MRNA tagging (intestine)
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE4150 | GEO | 2006/02/03
SECONDARY ACCESSION(S): PRJNA94995
REPOSITORIES: GEO
Similar Datasets
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: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: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 Keywords: other
2005-12-20 | GSE2626 | GEO
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
2010-06-05 | E-GEOD-2626 | biostudies-arrayexpress
Project description:The method of mRNA tagging was recently developed to isolate mRNA population from muscle tissues in Caenohabditis elegans. This method utilizes a FLAG-tagged poly(A)-binding protein (PABP), which can bind to poly(A)-tail of eukaryotic mRNA. Thus, the mRNA population from specific tissue, in which FLAG- tagged PABP is expressed, can be co-immunoprecipitated with FLAG-tagged PABP using FLAG-specific antibody. To evaluate the applicability of this method to isolate mRNA from specific tissue in Drosophila, we generated Rh1-GLA4/P{UAS-dPABP-FLAG} flies which express a FLAG-tagged PABP in photoreceptor cells R1-R6. We then prepared 4 individual mRNA samples (subset 1: GSM30900-30903)) presumably from photoreceptor cells of these flies by mRNA tagging method. We also prepared 4 individual mRNA samples (subset 2: GSM30832-30835) from whole heads of the Rh1-GAL4/P{UAS-dPABP-FLAG} flies, as well as 6 individual mRNA samples (subset 3: GSM30824-30828, GSM30830) from whole heads of wild type Canton-S flies. The total 14 mRNA samples were used to synthesize target separately and each of the resultant target was used to hybridize with 1 Drosophila Genome Array DrosGenome1 Affymetrix GeneChip. The raw data of the 14 microarray were imported to dChip program (version 1.3). The arrays were normalized to a common baseline array that has the median overall brightness. The expression value for each probe set on each chip was then calculated as model-based expression index (MBEI) by Perfect Match-only model. By comparing the results of subset 1 and subset 2, we found most known photoreceptor-specific genes were indeed enriched by mRNA tagging. Through the comparison of the results of subset 2 and subset 3, we found the mRNAs of most genes known to be involved in fly visual function were underrepresented in subset 2, which could be due to squelching effect of GAL4. By combining the data of subset 1, 2 and 3, we were able to identify 11 new photoreceptor cell-enriched genes. Keywords: other
2004-10-11 | GSE1790 | GEO
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)
2010-08-04 | E-GEOD-23252 | biostudies-arrayexpress
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
2010-08-04 | E-GEOD-23255 | 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)
2010-08-04 | E-GEOD-23253 | biostudies-arrayexpress
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)
2010-08-04 | E-GEOD-23287 | biostudies-arrayexpress
Project description:modENCODE_submission_657 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: NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1); Tissue: Coelomocytes (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: unc-119(ed1); wdEx638 [unc-119(+); unc-122::3XFLAG::PAB-1]; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Coelomocytes (L2)
2010-08-04 | E-GEOD-23281 | biostudies-arrayexpress