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| Status |
Public on Jul 16, 2020 |
| Title |
P15-2_scRNAseq |
| Sample type |
SRA |
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| Source name |
P15 optic lobe
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Canton S
Sex: female
age: P15%
tissue: P15 optic lobe
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| Treatment protocol |
No treatments.
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| Growth protocol |
Standard Drosophila rearing protocols.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Chromium™ Single Cell 3’ Reagent Kit v2 (10X Genomics)
Chromium™ Single Cell 3’ Reagent Kit v2 (10X Genomics)
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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 |
Fastq files were generated either with Illumina "bcl2fastq" (2.18) or CellRanger (2.1.1) "mkfastq".
Alignment and counting were performed with CellRanger (2.1.1 or 3.0.1) "count".
Normalization, scaling, dimensional reduction and clustering of the single-cell transcriptomes were performed using Seurat v3 (detailed in Methods).
Pupal single-cell transcriptomes were classified with a custom neural network (detailed in Methods).
Average gene expression levels and cluster markers were calculated for each cell type at each stage using Seurat v3.
Binarized expression values for each cell type were determined using mixture modeling (Davis et al., 2018)
Genome_build: ENSEMBL-release-88-BDGP6
Supplementary_files_format_and_content: Seurat objects (.rds format) provided for each stage include raw, normalized and scaled expression values for each cell in addition to the identities determined using different methods, as detailed in the paper. Excel files are provided for average and binarized expression levels and also for the cluster markers, where each stage is in a separate type.
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| Submission date |
Dec 31, 2019 |
| Last update date |
Jul 16, 2020 |
| Contact name |
Mehmet Neset Ozel |
| E-mail(s) |
[email protected]
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| Organization name |
New York University
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| Street address |
100 Washington Sq E
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platform ID |
GPL25244 |
| Series (2) |
| GSE142787 |
Neuronal diversity and convergence in a visual system developmental atlas (scRNA-seq) |
| GSE142789 |
Neuronal diversity and convergence in a visual system developmental atlas |
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| Relations |
| BioSample |
SAMN13703223 |
| SRA |
SRX7483480 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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