Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identiﬁcation of Drosophila TDF/Apt regulated genes in embryos

ABSTRACT: Drosophila tdf, another name apontic (apt), encodes a bZIP transcription factor that is required for the development of trachea, heart, head and neural system. However, little is known about the target of TDF/Apt. To identify theTDF/ Apt regulated genes, we compared expression profiles of mRNA purified from wild-type and tdf mutant embryos. Summary file is emtdf-yw.CHP.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE36917 | GEO | 2014/04/01

SECONDARY ACCESSION(S): PRJNA157091

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

IdentiM-oM-,M-^Acation of Drosophila TDF/Apt regulated genes in embryos

Project description:Drosophila tdf, another name apontic (apt), encodes a bZIP transcription factor that is required for the development of trachea, heart, head and neural system. However, little is known about the target of TDF/Apt. To identify theTDF/ Apt regulated genes, we compared expression profiles of mRNA purified from wild-type and tdf mutant embryos. Summary file is emtdf-yw.CHP. yw and tdf mutant embryos were selected at later stage of development for RNA extraction and hybridization on Affymetrix microarrays. We identified tdf mutant embryos using CyOact-GFP balancer chromosome.

2014-04-01 | E-GEOD-36917 | biostudies-arrayexpress

RNA-seq of NPs and NP-IDO-APT treated lymphocytes

Project description:To explore the effect of IDO-APT on T cell function, we conducted RNA transcriptome profiling of NPs, named as NP-Scr-APT in article, and NP-IDO-APT treated lymphocytes.

2023-08-08 | GSE222366 | GEO

The APT complex is involved in non-coding RNA transcription and is distinct from CPF [PAR-CLIP]

Project description:The 3′-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes but how these are coordinated remains poorly understood. Several subunits of the CPF including two protein phosphatases are also found in a related complex, the ‘associated with Pta1’ (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1 has functions separable from those of CPF. Syc1 plays a role in sn/snoRNA production whereas CPF processes the 3ʹ-ends of protein-coding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.

2018-09-17 | GSE114302 | GEO

The APT complex is involved in non-coding RNA transcription and is distinct from CPF [RNA-seq]

2018-09-17 | GSE114301 | GEO

The APT complex is involved in non-coding RNA transcription and is distinct from CPF [ChIP-seq]

2018-09-17 | GSE114303 | GEO

Drosophila melanogaster

Project description:Identiﬁcation of Drosophila TDF/Apt regulated genes in embryos

| PRJNA157091 | ENA

Identification of Drosophila Mid regulated genes in embryos

Project description:Drosophila midline(mid), encodes a T-box transcription factor that is required for cell fate specification and tissue morphogenesis during a series of developmental processes. However, little is known about the target of Mid. To identify the Mid regulated genes, we compared expression profiles of mRNA purified from wild-type and mid mutant embryos. Summary file is yw-mid.CHP.

2016-06-30 | GSE73802 | GEO

Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing

Project description:Microarray hybridization was used to compare RNA from mouse brains with opposite genotypes at the Mvb1 (Nxf1) modifier locus for known alternative processing events. 6 samples of total brain RNA, from 3 littermate pairs, were hybridized to splicing-sensitive microarrays *Addendum Depending on the analysis software used, these CEL files may not load correctly using default parameters. This is due to the custom chip type of MJAY not being used during the array scanning step. There are three workarounds known for this problem so far. 1) If using APT, use multiple --chip-type parameters. Specifically, --chip-type mjay --chip-type MJAY --chip-type MoEx-1_0-st-v1.1sq 2) Edit the CEL file by converting to text using the APT command apt-cel-convert, then replacing the MoEx-1_0-st-v1.1sq in the DatHeader line with MJAY (all caps). 3) Edit the .pgf, .clf, and antigenomics.bmp files to use the MoEx-1_0-st-v1.1sq array instead of MJAY for the chip_type and lib_set_name options. (works on AltAnalyze software)

2015-03-10 | E-GEOD-66696 | biostudies-arrayexpress

Fyn- and Abl-driven interactome and post-translational modifications of DCBLD1 and DCBLD2

Project description:Three related datasets are included, all from immunoprecipitations of FLAG-tagged DCBLD1 and DCBLD2 (human) from 293 cells. Letters at the end of file names denote regions of each gel lave from highest (“A”) to lowest (“B”-X) molecular weight. File names containing “SILAC” are part of a dataset composed of 3 biological replicates (“T1”,”T2”,”T3” in file name) run of 10% or 15% gels (“10” or “15” in file name). DCBLD1 or DCBLD2 were immunoprecipitated from cells alone (light SILAC condition) or with Fyn/Abl (heavy SILAC condition). “Mock”, “Fyn” alone, or “Abl” alone in file names denote control immunoprecipitates, in which the light condition was a mock transfection and the heavy was either a mock or had Fyn/Abl expressed alone. Trypsin was used as the proteolytic enzyme. File names beginning with “Label_free” are part of datasets from LC-MS/MS analysis of DCBLD1 or DCBLD2 immunoprecipitates from 293 lysates. Prior to LC-MS/MS analysis, immunoprecipitates were digested with trypsin and GluC. Only DCBLD1 and DCBLD2 protein bands were analyzed via LC-MS/MS. File names containing “zebrafish” are part of datasets from LC-MS/MS analysis of DCBLD2 immunoprecipitates from 293 extracts that were then incubated with zebrafish extracts. These datasets include tryptic peptides from both human and zebrafish proteins.

2020-08-07 | PXD017723 | Pride

Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment

Project description:Single-cell RNA-seq analysis of primary and metastatic (liver) human PDAC tumors, some pre-treatment and some post-chemotherapy. (Please note that although the file has "RAW" in the name these are the filtered results from CellRanger.)

2023-01-09 | GSE205013 | GEO

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