Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: TruSeq Synthetic Long-Reads for NA12878 (early stage data)

PROVIDER: PRJEB11287 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1050530_1.fastq.gz	Fastqsanger.gz
	ERR1050530_2.fastq.gz	Fastqsanger.gz
	ERR1050540_1.fastq.gz	Fastqsanger.gz
	ERR1050540_2.fastq.gz	Fastqsanger.gz
	ERR1050550_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 768

Similar Datasets

Project description:TruSeq Synthetic Long-Reads for NA12878

| PRJEB11299 | ENA

Drosophila melanogaster strain:yw cn,bw,sp

Project description:Drosophila melanogaster genome sequencing with TruSeq synthetic long-reads

| PRJNA235897 | ENA

A draft genome sequence of the elusive giant squid, Architeuthis dux

Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

2019-12-16 | PXD016522 | Pride

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis

Project description:Different Library Sample Preparation (LSP) allow the detection of a large common set of isoforms. However, each LSP also detects a smaller set of isoforms which are characterized both by lower coverage and lower FPKM than that observed for the common ones among LSPs. This characteristic is particularly critical in case of low input RNA NuGEN v2 LSP. The effect of statistical detection of alternative splicing considering low input LSP (NuGEN v2) with respect to high input LSP (TruSeq) was studied using a benchmark dataset, in which both synthetic reads and reads generated from high and low input LSPs were spiked-in. Statistical detection of alternative splicing was done using prototypes of bioinformatics analysis for isoform-reconstruction and exon-level analysis. Each available sample contains a total of 5 paired end replicates. 3 samples contain increasing numbers of spiked-in reads (20, 40, 80 millions) from NuGENv2 library preparation kit on a common TruSeq 1000ng background. 3 additional samples were built with the same approach, but spiked-in reads were collected from a TruSeq-based experiment. The remaining 6 samples follow the same approach of the previous 6, but the common background is based on a TruSeq library preparation on 100ng of material

2014-05-28 | E-GEOD-58001 | biostudies-arrayexpress

LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [Loop QC]

Project description:In this study, we used a barcoding-based synthetic long read (SLR) isoform sequencing approach (LoopSeq) to generate sequencing reads sufficiently long and accurate to identify isoforms using standard short read Illumina sequencers.

2021-05-05 | GSE155920 | GEO

LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [RNA-seq]

2021-05-05 | GSE155375 | GEO

LoopSeq Synthetic Long Read Sequencing Uncovers Isoform Modulation in the progression of Colon Cancer [LoopSeq]

2021-05-05 | GSE155919 | GEO

MeDIP sequencing of Ovis aries

Project description:We have completed the high quality reference genome for domestic sheep (Oar v3.1). Early-stage Illumina GA sequence platform sequenced less reads in high GC content regions than in other regions. To read through higher GC content regions, we generated 2 Gb MeDIP-seq data for filling gaps in sheep reference genome assembly.

2014-06-06 | E-GEOD-56644 | biostudies-arrayexpress

Homo sapiens

Project description:Expression data for early stage NSCLC

| PRJNA120673 | ENA

REVERSIR platform for the tailored control of GalNAc-siRNA conjugate pharmacology

Project description:Primary mouse hepatocytes were treated with 1 nM TTR-siRNA and 10 nM scrambled or TTR-REVERSIR by in vitro free uptake for 24 h. RNA extracted with the Purelink RNA kit (ThermoFisher) was used for cDNA library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the NextSeq500 desktop sequencer (Illumina), all according to manufacturers’ instructions. Raw RNA-seq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using fastq-mcf. Filtered reads were aligned to the Mus musculus genome (NCBIM37) using STAR with default parameters. Uniquely aligned reads were counted by featureCounts. Differential gene expression (DEG) analysis was performed by the R package DESeq2. Here, we report the rapid and potent reversal of GalNAc-siRNA-mediated RNAi activity in vivo with REVERSIR technology, which is based on short, synthetic high-affinity oligonucleotide complementary to the siRNA guide strand. The modular, sequence-specific nature of the REVERSIR platform has the potential to enhance the therapeutic profile of any long-acting GalNAc-siRNA conjugate to enable fine-tuned control of RNAi pharmacology

2018-05-02 | GSE110620 | 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