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A distinct and unique M2 transcriptional program expressed by tumor-associated macrophages

ABSTRACT: Description This series contains microarrays for tumor associated macrophages (TAMs) purified from 8 week old male C57/BL6N mice, 3 weeks after tumor implantation into the left hind limb. Peritoneal exudates cells (PECs) were also harvested from control C57/BL6N mice. The resulting adherent populations were maintained in culture and resting TAMs and PECs were treated for 4 hours with 100 ng/mL of LPS to promote macrophage activation. RNA isolation and cDNA microarrays: Total RNA was isolated from approximately 20x10e6 PEC and TAM cells using standard Trizol purification protocols (Invitrogen, Carlsbad, CA). Microarrays were manufactured at the NCI, Laboratory of Molecular Technology (Frederick MD). The 10,368 Mm UniGem2 set was printed on poly-lysine coated glass slides and hybridized according to NCI facility protocols. All slides were scanned using as Axon GenePix 4000 scanner (Axon Instruments, Foster city, CA) and resulting data was uploaded for analysis to the mAdb microarray database (http://madb.nci.nih.gov/). Keywords = tumor associated macrophage Keywords: other

ORGANISM(S): Mus musculus

PROVIDER: GSE2098 | GEO | 2005/01/31

SECONDARY ACCESSION(S): PRJNA91793

REPOSITORIES: GEO

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A distinct and unique M2 transcriptional program expressed by tumor-associated macrophages

Project description:Description This series contains microarrays for tumor associated macrophages (TAMs) purified from 8 week old male C57/BL6N mice, 3 weeks after tumor implantation into the left hind limb. Peritoneal exudates cells (PECs) were also harvested from control C57/BL6N mice. The resulting adherent populations were maintained in culture and resting TAMs and PECs were treated for 4 hours with 100 ng/mL of LPS to promote macrophage activation. RNA isolation and cDNA microarrays: Total RNA was isolated from approximately 20x10e6 PEC and TAM cells using standard Trizol purification protocols (Invitrogen, Carlsbad, CA). Microarrays were manufactured at the NCI, Laboratory of Molecular Technology (Frederick MD). The 10,368 Mm UniGem2 set was printed on poly-lysine coated glass slides and hybridized according to NCI facility protocols. All slides were scanned using as Axon GenePix 4000 scanner (Axon Instruments, Foster city, CA) and resulting data was uploaded for analysis to the mAdb microarray database (http://madb.nci.nih.gov/). Keywords = tumor associated macrophage

2010-06-10 | E-GEOD-2098 | biostudies-arrayexpress

GR mutation in mice changes the genome-wide epigenome of frontal cortex in a highly sex-specific manner

Project description:We found that the GR mutation leads to a changes of the DNA methylation landscape in frontal cortex of c57/bl6n male mice

2018-12-07 | GSE123460 | GEO

Differential Gene Up-regulation by HIF-1a and HIF-2a in HEK293T.

Project description:Cell lines. HEK293 human embryonic kidney cells were obtained from ATCC (American Type Culture Collection, Manassas, VA) and were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Heat inactivated, Hyclone, Logan, Utah) and 1X antibiotics/glutamine (100 units/ml penicillin, 100ug/ml streptomycin, 292ug/ml L-Glutamine sulfate, all from Invitrogen Corp, Carlsbad, CA.), under either hypoxic (1% O2) or normoxic (21% O2) conditions at 37C in a tissue culture incubator. Treatment. Cells treated in hypoxia for 16 hours or transfected with HIF-1a (HIF-1amut or HIF2a) plasmid. At the end of treatment, cells were collected and washed. Microarray studies. Total RNA samples were extracted from HEK293T cells grown in 1% or 21% O2 overnight and from transfected cells. Total RNA (20 µg) from each sample was synthesized into double-stranded cDNA with reverse transcriptase (Fairplay labeling kit, Stratagen, La Jolla, CA) using an oligo d(T) primer. The double stranded cDNA from untreated cells was labeled with Cy3 monofunctional reactive dye and that from hypoxia-treated or transfected cells was labeled with Cy5 monofunctinal reactive dye. The probe was hybridized to a long oligo array (Hs-Operon V2-vB1.1px.gal) containing 20K human transcripts (NCI Microarray Facility, Advanced Technology Center, Gaithersburg, MD) overnight at 42C . The slides were washed and spin-dried. Microarray slides were scanned with a GenePix 4000 microarray scanner (Axon Instruments, Union City, CA.). The microarray images were analyzed with GenePix 3.0 software and data analysis was performed with the MicroArray Database (mAdb) system hosted by the Center for Information Technology and Center for Cancer Research at the NCI. Keywords: other

2005-04-01 | GSE2020 | GEO

Mus musculus strain:C57/Bl6N

Project description:Mus musculus strain:C57/Bl6N Raw sequence reads

| PRJNA362527 | ENA

Expression data from vehicle tumor associated macrophages (TAM) VS PLX3397 treated-TAM.

Project description:To test the difference genes expression of TAMs obtained from orthotopically implanted hepa1-6 tumors in C57BL/6 mice.Isolated TAMs were obtained from orthotopically implanted hepa1-6 tumors in C57BL/6 mice. Specimens were minced with scissors and digested by incubation for 1 h at 37°C in high-glucose DMEM (Life Technologies, CA) containing 0.1% collagenase IV (Sigma). After being washed in medium plus 10% FBS, the cell suspension was forced through a graded series of meshes to obtain single-cell suspensions and centrifuged at 400 g for 30–40 minutes at 18–20°C on layers of Lympholyte-M (Cedarlane Labs, Burlington, Ontario, Canada), after which the upper layer was removed, thus leaving the lymphocyte layer undisturbed at the interface. TAMs were sorted using Fluorescence-activated cell sorting (FACS, Becton Dickinson, Franklin Lakes, NJ) with CD45+, CD11b+, and F4/80+ (Becton Dickinson) according to the protocol listed at http://www.immgen.org/Protocols/ImmGen%20Cell%20prep%20and%20sorting%20SOP.pdf . TAMs growing in DMEM supplemented with 10% FBS were tested to determine their biological characteristics. We used microarrays to detail the global programme of gene expression and identified vehicle-TAM and treated-TAM during this process.

2017-02-28 | GSE95406 | GEO

Transcriptome of irradiated keratinocyte stem cells

Project description:To characterise the response of keratinocyte stem cells to ionizing radiation, gene profiling was performed using oligonucleotide microarrays (26068 probes). Cells were seeded in culture plates after cell sorting, irradiated the next day (2 Gy at 15 hours in culture), and RNA was prepared 3 hours after exposure. LOWESS normalisation was applied. dye-swap hybridization were performed. Slides were scanned with a Genepix 4000 microarray scanner (Axon Instruments, Molecular devices, Sunnyvale, CA). For each hybridized spot, the Cy3 and Cy5 fluorescence values were obtained by using Genepix Pro 4.0 software (Axon Instruments) and were saved as a result file

2010-06-11 | E-GEOD-7693 | biostudies-arrayexpress

Murine macrophages: Peritoneal exudate macrophages (PECs) vs tumor-associated macrophages (TAMs)

Project description:Murine macrophages: Peritoneal exudate macrophages (PECs) vs tumor-associated macrophages (TAMs)

| PRJNA704618 | ENA

Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice - Plasma (part V)

Project description:Characterization and analysis of metabolomic, proteomic and metabolic profiles of C57/Bl6N mice fed various high fat diets

2017-07-26 | ST000901 | MetabolomicsWorkbench

Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice - Liver (part VI)

Project description:Characterization and analysis of metabolomic, proteomic and metabolic profiles of C57/Bl6N mice fed various high fat diets

2017-07-26 | ST000902 | MetabolomicsWorkbench

Identification of new markers of cutaneous melanoma invasion

Project description:T1C3 is a clonal cell line from a human melanoma tumor, expressing PNA lectin, and characterized by a high capacity of dermal invasion. IC8 is a clonal cell line from a human melanoma tumor, negative for PNA lectin, and non-invasive. To identify new gene markers involved in the mechanisms of early invasion, oligonuclotide microarrays were used to assess transcriptional chnages between the two cell lines. Dye-swap hybridization were performed. Slides were scanned with a Genepix 4000 microarray scanner (Axon Instruments, Molecular devices, Sunnyvale, CA). For each hybridized spot, the Cy3 and Cy5 fluorescence values were obtained by using Genepix Pro 4.0 software (Axon Instruments) and were saved as a result file.

2010-12-15 | E-GEOD-15802 | biostudies-arrayexpress

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