Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Illumina RNA-seq of polyA+ RNA from HAP1 cells

ABSTRACT: Illumina RNA-seq of polyA+ RNA from HAP1 cells

PROVIDER: PRJEB31661 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3218280_1.fastq.gz	Fastqsanger.gz
	ERR3218280_2.fastq.gz	Fastqsanger.gz
	ERR3218281_1.fastq.gz	Fastqsanger.gz
	ERR3218281_2.fastq.gz	Fastqsanger.gz
	ERR3218282_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

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

Nanopore RNA-seq of polyA+ RNA from HAP1 and HEK293 cell lines

Project description:Sequencing was performed to assess the ability of Nanopore direct cDNA and native RNA sequencing to characterise human transcriptomes. Total RNA was extracted from either HAP1 or HEK293 cells, and the polyA+ fraction isolated using oligodT dynabeads. Libraries were prepared using Oxford Nanopore Technologies (ONT) kits according to manufacturers instructions. Samples were then sequenced on ONT R9.4 flow cells to generate fast5 raw reads in the ONT MinKNOW software. Fast5 reads were then base-called using the ONT Albacore software to generate Fastq reads.

2019-03-14 | E-MTAB-7778 | biostudies-arrayexpress

Nanopore RNA-seq of polyA+ RNA from HAP1 and HEK293 cell lines

Project description:Nanopore RNA-seq of polyA+ RNA from HAP1 and HEK293 cell lines

| PRJEB31662 | ENA

RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells

Project description:We performed a genome-scale screen for suppressors of interferon stimulated gene (ISG) expression in human haploid cells (HAP1). Ubiquitin specific peptidase 14 (USP14) was a significant hit. In order to validate USP14 as a regulator of ISG expression, we created knockouts of USP14 in HAP1 cells using CRISPR-Cas9 and performed RNA-seq on coding RNA from USP14 KO and WT cells. This data was used to determine if ISGs were upregulated in USP14 KO HAP1 cells.

2017-07-25 | E-MTAB-5865 | biostudies-arrayexpress

RNA-seq of coding RNA from DDX6 knockout human haploid (HAP1) cells

Project description:We performed a genome-scale screen for suppressors of interferon stimulated gene (ISG) expression in human haploid cells (HAP1). DEAD-box helicase 6 (DDX6) was a significant hit. In order to validate DDX6 as a regulator of ISG expression, we created knockouts of DDX6 in HAP1 cells using CRISPR-Cas9 and performed RNA-seq on coding RNA from DDX6 KO and WT cells. This data was used to determine if ISGs were upregulated in DDX6 KO HAP1 cells.

2017-07-25 | E-MTAB-5867 | biostudies-arrayexpress

PolyA RNA-seq from differentiated iPSCs

Project description:PolyA RNA-seq from differentiated iPSCs

| PRJNA854943 | ENA

PolyA RNA-seq from Medulloblastoma cells ± EYA2 knockdown

Project description:PolyA RNA-seq from Medulloblastoma cells ± EYA2 knockdown

| PRJNA962875 | 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

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

ATAC sequencing of HAP1 cells

Project description:We analysed the global effect of CHD3-KO and SENP1-KO HAP1 cell lines compared to control cell line, on chromatin accessibility using ATAC-seq.

2018-08-05 | GSE111047 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data