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TranscriptomicsRNA Capture-Seq resolves the deep complexity of the human transcriptome (454)
Transcriptomic analyses have revealed an unexpected complexity of the human transcriptome, whose breadth and depth exceeds current RNA sequencing capacity 1-3. Here we combine tiling arrays and RNA sequencing technologies, in an approach we term RNA Capture-Seq, to enable the assembly and characteri...
ORGANISM(S): Homo sapiens 
2011-09-12 | E-GEOD-29040 | biostudies-arrayexpress
TranscriptomicsRNA Capture-Seq resolves the deep complexity of the human transcriptome (Illumina)
Transcriptomic analyses have revealed an unexpected complexity of the human transcriptome, whose breadth and depth exceeds current RNA sequencing capacity 1-3. Here we combine tiling arrays and RNA sequencing technologies, in an approach we term RNA Capture-Seq, to enable the assembly and characteri...
ORGANISM(S): Homo sapiens 
2011-09-12 | E-GEOD-29038 | biostudies-arrayexpress
TranscriptomicsK562 polyA RNA-Seq
RNA-Seq reads and TopHat (Trapnell et al. Bioinformatics 2009) alignments of K562 cell-line transcriptome. These were used to validate the expression of short peptides idenitified by Mass-Spectrometry in K562 cells. K562 polyA+ RNA (Batch 1) and total RNA (batch 2) was purchased from Ambion. We use...
ORGANISM(S): Homo sapiens 
2012-11-14 | E-GEOD-34740 | biostudies-arrayexpress
TranscriptomicsMouse CD4+/CD8+ thymocytes from miR-181a1/b1 KO vs WT
miR-181a1/b1, miR-181a2/b2, and miR-181c/d belong to a highly conserved family of microRNA clusters, yet their role in vivo is poorly understood. Here we show that the miR-181a1/b1 cluster is absolutely essential for NKT development and is a critical determinant of thymocyte proliferation, survival ...
ORGANISM(S): Mus musculus 
2014-04-09 | E-GEOD-41090 | biostudies-arrayexpress
TranscriptomicsComparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation
The equivalency of human induced pluripotent stem cells (hiPSCs) with human embryonic stem cells (hESCs) remains controversial. Here, we devised a strategy to assess the contribution of clonal growth, reprogramming method and genetic background to transcriptional patterns in hESCs and hiPSCs. Surpri...
ORGANISM(S): Homo sapiens 
2015-10-26 | E-GEOD-73211 | biostudies-arrayexpress
ProteomicsYoun_et_al_RNAbodies_SAINT3073_MSPLIT_DDA (Paired with MSV000081422)
This set of submissions contains the mass spectrometry files acquired using Data-Dependent Acquisition mode (DDA), which were paired with Data-Independent Acquisition mode (DIA) files (MSV000081422) for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA b...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-01-17 | MSV000081943 | MassIVE
ProteomicsYoun_et_al_RNAbodies_SAINT3105_Set1
This set of submissions contains the mass spectrometry files for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. BioID experiments were performed from Flp-In T-REx HEK293 cells and MS files were acquired on Orbitrap Elite and Orbitrap Velos.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-08-04 | MSV000081411 | MassIVE
ProteomicsYoun_et_al_RNAbodies_SAINT3090_MSPLIT_DDA (PAIRED with MSV000081414)
This set of submissions contains the mass spectrometry files acquired using Data-Dependent Acquisition mode (DDA), which were paired with Data-Independent Acquisition mode (DIA) files (MSV000081414) for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA b...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-01-17 | MSV000081947 | MassIVE
ProteomicsYoun_et_al_RNAbodies_SAINT3116
Youn et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies (Task 3116)
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-08-08 | MSV000081427 | MassIVE
ProteomicsYoun_et_al_RNAbodies_SAINT3112
Youn et al., High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies. MassIVE title: Youn_et_al_RNAbodies_SAINT3112
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-08-08 | MSV000081426 | MassIVE
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