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Sample GSM4240174 Query DataSets for GSM4240174
Status Public on Jul 16, 2020
Title Adult3_scRNAseq
Sample type SRA
 
Source name adult optic lobe
Organism Drosophila melanogaster
Characteristics strain: Canton S
Sex: female
age: 1-3 days old
tissue: adult optic lobe
Treatment protocol No treatments.
Growth protocol Standard Drosophila rearing protocols.
Extracted molecule polyA RNA
Extraction protocol Chromium™ Single Cell 3’ Reagent Kit v2 (10X Genomics)
Chromium™ Single Cell 3’ Reagent Kit v2 (10X Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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.
 
Submission date Dec 31, 2019
Last update date Jul 16, 2020
Contact name Mehmet Neset Ozel
E-mail(s) mehmetnesetozel@gmail.com
Organization name New York University
Street address 100 Washington Sq E
City New York
State/province New York
ZIP/Postal code 10003
Country USA
 
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
Relations
BioSample SAMN13703195
SRA SRX7483455

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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