Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 7

Integrative Oncogenomics of multiple myeloma

ABSTRACT: We used targeted capture and massively parallel sequencing of exomes of CD138 purified plasma cells and matched somatic DNA from 53 patients with Multiple Myeloma. 2281 variants were validated by 454 sequencing. The present study will validate an additional 5538 variants by targeted pull-down and sequencing. The normal and tumor samples will be indexed separately and pre-pooled in groups of 10 or 11. The sequence capture will use 5 reactions each for the normals and tumors. All normal samples will then be pooled and go thorugh one lane of HiSeq. Same for the tumors.

PROVIDER: EGAS00001000243 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Integrative Oncogenomics of multiple myeloma

Project description:We used targeted capture and massively parallel sequencing of exomes of CD138 purified plasma cells and matched somatic DNA from 17 patients with Multiple Myeloma. For each patient, an early tumor sample (at diagnosis) and a late one (at relapse) were available. For few of them, an additional late sample (2nd progression) was present. In total, the study has 52 samples. 1044 variants were validated by 454 sequencing. The present study will validate an additional 4630 variants by targeted pull-down and sequencing. All 52 samples will be indexed and then will be pre-pooled in groups of 5 or 6. The sequence capture will use 10 reactions. All samples will then be pooled and go thorugh one lane of HiSeq.

| EGAS00001000244 | EGA

Identification of SOX2-bound mRNA

Project description:In vitro pull down assay was performed using recombinant GST and GST fusion SOX2 protein to precipitate total RNA from urothelial carcinoma cell line BFTC905 Unbound RNA from both reactions and matrix-associated RNA from SOX2 pull down reaction was extracted using TRIZOL reagent

2011-10-26 | GSE33207 | GEO

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)

Project description:A pooled pull-down experiment for protein fragments, expressed with mRNA display, that bind Med15 or TFIID subcomplex

2021-04-26 | GSE173152 | GEO

Identification of SOX2-bound mRNA

2011-10-25 | E-GEOD-33207 | biostudies-arrayexpress

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Project description:Activation: A pooled screen for protein fragments that induce transcriptional activation of a reporter GFP gene. A pooled pull-down experiment for protein fragments, expressed with mRNA display, that bind Mediator Med15 or TFIID subcomplex. This SuperSeries is composed of the SubSeries listed below.

2021-04-26 | GSE173156 | GEO

Transcriptional termini of genes on chromosomes 21-22 (RACE mapping)

Project description:The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we first carried out 5’ and 3’ RACE reactions from 1193 exons from 492 genes in these chromosomes using RNA isolated from 11 normal tissues and 5 cell lines. An average of 3 to 4 RACE reactions (5’ and 3’) was carried out from each gene. The products of the RACE reactions were analyzed by hybridization to tiling arrays interrogating the non-repeat portions of these chromosomes at 17 nucleotide resolution. A total of 26,688 RACE reactions were performed and pooled to be placed on to 1020 tiling arrays For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2009-08-13 | GSE17600 | GEO

Comparative oncogenomics identifies breast tumors enriched in functional tumor initiating cells

Project description:The claudin-low subtype is a recently identified rare molecular subtype of human breast cancer that expresses low levels of tight and adherens junction genes and shows high expression of epithelial-to-mesenchymal transition (EMT) genes. These tumors are enriched in gene expression signatures derived from human tumor initiating cells (TIC) and human mammary stem cells. Through cross-species analysis, we discovered mouse mammary tumors that have similar gene expression characteristics as human claudin-low tumors and were also enriched for the human TIC signature. Such claudin-low tumors were similarly rare, but came from a number of distinct mouse models including the p53 null transplant model. Here we present a molecular characterization of fifty p53 null mammary tumors as compared to other mouse models and human breast tumor subtypes. Similar to human tumors, the murine p53 null tumors fell into multiple molecular subtypes including two basal-like, a luminal, a claudin-low, and a subtype unique to this model. The claudin-low tumors also showed high gene expression of EMT inducers, low expression of the miR-200 family, and low to absent expression of both claudin 3 and E-cadherin. These murine subtypes also contained distinct genomic DNA copy number changes some of which are similarly altered in their cognate human subtype counterpart. Finally, limiting dilution transplantation revealed that p53 null claudin-low tumors are highly enriched for TICs as compared to the more common adenocarcinomas arising in the same model, thus providing a novel preclinical mouse model to investigate the therapeutic response of TICs.

2011-08-15 | GSE27101 | GEO

Expression data from mouse SEOC tumors

Project description:We have developed mouse models for serous epithelial ovarian cancer (SEOC) based on conditional inactivation of p53 and Rb tumor suppression (RB-TS) in combination with or without Brca1/2 following injection of adenovirus expressing Cre recombinase into the ovarian bursa. These models develop metastatic (Stage IV) disease with key histopathological features resembling human SEOC.To determine whether these mouse tumors resemble human SEOC at the molecular level, we conducted global gene expression analysis on 27 ovarian carcinomas and 3 pooled normal ovarian surface epithelium samples (single epithelial layer isolated from ovarian surface by laser capture).

2013-04-19 | GSE46169 | GEO

Expression data from mouse SEOC tumors

2013-04-19 | E-GEOD-46169 | biostudies-arrayexpress

Comparative oncogenomics

Project description:Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer

| PRJEB30443 | ENA