Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix SNP array data for cell line and tumor genotype alignment

ABSTRACT: When characterizing novel cell lines, we used SNP genotyping alignment to compare the tumor to the resulting cell line. In order to do this pairwise comparison as each cell model was developed, we added additional data from the GEO database during the normalization step. These data were either tumor DNA or cancer cell line DNA. These samples were not part of a matched pair and so genotype alignment was not reported for these samples. The GEO Series and Sample numbers used for each sample grouping is as follows. Wood- Series: GSE21541; Samples: GSM533396, GSM533397, GSM533398, GSM533399, GSM533400, GSM533401, GSM533402, GSM533404, GSM533410. Ferry- Series: GSE16125; Samples: GSM403493, GSM403494, GSM403495, GSM403496, GSM403497, GSM403498, GSM403499, GSM403500, GSM403501. Jacket series 1: GSE15126; samples: GSM385517, GSM385518, GSM385519, GSM385520, GSM385521, GSM385522, GSM385523, GSM385524, GSM385525, GSM385526. Jacket series 2: GSE62407; Samples: GSM1526628, GSM1526648, GSM1526668. DF Series GSE39130; Samples: GSM956523, GSM956524, GSM956525, GSM956526, GSM956527, GSM956528.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85838 | GEO | 2018/08/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq alignment to individualized genomes

Project description:The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq. Illumina 100bp single-end liver RNA-seq from 277 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. In addition, Illumina 100bp single-end liver RNA-seq from 128 male 26-week old male mice (20 weeks for NZO strain) from each of the DO founder strains raised on standard chow or high fat diet (8 males per strain by diet group). Each sample was sequenced in 2-4x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.

2014-06-10 | E-GEOD-45684 | biostudies-arrayexpress

Evaluating sequence alignment for metaproteomics applications

Project description:This dataset was utilized to assess the performance of a novel de novo metaproteomics pipeline, which performs sequence alignment of de novo sequences from complete metaproteomics experiments. Traditionally, metaproteomics data annotation relies on database searching that requires sample-specific databases derived from whole metagenome sequencing experiments. Creating these databases, however, is a complex, time-consuming, and error prone process, which can introduce biases affecting the outcomes and conclusions, highlighting the need for alternative methods. The evaluated approach offers rapid and orthogonal insights into metaproteomics data.

2024-10-10 | PXD050548 | Pride

FOSL1 as a candidate target gene for 11q12 rearrangements in desmoplastic fibroblastoma

Project description:Global gene expression analysis of desmoplastic fibroblastoma (DF) and histologically similar tumors. FOSL1 is identified as a candidate target gene for the 11q12 rearrangments in DF. RNA was extracted from 3 frozen desmoplastic fibroblastoma (DF) biopsies and hybridized onto Affymetrix Human Gene 1.0 ST arrays. RNA from 6 myxofibrosarcoma (MFS), 6 desmoid fibromatosis (DFM), 5 solitary fibrous tumor (SFT) and 17 low-grade fibromyxoid sarcomas (LGFMS) were used as controls. The control dataset has been previously published and is available in the GEO database under Series accession GSE24369. The complete dataset representing: (1) the 3 desmoplastic fibroblastoma Samples and (2) the 34 control Samples from Series GSE24369 (re-processed using RMA), is linked below as a supplementary file.

2012-05-08 | E-GEOD-35162 | biostudies-arrayexpress

RNA-seq read alignment evaluation

Project description:RNA-seq read alignment evaluation

| PRJEB4265 | ENA

Screen for Ferry-associated RNAs

Project description:Goal: Identification of RNAs that are associated with the novel Ferry complex Methods: We performed a GST pulldown experiment, where GST-Ferry and GST were incubated with a HEK 293 cell lysate and extensively washed prior to elution. Subsequently, RNA was extracted from the elution and sequenced. Results: We identifed around 17 588 different transcripts and found a set of 252 mRNAs that are specifically enriched in the GST-Ferry sample. Conclusions: The Ferry complex seems to interact with a specific subset of mRNAs

2023-04-27 | GSE173422 | GEO

Prediction of Breast Cancer Estrogen Receptor Status using Machine Learning

Project description:Gene expression profiles were generated from 199 primary breast cancer patients. Samples 1-176 were used in another study, GEO Series GSE22820, and form the training data set in this study. Sample numbers 200-222 form a validation set. This data is used to model a machine learning classifier for Estrogen Receptor Status.

2013-01-01 | GSE29210 | GEO

Plant RNA-Seq alignment

Project description:The crop genomics RNA-Seq identification, alignment and visualisation pipeline

| PRJEB12852 | ENA

Protists RNA-Seq alignment

Project description:The protists genomics RNA-Seq identification, alignment and visualisation pipeline

| PRJEB15488 | ENA

RNA-seq alignment to individualized genomes

2014-06-10 | GSE45684 | GEO

RNA-seq read alignment evaluation

Project description:To assess the performance of read mapping software for RNA-seq, 26 spliced alignment protocols based on 11 programs and pipelines (BAGET, GEM, GSNAP, GSTRUCT, MapSplice, PALMapper, PASS, ReadsMap, SMALT, STAR and TopHat) were applied to four human and mouse transcriptome data sets.

2013-07-15 | E-MTAB-1728 | 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