Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1018951 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Citizen DNA Barcode Network (DNA Learning Center|Cold Spring Harbor Laboratory)
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Project description:Barcoding US Ants (DNA Learning Center|Cold Spring Harbor Laboratory)
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Project description:We selected 11 tissues from sorghum reference genome line BTX623 for comparative study between Maize and sorghum. These 11 tissues were selected at different development stages at Cold Spring Harbor Laboratory upland farm, RNA were extracted, library was made and sequenced on HiSeq2500 PE125 platform at Woodbury Genome Center.
2018-07-31 | E-MTAB-5956 | biostudies-arrayexpress
Project description:Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the expression profiles of both protein-coding and non-coding transcripts in 11 matched tissues using single-molecule long-read and deep RNA sequencing. In this study, maize B73 line was planted at Cold Spring Harbor Laboratory upland farm, 11 tissues together with previously reported six tissues were collected, RNA was extracted, library was made and sequenced on the HiSeq 2500 PE125 platform at Woodbury Genome Center.
2018-04-05 | E-MTAB-5915 | biostudies-arrayexpress
Project description:To understand the role of GCN2 in stress response, the total transcript and translation state were compared between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2015-12-01 | GSE52117 | GEO
Project description:To understand the role of GCN2 in regulating translation, we compared the polysome loading state and overall transcript level between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2015-12-01 | GSE52116 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE30567: ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19) GSE32931: ENCODE Cold Spring Harbor Labs Long RNA-seq (hg18) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series
2010-12-28 | E-GEOD-26284 | biostudies-arrayexpress
Project description:Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis. This work was supported by the Howard Hughes Medical Institute and by grants from the National Institutes of Health (R35GM144206), the National Science Foundation Plant Genome Research Program and the Robertson Research Foundation (to R.A.M.). Work in the Kouzarides laboratory is supported by a grant from Cancer Research UK (grant no. RG96894), in addition to benefiting from core support from the Wellcome Trust (WT203144) and Cancer Research UK (grant no. C6946/A24843). V.M. was funded by a Kay Kendall Leukemia Fund project grant (grant no. RG88664) and Cancer Research UK (grant no. RG96894). J.D. was funded by a grant from the Polish National Science Center (2020/39/D/NZ1/01918). We acknowledge assistance from the Cold Spring Harbor Laboratory Shared Resources, which are funded in part by the Cancer Center support grant (5PP30CA045508)
2023-08-07 | GSE222751 | GEO
Project description:Staphylococcus aureus is an opportunistic pathogen that can grow in wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilms forms and can cause many type of infections. Consequently, S. aureus must be able to adapt rapidly to these changing growth conditions, an ability largely driven at the posttranscriptional level. RNA helicases of the DEAD-box family play an important part in this process. In particular, CshA, which is part of the degradosome, is required for the rapid turnover of certain mRNAs and its deletion results in cold-sensitivity. To understand the molecular basis of this phenotype, we conducted a large genetic screen isolating 82 independent suppressors of cold growth. Full genome sequencing revealed the fatty acid synthesis pathway affected in many suppressor strains. Consistent with that result, sublethal doses of triclosan, a FASII inhibitor, can partially restore growth of a cshA mutant in the cold. Overexpression of the genes involved in branch-chained fatty acid synthesis was also able to suppress the cold-sensitivity. Using gas chromatography analysis of fatty acids, we observed an imbalance of straight and branch-chained fatty acids in the cshA mutant, compared to the wild-type. This imbalance is compensated in the suppressor strains. Thus, we reveal for the first time that the cold sensitive growth phenotype of a DEAD-box mutant can be explained, at least partially, by an improper membrane composition. The defect correlates with an accumulation of the pyruvate dehydrogenase complex mRNA, which is inefficiently degraded in absence of CshA. We propose that the resulting accumulation of acetyl- CoA fuels straight-chained fatty acid production at the expense of the branched ones. Strikingly, addition of acetate into the medium mimics the cshA deletion phenotype, resulting in cold sensitivity suppressed by the mutations found in our genetic screen or by sublethal doses of triclosan.
2020-04-21 | GSE133013 | GEO
Project description:Students at the cold spring harbor metabolomics course had fun running fecal and cecal samples in one experiment and embryo samples across development from mice.
2022-06-26 | MSV000089732 | GNPS