Intestine mRNA tagging
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE2626 | GEO | 2005/12/20
SECONDARY ACCESSION(S): PRJNA92139
REPOSITORIES: GEO
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Project description:mRNA tagging in the intestine of C. elegans. FLAG::PAB-1 was expressed from the intestine-specific promoter for ges-1 and used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine with anti-FLAG antibody on agarose beads. This mRNA was amplified, cDNA was synthesized and labeled with Cy5. Total RNA from the same strain, but without the IP was amplified and cDNA was synthesized and labeled with Cy3. These two samples were compared on C. elegans DNA printed arrays from the Stuart Kim lab. 1938 intestine-expressed genes were identified (p<0.001) after eight repeats of the experiment A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Type = replicate_design Series_overall_design: Computed
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Project description:For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab Set of arrays that are part of repeated experiments Keywords: Biological Replicate, mRNA tagging
2006-02-03 | GSE4150 | GEO
Project description:For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab
2006-01-04 | E-SMDB-3592 | biostudies-arrayexpress
Project description:For each experiment (as described in Pauli et al. 2006): Channel 1: whole worm lysate from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 Channel 2: mRNA immunoprecipitated from strain SD1084 carrying transgene Pges-1::FLAG::PAB-1 mRNA was amplified and hybridized to C. elegans DNA arrays from the Stuart Kim lab Set of arrays that are part of repeated experiments Biological Replicate Computed
2006-02-02 | E-GEOD-4150 | biostudies-arrayexpress
Project description:modENCODE_submission_463 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: SD1084 (engineered, target gene ges-1 tagged by 3xFlag::PAB-1); Tissue: Intestine (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs148 [(ges-1p::FLAG::PAB-1) +(sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1084 (engineered, target gene ges-1 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Intestine (L2)
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Project description:Binding of in vitro synthesized HAC1 mRNA was studied using protein microarray. 3 replicates, plus 3 reverse dye replicates An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. is_reverse: no: HAC1 mRNA Cy5 labeled; yes: HAC1 mRNA Cy3 labeled
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Project description:modENCODE_submission_462 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1); Tissue: Pan-neural (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs153 [(F25B3.3::FLAG::PAB-1) + (sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Pan-neural (L2)
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Project description:modENCODE_submission_465 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1); Tissue: body wall muscle; Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs146 [(myo-3p::FLAG::PAB-1) + (sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue body wall muscle
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Project description:modENCODE_submission_2454 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); Tissue: hypodermis (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119(ed1); wdEx626[unc-119+; dpy-7::3xFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue hypodermis (L3-L4)
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