Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1180498 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A PiggyBac transposon based screen in a murine pancreatic cancer model.This data has been described in the following article [doi:10.1038/ng.3164] and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/
2016-07-04 | E-ERAD-514 | biostudies-arrayexpress
Project description:Comparative Dynamic Transcriptome Analysis (cDTA) enables global analysis of newly synthesized RNA as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111) and reveals defects in transcription with much higher sensitivity than conventional steady-state methods. cDTA was carried out as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111), using the S. cerevisiae heterozygous Med17/med17delta strain (Euroscarf) transfected with plasmids pRS315-SRB4 or pRS315-srb4-ts as described in Larivi̬re et al. Nature. 2012 (DOI:10.1038/nature11670), and Y40343-wildtype (Euroscarf) or Med18-FRB-KanMX6 (Euroscarf) strains. Heatshock of SRB4 and srb4-ts strains was applied for 18 or 60 minutes at 37C prior to RNA labeling as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). To deplete the Med18 subunit from the nucleus, anchor-away experiments were performed by rapamycin treatment (1 ug/ml in 200 mL YPD) for 18 or 60 minutes at 30C prior to RNA labeling as described in Sun et al. Mol. Cell. 2013 (DOI:10.1016/j.molcel.2013.09.010). Data analysis was as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111).
2015-02-04 | E-MTAB-2942 | biostudies-arrayexpress
Project description:Relapse and acquired drug resistance in T-cell acute lymphoblastic leukemia (T-ALL) remains a significant clinical problem. The current study used a pre-clinical model of induction therapy for pediatric ALL in NOD/SCID mice (Samuels et al Blood Cancer Journal (2014) 4, e232; doi:10.1038/bcj.2014.52) to study the development of drug resistance. We performed transcription profiling by array of human CD45-positive lymphocytes from patients with acute pediatric lymphoblastic leukemia, xenografted in NOD/SCID mice treated with vincristine, daunorubicin, dexamethasone and L-asparagine. Both the primary-patient-derived and xenograft cells were analysed. The VLXD2 treatment regime is described in full in the protocols associated with this submission and in Samuels et al (Blood Cancer Journal (2014) 4, e232; doi:10.1038/bcj.2014.52). This study is an extension of E-MEXP-3916.
2017-05-01 | E-MTAB-4759 | biostudies-arrayexpress
Project description:RNA-Seq from lymphoblastoid cell lines for Gorilla, chimpanzee and bonobo species. This RNA-Seq data has been described in the following article: Scally et al., Nature 2012;483;7388;169-75, DOI: 10.1038/nature10842, and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/>
2013-01-09 | E-ERAD-129 | biostudies-arrayexpress
Project description:RT-PCR of platelet-poor plasma samples per Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, et al. Diverse human extracellular RNAs are widely detected in human plasma. Nat Commun 2016; 7. doi:10.1038/ncomms11106
2022-08-12 | GSE135758 | GEO
Project description:Here we used human cortical brain organoids to probe the longitudinal impact of GSK3 inhibition through multiple developmental stages. Chronic GSK3 inhibition increased the proliferation of neural progenitors and caused massive derangement of cortical tissue architecture. Cortical organoids were differentiated as previously described (Paşca et al., 2015, doi: 10.1038/nmeth.3415.).Chronic GSK3 inhibition was performed by adding CHIR99021 (Merck SML1046) to the medium at day 0 (1 microM) and kept throughout the differentiation process until reaching the respective collection timepoints (day 18, day 50, day 100).
2020-06-04 | E-MTAB-8325 | biostudies-arrayexpress
Project description:Here we used human cortical brain organoids to probe the longitudinal impact of GSK3 inhibition through multiple developmental stages. Chronic GSK3 inhibition increased the proliferation of neural progenitors and caused massive derangement of cortical tissue architecture. Cortical organoids were differentiated as previously described (Paşca et al., 2015, doi: 10.1038/nmeth.3415.). Chronic GSK3 inhibition was performed by adding CHIR99021 (Merck SML1046) to the medium at day 0 (1 microM) and kept throughout the differentiation process until reaching the respective collection timepoints (day 50, day 100).
2020-06-09 | E-MTAB-8337 | biostudies-arrayexpress
Project description:McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688)
| EGAD00001001300 | EGA
Project description:Taking the advantage that B16F10 cells retain the wild-type p53, we introduced the p53 partner into these cells, the p19Arf. Also, in order to induce a immune stimulation in experiments *in vivo*, we introduced the interferon-beta cDNA. This combination induced several benefits when compared to the use of these factors alone, as seen by propidium iodide staining, tunel staining, several gene expression analysis, tumor growth, mice survival, among others. Because of this, we had the interest to study the effects of the combination of p19Arf plus interferon-beta upon gene regulation of B16F10 cells, compared to the effects of these transgenes alone. Previous works from our group that show several benefits of p19Arf plus interferon-beta combination upon B16F10 cells are described in Merkel et al (2010) doi: 10.1186/1471-2407-10-316, Merkel et al (2013) doi:10.1038/cgt.2013.23 and Medrano et al (2016) doi: 10.1007/s00262-016-1807-8 .
2017-12-02 | E-MTAB-5399 | biostudies-arrayexpress
Project description:The stem cell lines were generated according to the principle described in Noggle et al., Nature 2011, Oct 5;478(7367):70-5. doi: 10.1038/nature10397. Title: Human oocytes reprogram somatic cells to a pluripotent state. Abstract: The exchange of the oocyte's genome with the genome of a somatic cell, followed by the derivation of pluripotent stem cells, could enable the generation of specific cells affected in degenerative human diseases. Such cells, carrying the patient's genome, might be useful for cell replacement. Here we report that the development of human oocytes after genome exchange arrests at late cleavage stages in association with transcriptional abnormalities. In contrast, if the oocyte genome is not removed and the somatic cell genome is merely added, the resultant triploid cells develop to the blastocyst stage. Stem cell lines derived from these blastocysts differentiate into cell types of all three germ layers, and a pluripotent gene expression program is established on the genome derived from the somatic cell. This result demonstrates the feasibility of reprogramming human cells using oocytes and identifies removal of the oocyte genome as the primary cause of developmental failure after genome exchange. The major difference to Noggle et al. are that these new stem cell lines are tetraploid rather than diploid. The main technical difference is the addition of cytochalasinB during artificial activation, preventing extrusion of the second polar body, thereby resulting in the retention of a diploid oocyte genome, rather than a haploid one. Adult somatic cells were transferred into non-enucleated oocytes and then activated in the presence of cytochalasinB. Addition of cytochalasinB inhibits extrusion of the second polar body, resulting in tetraploid eggs. The efficiency of development to the blastoycst stage is described in: Yamada et al., 2014, Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells, Nature. 2014 Jun 26;510(7506):533-6. doi: 10.1038/nature13287. Blastocysts developing from these were used for the derivation or pluripotent stem cell lines. Gene expression analysis was performed to demonstrate transcriptional reprogramming. These cell lines contain both somatic and oocyte genomes.
2014-08-12 | E-GEOD-60360 | biostudies-arrayexpress