Comparing the transcriptomic responses of Caenorhabditis elegans exposed to cadmium from L1 to L3 versus L1 to L4 stage
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ABSTRACT:
PROVIDER: PRJNA658134 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12478185_1.fastq.gz | Fastqsanger.gz | |||
| SRR12478185_2.fastq.gz | Fastqsanger.gz | |||
| SRR12478186_1.fastq.gz | Fastqsanger.gz | |||
| SRR12478186_2.fastq.gz | Fastqsanger.gz | |||
| SRR12478187_1.fastq.gz | Fastqsanger.gz |
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Project description:Cadmium is a naturally occurring heavy metal, and it is widely used in industry. Due to its persistent toxic effect, cadmium is classified as a category one human carcinogen. Its toxicity has been extensively studied in different organisms, including the nematode Caenorhabditis elegans. To investigate the transcriptomic responses following cadmium during early life exposure, C. elegans larval were exposed either from L1 to L3 stage or L1 to L4 stage to 20 µM cadmium chloride. RNAseq was applied to identified the changes of the transcriptome and the pathways which are specific to each stage. Overall, the result revealed that the highest responsive genes in both exposure scenario were linked to oxidative stress, lipid metabolism and ion binding. Additionally, some of these genes are well characterized and linked to specific functions, but some have no known function, however these uncharacterized genes are differentially expressed in both stages as a result of cadmium toxicity.Numerous transcripts were identified in one stage but not at the other. Furthermore, a general trend was observed where a larger number of genes were differentially expressed at L3 stage compared to L4, which suggest stage specific sensitivity in response to cadmium exposure.
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Project description:modENCODE_submission_659 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: N2; Tissue: reference (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue reference (L3-L4)
2010-08-04 | E-GEOD-23283 | 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_655 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: NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); Tissue: Dopaminergic neurons (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx637 [unc-119 (+); dat-1::3XFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue Dopaminergic neurons (L3-L4)
2010-08-04 | E-GEOD-23279 | biostudies-arrayexpress
Project description:modENCODE_submission_460 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: NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1); Tissue: PVD OLLs (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx460 [unc-119 (+); ser-2prom3B::3XFLAG::PAB-1]; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue PVD OLLs (L3-L4)
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Project description:To identify genes differentially expressed during L3 lethargus, we collected RNA during the third larval stage (L3) lethargus period, 37 hours after feeding developmentally-arrested L1 animals. Animals in lethargus were identified based on quiescence of locomotion and feeding. Additional time point for RNA collection was in the mid-L3 stage, 32 hours after feeding developmentally-arrested L1 animals. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 153 gene transcripts were up regulated, and 48 gene transcripts were down regulated, during the L3 lethargus period compared to the L3 stage (false discovery rate (FDR) < 0.05).
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Project description:To identify genes differentially expressed during L3 lethargus, we collected RNA during the third larval stage (L3) lethargus period, 37 hours after feeding developmentally-arrested L1 animals. Animals in lethargus were identified based on quiescence of locomotion and feeding. Additional time point for RNA collection was in the mid-L3 stage, 32 hours after feeding developmentally-arrested L1 animals. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 153 gene transcripts were up regulated, and 48 gene transcripts were down regulated, during the L3 lethargus period compared to the L3 stage (false discovery rate (FDR) < 0.05). There were 2 groups and 3x replication for each group, for 6 total samples. The groups were (1) L3 and (2) L3-lethargus. We compared L3-lethargus vs L3 using R/maanova. The permutation based p-values for each test were significant for FDRM-bM-^IM-$5%.
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2023-11-05 | GSE246726 | GEO