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| Status |
Public on Mar 09, 2023 |
| Title |
Mouse, carotid artery, scRNA-seq |
| Sample type |
SRA |
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| Source name |
Carotid artery
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| Organism |
Mus musculus |
| Characteristics |
tissue: Carotid artery
strain: C57BL/6
age: 11 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Eight carotid arteries were cut into small pieces in an enzyme mixture containing 125 U/mL collagenase type XI, 450 U/mL collagenase type I, 60 U/mL hyaluronidase type I-s and 60 U/mL DNase 1 in PBS containing Ca2+ and 20 mM Hepes (pH. 7.4) and subsequently incubated at 37 ◦C for 30 minutes in a total volume of 5 mL. Every 10 minutes the solution was resuspended by pipetting. Digestion was stopped with stopping solution (PBS; 2% FCS; 1 mM EDTA) and cell suspension was strained.
All scRNA-seq libraries were prepared using Chromium Single Cell 30 v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. In brief, the initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10x cell barcodes, UMI (unique molecular identifiers) and poly(dT) sequences. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Germany). Bulk cDNA was amplified using a Biometra Thermocycler TProfessional Basic Gradient with 96-Well Sample Block (98°C for 3min; cycled 14x: 98°C for 15 s, 67°C for 20 s, and 72°C for 1min; 72°C for 1min; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter, USA). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 30 v2 Reagent Kit, as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment were performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10x Genomics
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| Data processing |
Single-cell expression data were processed using the Cell Ranger Single Cell Software Suite (v2.1.1) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 30 gene counting. Sequencing reads were aligned to the mouse reference genome GRCh38 using the Cell Ranger suite with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Dec 12, 2022 |
| Last update date |
Mar 09, 2023 |
| Contact name |
Timothy Warwick |
| E-mail(s) |
warwick@vrc.uni-frankfurt.de
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| Organization name |
Goethe Universität Frankfurt am Main
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| Department |
Institute for Cardiovascular Physiology
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| Street address |
Theodor-Stern-Kai 7
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| City |
Frankfurt am Main |
| State/province |
Hesse |
| ZIP/Postal code |
60590 |
| Country |
Germany |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE220514 |
Carotid injury in mice |
| GSE220779 |
Single-cell transcriptome of the basal murine carotid artery |
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| Relations |
| BioSample |
SAMN32175310 |
| SRA |
SRX18658298 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6817309_104883-003-001_barcodes.tsv.gz |
7.7 Mb |
(ftp)(http) |
TSV |
| GSM6817309_104883-003-001_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM6817309_104883-003-001_matrix.mtx.gz |
97.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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