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I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells II

ABSTRACT: The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), exclusively expressed in intestinal progenitor cells. This method used UV cross-linked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4. When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identified 98.8% of transcripts found after progenitor cell sorting, and had low background noise despite being derived from whole animal lysate.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE160126 | GEO | 2020/12/11

REPOSITORIES: GEO

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I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells I

Project description:The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. We describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), exclusively expressed in intestinal progenitor cells. This method used UV cross-linked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4. Using I-KCKT-GAL4 based enhanced CLIP datasets provided here we mapped the RNA targets of a selective RNA binding protein, Fragile Mental Retardation Protein (FMRP).

2020-12-11 | GSE160125 | GEO

Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and Su(H) in wildtype, seq overexpressed and ttk-RNAi intestinal progenitor cells by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and comparing Su(H) binding sites between seq overexpressed and ttk-RNAi intestinal progenitor cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: Dam(Ctrl) , Ttk-Dam transgenes, Su(H)-Dam, Su(H)-Dam&seq and Su(H)-Dam&ttk-RNAi were expressed in intestinal progenitor cells by esg-Gal4.The guts within 2 days was used for DNA adenine methyltransferase identification (DamID), followed by deep sequencing analysis Results: Ttk suppresses neural specific Notch targets through suppressing Seq in intestinal progenitor cells

2021-02-23 | GSE130941 | GEO

Transcriptomic and proteomic analyses of colon inflammation in interleukin-10 gene-deficient mice

Project description:A total of 30 male IL10-/- (B6.129P2-Il10<tm1Cgn>/J) and 30 male C57 control (C57BL/6J) mice were obtained from The Jackson Laboratory (Bar Harbor, Maine, USA). All mice were between 28 and 35 days of age at the start of the study. For convenience and consistency in reporting, their age was defined as 35 days or 5 weeks of age. The mice were housed individually in standard shoebox size cages containing untreated wood shavings and maintained in an air-conditioned animal room with a 12-h light-dark cycle. Animals had free access to water and were fed an AIN-76A standard powder diet prepared in-house. This study was approved by the AgResearch Ruakura Animal Ethics Committee in Hamilton, New Zealand according to the Animal Protection Act (1960) and Animal Protection Regulations (1987) and amendments. Four days after arrival, all mice were inoculated orally with a mixture of Enterococcus faecalis strains and bacteria commonly found in the intestinal lumen to obtain a more consistent and reproducible intestinal inflammation. Mice were randomly assigned to five sampling groups (7, 8.5, 10, 12 and 14 weeks of age).

2009-09-10 | GSE17990 | GEO

Genome-wide DNA-binding analysis for Sox100B in intestinal stem cells by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for Sox100B in intestinal stem cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: DNA adenine methyltransferase identification (DamID) on Sox100B driven by ESG-Gal4 Results: 5046 significant genomic binding sites, corresponding to 3182 genes were identified via iDamID following Sox100B overexpression in progenitor cells compared to WT. About a third of these genes were in the list of significantly altered genes following Sox100B overexpression and/or depletion.

2020-05-18 | GSE130304 | GEO

Palmyrene Polychromy: Investigations of funerary portraits from Palmyra in the collections of the Ny Carlsberg Glyptotek

Project description:Two samples from the Beauty of Palmyra (IN 2795 – Ny Carlsberg Glyptotek, Copenhagen, Denmark) were collected from the surface coating, and partially the paint layer, in locations corresponding to paint residues from respectively the yellow paint (containing lead-based yellow pigment) and the red paint (containing haematite as pigment) of the headdress of the figure. The two samples were analysed using a palaeoproteomic protocol to investigate the use of a proteinaceous paint binder and/or the presence of other proteinaceous materials. The analysis led to the confident identification of collagen, probably indicating the use of animal glue as paint binder of the sample removed from red paint residues. Various animal keratins were also confidently identified in both samples. The presence of these proteins might be related to the manufacture of organic pigments, but also possibly to the use of a keratin-based glue as paint binder or surface coating, or even to the use of a paintbrush made with animal bristles.

2022-06-28 | PXD031280 | Pride

Application of Histone Interacting Domains as an Alternative to Antibodies (CIDOP-seq)

Project description:Application of Histone Modification Interacting Domains (HMIDs) as an Alternative to Antibodies. HMIDs and antibodies (taken from ENCODE) were used for precipitation of native chromatin (mononucleosomes) in order to study distinct histone marks. HMIDs used in this study are MPP8 Chromo domains and ATRX ADD (as H3K9me3 binders), Dnmt3a PWWP (as H3K36me3 binder) and CBX7 Chromo (as H3K27me3 binder).

2014-02-06 | E-MTAB-2143 | biostudies-arrayexpress

Cell type-specific gene expression profiling of Drosophila neurons [RNA-Seq]

Project description:Gene expression profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Gene expression profiles were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons in the adult Drosophila head using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Sequencing was performed with an Illumina HiSeq 2000.

2012-08-02 | E-GEOD-37027 | biostudies-arrayexpress

The E3 Ligase CUL3 physically interacts with TANGO10 protein in vivo

Project description:List of protein scores for putative TANGO10 interactors from mass spectrometry analysis of FLAG-tagged TANGO10 using either elav-GAL4 or tim-GAL4 at both ZT10 and ZT 22, as determined using Proteome Discoverer software (ThermoFisher). Fly heads from GAL4 heterozygotes were used as controls. The hits from FLAG-tagged twenty-four (TYF) proteomics were also excluded from the list to increase TANGO10-specificity. Proteins listed are those present in at least one elav-GAL4 sample and at least one tim-GAL4 sample but no negative controls.

2021-11-02 | PXD029326 | Pride

Genome-wide DNA-binding analysis for E(spl)m8 in intestinal stem cells by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for E(spl)m8 in intestinal stem cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: DNA adenine methyltransferase identification (DamID) on E(spl)m8 driven by Dl-Gal4 Results:

2018-02-02 | GSE102568 | GEO

Cell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq]

Project description:Chromatin profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Cell type-specific histone modification maps were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Three histone modifications were profiled: H3K4me3, H3K27ac, and H3K27me3. Sequencing was performed with an Illumina HiSeq 2000.

2012-08-02 | E-GEOD-37032 | biostudies-arrayexpress

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