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| Status |
Public on Dec 15, 2023 |
| Title |
snRNA-seq, D. simulans central brain, biol rep5 |
| Sample type |
SRA |
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| Source name |
central brain
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| Organism |
Drosophila simulans |
| Characteristics |
tissue: central brain
genotype: DSSC 14021-0251.004
treatment: standard fly food
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| Growth protocol |
Standard fly growth medium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Newly-eclosed 30-50 male and female adult flies were collected and placed together for mating, followed by sorting by sex on day 5. The central brains of 20 mated female flies were dissected and collected in 100 μl Schneider’s medium, flash-frozen in liquid nitrogen, and stored at -80ºC for nuclear extraction. Sample homogenization, single-nucleus suspension, and nuclear sorting were performed using the standard protocol described in the Fly Cell Atlas (Li et al. 2022)
To obtain sequencing data from 10,000 nuclei, 15-20,000 nuclei were collected and loaded onto the Chromium Next GEM Chip (10x Genomics). Sequencing libraries were prepared with the Chromium Single Cell 3ʹ reagent kit v3.1 dual index, strictly following the manufacturer’s recommendations.
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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 |
Raw snRNA-seq data was first processed through Cell Ranger (v6.0.1, default parameters except --include-introns)
Assembly: D. simulans reference genome and transcriptome from FlyBase (release 2.02)
Supplementary files format and content: TSV files and matrix files
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| Submission date |
Dec 14, 2023 |
| Last update date |
Dec 15, 2023 |
| Contact name |
Daehan Lee |
| E-mail(s) |
phman1121@gmail.com
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| Organization name |
Sungkyunkwan University
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| Street address |
2066 Seobu-ro
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| City |
Suwon |
| State/province |
Gyeonggi |
| ZIP/Postal code |
16419 |
| Country |
South Korea |
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| Platform ID |
GPL27544 |
| Series (1) |
| GSE247965 |
Comparative single-cell transcriptomic atlases reveal conserved and divergent features of drosophilid central brains |
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| Relations |
| BioSample |
SAMN38847211 |
| SRA |
SRX22894423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7975651_Dsim5_barcodes.tsv.gz |
47.2 Kb |
(ftp)(http) |
TSV |
| GSM7975651_Dsim5_features.tsv.gz |
103.2 Kb |
(ftp)(http) |
TSV |
| GSM7975651_Dsim5_matrix.mtx.gz |
29.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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