Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

B Cell Methylome

ABSTRACT: Mouse B cells were isolated from the spleen and activated ex vivo. DNA was obtained from activated and control B cells with the Qiagen AllPrep kit. 1ug of DNA was sonicated with the Covaris Sonicator (300bp) and the Illumina library was prepared following a standard Illumina protocol with the NEB Next kit. The library was amplified 15x and gel-excised within the range of 200-500bp. 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/

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER:

PROVIDER: E-ERAD-90 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Reprogramming around an epigenetic barrier with TET1

Project description:Mouse Epiblast Stem Cells (EpiSCs) were reprogrammed to induced pluripotent stem cells (iPSCs) by overexpression of key pluripotency factors and the TET1 DNA hydroxylase. 0.2ug of extractd DNA was sonicated using the Covaris Sonicator (300bp) and the Illumina library was prepared following a standard Illumina protocol with the NEB Next kit and subjected to bisulfite treament. The library was amplified 12x and fragments smaller than 200 bp were removed by PEG precipitation on magnetic beads. 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/

2014-04-28 | E-ERAD-238 | biostudies-arrayexpress

Gene expression changes upon dietary restriction switch in mice

Project description:RNA was extracted from mice and mRNA isolated from 2ug total RNA. mRNA was processed to generate a library compatible with Illumina high throughput sequencing using a standard RNA-seq library generation protocol. Each library was amplified using indexed primers and samples were purified using AMPure XP beads. Libraries were pooled and quantified with Bioanalyzer and qPCR.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/

2014-01-07 | E-ERAD-209 | biostudies-arrayexpress

A method for automated High throughput ChIPseq

Project description:Setup and optimisation of a high throughput pipeline for ChIPseq. The protocol used is ChIP carried out using the Agilent Bravo robot with subsequent Ilumina sequencing library preparation.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/

2013-02-12 | E-ERAD-77 | biostudies-arrayexpress

Single cell transcriptomics in olfactory sensory neurons

Project description:High-throughput sequencing of individual olfactory sensory neurons from adult male mice.A multiplexed library of 72 single cells was prepared and purified using the Nextera XT DNA. 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/

2013-11-25 | E-ERAD-199 | biostudies-arrayexpress

Zea mays cultivar:W22 Transcriptome or Gene expression

Project description:Large scale transcriptomics study to establish gene expression in leaf tissue of W22 inbred line in Zea Mays. RNA was extracted from leaf tissue when the plants were at V6. Sequencing library was produced following the protocol mentioned in the following publication PMID:22039485

2015-04-29 | E-MTAB-4446 | biostudies-arrayexpress

In vivo RNA interference RNAi target sequencing of Trypanosoma brucei

Project description:A direct comparison of RNAi in vitro with RNAi in vivo is being performed using RNA interference (RNAi) target sequencing (RIT-Seq) of Trypanosoma brucei to identify all genes specifically required for growth in vivo (the infectome). Assembly of the bloodstream-form T. brucei RNAi library and the RNAi target sequencing (RIT-seq) approach in African trypanosomes were reported previously in Alsford, S. et al. High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 21, 915-924, 264 doi:gr.115089.110 [pii] 265 10.1101/gr.115089.110 (2011) and Alsford,S et al. High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature 482, 232236 doi:10.1038/nature10771 (2012). 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/

2014-01-21 | E-ERAD-110 | biostudies-arrayexpress

Transcriptome profiling of embryos from the Mouse Genetics Project DMDD

Project description:Total RNA was extracted from wildtype embryos of developmental stage E14.5 for baseline expression study relating to the Mouse Genetics Project (http://www.dmdd.org.uk/). Protocol: After DNase treatment, fragmented RNA was enriched for the 3 ends by pull down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 1 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 2 at the 5 end followed by 10 bases HBDVHBDVHB (using the single base code), then one of 96 eight base indexing tags, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. 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/

2014-07-28 | E-ERAD-278 | biostudies-arrayexpress

Transcriptome profiling of zebrafish muscle from wild type and tert knockout adults

Project description:Total RNA was extracted from dissected muscle from tert homozygous and wild type adult zebrafish. The 3' ends of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using IlluminaHiSeq paired-end sequencing. Protocol: Total RNA was extracted and DNase treated. Fragmented RNA was enriched for the 3 ends by pull down using a polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by PCR. 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/

2016-05-03 | E-ERAD-456 | biostudies-arrayexpress

Transcriptome profiling of zebrafish neural crest mutants

Project description:Total RNA was extracted from morpholigcally abnormal and wildtype sibling larvae of neural crest mutants derived from ENU mutagenesis. The 3 end of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using Illumina HiSeq paired-end sequencing. Protocol: Total RNA was extracted from zebrafish embryos using Trizol and DNase treated. Chemically fragmented RNA was enriched for the 3 ends by pulled down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 12 random bases, then an 8 base indexing tag, then CG and 14 T bases. An Illumina library with full adapter sequence was produced by 20 cycles of PCR. 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/

2014-04-28 | E-ERAD-243 | biostudies-arrayexpress

Mouse embryo transcript profile pilot study

Project description:Total RNA was extracted from adult mutant and wild type mouse embryos. The 3 end of fragmented RNA was pulled down using polyT oligos attached to magnetic beads, reverse transcribed, made into Illumina libraries and sequenced using Illumina HiSeq paired-end sequencing. Protocol: Total RNA was extracted from mouse embryos using Trizol and DNase treated. Chemically fragmented RNA was enriched for the 3 ends by pulled down using an anchored polyT oligo attached to magnetic beads. An RNA oligo comprising part of the Illumina adapter 2 was ligated to the 5 end of the captured RNA and the RNA was eluted from the beads. Reverse transcription was primed with an anchored polyT oligo with part of Illumina adapter 1 at the 5 end followed by 4 random bases, then one of six indexing tags and 14 T bases. An Illumina library with full adapter sequence was produced by 15 cycles of PCR. 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/

2014-04-14 | E-ERAD-71 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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