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GenomicsPol III ChIP-seq of liver cancer cell lines
This dataset has been designed to test whether codons in mRNAs and anticodons in tRNAs vary in order to maximize translation in specific cellular conditions in mammals. Prokaryotes and simple unicellular eukaryotes optimize their translational rates by adjusting the codons in the protein-coding tran...
ORGANISM(S): human 
2016-04-18 | E-MTAB-4046 | biostudies-arrayexpress
Genomics[E-TABM-722] Transcription factor binding evolution in five vertebrates
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. ArrayExpress Submission Date: Apr 07 2010 ArrayExpress Release Date: Apr 08 2010 Publication A...
ORGANISM(S): Gallus gallus Canis lupus familiaris Monodelphis domestica Homo sapiens Mus musculus 
2010-06-02 | GSE22078 | GEO
TranscriptomicsRNA-seq of liver tissue and liver cancer cell lines
This dataset has been designed to test whether codons in mRNAs and anticodons in tRNAs vary in order to maximize translation in specific cellular conditions in mammals. Prokaryotes and simple unicellular eukaryotes optimize their translational rates by adjusting the codons in the protein-coding tran...
ORGANISM(S): human 
2016-04-18 | E-MTAB-4052 | biostudies-arrayexpress
GenomicsPol III ChIP-seq mouse development
The genetic code is an abstraction of how mRNA codons and tRNA anticodons molecularly interact during protein synthesis; the stability and regulation of this interaction remains largely unexplored. Here, we quantitatively characterized the expression of m
ORGANISM(S): Mus musculus 
2014-08-08 | E-MTAB-2326 | biostudies-arrayexpress
TranscriptomicsRNA-seq mouse development
The genetic code is an abstraction of how mRNA codons and tRNA anticodons molecularly interact during protein synthesis; the stability and regulation of this interaction remains largely unexplored. Here, we quantitatively characterized the expression of mRNA and tRNA genes across developing mouse ti...
ORGANISM(S): Mus musculus 
2014-08-08 | E-MTAB-2328 | biostudies-arrayexpress
TranscriptomicsRNA Affinity Purification followed by sequencing (RAP-seq) allows identification of transcriptome-wide RBP binding sites using recombinant RBPs and purified total cellular RNA
RAPseq is a new in vitro method used to study RNA-protein interactions at scale. In RAPseq, a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP-Halo fusion is then incubated with fragmented native total RNA that retains endogenous s...
ORGANISM(S): Homo sapiens 
2023-12-29 | E-MTAB-10834 | biostudies-arrayexpress
TranscriptomicsMetastudy: Transcription profiling by array of human normal liver, HBV, HCV and haemochromatosis background cirrhotic and hematocellular carcinoma liver samples.
The experiment studies the changes of gene expression from normal liver to cirrhotic and hepatocellular carcinoma in three disease etiologies: HBV, HCV and haemochromatosis. This dataset is part of the TransQST collection.
ORGANISM(S): Homo sapiens 
2013-01-20 | E-MTAB-950 | biostudies-arrayexpress
TranscriptomicsRNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment
Biological replicates of liver spheroids derived from primary hepatocytes were treated with IFNa2 and/or baricitinib for 24 h and subsequently infected with Sars-CoV-2. The cells were harvested 48 h time after infection. Total RNA was extracted and sequenced with a strand-specific paired end RNA-seq...
ORGANISM(S): Homo sapiens 
2020-11-18 | E-MTAB-9711 | biostudies-arrayexpress
TranscriptomicsIn vitro RIP-seq for Zfp207 in mouse embryonic stem cells
in vitro RIP-seq assay of tagged Zfp207 performed in 2 technical replicates with Tag only and Input as negative controls. The input RNA used for the assay is total RNA extracted from mESC. The data provides information about the transcripts and the binding sites that Zfp207 has in the transcriptome ...
ORGANISM(S): Mus musculus 
2021-12-09 | E-MTAB-10113 | biostudies-arrayexpress
TranscriptomicsRNA-seq of human liver cancer cell lines after RBP-KD
Biological replicates of Human liver cancer cell lines HepG2 (n = 2) and Huh7 (n = 2) were treated with siRNA (KD) against CCT3, DDX39A, TOP2A, PKM, STMN1, HIST1H1C, NQO1, KPNA2, PEG10, IGF2BP1, and non-targeting (NT) control. Cells were harvested 48hrs after transfection. Total RNA was extracted an...
ORGANISM(S): Homo sapiens 
2021-12-23 | E-MTAB-9587 | biostudies-arrayexpress
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