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Let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC2]

ABSTRACT: We examined mRNA levels in wild-type and lin-28(xe192) animals throughout postembryonic development (0-44 h) with hourly resolution. Samples collected at 3 to 6 hours of development were used as one of the three biological replicates used to determine differentially expressed genes in lin-28(xe192) animals.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE315952 | GEO | 2026/06/10

REPOSITORIES: GEO

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let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [smallRNA-seq TC2]

Project description:We examined the levels of small RNAs in wild-type and lin-28(xe192) animals throughout postembryonic development (0-44 h) with hourly resolution. The first time points (0h to 23h) of this experiment were published previously and are accessible under the accession GSE245900 (Nahar et al. 2024). In that previous submission, all samples were sequenced twice to increase coverage (two fastq files per sample on SRA). The new samples published here (24h-44h) were only sequenced once and are thus compatible with the first sequencing round of GSE245900. While in this submission only the raw data of the new samples (24h-44h) are published, we included the time points 0h to 23h (considering only the first sequencing run, see above) in the processed data files. Due to the differences in sequencing depths between the two submissions, the intensity values for time points 0h to 23h are not identical even though they originate from the same biological samples.

2026-06-10 | GSE315956 | GEO

let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC5]

Project description:We examined mRNA levels using mRNA-seq in wild-type (N2), lin-28 mutant animals (HW2705) and animals that have the single GGAG motif (i.e. the putative LIN-28 binding motif) in the lin-46 5'UTR mutated to CTCC (HW3531).

2026-06-10 | GSE315955 | GEO

let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq RIPseq]

Project description:We identified 581 transcripts enriched ≥2-fold for LIN-28 binding in L1 animals.

2026-06-10 | GSE315949 | GEO

let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC1]

Project description:We examined gene expression changes using mRNA-seq in two different lin-28 mutant strains, lin-28(n719) and lin-28(xe192). Although both are considered genetic null mutants, their expression profiles differ substantially: lin-28(n719) (a point mutation affecting a splice site) shows many more dysregulated genes than lin-28(xe192) (a deletion of the entire lin-28 locus).

2026-06-10 | GSE315950 | GEO

let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning [mRNA-seq TC3_TC4]

Project description:We determined differentially expressed genes in lin-28(xe192) animals in the early developmental time window of 3 to 6 hours collected in three biological replicates, two included here (TC3, TC4) and one as part of a full developmental time course (TC1).

2026-06-10 | GSE315954 | GEO

Effect of lin-28 and lin-46 on miRNA profile in late L1 stage Caenorhabditis elegans

Project description:Comparison of miRNA profiles of wildtype and lin-28(n719); lin-46(ma164) Caenorhabditis elegans nematodes at the L1 stage

2012-02-09 | GSE35634 | GEO

Effect of lin-28 and lin-46 on miRNA profile in late L1 stage Caenorhabditis elegans

Project description:Comparison of miRNA profiles of wildtype and lin-28(n719); lin-46(ma164) Caenorhabditis elegans nematodes at the L1 stage Two genotypes, wildtype vs. mutant. Biological replicates: 3 wild type, 3 mutant, independently grown and harvested. One replicate per slide.

2012-02-09 | E-GEOD-35634 | biostudies-arrayexpress

Role of LIN-15A on the binding of LIN-15B and LIN-35

Project description:ChIP-seq was performed in C. elegans to characterize the genomic binding profiles of LIN-35 (DREAM complex), LIN-15B, and LIN-15A, and to assess their interdependencies. Experiments were conducted in wild-type animals and in lin-15A(fp31), lin-15B(n744), and lin-35(n745) null mutants. All three factors showed highly overlapping binding patterns, predominantly at promoter regions, and shared target genes enriched for metabolic and developmental pathways. Comparative analyses revealed reciprocal effects on binding between LIN-35 and LIN-15B, while loss of LIN-15A primarily resulted in increased LIN-35 and LIN-15B occupancy at a subset of loci, suggesting that LIN-15A modulates DREAM complex binding.

2026-03-31 | GSE325892 | GEO

let-7 and lin-46 are the essential targets of the LIN28 RNA-binding protein in temporal patterning

Project description:This SuperSeries is composed of the SubSeries listed below.

2026-06-09 | GSE315957 | GEO

LIN-14 mutants

Project description:A temporal gradient of the novel nuclear protein LIN-14 specifies the timing and sequence of stage-specific developmental events in Caenorhabditis elegans. The profound effects of lin-14 mutations on worm development suggest that LIN-14 directly or indirectly regulates stage-specific gene expression. We show that LIN-14 can associate with chromatin in vivo and has in vitro DNA binding activity. A bacterially expressed C-terminal domain of LIN-14 was used to select DNA sequences that contain a putative consensus binding site from a pool of randomized double-stranded oligonucleotides. To identify candidates for genes directly regulated by lin-14, we employed DNA microarray hybridization to compare the mRNA abundance of C. elegans genes in wild-type animals to that in mutants with reduced or elevated lin-14 activity. Five of the candidate LIN-14 target genes identified by microarrays, including the insulin/insulin-like growth factor family gene ins-33, contain putative LIN-14 consensus sites in their upstream DNA sequences. Genetic analysis indicates that the developmental regulation of ins-33 mRNA involves the stage-specific repression of ins-33 transcription by LIN-14 via sequence-specific DNA binding. These results reinforce the conclusion that lin-14 encodes a novel class of transcription factor. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2007-07-19 | GSE8520 | GEO

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