title: 4_RNA from posterior half of wild-type embryo

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Gene Expression of posterior half of wild-type embryo

hyb_protocol: 1.65 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 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 4x44K (G4122F) 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

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: 014868_D_F_20100617) to obtain background subtracted and spatially detrended Processed Signal intensities.  These data were analyzed further with the GeneSpring GX11.5 software (Agilent Technologies). Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array; 4, per-gene normalization, in which the data were normalized to control samples (wild-type).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Low RNA Input Fluorescent Linear Amplification 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: Jmjd3+/- mice were intercrossed and embryos were collected at E9.5 according to the time after mating and the somite number.

extract_protocol: After genotyping, total RNAs were extracted using RNeasy mini RNA purification kit (QIAGEN, Valencia, CA). RNA was quantified and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Embryos were collected at E9.5 and posterior half of embryos were frozen immediately at -80°C.

value: wild-type

tag: developmental stage

value: posterior half of embryo


title: 1_RNA from posterior half of Jmjd3-/- embryo

status: Public on Feb 23 2014

type: RNA

description: Gene Expression of posterior half of Jmjd3-/- embryo

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

tag: tissue


title: 21sp

city: Dresden

first: Astrid

last: Schuller

address: Zellescher Weg 20B

country: Germany

institute: TU-Dresden

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Arabidopsis Genome Oligo Microarrays (4x44K v3, AMADID 15059) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505B , Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 9.5.1.1 ) was used to read out and process the microarray image files.  The final normalized data include 37,685 relevant probes for detection of mRNA; 6,118 IDs marked as 'NA' or 'ignore' and 1,417 controls probes were excluded.

organism: Arabidopsis thaliana

source_name: Host cells with small plasmodia close to the central cylinder (21 dai)

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Seeds of Arabidopsis thaliana ecotype Col-0 were soaked on wet filter paper in a Petri dish at 8°C for 72 h and sown onto a mixture of peat containing compost and sand (volume ratio 5:2). Plants were grown in a growth chamber at 24°C with 12 h daylight period (100 µmol m-2 s-1) and at 18°C for 12 h in the dark. Air humidity was 60% and the plants were regularly watered with tap water.

extract_protocol: SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol:
After 14 days the plants were inoculated with 2 ml of a resting spore suspension (2x10^6 spores ml-1) of the Plasmodiophora brassicae (single spore isolate) isolate ‘e3’ as described by Fähling et al. (2003) and Graf et al. (2004). Control plants were watered with the corresponding phosphate buffer only (50 mM KH2PO4, pH 5,5 adjusted with 25 % K2HPO4). Brassica rapa L. ssp. pekinensis cv. ‘Granaat’ (ECD-05) was used for propagation of the P. brassicae isolate. The spores were isolated as described by Mithen and Magrath (1992). At defined time points roots were harvested and carefully washed with deionized water. Root material for RNA isolation was instantly frozen in liquid nitrogen whereas root material for paraffin embedding was instantly dissected and fixed.
Tissue fixation and dehydration; Tissue fixation was performed with the HOPE® Reagents (DCS, Innovative Diagnostic Systems, Hamburg, Germany). Transverse sections of the main roots of A. thaliana (< 5 mm3) were immediately submerged in 1,5 ml of ice-cold (0-4°C) HOPE® I and incubated on ice overnight. All following incubation steps were performed with pre-cooled solutions and done at 0-4°C. The next day HOPE® I solution was discarded and staining of the tissue was performed in 85% ethanol with a few crystals of Eosin (Eosin Y disodium salt, Sigma) for 30 min (the Eosin staining facilitated the recovery of the tissue within the cured paraffin wax blocks). After removal of the staining solution dehydration started with incubation in a pre-mixed HOPE® II / acetone solution (1,5 ml acetone (100%) + 1,5 µl HOPE® II) for 2 h. After the HOPE® II / acetone solution was discarded the tissue was incubated in ice-cold pure acetone for 3 h, replacing the acetone during this incubation step several times. Next acetone was replaced by pre-warmed low-melting paraffin (52-54°C) (DCS, Innovative Diagnostic Systems, Hamburg, Germany) and the tissue was incubated at 54°C (60°C) for 1 h. In the next step this paraffin wax was replaced by Paraplast X-Tra (Carl Roth GmbH, Karlsruhe, Germany) and kept at 54°C (60°C) for 1 h while replacing the paraffin once to twice. Then the paraffin wax including the tissue was poured in a mold and with pre-warmed needles the tissue was placed in the desired position at 54°C (60°C). The paraffin wax was cooled down for hardening at room temperature. The embedded tissue was stored until further use at 8°C with silica gel as desiccant.
Sectioning and slide preparation; Every surface of the microtome as well as every instrument that came in contact with the sections (e.g. blade, tweezers etc.) was cleaned with RNaseZAP® (Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany). The paraffin wax block was clamped directly in the “sample holder” of the microtome and sections of 12 – 20 µm were cut, taken off with tweezers and placed on a drop of 75% ethanol pipetted on a PEN-slide (PALM MembraneSlides PEN/NF, Carl Zeiss MicroImaging GmbH, Bernried, Germany). The PEN-slides were placed on a heating plate at 45°C and incubated until the sections get stretched. Excess of ethanol was poured off and the samples were air-dried at room temperature.  A better attachment of the sections onto the PEN-slides was achieved by placing the slides for a few seconds on a heating plate at 60°C until the paraffin started to melt. PEN-slides with mounted sections were stored at 8°C with silica gel as desiccant until Laser Microdissection and Pressure Catapulting (LMPC).
Laser Microdissection and Pressure Catapulting (LMPC) and sample processing for microarray hybridization; Before cells have been collected with Laser Microdissection and Pressure Catapulting (LMPC) paraffin wax was removed by incubation of PEN-slides with tissue sections in fresh xylene for 5-10 min. Slides were then air-dried under a fume hood for a few minutes and mounted at the PALM® MicroBeam system. Cells and tissue area of interest were selected with the PALM® RoboSoftware, microdissected and catapulted into the cap of a collection device (PALM AdhesiveCaps, Carl Zeiss MicroImaging GmbH, Bernried, Germany) located on top of the desired area. For every sample 200 to 300 cells have been collected. For each type of sample the laser focus adjustment was performed individually. For cutting and catapulting the menu “RoboLPC” has been used, with Laser power: 85 – 100, Laser focus: 74 – 79, Cells were lysed directly in the cap of the collection device using 6,4 µl SuperAmp Lysis Buffer  (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instruction and stored at -20°C.

tag: ecotype

tag: infected with

value: Plasmodiophora brassicae

tag: time point

value: 21 days after infection (dai)


title: 21c

source_name: Cortex from control roots (21 dai)

value: none (phosphate buffer only control)

value: Cortex from control roots


title: 3_RNA from posterior half of wild-type embryo


title: 9_RNA from posterior half of Jmjd3-/- embryo


title: 14lp

source_name: Hypertrophied host cells with large plasmodia in the cortex area (14 dai)

value: 14 days after infection (dai)


title: 14cci

source_name: Central cylinder from infected roots (14 dai)

value: Central cylinder from infected roots


title: 14sp

source_name: Host cells with small plasmodia close to the central cylinder (14 dai)


title: ileocecal_valve_patient10

status: Public on Feb 22 2014

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

country: USA

institute: Washington University in St Louis

hyb_protocol: Cy3 labeled, linearly amplified complementary RNA was synthesized and hybridized to Sureprint G3 Human Gene Expression 8 x 60K (Agilent) microarrays according to manufacturer's protocol.

scan_protocol: Arrays were scanned using a High Resolution C scanner

data_processing: Raw signal intensities were extracted with feature extraction v10.7 software with the protocol GE1_107_Sep09 and Grid 028004_D_F_20110819, to obtain spatially detrended signal intensities.

organism: Homo sapiens

source_name: Ileocecal valve

label_protocol: Labeling was performed with Cy3 according to the manufacturer protoocl for one color microarray based gene expression analysis (Agilent)

extract_protocol: Pinch biopsy that was snap frozen in Trizol for RNA extraction using chloroform purification and isopropanol extraction and purification using QIAgen Rneasy Mini Kit

value: Intestinal mucosa

tag: gender

value: Female

tag: age


title: sigmoid_colon_patient10

source_name: Sigmoid colon


title: sigmoid_colon_patient9

value: Male


title: appendiceal_orifice_patient23

source_name: Appendiceal orifice


title: ileocecal_valve_patient18


title: ileocecal_valve_patient23


title: appendiceal_orifice_patient18


title: sigmoid_colon_patient23


title: sigmoid_colon_patient22


title: terminal_ileum_patient18

source_name: Terminal ileum


title: sigmoid_colon_patient18


title: ileocecal_valve_patient22


title: appendiceal_orifice_patient22


title: terminal_ileum_patient22


title: terminal_ileum_patient23


title: 14c

source_name: Cortex from control roots (14 dai)


title: terminal_ileum_patient10


title: appendiceal_orifice_patient10


title: appendiceal_orifice_patient9


title: ileocecal_valve_patient9


title: terminal_ileum_patient9


title: terminal_ileum_patient17


title: Adipose-24 month-Myc heterozygous-technical replicate 1

city: Providence

first: Jeffrey

middle: Walter

last: Hofmann

state: RI

address: 70 Ship St

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

description: Each sample contains RNA pooled from 8 mice

hyb_protocol: The Hybridization Wash Stain kit from Affymetrix was used for hybridization according to the manufacturer's protocols.

scan_protocol: Arrays were scanned on a 3000 G7 scanner running  AGCC v3.2.4 software

data_processing: The data from all expression arrays were normalized using the Affymetrix Expression Console software package, and expression values for all genes were generated using the built-in RMA algorithm.

label: biotin

source_name: Adipose from a 24 month old Myc heterozygous mouse

label_protocol: The WT amplification kit from Life Technologies and the WT terminal labeling kit from Affymetrix were used according to the manufacturer's protocols.

growth_protocol: Mice were produced and housed in a specific pathogen-free (SPF), AAALAC-certified barrier facility. Animals are housed in plastic 27 cm x 27 cm cages which are held in HEPA-ventilated cage racks (maximum of 7 animals per cage). Animals are also housed in half-cages (maximum of 3 animals). Cages, bedding (Sani-chip hardwood bedding) and food (Purina Lab Chow # 5010) are sterilized by autoclaving. Food and water (also sterilized) are provided ad libitum. The same food is used for all animals, including pregnant and nursing mothers and weaned pups. Bedding is changed once per week. A light-dark cycle of 12 hours is used (7 AM On, 7 PM Off). Temperature is maintained at 70°F, and humidity at 50%.

extract_protocol: Fragments of tissues in the range of 20-50 mg were removed from samples kept at -80°C, carefully weighed on dry ice, and homogenized in Trizol reagent (Invitrogen) according to the supplier's instructions. Two homogenization methods were used. In the first, the tissue was hand-ground to a powder using a plastic homogenizer (Fisher 02-542-09) chilled in liquid nitrogen, and the powder was vigorously vortexed with Trizol reagent at room temperature. In the second, the tissue fragment was homogenized directly in Trizol reagent in a Fisher PowerGen 125 motorized homogenizer at room temperature. Equal amounts of total RNA from 5 to 8 male animals were pooled to create a representative sample with a final concentration of 100 ng/ul. The same animals were used for the analysis of all tissues. The pooled RNA samples were converted to cRNA targets using the 3' IVT Express kit from Affymetrix, hybridized to Mouse 1.0 Gene ST arrays, and scanned on a 3000 G7 scanner, all according to the manufacturer’s protocols.

tag: Sex

tag: strain

value: White adipose

value: 24 months

tag: genotype

value: Myc heterozygous


title: Adipose-24 month-Myc heterozygous-technical replicate 3


title: Muscle-24 month-Myc heterozygous-technical replicate 3

source_name: Muscle from a 24 month old Myc heterozygous mouse

value: Skeletal muscle


title: Adipose-24 month-Myc heterozygous-technical replicate 2


title: Muscle-24 month-Myc heterozygous-technical replicate 1


title: Liver-5 month-Myc heterozygous-technical replicate 2

description: Each sample contains RNA pooled from 5 mice

source_name: Liver from a 5 month old Myc heterozygous mouse

value: Liver

value: 5 months


title: Adipose-5 month-Myc heterozygous-technical replicate 3

source_name: Adipose from a 5 month old Myc heterozygous mouse


title: Adipose-24 month-wild type-technical replicate 3

source_name: Adipose from a 24 month old wild type mouse

value: Wild type


title: Liver-24 month-Myc heterozygous-technical replicate 2

source_name: Liver from a 24 month old Myc heterozygous mouse


title: Muscle-5 month-Myc heterozygous-technical replicate 2

source_name: Muscle from a 5 month old Myc heterozygous mouse


title: Liver-5 month-Myc heterozygous-technical replicate 3


title: Adipose-5 month-Myc heterozygous-technical replicate 1


title: Muscle-24 month-Myc heterozygous-technical replicate 2


title: Muscle-5 month-Myc heterozygous-technical replicate 1


title: Liver-5 month-Myc heterozygous-technical replicate 1


title: Liver-24 month-Myc heterozygous-technical replicate 3


title: Adipose-24 month-wild type-technical replicate 1


title: Adipose-5 month-wild type-technical replicate 3

description: Each sample contains RNA pooled from 6 mice

source_name: Adipose from a 5 month old wild type mouse


title: Adipose-5 month-wild type-technical replicate 2


title: Muscle-5 month-Myc heterozygous-technical replicate 3


title: Muscle-24 month-wild type-technical replicate 2

source_name: Muscle from a 24 month old wild type mouse


title: Adipose-5 month-Myc heterozygous-technical replicate 2


title: Adipose-24 month-wild type-technical replicate 2


title: Liver-24 month-Myc heterozygous-technical replicate 1


title: Adipose-5 month-wild type-technical replicate 1


title: Muscle-24 month-wild type-technical replicate 1


title: Muscle-24 month-wild type-technical replicate 3


title: Muscle-5 month-wild type-technical replicate 2

source_name: Muscle from a 5 month old wild type mouse


title: Muscle-5 month-wild type-technical replicate 3


title: Liver-5 month-wild type-technical replicate 3

source_name: Liver from a 5 month old wild type mouse


title: N167_Gly14_rep3

city: Sendai

first: Keiko

last: Nishizawa

address: Seiryo-machi 2-1,Aoba-ku

department: Department of Neurochemistry

institute: Tohoku University Graduate School of Medicine

hyb_protocol: An aliquot of 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent, following the manufacturers instructions. After completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture. Hybridization was performed with Agilent Whole Mouse Genome 4×44k ver.2 Oligo Microarrays (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and for 1 minute with 37°C GE Wash buffer 2 (Agilent). Then, the microarrys were dried immediately.

scan_protocol: Microarrays were scanned immediately with the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area, 61x21.6 mm; Scan resolution, 10 um; Dye channel, Green; Green PMT, 100%).

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: 026655_D_F_20100123) to obtain background-subtracted, spatially detrended Processed Signal intensities.

label_protocol: Total RNAs were amplified and labeled using Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Santa Clara, CA, USA).

growth_protocol: Mouse neuroblastoma cells infected with 22L scrapie prion (N167 cells) were cultured with Opti-MEMI medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Cells were lysed with RNAiso-plus reagent (Takara Bio Inc., Shiga, Japan). Total RNA was extracted using FastPure RNA (Takara Bio Inc.).

treatment_protocol: N167 cells were treated with either anti-prion compound Gly-9 or control compound Gly-14 at a dose of 5 μg/mL for three days.

tag: cell line

tag: cell type

value: Prion-infected neuroblastoma cells

tag: treated with

value: control compound Gly-14


title: N167_Gly14_rep4


title: Liver-5 month-wild type-technical replicate 1


title: N167_Gly14_rep1


title: Liver-24 month-wild type-technical replicate 1

source_name: Liver from a 24 month old wild type mouse


title: N167_Gly09_rep1

value: anti-prion compound Gly-9


title: Liver-24 month-wild type-technical replicate 3


title: N167_Gly14_rep2


title: N167_Gly09_rep4


title: sem-occult-met_4

status: Public on Feb 21 2014

city: Munich

first: Michael

last: Abend

state: Bavaria

address: Neuherbergstr. 11

institute: Bundeswehr Institute of Radiobiology

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing:
The quantile normalized, log2 transformed data were averaged across replicates, resulting in the columns group # (normalized). A pairwise comparison was analyzed. Group lymphogen was used as reference group and RNA expression of group occult was compared to this baseline.
To filter for genes with a robust differential expression between two compared groups, several parameters are taken into account:
Robust detection:
A probe is only considered if it is reliably detectable (“Detected” call, flag information from the Feature Extraction software) in all samples of one of the two compared groups. Specifically, if filtering for induction in group x compared to group y, the probe must be called “Detected” in all samples of group x. If filtering for repression, it must be called “Detected” in all samples of the reference group y.
Statistical significance:
Two filtering approaches were used that apply different stringency levels to the data set:
a) Stringent filtering:
A probe is only classified as induced in a specific comparison if its corrected p-value is ≤ 0.05 and if it has a Fold Change value ≥ 1.5 and 2, respectively. Analogously, a probe is classified as repressed if its corrected p-value is ≤ 0.05 and its Fold Change is ≤ -1.5 and -2, respectively. By using this stringent filtering, the multiple testing error is taken into account, and the false discovery (FDR) rate is controlled at a maximum level of 5%.
b) Non-stringent filtering:
Stringency was reduced by using the non-corrected instead of the corrected p-value. Using this approach, a probe is only classified as induced in a specific comparison if its (non-corrected) p-value is ≤ 0.05, and if it has a Fold Change value ≥ 1.5 and 2, respectively. Analogously, a probe is classified as repressed if its (non-corrected) pvalue is ≤ 0.05 and its Fold Change is ≤ -1.5 and -2, respectively.
By using this non-stringent filtering, the multiple testing error is not taken into account. Finally, several analysis tools from the PANTHER website, release 8.1 (accessible through http://www.pantherdb.org/) were applied for functional evaluation of differential regulation.

label: Cyanine-3-labeled cRNA

source_name: occult metastasis

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies).

extract_protocol: Not provided

value: biopsy taken from occult metastasis

value: male


title: Muscle-5 month-wild type-technical replicate 1


title: Liver-24 month-wild type-technical replicate 2


title: sem-occult-met_3


title: sem-occult-met_1


title: sem-lymph-met_4

source_name: lymphogen metastasis

value: biopsy taken from lymphogen metastasis


title: sem-occult-met_2


title: Liver-5 month-wild type-technical replicate 2


title: N167_Gly09_rep3


title: sem-lymph-met_2


title: sem-lymph-met_1


title: sem-lymph-met_3


title: Liver_PBS control_48 hr_Female_Rep2

city: San Diego

first: Dawn

last: Applegate

state: CA

address: 9855 Towne Centre Drive

institute: RegeneMed, Inc.

description: Vehicle control group for animals administered phenylhydrazine

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

source_name: Liver

label_protocol: Standard Affymetrix procedures

growth_protocol: Six week old male and female B6C3F1 mice (B6C3F1/Crl) were purchased from Charles River Laboratories (Raleigh, NC) and acclimated for one week prior to initiation of the study.  The animals were weighed and randomized into treatment groups to ensure the mean body weight in each group was approximately the same. Animals were housed three per cage except male mice which were house individually in shoe box cages and segregated by treatment group.  Alpha-dri cellulose bedding (Shepard Specialty Papers, Kalamazoo, MI) was used.  Animals had access to reverse osmosis water (Hydro Systems, Durham, NC) and pellet NIH-07 certified feed (Zeigler Brothers, Gardners, PA) ad libitum.  The animal room was kept within the standard temperature and humidity parameters (64 to 79°F with 30 to 70% relative humidity) and standard light cycle (0700-1900 hours).  Animal use in this study was approved by the Institutional Animal Use and Care Committee of The Hamner Institutes for Health Sciences and was conducted in accordance with the National Institutes of Health guidelines for the care and use of laboratory animals.  Animals were housed in fully-accredited American Association for Accreditation of Laboratory Animal Care (AAALAC) facilities.

extract_protocol: Total RNA was extracted and transcribed to cDNA

treatment_protocol: Mice were weighed, anesthetized with Ketamine (90 mg/kg) and Xylazine (10 mg/kg), and exsanguinated to obtain blood.  The right, caudate, and median lobes were placed in RNAlater (Ambion, Austin, TX).

value: 7 weeks

tag: compound

value: PBS control

tag: vehicle

value: PBS

tag: route

value: IP

tag: dose volume

value: 10 ml/kg

tag: time

value: 48 hours


title: Liver_PBS control_48 hr_Female_Rep1

value: Female


title: Liver_Cobalt chloride_48 hr_Female_Rep3

value: Cobalt Chloride

tag: cas number

tag: dose

value: 60 mg/kg

value: 0.9% saline


title: Liver_Cobalt chloride_48 hr_Female_Rep1


title: Liver_Cobalt chloride_48 hr_Female_Rep2


title: Liver_Lipopolysaccharide_6 hr_Female_Rep2

value: Lipopolysaccharide

value: 1 mg/kg

value: 6 hours


title: Liver_PBS control_6 hr_Female_Rep2

description: Vehicle control group for animals adminstered IL-6, lipopolysaccharide and TNFα


title: Liver_Lipopolysaccharide_6 hr_Female_Rep3


title: Liver_PBS control_6 hr_Female_Rep3


title: Liver_PBS control_48 hr_Female_Rep3


title: N167_Gly09_rep2

value: Prion-infected neuroblastoma cells

value: anti-prion compound Gly-9


title: Liver_IL-6_6 hr_Female_Rep3

value: 25 ug/kg


title: Liver_IL-6_6 hr_Female_Rep2


title: Liver_TNF-a_6 hr_Female_Rep3

value: Tumor necrosis factor-α

value: 50 ug/kg


title: Liver_IL-6_6 hr_Female_Rep1

value: 7 weeks


title: Liver_Lipopolysaccharide_6 hr_Female_Rep1

value: PBS


title: Liver_TNF-a_6 hr_Female_Rep2

value: IP


title: Liver_PBS control_6 hr_Female_Rep1

value: PBS control

value: 10 ml/kg


title: Liver_Phenylhydrazine_48 hr_Female_Rep3

value: Female

value: Phenylhydrazine

value: 100 mg/kg

value: 48 hours


title: Liver_0.9% saline control_72 hr_Female_Rep3

description: Vehicle control group for animals administered phenobarbital

value: 0.9% saline control

value: 0.9% saline

value: 72 hours


title: Liver_Phenylhydrazine_48 hr_Female_Rep1


title: Liver_TNF-a_6 hr_Female_Rep1

value: 6 hours


title: Liver_0.9% saline control_48 hr_Female_Rep1

description: Vehicle control group for animals administered cobalt chloride


title: Liver_0.9% saline control_48 hr_Female_Rep3


title: Liver_0.9% saline control_72 hr_Female_Rep1


title: Liver_Phenylhydrazine_48 hr_Female_Rep2


title: Liver_0.9% saline control_48 hr_Female_Rep2


title: Liver_0.9% saline control_72 hr_Female_Rep2


title: Liver_Phenobarbital_72 hr_Female_Rep2

value: Phenobarbital

value: 100 mg/kg/day


title: Liver_Phenobarbital_72 hr_Female_Rep3


title: Liver_Phenobarbital_72 hr_Female_Rep1


title: Liver_DMSO control_48 hr_Female_Rep1

description: Vehicle control group for animals administered TCDD

value: DMSO control

value: DMSO

value: 100 ul/kg


title: Liver_DMSO control_8 hr_Female_Rep1

description: Vehicle control group for animals administered ciprofibrate and WY-14,643

value: 7 weeks

value: Gavage

value: 8 hours


title: Liver_DMSO control_8 hr_Female_Rep2

value: 10 ml/kg


title: Liver_WY-14,643_8 hr_Female_Rep2

value: Female

value: 250 mg/kg


title: Liver_WY-14,643_8 hr_Female_Rep3


title: Liver_Ciprofibrate_8 hr_Female_Rep2

value: Ciprofibrate


title: Liver_DMSO control_48 hr_Female_Rep2

value: IP

value: 48 hours


title: Liver_DMSO control_48 hr_Female_Rep3


title: Liver_TCDD_48 hr_Female_Rep2

value: 10 ug/kg


title: Liver_WY-14,643_8 hr_Female_Rep1


title: Liver_TCDD_48 hr_Female_Rep1


title: Liver_DMSO control_8 hr_Female_Rep3


title: Liver_TCDD_48 hr_Female_Rep3


title: Liver_Ciprofibrate_8 hr_Female_Rep1


title: Liver_Corn oil control 2_24 hr_Female_Rep3

description: Vehicle control group for animals administered β-naphthoflavone

value: Corn oil control

value: Corn oil

value: 24 hours


title: Liver_Ciprofibrate_8 hr_Female_Rep3


title: Liver_PCB-153_48 hr_Female_Rep2

value: 80 mg/kg


title: Liver_Corn oil control 1_48 hr_Female_Rep3

description: Vehicle control group for animals administered aroclor 1260 and PCB-153


title: Liver_PCB-153_48 hr_Female_Rep1


title: Liver_Corn oil control 2_24 hr_Female_Rep1


title: Liver_Corn oil control 2_24 hr_Female_Rep2


title: Liver_Corn oil control 1_48 hr_Female_Rep2


title: Liver_Cobalt chloride_48 hr_Male_Rep3

value: Male

value: Cobalt Chloride

value: 60 mg/kg

value: 0.9% saline


title: Liver_β-Naphthoflavone_24 hr_Female_Rep2

value: 7 weeks

value: β-Naphthoflavone

value: 50 mg/kg


title: Liver_β-Naphthoflavone_24 hr_Female_Rep1

value: Female

value: 10 ml/kg


title: Liver_β-Naphthoflavone_24 hr_Female_Rep3


title: Liver_Corn oil control 1_48 hr_Female_Rep1


title: Liver_Aroclor 1260_48 hr_Female_Rep1

value: Aroclor 1260

value: 200 mg/kg


title: Liver_Aroclor 1260_48 hr_Female_Rep2

value: IP

value: 48 hours


title: Liver_Aroclor 1260_48 hr_Female_Rep3


title: Liver_PCB-153_48 hr_Female_Rep3


title: Liver_Cobalt chloride_48 hr_Male_Rep2


title: Liver_Cobalt chloride_48 hr_Male_Rep1


title: Liver_PBS control_6 hr_Male_Rep3

value: PBS control

value: PBS

value: 6 hours


title: Liver_PBS control_48 hr_Male_Rep1


title: Synovial tissue from rheumatoid arthritis joint 8  (RA_8)

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 8, labelled as RA_8

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: GCOS

source_name: synovial tissue from rheumatoid arthritis joint

label_protocol: 3-5 µg of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)

growth_protocol: tissues were immediately frozen in liquid nitrogen for subsequent RNA-extraction

extract_protocol: RNA was collected by using the RNeasy mini kit (Qiagen)

treatment_protocol: tissues were collected from joint replacement surgery in OA patients and synovecomy surgery in RA patients, normal synovium was collected early post mortem from macroscopically normal knee joints

tag: disease state

value: rheumatoid arthritis

tag: tissue

value: synovial tissue isolated from joint


title: Synovial tissue from rheumatoid arthritis joint 6  (RA_6)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 6, labelled as RA_6


title: Synovial tissue from rheumatoid arthritis joint 10  (RA_10)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 10, labelled as RA_10


title: Synovial tissue from rheumatoid arthritis joint 5  (RA_5)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 5, labelled as RA_5


title: Liver_PBS control_48 hr_Male_Rep2

value: Male


title: Liver_PBS control_48 hr_Male_Rep3


title: Synovial tissue from rheumatoid arthritis joint 4  (RA_4)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 4, labelled as RA_4


title: Liver_PBS control_6 hr_Male_Rep2


title: Liver_Lipopolysaccharide_6 hr_Male_Rep3

value: Lipopolysaccharide

value: 1 mg/kg


title: Synovial tissue from rheumatoid arthritis joint 7  (RA_7)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 7, labelled as RA_7


title: Liver_PBS control_6 hr_Male_Rep1

value: 7 weeks


title: Synovial tissue from rheumatoid arthritis joint 2  (RA_2)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 2, labelled as RA_2


title: Synovial tissue from rheumatoid arthritis joint 3  (RA_3)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 3, labelled as RA_3


title: Liver_IL-6_6 hr_Male_Rep3

value: 25 ug/kg


title: Liver_Lipopolysaccharide_6 hr_Male_Rep2


title: Synovial tissue from osteoarthritic joint 9  (OA_9)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 9, labelled as OA_9

source_name: synovial tissue from osteoarthritic joint


title: FAST/FLX_2

city: Ottawa

first: Paul

last: Craig

state: Ontario

address: 30 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

description: miRNA liver expression profile after fasting 7days, 540ng/L fluoxetine

hyb_protocol: The dried Cy3 labelled pellet was resuspended in 17ul nuclease-free H2O and 1ul Hyb Spike-In,  4.5 ul 10x GE blocking agent, and 22.5 ul 2x Hi-RPM Hybridization Buffer was added with the samples being heat shocked at 100oC for 5min, followed by quenching on ice for 5min. The samples were immediately loaded onto the 8x15K custom miRNA microarray (G4474A) and hybridized overnight for 20 hours at 55oC in a rotating Agilent hybridization oven set to 20 rpm. After hybridization, microarrays were dissasembled in GE wash buffer 1, then washed in GE wash buffer 1 at room temp for 5min, followed by a second wash in GE Wash buffer 2 at 37oC for 5 minutes. Slides were air dried and immediately placed in an ozone protected slide holder

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner (G2600D) using one colour scan setting for the 8x15K array slides (ScanArea 61x21.6mm, Scan resolution 5 uM) with the Green PMT channel set to 100%>

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol: miRNA_1100_Jul11 and Grid: 043253_D_F_20121224) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: Liver, fast, 7days, 540ng/L FLX

label_protocol: Cyanine-3 labelled miRNA was prepared from 0.5 ug total RNA using the miRNA microarray system with miRNA Complete labeling and Hyb kit from Agilent following the manufacturer's instructions. Samples were dried in a roto-vap centrifuge for 2 hrs prior to the hybridization protocol.

extract_protocol: Both total and miRNA was extracted using the Absolutely RNA miRNA kit (Agilent; Cat# 400814) following the explicit instructions of the manufacturer. Quantification of RNA was performed on the NanoDrop-1000 and RNA integrity and quality was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Zebrafish (n=20/tank; adult female) were placed in 4 separate 8L glass aquaria with sufficient aeration. 540 ng/L (from 1mg/L stock dissolved in H2O) was added to treatment tanks. Experiment consisted of static renewal for 7 days. All tanks were cleaned and 80% of water was replaced daily. After 7 days, zebrafish were removed, terminally anesthetized, and livers removed and immediately frozen in dry ice for RNA extraction.

value: Liver

tag: gender

value: Adult


title: Synovial tissue from osteoarthritic joint 10  (OA_10)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 10, labelled as OA_10


title: FAST/FLX_3

value: Female

tag: age


title: FAST/FLX_4


title: Liver_TNF-a_6 hr_Male_Rep3

tag: Sex

value: Tumor necrosis factor-α

value: 50 ug/kg

value: 10 ml/kg


title: Liver_Lipopolysaccharide_6 hr_Male_Rep1

tag: strain

value: IP


title: Synovial tissue from osteoarthritic joint 8  (OA_8)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 8, labelled as OA_8


title: Synovial tissue from rheumatoid arthritis joint 9  (RA_9)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 9, labelled as RA_9


title: Synovial tissue from rheumatoid arthritis joint 1  (RA_1)

description: Gene expression data of synovial tissue isolated from rheumatoid arthritis joint number 1, labelled as RA_1


title: FAST/FLX_1


title: Liver_IL-6_6 hr_Male_Rep1


title: FED/FLX_3

description: miRNA liver expression profile after fed 7days, 540ng/L fluoxetine

source_name: Liver, fed, 7days, 540ng/L FLX


title: FED/FLX_4


title: Liver_IL-6_6 hr_Male_Rep2


title: FED/FLX_2


title: FED/FLX_1


title: Liver_TNF-a_6 hr_Male_Rep2


title: Liver_TNF-a_6 hr_Male_Rep1


title: FAST_4

description: miRNA liver expression profile after fasted 7days, 0ng/L fluoxetine

source_name: Liver, fast, 7days, 0ng/L FLX


title: Synovial tissue from osteoarthritic joint 7  (OA_7)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 7, labelled as OA_7


title: Synovial tissue from osteoarthritic joint 5  (OA_5)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 5, labelled as OA_5


title: Synovial tissue from osteoarthritic joint 4  (OA_4)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 4, labelled as OA_4


title: Synovial tissue from osteoarthritic joint 6  (OA_6)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 6, labelled as OA_6


title: FAST_2


title: Liver_Phenylhydrazine_48 hr_Male_Rep2

value: Phenylhydrazine

value: 100 mg/kg

value: 48 hours


title: FAST_3


title: FAST_1


title: FED_4

description: miRNA liver expression profile after fed 7days, 0ng/L fluoxetine

source_name: Liver, fed, 7days, 0ng/L FLX


title: Liver_Phenylhydrazine_48 hr_Male_Rep3

value: PBS


title: FED_3


title: FED_2


title: FED_1


title: Liver_Phenylhydrazine_48 hr_Male_Rep1


title: Liver_0.9% saline control_72 hr_Male_Rep3

description: Vehicle control group for animals administered phenobarbital

value: 0.9% saline control

value: 0.9% saline

value: 72 hours


title: Synovial tissue from osteoarthritic joint 1  (OA_1)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 1, labelled as OA_1

value: osteoarthritis

value: synovial tissue isolated from joint


title: Liver_0.9% saline control_72 hr_Male_Rep2

value: 7 weeks

value: Male


title: Synovial tissue from osteoarthritic joint 2  (OA_2)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 2, labelled as OA_2


title: Synovial tisssue from healthy joint 10  (ND_10)

description: Gene expression data of synovial tissue isolated from healthy joint number 10, labelled as ND_10

source_name: synovial tissue from healthy joint

value: healthy control


title: Liver_0.9% saline control_48 hr_Male_Rep3

description: Vehicle control group for animals administered cobalt chloride


title: Synovial tisssue from healthy joint 7  (ND_7)

description: Gene expression data of synovial tissue isolated from healthy joint number 7, labelled as ND_7


title: 12 hour

city: Çankırı

first: tugba

last: gurkok

address: Uluyazı

department: biology

country: Turkey

institute: Çankırı Karatekin University

description: capsule

hyb_protocol: Hybridization was performed by following standard NimbleGen operating protocol.

scan_protocol: Scaning was performed by following standard NimbleGen operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185).

organism: Papaver somniferum

source_name: Papaver somniferum

label_protocol: Labeling was performed by following standard NimbleGen operating protocol.

growth_protocol: Seeds of Ofis 95 opium poppy were germinated in fruit trays then were transplanted to pots. All the plants were grown with 16/8 h day/night cycles at 20 °C/18 °C in green house

extract_protocol: Leaves and fruits were collected, and transferred directly into liquid nitrogen. The total RNA extractions were performed using the TRIzol® Reagent (Invitrogen, Cat No. 15596-026)

treatment_protocol: Before MeJa application leaves, stem and capsule were wounded with sterile pins and treated with 100 µM MeJa with MeJa (Sigma) in post anthesis period by spraying 100 µM MeJa until all parts of the plant were fully wet. 100 µM MeJa solutions was prepared in ethanol using 0.1% triton X-100. Control plants weres treated with equal volumes of 0.1% triton X-100 dissolved in ethanol.

tag: cultivar

value: Ofis 95

value: Leaves and fruits

tag: treatment

value: 12 hour


title: 3 hour

description: capsule

value: 3 hour


title: Liver_Phenobarbital_72 hr_Male_Rep3

value: Phenobarbital

value: 100 mg/kg/day

value: IP

value: 10 ml/kg


title: Liver_0.9% saline control_48 hr_Male_Rep2

value: 48 hours


title: Synovial tisssue from healthy joint 4  (ND_4)

description: Gene expression data of synovial tissue isolated from healthy joint number 4, labelled as ND_4


title: Liver_0.9% saline control_48 hr_Male_Rep1

value: 0.9% saline control


title: Liver_Phenobarbital_72 hr_Male_Rep1

value: 0.9% saline


title: Liver_DMSO control_48 hr_Male_Rep3

description: Vehicle control group for animals administered TCDD

value: DMSO control

value: DMSO

value: 100 ul/kg


title: Liver_Phenobarbital_72 hr_Male_Rep2

value: 7 weeks

value: 72 hours


title: Synovial tisssue from healthy joint 5  (ND_5)

description: Gene expression data of synovial tissue isolated from healthy joint number 5, labelled as ND_5

value: healthy control

value: synovial tissue isolated from joint


title: CLP YNG 2hr_r1

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: Gene expression data from WBC from mice

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using RMA. Analyzed using BRB array tools

source_name: CLP YNG 2hr r1

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

growth_protocol: Mus musculus 6 to 12 weeks

extract_protocol: Extraction of total RNA was performed with QIAGEN Rneasy mini kit according to the manufacturer's instructions.

treatment_protocol: Used the Cecal Ligation and Puncture (CLP) model and Cecal Slurry (CS) method

tag: sepsis model

value: CLP

tag: cell type

value: WBC

value: 6-12 weeks


title: Synovial tissue from osteoarthritic joint 3  (OA_3)

description: Gene expression data of synovial tissue isolated from osteoarthritic joint number 3, labelled as OA_3


title: 0 hour

description: capsule

value: Ofis 95

value: Leaves and fruits

value: 0 hour


title: Synovial tisssue from healthy joint 3  (ND_3)

description: Gene expression data of synovial tissue isolated from healthy joint number 3, labelled as ND_3


title: CLP YNG 2hr_r4

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r4


title: CLP YNG Day3_r3

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r3


title: Synovial tisssue from healthy joint 2  (ND_2)

description: Gene expression data of synovial tissue isolated from healthy joint number 2, labelled as ND_2


title: Synovial tisssue from healthy joint 9  (ND_9)

description: Gene expression data of synovial tissue isolated from healthy joint number 9, labelled as ND_9


title: Synovial tisssue from healthy joint 8  (ND_8)

description: Gene expression data of synovial tissue isolated from healthy joint number 8, labelled as ND_8


title: Synovial tisssue from healthy joint 1  (ND_1)

description: Gene expression data of synovial tissue isolated from healthy joint number 1, labelled as ND_1


title: Liver_0.9% saline control_72 hr_Male_Rep1

value: Male

tag: compound

value: IP

value: 10 ml/kg


title: CLP YNG 2hr_r2

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r2


title: CLP YNG Day3_r2

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r2


title: Liver_DMSO control_48 hr_Male_Rep1

tag: vehicle

value: 48 hours


title: CLP YNG 2hr_r3

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r3


title: CLP YNG Day3_r1

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r1


title: Control

description: capsule

value: Control


title: Synovial tisssue from healthy joint 6  (ND_6)

description: Gene expression data of synovial tissue isolated from healthy joint number 6, labelled as ND_6


title: CLP YNG Day1_r4

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r4


title: Liver_DMSO control_48 hr_Male_Rep2

source_name: Liver

value: DMSO control

value: DMSO

tag: route


title: Liver_DMSO control_8 hr_Male_Rep2

description: Vehicle control group for animals administered ciprofibrate and WY-14,643

value: 7 weeks

value: Gavage

tag: dose volume

value: 8 hours


title: Liver_DMSO control_8 hr_Male_Rep1

tag: time


title: CLP YNG Day1_r3

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r3


title: CLP YNG Day1_r2

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r2


title: CLP YNG Day3_r4

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r4


title: CS YNG Day3_r3

description: Gene expression data from WBC from mice

source_name: CS YNG Day3 r3

value: CS


title: CS YNG Day3_r2

description: Gene expression data from WBC from mice

source_name: CS YNG Day3 r2


title: Liver_DMSO control_8 hr_Male_Rep3


title: CLP YNG Day1_r1

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r1

value: CLP


title: CS YNG Day3_r4

description: Gene expression data from WBC from mice

source_name: CS YNG Day3 r4

value: WBC


title: Liver_WY-14,643_8 hr_Male_Rep3

tag: cas number

value: 250 mg/kg


title: HeLa_siSIN3B_48hr_ rep 2

city: Nagoya

first: Jun-ichi

last: Nakayama

state: Aichi

address: 1 Yamanohata, Mizuho

department: Graduate School of Natural Sciences

institute: Nagoya city University

description: HeLa cells transfected with siSIN3B

hyb_protocol: Labeled cRNAs were hybridized for 17 hours at 65°C and 10 RPM on the Agilent SurePrint G3 Human GE 8x60K Microarray slide (Agilent Technologies) using the Agilent’s Microarray Hybridization Oven.

scan_protocol: Slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies) according to the Agilent_G3_GX_1Color protocol.

data_processing: Images were processed using Feature Extraction Software, and further analyzed using GeneSpring GX (all from Agilent Technologies).

source_name: HeLa cells, 48hr, siSIN3B, replicate 2

label_protocol: Total RNA (100ng) was amplified and cyanine 3-CTP labeled with the One Color Low Input Quick Amp Labeling Kit. Dye incorporation and cRNA yield were checked with the NanoDrop 2000.

extract_protocol: RNA was isolated from siRNA treated HeLa cells in Trizol (Invitrogen), re-purified using the RNeasy Micro kit (Qiagen), and total RNA quality was assessed with the Agilent 2100 bioanalyzer prior to microarray analysis. Samples with a RIN value of greater than or equal to 8.0 were deemed to be acceptable for microarray analysis.

tag: cell line

value: HeLa


title: CS YNG Day1_r4

description: Gene expression data from WBC from mice

source_name: CS YNG Day1 r4

value: 6-12 weeks


title: CS YNG Day3_r1

description: Gene expression data from WBC from mice

source_name: CS YNG Day3 r1


title: Liver_WY-14,643_8 hr_Male_Rep2

tag: dose


title: HeLa_siJARID1A_48hr_ rep 1

description: HeLa cells transfected with siJARID1A

source_name: HeLa cells, 48hr, siJARID1A, replicate 1


title: CS YNG 2hr_r3

description: Gene expression data from WBC from mice

source_name: CS YNG 2hr r3


title: HeLa_siCHD4_48hr_ rep 2

description: HeLa cells transfected with siSIN3B

source_name: HeLa cells, 48hr, siCHD4, replicate 2


title: HeLa_siSIN3B_48hr_ rep 1

description: HeLa cells transfected with siSIN3B

source_name: HeLa cells, 48hr, siSIN3B, replicate 1


title: HeLa_siJARID1A_48hr_ rep 2

description: HeLa cells transfected with siJARID1A

source_name: HeLa cells, 48hr, siJARID1A, replicate 2


title: CS YNG Day1_r1

description: Gene expression data from WBC from mice

source_name: CS YNG Day1 r1


title: CS YNG Day1_r2

description: Gene expression data from WBC from mice

source_name: CS YNG Day1 r2


title: CS YNG Day1_r3

description: Gene expression data from WBC from mice

source_name: CS YNG Day1 r3


title: HeLa_siCHD4_48hr_ rep 1

description: HeLa cells transfected with siSIN3B

source_name: HeLa cells, 48hr, siCHD4, replicate 1


title: Liver_TCDD_48 hr_Male_Rep3

source_name: Liver

value: 10 ug/kg

value: 100 ul/kg


title: CS YNG 2hr_r2

description: Gene expression data from WBC from mice

source_name: CS YNG 2hr r2


title: CS YNG 2hr_r4

description: Gene expression data from WBC from mice

source_name: CS YNG 2hr r4


title: Liver_WY-14,643_8 hr_Male_Rep1

value: Male


title: CS YNG 2hr_r1

description: Gene expression data from WBC from mice

source_name: CS YNG 2hr r1


title: HeLa_siControl_48hr_ rep 2

description: HeLa cells transfected with siControl

source_name: HeLa cells, 48hr, siControl, replicate 2

value: siControl


title: Control_r4

description: Gene expression data from WBC from mice

source_name: Control r4

value: control


title: Liver_TCDD_48 hr_Male_Rep2

value: IP

value: 48 hours


title: Control_r2

description: Gene expression data from WBC from mice

source_name: Control r2


title: Control_r1

description: Gene expression data from WBC from mice

source_name: Control r1


title: HeLa_siControl_48hr_ rep 1

description: HeLa cells transfected with siControl

source_name: HeLa cells, 48hr, siControl, replicate 1


title: Liver_TCDD_48 hr_Male_Rep1

value: DMSO


title: Control_r3

description: Gene expression data from WBC from mice

source_name: Control r3


title: Liver_Ciprofibrate_8 hr_Male_Rep3

value: 7 weeks

value: Ciprofibrate

value: 10 ml/kg


title: NIH3T3 cells in G1 phase,  rep3

city: Boston

first: Toshihiko

last: Oki

state: MA

address: 185 Cambridge Street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

description: Gene expression data from NIH3T3 cells in G1 phase in the middle of G0-G1 transition

hyb_protocol: 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (bioB, bioC, bioD, cre). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip® Scanner 3000 7G.. Chip analysis was performed using the Affymetrix GeneChip® Operating Software v1.4.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: NIH3T3 cells in G1 phase

label_protocol:
NIH3T3-G0_1-3 and NIH3T3-G1_1-3: Biotinylated cRNA were prepared with The GeneChip® 3’IVT Express Kit (Affymetrix) according to  the standard Affymetrix protocol Rev.8 from 100 ng total RNA.
NIH3T3-G0_4 and NIH3T3C1_4: Biotinylated cRNA were prepared with The GeneChip® IVT Express Kit (Affymetrix) according to  the standard Affymetrix protocol Rev.3 from 1 mg total RNA.

growth_protocol: NIH3T3 cells transduced with mVenus-p27K- and mCherry-hCdt1(30/120) were cultured for 5 hours in the medium containing 10% FBS (DMEM/10%FCS) after they were cultured in the media without serum.

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

treatment_protocol: mVenus(+)/mCherry(+) NIH3T3 (G0) cells and mVenus(-)/mCherry(+) NIH3T3 (G1) cells were sorted by FACS Aria (Becton Dickinson)

tag: growth phase


title: Liver_Ciprofibrate_8 hr_Male_Rep2

value: Gavage

value: 8 hours


title: NIH3T3 cells in G1 phase,  rep4


title: Liver_Ciprofibrate_8 hr_Male_Rep1


title: NIH3T3 cells in G1 phase,  rep2


title: spt20D vs WT in SM_1

city: New Delhi

first: Krishnamurthy

last: Natarajan

state: Delhi

address: 314/325, School of life sciences, JNU

department: School of life sciences

country: India

institute: Jawaharlal Nehru University

description: Biological replicate 1 of 2. Comparison of wildtype SPT20 vs spt20D strain in SM.

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom Saccharomyces cerevisiae 8x15k Gene expression Array (AMADID: 016333) designed by Genotypic Technology Private Limited.  About 300ng of Cy3 labeled samples and 300ng of Cy5 labeled samples were pooled, fragmented and hybridized using the Gene Expression Hybridization kit (Agilent Part Number 5188-5242) in Agilent’s Surehyb Chambers at 65°C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327), and dried.

scan_protocol: The slides were scanned using the Agilent Microarray Scanner G2505C at 5mm resolution.

data_processing: The scanned images were processed in the Feature Extraction Software v10.7.3.1, and the raw data was obtained.  Data normalization was done using GeneSpring GX v11.5  (Agilent) using the recommended (Lowess) normalization.

organism: Saccharomyces cerevisiae

label_protocol: The total RNA were labeled using the Agilent Quick Amp Kit PLUS (Part number: 5190-0424). Five hundred nanograms each of the samples were reverse transcribed at 40°C and  converted to double stranded cDNA was primed using oligodT tagged with a T7 polymerase promoter.  The double-stranded cDNA was used as template in an in vitro transcription reaction at 40°C to generate cRNA. The samples were labeled with Cy3-CTP or Cy5-CTP (Agilent) during this step. Labeled cRNA was cleaned up and quality assessed for yields and specific activity using Nanodrop.

growth_protocol: Yeast strains were cultured in Synthetic Complete (SC)-Leu-Ile-Val medium for 36h at 30°C, 220 rpm.  Fresh cultures were inoculated in duplicate with the pre-culture, for the wild-type at an OD600 of 0.04, and for the taf9-tCRD2 strain at an OD600 of 0.08.  Untreated wild-type and taf9-tCRD2 cultures were harvested at an OD600 of 0.5.  For SM treatment, cultures were grown to an OD600 of 0.5 and induced with Sulfometuron Methyl (SM) for 2h at 30°C and harvested by rapid filtration on sterile Millipore 0.45mm filter disks, and frozen at -80°C.

extract_protocol: Total RNA was extracted by hot-phenol extraction method as follows.  Cells were washed with AE buffer and about 10 OD equivalent of cells were re-suspended in 500µl of AE buffer, 33.4µl of 25% (w/v) SDS and 500µl phenol equilibrated with AE buffer.  The mixture was vortexed and incubated in a water bath set to 65°C for 10 min with vortexing every 1-2 min.  The mixtures were rapidly cooled on ice and centrifuged at RT for 10 min at 13,000 rpm.  The resulting aqueous phase was collected, ~0.542 ml chloroform added to the supernatant, mixed, centrifuged at RT for 10 min and the aqueous phase collected.  About 1/10th volume of 3M NaOAc (pH 5.3) and an equal volume of isopropanol were added, mixed, immediately centrifuged at 13,000 rpm for 45 min at 4°C.  The pellet was washed with chilled 70% ethanol and centrifuged at 13,000 rpm for 20 min at 4°C.  The pellet was air-dried and re-suspended in 50µl of 0.1% (w/v) DEPC treated, autoclaved, double-distilled water, and purified using RNeasy kit from Qiagen.  The RNA samples were quantitated in a Nanodrop spectrophotometer and the integrity was assessed on an agarose gel, as well as on the Agilent 2100 Bioanalyzer.

treatment_protocol: Sulfometuron Methyl, an inhibitor of ILV2 gene product,  causes isoleucine-valine starvation, and consequent induction of Gcn4.  The SM treatment was done as per the Growth protocol.

tag: genotype

value: +Sulfometuron Methyl

value: WT


title: Liver_Corn oil control 2_24 hr_Male_Rep2

description: Vehicle control group for animals administered β-naphthoflavone

tag: age

value: corn oil control

value: Corn oil

value: 24 hours


title: Liver_Corn oil control 2_24 hr_Male_Rep3

tag: Sex


title: taf9-tCRD2 vs TAF9 in SM_1

description: Biological replicate 1 of 4. Comparison of wildtype and mutant TAF9 strains in SM


title: Liver_Corn oil control 1_48 hr_Male_Rep3

description: Vehicle control group for animals administered aroclor 1260 and PCB-153

tag: strain


title: Liver_Corn oil control 1_48 hr_Male_Rep2


title: NIH3T3 cells in G0 phase,  rep3

description: Gene expression data from NIH3T3 cells in G0 phase in the middle of G0-G1 transition

source_name: NIH3T3 cells in G0 phase


title: taf9-tCRD2 vs TAF9 in SM_4

description: Biological replicate 4 of 4. Comparison of wildtype and mutant TAF9 strains in SM


title: Liver_Corn oil control 1_48 hr_Male_Rep1


title: taf9-tCRD2 vs TAF9 in SM_2

description: Biological replicate 2 of 4. Comparison of wildtype and mutant TAF9 strains in SM


title: taf9-tCRD2 vs TAF9 in SM_3

description: Biological replicate 3 of 4. Comparison of wildtype and mutant TAF9 strains in SM


title: Liver_Corn oil control 2_24 hr_Male_Rep1


title: NIH3T3 cells in G1 phase,  rep1


title: spt20D vs WT in SM_2

description: Biological replicate 2 of 2. Comparison of wildtype SPT20 vs spt20D strain in SM.


title: NIH3T3 cells in G0 phase,  rep2


title: NIH3T3 cells in G0 phase,  rep4


title: taf9-tCRD2 SM-induced vs uninduced_4

description: Biological replicate 4 of 4. Comparison of mutant taf9-tCRD2 in SM inducing versus uninducing conditions.

value: -Sulfometuron Methyl


title: Liver_PCB-153_48 hr_Male_Rep1

value: Male

value: 80 mg/kg


title: Liver_PCB-153_48 hr_Male_Rep2


title: Liver_PCB-153_48 hr_Male_Rep3


title: NIH3T3 cells in G0 phase,  rep1


title: taf9-tCRD2 SM-induced vs uninduced_2

description: Biological replicate 2 of 4. Comparison of mutant taf9-tCRD2 in SM inducing versus uninducing conditions.


title: Liver_β-Naphthoflavone_24 hr_Male_Rep3

value: β-Naphthoflavone

value: 50 mg/kg


title: Liver_β-Naphthoflavone_24 hr_Male_Rep2

value: IP


title: taf9-tCRD2 SM-induced vs uninduced_1

description: Biological replicate 1 of 4. Comparison of mutant taf9-tCRD2 in SM inducing versus uninducing conditions.


title: WT SM-induced vs uninduced_4

description: Biological replicate 4 of 4. Comparison of wildtype TAF9 in SM inducing versus uninducing conditions.


title: taf9-tCRD2 SM-induced vs uninduced_3

description: Biological replicate 3 of 4. Comparison of mutant taf9-tCRD2 in SM inducing versus uninducing conditions.


title: WT SM-induced vs uninduced_3

description: Biological replicate 3 of 4. Comparison of wildtype TAF9 in SM inducing versus uninducing conditions.


title: Patient H3T

city: Beijing

first: Hanjiang

last: Fu

address: 27 Taiping Road

department: Department of Biochemistry and Molecular Biology

country: China

institute: Beijing Institute of Radiation Medicine

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity LncRNAs and mRNA were filtered.

source_name: hepatocellular carcinoma

label_protocol: 1ug of total RNA was reverse transcripted into cDNA with T7 Promoter Primer and MMLV-Rtase, and then was labled with T7 polymerase and Cyanine-3-CTP.

extract_protocol: HCC and adjacent normal tissues were prefrozen with liquid nitrogen, ground into powder with mortar, extracted with Trizol regeant according its protocal.

tag: tissue

value: hepatocellular carcinoma

tag: tumer size

tag: hbsag

value: Positive

tag: hcv-ab

value: Negative

value: 52 years


title: WT SM-induced vs uninduced_1

description: Biological replicate 1 of 4. Comparison of wildtype TAF9 in SM inducing versus uninducing conditions.

tag: treatment


title: WT SM-induced vs uninduced_2

description: Biological replicate 2 of 4. Comparison of wildtype TAF9 in SM inducing versus uninducing conditions.


title: Patient H3N

source_name: human HCC adjacent normal tissue

value: human HCC adjacent normal tissue


title: Liver_β-Naphthoflavone_24 hr_Male_Rep1

value: 7 weeks

tag: compound

tag: vehicle

value: 10 ml/kg


title: Patient H2N

value: 64 years


title: Patient H2T


title: Liver_Aroclor 1260_48 hr_Male_Rep2

value: Aroclor 1260

value: 200 mg/kg

tag: route

tag: dose volume

value: 48 hours


title: Patient H1N

value: 37 years


title: Liver_Aroclor 1260_48 hr_Male_Rep1

value: Male

tag: cas number

value: Corn oil

tag: time


title: Liver_Aroclor 1260_48 hr_Male_Rep3

tag: dose


title: Patient H1T


title: saliva_LA17

status: Public on Feb 20 2014

type: genomic

city: Cambridge

first: Christina

middle: A

last: Eichstaedt

address: Fitzwilliam Street

department: Biological Anthropology

institute: University of Cambridge

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

molecule: genomic DNA

source_name: 1 ml saliva, lysed

label_protocol: Followed Illumina standard protocol

growth_protocol: Saliva mixed with equal volume of lysis buffer (Quinque et al. 2006) to allow storage at room temperature

extract_protocol: Qiagen DNA Investigator Kit scaled up for 2 ml buffer-saliva mixture

treatment_protocol: Storage at room temperature for 2 weeks, 1-3 weeks at 4°C, centrifugation

tag: gender

value: female

tag: sampling location

value: Carboncito, Argentina

tag: sampling type

value: Low altitude sample


title: saliva_LA18

value: male


title: saliva_LA15

value: Dragones, Argentina


title: saliva_LA12


title: saliva_LA2

value: Embarcación, Argentina


title: saliva_LA23

value: Misión Chaqueña, Argentina


title: saliva_LA21


title: saliva_LA14


title: saliva_LA5


title: saliva_LA13


title: saliva_LA20


title: saliva_LA11


title: saliva_LA24


title: saliva_HA23

value: Tolar Grande, Argentina

value: High altitude sample


title: saliva_LA22


title: saliva_LA16


title: saliva_LA6


title: saliva_HA21


title: saliva_LA8


title: saliva_LA19


title: saliva_LA7


title: saliva_LA3


title: saliva_HA22


title: saliva_HA24


title: saliva_LA9


title: lower airway_Patient ID: UG1705

city: San Francisco

first: Shoko

last: Iwai

address: 513 Parnassus Ave.

department: Medicine

institute: University of California San Francisco

description: 16S ribosomal RNA gene is amplified prior to fragmentation and hybridization.

hyb_protocol: Hybridization solution contained 100 mM MES (N-morpholinoethanesulfonic acid), 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20, pH 6.6 (referred to as 1x MES). In addition, the solution contained 0.1 mg of herring sperm DNA (Promega)/ml, 0.5 mg of acetylated bovine serum albumin (BSA; Invitrogen)/ml, and 50 pM control oligonucleotide B2 (Affymetrix). Hybridization was carried out at 45°C for 16 h with mixing on a rotary mixer at 60 rpm. Following hybridization, the sample solution was removed and the array was washed and stained in a GeneChip Fluidics Station (Affymetrix). In brief, to enhance the signals, 10 ug of streptavidin (Vector Laboratories)/ml and 2 mg of BSA/ml in 1x MES were used as the first staining solution. After the streptavidin solution was removed, an antibody mix was added as the second stain, containing 0.1 mg of goat immunoglobulin G (Sigma-Aldrich)/ml, 5 ug of biotinylated anti-streptavidin antibody (Vector Laboratories)/ml, and 2 mg of BSA/ml in 1x MES. Nucleic acid was fluorescently labeled by incubation with 10 ug of streptavidin R-phycoerythrin conjugate (Molecular Probes)/ml and 2 mg of BSA/ml in 1x MES.

scan_protocol: The arrays were scanned at 570 nm with a resolution of 3 um with a GeneChip Scanner 3000 (GCS 3000; Affymetrix).

data_processing: Fluorescence intensities were normalized to spike-in control oligonucleotides provided by SecondGenome, Inc. (San Bruno, CA, USA) using the proprietary PhyCA processing technique developed by SecondGenome, Inc, which utilizes aggregate measures (“r scores”) that incorporate mismatch probe fluorescence intensity as well as distribution of total chip fluorescence. Quartile r score cutoffs were chosen based on r scores retrieved for control probes spiked-in at known concentrations, as recorded from all Phylochip microarrays of the current study, and were as follows: rQ1 > .31, rQ2 > .56, rQ3 > .80.

source_name: lower airway_HIV-infected patient with pneumonia

label_protocol: DNA was resuspended in 96 ul of 30 mM MOPS (morpholinepropanesulfonic acid, pH 7.5), and 4 ul of a 50 mM polyethylene oxide-iodoacetyl biotin (Pierce Chemical) solution was added to introduce the biotin label. The reaction mixture was incubated at 37°C for 1 h, and the labeled DNA was subsequently ethanol precipitated and washed twice with 70% ethanol to remove unreacted biotin compounds.

extract_protocol: Cell pellets obtained by centrifugation was resuspended in 600ul RLT Plus buffer (Qiagen, CA) and transferred to Lysis Matrix B (MP Biomedicals, OH) tubes. Samples were subjected to 30 seconds of bead beating at 5.5 m/second, followed by centrifugation for one minute at 400 rcf. Supernatant was transferred to the AllPrep DNA (Qiagen, CA) spin column and nucleic acid purification was carried out according to the manufacturer's instructions. Nucleic acid concentrations were determined using a NanoDrop spectophotometer (Thermo Scientific, MA).

treatment_protocol: Bronchoscopy with bronchoalveolar lavage (BAL) was performed in the sub-segment that was most involved on chest imaging or the right middle lobe if the imaging revealed diffuse pneumonia. A 15 ml aliquot of BAL fluid was promptly mixed with 30 mL of RNAlater solution (Life Technologies, Carlsbad, CA) and placed at 4ºC for 16 hours, prior to storage at -80ºC until processed for microbiome profiling

tag: subject id

tag: subject status

value: Ugandan HIV-infected patients with pneumonia

value: bronchoalveolar lavage


title: lower airway_Patient ID: UG1690

tag: tissue


title: saliva_LA25


title: saliva_HA25

value: Olacapato, Argentina


title: lower airway_Patient ID: UG1689


title: lower airway_Patient ID: UG1711


title: SM009_B6_Mock_d7_2

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: Study, mouse strain, infection, sample dpi, replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

value: Lung

tag: genetic background

tag: genotype

value: wild type

value: Mock


title: lower airway_Patient ID: UG1674


title: saliva_LA1


title: saliva_LA10


title: SM009_B6_Mock_d7_1


title: SM009_B6_Mock_d4_1


title: lower airway_Patient ID: UG1652


title: lower airway_Patient ID: UG1651


title: lower airway_Patient ID: UG1628


title: lower airway_Patient ID: UG1640


title: lower airway_Patient ID: UG1634


title: SM009_B6_Mock_d4_2


title: lower airway_Patient ID: UG1618


title: SM009_B6_MA15_d4_3


title: SM009_B6_MA15_d7_2


title: SM009_B6_MA15_d7_4


title: lower airway_Patient ID: UG1601


title: lower airway_Patient ID: UG1623


title: lower airway_Patient ID: UG1571


title: SM009_B6_MA15_d4_2


title: SM009_B6_MA15_d4_4


title: SM009_PLAT_Mock_d7_1

value: PLAT KO


title: SM009_PLAT_Mock_d7_2


title: SM009_PLAT_Mock_d4_2


title: saliva_LA4


title: lower airway_Patient ID: UG1563


title: lower airway_Patient ID: UG1550


title: lower airway_Patient ID: UG1500


title: lower airway_Patient ID: UG1555


title: SM009_PLAT_Mock_d4_1


title: saliva_HA20


title: SM009_PLAT_MA15_d7_4


title: saliva_HA19


title: lower airway_Patient ID: UG1499


title: lower airway_Patient ID: UG1586


title: lower airway_Patient ID: UG1488


title: saliva_HA16

value: San Antonio de los Cobres, Argentina


title: lower airway_Patient ID: UG1492


title: saliva_HA14


title: SM009_PLAT_MA15_d4_3


title: SM009_PLAT_MA15_d7_1


title: SM009_PLAT_MA15_d4_4


title: SM009_PLAT_MA15_d7_2


title: SM004_B6_MA15_d7_1

source_name: Study name, mouse strain/mutation, infection, sample dpi, replicate


title: saliva_HA11

value: female


title: saliva_HA2


title: saliva_HA17


title: saliva_HA7


title: lower airway_Patient ID: UG1477


title: saliva_HA15


title: SM004_B6_MA15_d4_4


title: saliva_HA9


title: saliva_HA18


title: lower airway_Patient ID: UG1472


title: saliva_HA6


title: lower airway_Patient ID: UG1454


title: saliva_HA12


title: saliva_HA1


title: lower airway_Patient ID: UG1438


title: lower airway_Patient ID: UG1442


title: SM004_B6_MA15_d4_3


title: lower airway_Patient ID: UG1436


title: saliva_HA13


title: SM004_B6_MA15_d4_1


title: saliva_HA8


title: saliva_HA5


title: saliva_HA10


title: lower airway_Patient ID: UG1435


title: saliva_HA3


title: SM004_B6_MA15_d4_2


title: SM004_PAI1_Mock_d7_1

value: PAI1 KO


title: SM004_PAI1_Mock_d7_2


title: lower airway_Patient ID: UG1424


title: SM004_PAI1_Mock_d4_1


title: lower airway_Patient ID: UG1420


title: lower airway_Patient ID: UG1416


title: SM004_PAI1_MA15_d7_3


title: SM004_PAI1_Mock_d4_2


title: SM004_PAI1_MA15_d7_2


title: lower airway_Patient ID: UG1397


title: lower airway_Patient ID: UG1360


title: SM004_PAI1_MA15_d7_1


title: lower airway_Patient ID: UG1290


title: lower airway_Patient ID: UG1325


title: lower airway_Patient ID: UG1292


title: lower airway_Patient ID: UG1289


title: saliva_HA4


title: SM004_PAI1_MA15_d4_2


title: lower airway_Patient ID: UG1328


title: lower airway_Patient ID: UG1266


title: SM004_PAI1_MA15_d4_3


title: lower airway_Patient ID: UG1254


title: lower airway_Patient ID: UG1242


title: lower airway_Patient ID: UG1243


title: SM004_PAI1_MA15_d4_4


title: lower airway_Patient ID: UG1222


title: SM004_TIMP1_Mock_d4_2

value: TIMP1 KO


title: lower airway_Patient ID: UG1216


title: SM004_TIMP1_Mock_d4_1


title: SM004_PAI1_MA15_d4_1


title: lower airway_Patient ID: UG1200


title: lower airway_Patient ID: UG1262


title: SM004_TIMP1_Mock_d7_1


title: SM004_B6_Mock_d7_4


title: SM004_TIMP1_MA15_d7_1


title: SM004_B6_Mock_d7_3


title: lower airway_Patient ID: UG1197


title: SM004_B6_Mock_d7_2


title: lower airway_Patient ID: UG1186


title: lower airway_Patient ID: UG1194


title: SM004_TIMP1_MA15_d7_3


title: SM004_TIMP1_MA15_d7_2


title: SM004_B6_Mock_d7_1


title: lower airway_Patient ID: UG1483


title: SM004_B6_Mock_d4_4


title: SM004_TIMP1_Mock_d7_2


title: lower airway_Patient ID: UG1175


title: lower airway_Patient ID: UG1171


title: lower airway_Patient ID: UG1168


title: lower airway_Patient ID: UG1169


title: lower airway_Patient ID: UG1176


title: lower airway_Patient ID: UG1165


title: SM004_B6_Mock_d4_1


title: lower airway_Patient ID: UG1142


title: lower airway_Patient ID: UG1166


title: SM004_TIMP1_MA15_d4_4


title: SM004_B6_MA15_d7_4


title: SM004_B6_Mock_d4_3


title: SM004_TIMP1_MA15_d4_3


title: SM004_B6_MA15_d7_3


title: lower airway_Patient ID: UG1138


title: SM004_TIMP1_MA15_d7_4


title: SM004_B6_Mock_d4_2


title: SM004_TIMP1_MA15_d4_1


title: SM007_CXCR3_mock_d2_3

description: US23502418_251486837119_S01_GE1_107_Sep09_1_2.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

source_name: CXCR3 KO_mock_d2

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Ten-week-old mice were infected by intranasal instillation of 10^5 PFU of  SARS MA15 in 50 µl of PBS or mock-infected with PBS alone.  At days 4 and 7 days post-infection, lungs were harvested.

treatment_protocol: Specific lobes of the lung from each animal were harvested and briefly rinse tissue in cold (4C) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4C incubation for overnight, samples were stored at -80C further processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

tag: strain background

tag: genotype/variation

value: CXCR3 knockout

tag: age

value: 10 wks

tag: infection

value: Mock (PBS alone)

tag: time point

value: 2 days post infection

value: lung


title: SM007_CXCR3_MA15_d7_3

description: US23502418_251486837119_S01_GE1_107_Sep09_1_1.txt

source_name: CXCR3 KO_MA15_d7

value: SARS MA15

value: 7 days post infection


title: SM007_CXCR3_MA15_d7_1

description: US23502418_251486836926_S01_GE1_107_Sep09_1_2.txt


title: SM007_CXCR3_mock_d2_2

description: US23502418_251486837118_S01_GE1_107_Sep09_1_1.txt


title: SM007_CXCR3_mock_d4_1

description: US23502418_251486837116_S01_GE1_107_Sep09_1_3.txt

source_name: CXCR3 KO_mock_d4

value: 4 days post infection


title: SM007_CXCR3_mock_d7_3

description: US23502418_251486836928_S01_GE1_107_Sep09_1_3.txt

source_name: CXCR3 KO_mock_d7


title: SM004_TIMP1_MA15_d4_2

tag: treatment


title: SM007_CXCR3_MA15_d7_4

description: US23502418_251486837120_S01_GE1_107_Sep09_1_2.txt


title: SM007_CXCR3_mock_d7_2

description: US23502418_251486837117_S01_GE1_107_Sep09_1_3.txt


title: SM007_CXCR3_MA15_d7_2

description: US23502418_251486837117_S01_GE1_107_Sep09_1_4.txt


title: SM007_CXCR3_mock_d7_1

description: US23502418_251486836926_S01_GE1_107_Sep09_1_3.txt


title: SM007_CXCR3_mock_d4_2

description: US23502418_251486837117_S01_GE1_107_Sep09_1_2.txt


title: SM007_CXCR3_MA15_d4_2

description: US23502418_251486836928_S01_GE1_107_Sep09_1_2.txt

source_name: CXCR3 KO_MA15_d4


title: SPFs11+DLD-1

city: Chiba

first: Youichi

last: Higuchi

address: 6-5-1 Kashiwanoha, Kashiwa

institute: Research Center for Innovative Oncology National Cancer Center Hospital East

description:
CoSS11_D
Colon subperitoneal fibroblasts stimulated with DLD-1 cultured medium

hyb_protocol: The procedures for target hybridization, washing, and staining with signal amplification were conducted according to the supplier's protocols.

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The intensity of each feature of the array was calculated using GeneSpring GX Software, version 12.5 (Agilent).

source_name: Colon subperitoneal fibroblasts_DLD-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using a 30 IVT Express Kit.

growth_protocol: All fibroblasts were grown and maintained in MF-medium (Toyobo), and all experiments were performed with cells within 6 passages.

extract_protocol: TRIzol / RNeasy minicolumn protocol (QIAGEN) were performed according to the manufacturer's instructions.

treatment_protocol: 5.0×10^5 fibroblasts cells were plated on 10cm dish and cultured in DMEM (Sigma) with 10% FBS (Sigma) and 1% penicillin streptomycin (Sigma) for 48h. Then, the medium were changed into DMEM without FBS and penicillin streptomycin and cultured for 24h. The medium were changed again and cultured for 24h, as non-stimulated samples. The stimulated samples were extracted from the fibroblasts treated with DLD-1 cultured medium for 24h.

value: 58 years

tag: cell type

value: Human colon subperitoneal fibroblasts

tag: stimulated with

value: colon cancer cell line (DLD-1) cultured medium


title: SPFs8+DLD-1

description:
CoSS8_D
Colon subperitoneal fibroblasts stimulated with DLD-1 cultured medium

value: 71 years


title: SM007_CXCR3_MA15_d4_3

description: US23502418_251486836927_S01_GE1_107_Sep09_1_4.txt


title: SM007_CXCR3_MA15_d2_3

description: US23502418_251486836929_S01_GE1_107_Sep09_1_3.txt

source_name: CXCR3 KO_MA15_d2


title: SM007_CXCR3_MA15_d2_1

description: US23502418_251486836930_S01_GE1_107_Sep09_1_4.txt


title: SPFs4+DLD-1

description:
CoSS4_D
Colon subperitoneal fibroblasts stimulated with DLD-1 cultured medium

value: 61 years

value: male


title: SPFs11

description:
CoSS11_N
Colon subperitoneal fibroblasts without stimulating

source_name: Colon subperitoneal fibroblasts_Normal

value: female

value: none (control media)


title: SM007_B6_mock_d7_1

description: US23502418_251486837116_S01_GE1_107_Sep09_1_1.txt

value: wild-type


title: SPFs4

description:
CoSS4_N
Colon subperitoneal fibroblasts without stimulating


title: SM007_B6_mock_d7_3

description: US23502418_251486836927_S01_GE1_107_Sep09_1_2.txt


title: SMFs11+DLD-1

description:
CoSM11_D
Colon submucosal fibroblasts stimulated with DLD-1 cultured medium

source_name: Colon submucosal fibroblasts_DLD-1

value: Human colon submucosal fibroblasts


title: SM007_B6_mock_d4_3

description: US23502418_251486837118_S01_GE1_107_Sep09_1_2.txt

value: 10 wks


title: SMFs11

description:
CoSM11_N
Colon submucosal fibroblasts without stimulating

source_name: Colon submucosal fibroblasts_Normal


title: SMFs8+DLD-1

description:
CoSM8_D
Colon submucosal fibroblasts stimulated with DLD-1 cultured medium


title: SMFs4+DLD-1

description:
CoSM4_D
Colon submucosal fibroblasts stimulated with DLD-1 cultured medium


title: SM007_B6_mock_d7_2

description: US23502418_251486836929_S01_GE1_107_Sep09_1_1.txt

value: Mock (PBS alone)


title: SM007_CXCR3_MA15_d2_2

description: US23502418_251486836926_S01_GE1_107_Sep09_1_1.txt

value: CXCR3 knockout

value: 2 days post infection


title: SM007_B6_mock_d2_2

description: US23502418_251486836927_S01_GE1_107_Sep09_1_1.txt

value: lung


title: SMFs4

description:
CoSM4_N
Colon submucosal fibroblasts without stimulating


title: SM007_B6_mock_d2_1

description: US23502418_251486837118_S01_GE1_107_Sep09_1_3.txt


title: SM007_B6_MA15_d7_3

description: US23502418_251486836929_S01_GE1_107_Sep09_1_2.txt

value: SARS MA15

value: 7 days post infection


title: HUVEC_DMSO_rep1

city: Columbia

first: Henry

middle: Rhodes

last: Bateman

state: SC

address: 6439 Garners Ferry Road

department: Cell Biology & Anatomy

institute: University of South Carolina

description: Gene expression data from HUVECs

hyb_protocol: Samples were hybridized overnight to GeneChips in accordance with Affymetrix protocols.

scan_protocol: Post hybridization washing, staining and fluorescence scanning were performed using Affymetrix instrumentation in accordance with manufacturer recommendations.

data_processing: Microarray data were normalized by RMA to obtain normalized hyb intensity values and by Mas5 to obtain detection (presence/absence) scoring.  Normalized data and A/P calls were imported into dchip for comparative analyses.

source_name: HUVECs exposed to Vehicle Control

label_protocol: Total RNA (2 micrograms) was converted into biotin-labeled cRNA using the SuperScript II cDNA synthesis kit (Invitrogen, Carlsbad, CA) and the Enzo HighYield in vitro transcription amplification kit (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: HUVECs were cultured on gelatin-coated Petri plates in endothelial cell medium supplemented with fetal bovine serum (FBS) and growth factors.  The endothelial cell media was replaced every 2-3 days, and the cells were passaged after complete confluence was reached.  Confluent plates were trypsinized and split, and the cells were cultured until the fourth passage was reached.

extract_protocol: RNA isolation was completed with the RNeasy Mini kit from Qiagen.  The cells were lysed, and RNA was isolated by using the RNeasy spin columns and following the protocol provided by Qiagen.

treatment_protocol: Confluent plates of HUVECs (four total plates) were chosen for the microarray experiments.  Two of the plates received fresh medium containing vehicle control (1:1000 diluted DMSO), and the remaining plates received fresh medium containing 100 µM SsnB.  The plates were incubated for 24 h to allow SsnB to have an effect on cellular gene expression.

value: Primary Human Umbilical Vein Endothelial Cells

value: Sparstolonin B


title: HUVEC_SsnB_rep1

description: Gene expression data from HUVECs

source_name: HUVECs exposed to SsnB

value: control


title: SPFs8

description:
CoSS8_N
Colon subperitoneal fibroblasts without stimulating

value: 71 years

value: Human colon subperitoneal fibroblasts


title: HUVEC_SsnB_rep2

description: Gene expression data from HUVECs


title: SM007_B6_mock_d4_1

description: US23502418_251486837116_S01_GE1_107_Sep09_1_4.txt

value: 4 days post infection


title: SM007_B6_mock_d2_3

description: US23502418_251486837119_S01_GE1_107_Sep09_1_4.txt


title: SM007_B6_MA15_d7_2

description: US23502418_251486836928_S01_GE1_107_Sep09_1_1.txt


title: HCAEC_DMSO_rep1

description: Gene expression data from HCAECs

source_name: HCAECs exposed to Vehicle Control

growth_protocol: HCAECs were cultured on gelatin-coated Petri plates in endothelial cell medium supplemented with fetal bovine serum (FBS) and growth factors.  The endothelial cell media was replaced every 2-3 days, and the cells were passaged after complete confluence was reached.  Confluent plates were trypsinized and split, and the cells were cultured until the fourth passage was reached.

treatment_protocol: Confluent plates of HCAECs (six total plates) were chosen for the microarray experiments.  Two of the plates received fresh medium containing vehicle control (1:1000 diluted DMSO), and the remaining plates received fresh medium containing 100 µM SsnB.  The plates were incubated for 24 h to allow SsnB to have an effect on cellular gene expression.

value: Primary Human Coronary Artery Endothelial Cells


title: SM007_B6_mock_d4_2

description: US23502418_251486836926_S01_GE1_107_Sep09_1_4.txt


title: HUVEC_DMSO_rep2

description: Gene expression data from HUVECs


title: SMFs8

description:
CoSM8_N
Colon submucosal fibroblasts without stimulating

value: female

value: none (control media)


title: HCAEC_DMSO_rep3

description: Gene expression data from HCAECs


title: HCAEC_SsnB_rep3

description: Gene expression data from HCAECs

source_name: HCAECs exposed to SsnB


title: HCAEC_DMSO_rep2

description: Gene expression data from HCAECs


title: SM007_B6_MA15_d2_3

description: US23502418_251486837116_S01_GE1_107_Sep09_1_2.txt

value: wild-type


title: SM007_B6_MA15_d4_1

description: US23502418_251486836927_S01_GE1_107_Sep09_1_3.txt

value: 10 wks


title: HCAEC_SsnB_rep2

description: Gene expression data from HCAECs


title: SM007_B6_MA15_d4_2

description: US23502418_251486836928_S01_GE1_107_Sep09_1_4.txt


title: Disome 15 ubp6∆ vs. wild-type

city: worcester

first: Eduardo

middle: M

last: Torres

address: 364 Plantation Street, LRB-523

department: Department of Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description: Grown in YEPD at 30 degrees

hyb_protocol: Equal masses of differentially labeled control and sample cRNA were combined such that each sample contained at least 2.5 pmol dye. Samples were mixed with control targets, fragmented, combined with hybridization buffer, and applied to a microarray consisting of 60mer probes for each yeast open reading frame (Agilent). Microarrays were rotated at 60?C for 17 hours in a hybridization oven (Agilent). Arrays were then washed according to the Agilent SSPE wash protocol, and scanned on an Agilent scanner.

scan_protocol: Scanned on an Agilent G2505B Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extractor A.7.5.1

organism: Saccharomyces cerevisiae W303

source_name: Disome 15 ubp6∆

label_protocol: 325 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Reactions were performed as directed except using half the recommended reaction volume and one quarter the recommended Cy-CTP amount. Dye incorporation and yield were measured with a Nanodrop spectrophotometer.

growth_protocol: Cells grown in YEPD at 30 degrees

extract_protocol: Filters were incubated for 1 hour at 65oC in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mM Tris, pH 7.5) and acid phenol. The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf). Total RNA was then ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit.

value: Disome 15 ubp6∆

value: day 1

source_name: whole cells

value: whole cells


title: Disome 13 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 13 ubp6∆

value: Disome 13 ubp6∆


title: Disome 12 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 12 ubp6∆

value: Disome 12 ubp6∆


title: Disome 16 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 16 ubp6∆

value: Disome 16 ubp6∆


title: Disome 11 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 11 ubp6∆

value: Disome 11 ubp6∆


title: Disome 14 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 14 ubp6∆

value: Disome 14 ubp6∆


title: HCAEC_SsnB_rep1

description: Gene expression data from HCAECs

value: control


title: SM007_B6_MA15_d2_2

description: US23502418_251486837119_S01_GE1_107_Sep09_1_3.txt

value: SARS MA15

value: 2 days post infection

value: lung


title: Disome 10 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 10 ubp6∆

value: Disome 10 ubp6∆


title: Disome 9 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 9 ubp6∆

value: Disome 9 ubp6∆


title: SM007_B6_MA15_d7_1

description: US23502418_251486836930_S01_GE1_107_Sep09_1_1.txt

value: 7 days post infection


title: Disome 8 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 8 ubp6∆

value: Disome 8 ubp6∆


title: Disome 5 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 5 ubp6∆

value: Disome 5 ubp6∆


title: T1DControl18_2

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: 750 ng each cDNA was hybridized to Human HT-12 Expression BeadChips, version 3 (Illumina, cat. no BD-103-0603) at 58 °C overnight (18 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A. Hybridizations were detected with 1 ug/ml Cyanine3-streptavidine (GE Healthcare Biosciences cat. no PA43001).

scan_protocol: Chips were scanned with Illumina Bead Array Reader, BeadScan software version 3.5. The numerical results were extracted with GenomeStudio2008 v1 without any normalization or background subtraction.

data_processing: The intensities were quantile normalized and log2-transformed using R/Bioconductor.

label_protocol: 100 ng total RNA was amplified to cDNA with Ovation RNA Amplification System V2 (NuGEN, cat. no 3100-60), including Ovation Whole Blood Reagent (cat. no 1300-60). The amplified cDNA was labelled according to NuGEN’s Illumina Solution protocol, Application Note #2.

growth_protocol: 2.5 ml of venous blood was drawn into PAXgene Blood RNA tubes (PreAnalytix Switzerland), at the Type 1 Diabetes Prediction and Prevention (DIPP) study clinic, Turku, Finland. The samples were incubated for 2 hours at RT and then stored at -70 °C until analyzed.

extract_protocol: Total whole-blood RNA was extracted from the samples using PAX gene RNA Blood RNA kit (Qiagen, Germany) according to manufacturer's instructions. RNA quality and quantity was determined using Nano Drop ND-1000 (Nano Drop Technologies, USA) and Experion Automated Electrophoresis System (Bio-Rad Laboratories, Finland).

tag: case/control pair

tag: age at sample (months)

tag: time from seroconversion (months)

value: no seroconversion

tag: time from t1d diagnosis (months)

value: no diagnosis

value: male

value: peripheral blood

tag: hla-dqb1 genotype


title: T1DControl17B_4

tag: gender


title: T1DControl17B_3

tag: tissue


title: Disome 1 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 1 ubp6∆

value: Disome 1 ubp6∆

value: day 1

value: whole cells


title: T1DCase18_4


title: T1DCase18_2


title: T1DCase18_1


title: T1DControl18_3


title: T1DCase18_3


title: Disome 2 ubp6∆ vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 2 ubp6∆

value: Disome 2 ubp6∆


title: SM007_B6_MA15_d2_1

description: US23502418_251486836930_S01_GE1_107_Sep09_1_3.txt

value: wild-type

value: 10 wks


title: T1DCase18_5


title: T1DControl18_1


title: T1DControl17A_4


title: T1DControl17B_1


title: T1DControl17B_2


title: T1DControl17A_6


title: T1DControl17A_5


title: Disome 11 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 11

value: Disome 11


title: T1DControl17A_2


title: Disome 16 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 16

value: Disome 16


title: Disome 13 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 13

value: Disome 13


title: Granulocyte Rep2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

hyb_protocol: Cy5-labeled RNA was hybridized to SurePrint G3 Mouse GE 8x60K arrays

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing:
Agilent Feature Extraction Software was used to quantify expression and local background levels for each probe of each sample. Background subtracted expression values were then quantile normalized. Values that did not show significant expression above background (p<0.05 and at least 2.6 fold above background’s standard deviation) were considered not significantly detected and floored to the minimal significantly detected (MSD) value (MSD = 4.6). Expression values were log2 transformed for further analysis.
The processed data used to draw the conclusions in the published study are restricted to noncoding genes identified by us (accession IDs TCONS_xxxxxxx) and coding genes already present on the array.

source_name: Gr1+ Granulocyte

label_protocol: RNA was labeled with Cy5 using the manufacturer's standard labeling kits and protocol

extract_protocol: Total RNA was extracted using RNeasy Mini column kits

value: Granulocyte

value: Adult bone marrow

value: 8 - 12 weeks

tag: strain


title: Disome 14 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 14

value: Disome 14


title: Disome 12 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 12

value: Disome 12

source_name: whole cells


title: Disome 5 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 5

value: Disome 5


title: T1DCase17_4

value: male


title: Disome 9 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 9

value: Disome 9


title: T1DControl16_8

value: no seroconversion

value: no diagnosis

value: peripheral blood


title: Disome 15 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 15

value: Disome 15

value: day 1

value: whole cells


title: T1DControl17A_1


title: T1DControl16_9


title: T1DControl16_7


title: T1DCase17_2


title: Granulocyte macrophage progenitor Rep2

source_name: Lin- cKit+ Scal- CD16/32(high) CD34(high) Granulocyte Macrophage Progenitor

value: Granulocyte macrophage progenitor


title: T1DControl17A_3


title: T1DControl16_6


title: Disome 10 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 10

value: Disome 10


title: Disome 1 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 1

value: Disome 1


title: Disome 2 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 2

value: Disome 2


title: Granulocyte Rep1

value: Granulocyte

value: Adult bone marrow


title: T1DCase17_1


title: Granulocyte macrophage progenitor Rep1

value: 8 - 12 weeks


title: Granulocyte Rep3


title: Disome 8 vs. wild-type

description: Grown in YEPD at 30 degrees

source_name: Disome 8

value: Disome 8


title: T1DCase17_3


title: Late erythroblast Rep3

source_name: Ter119+ FSC low CD44 mid Late Erythroblast

value: Late erythroblast


title: T1DControl16_3

value: male


title: T1DControl16_2


title: T1DControl16_5


title: T1DControl16_4


title: Late erythroblast Rep2


title: Megakaryocyte erythroid progenitor Rep2

source_name: Lin- cKit+ Scal- CD16/32(low) CD34(low) Megakaryocyte erythroid progenitor

value: Megakaryocyte erythroid progenitor


title: Late erythroblast Rep1


title: T1DCase16_9


title: Megakaryocyte erythroid progenitor Rep3


title: T1DControl16_1

value: no seroconversion


title: Early erythroblast Rep1

source_name: Ter119+ FSC high CD44 high Early Erythroblast

value: Early erythroblast


title: Early erythroblast Rep2


title: T1DCase16_6

value: peripheral blood


title: Common myeloid progenitor Rep3

source_name: Lin- cKit+ Scal- CD16/32(low) CD34(high) Common myeloid progenitor

value: Common myeloid progenitor


title: T1DCase16_5


title: Megakaryocyte erythroid progenitor Rep1


title: T1DCase16_7


title: Hematopoietic stem and multipotent progenitor cells Rep2

source_name: Lin- cKit+ Sca1+ cells


title: Hematopoietic stem and multipotent progenitor cells Rep3


title: T1DCase16_8


title: Hematopoietic stem and multipotent progenitor cells Rep1


title: Common myeloid progenitor Rep1


title: T1DCase16_2


title: T1DCase15_8

value: female


title: T1DCase16_4


title: T1DCase16_3


title: T1DCase16_1


title: T1DControl15_5

value: no diagnosis


title: T1DControl15_3


title: T1DControl15_4


title: T1DControl15_1


title: Common myeloid progenitor Rep2