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| Status |
Public on Jan 17, 2023 |
| Title |
A10_VDJ |
| Sample type |
SRA |
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| Source name |
T lymphocytes from heart
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| Organism |
Mus musculus |
| Characteristics |
strain: Balb/C
library type: VDJ recombination
cell type: T lymphocytes from heart
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| Extracted molecule |
total RNA |
| Extraction protocol |
Heart and medistinal lymph nodes were collected from TCR-M transferred adult mice at 5 and 7 days post myocardial infarction surgery. All tissue was kept in HBSS/BSA 0.5% at 4°C until processing. Heart samples were digested in collagenase II 1000U/mL for 30 minutes, at 37ºC. After digestion, both tissues were grinded through a 30um mesh and seeded in a plate for FACS staining. Each condition (e.g Heart, 5d, MI) was stained with Hashtag TotalSeq C antibody to enable multiplexing. T-helper cells defined ad live, lineage (CD11b,CD8a,CB220) negative and CD4+ and TCR-M cells defined as live, lineage negative, CD4+ Thy1.1+ were FACS sorted from pooled heart and MedLN samples. After sorting, cells were combined in different ratios for single cell RNA sequencing application.
The same multiplexed sample were processed in parallel in 2 sets of libraries (set 1: A7, A9, A1 and set 2: A8, A10, A2). Libraries were generated with the Chromium Next GEM Single Cell 5’ Reagents Kit v2 Chemistry according to manufacturer ´s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The sequencing data was processed using CellRanger software (version 6.0.1).
Genome_build: mm10-2020-A for GEX and GRCm38 5.0.0 for V(D)J
Supplementary_files_format_and_content: tsv; gene barcode matrices and feature barcode matrix
Supplementary_files_format_and_content: csv;High-level descriptions of each clonotype and annotations of each high-confidence, cellular contig.
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| Submission date |
Mar 07, 2022 |
| Last update date |
Jan 17, 2023 |
| Contact name |
Antoine-Emmanuel Saliba |
| E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
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| Phone |
+49-931-31-81341
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| Organization name |
Helmholtz Institute for RNA-based Infection Research
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| Street address |
Josef-Schneider-Straße 2 / D15
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE198059 |
Deep phenotypin heart-specific Tregs |
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| Relations |
| BioSample |
SAMN26509210 |
| SRA |
SRX14400813 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5937023_A10_clonotypes.csv.gz |
227.4 Kb |
(ftp)(http) |
CSV |
| GSM5937023_A10_filtered_contig_annotations.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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