title: Zebra finch, HVc, (LD), biological rep5

description: HVC was dissected from cryosections


title: Subordinate male urine stimulation, OB brain tissue, replicate 5

status: Public on Feb 01 2014

type: RNA

city: Lisboa

first: José Miguel

last: Simões

address: Rua Jardim do Tabaco 34

department: Eco-Ethology Research Unit

country: Portugal

institute: ISPA - Instituto Universitário

description: Samples from blank stimulations (control) collected from eight different individuals (for both areas) were pooled and aliquoted to be used as reference in a reference based array design

hyb_protocol: A reference and experimental sample were competitively hybridized at 65oC overnight to a 19K A. burtoni cDNA microarray (GEO platform GPL6416) constructed from brain-specific and mixed tissue libraries representing a total of 17,712 cichlid-specific features

scan_protocol: Microarrays were scanned with an Axon 4000B scanner (Axon Instruments) using Genepix 4.0 software (Axon Instruments).

data_processing: Microarray data were processed using the LIMMA software package (v3.12.0; [62] in R (v2.15.0; the R Foundation for Statistical Computing, 2012).  Background-subtracted mean intensities were calculated using the minimum method and further normalized using within-array loess normalization. After this normalization step, Bayesian analysis was used to calculate gene expression levels using the ratios of intensities measured. Finally, to compare between expression profiles for the different olfactory stimulations, unsupervised hierarchical clustering analysis were done using the hclust function in R/Bioconductor.

molecule: total RNA

organism: Oreochromis mossambicus

source_name: OB Brain, SUB stimuli

label_protocol: mRNA (500 ng) from each experimental sample or reference were reverse transcribed using SuperScript II (Invitrogen) and labeled. Following this reverse transcription, RNA was hydrolyzed and purified before being dye-coupled with Cy3 or Cy5 post-labeling Reactive Dye Pack (Amersham).

growth_protocol: Mixed-sex groups which were kept in tanks with gravel substrate, which promotes nest digging by males and the establishment of territories and social hierarchies, at a temperature of 26 ± 2◦C and a 12L:12D photoperiod. Fish were fed twice daily with commercial cichlid sticks.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Dominant males were chemically stimulated with social relevant stimuli while electro-olfactograms measured their electrical activity at the level of the olfactory rosette. After stimulation the fish were killed, their brains dissected and brain samples were microdissected for analysis.

tag: brain tissue

value: OB

tag: olfactory stimuli

value: subordinate male urine

source_name: OB Brain, blank stimuli


title: asthma patient-3

city: Changsha

first: Yang

last: Xiang

state: Hunan

address: 110 Xiangya Road

department: Physiology

country: China

institute: Central South University

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L19a were spread on each chip.
Biotin-16-dUTP

hyb_protocol: a. Warm the GEAhyb Hybridization Solution(3 ml for each array) to 60 °C to allow complete dissolution of the buffer components.  b. Heat the sheared salmon sperm DNA at 100 °C for 5 min and immediately chill on ice. Add the heat-denatured salmon sperm DNA to the pre-warmed GEAhyb Hybridization Solution to a final concentration of 100 µg/ml. Keep the GEAprehyb solution at 60 °C until needed.  c. Pre-wet the array membrane by adding roughly 5 ml of deionized water to the hybridization tube.  d. Discard the deionized water from the hybridization tube. Add 2 ml of the GEAprehyb solution, and vortex the tube gently for a few seconds.  e. Pre-hybridize in the hybridization oven at 60 °C for 1.5 hours with continuous agitation at 6 rpm.  f. Discard the GEAprehyb from the hybridization tube. Add the entire volume of denatured cDNA probe to 0.75 ml of pre-warmed GEAprehyb. Mix well and hybridize overnight (12 hours) at 60 °C with continuous agitation at 6 rpm.  g. Discard the GEAhyb solution from the hybridization tube. Wash the membrane twice with 5 ml Wash Solution 1 at 60 °C with 30 to 40 rpm agitation for 15 minutes each. Vortex the tube gently with each wash.  h. Discar Wash Solution 1. Wash the membrane twice with 5 ml Wash Solution 2 at 60 °C with 30 to 40 rpm agitation for 15 minutes each. Vortex the tube gently with each wash.

scan_protocol: After discarding the last wash, immediately add 1.5 ml GEAblocking Solution Q. Incubate for 40 min with continuous agitation.   Binding of alkaline phosphatase-conjugated streptavidin (AP)  Prepare Binding Buffer: Dilute 5X Buffer F five-fold to prepare excess 1X Buffer F. Dilute AP 1:7,500 into 1X Buffer F.  Discard the GEAblocking Solution Q from the tube. Add 2 ml Binding Buffer, and incubate for 10 min with continuous but gentle agitation.  Washing: Wash the membrane four times with 4 ml 1X Buffer F for 5 min with gentle agitation. Vortex the tube gently after each addition of fresh 1X Buffer F. Rinse or wash twice with 3 ml Buffer G.  Detection: Add 1.0 ml CDP-Star chemiluminescent substrate to the hybridization tube. Incubate at room temperature for 2 min.  Blot the membrane on a piece of filter paper to remove excess CDP-Star Solution. Place the membrane between two plastic sheets and smooth out any bubbles. Expose it on the X-ray film.  After exposing the membrane to X-ray film, use a desktop scanner to convert the image into a grayscale TIFF file. Be sure to save this file. Convert the image of spots into numerical data using the free ScanAlyze software. Save the raw data as a Microsoft Excel file.

data_processing: Use GEArray Analyzer software for background subtraction and data normalization. Each GEArrayTM Q Series membranes are spotted with negative controls (pUC18 DNA and blanks) and housekeeping genes, including β-actin, GAPDH, cyclophilin A and ribosomal protein L13a. All raw signal intensities should be corrected for background by subtracting the minimum value to avoid the appearance of negative numbers. All signal intensities should also be normalized to that of a housekeeping gene. These corrected, normalized signals can then be used to estimate the relative abundance of particular transcripts.

label: biotin

organism: Homo sapiens

source_name: peripheral blood leucocytes

label_protocol: 5.0 µg  of total RNA was reverse-transcribed using MMLV Reverse Transcriptase (Promega) in the presence of 2μl Biotin-16-dUTP (1mM)

extract_protocol: RNA was extracted from leucocytes in peripheral blood of 4 normal adults and 6 asthma patients by using TRIzol Reagent.

tag: cell type

value: peripheral blood leucocytes

tag: age

value: 30 years

tag: Sex

value: Female

tag: diagnosis

value: asthma


title: Dominant male urine stimulation, OB brain tissue, replicate 2

source_name: OB Brain, DOM stimuli

value: Dominant male urine


title: asthma patient-1

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L17a were spread on each chip.
Biotin-16-dUTP

value: 47 years


title: asthma patient-2

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L18a were spread on each chip.
Biotin-16-dUTP

value: 39 years


title: L5_1

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

hyb_protocol: 1.65 ug of Cy3-labeled (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 4 - 180 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan settings for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039425_D_F_20120307) to obtain mean Green intensities and median Green background intesities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizion was done.

organism: Folsomia candida

source_name: total RNA from 30 animals

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container; containing a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: sample type

value: field polluted soil


title: healthy adult -4

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L16a were spread on each chip.
Biotin-16-dUTP

value: 34 years

value: Male

value: healthy


title: Zebra finch, HVc, (LD), biological rep3

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

country: Germany

institute: Max Planck Institute for Ornithology

description: HVC was dissected from cryosections

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing:
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: E26R1204 Genomatix GmbH (http://www.genomatix.de)
ZF processed data files (ZF_HVc_to_ento.txt, ZF_Testo_HVCvsENTO.txt) on Series record, are the significance results obtained by ChipInspector.
The differential expression was analyzed using the group-wise exhaustive analysis i.e., HVc samples group compare to Ento samples group with False Discovery Rate set to zero and 10-significant probe minimum coverage. These result files consist in the table of transcripts and the fold changes for every data combination, also chromosome location (in TGU), Gene ID, Gene Symbol.
The statistic algorithm in ChipInspector is a T-test with a permuted artificial background. It is based on and enhances the original SAM algorithm by Tusher et al. (2001): Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98(9), pp 5116-5121. Exhaustive matching of the experiments introduces a second level of data volume enhancing. This means it is using the complete set of available data points by matching the values from every condition experiment to the values from every control experiment. This gives the results greater confidence and therefore increases the number of values that are recognized as significant (higher number of significant genes with lower FDR) (http://www.genomatix.de).

organism: Taeniopygia guttata

source_name: HVC

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult zebra finches housed in long light cycles in aviaries

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80 C till RNA preparation.

treatment_protocol: Testosterone

value: adult

tag: tissue

value: HVC

tag: light cycle

value: long day

tag: treatment

value: No treatment


title: Subordinate male urine stimulation, OB brain tissue, replicate 4

value: OB


title: L3_1


title: L4_2


title: Dominant male urine stimulation, OB brain tissue, replicate 1


title: healthy adult -3

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L15a were spread on each chip.
Biotin-16-dUTP

value: 26 years


title: Zebra finch, HVc, (LD), biological rep2

description: HVC was dissected from cryosections


title: Subordinate male urine stimulation, OB brain tissue, replicate 2

value: subordinate male urine


title: Subordinate male urine stimulation, OB brain tissue, replicate 3


title: Post-ovulatory female scent stimulation, OB brain tissue, replicate 3

source_name: OB Brain, POST stimuli

value: post-ovulatory female scent


title: Zebra finch, HVc, (LD), biological rep4

description: HVC was dissected from cryosections


title: L2_2


title: LUFA_1

value: LUFA2.2 soil


title: healthy adult -2

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L14a were spread on each chip.
Biotin-16-dUTP

value: peripheral blood leucocytes

value: 52 years


title: Subordinate male urine stimulation, OB brain tissue, replicate 1


title: L1_2


title: LUFA_2


title: Post-ovulatory female scent stimulation, OB brain tissue, replicate 2


title: Zebra finch, HVc, (LD), biological rep1

description: HVC was dissected from cryosections


title: L4_1


title: Retentostat IMK313 day20 -2

status: Public on Jan 31 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: S. cerevisiae rim15  anaerobic glucose-limited retentostat with a dilution rate of 0.025h-1 day 20

hyb_protocol: Hybridization, washing and scanning of Affymetrix chips was performed following the manufacturer’s instructions.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

label: Biotin-Streptavidin

organism: Saccharomyces cerevisiae

source_name: Anaerobic glucose-limited retentostat pH5.0 day 20, 30°, S. cerevisiae rim15 (MB009)

growth_protocol: The prototrophic laboratory strain Saccharomyces cerevisiae CEN.PK113-7D and its rim15 mutant were cultivated using the method described by (Boender et al.,  2011. FEMS Yeast Res. 11: 603-620) Briefly Anaerobic glucose-limited retentostats with a dilution rate of 0.025 h-1 and a working volume of 1.4 litre were performed in triplicate. Duplicate retentostat cultures were started from independent anaerobic, glucose-limited chemostat cultures grown at the same dilution rate by redirecting the effluent through an AppliSense Sample Filter assembly (0.22 µm pore size, Applikon, Schiedam, The Netherlands) instead of through the standard effluent tube. The synthetic medium was supplemented with 50 g.l-1 of glucose and 1.5 ml.l-1 of a 20 % (wt.wt-1) solution of the antifoaming agent Struktol J673 (Schill and Seilacher AG, Hamburg, Germany).

extract_protocol: For each array, total RNA was extracted from a single tube using the hot-phenol method (Schmitt et al., 1990, Nucleic Acids Res., 18: 3091–3092).  mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix GeneChip Expression Analysis Technical Manual, 2000, Affymetrix, Santa Clara, CA

treatment_protocol: Sampling for transcriptome analysis from anaerobic retentostat cultures at different timepoints, was performed as previously described, using liquid nitrogen for rapid quenching of metabolism (Boender et al., 2011 Biochim Biophys Acta 1813(12):2133-2144). Samples were stored at -80°C in a mixture of phenol/chloroform and TEA buffer until further processing for total RNA extraction.

tag: strain

value: rim15 deletion mutant


title: L2_1


title: Zebra finch, Entopallium, testosterone, (LD), biological rep4

description: Entopallium was dissected from cryosections

source_name: Entopallium

value: Entopallium

value: testosterone


title: Liver_FXR WB KO_GW4064_Rep3

city: Piscataway

first: Grace

last: Guo

state: NJ

address: 170 Frelinghuysen Road

country: USA

institute: Rutgers University

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

label: Biotin

organism: Mus musculus

source_name: FXR KO mouse, liver

label_protocol: Standard Affymetrix procedures

growth_protocol: Mice were bred and maintained in the laboratory animal research facility at the University of Kansas Medical Center in rooms under a 12-hour light-dark cycle. FXR was activated by treatment with the FXR synthetic agonist, GW4064, at 150 mg/kg. GW4064 or vehicle was administered by oral gavage at 6 p.m., followed by a second administration at 8 a.m. the next morning.  Two hours later, the liver was harvested.

extract_protocol: Total RNA was extracted and transcribed to cDNA

tag: genotype

value: Whole body Fxr KO

value: Liver

value: 10-16 weeks

tag: route

value: Oral gavage

tag: dose

value: 150 mg/kg

tag: genetic background


title: L6_1

value: field polluted soil


title: Liver_FXR WB KO_GW4064_Rep1

value: Male


title: Liver_FXR WB KO_GW4064_Rep2


title: healthy adult -1

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L13a were spread on each chip.
Biotin-16-dUTP

value: 43 years

value: Female

value: healthy


title: L1_1


title: Retentostat IMK313 day20 -1

source_name: Anaerobic glucose-limited retentostat pH5.0 day 20, 30°, S. cerevisiae rim15 (MB008)

label_protocol: Hybridization, washing and scanning of Affymetrix chips was performed following the manufacturer’s instructions.


title: Post-ovulatory female scent stimulation, OB brain tissue, replicate 1

value: OB

value: post-ovulatory female scent


title: Liver_FXR WB KO_Vehicle_Rep2

value: Vehicle

value: 0 mg/kg


title: Retentostat IMK313 day16 -2

description: S. cerevisiae rim15  anaerobic glucose-limited retentostat with a dilution rate of 0.025h-1 day 16

source_name: Anaerobic glucose-limited retentostat pH5.0 day 16, 30°, S. cerevisiae rim15 (MB009)

value: rim15 deletion mutant


title: Liver_FXR WB KO_Vehicle_Rep3


title: Liver_FXR WB KO_Vehicle_Rep1


title: Retentostat IMK313 day9 -1

description: S. cerevisiae rim15  anaerobic glucose-limited retentostat with a dilution rate of 0.025h-1 day 9

source_name: Anaerobic glucose-limited retentostat pH5.0 day 9, 30°, S. cerevisiae rim15 (MB008)


title: Retentostat IMK313 day9 -2

source_name: Anaerobic glucose-limited retentostat pH5.0 day 9, 30°, S. cerevisiae rim15 (MB009)


title: Liver_LiverFXR null_GW4064_Rep3

description: Tissue-specific Fxr KO mice generated with specific disruption of the Nr1h4 gene in hepatocytes and cross-breeding Fxr floxed/floxed mice with albumin cre (+) mice

source_name: AFXR Cre+ mouse, liver

value: Liver Fxr KO


title: Chemostat IMK313 -2

description: S. cerevisiae rim15  anaerobic glucose-limited chemostat with a dilution rate of 0.025h-1.

source_name: Anaerobic glucose-limited chemostat pH5.0, 30°, S. cerevisiae rim15 (MB014)


title: L3_3


title: Liver_LiverFXR null_GW4064_Rep2


title: Retentostat IMK313 day2 -1

description: S. cerevisiae rim15  anaerobic glucose-limited retentostat with a dilution rate of 0.025h-1 day 2

source_name: Anaerobic glucose-limited retentostat pH5.0 day 2, 30°, S. cerevisiae rim15 (MB008)


title: Liver_LiverFXR null_GW4064_Rep1


title: Chemostat IMK313 -3

source_name: Anaerobic glucose-limited chemostat pH5.0, 30°, S. cerevisiae rim15 (MB011)


title: Chemostat IMK313 -1

source_name: Anaerobic glucose-limited chemostat pH5.0, 30°, S. cerevisiae rim15 (MB010)


title: Liver_LiverFXR null_Vehicle_Rep3


title: Liver_LiverFXR null_Vehicle_Rep2


title: Liver_WT_Vehicle_Rep2

source_name: Wildtype mouse, liver

value: Wildtype


title: Liver_WT_GW4064_Rep3


title: Liver_WT_GW4064_Rep1


title: Liver_WT_GW4064_Rep2


title: Liver_WT_Vehicle_Rep3


title: Breast cancer_Breast Cancer 121T

status: Public on Jan 07 2014

city: New Taipei City

first: Chi-Cheng

last: Huang

address: No.2, Lane 59, Jiancheng Rd. Xizhi Dist.

department: Department of Medical Education and Research

country: Taiwan

institute: Cathay General Hospital SiJhih

description: Gene expression data from breast cancer tissues without chemotherapy.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software, summarized by Robust Multichip Average (RMA) algorithm and further normalized by quantile normalization.

source_name: Breast cancer tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA.

extract_protocol: Total RNA was extracted from frozen specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA). Purification of RNA was performed using RNeasy® mini kits (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: The frozen bulk tumor samples were confirmed to contain at least 90% viable tumor by area on histologic thin sections.

value: Breast

tag: predicted risk

value: low

tag: hu306 classification

value: Basal-like subtype

value: over-expression

tag: er

value: negative

tag: survival time (year)

tag: event

value: disease-free

tag: status

value: alive


title: Breast cancer_Breast Cancer 119T

value: high

value: Luminal A

value: normal

value: positive


title: SP cells from SUPM2 ALCL cell line

status: Public on Jan 15 2014

city: Cambridge

first: Naushad

last: Moti

state: Cambridgeshire

address: Hills Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

description: gene expression data from SP cells

hyb_protocol: 10 ug of cRNA was hybridized on Human Gene ST 1.0 169 format cartridge from Affymetrix (P/N 901087) using GeneChip Hybridization Wash and Stain Kit (Affymetrix P/N 900720) and then washed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Genechips were finally scanned on the GeneScan 3000 (Affymetrix).

data_processing: RMA normalization using HuGene 1.0 st v1 library were performed separately for each sample after Affymetrix CEL files were uploaded to bioconductor. This was followed by filtering out the controls on the ST array and carrying out one-way ANOVA and clustering analysis

source_name: SUPM2 ALCL cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Cells were grown in RPMI 1640+10% FCS+P/S until the cells reached log phase.

extract_protocol: Qiagen RNA extraction method was used using Qiacube fully automated sample prep. For QC your samples were processed on the Bioanalyzer 2100 (Agilent) using the RNA Pico Kit from Agilent technologies (P/N 5067-1513)  Then the samples were analysed using the Nugen Kits (Ovation Pico WTA system P/N 3300– WT-Ovation Exon Module P/N 2000 and Encore Biotin Module P/N 4200)

treatment_protocol: Cells were stained with Hoechst 33342 dye for required period of time and analysed using flow cytometry. Required SP and MP cells were FACS sorted into PBS.

tag: cell line

value: SUPM2 ALCL

tag: cell population

value: Side population cells


title: Breast cancer_BH0396-4

value: Luminal B


title: MP cells from Karpas299 ALCL cell line

description: gene expression data from MP cells

source_name: Karpas299 ALCL cell line

value: Karpas299 ALCL

value: Main population cells


title: Breast cancer_BH0396-7

value: death


title: Breast cancer_BH0396-6

value: Breast


title: Liver_WT_Vehicle_Rep1

value: Wildtype

value: Liver

tag: age

value: 10-16 weeks

tag: Sex

value: Male

value: Vehicle

value: Oral gavage

value: 0 mg/kg


title: Liver_LiverFXR null_Vehicle_Rep1

value: Liver Fxr KO

tag: tissue


title: Breast cancer_BH0396-5

value: low

value: Uncla

value: normal

value: disease-free

value: alive


title: Breast cancer_Breast Cancer 108T

value: Normal breast-like

value: over-expression

value: negative


title: MP cells from SUPM2 ALCL cell line

description: gene expression data from MP cells

value: SUPM2 ALCL

value: Main population cells


title: SP cells from Karpas299 ALCL cell line

description: gene expression data from SP cells

value: Karpas299 ALCL

value: Side population cells


title: Breast cancer_BH0394-6

value: Breast

value: Luminal B

value: positive


title: Breast cancer_BH0396-10


title: Breast cancer_BH0394-4

value: Luminal A


title: MP cells from DEL ALCL cell line

description: gene expression data from MP cells

source_name: DEL ALCL cell line

value: DEL ALCL


title: Breast cancer_BH0396-1

value: low


title: Breast cancer_BH0394-5


title: SP cells from DEL ALCL cell line

description: gene expression data from SP cells


title: Breast cancer_BH0396-3

value: Uncla


title: Breast cancer_BH0394-7


title: Breast cancer_BH0394-10

value: high


title: Breast cancer_BH0354-3

value: normal

value: recurrence, metastasis,  or disease-specific mortality

value: death


title: Breast cancer_BH0396-2

value: over-expression

value: disease-free

value: alive


title: Breast cancer_BH0354-1


title: Breast cancer_BH0394-8


title: Breast cancer_BH0394-1


title: Breast cancer_BH0354-4

value: negative


title: Retentostat IMK313 day2 -2

source_name: Anaerobic glucose-limited retentostat pH5.0 day 2, 30°, S. cerevisiae rim15 (MB009)

value: rim15 deletion mutant


title: Breast cancer_BH0394-2


title: Breast cancer_BH0394-3


title: Breast cancer_BH0394-9


title: Breast cancer_BH0344-7


title: Breast cancer_BH0344-9


title: Breast cancer_BH0354-2


title: Breast cancer_BH0344-2


title: Breast cancer_BH0344-3


title: Breast cancer_BH0312-8


title: Breast cancer_BH0344-10


title: Breast cancer_BH0344-4


title: Breast cancer_BH0312-7

value: Basal-like subtype


title: Breast cancer_BH0312-6

value: Breast


title: Breast cancer_76 cancer


title: Breast cancer_7 cancer

value: Luminal B


title: Retentostat IMK313 day16 -1

source_name: Anaerobic glucose-limited retentostat pH5.0 day 16, 30°, S. cerevisiae rim15 (MB008)


title: Breast cancer_BH0312-4

value: Normal breast-like

value: positive


title: Breast cancer_72 cancer


title: Breast cancer_BH0312-10


title: Breast cancer_BH0312-11

value: Luminal A


title: Breast cancer_75 cancer


title: Breast cancer_64 cancer


title: Breast cancer_70 cancer


title: Breast cancer_66 cancer

value: low


title: Breast cancer_BH0312-12


title: Breast cancer_65 cancer


title: Breast cancer_90T


title: Breast cancer_59 cancer


title: Breast cancer_28 cancer


title: Breast cancer_9 cancer


title: Breast cancer_62 cancer


title: Breast cancer_8 cancer


title: Breast cancer_58 cancer


title: Breast cancer_BH0312-3


title: Breast cancer_78 cancer2


title: Breast cancer_48 cancer


title: Breast cancer_69 cancer


title: Breast cancer_22 cancer


title: Breast cancer_BH0312-9


title: Breast cancer_154T


title: Breast cancer_23 cancer


title: Breast cancer_45 cancer


title: Breast cancer_15 cancer


title: Breast cancer_14 cancer


title: Breast cancer_153T


title: Breast cancer_135T


title: Breast cancer_134T


title: Breast cancer_128T

value: Uncla


title: Breast cancer_151T

value: high


title: Breast cancer_12 cancer

value: normal


title: Breast cancer_136T


title: Breast cancer_112T


title: Breast cancer_129T


title: Breast cancer_140T


title: Breast cancer_142T


title: Breast cancer_111T


title: Breast cancer_13 cancer

value: recurrence, metastasis,  or disease-specific mortality


title: Breast cancer_133T


title: Breast cancer_120T

value: death


title: Breast cancer_10 cancer


title: Breast cancer_BH0312-13


title: N3611

status: Public on Nov 24 2013

type: genomic

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing:
GenomeStudio v2011.1 and Methylation module (within GenomeStudio) v1.9 was used to generate RAW_nonorm_nobg.txt and GenomeStudio_norm_bg.txt (linked as supplementary files on Series record). GenomeStudio's default parameters were used.
GenomeStudio_norm_bg.txt AVG_Beta values were then quantile normalized to minimize batch effect (as the samples were run on different arrays).
The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg18 (NCBI36) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately.
The quantile normalized Beta values form the basis of the study's conclusions.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Control

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by phenol-chloroform extraction and ethanol precipitation

value: 64 years

tag: disease status

value: Control

value: Frontal lobe white matter

tag: gender

value: Male

tag: ms subtype

value: Not applicable

tag: ms duration

tag: post mortem interval

value: 17.5 hours

tag: additional diagnosis

value: coronary artery disease, lymphoma


title: PDC022

value: 71 years

value: Unknown

tag: additional diagnosis:


title: N3589

value: 53 years

value: 15 hours

value: melanoma


title: N3602

value: 66 years

value: 13.1 hours

value: metastatic larynx cancer, type 1 diabetes mellitus


title: N3606

value: 11.5 hours

value: chronic obstructive pulmonary disease


title: N3535

value: 81 years

value: 14 hours

value: non-hodgkin’s lymphoma


title: N3529

value: 58 years

value: Control

value: Frontal lobe white matter

value: Male

value: 9 hours

value: colon cancer


title: N3175

value: 54 years

value: Female

value: Not applicable

value: 21.5 hours

value: hypothyroidism, pancytopenia, type 1 diabetes mellitus


title: N3406

value: 72 years

value: 20.1 hours

value: breast cancer, congestive heart failure, tuberous sclerosis complex


title: PDC05

value: Unknown

value: cervical ependymoma


title: N3558

value: 59 years

value: 19.5 hours

value: non-hodgkin’s lymphoma


title: MS060

source_name: Multiple sclerosis

value: 55 years

value: Multiple sclerosis

value: Frontal lobe white matter

value: Secondary Progressive

value: 43 years

value: 16 hours

value: unknown


title: PDC08

value: 71 years

value: Control

value: Female

value: Not applicable

value: cerebral atherosclerosis


title: MS2946

value: Male

value: Primary Progressive

value: 12 years

value: 15 hours

value: dementia


title: MS122

value: 44 years

value: 10+ years

value: bronchopneumonia


title: MS104

value: 53 years

value: Multiple sclerosis

value: Frontal lobe white matter

value: Secondary Progressive

value: 11 years

value: 12 hours

value: urinary tract infection


title: N3482

value: 79 years

value: Control

value: Female

value: Not applicable

value: 14 hours

value: coronary heart disease, hypertension


title: CO51

value: 68 years

value: Male

value: 24 hours

value: ischemic heart disease


title: N3543

value: 73 years

value: chronic obstructive pulmonary disease


title: CO36

value: Frontal lobe white matter

value: 30 hours

value: coronary artery disease, cor pulmonale, idiopathic pulmonary fibrosis


title: N3348

value: 76 years

value: 9 hours

value: coronary heart disease, hypertension, type 1 diabetes mellitus


title: CO14

value: 64 years

value: Control

value: 18 hours

value: myocardial infarction, transient ischemic attack


title: MS083

value: 54 years

value: Multiple sclerosis

value: Primary Progressive

value: 16 years

value: 13 hours

value: bronchopneumonia


title: MS100

value: 46 years

value: Male

value: Secondary Progressive

value: 8 years

value: 7 hours

value: acute polyarthritis, peptic ulceration, pneumonia


title: MS3502

value: 78 years

value: Frontal lobe white matter

value: 52 years

value: 15.5 hours

value: bell’s palsy, cerebral vascular accident, seizure disorder


title: N3276

value: 54 years

value: Control

value: Not applicable

value: 19 hours

value: coronary heart disease, chronic kidney disease, peripheral vascular disease


title: MS286

value: 45 years

value: Multiple sclerosis

value: 16 years

value: unknown


title: MS141

value: Unknown

value: Male


title: MS097

value: 55 years

value: Secondary Progressive

value: 22 years

value: 31 hours

value: bronchopneumonia


title: MS273

value: 61 years

value: Frontal lobe white matter

value: Primary Progressive

value: 31 years

value: 24 hours

value: septicemia, urinary tract infection


title: MS231

value: 59 years

value: Female

value: 27 years

value: 12 hours


title: Jejunum tissue: SIV infected, untreated macaque biological rep 2

status: Public on Nov 01 2013

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from SIV infected, untreated macaque jejunum tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus macaque 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneSpring software, version 9

organism: Macaca mulatta

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: One SIV infected macaque (30378) was administered antiretroviral therapy beginning at 6 weeks post-infection, and two SIV infected macaques (33162 and 34540) were administered antiretroviral therapy beginning at 10 weeks post-infection

value: jejunal mucosa

value: 4-6 years


title: miRNA-tumour-P91_rep1

status: Public on Sep 30 2013

city: Pomezia(Rome)

first: Emanuele

last: de Rinaldis

address: Via Pontina

country: Italy

institute: IRBM (MERCK)

hyb_protocol: Samples were hybridized to Agilent Human miRNA Microarray Rel12.0 (Agilent Tech. Inc.) at 55oC, for 20 hours according to the manufacturer’s instructions.

scan_protocol: After washing microarray slides array scanning was performed by Agilent DNA Microarray Scanner G2565BA (Agilent Tech. Inc.).

data_processing: Feature extraction and data processing was performed with default scenario for Agilent Human MiRNA Microarray Rel12.0 by Feature Extraction Software 9.5.3 (Agilent Tech. Inc.) to calculate gProcessed signal. miRNA data were then post-processed using the AgiMicroRna (www.aroma-project.org) R package. Quality of individual arrays was assessed by visual evaluation of RLE (relative log expression), NUSE (normalised unscaled standard error) and hierarchical clustering plots. Robust Multichip Analysis (RMA) methodology  was used to remove the array signal background, followed by quantile normalisation to correct for inter-arrays global differences and by miRNA level summarisation. miRNAs not detected or having saturated signal in more than 10 samples were filtered out. Replicated samples for the same patient were averaged.

label_protocol: Total RNA was dephosphorylated, denaturated and Cyanine3-pCp ligated according to the manufacturer’s instructions using miRNA Complete Labeling and Hyb Kit (Agilent Tech. Inc.).

extract_protocol: Total RNA extraction from fresh-frozen samples was performed after tissue homogenization with Qiagen miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) completed with optional on-column DNase digestion carried out by RNase-Free DNase Set (Qiagen GmbH).

tag: pam50 subtype assignment

tag: patient id

tag: path. review % of tumour cells

tag: node positive

value: FALSE

tag: grade

tag: traditional histological type

value: NST


title: miRNA-tumour-P79_rep1

value: TRUE


title: miRNA-tumour-P48_rep1


title: LNCaP_DCC_1+R1881_1

status: Public on Oct 22 2013

city: Copenhagen

first: Charlotte

last: Svensson

state: Please select one

address: Blegdamsvej 3

department: Novo Nordisk foundation center for protein research

country: Denmark

institute: University of copenhagen

description:
androgen status, negative
LNCaP grown in DCC (steroid-depleted) medium_No1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LNCaP, DCC serum containing medium + R1881 treated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LNCaP cells wre grown in RPMI1648 supplemented with 10%FBS or alternatively supplemented with 5% dextran-coated charcoal stripped(DCC) FBS.

extract_protocol: Qiagen's RNAeasy RNA extraction kit

treatment_protocol: Steroid depletion was achieved by incubating with DCC containing medium for 5 days and treatment of DCC cultured cells with synthestic androgen (R1881, 10nM) was perfomed overnight (16h).

tag: cell line

value: LNCaP

tag: treatment


title: miRNA-tumour-P95_rep1


title: miRNA-tumour-P11_rep1

value: APOCRINE/LOBULAR

value: Breast Cancer


title: MS093

tag: age

value: 57 years

value: Multiple sclerosis

value: Frontal lobe white matter

value: Secondary Progressive

value: 26 years

value: 25 hours

value: pneumonia


title: miRNA-tumour-P83_rep2


title: miRNA-tumour-P130_rep1


title: LNCaP_DCC_1

description:
androgen status, positive
LNCaP grown in DCC medium treated with R1881_1

source_name: LNCap, DCC serum containing medium

value: DCC serum containing medium


title: miRNA-tumour-P112_rep1


title: miRNA-tumour-P70_rep1


title: miRNA-tumour-P68_rep1


title: MS109

value: 60 years

tag: tissue

value: Female

value: 25 years

value: 22 hours

value: cerebral atherosclerosis, myocardial infarction


title: miRNA-tumour-P157_rep1

value: FALSE

value: NST


title: miRNA-tumour-P69_rep1

value: TRUE


title: miRNA-tumour-P67_rep1


title: miRNA-tumour-P64_rep1


title: miRNA-tumour-P63_rep1


title: miRNA-tumour-P59_rep1


title: miRNA-tumour-P56_rep1


title: miRNA-tumour-P71_rep1


title: miRNA-tumour-P18_rep2


title: MS076

value: 49 years

tag: disease status

value: 18 years

value: 31 hours

value: chronic renal failure, heart disease


title: miRNA-tumour-P58_rep1

value: PLEOMORPHIC   LOBULAR


title: miRNA-tumour-P66_rep1


title: miRNA-tumour-P55_rep1


title: miRNA-tumour-P62_rep1


title: miRNA-tumour-P60_rep1

value: MEDULLARY LIKE


title: MS3010

value: 50 years

value: Multiple sclerosis

value: Frontal lobe white matter

tag: gender

value: Secondary Progressive

value: 24 years

value: 15 hours

value: unknown


title: MS2765

value: 51 years

value: Female

tag: ms subtype

value: Chronic Progressive

value: 32 years

value: 9 hours


title: MS342

value: 35 years

tag: ms duration

value: 5 years


title: MS3840

value: 61 years

value: Primary Progressive

value: 17 years

tag: post mortem interval

value: 22.8 hours

value: chronic urinary tract infection, pneumonia


title: MS088

value: 54 years

value: Multiple sclerosis

value: Frontal lobe white matter

value: Unknown

value: 22 hours

tag: additional diagnosis

value: bronchopneumonia


title: MS3931

value: 74 years

value: Female

value: 11 years

value: 9.5 hours

value: pneumonia


title: miRNA-tumour-P98_rep1

value: TRUE

value: NST

value: Breast Cancer


title: miRNA-tumour-P2_rep1


title: miRNA-tumour-P35_rep1

value: METAPLASTIC - SQUAMOUS


title: miRNA-tumour-P27_rep1

value: FALSE


title: miRNA-tumour-P47_rep1


title: miRNA-tumour-P24_rep1


title: miRNA-tumour-P167_rep1


title: miRNA-tumour-P81_rep2


title: miRNA-tumour-P57_rep1


title: miRNA-tumour-P40_rep1


title: MS062

value: 49 years

value: Secondary Progressive

value: 19 years

value: 10 hours

value: respiratory infection


title: miRNA-tumour-P113_rep1


title: miRNA-tumour-P101_rep1


title: miRNA-tumour-P121_rep1


title: MS377

value: 50 years

value: Multiple sclerosis

value: Frontal lobe white matter

value: Unknown

value: 22 hours


title: miRNA-tumour-P102_rep1


title: miRNA-tumour-P149_rep1


title: miRNA-tumour-P155_rep1


title: miRNA-tumour-P127_rep1


title: MS4218

value: 63 years

value: Female

value: Chronic Progressive

value: 18 years

value: 15 hours

value: cerebral atherosclerosis, chronic urinary tract infection


title: MS2771

value: 64 years

value: 33 years

value: 17.3 hours

value: unknown


title: MS058

value: 51 years

value: Secondary Progressive

value: 21 years


title: MS094

value: 42 years

value: Multiple sclerosis

value: Primary Progressive

value: 6 years

value: 11 hours

value: bronchopneumonia


title: miRNA-tumour-P74_rep1

value: TRUE

value: NST

value: Breast Cancer


title: miRNA-tumour-P99_rep1

value: FALSE


title: miRNA-tumour-P150_rep1


title: miRNA-tumour-P156_rep1


title: miRNA-tumour-P26_rep1


title: miRNA-tumour-P61_rep1


title: miRNA-tumour-P141_rep2


title: MS4201

value: 75 years

value: Frontal lobe white matter

value: Female

value: Chronic Progressive

value: 29 years

value: 13.8 hours

value: chronic urinary tract infection, hypertension, hypothyroidism, migraine


title: miRNA-tumour-P37_rep1


title: miRNA-tumour-P152_rep1


title: miRNA-tumour-P146_rep1

value: LOBULAR


title: miRNA-tumour-P29_rep1


title: miRNA-tumour-P111_rep1


title: miRNA-tumour-P163_rep1


title: miRNA-tumour-P162_rep1


title: miRNA-tumour-P109_rep2


title: miRNA-tumour-P87_rep1


title: miRNA-tumour-P123_rep1

value: INTRACYSTIC PAPILLARY CARCINOMA


title: miRNA-tumour-P173_rep1


title: miRNA-tumour-P166_rep1


title: miRNA-tumour-P109_rep1


title: miRNA-tumour-P165_rep1

value: MIXED NST + INV. PAPILLARY + INV. MICROPAPILLARY


title: miRNA-tumour-P168_rep1


title: miRNA-tumour-P141_rep1


title: miRNA-tumour-P161_rep1


title: miRNA-tumour-P158_rep1

value: INVASIVE TUBULAR/CRIBRIFORM


title: miRNA-tumour-P106_rep2


title: miRNA-tumour-P53_rep1


title: miRNA-tumour-P20_rep1


title: miRNA-tumour-P14_rep1


title: miRNA-tumour-P41_rep1


title: miRNA-tumour-P13_rep1


title: miRNA-tumour-P120_rep1


title: miRNA-tumour-P6_rep1


title: miRNA-tumour-P93_rep1


title: miRNA-tumour-P9_rep1


title: miRNA-tumour-P7_rep1


title: miRNA-tumour-P73_rep1


title: miRNA-tumour-P106_rep1


title: miRNA-tumour-P124_rep1


title: miRNA-tumour-P148_rep1


title: miRNA-tumour-P105_rep1


title: miRNA-tumour-P119_rep1


title: miRNA-tumour-P153_rep1


title: miRNA-tumour-P45_rep1

value: INVASIVE PAPILLARY


title: miRNA-tumour-P51_rep1


title: miRNA-tumour-P46_rep1

value: MEDULLARY LIKE


title: miRNA-tumour-P54_rep1


title: miRNA-tumour-P22_rep1

value: TRUE


title: miRNA-tumour-P49_rep1

value: NST


title: miRNA-tumour-P154_rep1

value: MIXED NST AND TUBULAR


title: miRNA-tumour-P1_rep1


title: miRNA-tumour-P159_rep1

value: Breast Cancer


title: miRNA-tumour-P50_rep1


title: miRNA-tumour-P42_rep1

value: FALSE

value: SALIVARY GLAND FEATURES


title: miRNA-tumour-P43_rep1


title: miRNA-tumour-P39_rep1


title: miRNA-tumour-P38_rep1


title: miRNA-tumour-P65_rep1


title: miRNA-tumour-P52_rep1


title: miRNA-tumour-P36_rep1


title: miRNA-tumour-P34_rep1


title: miRNA-tumour-P44_rep1


title: miRNA-tumour-P33_rep1


title: miRNA-tumour-P32_rep1


title: miRNA-tumour-P31_rep1


title: miRNA-tumour-P30_rep1


title: miRNA-tumour-P28_rep1


title: miRNA-tumour-P25_rep1


title: miRNA-tumour-P23_rep1


title: miRNA-tumour-P21_rep1


title: miRNA-tumour-P19_rep1

value: METAPLASTIC


title: miRNA-tumour-P134_rep2


title: miRNA-tumour-P18_rep1


title: miRNA-tumour-P3_rep1


title: miRNA-tumour-P15_rep1


title: miRNA-tumour-P17_rep1

value: MIXED NST AND METAPLASTIC


title: miRNA-tumour-P117_rep1


title: miRNA-tumour-P144_rep1


title: miRNA-tumour-P5_rep1


title: miRNA-tumour-P16_rep1


title: miRNA-tumour-P140_rep1


title: miRNA-tumour-P134_rep1


title: miRNA-tumour-P132_rep1


title: miRNA-tumour-P8_rep1


title: miRNA-tumour-P128_rep1


title: miRNA-tumour-P104_rep1


title: miRNA-tumour-P78_rep1


title: miRNA-tumour-P139_rep1


title: miRNA-tumour-P89_rep1


title: miRNA-tumour-P107_rep1


title: miRNA-tumour-P151_rep1


title: miRNA-tumour-P97_rep1


title: miRNA-tumour-P82_rep1


title: miRNA-tumour-P12_rep1


title: miRNA-tumour-P10_rep1

value: R_ METAPLASTIC CARCINOMA; L_NST


title: miRNA-tumour-P108_rep1


title: miRNA-tumour-P84_rep1


title: miRNA-tumour-P122_rep1


title: miRNA-tumour-P115_rep1


title: miRNA-tumour-P169_rep1


title: miRNA-tumour-P137_rep1


title: miRNA-tumour-P172_rep1


title: miRNA-tumour-P145_rep1


title: miRNA-tumour-P76_rep2


title: miRNA-tumour-P138_rep1


title: miRNA-tumour-P80_rep1

value: PLEOMORPHIC LOBULAR


title: miRNA-tumour-P81_rep1


title: miRNA-tumour-P114_rep1


title: miRNA-tumour-P100_rep1


title: miRNA-tumour-P85_rep1


title: miRNA-tumour-P136_rep1


title: miRNA-tumour-P83_rep1


title: miRNA-tumour-P160_rep1


title: miRNA-tumour-P86_rep1


title: miRNA-tumour-P133_rep1


title: miRNA-tumour-P164_rep1


title: miRNA-tumour-P142_rep1


title: miRNA-tumour-P135_rep1


title: miRNA-tumour-P96_rep1


title: miRNA-tumour-P126_rep1


title: miRNA-tumour-P110_rep1


title: miRNA-tumour-P125_rep1


title: miRNA-tumour-P94_rep1

value: METAPLASTIC MATRIX PRODUCING


title: miRNA-tumour-P131_rep1


title: miRNA-tumour-P77_rep1


title: miRNA-tumour-P103_rep1


title: miRNA-tumour-P170_rep1


title: miRNA-tumour-P143_rep1


title: miRNA-tumour-P4_rep1


title: miRNA-tumour-P171_rep1


title: miRNA-tumour-P118_rep1


title: miRNA-tumour-P129_rep1


title: miRNA-tumour-P88_rep1


title: miRNA-tumour-P147_rep1


title: miRNA-tumour-P72_rep1


title: miRNA-tumour-P76_rep1


title: miRNA-tumour-P116_rep1


title: miRNA-tumour-P92_rep1


title: miRNA-tumour-P90_rep1


title: miRNA-tumour-P75_rep1


title: Mesothelioma_3

status: Public on Sep 06 2013

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from spontaneous malignant mesotheliomas

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

organism: Rattus norvegicus

source_name: spontaneous malignant mesotheliomas

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

extract_protocol: RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples.   RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.

tag: strain

tag: sample type

value: spontaneous malignant mesotheliomas


title: Mesothelioma_5


title: Fred-PE_control_6

description: Gene expression from normal Fred-PE mesothelial cell culture

source_name: normal Fred-PE mesothelial cell culture (control)

value: normal Fred-PE mesothelial cell culture


title: Mesothelioma_4


title: Mesothelioma_2


title: Fred-PE_control_5


title: Mesothelioma_1


title: Fred-PE_control_4


title: Fred-PE_control_3


title: Fred-PE_control_1


title: Fred-PE_control_2


title: DLPFC-8

status: Public on Aug 08 2013

middle: M

last: Montano

state: United States

address: 855 N Wolfe Street

department: Molecular Medicine

institute: Johns Hopkins School of Medicine

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.
processed data: quantile normalized p (percent methylation) value

source_name: Input fraction from DLPFC-8

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: brain region

value: DLPFC

tag: cell type

value: Whole Tissue

tag: Sex

value: M

tag: race

value: C

source_name: DLPFC-8 methyl-depleted


title: DLPFC-14

source_name: Input fraction from DLPFC-14

value: F

source_name: DLPFC-14 methyl-depleted


title: DLPFC-16

source_name: Input fraction from DLPFC-16

source_name: DLPFC-16 methyl-depleted


title: DLPFC-17

source_name: Input fraction from DLPFC-17

source_name: DLPFC-17 methyl-depleted


title: STG-15

source_name: Input fraction from STG-15

value: STG

source_name: STG-15 methyl-depleted


title: STG-17

source_name: Input fraction from STG-17

source_name: STG-17 methyl-depleted


title: DLPFC-13

source_name: Input fraction from DLPFC-13

source_name: DLPFC-13 methyl-depleted


title: DLPFC-7

source_name: Input fraction from DLPFC-7

source_name: DLPFC-7 methyl-depleted


title: DLPFC-10

source_name: Input fraction from DLPFC-10

source_name: DLPFC-10 methyl-depleted


title: DLPFC-15

source_name: Input fraction from DLPFC-15

source_name: DLPFC-15 methyl-depleted


title: DLPFC-19

source_name: Input fraction from DLPFC-19

source_name: DLPFC-19 methyl-depleted


title: HF-14

source_name: Input fraction from HF-14

value: HF

source_name: HF-14 methyl-depleted


title: DLPFC-20

source_name: Input fraction from DLPFC-20

source_name: DLPFC-20 methyl-depleted


title: DLPFC-11

source_name: Input fraction from DLPFC-11

source_name: DLPFC-11 methyl-depleted


title: HF-8

source_name: Input fraction from HF-8

source_name: HF-8 methyl-depleted


title: DLPFC-2

source_name: Input fraction from DLPFC-2

source_name: DLPFC-2 methyl-depleted


title: DLPFC-1

source_name: Input fraction from DLPFC-1

source_name: DLPFC-1 methyl-depleted


title: STG-18

source_name: Input fraction from STG-18

source_name: STG-18 methyl-depleted


title: HF-13

source_name: Input fraction from HF-13

value: AA

source_name: HF-13 methyl-depleted


title: HF-5

source_name: Input fraction from HF-5

source_name: HF-5 methyl-depleted


title: HF-11

source_name: Input fraction from HF-11

source_name: HF-11 methyl-depleted


title: HF-1

source_name: Input fraction from HF-1

source_name: HF-1 methyl-depleted


title: HF-2

source_name: Input fraction from HF-2

source_name: HF-2 methyl-depleted


title: DLPFC-12

source_name: Input fraction from DLPFC-12

source_name: DLPFC-12 methyl-depleted


title: STG-3

source_name: Input fraction from STG-3

source_name: STG-3 methyl-depleted


title: HF-10

source_name: Input fraction from HF-10

source_name: HF-10 methyl-depleted


title: HF-4

source_name: Input fraction from HF-4

source_name: HF-4 methyl-depleted


title: DLPFC-3

source_name: Input fraction from DLPFC-3

source_name: DLPFC-3 methyl-depleted


title: HF-12

source_name: Input fraction from HF-12

source_name: HF-12 methyl-depleted


title: HF-3

source_name: Input fraction from HF-3

source_name: HF-3 methyl-depleted


title: HF-(-)-3

source_name: Input fraction from HF-(-)-3

value: NeuN-Neg

source_name: HF-(-)-3 methyl-depleted


title: HF-(+)-3

source_name: Input fraction from HF-(+)-3

value: NeuN-Pos

source_name: HF-(+)-3 methyl-depleted


title: STG-(-)-20

source_name: Input fraction from STG-(-)-20

source_name: STG-(-)-20 methyl-depleted


title: HF-(-)-7

source_name: Input fraction from HF-(-)-7

source_name: HF-(-)-7 methyl-depleted


title: HF-(+)-2

source_name: Input fraction from HF-(+)-2

source_name: HF-(+)-2 methyl-depleted


title: STG-20

source_name: Input fraction from STG-20

source_name: STG-20 methyl-depleted


title: HF-(+)-7

source_name: Input fraction from HF-(+)-7

source_name: HF-(+)-7 methyl-depleted


title: HF-(-)-2

source_name: Input fraction from HF-(-)-2

source_name: HF-(-)-2 methyl-depleted


title: HF-(+)-6

source_name: Input fraction from HF-(+)-6

source_name: HF-(+)-6 methyl-depleted


title: STG-(-)-22

source_name: Input fraction from STG-(-)-22

source_name: STG-(-)-22 methyl-depleted


title: DLP-(+)-18

source_name: Input fraction from DLP-(+)-18

source_name: DLP-(+)-18 methyl-depleted


title: HF-(-)-6

source_name: Input fraction from HF-(-)-6

source_name: HF-(-)-6 methyl-depleted


title: DLPFC-9

source_name: Input fraction from DLPFC-9

source_name: DLPFC-9 methyl-depleted


title: HF-6

source_name: Input fraction from HF-6

source_name: HF-6 methyl-depleted


title: DLPFC-6

source_name: Input fraction from DLPFC-6

source_name: DLPFC-6 methyl-depleted


title: STG-(+)-1

source_name: Input fraction from STG-(+)-1

source_name: STG-(+)-1 methyl-depleted


title: DLP-(+)-9

source_name: Input fraction from DLP-(+)-9

source_name: DLP-(+)-9 methyl-depleted


title: DLP-(-)-6

source_name: Input fraction from DLP-(-)-6

source_name: DLP-(-)-6 methyl-depleted


title: DLPFC-5

source_name: Input fraction from DLPFC-5

source_name: DLPFC-5 methyl-depleted


title: DLP-(+)-6

source_name: Input fraction from DLP-(+)-6

source_name: DLP-(+)-6 methyl-depleted


title: DLP-(-)-5

source_name: Input fraction from DLP-(-)-5

source_name: DLP-(-)-5 methyl-depleted


title: DLP-(-)-9

source_name: Input fraction from DLP-(-)-9

source_name: DLP-(-)-9 methyl-depleted


title: STG-(-)-1

source_name: Input fraction from STG-(-)-1

source_name: STG-(-)-1 methyl-depleted


title: HF-7

source_name: Input fraction from HF-7

source_name: HF-7 methyl-depleted


title: STG-1

source_name: Input fraction from STG-1

source_name: STG-1 methyl-depleted


title: STG-22

source_name: Input fraction from STG-22

source_name: STG-22 methyl-depleted


title: DLP-(+)-5

source_name: Input fraction from DLP-(+)-5

source_name: DLP-(+)-5 methyl-depleted


title: STG-(+)-20

source_name: Input fraction from STG-(+)-20

source_name: STG-(+)-20 methyl-depleted


title: DLP-(-)-18

source_name: Input fraction from DLP-(-)-18

source_name: DLP-(-)-18 methyl-depleted


title: STG-(+)-22

source_name: Input fraction from STG-(+)-22

source_name: STG-(+)-22 methyl-depleted


title: 80(-)-20(+)

source_name: Input fraction from  80(-)-20(+)

value: Calibration mix NeuN-Pos and NeuN-Neg

source_name: 80(-)-20(+) methyl-depleted


title: DLPFC-18

source_name: Input fraction from DLPFC-18

source_name: DLPFC-18 methyl-depleted


title: 40(-)-60(+)

source_name: Input fraction from  40(-)-60(+)

source_name: 40(-)-60(+) methyl-depleted


title: High Mg2+ 4 days  treatment

status: Public on Aug 02 2013

type: SRA

city: Hangzhou

first: Gulei

last: Jin

state: Zhejiang

address: Yuhangtang Road 388#

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using tophat 2.0.8 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: TAIR v10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Arabidopsis thaliana

growth_protocol: All plants were grown in the controlled-environment growth chambers (Conviron E7/2, Winnipeg, Manitoba, Canada) with a humidity of 80%, a daily cycle of 24 °C, 10-h day and 20 °C, 14-h night. The daytime light intensity was 120 µmol photons m−2 s−1. The wild ecotype line was from the Nottingham Arabidopsis Stock Centre (http://nasc.nott.ac.uk).

extract_protocol:
The roots were ground in liquid nitrogen and total RNA was subsequently extracted with RNAisoPlus reagent from 70 mg of tissue powder according to the manufacturer’s instructions (Takara, Otsu, Shiga, Japan). All RNA samples were checked for DNA contamination.
Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.

treatment_protocol: Roots were sampled from five-week-cultivated Arabidopsis after 4 d and 7 d treatment of low Mg (supplied with 0.5 μM Mg2+) and high Mg (supplied with 10 mM Mg2+).

value: Root

tag: time

value: 4 day


title: Low Mg2+ 4 days treatment


title: STG-2

source_name: Input fraction from STG-2

source_name: STG-2 methyl-depleted


title: wild type vs uppS-RBS (A to C) rep2 dye-swap

status: Public on Apr 01 2013

city: Ithaca

first: John

middle: D.

last: Helmann

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

description:
rep2 dye-swap
Fold change was calculated by dividing the uppS-RBS (A to C) mutant value by the WT value.

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95°C and hybridized 16-18 hours at 42°C to DNA microarray slides which had been prehybridized for at least 30 min at 42°C in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42°C, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.) Raw data files were produced from the scanned images using the GenePix Pro 6.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 6.0 software package such that the ratio of medians of all features was equal to 1. Fold changes equal to average of mutant/average of wild type. Ave represents the average of medians for duplicate spots (minus median of background).

label: Alexa Fluor 555

organism: Bacillus subtilis

source_name: uppS-RBS (A to C)

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 microgram of total RNA. Total cDNA was labeled overnight with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen)

extract_protocol: The cell cultures were grown to an OD600 of 0.4 in LB broth with agitation. RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNase free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

tag: genotype/variation

value: uppS-RBS (A to C)

label: Alexa Fluor 647

source_name: wild type

value: wild type


title: STG-7

source_name: Input fraction from STG-7

source_name: STG-7 methyl-depleted


title: STG-24

source_name: Input fraction from STG-24

source_name: STG-24 methyl-depleted


title: 0(-)-100(+)

source_name: Input fraction from  0(-)-100(+)

source_name: 0(-)-100(+) methyl-depleted


title: STG-4

source_name: Input fraction from STG-4

source_name: STG-4 methyl-depleted


title: STG-29

source_name: Input fraction from STG-29

source_name: STG-29 methyl-depleted


title: wild type vs uppS-RBS (A to C) rep1 dye-swap

description:
rep1 dye-swap
Fold change was calculated by dividing the uppS-RBS (A to C) mutant value by the WT value.


title: wild type vs uppS-RBS (A to C) rep2

description:
rep2
Fold change was calculated by dividing the uppS-RBS (A to C) mutant value by the WT value.


title: STG-10

source_name: Input fraction from STG-10

source_name: STG-10 methyl-depleted


title: wild type vs uppS-RBS (A to C) rep1

description:
rep1
Fold change was calculated by dividing the uppS-RBS (A to C) mutant value by the WT value.


title: STG-19

source_name: Input fraction from STG-19

source_name: STG-19 methyl-depleted


title: STG-23

source_name: Input fraction from STG-23

source_name: STG-23 methyl-depleted


title: STG-25

source_name: Input fraction from STG-25

source_name: STG-25 methyl-depleted


title: MP cells from SUDHL-1 ALCL cell line, rep 3

status: Public on Jun 25 2012

description: gene expression data from MP cells

source_name: SUDHL-1 ALCL cell line

tag: cell line

value: ALCL cell line SUDHL-1

tag: cell population

value: Main population cells


title: STG-26

source_name: Input fraction from STG-26

tag: age

source_name: STG-26 methyl-depleted


title: STG-9

source_name: Input fraction from STG-9

source_name: STG-9 methyl-depleted


title: STG-28

source_name: Input fraction from STG-28

source_name: STG-28 methyl-depleted


title: MP cells from SUDHL-1 ALCL cell line, rep 2

description: gene expression data from MP cells


title: STG-31

source_name: Input fraction from STG-31

source_name: STG-31 methyl-depleted


title: 100(-)-0(+)

source_name: Input fraction from  100(-)-0(+)

value: DLPFC

source_name: 100(-)-0(+) methyl-depleted


title: STG-14

source_name: Input fraction from STG-14

value: Whole Tissue

source_name: STG-14 methyl-depleted


title: STG-8

source_name: Input fraction from STG-8

source_name: STG-8 methyl-depleted


title: WT vs rpoC (G1122D) rep2

status: Public on Jun 15 2012

description:
rep2
Fold change was calculated by dividing the rpoC (G1122D) mutant value by the WT value.

source_name: WT

value: WT

source_name: rpoC (G1122D)

value: rpoC (G1122D)


title: STG-32

source_name: Input fraction from STG-32

value: F

value: C

source_name: STG-32 methyl-depleted


title: STG-6

source_name: Input fraction from STG-6

value: STG

value: M

source_name: STG-6 methyl-depleted


title: SP cells from SUDHL-1 ALCL cell line, rep 2

description: gene expression data from SP cells

source_name: SUDHL-1 ALCL cell line

value: Side population cells


title: WT vs rpoC (G1122D) rep1 dye-swap

description:
rep1 dye-swap
Fold change was calculated by dividing the rpoC (G1122D) mutant value by the WT value.


title: WT vs rpoC (G1122D) rep2 dye-swap

description:
rep2 dye-swap
Fold change was calculated by dividing the rpoC (G1122D) mutant value by the WT value.


title: WT vs rpoC (G1122D) rep1

description:
rep1
Fold change was calculated by dividing the rpoC (G1122D) mutant value by the WT value.


title: STG-5

source_name: Input fraction from STG-5

value: AA

source_name: STG-5 methyl-depleted


title: IDD patient 3

status: Public on Jan 01 2012

city: Xi'an

first: Hai-Qiang

last: Wang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

description:
Biological replicate 3 of 3. Degenerative human nucleus pulposus cells harvested following digestion of nucleus pulposus with pronase and collagenase II.

WDN

hyb_protocol: The labeled samples were hybridized on the miRCURY LNA™ microRNA Array V11.0.

scan_protocol: Hybridization signals were detected by fluorescence using an Axon GenePix 4000B microarray scanner. Scanner images were quantified by GenePix Pro 6 (Molecular Devices).

data_processing: The intensity of green signal was calculated after background subtraction and the median value of four replicated spots of each probe on the same slide had been calculated. We used Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

source_name: Nucleus pulposus cells, degenerative

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon) according to manufacturer's instructions.

extract_protocol: Nucleus pulposus (NP) cells were isolated by enzymatic digestion of collected human NP for 40 min at 37 °C in PBS with 0.25% pronase (Gibco-BRL) and subsequently for 4 h in PBS with 0.025% collagenase type II (Invitrogen). Total RNA of NP cells was extracted using Trizol(Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

tag: tissue

value: Nucleus pulposus

tag: condition

value: degenerative

tag: disease

value: intervertebral disc degeneration (IDD)

value: female

tag: degeneration grading

value: Grading IV


title: IDD patient 1

description:
Biological replicate 1 of 3. Degenerative human nucleus pulposus cells harvested following digestion of nucleus pulposus with pronase and collagenase II.
WYS

tag: gender


title: Control patient 3

description:
Biological replicate 3 of 3. Control human nucleus pulposus cells harvested following digestion of nucleus pulposus with pronase and collagenase II.
CMN2

source_name: Nucleus pulposus cells, control

value: control

value: scoliosis

value: Grading II


title: Control patient 2

description: Biological replicate 2 of 3. Control human nucleus pulposus cells harvested following digestion of nucleus pulposus with pronase and collagenase II.


title: Control patient 1

description:
Biological replicate 1 of 3. Control human nucleus pulposus cells harvested following digestion of nucleus pulposus with pronase and collagenase II.
WR


title: WT vs delta rocG delta gudB   rep2

status: Public on Dec 13 2011

tag: genotype

value: wt

source_name: delta rocG delta gudB

value: delta rocG delta gudB


title: WT vs delta rocG delta gudB   rep1

tag: strain


title: Control

tag: treatment

value: Control

value: Root

value: 4 day


title: 168 + lys vs 168 - lys rep2 dyeswap

status: Public on Aug 23 2011

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.) Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing:
Red/green fluorescence intensity values were normalized  using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1
Fold changes equal to average of induced/average of non induced.  Ave represents the average of medians for duplicate spots (minus median of background).

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: The cell cultures were grown to an OD600 of 0.4 in LB broth with agitation.

treatment_protocol: The cultures were treated with either lysozyme or xylose for 20 min. The non induced cultures were incubated for 20 min without treatment. RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

value: wildtype

value: 20 min + lys

value: 20 min - lys


title: 168 + lys vs 168 - lys rep1 dyeswap

extract_protocol: RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).


title: STG-21

source_name: Input fraction from STG-21

tag: brain region

value: STG

value: Whole Tissue

value: F

value: C

source_name: STG-21 methyl-depleted


title: delta7 P-sigV + xyl vs delta7 P-sigV - xyl rep2 dyeswap

source_name: delta7 P-sigV

value: delta7 P-sigV

value: 20 min + xyl

value: 20 min - xyl


title: 168 + lys vs 168 - lys rep1


title: WT_(+MOE)_vs_WT_(-MOE)_rep3

status: Public on Jun 17 2011

description: Biological replicate 3 of 3

data_processing: Red/green fluorescence intensity values were normalized using the GenePix Pro 6.0 software package such that the ratio of medians of all features was equal to 1. Fold changes equal to average of moenomycin treated samples  (635) / average of untreated samples (532). Ave represents the average of medians for duplicate spots (minus median of background).

source_name: WT/-MOE

extract_protocol: Cells were grown to mid-log phase (OD600 0.4) and split into 2 flasks. One flask was treated with 1 µg/ml moenomycin for 15 minutes. Total RNA was isolated using the RNeasy Mini Kit (Qiagen Sciences, Maryland). After DNase treatment with TURBO DNA-freeTM (Ambion), RNA concentrations were quantified using a NanoDrop spectrophotometer (NanoDrop Tech. Inc., Wilmington, DE). cDNA was synthesized from 20 µg total RNA and differentially labeled according to manufacturer’s instructions with the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen). Before and after indirect labeling with Alexa Fluor 555 or Alexa Fluor 647 (at least 3 h at room temperature) cDNA was purified using the Qiagen MinElute PCR Purification Kit (Qiagen, Maryland) and quantified via NanoDrop.

value: wild-type

source_name: WT/+MOE


title: delta7 P-sigV + xyl vs delta7 P-sigV - xyl rep1


title: STG-16

source_name: Input fraction from STG-16

tag: cell type

source_name: STG-16 methyl-depleted


title: STG-11

source_name: Input fraction from STG-11

tag: Sex

source_name: STG-11 methyl-depleted


title: MP cells from SUDHL-1 ALCL cell line, rep 1

description: gene expression data from MP cells

value: ALCL cell line SUDHL-1

value: Main population cells


title: delta7 P-sigV + xyl vs delta7 P-sigV - xyl rep3 dyeswap


title: delta7 P-sigV + xyl vs delta7 P-sigV - xyl rep3


title: delta7 P-sigV + xyl vs delta7 P-sigV - xyl rep1 dyeswap


title: 168 + lys vs 168 - lys rep3


title: WT_(+MOE)_vs_WT_(-MOE)_rep2

description: Biological replicate 2 of 3


title: 168 + lys vs 168 - lys rep2


title: STG-12

source_name: Input fraction from STG-12

tag: race

source_name: STG-12 methyl-depleted


title: 20(-)-80(+)

source_name: Input fraction from  20(-)-80(+)

value: DLPFC

value: Calibration mix NeuN-Pos and NeuN-Neg

source_name: 20(-)-80(+) methyl-depleted


title: delta7 P-sigV + xyl vs delta7 P-sigV - xyl rep2


title: DapR1(+DAP)_vs_DapR1(-DAP)_rep3

status: Public on Jun 16 2011

description: Biological replicate 3 of 4 of daptomycin resistant mutant DapR1 with and without daptomycin treatment.

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 6.0 software package such that the ratio of medians of all features was equal to 1. Fold changes equal to average of daptomycin treated samples  (635) / average of untreated samples (532) or average of wild type (532) / average of mutants (635) excluding dye swap experiment which was average of wild type (635) / average of mutant (532). Ave represents the average of medians for duplicate spots (minus median of background).

extract_protocol: Total RNA was isolated from Bacillus subtilis 168 and DapR1 grown to mid-log phase (OD600 of 0.4) using the RNeasy Mini Kit (Qiagen Sciences, Maryland). After DNase treatment with TURBO DNA-freeTM (Ambion), RNA concentrations were quantified using a NanoDrop spectrophotometer (NanoDrop Tech. Inc., Wilmington, DE). cDNA was synthesized from 20 µg total RNA and differentially labeled according to manufacturer’s instructions with the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen). Before and after indirect labeling with Alexa Fluor 555 or Alexa Fluor 647 (at least 3 h at room temperature) cDNA was purified using the Qiagen MinElute PCR Purification Kit (Qiagen, Maryland) and quantified via NanoDrop.

value: DapR1 (daptomycin resistant mutant)


title: DapR1(+DAP)_vs_DapR1(-DAP)_rep4

description: Biological replicate 4 of 4 of daptomycin resistant mutant DapR1 with and without daptomycin treatment.


title: WT_(+MOE)_vs_WT_(-MOE)_rep1

description: Biological replicate 1 of 3


title: DapR1(+DAP)_vs_DapR1(-DAP)_rep2

description: Biological replicate 2 of 4 of daptomycin resistant mutant DapR1 with and without daptomycin treatment.


title: DapR1(+DAP)_vs_DapR1(-DAP)_rep1

description: Biological replicate 1 of 4 of daptomycin resistant mutant DapR1 with and without daptomycin treatment.


title: WT(+DAP)vsDapR1(+DAP)_rep2

description: Biological replicate 2 of 2 of Bacillus subtilis compared to daptomycin resistant mutant DapR1 with daptomycin treatment.

source_name: WT/+DAP


title: WT(+DAP)vsDapR1(+DAP)_rep1

description: Biological replicate 1 of 2 of Bacillus subtilis compared to daptomycin resistant mutant DapR1 with daptomycin treatment.


title: Fur vs. Fur FbpABC replicate 3 (dye swap)

status: Public on Feb 19 2011

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined  plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

data_processing: Red/green fluorescence intensity values were normalized such that the ratio of medians of all features was equal to 1

source_name: fur fbpABC, LB, mid-log

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 μg of total RNA. Total cDNA was labeled overnight with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen)

extract_protocol: RNA isolation and was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

tag: mutation

value: fur fbpABC

source_name: fur, LB, mid-log

value: fur


title: Fur vs. Fur FbpC replicate 2

source_name: fur fbpC, LB, mid-log

value: fur fbpC


title: Fur vs. Fur FbpC replicate 1


title: WT(-DAP)vsDapR1(-DAP)_rep2

description: Biological replicate 2 of 2 of Bacillus subtilis compared to daptomycin resistant mutant DapR1.

source_name: WT/-DAP

tag: genotype/variation


title: Fur vs. Fur FbpAB replicate 2

source_name: fur fbpAB, LB, mid-log

value: fur fbpAB


title: WT vs. Fur replicate 3 (dye swap)

status: Public on Mar 23 2011

source_name: WT, LB, mid-log

value: WT


title: Fur vs. Fur FbpAB replicate 1


title: WT(-DAP)vsDapR1(-DAP)_rep1

description: Biological replicate 1 of 2 of Bacillus subtilis compared to daptomycin resistant mutant DapR1.


title: Fur vs. Fur FbpC replicate 3 (dye swap)


title: Fur vs. Fur FsrA replicate 2

source_name: fur fsrA, LB, mid-log

value: fur fsrA


title: IDD patient 2

description:
Biological replicate 2 of 3. Degenerative human nucleus pulposus cells harvested following digestion of nucleus pulposus with pronase and collagenase II.
MHC

source_name: Nucleus pulposus cells, degenerative

value: Nucleus pulposus

value: degenerative

value: intervertebral disc degeneration (IDD)

value: female

value: Grading IV


title: WT vs. Fur replicate 2


title: SP cells from SUDHL-1 ALCL cell line, rep 1

description: gene expression data from SP cells

source_name: SUDHL-1 ALCL cell line

tag: cell line

value: Side population cells


title: Fur vs. Fur FbpABC replicate 1


title: WT vs. Fur replicate 1


title: Fur vs. Fur FbpABC replicate 2


title: STG-30

source_name: Input fraction from STG-30

value: STG

value: Whole Tissue

value: F

value: C

source_name: STG-30 methyl-depleted


title: STG-13

source_name: Input fraction from STG-13

source_name: STG-13 methyl-depleted


title: 60(-)-40(+)

source_name: Input fraction from  60(-)-40(+)

value: DLPFC

value: Calibration mix NeuN-Pos and NeuN-Neg

source_name: 60(-)-40(+) methyl-depleted


title: Fur vs. Fur FbpAB replicate 3 (dye swap)

value: fur


title: Fur vs. Fur FsrA replicate 1


title: WT(+van)vsspx(+van)_rep1

status: Public on Dec 05 2008

description: Alexa Fluor 555 (WT/+van) / 647 (spx/+van)

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1

source_name: WT/+van

extract_protocol: The cell cultures were grown to an OD600 of 0.4 and split into 2 flasks with equal volume, vancomycin was added to 1 flask to a final concentration of 2 microgram/ml and cells were harvested 10 min after treatment. RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

tag: WT/+van

label: alexa Fluor 647

source_name: spx/+van

tag: spx/+van


title: WT(+van)vsspx(+van)_dyeswap

description: Alexa Fluor 647 (WT/+van) / 555 (spx/+van)

label: alexa Fluor 555


title: WT(-van)vssigM(-van)_rep3

description: Alexa Fluor 555 (WT/-van) / 647 (sigM/-van)

source_name: WT/-van

tag: WT/-van

source_name: sigM/-van

tag: sigM/-van


title: WT(-van)vsspx(-van)_rep2

description: Alexa Fluor 555 (WT/-van) / 647 (spx/-van)

source_name: spx/-van

tag: spx/-van


title: WT(-van)vsspx(-van)_rep1


title: WT(-van)vssigM(-van)_rep2


title: 1 Day 18.5

status: Public on Oct 30 2010

city: Dallas

first: Carole

middle: R

last: Mendelson

state: TX

address: 5323 Harry Hines Blvs

department: Biochemistry

institute: University of Texas Southwestern Medical Center

hyb_protocol: Hybridization was performed by the UT Southwestern Microarray Core facility according to Illumina's protocol

scan_protocol: Scanning was performed by the UT Southwestern Microarray Core facility according to Illumina's protocol

data_processing: Data was initially processed using Illumina Bead studio software where it was quantile normalized and background subtracted.  Downstream analysis was done using Bioconductor.

label_protocol: Total mRNA labeling was performed by the UT Southwestern Microarray Core facility using Illumina labeling kit according to manufacturer's protocol.

extract_protocol: Mouse uterus was lysed in Trizol and mRNA was extracted using Qiagen RNA mini kit according to the manufacturers protocol.

tag: tissue

value: uterus

tag: developmental stage

value: 18.5 days post coitum


title: 3 Day 18.5


title: 2 Day 18.5


title: 2 Day 15.5

value: 15.5 days post coitum


title: WT(+van)vssigM(+van)_rep3

description: Alexa Fluor 555 (WT/+van) / 647 (sigM/+van)

source_name: sigM/+van

tag: sigM/+van


title: WT(-DAP)vsWT(+DAP)_rep3_normalized

status: Public on Dec 11 2008

description: Alexa Fluor 647 (WT-DAP) / 555 (WT+DAP)

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.). Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1.

source_name: untreated

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 microgram of total RNA. Total cDNA was labeled overnight with Alexa Fluor 647 or Alexa Fluor 555 (Invitrogen).

extract_protocol: The cell cultures were grown to an OD600 of 0.4 and split into 2 flasks with equal volume, daptomycin was added to 1 flask to a final concentration of 1 µg/ml and cells were harvested 20 min after treatment. RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

tag: WT (-DAP)

source_name: daptomycin treated

tag: WT (+DAP)


title: 3 Day 15.5


title: Control, 3 month: 251959710087_GE1-v5_95_Feb07_1_4

status: Public on Jul 30 2010

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: 1 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 021219_G2_D_F_20080811.xml to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by 75th percentile shift and conduct baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA with Benjamini-Hochberg multiple-tests correction to test for significant differential expression of microarray targets.  The resulting gene list was utilized to conduct pair-wise comparisons to determine statistically significant differences in gene expression between control and RDX-exposed fish within each time point via unpaired t-test and 2-fold cutoff.

organism: Pimephales promelas

source_name: Control, 3 month

growth_protocol: Fathead minnow were maintained in 10 gallon aquaria including glass wool filtration systems, air stones, breeding substrates (3 PVC pipe cut in longitudinal section) where water changes were conducted every 28d.  Fish were fed frozen brine shrimp daily.

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 2 male and 4 female adult fish were allocated to each experimental unit (10 gallon aquarium).  Eight experimental units were maintained as controls and another 8 were dosed with RDX that averaged 0.83mg/L over the course of the year long Assay.  5 male fish were collected from each the control and RDX-exposure condition at 1d, 1mo, 3mo, 6mo, 9mo, and 12 mo time periods.  Both liver and brain tissues were collected and immediately transferred to RNA Later (Ambion, Austin TX) and RNA fixed following manufacturer's recommendations.

value: liver


title: WT(+van)vssigM(+van)_rep2


title: Control, 3 month: 251959710083_GE1-v5_95_Feb07_2_1


title: Control, 3 month: 251959710083_GE1-v5_95_Feb07_1_3


title: Control, 3 month: 251959710088_GE1-v5_95_Feb07_1_2


title: sigM(-van)vssigM(+van)_rep2

description: Alexa Fluor 555 (sigM/-van) / 647 (sigM/+van)


title: WT(+DAP)vsWT(-DAP)_rep2_normalized

description: Alexa Fluor 647 (WT+DAP) / 555 (WT-DAP)


title: WT(+DAP)vsWT(-DAP)_rep1_normalized

description: Alexa Fluor 647 (WT+DAP) / 555 (WT-DAP)


title: WT(-van)vssigM(-van)_rep1


title: 1 Day 15.5


title: Control, 3 month: 251959710086_GE1-v5_95_Feb07_2_2


title: WT(+van)vssigM(+van)_rep1


title: sigM(-van)vssigM(+van)_rep1


title: WT(-van)vsWT(+van)_rep2

description: Alexa Fluor 555 (WT/-van) / 647 (WT/+van)


title: 168 + lys vs 168 - lys rep3 dyeswap

value: wildtype

tag: condition

value: 20 min + lys

value: 20 min - lys


title: SP cells from SUDHL-1 ALCL cell line, rep 3

description: gene expression data from SP cells

data_processing: RMA normalization using HuGene 1.0 st v1 library were performed separately for each sample after Affymetrix CEL files were uploaded to bioconductor. This was followed by filtering out the controls on the ST array and carrying out one-way ANOVA and clustering analysis

extract_protocol: Qiagen RNA extraction method was used using Qiacube fully automated sample prep. For QC your samples were processed on the Bioanalyzer 2100 (Agilent) using the RNA Pico Kit from Agilent technologies (P/N 5067-1513)  Then the samples were analysed using the Nugen Kits (Ovation Pico WTA system P/N 3300– WT-Ovation Exon Module P/N 2000 and Encore Biotin Module P/N 4200)

value: ALCL cell line SUDHL-1

tag: cell population


title: WTvsQuad_dyeswap

status: Public on Oct 09 2008

source_name: ugtPmprFpssAywnE quadruple mutant

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 mg of total RNA. Total cDNA was labeled overnight with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen)

tag: ugtPmprFpssAywnE quadruple mutant

source_name: wild type

tag: wild type


title: WT(-van)vsWT(+van)_rep1


title: WTvsTriple_dyeswap

source_name: mprFpssAywnE triple mutant

tag: mprFpssAywnE triple mutant


title: WTvsUgtP_dyeswap

source_name: ugtP single mutant

tag: ugtP single mutant


title: WTvsUgtP_rep1


title: WTvsQuad_rep2


title: WTvsTriple_rep2


title: WTvsQuad_rep1


title: WTvsTriple_rep3


title: WTvsTriple_rep1


title: WTvsUgtP_rep2


title: WTvsUgtP_rep3


title: WTvsQuad_rep3


title: Fur vs. Fur FsrA replicate 3 (dye swap)

source_name: fur, LB, mid-log

tag: strain

tag: mutation

source_name: fur fsrA, LB, mid-log

value: fur fsrA