title: hippocampus_HE_rep5

city: Hangzhou

first: Chengliang

address: No. 866th, Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: brain hippocampus

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One‐Color (Cat#5190‐2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: ICR mice were housed in cages on 12-hour light/dark cycle with temperature of 21-23 and humidity of 54-56%. They were provided food and water ad libitum.

extract_protocol: Total RNAs were extracted from hippocampus tissue using TRIzol reagent (ThermoFisher, 15596018), and followed with purification by RNeasy mini kit (Qiagen, 74106) and RNase-Free DNase Set (Qiagen, 79254) according to the manufacturer’s instruction. The concentration and quality of RNA was checked by NanoDrop 2000 (ThermoFisher) and electrophoresis though denaturing gels.

treatment_protocol: The pregnant mice were randomly divided into the negative control group (NC group) and high estradiol group (HE group). Mice of HE group were orally administrated with estradiol valerate (sigma) which was dissolved in corn oil at a dose of 100ug/kg/day from day of E5.5 to E11.5.  Mice of NC group received an equal volume of corn oil.

tag: group

value: maternal excessive estradiol exposure group

tag: Sex

value: male

value: ICR

value: brain

value: adult


title: MFB003_MOCK_12HRS_RNA_A

status: Public on Jun 27 2017

type: RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

country: USA

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

molecule: total RNA

organism: Homo sapiens

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 1

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: Cells were infected with a multiplicity of infection of 5 PFU.

tag: cell type

value: primary fibroblasts

tag: time

tag: virus

value: Mock


title: hippocampus_HE_rep3

last: Zhou

state: Zhejiang

country: China

organism: Mus musculus

tag: strain

tag: tissue

tag: age


title: MFB003_MOCK_12HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 3


title: MFB003_icMERS_12HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 5

value: icMERS


title: MFB003_MOCK_12HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 4


title: hippocampus_NC_rep5

value: normal control


title: hippocampus_HE_rep4


title: hippocampus_NC_rep4


title: MFB003_icMERS_24HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 2


title: hippocampus_HE_rep2


title: MFB003_MOCK_12HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 5


title: hippocampus_HE_rep1


title: MFB003_MOCK_12HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 2


title: hippocampus_NC_rep3


title: MFB003_icMERS_12HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 3


title: YYy310spont9W3

type: genomic

city: Los Angeles

first: Yi

last: Yin

state: CA

address: 695 Charles E. Young Dr. S.

department: Human Genetics

institute: University of California, Los Angeles

description: Genotype of YYy310spont9W3

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222, pre-warmed to 37C).

scan_protocol: We acquired the microarray images with a GenePix 4000B scanner and analyzed the images with the GenePix Pro 6.0 software

data_processing:
The data generated by GenePix Pro were exported to text files and analyzed with R. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average ratio of the entire probe set.
Ratio of the medians (635 nm/532 nm).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: cell culture of strain YYy310spont9W3

label_protocol: The DNA was labeled using either Cy3-dUTP (control) or Cy5-dUTP (samples) using Invitrogen Bioprime Array CGH Genome Labeling Module using the kit protocol.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Approximately 55 mg of the pelleted culture was resuspended in 500 ml of a melted agarose solution (0.5% low melt agarose, 100 mM EDTA pH 7.5 at approximately 42°), and then 20 μl of a 25 mg/ml Zymolase solution was added. This cell-agarose mixture was distributed into five plug molds and allowed to solidify. The plugs were then incubated in 700 μl of an EDTA/Tris solution (500 mM EDTA, 10 mM Tris, pH 7.5) for 5 hours at 37°. We then add 400 μl of a sarcosyl/proteinase K solution (5% sarcosyl, 5 mg/ml proteinase K, 500 mM EDTA pH 7.5) to the tubes containing the plugs, and incubate at 50° for 12 hours. DNA was isolated from three plugs per strain using the Fermentas Life Sciences GeneJet Gel Extraction Kit. Following the addition of the “Binding” buffer from the kit, the samples were incubated at room temperature (~25°) until the agarose had melted and were then incubated on ice for 5 minutes. These samples were sonicated using a BioRupter sonicater for two 15-minute sessions of 30-second high pulses, followed by 30 seconds without sonication, resulting in DNA fragments of about 200-300 bp. Following sonication, the samples were treated according to the kit protocol.

treatment_protocol: Yeast cells were collected after culture in YPD medium for 20 hours.

source_name: cell culture of JSC24-2

tag: reference strain


title: YYy310spont9R3

description: Genotype of YYy310spont9R3

source_name: cell culture of strain YYy310spont9R3


title: YYy310spont9W1

description: Genotype of YYy310spont9W1

source_name: cell culture of strain YYy310spont9W1


title: YYy310spont9R1

description: Genotype of YYy310spont9R1

source_name: cell culture of strain YYy310spont9R1


title: MFB003_icMERS_12HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 4


title: MFB003_MOCK_0HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 2


title: MFB003_MOCK_0HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 4


title: YYy310spont9W1-1

description: Genotype of YYy310spont9W1-1

source_name: cell culture of strain YYy310spont9W1-1


title: YYy310spont9W3-1

description: Genotype of YYy310spont9W3-1

source_name: cell culture of strain YYy310spont9W3-1


title: YYy310spont9R3-1a

description: Genotype of YYy310spont9R3-1a

source_name: cell culture of strain YYy310spont9R3-1a


title: MFB003_icMERS_0HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 4


title: hippocampus_NC_rep1

source_name: brain hippocampus


title: MFB003_icMERS_12HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 2


title: MFB003_MOCK_0HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 5


title: hippocampus_NC_rep2


title: MFB003_MOCK_0HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 3


title: MFB003_icMERS_0HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 2


title: MFB003_icMERS_12HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 1


title: YYy310spont6W4

description: Genotype of YYy310spont6W4

source_name: cell culture of strain YYy310spont6W4

source_name: cell culture of JSC24-2


title: MFB003_MOCK_0HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 1


title: YYy310spont9R1-1a

description: Genotype of YYy310spont9R1-1a

source_name: cell culture of strain YYy310spont9R1-1a


title: MFB003_icMERS_0HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 1


title: MFB003_icMERS_0HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 3


title: H10-4 Normal

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label: biotin

source_name: Normal

label_protocol: GeneChip Affymetrix protocol. AmplificationCycles(2Amp).

extract_protocol: GeneChip Affymetrix protocol.

tag: individual (patient id)

tag: disease state

value: Normal

tag: technique

value: Vivo

tag: origin

value: RU


title: YYy310spont6W4-1

description: Genotype of YYy310spont6W4-1

source_name: cell culture of strain YYy310spont6W4-1


title: H14-4 Normal


title: H12-4 Normal


title: H13-4 Normal


title: H11-4 Normal


title: MFB003_icMERS_0HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 5


title: YYy310spont6W1

description: Genotype of YYy310spont6W1

source_name: cell culture of strain YYy310spont6W1


title: YYy310spont6W1-2

description: Genotype of YYy310spont6W1-2

source_name: cell culture of strain YYy310spont6W1-2


title: YYy310spont6R4

description: Genotype of YYy310spont6R4

source_name: cell culture of strain YYy310spont6R4


title: YYy310.9-G1-15J-5W2

description: Genotype of YYy310.9-G1-15J-5W2

source_name: cell culture of strain YYy310.9-G1-15J-5W2


title: YYy310.9-G1-15J-5W1

description: Genotype of YYy310.9-G1-15J-5W1

source_name: cell culture of strain YYy310.9-G1-15J-5W1


title: ptoluidine120_rep2

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: ptoluidine treated 120 mg/kg R. norvegicus sample

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Affymetrix Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized separately for each chemical.

organism: Rattus norvegicus

source_name: liver, ptoluidine 120mg/kg

label_protocol: One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

growth_protocol: At the start of the study, the animals were 5–6 weeks of age. The animals were housed 2 per cage. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) were made available ad libitum. The care of animals on this study was according to National  Institutes of Health (NIH) procedures as described in the ‘‘The  U.S. Public Health Service Policy on Humane Care and Use of  Laboratory Animals,’’ available from the Office of Laboratory  Animal Welfare, NIH, Department of Health and Human Services,  RKLI, Bethesda, MD or online at http://grants.nih.gov/  grants/olaw/olaw.htm#pol.

extract_protocol: The liver was harvested and weighed, and then, a representative section from the midline of the left lateral hepatic lobe was collected and fixed in 10 % neutral buffered formalin for histology. Hematoxylin and eosin (H&E)-stained sections (5 μm) were examined by a board certified pathologist. Three samples (approximately 3–4 mm cubes) were dissected from the remaining left lateral hepatic lobe and flash-frozen in liquid nitrogen and stored at −80 °C until RNA extraction. RNA was extracted from frozen samples using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A, Carlsbad, CA) according to the manufacturer’s protocol. RNA concentration and quality were measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples were aliquoted and stored at −80 °C until they were analyzed for gene expression studies.

treatment_protocol: DMPT (lot #C15Y012, Alfa Aesar, Ward Hill, MA) and p-toluidine (lot #STBB8127V, Sigma-Aldrich, Allentown, PA) were prepared for oral gavage administration in corn oil (Lot# 12-542; Welch, Holme & Clark Co., Inc. Newark, NJ) to deliver DMPT at doses of 0, 1, 6, 20, 60, or 120 mg/kg/day for 5 consecutive days to male F344/N rats in a volume of 2.5-ml/kg body weight.

tag: agent

value: ptoluidine

tag: dose

value: liver


title: MFB003_icMERS_36HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 3


title: YYy310spont6R4-1

description: Genotype of YYy310spont6R4-1

source_name: cell culture of strain YYy310spont6R4-1


title: GM Melanoma

source_name: Melanoma

value: GM

value: Melanoma

value: Tumor

value: Charite-DH


title: ptoluidine120_rep3


title: ptoluidine120_rep4


title: LB23 Normal


title: KP Melanoma

value: KP


title: YYy310.9-G1-15J-5W2-1a

description: Genotype of YYy310.9-G1-15J-5W2-1a

source_name: cell culture of strain YYy310.9-G1-15J-5W2-1a

source_name: cell culture of JSC24-2


title: TS Melanoma

value: TS


title: ptoluidine60_rep5

description: ptoluidine treated 60 mg/kg R. norvegicus sample

source_name: liver, ptoluidine 60mg/kg


title: ptoluidine120_rep5


title: YYy310.9-G1-15J-5W1-1a

description: Genotype of YYy310.9-G1-15J-5W1-1a

source_name: cell culture of strain YYy310.9-G1-15J-5W1-1a


title: ptoluidine120_rep1


title: YYy310.9-G1-15J-5R2

description: Genotype of YYy310.9-G1-15J-5R2

source_name: cell culture of strain YYy310.9-G1-15J-5R2


title: YYy310spont6R2

description: Genotype of YYy310spont6R2

source_name: cell culture of strain YYy310spont6R2


title: HH Melanoma

value: HH


title: YYy310spont6R2-3

description: Genotype of YYy310spont6R2-3

source_name: cell culture of strain YYy310spont6R2-3


title: ptoluidine60_rep4


title: GB Melanoma

value: GB


title: YYy310.9-G1-15J-5R2-1a

description: Genotype of YYy310.9-G1-15J-5R2-1a

source_name: cell culture of strain YYy310.9-G1-15J-5R2-1a


title: YYy311spont32W2-6a

description: Genotype of YYy311spont32W2-6a

source_name: cell culture of strain YYy311spont32W2-6a


title: YYy311spont32W2

description: Genotype of YYy311spont32W2

source_name: cell culture of strain YYy311spont32W2


title: YYy310spont4W2

description: Genotype of YYy310spont4W2

source_name: cell culture of strain YYy310spont4W2


title: YYy310spont4W2-1

description: Genotype of YYy310spont4W2-1

source_name: cell culture of strain YYy310spont4W2-1


title: YYy310.9-G1-15J-5R1-1a

description: Genotype of YYy310.9-G1-15J-5R1-1a

source_name: cell culture of strain YYy310.9-G1-15J-5R1-1a


title: YYy310.9-G1-15J-17W4

description: Genotype of YYy310.9-G1-15J-17W4

source_name: cell culture of strain YYy310.9-G1-15J-17W4


title: YYy311spont32R6

description: Genotype of YYy311spont32R6

source_name: cell culture of strain YYy311spont32R6


title: YYy310.9-G1-15J-5R1

description: Genotype of YYy310.9-G1-15J-5R1

source_name: cell culture of strain YYy310.9-G1-15J-5R1


title: YYy310spont4W1

description: Genotype of YYy310spont4W1

source_name: cell culture of strain YYy310spont4W1


title: YYy310.9-G1-15J-17W4-1a

description: Genotype of YYy310.9-G1-15J-17W4-1a

source_name: cell culture of strain YYy310.9-G1-15J-17W4-1a


title: YYy311spont32W1

description: Genotype of YYy311spont32W1

source_name: cell culture of strain YYy311spont32W1

source_name: cell culture of JSC24-2


title: YYy311spont32R1

description: Genotype of YYy311spont32R1

source_name: cell culture of strain YYy311spont32R1


title: YYy311spont32R6-1a

description: Genotype of YYy311spont32R6-1a

source_name: cell culture of strain YYy311spont32R6-1a


title: YYy311spont32W1-4a

description: Genotype of YYy311spont32W1-4a

source_name: cell culture of strain YYy311spont32W1-4a


title: ptoluidine60_rep1

source_name: liver, ptoluidine 60mg/kg


title: YYy310spont4W1-3

description: Genotype of YYy310spont4W1-3

source_name: cell culture of strain YYy310spont4W1-3


title: LH Melanoma

source_name: Melanoma

value: LH


title: YYy310.9-G1-15J-17W1

description: Genotype of YYy310.9-G1-15J-17W1

source_name: cell culture of strain YYy310.9-G1-15J-17W1


title: YYy310spont4R3-4a

description: Genotype of YYy310spont4R3-4a

source_name: cell culture of strain YYy310spont4R3-4a


title: ptoluidine60_rep2


title: YYy310.9-G1-15J-17W1-1a

description: Genotype of YYy310.9-G1-15J-17W1-1a

source_name: cell culture of strain YYy310.9-G1-15J-17W1-1a


title: YYy311spont32R1-1a

description: Genotype of YYy311spont32R1-1a

source_name: cell culture of strain YYy311spont32R1-1a


title: ptoluidine60_rep3


title: ptoluidine20_rep4

description: ptoluidine treated 20 mg/kg R. norvegicus sample

source_name: liver, ptoluidine 20mg/kg


title: ptoluidine20_rep5


title: ptoluidine20_rep3


title: YYy310spont4R3

description: Genotype of YYy310spont4R3

source_name: cell culture of strain YYy310spont4R3


title: YYy311spont30W3-7a

description: Genotype of YYy311spont30W3-7a

source_name: cell culture of strain YYy311spont30W3-7a


title: YYy311spont30W3

description: Genotype of YYy311spont30W3

source_name: cell culture of strain YYy311spont30W3


title: ptoluidine20_rep1


title: ptoluidine6_rep5

description: ptoluidine treated 6 mg/kg R. norvegicus sample

source_name: liver, ptoluidine 6mg/kg


title: YYy310.9-G1-15J-17R3

description: Genotype of YYy310.9-G1-15J-17R3

source_name: cell culture of strain YYy310.9-G1-15J-17R3


title: YYy311spont30W1

description: Genotype of YYy311spont30W1

source_name: cell culture of strain YYy311spont30W1

source_name: cell culture of JSC24-2


title: YYy310spont4R1-1

description: Genotype of YYy310spont4R1-1

source_name: cell culture of strain YYy310spont4R1-1


title: YYy310.9-G1-15J-17R1

description: Genotype of YYy310.9-G1-15J-17R1

source_name: cell culture of strain YYy310.9-G1-15J-17R1


title: YYy310.9-G1-15J-17R3-1a

description: Genotype of YYy310.9-G1-15J-17R3-1a

source_name: cell culture of strain YYy310.9-G1-15J-17R3-1a


title: YYy310spont38W1

description: Genotype of YYy310spont38W1

source_name: cell culture of strain YYy310spont38W1


title: ptoluidine20_rep2


title: YYy310spont4R1

description: Genotype of YYy310spont4R1

source_name: cell culture of strain YYy310spont4R1


title: YYy310spont38W5

description: Genotype of YYy310spont38W5

source_name: cell culture of strain YYy310spont38W5


title: YYy311spont30R2

description: Genotype of YYy311spont30R2

source_name: cell culture of strain YYy311spont30R2


title: YYy310spont38W5-6

description: Genotype of YYy310spont38W5-6

source_name: cell culture of strain YYy310spont38W5-6


title: YYy311spont30W1-1a

description: Genotype of YYy311spont30W1-1a

source_name: cell culture of strain YYy311spont30W1-1a


title: YYy310.9-G1-15J-17R1-1a

description: Genotype of YYy310.9-G1-15J-17R1-1a

source_name: cell culture of strain YYy310.9-G1-15J-17R1-1a


title: YYy310spont38R2

description: Genotype of YYy310spont38R2

source_name: cell culture of strain YYy310spont38R2


title: YYy310spont38R2-1

description: Genotype of YYy310spont38R2-1

source_name: cell culture of strain YYy310spont38R2-1


title: YYy310spont38W1-1

description: Genotype of YYy310spont38W1-1

source_name: cell culture of strain YYy310spont38W1-1


title: YYy310spont38R1-3

description: Genotype of YYy310spont38R1-3

source_name: cell culture of strain YYy310spont38R1-3


title: YYy310spont1W2

description: Genotype of YYy310spont1W2

source_name: cell culture of strain YYy310spont1W2


title: YYy310.9-G1-15J-12W1-2a

description: Genotype of YYy310.9-G1-15J-12W1-2a

source_name: cell culture of strain YYy310.9-G1-15J-12W1-2a


title: YYy310.9-G1-15J-12R5

description: Genotype of YYy310.9-G1-15J-12R5

source_name: cell culture of strain YYy310.9-G1-15J-12R5

source_name: cell culture of JSC24-2


title: YYy310.9-G1-15J-12W1

description: Genotype of YYy310.9-G1-15J-12W1

source_name: cell culture of strain YYy310.9-G1-15J-12W1


title: YYy310.9-G1-15J-12W7-2b

description: Genotype of YYy310.9-G1-15J-12W7-2b

source_name: cell culture of strain YYy310.9-G1-15J-12W7-2b


title: YYy310.9-G1-15J-12W7

description: Genotype of YYy310.9-G1-15J-12W7

source_name: cell culture of strain YYy310.9-G1-15J-12W7


title: YYy310spont38R1

description: Genotype of YYy310spont38R1

source_name: cell culture of strain YYy310spont38R1


title: ptoluidine6_rep1

source_name: liver, ptoluidine 6mg/kg


title: ptoluidine1_rep2

description: ptoluidine treated 1 mg/kg R. norvegicus sample

source_name: liver, ptoluidine 1mg/kg


title: ptoluidine6_rep2


title: ptoluidine1_rep5


title: ptoluidine6_rep4


title: YYy311spont30R1-1a

description: Genotype of YYy311spont30R1-1a

source_name: cell culture of strain YYy311spont30R1-1a


title: YYy311spont27W1

description: Genotype of YYy311spont27W1

source_name: cell culture of strain YYy311spont27W1


title: YYy310.9-G1-15J-12R5-1a

description: Genotype of YYy310.9-G1-15J-12R5-1a

source_name: cell culture of strain YYy310.9-G1-15J-12R5-1a


title: YYy311spont30R2-1a

description: Genotype of YYy311spont30R2-1a

source_name: cell culture of strain YYy311spont30R2-1a


title: ptoluidine1_rep4


title: ptoluidine6_rep3


title: ptoluidine1_rep3


title: YYy311spont27W2

description: Genotype of YYy311spont27W2

source_name: cell culture of strain YYy311spont27W2


title: YYy311spont27W2-1a

description: Genotype of YYy311spont27W2-1a

source_name: cell culture of strain YYy311spont27W2-1a


title: YYy311spont30R1

description: Genotype of YYy311spont30R1

source_name: cell culture of strain YYy311spont30R1


title: ptoluidine1_rep1


title: YYy311spont27W1-18

description: Genotype of YYy311spont27W1-18

source_name: cell culture of strain YYy311spont27W1-18


title: YYy310.9-G1-15J-12R3

description: Genotype of YYy310.9-G1-15J-12R3

source_name: cell culture of strain YYy310.9-G1-15J-12R3


title: ptoluidine_Veh_rep5

description: R. norvegicus ptoluidine vehicle control sample

source_name: liver, ptoluidine vehicle control

value: ptoluidine vehicle control

value: control


title: YYy310spont1W2-2

description: Genotype of YYy310spont1W2-2

source_name: cell culture of strain YYy310spont1W2-2

source_name: cell culture of JSC24-2


title: ptoluidine_Veh_rep4


title: YYy310.9-G1-15J-12R3-2a

description: Genotype of YYy310.9-G1-15J-12R3-2a

source_name: cell culture of strain YYy310.9-G1-15J-12R3-2a


title: YYy310spont1W1

description: Genotype of YYy310spont1W1

source_name: cell culture of strain YYy310spont1W1


title: YYy310.10-G1-15J-23W3

description: Genotype of YYy310.10-G1-15J-23W3

source_name: cell culture of strain YYy310.10-G1-15J-23W3


title: YYy310spont1W1-2

description: Genotype of YYy310spont1W1-2

source_name: cell culture of strain YYy310spont1W1-2


title: YYy311spont27R3

description: Genotype of YYy311spont27R3

source_name: cell culture of strain YYy311spont27R3


title: ptoluidine_Veh_rep3


title: ptoluidine_Veh_rep2


title: YYy311spont27R3-1a

description: Genotype of YYy311spont27R3-1a

source_name: cell culture of strain YYy311spont27R3-1a


title: YYy311spont27R1

description: Genotype of YYy311spont27R1

source_name: cell culture of strain YYy311spont27R1


title: YYy310.10-G1-15J-23W1

description: Genotype of YYy310.10-G1-15J-23W1

source_name: cell culture of strain YYy310.10-G1-15J-23W1


title: YYy310.10-G1-15J-23W3-2a

description: Genotype of YYy310.10-G1-15J-23W3-2a

source_name: cell culture of strain YYy310.10-G1-15J-23W3-2a


title: YYy310spont1R1-1

description: Genotype of YYy310spont1R1-1

source_name: cell culture of strain YYy310spont1R1-1


title: YYy310.10-G1-15J-23W1-1a

description: Genotype of YYy310.10-G1-15J-23W1-1a

source_name: cell culture of strain YYy310.10-G1-15J-23W1-1a


title: YYy310spont1R3-1

description: Genotype of YYy310spont1R3-1

source_name: cell culture of strain YYy310spont1R3-1


title: YYy311spont25W2

description: Genotype of YYy311spont25W2

source_name: cell culture of strain YYy311spont25W2


title: YYy310.10-G1-15J-23R6

description: Genotype of YYy310.10-G1-15J-23R6

source_name: cell culture of strain YYy310.10-G1-15J-23R6


title: YYy310.10-G1-15J-23R7

description: Genotype of YYy310.10-G1-15J-23R7

source_name: cell culture of strain YYy310.10-G1-15J-23R7


title: YYy310.10-G1-15J-23R7-1a

description: Genotype of YYy310.10-G1-15J-23R7-1a

source_name: cell culture of strain YYy310.10-G1-15J-23R7-1a


title: YYy311spont27R1-1a

description: Genotype of YYy311spont27R1-1a

source_name: cell culture of strain YYy311spont27R1-1a

source_name: cell culture of JSC24-2


title: YYy311spont25W1

description: Genotype of YYy311spont25W1

source_name: cell culture of strain YYy311spont25W1


title: YYy311spont25W1-3a

description: Genotype of YYy311spont25W1-3a

source_name: cell culture of strain YYy311spont25W1-3a


title: YYy310.10-G1-15J-23R6-3a

description: Genotype of YYy310.10-G1-15J-23R6-3a

source_name: cell culture of strain YYy310.10-G1-15J-23R6-3a


title: YYy311spont25SP3-1a

description: Genotype of YYy311spont25SP3-1a

source_name: cell culture of strain YYy311spont25SP3-1a


title: YYy310spont1R3

description: Genotype of YYy310spont1R3

source_name: cell culture of strain YYy310spont1R3


title: YYy310spont1R1

description: Genotype of YYy310spont1R1

source_name: cell culture of strain YYy310spont1R1


title: DMPT120_rep5

description: DMPT treated 120 mg/kg R. norvegicus sample

source_name: liver, DMPT 120mg/kg

value: DMPT


title: DMPT120_rep3


title: YYy310.10-G1-15J-18W4

description: Genotype of YYy310.10-G1-15J-18W4

source_name: cell culture of strain YYy310.10-G1-15J-18W4


title: YYy311spont25W2-1a

description: Genotype of YYy311spont25W2-1a

source_name: cell culture of strain YYy311spont25W2-1a


title: YYy310.10-G1-15J-18W4-9a

description: Genotype of YYy310.10-G1-15J-18W4-9a

source_name: cell culture of strain YYy310.10-G1-15J-18W4-9a


title: YYy310.10-G1-15J-18W1

description: Genotype of YYy310.10-G1-15J-18W1

source_name: cell culture of strain YYy310.10-G1-15J-18W1


title: DMPT120_rep2


title: YYy311spont25SP17-2a

description: Genotype of YYy311spont25SP17-2a

source_name: cell culture of strain YYy311spont25SP17-2a


title: DMPT120_rep4


title: DMPT60_rep5

description: DMPT treated 60 mg/kg R. norvegicus sample

source_name: liver, DMPT 60mg/kg


title: DMPT60_rep4


title: ptoluidine_Veh_rep1

source_name: liver, ptoluidine vehicle control


title: YYy311spont21W4

description: Genotype of YYy311spont21W4

source_name: cell culture of strain YYy311spont21W4


title: YYy311spont25R3-2a

description: Genotype of YYy311spont25R3-2a

source_name: cell culture of strain YYy311spont25R3-2a


title: DMPT120_rep1


title: YYy310.10-G1-15J-18W1-13a

description: Genotype of YYy310.10-G1-15J-18W1-13a

source_name: cell culture of strain YYy310.10-G1-15J-18W1-13a

source_name: cell culture of JSC24-2


title: YYy311spont21W4-14a

description: Genotype of YYy311spont21W4-14a

source_name: cell culture of strain YYy311spont21W4-14a


title: YYy311spont25SP17

description: Genotype of YYy311spont25SP17

source_name: cell culture of strain YYy311spont25SP17


title: YYy310.10-G1-15J-18R2-1a

description: Genotype of YYy310.10-G1-15J-18R2-1a

source_name: cell culture of strain YYy310.10-G1-15J-18R2-1a


title: YYy311spont21W1

description: Genotype of YYy311spont21W1

source_name: cell culture of strain YYy311spont21W1


title: YYy310.10-G1-15J-18R2

description: Genotype of YYy310.10-G1-15J-18R2

source_name: cell culture of strain YYy310.10-G1-15J-18R2


title: YYy310.10-G1-15J-18R1

description: Genotype of YYy310.10-G1-15J-18R1

source_name: cell culture of strain YYy310.10-G1-15J-18R1


title: DMPT60_rep2


title: DMPT60_rep1


title: DMPT60_rep3


title: YYy310.10-G1-15J-18R1-1a

description: Genotype of YYy310.10-G1-15J-18R1-1a

source_name: cell culture of strain YYy310.10-G1-15J-18R1-1a


title: YYy310.10-G1-15J-17W2

description: Genotype of YYy310.10-G1-15J-17W2

source_name: cell culture of strain YYy310.10-G1-15J-17W2


title: YYy311spont21R2-1a

description: Genotype of YYy311spont21R2-1a

source_name: cell culture of strain YYy311spont21R2-1a


title: YYy311spont21R2

description: Genotype of YYy311spont21R2

source_name: cell culture of strain YYy311spont21R2


title: YYy311spont21W1-1a

description: Genotype of YYy311spont21W1-1a

source_name: cell culture of strain YYy311spont21W1-1a


title: YYy311spont21R1-1a

description: Genotype of YYy311spont21R1-1a

source_name: cell culture of strain YYy311spont21R1-1a


title: YYy310.10-G1-15J-17W1-1a

description: Genotype of YYy310.10-G1-15J-17W1-1a

source_name: cell culture of strain YYy310.10-G1-15J-17W1-1a


title: DMPT20_rep3

description: DMPT treated 20 mg/kg R. norvegicus sample

source_name: liver, DMPT 20mg/kg


title: YYy310.10-G1-15J-17W1

description: Genotype of YYy310.10-G1-15J-17W1

source_name: cell culture of strain YYy310.10-G1-15J-17W1


title: YYy311spont21R1

description: Genotype of YYy311spont21R1

source_name: cell culture of strain YYy311spont21R1


title: DMPT20_rep5


title: YYy310.10-G1-15J-17W2-1a

description: Genotype of YYy310.10-G1-15J-17W2-1a

source_name: cell culture of strain YYy310.10-G1-15J-17W2-1a

source_name: cell culture of JSC24-2


title: YYy310.10-G1-15J-17R9-3a

description: Genotype of YYy310.10-G1-15J-17R9-3a

source_name: cell culture of strain YYy310.10-G1-15J-17R9-3a


title: YYy311spont10W2

description: Genotype of YYy311spont10W2

source_name: cell culture of strain YYy311spont10W2


title: YYy310.10-G1-15J-17R9

description: Genotype of YYy310.10-G1-15J-17R9

source_name: cell culture of strain YYy310.10-G1-15J-17R9


title: YYy311spont10W2-1a

description: Genotype of YYy311spont10W2-1a

source_name: cell culture of strain YYy311spont10W2-1a


title: YYy311spont10W1

description: Genotype of YYy311spont10W1

source_name: cell culture of strain YYy311spont10W1


title: YYy310.10-G1-15J-17R1

description: Genotype of YYy310.10-G1-15J-17R1

source_name: cell culture of strain YYy310.10-G1-15J-17R1


title: DMPT20_rep1


title: DMPT20_rep4


title: YYy310.10-G1-15J-17R1-1a

description: Genotype of YYy310.10-G1-15J-17R1-1a

source_name: cell culture of strain YYy310.10-G1-15J-17R1-1a


title: DMPT6_rep4

description: DMPT treated 6 mg/kg R. norvegicus sample

source_name: liver, DMPT 6mg/kg


title: DMPT6_rep5


title: DMPT20_rep2


title: DMPT6_rep3


title: DMPT6_rep2


title: YYy310.10-G1-15J-14W2

description: Genotype of YYy310.10-G1-15J-14W2

source_name: cell culture of strain YYy310.10-G1-15J-14W2


title: YYy311spont10R2-1a

description: Genotype of YYy311spont10R2-1a

source_name: cell culture of strain YYy311spont10R2-1a


title: YYy311spont10R1-1a

description: Genotype of YYy311spont10R1-1a

source_name: cell culture of strain YYy311spont10R1-1a


title: YYy310.10-G1-15J-14W2-1a

description: Genotype of YYy310.10-G1-15J-14W2-1a

source_name: cell culture of strain YYy310.10-G1-15J-14W2-1a


title: YYy311spont10W1-1a

description: Genotype of YYy311spont10W1-1a

source_name: cell culture of strain YYy311spont10W1-1a


title: YYy310.10-G1-15J-14R2

description: Genotype of YYy310.10-G1-15J-14R2

source_name: cell culture of strain YYy310.10-G1-15J-14R2


title: YYy310.10-G1-15J-14W1-2a

description: Genotype of YYy310.10-G1-15J-14W1-2a

source_name: cell culture of strain YYy310.10-G1-15J-14W1-2a


title: YYy310.10-G1-15J-14R2-1a

description: Genotype of YYy310.10-G1-15J-14R2-1a

source_name: cell culture of strain YYy310.10-G1-15J-14R2-1a


title: YYy310.10-G1-15J-14W1

description: Genotype of YYy310.10-G1-15J-14W1

source_name: cell culture of strain YYy310.10-G1-15J-14W1

source_name: cell culture of JSC24-2


title: DMPT1_rep4

description: DMPT treated 1 mg/kg R. norvegicus sample

source_name: liver, DMPT 1mg/kg


title: YYy311spont10R2

description: Genotype of YYy311spont10R2

source_name: cell culture of strain YYy311spont10R2


title: YYy311spont10R1

description: Genotype of YYy311spont10R1

source_name: cell culture of strain YYy311spont10R1


title: DMPT1_rep3


title: DMPT1_rep1


title: DMPT_Veh_rep4

description: R. norvegicus DMPT vehicle control sample

source_name: liver, DMPT vehicle control

value: DMPT vehicle control


title: YYy310.10-G1-15J-14R1-1a

description: Genotype of YYy310.10-G1-15J-14R1-1a

source_name: cell culture of strain YYy310.10-G1-15J-14R1-1a


title: DMPT1_rep2


title: DMPT_Veh_rep2


title: DMPT1_rep5


title: YYy310.10-G1-15J-14R1

description: Genotype of YYy310.10-G1-15J-14R1

source_name: cell culture of strain YYy310.10-G1-15J-14R1


title: DMPT_Veh_rep3


title: DMPT_Veh_rep5


title: DMPT6_rep1

source_name: liver, DMPT 6mg/kg


title: Touch-petiole base rep3

status: Public on Jun 26 2017

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: The samples were hybridized to the Affymetrix Gene 1.1 ST Arabidopsis Array Plate and washed on an Affymetrix GeneAtlas system followed by scanning of arrays at AROS Applied Biotechnology (http://arosab.com/services/microarrays/gene-expression/).

scan_protocol: Array scanning has deen done according to the instruction of the manufacturer (Affymetrix).

data_processing: Data analysis was performed by using the R environment and Bioconductor.

organism: Arabidopsis thaliana

source_name: Arabidopsis petiole base, Touch

label_protocol: Single-stranded cDNA was generated from the amplified cRNA, fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (140 µmol / m2 / s, 20°C, 70% RH, R:FR 2.3), 15 h dark) where they were transferred to individual pots 11 d after sowing and grew another 17 d.

extract_protocol: The lamina tip (top 2.5 mm) and petiole base (basal 1.5 mm) of the fifth-youngest leaf plants were harvested for RNA isolation after 5 h of light treatments (W (control), W+FRtip, W+FRwhole). Total RNA was isolated from the tissue by using the RNeasy plant mini kit (Qiagen Germany). 3 independent biological replicates per treatment X tissue combination.

treatment_protocol: Plants were grown single in pots. Leaf tip and petiole base from the same leaf of 28 d old plants were harvested 5h after start of the light or the touch treatments (white light or touch  (PAR: 140 µmol / m2 / s and R:FR 2.3. local FR or Whole FR condition (PAR: 140 µmol / m2 / s and R:FR 2.3 and R:FR 0,05 in the leaf tip or the the whole rosette plant respectively)

value: petiole base

tag: treatment

value: Touch


title: Local FR-petiole base rep2

source_name: Arabidopsis petiole base, Local FR

value: Local FR


title: Whole FR-petiole base rep3

source_name: Arabidopsis petiole base, Whole FR

value: Whole FR


title: Local FR-leaf tip rep3

source_name: Arabidopsis leaf tip, Local FR

value: leaf tip


title: DMPT_Veh_rep1

value: liver


title: Whole FR-leaf tip rep2

source_name: Arabidopsis leaf tip, Whole FR


title: Touch-leaf tip rep3

source_name: Arabidopsis leaf tip, touch


title: Control-petiole base rep3

source_name: Arabidopsis petiole base, Control

value: Control


title: Local FR-petiole base rep3


title: Touch-petiole base re2


title: Whole FR-leaf tip rep3


title: Local FR-leaf tip rep2


title: Whole FR-petiole base rep2


title: Local FR-petiole base rep1


title: Control-leaf tip rep2

source_name: Arabidopsis leaf tip, Control


title: Touch-leaf tip rep2


title: Touch-petiole base rep1


title: Touch-leaf tip rep1


title: Control-petiole base rep1


title: Local FR-leaf tip rep1


title: Whole FR-petiole base rep1


title: Whole FR-leaf tip rep1


title: Control-leaf tip rep1


title: shR-ING5_1

status: Public on Jun 24 2017

city: Vancouver

first: Fangwu

last: Wang

address: 675 W 10th Ave

country: Canada

institute: UBC

hyb_protocol: Labelled cDNA is hybridized to the Gene 2.0 ST arrays and washed, stained using the fluidics station.

scan_protocol: Stained Gene 2.0 ST arrays are scanned by the scanner.

data_processing:
Probe cell intensity data (CEL) from arrays are analyzed in the Affymetrix Expression Console software at gene level. CHP files are created using iterplier algorithm. Gene level differential expression analysis is performed by Affymetrix Transcriptome Console software.
affymetrix-algorithm-name = iterplier-gene-full
affymetrix-algorithm-version = 2.0
affymetrix-array-type = HuGene-2_0-st
program-name = Expression Console
program-version = 1.4.1.46

source_name: Glioblastoma

label_protocol: 400ng RNA from each sample is used for cDNA amplification and labeling. Sense RNA is synthesized using an amplication kit and further labelled with biotin at fragmented double-stranded cDNA ends.

growth_protocol: shRNA BTIC lines are grown and maintained in serum free medium supplemented with FGF, EGF and Heparin.

extract_protocol: Total RNA was isolated by phenol chloroform extraction and genome DNA removed by RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: shRNA BTIC lines are induced by doxycycline for seven days for optimal shRNA expression.

tag: cell line

value: Brain Tumor Initiating Cell Line (BTICs)

tag: tissue source

value: brain; glioblastoma

tag: genotype/variation

value: shRNA targeting ING5


title: CD34+CD38-CD133+GPI-80+_rep3

status: Public on Jun 23 2017

city: Hirakata

first: Yoshikazu

last: Matsuoka

address: 2-5-1 shinmachi

country: Japan

institute: Kansai Medical University

hyb_protocol: 1 - 6.5 ng of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) （the Agilent DNA Microarray Scanner (G2565CA)）using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1（10.10.1.1） (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Cord Blood

label_protocol: cDNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from 20ng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0ug cDNA using SureTag Complete DNA Labeling Kit (Agilent) （Genomic DNA Enzymatic Labeling Kit (Agilent)）according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA from 3.4 x 10^4 to 5 x 10^4 18Lin-CD34+CD38-CD133+GPI-80+, 18Lin-CD34-CD133+GPI-80+ and 18Lin-CD34+CD38-CD133- cells were extracted using an RNeasy Plus Micro kit (QIAGEN).

treatment_protocol: Eighteen Lin-CD34+CD38-CD133+GPI-80+, 18Lin-CD34-CD133+GPI-80+ and 18Lin-CD34+CD38-CD133- cells were isolated from human cord blood using FACS.

value: Human cord blood

tag: cell population

tag: cell type

value: CD34+ HSC


title: CD34+CD133-_rep3

value: non-HSC


title: CD34+CD133-_rep2


title: shR-ING5_2


title: CD34-CD133+GPI-80+_rep2

value: CD34- HSC


title: CD34-CD133+GPI-80+_rep3


title: Control-petiole base rep2


title: shR-ctr_1

value: control shRNA


title: shR-ctr_2


title: CD34+CD38-CD133+GPI-80+_rep2


title: Lesional Skin Biopsy [45583004502_D57]

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

description: Sample name: 57

hyb_protocol: Labeled samples were hybridized to GeneChip HT_HG-U133+PM microarrays.

scan_protocol: Hybridizaed microarrays were scanned using a GeneTitan instrument (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Lesional Skin Biopsy

label_protocol: Labeled complementary DNA was generated using a NuGEN Ovation kit (NuGen Technologies) according to the manufacturer's instructions.

extract_protocol: Frozen skin samples were disrupted with a Multi-Sample Bio Pulverizer (Research Products International) and homogenized with a TissueRuptor (Qiagen). Total RNA was isolated using the mirVana Micro-RNA Isolation kit (Applied Biosystems), modified to include on-column DNase treatment with RNase-free DNase (Qiagen).

treatment_protocol: The study was designed as a phase I randomized, double-blind, placebo-controlled crossover study of the pharmacodynamics, safety, and clinical efficacy of AMG 811 in patients with DLE. Patients received a single subcutaneous dose of AMG 811 (180 mg) or placebo. The patients in sequence 1 received AMG 811 followed by placebo, while those in sequence 2 received placebo followed by AMG 811.

value: skin

tag: diagnosis

value: Discoid Lupus Erythematosus

tag: skin lesion status

value: Lesional

tag: sbj

tag: visit name

value: 0 mg

tag: sequence

value: Placebo on Day 1 followed by AMG811 (D85)


title: Lesional Skin Biopsy [45583002001_D15]

description: Sample name: 60

tag: tissue

value: AMG811 on Day 1 followed by Placebo (D85)


title: Lesional Skin Biopsy [45583002001_D-1]

description: Sample name: 58


title: CD34-CD133+GPI-80+_rep1


title: Non-lesional Skin Biopsy [45583002001_D-1]

description: Sample name: 59

source_name: Non-lesional Skin Biopsy

value: Non-lesional


title: Lesional Skin Biopsy [45583002000_D15]

description: Sample name: 52


title: Non-lesional Skin Biopsy [45583004502_D-1]

description: Sample name: 55


title: Lesional Skin Biopsy [45583004502_D15]

description: Sample name: 56


title: MHAE003_MOCK_36HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 2

value: Primary human airway epithelial cells

tag: time

tag: virus

value: Mock


title: Lesional Skin Biopsy [45583004501_D57]

description: Sample name: 49


title: CD34+CD133-_rep1


title: Lesional Skin Biopsy [45583002000_D57]

description: Sample name: 53


title: Non-lesional Skin Biopsy [45583002000_D-1]

description: Sample name: 51


title: Lesional Skin Biopsy [45583004502_D-1]

description: Sample name: 54


title: Lesional Skin Biopsy [45583004501_D15]

description: Sample name: 48


title: Lesional Skin Biopsy [45583002000_D-1]

description: Sample name: 50


title: Non-lesional Skin Biopsy [45583004501_D-1]

description: Sample name: 47


title: CD34+CD38-CD133+GPI-80+_rep1


title: Lesional Skin Biopsy [45583002504_D57]

description: Sample name: 43


title: Lesional Skin Biopsy [45583004501_D-1]

description: Sample name: 46


title: Lesional Skin Biopsy [45583002504_D15]

description: Sample name: 42


title: Control-leaf tip rep3

value: leaf tip

value: Control


title: Lesional Skin Biopsy [45583002502_D57]

description: Sample name: 31


title: Lesional Skin Biopsy [45583002504_D-1]

description: Sample name: 40


title: Lesional Skin Biopsy [45583002502_D15]

description: Sample name: 30


title: Lesional Skin Biopsy [45583002503_D15]

description: Sample name: 39


title: Non-lesional Skin Biopsy [45583002503_D-1]

description: Sample name: 33


title: Non-lesional Skin Biopsy [45583004500_D-1]

description: Sample name: 45


title: Non-lesional Skin Biopsy [45583002502_D-1]

description: Sample name: 29


title: Non-lesional Skin Biopsy [45583002504_D-1]

description: Sample name: 41


title: Lesional Skin Biopsy [45583001500_D-1]

description: Sample name: 35


title: Non-lesional Skin Biopsy [45583001500_D-1]

description: Sample name: 36


title: Lesional Skin Biopsy [45583001500_D15]

description: Sample name: 37


title: Lesional Skin Biopsy [45583002503_D-1]

description: Sample name: 32


title: Lesional Skin Biopsy [45583001500_D57]

description: Sample name: 38


title: Lesional Skin Biopsy [45583002502_D-1]

description: Sample name: 28


title: Lesional Skin Biopsy [45583001001_D-1]

description: Sample name: 24


title: Lesional Skin Biopsy [45583002503_D57]

description: Sample name: 34


title: Lesional Skin Biopsy [45583001001_D57]

description: Sample name: 27


title: Lesional Skin Biopsy [45583001001_D15]

description: Sample name: 26


title: Lesional Skin Biopsy [45583004500_D-1]

description: Sample name: 44


title: Lesional Skin Biopsy [45583002501_D15]_2

description: Sample name: 23


title: Non-lesional Skin Biopsy [45583002501_D-1]_2

description: Sample name: 22


title: Lesional Skin Biopsy [45583002501_D-1]_2

description: Sample name: 21


title: Lesional Skin Biopsy [45583002501_D15]_1

description: Sample name: 19


title: Non-lesional Skin Biopsy [45583002501_D-1]_1

description: Sample name: 18


title: Non-lesional Skin Biopsy [45583001001_D-1]

description: Sample name: 25


title: Lesional Skin Biopsy [45583002501_D57]

description: Sample name: 20


title: MP_CD64+_rep1

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Macrophages from SI, CD64+

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: Macrophage, CD64+

label_protocol: Affymetrix WT Terminal Labeling Kit

extract_protocol: Small Intestines were excised from steady state mice. Fat and Peyer's patches were removed and guts were then open longitudinally and cut into pieces of ~5mm. Epithelial cells were removed by 2 x 20 min incubations in HBSS 2mM EDTA at 37C. Lamina Proporia cells were then isolated via digestion with 0.8mg/ml Collagenase VIII and 30ug/ml DNase (20-30mins at 37C). Cell suspensions were filtered over a 40um filter and cells were stained for FACS.

value: Small Intestine


title: Lesional Skin Biopsy [45583001000_D-1]

description: Sample name: 9


title: Non-lesional Skin Biopsy [45583000503_D-1]

description: Sample name: 6


title: Non-lesional Skin Biopsy [45583002500_D-1]

description: Sample name: 14


title: DC_CD64-CD103-CD11b+_rep3

description: Dendritic cell from SI, CD64-CD103-CD11b+

source_name: Dendritic cell, CD64-CD103-CD11b+


title: Lesional Skin Biopsy [45583002500_D15]

description: Sample name: 15


title: DC_CD64-CD103-CD11b-_rep1

description: Dendritic cell from SI, CD64-CD103-CD11b-

source_name: Dendritic cell, CD64-CD103-CD11b-


title: Lesional Skin Biopsy [45583000500_D15]

description: Sample name: 3


title: Lesional Skin Biopsy [45583001000_D57]

description: Sample name: 12


title: DC_CD64-CD103-CD11b-_rep3


title: MP_CD64+_rep2

description: Macrophages from SI, CD64+


title: Lesional Skin Biopsy [45583002501_D-1]_1

description: Sample name: 17


title: Non-lesional Skin Biopsy [45583000500_D-1]

description: Sample name: 2


title: Lesional Skin Biopsy [45583000503_D57]

description: Sample name: 8


title: Lesional Skin Biopsy [45583000503_D-1]

description: Sample name: 5


title: MP_CD64+_rep3

description: Macrophages from SI, CD64+


title: DC_CD64-CD103+CD11b-_rep3

description: Dendritic cell from SI, CD64-CD103+CD11b-

source_name: Dendritic cell, CD64-CD103+CD11b-


title: DC_CD64-CD103-CD11b-_rep2


title: Lesional Skin Biopsy [45583001000_D15]

description: Sample name: 11


title: DC_CD64-CD103-CD11b+_rep2


title: Lesional Skin Biopsy [45583002500_D57]

description: Sample name: 16


title: Lesional Skin Biopsy [45583000500_D57]

description: Sample name: 4


title: Lesional Skin Biopsy [45583000500_D-1]

description: Sample name: 1


title: Non-lesional Skin Biopsy [45583001000_D-1]

description: Sample name: 10


title: Lesional Skin Biopsy [45583000503_D15]

description: Sample name: 7


title: DC_CD64-CD103+CD11b-_rep2


title: DC_CD64-CD103-CD11b+_rep1


title: DC_CD64-CD103+CD11b+_rep3

description: Dendritic cell from SI, CD64-CD103+CD11b+

source_name: Dendritic cell, CD64-CD103+CD11b+


title: blood [91166005056_D57]

hyb_protocol: Overnight hybridizations at 65C per manufacturer’s instructions

scan_protocol: All arrays were scanned on the Agilent Surescaner Scanner (Agilent p/n G2600D). Agilent Scan Control Software version 9.1.5.1 was used for array scanning. Array files were processed using Agilent Feature Extraction software 11.0.1.1.

data_processing: The scanned images were analyzed using default parameters (protocol GE1-v1_91 and Grid: 026822_D_F_20100209) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Blood

label_protocol: Samples were labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color (Agilent Cat # 5188-5339) per manufacturer’s instructions.

extract_protocol: Total RNA was isolated from PAXgene whole blood tubes (BD Cat # 762165) using the PAXgene RNA Kit. (Qiagen Cat # 762164) on the Qiacube automated sample prep system

value: blood


title: DC_CD64-CD103+CD11b-_rep1


title: Lesional Skin Biopsy [45583002500_D-1]

description: Sample name: 13


title: blood [91166009052_D15]


title: blood [91166005056_D-1]


title: blood [91166005059_D-1]


title: blood [91166009052_D1.6]


title: blood [91166005057_D2]


title: blood [91166009052_D2]


title: blood [91166009052_D141]


title: blood [91166005056_D2]


title: DC_CD64-CD103+CD11b+_rep2


title: blood [91166005057_D113]


title: DC_CD64-CD103+CD11b+_rep1


title: blood [91166009052_D113]


title: blood [91166005059_D197]


title: blood [91166005059_D141]


title: blood [91166009055_D2]


title: blood [91166005057_D1.6]


title: blood [91166005057_D99]


title: blood [91166005057_D29]


title: blood [91166005057_D141]


title: blood [91166005056_D99]


title: blood [91166005056_D85]


title: blood [91166005056_D15]


title: blood [91166009052_D29]


title: blood [91166005057_D1]


title: blood [91166009052_D57]


title: blood [91166005056_D1]


title: blood [91166005059_D15]


title: blood [91166005057_D85.6]


title: blood [91166005057_D15]


title: blood [91166009052_D-1]


title: blood [91166009055_D1]


title: blood [91166009055_D29]


title: blood [91166005059_D85.6]


title: blood [91166005056_D29]


title: blood [91166009055_D57]


title: blood [91166005059_D29]


title: blood [91166005056_D141]


title: blood [91166005059_D99]


title: blood [91166005059_D85]


title: blood [91166005057_D197]


title: blood [91166005059_D1]


title: blood [91166005059_D1.6]


title: blood [91166009052_D1]


title: blood [91166005056_D113]


title: blood [91166005057_D-1]


title: blood [91166009052_D197]


title: blood [91166009055_D1.6]


title: blood [91166005056_D85.6]


title: blood [91166005057_D85]


title: blood [91166005057_D57]


title: blood [91166005056_D197]


title: blood [91166009052_D85]


title: blood [91166005059_D57]


title: blood [91166005056_D1.6]


title: blood [91166009055_D-1]


title: blood [91166002053_D99]


title: blood [91166005059_D2]


title: blood [91166002053_D85.6]


title: blood [91166002051_D1.6]


title: blood [91166009055_D15]


title: blood [91166001051_D99]


title: blood [91166005051_D29]


title: blood [91166003051_D85]


title: blood [91166005051_D2]


title: blood [91166002051_D85]


title: blood [91166002053_D197]


title: blood [91166005055_D1.6]


title: blood [91166005051_D15]


title: blood [91166005055_D2]


title: blood [91166005052_D141]


title: blood [91166003051_D1]


title: blood [91166005051_D197]


title: blood [91166002051_D57]


title: blood [91166005052_D113]


title: blood [91166005055_D-1]


title: blood [91166002051_D197]


title: blood [91166005051_D85.6]


title: blood [91166002051_D141]


title: blood [91166005055_D85.6]


title: blood [91166001051_D113]


title: blood [91166002053_D1.6]


title: blood [91166005052_D1.6]


title: blood [91166003051_D197]


title: blood [91166003051_D29]


title: blood [91166005055_UNSCH]

value: UNSCH


title: blood [91166001051_D15]


title: blood [91166002053_D57]


title: blood [91166005051_D85]


title: blood [91166002053_D29]


title: blood [91166005055_D29]


title: blood [91166003051_D141]


title: blood [91166005051_D1.6]


title: blood [91166003051_UNSCH]


title: blood [91166001051_D197]


title: blood [91166005055_D57]


title: blood [91166005051_D99]


title: blood [91166005052_D-1]


title: blood [91166003051_D85.6]


title: blood [91166005051_D1]


title: blood [91166002053_D2]


title: blood [91166005055_D1]


title: blood [91166002051_D2]


title: blood [91166005055_D85]


title: blood [91166002053_D-1]


title: blood [91166005055_D15]


title: blood [91166001051_D57]


title: blood [91166001056_D29]


title: blood [91166002051_D85.6]


title: blood [91166005055_D141]


title: blood [91166005055_D197]


title: blood [91166005052_D1]


title: blood [91166001056_D85]


title: blood [91166005052_D15]


title: blood [91166003051_D-1]


title: blood [91166001051_D1]


title: blood [91166002051_D29]


title: blood [91166001056_D2]


title: blood [91166005051_D113]


title: blood [91166002051_D-1]


title: blood [91166005052_D99]


title: blood [91166003051_D113]


title: blood [91166002053_D113]


title: blood [91166005052_D57]


title: blood [91166005052_D85.6]


title: blood [91166005055_D113]


title: blood [91166001056_D197]


title: blood [91166003051_D99]


title: blood [91166002053_D85]


title: blood [91166001056_D141]


title: blood [91166005052_D197]


title: blood [91166002051_D113]


title: blood [91166003051_D57]


title: blood [91166001056_D99]


title: blood [91166002053_D141]


title: blood [91166005051_D141]


title: blood [91166002053_D15]


title: blood [91166001051_D1.6]


title: blood [91166002053_D1]


title: blood [91166002051_D15]


title: blood [91166005051_D-1]


title: blood [91166005052_D85]


title: blood [91166002051_D99]


title: lung CD8 T cells d21post Mtb infection rep2

status: Public on Jun 22 2017

city: Hamilton

first: Zhou

last: Xing

state: Ontario

address: 1280 Main street

department: Pathology and molecular Medicine

institute: McMaster University

description: MoGene2_062215H_ZX8_d21-8.rma-gene-full-Signal

hyb_protocol: 16hr at 45C washing FS450_0002

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Preprocessing was done by using Affymetrix Expression Console Software 1.4: with RMA-Gene procedure; the values were Log2-transformed.

label: Biotin-allonamide Triphosphate

source_name: lung CD8 T cells d21 post Mtb infection

label_protocol: Biotin Allonamide Triphosphate

growth_protocol: mice were housed in a specific pathogen free level B facility at McMaster University.

extract_protocol: RNA from purified CD8 T cells was isolated using RNeasy® Mini Kit (Qiagen, Germantown, MD, USA) Sample preparation-Affymetrix WT PLUS kit

tag: strain

value: BALB/C

tag: Sex

value: Female

tag: age

value: lung CD8 T cells

tag: infected with

value: Mycobacterium tuberculosis

tag: time point

value: d21 post Mtb infection


title: blood [91166001051_D29]

value: Discoid Lupus Erythematosus


title: lung CD8 T cells d21 post Mtb infection rep3

description: MoGene2_062215H_ZX9_d21-9.rma-gene-full-Signal


title: lung CD8 T cells d7 post Mtb infection rep2

description: MoGene2_062215H_ZX5_d7-5.rma-gene-full-Signal

source_name: lung CD8 T cells d7 post Mtb infection

value: d7 post Mtb infection


title: lung CD8 T cells d21 post Mtb infection rep1

description: MoGene2_062215H_ZX7_d21-7.rma-gene-full-Signal


title: RPB11_alpha_30C

city: Madison

first: David

last: Brow

state: WI

address: 420 Henry Mall, Room 1135

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

description:
Two biological replicates:
RPB11_1_alpha_30C
RPB11_2_alpha_30C

hyb_protocol: The array hybridization to Affymetrix GeneChip S.cerevisiae Tiling 1.0R Array was performed as described in the Affymetrix manual.

scan_protocol: The tiling arrays were scanned by the Microarray Core Facility at the University of Virginia according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1) using parameters: two sided, 50 bp bandwidth and PM/MM. The normalized and smoothed RNA levels of each sample were calculated following the TAS user guide available on the Affymetrix website. The intensities on the arrays of the two biological replicates were quantile normalized, and then the data were linearly scaled to a target median intensity of 100. The S. cerevisiae Tiling 1.0R Array has paired perfect match (PM) and mismatch (MM) probes, and MM probes serve as background. TAS applied the Wilcoxon Signed-Rank test to the normalized log2(max(PMi-MMi,1)) value whose genomic coordinate i fell within a designated 101-bp smoothing window to calculate the log transformed probability (-10log10(p-value)) that the RNA was detected above the noise level. The associated Hodges-Lehmann estimator was used to compute the signal intensity. If the estimate s of signal location is over 1, it was transformed to log2(s) for the RNA level. Otherwise, 0 was assigned for the RNA level.
Sc3_updated.bpmap: The genomic map (BPMAP) file in Affymetrix Tiling Analysis Software (TAS) version 1.1 was used to analyze intensity data in the raw microarray CEL files and evaluate the signal for each interrogated genomic position. Because the S. cerevisiae Tiling 1.0R Array is based on the reference genome sequence UCSC sacCer1 (released Oct. 2003) and there have been changes in later versions, the UCSC sacCer3 sequence (released Apr. 2011) was used to update the BPMAP file so that every probe on the chip that has a unique perfect match to the sacCer3 genome was assigned to its correct chromosomal location. The BPMAP file was updated by the function “remap” of the Bioconductor software package “Starr” to make the final updated "Sc3_updated.bpmap" file.
The resulting WIG files are converted directly from the .txt fles generated by the Affymetrix Tiling Analysis Software (v. 1.1) using parameters: two sided, 50 bp bandwidth and PM/MM.

label: Biotin

source_name: rpb11-E108G, none

label_protocol: The Affymetrix GeneChip Whole Transcript Double-Stranded cDNA Synthesis Kit was used as recommended by the manufacturer for model organisms. First and second strand cDNA was synthesized from random-sequence primers using dNTPs doped with dUTP. The product dsDNA was fragmented to an approximate length of 25 to 100 basepairs by treatment with uracil DNA glycosylase and apurinic endonuclease. The DNA fragments were then indirectly end-labeled with phycoerythrin.

growth_protocol: Cells were grown in exponential phase for at least 2 generations in YEPD at 30ºC to an OD600 of 1.0

extract_protocol: Total RNA was isolated using hot-acid phenol extraction in Schmitt et al. 1990.

treatment_protocol: Cells were shifted to 35ºC for 45 minutes and pelleted by centrifugation, except the Rpb11 mutant, which was grown continuously at 30ºC.

tag: cell line

value: RPB11 mutant

tag: treatment

tag: fraction

value: whole cell


title: Grafted drought moderate tolerant grapevine rootstock (5BB) under drought stress (DS)_replication2

city: tokat

first: Kubilay

last: Yıldırım

address: tasliciftlik kampusu

country: Turkey

institute: gaziosmanpasa university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Vitis cinerea var. helleri x Vitis riparia

source_name: drought treated roots of grafted 5BB at 5-10% field capacity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: drought tolerant 110R and senstive 5BB rootstocks were firstly grafted with sultana seedless . After callusing and rooting, grafted and non-grafted  plants were grown for two year in 20 L pots filled with soil (clay loam (pH 6.4) with 0.0062 dS/m EC, 1.9 % organic carbon content) perlite mixture (4:1).  All the experiments were carried out in semi-controlled greenhouse.

extract_protocol: roots collected from control and drought treated plants were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al (2007).

treatment_protocol: Droguth treatment applied to plants by completely witholding irrigation from the pots. Sampling was done when the soil water content of the pots decreased to 5-10% at the end of drought treatment. Control condition was created by well irrigation of the replicates at the field capacity.

tag: grapevine rootstock

tag: genotype/phenotype

value: grafted moderate drought tolerant

tag: growth condition

value: under drought stress (DS)

value: two year old grafted and rooted cuttings

value: root


title: blood [91166003051_D2]

tag: diagnosis

tag: sbj

value: Placebo on Day 1 followed by AMG811 (D85)


title: lung CD8 T cells d0 post Mtb infection rep3

description: MoGene2_062215H_ZX3_d0-3_2.rma-gene-full-Signal

source_name: lung CD8 T cells d0 post Mtb infection

tag: cell type

value: d0 post Mtb infection


title: lung CD8 T cells d7 post Mtb infection rep3

description: MoGene2_062215H_ZX6_d7-6.rma-gene-full-Signal


title: SSU72_alpha_35C

description:
Two biological replicates:
SSU72_1_alpha_35C
SSU72_2_alpha_35C

source_name: ssu72-G33A, cells were shifted to 35°C for 45 minutes

tag: genotype/variation

value: SSU72 mutant

value: Cells were shifted to 35°C for 45 minutes


title: lung CD8 T cells d0 post Mtb infection rep1

description: MoGene2_062215H_ZX1_d0-1.rma-gene-full-Signal

value: BALB/C


title: Grafted drought moderate tolerant grapevine rootstock (5BB) under drought stress (DS)_replication1

tag: tissue


title: grafted drought sensitive grapevine rootstock (41B) under well watered condition (WWP)_replication 2

organism: Vitis cinerea var. helleri x Vitis vinifera

source_name: roots of grafted 41B grown under well watered control condition at 90-100% field capacity

value: grafted drought sensitive

value: under well watered period (WWP)


title: lung CD8 T cells d0 post Mtb infection rep2

description: MoGene2_062215H_ZX2_d0-2.rma-gene-full-Signal

value: Female

value: lung CD8 T cells

value: Mycobacterium tuberculosis


title: Grafted drought tolerant grapevine rootstock (110R) under well watered period (WWP)_replication2

organism: Vitis cinerea var. helleri x Vitis rupestris

source_name: roots of grafted 110R grown under well watered control condition at 90-100% field capacity

value: grafted drought tolerant


title: Grafted drought moderate tolerant grapevine rootstock (5BB) under well watered period (WWP)_replication1

source_name: roots of grafted 5BB grown under well watered control condition at 90-100% field capacity


title: Grafted drought sensitive grapevine rootstock (41B) under drought stress (DS)_replication 1

source_name: drought treated roots of grafted 41B at 5-10% field capacity


title: NRD1_alpha_35C

description:
Two biological replicates:
NRD1_1_alpha_35C
NRD1_2_alpha_35C

source_name: nrd1-V368G, cells were shifted to 35°C for 45 minutes

value: NRD1 mutant


title: NAB3_alpha_35C

description:
Two biological replicates:
NAB3_1_alpha_35C
NAB3_2_alpha_35C

source_name: nab3-F371L/P374T, cells were shifted to 35°C for 45 minutes

value: NAB3 mutant

value: whole cell


title: Grafted drought sensitive grapevine rootstock (41B) under drought stress (DS)_replication 2

value: under drought stress (DS)


title: grafted drought sensitive grapevine rootstock (41B) under well watered condition (WWP)_replication 1

value: two year old grafted and rooted cuttings


title: lung CD8 T cells d7 post Mtb infection rep1

description: MoGene2_062215H_ZX4_d7-4.rma-gene-full-Signal

value: d7 post Mtb infection


title: Grafted drought moderate tolerant grapevine rootstock (5BB) under well watered period (WWP)_replication2

value: grafted moderate drought tolerant

value: root


title: blood [91166003051_D1.6]

value: blood

value: Discoid Lupus Erythematosus

tag: visit name

tag: sequence

value: Placebo on Day 1 followed by AMG811 (D85)


title: Grafted drought tolerant grapevine rootstock (110R) under well watered period (WWP)_replication1


title: HRP1_alpha_35C

description:
Two biological replicates:
HRP1_1_alpha_35C
HRP1_2_alpha_35C

source_name: hrp1-L205S, cells were shifted to 35°C for 45 minutes

value: HRP1 mutant

value: Cells were shifted to 35°C for 45 minutes


title: SEN1_a_35C

description:
Two biological replicates:
SEN1_1_a_35C
SEN1_2_a_35C

source_name: sen1-E1597K, cells were shifted to 35°C for 45 minutes

value: SEN1 mutant


title: WT_alpha_30C

description:
Two biological replicates:
WT_1_alpha_30C
WT_2_alpha_30C

source_name: 46alpha, none

value: WT


title: WT_a_35C

description:
Two biological replicates:
WT_1_a_35C
WT_2_a_35C

source_name: 46a, cells were shifted to 35°C for 45 minutes


title: WT_alpha_35C

description:
Two biological replicates:
WT_1_alpha_35C
WT_2_alpha_35C

source_name: 46alpha, cells were shifted to 35°C for 45 minutes


title: Grafted drought tolerant grapevine rootstock (110R) under drought stress (DS)_replication1

source_name: drought treated roots of grafted 110R at 5-10% field capacity


title: GW501516_2

status: Public on Jun 21 2017

city: Boston

first: Lingling

last: Dai

state: MA

address: 665 Huntington Avenue

institute: Harvard T.H. Chan School of Public Health

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with GW501516. It is the second of three replicates used in this experiment, each from separate culture.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown in DMEM mudium with 10% FBS

extract_protocol: Total RNA was extracted using the PrepEase RNA Spin Kit (USB)

tag: genotype

value: cell line:Ppard-overexpressing RAW 264.7 cells

tag: phenotype

value: treated with GW501516


title: Vehicle_2

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with vehicle. It is the second of three replicates used in this experiment, each from separate culture.

value: treated with vehicle


title: Il4_3

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with Il-4. It is the third of three replicates used in this experiment, each from separate culture.

value: treated with Il-4


title: GW501516_3

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with GW501516. It is the third of three replicates used in this experiment, each from separate culture.


title: Il4_1

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with Il-4. It is the first of three replicates used in this experiment, each from separate culture.


title: GW501516_1

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with GW501516. It is the first of three replicates used in this experiment, each from separate culture.


title: leaf_eggs_Friesland_rep2

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, twice the fluorescence value of the 90% percentile of non-labelled hairpin DNA probes (dark-corner spots) was set as limit of detection on each microarray. Probes that did not exceed this threshold in at least in two replicates of at least one treatment group were considered non-expressed and removed from further analysis in the paper. Background-correction and normalization across arrays was then performed after removal of the non-expressed genes. In the publication, assignment of the longest contig to the respective oligo in case of multiple matching contigs for averaging and and GO-term annotation was performed after removal of the non-expressed genes.

organism: Solanum dulcamara

source_name: leaf, S. exigua oviposited

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.

growth_protocol: Solanum dulcamara plants were grown from seeds in a greenhouse at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol/ m s. For germination, seeds were incubated at 4°C on sterile wet sand for 12 days.

extract_protocol: Total RNA was extracted from powdered tissue samples (50 mg) pooled from three to four plants (resulting in 5-6 biological replicates) with a TRIzol® Reagent-based RNA extraction followed by a DNase digestion with TURBO DNA-freeTM (both Ambion® Life Technologies). The RNA was additionally cleaned up using the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Equal amounts of RNA from 1-3 biological replicates were pooled to obtain 3 replicates for hybridisation. All RNA samples had a RNA integrity index between 7.3 and 8.0 in an electrophoretic analysis with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA)

treatment_protocol: For oviposition, the 3rd fully developed leaf from the top was placed through slits into a flight cage with either 40 male and 40 female moths (for egg deposition) or with 80 male moths (for control plants) overnight. After 72 hours, the eggs were carefully removed  a 13mm leaf disc  including the site of oviposition was sampled using a cork-borer. Leaf material was flash frozen in liquid nitrogen immediately after the eggs had been carefully removed using a fine paintbrush.

tag: plant population

value: Friesland

value: leaf


title: Il4_2

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with Il-4. It is the second of three replicates used in this experiment, each from separate culture.


title: Vehicle_1

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with vehicle. It is the first of three replicates used in this experiment, each from separate culture.


title: YDBS/MCAO group, biological rep1

city: Xi’an

first: Tianlong

last: Liu

address: No. 127 West Changle Road

department: Pharmacy

institute: Xijing Hospital

hyb_protocol: It was processed for hybridization with the GeneChip® Rat Gene 2.0 ST Array (Affymetrix) by using a GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: The arrays were washed and scanned by an Affymetrix GeneChip Command Console.

data_processing: The raw data were normalized by the log scale robust multi-array analysis (RMA) method with the Expression Console software version 1.1 (Affymetrix).

source_name: Blood was drawn from the abdominal aorta after 24 h reperfusion

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® 3' IVT PLUS Reagent Kit, Affymetrix).

growth_protocol: Male Sprague-Dawley (SD) rats, weighing 250–280g, were kept in plastic cages at 22 ± 2 °C with free access to pellet food and water and on a 12 h light/dark cycle.

extract_protocol: Total RNA in the blood was isolated using TRIpure LS blood (liquid sample) RNA extraction reagent according to the manufacture's protocol.

treatment_protocol: Rats in QDBS group were treated with exhaustive swimming exercising once a day for 21 days, while the YDBS model rats were intramuscularly injected with hydrocortisone (45mg/kg) one time per day for 13 days, followed by subcutaneous injection of epinephrine (0.36mg/kg) for 1 day. On the next day of that, the middle cerebral artery occlusion (MCAO) was performed.

tag: strain/background

value: Sprague-Dawley

tag: gender

value: male

tag: group

value: YDBS/MCAO


title: QDBS/MCAO group, biological rep3

value: QDBS/MCAO


title: leaf_control_Siethen_rep3

source_name: leaf, undamaged control

value: Siethen


title: QDBS/MCAO group, biological rep2

value: blood


title: ACINAR

city: Kyoto

first: Takahisa

last: Maruno

state: Kyoto

address: 54 Syogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and hepatology

institute: Kyoto university

description: Gene expression of acinar cells 48 hours after caerulein pancreatitis

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized   on GeneSpring GX 14.5 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: dissected acinar cells, caerulein pancreatitis, 48h

label_protocol: RNA was amplified from 1.181 ng by using an Ovation Pico WTA System V2 (NuGEN, San Carlos, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0 ug cDNA using SureTag Complete DNA Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from dissected tissue using the RNeasy Micro Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: acinar


title: DUCT

description: Gene expression of ductal cells 48 hours after caerulein pancreatitis

hyb_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0 ug cDNA using SureTag Complete DNA Labeling Kit (Agilent Technologies).

source_name: dissected ductal cells, caerulein pancreatitis, 48h

value: ductal


title: YDBS/MCAO group, biological rep3


title: Control (Sham) group, biological rep1

value: Sham


title: leaf_eggs_Erkner_rep1

value: Erkner


title: Vehicle_3

description: This sample is of Ppard-overexpressing RAW 264.7 cells treated with vehicle. It is the third of three replicates used in this experiment, each from separate culture.


title: YDBS/MCAO group, biological rep2


title: leaf_eggs_Siethen_rep3


title: blood [91166005051_D57]

source_name: Blood

value: Discoid Lupus Erythematosus

value: AMG811 on Day 1 followed by Placebo (D85)


title: QDBS/MCAO group, biological rep1


title: Control (Sham) group, biological rep3


title: leaf_control_Friesland_rep2


title: ADM

description: Gene expression of ADM cells 48 hours after caerulein pancreatitis

source_name: dissected ADM cells, caerulein pancreatitis, 48h

value: ADM


title: leaf_control_Erkner_rep1


title: Control (Sham) group, biological rep2


title: Resistant clone C#6, biological rep3

status: Public on Jun 20 2017

city: Salamanca

first: Sara

last: García-Alonso

state: Salamanca

address: Campus Miguel de Unamuno s/n

country: Spain

institute: Centro de Investigación del Cáncer

description: Gene expression data from T-DM1 resistant clone, C#6, derived from BT474 cell line

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Data were processed using the RMA algorithm implemented in the Affimetrix Expression Console (version 1.4.1; Affymetrix). Differentially expressed genes were identified using Transcriptome Analysis Console (TAC version 3.0; Affymetrix).

source_name: Breast cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell lines were cultured at 37°C in a humidified atmosphere in the presence of 5% CO2 and 95% air. Cells were grown in Dulbecco´s Modified Eagle´s Medium (DMEM) supplemented with 10% FBS, 100 mU/mL penicillin and 100 µg/mL streptomycin.

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

treatment_protocol: T-DM1 resistant clones were derived from parental cells by prolonged exposure to T-DM1 following an initial dose-response study of T-DM1 (0.1 nM - 100 nM) over 5 days. Resistant BT474 T-DM1R cell lines were obtained by single-cell cloning and continuously cultured in the presence of 5 nM T-DM1 for 3 months. Clones were routinely tested for resistance.

tag: drug resistance

value: T-DM1 resistant clone

tag: cell line


title: Resistant clone C#6, biological rep1


title: Resistant clone C#6, biological rep2


title: Resistant clone C#3, biological rep3

description: Gene expression data from T-DM1 resistant clone, C#3, derived from BT474 cell line


title: Resistant clone C#2, biological rep2

description: Gene expression data from T-DM1 resistant clone, C#2, derived from BT474 cell line


title: Resistant clone C#1, biological rep2

description: Gene expression data from T-DM1 resistant clone, C#1, derived from BT474 cell line


title: Resistant clone C#1, biological rep3


title: Resistant clone C#2, biological rep3


title: Resistant clone C#2, biological rep1


title: Resistant clone C#1, biological rep1


title: Resistant clone C#3, biological rep2


title: Parental cell line, biological rep1

description: Gene expression data from parental cell line BT474

value: Parental sensitive cell line


title: Parental cell line, biological rep2


title: Parental cell line, biological rep3


title: CP-1A

city: Hong Kong

first: Thomas

middle: HY

last: Leung

address: Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: Obstetrics and Gynaecology

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression

hyb_protocol: Service by the Centre for Genomic Sciences, The University of Hong Kong

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method

source_name: cell line

growth_protocol: CP-1A cells growth in MEM-HG medium supplemented with FBS, CP-1S cells growth in DMEM-F12 medium supplemented with EGF, bFGF, insulin and BSA

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

value: attached

tag: disease state

value: Cervical cancer


title: NR8383_Egr rep 2

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 24hr in EGr-exposed rat alveolar macrophages

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4.

source_name: Rat alveolar macrophages, 24hr, EGr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Rat alveolar macrophages NR8383 were seeded into each well of a 96-well plate and grown in the F-12K with 10% heat-inactivated fetal bovine serum medium for 24 hours.

extract_protocol: After 24 hours, total RNA was extracted from the cells using the RNeasy mini (Qiagen, Tokyo, Japan) according to the manufactures instructions. Total RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The culture medium were replaced by four kinds of the working solutions including  exfoliated graphene (EGr), respectively. These working solutions were dissolved in 1mg/mL bovine serum albumin (BSA). Cell concentrations at this point were approximately 2.0 x 10^5 cells/mL. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell

value: Rat alveolar macrophages  (NR8384)

tag: treatment

value: EGr

tag: time


title: cell culture after 15 days  - biological rep 2

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description: Poricine oviductal epithelial cells gene expression after 15 days of cell culture

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Canine Gene 1.1 ST Array Strip (48°C/20 h), washed and stained using the Affymetrix GeneAtlas Fluidics Station according to the manufacturer technical protocol

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cell files were submied to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

organism: Sus scrofa

source_name: 9 month old crossbred gilts

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: In this study we used landrace crossbred gilts (n=45) at the age of about nine month and which displayed two regular estrous cycles, collected from a commercial herd.

extract_protocol: Total RNA was extracted from samples using TRI Reagent (Sigma, St Louis, MO, USA) and RNeasy MinElute cleanup Kit (Qiagen, Hilden, Germany). Subsequently total RNA (100 ng) from each pooled sample was subjected to two round, sense cDNA amplification (Ambion® WT Expression Kit).

treatment_protocol: Epithelial cells were surgically removed using sterile surgical blades. Then the epithelium was incubated with collagenase I (Sigma Aldrich, Madison, USA) in DMEM (Sigma Aldrich, Madison, USA) for 1 hour. Next, the cells were centrifuged and incubated with 0.5% Trypsin/EDTA (Sigma Aldrich, Madison, USA). The final cell pellet was suspended in DMEM with 10% FBS, 10000 U/mL penicillin, 100 µg/mL streptomycin and 25 µg/mL amphotericin B. The cells were cultured at 37oC in humidified atmosphere of 5% CO2.

value: Porcine oviductal epithelial cells


title: NR8383_Egr rep 3


title: NR8383_Control for EGr rep 4

description: Gene expression after 24hr in rat alveolar macrophages as cotrol for EGr

source_name: Rat alveolar macrophages, 24hr, control for EGr

value: Rat alveolar macrophages  (NR8383)

value: Control for EGr


title: cell culture after 30 days  - biological rep 1

description: Poricine oviductal epithelial cells gene expression after 30 days of cell culture


title: NR8383_Control for EGr rep 3


title: cell culture after 7 days  - biological rep 2

description: Poricine oviductal epithelial cells gene expression after 7 days of cell culture


title: NR8383_Egr rep 4


title: cell culture after 30 days  - biological rep 2


title: NR8383_Egr rep 1


title: cell culture after 24h  - biological rep 2

description: Poricine oviductal epithelial cells gene expression after 24h of cell culture


title: cell culture after 24h - biological rep 1


title: cell culture after 7 days  - biological rep 1


title: cell culture after 15 days  - biological rep 1


title: CP-1S

description: Gene expression

scan_protocol: Service by the Centre for Genomic Sciences, The University of Hong Kong

value: spheroid


title: NR8383_Control for EGr rep 2


title: NR8383_Control for EGr rep 1


title: WT_Colon_MF_Rep2

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description: miRNA expression in colon macrophages

hyb_protocol: Labeled RNA was hybridized with a 8X15 mouse miRNA array rel v19 (design number 046065) at 55Â°C and 20 rpm for 20 hours, and then washed according to the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on Agilent Technologies Scanner G2505B US22502692 using 5uM resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 029152_D_F_20100702) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Colon, isolated MF, Replicate 2

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

growth_protocol: Different macrophage populations were freshly isolated from WT mice  (C57BL6/J) grown in SPF conditions.

extract_protocol: The miRNeasy total RNA extraction kit (Qiagen) was used for RNA isolation.

treatment_protocol: Cells were isolated ex vivo and cells were directly isolated within a total range of time of 5h.

tag: tissue specific cells

value: Colon macrophages

value: male

tag: age

value: 6 weeks


title: WT_Colon_MF_Rep1

description: miRNA expression in colon macrophages

source_name: Colon, isolated MF, Replicate 1


title: WT_Liver_MF_Rep2

description: miRNA expression in liver macrophages (KC)

source_name: Liver, isolated MF, Replicate 2

value: Liver macrophages


title: WT_Liver_MF_Rep1

source_name: Liver, isolated MF, Replicate 1


title: WT_MG_Rep2

description: miRNA expression in brain microglia

source_name: Brain, isolated MG, Replicate 2

value: Brain microglia


title: WT_MG_Rep1

description: miRNA expression in brain microglia

source_name: Brain, isolated MG, Replicate 1


title: HG+Ad-Ctrl

city: Jinan

first: Min

state: Shandong

address: wen hua xi road 44

department: Department of Pharmacology

institute: Shandong University School of Medicine

description: RPMI Medium 1640 basic(1*) from gibco

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 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 immediately by brief centrifugation.

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

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

source_name: Podocytes (Ad-Ctrl transfection) were cultured in 1640 medium for 24h with high glucose

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

growth_protocol: Overexpression of Sirt6 by a Sirt6-adenovirus transfection was used in this study. Podocytes (Ad-Ctrl or Ad-Sirt6 transfection) were cultured in 1640 medium for 24h with or without high glucose

extract_protocol: Total RNA was isolated from podocytes using TRIzol reagent (Invitrogen).

treatment_protocol: High glucose (a final concentration of  40 mmol/l in culture medium);

tag: cell type

value: podocyte

tag: transfected with

value: Control adenovirus

value: high glucose


title: Ad-Sirt6

description: RPMI Medium 1640 basic(1*) from gibco

source_name: Podocytes (Ad-Sirt6 transfection) were cultured in 1640 medium for 24h without high glucose


title: Grafted drought tolerant grapevine rootstock (110R) under drought stress (DS)_replication2

source_name: drought treated roots of grafted 110R at 5-10% field capacity

tag: grapevine rootstock

tag: genotype/phenotype

value: grafted drought tolerant

tag: growth condition

value: under drought stress (DS)

value: two year old grafted and rooted cuttings

tag: tissue

value: root


title: HG+Ad-Sirt6

description: RPMI Medium 1640 basic(1*) from gibco

source_name: Podocytes (Ad-Sirt6 transfection) were cultured in 1640 medium for 24h with high glucose


title: Ad-Ctrl

description: RPMI Medium 1640 basic(1*) from gibco

source_name: Podocytes (Ad-Ctrl transfection) were cultured in 1640 medium for 24h without high glucose


title: AGILENT_HUMAN_AR NO TX 18

city: Aguascalientes

first: Noe

last: Macias-Segura

state: Aguascalientes

address: Av. Universidad #940 ciudad universitaria cp20131

department: Physiology

country: Mexico

institute: Universidad Autonoma de Aguascalientes

description: Gene expression from human whole blood

hyb_protocol: Hybridization protocol was carried out following the supliers instruction from the one-color low input RNA labeling kit (Agilent)

scan_protocol: Inmediately after wash step the microarrays were scaned in the Agilent G4900DA SureScan Microarray Scanner equipment (Agilent) following the supliers intructions and the default parameters.

data_processing: The median intensity values from the microarray images were obtained using the Feature extraction software (Agilent) version 11.5.1.1 following the supliers instructions and default parameters using the protocol GE1_1105 and grid 026652_D_F_20140228.

source_name: Peripheral blood, patient with RA untreated

label_protocol: Total RNA exracted from samples was labeled with Cy3 under suplier instructions folowing the protocol of one sample low input RNA labeling kit (Agilent), and purified with QIAmp mini-columns (QIAGEN). Dye incorporation and RNA yield were measured by Nanodrop 1000 (Thermo scientific)

extract_protocol: Total RNA was extracted and proceced in QIAmp RNA mini-columns according the suplier intructions (QIAGEN, 2014) and the integrity was measured with the RNA 6000 nano kit in a Bioanalyzer 2100 (Agylent technologies)

treatment_protocol: Whole blood from al the subject was obtained in EDTA colection tubes and 1ml of RNA later was added to preserve the RNA.

value: whole blood

value: Female

tag: clinical stage

value: RA patient, less than one year of evolution untreated


title: AGILENT_HUMAN_AR NO TX 20

description: Gene expression from human whole blood

tag: gender

value: Male


title: AGILENT_HUMAN_ AR NO TX 19

description: Gene expression from human whole blood


title: AGILENT_HUMAN_AR NO TX 16

description: Gene expression from human whole blood


title: AGILENT_HUMAN_ AR NO TX 15

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP- 12

description: Gene expression from human whole blood

source_name: Peripheral blood, relative ACPA negative

value: Healthy relatives


title: AGILENT_HUMAN_CONTROL CCP- 11

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP- 10

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP+ 7

description: Gene expression from human whole blood

source_name: Peripheral blood, relative ACPA postive

value: Relative in preclinical autoimmune stage


title: AGILENT_HUMAN_CONTROL CCP+ 5

description: Gene expression from human whole blood


title: AGILENT_HUMAN_AR NO TX 14

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP- 13

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP+ 3

description: Gene expression from human whole blood


title: AGILENT_HUMAN_CONTROL CCP+ 6

description: Gene expression from human whole blood