Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq on D5 C. elegans in WT(N2), alg-1(gk214), alg-2(ok304)

ABSTRACT: RNA-seq on D5 C. elegans in WT(N2), alg-1(gk214), alg-2(ok304)

PROVIDER: PRJNA448899 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6949390.fastq.gz	Fastqsanger.gz
	SRR6949382.fastq.gz	Fastqsanger.gz
	SRR6949383.fastq.gz	Fastqsanger.gz
	SRR6949384.fastq.gz	Fastqsanger.gz
	SRR6949385.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

RNA-seq on D5 C. elegans in WT(N2), alg-1(gk214), alg-2(ok304)

Project description:In order to examine the misregulation of genes in loss of function alg-1 and alg-2 versus WT, RNA-seq was performed on D5 C.elegans in WT(N2), alg-1(gk214), alg-2(ok304)

2018-05-01 | GSE112753 | GEO

miRNAs associated with ALG-1 and ALG-2 in adult C. elegans

Project description:Investigated the specific miRNAs that are assocaited with ALG-1 and ALG-2 in adult (D5) C. elegans. ALG-1 and ALG-2 were IP-ed from D5 collected C.elegans, RNA was isolated and used for small RNA sequencing. Two biological replicates were used.

2018-05-01 | GSE112754 | GEO

Purification of TAP::ALG-1 complexes and associated RNA from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2) animals

2012-03-01 | GSE32941 | GEO

Purification of TAP::ALG-1 complexes and associated RNA from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2) animals

Project description:To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein We purified TAP::ALG-1 complexes from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2, serving as a mock control) animals and hybridized the associated mRNAs to two-color microarrays RNA isolated from WS4303 and N2 (mock control) animals was analyzed for each IP sample and for each total worm extract sample. Three independent biological replicates have been performed. Long-oligo whole-genome C. elegans arrays, produced by the Genome Sequencing Center at Washington University in St. Louis (http://genome.wustl.edu/genome/celegans/microarray/ma_gen_info.cgi), were used for analysis. Log2 ratios (immunopurified RNA over total RNA from extract) were calculated for each gene. Microarrays generated from WS4303 animals were compared to microarrays generated from N2 mock control animals by a Student’s two sample t test.

2012-03-01 | E-GEOD-32941 | biostudies-arrayexpress

Developmental characterization of the microRNAs-specific C. elegans Argonautes alg-1 and alg-2

Project description:This study analyzes miRNA association with ALG-1 and ALG-2 in different stages during larval development of C. elegans

2012-02-03 | GSE35505 | GEO

Developmental characterization of the microRNAs-specific C. elegans Argonautes alg-1 and alg-2

Project description:This study analyzes miRNA association with ALG-1 and ALG-2 in different stages during larval development of C. elegans Staged animals (L1, L2, L3, L4) - the alg-2 mutant expressing tagged-ALG-2, alg-1 mutant, and wild type controls - were lysed. ALG-1 IP or ALG-2 (GFP) IP was performed using tags from all four samples at all four timepoints. Small RNAs were released from antibodies and 5' end-labelled with AlexaFluor532. Labelled RNA was hybridized to a custom microRNA microarray platform to quantify miRNA content.

2012-02-03 | E-GEOD-35505 | biostudies-arrayexpress

ALG-5 is a miRNA-associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline

Project description:Caenorhabditis elegans contains twenty-five Argonautes, of which, only ALG-1 and ALG-2 are known to interact with miRNAs. ALG-5 belongs to the AGO subfamily of Argonautes that includes ALG-1 and ALG-2, but its role in small RNA pathways is unknown. We analyzed by high-throughput sequencing the small RNAs associated with ALG-5, ALG-1, and ALG-2, as well as changes in mRNA expression in alg-5, alg-1, and alg-2 mutants.

2017-06-09 | GSE98935 | GEO

Transcriptional profiling of Caenorhabditis elegans in control (20°C) and heat shock (35°C) of N2 (WT) and miR-85(n4117) animals

Project description:Transcriptional profiling of N2 (WT) and miR-85(m4117) Caenorhabditis elegans at larval stage 4 (L4) compared at either control temperature (20°C) or after 3hr HS (35°C).

2021-07-26 | GSE168073 | GEO

Expression data from ageing wt N2 Bristol Caenorhabditis elegans population.

Project description:Expression data from ageing wt N2 Bristol Caenorhabditis elegans population.

| PRJNA685423 | ENA

Modeling neurodevelopmental disorder-associated human AGO1 mutations in C. elegans Argonaute alg-1. [RNA-Seq]

Project description:MicroRNAs (miRNA) associate with Argonaute proteins and negatively regulate gene expression by base pairing with complementary sequences in the 3’ UTRs of target genes. De novo coding variants in the human Argonaute gene AGO1 were reported to cause neurodevelopmental disorder (NDD) with intellectual disability (ID). Most of the altered amino acids are conserved between the miRNA associated Argonautes in H. sapiens and C. elegans, suggesting that the human AGO1 mutations could disrupt evolutionarily conserved functions in miRNA biogenesis or target repression. We genetically modeled four human AGO1 mutations in C. elegans by introducing identical mutations into the C. elegans AGO1 homolog, ALG-1. These alg-1 NDD mutations caused phenotypes in C. elegans indicative of disrupted miRNA processing, miRISC formation, and/or target repression. We show that the alg-1 NDD mutations are antimorphic as they cause developmental and molecular phenotypes stronger than those exhibited by the alg-1 null mutants, likely by sequestrating functional miRNA silencing complex (miRISC) components into non-functional complexes that fail to confer robust gene repression. The alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles, both in overall abundances and ALG-1 NDD association, accompanied by perturbation of downstream gene expression, including altered translational efficiency and/or mRNA abundance. The perturbed genes include those with human orthologs whose dysfunction is associated with NDD. These cross-clade genetic studies illuminate fundamental Argonaute functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.

2023-12-30 | GSE252065 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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