Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ECM Culture of Normal Breast Lines

ABSTRACT: We cultured htertHME, HME2, PCS600010, and MCF10A cells in decellularized ECM scaffolds generated by BJ fibroblasts or on an uncoated, plastic cell culture dish (Unc) to analyze the potential effects of ECM signalling breast cancer development. Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

ORGANISM(S): Homo sapiens

PROVIDER: GSE152860 | GEO | 2024/06/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

ECM mediated FGF-induced estrogen receptor activity and therapy response

Project description:We wanted to investigate the effects of stromal signaling on ER+ breast cancer cells as recent work implicates the tumor microenvironment in the acquisition of resistance to endocrine therapy. We desired to examine the effects of both coculture with fibroblasts, and 2.5D monoculture of breast cancer cells on decellularized, fibroblast-derived extracellular matrix scaffolds. We cultured MCF7 cells alone (Unc_#_Mono) or in coculture (Co_#) with BJ fibroblasts to examine stromal signalling on ER+ breast cancer. Cocultured MCF7 were isolated by magnetically activated cell sorting. We also cultured MCF7 cells in decellularized ECM scaffolds generated by BJ fibroblasts (ECM1_#) or IMR90 fibroblasts (ECM2_#) or on an uncoated, plastic cell culture dish (Unc_#). Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 14 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

2019-12-31 | GSE137528 | GEO

Analysis of Transcriptome in hematopoietic stem cells after radiation injury with treatment of EGF or saline

Project description:Purpose: This study is designed to understand whether Epidermal Growth Factor treatment alters the transcriptome of hematopoietic stem cells after radiation injury Method: RNA was extracted from C57BL/6J mice at six weeks post 500cGy total body radiation and Epidermal Growth Factor or saline subcutaneous treatment. Libraries for RNA-Seq were prepared with Clontech kit. The data was sequenced on NextSeq500 for a paired-end 75bp read run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program. The Partek flow and Ingenuity Pathway Analysis (IPA) were used for bioinformatics methods and data analysis, respectively. The reads were mapped to the latest UCSC transcript set using STAR - 2.7.2a and GRCm38.97.

2020-07-29 | GSE146371 | GEO

A novel fate-mapping approach allows intratumoral profiling of hypoxic cells

Project description:We designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Tumors were resected 2 weeks post-implantation, mechanically disrupted and digested with collagenase to obtain a cell suspension. The cell suspension was enriched using magnetic-activated cell sorting (MACS) and DsRed+ cells were isolated from GFP+ cells by fluorescence-activated cell sorting (FACS) directly into Tris Reagent (Zymo Research). Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

2019-02-16 | GSE126609 | GEO

A novel fate-mapping approach allows intratumoral profiling of hypoxic cells II

Project description:We designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Metastatic lungs were resected 2 weeks after primary tumor removal, mechanically disrupted and digested with collagenase to obtain a cell suspension. The cell suspension was enriched using magnetic-activated cell sorting (MACS) and DsRed+ cells were isolated from GFP+ cells by fluorescence-activated cell sorting (FACS) directly into Tris Reagent (Zymo Research). Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

2019-08-27 | GSE136372 | GEO

A consensus hypoxia signature in breast cancer

Project description:We exposed a panel of 32 breast cancer cell lines or normal human mammary epithelial cells to 20% or 1% O2 concentration for 24h. Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with DNase I (Ambion). All samples had a RIN value of >9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

2018-12-26 | GSE111653 | GEO

Difference in characteristics between Endocardially-derived cardiac tissue macrophages (EcTMs) and non-Endocardially-derived cardiac tissue macrophages (non EcTMs)

Project description:[Purpose] To define the traditional profile of EcTMs, RNA seq analysis were parformed on EcTMs and non EcTMs at postnatal day28. [Method] The workflow consists of first-strand synthesis, template switching, adaptor ligation, cleavage of ribosomal cDNA and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on an Illumina Nextseq500 a single read 75 run. Data quality check was conducted on Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program. Reads were aligned to the UCSC mm10 reference genome map using TopHat. DEseq2 was used to identify differentially expressed genes of EcTMs compared to non-EcTMs. 36 upregulated genes in EcTMs compared to non-EcTMs with a padj < 0.05 were subsequently clustered and visualized using R. Gene ontology functional analyses were performed using the database for annotation, visualization, and integrated discovery (DAVID) online tool.[Result] 40 genes were differentially expressed between the two groups: 36 were higher and 4 genes were lower in EcTMs compared to non-EcTMs. Gene Ontology analysis revealed that EcTMs were enriched for genes related to antigen presentation, lysosomes, and phagosomes (H2-Ab1, H2-Aa, H2-Eb1, CD74, Laptm5). [Conclusion] EcTMs would have higher potential for presenting antigen and phagositosis compared to non EcTMs.

2019-02-27 | GSE100495 | GEO

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

Project description: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).

2018-11-15 | GSE89857 | GEO

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

Microbes Malnutrition Microglia

Project description:This study examines the role of early exposure to gut microbes and poor diet on microglial function in mice. Groups = control (CON), malnourished (MAL), and malnourished + microbial exposure (E/MALBG). CD11b+ cells (microglial enrichment) were isolated from whole mouse brains (Adult Brain Disruption Kit, Miltenyi Biotec). After sample quality control (Agilent 2100 Bioanalyzer), qualifying samples were sent for RNA-Seq (Illumina NextSeq 500 with Paired End 42bp × 42bp reads; demultiplexed: Illumina's bcl2fastq2). Following alignment against mouse reference genes (STAR aligner), DEG analyses was conducted using the DESeq2 pipeline.

2021-05-31 | GSE138182 | 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

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