Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Loss of KDM4B Exacerbates Bone-Fat Imbalance and Mesenchymal Stem Cell Exhaustion in Skeletal Aging [RNA-seq]

ABSTRACT: Primary mMSCs were cultured in control medium (Con), containing DMEM and 15% FBS, or were subjeucted to osteogenic induction (OI) for 2 days. RNA was isolated using RNeasy Mini Kit (Qiagen, Cat#74104) from three biological replicates of primary MSCs from Prx1Cre;Kdm4bf/f mice and control mice. Total RNA was then purified with Dynabeads™ mRNA Purification Kit (Invitrogen, Cat#61006). RNA-seq libraries were constructed using Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems, Cat#KK8400), and sequenced using an illumina HiSeq 3000 sequencer at the Technology Center for Genomics & Bioinformatics (TCGB) core at UCLA.

ORGANISM(S): Mus musculus

PROVIDER: GSE104258 | GEO | 2021/02/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this work is comprehensive analysis of target genes co-regulated by CREB1 and FoxA1 in prostate cancer cell models, tissues, and circulating tumor cells (CTCs). Expression of CREB1/FoxA1 target genes corresponds with disease recurrence and aggressive clinical features. Methods: LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. For RNA-seq, cells are transfected with FoxA1,CREB1 specific or nonspecific siRNA and total RNA is extracted with Qiangen RNeasy Mini kit(cat 74104) and library is generated with TruSeq RNA Sample Preparation Kit v2 from Illumina(cat RS-122-2001). For Chip-seq, LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. After crosslinking with 1% formaldehyde, ChIP was performed. the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks.

2016-01-13 | GSE63034 | GEO

shRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

Project description:Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls. Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method. Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis.

2013-12-26 | GSE53658 | GEO

antiOsLIC collar chip

Project description:30 collars were taken from wild type plants or antiOsLIC transgenic plants respectively. One collar from one plant only. The leaves are just sprout 2-3 cm (about 1-2 days) from the stem. For measuring the genes expression level, Wild type plants were taken as control. The developing collar from both line2 of OsLIC antisense transgenic plants and wild type were harvested at the heading stage. The position of the collar was about 1cm above the last developed collar. Total RNA was extracted from the collars using TRIzol regeant (Invitrogen, P/N 15596-018, USA) and purified by using Qiagen RNeasy columns (QIAGEN, Cat. NO. 74104). All the processes for cDNA and cRNA synthesis, cRNA fragmentation, hybridization, washing and staining, and scanning, were conducted according to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix). Poly-A RNA Control Kit and the One-Cycle cDNA Synthesis kit were used in this experiment as described in the website: http://www.affymetrix.com/products/arrays/specific/rice.affx.

2008-12-22 | GSE12097 | GEO

CD6 co-stimulation of human peripheral blood mononuclear cells

Project description:Difference in gene expression profile between 30000 freshly isolated human PBMCs stimulated with the immobilized anti-CD3 mAb (0.25Âµg/ml) alone (lane 1), along with ALCAM-Fc (1Âµg/ml) (lane 2), IL-2 (2.5ng/ml) (lane 4) or both (lane 3) or compared to unstimulated cells (lane 5), incubated for 72 h. Organism used: Human Slides: Human 8x15k Arrays Starting material: Human peripheral blood mononuclear cells RNA Samples used: Pooled 1 â Unstimulated, Anti-CD3, Anti-CD3 + IL-2, Anti-CD3 + ALCAM, Anti-CD3 +ALCAM + IL-2. Labeling kit: Agilentâs Quick-Amp labeling Kit (p/n5190-0444) Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis) Total RNA and cRNA Purification Kit: Hybridization Kit: Qiagenâs RNeasy minikit Cat#74104 RNA quality was checked using Bioanalyzer.

2010-05-18 | E-GEOD-16331 | biostudies-arrayexpress

BRD4 regulates the osteogenic differentiation of MSCs

Project description:MSCs were lysed in cell lysis buffer for Western blotting and IP (Beyotime, Cat. No. P0013). A Dynabeads™ protein G immunoprecipitation kit (Invitrogen, Cat. No. 10007D) was used for Co-IP according to the manufacturer’s instructions. Dynabeads were resuspended and placed on a magnet to remove the supernatant then incubated with Ab Binding & Washing Buffer containing an anti-BRD4 antibody for 10 min at room temperature with rotation. The supernatant was removed by placing tubes on a magnet, and the Dynabeads-antibody complex was washed with Ab Binding & Washing Buffer. MSC lysates were added to the Dynabeads-antibody mixture and incubated for 10 min at room temperature with rotation. The supernatant was removed, the Dynabeads-antibody complex mixture was washed with washing buffer, and the proteins were separated using a standard SDS–PAGE system.

2022-06-16 | PXD034615 | iProX

Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence

2016-01-13 | E-GEOD-63034 | biostudies-arrayexpress

shRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

2013-12-26 | E-GEOD-53658 | biostudies-arrayexpress

Loss of KDM4B Exacerbates Bone-Fat Imbalance and Mesenchymal Stem Cell Exhaustion in Skeletal Aging [ChIP-seq]

Project description:Mesenchymal stem/stromal cells (MSCs) are multipotent progenitor cells with multilineage differentiation potentials. We previously reported histone demethylases KDM4B promoted osteogenesis and inhibited adipogenesis of human MSCs. To identify genome-wide enrichments of KDM4B and the changes in H3K9me3 marks when loss of KDM4B, Primary MSCs were isolated from Prx1Cre; Kdm4bf/f mice and control mice. ChIP-seq assay was performed using KDM4B, H3K9me3 and H3 antibody, respectively.

2021-02-10 | GSE104257 | GEO

RNA-seq profiles of B cells and naive and activated T cells from human peripheral blood

Project description:Mature B cells, CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors. Naive CD4+ and CD8+ T cells were cultured for three days in the presence of Dynabeads Human T-Activator CD3/CD28 beads (Life Technologies, cat. no. 111.31D) to induce activation. The B cells and naive and activated T cells were profiled by whole transcriptome RNA-seq.

2021-01-21 | GSE126116 | GEO

Modulation of microglia-mediated amyloid-beta clearance with nanoformulated polyphenol through the SIRT1-LDLR pathway

Project description:Light-controlled in situ synthesis of DNA microarrays (Affymetrix GeneChip® Mouse Genome 430 2.0) were performed to determine the altered gene expression. Affymetrix algorithm and multiple analysis comparison software were used for assessing gene expression differences, and mRNAs that increased or decreased in the brains of NP(α-M)-treated mice relative to that in the brains of Blank-NP-treated mice were identified. For the assay, total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions. Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

2018-09-14 | GSE119904 | GEO

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