Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Drosophila melanogaster testis with or without tbrd-1 knock out or tplus3a/b knock out

ABSTRACT: Many protein complexes are involved in gene regulation during Drosophila spermatogenesis. tplus3a and tplus3b code for Plus3 domain proteins and are enriched in spermatocytes. Male flies ∆tplus3a/b carrying deletions of both genes in trans to deficiency Df(2L)BSC151 show severely reduced fertility. tbrd-1 is known to regulate hundreds of genes during spermatogenesis in cooperation with tTAFs. To gain more insight into the regulatory mechanisms during spermatogenesis we used RNA from testes of ∆tplus3a/b/Df(2L)BSC151 and tbrd-11 mutant flies for RNAseq in comparison to w1118 wild-typic control. RNA was isolated with Trizol from 200 Testes dissected from w1118, homozygous tbrd-11 mutants or ∆tplus3a/b/Df(2L)BSC151. After DNAse I digestion RNA was purified and RNAseq was performed in three replicates. Genotype Description: w1118: wild-typic control tbrd-11: homozygous tbrd-11 mutants (knock-out through P{EPgy2}tbrd-11, as described in Leser et al., 2012) ∆tplus3a/b/Df(2L)BSC151: CRISPR/Cas9 deletion mutants, representing knock-out of both tplus3 and tplus3b. Male flies y1cho2v1;∆tplus3a/b/CyO were crossed with virgin females w1118;Df(2L)BSC151/CyO. Male offspring with w1118;∆tplus3a/b/Df(2L)BSC151 were used for RNAseq.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Boris Lamp

PROVIDER: E-MTAB-7013 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis in transgenerational epigenetic inheritance

Project description:The study was performed towards understanding transgenerational epigenetic inheritance at transcriptome level. The founder males of F0 generation (actin-GAL4/Pin; UASRNAi-mts/+), and the resulting, male-line derived F1 (Pin/+; +/+), and F2 (+/+; +/+) generation individuals were used as test lineage, and the wild-type w1118 progeny as control lineage flies. The fly strains used for generating founder F0 line included Pin/CyO-dYFP; UASRNAi-mts/MKRS, actin-GAL4/CyO; +/+, and w1118. Precursor strains, as appropriate, were outcrossed with w1118 to minimize genetic background differences.

2024-01-05 | GSE222543 | GEO

DNA-Seq of DrosDel deficiency lines and w1118 lines

Project description:DNASeq reads from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies). Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_DNASeq_biological replicate #. We sequenced DNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).

2012-04-03 | E-GEOD-31550 | biostudies-arrayexpress

Expression profiling of DHR38-dependent transcripts in Drosophila larvae

Project description:Transcriptional profiling of Drosophila third instar larvae comparing control (w1118) and DHR38 mutants (DHR38Y214/Df(2)KetelRX32)

2010-12-01 | GSE23047 | GEO

Expression profiling of DHR38-dependent transcripts in Drosophila larvae

Project description:Transcriptional profiling of Drosophila third instar larvae comparing control (w1118) and DHR38 mutants (DHR38Y214/Df(2)KetelRX32)

2010-12-01 | GSE23047 | GEO

Drosophila 16-20 hrs embryos: DHR3G60S/Df(2R)12 vs. w1118

Project description:Transcriptional profiling of 16-20 hrs Drosophila embryos comparing control (w1118) and DHR3 mutants (DHR3G60S/Df(2R)12)

2009-12-01 | GSE18577 | GEO

RNA-Seq on Illumina platform of Drosophila DrosDel deficiency lines

Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Illumina platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).

2012-04-03 | E-GEOD-31549 | biostudies-arrayexpress

Transcription profiling of Drosophila deficiency hemizygotes and a duplication hemizygote reveals buffering of segmental and chromosomal aneuploidies in Drosophila melanogaster

Project description:Chromosomal instability which involves deletion and duplication of chromosomes or chromosome parts is a common feature of cancers, and deficiency screens are commonly used as a method to find genes involved in different biological pathways. Still, how gene expression from whole chromosomes or large chromosomal domains is affected by deficiencies, duplications or chromosome loss is largely unknown. Using expression microarrays of deficiency hemizygotes and a duplication hemizygote we show that expressed genes are significantly buffered when present in a deficiency hemizygote and that the buffering effect is general and not mainly caused by feedback regulation of individual genes. Differentially expressed genes are in general better buffered than ubiquitously expressed genes when present in one copy. When present in three copies, differentially expressed genes are in general less buffered than ubiquitously expressed genes. Furthermore, we show that the 4th chromosome is compensated in response to dose differences. Our results suggest that general mechanisms exist to stimulate and to repress gene expression of aneuploidy regions and on the 4th chromosome this compensation is mediated by POF (Painting of Fourth). Experiment Overall Design: We prepared total RNA from flies heterozygous for three different deletions, Df(2L)J-H, Df (2L)ED4470, Df(2L)ED4651, flies heterozygous for the duplication Dp(2;2)Cam3 and flies with only one chromosome 4, or three copies of the 4th chromosome, as well as from wild type control flies. Three biological replicates of all genotypes were prepared.

2009-04-03 | E-GEOD-14517 | biostudies-arrayexpress

DNA-Seq of DrosDel deficiency lines and w1118 lines

2012-04-03 | GSE31550 | GEO

RNA-Seq on SOLiD platform of DrosDel deficiency and w1118 flies

Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the SOLiD platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform_technical replicate. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies). The same sample was sequenced across two flow cells on the SOLiD platform.

2012-04-03 | E-GEOD-31401 | biostudies-arrayexpress

Buffering and proteolysis are induced upon segmental haploidy in Drosophila melanogaster.

Project description:Aneuploidy, i.e., variation in the number of individual chromosomes (chromosomal aneuploidy) or chromosome segment (segmental aneuploidy) is associated with developmental abnormalities and reduced fitness in all species examined, is the leading cause of miscarriages and mental retardations and a hallmark of cancer. Despite their documented importance in disease the effects of aneuploidies on the transcriptome remains largely unknown. Here we have examined the expression output in seven deficiency heterozygotes as single deficiencies and in all pairwise combinations. The results show that genes in one copy are buffered, i.e., are expressed above the expected 50% expression level compared to wild type and the buffering is general and not influenced by additional haploid regions. Long genes are significantly better buffered than short genes and our analysis suggests that gene length is the primary determinant for the degree of buffering. For short genes the degree of buffering depends on expression level and expression pattern. Furthermore, the results show that in deficiency heterozygotes the expression of genes involved in proteolysis is enhanced and negatively correlates with the degree of buffering. Our results suggest that proteolysis is a general response induced by aneuploidy. We prepared total RNA from flies heterozygous for seven different deletions, Df(3R)ED10953, Df(2L)ED4559, Df(2R)ED1770, Df(2R)ED1612, Df(2L)ED3, Df(3R)ED5071 or Df(3R)ED7665 in two or three single biological replicates or in pairwise combinations, as well as from six biological replicates of wild type control flies.

2012-04-04 | E-GEOD-34400 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data