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

Gene expression data from 4T1 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble) or two shRNAs targeting TM4SF1 (shTM4SF1-1 and shTM4SF1-5) and from 4TO7 cells stably expressing with or without TM4SF1

ABSTRACT: Compare the gene expression profile between shscramble with shTM4SF1 knockingdown 4T1 cells and between 4TO7 cells stably expressing with or without TM4SF1 Compare the gene expression profile between shscramble with shTM4SF1 knockingdown 4T1 cells and between 4TO7 cells stably expressing with or without TM4SF1

ORGANISM(S): Mus musculus

SUBMITTER: Jeffrey Zhao

PROVIDER: E-GEOD-62730 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Glucocorticoid Receptor Confers Resistance to Anti-Androgens by Bypassing Androgen Receptor Blockade.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-27 | E-GEOD-52169 | biostudies-arrayexpress

Dexamethasone treatment of VCaP prostate cells

Project description:The treatment of advanced prostate cancer has been transformed by novel antiandrogen therapies such as enzalutamide. We identified glucocorticoid receptor (GR) activity as modulator of enzalutamite sensitivity in the VCaP prostate cancer cell line. The GR agonist dexamethasone was sufficient to confer enzalutamide resistance whereas a GR antagonist restored sensitivity. These expression profiling data demonstrate that GR transcriptional activity overlaps with that of AR in the VCAP model. VCAP cells growing in complete media were treated with the indicated drugs in biological triplicates for 24 hours prior to harvest.

2013-12-27 | E-GEOD-51872 | biostudies-arrayexpress

Androgen and Glucocorticoid stimulation of LREX' cells in vitro

2013-12-27 | E-GEOD-51871 | biostudies-arrayexpress

LNCAP/AR and a LnCAP/AR subline (LREX') with acquired resistance to 2nd generation antiandrogens

Project description:The treatment of advanced prostate cancer has been transformed by novel antiandrogen therapies such as enzalutamide. Using the LnCaP/AR xenograft model, we identified induction of glucocorticoid receptor (GR) expression as a common feature of drug resistant tumors. From a resistant xenograft tumor, we derived a GR expressing resistant subline called LREX' which maintains the resistant phenotype. mRNA expression was used to characterize resistant tissues. LnCaP/AR cells were injected into castrate mice and tumors were established. Mice were then treated with vehicle (Con), 4 days of anti-androgen (ARN-509 10mgkg), or were maintained on anti-androgen (10mg/kg ARN-509 or enzalutamide) until emergence of resistance. Resistant tissues continued to be exposed to anti-androgen through time of harvest. LREX' (LnCaP/AR Resistant to Enzalutamide Xenograft Derived) was derived from an enzalutamide resistant xenograft and was re-injected into castrate mice undergoing continual treatment with enzalutamide. The GR probe on the Illumina array failed to detect GR expression. Therefore, GR expression as determined by qPCR is annotated separately. Of the 10 control tissues, 8 were analyzed twice (technical duplicates annotated as A and B).

2013-12-27 | E-GEOD-51873 | biostudies-arrayexpress

Directed differentiation of oligodendrocytes from human embryonic stem cells

Project description:Here we compare the transcriptional profile of the undifferentiated hESC with the anterior oligodendroctes derived from the hESC using our new differentiation protocol. Total RNA was isolated from undifferentiated hES cells and from hES derived oligodendrocytes, 70 days old and FACS sorted for O4 marker. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

2015-02-01 | E-GEOD-63318 | biostudies-arrayexpress

Directed differentiation of human pluripotent stem cells into cortical interneurons

Project description:Here we demonstrate the highly efficient derivation of human cortical interneurons in a NKX2.1::GFP hESC reporter line. Manipulating the timing of SHH activation yields three distinct GFP+ populations with specific transcriptional profiles, neurotransmitter phenotypes and migratory behaviors. Total RNA was isolated at day 18 of differentiation from FACS sorted NKX2.1::GFP+ cells from three varying differentiation conditions and a “No SHH” condition (no sonic hedgehog treatment) that did not contain any GFP-expressing cells (Trizol, Sigma). Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

2013-12-31 | E-GEOD-46098 | biostudies-arrayexpress

Directed differentiation of placode from human embryonic stem cells

Project description:Here we compare the transcriptional profile during the differentiation of hESC into neuroepithelial cells (NSB) (Chambers et. al 2009 Nature Biotechnology) with our new placode differentiation (PIP). Total RNA was isolated at day 1,3, 5 (NSB), 5 (PIP), 7 (NSB), 7 (PIP), 9 (NSB), 9 (PIP), 11 (NSB) and 11 (PIP) of differentiation using Trizol. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

2013-12-04 | E-GEOD-51533 | biostudies-arrayexpress

Cohesin recruits the Esco1 acetyltransferase genomewide to repress transcription and promote cohesion in somatic cells

Project description:The cohesin complex links DNA molecules and plays key roles in the organization, expression, repair, and segregation of eukaryotic genomes. In vertebrates the Esco1 and Esco2 acetyltransferases both modify cohesin’s Smc3 subunit to establish sister chromatid cohesion during S phase, but differ in their N-terminal domains and expression during development and across the cell cycle. Here we show that Esco1 and Esco2 also differ dramatically in their interaction with chromatin, as Esco1 is recruited by cohesin to over 11,000 sites, whereas Esco2 is infrequently enriched at REST/NRSF target genes. Esco1’s colocalization with cohesin occurs throughout the cell cycle and depends on two short motifs (the A-box and B-box) present in and unique to all Esco1 orthologs. Deleting either motif led to the derepression of Esco1-proximal genes and functional uncoupling of cohesion from Smc3 acetylation. In contrast, other mutations that preserved Esco1’s recruitment separated its roles in cohesion establishment and gene silencing. We conclude that Esco1 uses cohesin as both a substrate and a scaffold for coordinating multiple chromatin-based transactions in somatic cells. Total RNA was isolated after treatment with indicated siRNAs, or transfection reagent only for control samples. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to manufacturer instructions.

2015-08-25 | E-GEOD-71420 | biostudies-arrayexpress

Gene expression in teratogenic exposures: a new approach to understanding individual risk

Project description:The phenomenon of partial or incomplete penetrance is common to many paradigms of exposure to teratogens, where only some of the exposed individuals exhibit developmental defects. We here argue that the most widely used experimental approaches in reproductive toxicology do not take partial penetrance into account, and are thus likely to miss differences between affected and unaffected individuals that contribute to susceptibility for teratogenesis. We propose that focus on the variation between exposed individuals could help to discover factors that may play a causative role for abnormal developmental processes that occur with incomplete penetrance. Total RNA was extracted from individual embryos E10.5 derived from normal and diabetic pregnancies. A total of 8 sample pools were created, 4 resultiing from normal (C1-C4) and 4 from diabetic (E1-E4) pregnancies. Each pool consisted of RNA from 4 embryos obtained from 4 different pregnancies. Samples E5-E8 consisted of individual embryos with NT defects obtained from diabetic pregnancies.

2013-12-31 | E-GEOD-50600 | biostudies-arrayexpress

Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling (Illumina)

Project description:Here we profile prostate cancers derived from GEM models of prostate cancer representative of human prostate cancer Total RNA was isolated from established prostate cancers in 3 GEM models of prostate cancer - PB-MYC, Pten-/-, Pten-/- p53-/-

2015-02-20 | E-GEOD-61379 | 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