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ProteomicsLong read proteogenomics to characterize protein isoform diversity in human umbilical vein endothelial cells (HUVECs)
Mass spectrometry-based proteomics sample preparation Harvested HUVECs, approximately 5 million cells each, were pelleted and frozen at -80C. The sample pellet was lysed according to the Filter Aided Sample Preparation (FASP) protocol.59 Lysis buffer used in the FASP was changed to 6% SDS, 150 mM DT...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-04-28 | MSV000089326 | MassIVE
TranscriptomicsThe Genetic Basis of Rapidly Evolving Male Genital Morphology in Drosophila
Deep sequencing of total RNA extracted from the genital discs of males for each of the following strains : Drosophila sechellia, Drosophila mauritiana, hybrid introgression line 3Q1(A) and hybrid introgression line Q1(A) Analysis of poly(A)+ RNA for three independent biological replicates of sequenc...
ORGANISM(S): Drosophila sechellia 
2011-07-22 | E-GEOD-28663 | biostudies-arrayexpress
ProteomicsLong-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
Deregulated gene expression is a hallmark of cancer, however most studies to date have analyzed short-read RNA-sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short read RNA sequencing to comprehensively survey the tra...
ORGANISM(S): Homo sapiens (Human) 
2021-02-02 | PXD023373 | Pride
Isoform sequencing (iso-seq) Alternative promoters Gastric cancer Long-read sequencing 
TranscriptomicsProfile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus
In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied fo...
ORGANISM(S): Gossypium hirsutum 
2012-07-16 | E-GEOD-31062 | biostudies-arrayexpress
GenomicsGenome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.
Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and m...
ORGANISM(S): Homo sapiens 
2011-04-04 | E-GEOD-28286 | biostudies-arrayexpress
ProteomicsTranscriptome innovations in primates revealed by single-molecule long-read sequencing
We produced an extensive transcript catalog for LCLs of 5 primate species by leveraging isoform sequencing and short-read RNA-seq. The curated transcriptomes were used to assist mass spectrometry protein identifications.
ORGANISM(S): Pan troglodytes (Chimpanzee) Homo sapiens (Human) Pongo pygmaeus (Bornean orangutan) Gorilla gorilla Macaca mulatta (Rhesus macaque) 
2022-05-31 | PXD031213 | Pride
Iso-seq Primates Proteomics Isoforms Lcls 
GenomicsTemperature-dependent alternative splicing of FLM controls flowering in Arabidopsis thaliana
How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperatu...
ORGANISM(S): Arabidopsis thaliana 
2013-09-19 | E-GEOD-48082 | biostudies-arrayexpress
TranscriptomicsRNA at 92 M-BM-0C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.
The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transc...
ORGANISM(S): Pyrococcus abyssi 
2014-05-31 | E-GEOD-58131 | biostudies-arrayexpress
TranscriptomicsGlobal transcriptomic changes following N-deprivation in Nannochloropsis oceanica IMET1: Illumina sequencing
Limited systems-level understanding of oil synthesis in wild oleaginous algae has hindered the development of microalgal feedstock. Nannochloropsis is a small unicellular microalgae widely distributed in oceans and fresh water. In many large-scale and pilot-scale outdoor cultivation facilities, Nann...
ORGANISM(S): Nannochloropsis oceanica 
2014-05-14 | E-GEOD-42508 | biostudies-arrayexpress
ProteomicsEnhancing the cardiac pig transcriptome by long-read sequencing and in-depth proteomics
Clinically translatable large animal models have become indispensable for cardiovascular research, clinically relevant proof of concept studies and for novel diagnostic and therapeutic interventions. In particular, the pig as emerged as an essential cardiovascular disease model, because its heart, c...
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2020-10-29 | PXD018985 | Pride
Pig Tmt Annotation Proteomics Transcriptomics Cardiac Nanopore Lcms 
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