title: 0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 1

description:
CHIPEXP_NAME: 230_2_050531tpj_53h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 24
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 2

status: Public on Jun 02 2007

type: RNA

city: Nutley

first: Charu

last: Kanwal

state: NJ

address: 340 Kingsland Street

department: RIGG

country: USA

institute: Hoffman-La Roche

description:
CHIPEXP_NAME: 230_2_050531tpj_39h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip scanner 3000

data_processing: Chips were pre-processed using robust multichip analysis. Normalized data were fit to a linear model with dose and time contrasts using the GLM procedure of SAS 9.1 (SAS Institute, Carey NC)

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Extraction of total RNA was performed from the heart tissues using RNAeasy Mini kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: The tissues from the necropsy were stored in RNA later (Ambion)

tag: Wistar Han

tag: Crl:Wi(Han), Male, tissue

value: Heart


title: Enriched germ cells Replicate 2, dye-swap

city: Chunan, Miaoli

first: Wen-chuan

last: Lee

address: 52 Ke-dung 2nd Rd.

department: Division of Biotechnology

country: Taiwan

institute: Animal Technology Institute Taiwan

description: Biological replicate 2 of 3, technical replicate (dye-swap)

hyb_protocol: The labeled targets were mixed with 5 x SSC, 200 μg/mL of both human Cot-1 DNA and poly-A, and 0.12 % SDS in a total volume of 75 μL.  Place a coverslip (LifterSlip, Erie Scientific Co.) onto a cDNA microarray.  After boiling for 2 min and short cooling with tape water, the hybridization mixture was transferred steadily to the covered slide.  Place the assembly to Hybchamber (Genomic Solutions) and deposit 15 μL of 3 x SSC into the reservoir grooves for moisture maintaining.  Submerge the assembled hybridization chamber in water bath of 65C for 14 h to 16 h.  After hybridization, the slide assembly was submerged shortly in Wash 1 (0.5 x SSC, 0.01 % SDS, 55C) to detach the coverslip, then washed sequentially by dipping the slide up-and-down in: Wash 1, 2 min; Wash 2 (0.5 x SSC), 3 min; Wash 3 (0.1 x SSC), 3 min and twice 1 min and Wash 4 (0.01 x SSC) shortly.

scan_protocol: Scanned on an GenePix Personal 4100A (Molecular Devices) Images were quantified using GenePix Pro 6.1

data_processing: Normalization: Ratio of all features is 1. Features with SNR>3 were collected for further analysis.

label: Alexa FluorR 647

organism: Sus scrofa

source_name: Enriched germ cells, control (34C), 1 h

label_protocol:
About 250 ng of total RNA with amplified to antisense RNA (aRNA) with SuperScript RNA Amplification System (Invitrogen) as recommended by the manufacturer.  2 μg of aRNA, spiking with 2 μg of test RNA (Universal ScoreCard, GE Healthcare), was labeled with SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s instructions.
!Sample_source_name_ch2 = Enriched germ cells, control (34C), 1 h

growth_protocol: Enriched germ cells were cultured in DMEM/F12 medium supplemented with 10 % fetal bovine serum at 34C.

extract_protocol: RNeasy mini kit

treatment_protocol: enriched germ cells were incubated at 34C CO2 incubator parallel.

tag: Cells prepared

tag: Breed

value: Duroc

tag: Animal

tag: Age

value: 67 days

tag: Tissue

value: testis

label: Alexa FluorR 555

source_name: Enriched germ cells, heat shock (39C), 1 h

treatment_protocol: enriched germ cells were moved to 39C oven for 1 h, then transferred back to 34C CO2 incubator for 2 h.


title: 0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 4

description:
CHIPEXP_NAME: 230_2_050531tpj_41h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 3 hour time point, biological replicate 1

description:
CHIPEXP_NAME: 230_2_050531tpj_7h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 5

description:
CHIPEXP_NAME: 230_2_050531tpj_37h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143

source_name: 0.5 mg/kg/ml Isoproterenol treatment for 1 hour,  biological rep 5


title: 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 1

description:
CHIPEXP_NAME: 230_2_050531tpj_33h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143

source_name: 0.5 mg/kg/ml Isoproterenol treatment for 1 hour


title: vehicle treatment, 3 hour time point, biological replicate 3

description:
CHIPEXP_NAME: 230_2_050531tpj_9h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143


title: 0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 3

description:
CHIPEXP_NAME: 230_2_050531tpj_40h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143


title: Enriched germ cells Replicate 3, dye-swap

description: Biological replicate 3 of 3, technical replicate (dye-swap)

value: 89 days

label_protocol: About 250 ng of total RNA with amplified to antisense RNA (aRNA) with SuperScript RNA Amplification System (Invitrogen) as recommended by the manufacturer.  2 μg of aRNA, spiking with 2 μg of test RNA (Universal ScoreCard, GE Healthcare), was labeled with SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s instructions.


title: vehicle treatment, 1 hour time point, biological replicate 3

description:
CHIPEXP_NAME: 230_2_050531tpj_6h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143

source_name: cardiac muscle, treated with vehicle, dissected after 1 hr


title: 0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 1

description:
CHIPEXP_NAME: 230_2_050531tpj_38h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 3 hour time point, biological replicate 2

description:
CHIPEXP_NAME: 230_2_050531tpj_8h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 3
PROJECT: ISO_TG
STUDY_NO: 9143


title: Enriched germ cells Replicate 3

description: Biological replicate 3 of 3


title: 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 4

description:
CHIPEXP_NAME: 230_2_050531tpj_36h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143

source_name: 0.5 mg/kg/ml Isoproterenol treatment for 1 hour,  biological rep 4


title: PGF2alpha (3 injections) at a dose of at 59 µg/kg BW for 24 h_3

city: Bangalore

first: priyanka

last: samji

state: Karnataka

address: Malleswaram

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

description: Probe level measurements produced by Affymetrix microarray suite 5.0. Analysis performed at level of raw signals (See Affymetrix Microarray suite 5.0 reference on web site for description).

scan_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001) using scanner 3000 series

data_processing: MAS5.0, data was normalized with standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

organism: Macaca radiata

source_name: CL from female bonnet monkeys at 24 h following PGF2alpha treatment

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma Aldrich Co., St.Louis, MO) followed by clean up step using RNeasy mini purification kit (# 74104, Qiagen).

treatment_protocol: For the purpose of microarray analysis, PGF2alpha (3 injections) at a dose of 59 µg/kg BW was administered i.m. to female monkeys on day 10 of luteal phase (n=3). At 24 h following  PGF2alpha administration, CL was collected and immediately cut into 4-5 pieces and snap frozen in liquid nitrogen.

tag: CL collected from female bonnet monkey 24 h post PGF2alpha treatment


title: 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 3

description:
CHIPEXP_NAME: 230_2_050531tpj_35h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143


title: Vehicle control (PBS) for 24 h_6

hyb_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

source_name: CL from female bonnet monkeys at 24 h following VEH administration

treatment_protocol: For the purpose of microarray analysis, PBS as VEH (control) was administered i.m. to female monkeys on day 10 of luteal phase (n=3). At 24 h following VEH administration, CL was collected and immediately cut into 4-5 pieces and snap frozen in liquid nitrogen.


title: Enriched germ cells Replicate 1, dye-swap

description: Biological replicate 1 of 3, technical replicate (dye-swap)

value: 76 days


title: Vehicle control (PBS) for 24 h_4

label_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

tag: CL from female bonnet monkeys at 24 h following VEH administration


title: vehicle treatment, 1 hour time point, biological replicate 1

description:
CHIPEXP_NAME: 230_2_050531tpj_4h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143


title: vehicle treatment, 1 hour time point, biological replicate 2

description:
CHIPEXP_NAME: 230_2_050531tpj_5h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143


title: Enriched germ cells Replicate 1

description: Biological replicate 1 of 3


title: 0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 2

description:
CHIPEXP_NAME: 230_2_050531tpj_34h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143


title: PGF2alpha (3 injections) at a dose of at 59 µg/kg BW for 24 h_2


title: Vehicle control (PBS) for 24 h_5


title: PGF2alpha (3 injections) at a dose of 59 µg/kg BW_1

source_name: CL from female bonnet monkey 24 h post PGF2alpha treatment


title: Enriched germ cells Replicate 2

description: Biological replicate 2 of 3


title: MLN_ST infected pig, 21 dpi, rep1

status: Public on Jun 01 2007

city: Ames

first: Christopher

middle: K

last: Tuggle

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

description: Gene expression data from the mesenteric lymph nodes of Salmonella Typhimurium infected pig, 21 dhpi post-infection

hyb_protocol: Following fragmentation, 6.5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip® Porcine Genome Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: biotin

source_name: mesenteric lymph nodes, 21d post infected pig

label_protocol: Biotinylated cRNA were prepared by the GeneChip® One-Cycle target labeling kit according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Total RNA was isolated from ~200 mg of porcine MLN tissues by using the RNeasy Midi kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) based on the manufacture’s protocol

treatment_protocol: Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA, and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed twice on rectal swabs before the experiments. At seven weeks of age, 3 pigs were randomly allocated to the non-infected group and 12 to the infected group. The three non-infected control pigs were necropsied 2 days prior to experimental infection. On day0, pigs in the infected groups were intranasally challenged with 1 x 109 CFU of S. Typhimurium ?4232. A randomly chosen group of three infected pigs were necropsied at each time point of 8 hpi, 24 hpi, 48 hpi and 21 dpi, respectively

value: 7 weeks old pigs were used for this experiment


title: MLN_ST infected pig, 8 hpi, rep3

description: Gene expression data from the mesenteric lymph nodes of Salmonella Typhimurium infected pig, 8 hpi post-infection

source_name: mesenteric lymph nodes, 8h post infected pig


title: MLN_ST infected pig, 48 hpi, rep2

description: Gene expression data from the mesenteric lymph nodes of Salmonella Typhimurium infected pig, 48 hpi post-infection

source_name: mesenteric lymph nodes, 48h post infected pig


title: MLN_ST infected pig, 21 dpi, rep2


title: MLN_ST infected pig, 48 hpi, rep1


title: MLN_ST infected pig, 24 hpi, rep2

description: Gene expression data from the mesenteric lymph nodes of Salmonella Typhimurium infected pig, 24 hpi post-infection

source_name: mesenteric lymph nodes, 24h post infected pig


title: MLN_ST infected pig, 8 hpi, rep2


title: MLN_ST non_infected pig, rep3

description: Gene expression data from the mesenteric lymph nodes of non-infected pig

source_name: mesenteric lymph nodes, non-infected pig


title: MLN_ST infected pig, 48 hpi, rep3


title: H9 hES cells

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: Data are average intensity values from three replicate cell cultures / hybridisations. A commercial RNA pool (human universal RNA, Stratagene) was used as control.

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 17h at 55 degC

scan_protocol: Using an Illumina scanner; gain factor: 2.5

data_processing: In BeadStudio 1.0 raw data were background subtracted and normalised using the "rank invariant" algorithm. Value = "null" denotes expression below background (p < 0.01).

organism: Homo sapiens

source_name: cell line H9

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 300ng of total RNA; IVT: 6h

growth_protocol: hES cells grown in MEF-conditioned medium on Matrigel. Partially differentiated colonies were manually removed from the cultures prior to RNA isolation.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion following the manufacturer's instructions

tag: undifferentiated H9 human embryonic stem cells, passage 47


title: MLN_ST non_infected pig, rep2


title: MLN_ST infected pig, 21 dpi, rep3


title: Hepatopancreas of X-organ-extirpated, premolted vs. intermolted males

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description: Evaluated Gene expression ratio between hepatopncreas tissues of XO-SG extirpated premolted and intact intermolt males was part of a broader experiment which includes males in five experimental conditions. Individual variability was integrated into the hybridization design, by using RNA populations of 3 individual crayfish males for each of four experimental conditions: injected-premolted, injected-postmolted, extirpated-premolted and extirpated-postmolted males. Three pools of reference intermolt individuals were used: Ref pool 1 contained RNA from 6 individuals whereas each of Ref pools 2 and 3 contained 3 individuals. Three hybridization sets, each composed of 8 slides, were carried out. In each set, one individual from each treatment was compared to one of the Ref pools, and in addition the treated individuals were compared to each other, totaling 8 slides. The design was balanced with respect to the dye labeling of the RNA populations, such that each individual RNA population was labeled with one dye on one slide and with the other dye in two other slides. The data table of this sample, comparing hepatopncreas tissues of XO-SG extirpated premolted and intact intermolt males, is part of an integrative analysis of the entire 24 slides set, resulting with eight binary comparisons among experimental conditions (see data processing below).

hyb_protocol: Microarray slides were incubated with pre-hybridization solution (1% BSA; 5x SSC; 0.1% SDS, 25% formamide) for 2h at 42oC to block non-specific DNA interactions, reducing background fluorescence, followed by two short rinses in water, one in ethanol and drying by mild centrifugation of vertical slides. Dual-labeled solutions, aimed at binary comparisons between two experimental conditions, were prepared by mixing the two compared labeled cDNA populations, followed by 1:1 dilution with hybridization solution containing 200 µg/ml salmon sperm DNA, 10x SSC, 0.2% SDS, 50% formamide. The heat denatured hybridization mixture (3' at 95oC) was layered onto the microarray, covered (Lifterslip, Erie Scientific; #25x60-2-4789) and incubated over night at 42°C in humidified hybridization chamber (Corning). Following incubation, slides were washed as follows: 5’ at 42°C in x2 SSC - 0.1% SDS, mild shaking for 10’ at room temperature in x0.1 SSC - 0.1% SDS; mild shaking 4x for 5’ at room temperature in x0.1 SSC, ending by two quick dips, one in water and one in ethanol. The slides were dried by centrifugation.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX software (Axon), which provided also weight index of the quality for each hybridized spot.

data_processing: Data analysis was conducted under the R/BioConductor environment (Gentleman et al., 2005). Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each unique spot across a binary comparison was carried out using the LIMMA package (Linear Models for Microarray data Analysis; Smyth, 2004). GENEPIX quantified image files were imported into LIMMA, spots with quality flags < -49 were marked as unreliable, and the Cy5 and Cy3 intensities within each slide were normalized using the print-tip Loess method. No background correction was applied. LIMMA calculated for each spot on an individual slide an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an emission intensity A-value [A=(log2(Cy5)*Cy3))/2]. Subsequently, LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. Inter-duplicate correlation method was used at the linear modeling step. A meanA value, which is the average spot emission intensity across the analyzed experiment, was calculated for each unique spot and only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. The LIMMA summary statistics of each unique spot included an estimated average M-value across each binary comparison associated to two statistical parameters: B statistic, the log-odds that the spot is differentially expressed and p-value, derived from a moderated t-statistic after multiple testing correction according to Benjamini and Hochberg (1995). All these parameters are found in the sample data table.

label: Cy3 and Cy5 alternatively in different slides (see Description below)

molecule: polyA RNA

organism: Cherax quadricarinatus

source_name: Hepatopancreas from X-organ-extirpated-premolted males

label_protocol: Messenger RNA was labeled by the fluorescent dyes Cy3 and Cy5, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70oC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42oC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65oC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the fluorescent dyes Cy3 or Cy5 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA23001 / PA25001 for Cy3 and Cy5, respectively) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 550 nm (Cy3) and 650 nm (Cy5) for labeling intensity measurement.

growth_protocol: C. quadricarinatus males were maintained in captivity, before and during the experiment at 28oC, with a photoperiod of 14L:10D

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyTtract kit (Promega) was used for mRNA extraction from total RNA solutions

treatment_protocol: The XO-SG complex was extirpated from three adult males sacrificed at premolt. Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. The experiment was terminated by sacrifice of the males, dissecting their hepatopancreas and its immediate freezing in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue.

tag: Hepatopancreas of X organ-sinus gland-extirpated C. quadricarinatus males were dissected at premolt and snap frozen in liquid nitrogen.

source_name: Hepatopancreas from intermolt males

treatment_protocol: Molt stage was monitored by X-ray of gastrolith size and by evaluating ecdysteroid level in the hemolymph. Twelve intermolt males were sacrificed and their hepatopancreas was dissected and immediately frozen in liquid nitrogen. Total RNA and mRNA were purified later starting from the frozen tissue, pooled into three mRNA groups of 6, 3 and 3 males.

tag: Hepatopancreas of intact intermolt C. quadricarinatus males were dissected and snap frozen in liquid nitrogen.


title: Universal Reference RNAs

description: Data are average intensity values from two hybridisations.

source_name: Universal Reference RNAs (Stratagene)

extract_protocol: Absolutely RNA Kit (Stratagene) followed by DNase treatment

tag: commercially available pool of RNAs from 10 different human cell lines (Stratagene #740000)


title: SOX2 knock-down in NCCIT hEC cells

description: The control for this knock-down experiment is named NCCIT hEC cells mock-treated. Values are means of three biological replicates.

source_name: cell line NCCIT

growth_protocol: high-glucose DMEM supplemented with 10% FCS, 2mM L-glutamine, penicillin-streptomycin

treatment_protocol: Cells were seeded at 70,000/sqcm and treated with esiRNA against SOX2 message complexed with Hyperfect transfection reagent (Qiagen), following the vendor's recommendations. Medium was changed the following day and cells harvested at day 2.5

tag: human embryonic carcinoma cell line NCCIT


title: MLN_ST non_infected pig, rep1


title: MLN_ST infected pig, 24 hpi, rep3


title: MLN_ST infected pig, 8 hpi, rep1


title: NANOG knock-down in NCCIT hEC cells

treatment_protocol: Cells were seeded at 70,000/sqcm and treated with esiRNA against NANOG message complexed with Hyperfect transfection reagent (Qiagen), following the vendor's recommendations. Medium was changed the following day and cells harvested at day 2.5


title: MLN_ST infected pig, 24 hpi, rep1


title: OCT4 knock-down in NCCIT hEC cells

treatment_protocol: Cells were seeded at 70,000/sqcm and treated with esiRNA against OCT4 message complexed with Hyperfect transfection reagent (Qiagen), following the vendor's recommendations. Medium was changed the following day and cells harvested at day 2.5


title: NCCIT hEC cells mock-treated

description: This sample presents the mock control for three transcription factor knock-downs in hEC cells. Values are means of three biological replicates.

treatment_protocol: Cells were seeded at 70,000/sqcm and treated with Hyperfect transfection reagent (Qiagen). Medium was changed the following day and cells harvested at day 2.5


title: NHGRI_WT_WT_pool_3-45-73

city: Bethesda

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Men1 wildtype vs Men1-null expression

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs in 30 ul DEPC H20 are denatured for 2 minutes. 15 ul 20X SSC, 5 ul 100% Formamide, 0.5 ul 10% SDS, and 4 ul DEPC H20 are added and the mixture hybridized on the array slide under a coverslip at 65 degre for 16 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray

organism: Mus musculus

source_name: WT, pooled

label_protocol: 15-25 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Fluoro dUTP (Cy3/Cy5), after NaOH RNA hydrolysis, the labeled cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104)

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: Mouse embryo Fibroblast (MEF) cell line of wild type from early stage E9.5

tag: Mouse embryo Fibroblast (MEF) cell line of Men1-Null from early stage E9.5


title: NHGRI_50W_50W_3-45-72

description: Men1 wildtype vs Men1-null expression


title: NHGRI_WT_Null_pool_DyeSwap_3-45-80

description: Men1 wildtype vs Men1-null expression

source_name: Null, pooled


title: NHGRI_Null_Null_pool_3-45-74

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_17N_3-45-64

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_40N_3-45-65

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_12N_3-45-63

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_17N_DyeSwap_3-45-60

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_47N_DyeSwap_3-45-70

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_47N_DyeSwap_3-45-62

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_40N_DyeSwap_3-45-61

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_12N_DyeSwap_3-45-59

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_47N_3-45-66

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_40N_DyeSwap_3-45-69

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_17N_DyeSwap_3-45-68

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_47N_DyeSwap_3-45-37

description: Men1 wildtype vs Men1-null expression


title: NHGRI_WT_Null_pool_3-45-79

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_47N_3-45-58

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_12N_3-45-55

description: Men1 wildtype vs Men1-null expression


title: NHGRI_50W_12N_DyeSwap_3-45-67

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_17N_3-45-56

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_40N_DyeSwap_3-45-36

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_12N_DyeSwap_3-45-34

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_17N_DyeSwap_3-45-35

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_47N_3-45-33

description: Men1 wildtype vs Men1-null expression


title: NHGRI_46W_40N_3-45-57

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_12N_3-45-30

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_40N_3-45-32

description: Men1 wildtype vs Men1-null expression


title: NHGRI_26W_17N_3-45-31

description: Men1 wildtype vs Men1-null expression


title: NHGRI_10W_47N_DyeSwap_3-45-47

description: Men1 wildtype vs Men1-null expression


title: NHGRI_10W_12N_DyeSwap_3-45-44

description: Men1 wildtype vs Men1-null expression


title: NHGRI_10W_17N_DyeSwap_3-45-45

description: Men1 wildtype vs Men1-null expression


title: NHGRI_10W_40N_DyeSwap_3-45-46

description: Men1 wildtype vs Men1-null expression


title: NHGRI_10W_17N_3-45-39

description: Men1 wildtype vs Men1-null expression


title: NHGRI_10W_40N_3-45-40

description: Men1 wildtype vs Men1-null expression


title: Saccharomyces cerevisiae MA-A3 MA-A0

city: Cambridge

first: Christian

last: Landry

state: MA

address: 16 Divinity avenue

department: OEB

institute: Harvard University

description: see Landry et al.

hyb_protocol: Genisphere 3DNA System

scan_protocol: Axon scnanner and Genepix

data_processing: Spots of bad quality were given negative flags

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae MA-A3

label_protocol: Genisphere 3DNA System

extract_protocol: See Townsend, Cavalieri and Hartl 2003, PMID: 12716989: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=12716989

tag: Saccharomyces cerevisiae MA-A3

source_name: Saccharomyces cerevisiae MA-A0

tag: Saccharomyces cerevisiae MA-A0


title: Saccharomyces cerevisiae MA-A3 MA-A1

description: see Landry et al.

source_name: Saccharomyces cerevisiae MA-A1

tag: Saccharomyces cerevisiae MA-A1


title: Saccharomyces cerevisiae MA-A8 MA-A1

description: see Landry et al.

source_name: Saccharomyces cerevisiae MA-A8

tag: Saccharomyces cerevisiae MA-A8


title: Saccharomyces cerevisiae MA-A4 MA-A8

description: see Landry et al.

source_name: Saccharomyces cerevisiae MA-A4

tag: Saccharomyces cerevisiae MA-A4


title: Saccharomyces cerevisiae MA-A0 MA-A8

description: see Landry et al.


title: Saccharomyces cerevisiae MA-A8 MA-A3

description: see Landry et al.


title: Saccharomyces cerevisiae MA-A1 MA-A4

description: see Landry et al.


title: NHGRI_10W_47N_3-45-42

description: Men1 wildtype vs Men1-null expression


title: Saccharomyces cerevisiae MA-A1 MA-A0

description: see Landry et al.


title: Saccharomyces cerevisiae MA-A4 MA-A3

description: see Landry et al.


title: E. histolytica strain HM1 heat shock replicate 1

status: Public on Mar 01 2007

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

state: CA

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Entamoeba histolytica HM-1:IMSS trophozoites subjected to heat shock at 42C for 1 hour

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

organism: Entamoeba histolytica

source_name: HM-1:IMSS heat shock 42C for 1 hour

label_protocol: Affymetrix single amplification

tag: Strain

tag: Media

value: TYI

tag: Heat shock 42C for 1 hour


title: E. histolytica strain HM1 heat shock replicate 2


title: Saccharomyces cerevisiae MA-A0 MA-A4

description: see Landry et al.


title: Allo-25-1

status: Public on Oct 08 2005

city: Minneapolis

first: Jeff

last: Lande

state: MN

address: 420 Washington Avenue SE

department: Medicine

institute: University of Minnesota

description: Day 25 Allograft

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Bioconductor - GCRMA version 1.1.3

source_name: tracheal tissue

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: TRIzol w/ Qiagen RNeasy cleanup

tag: Male 6-8 week BALB/c grafts in Male 6-8 week C57Bl/6 host


title: Allo-25-5

description: Day 25 Allograft


title: Allo-14-5

description: Day 14 Allograft


title: Allo-25-2

description: Day 25 Allograft


title: Allo-14-3

description: Day 14 Allograft


title: Allo-25-3

description: Day 25 Allograft


title: NHGRI_10W_12N_3-45-38

description: Men1 wildtype vs Men1-null expression


title: Allo-25-4

description: Day 25 Allograft


title: Allo-4-5

description: Day 4 Allograft


title: Iso-25-3

description: Day 25 Isograft

tag: Male 6-8 week BALB/c grafts in Male 6-8 week BALB/c host


title: Iso-25-5

description: Day 25 Isograft


title: Iso-25-2

description: Day 25 Isograft


title: Allo-14-2

description: Day 14 Allograft


title: Allo-14-1

description: Day 14 Allograft


title: Allo-4-3

description: Day 4 Allograft


title: Iso-25-1

description: Day 25 Isograft


title: Allo-4-1

description: Day 4 Allograft


title: Allo-4-2

description: Day 4 Allograft


title: Iso-14-5

description: Day 14 Isograft


title: Allo-14-4

description: Day 14 Allograft


title: Iso-14-4

description: Day 14 Isograft


title: Allo-4-4

description: Day 4 Allograft


title: Iso-25-4

description: Day 25 Isograft


title: Iso-14-3

description: Day 14 Isograft


title: Iso-14-1

description: Day 14 Isograft


title: Iso-14-2

description: Day 14 Isograft


title: Iso-4-5

description: Day 4 Isograft


title: Iso-4-1

description: Day 4 Isograft


title: Iso-4-2

description: Day 4 Isograft


title: Iso-4-3

description: Day 4 Isograft


title: Native-0-5

description: Normal (untransplanted) trachea

tag: Male 6-8 week BALB/c trachea


title: Native-0-2

description: Normal (untransplanted) trachea


title: Native-0-4

description: Normal (untransplanted) trachea


title: Native-0-1

description: Normal (untransplanted) trachea


title: Native-0-3

description: Normal (untransplanted) trachea


title: Iso-4-4

description: Day 4 Isograft


title: BAL_47c_A0B1

status: Public on Nov 30 2004

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection).
One of three samples from the same patient, different visits.

source_name: Bronchoalveolar lavage cells


title: BAL_33_A0B1

description: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection).


title: BAL_45a_A1B0

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection).
One of two samples from the same patient, different visits.


title: BAL_44b_A0B0

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).
One of two samples from the same patient, different visits


title: BAL_45b_A2B0

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection).
One of two samples from the same patient, different visits


title: BAL_42_A0B0

description: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).


title: BAL_47a_A0B0

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).
One of three samples from the same patient, different visits.


title: BAL_44a_A0B0


title: BAL_39_A0B1


title: BAL_40_A0B0


title: BAL_46_A2B0

description: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection).


title: BAL_47b_A0B1


title: BAL_41_A1B0

description: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection).


title: BAL_3_A1B0


title: BAL_19_A0B0


title: BAL_21_A0B0


title: BAL_25_A0B0


title: BAL_31_A0B1


title: BAL_20a_A1B1

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection).
One of two samples from the same patient, different visits.


title: BAL_43_A0B0


title: BAL_20b_A1B1


title: BAL_27b_A2B1

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=1 (Acute rejection).
One of two samples from the same patient, different visits


title: BAL_4_A0B0


title: BAL_26_A2B0


title: BAL_29_A1B0


title: BAL_27a_A0B0


title: BAL_18_A1B0


title: BAL_12_A1B0


title: BAL_1_A0B0


title: BAL_17_A0B0


title: BAL_37_A1B1

description: Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection)


title: BAL_15a_A0B1

description:
Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection).
One of two samples from the same patient, different visits.


title: BAL_15b_A0B0


title: BAL_13_A0B0


title: Bladder tumor 01015T_E (44g2)

status: Public on Jun 15 2007

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Gene expression data from a bladder tumor compared to a common reference sample

hyb_protocol: Described in: Dyrskjot L, Zieger K, Kruhoffer M, Thykjaer T, Jensen JL, Primdahl H, Aziz N, Marcussen N, Moller K, Orntoft TF. A molecular signature in superficial bladder carcinoma predicts clinical outcome. Clin Cancer Res. 2005 Jun 1;11(11):4029-36. PMID: 15930337

scan_protocol: Arrays were scanned using a ScanArray4000 scanner - settings: Cy5: 54% PMT, 100% laser power and Cy3: 78% PMT, 100% laser power

data_processing: Raw data were generated using TIGR Spotfinder 2.23 and raw data were lowess print-group normalized using TIGR MIDAS 2.19

source_name: Bladder tumor biopsy

extract_protocol: Total RNA extraction using standard protocols

tag: Bladder tumor

tag: Patient clinical information can be found in a Series supplementary file

source_name: Universal human reference RNA (Stratagene)

extract_protocol: Total RNA from Stratagene Universal human reference RNA

tag: reference sample


title: Blood Pool vs Blood_Sample_44

status: Public on Jun 13 2007

city: Seattle

first: Valur

last: Emilsson

state: WA

address: 401 Terry Avenue N

department: Genetics

institute: Merck

description: The genetics of human gene expression from population based tissue sampling

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Blood

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Blood Pool


title: Adipose Pool vs Adipose_Sample_565

source_name: Adipose

tag: Adipose Pool