Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global gene expression profile of primary mouse lung and small cell lung cancer (SCLC) tissues

ABSTRACT: Mouse SCLCs were induced by lentiviral vector expressing luciferase-Mycl-shp53-shRb or IkBaM-Mycl-shp53-shRb. Tumor tissues were isolated from mice that reached clinical endpoints. RNA was isolated using the RNeasy kit according to manufacturer’s protocol with the addition of DNase (Direct-zol). cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina). RNA sequencing was performed using a HiSeq 2500 Sequencing System (Illumina).

ORGANISM(S): Mus musculus

PROVIDER: GSE89857 | GEO | 2018/11/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Global gene expression profile of primary mouse brain and glioblastoma tissues

Project description:Mouse glioblastomas were induced by lentiviral vector expressing HrasG12V and shRNA against p53. Tumor tissues were isolated from mice reached clinical endpoints. RNA was isolated using the RNeasy kit according to manufacturer’s protocol with the addition of DNase (Qiagen). cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina). RNA sequencing was performed using a HiSeq 2500 Sequencing System (Illumina).

2016-09-15 | GSE73127 | GEO

NFIB is a driver of SCLC initiation, progression and metastasis in mouse and marks metastatic disease in patients

Project description:Small Cell Lung Cancer (SCLC) is the most aggressive type of lung cancer with early metastatic dissemination and invariable development of resistant disease for which no effective treatment is available to date. Mouse models of SCLC based on inactivation of Rb1 and Trp53 developed earlier showed frequent amplifications of two transcription factor genes: Nfib and Mycl. Overexpression of Nfib but not Mycl in SCLC mouse results in an enhanced and altered metastatic profile, and appears to be associated with genomic instability. NFIB promotes tumor heterogeneity with the concomitant expansive growth of poorly differentiated, highly proliferative, and invasive tumor cell populations. Consistent with the mouse data, NFIB expression in high-grade human neuroendocrine carcinomas correlates with advanced stage III/IV disease warranting its further assessment as a potentially valuable progression marker in a clinical setting. Genomic DNA from mouse small cell lung tumor samples was analyzed by mate pair sequencing and low coverage sequencing. And RNA from Nfib overexpressing mouse small cell lung cancer cell lines was further analyzed for high quality RNA profiles using Illumina Hiseq2500. This series contains only RNA-seq data.

2016-07-29 | E-GEOD-82005 | biostudies-arrayexpress

RNA Expression Profiling Of Normal Mouse Live Across a Reproductive Cycle

Project description:Purpose: To perform RNA-Seq expression profiling of the normal rodent liver at nulliparous, lactation, and involution day 6 reproductive stages. Methods: RNA was extracted and isolated from flash frozen murine liver using the Direct-zol RNA MiniPrep kit. An input of 100ng of RNA was used for library preparation. Library construction was performed by Novogene using a NEBNext® Ultra RNA Library Prep Kit for Illumina. Qualified libraries were sequenced on an Illumina Novaseq6000 Platform using a paired-end 150 run. Results: We identified gene pathway differences bile acid production and FGFR4 signaling between different reproductive stages with upregulation of these pathways during lactation. Additionally, individual genes involved with promoting bile acid synthesis were elevated at lactation whereas genes associated with inhibiting bile acid synthesis were reduced during lactation and elevated during involution.

2021-11-15 | GSE188680 | GEO

RNA-seq of RS4:11 cell line populations that are unedited (SPI1 +/+), mono (SPI1 +/-) and biallelicaly edited (SPI1 -/-)

Project description:The goal of the experiment was to identify which genes are differentially expressed between the unedited and SPI1-edited populations. The RS4:11 cell line was edited both mono and biallelicaly via electroporation with guides and Cas9. Following editing, RNA from unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were extracted through the Direct-zol RNA Microprep kit. cDNA libraries for sequencing were then prepared using the TruSeq Stranded mRNA Library Prep Kit and the IDT for Illumina-TruSeq RNA UD Indexes (Illumina). Samples were then sequenced on the Illumina NovaSeq platform.

2021-03-24 | E-MTAB-8677 | biostudies-arrayexpress

NFIB is a driver of SCLC initiation, progression and metastasis in mouse and marks metastatic disease in patients

2016-07-29 | GSE82005 | GEO

Bulk RNA-Sequencing of mouse large intestinal lymphatics (capillaries and collectors)

Project description:Purpose: Profile global gene expression of intestinal lymphatics to compare with published datasets Methods: Intestinal tissues were digested, lymphatic endothelial cells were sorted using lymphatic markers including CD31, Podoplanin, Lyve1. Total RNA was isolated from sorted cells using the Direct-Zol RNA MiniPrep kit (Zymo). Samples were submitted for bulk RNA-Sequencing. Conclusions: Gobal gene expression profile of intestinal lymphatics for further comparison with published datasets

2022-06-21 | GSE199082 | GEO

Mouse wound healing [RNA-seq]

Project description:Purpose: To explore the changes of genes expression in different time points during mouse wound healing. Two wounds tissue from one animal were pooled, three animals were used per time point. The wounds tissue was collected on day 0, 1, 3, 5, 7 after cutting. Skin was cleaned of muscle and fat tissue; total RNA was extracted using the RNeasy mini kits (Qiagen), purified using Direct-zol RNA MiniPrep kit (Zymo Research). Next-generation libraries were prepared using the VAHTS TM mRNA-seq V2 Library Prep Kit for Illumina (Vazyme, #NR601). RNA-seq libraries were run on an Illumina HiSeq X-Ten next-generation sequencer. Analysis of RNA-seq data was done using the DESeq package in R.

2020-06-05 | GSE128193 | GEO

3prime RNA-seq of murine SCLC cell line modified with CRISPR-activation of Myc, Mycl or Mycn

Project description:In cells derived from a genetically engineered Rb1 and Trp53 loss mouse model of SCLC (RP) expression of one of the three MYC family members induced from the endogenous locus using CRISPR activation. Cells were first stably transfected with the lenti-MS2-p65-HSF1 activator plasmid. Respective sgRNAs targeting either Myc, Mycl or MYCN were then cloned into the lentiSAMv2 system and transfected separately into the MS2-p65-HSF1 cells using lentiviral delivery.

2019-07-09 | E-MTAB-7411 | biostudies-arrayexpress

Dlx1/2-Dependent Expression of Meis2 Promotes Neuronal Fate Determination in the Mammalian Striatum [RNA-seq]

Project description:Purpose:To asses changes in gene expression profiles from the E14.5 littermate controls LGE and Meis2-CKO mice. Methods:The LGEs from E14.5 Meis2-CKO mutant and Control brains (n = 4 per group) were dissected, and RNA was isolated with the Direct-zol RNA Miniprep kit (Zymo, catalog #R2050) following the manufacturer’s instructions. Results: Identified 161 genes with downregulated RNA expression and 94 genes with upregulated RNA expression

2021-08-19 | GSE182335 | GEO

FACS Sequencing Analysis of DCX+ cells in the DG of Wild Type and Fmr1-/y; Dcx-DsRed mice

Project description:Purpose: The goals of this study are to investigate the molecular mechanism underlying FMRP-regulated maturation of newborn neurons Methods: DG tissue were isolated from 6-7 weeks old Fmr1-/y; Dcx-DsRed mice and their WT littermates. All cell populations were isolated into single cells using a Becton Dickinson FACS Aria II contained in a Biosafety Carbinet using 20 psi pressure and 100-μm nozzle aperture. 10,000 total alive or Dcx-DsRed+ alive Cells were collected directly in Trizol. Total RNA from the sorted cell was isolated using the Direct-zol™ RNA MiniPrep Kit. Strand-specific, poly(A) selected cDNA libraries were generated using Nugen Ovation® Ultralow Library Systems (Illumina) according to the manufacturer’s protocol. Cluster generation and high-throughput sequencing were performed on a HiSeq 2500 (Illumina), using the paired-end 100 bp protocol. Reads were aligned to the mouse genome GRCm38 with annotation from Gencode. Results: RNA isolated from DsRed+ cells were subjected to next generation sequencing and 519 differentially expressed (DE) genes were identified that showed significant changes (FDR-adjusted P < 0.05) between Fmr1 KO and WT cells.

2019-01-31 | GSE117111 | GEO

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