EGAS00001002210-sc-2019-05-31T14:06:06Z - samples
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ABSTRACT:
PROVIDER: EGAD00001005055 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The goals of this study is to investigate the prevalence and heritability of age-related clonal haemopoeisis (ARCH) in healthy elderly individuals.We will use a bespoke bait set to pull down DNA regions of interest in whole blood samples combined with HiSeq at a deep level . By correlating findings from each individual to their respective twin we hope to elucidate whether heritable traits influence the development of ARCH.
a. 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/
| EGAS00001002210 | EGA
Project description:We are investigating the possible role of ribonucleoprotein-bound RNAs on the pathogenesis of AML. This study uses antibody-pulldown of specific ribonucleoproteins followed by RANSeq. We hope to describe this interaction in wild type cells befire studying the effects of specific mutations 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/
2014-03-25 | E-ERAD-226 | biostudies-arrayexpress
Project description:We aim to identify the sequence of changes in gene expression associated with increasing virulence over successive blood passages. With the B cell-deficient mice we hope to establish how a reduction in immune pressure changes the response of the parasite. This work is in collaboration with Jean Langhorne at NIMR.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/
2014-08-27 | E-ERAD-288 | biostudies-arrayexpress
Project description:Various test protocols to improve the 3' pull down transcript profiling protocol, aiming to produce a pipeline library prep protocol. 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/ 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 polyToligo 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 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/
2015-04-21 | E-ERAD-384 | biostudies-arrayexpress
Project description:Total RNA was extracted from wild type and mutant zebrafish embryos. Double stranded cDNA representing the 3' ends of transcripts was made by a variety of methods, including polyT priming and 3' pull down on magentic beads. Some samples included indexing test experiments where a sequence barcode was placed within one of the sequence reads. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD 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/
2013-05-13 | E-ERAD-84 | biostudies-arrayexpress
Project description:RNA was isolated from Xenopus tropicalis rax mutants and wild type siblings. We have identified by tilling a Xenopus tropicalis rax mutant in which the gene has a premature stop codon before the homeobox domain. The rax gene is essential for eye development and has been identified as a causative gene for human ocular malformations such as anophthalmia and microphthalmia. The phenotype of the X.tropicalis mutant replicates the human condition with complete loss or small eyes. By analysis of the full RNA complement of rax mutants compared to wild type siblings we hope to gain a better understanding of the role of rax during eye development and the genes that it regulates. This is part of an ongoing collaboration with Dr Robert Grainger, University of Virginia. 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 www.sanger.ac.uk/datasharing/
2011-01-19 | E-ERAD-0 | biostudies-arrayexpress
Project description:Protocol: Total RNA was extracted from mouse embryos and DNase treated. 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/
2014-09-02 | E-ERAD-272 | biostudies-arrayexpress
Project description:Over expression of prl3 by use of outcrossed tg(actin:prl3) fish comparing prl3 overexpression to wild type siblings. 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/
2016-05-17 | E-ERAD-455 | biostudies-arrayexpress
Project description:This project carries out the pilot CRISPR/Cas9 screens in the K562 background. Its goals are to confirm that positive controls work, and to assess the effects of experimental parameters (listed below) on the sequencing-based fitness readout. We test 1) length of selection 2) biological replicates 3) sampling variation during bottlenecks 4) sampling variation during DNA preparation 5) sequencing depth to inform the setup for the next round of experiments. To do so, we propose to sequence 13 samples (6 timepoints, 2 biological replicates, 2 severe bottlenecks during growth, 2 bottlenecks during DNA preparation, and the screening library itself) on two lanes of HiSeq, using 19bp reads. The sequencing libraries are prepared in our lab.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-459 | biostudies-arrayexpress
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