 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 02, 2023 |
| Title |
gene expression library 1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line, PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line, PBMC
cell line: PC9 (CMOs 303), HTB178 (CMOs 305), CRL5868 (CMOs 304), DV90 (CMOs 306), HCC78 (CMOs 307), A549 (CMOs 301), CCL-185-IG (CMOs 302), PBMC (CMOs 308)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The libraries were constructed using CellPlex technology from 10XGenomics. We used four reactions of Chromium Next GEM Single Cell 3' Kit v3.1, combined with 3' CellPlex Kit. We generated four expression libraries (1740FL-306-01-01, 1740FL-306-01-02, 1740FL-306-01-03, 1740FL-306-01-04) and four multiplexing libraries (1740FL-306-01-09, 1740FL-306-01-10, 1740FL-306-01-11, 1740FL-306-01-12). These are the cell lines analysed and the associated CellPlex barcode: PC9 (CMOs 303), HTB178 (CMOs 305), CRL5868 (CMOs 304), DV90 (CMOs 306), HCC78 (CMOs 307), A549 (CMOs 301), CCL-185-IG (CMOs 302), PBMC (CMOs 308). As part of the supplementary data the file multi_gex.csv describes all the required parameters to run cellranger for multiplexed samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
data generated using cell plex technology from 10XGenomics
PC9_barcodes.tsv, HTB178_barcodes.tsv, CRL5868_barcodes.tsv, DV90_barcodes.tsv, HCC78_barcodes.tsv, A549_barcodes.tsv, CCL-185-IG_barcodes.tsv, PBMCs_barcodes.tsv
PC9_features.tsv, HTB178_features.tsv, CRL5868_features.tsv, DV90_features.tsv, HCC78_features.tsv), A549_features.tsv, CCL-185-IG_features.tsv, PBMCs_features.tsv
PC9_matrix.mtx.gz, HTB178_matrix.mtx.gz, CRL5868_matrix.mtx.gz, DV90_matrix.mtx.gz, HCC78_matrix.mtx.gz, A549_matrix.mtx.gz, CCL-185-IG_matrix.mtx.gz, PBMCs_matrix.mtx.gz
|
| Data processing |
from fastq to count matrix: cellranger v7.1.0
Cell ranger is available in docker image repbioinfo/cellranger.2023.7.1.0 at https://hub.docker.com/ (docker pull repbioinfo/cellranger.2023.7.1.0)
The sample sheet required by cellranger is available in the supplementary file: multi_gex.csv. The string to execute the conversion from fastq to counts in docker are: 1) access to the docker container :docker run -v /fastq_folder_somewhere_in_your_server:/data -v /somewhere_in_your_server/the-folder_with_the_10Xgenomics_human_genome_assembly_built/:/genomes -it repbioinfo/cellranger.2023.7.1.0 /bin/bash ; 2) execute cellranger cellranger multi --id=BE1 --csv=/data/multi_gex.csv
The barcode.tsv files were edited indicating the name of the cell lines.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: 10XGenomics sparse matrix format
Supplementary files format and content: multi_gex.csv configuration file required to run cellranger multi
|
| |
|
| Submission date |
Sep 20, 2023 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
raffaele.calogero@unito.it
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE243665 |
A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity |
|
| Relations |
| BioSample |
SAMN37482922 |
| SRA |
SRX21841442 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
