Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq Neo antigen discovery in mouse lung cancer

ABSTRACT: In this experiment we have sequenced the MCA205 cell line. Here we exome and transcriptome sequenced this line to identify potential neo-antigens.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER:

PROVIDER: E-ERAD-468 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Neo antigen discovery in mouse lung cancer

Project description:In this experiment we have generated a mouse lung cancer cell line carrying p53 and K-Ras alleles. Here we exome and transcriptome sequenced this line to identify potential neo-antigens.

2015-10-13 | E-ERAD-394 | biostudies-arrayexpress

Transcriptome of Arabidopsis bam1 and bam2 mutants for study of early anther development

Project description:Genome-wide transcriptomes of the bam1, bam2 single and bam1 bam2 double mutants were sequenced and analyzed to uncover locus-associated gene expression variations, providing support for different fates of the duplicated BAM1 and BAM2 genes, including sub-/neofunctionalization after duplication.

2015-03-13 | E-MTAB-4435 | biostudies-arrayexpress

The Transcriptome of PLX4032 resistance

Project description:We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative.

2013-06-07 | E-ERAD-138 | biostudies-arrayexpress

Solanum lycopersicum strain:M82 Transcriptome or Gene expression

Project description:We sequenced mRNA from immature green (15 days after anthesis) and red (Breaker+10 days) tomato (Solanum lycopersicum) fruit tissues from plants over-expressing SlGLK1 and SlGLK2 and from control plants 'M82' to compare gene expression levels between transgenic fruit and the control. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2013-06-01 | E-MTAB-4819 | biostudies-arrayexpress

Tel AML1 mtumours

Project description:This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/In this experiment we sequenced the transcriptomes of mouse Tel-AML1 tumours to identify transcriptional profiles associated with the development of B-ALL.

2014-08-12 | E-ERAD-264 | biostudies-arrayexpress

Oryza sativa Japonica strain:EFR-XA21 | cultivar:Kitaake Transcriptome or Gene expression

Project description:We analyzed the transcriptomic profile of EFR:XA21:GFP rice lines treated with elf18 to identify genes differentially regulated during this response. We sequenced cDNA from EFR:XA21:GFP leaves treated with 500 nM elf18 for 0.5, 1, 3, 6, and 12 h. We also included untreated EFR:XA21:GFP and Kitaake as controls. Note: All samples in SRA were assigned the same sample accession (SRS843490). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

2015-02-12 | E-MTAB-5170 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:Transcriptome of Zea mays genotypes under control and stress conditions. Stress conditions include heat, cold, salt, and UV. We extracted and sequenced RNA from 14 day old seedlings of inbred lines B73, Mo17 and Oh43 grown using standard conditions as well as seedlings that had been subjected to cold (5Â°C for 16 hours), heat (50Â°C for 4 hours), high salt (watered with 300 mM NaCl 20 hours prior to collection) or UV stress (2 hours). For each stress the plants were sampled immediately following the stress treatment and there were no apparent morphological changes in these plants relative to control plants.

2015-01-31 | E-MTAB-4258 | biostudies-arrayexpress

Characterization of transcriptional reprogramming of Vitis vinifera during Trichoderma-induced resistance and in response to Plasmopara viticola using RNA-Seq

Project description:We have carried out a global transcriptional analysis of grapevine resistance induced by Trichoderma harzianum T39 against Plasmopara viticola using high-throughput Illumina sequencing technology. Four samples were analyzed: control (C), T39-treated (T39), P. viticola-inoculated control (C+P.v.) and P. viticola-inoculated T39-treated (T39 P.v.) plants. Three biological replicates (named A, B and C) were analyzed for each sample and sequenced twice (named 1 and 2). Reads were aligned to the Pinot Noir ENTAV 115 genome and then analyzed to measure gene expression levels. Differentially expressed genes have been identified by statistical analysis.

2012-06-27 | E-MTAB-4324 | biostudies-arrayexpress

Triticum urartu strain:PI 428198 Genome sequencing and Transcriptome or Gene expression

Project description:For this project, we have sequenced, assembled and annotated a transcriptome of a diploid wheat Triticum urartu accession PI 428198. The sequencing libraries were prepared from shoot and root tissues harvested from 2-3 week old seedlings. All sequencing was carried out on the Illumina HiSeq platform using the 100 bp pair-end protocol (248.5 million reads). The assembly was constructed using a multiple k-mer approach with a de novo assembly algorithm implemented in CLC Genomics Workbench 5.5 and additional redundancy reduction with CD-HIT and blast2cap3 programs. Open reading frames and proteins were predicted using BLASTX searches and a findorf algorithm.

2013-06-11 | E-MTAB-5037 | biostudies-arrayexpress

Detection of large intergenic non-coding RNA

Project description:Members of the ARGONAUTE gene family are known to have roles in RNA-mediated silencing during development. One of these, MEL1, was shown to be germ-cell specific and essential for progression through sporogenesis at both premeiotic mitosis and meiosis. To understand how the MEL1 gene product is responsible for these effects requires analysis of the changes of the transcriptome. The mel1 gene was identified by TOS 17 insertion mutagenesis of Oryza sativa Japonica, cultivar Nipponbare. The TOS 17 insertion line of mel1 and the wild-type parent were the sources of RNA. RNA was extracted from rice panicle (3 cM) of rice grown under natural conditions in rice fields. Small RNAs associated with MEL1 and small RNAs in total RNA were sequenced by Illumina GAII.

2014-04-22 | E-MTAB-4365 | 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