|
| Status |
Public on Apr 07, 2024 |
| Title |
3 layer spheroid channel 1 [3-1-GEX_S1_L002] |
| Sample type |
SRA |
| |
|
| Source name |
3 layer spheroid channel 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: Epithelial
library type: mRNA
|
| Treatment protocol |
10 samples were labelled with unique short barcoded oligonucleotides (SBOs) for multiplexing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Spheroids were dissociated with TryplE and resuspended in 0.04% w/v BSA. Cells from each sample were pooled together in equal numbers at a final concentration of 2,000 cells/μL.
Cells were loaded onto a 10x Genomics Chromium Controller, Chip K (PN 1000286) and libraries were prepared using the Chromium Next GEM single cell 5’ kit v2 (PN1000263/1000265). Libraries from SBOs were prepared using the 5’ Feature Barcode kit (PN 1000256) following manufacturer guidelines. Illumina iSeq 100 platform was used for initial QC of the libraries and deeper sequencing was conducted on Illumina NovaSeq 6000 in the vendor recommended format to reach up to 50,000 reads per cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3-1-GEX_S1_L002
Channel 2
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
C2_barcodes.tsv.gz
C2_features.tsv.gz
C2_matrix.mtx.gz
|
| Data processing |
Fastq files were generated with Illumina bcl2fastq v2.20.0.422, allowing 1 mismatch in each index.
Transcript alignment and generation of gene count and feature barcode matrices were performed using 10x Genomics Cell Ranger count v6.0.2. Output from four channels was combined either with Cell Ranger aggr (for data QC and initial exploration), or Seurat v4.1.0 in R for all further downstream analysis.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
|
| |
|
| Submission date |
Oct 15, 2023 |
| Last update date |
Apr 07, 2024 |
| Contact name |
Jessica King |
| E-mail(s) |
jessicaking736@gmail.com, jessica.king@research.uwa.edu.au
|
| Organization name |
University of Western Australia
|
| Department |
School of Molecular Sciences
|
| Street address |
35 Stirling Hwy
|
| City |
Crawley |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE245416 |
Polymer-mediated oligo delivery enables construction of spatially encoded 3D cultures for analysis by single-cell RNA sequencing |
|
| Relations |
| BioSample |
SAMN37819494 |
| SRA |
SRX22094460 |
