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TranscriptomicsRNA-seq analysis of differentiating human erythroblasts
Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages:  proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromat...
ORGANISM(S): Homo sapiens 
2013-12-25 | E-GEOD-53635 | biostudies-arrayexpress
TranscriptomicsMultiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within com...
ORGANISM(S): Bacillus subtilis 
2011-08-26 | E-GEOD-31573 | biostudies-arrayexpress
TranscriptomicsDeep RNA Sequencing of native mouse podocytes and non-podocytes glomerular cells
Purpose: Next-generation sequencing (NGS) was used to define the transcriptome of native mouse podocytes and non-podocytes glomerular cells as part of a project aiming to define the molecular fingerprint of mouse podocytes. Method: Glomeruli from 29 Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J x hNPHS...
ORGANISM(S): Mus musculus 
2019-01-01 | E-MTAB-5457 | biostudies-arrayexpress
TranscriptomicsTranscript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 m...
ORGANISM(S): Mus musculus 
2010-04-14 | E-GEOD-20846 | biostudies-arrayexpress
TranscriptomicsDifferential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Agilent]
High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-...
ORGANISM(S): Homo sapiens 
2012-12-11 | E-GEOD-37690 | biostudies-arrayexpress
TranscriptomicsDifferential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Illumina]
High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-...
ORGANISM(S): Homo sapiens 
2012-12-11 | E-GEOD-37703 | biostudies-arrayexpress
TranscriptomicsHuman intestinal tissue with adult stem cell properties derived from pluripotent stem cells
Genetically engineered human pluripotent stem cells (hPSCs) have been proposed as a source for transplantation therapies and are rapidly becoming valuable tools for human disease modeling. However, many of the potential applications are still limited by the lack of robust differentiation paradigms t...
ORGANISM(S): Homo sapiens 
2014-04-24 | E-GEOD-56930 | biostudies-arrayexpress
TranscriptomicsDifferential Gene and Transcript Expression Analysis with TopHat and Cufflinks
This submission includes the sample data for a protocol covering differential expression analysis with TopHat and Cufflinks. The protocol also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-Seq analysis results. While the pro...
ORGANISM(S): Drosophila melanogaster 
2011-09-09 | E-GEOD-32038 | biostudies-arrayexpress
TranscriptomicsRNA-seq from ENCODE/Caltech
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (mailto:georgi@caltech.edu for data coordination/informatics/experimental questions, mailto:diane@caltech.edu for informatics questions, mailto:bawilli_91125@yahoo.com for experimental...
ORGANISM(S): Homo sapiens 
2012-07-12 | E-GEOD-33480 | biostudies-arrayexpress
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