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| Status |
Public on Jun 03, 2023 |
| Title |
TGS - RCC1 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: NA
cell type: nuclei of tumor
genotype: unknown
tumor stage: Primary RCC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single nuclei of cell lines were prepared by following the 10X Genomics protocol(CG000365 Rev C). Single nucleus suspensions of frozen tumor tissues were prepared according to the method as previously described (dx.doi.org/10.17504/protocols.io.t3aeqie)
NGS libraries were prepared by following 10X genomics 3'scRNAseq protocol. For Nanopore long-read sequencing, cDNA libraries were prepared with SQK-LSK110 ligation sequencing kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Description |
scNanoRNAseq
NP6
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| Data processing |
For NGS, the reads are analyzed by cellranger-arc 4.0 to generate gene expression matrix.
For Nanopore, the reads are analyzed by scNanoGPS to generate gene expression, isoform, SNV matrices. The detailed process is described at: https://github.com/gaolabtools/scNanoGPS_v0.10/ .
deconvolution into single cells
make consensus sequencces of single molecules
calculate same cell multiomics
Assembly: GRCh38
Supplementary files format and content: NGS: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Nanopore: matrix.tsv.gz, matrix_isoform.tsv.gz, matrix_SNV.vcf.gz
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| Submission date |
Sep 08, 2022 |
| Last update date |
Jun 04, 2023 |
| Contact name |
Ruli Gao |
| E-mail(s) |
[email protected]
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| Organization name |
Northwestern University
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| Department |
Department of Biochemistry and Molecular Genetics
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| Lab |
Ruli Gao
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| Street address |
Simpson Querrey, 7th Floor
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE212945 |
High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors. |
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| Relations |
| BioSample |
SAMN30728958 |
| SRA |
SRX17495529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6564302_NP6_matrix.tsv.gz |
11.2 Mb |
(ftp)(http) |
TSV |
| GSM6564302_NP6_matrix_SNV.vcf.gz |
18.2 Mb |
(ftp)(http) |
VCF |
| GSM6564302_NP6_matrix_isoform.tsv.gz |
25.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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