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TranscriptomicsRibosome profiling of the genome-reduced bacterium Mycoplasma pneumoniae
In order to study quantitatively the translation efficiency in the genome-reduced bacterium Mycoplasma pneumoniae, we performed ribosome profiling (ribo-seq) in standard growth conditions. We first tested whether the ribosome profiling method could be applied to M. pneumoniae and assessed the qualit...
ORGANISM(S): Escherichia coli K-12 
2023-07-01 | E-MTAB-11935 | biostudies-arrayexpress
TranscriptomicstRNAs quantification by hydro-tRNA-seq in the genome-reduced bacterium Mycoplasma pneumoniae
We measured abundances of tRNAs by means of hydro-tRNA-seq (Gogakos et al., 2017), a method based on partial alkaline RNA hydrolysis that generates fragments suitable for sequencing, in the genome-reduced bacterium Mycoplasma pneumoniae.
ORGANISM(S): Mycoplasma pneumoniae M129 
2023-06-29 | E-MTAB-11930 | biostudies-arrayexpress
TranscriptomicsRNA-seq of Lon and FtsH conditional mutants of Mycoplasma pneumoniae under depleting and inducing conditions
Using Mycoplasma pneumoniae as a model organism, we conditionally depleted the two essential ATP-dependent proteases (Lon and FtsH) of this bacterium, by engineering three strains carrying a Lon and/or FtsH inducible expression locus. An integrative comparative study combining label-free shotgun pro...
ORGANISM(S): Mycoplasma pneumoniae M129 
2020-11-10 | E-MTAB-8537 | biostudies-arrayexpress
TranscriptomicsRNA-seq differential expression analysis of tmRNA (ssrA) mutants in the genome-reduced bacterium Mycoplasma pneumoniae
We used a combination of genetic and proteomic approaches to characterize tmRNA (ssrA) activity in the genome-reduced bacterium Mycoplasma pneumoniae. For this, we generated tmRNA mutants encoding a tag resistant to proteolysis. Endogenous protein tagging by the mutant tmRNA gene (ssrAmk) was then e...
ORGANISM(S): Mycoplasma pneumoniae 
2021-08-09 | E-MTAB-10111 | biostudies-arrayexpress
TranscriptomicsMethylation profiling data from medulloblastoma tumor samples
Smoothened (SMO)-inhibitors recently entered clinical trials for sonic-hedgehog driven medulloblastoma (SHH-MB). Clinical response appears highly variable. To understand the mechanism(s) of primary resistance and to identify pathways co-operating with aberrant SHH-signaling, we sequenced a large coh...
ORGANISM(S): Homo sapiens 
2014-09-02 | E-GEOD-49377 | biostudies-arrayexpress
GenomicsGenetic landscape of pediatric Medulloblastoma
Medulloblastoma is a heterogenous disease made up of at least four distinct subtypes of disease which appear to exploit and disrupt naturally occurring developmental pathways of cellular growth and hindbrain development. To better understand the driver mutations of this disease, we performed whole g...
EGAS00001000347 | EGA
TranscriptomicsHuman medulloblastoma samples
Purpose Integrated genomics approaches have identified at least four distinct biological variants in medulloblastoma: WNT, SHH, group C, and group D. Non-WNT/Non-SHH tumors are associated with metastatic dissemination and an unfavorable prognosis. Additional markers may enhance outcome prediction in...
ORGANISM(S): Homo sapiens 
2011-07-01 | E-GEOD-28245 | biostudies-arrayexpress
GenomicsRNA-SEQ_DATA_SET_rain_PA_2012_10_22 - samples
Pilocytic Astrocytoma ICGC PedBrain RNA sequencing
EGAD00001000617 | EGA
GenomicsDATA_SET_ICGC_PedBrain_Tumor_Low-Grade_Astrocytoma_Study - samples
Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood
EGAD00001000271 | EGA
GenomicsWGS-SEQ_DATA_SET_rain_PA_2012_10_22 - samples
Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing
EGAD00001000616 | EGA
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