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GenomicsDNA-seq of an ELMSeq reporter cassette to study impact of C-terminal sequence variations on protein abundance
A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. The regions of 6 nt upstream and 6 nt downstream the stop codon were randomized to study their effect on gene expression. The ELMSeq reporter cassette was composed of: promoter - dam - random N...
ORGANISM(S): Mycoplasma pneumoniae 
2020-05-04 | E-MTAB-8223 | biostudies-arrayexpress
TranscriptomicsDynamics of the chili pepper transcriptome during fruit development
Background The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Chili pepper is an economically and culturally important horticultural crop as well as ...
ORGANISM(S): Capsicum annuum 
2014-02-21 | E-GEOD-54123 | biostudies-arrayexpress
TranscriptomicsHydro-tRNAseq of human cell lines HACAT and HepG2
To quantify tRNA expression, we perform hydro-tRNA sequencing (Gogakos et al. 2017) in HACAT (keratinoytes) and HepG2 (liver) human cell lines. This study contains 6 samples. Three replicates for each of the five cell lines. This data complements our previously published data (GEO: GSE137834), whic...
ORGANISM(S): Homo sapiens 
2021-03-15 | E-MTAB-9905 | biostudies-arrayexpress
TranscriptomicsTransposon random mutagenesis of Mycoplasma pneumoniae M129. Samples sequenced for passage numbers 1, 2, 3, 4, 6, 8 and 10, two biological replicates per passage and two technical replicates for passages 2-4.
Controlled dataset covering multiple passage conditions, from the genome-reduced bacterium Mycoplasma pneumoniae, to test and validate two new software tools: FASTQINS and ANUBIS. These computational tools allow the generation of insertion profile datasets from raw transposon sequencing data, detect...
ORGANISM(S): Mycoplasma pneumoniae M129 
2020-08-28 | E-MTAB-8918 | biostudies-arrayexpress
ProteomicsHs_ErbB_Network
Human ErbB network proteins in three cell types
ORGANISM(S): Homo Sapiens (human) 
2014-12-31 | PAe005020 | PeptideAtlas
TranscriptomicsDNA sequencing to validate random deletions in Mycoplasma pneumoniae
We present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of Lox sites by transposon mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the nat...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-18 | E-MTAB-9582 | biostudies-arrayexpress
GenomicsSynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes
This sample was prepared with a modified version of the Tn4001 transposon commonly used in Mycoplasmas. This transposon is described to work more efficiently in Mycoplasma agalactiae and, by extension, in other Mycoplasma species. This sample was prepared transforming this bacteria with a newly desi...
ORGANISM(S): Mycoplasma agalactiae 
2019-11-15 | E-MTAB-7425 | biostudies-arrayexpress
TranscriptomicsRNASeq of multiple Mycoplasma species in wild-type condition including: Mycoplasma pneumoniae, Mycoplasma genitalium, Mycoplasma hyopneumoniae, Mycoplasma capricolum, Mycoplasma gallisepticum, Mycoplasma mycoides
The discovery of small open reading frames (smORFs) encoding for polypeptides (SEPs; <100aa) highlights that the coding capacity of the genomes has been underestimated. Most ORF-finding algorithms have historically set a minimum threshold length of 100 aa. As consequence, some transcripts encoding f...
ORGANISM(S): Mycoplasma gallisepticum str. R(high) 
2018-11-16 | E-MTAB-6203 | biostudies-arrayexpress
ProteomicsProteome wide measurements of protein half-lives in Mycoplasma pneumoniae
We obtained proteome wide measurements of protein half-lives in M. pneumoniae by performing pulse-chase experiments following SILAC methods. We estimated degradation rates of individual proteins by measuring the increase in light protein compared to heavy protein labeling along the growth curve.
ORGANISM(S): Mycoplasma pneumoniae (strain ATCC 29342 / M129) 
2020-11-24 | PXD016386 | Pride
Degradation rates Protein half-life Silac 
ProteomicsPRM of eGFP and mCherry in human cells
We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enric...
ORGANISM(S): Homo sapiens (Human) 
2023-02-24 | PXD037866 | Pride
Lc-msms Prm Lung Kidney Human 
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