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| Status |
Public on Nov 15, 2019 |
| Title |
Single cell transcriptome atlas of the Drosophila larval brain |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The cellular composition of the brain and how it is affected by starvation, remains largely unknown. Here we introduce a single-cell transcriptome atlas of the entire Drosophila melanogaster first instar larval brain. We first assigned cell type identity based on the expression of previously characterized marker genes, allowing us to distinguish five major groups: neural progenitors cells, differentiated neurons, glial cells, undifferentiated neurons as well as non-neural cells corresponding to organs and structures located adjacent to the brain. All major classes were further subdivided into multiple subtypes based on cluster analysis, revealing critical biological features of various cell types. Moreover, we included two different feeding conditions: normal fed versus starved. After starvation, the transcriptional profile of several cell clusters were altered, while the overall composition of the brain remains unaffected. Intriguingly, different cell clusters show very distinct responses to starvation, suggesting the presence of cell-specific programs for nutrition availability. Establishing a single-cell transcriptome atlas of the larval brain provides a powerful tool to explore cell diversity, assess genetic profiles of neurogenic, neuronal and glial cell types. The analysis of neurotransmitters, neuropeptides and their respective receptors may further open the doors for functional studies.
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| Overall design |
scRNA-seq (10x Genomics - Single Cell 3’ Chemistry v2 ) of the Drosophila larval brain at different feeding conditions
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| Contributor(s) |
Brunet Avalos C, Bruggmann R, Simon SG, Maier G |
| Citation(s) |
31746739 |
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| Submission date |
Jul 23, 2019 |
| Last update date |
May 14, 2020 |
| Contact name |
Simon Sprecher |
| E-mail(s) |
simon.sprecher@unifr.ch
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| Organization name |
University of Fribourg
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| Department |
Biology
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| Lab |
Sprecher Lab
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| Street address |
Chemin du Musée 10
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| City |
Fribourg |
| State/province |
Fribourg |
| ZIP/Postal code |
1700 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
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| Samples (7)
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| GSM3964166 |
First instar larval brain cells, Normal condition (scRNAseq) 1 - sample 1 |
| GSM3964167 |
First instar larval brain cells, Normal condition (scRNAseq) 2 - sample 2 |
| GSM3964168 |
First instar larval brain cells, Normal condition (scRNAseq) 3 - sample 3 |
| GSM3964169 |
First instar larval brain cells, Starvation condition (scRNAseq) 1 - sample 4 |
| GSM3964170 |
First instar larval brain cells, Starvation condition (scRNAseq) 2 - sample 5 |
| GSM4132287 |
First instar larval brain cells, Normal condition (scRNAseq) 4 - sample 6 |
| GSM4132288 |
First instar larval brain cells, Starvation condition (scRNAseq) 3 - sample 7 |
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| Relations |
| BioProject |
PRJNA556226 |
| SRA |
SRP216038 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE134722_FirstInstarLarvalBrainNormalCondition_aggr_10X_barcodes.tsv.gz |
17.3 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainNormalCondition_aggr_10X_genes.tsv.gz |
129.1 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainNormalCondition_aggr_10X_matrix.mtx.gz |
16.1 Mb |
(ftp)(http) |
MTX |
| GSE134722_FirstInstarLarvalBrainNormalCondition_finalaggr_10X_barcodes.tsv.gz |
21.7 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainNormalCondition_finalaggr_10X_genes.tsv.gz |
129.1 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainNormalCondition_finalaggr_10X_matrix.mtx.gz |
25.5 Mb |
(ftp)(http) |
MTX |
| GSE134722_FirstInstarLarvalBrainStarvationCondition_aggr_10X_barcodes.tsv.gz |
16.2 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainStarvationCondition_aggr_10X_genes.tsv.gz |
129.1 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainStarvationCondition_aggr_10Xmatrix.mtx.gz |
23.8 Mb |
(ftp)(http) |
MTX |
| GSE134722_FirstInstarLarvalBrainStarvationCondition_finalaggr_10X_barcodes.tsv.gz |
20.8 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainStarvationCondition_finalaggr_10X_genes.tsv.gz |
129.1 Kb |
(ftp)(http) |
TSV |
| GSE134722_FirstInstarLarvalBrainStarvationCondition_finalaggr_10X_matrix.mtx.gz |
29.3 Mb |
(ftp)(http) |
MTX |
| GSE134722_RAW.tar |
55.1 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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