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| Status |
Public on Nov 15, 2021 |
| Title |
snRNAseq_JW03_iris_constricted_RP1 |
| Sample type |
SRA |
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| Source name |
Adult iris
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| Organism |
Mus musculus |
| Characteristics |
tissue: iris
genotype: WT
protocol: constricted
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| Extracted molecule |
total RNA |
| Extraction protocol |
Five or six irise a femalemice were rapidly dissected in ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH). The tissue was minced with a razor blade and Dounce homogenized using a loose-fitting pestle in 5 ml of homogenization buffer supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and EDTA-free protease inhibitor (Roche 11 836 170 001), and 60 U/mL RNasin Plus RNase Inhibitor (Promega N2611). A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further homogenized with five strokes of a tight-fitting pestle. The sample was filtered through a 50 μm filter (CellTrix, Sysmex, 04-004-2327), underlayed with solutions of 30% and 40% iodixanol in homogenization buffer (Sigma D1556), and centrifuged at 10,000 x g for 18 minutes in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface, diluted with 2 volumes of homogenization buffer and concentrated by centrifugation for 10 min at 0.5 x g at 4°C. snRNA-seq sequencing libraries were constructed using the 10X Genomics Chromium single cell 3’ v3 kit.
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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 |
Reads were aligned to a mm10 pre-mRNA index using Cellranger version 3.1.0. Libraries were merged using Cellranger and data was analyzed using the Seurat R package.
Genome_build: mm10
Supplementary_files_format_and_content: expression_data.mtx
Supplementary_files_format_and_content: cell_metadata
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| Submission date |
Sep 08, 2021 |
| Last update date |
Nov 15, 2021 |
| Contact name |
Amir Rattner |
| E-mail(s) |
arattne1@jhmi.edu
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| Phone |
4105995777
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| Organization name |
Johns Hopkins University
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| Street address |
725 North Wolfe St.
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| City |
Baltimore |
| State/province |
MD - Maryland |
| ZIP/Postal code |
21208 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE183690 |
A transcriptome atlas of the mouse iris at single cell resolution defines cell types and the genomic response to pupil dilation |
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| Relations |
| BioSample |
SAMN21357883 |
| SRA |
SRX12105462 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5567781_snRNAseq_JW03_iris_constricted_RP1_cell_metadata.tsv.gz |
235.8 Kb |
(ftp)(http) |
TSV |
| GSM5567781_snRNAseq_JW03_iris_constricted_RP1_expression_data.mtx.gz |
19.7 Mb |
(ftp)(http) |
MTX |
| GSM5567781_snRNAseq_JW03_iris_constricted_RP1_gene_metadata.tsv.gz |
135.0 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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