title: Quadruple rrm experience - Transcriptomic study of a quadruple rrm mutant which belong to a new family of AGO hook proteins

status: Public on Apr 16 2011

first: Eddy

last: Blondet

summary:
rs10-01_rrm - quadruple rrm experience - What is the role of the RRM protein family in plants? Plants were grown on soil in controlled environment under LD (16 h light/8 h dark) and the rosette leaves (8-leaf stage seedlings) were collected for RNA preparation.

Keywords: normal vs transgenic comparison


title: Normalization of whole-genome SNP data from acute monocytic leukemia patients for exome sequencing

status: Public on Feb 12 2011

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

country: China

institute: Shanghai Jiao Tong University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: With the whole genome SNPs array information, we could evaluate the sensitivity and specificity of the point mutation we conclude from the  next-generation sequencing data. Furthermore, we could use the true positive mutation as our guidance to exclude the most unreliable single nucleotide variation detected from sequence. After the process, we could promise a very high specificity under minimum loss of sensitivity.

overall_design: To evaluate the sensitivity and specificity of point mutaions detected through the next-generation sequencing data from nine cases of M5 leukemia patients.

first: Zhu

last: Chen

first: Sai-Juan


title: wt vs. mutants 09-DNA methylation and small RNAs

status: Public on Apr 01 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: rs09-10_fwa - wt vs mutants 09. Impact of loss of DNA methylation and small interference RNAs (siRNAs) in gene expression. Determination of the genes misregulated upon ectopic expression of the FWA imprinted gene. Mutants impaired for the DNA methylation maintenance pathway and RNA interference machinery were compared to mutants simultaneously impaired for both. Impact of FWA and SDC ectopic expression.

overall_design: 15 dye-swaps. fwa-d, gain of function epimutation, gene knock-in (transgenic), gene knockout.

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Vincent

last: Colot

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: gemsupv2-PLASMAR - Biodiversity and functional genomics of endogenous small RNAs induced upon biotic and abiotic stresses in plants

status: Public on Jan 08 2011

summary: au09-04_geminisilsup2 - gemsupv2 - Determine the level of expression in transgenic plants expressing geminviral gene silencing suppressors. One transgenic line of Arabidopsis overexpressing the geminiviral silencing suppressor V2 was grown in addition to a control, and their total RNA was extracted in order to study their genetic expression profiles.

overall_design: 3 dye-swaps - gene knock-in (transgenic).

first: Botella

last: Miguel


title: Expression data from porcine red and white muscle

status: Public on Jan 29 2011

city: Wuhan

first: Bo

last: Zuo

address: Shizishan Street

institute: HZAU

summary:
In meat animal production, favourable meat traits such as color and, in the pig in particular, tenderness have been found to closely associate with the greater abundance of red or highly oxidative fibres. Red muscles possess higher lipid concentration (intra- and inter-fibre fat) which is associated with more tender and juicy meat. In addition, individuals with muscles that are abundant in oxidative type I fibres are associated with favourable metabolic health, and are less likely to predispose to obesity and insulin resistance. Collectively, understanding the molecular processes that govern the expression of specific fiber types and the phenotypic characteristics of muscles is important in agricultural and medical fields.
In this study, a genome-wide investigation of the porcine differential expression between two red (soleus, SE) and white (longissimus dorsi, LD) muscle was conducted using the Affymetrix GeneChip® Porcine Genome Array containing oligonucleotides representing approximately 24123 transcripts from 20201 S. scrofa genes

overall_design: Three meishan gilts from the same litter were slaughtered at the 150 days of age by electrical stunning and exsanguination, in compliance with national regulations applied in commercial slaughtering. Immediately after slaughter, two muscles with different locations, functions, and biochemical properties were sampled: the longissimus at the last rib level, a fast twitch glycolytic muscle involved in voluntary movements of the back, and the deep portion of the SE, a oxydolytic muscle.

first: Zuo

last: Bo

first: Li

last: Yang


title: zf1 experiment

status: Public on Jan 01 2011

city: Evry

address: 2 rue Gaston crémieux

summary:
rs09-03_zf1 - zf1 experiment - Transcriptome analysis of mutants for novel AGO-hook type proteins in Arabidopsis thaliana - Plants were grown on soil in controlled environment under LD (16 h light/8 h dark) and the rosette leaves (8-leaf stage seedlings) were collected for RNA preparation

Keywords: normal vs transgenic comparison

overall_design: 4 dye-swap - CATMA arrays

first: Patrick

last: Achard

first: Thierry

last: Lagrange

middle: P

middle: L


title: Population genetics context of ancient human genome sequence of an extinct Palaeo-Eskimo

status: Public on Nov 30 2010

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

summary: To study the population genetics context of the Saqqaq individual we carried out Illumina Bead-Array-based genotyping on four native North American and twelve north Asian populations.

overall_design: 169 samples are analysed on two different Illumina platforms.

first: Richard

last: Villems

first: Eske

last: Willerslev


title: upregulation of transcripts in the absence of prc2 repressory complex-Dissecting the role of the polycomb repressor

status: Public on Dec 01 2010

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

summary:
rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT.

Keywords: gene knock out

overall_design: 6 dye-swap - CATMA arrays

first: Daniel

last: Bouyer

first: Arp

last: Schnittger


title: Comparative transcriptome analysis of dedifferentiation in porcine mature adipocytes and follicular granulosa cells

status: Public on Mar 10 2011

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

country: Japan

institute: Research Organization of Information and Systems

summary:
Cellular dedifferentiation signifies the withdrawal of cells from a specific differentiated state into a ‘stem cell’-like undifferentiated state. However, the mechanism of dedifferentiation remains obscure. We showed that mature adipocytes (MA) and follicular granulosa cells (GC), which have distinct functions in vivo, can dedifferentiate during culture in vitro and acquire multipotency.
We investigated the dedifferentiation mechanism of MA and GC using global gene expression analyses.

overall_design: Using Affymetrix porcine genome array, we compared global gene expression profiles during dedifferentiation to search for particular biological functions in genes of which  expression intensities were increased or decreased by MA and GC dedifferentiation.

first: Yoshinao

last: Oki

first: Hidemasa

last: Bono

first: Koichiro

last: Kano


title: mutants versus wt - Transcriptome analysis of mutants impaired in post-transcriptional gene silencing (PTGS)

first: Soubigou-Taconnat

last: Ludivine

summary: ra09-03_sgs - mutants versus wt - Identification of new genes regulated by SGS1 and SGS6/UBP5 (two genes involved in PTGS) by analysis of the transcriptomes of sgs1 and sgs6 mutants compared to wild-type plants in the shoots of seedlings. The comparison between the transcriptomes of sgs3, chr11, chr17 simple mutants impaired differently in PTGS and development (juvenile-to-adult transition and bolting), and the transcriptomes of the sgs3 chr11, sgs3 chr17 double mutants showed additive effects on development (juvenile-to-adult transition and bolting), which allows a better understanding of the genetic link existing between SGS3 and its potential partners, CHR11 (which interacts with SGS3 in a two-hybrid assay and BiFC) and CHR17, 2 homologous proteins of the SWI/SNF2 family. Transcriptome comparison between mutants and wild-type plants L1 in the shoots of seedlings.

overall_design: 14 dye-swaps - gene knock-in (transgenic).

first: Herve

last: Vaucheret

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: S2_RNA_expression_Tiling_Array

status: Public on Nov 18 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

type: Expression profiling by genome tiling array

summary:
modENCODE_submission_2769
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes.  Labeled cDNA and labeled genomic DNA were hybridized to NimbleGen microarrays (2-color hybridizations).  These experiments are used as controls for nucleosome salt fractionations.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC

first: Steven

last: Henikoff

first: Jorja

first: Kami

last: Ahmad


title: Overexpression of pten2a: The signaling pathway of TOR/PTEN in Arabidopsis

summary: gnp_blan06_torpten - overexpression of pten2a - The impact of the TOR pathway on growth and stress responses. - Comparaison control versus overexpressor. The overexpressor has a male phenotype of sterility.

overall_design: 3 dye-swap - gene knock in (transgenic)

first: Christian

last: Meyer


title: lst8 - The signalisation way TOR/PTEN in Arabidopsis

status: Public on Dec 08 2010

summary: gnp_blan06_torpten - lst8 - The impact of the TOR pathway on growth and stress responses. Comparison between the lst8 mutant vs. WT in short day and in long day conditions.

overall_design: 8 dye-swaps - gene knock out.


title: Kc 600 mM Salt Extracted Chromatin Pellet

type: Genome binding/occupancy profiling by genome tiling array

summary:
modENCODE_submission_2757
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line Kc167; biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1 to 2 hours

first: Akiko

last: Sakai

first: Gabriel

last: Loeb


title: Kc_600_mM_Salt_Extracted_Chromatin

summary:
modENCODE_submission_2756
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line Kc167; biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1 to 2 hours


title: Porcine spleen_Streptococcus suis serotype 2 infected_3 days

status: Public on Nov 24 2010

first: Meilin

last: Jin

address: 1 Shizishan Street, Wuhan, Hubei, 430070, P.R. China

institute: Huazhong Agricultural University

summary:
Streptococcus suis serotype 2 (SS2), a major swine pathogen and an emerging zoonotic agent, has greatly challenged global public health. Systematical information about host immune response to the infection is important for understanding the molecular mechanism of diseases.
Here, we investigated the global expression changes in spleen following SS2 infection using the Affymetrix Porcine Genechip. Our findings indicate previously unrecognized gene transcription changes in case of SS infection in vivo. Our data should provide new clues for immune response in mammals and identification of candidate genes related to SS resistance.

overall_design: All animal tissue collection procedures were performed according to protocols approved by The Hubei Province, PR China for Biological Studies Animal Care and Use Committee. Piglets at 35 days old were determined to be S.suis 2-free by antibody-based ELISA before artificial bacterial challenges. Each piglet was intranasally challenged with 2×106 colony-forming units (CFU) per millilitre of SS2 strain 05ZY or ΔHP0197. A total of 4 piglets were challenged with 05ZY, 4 were challenged with ΔHP0197, and 4 pigs were used as controls. These three groups were raised in isolated facilities. Nine microarrays were used in the experiment, corresponding to the RNAs from spleen tissues of piglets with arthritis after SS2 infection and spleen tissues of piglets with no clinical signs and three controls.

first: Ran

last: Li

first: Anding

last: Zhang

first: Bo

last: Chen

first: Liu

last: Teng

first: Ya

last: Wang

first: Huanchun


title: Kc H2Av Knockdown 600 mM Salt Extracted Chromatin Pellet

summary:
modENCODE_submission_2760
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: Kc H2Av Knockdown 600 mM Salt Extracted Chromatin

summary:
modENCODE_submission_2759
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: Fly wing disc 80 mM Salt Extracted Chromatin

summary:
modENCODE_submission_2513
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: ML-DmD16-c3; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line ML-DmD16-c3; biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 80 mM; extraction time (sampling_time_point) 1-2 hours


title: Fly wing disc 600 mM Salt Extracted Chromatin Pellet

summary:
modENCODE_submission_2516
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: ML-DmD16-c3; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line ML-DmD16-c3; biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1-2 hours


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin

summary:
modENCODE_submission_2511
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: B3(made_by : Paul Talbert description : A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags : Transposon transgene : Histone H3.3::biotin-recognition-peptide outcross : New Line genotype : y w; A5C-GAL4/cyO; B3 official name : B3 ); Genotype: y w; A5C-GAL4/cyO; B3; Transgene: Histone H3.3::biotin-recognition-peptide;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1-2 hours


title: Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin

summary:
modENCODE_submission_2508
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: Fly_embryos_1-3_hr_600_mM_Salt_Extracted_Chromatin_Pellet

summary:
modENCODE_submission_2509
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: B3(made_by : Paul Talbert description : A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags : Transposon transgene : Histone H3.3::biotin-recognition-peptide outcross : New Line genotype : y w; A5C-GAL4/cyO; B3 official name : B3 ); Genotype: y w; A5C-GAL4/cyO; B3; Transgene: Histone H3.3::biotin-recognition-peptide;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1-2 hours


title: rnai tor time course - The signalization way TOR/PTEN in Arabidopsis

status: Public on Jan 07 2011

first: Soubigou-Taconnat

last: Ludivine

summary: gnp_blan06_torpten - rnai tor time course - The impact of the TOR pathway on growth and stress responses. Modification of translational and transcriptional profiles in Tor-inducible RNAi mutants and identification of TOR targets.

overall_design: 28 dye-swaps - normal vs. rnai mutant comparison.

first: Ludivine

first: Jean-Pierre


title: Kc H2Av Knockdown RNA Expression Tiling Array

first: DCC

summary:
modENCODE_submission_2761
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes.  Labeled cDNA and labeled genomic DNA were hybridized to NimbleGen microarrays (2-color hybridizations).  These experiments are used as controls for nucleosome salt fractionations.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: dsRNA (synthetic_RNA) CG5499_RNAi; Cell Line Kc167


title: Kc_RNA_Expression_Tiling_Array

summary:
modENCODE_submission_2758
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes.  Labeled cDNA and labeled genomic DNA were hybridized to NimbleGen microarrays (2-color hybridizations).  These experiments are used as controls for nucleosome salt fractionations.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line Kc167

first: Steven


title: Homozygosity mapping in a consanguineous family with osteogenesis imperfecta (OI)

status: Public on Nov 01 2010

city: Madrid

first: Victor

last: Martinez-Glez

address: Paseo la Castellana 261

department: INGEMM

country: Spain

institute: HULP

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Homozygosity mapping using genome-wide SNP arrys is a useful tool to map causative genes of mendelian disorders in consanguineous patients
To search for LOH (loss of heterozygosity) regions we hybridized genomic DNA from a OI patient and a normal sibling against Human610quad beadarrays  from Illumina (www.illumina.com). Genotyping data was analyzed with BeadStudio software (www.illumina.com)

overall_design: Genomic DNAs from OI affected individual and non-affected sibling were hybridized each on an Illumina Human610Quad Genotyping BeadChip. Image data was analyzed using Beadstudio 3.1.3 software. CNV and LOH (larger than 1 Mb) analysis was performed using the cnvPartition 2.3.4. It was considered as a region of interest those showing LOH in the affected individual but not in the non-affected sibling.

last: Ruiz-Perez

first: Pablo

last: Lapunzina


title: Fly wing disc 600 mM Salt Extracted Chromatin

summary:
modENCODE_submission_2515
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: ML-DmD16-c3; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line ML-DmD16-c3; biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1-2 hours

first: Jorja

first: Kami


title: Gene expression affected by the AtWOX14 gene mutation

status: Public on Oct 01 2010

summary:
au09-02_wox14 - wox13 orthologous group - The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Our scope is to establish a functional link to organ initiation and development in Arabidopsis by identifying genes that are deregulated in the wox14 mutant background. - Transcriptome analyses of the transposon donor line N8514 and the wox14 mutant seedlings grown for 6 and 10 days (growth stages 1.02 and 1.04) in LD condition (i. e. 4 days of cold treatment on 0.5 MS medium, 1% sucrose, 0.7% agar + respectively 6 and 10 days of in vitro growth in LD condition).

Keywords: gene knock out

overall_design: 8 dye-swap - CATMA arrays

last: Taconnat

last: Renou

first: Yves

last: Deveaux

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Fly wing disc 150 mM Salt Extracted Chromatin

last: modENCODE

summary:
modENCODE_submission_2514
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: ML-DmD16-c3; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Female;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: Cell Line ML-DmD16-c3; biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 150 mM; extraction time (sampling_time_point) 1-2 hours

last: Henikoff

first: Akiko

last: Sakai

first: Gabriel

last: Ahmad


title: Fly_embryos_4-6_hr_600_mM_Salt_Extracted_Chromatin_Pellet

summary:
modENCODE_submission_2512
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: B3(made_by : Paul Talbert description : A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags : Transposon transgene : Histone H3.3::biotin-recognition-peptide outcross : New Line genotype : y w; A5C-GAL4/cyO; B3 official name : B3 ); Genotype: y w; A5C-GAL4/cyO; B3; Transgene: Histone H3.3::biotin-recognition-peptide;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1-2 hours

last: Loeb


title: Fly_embryos_4-6_hr_150_mM_Salt_Extracted_Chromatin

summary:
modENCODE_submission_2510
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: B3(made_by : Paul Talbert description : A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags : Transposon transgene : Histone H3.3::biotin-recognition-peptide outcross : New Line genotype : y w; A5C-GAL4/cyO; B3 official name : B3 ); Genotype: y w; A5C-GAL4/cyO; B3; Transgene: Histone H3.3::biotin-recognition-peptide;  NUMBER OF REPLICATES: 2;  EXPERIMENTAL FACTORS: biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 150 mM; extraction time (sampling_time_point) 1-2 hours


title: Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin

summary:
modENCODE_submission_2507
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin.  Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes.  Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions.  Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Strain: B3(made_by : Paul Talbert description : A strain that expresses a conditionally expressed biotin-tagged histone H3.3.  The strain also contains the E. coli BirA gene that is expressed under the control of a GAL4 UAS. tags : Transposon transgene : Histone H3.3::biotin-recognition-peptide outcross : New Line genotype : y w; A5C-GAL4/cyO; B3 official name : B3 ); Genotype: y w; A5C-GAL4/cyO; B3; Transgene: Histone H3.3::biotin-recognition-peptide;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: biochemical fraction (extract) soluble fraction; sodium chloride concentration (Compound) 150 mM; extraction time (sampling_time_point) 1-2 hours


title: A statistical method for detecting genomic aberrations in heterogeneous tumour samples from single nucleotide polymorphism genotyping data

status: Public on Aug 25 2010

city: Oxford

first: Christopher

last: Yau

address: 1 South Parks Road

department: Department of Statistics

country: United Kingdom

institute: University of Oxford

summary: SNP array analysis of microdissected tumor vs stroma vs surgically obtained tumor

overall_design: DNA was extracted from total tumor material, from microdissected stroma and microdissected, pure tumor tissue

first: Graham

last: Steers

first: Adrian

last: Harris

first: Jiannis

last: Ragoussis

first: Ghazala

last: Mirza

middle: C

last: Holmes


title: L2 glutamate receptor expressing neurons tiling array

status: Public on Aug 05 2010

summary:
modENCODE_submission_658
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: NC1842 (engineered, target gene glr-1 tagged by 3xFlag::PAB-1); Tissue: Glutamate receptor expressing neurons (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: unc-119 (ed1); [unc-119 (+); glr-1::3XFLAG::PAB-1]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1842 (engineered, target gene glr-1 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Glutamate receptor expressing neurons (L2)

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: Effect of earthworms on Arabidopsis transcriptome

first: Soubigou-Taconnat

last: Ludivine

summary:
au07-05_groundworms - groundworms - Do earthworms affect plant growth through signal molecules? - Plants were grown in a sandy soil from the Centre de Recherche en Ecologie Expérimentale et Prédictive (CEREEP, France), in the presence or absence of earthworms. Soil was dried and sieved at 2 mm before to be put in the pots. There was 2 levels of treatment (presence or absence of earthworms in the soil), and 5 plants per treatments.

Keywords: treated vs untreated comparison

overall_design: 4 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Manuel

last: Blouin

last: Balzergue

last: Martin-Magniette


title: Genomic expression study of regenerated endothelial cells in high cholesterol-fed and fish oil-rich groups

status: Public on Oct 18 2010

city: Hong Kong

first: Mary

last: Lee

address: 21 sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: Experiments on primary cultures of native and regenerated endothelial cells demonstrated genomic changes in the latter related to vasomotor control, coagulation, oxidative stress, lipid metabolism and extracellular matrix. However, the genomic changes caused by the combination of either hyperlipidemia or supplementation with polyunsaturated fatty acids and endothelial regeneration are unknown.The present experiments were designed to test the hypothesis that endothelial regeneration process is affected differentially at the genomic level by the exposure to either high cholesterol or PUFA-rich diet in vivo.

overall_design:
This study consists of three treatment groups, the control (n=8), high cholesterol-fed (CHL;n=6) and PUFA-rich (FO; n=6) groups. Native (LCX) and regenerated (LAD) samples of each animal from each treatment group was analyzed and followed by statistical analysis (paired t test) of all the animals from each group. The analytical results (N vs R) from each group would then be compared to that of the control group. Native cells from control group would also be compared to the native cells of the other animal groups (CHL/FO).

Supplementary files:
Comparisons of fish oil vs ctrl and high cholesterol vs ctrl.

middle: Y


title: L2_intestine_tiling_array

first: DCC

last: modENCODE

summary:
modENCODE_submission_463
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: SD1084 (engineered, target gene ges-1 tagged by 3xFlag::PAB-1); Tissue: Intestine (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs148 [(ges-1p::FLAG::PAB-1) +(sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1084 (engineered, target gene ges-1 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Intestine (L2)


title: Cystic Fibrosis Pigs Develop Lung Disease and Exhibit Defective Bacterial Eradication at Birth

status: Public on Sep 17 2010

city: Iowa City

first: Shyam

last: Ramachandran

address: 240G EMRB

department: Pediatrics

country: USA

institute: Univ of Iowa

summary: Lung disease causes most of the morbidity and mortality in cystic fibrosis (CF). However, understanding its pathogenesis has been hindered by lack of an animal model with characteristic features of CF. To overcome this problem, we recently generated pigs with targeted CFTR genes. We now report that within months of birth, CF pigs spontaneously develop hallmark features of CF lung disease including airway inflammation, remodeling, mucus accumulation, and infection. Their lungs contained multiple bacterial species, suggesting an equal opportunity host defense defect. In humans, the temporal and/or causal relationships between inflammation and infection have remained uncertain. To investigate these processes, we studied newborn pigs. Their lungs showed no inflammation, but were less often sterile than controls. Moreover, after intrapulmonary bacterial challenge, CF pigs failed to eradicate bacteria as effectively as wild- type pigs. These results suggest that impaired bacterial elimination is the pathogenic event that initiates a cascade of inflammation and pathology in CF lungs. Finding that CF pigs have a bacterial host defense defect within hours of birth provides an exciting opportunity to further investigate pathogenesis and to test therapeutic and preventive strategies before secondary consequences develop.

overall_design: Pig model of human CF lung disease

middle: A

last: Stoltz

middle: K

last: Meyerholz

first: Alejandro

last: Pezzulo

last: Rogan

first: Greg

middle: J

last: Davis

first: Robert

last: Hanfland

first: Chris

last: Wohlford-Lenane

first: Cassie

last: Dohrn

first: Jennifer

last: Bartlett

first: George

last: Nelson

first: Eugene

middle: H

last: Chang

first: Peter

last: Taft

first: Paula

middle: S

last: Ludwig

first: Mira

last: Estin

first: Emma

middle: E

last: Hornick

first: Janice

last: Launspach

first: Melissa

last: Samuel

first: Tatiana

last: Rokhlina

first: Philip

last: Karp

first: Lynda

last: Ostedgaard

first: Aliye

last: Uc

first: Timothy

middle: D

last: Starne

first: Alexander

middle: R

last: Horswill

first: Kim

last: Brogde

first: Randall

last: Prather

first: Sandra

last: Richter

first: Joel

last: Shilyansky

first: Paul

middle: B

last: McCray

first: Joseph

last: Zabner

first: Michael

last: Welsh


title: L2_panneural_tiling_array

first: DCC

last: modENCODE

summary:
modENCODE_submission_462
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: SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1); Tissue: Pan-neural (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs153 [(F25B3.3::FLAG::PAB-1) + (sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1241 (engineered, target gene F25B3.3 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Pan-neural (L2)

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: The microRNA profile analysis of the function of HMGA2 in immortalized human ovarian surface epithelial cell lines

status: Public on Sep 11 2010

city: Chicago

first: Jingjing

last: Wu

state: IL

address: 303 E. Chicago Avenue

department: pathology

institute: northwestern university

summary: To identify HMGA2-regulated downstream target microRNAs, we compared the difference of microRNA profiles between ovarian surface epithelial cells without HMGA2 (T29) and cells with HMGA2 (T29A2).

overall_design: Immortalized ovarian surface epithelial cells (named T29) were transfected with HMGA2 retrovirus vector pBabe-HMGA2 (named T29A2). Then cells were harvested for RNA isolation for microRNA expression analysis.

first: Jianjun

last: Wei


title: Mechanisms underlying the sparing of masticatory muscle function relative to biceps femoris muscle in an experimental critical illness model

status: Public on Sep 21 2010

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

summary:
Background: The aim of this study is to improve our understanding of the mechanisms underlying the sparing of masticatory muscles relative to limb muscles in ICU patients with acute quadriplegic myopathy (AQM) by using a unique porcine ICU model, i.e., 5-day longitudinal experiments where animals are sedated, mechanically ventilated and exposed to factors triggering AQM, such as muscle unloading, endotoxin-induced sepsis, and systemic exposure to CS and NMBA.

Results: An altered expression was notably observed in  heat-shock proteins genes, sarcomeric proteins and myostatin genes were noticed. Hence, modifications in heat-shock proteins, sarcomeric proteins and myostatin genes are in sharp contrast to alterations in the limb muscles and it is postulated that elevated heat-shock proteins and decreased sarcomeric protein and myostatin genes play a protective role in the masticatory muscle relative to limb muscle in ICU patients with AQM.

Conclusions: This intervention had no significant effect on masseter muscle fiber size or force-generation capacity.  This is in sharp contrast to the dramatic decrease observed in specific force in limb muscle fibers from the same animals.  However, significant differences were observed between the craniofacial and the limb muscle with a masseter muscle specific regulation of i) transcriptional and growth factors like RUNX1, FOXO1A, TBX1, PGC1-β and myostatin, ii) several heat shock protein genes like HSP 90, HSP 105/110 and αB-crystallin, iii) a matrix metalloproteinase inhibitor (TIMP2) and iv) oxidative stress responsive elements such as SRXN1 and SOD2.  These muscle-type specific differences, the alterations in heat shock protein, sarcomeric protein and myostatin genes are forwarded as important factors underlying the sparing of masticatory muscles compared with limb muscles in critically ill ICU patients with Acute Quadriplegic Myopathy.

Keywords: Treatment, immobilization, muscle function.

overall_design:
Five female domestic piglets (Sus scrofa, average body weight 26.9 kg) were used in this study. Five subjects were included for masseter muscle and same four subjects were included for the biceps femoris muscle.
Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period. A neuromuscular blocking agent (NMBA) was administered as a continuous infusion of pancuronium bromide 0.1mg/kg/h (Pavolun; Organon, Boxtel, The Netherlands) for 5days while a corticosteroid (CS) was given as bolus doses of betamethasone 0.1 mg/kg (Betapred; GSK, Slona, Sweden) twice daily for 5days.Endotoxemia was induced by a continuous infusion of Escherichia coli endotoxin, serotype O26:B6 (Sigma Labkemi, Stockholm, Sweden) at 36 µg/kg/h for 1h.

Variables [biceps femoris muscle]:
AQM control: RLPA-Day1_N_CS_S-1PC.CEL(porcine), RLPA-Day1_N_CS_S-2PC.CEL(porcine), RLPA-Day1_N_CS_S-3PC.CEL(porcine), RLPA-Day1_N_CS_S-4PC.CEL(porcine).
AQM treatment: RLPA-Day5_N_CS_S-1PC.CEL(porcine), RLPA-Day5_N_CS_S-2PC.CEL(porcine), RLPA-Day5_N_CS_S-3PC.CEL(porcine), RLPA-Day5_N_CS_S-4PC.CEL(porcine).

first: Sudhakar

last: Aare

first: Varuna

last: Banduseela

first: Julien

last: Ochala

first: Hanna

last: Goransson

first: Holly

last: Norman

first: Peter

last: Radell

first: Lars

middle: I

last: Eriksson

first: Yi-Wen

last: Chen

first: Eric

last: Hoffman

last: Larsson


title: Analysis of 30nm Chromatin Structure in Female Human Lymphoblastoid Cells

status: Public on Aug 27 2010

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

type: Genome binding/occupancy profiling by SNP array

summary: Analysis of 30nm Chromatin Structure in Female Human SATO3 Lymphoblastoid Cells

overall_design: Single Input and Replicate Open Chromatin Samples Prepared from Cell Line


title: L3-L4_PVD_OLL_neuron_tiling_array

first: DCC

last: modENCODE

summary:
modENCODE_submission_460
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: NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1); Tissue: PVD OLLs (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx460 [unc-119 (+); ser-2prom3B::3XFLAG::PAB-1]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1021 (engineered, target gene ser-2 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue PVD OLLs (L3-L4)

first: Bob

last: Waterston

first: David

last: Miller

first: Mark

last: Gerstein

last: Wilson


title: L2_excretory_cell_tiling_array

summary:
modENCODE_submission_464
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: NC1598 (engineered, target gene clh-4 tagged by 3xFlag::PAB-1); Tissue: Excretory cell (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: wdIs47 [clh-4::3XFLAG::PAB-1 + rol-6 (su1006)]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1598 (engineered, target gene clh-4 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Excretory cell (L2)

first: Mike

first: Ashish

last: Argiwal

first: Valerie

last: Reinke


title: silencing mutants-Transcriptome analysis of silencing mutants and endogenous hairpin KO insertion.

status: Public on Sep 15 2010

first: Soubigou-Taconnat

last: Ludivine

summary:
rs09-06_silencing-muntants - silencing mutants - Find endogenous targets of SDE3, SDE5 and IR71. - Lines IR71 KO n°3, smd8#25, sde3 (Col-0), sde5 (Col-0), Suc-SUL(Col-0) and Col-0 were grown for 11 days on MS solid medium, seedlings were then transferred in MS liquid medium and harvested 2.5 days after.

Keywords: genotype comparaison

overall_design: 8 dye-swap - CATMA arrays

first: Olivier

last: Voinnet

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Young Adult Cephalic sheath (CEPsh) tiling array

summary:
modENCODE_submission_660
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: OS3991 (engineered, target gene hlh-17 tagged by 3xFlag::PAB-1); Tissue: CEPsh (YA); Developmental Stage: Young Adult 20dC 72hr post-L1; Genotype: unc-119 (ed1); nsIs191 [unc-119 (+); hlh-17::3XFLAG::PAB-1]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain OS3991 (engineered, target gene hlh-17 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage Young Adult 20dC 72hr post-L1; Tissue CEPsh (YA)


title: L3-L4_reference_tiling_array

summary:
modENCODE_submission_659
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 (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue reference (L3-L4)


title: Transciptomic analysis of the hal4hal5 mutant of Saccharomyces cerevisiae

status: Public on Jul 17 2010

city: Barcelona

first: Jorge

last: Pérez-Valle

state: Barcelona

address: Parc Cientific de Barcelona, C/. Baldiri Reixac 10

department: RNA lab

institute: IBMB (CSIC)

summary: The yeast protein kinases Sat4/Hal4 and Hal5 are required for the plasma membrane stability of the K+ transporter Trk1 and some amino acid and glucose permeases. The transcriptomic analysis presented here indicates alterations in the general control of both nitrogen and carbon metabolism. Accordingly, we observed reduced uptake of methionine and leucine in the hal4 hal5 mutant. This decrease correlates with activation of the Gcn2-Gcn4 pathway, as measured by expression of the lacZ gene under the control of the Gcn4 promoter. However, with the exception of methionine biosynthetic genes, few amino acid biosynthetic genes are induced in the hal4 hal5 mutant, whereas several genes involved in amino acid catabolism are repressed. Concerning glucose metabolism, we found that this mutant exhibits derepression of respiratory genes in the presence of glucose, leading to an increased activity of mitochondrial enzymes, as measured by SDH activity. In addition, the reduced glucose consumption in the hal4 hal5 mutant correlates with a more acidic intracellular pH and with low activity of the plasma membrane H+-ATPase. As a compensatory mechanism for the low glycolytic rate, the hal4 hal5 mutant overexpresses the HXT4 high affinity glucose transporter and the hexokinase genes. These results indicate that the hal4 hal5 mutant presents defects in the general control of nitrogen and carbon metabolism, which correlate with reduced transport of amino acids and glucose, respectively. A more acidic intracellular pH may contribute to some defects of this mutant.

overall_design: Four biological replicates were used to assess diferentially expression between wild type yeast strain and the hal4hal5 mutant strain for three sample sets: 1) cells grown in YPD pH 4.5 and BY4741 genetic background, 2) cells grown in YPD pH 4.5 and W303 genetic background, 3) cells grown in YPD pH 6.0 and W303 genetic background. Differentially expressed genes were identified using one-class significant analysis of microarrays (SAM; Tusher et al, 2004)

first: Joaquin

last: Ariño

first: Lynne

last: Yenush

first: Ramón

last: Serrano


title: L3-L4_dopaminergic_neuron_tiling_array

first: DCC

last: modENCODE

summary:
modENCODE_submission_655
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: NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); Tissue: Dopaminergic neurons (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119 (ed1); wdEx637 [unc-119 (+); dat-1::3XFLAG::PAB-1]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1700 (engineered, target gene dat-1 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue Dopaminergic neurons (L3-L4)


title: L2_coelomocytes_tiling_array

summary:
modENCODE_submission_657
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: NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1); Tissue: Coelomocytes (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: unc-119(ed1); wdEx638 [unc-119(+); unc-122::3XFLAG::PAB-1]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1668 (engineered, target gene unc-122 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue Coelomocytes (L2)

first: Bob

last: Waterston


title: Expression data from porcine diaphragm and Psoas major tissue of Iberian males and females fed with two feeding levels

status: Public on Jul 30 2010

first: Ana

last: Fernandez

state: Madrid

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

institute: INIA

summary: The aim of this study was to identify genes, gene clusters and networks involved in sexual dimorphism and in the response to nutritional restriction in porcine skeletal muscles, through the analysis of gene expression differences. Full sib Iberian piglets from three litters composed of two males and two females per family were randomly assigned to two dietary treatments which differed in the feeding level during 15 wk. At the end of the trial, 27 wk of age, significant phenotypic differences  were detected between genders and between feeding levels for growth, fatness, fatty acid composition and primary cuts weights. RNA samples from two skeletal muscles, diaphragm and Psoas major, were hybridized with Affymetrix microarrays and the expression data were analyzed using a mixed model and a FDR<0.01.  The successfully performed validations by qRT-PCR of six selected genes supported the reliability of our microarray results. Ina a first step, the main gene expression differences between both muscles were established, identifying 181 differentially expressed genes, which represented almost exclusively anatomical structural differences. The analysis between genders reported expression differences of 59 unique genes, mainly implicated in muscle growth and stress response, including well known genes, such as IGF1, apart from others potentially associated to meat quality such as ANKRD1. The analysis of the feeding level effect restriction reported up-regulation of 76 genes and down-regulation of other 60 genes. Functional annotation showed that the moderated nutritional restriction applied led to a reduced growth through down-regulation of key genes implicated in enhancing growth and up-regulation of genes implicated in inhibiting growth. Besides, the restriction led to an increase of muscular aminoacid metabolism and decrease of lipid metabolism as adaptive response. Changes in expression patterns of genes determining meat characteristics, such as PDK4 implicated in water holding, CTSD associated to muscle transformation during meat processing and SCD involved in the determination of fatty acids profiles, were also reported. Finally, we identify relevant expression differences in ADAM12, CA2, UCHL1 and ESRRG genes, which are involved in human obesity and have not been previously studied in pig.

overall_design: 16 skeletal muscle samples, diaphragm and psoas major, from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 20% restriction.

last: Fernández

first: Almudena

first: Clemente

last: Lemus-Flores

first: Carmen

last: Barragán

first: MCarmen

last: Rodríguez

first: Cristina

last: Óvilo

first: Luis

last: Silió


title: L2_A-class_neurons_tiling_array

summary:
modENCODE_submission_469
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: NC694 (engineered, target gene unc-119 tagged by 3xFlag::PAB-1); Tissue: L2-A-class; Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: unc-119(ed1) III; wdEx257. Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC694 (engineered, target gene unc-119 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue L2-A-class

first: David

last: Miller

first: Mark

last: Gerstein

first: Mike

last: Wilson

first: Ashish

last: Argiwal

first: Valerie

last: Reinke


title: Comparative transcriptomic profiling of peripheral blood mononuclear cells (PBMNCs) isolated from pigs exposed to a high-fat diet (H-F) or to a high-fat diet plus resveratrol (H-F+RES)

status: Public on Aug 09 2010

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

institute: CEBAS-CSIC

summary: We used Affymetrix microarrays to investigate gene expression changes in PBMNCs isolated from female and male pigs to determine significant modulatory effects that may have been induced by the intake of resveratrol during 9 months in high-fat fed animals .

overall_design: The aim of this work was to determine whether the intake of dietary levels of resveratrol (RES) exerted any modulatory effects, at the level of gene expression, in PBMNCs isolated from female and male pigs exposed to a H-F diet for 9 months. We first isolated PBMNCs, and the corresponding total RNA, from 5 female pigs and 5 male pigs at time 0 (beginning of the experiment) to determine basal gene expression levels and to compare sex differential gene expression. Animals designated to the control group were then fed a normal chow (5% beef tallow) for 9 months. Animals in the H-F diet were fed a chow with 20% of beef tallow and animals in the H-F diet supplemented with resveratrol were fed the 20% fat diet plus resveratrol (8 mg/Kg body weight per day). From each group, PBMNCs were isolated from 2 female and 2 male animals. Pure RNA was extracted from the PBMNCs for microarrays analyses (Affymetrix) and gene differential expression determined between the H-F fed animals and CT animals (to determine the effects of fat consumption) and between the H-F fed animals supplemented with RES and the H-F group (to determine the effects of RES on the fat consumption).

first: María

last: Azorín-Ortuño

first: Juan-Carlos

last: Espín de Gea


title: Young Adult reference tiling array

first: DCC

last: modENCODE

summary:
modENCODE_submission_656
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 (YA); Developmental Stage: Young Adult 20dC 72hr post-L1; Genotype: wild type; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 20; Developmental Stage Young Adult 20dC 72hr post-L1; Tissue reference (YA)


title: L2_body_wall_muscle_tiling_array

summary:
modENCODE_submission_465
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: SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1); Tissue: body wall muscle; Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: gaIs146 [(myo-3p::FLAG::PAB-1) + (sur-5::GFP)]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain SD1075 (engineered, target gene myo-3 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue body wall muscle

first: Bob

last: Waterston


title: L2_GABA_motor_neurons_tiling_array

summary:
modENCODE_submission_466
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: NC1627 (engineered, target gene C04G2.1 tagged by 3xFlag::PAB-1); Tissue: GABA neurons (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: dpy-5 (e907); wdIs31 [dpy-5 (+); pC04G2.1::3XFLAG::PAB-1]dpy-5 (e907); wdIs31 [dpy-5 (+); pC04G2.1::3XFLAG::PAB-1]; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1627 (engineered, target gene C04G2.1 tagged by 3xFlag::PAB-1); temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue GABA neurons (L2)


title: ralstonia infection-characterisation of wat1 mutant

status: Public on Aug 01 2010

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

summary:
rs08-04_wat1-ralstonia - ralstonia infection - identification of the role of the plant cell wall in the interactions between plants and pathogenic agents - Comparison between the mutant and the wt at different time after infection with ralstonia bacteria

Keywords: treated vs untreated comparison

overall_design: 20 dye-swap - CATMA arrays

first: Deborah

last: Goffner

first: Jean-Pierre

last: Renou

first: Marie-Laure

last: Martin-Magniette


title: L3-L4_hypodermis_tiling_array

summary:
modENCODE_submission_2454
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: NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); Tissue: hypodermis (L3-L4); Developmental Stage: L3-L4 larva 20dC 22h 23dC 24hr post-L1; Genotype: unc-119(ed1); wdEx626[unc-119+; dpy-7::3xFLAG::PAB-1]; Sex: Hermaphrodite;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain NC1790 (engineered, target gene dpy-7 tagged by 3xFlag::PAB-1); temperature 23; Developmental Stage L3-L4 larva 20dC 22h 23dC 24hr post-L1; Tissue hypodermis (L3-L4)


title: L2_reference_tiling_array

summary:
modENCODE_submission_461
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 (L2); Developmental Stage: larva mid-L2 20dC 22h post-L1; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  NUMBER OF REPLICATES: 3;  EXPERIMENTAL FACTORS: Antibody EZview Red ANTI-FLAG® M2 Affinity Gel (target is FLAG); Strain N2; temperature 20; Developmental Stage larva mid-L2 20dC 22h post-L1; Tissue reference (L2)


title: Transcript profiling in the liver of piglets fed carnitine

status: Public on Jul 15 2010

city: Jena

first: Steffen

last: Priebe

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Hans-Knöll-Institute (HKI)

summary:
Carnitine is a water soluble quaternary amine which is essential for normal function of all tissues.
Besides improving performance characteristics of livestock animals carnitine has attracted scientific interest due to several health-related effects, like protection against neurodegeneration, mitochondrial decay, and oxidative stress, improvement of glucose tolerance and insulin sensitivity as well as reduction of hepatic steatosis.
To gain insight into mechanisms through which carnitine exerts its beneficial metabolic effects, we fed piglets either a control or a carnitine supplemented diet, and analyzed the transcriptome in the liver, which plays a central role in whole body metabolism.

overall_design: Total RNA was isolated from pig liver samples for hybridization on Affymetrix GeneChip porcine genome arrays. Two RNA pools, each for the control group and the carnitine group, were used. Each RNA pool comprised RNA from 4 pigs.

first: Janine

last: Keller

first: Robert

last: Ringseis

first: Reinhard

last: Guthke

first: Holger

last: Kluge

first: Klaus

last: Eder


title: Interactions between H2O2 and glutathione in gene expression

status: Public on Jul 22 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

institute: INRA

summary:
rs08-03_glutathion - glutathion - How does glutathione content or reduction state affect H2O2-induced changes in the transcriptome? - Three single Arabidopsis mutants were used: cat2, knockout for catalase2 and so enriched in H2O2; cad2, defective in glutathione content; cytGR, knockout for cytosolic glutathione reductase. Cat2 was crossed with cad2 and cyt GR, and col0, 3 single mutants, and 2 double mutants were sampled in controlled growth conditions either in 8h or 16h photoperiod.

Keywords: gene knock out

overall_design: 20 dye-swap pairs - CATMA arrays: 40 arrays

first: Graham

last: Noctor

first: Eddy

last: Blondet


title: Expression data from pig mesenteric lymph nodes

status: Public on Jun 11 2010

city: nanjing

first: fang

last: tian

state: jiangsu

address: hanzhong road No.140

institute: nanjing medical university

summary:
The mesenteric lymph nodes  represent the immune response to eggs in schistosome infections,and the analysis of gene expression profiles of the mesenteric lymph nodes from the Vac-Cha (vaccinated with UV attenuated cercariae and challenged with normal cercariae)and Inf-Con (infected with normal cercariae) groups.
We used microarrays to detail the global programme of gene expression and identified distinct classes of up-regulated and down-regulated genes.

overall_design:
The mesenteric lymph nodes surrounding the cecum from the Vac-Cha and Inf-Con groups were collected at week 8 post challenge and used to analyze the gene profile with Affymetrix microarrays. We sought to obtain the different genes expression profiles between the Vac-Cha group and Inf-Con group.The Vac-Cha group is three pigs vaccinated with UV attenuated Schistosoma japonicum cercariae and challenged with normal Schistosoma japonicum cercariae, and the Inf-Con group is three pigs infected with normal cercariae.  Samples pooled per group.

A list of differentially-regulated genes can be found in the supplementary file below.

first: Fang

last: Tian

first: Minjun

last: Ji

first: Guanling

last: Wu


title: Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering (S. cerevisiae, C. glabrata, K. lactis)

status: Public on Jul 08 2010

city: La Jolla

first: Dwight

last: Kuo

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary:
Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure.

Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity.

We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus
Kluyveromyces lactis

overall_design: There are three yeast species being studied. Each species has three biological replicates. Each biological replicate has 6 time points (0,1/3,2/3,1,2,4). These time points are combined in equal proportions to form a species and replicate specific “Reference Pool”. Each time point (except time 0) is compared against the Reference Pool. We also perform dye-swapped technical replicates for each biological replicate.


title: quinolinate-Deregulation of NAD biosynthesis

status: Public on Jul 01 2010

first: Sandra

last: Pelletier

summary:
rs09-02_quinolinate - quinolinate - Study of the impact of an inductible increase in the NAD concentration in arabidopsis - Comparison between the mutant or the control after a quinolinate treatment

Keywords: treated vs untreated comparison,wt vs mutant comparison

overall_design: 6 dye-swap - CATMA arrays

first: Bertrand

last: Gakière


title: CATCH-IT method for measuring nucleosome turnover

status: Public on May 27 2010

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary:
Direct measurement of nucleosome turnover dynamics by using co-translational incorporation of the methionine (Met) surrogate azidohomoalaine (Aha) into proteins and subsequent ligation of biotin to Aha-containing proteins through the [3+2] cycloaddition reaction between the azide group of Aha and an alkyne linked to biotin. To measure turnover rates, we treat cells briefly with Aha, couple biotin to nucleosomes containing newly incorporated histones, affinity purify with strepavidin, wash stringently to remove non-histone proteins and H2A/H2B dimers, and analyze the affinity-purified DNA using tiling microarrays. We call this strategy 'CATCH-IT' for Covalent Attachment of Tags to Capture Histones and Identify Turnover.

Keywords: Chromatin affinity-purification on microarray

overall_design: All experiments were done using strepavidin pulldown DNA cohybridized with total input DNA to the same array. Two channels per array, Cy5 and Cy3, were used in each experiment.

first: Steven

first: Roger

last: Deal


title: mutant comparison - characterisation of wat1 mutant

summary:
rs08-04_wat1-ralstonia - mutant comparison - identification of the role of the plant cell wall in the interactions between plants and pathogenic agents - wt versus mutant comparison in the leaf and the root

Keywords: wt vs mutant comparison

first: Deborah

last: Goffner

first: Jean-Pierre

last: Renou

first: Marie-Laure

last: Martin-Magniette


title: Expression data from neonatal pig skeletal muscle

status: Public on Jun 22 2010

city: chongqing

first: shi

last: ping

address: beibei

department: school of life science

institute: southwest university

summary:
Muscle development and growth is an economically important process in the pig.The neonatal period is another important stage for the pig when the most rapid gain occurring in skeletal muscle.Gene expresseion changes during fetal and postnatal skeletal muscle development that can be used to enhance pig production efficiency, as well as for comparative developmental biology using the pig as a model for other mammalian species.
We used microarrays to detail the global programme of gene expression level at different stages of postnatal development.

overall_design: Pig skeletal muscles were selected at different stages of post-natal development for RNA extraction and hybridization on Affymetrix microarrays.So,we sampled at four time-points: within 24 hours after birth (0d),7 days after birth (7d), 14 days after birth (14d), 21 days after birth (21d).

first: Caode

last: Jiang

first: Ping

last: Shi