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| Status |
Public on Jun 05, 2024 |
| Title |
PCLD6, scTCRseq |
| Sample type |
SRA |
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| Source name |
Bronchoalveolar cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Bronchoalveolar cells
disease state: Post-COVID-19 lung disease
radiology: Fibrotic
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Flexible fibreoptic bronchoscopy was used to obtain bronchoalveolar lavage (BAL) samples by instillation of up to 240 ml of warmed normal saline into a lung segment affected by the predominant radiological abnormality. Aspirated BAL fluid was cooled to 4°C and filtered through a cell strainer to remove particulate debris before centrifugation. After removal of the supernatant, cells were resuspended in PBS. Cell count and viability were determined by Trypan blue staining and erythrocytes removed where indicated, using red cell lysis buffer. Cells were resuspended at 2 x10^6 per ml for downstream processing. 20,000 cells per sample were loaded on to the Chromium controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs).
Single-cell partitioning, reverse transcription, cDNA amplification and library construction were performed using the Chromium Single-cell 5’ Reagent kits v1.1 and v2 (10x Genomics) according to the manufacturer’s instructions. T cell receptor (TCR) V(D)J segments were enriched from amplified cDNA using Chromium Single-Cell V(D)J Enrichment kits v1.1 and v2 (10x Genomics) per the manufacturer’s protocol.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
10x Genomics
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| Data processing |
library strategy: TCR-seq
Raw sequencing files were demultiplexed using BCL Convert v3.7.5 (Illumina) or Cell Ranger version 6.1.1 using the “mkfastq” script. Transcript alignment and quantitation against the GRCh38 human genome assembly was performed using Cell Ranger “multi” for samples with gene expression and T cell VDJ data or Cell Ranger “count” for samples with gene expression data only.
Assembly: GRCh38
Supplementary files format and content: .h5 files are raw count matrices generated by Cell Ranger count or multi, rows are features and columns are cells; .csv files are TCR contig and clonotype annotations generated by Cell Ranger multi.
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| Submission date |
Mar 27, 2023 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Gillian S Tomlinson |
| E-mail(s) |
g.tomlinson@ucl.ac.uk
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| Organization name |
University College London
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| Department |
Infection and Immunity
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| Street address |
Gower Street
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| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE228236 |
Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease |
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| Relations |
| BioSample |
SAMN33924932 |
| SRA |
SRX19780689 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7117564_pcld6_clonotypes.csv.gz |
4.1 Kb |
(ftp)(http) |
CSV |
| GSM7117564_pcld6_filtered_contig_annotations.csv.gz |
30.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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