 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 14, 2023 |
| Title |
20% sample long-read |
| Sample type |
SRA |
| |
|
| Source name |
Lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung adenocarcinoma
cell line: mixture of cell lines: H2228, H1975, A549, H838, HCC827
|
| Treatment protocol |
Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.
|
| Growth protocol |
The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin. The cells were grown independently at 37C with 5% carbon dioxide until near 100% confluency.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The cell lines were mixed to achieve 16,000 nuclei captured, 9,700 nuclei in total, following the 10X Genomics nuclei preparation protocol.
GEX + ATAC: 10X Genomics Chromium nextgeM Single Cell Multiome ATAC + Gene Expression kit, Illumina NextSeq 500 sequencing chemistry v2.5. Long reads: Full length cDNA was obtained using 10X Multiome protocol to step 6. Elongation time was changed to 6 minutes. The ligation sequencing kit (SQK-LSK110) was used with the supplied ONT protocol. Libraries were loaded on 1 PromethION R9.4 flow cell and sequenced with ONT PromethION.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Description |
long_20
scM2_20_FLAMES_stats.txt
|
| Data processing |
GEX + ATAC: base calling and quality scoring were performed using Illumina Real-Time Analysis on board software (version 2.11.3).
Raw base call files were demultiplexed into FASTQ files using the mkfastq pipeline in Cellranger ARC (version 2.0.0).
Reads were aligned to the human reference genome, filtering, barcode counting, peak calling were performed, and gene counts were generated using the count pipeline in CellRanger ARC (version 2.0.0).
Long reads: MinKNOW PromethION Release (version 20.06.9), base calling with Guppy (version 5.0.12).
Cell barcode matching and counting was performed with FLAMES (version 0.1.0, https://github.com/LuyiTian/FLAMES).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files with cell-associated barcodes, features, and matrix outputs from CellRanger.
Supplementary files format and content: scM2_20_FLAMES_stats.txt: comma-delimited file with cell IDs and counts
|
| |
|
| Submission date |
Jan 30, 2023 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Matthew Ritchie |
| E-mail(s) |
[email protected]
|
| Organization name |
The Walter and Eliza Hall Institute of Medical Research
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE224045 |
Designing a single cell ATAC-Seq (scATAC-Seq) dataset to validate long read RNA-Seq isoforms and benchmark scATAC-Seq analysis methods II |
|
| Relations |
| BioSample |
SAMN32960175 |
| SRA |
SRX19215447 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
