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UnknownTPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository.
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S-EPMC8220791 | biostudies-literature
TranscriptomicsPromoter hypermethylation of TERT is associated with hepatocellular carcinoma in the Han Chinese population
A recent study by Castelo-Branco, P., et al. Methylation of the TERT promoter and risk stratification of childhood brain tumours: an integrative genomic and molecular study. Lancet Oncol 2013;14:534-542 found upstream of the transcription start site (UTSS) hypermethylation of TERT is associated with...
ORGANISM(S): Homo sapiens 
2015-01-03 | E-GEOD-63863 | biostudies-arrayexpress
Genomics5933aad4-f4a1-4e3f-8f14-c5d913f0f111 - samples
FPKM expression values of the CUP/reference/validation cohort used for tissue-of-origin prediction based on transcriptomic data
EGAD00001008638 | EGA
TranscriptomicsWidespread genetic epistasis among cancer genes.
We performed NGS-based transcript profiling (RNA-seq) to profile transcripts that are expressed in MCF10A cells. 12,332 genes with FPKM>1 were considered as expressed in MCF10A cells. mRNA profiles of MCF10A cells were generated by deep sequencing using Illumina Hiseq 2000.
ORGANISM(S): Homo sapiens 
2014-08-01 | E-GEOD-58834 | biostudies-arrayexpress
TranscriptomicsNuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity
The nuclear pore complex (NPC) has dual roles in nucleocytoplasmic transport and chromatin organisation. In many eukaryotes the coiled coil Mlp/Tpr proteins of the NPC nuclear basket have specific roles in interactions with chromatin and defining specialised regions of active transcription, while Ml...
ORGANISM(S): Trypanosoma brucei 
2014-04-03 | E-GEOD-56436 | biostudies-arrayexpress
TranscriptomicsRNA-seq of adult baboon subventricular zone primary cells
Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) ...
ORGANISM(S): Papio anubis 
2014-07-16 | E-GEOD-58527 | biostudies-arrayexpress
TranscriptomicsProcessed RNA-seq of 95 lung adenocarcinoma samples
The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions. Libraries were prepared using the Illumina TruSeq stranded mRNA protocol and sequenced on the NovaSeq 6000 system at the Center for Translational Genomics (www.ctg.lu.se) in Lund, Sweden. Demulti...
ORGANISM(S): Homo sapiens 
2026-02-08 | E-MTAB-16082 | biostudies-arrayexpress
TranscriptomicsEvolution and Pathogenic Mechanism of Rice Sheath Blight Pathogen
Analysis of RNA expression of Rhizoctonia solani AG1 IA. mRNA-seq of R. solani AG1 IA at 6 timepoints during the plant infection were sequenced. Cufflinks was used for calculating expected fragments per kilobase of transcript per million fragments sequenced (FPKM) values. Expression and regulation w...
ORGANISM(S): Rhizoctonia solani AG-1 IA 
2013-01-28 | E-GEOD-32577 | biostudies-arrayexpress
TranscriptomicsGene expression of M. acetivorans producing ANME-1 Mcr during growth on methane vs. growth on methanol
Our goal is to convert methane efficiently into liquid fuels that may be more readily transported. Since aerobic oxidation of methane is less efficient, we focused on anaerobic processes to capture methane, which are accomplished by anaerobic methanotrophic archaea (ANME) in consortia. However, no p...
ORGANISM(S): Methanosarcina acetivorans 
2015-12-20 | E-GEOD-66445 | biostudies-arrayexpress
TranscriptomicsNext Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Jmjd6-/- Thymic stromal Transcriptomes
The goals of this study are to comprehensively identify genes controlled by Jmjd6 in the thymic stroma, and to identify a novel alternative splicing mechanism. Methods: Samples were WT and Jmjd6-/- fetal thymus organ culture with (2 samples for each category) or without (1 sample for each category)...
ORGANISM(S): Mus musculus 
2015-10-22 | E-GEOD-61444 | biostudies-arrayexpress
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