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General Information
Name
scRNAseq_2020_Cattenoz_WI_seq_clustering
Species
D. melanogaster
Result type
FlyBase ID
FBlc0003737
Project
Data Provider
Title
Clustering analysis of hemocytes from wasp-infested third instar larvae
Status
Current
Accessions
    Biosample Source
    Overview
    Sex
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Sample preparation

    Staged larvae were infested at the L2 stage (48-56 h AEL) for 2 h at 20oC with 20 female wasps (L. boulardi) per 100 Drosophila larvae. Following infestation, the larvae were raised at 25oC until the wandering L3 stage, where 20 female larvae were collected and bled in Schneider medium complemented with N-phenylthiourea on ice. Both circulating and resident pools of hemocytes were collected by first puncturing the cuticle to release the circulating hemocytes, then by scrapping the cuticle with fine forceps to release the resident hemocytes (FBrf0230406). After bleeding, the hemolymph was filtered on a 100um-mesh to remove cell aggregates and wasp eggs.

    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    Hemocytes from wasp-infested third-instar larvae
    Data Analyzed
    Key genes
    Protocol

    For each condition, single-cell RNA-seq libraries were prepared from 10,000 cells using the Chromium Single Cell 3' Reagent Kits v2 (10x Genomics).

    Mode of Assay

    RNA-seq libraries were sequenced on the Illumina HiSeq 4000 platform with paired-end 100 bp reads.

    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    Single-cell RNA-seq of hemocytes from wasp-infested third instar larvae
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis

    Reads were processed using Cell Ranger v3.0.1 (10x Genomics). They were mapped to the Drosophila melanogaster reference genome BDGP6_ens95. For quality filtering, cells with less than 200 UMI were removed. Further analysis was performed using Seurat v3 (https://satijalab.org/seurat/). Dimensionality reduction and clustering were performed by computing 20 principal components and with a clustering resolution of 0.55.

    Comments
    Associated Data
    Size
    8214 Number of cells in sample retained for analysis
    Files
    Additional Information
    Synonyms and Secondary IDs (2)
    Reported As
    Symbol Synonym
    scRNAseq_2020_Cattenoz_WI_seq_clustering
    Name Synonyms
    Clustering analysis of hemocytes from wasp-infested third instar larvae
    Secondary FlyBase IDs
      References (1)