Transcriptomic signatures of flight muscle, brain and leg tissues during Drosophila pupal development
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PROVIDER: PRJNA799594 | ENA |
REPOSITORIES: ENA
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Project description:Alternative splicing produces multiple, distinct mRNA transcripts from the same gene locus. To explore tissue-type specific gene expression and alternative splicing, we generated mRNA-Seq data from pupal tissues dissected from Drosophila. This allowed us to compare expression between dissected, highly enriched brain and indirect flight muscle (IFM) samples as well as whole legs. Bioinformatic analysis allowed us to characterize tissue-specific differences in gene expression as well as alternative splicing among the three tissues, as well as to identify a multitude of novel splicing events that are not currently contained in the Drosophila annotation. This suggests that tissue or cell-type specific sequencing at multiple timepoints during the fly life cycle will help extend existing annotations, and novel splice junction discovery is an important consideration in mRNA-Seq data analysis.
2022-01-25 | GSE194199 | GEO
Project description:To complement our existing data on developmental gene expression changes in flight muscle (IFM) development in Drosophila (GSE107247, GSE63707), we performed mRNA-Seq on dissected leg samples at three stages during pupal development (30, 50 and 72h APF). We further sequenced an additional timepoint at 24h APF for RNAi knockdown of aret (Bru1) in flight muscle. Comparison of splicing and expression profiles of sarcomeric genes allowed us to identify muscle-type specific differences in gene and isoform expression between fibrillar flight muscle and tubular leg muscle. We can further trace the dynamics of exon usage in sarcomere genes across the developmental timecourse, allowing us to identify events the switch during muscle differentiation and maturation.
2020-01-11 | GSE143430 | GEO
Project description:In Drosophila, fibrillar flight muscles (IFMs) enable flight, while tubular muscles mediate other body movements. Here, we use RNA-sequencing and isoform-specific reporters to show that spalt major (salm) determines fibrillar muscle physiology by regulating transcription and alternative splicing of a large set of sarcomeric proteins. We identify the RNA binding protein Arrest (Aret, Bruno) as downstream of salm. Aret shuttles between cytoplasm and nuclei, and is essential for myofibril maturation and sarcomere growth of IFMs. Molecularly, Aret regulates IFM-specific transcription and splicing of various sarcomeric targets, including Stretchin and wupA (TnI), and thus maintains muscle fiber integrity. As Aret and its sarcomeric targets are evolutionarily conserved, similar principles may regulate mammalian muscle morphogenesis. 9 samples from Drosophila melanogaster were analyzed in duplicate: control dissected wildtype flight muscle at 30h APF, 72h APF and 0 day adult, jump muscle and whole leg from 1d adult and RNAi/mutant conditions for salm (1d flight muscle) and aret (30h, 72h and 1d flight muscle)
2014-12-23 | E-GEOD-63707 | biostudies-arrayexpress
Project description:Transcriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrated a requirement of neuronal SOCE for Drosophila flight. We identified the early pupal stage to be critical and used RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. We down-regulated dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system for a 24h period during pupal development, and compared wild type and knockdown transcriptional profiles, immediately after knockdown as well as after a 36h recovery period. We found that dStim knockdown altered the expression of a number of genes. We also characterized one of the down-regulated genes, Ral for its role in flight. Thus, we identify neuronal SOCE as a mechanism that regulates expression of a number of genes during the development of the pupal nervous system. These genes can be further studied in the context of pupal nervous system development.
2017-03-21 | GSE89168 | GEO
Project description:Honey bees move through a series of in-hive tasks (M-bM-^@M-^\nursingM-bM-^@M-^]) to outside tasks (M-bM-^@M-^\foragingM-bM-^@M-^]) that coincident with an intense increase in metabolic activity. Social context can cause worker bees to speed up, or slow down this process and foragers may revert back to their earlier in hive tasks accompanied by reversion to earlier physiological states. To determine if the transcriptional profile of forager bees can revert, or if the effects of flight on gene expression are irreversible, we used whole-genome microarrays. Brain tissue and flight muscle exhibited independent patterns of expression during behavioral transitions, with patterns of expression in the brain reflecting both age and behavior, while flight muscle exhibited primarily age-related patterns of expression. Our data suggest that the transition from little to no flight (nurse) to intense flight (forager), rather than the amount of flight has a major effect on gene expression. Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. These data suggest an epigenetic control and energy balance role in honey bee functional senescence. Brains and thoraces from the same individuals of all behavioral groups were compared on a total of 132 arrays. The samples were hybridized against each other using a loop design. The groups tested are outlined as follows: Typical aged nurse 'YN' (8-10 days old; <1 day flight experience), Precocious forager 'PF' (8 to 10 days old; 2 to 3 days flight experience), Overaged nurse 'ON' (19 to 22 days old; < 1 day flight experience), Forager - low flight 'TFL' (19 to 22 days old; 2 to 3 days flight experience), Forager - high flight 'TFH' ( 19 to 22 days old; 7 to 9 days flight experience), Forager - old 'OF' (25 to 26 days old; 10 to 12 days flight experience), Reverted nurse 'RN' (25 to 26 days old; 7 to 9 days flight experience). The comparisons are outlined as follows: YN:ON (6 arrays), ON:RN (6 arrays), RN:TFH (6 arrays), TFH:TFL (6 arrays), TFL:PF (6 arrays), PF:YN (6 arrays), ON:TFL (12 arrays), YN:OF (6 arrays), OF:RN (6 arrays), RN:YN (6 arrays). Each comparison was done for individual brains and thoraces. Total: 132 arrays
2012-10-01 | E-GEOD-40650 | biostudies-arrayexpress
Project description:Leg muscle mdx and control: 7,14,23 day Keywords: other
2004-02-05 | GSE1018 | GEO
Project description:Honey bees move through a series of in-hive tasks (“nursing”) to outside tasks (“foraging”) that coincident with an intense increase in metabolic activity. Social context can cause worker bees to speed up, or slow down this process and foragers may revert back to their earlier in hive tasks accompanied by reversion to earlier physiological states. To determine if the transcriptional profile of forager bees can revert, or if the effects of flight on gene expression are irreversible, we used whole-genome microarrays. Brain tissue and flight muscle exhibited independent patterns of expression during behavioral transitions, with patterns of expression in the brain reflecting both age and behavior, while flight muscle exhibited primarily age-related patterns of expression. Our data suggest that the transition from little to no flight (nurse) to intense flight (forager), rather than the amount of flight has a major effect on gene expression. Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. These data suggest an epigenetic control and energy balance role in honey bee functional senescence.
2012-10-01 | GSE40650 | GEO
Project description:Transcriptional profiling comparing adult wild-type indirect flight muscle (IFM) with wild-type leg muscle and salm RNAi IFM (Mef2-GAL4, UASsalmIR). We used 2 different salm hairpin constructs for the experiments, TF3029 and TF101052, both available from the VDRC Drosophila stock centre.
2011-03-01 | GSE27502 | GEO
Project description: Not available
| S-EPMC5034364 | biostudies-literature
Project description:Transcriptional profiling comparing adult wild-type indirect flight muscle (IFM) with wild-type leg muscle and salm RNAi IFM (Mef2-GAL4, UASsalmIR). We used 2 different salm hairpin constructs for the experiments, TF3029 and TF101052, both available from the VDRC Drosophila stock centre. Experiments were done in biological duplicates + 1 technical replicate (1 labeled sample was hybridized on a different array)
2011-03-01 | E-GEOD-27502 | biostudies-arrayexpress