title: proliferating leaf, control, biological rep1

description: leaf size around 0.1mm2

value: control


title: Fog1ki/ki MEP, biological rep3

status: Public on Apr 11 2010

type: RNA

city: Philadelphia

first: Gregory

middle: D

last: Gregory

state: PA

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

country: USA

institute: Children's Hospital of Philadelphia

description: Gene expression data from Fog1 ki/ki MEP cells

hyb_protocol: Probes were hybridized to Affymetrix Mouse Gene ST1.0 array chips.

scan_protocol: All samples were amplified, labeled, hybridized, and scanned at the Penn Microarray Facility (University of Pennsylvania) according to manufacturer’s protocol.

data_processing: The raw data (.CEL files) were processed by R/Bioconductor (www.bioconductor.org), using the xps package. The probe-level data were normalized and summarized into transcript-level data by the robust multichip analysis (RMA) method. Processed data was log2-transformed for statistical analysis. Differential expression of transcripts between two sample groups was evaluated by the samr package of R/Bioconductor, and genes with a Significance Analysis of Microarray (SAM) p value of <0.01 and a fold-change ≥1.5 were used for further analysis.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lineage neg, kit pos, Sca1 neg, CD34 neg, FcgrII/III low MEP cells from Fog1 ki/ki bone marrow

label_protocol: RNA was amplified using the WT-Ovation Pico System from NuGEN. Sense transcript (ST)-cDNA was generated using the WT-Ovation Exon Module. ST-cDNA was subsequently fragmented and 3’ labeled with biotin using the WT-Ovation Biotin Module V2 (NuGEN).

growth_protocol: Flow cytometry assisted cell sorting of MEP from Fog1+/+ and Fog1 ki/ki bone marrow was performed. Cells were sorted into serum free media prior to counting and RNA extraction.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue origin

value: bone marrow

tag: strain

tag: cell type

value: megakaryocyte-erythroid progenitor


title: seedling, mannitol, biological rep3

city: Gent

first: aleksandra

last: skirycz

address: Technologiepark 927

department: Plant System Biology

country: Belgium

institute: Ghent University

description: wild type seedling 1.03 vegetative part

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)

organism: Arabidopsis thaliana

source_name: Wild type, seedling, stress

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: Biosources were dissected in RNAlater, Trizol extraction (Invitrogen) followed by clean-up by RNeasy plant mini kit (Qiagen) , according to manufacturer protocol

treatment_protocol: plant were grown on MS medium with 25mM mannitol under 16 h light/ 8 h dark cycle at 22°C

tag: stress

value: osmotic stress

tag: ecotype

tag: tissue

value: seedling (vegetative part)

tag: developmental stage

value: stage 1.03

tag: genotype

value: wild-type


title: 334649, mytotubes #165, BHLHB3 vs GFP

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description:
Human primary myotubes culture #165 infected with BHLHB3 for 48hours vs Human primary myotubes culture #165 infected with GFP for 48hours
Date:2007/12/10

hyb_protocol: Agilent : 1500.0 ng of labelled nucleic acid was hybridized at 62 degree_C during 17 hours.

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Normalized using a global Lowess method.

organism: Homo sapiens

label_protocol: Fluorescent probes were synthesized by chemical coupling of 5ug aminoallyl aRNA with cyanine 3 (Cy3) or Cy5 dyes and purified using Rneasy Mini Kit (Qiagen).

growth_protocol: Myotubes were prepared from a human skeletal muscle biopsy.

extract_protocol: Trizol

treatment_protocol: After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing BHLHB3.

value: subject #165

tag: Tissue

value: Human primary myotubes culture

treatment_protocol: After 7 days of differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing GFP.


title: PBMC 05 PUFA baseline

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using RMA

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 05

label_protocol: TThe Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

extract_protocol: PBMCs were lysed in Qiagen RLT buffer and homogenized using seringes with 0.4 mm needles, whereafter purified total RNA was isolated using Qiagen RNEasy columns

treatment_protocol: Subjects were given a shake containing either SFA or PUFA as the fatty acid source as a single challange consumption

tag: Male, 18-27 years of age


title: expanding leaf, control, biological rep1

description: leaf size around 7mm2

source_name: Wild type, expanding leaf, control

value: expanding leaf (3rd true leaf)

value: leaf 3_15DAS plants


title: Fog1ki/ki MEP, biological rep2


title: expanding leaf,mannitol, biological rep1

description: leaf size around 7mm2

source_name: Wild type, expanding leaf, stress


title: seedling, mannitol, biological rep2

description: wild type seedling 1.03 vegetative part


title: 20D +/- pool vs F53

description: Biological replicate 1 dye swap

hyb_protocol: 1µg of labelled nucleic acid was hybridized in 2X Agilent Hybridation Buffer at 67 degree_C during 17 hours

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were quantified using Genepix pro 6.0

data_processing: Lowess normalization.

source_name: 20D +/- pool

label_protocol: One microgram of total RNA  was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine (Cy)3 or Cy5 dyes, following a dye switch experimental plan. Fluorescent probes were purified using Rneasy minikit (Qiagen)

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions

value: testis


title: seedling, mannitol, biological rep1

description: wild type seedling 1.03 vegetative part


title: PBMC 04 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 04


title: F57  vs 20D +/- pool

description: Biological replicate 3


title: seedling, control, biological rep3

description: wild type seedling 1.03 vegetative part

source_name: Wild type, seedling, control


title: PBMC 03 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 03


title: Fog1+/+ MEP, biological rep2

description: Gene expression data from Fog1+/+ MEP cells

source_name: Lineage neg, kit pos, Sca1 neg, CD34 neg, FcgrII/III low MEP cells from Fog1+/+ bone marrow


title: seedling, control, biological rep2

description: wild type seedling 1.03 vegetative part


title: F56  vs 20D +/- pool

description: Biological replicate 2


title: Fog1ki/ki MEP, biological rep1


title: PBMC 02 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 02


title: Fog1+/+ MEP, biological rep1


title: F53  vs 20D +/- pool

description: Biological replicate 1


title: Fog1+/+ MEP, biological rep3


title: WAT-biopsy- weight stable control_V37_B

status: Public on Apr 10 2010

city: Update

first: Ingrid

last: Dahlman

address: Update

country: Sweden

institute: Karolinska Institute

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median

source_name: abdominal subcutaneous adipose tissue

label_protocol: Total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNA was extracted using the Nucleospin RNA11 kit (Macherey-Nagel, Duren, Germany). RNA samples were treated with RNase-free DNase (Macherey-Nagel).

tag: nutritional status

value: weight stable control


title: WAT-biopsy- weight stable control_V53_B


title: seedling, control, biological rep1

description: wild type seedling 1.03 vegetative part


title: WAT-biopsy- weight stable control_V38_B


title: WAT-biopsy- weight stable control_V40_B


title: WAT-biopsy- weight stable control_V43_B


title: WAT-biopsy- weight stable control_V44_B


title: WAT-biopsy- weight stable control_V10_B


title: WAT-biopsy- weight stable control_V20_B


title: WAT-biopsy- weight stable control_V15_B


title: WAT-biopsy- weight stable control_V26_B


title: WAT-biopsy- weight stable control_V41_B


title: WAT-biopsy- weight stable control_V3_B


title: WAT-biopsy- weight stable control_V4_B


title: WAT-biopsy- weight stable control_V7_B


title: WAT-biopsy- cachexia_V49_A

value: cachexia


title: PBMC 01 PUFA baseline

source_name: Peripheral blood mononuclear cells, PUFA shake, baseline, individual 01


title: WAT-biopsy- cachexia_V51_A


title: WAT-biopsy- cachexia_V46_A


title: WAT-biopsy- cachexia_V36_A


title: WAT-biopsy- cachexia_V18_A


title: WAT-biopsy- cachexia_V28_A


title: WAT-biopsy- cachexia_V16_A


title: WAT-biopsy- cachexia_V12_A


title: WAT-biopsy- cachexia_V17_A


title: WAT-biopsy- cachexia_V5_A


title: WAT-biopsy- cachexia_V2_A


title: WAT-biopsy- cachexia_V24_A


title: PBMC 21 PUFA 6 h after intake

source_name: Peripheral blood mononuclear cells, PUFA shake, 6 hours after intake, individual 21


title: EML.D417.48H

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

institute: Institut Paoli-Calmettes

description: EML

hyb_protocol: see Affymetrix standard protocols, www.affymetrix.com

data_processing: RMA. Controls were removed, like all genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples and a SD less than 0.15 on log2-transformed data. Thus, 10861 probe sets were selected and analysed.

source_name: lymphohematopoietic cell line

growth_protocol: EML cells were grown in RPMI 1640 medium supplemented with 20% FBS and 250 ng/ml murine SCF. COS-7, R4 MEFs, Phoenix A, and GP+E-86 retrovirus-packaging cell lines were maintained in Dulbecco's modified Eagle's medium supplemented with 10% FBS and 0.5 mg/ml sodium pyruvate. All of the media and sera were purchased from Invitrogen.

extract_protocol: Qiagen RNeasy mini kits. On column, DNase digestion was used.

treatment_protocol: EML cells were transduced by using PhoenixTM retroviral expression system (ATCC, LGC-Standards, France). Phoenix cells were first transfected with pLXSN vectors containing the c-kit constructs or pMSCVpuro- (Myr)EGFP-AKT by using Fugene 6 (Roche Applied Science, Indianapolis) according to the manufacturer’s instructions. 48 hours later, retroviral supernatants were used to infect EML cells. 24 hours after transfection, cells were selected with 0.4 mg/mL (EML cells) of geneticin (Invitrogen SARL, France) for 14 days. EML cells transfected with KIT mutants were further grown in growth factor-free medium in order to obtain autonomous populations. Cells expressing KIT variants were selected by using ARIA cell sorter (Becton Dickinson, San Jose, CA) to obtain homogenous populations.

tag: cell line

value: EML

tag: genotype/variation

value: Del417-419insY KIT mutant

tag: time point

value: 48 hours

tag: agent

value: 250 ng/mL SCF


title: WAT-biopsy- cachexia_V25_A


title: EML.D816V.48H

description: EML

scan_protocol: see Affymetrix standard protocols, www.affymetrix.com

value: D816V KIT mutant


title: EML.D816V

description: EML

label_protocol: see Affymetrix standard protocols, www.affymetrix.com


title: EML.D417

description: EML


title: JWY7_xylose_t48

status: Public on Apr 09 2010

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79250.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Agilent Feature Extraction

organism: Saccharomyces cerevisiae

source_name: pooled reference (all 120 samples)

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: pooled reference (all 120 samples)

tag: elapsed time

value: positive, XDH1 present

tag: media

value: 2% xylose in Minimal


title: JWY3_nc_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79151.gif

value: no carbon source in Minimal


title: JWY1_nc_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79128.gif

value: xylose negative, XDH1 absent


title: JWY15_nc_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79293.gif


title: JWY15_xylose_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79263.gif


title: JWY14_xylose_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79286.gif


title: JWY1_nc_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79133.gif


title: JWY1_xylose_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79267.gif


title: JWY15_xylose_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79291.gif


title: JWY14_nc_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79295.gif


title: JWY7_xylose_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79183.gif


title: JWY15_nc_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79297.gif


title: JWY3_nc_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79156.gif


title: JWY14_nc_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79258.gif


title: JWY7_xylose_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79181.gif


title: JWY1_nc_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79132.gif


title: JWY5_nc_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79163.gif


title: JWY1_xylose_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79126.gif


title: JWY14_xylose_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79269.gif


title: JWY15_nc_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79276.gif


title: JWY3_nc_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79153.gif


title: JWY14_xylose_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79255.gif


title: JWY5_nc_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79179.gif


title: JWY1_nc_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79137.gif


title: JWY14_nc_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79265.gif


title: JWY7_xylose_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79180.gif


title: JWY7_xylose_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79253.gif


title: JWY15_nc_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79299.gif


title: JWY14_nc_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79305.gif


title: JWY5_nc_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79161.gif


title: JWY5_xylose_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79172.gif


title: JWY15_xylose_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79315.gif


title: JWY7_nc_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79279.gif


title: JWY15_nc_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79280.gif


title: JWY15_xylose_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79289.gif


title: JWY3_nc_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79150.gif


title: JWY1_xylose_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79119.gif


title: JWY15_xylose_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79285.gif


title: JWY1_xylose_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79125.gif


title: JWY3_nc_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79154.gif


title: JWY3_nc_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79155.gif


title: JWY5_xylose_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79170.gif


title: JWY15_nc_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79317.gif


title: JWY5_nc_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79176.gif


title: JWY1_nc_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79130.gif


title: JWY5_nc_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79178.gif


title: JWY14_nc_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79301.gif


title: self_self_ref10_11

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79312.gif


title: JWY15_xylose_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79307.gif


title: JWY3_nc_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79146.gif


title: JWY1_nc_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79270.gif


title: JWY3_xylose_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79275.gif


title: JWY15_xylose_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79313.gif


title: JWY5_nc_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79167.gif


title: JWY1_xylose_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79121.gif


title: JWY15_xylose_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79261.gif


title: JWY14_nc_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79310.gif


title: JWY7_xylose_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79182.gif


title: JWY5_xylose_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79166.gif


title: JWY7_xylose_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79256.gif


title: JWY1_xylose_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79118.gif


title: JWY3_xylose_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79149.gif


title: Pou4f1+/+ cells, transduced with MSCV-Pou4f1 virus_WT-POU_87

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: WT POU 112108-0900823

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Raw probe intensities were background-corrected, quantile-normalized, and summarized using the R function rma.

label_protocol: RNA was linear amplified

growth_protocol: Fetal liver cells were removed, subjected to red cell lysis, and grown for 48h in RPMI 20% FBS, 1% L-Glutamine supplemented with 10 ng/mL interleukin-6, 100 ng/mL SCF, 6 ng/mL IL3, 50 ng/mL FLT3 ligand and 10 ng/mL TPO

extract_protocol: Trizol LS (Invitrogen)

treatment_protocol: Cells were transduced two consecutive days with  MSCV-based retroviruses and sorted on GFP 48 hours later.

value: MSCV-Pou4f1 virus

tag: tissue type

value: fetal liver


title: JWY7_nc_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79272.gif


title: Pou4f1-/- cells, transduced with control virus_KO_MSCV_83

description: KO MSCV 73-010909-0900819

value: control virus


title: Pou4f1+/+ cells, transduced with MSCV-Pou4f1 virus_WT-POU_82

description: WT-POU 74-010909-0900818


title: Pou4f1-/- cells, transduced with control virus_KO_MSCV_84

description: KO MSCV 74-010909-0900820


title: Pou4f1+/+ cells, transduced with control virus_Wt-MSCV_81

description: WT-MSCV 74-010909-0900817


title: Pou4f1+/+ cells, transduced with control virus_Wt-MSCV_85

description: WT MSCV 112108-0900821


title: Pou4f1-/- cells, transduced with control virus_KO_MSCV_86

description: KO MSCV 112108-0900822


title: Pou4f1+/+ cells, transduced with MSCV-Pou4f1 virus_WT-POU_80

description: WT-POU 73-010909-0900816


title: JWY14_xylose_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79271.gif


title: JWY1_nc_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79135.gif


title: JWY14_xylose_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79282.gif


title: Pou4f1+/+ cells, transduced with control virus_Wt-MSCV_79

description: WT-MSCV 73-010909-0900815


title: JWY5_nc_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79294.gif


title: JWY14_xylose_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79259.gif


title: JWY7_xylose_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79248.gif


title: JWY7_nc_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79257.gif


title: JWY15_xylose_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79287.gif


title: JWY3_nc_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79157.gif


title: JWY7_nc_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79268.gif


title: JWY5_nc_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79169.gif


title: JWY3_xylose_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79139.gif


title: JWY15_xylose_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79290.gif


title: JWY1_nc_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79129.gif


title: JWY7_nc_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79260.gif


title: JWY3_nc_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79152.gif


title: JWY15_nc_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79264.gif


title: JWY5_nc_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79171.gif


title: JWY7_nc_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79251.gif


title: JWY7_xylose_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79262.gif


title: JWY1_xylose_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79123.gif


title: JWY14_xylose_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79252.gif


title: LCL from discordant monozygotic co-twin of A_361 (HI0360)

type: other

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

description: miRNA profiling

hyb_protocol: Hybridization was performed according to the mirVana™ miRNA Probe Set protocol (Ambion).

scan_protocol: The microarrays were scanned with a ScanArray 5000 fluorescence scanner (PerkinElmer, Waltham, MA).

data_processing: The raw pixel intensity images were analyzed using IPLab image processing software package (Scanalytics, Fairfax, VA). The program performs statistical methods that have been previously described to locate specific miRNAs on the array, measure local background for each of them, and subtract the respective background from the spot intensity value (average of triplicate spots). Besides the background subtraction, the IPLab program was also used for within-array normalization and data filtering. Fluorescence ratios within the array were normalized according to a ratio distribution method at confidence level = 99.00. The filtered data from the IPLab program were then uploaded into R version 2.6.1 software package to perform array normalization across all of the samples based upon quantile-quantile (Q-Q) plots, using a procedure known as quantile normalization. After normalization, 1,237 miRNAs were detectable above background.

molecule: other

source_name: Lymphoblastoid Cell Line (LCL) derived from lymphocytes of individuals from Autism Genetic Resource Exchange (AGRE)

label_protocol: miRNA labeling and microarray hybridization were performed using Ambion’s miRNA Labeling Kit and Bioarray Essential Kit, respectively, according to the manufacturer’s instructions. Briefly, a 20-50-nucleotide tail was added to the 3’end of each miRNA in the sample using E.coli Poly (A) Polymerase. The amine-modified miRNAs were then purified and coupled to amine-reactive NHS-ester CyDye fluors (Amersham Biosciences, Piscataway, NJ). A reference design was used for microarray hybridization in this study.  The sample miRNAs were coupled with Cy3, whereas the common reference miRNA was coupled with Cy5, and two-colored miRNA microarray analyses were carried out by cohybridizing an equal amount of both miRNA samples onto one slide.

growth_protocol: LCL derived from peripheral lymphocytes of 14 male subjects were obtained from the Autism Genetic Resource Exchange (AGRE, Los Angeles, CA). The subjects included three pairs of monozygotic twins discordant for diagnosis of autism, a normal sibling for 2 of the twin pairs, two pairs of autistic and unaffected siblings, and a pair of normal monozygotic twins. These cell lines had all been used previously for gene expression profiling and thus allowed us to compare miRNA expression profiles with mRNA expression levels across the affected and control samples from both studies.  The frozen cells were cultured in L-Glutamine-added RPMI 1640 (Mediatech Inc., Herndon, VA) with 15% triple-0.1 μm-filtered fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA) and 1% penicillin-streptomycin-amphotericin (Mediatech). According to the protocol from the Rutgers University Cell and DNA Repository (which contains the AGRE samples), cultures were split 1:2 every three to four days, and cells were harvested for miRNA isolation three days after a split, while the cell lines were in logarithmic growth phase. All cell lines were cultured and harvested at the same time with the same procedures and reagents to minimize the differences in miRNA expression that might occur as a result of different cell and miRNA preparations.

extract_protocol: LCLs were disrupted in TRIzol Reagent (Invitrogen, Carlsbad, CA) and miRNAs were then extracted from the TRIzol lysate using the mirVana miRNA Isolation Kit (Ambion, Austin, TX)   according to the manufacturers’ protocols. Briefly, ethanol (100%) was added to TRIzol-extracted, purified RNA in water to bring the samples to 25% ethanol and the mixture was then passed through the mirVana glass-fiber filter which allowed passage of small RNA in the filtrate.  Ethanol was added to the filtrate to increase the ethanol concentration to 55%, and the mixture was passed through the second glass-fiber filter which immobilized the small RNAs. After washing, the immobilized small RNAs were eluted in DNase-RNase-free water (Invitrogen), yielding an RNA fraction highly enriched in small RNA species ( 200 nt). The concentration of the small RNAs in the final fraction was then measured with a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE).  To enable comparison of miRNA expression patterns across all of the samples, equal amounts of miRNAs from unaffected siblings and normal control individuals were pooled to make a common reference miRNA that was co-hybridized with each sample on the miRNA microarray.

tag: gender

value: male

tag: individual

source_name: Pooled control miRNA

tag: sample type

value: common reference


title: LCL from discordant monozygotic co-twin of A_809 (HI0810)

description: miRNA profiling


title: LCL from unaffected sibling of A_2769 (HI2772)

description: miRNA profiling

value: unaffected sibling of A_2369 (HI2357)


title: JWY1_nc_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79134.gif


title: JWY1_nc_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79131.gif


title: JWY3_xylose_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79142.gif


title: LCL from unaffected sibling of A_2369 (HI2357)

description: miRNA profiling


title: JWY15_xylose_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79266.gif


title: JWY14_nc_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79304.gif


title: JWY3_xylose_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79144.gif


title: JWY3_xylose_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79145.gif


title: JWY1_xylose_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79127.gif


title: LCL from unaffected sibling of A_809 (HI0813)

description: miRNA profiling

value: unaffected sibling of A_809 (HI0813)


title: JWY14_xylose_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79296.gif


title: LCL from unaffected sibling of A_366 (HI0365)

description: miRNA profiling

value: unaffected sibling of A_366 (HI0365)


title: JWY5_xylose_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79284.gif


title: JWY5_xylose_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79164.gif


title: JWY3_xylose_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79147.gif


title: LCL from autistic individual  No.2769 (HI2769)

description: miRNA profiling

value: autistic individual  No.2769 (HI2769)


title: LCL from normal monozygotic co-twin of C_2744 (HI2745)

description: miRNA profiling


title: LCL from normal individual No.2744 (HI2744)

description: miRNA profiling

value: normal individual No.2744 (HI2744)


title: LCL from discordant monozygotic co-twin of A_2369 (HI2368)

description: miRNA profiling


title: LCL from autistic individual  No.2369 (HI2369)

description: miRNA profiling

value: autistic individual  No.2369 (HI2369)


title: LCL from autistic individual  No.809 (HI0809)

description: miRNA profiling

value: autistic individual  No.809 (HI0809)


title: JWY14_nc_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79298.gif

value: pooled reference (all 120 samples)


title: JWY1_xylose_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79122.gif


title: JWY3_nc_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79278.gif

value: positive, XDH1 present


title: JWY5_xylose_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79173.gif

value: 2% xylose in Minimal


title: LCL from autistic individual  No.361 (HI0361)

description: miRNA profiling

value: autistic individual  No.361 (HI0361)


title: JWY3_xylose_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79138.gif


title: JWY7_xylose_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79247.gif


title: JWY15_nc_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79303.gif

value: xylose negative, XDH1 absent

value: no carbon source in Minimal


title: LCL from autistic individual  No.366 (HI0366)

description: miRNA profiling

value: autistic individual  No.366 (HI0366)


title: JWY1_xylose_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79124.gif


title: JWY5_xylose_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79158.gif


title: JWY3_nc_t24

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79148.gif


title: JWY14_xylose_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79288.gif


title: JWY5_xylose_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79168.gif


title: JWY14_xylose_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79300.gif


title: HEK293 5-azaC H3K27me3 [ChIP-chip]

type: genomic

city: Seattle

first: Vitalina

last: Komashko

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: Antibody: rabbit polyclonal H3K27me3 IgG (Millipore cat # 07-449; 3 ug per ChIP assay). No secondary

hyb_protocol: 6 ug of the Cy5-labeled ChIP sample and 6 ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 18 μl of NimbleGen Hybridization Buffer (NimbleGen Systems).After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems) and dried by centrifugation.

scan_protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)

data_processing: Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel

molecule: genomic DNA

source_name: H3K27me3 ChIP DNA from HEK293 cells treated with 5 uM 5-azacytidine for 8 days

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

growth_protocol: DMEM, 10% FBS, 2mM L-glutamine, 1% penicillin/streptomycin

extract_protocol: ChIP assay was performed following the ChIP protocol provided athttp://www.genomecenter.ucdavis.edu/farnham   and http://genomecenter.ucdavis.edu/expression_analysis.

treatment_protocol: 5-azacytidine was purchased from Sigma (cat # 2385) and dissolved in 50% acetic acid. HEK293 cells were treated with 5uM 5-azacytidine dissolved in medium for 8 days; medium was changed daily.

tag: treatment

value: 5uM 5-azacytidine for 8 days

tag: antibody

source_name: Total input DNA from HEK293 cells treated with 5uM 5-azacytidine for 8 days


title: E. coli 8624 sidA deletion mutant + AHL

first: David

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
All protocols were done according to manufacturer's specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli

source_name: E. coli 8624 sdiA deletion mutant + AHL

extract_protocol: Ambion RiboPure RNA Isolation

tag: Escherichia coli 8624 sdiA deletion mutant grown in DMEM with AHL


title: HEK293 aa H3K27me3 [ChIP-chip]

source_name: H3K27me3 ChIP DNA from HEK293 cells treated with 50% acetic acid (control)

treatment_protocol: Cells were treated with 50% acetic acid for the same time periods as the cells treated with 5-azacytidine. Amount of acetic acid was the same by volume as used for 5-azacytidine

value: 50% acetic acid

source_name: Total input DNA from HEK293 cells treated with 50% acetic acid


title: HEK293 aa 5-meC [ChIP-chip]

description: Extraction protocol specific to MeDIP samples: genomic DNA was extracted by shaking cells in digestion buffer (100mM NaCl, 10mM TrisCl, pH 8, 25mM EDTA, pH 8, 0.5% SDS) and 0.1 mg/ml Proteinase K for 12-18 hours at 50C and purified using phenol-chlorophorm extraction method. Extracted DNA was sonicated to an average size of 500 bp, denatured at 95C for 10 min and quickly chilled on ice. Immunoprecipitation of methylated DNA was performed with 4 ug mouse monoclonal 5-Methylcytidine (Eurogentec cat# BI-MECY-0100) antibody per 4 ug of sonicated genomic DNA using the same buffers as for the ChIP assays. The secondary rabbit anti-mouse IgG was purchased from MP Biomedicals (cat # 55436). Incubation with primary antibody was performed for 2 hours and for 1 hour with the secondary antibody. Antibody-DNA complexes were captured using Staph A cells, then the DNA was washed, eluted and incubated with Proteinase K. The non-specific rabbit IgG used as a negative control in the ChIP and MeDIP assays was purchased from Alpha Diagnostics (cat # 20009-5).

source_name: 5-meC MeDIP DNA from HEK293 cells treated with 50% acetic acid (control)

growth_protocol: Cells were treated with 50% acetic acid for the same time periods as the cells treated with 5-azacytidine. Amount of acetic acid was the same by volume as used for 5-azacytidine

treatment_protocol: Total input DNA from HEK293 cells treated with 50% acetic acid


title: self_self_ref10_12

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79314.gif


title: JWY14_nc_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79273.gif

tag: genotype


title: HEK293 aa H3K9me3 [ChIP-chip]

description: Antibody: rabbit polyclonal H3K9me3 IgG (Abcam cat # ab8898; 3 ug per ChIP assay). No secondary

source_name: H3K9me3 ChIP DNA from HEK293 cells treated with 50% acetic acid (control)


title: HEK293 5-azaC H3K9me3 [ChIP-chip]

source_name: H3K9me3 ChIP DNA from HEK293 cells treated with 5 uM 5-azacytidine for 8 days

growth_protocol: 5-azacytidine was purchased from Sigma (cat # 2385) and dissolved in 50% acetic acid. HEK293 cells were treated with 5uM 5-azacytidine dissolved in medium for 8 days; medium was changed daily.

treatment_protocol: Total input DNA from HEK293 cells treated with 5uM 5-azacytidine for 8 days


title: JWY7_nc_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79274.gif


title: JWY14_nc_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79277.gif


title: JWY3_xylose_t24_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79316.gif


title: JWY7_nc_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79249.gif


title: self_self_ref10_10

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79311.gif


title: E. coli 8624 sidA deletion mutant

hyb_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: E. coli 8624 sdiA deletion mutant

tag: Escherichia coli 8624 sdiA deletion mutant grown in DMEM


title: JWY3_xylose_t40

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79143.gif


title: JWY7_nc_t32

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79254.gif


title: JWY15_nc_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79318.gif


title: JWY5_xylose_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79159.gif


title: JWY7_nc_t72

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79283.gif


title: JWY15_nc_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79309.gif


title: JWY15_nc_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79308.gif


title: JWY7_xylose_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79302.gif


title: JWY3_xylose_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79140.gif


title: JWY14_nc_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79281.gif


title: JWY5_xylose_t8

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79162.gif


title: Simi White (788) Positive Pool vs Negative Pool

description: gDNA from a pooled set of "xylose positive" and "xylose negative" segregants from laboratory crossed to a wine strain of S. cerevisiae

hyb_protocol: standard Affymetrix protocols (done by Stanford Peptide and Nucleic Acid Facility)

data_processing: a simple ratio of the log2 intensities (negative/positive) was calculated for every position in the genome and plotted in R to look visually for peaks in hybridization intensity in the negative pool versus the positive pool.  The positive pool was normalized to the average difference per chromosome between the intensities of the negative vs. positive pool.

source_name: xylose positive segregant pool

label_protocol: 10 micrograms of gDNA  were digested for 5 min @ 37C with DNaseI (Invitrogen) diluted 1:5 in water.  Fragmented gDNA was labeled with 1 nmol of biotin-11-ddATP (Perkin Elmer, Boston, MA) using 30 units of terminal transferase (Promega, Madison, WI)

extract_protocol: Xylose positive segregants of Simi White (Lallemand) were crossed once to S288c (GSY147), and the resulting diploids were then sporulated.  F2 segregants were scored for xylose utilization in a TECAN plate reader.  1.5mL of overnight YPD culture of each segregant grown was spun down, resuspended, and frozen in 300μL of sorbitol solution (0.9M sorbitol, 0.1M Tris pH 8, 0.1M EDTA).  Samples were pooled by phenotype at this stage and genomic DNA was extracted as described (Treco, D.A., Curr. Protoc. Mol. Biol. Vol. 5:13.11. 1989).  The pools contained 39 positives and 39 negatives for Simi White.

tag: cross

value: "Simi White" x S288c

tag: phenotype

value: xylose positive

value: xylose negative

source_name: xylose negative segregant pool


title: JWY7_nc_t0_repeat

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79306.gif


title: JWY1_nc_t64

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79136.gif


title: JWY5_nc_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79165.gif


title: JWY14_xylose_t48

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79292.gif


title: HEK293_5azaC-4days_rep1 [gene expression]

description: SAMPLE 5

hyb_protocol: Array hybridization was performed by the Expression Analysis Core at UC Davis (http://genomecenter.ucdavis.edu/expression_analysis/) according to standard Illumina protocols

scan_protocol: Scanning was performed by the Expression Analysis Core at UC Davis (http://genomecenter.ucdavis.edu/expression_analysis/) according to standard Illumina protocols

data_processing: RNA hybridization signals were generated using BeadStudo Gene Expression Module v.3.2.3 (Illumina). To normalize gene expression data  we used the R Project for Statistical Computing v.2.7.0 (http://www.r-project.org/) and Bioconductor package (http://www.bioconductor.org/) beadarray. Quantile method was used for normalization, data was log2 transformed (beadarray package).

source_name: HEK293 cells treated with 5uM 5-azacytidine for 4 days, biological replicate 1

label_protocol: Biotinylated RNA was prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: The human HEK293 embryonal kidney cells were obtained from Dr David Segal's laboratory at the Genome and Biomedical Science Facility, UC Davis (ATCC cat# CRL-1573) and grown in DMEM, 10% FBS, 2mM L-glutamine and 1% penicillin/streptomycin

extract_protocol: Total RNA was prepared from 5x10e6 cells using RNAeasy Kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: 5-azacytidine was purchased from Sigma (cat # 2385) and dissolved in 50% acetic acid. HEK293 cells were treated with 5uM 5-azacytidine dissolved in medium for 4 days; medium was changed daily.

tag: cell type

value: HEK293 cells

tag: dose

tag: time

value: 4 days


title: JWY1_xylose_t16

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79120.gif

tag: reference


title: JWY5_xylose_t0

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79160.gif

tag: elapsed time


title: HEK293_5azaC-8days_rep2 [gene expression]

description: SAMPLE 4

source_name: HEK293 cells treated with 5uM 5-azacytidine for 8 days, biological replicate 2

tag: agent

value: 8 days


city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

country: Israel

institute: Hebrew University

description: Gene expression data from undifferentiated BJ-TERT derived induced pluripotent stem cell line 28 replicate 1

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

label_protocol: 300ng total RNA, Affymetrix protocol

growth_protocol: standard HESC growth conditions as described in Pick et al. (2009). iPSC lines were induced by infection with a combinationn of the human OCT4, SOX2, MYC and KLF4 genes packaged in pMXs retroviral vectors, as described in Pick et al. (2009)

extract_protocol: Tri reagent

treatment_protocol: total RNA was isolated from undifferentiated pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.

value: Undifferentiated human induced pluripotent stem cells

tag: age

value: passage 15

tag: cell line


description: Gene expression data from undifferentiated H9 Human embryonic stem cells replicate 2

value: Undifferentiated human embryonic stem cells

value: passage 42

value: H9 Human embryonic stem cells


title: HEK293_5azaC-8days_rep1 [gene expression]

description: SAMPLE 3

source_name: HEK293 cells treated with 5uM 5-azacytidine for 8 days, biological replicate 1


title: E. coli 8624 WT + AHL

description:
All protocols were done according to manufacturer's specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: E. coli 8624 + AHL

tag: Escherichia coli 8624 grown in DMEM with AHL


description: Gene expression data from undifferentiated primary foreskin fibroblast derived induced pluripotent stem cell line 1

value: passage 5


description: Gene expression data from undifferentiated BJ-TERT derived induced pluripotent stem cell line 29

value: passage 14


description: Gene expression data from undifferentiated induced pluripotent stem cell clone IMR9.4

hyb_protocol: Affymetrix protocol, 11ug cRNA

data_processing: Affymetrix Expression Console MAS5

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: Cells were maintained on mitomycin C (MMC)-inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)].  Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).

extract_protocol: total RNA from 3975.2 p9 and 3975.4 p6 was isolated using Stratagene RNA isolation kit,  RNA from IMR9.4 p9 was isolated using Qiagen Rneasy mini kit

value: Undifferentiated induced pluripotent stem cells

value: passage 9


title: JWY5_nc_t56

description:
Simple annotation: Carbon sources, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79177.gif

source_name: pooled reference (all 120 samples)

value: pooled reference (all 120 samples)

value: xylose negative, XDH1 absent

tag: media

value: no carbon source in Minimal


description: Gene expression data from undifferentiated BJ-TERT derived induced pluripotent stem cell line 28 replicate 2


description: Gene expression data from undifferentiated induced pluripotent stem cell clone 3975.4

value: passage 6


description: Gene expression data from undifferentiated H9 Human embryonic stem cells replicate 3


description: Gene expression data from undifferentiated H9 Human embryonic stem cells replicate 1


title: HEK293_aa_rep1 [gene expression]

description: SAMPLE 1

source_name: HEK293 cells treated with 50% acetic acid (control), biological replicate 1

treatment_protocol: Cells were treated with 50% acetic acid, medium was changed daily   Amount of acetic acid was the same by volume as used for 5-azacytidine

value: control (50% acetic acid)


title: Mut.nt.3

status: Public on Apr 08 2010

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
Q111 striatal cell line treated with control
4068264015_D

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

label: Biotin

source_name: Mut, nt

label_protocol: Illumina protocol

extract_protocol: Q7 and Q111 have been treated with ZDON (50µM) or Boc-DON (50µM) or cystamine (250µM) for 12 hours. Cells were washed with cold PBS and RNA has been extracted with the RNAgents Total RNA Isolation System Kit (Promega), as directed by the manufacturer. Briefly, cells were lysed in chilled Denaturating Solution and the RNA was precipitated and isolated through Phenol:Chloroform:Isoamyl Alchool extraction.

treatment_protocol: Cells were treated with ZDON, Boc-DON, CystamineA, and Control

value: Control


description: Gene expression data from undifferentiated induced pluripotent stem cell clone 3975.2


description: Gene expression data from undifferentiated induced pluripotent stem cell clone hIPS18_P10_CM

source_name: undifferentiated induced pluripotent stem cell clone hIPS18 after 10 passages growth in mouse embryonic fibroblasts conditioned medium

value: passage 63


title: Mut.z.3

description:
Q111 striatal cell line treated with ZDON
4068264015_B

source_name: Mut, z

value: ZDON


title: WT.z.3

description:
Q7 striatal cell line treated with ZDON
4068264015_F

source_name: WT, z

value: Q7 (WT)


title: WT.cystA.3

description:
Q7 striatal cell line treated with CystamineA
4068264015_E

source_name: WT, cystA

value: CystamineA


title: HEK293_aa_rep2 [gene expression]

description: SAMPLE 2

value: HEK293 cells


title: WT.cystA.2

description:
Q7 striatal cell line treated with CystamineA
4068264031_F


title: WT.boc.2

description:
Q7 striatal cell line treated with Boc-DON
4068264031_H

source_name: WT, boc

value: Boc-DON


title: Mut.cystA.3

description:
Q111 striatal cell line treated with CystamineA
4068264015_A

source_name: Mut, cystA


title: Mut.boc.3

description:
Q111 striatal cell line treated with Boc-DON
4068264015_C

source_name: Mut, boc


title: Mut.boc.2

description:
Q111 striatal cell line treated with Boc-DON
4068264031_E


title: WT.nt.3

description:
Q7 striatal cell line treated with control
4068264015_H

source_name: WT, nt


title: Mut.cystA.2

description:
Q111 striatal cell line treated with CystamineA
4068264031_G


title: WT.nt.2

description:
Q7 striatal cell line treated with control
4068264031_C


title: Mut.nt.2

description:
Q111 striatal cell line treated with control
4068264031_B


title: WT.z.2

description:
Q7 striatal cell line treated with ZDON
4068264031_A


title: HEK293_5azaC-4days_rep2 [gene expression]

description: SAMPLE 6

source_name: HEK293 cells treated with 5uM 5-azacytidine for 4 days, biological replicate 2

value: 4 days


title: Mut.nt.1

description:
Q111 striatal cell line treated with control
4068264040_E


title: Mut.boc.1

description:
Q111 striatal cell line treated with Boc-DON
4068264040_F


title: Mut.z.1

description:
Q111 striatal cell line treated with ZDON
4068264040_G


title: WT.nt.1

description:
Q7 striatal cell line treated with control
4068264040_A


title: WT.z.1

description:
Q7 striatal cell line treated with ZDON
4068264040_C


title: Mut.z.2

description:
Q111 striatal cell line treated with ZDON
4068264031_D


title: Mut.cystA.1

description:
Q111 striatal cell line treated with CystamineA
4068264040_H


title: WT.cystA.1

description:
Q7 striatal cell line treated with CystamineA
4068264040_D


title: WT.boc.1

description:
Q7 striatal cell line treated with Boc-DON
4068264040_B


title: Puerto Rican 19

city: New York

first: Harry

last: Ostrer

state: NY

address: 550 First Avenue, MSB 136

department: Department of Pediatrics

institute: NYU Langone Medical Center

description: sample id: D0016206

hyb_protocol: Extraction of DNA from peripheral blood at North Shore - Long Island Jewish, following standard Illumina labeling, hybridization, scanning, and genotype protocol.  See illumina.com

data_processing: Genotyped using Illumina 610-Quad Genotyping BeadChips, which use the SNPs on the 550-v3 Genotyping BeadChip plus an additional 60,000 SNPs for CNV not analyzed in present study.  See illumina.com

source_name: NYHP

label_protocol: standard Illumina protocol

tag: gender

value: Male

tag: tissue

value: Peripheral blood

tag: disease state

value: Healthy control


title: Puerto Rican 2

description: sample id: D0004387

scan_protocol: Extraction of DNA from peripheral blood at North Shore - Long Island Jewish, following standard Illumina labeling, hybridization, scanning, and genotype protocol.  See illumina.com


title: Puerto Rican 24

description: sample id: D0021343

extract_protocol: Extraction of DNA from peripheral blood at North Shore - Long Island Jewish, following standard Illumina labeling, hybridization, scanning, and genotype protocol.  See illumina.com


title: Puerto Rican 12

description: sample id: D0012663


title: Puerto Rican 16

description: sample id: D0014724


title: Puerto Rican 8

description: sample id: D0010754


title: Puerto Rican 22

description: sample id: D0019673


title: Puerto Rican 18

description: sample id: D0016090


title: Puerto Rican 4

description: sample id: D0004522


title: Puerto Rican 26

description: sample id: D0022009


title: Puerto Rican 25

description: sample id: D0021827


title: Puerto Rican 27

description: sample id: D0022087


title: Puerto Rican 10

description: sample id: D0010785


title: Puerto Rican 5

description: sample id: D0010430


title: Puerto Rican 6

description: sample id: D0010572


title: Puerto Rican 17

description: sample id: D0015501


title: Puerto Rican 23

description: sample id: D0021237


title: Puerto Rican 14

description: sample id: D0013360


title: Puerto Rican 3

description: sample id: D0004510


title: Puerto Rican 9

description: sample id: D0010760


title: Puerto Rican 1

description: sample id: D0002987


title: Puerto Rican 20

description: sample id: D0017383


title: Puerto Rican 15

description: sample id: D0014630


title: Puerto Rican 21

description: sample id: D0017472


title: Ecuadorian 20

description: sample id: D0024695


title: Puerto Rican 13

description: sample id: D0013354


title: Puerto Rican 11

description: sample id: D0010923

value: Female


title: Ecuadorian 19

description: sample id: D0020846


title: Puerto Rican 7

description: sample id: D0010742


title: Ecuadorian 17

description: sample id: D0020655


title: Ecuadorian 10

description: sample id: D0013765


title: Ecuadorian 14

description: sample id: D0017286


title: Ecuadorian 18

description: sample id: D0020753


title: Ecuadorian 13

description: sample id: D0017270


title: Ecuadorian 9

description: sample id: D0013293


title: Ecuadorian 11

description: sample id: D0016073


title: Dominican 25

description: sample id: D0017258


title: Ecuadorian 4

description: sample id: D0010717


title: Ecuadorian 2

description: sample id: D0009809


title: Ecuadorian 8

description: sample id: D0012402


title: Dominican 22

description: sample id: D0011113


title: Dominican 24

description: sample id: D0017077


title: Ecuadorian 6

description: sample id: D0011036


title: Ecuadorian 15

description: sample id: D0017592


title: Ecuadorian 16

description: sample id: D0019481


title: Dominican 19

description: sample id: D0011034


title: Dominican 26

description: sample id: D0018717


title: Dominican 20

description: sample id: D0011038


title: Dominican 21

description: sample id: D0011098


title: Ecuadorian 12

description: sample id: D0016094


title: Dominican 23

description: sample id: D0015122


title: Ecuadorian 1

description: sample id: D0009798


title: Dominican 18

description: sample id: D0011033


title: Rhodobacter capsulatus SBRM1 Stationary 1

city: St. John's

first: Ryan

middle: G

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

country: Canada

institute: Memorial University

description: Target preparation, labeling, hybridization and scanning performed at Michael Smith Genome Science Center, Vancouver, BC

hyb_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 6: Prokaryotic Target Hybridization, page 119-126

scan_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 7: Prokaryotic Arrays: Washing, Staining and Scanning page 127-152.

data_processing:
Raw data was RMA normalized after scanning
Analyzed using GeneSpring v7.2 (Agilent Technologies)
Further normalized in GeneSpring (per chip) to the 50th percentile

organism: Rhodobacter capsulatus

source_name: R. capsulatus SBRM1 Stationary growth phase

label_protocol: As per described in Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev. 2) - Chapter 5: Prokaryotic Target Preparation, page 101-118

growth_protocol: Growth Conditions: YPS medium, Photosynthetic

extract_protocol: As per described in RNeasy Mini Handbook 3rd Ed (Qiagen Inc.), Protocol for Isolation of Total RNA from Bacteria, pages 56-60.

tag: strain

value: SBRM1 (SB1003 ctrA mutant)

tag: growth phase

value: Stationary


title: Ecuadorian 5

description: sample id: D0011035


title: Rhodobacter capsulatus SBRM1 Stationary 3


title: Rhodobacter capsulatus SBRM1 Stationary 2


title: Dominican 17

description: sample id: D0010990


title: Rhodobacter capsulatus SBRM1 Log 2

source_name: R. capsulatus SBRM1 Logarithmic growth phase

value: Logarithmic


title: Rhodobacter capsulatus SBRM1 Log 3


title: Rhodobacter capsulatus SB1003 Stationary 3

source_name: R. capsulatus SB1003 Stationary growth phase


title: Rhodobacter capsulatus SBRM1 Log 1


title: Hyperox.inf.2

city: Canberra

first: Yuan

last: Zhu

state: ACT

address: Bldg 46, RSBS, ANU

department: Research School of Biology

country: Australia

institute: Australian National University

description: mouse retina, hyperoxia exposed, inferior half, rep 2

hyb_protocol: 7.5 ug of fragmented and labeled DNA target were used. Heat hybridization mixture at 99ْC for 5 mins (in lab heat block), then cool to 45ْC (in lab heat block) for 5 mins and centrifuge at max speed for 5 min. Inject approx 100uL of sample into array. Tough Spot the holes over the septa and immediately place the array in 45ْC hybridization oven at 60rpm for 17hours. Arrays were washed and stained in the Fluidics Station using the Prime_450 protocol.

scan_protocol: Arrays were scanned using the Affymetrix Launcher. For Mouse, use MoGene 1_0-st-v1 universal Module and the FS450_0007 fluidics protocol.

data_processing: CEL files were imported into Partek Genomics Suite, with the following normalization of their configuration: Probes to import - interrogating probes; Probe filtering - include core; Background correction - RMA background; Log base - 2; Probeset summarization - Median Polish.

label_protocol: Staining, hybridization, washing and scanning of the array were performed at the Biomolecular Resource Facility at the John Curtin School of Medical Research, Australian National University, following manufacturers’ protocols. Biotinylated sense-strand DNA targets from the entire expressed genome were prepared from 100ng total RNA, according to the Affymetrix Whole Transcript (WT) Sense Target labeling Assay Manual.

growth_protocol: C57BL/6J mice, a hyperoxia-vulnerable strain , were used for this study. Mice were raised in dim cyclic illumination (12 hr 5 lux, 12 hr dark) and maintained in this level of lighting during the period of experiment.

extract_protocol: RNA extraction was performed using a combination of TRIzol Reagent (Invitrogen™ life technologies, Carlsbad, CA) and RNAqueous-micro kit (Ambion, Foster City, CA). TRIzol was used to isolate the RNA and the RNAqueous kit was used to purify and DNase-treat the RNA.

treatment_protocol: At the age of P (postnatal) 83-90, some mice were exposed to constant hyperoxia (75% O2) for 14 days. Oxygen-exposed animals were euthanized at the end of the period of hyperoxia; controls were euthanized at the same age. Retinas were removed and divided into superior and inferior halves. Retinal samples from 2 animals (1 male and 1 female) were pooled for each condition.

tag: treatment

value: Hyperoxia

value: inferior retina


title: Hyperox.sup.2

description: mouse retina, hyperoxia exposed, superior half, rep 2

value: superior retina


title: Dominican 16

description: sample id: D0010987


title: Rhodobacter capsulatus SB1003 Stationary 2


title: Dominican 27

description: sample id: D0022095


title: Dominican 12

description: sample id: D0010865


title: Rhodobacter capsulatus SB1003 Stationary 1


title: Rhodobacter capsulatus SB1003 Log 3

source_name: R. capsulatus SB1003 Logarithmic growth phase


title: Rhodobacter capsulatus SB1003 Log 2


title: control.sup.2

description: mouse retina, under normoxia condition, superior half, rep 2

value: Control (normoxia)


title: Dominican 13

description: sample id: D0010876


title: Dominican 14

description: sample id: D0010980


title: Rhodobacter capsulatus SB1003 Log 1

data_processing:
Raw data was RMA normalized after scanning
Analyzed using GeneSpring v7.2 (Agilent Technologies)
Further normalized in GeneSpring (per chip) to the 50th percentile.

extract_protocol: As per described in RNeasy Mini Handbook (Qiagen Inc.), Protocol for Isolation of Total RNA from Bacteria, pages 56-60.


title: Hyperox.inf.1

description: mouse retina, hyperoxia exposed, inferior half, rep 1


title: Dominican 15

description: sample id: D0010984


title: Ecuadorian 7

description: sample id: D0011419


title: control.inf.2

description: mouse retina, under normoxia condition, inferior half, rep 2


title: SYNW1019_mutant_bsy89280d0055_rep6

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

institute: Macquarie University

description: This slide measures gene expression of a ptrA mutant under phosphorus-deplete conditions as compared to gene expression of wild-type WH8102 under the same conditions.

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a total of 8 70-mers at 2 ng/microliter each.  The sequences are:  At2g14610a_219_rev - AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGGACAA; At2g14610b_265_rev - AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev - TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev - CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG). Dry using a speed vac. Make pre-hybridization buffer by combining: 0.5 g BSA; 37 mL DEPC water; 12.5 mL 20X SSC; 0.5 mL 10% SDS. Incubate pre-hybridization buffer for 20 minutes at 42 degrees C. Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar. Incubate for 20 minutes at 42 degrees C. Make hybridization buffer by combining: 500 microliters fomamide; 250 microliters 20X SSC; 10 microliters 10% SDS; 240 microliters DEPC water. Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter. Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer. Add 60 microliters hybridization buffer to speed vac-dried probes. Put slide into pre-hybridization buffer in coplin jar. Incubate for 45 minutes at 42 degrees C. Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand. Dry slide by spinning. Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature. Dip in 100% EtOH and dry with a Chem Wipe. Heat probes for 15 minutes at 95 degrees C with occassional "flicking" to resuspend probes. Remove probes from heat block and centrifuge for 2 minutes at 15,000g. Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip. Hybridize overnight at 42 degrees C. Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C. Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature. Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature. Dry slide by spinning.

scan_protocol: Slide were scanned at 10 micrometer resolution using an Axon 4000B scanner with GenePix 4.0 software.

data_processing: Tiff images were processed using TIGR-Spotfinder (www.tigr.org/software) with Otsu thresholding, a minimum spot size of 10 and a maximum spot size of 15, and applying the default quality control filter options.  The data were normalized ignoring controls with the LOWESS algorithm in block mode with a smooth parameter of 0.33 by using TIGR-MIDAS (www.tigr.org/software).

organism: Parasynechococcus marenigrum WH 8102

source_name: wild type WH8102 MO8r-WH8102-w5

label_protocol:
Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the MegaScript Kit (Ambion) by combining for Cy5 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
4.7 microliters 13.279 ng/microliter ltp6 RNA;
11.8 microliters 21.313 ng/microliter rcp1 RNA;
40.7 microliters 23.23 ng/microliter nac RNA;
4.6 microliters 18.177 ng/microliter xcp2 RNA;
14.7 microliters 11.436 ng/microliter prk RNA;
18.9 microliters 11.084 ng/microliter tim RNA;
826.5 microliters water.
And for Cy3 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
1.6 microliters 13.279 ng/microliter ltp6 RNA;
3.9 microliters 21.313 ng/microliter rcp1 RNA;
13.6 microliters 23.23 ng/microliter nac RNA;
13.9 microliters 18.177 ng/microliter xcp2 RNA;
44.1 microliters 11.436 ng/microliter prk RNA;
56.8 microliters 11.084 ng/microliter tim RNA;
788.1 microliters water.
To label RNA sample combine:
4 micrograms RNA;
2 microliters 3 mg/mL random hexamers (Invitrogen);
2 microliters arabidopsis spike-in control RNA;
DEPC water to a final volume to 17.5 microliters.
Mix and incubated at 70 degrees C for 10 minutes.
Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.
Add:
6 microliters 5X Superscript II buffer (Invitrogen);
3 microliters 0.1 M dithiothreitol;
1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;
2 microliters SuperScript II (Invitrogen).
Mix and incubated overnight at 42 degrees C.
Add:
10 microliters 1 M NaOH;
10 microliters 0.5 M EDTA.
Incubate for 15 minutes at 65 degrees C.
Add:
25 microliters 1 M Tris pH 7.4;
400 microliters PB buffer (Qiagen).
Apply sample to QIAquick column (Qiagen).
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4 with 9.5 mL 1M K2HPO4).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Dry sample using a speed vac.
Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).
Allow the sample to resuspend for 15 minutes at room temperature.
Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.
Incubate for 1 hour at room temperature in the dark.
Add 4.5 microliters 4 M hydroxylamine.
Incubate for 15 minutes at room temperature in the dark.
Add:
35 microliters 100 mM NaOAc pH 5.2;
500 microliters PB buffer.
Apply to Qiaquick column.
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters PE buffer (Qiagen).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters EB buffer (Qiagen).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Check quality of probes spectrophotometrically from 200nm to 700nm.
Store at -80 degrees C.

growth_protocol: Cells were grown in 1 liter of artificial seawater (SOW) containing 4.5 millimolar NaNO3, 90 micromolar Na2PO4, 100 micromolar NH4Cl, 13.4 micromolar Na2EDTA, 10 micromolar Na2CO3, and 10 micromolar phosphate to just after onset of phosphatase activity in wild-type WH8102 (~125-150 hours after inoculation).

extract_protocol: RNA was extracted from one litre of harvested exponential phase cells using Trizol (Invitrogen) according to the manufacturer's recommendation. RNA was resuspended in 100 microliters DEPC-treated water. RNA was digested twice with DNase I (Qiagen) using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA yield and purity were determined by measuring optical density spectrophotometrically at 260 and 280 nm. RNA was stored at -80 degrees C.

value: wild type

source_name: ptrA mutant MO7r-synw1019-p5

value: ptrA mutant


title: Hyperox.sup.1

description: mouse retina, hyperoxia exposed, superior half, rep 1


title: A.niger_pH5_xylose_8xNH4Cl_-1.5h

city: Zeist

first: Machtelt

last: Braaksma

address: Utrechtseweg 48

institute: TNO

description: the time indicated at the sample title indicates the time point each sample was collected prior to (-xh) or after (+xh) carbon souce depletion.

hyb_protocol: Washing, staining, and hybridization was done according to the Hybridization, Wash, and Stain kit (Affymetrix) according to the manufacturers' recommendations.

scan_protocol: Arrays were scanned on an Agilent G2500A Gene Array scanner. Pixel value was 3 um, wavelength 570 nm.

data_processing: Raw signal intensities, detection p-values, and present/absent calls were derived using Microarray Suite Software version MAS5 (Affymetrix).

organism: Aspergillus niger

source_name: A.niger, pH5, xylose, 8xNH4Cl, late exponential growth phase

label_protocol: Extracted total RNA was processed using the Bioarray High Yield RNA transcript labeling kit (Enzo). 15 ug of cRNA was used for labeling.

growth_protocol: Fermentor cultures were grown in minimal medium (MM) at a constant temperature of 30 ± 0.5 ºC and with differing combinations of carbon source (either 277,5 mM glucose or 333,0 mM xylose), nitrogen source (NH4Cl or NaNO3) and nitrogen concentration (4x: 282·4 mM; 8x: 564·8 mM), and pH (pH4 or pH5) of the medium (M. Braaksma, A.K. Smilde, M.J. van der Werf, P.J. Punt, submitted for publication). Fermentor inoculum was pre-cultured in baffled 500 ml Erlenmeyer flasks containing 100 ml MM (pH6.5) supplemented with the carbon source and nitrogen source concentrations corresponding to fermentor conditions. These flasks were inoculated with 10^6 spores per liter and incubated in a rotary shaker at 125 rpm until approximately half of the available carbon source was consumed. Fermentor cultures were carried out in 6.6-liter fermentors (New Brunswick Scientific) with 5.0 liters of MM. The fermentors were inoculated with 4% (weight/vol) pre-culture. To prevent foaming, 1% (vol/vol) Struktol J-673 antifoam was added to the medium and additional antifoam was added during cultivation when necessary. Each fermentor was sparged with 75 liters/h of air with the stirrer speed set at 400 rpm at the start of the cultivation. When dissolved oxygen tension levels dropped below 20%, the stirrer speed was automatically increased to maintain oxygen tension at 20% or until the maximum of 1000 rpm was reached. The pH was controlled by automatic addition of 8 M KOH or 1.5 M H3PO4. The culture was allowed to grow for at least twice the time it took to consume all carbon source.

extract_protocol: Frozen mycelium was ground using a mortar and pestle, followed by a trizol-chloroform extraction using the Qiagen Rneasy mini columns according to the “yeast protocol”.

treatment_protocol: Samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion. The amount of sample collected depended on the concentration of biomass atthat time point. Collected samples were quenched immediately in methanol at -45 ºC as described previously (Pieterse B., R. H. Jellema, M. J. van der Werf. 2006. Quenching of microbial samples for increased reliability of microarray data. J. Microbiol. Methods 64:207-216.) and centrifuged at -20 ºC to remove supernatant. Biomass was frozen into liquid nitrogen and stored at -80 ºC until further use.

tag: carbon source

value: xylose

tag: nitrogen source

tag: nitrogen concentration

tag: ph of the medium

tag: time point relative to carbon source depletion


title: Dominican 11

description: sample id: D0010858


title: SYNW1019_mutant_bsy89280d0054_rep5


title: Dominican 6

description: sample id: D0010751


title: control.sup.1

description: mouse retina, under normoxia condition, superior half, rep 1


title: control.inf.1

description: mouse retina, under normoxia condition, inferior half, rep 1


title: SYNW1019_mutant_bsy89280d0053_rep3

source_name: wild type WH8102 MO4r-WH8102-wt2

source_name: ptrA mutant MO2r-synw1019-p2


title: A.niger_pH4_glucose_8xNH4Cl_+23.5h_rep2

source_name: A.niger, pH4, glucose, 8xNH4Cl, late stationairy growth phase

value: glucose


title: A.niger_pH5_glucose_8xNH4Cl_-1.5h

source_name: A.niger, pH5, glucose, 8xNH4Cl, late exponential growth phase


title: UMASS Hall

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

description: GFF file shows signal intensities for both channels.

hyb_protocol: Arrays were co-hybridized with both Cy3-labeled DNA (experimental strain) and Cy5-labeled DNA (reference strain) for 14 hours at 42C.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner at 532nm and 635nm.

data_processing: Signal intensities were extracted and normalized log2 ratio data were obtained using Nimblescan v. 2.3 software (Nimblegen).

organism: Clostridium botulinum

source_name: UMASS Hall

label_protocol: 1 ug of genomic DNA was labled with Cy3 random primers and Klenow fragments

extract_protocol: Epicenter MasterPure DNA Purification kit (Madison, WI)

value: UMASS Type A

tag: toxin subtype

source_name: ATCC 3502

label_protocol: 1 ug of genomic DNA was labled with Cy5 random primers and Klenow fragments

value: ATCC 3502 Type A


title: Dominican 8

description: sample id: D0010766

value: Male


title: SYNW1019_mutant_bsy89280d0052_rep2


title: Dominican 10

description: sample id: D0010857

value: Peripheral blood


title: A.niger_pH4_glucose_8xNH4Cl_+23.5h_rep1


title: A.niger_pH4_glucose_8xNH4Cl_-0.5h_rep2

source_name: A.niger, pH4, glucose, 8xNH4Cl, late exponential growth phase


title: Dominican 1

description: sample id: D0010169

value: Healthy control


title: Dominican 9

description: sample id: D0010855


title: A.niger_pH4_glucose_8xNH4Cl_-0.5h_rep1


title: Dominican 4

description: sample id: D0010729


title: A.niger_pH4_xylose_8xNH4Cl_+22.5h

source_name: A.niger, pH4, xylose, 8xNH4Cl, late stationairy growth phase


title: A.niger_pH4_xylose_4xNH4Cl_+23h

source_name: A.niger, pH4, xylose, 4xNH4Cl, late stationairy growth phase


title: Dominican 2

description: sample id: D0010722

source_name: NYHP


title: A.niger_pH5_xylose_8xNaNO3_+2h

source_name: A.niger, pH5, xylose, 8xNaNO3, stationairy growth phase


title: Ecuadorian 3

description: sample id: D0010017


title: SYNW1019_mutant_bsy89255d0024_rep4


title: Dominican 3

description: sample id: D0010727


title: SYNW1019_mutant_bsy89255d0023_rep1


title: Dominican 7

description: sample id: D0010752


title: A.niger_pH4_glucose_4xNaNO3_+25.5h

source_name: A.niger, pH4, glucose, 4xNaNO3, late stationairy growth phase


title: Colombian 26

description: sample id: D0025102


title: A.niger_pH4_glucose_4xNaNO3_+55.5h


title: A.niger_pH5_glucose_4xNH4Cl_+3.75h

source_name: A.niger, pH5, glucose, 4xNH4Cl, late exponential growth phase


title: A.niger_pH5_glucose_8xNaNO3_-1h

source_name: A.niger, pH5, glucose, 8xNaNO3, late exponential growth phase


title: A.niger_pH5_xylose_4xNH4Cl_-3.5h

source_name: A.niger, pH5, xylose, 4xNH4Cl, late exponential growth phase


title: Dominican 5

description: sample id: D0010733


title: A.niger_pH4_xylose_4xNaNO3_+13h

source_name: A.niger, pH4, xylose, 4xNaNO3, late stationairy growth phase


title: A.niger_pH4_glucose_4xNH4Cl_+24h

source_name: A.niger, pH4, glucose, 4xNH4Cl, late stationairy growth phase


title: A.niger_pH4_xylose_8xNaNO3_+22.5h

source_name: A.niger, pH4, xylose, 8xNaNO3, late stationairy growth phase


title: A.niger_pH5_xylose_4xNaNO3_0h

source_name: A.niger, pH5, xylose, 4xNaNO3, stationairy growth phase


title: A.niger_pH5_glucose_4xNaNO3_+5h

source_name: A.niger, pH5, glucose, 4xNaNO3, stationairy growth phase


title: Colombian 19

description: sample id: D0017450


title: Colombian 23

description: sample id: D0018876


title: A.niger_pH4_glucose_8xNaNO3_-1h

source_name: A.niger, pH4, glucose, 8xNaNO3, late exponential growth phase


title: Colombian 21

description: sample id: D0018861


title: Colombian 24

description: sample id: D0024360


title: Colombian 18

description: sample id: D0016011


title: Colombian 17

description: sample id: D0015717


title: PC-deficient mutant_virulence-induced_rep3

status: Public on Apr 07 2010

city: Bochum

first: sonja

last: klüsener

address: Universitätsstrasse 150

country: Germany

institute: Ruhr-Universität Bochum

description: This sample is of Agrobacterium tumefaciens str. C58 DpmtA Dpcs mutant in which the PC-biosynthesis genes pmtA (ATU0300) and pcs (ATU1793) are deleted. The cells were grown under virulence-induced conditions. It is the third of three mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems, Inc (Madison, USA) according to the NimbleGenTM Arrays User´s Guide for Gene Expression Analysis (Version 3.0).

scan_protocol: Array scanning was performed by NimbleGen Systems, Inc (Madison, USA) according to the NimbleGenTM Arrays User´s Guide for Gene Expression Analysis (Version 3.0).

data_processing:
The raw data (.pair file) was subjected to RMA and quantile normalization (Nimble ScanTM). Data were further analyzed using the GeneSpring gene expression analysis software Version 7.3 (Agilent). The experiment was normalized with the default settings for Affymetrix arrays. First, data was transformed to set measurements of below 0.01 to 0.01 followed by a per-chip normalization to the 50th percentile and a per-gene normalization to median.
For statistical comparisons, the student t-test with a P-value threshold of 0.05 was applied. Comparing cultivation conditions, genes were considered to be differentially expressed at a fold change of >±2.

organism: Agrobacterium fabrum str. C58

label_protocol: cDNA production and cDNA labeling were performed by NimbleGen Systems, Inc (Madison, USA) according to the NimbleGenTM Arrays User´s Guide for Gene Expression Analysis (Version 3.0).

growth_protocol: A. tumefaciens C58 wild type and mutant (DpmtA Dpcs) cells were grown in 50 ml AB minimal medium (Schmidt-Eisenlohr et al. 1999, J. Bacteriol. 181:7485-92) to an OD600 nm of 0.2 at 30°C. To induce virulence gene expression 0.1 mM acetosyringone was added. Control cultures (non-induced) were treated with solvent (DMSO) only. Cells were further incubated for 16 h at 23°C.

extract_protocol: Total RNA was isolated with the hot phenol-extraction procedure described previously (Babst et al. 1996, Mol. Microbiol. 19:827-39). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 200 µg) was treated with 100 U of recombinant DNase I (Roche, Mannheim, Germany) for 30 min at 37°C in a reaction volume of 110 µl. SUPERase•InTM (100 U; Ambion, Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen, Hilden, Germany) and the eluted RNA was checked again for integrity by agarose gel electrophoresis.

tag: genotype

value: DpmtA Dpcs deletion mutant

tag: phenotype

value: motility defect; altered biofilm formation and stress adaptation


title: PC-deficient mutant_virulence-induced_rep2

description: This sample is of Agrobacterium tumefaciens str. C58 DpmtA Dpcs mutant in which the PC-biosynthesis genes pmtA (ATU0300) and pcs (ATU1793) are deleted. The cells were grown under virulence-induced conditions. It is the second of three mutant biological replicates used in this experiment, each from separate cultures.


title: Colombian 16

description: sample id: D0014721


title: Es16, Ectocarpus siliculosus tiling array Chip8

city: Los Altos

first: Manoj

last: Samanta

address: 2240 Homestead Court #309

institute: Systemix Institute

description: A High-Resolution Transcriptome Map of the Ectocarpus siliculosus

hyb_protocol: Hybridization was performed by Nimblegen at their Iceland core facility using Nimblegen protocol.

scan_protocol: Features were scanned using Nimblescan software.

data_processing: Custom software tools were used for data processing. Quantile normalization was performed with data on all arrays.

organism: Ectocarpus siliculosus

source_name: genomic DNA from ectocarpus

label_protocol: Standard Nimblegen protocol was used to generate labeled DNA from genomic DNA.

extract_protocol: Genomic DNA was extracted from cells of ectocarpus. The DNA extraction protocol described by Apt et al.^2 was optimised for the Ec 32 strain. About one gram of tissue was ground to a powder under liquid nitrogen in a mortar and pestle using sand. After addition of 2 ml of extraction buffer (100 mM Tris-HCl pH 7.5, 1.5 M NaCl, 2% CTAB, 50 mM EDTA pH 4.5, 50 mM DTT) the tissue was extracted further in a Wheaton glass grinding tube. Extraction buffer was then added to 15 ml final volume, the sample shaken vigorously for 10 min and then incubated at 55°C for 2 hours in the presence of 25 units of proteinase K. After extraction with 1 volume of chloroform:isoamyl alcohol (24:1), polysaccharides were precipitated with 0.3 volumes of 100% ethanol and the chloroform-isoamyl alcohol extraction repeated. RNA was then removed by incubation overnight at 20°C in 4M LiCl and 1% beta-mercaptoethanol and centrifugation at 13,000 rpm for 30 min. The DNA was then precipitated from the supernatant by addition of 0.8 volumes of isopropanol, redissolved in 500 µl of Tris EDTA buffer, extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then with chloroform:isoamyl alcohol (24:1) and precipitated in 0.3 M sodium acetate and 71% ethanol. The DNA was then purified on a CsCl gradient.

tag: control

value: Genomic DNA from Ectocarpus siliculosus genome


title: 36 Days Treatment, Replicate 2 (Dye Flip)

city: Bonn

first: Uta

last: Strübing

address: Sigmund-Freud-Str. 25

department: Institute for Medical Microbiology, Immunology and Parasitology

institute: University Hospital Bonn

description:
Dye-flip replicate 2 of 2. RNA from 36 days tetracycline-treated L. sigmodontis was compared to age-matched untreated worms.
Day36_rep2

hyb_protocol: Each sample pair (~24 µl) was resuspended in formamide-based  hybridization buffer (vial 7-Genisphere) (26 µl) and Array 50dT blocker (Genisphere) (2 µl). Two hybridizations were carried out in a sequential manner. The primary hybridization was performed by adding 48 µl of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43°C for 16-20 hours at high humidity in the dark. Prior to the secondary hybridization, slides were gently submerged into 2X SSC, 0.2% SDS (at 43°C) for 11 min., transferred to 2X SSC (at room temperature) for 11 min., transferred to 0.2X SSC (at room temperature) for 11 min., and then spun dry by centrifugation. Secondary hybridization was carried out using the complimentary capture reagents provided in the 3DNA Array 900 kit (Genisphere). For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 µl), 3DNA capture reagent with Cy5 (2.5 µl), SDS-based hybridization buffer (vial 6-Genisphere) (26 µl), and nuclease-free water (21 µl). The secondary hybridization solution was incubated in the dark at 80°C for 10 min., then 50°C for 15 min. Hybridization was performed by adding 48 µl secondary hybridization solution to the slide under a supported glass coverslip at 65°C for 4 hours at high humidity in the dark. At hybridization termination, arrays were gently submerged into 2X SSC, 0.2% SDS (at 65°C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temperature) for 11 min., and then spun dry by centrifugation.

scan_protocol: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence. Laser power was kept constant for Cy3/Cy5 scans and PMT was varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low PMT setting scan was also performed to recover signal from saturated elements.  Gridding and analysis of images was performed using ScanArray v3.0 (Perkin Elmer).

data_processing: For determining foreground and background intensities of each spot, the adaptive circle spot-finding algorithm was used. Data were normalized using LOWESS. Spots that passed the criteria of an intensity unit > 200 and signal to background ratio > 2 in one of the two channels were marked as “present” and were included in further analyses. Since a cross-species hybridization was performed, only approximately 20% of the cDNA hybridized to the oligos on the array. The log2 transformed values of the normalized and background subtracted ratio of intensities (treated vs. untreated) were used for identification of significant changes in gene expression applying Significance Analysis of Microarrays (SAM, version 3.02, Tusher et al., 2001). The one-class response type was used with a false discovery rate (FDR) ≤ 5% (= q-value ≤ 0.05). The resulting data were filtered for genes having a minimum 2-fold gene expression change.

organism: Litomosoides sigmodontis

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 36 days Tet

label_protocol: First strand cDNA was generated by oligo-dT primed reverse transcription (Superscript II, Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere), with Cy3 or Cy5  specific oligo sequences attached to the oligo-dT Primer. One µl of fluorophore specific oligo-dT primer was added to 2 µg of total RNA and the solution was incubated at 80°C for 5 minutes and then cooled on ice for 2 minutes. 0.5 µl RNase inhibitor (Superase-In, Ambion), 2 µl 5x first strand buffer, 0.5 µl dNTP mix (10 mM each dATP, dCTP, dGTP and dTTP), 1 µl 0.1M DTT and 0.5 µl Superscript II RNase H- Reverse Transcriptase were added to each sample. Reverse transcription was carried out at 42°C for 2 hours. The reaction was terminated by adding 1.0 µl of 1.0 M NaOH/100 mM EDTA and incubation at 65°C for 10 minutes following a neutralization with 1.2 µl 2M Tris-HCL, pH 7.5.

growth_protocol: Fully permissive IL-5 KO BALB/c mice (6-8 weeks old) were infected with Litomosoides sigmodontis by mites (Ornithonyssus bacoti) carrying the infective L3 larvae.

extract_protocol: Total RNA was isolated from 5-10 female L. sigmodontis using the Trizol (Invitrogen GmbH, Karlsruhe, Germany) extraction method, following the manufacturer’s protocol with some modifications. Briefly, nematodes in 800 µl Trizol reagent were transferred to 2 ml tubes containing 0.5 mm glass beads and homogenized in a Precellys 24 homogenizer (Peqlab, Erlangen, Germany) 4 x 10 s at 5000 rpm. Instead of chloroform, 80 µl of 1-brom-3-chloro-propane (Sigma-Aldrich, Steinheim, Germany) was used to separate the homogenate into RNA-containing aqueous and DNA containing organic phases. For precipitation of RNA, linear acrylamide (Applied Biosystems, Foster City, USA) was used as co-precipitant with a final concentration of 9 µg/ml and 1 volume isopropanol (Merck, Darmstadt, Germany). RNA was treated with RNAse-free DNAse I (Applied Biosystems) for 1 h at 37°C, followed by clean-up and concentration of the RNA with the RNeasy Minelute kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. Total RNA quality was then determined by an Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer's recommendations.

treatment_protocol: Tetracycline (Tet) treatment of mice started around day 60, when worms were patent and microfilaria are seen in blood of infected mice. Mice were treated daily for 36 days with intraperitoneal injections of 1mg Tet in 200 µl PBS (50mg Tet/kg). At days 6, 15 and 36 after start of Tet treatment, worms from untreated control and Tet-treated mice were recovered from the thoracic cavity. Female worms were snap frozen in liquid nitrogen and stored at -80°C for subsequent RNA isolation.

value: female

tag: developmental stage

value: adult

value: whole body

value: tetracycline treated

tag: timepoint

value: 36 days

source_name: female adult worms from patent infections in Balb/C IL5 knockout mice, 36 days untreated

value: untreated