title: Array-based cross-species hybridization between genera of Rhabditidae (Nematoda)

status: Public on Aug 18 2010

city: Manhattan

first: Michael

last: Herman

state: KS

address: 266 Chalmers Hall

department: Division of Biology

institute: Kansas State University, Ecological Genomics Institute

summary: The objective of this work was to determine the effectiveness of cross-hybridization of gDNA from five native soil nematodes to an Affymetrix Caenorhabditis elegans tiling array. Cross-hybridization experiments using C. briggsae, for which genome information is available, allowed hybridisation intensities to be correlated with known sequence differences. Initial analysis of data by conventional array-based Comparative Genomic Hybridization (aCGH) techniques at the chip level lead to misleading results due to an artefact from the combination of scaling, bandwidth smoothing, and differential GC content in exon and intron regions. To circumvent this artefact, individual probes were instead normalized and centered by adjusting for probe-specific thermodynamic binding affinity. However, cross-hybridization of C. briggsae DNA revealed that the resultant probe intensities alone were still uncorrelated to sequence similarity below 90% identity. Below 90% similarity, all probes hybridize uniformly poorly, and above 90% similarity the hybridization differences are not large enough to detect over background, therefore, no 'threshold' ratio of hybridization intensity was successful at identifying probes with similarity to the heterologous genome. In light of the observations described here, we suggest that the criteria for replication and verification of gene expression profiles generated from cross-species microarray hybridizations be more stringent than typically adopted for con-specific hybridizations.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans
Oscheius sp. FVV-2
Oscheius tipulae
Mesorhabditis sp. MAH-2010
Acrobeloides sp. MAH-2010
Chiloplacus sp. MAH-2010

overall_design: Genomic DNA from Caenorhabditis elegans N2 (Bristol), C. elegans CB4856 (Hawaiian), C. briggsae AF16, Oscheius tipulae KS585, Oscheius FVV-2 KS555, Mesorhabditis sp. KS587, Acrobeloides sp. KS586, and Chiloplacus sp. KS584 were hybridized onto C. elegans Affymetrix tiling array (two replicate chips were performed for each species).

first: Brian

last: Darby

first: Kenneth

last: Jones

first: Dave

last: Wheeler


title: Pacific salmon gill samples

status: Public on Dec 31 2010

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

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

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Refer to individual Series


title: embryo hypodermal cells tiling array

status: Public on Aug 05 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

type: Expression profiling by genome tiling array

summary:
modENCODE_submission_662
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: DM8001 (engineered, target gene dpy-7 tagged by GFP); Tissue: hypodermis; Developmental Stage: Mixed stage of embryos 20dC; Genotype: raIs/[rol-6(SU1006)+Pdpy-7::GFP]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain DM8001 (engineered, target gene dpy-7 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue hypodermis

first: Bob

last: Waterston

first: David

last: Miller

first: Mark

last: Gerstein

first: Mike

last: Wilson

first: Ashish

last: Argiwal

first: Valerie

last: Reinke


title: Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers

status: Public on Jun 13 2011

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: Purpose:  Small bowel adenocarcinoma (SBA) is a rare cancer and consequently the number of clinical trials has been very limited due to the small numbers of patients. Chemotherapy regimens are currently rather arbitrarily chosen between either a colorectal (CRC) or a gastric cancer (GC) regimen. Chromosomal copy number aberrations are a hallmark of solid tumours and can be measured by array comparative genomic hybridization (aCGH).  The aim of the present study is to investigate whether genome-wide copy number aberrations of SBA are more similar to CRC or GC in order to support treatment of SBA according to either regimen.   Experimental Design:  A total of 85 GCs, CRCs and SBAs were selected from existing in house aCGH datasets based on array quality and clinical parameters. Differences and similarities in gains and losses of the three tumor types were analyzed using supervised and unsupervised analysis.   Results:  Hierarchical clustering revealed substantial overlap of chromosomal copy number profiles between SBA and CRC and less overlap between SBA and GC. Chromosome 13q13.2-q31.3 is primarily gained in SBA and CRC and the strongest feature discriminating SBA from GC. Further strong discriminating copy number characteristics are aberrations at chromosomes 1p36.3-p34.3, 4p15.3-q35.2, 9p24.3-p11.1 and 17p13.3-p13.2.   Conclusions:  SBA is more similar to CRC than to GC, based on genome-wide copy number aberrations. These data provide molecular support for treatment of SBA according to a CRC regimen.

overall_design: 29 gastric adenocarcinomas on 5K or 6K BAC arrays of which 2 samples are also done on 30K oligonucleotide arrays as control samples, 29 colorectal adenocarcinomas on 5K or 6K BAC arrays of which 2 samples are also done on 30K oligonucleotide arrays as control, 27 small bowel adenocarcinomas done on 30K oligonucleotide arrays of which 2 samples are also done on 5K BAC arrays as control.

first: Josien

middle: C

last: Haan

first: Tineke

middle: E

last: Buffart

middle: P

last: Eijk

middle: A

last: van de Wiel

first: Peter

last: Howdle

first: Chris

last: Mulder

first: Cornelis

middle: J

last: vandeVelde

first: Phil

last: Quirke

first: Iris

middle: D

last: Nagtegaal

first: Nicole

last: vanGrieken

first: Heike

last: Grabsch

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: embryo germline precursor cells tiling array

first: DCC

last: modENCODE

summary:
modENCODE_submission_661
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: SS747 (engineered, target gene pie-1 tagged by GFP); Tissue: germ line precursor (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: bnIs1 (pie-1p8::GFP::PGL-1+unc119); Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain SS747 (engineered, target gene pie-1 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue germ line precursor (embryonic)

first: Bob

last: Waterston

first: David

last: Miller

last: Gerstein

last: Wilson


title: embryo A-class motor neurons tiling array

summary:
modENCODE_submission_654
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC300 (engineered, target gene unc-119 tagged by GFP); Tissue: unc-4 neurons (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: wdIs5[unc-4::GFP; dpy-20(e1282)]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain NC300 (engineered, target gene unc-119 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue unc-4 neurons (embryonic)

first: Mark

first: Mike

first: Ashish

last: Argiwal

last: Reinke


title: pathogen_controlOP50_25dC_24hr_exposure_post-adulthood_N2_tiling_array

summary:
modENCODE_submission_491
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels.  Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: GrowthCondition E. coli (OP50); Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1; Strain N2; age 24

first: Valerie


title: pathogen_controlOP50_25dC_48hr_exposure_post-adulthood_N2_tiling_array

summary:
modENCODE_submission_490
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels.  Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: GrowthCondition E. coli (OP50); Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1; Strain N2; age 48


title: pathogen_Smarcescens_25dC_24hr_exposure_post-adulthood_N2_tiling_array

summary:
modENCODE_submission_489
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels.  Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: GrowthCondition S. marcescens (Db11); Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1; Strain N2; age 24


title: pathogen_Efaecalis_25dC_24hr_exposure_post-adulthood_N2_tiling_array

summary:
modENCODE_submission_487
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels.  Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: GrowthCondition E. faecalis (OG1RF); Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1; Strain N2; age 24


title: pathogen_Smarcescens_25dC_48hr_exposure_post-adulthood_N2_tiling_array

summary:
modENCODE_submission_488
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels.  Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: GrowthCondition S. marcescens (Db11); Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1; Strain N2; age 48


title: L1_20dC_0hrs_post-L1_N2_tiling_array

summary:
modENCODE_submission_484
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: larva mid-L1 25dC 4.0 hrs post-L1; Genotype: wild type; Sex: Unknown;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage larva mid-L1 25dC 4.0 hrs post-L1


title: gonad-only_young_adult_20dC_42hrs_post-L1_N2_tiling_array

summary:
modENCODE_submission_481
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: Gonad; Developmental Stage: Young Adult 20dC 42 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage Young Adult 20dC 42 hrs post-L1; Tissue Gonad


title: late_embryo_20dC_6-12hrs_post-fertilization_N2_tiling_array

summary:
modENCODE_submission_479
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: late embryo 20dC 4.5 hrs post-early embryo; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage late embryo 20dC 4.5 hrs post-early embryo


title: male_mid_L4_25dC_36hrs_post-L1_CB4689_tiling_array

summary:
modENCODE_submission_478
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: dpy28(y1);him-8(e1489); Developmental Stage: Male larva mid-L4 25dC 30 hrs post-L1; Genotype: dpy-28(y1);him-8(e1489); Sex: Male;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain dpy28(y1);him-8(e1489); Developmental Stage Male larva mid-L4 25dC 30 hrs post-L1


title: early_embryo_20dC_0-4hrs_post-fertilization_N2_tiling_array

summary:
modENCODE_submission_476
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: early embryo; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage early embryo


title: soma-only_mid-L4_25dC_36hrs_post-L1_JK1107_tiling_array

summary:
modENCODE_submission_485
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: JK1107; Developmental Stage: larva mid-L4 25dC 34.25 hrs post-L1; Genotype: glp-1(q224) III; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain JK1107; Developmental Stage larva mid-L4 25dC 34.25 hrs post-L1


title: pathogen_Pluminscens_25dC_24hr_exposure_post-adulthood_N2_tiling_array

summary:
modENCODE_submission_486
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels.  Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: GrowthCondition P. luminescens (Hb); Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1; Strain N2; age 24


title: mid-L4_25dC_36hrs_post-L1_N2_tiling_array

summary:
modENCODE_submission_473
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: larva mid-L4 25dC 34.25 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage larva mid-L4 25dC 34.25 hrs post-L1


title: embryo_GABA_motor_neurons_tiling_array

summary:
modENCODE_submission_468
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: CZ1200 (engineered, target gene unc-25 tagged by GFP); Tissue: GABA neurons (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: juIs76 II; lin-15(n765) X. Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain CZ1200 (engineered, target gene unc-25 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue GABA neurons (embryonic)

first: Frank


title: mid-L2_25dC_14hrs_post-L1_N2_tiling_array

summary:
modENCODE_submission_472
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: larva mid-L2 25dC 17.75 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage larva mid-L2 25dC 17.75 hrs post-L1


title: young_adult_25dC_42hrs_post-L1_N2_tiling_array

summary:
modENCODE_submission_475
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Young Adult (pre-gravid) 25dC 46 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage Young Adult (pre-gravid) 25dC 46 hrs post-L1


title: embryo dopaminergic neurons tiling array

summary:
modENCODE_submission_467
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: BY200 (engineered, target gene dat-1 tagged by GFP); Tissue: dopaminergic neurons (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: dat-1::GFP (pRN2003); Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain BY200 (engineered, target gene dat-1 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue dopaminergic neurons (embryonic)


title: embryo AVA neurons tiling array

summary:
modENCODE_submission_459
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NC1749 (engineered, target gene rig-3 tagged by GFP); Tissue: embryo-AVA; Developmental Stage: Mixed stage of embryos 20dC; Genotype: OH4326[otEx239(rig-3::GFP) pha-1(e2123)III] VH804[hdIs32(glr-1::DsRed2); Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain NC1749 (engineered, target gene rig-3 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue embryo-AVA


title: embryo intestine tiling array

summary:
modENCODE_submission_457
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: JR1130 (engineered, target gene elt-2 tagged by GFP); Tissue: intestinal cells; Developmental Stage: Mixed stage of embryos 20dC; Genotype: wIs84 [elt-2::GFP ]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain JR1130 (engineered, target gene elt-2 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue intestinal cells


title: embryo body wall muscle tiling array (v2)

summary:
modENCODE_submission_470
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: PD4251 (engineered, target gene myo-3 tagged by GFP); Tissue: body wall muscle; Developmental Stage: Mixed stage of embryos 20dC; Genotype: ccIs4251 [(myo-3::GFP-LacZ) I ; dpy-20(e1282) IV.]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain PD4251 (engineered, target gene myo-3 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue body wall muscle


title: mid-L2_polA_enriched_20dC_14hrs_post-L1_N2_tiling_array

summary:
modENCODE_submission_477
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: larva mid-L2 25dC 17.75 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Strain N2; Developmental Stage larva mid-L2 25dC 17.75 hrs post-L1


title: embryo all cells reference tiling array

summary:
modENCODE_submission_456
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (embryo); Developmental Stage: Mixed stage of embryos 20dC; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain N2; temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue reference (embryo)


title: embryo coelomocytes tiling array

summary:
modENCODE_submission_458
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: TV1112 (engineered, target gene unc-122 tagged by RFP); Tissue: coelomocytes; Developmental Stage: Mixed stage of embryos 20dC; Genotype: wyIs58 (opt-3::GFP::RAB-3; unc-122::RFP); Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain TV1112 (engineered, target gene unc-122 tagged by RFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue coelomocytes


title: embryo panneural tiling array

summary:
modENCODE_submission_455
This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: Transcript tiling array analysis

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: NW1229 (engineered, target gene F25B3.3 tagged by GFP); Tissue: panneural; Developmental Stage: Mixed stage of embryos 20dC; Genotype: evIs111 [F25B3.3::GFP]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Strain NW1229 (engineered, target gene F25B3.3 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue panneural


title: Salvelinus Microarray experiment: cross-specific transcriptome in hybrids

status: Public on Jul 01 2010

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

department: Biology

institute: Laval university

summary: The genetic mechanisms underlying hybridization are poorly understood despite their potentially important roles in speciation processes, adaptative evolution, and agronomical innovation. In this study, transcription profiles were compared among three populations of brook charr and their hybrids using microarrays to assess the influence of hybrid origin on modes of transcription regulation inheritance and on the mechanisms underlying growth. We found that twice as many transcripts were differently expressed between the domestic strain and the two wild populations (Rupert and Laval) than between wild ones, despite their deeper genetic distance. This could reflect the consequence of artificial selection during domestication. We detected that hybrids exhibited strikingly different patterns of mode of transcription regulation, being mostly additive (94%) for domestic × Rupert, and non-additive for Laval × domestic (45.7%) and Rupert × Laval hybrids (37.5%). Both heterosis and outbreeding depression for growth were observed among the crosses. Our results indicated that prevalence of dominance in transcription regulation seems related to growth heterosis, while prevalence of transgressive transcription regulation may be more related to outbreeding depression. Our study clearly shows, for the first time in vertebrates, that the consequences of hybridization on both the transcriptome level and the phenotype are highly dependent on the specific genetic architectures of crossed populations and therefore hardly predictable.

overall_design: Comparison between six crosses using a loop design: direct comparison of hybrids vs parental populations fishes for 8 families. Each individual was technically replicated on two bi-coloured distinct microarrays and dye-swapped.

first: Bérénice

last: Bougas

first: Sarah

last: Granier

first: Céline

last: Audet

first: Louis

last: Bernatchez


title: Amniotic fluid and necrotizing enterocolitis in preterm pigs

status: Public on Mar 01 2010

city: Frederiksberg

first: Jayda

last: Siggers

state: C

address: Roligehdsvej 30

department: Human Nutrition

country: Denmark

institute: University of Copenhagen

summary:
Preterm neonates are susceptible to gastrointestinal (GI) disorders such as necrotizing enterocolitis (NEC). Maternal milk, and especially colostrum, protects against NEC via growth promoting, immunomodulatory and antimicrobial factors. The fetal enteral diet, amniotic fluid (AF), contains similar bioactive components and we hypothesized that postnatal AF administration would reduce inflammatory responses and NEC in preterm neonates. Thirty preterm pigs (92% gestation) were delivered by caesarean section and fed total parental nutrition (TPN) for 48 h followed by enteral porcine colostrum (COLOS, n=7), infant formula (FORM, n=13) or formula + porcine AF (AF, n=10). Using a previously validated model of NEC in preterm pigs, we determined the structural, functional, microbiological and immunological responses to AF when administered prior to and after introduction of a suboptimal enteral formula diet.

Keywords: Healthy versus inflammed tissues in relation to necrotizing enterocolitis

overall_design: Pigs from each treatment group (COLOS, n=4; FORM, n=6; and AF, n=7) were randomly selected for microarray analysis of frozen distal small intestine samples. The FORM group was further divided into formula-fed healthy pigs (F-HEA, n=3) and formula-fed NEC pigs (F-NEC, n=3) in order to compare sick versus healthy formula fed pigs. Equal amounts of total distal small intestinal RNA from all pigs were pooled to make the reference sample. Samples and reference pool were labelled with Oyster 550 and 650, respectively. The in-house spotted porcine oligonucleotide microarray version 4 (POM4) is a low density microarray consisting of 384 different oligonucleotide probes representing more than 200 different immune related genes.

first: Mette

last: Boye

first: Per

middle: T

last: Sangild

first: Kerstin

last: Skovgaard

first: Richard


title: Lake Whitefish microarray experiment: dwarf vs normal ecotypes

status: Public on Mar 31 2010

first: Jérôme

last: St-Cyr

state: Québec

address: 1030, Avenue de la Médecine

department: Biologie

institute: Université Laval

summary: Despite the progress achieved in elucidating the ecological mechanisms of adaptive radiation, there has been little focus on documenting the extent of adaptive differentiation in physiological functions during this process. Moreover, a thorough understanding of the genomic basis underlying phenotypic adaptive divergence is still in its infancy. One important evolutionary process for which causal genetic mechanisms are largely unknown pertains to life-history trade-offs. We analysed patterns of gene transcription in liver tissue of sympatric dwarf and normal whitefish from two natural lakes, as well as from populations reared in controlled environments, using a 16 006-gene cDNA microarray in order to: (i) document the extent of physiological adaptive divergence between sympatric dwarf and normal species pairs, and (ii) explore the molecular mechanisms of differential life history trade-offs between growth and survival potentially involved in their adaptive divergence. In the two natural lakes, 6.45% of significantly transcribed genes showed regulation either in parallel fashion (2.39%) or in different directions (4.06%). Among genes showing parallelism in regulation patterns, we observed a higher proportion of over-expressed genes in dwarf relative to normal whitefish (70.6%). Patterns observed in controlled conditions were also generally congruent with those observed in natural populations. Dwarf whitefish consistently showed significant over-expression of genes potentially associated with survival through enhanced activity (energy metabolism, iron homeostasis, lipid metabolism, detoxification), whereas more genes associated with growth (protein synthesis, cell cycle, cell growth) were generally down-regulated in dwarf relative to normal whitefish. Overall, parallelism in patterns of gene transcription, as well as patterns of interindividual variation across controlled and natural environments, provide strong indirect evidence for the role of selection in the evolution of differential regulation of genes involving a vast array of potentially adaptive physiological processes between dwarf and normal whitefish. Our results also provide a first mechanistic, genomic basis for the observed trade-off in life-history traits distinguishing dwarf and normal whitefish species pairs, wherein enhanced survival via more active swimming, necessary for increased foraging and predator avoidance, engages energetic costs that translate into slower growth rate and reduced fecundity in dwarf relative to normal whitefish.

overall_design: Direct comparison of Dwarf vs Normal ecotypes. Samples comes from two natural environments (two different lakes) and one controled environement.

first: Jerome

first: Derôme

last: Nicolas


title: Gene expression profile of alg-3(tm1155);alg-4(ok1041) animals compared to wild type

status: Public on Feb 24 2010

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

country: USA

institute: University of Massachusetts Medical School

summary: Gametogenesis is thermosensitive in numerous metazoa ranging from worms to man.  In C. elegans a variety of germ-line nuage- (P-granule) -associated RNA-binding proteins including the Piwi-clade Argonaute, PRG-1, have been implicated in temperature-dependent fertility.  Here, we describe the role of two AGO-class paralogs, alg-3 (T22B3.2) and alg-4 (ZK757.3) in promoting male fertility at elevated temperatures.  A rescuing GFP::alg-3 transgene is localized in P-granules beginning at the late pachytene stage of male gametogenesis. alg-3/4 double mutants lack a subgroup of small RNAs, named 26G-RNAs, which target and appear to down-regulate numerous spermatogenesis-expressed mRNAs. These findings add to a growing number of AGO pathways required for temperature-dependent fertility in C. elegans and support a model in which AGOs and their small RNA co-factors function to promote robustness in gene-expression networks.

overall_design: Total RNA was extracted from C. elegans alg-3(tm1155);alg-4(ok1041) double-mutant and N2 wild type animals.

first: Colin

last: Conine


title: Azole Resistance Mechanism in Candida glabrata Oropharyngeal Isolates

status: Public on Jul 07 2010

city: Bethesda

first: Huei-Fung

last: Tsai

state: MD

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

summary: Microarray was used to analyze azole resistance of Candida glabrata oropharyngeal isolates from 7 hematopoietic stem cell transplant recipients receiving fluconazole prophylaxis. Transcriptional profiling of the sequential-paired clinical isolates by microarray revealed 19 genes upregulated in the majority of resistant isolates compared to their paired-susceptible isolates. All seven resistant isolates had greater than two fold upregulation of CgPDR1, a master transcriptional regulator of PDR network, and all 7 resistant isolates showed upregulation of known CgPDR1-target genes. The altered transcriptome can be explained in part by the observation that all 7 resistant isolates had acquired a single nonsynonymous mutation in their CgPDR1 ORF. Four mutations occurred in the regulatory domain (L280P, L344S, G348A, S391L) and one in the activation domain (G943S) while two mutations (N764I, R772I) occurred in an undefined region. Association of azole resistance and the CgPDR1 mutations was investigated in the same genetic background by introducing the CgPDR1 sequences from one sensitive and five resistant isolates into a laboratory azole-sensitive strain (cgpdr1) via integrative transformation. The cgpdr1 strain was restored to wild-type fluconazole susceptibility when transformed with CgPDR1 from the susceptible isolate but became resistant when transformed with CgPDR1 from the resistant isolates. However, despite the identical genetic background, upregulation of CgPDR1 and CgPDR1-target genes varied between the 5 transformants, independent of the domain locations in which the mutations occurred. In sum, gain-of-function mutations in CgPDR1 not only contributed to the clinical azole resistance but different mutations had varying degrees of impact on the CgPDR1-target genes.

overall_design: Seven pairs of oropharyngeal sequential isolates were chosen for study because each pair came from an individual hematopoietic stem cell transplant recipient receiving fluconazole. Seven groups consisted of 5 biological replicates in which a sensitive sample was paired with a resistant sample. Each group included 1 to 2 reciprocally labeled samples.


title: Conservation genomics of Atlantic salmon

status: Public on Nov 25 2009

city: West Vancouver

first: Wendy

last: Tymchuk

state: BC

address: 4160 Marine Drive

department: Science

institute: Fisheries & Oceans Canada

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

overall_design: Refer to individual Series


title: Hepatic Gene Expression in Rainbow Trout (Oncorhynchus mykiss) Exposed to Different Hydrocarbon Mixtures

status: Public on Dec 15 2009

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

country: Australia

institute: CSIRO

summary: Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i  dentified gene expression profiles resulting from hydrocarbon exposure.  These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures.  Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils.

overall_design: Two channel experiment; control versus exposed (samples were time matched).  3 biological replicates, three technical replicates for both exposed and control fish.  Samples were paired at random. One replicate per array

first: Mark

last: Lampi


title: Conservation genomics of Atlantic salmon (Year One)

summary: Due to difficulties inherent in designating conservation units for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species.  In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy.  In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression.  Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Uplands region.  There was also support for more refined population structure; there was some differentiation in both microsatellite and gene expression patterns between salmon from rivers in the two regions of the inner Bay of Fundy: Chignecto Bay and Minas Basin.  Consistent patterns apparent in the genetic and transcriptomic dataset indicate that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of unique genetic legacies between regions of the inner Bay of Fundy, and even between individual rivers within a region.  Consistency of the microarray data across two years helps to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation.

overall_design: Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada.  In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total).  This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides.  Therefore, in year one a total of 40 slides were used.  Because of the large number of strains assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).

first: Patrick

last: O'Reilly

first: Jesse

last: Bitman

first: Danielle

last: MacDonald

first: Patricia

middle: M

last: Schulte


title: A point mutation in the agr locus caused previously reported phenotypes in Staphylococcus aureus pneumonia

status: Public on Dec 31 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The role of Panton‐Valentine leukocidin (PVL) in Staphylococcus aureus pathogenesis is controversial. Here, we show that an unintended point mutation in the agr P2 promoter of S.aureus caused the phenotypes in gene regulation and murine pneumonia attributed to PVL by Labandeira‐Rey et al. (Science 315:1130‐3, 2007). In agreement with previous studies that failed to detect similar effects of PVL using community‐associated methicillin‐resistant S. aureus strains, we found no significant impact of PVL on gene expression or pathogenesis after we repaired the mutation. These findings further contribute to the idea that PVL does not have a major impact on S. aureus pathogenesis and resolve debate about its role in murine infection models. Moreover, our results demonstrate that a single nucleotide polymorphism in an intergenic region can dramatically impact bacterial physiology and virulence. Finally, our work emphasizes the need to frequently evaluate the integrity of the S. aureus agr locus.

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: 7 hour growth, with 5 different strain comparisons

first: Amer

last: Villaruz

first: Juliane

middle: B

last: Wardenburg

first: Burhan

last: Khan

first: Adeline

middle: R

last: Whitney

first: Daniel

first: Donald

last: Gardner

first: Frank

last: DeLeo

first: Michael

last: Otto


title: Conservation genomics of Atlantic salmon (Year Two)

overall_design: Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada.  In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total).  This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides.  Therefore, in year one a total of 40 slides were used.  Because of the large number of populations assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).


title: Replication Timing Reveal An Epigenetic Commitment To Differentiation Prior To Germ Layer Specification (WG_CGH, RT)

city: Tallahassee

first: David

middle: M.

last: Gilbert

state: Florida

address: 319 Stadium Drive

institute: Florida State University

summary: Differentiation of mouse embryonic stem cells (mESCs) is accompanied by global changes in replication timing. To elucidate this reorganization process and explore its potential impact on mouse development, we constructed genome-wide replication-timing profiles of 15 independent mouse cell types representing nine different stages of early mouse development, including all three germ layers. Overall, 45% of the genome exhibits significant changes in replication timing between cell types, indicating that replication-timing regulation is more extensive than previously estimated from neural differentiation. Intriguingly, analysis of early and late epiblast cell culture models suggest that the earliest changes in development include extensive lineage-independent early-to-late replication switches that are completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors (Oct4/Nanog/Sox2). These changes were stable in all subsequent lineages and involved a class of irreversibly silenced genes that were re-positioned closer to the nuclear periphery. Lineage-specific, late-to-early and early-to-late replication switches followed, which created cell-type specific replication profiles. Importantly, partially reprogrammed induced pluripotent stem cells (piPSCs) failed to restore ESC-specific replication timing and transcription programs particularly within regions of lineage-independent early-to-late replication changes, as well as the inactive X-chromosome. We conclude that lineage-independent, early-to-late replication-timing switches that occur in the post-implantation epiblast embody an epigenetic commitment to differentiation prior to germ layer specification.

overall_design: 22 cell lines, with a total of 36 individual replicates (i.e. 14 in duplicates, 8 in single replicates)

first: Ichiro

last: Hiratani

first: Tyrone

last: Ryba


title: Genome-Wide Dynamics of Replication Timing Revealed by In Vitro Models of Mouse Embryogenesis (Expression)

summary: Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of lineage-independent early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors (Oct4/Nanog/Sox2) and coinciding with the emergence of compact chromatin near the nuclear periphery. These changes were conserved in all subsequent lineages and involved a group of irreversibly down-regulated genes, at least some of which were repositioned closer to the nuclear periphery. Importantly, many genomic regions of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication timing and transcription programs. These regions were enriched for lineage-independent early-to-late changes, which in female cells included the inactive X-chromosome. Taken together, we demonstrate that replication-timing changes are extensive during development. Moreover, a distinct set of lineage-independent, early-to-late changes completed in and stably maintained after the post-implantation epiblast stage is difficult to reprogram and therefore coincides with an epigenetic commitment to differentiation prior to germ layer specification.

overall_design: 8 cell lines, with a total of 14 individual replicates (i.e. 6 in duplicates, 2 in single replicates)


title: Gene expression profile of csr-1(tm892) animals compared to wild type

status: Public on Oct 02 2009

first: Julie

last: Claycomb

address: 373 Plantation Street Biotech2 Suite 219

summary: RNAi-related pathways regulate diverse processes, from developmental timing to transposon silencing. Here, we show that in C. elegans the Argonaute CSR-1, the RNA-dependent RNA polymerase EGO-1, the Dicer-related helicase DRH-3, and the Tudor-domain protein EKL-1 localize to chromosomes and are required for proper chromosome segregation. In the absence of these factors chromosomes fail to align at the metaphase plate and kinetochores do not orient to opposing spindle poles. Surprisingly, the CSR-1 interacting small RNAs (22G-RNAs) are antisense to thousands of germline-expressed protein-coding genes. Nematodes assemble holocentric chromosomes in which continuous kinetochores must span the expressed domains of the genome. We show that CSR-1 interacts with chromatin at target loci, but does not down-regulate target mRNA or protein levels.  Instead, our findings support a model in which CSR-1 complexes target protein-coding domains to promote their proper organization within the holocentric chromosomes of C. elegans.

overall_design: Total RNA was extracted from C. elegnas csr-1(tm892) and wild type animals

first: Craig

last: Mello


title: The heat shock response of killifish (Fundulus heteroclitus): candidate gene and heterologous microarray approaches.

status: Public on Oct 30 2009

first: Wendy

last: Tymchuk

summary:
Subspecies of the Atlantic killifish, Fundulus heteroclitus, differ in their maximum thermal tolerance.  To determine whether there is a link between the heat shock response (HSR) and maximum thermal tolerance, we exposed 20ºC acclimated killifish from these subspecies to a 2hr heat shock at 34ºC and examined gene expression during heat shock and recovery using real time quantitative PCR and a heterologous cDNA microarray designed for salmonid fishes.

Keywords: Expression profiling by array

overall_design: Microarray analyses were performed on four individual fish per subspecies of killifish (northern and southern) prior to heat shock (control) and after 60 minutes of heat shock, hybridized (one slide per individual) against a common reference RNA pool composed of an equal amount of RNA from all samples in the analysis.

first: Timothy

last: Healy

first: Edward

last: Osborne


title: The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

status: Public on Sep 11 2009

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

summary: Microbiota-induced cytokine responses participate in gut homeostasis, but the cytokine balance at steady-state and the role of individual bacterial species in setting the balance remain elusive. Using gnotobiotic mouse models, we provide a systematic analysis of the role of microbiota in the induction of cytokine responses in the normal intestine. Colonization by a whole mouse microbiota orchestrated a broad spectrum of pro-inflammatory (Th1, Th17) and regulatory T cell responses. Unexpectedly, most tested complex microbiota and individual bacteria failed to efficiently stimulate intestinal cytokine responses. A potent cytokine-inducing function was however associated with non-culturable host-specific species, the prototype of which was the Clostridia-related Segmented Filamentous Bacterium, and this bacterial species recapitulated the coordinated maturation of T cell responses induced by the whole mouse microbiota. Our study demonstrates the non-redundant role of microbiota members in the regulation of gut immune homeostasis.

overall_design:
Germfree (GF) female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of fresh anaerobic cultures of fecal homogenate from SFB mono-associated mice, fresh feces from Cv mice (Cvd) or from a healthy human donor (Hum). All mice were sacrificed on d8, 20 and 60 post-colonization in parallel to age-matched Cv and GF controls.
RNA was extracted from ileal tissue, and processed to biotin-labelled cRNA, and then hybridized to the NuGO array (mouse) NuGO_Mm1a520177. Microarray analysis compared gene expression in ileum tissue of all the treatment groups GF, Cv, Cvd, Hum and SFB (N=3 per treatment group per time-point).
Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.

first: Valérie

last: Gaboriau-Routhiau

first: Sabine

last: Rakotobe

first: Emelyne

last: Lécuyer

first: Imke

last: Mulder

first: Annaïg

last: Lan

first: Chantal

last: Bridonneau

first: Violaine

last: Rochet

first: Annamaria

last: Pisi

first: Marianne

last: De Paepe

first: Giovanni

last: Brandi

first: Gérard

last: Eberl

first: Johannes

last: Snel

first: Nadine

last: Cerf-Bensussan


title: Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil

first: Sharon

last: Hook

summary: Time is often not characterized as a variable in ecotoxicogenomic studies.  In this study, the temporal kinetics in gene expression were determined during exposure to crude oil and a subsequent recovery period. Juvenile rainbow trout, Oncorhynchus mykiss, were exposed for 96 hours to the water accomodated fractions of 0.4, 2 or 10 mg l-1 crude oil loadings.  Following 96 h of exposure, fish were transferred to recovery tanks for 96 h.  Gill and liver samples were collected after 24 and 96 h of exposure, and after 96 h of recovery for RNA extraction and microarray analysis.  Fluorescently labeled cDNA was hybridized against matched controls, using salmonid cDNA arrays.  Each exposure scenario generated unique patterns of altered gene expression.  More genes responded to crude oil in the gill than in liver.  In the gill, 1137 genes had altered expression at 24 hours, 2003 genes had altered expression levels at 96 h of exposure, yet by 96 h of recovery, no genes were significant  ly altered in expression.  The Gene Ontology terms associated with gill-responsive genes implicated membrane narcosis, a toxic mechanism for crude oil.  By contrast, in the liver at 10 mg l-1, only five genes were changed at 24 h, yet 192 genes had altered expression after 96 h recovery.  At 2 mg l-1 in the liver, many genes had altered regulation at all three timepoints.  The 0.4 mg l-1 loading also showed 289 genes upregulated at 24 h after exposure.  The Gene Ontology terms associated with altered expression in the liver suggested that the processes of protein synthesis, xenobiotic metabolism, and oxidoreductase activity were altered.  The concentration-responsive expression profile of cytochrome P450 1A, a biomarker for oil exposure, did not predict the majority of gene expression profiles in any tissue or dose, since direct relationships with dose were not observed for most genes.  While the genes and their associated functions agree with known modes of toxic action for crude oil, the gene lists obtained do not agree with our previously published work, presumably due to array analysis procedures.  These results demonstrate that changes in gene expression with time and dose should be characterized in controlled laboratory settings before responses from field collected organisms are interpreted, and that processes for analyzing microarray data need to be developed such that standardized gene lists are developed, or that analysis is gene list independent  before arrays are as a monitoring tool.

overall_design: Two channel experiment; Control versus exposed (samples were time matched).  3 biological replicates, two technical replicates for both exposed and control fish.  Exposed and cotrol samples were paired so that fish had been sacrificed at the same time, but otherwise, samples were paired at random. One replicate per array

first: Mark

last: Lampi


title: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the brain transcriptome

status: Public on Jul 03 2009

first: Wendy

last: Tymchuk

summary: Domestication has produced faster-growing strains of animals for use in agriculture, but selection has been applied with little knowledge of the underlying genetic changes that arose throughout the process.  Mammals and birds have been domesticated for thousands of years whereas fish have been domesticated only recently; therefore, wild progenitor strains remain for comparison. Rainbow trout (Oncorhynchus mykiss) have undergone intensive selection and domesticated strains grow more rapidly than extant wild strains. To assess physiological pathways altered by domestication, whole-genome mRNA expression was measured in brain, muscle and liver of size-matched domestic and wild trout using a 16K (cGRASP) salmonid microarray.  A large number of genes differed between strains, ranging from 3% of genes in brain to 9% in muscle.  Domestic fish had more down-regulated genes in the brain relative to wild fish, whereas more genes were up-regulated in domestic liver and muscle.  Relative to wild fish, there was a down-regulation of cell division and an up-regulation of structural genes in the brain of domestic fish.  In liver from domestic fish, there was an up-regulation of genes related to transport with a down-regulation of lipid binding.  Analysis of the functional categories for muscle indicated that most pathways, including pathways related to metabolism and catabolism, were up-regulated in domestic fish.  Comparison of these results to other genomic studies on transgenic, domestic and wild salmonids suggests that similar physiological pathways are altered systemically to support faster rates of growth, regardless of the underlying genetic alteration that has caused the altered growth.

overall_design: Microarray analyses were performed on nine individual fish per group of wild type and domestic rainbow trout hybridized (one slide per individual) against a common wild-type RNA pool.

first: Dionne

last: Sakhrani

first: Robert

middle: H

last: Devlin


title: Normal and shortened photoperiods in liver, ovary, and pituitarty

summary: This study compared changes in gene expression in an oviparous female fish, the rainbow trout (Oncorhynchus mykiss), under two different photoperiod treatments, a natural photoperiod (NP) and a shortened photoperiod (SP; 60% of NP). Gene expression in the liver, ovary and pituitary were measured at one-four week intervals over the course of the reproductive cycle in each treatment. Total RNA was harvested from these tissues, cDNA prepared, and hybridized on the 16K GRASP cDNA microarray. Established indices of reproductive development (ovulation, gonadosomatic index, mean oocyte diameter, and plasma hormone levels) were also measured. The SP fish failed to ovulate and their reproductive trajectory was clearly different from the NP group, which ovulated as expected. A comparative examination of the reproductive indices in both groups shows that ovarian development initiated in the SP group and proceeded relatively normally for about two-thirds of the reproductive cycle. Plasma follicle-stimulating hormone levels were higher in the SP fish from the cycle onset. This may have dampened E2 synthesis, preventing the positive feedback signal on the pituitary for the normal, rapid increase in luteinizing hormone late in the cycle.  Transcriptome analysis used an unsupervised k-means hierarchical clustering method to visualize changes in gene expression in the different organs from the NP fish that were assumed to represent the normal pattern leading to successful ovary development. In the NP, fish four, five, and six unique gene clusters were identified in the liver, ovary, and pituitary, respectively. These clusters ranged in size from 22 genes in one of the pituitary clusters to 302 genes in the liver.  These clusters were then applied to the SP fish to determine if and how they were altered.  The expression patterns of most genes in the SP fish were notably altered from the first time point. A SP in female rainbow trout initiated a rapid change in tr  anscript levels within the liver, ovary, and pituitary, leading to ovarian failure and apparently disrupting normal endocrine signaling between the pituitary and ovary.

overall_design:
Normal photoperiod: Two channel experiment; T=0 versus T= up to 330 days post spawn.  3 biological replicates for the later time points paired with a pooled laboratory standard t=0 control. One replicate per array
Shortened photoperiod: Two channel experiment; T=0 versus T= up to 216 days post spawn.  3 biological replicates for the later time points paired with a pooled laboratory standard t=0 control. One replicate per array

first: Irvin

last: Schultz

first: James

last: Nagler


title: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the liver transcriptome

overall_design: Microarray analyses were performed on seven individual fish per group of wild type and domestic rainbow trout hybridized (one slide per individual) against a common wild-type RNA pool.


title: Rho directs widespread termination of intragenic and stable RNA transcription

status: Public on Jun 23 2009

city: Madison

first: Jason

middle: Matthew

last: Peters

state: WI

address: 1550 Linden Drive

department: Biochemistry

institute: UW-Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP).  Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM).  We found ~200 Rho-terminated loci that were divided evenly into two classes: intergenic (at the ends of genes) and intragenic (within genes).  The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis.  The intragenic class of terminators included a novel set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene.  These Rho-terminated antisense transcripts point to a novel role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta or Beta' subunit) in cells treated with 20ug/ml bicyclomycin or untreated cells.  Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 4 datasets.

first: Rachel

last: Mooney

first: Pei

middle: F

last: Kuan

first: Jennifer

middle: L

last: Rowland

first: Sunduz

last: Keles

last: Landick


title: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the muscle transcriptome

overall_design: Microarray analyses were performed on six individual fish per group of wild type and domestic rainbow trout hybridized (one slide per individual) against a common wild-type RNA pool.


title: Expression comparison between C. elegans drh-3(ne4253) and wild-type

status: Public on Oct 01 2009

first: Craig

last: Mello

type: Non-coding RNA profiling by genome tiling array

summary: Endogenous small RNAs (endo-siRNAs) interact with Argonaute (AGO) proteins to mediate sequence-specific regulation of diverse biological processes. Here, we combine deep-sequencing and genetic approaches to explore the biogenesis and function of endo-siRNAs in C. elegans. We describe conditional alleles of the dicer-related helicase, drh-3, that abrogate both RNA interference and the biogenesis of endo-siRNAs, called 22G-RNAs. DRH-3 is a core component of RNA-dependent RNA polymerase (RdRP) complexes essential for several distinct 22G-RNA systems. We show that in the germ-line, one system is dependent on worm-specific AGOs, including WAGO-1, which localizes to germ-line nuage structures called P-granules. WAGO-1  silences certain genes, transposons, pseudogenes and cryptic loci. Finally, we demonstrate that components of the nonsense-mediated decay pathway function in at least one WAGO-mediated surveillance pathway. These findings broaden our understanding of the biogenesis and diversity of 22G-RNAs and suggest novel regulatory functions for small RNAs.

overall_design: Total RNA was extracted from C. elegans drh-3(ne4253) and wild type animals

first: Weifeng

last: Gu


title: Domestication causes large-scale effects on gene expression in rainbow trout

overall_design: Refer to individual Series


title: Domestication and growth hormone transgenesis cause similar changes in gene expression profiles in coho salmon

status: Public on Mar 09 2009

summary:
By directly comparing gene expression in wild type, domestic, and GH transgenic strains of salmon, we have found that domestication and GH transgenesis are modifying similar genetic pathways. Genes in many different physiological pathways show modified expression in domestic and GH transgenic strains relative to wild-type, but effects are strongly correlated. Genes specifically involved in growth regulation (IGF-I, GHR, IGF-II, THR) are also concordantly regulated in domestic and transgenic fish, and both strains show elevated levels of circulating IGF-I. Muscle expression of GH in nontransgenic strains was found to be elevated in domesticated fish relative to wild type, providing a possible mechanism for growth enhancement. These data have implications for genetic improvement of existing domesticated species as well as regulation of emerging transgenic strains.

Keywords: Expression profiling by array

overall_design: Microarray analyses were performed on four or five individual fish per group of wild type, domesticated, and GH transgenic salmon hybridized (one slide per individual) against a common wild-type RNA pool.

first: Matthew

last: Rise

first: Benjamin

last: Goh


title: Identification of pathways and transcription factors relevant to gut inflammation and anti-inflammatory probiotics

status: Public on Jul 29 2009

first: Caroline

last: Reiff

address: Greenburn Road

department: Gut Health

institute: Rowett Institute of Nutrition and Health

summary: Using Affymetrix data analysis, important signalling pathways and transcription factors relevant to gut inflammation and anti-inflammatory action of probiotics were identified using the clinically validated probiotic VSL#3 and the IL10-knockout mouse, an animal model for inflammatory bowel disease. VSL#3 increased expression of genes involved in PPAR signalling and metabolism of xenobiotics and decreased expression of genes involved in immune response/inflammatory response.

overall_design:
IL10-knockout (IL10-KO) and wildtype (WT) mice housed under specific pathogen-free (SPF) conditions were sacrificed at 24 weeks by cervical dislocation.

The study is comprised of two independent Microarray experiments.

Microarray experiment1 compares gene expression of IL10-KO and WT colon tissue. For microarray analysis RNA was extracted from the colon tissue of each mouse (WT n=7, IL10-KO n=6).

Microarray experiment2 compares gene expression of WT and IL10-KO mice fed with either placebo or probiotic VSL#3. IL10-KO and WT mice were fed with placebo or 1.3x109 cfu of lyophilized VSL#3 bacteria post weaning for 21 weeks. For microarray analysis RNA was extracted from the caecum tissue of each mouse (WT Placebo n=6, IL10-KO Placebo n=6, IL10-KO VSL#3 n=6).

first: Elaina

last: Collie-Duguid

first: Denise

last: Kelly


title: Response of ethanologenic E coli strains LY180 and EMFR9 to furfural

status: Public on Aug 25 2009

city: Gainesville

first: Peter

middle: Christopher

last: Turner

state: FL

address: Bldg 981, Museum Road

department: Micro and Cell Science

institute: University of Florida

summary:
The data explore the transcriptional response of strain LY180 and the furfural-resistant derivative EMFR9 to 0.5 g/L furfural
LY180 and EMFR9 and differences in their expression profiles are described in Miller, E. N., L. R. Jarboe, L. P. Yomano, S. W. York, K. T. Shanmugam, and L. O. Ingram. 2009. Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli. Appl Environ Microbiol 75:4315-23.  The response of LY180 to furfural is described in Miller, E. N., L. R. Jarboe, P. C. Turner, P. Pharkya, L. P. Yomano, S. W. York, D. Nunn, K. T. Shanmugam, and L. O. Ingram. 2009. Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol., 2009.

overall_design:
Total RNA was prepared from cultures of LY180 and EMFR9 immediately before and 15 min after addition of furfural to 0.5 g/L.  The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.

Data from replicate 1 (OID 8641) and replicate 2 (OID 14117) was analyzed independently.

first: Elliot

middle: N

last: Miller

first: Laura

last: Jarboe

first: Lonnie

middle: O

last: Ingram


title: Transcriptional factor FOXO3a controls the persistance of memory CD4+ T cells in HIV infection

status: Public on Mar 04 2009

city: Cleveland

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary:
Persistence of memory CD4+ T cells in ECs was coupled with the inactivation of FOXO3a transcriptional activities, which we have previously identified as a critical regulator of TCM survival. Indeed, expression levels of transcriptional targets of FOXO3a, endowed with pro-apoptotic and anti-proliferative functions, were lower in TCM and TEM from ECs as compared to ST individuals. Silencing the transcriptionally active form of FOXO3a by siRNA rescued TCM and TEM of STs from Fas-mediated apoptosis. Moreover the expression of FOXO3a dominant negative form (FOXO3a Nt) rescued the long-term survival of TCM from STs as these cells persisted as long as those derived from ECs. Overall, these studies indicate that FOXO3a activation is an important mediator of the shortened survival and heighteined turnover of TCM and TEM in chronic HIV infection. Targeting this pathway may provide a strategy to preserve memory T cell numbers in HIV infection.
Keywords: comparative gene profile, cell-type comparison

overall_design: Isolation of CD4+T cell sub-populations. Peripheral blood mononuclear cells (PBMCs) from healthy adult individuals were isolated by Ficoll-HyPaque (Pharmacia) density gradient. We first enriched for CD4+ T cells using negative immunomagnetic beads selection (Automacs, Myltenii), cells were then labeled with anti-CD4-APCcy7, anti-CD45RA-ECD, anti-CD27-FITC and anti-CCR7-PEcy7 and sorted into Naive cells described as CD4+, CD45RA+, CD27+ and CCR7+, Central Memory cells (TCM) described as CD4+, CD45RA-, CD27+ and CCR7+ cells and Effector Memory cells (TEM) described as CD4+, CD45RA-, CD27- and CCR7- cells. Sorting was performed using a BDAria (BD Pharmingen). Purity of the TCM and TEM sub-populations was ranging from 96 to 99%. All procedures were done at 4 degrees C to avoid any changes in cell phenotype or gene expression. Sample RNA was extracted using an RNA extraction kit (Quiagen), then amplified using the MessageAmp RNA kit (Ambion) as per the manufacturer’s instructions. The amplified RNA (aRNA) was then verified for quality and quantity using the Agilent Bioanalyser and measuring the OD. Universal human RNA (Stratagene) was also prepared in the same way. Sample probes were prepared by direct labelling with 3 µg of the aRNA Cy-5 (R values) fluorescent dye while the universal RNA probes were prepared by direct labelling of universal aRNA with Cy-3 (G values). All patient samples were hybridized against amplified universal RNA at 37 ºC for 18h on a custom human Immune array. Detailed information on the labeling and hybridization procedures can be obtained at the Microarray Centre web page (University Health Network).

first: Julien

last: van Grevenyngh

first: Francesco

last: Procopio

first: Zhong

last: He

first: Catherine

last: Riou

first: Yuwei

last: Zhang

first: Sylvain

last: Gimmig

first: Genevieve

last: Boucher

first: Yu

last: Shi

first: Bader

last: Yassine-Diab

first: Nicolas

last: Chomont

first: Elias

last: Said

first: Lydie

last: Trautmann

first: Mohamed

last: El Far

first: Mohamed-Rachid

last: Boullassel

first: Jean-Pierre

last: Routy

middle: K

last: Haddad

first: Rafick-Pierre

last: Sekaly


title: Phase I Clinical Trial of ES-285

status: Public on Apr 01 2009

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

summary:
Phase I Safety, Pharmacokinetic and Pharmacogenomic Trial of ES-285, a Novel Marine Cytotoxic Agent Administered as an Infusion over 24 h Every 21 Days in Patients with Solid Tumors

Purpose: A dose-escalation, phase I study evaluated the safety, pharmacokinetics,
pharmacogenomics and efficacy of ES-285, a novel agent isolated from a marine mollusc, in adult cancer patients.
Experimental design: Patients received a 24-hour i.v. infusion of ES-285 once every 3 weeks until disease progression or unacceptable toxicity. The starting dose was 4mg/m2. Dose escalation proceeded according to the worst toxicity observed in the previous cohort.
Results: 28 patients were treated with 72 courses of ES-285 across 8 dose levels. No doselimiting toxicities (DLTs) were seen between 4mg/m2 and 128mg/m2. Two out of 4 patients treated at 256mg/m2 had dose-limiting reversible grade 3 transaminitis; one patient at 256mg/m2 also had transient grade 3 central neurotoxicity. One of 3 patients subsequently treated at 200mg/m2 died following drug-related central neurotoxicity. Pharmacokinetic studies indicated dose-proportionality with high volume of distribution (median Vss at 256mg/m2 was 2389L, range 1615-4051L) and long elimination half life (median t1/2 at 256mg/m2 was 29h, range 21-32h). The 3 patients with DLT had the highest drug exposure. Pharmacogenomic studies of paired surrogate tissue samples identified changes in gene expression following treatment that correlated with increasing dose. Pre-treatment 59- and 49-gene sets were identified in blood and skin respectively, that may predict DLT. Disease stabilisation for 6 to 18 weeks was recorded in 9 patients.
Conclusion: Using this schedule, 128 mg/m2 was considered safe and feasible. At this dose, pharmacologically relevant concentrations of drug were safely achieved with pharmacogenomic studies indicating changes in the expression of genes of potential biological relevance.

Keywords: dose response

overall_design: 104 samples  - Total RNA extracted from blood samples and skin biopsies, then amplified, labelled and hybridised to 22k cDNA gene expression microarrays. All samples were compared to Stratagene Human Reference RNA.

first: Richard

last: Baird


title: Molecular pharmacology of phosphatidylinositol 3-kinase inhibition in human glioma

status: Public on Apr 21 2009

summary:
Gliomas are primary brain tumors with poor prognosis that
exhibit frequent abnormalities in phosphatidylinositol 3-kinase
(PI3 kinase) signaling. We investigated the molecular mechanism
of action of the isoform-selective class I PI3 kinase and mTOR
inhibitor PI-103 in human glioma cells. The potent inhibitory
effects of PI-103 on the PI3 kinase pathway were quantified.
PI-103 and the mTOR inhibitor rapamycin both inhibited ribosomal
protein S6 phosphorylation but there were clear differences
in the response of upstream components of the PI3 kinase pathway,
such as phosphorylation of Thr308-AKT, that were inhibited by
PI-103 but not rapamycin. Gene expression profiling identified
altered expression of genes encoding regulators of the cell cycle
and cholesterol metabolism, and genes modulated by insulin or
IGF1 signaling, rapamycin treatment or nutrient starvation. PI-103
decreased expression of positive regulators of G1/S phase progression
and increased expression of the negative cell cycle regulator
p27kip1. A reversible PI-103-mediated G1 cell cycle arrest occurred
without significant apoptosis, consistent with the altered gene
expression detected. PI-103 induced vacuolation and processing
of LC-3i to LC-3ii, which are features of an autophagic response.
In contrast to PI-103, LY294002 and PI-387 induced apoptosis,
indicative of likely off-target effects. PI-103 interacted synergistically
or additively with cytotoxic agents used in the treatment of
glioma, namely vincristine, BCNU and temozolomide. Compared
to individual treatments, the combination of PI-103 with temozolomide
significantly improved the response of U87MG human
glioma xenografts. Our results support the therapeutic potential
for PI3 kinase inhibitors with a PI-103-like profile as therapeutic
agents for the treatment of glioma.

Keywords: Key words: PI-103, glioma, PI3 kinase, mTOR, cell cycle, cytostasis

overall_design: 38 samples  - All treated samples were compared to untreated parental cells

first: Sandrine

last: Guillard

first: Paul

last: Clarke

first: Robert

last: te Poele

first: Zahra

last: Mohri

first: Lynn

last: Bjerke

first: Melanie

last: Valenti

first: Florence

last: Raynaud

first: Suzanne

last: Eccles

last: Workman


title: Brain eQTL analysis of lake whitefish species-pairs (Coregonus sp.)

status: Public on Sep 01 2008

city: Quebec

first: Andrew

last: Whiteley

state: Quebec

address: Pavillon Marchand

institute: Universite Laval

summary:
We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.).  Our goals were to elucidate the genomic distribution and sex-specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex-bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between sexes.  Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed.  We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development based on co-localization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations.  88% of eQTL-phenotypic QTL co-localization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs.  Hotspots co-localized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc finger protein in one case, control gene expression directly related to adaptive phenotypic divergence.  We observed little evidence of co-localization of brain eQTL with behavioral QTL, which provides insight on the genes identified by behavioral QTL studies.  These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological differences appear to play a key role in this divergence.

Keywords: eQTL mapping, gene expression, linkage mapping, adaptive radiation, Coregonus, microarrays

overall_design: The objective of this study was to elucidate the genomic distribution and sex-specificity of brain eQTL in dwarf and normal lake whitefish. Dissected brain tissue (250-350 mg) was sampled for 55 individuals from a hybrid x dwarf backcross mapping family. We used a loop design (YANG and SPEED 2002; CHURCHILL 2002) to maximize the number of sampled meioses. Each of 55 samples was technically replicated on two distinct slides, while performing dye swapping (Cy3 and Alexa) to estimate the dye intensity variation bias. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (KERR et al. 2000).  We used a previously generated linkage map based on the same backcross individuals for which gene expression was measured.  eQTL mapping was performed with QTL Cartographer.


title: Genetic alteration in recurrent melanoma - part 2

status: Public on Jul 22 2008

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary:
Studying a unique case of metastatic melanoma, we observed that cell lines derived from metachronous metastases arising over a decade retained a central core of genetic stability in spite of divergent phenotypes. In the present study we expanded our previous observations comparing these autologous cell lines of clonal derivation with heterologous ones and correlated array Comparative Genomic Hybridization with gene expression profiling to determine their relative contribution to the dynamics of disease progression. aCGH and gene expression profiling were performed on autologous cell lines and heterologous melanoma cell lines originated from other patients. A striking correlation existed between total extent of genetic imbalances, global transcriptional patterns and cellular phenotypes; they did not follow a strict temporal progression but stemmed independently at various time points from a central core of genetic stability best explained according to the cancer stem cell hypothesis; although their contribution was intertwined, genomic imbalances detectable by aCGH contributed only 25% of the transcriptional traits determining autologous tumors distinctiveness. Our study provides important insights about the dynamics of cancer progression and supports the development of targeted anti-cancer therapies against stable genetic factors determining the individuality of each patient’s disease that are maintained throughout the end stage of disease.
Keywords: genetic modification design

overall_design: We report the analysis of gene expression profiling of melanoma cell lines obtained from metastsases of a long term survivor melanoma patient and other melanoma cell lines. RNA was amplified and hybridized to 17.5K cDNA arrays.


title: Sprouting process in potato tuber

status: Public on Feb 13 2008

city: Rockville

first: Jia

last: Liu

address: 9712 Medical Center Drive

institute: Plant Genomics

summary:
Dormant/sprouting bud or eye tissue was collected from field grown Russet Burbank tubers using melon baler. These tubers after harvest washed with 5% Clorox, dried and stored at room temperature and allowed to sprout. Tissue samples were collected from dormant and sprouting eye at different physiological stages (based on length of the sprout) of sprouting. RNA was extracted using a hot phenol method and treated with DNAse. RNA extracted from different stages of sprouting potato tubers was used as query samples. RNA collected from non-sprouting eyes of potato tubers was used as reference samples  Information on RNA samples. Plant species: S. tuberosum CV Russet Burbank. Tissue harvested: Tissue was harvested from the dormant/sprouting bud/eye using ½ inch melon baler. Time points:  Dormant eyes –Stage 1 Initiating buds/sprouts – Stage 2 Sprouts (1/8 inch) – Stage 3 Sprouts (1/4 inch) – Stage 4 Sprout callus (1/4 inch) – Stage 5 Sprouts (1/2 inch) – Stage 6. Growth conditions: Field grown. Replicate information:  Biological replicates; A, B and C
Keywords: Direct comparison

overall_design: 15 hybs total

first: Sastry

last: Jayanty