
CD45+ liver immune cells were isolated from liver tissues of patients with advanced liver disease and HCC by flow cytometry.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
scRNA-Seq was performed by Single-Cell Discoveries B.V. using SORT-seq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
UST-AS-002
SORT-seq (partially robotized version of the CEL-seq2 protocol).
gene_counts_matrix.tsv
|
| Data processing |
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA (Anders and Huber, 2010).
Data was demultiplexed as described in Grün et al. 2014.
Mapping and generation of count tables was automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: gene_counts_matrix.tsv: Matrix table with raw gene counts for every gene and every cell of every sample.
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Frank Jühling |
| E-mail(s) |
juehling@unistra.fr
|
| Organization name |
Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110
|
| Street address |
3 Rue Koeberlé
|
| City |
Strasbourg |
| ZIP/Postal code |
67000 |
| Country |
France |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE66843 |
A cell-based model unravels drivers for hepatocarcinogenesis and targets for clinical chemoprevention |
| GSE173671 |
A human liver cell-based system modeling a clinical prognostic liver signature combined with single-cell RNA-Seq for discovery of liver disease therapeutics |
|
| Relations |
| BioSample |
SAMN18940743 |
| SRA |
SRX10723954 |
