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| Status |
Public on Dec 16, 2021 |
| Title |
KR08_A |
| Sample type |
SRA |
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| Source name |
Targeted Sequencing (TAP-Seq) SARS-CoV2
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
condition: COVID-19
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| Treatment protocol |
Snap-frozen COVID-19 patient autopsy kidney tissue was obtained from the pathology department at Radboud UMC Nijmegen, the Netherlands. A small piece of kidney tissue (ca. 2x2x2 mm) was thawed in PBS and crushed using a glass douncer and tube (Duran Wheaton Kimble Life Sciences, Wertheim/Main, Germany). After passing the single cell suspension through a 70 µm cell strainer (Greiner), the suspension was centrifuged at 4ºC and 300xg for 5 min. Subsequently, the supernatant was discarded and the cell pellet was resuspended in Nuc101 cell lysis buffer supplemented with RNase and protease inhibitors (Recombinant RNase Inhibitor and Superase RNase Inhibitor, Thermo Fisher, and cOmplete Protease Inhibitor, Roche) incubated for one minute and centrifuged at 4ºC and 500xg for 5 min. After discarding the supernatant, the nuclei were carefully resuspended in PBS containing 1% (v/v) UltraPure BSA (Invitrogen Ambion, Thermo Fisher) and Protector RNase inhibitor (Sigma Aldrich), counted, and used in the usual single cell RNA sequencing workflow (10x Genomics, v3.1).
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| Extracted molecule |
total RNA |
| Extraction protocol |
All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The Cell Ranger Software Suite (version 3.1.0) was used for processing sequencing information and single cell barcodes.
Seurat (version 3.2.2) was used to integrate the scRNA-seq data and predict cell labels.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes: barcodes present in input data
Supplementary_files_format_and_content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line. The rest of the lines represent nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to the number of cut sites.
Supplementary_files_format_and_content: genes: a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively.
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| Submission date |
Sep 03, 2021 |
| Last update date |
Dec 16, 2021 |
| Contact name |
Ivan Gesteira Costa |
| E-mail(s) |
ivan.costa@rwth-aachen.de
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| Phone |
+49 241 80 89337
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| Organization name |
UKA RWTH Aachen
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| Department |
Joint Research Center for Computational Biomedicine
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| Lab |
Institute for Computational Genomics
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| Street address |
Pauwelsstr. 19
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| City |
Aachen |
| State/province |
Northrhine-Westphalia |
| ZIP/Postal code |
52074 |
| Country |
Germany |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE167747 |
SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids |
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| Relations |
| BioSample |
SAMN21217738 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5557002_KR08_A.tar.gz |
8.2 Kb |
(ftp)(http) |
TAR |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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