title: Mouse cortex transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCT001_miRNA]

status: Public on Mar 12 2016

overall_design: Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 2 and 4 days post-infection. This study (WCT001) and GSE77160 (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77160 (WCB001). Infectivity (titer) and pathology are measured from the tissue in WCT001 (i.e., this experiment).

first: Kelly

last: Stratton


title: Human Calu-3 cell transcriptome response to wild-type pandemic H1N1 (A/California/04/2009), natural isolate [mRNA]

status: Public on May 26 2016

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

country: USA

institute: PNNL

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with wild-type pandemic H1N1 (A/California/04/2009), natural isolate.

overall_design: Human Calu-3 cells were seeded at  1 x 10^6 cells per well on 6 well plates 2 days before infection. Cells were infected with an MOI of 3. After infection, wash and replace with 2 ml of DMEM-F12 + .3% BSA and 1 ug/ml TPCK-trypsin. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 7, 12,  24, 36, and 48 hr post-infection.

first: Kevin

last: Walters

first: Allison

last: Thompson

first: Katrina

middle: M

last: Waters

first: Amie

middle: J

last: Eisfeld

first: Yoshihiro

last: Kawaoka


title: Human U937 cell transcriptome response to Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus [miRNA]

status: Public on May 06 2016

summary: The purpose is to obtain samples for microRNA analysis in human U937 cells infected with Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus.

overall_design: Human U937 cells (monocyte-like) expressing the Ebola VP30 protein were infected with Zaire Ebola virus wild-type (wild) in the ΔVP30 background and Δmucin virus (encodes a GP lacking the mucin domain) (mucin) in the Ebola ΔVP30 background. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 8, 18, and 30 h post-infection.

first: Pete

last: Halfmann


title: Human Calu-3 cell transcriptome response to a wild type infectious clone of H5N1 Influenza virus and mutant H5N1 viruses [miRNA]

status: Public on Feb 20 2016

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with wild-type A/Vietnam/1203/2004 (H5N1; 'VN1203'; derived by reverse genetics), PB2-K627E (627K is a mammalian-adapting mutation that increases polymerase replicatve activity; '627E' is typically found in avian species), and NS1-trunc124 (this 'NS1' protein has a 90 amino acid truncation at the C-terminus).

overall_design: Human Calu-3 cells were seeded at  1 x 10^6 cells per well on 6 well plates 2 days before infection. Prior to infection, washed cells 2 times with PBS, and then infected with a multiplicity of infection of 1. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 7, 12, and 24 hr post-infection.


title: Mouse popliteal lymph node transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [microRNA]

status: Public on Mar 19 2016

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse cortex infected with wild-type West Nile virus (WNV; WNV-NY99 382), and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt).

overall_design: Mice are inoculated with WNV in both hind footpads at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in triplets in parallel with infected samples. Time points: 1 and 2 days post-infection.

first: Larissa

last: Thackray

first: Michael

last: Diamond


title: Mouse cortex transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCT001_mRNA]

status: Public on Mar 04 2016

overall_design: Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 1, 2, 4, and 6 days post-infection. This study (WCT001) and GSE77192 (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77192 (WCB001). Infectivity (titer) and pathology are measured from the tissue in WCT001 (i.e., this experiment).


title: Primary human microvascular endothelial cell transcriptome (microRNA) response to wild type MERS-CoV (icMERS-CoV EMC2012)

status: Public on Apr 06 2016

summary: The purpose is to obtain samples for microRNA analysis in primary human microvascular endothelial cells infected with wild type MERS-CoV (icMERS).

overall_design: Human microvascular endothelial cells were infected with a multiplicity of infection of 5 PFU per cell.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 12 and 24 h post-infection. MERSCOV002.0P references the write up of the experimental procedure.

first: Ralph

last: Baric

first: Amy

last: Sims


title: Mouse cerebellum transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCB001_microRNA]

status: Public on Feb 21 2016

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse cerebellum infected with wild-type West Nile virus (WNV; WNV-NY99 382), and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt).

overall_design: Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 2 and 4 days post-infection. GSE77161 (WCT001) and this study (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77161 (WCT001). Infectivity (titer) and pathology are measured from cortex tissue in GSE77161 (WCT001).


title: Mouse cerebellum transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCB001_mRNA]

status: Public on Feb 15 2016

overall_design: Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 1, 2, 4, and 6 days post-infection. GSE77193 (WCT001) and this study (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77193 (WCT001). Infectivity (titer) and pathology are measured from cortex tissue in GSE77193 (WCT001).


title: Foxc1 reinforces quiescence in hair follicle stem cells

status: Public on Feb 05 2016

city: Boulder

first: Li

last: Wang

state: CO

address: 347 UCB

institute: University of Colorado, Boulder

type: Expression profiling by high throughput sequencing

summary: Quiescent stem cells are periodically activated to maintain tissue homeostasis or occasionally called into action upon injury. Molecular mechanisms that constitutively maintain stem cell identity or promote stem cell proliferation and differentiation upon activation have been extensively studied. However, it is unclear how quiescent stem cells maintain identity and reinforce quiescence when they transition from quiescence to activation. Here we show mouse hair follicle stem cell compartment induces a transcription factor, Foxc1, when activated. Importantly, deletion of Foxc1 in the activated but not quiescent stem cells compromises stem cell identity, fails to re-establish quiescence and subsequently drives premature stem cell activation.These findings uncover a dynamic, cell-intrinsic mechanism employed by hair follicle stem cells to reinforce stemness in response to activation.

overall_design: Poly(A)-enriched transcriptome RNA-seq on HFSCs isolated in WT and K14Cre cKO mice at anagen and early telogen stage of hair cycle.

first: Julie

middle: A

last: Siegenthaler

first: Robin

middle: D

last: Dowell

first: Rui

last: Yi


title: Sox2 signature in SHH medulloblastomas

status: Public on Dec 31 2015

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

summary: Affymetrix Human Gene 1.1 ST Array profiling of 83 primary SHH-driven medulloblastoma samples.

overall_design: Total RNA was extracted from primary medulloblastoma samples and hybridized to Affymetrix Human Gene 1.1 ST Arrays (24-Array Plates) according to the manufacturer's instructions.

first: Robert

last: Vanner

first: Paul

last: Northcott

first: Peter

middle: B

last: Dirks

last: Taylor


title: Primary mouse myeloid dendritic cell transcriptome response to a wild type infectious clone of West Nile virus (WNVMT) and mutant virus (WNVE218A).

first: Natalie

last: Heller

summary: The purpose is to obtain samples for mRNA analysis in primary mouse myeloid dendritic cells infected with wild type West Nile virus (WNVMT) and mutant virus (WNVE218A).

overall_design:
Mouse (C57Bl/6J) primary myeloid dendritic cells (D10 after seeding of leukocytes from bone marrow) were seeded at 2 x 10^5 cells per well of non-tc treated 12-well plate in 0.8 mL R10 DC media after infection at a multiplicity of infection of 500.  Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 1, 8, 12 and 24 h post-infection.

There were two independent biological replicates of the entire procedure. This study (WDC011) is a biological replicate of another (WDC010; GSE74628).

first: Kelly

last: Stratton

last: Waters


title: Human Calu-3 cell transcriptome response to a wild type infectious clone of H5N1 Influenza virus and mutant H5N1 viruses [mRNA]

status: Public on Jan 30 2016

first: Kevin

last: Walters

first: Katrina

first: Amie

last: Eisfeld

last: Kawaoka


title: Mouse primary myeloid dendritic cell transcriptome response to a wild type infectious clone of West Nile virus (WNVMT) and mutant virus (WNVE218A).

status: Public on Nov 04 2015

overall_design:
Mouse (C57Bl/6J) primary amyeloid dendritic cells (D10 after seeding of leukocytes from bone marrow) were seeded at 2 x 10^5 cells per well of non-tc treated 12-well plate in 0.8 mL R10 DC media after infection at a multiplicity of infection of 500.  Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 1, 8, 12 and 24 h post-infection.

There were two independent biological replicates of the entire procedure. This study (WDC010) is a biological replicate of another (WDC011; GSE75222).

first: Larissa

last: Thackray

last: Diamond

first: Yoshihiro


title: Mouse lung tissue transcriptome response to influenza H5N1 [miRNA]

status: Public on Aug 06 2015

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse lung infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203').

overall_design: Groups of 22-week-old C57BL/6 mice were infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203').Infections were done at 10^4 PFU/mouse in 50 μl PBS. Time points were 1, 2, 4, and 7 d.p.i. There were 5 mice for all infection groups and 3 mice for all mock groups. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.


title: Immortalized human hepatocyte (IHH) microRNA response to interferon alpha treatment

summary: The purpose of this experiment was to obtain samples for microRNA analysis in IHH cells infected with human interferon alpha.

overall_design: Immortalized human hepatocyte (IHH) cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection.  Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences).  Mock-treated cells were given normal culture medium only.  Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection

last: Halfmann


title: Mouse lung tissue transcriptome response to influenza H5N1 [miRNA] (AmbryGenetics)

status: Public on Sep 05 2015

overall_design: Groups of 22-week-old C57BL/6 mice were infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203'). Infections were done at 10^4 PFU/mouse in 50 μl PBS. Time points were 1, 2, 4, and 7 d.p.i. There were 5 mice for all infection groups and 3 mice for all mock groups. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.


title: Mouse lung tissue transcriptome response to influenza H5N1 and mutants [mRNA](Agilent-026655)

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse lung infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203') and VN1203-NS1trunc124.

overall_design: Groups of 22-week-old C57BL/6 mice were infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203') and VN1203-NS1trunc124 (an NS1 protein with a 90 amino acid truncation at the C-terminus). Infections were done at 10^4 PFU/mouse in 50 μl PBS. Time points were 1, 2, 4, and 7 d.p.i. There were 5 mice for all infection groups and 3 mice for all mock groups. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.


title: Comparison against 186 canid whole genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

status: Public on Jul 30 2015

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

summary: Whole genome sequencing of CTVT, breed dogs, and wild canids reveals pathways that are important in cancer cell survival. Comparison of these mutations with breed dogs shows that the original tumor came from a dog very similar to one of the modern Arctic breeds.

overall_design: DNA was collected from pedigreed dogs of the Alaskan Malamute (AMAL) and Siberian Husky (HUSK) breeds living in North America. SNPs were genotyed using the Illumina CanineHD SNP chip. These SNPs were compared to published data and seqeunced mutations from CTVT by principal component alnalysis to identify the breed of the CTVT originator.

first: Elaine

last: Ostrander


title: Mouse lung tissue transcriptome response to influenza H5N1 and mutants [mRNA](Agilent-028005)

status: Public on Aug 13 2015


title: Immortalized human hepatocyte (IHH) mRNA response to interferon alpha treatment

summary: The purpose of this experiment was to obtain samples for mRNA analysis in IHH cells infected with human interferon alpha.


title: Mouse lung tissue transcriptome response to H1N1, H5N1, and mutants [miRNA]

status: Public on Jun 18 2015

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse lung infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203'), VN12013-PB2-627E, VN1203-NS1trunc124, and WT A/California/04/2009 (H1N1; 'CA04').

overall_design: Groups of 22-week-old C57BL/6 mice were infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203'), VN12013-PB2-627E, VN1203-NS1trunc124, and WT A/California/04/2009 (H1N1; 'CA04').Infections were done at 176 PFU/mouse for VN1203, 70 PFU/mouse for VN1203-PB2-627E, 1100 PFU/mouse for VN1203-NS1trunc124, and 10^4 PFU/mouse for CA04. Time points were 1, 2, 4, and 7 d.p.i. There were 8 mice for all infection groups and 5 mice for all mock groups. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.


title: IHH microRNA response to genetically-reconstructed Zaire Ebola viruses [miRNA]

summary:
The purpose of this experiment was to obtain samples for mRNA analysis in IHH cells infected with Zaire Ebola virus and mutants:
Zaire Ebola virus: This wild-type Ebola virus - strain Mayinga - was isolated from a fatal human case in Zaire (now known as the Democratic Republic of Congo) in 1976
Zaire Ebola virus, VP35 R312A possesses a R312A mutation in the VP35 protein.
Zaire Ebola virus, delta sGP. Lacks the ability to produce non-structural protein, the secreted glycoprotein (sGP).
Zaire Ebola virus, delta mucin.  Lacks the mucin-like domain (MLD), which contains both N-linked and O-linked glycosylation sites, for the glycoproteins.

overall_design: Overview of Experiment: Cells: Immortalized Human Hepatocytes (IHH); seed 60,000 cells per well in a 24-well plate. Infected with a multiplicity of infection (MOI) of 0.5. After infection, 3x wash with PBS and replace with 5% FCS DMEM without NaPyr or NEAA. Time matched mocks done in triplicate from same cell stock as rest of samples. Time Points = 0, 6, 12, 24, 48, and 72 hrs post infection in triplicate.


title: IHH mRNA response to genetically-reconstructed Zaire Ebola viruses [mRNA]


title: Human Calu-3 cell transcriptome response to human interferon α [miRNA]

status: Public on Jun 25 2015

summary: The purpose is to obtain samples for mRNA and miRNA analysis with and without interferon α treatment; in parallel, to obtain cell pellets to forward to PNNL for use in top-down proteomics pilot experiments

overall_design: Human Calu-3 cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection. Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences).  Mock-treated cells were given normal culture medium only.  Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in quadruplet; time-matched mocks were collected in quadruplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection


title: Human Calu-3 cell micro RNA transcriptome response to a wild type infectious clone of H7N9 Influenza virus and mutant H7N9 viruses

status: Public on May 20 2015

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with WT A/Anhui/1/2013 (H7N9; 'AH1'), and AH - NS1-103F/106M.

overall_design: Human Calu-3 cells were seeded at 1 x 10^6 cells per well on 6 well plates 2 days before infection. Prior to infection, washed cells 2 times with PBS, and then infected with a multiplicity of infection of 1.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 7 and 12 h post-infection


title: Mouse lung tissue transcriptome response to H1N1, H5N1, and mutants [mRNA]

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse lung infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203'), VN1203-NS1trunc124, and WT A/California/04/2009 (H1N1; 'CA04').

overall_design: Groups of 22-week-old C57BL/6 mice were infected with WT A/Vietnam/1203/2004 (H5N1; 'VN1203'), VN12013-PB2-627E, VN1203-NS1trunc124, and WT A/California/04/2009 (H1N1; 'CA04').Infections were done at 176 PFU/mouse for VN1203, 1100 PFU/mouse for VN1203-NS1trunc124, and 10^4 PFU/mouse for CA04. Time points were 1, 2, 4, and 7 d.p.i. There were 5 mice for all infection groups and 3 mice for all mock groups. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.


title: Human Calu-3 cell transcriptome response to a wild type infectious clone of H7N9 Influenza virus and mutant H7N9 viruses

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in human Calu-3 cells infected with WT A/Anhui/1/2013 (H7N9; 'AH1'), AH - NS1-103F/106M, and AH1 - 691 (ferret adapted virus).

overall_design: Human Calu-3 cells were seeded at 1 x 10^6 cells per well on 6 well plates 2 days before infection. Prior to infection, washed cells 2 times with PBS, and then infected with a multiplicity of infection of 1.  Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 7, 12 and 24 h post-infection


title: Mouse lung tissue transcriptome response to a wild type infectious clone of H7N9 Influenza virus and mutant H7N9 viruses [microRNA]

status: Public on May 16 2015

summary: The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse lung infected with WT A/Anhui/1/2013 (H7N9; 'AH1'), AH - NS1-103F/106M, and AH1 - 691 (ferret adapted virus).

overall_design: Groups of 22-week-old C57BL/6 mice were infected with the H7N9 Influenza WT A/Anhui/1/2013 (H7N9; 'AH1'), AH - NS1-103F/106M, and AH1 - 691 (ferret adapted virus). Infections were done at 10^4 PFU or time-matched mock infected. Time points were 1, 2, 4 and 7 d.p.i. There were 5 animals/dose/time point. Lung samples were collected for virus load, transcriptional and proteomics analysis. Weight loss and animal survival were also monitored.


title: Human Calu-3 cell transcriptome response to human interferon α [mRNA]

overall_design: Human Calu-3 cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection.  Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences).  Mock-treated cells were given normal culture medium only.  Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in quadruplet; time-matched mocks were collected in quadruplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection


title: Deletion of TIPARP increases sensitivity to dioxin-induced hepatosteatosis and lethality

status: Public on May 14 2015

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

summary: The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that mediates the toxic effects of the environmental contaminant, dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin; TCDD). Dioxin causes a diverse range of toxic responses, including hepatic damage and lethal wasting syndrome; however, the mechanisms of dioxin-induced toxicity are still unknown. Here we show that the loss of TCDD-inducible poly(ADP-ribose) polymerase (TIPARP; ARTD14), an ADP-ribosyltransferase and AHR repressor, increases sensitivity to dioxin-induced toxicity and lethality. Tiparp-/- mice treated with a single injection of 100 mg/kg dioxin display an accelerated lethal wasting syndrome with no Tiparp-/- mice surviving beyond day 5; all Tiparp+/+ mice survived up to 30 days post treatment. Tiparp-/- mice displayed dramatic increases in liver steatosis and hepatotoxicity. At the molecular level, TIPARP selectively ADP-ribosylates AHR, but not AHR nuclear translocator (ARNT) and the Tiparp-dependent repression of AHR is reversed by the ADP-ribosylase and macrodomain containing protein MacroD1, but not MacroD2. These results describe previously unidentified roles for Tiparp, MacroD1, and ADP-ribosylation in AHR signaling, dioxin toxicity and lethality.

overall_design: 12 samples were analyzed. There were 4 treatment groups and each treatment group was done in triplicate. Gene expression changes were determine in hepatic RNA isolated from (1) corn oil treated C57BL/6;129Sv mice; (2) 30 ug/kg/bw 2,3,7,8-Tetrachlorodibenzo-p-dioxin C57BL/6;129Sv mice; (3) corn oil treated C57BL/6;129Sv Tiparp-/- mice; and (4) 30 ug/kg/bw 2,3,7,8-Tetrachlorodibenzo-p-dioxin C57BL/6;129Sv Tiparp-/- mice

first: Shaimaa

last: Ahmed

first: Debbie

last: Bott

first: Yang

last: Yang


title: Mouse granule cell neuron transcriptional response to wild-type West Nile virus (WNV-NY) and mutant virus WNV E218A (microRNA)

status: Public on Apr 29 2015

summary: The purpose is to obtain samples for transcriptional analysis in triplicate wells using wild type West Nile virus (WNV NY99 clone 382; WNVWT) and mutant virus (WNVE218A) in mouse granule cell neurons. This data set comprises two complete biological replicate experiments conducted in the same conditions and with data processed independently.

overall_design: Granule cell neurons from day 6 C57Bl/6J mouse pups are infected with plasmid-derived wild type West Nile virus NY99 clone 382 (WNVWT) or plasmid-derived isogenic E218A mutant West Nile virus NY99 clone 382 (WNVE218A) with multiplicity of infection (MOI) 250.  Three technical replicates were performed at each of 1, 8, 12 and 24 hrs post infection. Time matched mocks done in triplicate are treated with mockulum: cell media concentrated through ultracentrifugation and diluted as virus. mRNA is sampled at all time points; microRNA is sampled at 12 hours post-infection. There were two independent biological replicates of the entire procedure, distinguished by sample name prefixes ('WGCN002' and 'WGCN003') and the biological_replicate characteristic field.

first: Michael


title: Mouse granule cell neuron transcriptional response to wild-type West Nile virus (WNV-NY) and mutant virus WNV E218A (mRNA)


title: Mouse lung tissue transcriptome response to a wild type infectious clone of H7N9 Influenza virus and mutant H7N9 viruses [mRNA]


title: Mouse cortical neuron transcriptional response to wild-type West Nile virus (WNV-NY) and mutant virus WNV E218A [mRNA]

status: Public on Apr 04 2015

summary: The purpose is to obtain samples for transcriptional analysis in triplicate wells using wild type West Nile virus (WNV NY99 clone 382; WNVWT) and mutant virus (WNVE218A) in mouse cortical neurons. This data set comprises two complete biological replicate experiments conducted in the same conditions and with data processed independently.

overall_design: Primary cortical neurons from C57Bl/6J mouse embryos (age E15) are infected with plasmid-derived wild type West Nile virus NY99 clone 382 (WNVWT) or plasmid-derived isogenic E218A mutant West Nile virus NY99 clone 382 (WNVE218A) with multiplicity of infection (MOI) 250.  Three technical replicates were performed at each of 1, 8, 12 and 24 hrs post infection. Time matched mocks done in triplicate are treated with mockulum: cell media concentrated through ultracentrifugation and diluted as virus. mRNA is sampled at all time points; microRNA is sampled at 12 hours post-infection. There were two independent biological replicates of the entire procedure, distinguished by sample name prefixes ('WCN002' and 'WCN003') and the biological_replicate characteristic field.


title: Mouse cortical neuron transcriptional response to wild-type West Nile virus (WNV NY99 clone 382) and mutant virus WNV E218A [microRNA]


title: Human Calu-3 cell transcriptome response to a wild type infectious clone of Middle Eastern Respiratory Syndrome (icMERS) coronavirus and icMERS mutant viruses

status: Public on Feb 04 2015

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
The purpose of this experiment was to obtain samples for transcriptome analysis using wild type infectious clone of Middle Eastern Respiratory Syndrome  (icMERS) coronavirus and icMERS mutant viruses: icMERS-RFP, icMERS-dNSP16, icMERS-d4B, and icMERS-d3-5.
For protocol details, please search for the protocol ID at https://systemsvirology.org.

overall_design: Overview of Experiment: Cells: 2B4 Calu-3 cells; seed 5 x 10^5 cells per well on 6 well plates 2 days before infection. Prior to infection, washed cells 2 times with PBS, and then infected with a multiplicity of infection of 5.  Time matched mocks done in triplicate from same cell stock as rest of samples using culture medium. Time points: 0, 7, 12 and 24 h post-infection (For miRNA: 7, 12 hours only)

first: Ralph

middle: S

last: Baric

first: Vineet

last: Menachery

first: Amy

middle: C

last: Sims


title: Immortalized Human Hepatocyte (IHH) transcriptome response to wild-type Ebola viruses Zaire Ebola (ZEBOV '76) and Reston Ebola (REBOV '08)

first: Natalie

last: Heller

summary: The purpose of this experiment was to obtain samples for transcriptome analysis using wild-type viruses: Zaire Ebola (ZEBOV '76) and Reston Ebola (REBOV '08).

overall_design: Overview of Experiment: Cells: Immortalized Human Hepatocytes (IHH); seed 60,000 cells per well in a 24-well plate. Infected with a multiplicity of infection (MOI) of 0.5. After infection, 3x wash with PBS and replace with 5% FCS DMEM without NaPyr or NEAA. Time matched mocks done in triplicate from same cell stock as rest of samples. Time Points = 0, 8, 24, 48, and 72 hrs post infection in triplicate. (For miRNA: 8, 24, 48, 72 hours.)

first: Peter


title: Expression and Prognostic impact of LncRNAs in Acute Myeloid Leukemia

status: Public on Jan 01 2015

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

summary: Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides located within the intergenic stretches or overlapping antisense transcripts of protein coding genes. LncRNAs are involved in numerous biological roles including imprinting, epigenetic regulation, apoptosis and cell-cycle. To determine whether lncRNAs are associated with clinical features and recurrent mutations in older patients (aged ≥60 years) with cytogenetically normal (CN) acute myeloid leukemia (AML), we evaluated lncRNA expression in 148 untreated older CN-AML cases using a custom microarray platform.

overall_design:
In this study, we analyzed a large set of older CN-AML patients using custom lncRNA microarrays to investigate whether lncRNA expression is associated with clinical features, molecular abnormalities and outcome and to build a prognostic lncRNA signature that was subsequently validated using RNA sequencing.

This submission represents RNA-Seq component of study.

first: Ramiro

last: Garzon

first: Stefano

last: Volinia

first: Dimitrios

last: Papaioannou

first: Deedra

last: Nicolet

first: Jessica

last: Kohlschmidt

first: Pearlly

last: Yan

first: Krzysztof

last: Mrózek

first: Donna

last: Bucci

first: Andrew

last: Carroll

first: Maria

middle: R

last: Baer

first: Meir

last: Wetzler

first: Thomas

middle: H

last: Carter

first: Bayard

middle: L

last: Powell

first: Jonathan

middle: E

last: Kolitz

first: Joseph

middle: O

last: Moore

first: Ann-Kathrin

first: James

last: Blachly

first: William

last: Blum

last: Caligiuri

first: Richard

last: Stone

first: Guido

last: Marcucci

first: Carlo

last: Croce

first: John

last: Byrd

first: Clara

last: Bloomfield


title: miRNA gene expression profile of ApoE-/- mice during neointima formation

status: Public on Nov 28 2014

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

summary: In order to identify microRNAs involved in neointima formation in mice with an atherogenic background, wire-induced carotid injury was performed in ApoE-/- mice on western-type diet. Uninjured carotid arteries served as control. RNA was isolated after 1, 7, 14, and 28 days (n=3-4 each group) and hybridized to an Agilent microRNA microarray (Sanger v12). Significantly regulated microRNAs (>2-fold) over time (P<0.05; ANOVA and Benjamini-Hochberg correction) were clustered by K-means algorithm. Distinct groups of similarly regulated microRNAs were detected in the course of neointima formation in hyperlipidemic mice.

overall_design: miRNA gene expression profile of ApoE-/- mice were measured at 1, 7, 14, 28 days after vascular injury.  3 to 4  animals per group were used for each time points.

first: Schober

last: Andreas

first: Nazari-Jahantigh

last: Malihe

first: Zhou

last: Zhe


title: Gene expression profiling study by RNA-seq in colorectal cancer

status: Public on Aug 31 2014

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The objective of this study is to identify a prognostic signature in colorectal cancer (CRC) patients with diverse progression and heterogeneity of CRCs. We generated RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) from 18 CRC patients and, from the RNA-seq data, identified significant genes associated with aggressiveness of CRC. Through diverse statistical methods including generalized linear model likelihood ratio test, two significantly activated regulators were identified. In the validation cohorts, two activated regulators were independent risk factors and potential chemotherapy-sensitive agenets in colorectal cancers.

overall_design: RNA-seq data of 54 samples (normal colon, primary CRC, and liver metastasis) were generated from 18 CRC patients. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).

first: Jeong-Hwan

first: Seon-Young

first: Jin-Cheon


title: Transcriptomic studies to characterize the gene expression landscape of psoriasis

status: Public on Dec 10 2014

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design:
Refer to individual Series

Please note that some samples are from the same patient (e.g. M7832 and M7832_uninvolved), but they are from two different parts of the body (i.e. lesional skin vs. uninvolved skin), which was indicated in the sample title.


title: Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin

summary: Together with the GSE54456 data, we used in total RNA-seq data from 99 lesional psoriatic, 27 uninvolved psoriatic, and 90 normal skin biopsies and applied computational approaches to identify and characterize expressed lncRNAs.

overall_design: 7 psoriatic, 27 uninvolved, and 8 normal skin samples

middle: T

last: Elder

first: Goncalo

last: Abecasis

first: Rajan

middle: P

last: Nair


title: Expression data from Saccharomyces cerevisiae expressing Candida albicans Nik1p comparing osmotic stress and fludioxonil treatment

status: Public on Feb 01 2014

city: Braunschweig

first: Anna

last: Buschart

address: Inhoffenstr. 7

department: BiSA

institute: Helmholtz-Centre for Infection Research

summary: Fungal group III histidine kinases are the molecular targets of some classes of fungicides. In contrast to the yeast Saccharomyces cerevisiae, the fungal pathogen Candida albicans possesses a group III histidine kinase, CaNik1p, also called Cos1p. To investigate the function of CaNIK1, the gene was expressed in S. cerevisiae. The transformants became susceptible to antifungal compounds to which the wild-type strain is resistant. The susceptibility was related to the activation of the MAP kinase Hog1p of the osmotic stress response pathway. Gene expression analysis revealed a strong overlap of the responses to osmotic stress and to fludioxonil at early time points. While the response to fludioxonil persisted, the response to osmotic stress was diminished with time.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. cerevisiae expressing Candida albicans Nik1p were treated with 10 µg/ml fludioxonil. As a comparison, another culture of S. cerevisiae expressing Candida albicans Nik1p was treated with 1 M sorbitol to induce osmotic stress response. One culture remained untreated as a control. From all cultures, samples  were taken after a duration of 15, 30 and 60 min.

first: Katja

last: Gremmer

first: Joop

last: van den Heuvel

first: Peter

last: Müller

first: Ursula

last: Bilitewski


title: Transcriptome analysis of psoriasis in a large case-control sample:  RNA-seq provides insights into disease mechanisms

status: Public on Jan 29 2014

summary:
To increase our understanding of psoriasis, we utilized RNA-seq to assay the transcriptomes of lesional psoriatic and normal skin. We sequenced polyadenylated RNA-derived cDNAs from 92 psoriatic and 82 normal punch biopsies, generating an average of ~38 million single-end 80-bp reads per sample. Comparison of 42 samples* examined by both RNA-seq and microarray [GSE13355] revealed marked differences in sensitivity, with transcripts identified only by RNA-seq having much lower expression than those also identified by microarray. RNA-seq identified many more differentially expressed transcripts enriched in immune system processes.  Weighted gene co-expression network analysis (WGCNA) revealed multiple modules of coordinately expressed epidermal differentiation genes, overlapping significantly with genes regulated by the long non-coding RNA TINCR, its target gene, staufen-1 (STAU1), the p63 target gene ZNF750, and its target KLF4. Other coordinately expressed modules were enriched for lymphoid and/or myeloid signature transcripts and genes induced by IL-17 in keratinocytes. Dermally-expressed genes were significantly down-regulated in psoriatic biopsies, most likely due to expansion of the epidermal compartment. These results demonstrate the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and co-expression analysis.
*The list of 42 samples examined by both RNA-seq and microarray is provided in the 'MAoverlappedsamples.txt'.

overall_design: 92 psoriatic and 82 normal skin samples

first: James


title: Genome wide expression profile in cervical cancer patients (staged, locally advanced)

status: Public on May 01 2014

city: MEXICO, D.F.

first: JORGE

last: FERNANDEZ-RETANA

address: AV. SAN FERNANDO No22 COL SECCION XVI

department: INVESTIGACION BASICA

country: Mexico

institute: INSTITUTO NACIONAL DE CANCEROLOGIA

summary: Gene expression profile in Locally Advanced Cervical Cancer patients

overall_design: The RNA total samples were obtain from 89 biopsies of patients with locally advanced cervical cancer (staged).

first: Jorge

last: Fernandez-Retana

first: Carlos

last: Perez-Plasencia


title: Downregulation of CK2-Beta is sufficient to drive epithelial-to-mesenchymal transition through Snail 1 induction

status: Public on May 07 2012

city: GRENOBLE

first: Odile

last: FILHOL

address: 17, rue des martyrs

department: BIG

country: France

institute: INSERM-CEA

summary: To understand how CK2β silencing promotes a mesenchymal phenotype in human epithelial cells, like TGFβ does, we have employed whole genome microarray expression profiling as a discovery platform to compare genes regulated in CK2β-depleted cells and in TGFβ-treated cells.  To do so, we began by deriving individual gene expression signatures of WT-, TGFβ-treated, CK2β-depleted or CK2β-depleted and rescued with chicken CK2β, whose expression is not affected by the shRNA  in MCF10A cells, and cataloguing genes exhibiting at least a 1.5-fold up- or down-regulation under each experimental condition. We observed that EMT triggered by TGFβ1 or CK2β-depletion induced an overlapping set of changes in gene expression.  Of ~25,000 unique genes tested, we found ~1,200 genes whose expression was significantly modulated in TGFβ1-treated or CK2β-depleted cells as compared to Mock-cells. Of the 439 genes down-regulated in TGFβ1-treated cells, 74 genes (17%) were also repressed in CK2β-depleted MCF10A cells and 45 genes (10%) were commonly up-regulated. As expected, among commonly regulated genes, several mesenchymal genes (CDH2, FN1, MYL9, VIM) were upregulated, whereas epithelial genes such as CDH1, CDH3, CLDN1, CLDN7, OCLN, KRT5, KRT6B, COL2A1 and MUC1, were inversely turned down. The expression of the EMT-inducing transcription factors, Snail and Zeb, was also significantly up-regulated in accordance with the repression of their known target genes. While showing similar phenotypes, the genetic program of TGFβ1-treated or CK2β-depleted MCF10A cells also exhibited distinct features. These results highlight that in addition to TGFβ1-regulated genes, CK2β-depletion may affect alternative pathways.

overall_design: The microarray analysis was performed with RNAs isolated from parental MCF10A cells and the following MCF10A-derived cells: ΔCK2β- and TGFβ1-treated cells (2ng/ml for 72h) and each from two independent cell cultures (duplicates).

first: A

last: Deshiere

first: E

last: Duchemin-Pelletier

last: Spreux

first: D

last: Ciais

first: F

last: Combes

first: I

last: Mikaelian

first: S

last: Giusiano

first: C

last: Charpin

first: J

last: Boutonnat

last: Cochet

first: O

last: Filhol

first: Y

last: Vandenbrouck

last: Couté


title: Peripheral blood gene expression changes during allergen inhalation challenge in atopic asthmatic individuals

status: Public on Oct 15 2012

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary:
Background: Allergen inhalation challenge in mild asthmatics induces airflow obstruction, airway hyperresponsiveness and inflammation, providing a model for hypothesis-generating experiments to understand regulation of these responses.  We have sought to evaluate the peripheral whole blood transcriptome, post-challenge compared to pre-challenge, and to determine the effect of globin mRNA reduction methodology.   Methods: Asthmatic subjects (20-60 years of age, with stable, mild allergic asthma, n=17) underwent allergen inhalation challenges.  All subjects had an early asthmatic response of ≥ 20% fall in FEV1; most had a late phase response of ≥ 15% fall in FEV1.  Blood was collected immediately prior to, and two hours after allergen challenge.  Transcriptome analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST arrays, with and without globin mRNA reduction (PAX-GR and PAX-NGR, respectively) in 4 subjects. Replication studies for expression of nine genes contributing to the top canonical pathway, Nrf2-mediated oxidative stress response pathway, were performed with 5 independent subjects with microarray data, also with the same 4 subjects had microarray results and 8 other independent subjects with QPCR. Data were analyzed using paired t-test and Partek® Genomics Suite™.
Results: The number of differentially expressed probe sets from PAX-NGR samples was twice that of PAX-GR samples.  Paired analysis of each subjects' pre- and post-sample additionally demonstrated twice the power to detect differentially expressed probe sets.  The Nrf2-mediated oxidative stress response pathway was identified as the top canonical pathway in the PAX-NGR samples. ATP-binding cassette sub-family C member 1 (ABCC1) gene was significantly reduced two hours after allergen challenge in the 5 subjects’ microarray dataset and the 2 QPCR replication datasets with P < 0.05.   Conclusions: Globin mRNA reduction does not provide benefits to detect differentially expressed genes during allergen inhalation challenge. Allergen inhalation challenge is associated with decreased peripheral blood cell transcript level of ABCC1 gene.

overall_design:
26 array were analyzed. We first identified differentially expreed genes  between post- and pre-challenge samples from 4 asthmatic subjects by using globin reduction
samples and non-globin reduction samples (16 arrays). Then we replicated our findings using 10 arrays from 5 asthmatic subjects challenged with allergen. Includes 4 normal blood samples.

last: Kam

last: He

last: Ruan

first: G

last: Gauvreau

first: P

last: O'Byrne

first: M

last: FitzGerald


title: High-resolution genome-wide mapping of AHR and ARNT binding sites by ChIP-Seq

status: Public on Oct 24 2012

first: Jason

last: Matthews

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT) activated complex regulates genes in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHR has also emerged as a potential therapeutic target for the treatment of human diseases and different cancers, including breast cancer. To better understand AHR and ARNT signaling in breast cancer cells, we used chromatin immunoprecipitation linked to high throughput sequencing to identify AHR- and ARNT-binding sites across the genome in TCDD treated MCF-7 cells. We identified 2,594 AHR-bound, 1,352 ARNT-bound and 882 high confidence AHR/ARNT co-bound regions. No significant differences in the genomic distribution of AHR and ARNT were observed. Approximately 60% of the co-bound regions contained at least one core AHRE, 5'-GCGTG-3'. AHR/ARNT peak density was the highest within 1 kb of transcription start sites (TSS); however, a number of AHR/ARNT co-bound regions were located as far as 100 kb from TSS. De novo motif discovery identified a symmetrical variation of the AHRE (5'-GTGCGTG-3'), as well as FOXA1 and SP1 binding motifs. Microarray analysis identified 104 TCDD responsive genes where 98 genes were up-regulated by TCDD. Of the 104 regulated genes, 69 (66.3%) were associated with an AHR- or ARNT-bound region within 100 kb of their TSS. Overall our study identified AHR/ARNT co-bound regions across the genome, revealed the importance but not absolute requirement for an AHRE in AHR/ARNT interactions with DNA, and identified a modified AHRE motif, thereby increasing our understanding of AHR/ARNT signaling pathway.

overall_design: Examination of genome-wide AHR and ARNT binding pattern in MCF-7

first: Raymond

last: Lo


title: Comparison analysis of B. japonicum mutant and wild type grown under different conditions

status: Public on Nov 15 2007

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

summary:
part of GSE8478: Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Bradyrhizobium japonicum
Glycine max

overall_design: Refer to individual Series


title: Expression profiling of Gastric Cancers

status: Public on Jul 25 2005

city: SG

first: Amit

last: Aggarwal

department: Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre of Singapore

summary:
124 gastric biopsies comprising of Normals, Intestinal Metaplasia, Chronic Gastritis and Carcinomas are profiled.

The ratio metric is given by (Biological sample / Universal Reference). The Biological Samples are labeled with Cy5 (Green) and the Pooled Normal Biopsies  RNA is always labeled with Cy3 (Red).
The arrays were scanned using a ScanArray 5000 scanner (Perkin-Elmer) and data extraction was done using Quantarray (GSI Lumonics). Subsequently, the data was imported into GeneSpring (Silicon Genetics) and intensity dependent LOWESS normalization was performed. The 7383 genes were filtered using an intensity in the reference channel (Cy3) of 300. This corresponded to 2 standard deviations above the mean for the background signal. Background singal was calculated using the empty wells/spots on the array and the average of 4 different positions on the slide were used.
Keywords: other

first: Alex

last: Boussioutas

first: David

last: Bowtell


title: Expression data from mouse gastric tumor models

status: Public on Jul 02 2009

city: Tsukuba

first: Hiraku

last: Itadani

address: Okubo 3

country: Japan

institute: Banyu Tsukuba Research Institute

summary:
Transgenic mice with prostaglandin E2 pathway in stomach develops gastric tumors. Simultaneous activation of both Wnt pathway and prostaglandin E2 pathway causes gastric adenocarcinoma. Combination of prostaglandin E2 pathway activation and suppression of BMP pathway leads to the development of gastric hamartomas.
We used microarrays to find the mechanism of these tumor development and to evaluate whether these mouse models recapitulate human gastric tumors.

overall_design: Glandular stomach from three C57BL/6 wild-type, five K19-Wnt1 transgenic, three K19-C2mE, five K19-Wnt1/C2mE, two K19-Nog, and three K19-Nog/C2mE transgenic mice were used. All mice were female at 18-65 weeks of age.

first: Hiroko

last: Oshima

first: Masanobu

first: Hidehito

last: Kotani


title: MicroRNA profiling of mouse bone marrow-derived mast cells during mucosal differentiation and IgE-mediated activation

status: Public on Jan 01 2011

city: Budapest

first: Viktor

last: Molnár

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
The aim of this study was to investigate microRNA expression pattern and its functional relevance on the commitment toward mucosal differentiation and on IgE-mediated activation of mast cells.
To identify microRNA genes the expression of which change during the differentiation and activation of murine primary mast cells in vitro, the putative committed progenitors (c-kit+ cells isolated on day 6 from differentiating cultures), immature mast cells (BMMC), mucosal-type mast cells (MMC), and IgE-activated mast cells were compared by Agilent microRNA array.

overall_design: RNA was isolated by miRNeasy (Qiagen) from:   1) c-kit+ cells, isolated from differentiating cultures (in the presence of IL3 and SCF) derived from the bone marrow using MACS column purification,   2) immature BMMCs obtained by cultivation of bone marrow cells in the presence of IL3 and SCF for 4 weeks,   3) mucosal-type mast cells by additional differentiation of immature BMMCs for 5 days by supplementation of IL9 and TGFbeta, and  4) activated mast cells by presensitization with anti-DNP IgE followed by IgE-crosslinking by DNP-antigen challenge for 2 hours.   Agilent microRNA microarray was run on these experimental groups. Four biological replicates were included in every experimental group.

first: Barbara

last: Érsek

first: Zoltán

last: Wiener

first: Krisztina

last: Hegyi

first: András

last: Falus


title: Expression data of wild type and DDR-1-KO mice TMJ-cartilage

status: Public on Jan 25 2012

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

institute: University Göttingen

summary: The discoidin domain receptor 1 (DDR-1) deficient mice exhibit a high incidence of osteoarthritis (OA) in the temporomandibular joint (TMJ) already at early age. Young DDR-1 knock-out mice show typical histological signs of OA, like, surface fissures, loss of proteoglycans, cluster formation of the chondrocytes, altered collagen types as well as atypical arrangement of the collagen fibrils. The isolated chondrocytes from the TMJ exhibit an osteoarthritic character with high amounts of Runt-related transcription factor 2 (runx-2) and collagen type I compared to low levels of SRY (sex determining region Y)-box 9 (sox-9) and aggrecan. Especially, the amount of discoidin domain receptor 2 (DDR2) is increased, which is key player of OA in this model. The gene expression as well as the proteins of the DDR-1-deficient chondrocytes from the TMJ could be influenced by a three dimensional matrix, combined with a knockdown of runx-2 or the stimulation with components of the extracellular matrix, for example nidogen-2. These manipulations caused the osteoarthritic chondrocytes of DDR-1-deficient mice to change their gene expression towards a signature of more physiological cartilage and will open new possibilities for future regenerative treatment options of temporomandibular disorders like OA of the TMJ.

overall_design:
We used microarrays to detect the differences in gene-expression of wild type and Discoidin Domain Receptor 1 Tyrosine Kinase (DDR-1)-KO mice TMJ-cartilage.
RNA was extracted directly of the madibular condyle cartilage

first: Boris

last: Schminke


title: Genome-wide CNVs within and between breeds

status: Public on Mar 31 2011

city: Seattle

first: Tom

last: Nicholas

state: WA

address: Foege Building S-250, Box 355065 3720 15th Ave NE

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: This study used two different NimbleGen platforms to identify canine CNVs.  The first identifies genome-wide CNVs while the second genotypes all known canine CNVs in a large panel of dogs from multiple breeds.

sample_organism:
Canis lupus
Canis lupus familiaris

overall_design: The genome-wide microarray used was designed by NimbleGen.  The genotyping chip was created by tiling all available probes to all known CNVs identified here and in previous studies.

first: T


title: Populus balsamifera developmental tissue series

status: Public on Jan 15 2009

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

institute: University of Toronto

summary: This study examined the transcriptome level attributes of a variety of Populus balsmifera tissues and organs. The tissues include seedlings grown under three light regimes, young leaves, mature leaves, roots, differentiating xylem, female catkins, and male catkins.

overall_design: In total 27 samples were analysed including 9 tissues with 3 biological replicates for each tissue. The samples were hybridised to the Affymetrix GeneChip Poplar Genome Array.

first: Olivia

last: Wilkins


title: Contribution of HSD17B12 for estradiol biosynthesis in human breast cancer

status: Public on Dec 31 2008

city: Sendai

first: Shuji

last: Nagasaki

state: Miyagi-ken

address: 2-1 Seiryo-machi, Aoba-ku

institute: Tohoku University Graduate School of Medicine

summary: 17beta-hydroxysteroid dehydrogenase type12 (HSD17B12) has been demonstrated to be involved in regulation of in situ biosynthesis of estradiol (E2). HSD17B12 expression was reported in breast carcinomas but its functions have remained unknown. Therefore, we examined the correlation between mRNA expression profiles determined by microarray analysis and tissue E2 concentrations obtained from 16 postmenopausal breast carcinoma cases in order to analyze an association of the enzyme expression with intratumoral E2 production. No significant correlations were detected between intratumoral HSD17B12expression and E2 concentration.These findings suggest that the presence of HSD17B12 in carcinoma cells contributes to a development of human breast carcinoma via a pathway other than in situ E2 biosynthesis.

overall_design:
Gene expression profiles of LCM samples in isolated carcinoma cells in 16 breast carcinoma cases were examined using microarray analysis. Breast carcinomas were rapidly embedded in Tissue-Tek optimal cutting temperature compound (Sakura Finetechnical Co. Ltd., Tokyo, Japan) and frozen sectioned at a thickness of 8micro m. Approximately 5000 cells were laser transferred from these isolated specimens. Isolated total RNA was applied microarray analysis. Sample preparation and processing were performed essentially as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetix, Inc., Santa Clara, CA). The labeled cRNA samples were hybridized to the complete human U133 GeneChip set (Affymetrix), including 22,215 and 22,577 genes. In our present study, we focused on mRNA expression of 156 genes which is annotated according to Gene Ontology database (steroid biosynthetic process, accession No.6694) as genes involved in steroid biosynthesis, and HSD17B12 unregistered in Gene Ontology accession No.6694.
  The gene expression profiles of the patients with breast cancer in which tissue estradiol was under detection limit (2 patients) was averaged, and applied to an analysis. 15 gene expression profiles of 16 breast carcinomas examined were arranged according to the levels of tissue estradiol concentration, and the clustering analysis between each gene was performed using GeneSpring GX 7.3.1 (Agilent Technologies, Waldbronn, Germany).

first: Takashi

last: Suzuki

first: Yasuhiro

last: Miki

first: Kunio

last: Kitada

first: Takanori

last: Ishida

first: Noriaki

last: Ohuchi

first: Hironobu

last: Sasano


title: Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules

status: Public on Jul 14 2007

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

summary:
Expression data from B. japonicum soybean root nodules including  a nodulation time-course experiment with soybean nodules harvested at 10, 13, 21 and 31 dpi and transcriptome of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma 54. Two reference data sets were established using B. japonicum cells grown in PSY medium under either aerobic or micro-aerobic conditions.
Keywords: genetic modification, time course, growth conditions

overall_design: B. japonicum transcriptome was determined under free-living and symbiotic conditions including mutant analysis (sigma 54) and nodulation time-course experiments

first: G

last: Pessi

first: C

last: Ahrens

first: H

first: A

last: Lindemann

first: F

last: Hauser

middle: M

last: Fischer

last: Hennecke


title: Modeling Host Responses to Understand Severe Human Virus Infections

status: Public on Feb 04 2015

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus