Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PolyA Sequencing of K562 Cells

ABSTRACT: PolyA Sequencing of K562 Cells

PROVIDER: PRJNA607080 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11096665.fastq.gz	Fastqsanger.gz
	SRR11096666.fastq.gz	Fastqsanger.gz
	SRR11096667.fastq.gz	Fastqsanger.gz
	SRR11096668.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

PolyA Sequencing of K562 Cells

Project description:RNA chemical structure analysis using icSHAPE and icLASER reveals hexameric sequences that have structure differences inside and outside of cells. One such sequence that had higher in-cell reactivity was the sites of polyadenylation or PAS sequence within the 3’-UTRs. We aimed to understand this difference as we postulated it could be utilized to predict transcriptome-wide polyadenylation. To obtain direct positions with high polyadenylation sequence signal, we generated the first polyadenylation sequencing data (PAS-seq) for K562 cells. PAS-seq uses polyA tail priming to identify the sites of polyA tail selection directly. Inspection of PAS reads demonstrated clear buildup of read depth at the 3’-end of transcripts and we obtained sites of high PAS read depth and low PAS read depth.

2021-08-04 | GSE145400 | GEO

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-sequencing in Jurkat cells upon CDK12 depletion.

Project description:PolyA-sequencing in Jurkat cells upon CDK12 depletion.

| PRJNA679028 | ENA

Small RNA sequencing of human K562 cells transduced with lentiviral vectors overexpressing RUNX1

Project description:miRNA-Sequencing of RUNX1 overexpressing K562 cells were compared to K562 cells transduced with an empty vector control to analyse the differential expression of miRNAs in hematopoiesis. K562 cells were transduced either with an empty lentiviral vector as control or a lentiviral vector overexpressing human RUNX1. The samples were biological triplicates and the results were validated by qRT-PCR using SYBR green.

2016-06-01 | E-GEOD-70942 | biostudies-arrayexpress

Genome-wide mapping of RNA Pol III binding site (K562)

Project description:We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase III in K562 cells. We have also generated a sequenced input DNA datasets for K562 cells. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase III in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.

2009-12-31 | E-GEOD-19548 | biostudies-arrayexpress

K562 polyA RNA-Seq

2012-11-14 | GSE34740 | GEO

Homo sapiens strain:K562 cells

Project description:MLV integration sites in human K562 cells

| PRJNA188712 | ENA

Next Generation Sequencing of Ctrl and K562 DROSHA knockdown cells

Project description:Next Generation Sequencing of Ctrl and K562 DROSHA knockdown cells

| PRJNA674591 | ENA

Transcriptome sequencing of K562 cells stably expressing SUMO negative MYB

Project description:Transcriptome sequencing of K562 cells stably expressing SUMO negative MYB

| PRJNA512467 | ENA

Human K562 cells overexpressing ETO2

Project description:microRNA profiling of human K562 cells comparing control or ETO2-overexpressed cells Two-condition experiment, K562-pcDNA vs. K562-pcDNA-ETO2, Biological replicates: 1, 1 pcDNA, 1 pcDNA-ETO2, independently.

2014-10-01 | E-GEOD-51485 | biostudies-arrayexpress

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