The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis

Experiment ID:SRP269777
Technology:scRNA-Seq
Description:In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.
DOI:10.1016/j.celrep.2021.109039
Source:SRP269777 SRA
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scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogasterscRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
SRX8657660FBbt:00100533 type II neuroblast (Drosophila)typeIIUBERON:6001920 insect embryonic/larval brainbrainFBdv:00007007 late third instar larval stage (fruit fly)3rd instar larvaNA[;;R9D11-Gal4/UAS-hH2B::2xmNG]NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired384758486348924578030678604382012786.5Browse results
SRX8657660FBbt:00110571 optic lobe forming neuroblast (Drosophila)OLUBERON:6001920 insect embryonic/larval brainbrainFBdv:00007007 late third instar larval stage (fruit fly)3rd instar larvaNA[;;R9D11-Gal4/UAS-hH2B::2xmNG]NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMECELL0paired384758486348924578027212561334212956Browse results
SRX9904377FBbt:00100533 type II neuroblast (Drosophila)typeIIUBERON:6001920 insect embryonic/larval brainbrainFBdv:00007007 late third instar larval stage (fruit fly)3rd instar larvaNA[;;R9D11-Gal4/UAS-hH2B::2xmNG]NANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired381823225352134454020292362325312347Browse results
SRX9904377FBbt:00110571 optic lobe forming neuroblast (Drosophila)OLUBERON:6001920 insect embryonic/larval brainbrainFBdv:00007007 late third instar larval stage (fruit fly)3rd instar larvaNA[;;R9D11-Gal4/UAS-hH2B::2xmNG]NANADrosophila melanogasterNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0paired38182322535213445405904322181711849Browse results

Showing 1 to 4 of 4 entries

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