Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of cultured cells derived from Parkinson's disease patients [PolyA RNA-seq]

ABSTRACT: RNA-seq of cultured cells derived from Parkinson's disease patients [PolyA RNA-seq]

PROVIDER: PRJNA434415 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Small RNA profiling from cultured cells and tissues derived from Parkinson's disease patient [small RNA-seq]

Project description:Small RNA profiling from cultured cells and tissues derived from Parkinson's disease patient [small RNA-seq]

| PRJNA434419 | ENA

HeLa cell polyA- RNA-seq

Project description:Coilin iCLIP data revealed 42 novel human snoRNAs of intronic origin. To validate their expression and estimate abundance of novel and annotated snoRNAs, we performed RNA-seq on polyA- and rRNA-depleted RNA isolated from HeLa cells. Results show that expression of novel snoRNAs is comparable to the previously annotated snoRNAs. 1 replicate of RNA depleted of polyA and ribosomal RNA.

2014-11-06 | E-GEOD-58450 | biostudies-arrayexpress

Illumina RNA-seq of polyA+ RNA from HAP1 cells

Project description:Illumina RNA-seq of polyA+ RNA from HAP1 cells

| PRJEB31661 | ENA

RNA-seq in putamen of Parkinson's disease patients

Project description:We performed RNA-seq on total RNA from tissue samples from putamen of the brain from Parkinson's disease patients.

2020-02-01 | GSE134390 | GEO

Illumina RNA-seq of polyA+ RNA from HAP1 cells

Project description:Illumina RNA-seq was performed on polyA+ RNA isolated from the human HAP1 cell line

2019-03-14 | E-MTAB-7757 | biostudies-arrayexpress

polyA-RNA-seq from mESC treated with doxorubicin

Project description:polyA-RNA-seq from mESC treated with doxorubicin

| PRJNA627712 | ENA

Human Dorsal Root Ganglion PolyA RNA Seq Dataset

Project description:Human Dorsal Root Ganglion PolyA RNA Seq Dataset

| PRJNA326560 | ENA

RNA-seq in putamen of Parkinson's disease patients

Project description:RNA-seq in putamen of Parkinson's disease patients

| PRJNA555099 | ENA

K562 polyA RNA-Seq

Project description: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 used oligo (dT)-selected polyA+ RNA to construct libraries for RNA-Seq.We then profiled the transcriptome of polyadenylated mRNA-Seq using Illumina sequencing platforms. We then used the sequenced reads to reconstruct the transcriptome using the Cufflinks de-novo assembler (Trapnell et al. Nat.Bio.Tech. 2010). Recent computational and ribosome profiling analyses suggest that many short open reading frames (sORFs) in eukaryotic genomes are translated. However, evidence that these sORFs produce stable polypeptides is lacking. Here we develop a strategy to discover and validate novel sORF-encoded polypeptides (SEPs) in human cells. In total, we detect 117 SEPs, 114 of which are novel, varying in length from 15 to 149 amino acids. Of these, 10 SEPs (0.5%) are derived from long intergenic non-coding RNAs (lincRNAs). We also observe the presence of polycistronic genes and the widespread use of non-AUG start codons, which is a phenomenon historically thought to be rare in the mammalian genome. Quantitative measurements reveal that SEPs can be found at concentrations between ~10-2000 copies per cell, which is within the range of typical cellular proteins. We confirm the translation of a number of these SEPs through heterologous expression of their encoding cDNAs. We also discover that several SEPs possess properties characteristic of functional proteins. These results demonstrate that human sORFs produce numerous stable polypeptides, revealing that the human proteome is larger and more diverse than previously appreciated.

2012-11-14 | E-GEOD-34740 | biostudies-arrayexpress

PolyA+ RNA-seq in ALL-SIL upon TLX1 knockdown

Project description:PolyA+ RNA-seq in ALL-SIL upon TLX1 knockdown

| PRJNA434171 | ENA