title: HCT116 wild type 5x2Gy irradiation replicate 2

description:
HCT116 wild type were irradiated with fractionated 5 x 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.
HCT116_wt_5x2Gy_rep2


title: HCT116 p53 minus 2Gy irradiation replicate 2

status: Public on Aug 29 2017

type: RNA

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description:
HCT116 p53 minus were irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.
HCT116_p53minus_2Gy_rep2

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Human Gene Expression (v2) 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal cancer HCT116 p53 minus cells non-irradiated

label_protocol: 1 μg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion). cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: Cells were cultured in RPMI-1640 cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2mM glutamine (Gibco), 100 IU/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from harvested cells using Quick-RNA MiniPrep kit (ZYMO RESEARCH) according to the manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Inhibition of p53 gene expression in HCT116, a human colorectal cancer cell line was done using RNA interference (shRNA). The cell line that showed greatest reduction (85-90%) of p53 expression were treated with single (2 Gy) or fractionated (5 x 2Gy) doses of ionizing radiation.

tag: cell line/genotype

value: HCT116 p53 minus

tag: origin

value: Colorectal cancer

tag: treatment

value: Control

source_name: Colorectal cancer HCT116 p53 minus cells irradiated with 2 Gy

value: single dose of 2Gy


title: HCT116 wild type 2Gy irradiation replicate 1

description:
HCT116 wild type were irradiated with single 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.
HCT116_wt_2Gy_rep1

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Whole Human Genome Microarrays 4x44k (Agilent) for 17 hours at 65°C using HS 400 hybridization station (Tecan).

source_name: Colorectal cancer HCT116 cells non-irradiated

extract_protocol: Total RNA was isolated from harvested cells using Quick-RNA MiniPrep kit (ZYMO RESEARCH) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Cell were treated with single (2 Gy) or fractionated (5x2 Gy) doses of ionizing radiation

tag: cell line

source_name: Colorectal cancer HCT116 cells irradiated with 2 Gy


title: HCT116 p53 minus 2x5Gy irradiation replicate 1

description:
HCT116 p53 minus were irradiated with fractionated 5 x 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.
HCT116_p53minus_5x2Gy_rep1

source_name: Colorectal cancer HCT116 p53 minus cells irradiated with 5x2 Gy

value: fractionated dose of 5x2Gy


title: Ptch mutant [090410MJA_moe430-2.0_100795-03]

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Academic Medical Center

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
3.090410MJA_moe430-2.0_100795-03.CEL.KO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized. The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, and staining of the chips. The Affymetrix Mouse Genome 430-2.0 Arrays are used for hybridization.

scan_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for scanning of the chips.

data_processing: The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips, and provide the data stored in DTT format and Cell Intensity File (*.cel) for each GeneChip processed.

label: Biotin

organism: Mus musculus

source_name: Ptch mutant_whole colons

label_protocol: The Affymetrix 3’ IVT-Express labeling Kit (#901229) is used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng is used for the labeling experiments.

extract_protocol: RNA from the colons was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Rosa26-CreERT2-Ptch1+/+ and Rosa26-CreERT2-Ptch1fl/fl mice were intraperitoneally injected with 1 mg tamoxifen for 5 consecutive days. At day 12 animals were sacificed and colons were isolated.

tag: strain  background

value: mixed C57BL/6  X Balb/c

tag: genotype/variation

value: Patched1 knockout

tag: tissue

value: whole colons

tag: timepoint

value: 12 days after the start of the induction with tamoxifen


title: Ptch mutant [090410MJA_moe430-2.0_100795-06]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
6.090410MJA_moe430-2.0_100795-06.CEL.KO


title: HCT116 wild type 2Gy irradiation replicate 2

description:
HCT116 wild type were irradiated with single 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.
HCT116_wt_2Gy_rep2


title: HCC_HBV Tg mouse_18M_rep3

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

country: Japan

institute: University of Fukui

description: Biological replicate 3 of 5.

hyb_protocol: Samples (0.75 ug each) of Cy3- and Cy5-labeled targets were combined and hybridized to an Agilent catalog 44K feature mouse oligo array for 17 h at 60°C. In each assay, a hepatic RNA sample from an experimental animal was hybridized against a pooled RNA sample composed of equal amounts of RNA from the livers of five unmanipulated 7-month-old control Tg liver mixture.

scan_protocol: Data were extracted from the resulting images using Agilent's Feature Extraction Software (Agilent Technologies).

data_processing:
Expression analysis for all replicate microarray experiments was performed with GeneSpring GX, where its expression ratio (experiment group = Cy5 / control group = Cy3) was calculated and converted using the base two logarithm.
If flags (gIsPosAndSignif, rIsPosAndSignif, gIsWellAboveBG, or rIsWellAboveBG), indicating as reliable fluorescence probes, were 0, those probes were eliminated from the obtained data as well as probes with 1 or -1 in ControlType. For the logarithm ratio of each chronological sample in the unmanipulated control Tg mix, two color microarray analysis was performed by setting the samples with log2 ratios of 0. False Discovery Rate (FDR) with Welch P-values and RankProd FDR were respectively corrected for multiple testing with Benjamin-Hochberg (BH) procedure and RankProduct. While Welch P-values were calculated from TM4 MeV_4_6_1, R was used for RankProduct FDR.

source_name: HCC, HBV Tg mouse, 18M

label_protocol: One ug of total RNA from control and experimental animals was separately amplified and labeled with either Cy3- or Cy5-labeled CTP (Perkin Elmer, Wellesley, MA, USA) with an Agilent low input linear amplification kit (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s protocol.

extract_protocol: Total RNA was isolated from snap-frozen hepatic parenchyma and HCC tissues. Total RNA was resuspended in DEPC water, cleaned up with a Qiagen RNeasy column, and quantified by UV-Vis spectroscopy.

tag: duration

value: 18 months

value: Hepatocellular carcinoma

tag: strain

source_name: Unmanipulated 7-month-old control Tg liver mixture

tag: age

value: 7 months

value: Liver


title: Liver_HBV Tg mouse_18M_rep2

description: Biological replicate 2 of 5.

source_name: Liver, HBV Tg mouse, 18M


title: Liver_HBV Tg mouse_15M_rep2

description: Biological replicate 2 of 5.

source_name: Liver, HBV Tg mouse, 15M

value: 15 months


title: HCC_HBV Tg mouse_18M_rep5

description: Biological replicate 5 of 5.


title: Liver_HBV Tg mouse_15M_rep5

description: Biological replicate 5 of 5.


title: HCC_HBV Tg mouse_18M_rep4

description: Biological replicate 4 of 5.


title: Liver_HBV Tg mouse_15M_rep3

description: Biological replicate 3 of 5.


title: HCT116 p53 minus 2Gy irradiation replicate 1

description:
HCT116 p53 minus were irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.
HCT116_p53minus_2Gy_rep1


title: Liver_HBV Tg mouse_18M_rep4

description: Biological replicate 4 of 5.


title: Liver_HBV Tg mouse_12M_rep4

description: Biological replicate 4 of 5.

source_name: Liver, HBV Tg mouse, 12M

value: 12 months


title: Liver_HBV Tg mouse_12M_rep1

description: Biological replicate 1 of 5.


title: Liver_HBV Tg mouse_15M_rep4

description: Biological replicate 4 of 5.


title: Liver_HBV Tg mouse_9M_rep3

description: Biological replicate 3 of 5.

source_name: Liver, HBV Tg mouse, 9M

value: 9 months


title: Liver_HBV Tg mouse_18M_rep3

description: Biological replicate 3 of 5.


title: Liver_HBV Tg mouse_18M_rep1

description: Biological replicate 1 of 5.


title: HCC_HBV Tg mouse_18M_rep1

description: Biological replicate 1 of 5.


title: Liver_HBV Tg mouse_18M_rep5

description: Biological replicate 5 of 5.


title: Liver_HBV Tg mouse_15M_rep1

description: Biological replicate 1 of 5.


title: Liver_HBV Tg mouse_9M_rep2

description: Biological replicate 2 of 5.


title: Liver_HBV Tg mouse_6M_rep4

description: Biological replicate 4 of 5.

source_name: Liver, HBV Tg mouse, 6M

value: 6 months


title: Liver_HBV Tg mouse_12M_rep5

description: Biological replicate 5 of 5.


title: Liver_HBV Tg mouse_9M_rep1

description: Biological replicate 1 of 5.


title: Liver_HBV Tg mouse_6M_rep5

description: Biological replicate 5 of 5.


title: Liver_HBV Tg mouse_12M_rep2

description: Biological replicate 2 of 5.


title: Liver_HBV Tg mouse_9M_rep5

description: Biological replicate 5 of 5.


title: Liver_HBV Tg mouse_9M_rep4

description: Biological replicate 4 of 5.


title: Liver_HBV Tg mouse_12M_rep3

description: Biological replicate 3 of 5.


title: HCT116 wild type 2Gy irradiation replicate 3

description:
HCT116 wild type were irradiated with single 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.
HCT116_wt_2Gy_rep3


title: Liver_HBV Tg mouse_6M_rep3

description: Biological replicate 3 of 5.


title: Liver_HBV Tg mouse_3M_rep5

description: Biological replicate 5 of 5.

source_name: Liver, HBV Tg mouse, 3M

value: 3 months


title: Liver_HBV Tg mouse_6M_rep2

description: Biological replicate 2 of 5.


title: Carotid-1

city: Sao Paulo

first: Vinicius

last: Bassaneze

state: SP

address: Av. Dr. Eneas de Carvalho Aguiar, 44

department: Cardiopneumology

country: Brazil

institute: Heart Institute

description: Samples obtained from wistar rats

hyb_protocol: Ten microgram of fragmented cRNA was incubated with slide array for 24h at 37 ºC, under 300 RPM shaking to ensure homogenization.

scan_protocol: Slides were scanned using GenePix 4000B Array Scanner using Scan Codelink settings.

data_processing: The raw data were normalized using CyclicLoess, the most effective method for CodeLink Bioarray data. Data was also filtered for good intensity of the signal and removing genes with a low-intensity signal in at least 50% of the samples of each group.

organism: Rattus norvegicus

source_name: Carotid

label_protocol: Biotin-labelled cRNA was produced form 1 ug of total RNA. First and second-strand cDNA was synthesized  according to manufacturer’s instruction. cRNA was obtained by in vitro transcription reaction.

growth_protocol: Wistar rats (250-350g) were anesthetized with a mixture of ketamine (50 mg/kg) and xylazine (10mg/kg).

extract_protocol: Arterialized vein segments were collected at 3 days (n=3) and 28 days (n=3) after surgery. Normal jugular veins (n=5) and carotid arteries (n=2) were used as controls.

treatment_protocol: The right external jugular vein was connected to the common carotid artery by end-to-end anastomosis using a 10.0 silk suture (Ethicon Inc., Somerville, NJ).

value: Wistar

value: Carotid artery

tag: time

value: ND

tag: status

value: Reference Control


title: Carotid-2

description: Samples obtained from wistar rats


title: Liver_HBV Tg mouse_3M_rep2

description: Biological replicate 2 of 5.


title: Jugular-3Days-3

description: Samples obtained from wistar rats

value: Jugular vein

value: 3 days

value: arterialized


title: Liver_HBV Tg mouse_3M_rep4

description: Biological replicate 4 of 5.


title: Liver_HBV Tg mouse_3M_rep3

description: Biological replicate 3 of 5.


title: Liver_HBV Tg mouse_6M_rep1

description: Biological replicate 1 of 5.


title: Jugular-28Days-1

description: Samples obtained from wistar rats

value: 28 days


title: Jugular-3Days-2

description: Samples obtained from wistar rats


title: Liver_HBV Tg mouse_1M_rep4

description: Biological replicate 4 of 5.

source_name: Liver, HBV Tg mouse, 1M

value: 1 month


title: Jugular-28Days-2

description: Samples obtained from wistar rats


title: BV2 microglia / LPS replicate 3

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

country: USA

institute: Florida Agricultural & Mechanical University

description: Mouse, brain, microglial cells transformed by recombinant retrovirus (v-raf/v-mic), phenotype functional markers of macrophages.

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, ThermoFisher Scientific)

data_processing: The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific)

source_name: BV2 Microglia cells - LPS 1 ug/ml @ 24 Hours

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: BV-2 microglia (BV-2) cells were cultured in DMEM high glucose media [glucose 4500 mg/L] containing 5% FBS, 4 mM L-glutamine, and penicillin/streptomycin (100 U/0.1 mg/mL). Culture conditions were maintained at 37 °C in 5% CO2/atmosphere and every 2–3 days, the media was replaced and cells sub-cultured. For experiments, plating media consisted of DMEM (minus phenol red) [glucose 4500 mg/L], 2.5% FBS and penicillin/streptomycin (100 U/0.1 mg/mL).

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: LPS O111:B4 was prepared in HBSS at 1 mg/mL and stored at –20 °C. For experiments, LPS was added to the culture media at a working concentration of 1μg/mL.

tag: cell type

value: BV2 microglia cells

tag: agent

value: LPS


title: Jugular-28Days-3

description: Samples obtained from wistar rats


title: BV2 microglia / LPS replicate 1


title: BV2 microglia Control replicate2

source_name: BV2 Microglia cells - Resting

value: control


title: Liver_HBV Tg mouse_1M_rep2

description: Biological replicate 2 of 5.

value: Liver

value: 7 months


title: Liver_HBV Tg mouse_3M_rep1

description: Biological replicate 1 of 5.


title: Jugular-3Days-1

description: Samples obtained from wistar rats


title: Jugular-5

description: Samples obtained from wistar rats

source_name: Jugular


title: Liver_HBV Tg mouse_1M_rep5

description: Biological replicate 5 of 5.


title: BV2 microglia / LPS replicate 2


title: Jugular-3

description: Samples obtained from wistar rats


title: Jugular-4

description: Samples obtained from wistar rats


title: BV2 microglia Control replicate1


title: BV2 microglia Control replicate3


title: Liver_HBV Tg mouse_7d_rep3

description: Biological replicate 3 of 5.

source_name: Liver, HBV Tg mouse, 7d

value: 7 days


title: Liver_HBV Tg mouse_1M_rep1

description: Biological replicate 1 of 5.


title: Liver_HBV Tg mouse_1M_rep3

description: Biological replicate 3 of 5.


title: Liver_HBV Tg mouse_7d_rep4

description: Biological replicate 4 of 5.


title: Liver_HBV Tg mouse_7d_rep5

description: Biological replicate 5 of 5.


title: Liver_HBV Tg mouse_7d_rep1

description: Biological replicate 1 of 5.


title: Jugular-2

description: Samples obtained from wistar rats


title: Jugular-1

description: Samples obtained from wistar rats


title: Liver_HBV Tg mouse_7d_rep2

description: Biological replicate 2 of 5.


title: R16_FHS

status: Public on Aug 26 2017

city: Cleveland

first: Ulrich

last: Hopfer

state: Ohio

address: 10900 Euclid Ave.

department: Physiology&Biophysics

institute: Case Western Reserve University

description: Gene expression data from the renal cortex of rats given Fructose and High-Salt Chow

hyb_protocol: Following fragmentation and labeling, 5.5 micro-g of cDNA were hybridized for 16 hrs at 45C on RaGene-2_0 st Array. GeneChips were washed and stained in the Affymetrix Fuidics Station 450

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Expression Console build 1.4.1.46; gene level analysis; summarization method: median polish; normalization: sketch quartile; probe array type: Affymetrix RaGene-2_0 st

label: biotin

source_name: Kidney Cortex

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Plus protocol  from 150 ng total RNA (GeneChip WT PLUS reagent Kit, Affymetrix)

growth_protocol: Animals were housed under normal rat housing conditions with 12 hours of dark/light cycle, and two animals per cage.

extract_protocol: total RNA with Qiagen miRNeasy Mini Kit #217004

treatment_protocol: No particular treatment other than dietary described in Overall Design.

value: Sprague Dawley

tag: Sex

value: Male

value: 7 weeks

value: renal cortex

tag: diet

value: Fructose and High-Salt Chow


title: R09_CHS

description: Gene expression data from the renal cortex of rats given Water and High-Salt Chow

value: Water and High-Salt Chow


title: HCC_HBV Tg mouse_18M_rep2

description: Biological replicate 2 of 5.

value: 18 months

value: Hepatocellular carcinoma


title: CA 100uM

city: Beijing

first: SHUAI

last: HUANG

address: Nanwei Road NO2

country: China

institute: Institute of Materia Medica,Chinese Academy of Medical Sciences/Peking Union Medical College

description: Expression data from huh cells CA 100uM treated

hyb_protocol: 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.The hybridized arrays were washed, fixed.

scan_protocol: The chips were scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: MIHA cells with CA100uM treated

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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

growth_protocol: The non-cancer cell MIHA was cultured in the RIPA-1640 medium supplemented with 10% fetal calf serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL)

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

treatment_protocol: Cells were treated with CA (50 μΜ and 100 μΜ) for 24 hrs, trypsinized and re-suspend in serum-free medium.

value: MIHA cells


title: R10_CHS


title: Untreated Control

description: Expression data from huh cells without CA treated

source_name: MIHA cells without CA treated

value: untreated


title: R11_CHS


title: R12_CHS


title: R07_FNS

description: Gene expression data from the renal cortex of rats given Fructose and Standard Chow

value: Fructose and Standard Chow


title: CA 50uM

description: Expression data from huh cells CA 50uM treated

source_name: MIHA cells with CA 50uM treated


title: R05_FNS


title: Region 2, control embryos replicate 2

city: Lisboa

first: Rita

last: Pinto

state: Lisboa

address: Faculdade de Medicina da Universidade de Lisboa Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: Region 2 samples were obtained by microdissecting zebrafish embryos below the last formed somite pair (not included). All tailbud region, presomitic mesoderm and Kupffer's Vesicle are included

hyb_protocol: 3,5 µg of end-labeled, fragmented cDNA was used in a 150-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips and GeneChip Expression 3´-Amplification Reagents Hybridization Control Kit; Affymetrix) and hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips; Affymetrix) were used on an Affymetrix GeneAtlas system, followed by scanning of the array strips.

scan_protocol: Scanning was performed according to the manufacturer's instruction (Affymetrix) using a Affymetrix Gene ChIP Scanner 3000 7G

data_processing: All samples were analyzed with Affymetrix Zebrafish Gene 1.1 ST Array Strip (Thermo Fisher). The raw data (CEL files) was analyzed with Affymetrix Expression Console Software and Affymetrix Transcriptome Analysis Console Software (Thermo Fisher) and R. Statistical analysis was performed using ANOVA and False Discovery Rate correction (FDR). Only genes with a fold change (FC) higher than 2 or lower than -2, with P<0.05 and FDR<0.05 were considered.

organism: Danio rerio

source_name: Wildtype, Region 2, with a 30 minute heat-shock at 39ºC

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Zebrafish Gene 1.1 ST Array Strips by using the Affymetrix Genechip WT Plus Reagent Kit (Santa Clara, CA, USA), according to the manufacturer’s protocols. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (WT Amplification kit Module; Affymetrix). 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis (WT Amplification kit Module; Affymetrix). 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit ; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Embryos were grown at 28ºC until bud-stage. After heat-shock (treatment) they were placed at 28ºC until the desired stage of development.

extract_protocol: Between the period of 2 hours and 2 hours 30 minutes after heat-shock, zebrafish embryos were microdissected as described (Picker et al., 2009). Tissues from Region 1 and Region 2 were kept in TRIzol (Thermo Fisher) at -70ºC. We used a pool of 100 pieces from Region 1 and 100 pieces from Region 2. Three biological replicates of each condition (gain-of-function and wildtype) were used. Total RNA was extracted using TRIzol (Thermo Fisher) and further purified with RNA Clean & Concentrator-5 kit (Zymo Research).

treatment_protocol: Embryos were heat-shock, at bud-stage, during 30 minutes at 39ºC.

value: between 3 and 4 somite stage

value: Tailbud, Presomitic mesoderm, Kupffer's Vesicle and all associated tissues

tag: genotype

value: wildtype


title: R08_FNS


title: Region 2, control embryos replicate 1


title: Region 2, transgenic embryos replicate 3

source_name: Transgenic, Region 2, with a 30 minute heat-shock at 39ºC


title: R13_FHS


title: R15_FHS


title: Region 2, transgenic embryos replicate 1


title: Region 2, transgenic embryos replicate 2


title: Region 2, control embryos replicate 3


title: R14_FHS


title: R06_FNS


title: SS101_biological rep_4

city: Wageningen

first: Desalegn

middle: W

last: Etalo

state: Gelderland

address: Droevendaalsesteeg 10

department: Microbial Ecology

institute: Netherlands Institute of Ecology

description: Gene expression profile of plants inoculated with Pseudomonas fluorescens strain SS101 that promote growth and  ISR

hyb_protocol: For the Affymetrix Arabidopsis genome GeneChip array analysis (ServiceXS), amplification and labelling of the RNA samples as well as hybridization, staining, and scanning were performed according to the manufacturer’s specifications.

data_processing: The raw array data (CEL files) were normalized  using the RMA probe summarization algorithm in R programme using Bioconductor package

organism: Arabidopsis thaliana

source_name: Arabidopsis root tip

growth_protocol: Seeds of Arabidopsis thaliana Columbia-0 (Arabidopsis) were surface sterilized for three hours by placing seeds in opened Eppendorf tubes in a desiccator jar. Two 100-ml beakers each containing 50 ml commercial bleach was placed inside and 1.5 ml concentrated HCl was added to each beaker. The desiccator jar was closed and the seeds were sterilized by chlorine gas. After 4 h, seeds were transferred on water-saturated filter paper in petri dishes followed by a 3-day treatment at 4 °C. Seeds were sown on plates containing 50 ml half-strength Murashige Skoog (MS) medium (Murashige and Skoog, 1962).

extract_protocol: RNA was isolated from the frozen shoot tissues with Trizol reagent (Invitrogen). The RNA samples were further purified using the NucleoSpin RNA II kit (Macherey-Nagel).

treatment_protocol: The root tips of one week seedlings were inoculated with 2 µl Pf.SS101 cell suspensions, 2 µl of the cysH mutant (20H12) and in the control treatement seedlings were inoculated with 2 µl of 10 mM MgSO4.

value: shoot

value: inoculated with Pf. SS101 18 dpi


title: R04_CNS

description: Gene expression data from the renal cortex of rats given Water and Standard Chow

value: Water and Standard Chow


title: HuH7 cells infected with lenti-Ctrl

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

description: Gene expression after 6 days in HuH7 cells infected with lentivirus lenti-Ctrl.

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 Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

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=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: HuH7 cells, lenti-Ctrl

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: HuH7 (Human hepatocarcinoma cell) cells were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The expression of HNF1α was increased or decreased in HuH7 cells by lentivirus carrying HNF1α or shHNF1α, respectively.

value: hepatocellular carcinoma cell line

tag: infection

value: lenti-Ctrl


title: HuH7 cells infected with lenti-HNF1α

description: Gene expression after 6 days in HuH7 cells infected with lentivirus lenti-HNF1α.

source_name: HuH7 cells, lenti-HNF1α


title: HuH7 cells infected with lenti-shHNF1α

description: Gene expression after 6 days in HuH7 cells infected with lentivirus lenti-shHNF1α.

source_name: HuH7 cells, lenti-shHNF1α


title: HuH7 cells infected with lenti-shNC

description: Gene expression after 6 days in HuH7 cells infected with lentivirus lenti-shNC.

source_name: HuH7 cells, lenti-shNC

value: lenti-shNC


title: Region 1, control embryos replicate 3

description: Region 1 samples were obtained by microdissecting zebrafish embryos between the first and last somite. All somites and associated lateral and ventral tissues are present.

source_name: Wildtype, Region 1, with a 30 minute heat-shock at 39ºC

value: Somites and all associated tissues


title: R01_CNS

value: Sprague Dawley

value: Male

value: 7 weeks

value: renal cortex


title: SS101_biological rep_3

scan_protocol: For the Affymetrix Arabidopsis genome GeneChip array analysis (ServiceXS), amplification and labelling of the RNA samples as well as hybridization, staining, and scanning were performed according to the manufacturer’s specifications.

tag: treatment


title: Region 1, transgenic embryos replicate 3

source_name: Transgenic, Region 1, with a 30 minute heat-shock at 39ºC


title: Control_biological rep_2

description: Gene expression profile of plants treated with MgSO4 (control)

label_protocol: For the Affymetrix Arabidopsis genome GeneChip array analysis (ServiceXS), amplification and labelling of the RNA samples as well as hybridization, staining, and scanning were performed according to the manufacturer’s specifications.

value: treated with 10 mM MgSO4 18 dpi


title: Control_biological rep_1


title: Region 1, transgenic embryos replicate 1


title: endothelial cell_5 nm silver_rep3

city: Seoul

first: Jiyoung

last: Jang

state: Seodaemungu

address: 50-1 Yonseiro

department: Microbiology

country: South Korea

institute: Yonsei university

description: Gene expression data from 5 nm silver nanoparticles exposed human endothelial cell

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: endothelial cell_exposure to 5 nm silver nanoparticles at approximately LD50 for 6 h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: EA.hy926 cells were plated on 60-mm petri dishes (4.5 x 10^5 cells) overnight.

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's guidelines.

treatment_protocol: EA.hy926 cells were exposed to silver nanoparticles at approximately LD50 concentration for 6 hours.

tag: cell line

value: somatic human umbilical vein endothelial cells

tag: morphology

value: endothelial


title: Control_biological rep_3


title: SS101_biological rep_1


title: Region 1, control embryos replicate 2

value: between 3 and 4 somite stage


title: Control_biological rep_4


title: Region 1, control embryos replicate 1


title: Region 1, transgenic embryos replicate 2


title: MDA-MB-231 Cells YM-155 at 20 Hours Triplicate 3

description: Gene expression data from MDA-MB-231 cells grown under variable experimental treatment

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner  (Affymetrix, ThermoFisher Scientific)

data_processing: The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific). RMA data provided.

source_name: MDA-MB-231 ATCC® HTB-26™ cells - YM-155 14.6ng/ml @ 20 Hours

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 10% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C in 95% atmosphere and 5% CO2, having been sub-cultured every three to five days.

treatment_protocol: YM-155 was dissolved in DMSO [20mg/mL] and all subsequent dilutions were carried out using sterile HBSS. Toxicity values were acquired over time and concentration and the LC50s were determined by regression analysis.  For whole transcriptome studies, gradual increments totaling 83 ng/ml of YM-155 was added to the cells and morphological changes were monitored every hour to ensure no cell death was evident. At 8 hours, the cells retained morphological shape, flask attachment and had no obvious signs of cell death.  Cells were rapidly washed in HBSS 3 times, spun and frozen at -80 °C. For 20 hour studies – cells were treated with the LC50 14.6 ng/ml , and cells were rapidly washed in HBSS 3 times, spun and frozen at -80 °C.

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: MDA-MB-231 Cells YM-155 at 8 Hours Triplicate 3

source_name: MDA-MB-231 ATCC® HTB-26™ cells - YM-155 83ng/ml @ 8 Hours


title: MDA-MB-231 Cells YM-155 at 20 Hours Triplicate 1

source_name: MDA-MB-231 ATCC® HTB-26™ cells - YM-155 14.6 ng/ml @ 20 Hours


title: R03_CNS

source_name: Kidney Cortex


title: endothelial cell_100 nm silver_rep2

description: Gene expression data from 100 nm silver nanoparticles exposed human endothelial cell

source_name: endothelial cell_exposure to 100 nm silver nanoparticles at approximately LD50 for 6 h


title: SS101_biological rep_2


title: endothelial cell_5 nm silver_rep1


title: MDA-MB-231 Cells YM-155 at 20 Hours Triplicate 2

treatment_protocol: YM-155 was dissolved in DMSO [20mg/mL] and all subsequent dilutions were carried out using sterile HBSS. Toxicity values were acquired over time and concentration and the LC50s were determined by regression analysis.  For whole transcriptome studies, gradual increments totaling 83ng/ ml of YM-155 was added to the cells and morphological changes were monitored every hour to ensure no cell death was evident. At 8 hours, the cells retained morphological shape, flask attachment and had no obvious signs of cell death.  Cells were rapidly washed in HBSS 3 times, spun and frozen at -80 °C. For 20 hour studies – cells were treated with the LC50 14.6 ng/ml , and cells were rapidly washed in HBSS 3 times, spun and frozen at -80 °C.


title: endothelial cell_control_rep3

description: Gene expression data from non-exposed human endothelial cell

source_name: endothelial cell_non exposure


title: 20H12_biological rep_4

description: Gene expression profile of plants inoculated with cysH mutant bacteria that fail to promote growth and  ISR

value: inoculated with cysH mutant 18 dpi


title: endothelial cell_5 nm silver_rep2


title: endothelial cell_100 nm silver_rep1


title: MDA-MB-231 Cells YM-155 at 8 Hours Triplicate 2

treatment_protocol: YM-155 was dissolved in DMSO [20mg/mL] and all subsequent dilutions were carried out using sterile HBSS. Toxicity values were acquired over time and concentration and the LC50s were determined by regression analysis.  For whole transcriptome studies, gradual increments totaling 83ng/ml of YM-155 was added to the cells and morphological changes were monitored every hour to ensure no cell death was evident. At 8 hours, the cells retained morphological shape, flask attachment and had no obvious signs of cell death.  Cells were rapidly washed in HBSS 3 times, spun and frozen at -80 °C. For 20 hour studies – cells were treated with the LC50 14.6 ng/ml , and cells were rapidly washed in HBSS 3 times, spun and frozen at -80 °C.


title: endothelial cell_100 nm silver_rep3


title: 20H12_biological rep_3

value: shoot


title: MDA-MB-231 Cells Control Triplicate3

source_name: MDA-MB-231 ATCC® HTB-26™ cells - No treatment


title: MDA-MB-231 Cells YM-155 at 8 Hours Triplicate 1


title: 20H12_biological rep_2


title: endothelial cell_control_rep1


title: MDA-MB-231 Cells Control Triplicate2


title: 20H12_biological rep_1


title: endothelial cell_control_rep2


title: CNV-RPE-88 rep4

status: Public on Aug 25 2017

city: Freiburg

first: Gottfried

last: Martin

address: Killianstr. 5

department: Klinik für Augenheilkunde

country: Germany

institute: Universitätsklinikum Freiburg

description: patient age 83 years, male, classic CNV with greatest linear diameter of 2 optic disc diameters, no previous treatment for AMD, no ocular comorbidity or complications

hyb_protocol: Samples were hybridized according to the Agilent 4x44k expression arrays protocol.

scan_protocol: Arrays were scanned with an Agilent scanner G2505C. Spots were detected with the Agilent Feature Extraction software.

data_processing: Raw data were processed by the Bioconductor package Agi4x44PreProcess_1.22.0 with standard settings to get the PocessedData.txt file

source_name: CNV-derived retina pigment epithelial cells

label_protocol: Samples were labeled with Cy3.

growth_protocol: Cells of CNV-RPE, ARPE-19, and hRPE were cultured in DMEM / Ham’s F-12 medium (Biochrom, Berlin, Germany) containing 10% fetal bovine serum (FBS, Biowest, Nuaillé, France), 1% L-Glutamin 200 mM (Biochrom), 1% penicillin/streptomycin (10.000 U/ml / 10.000 µg/ml, Gibco, Life Technologies, Karlsruhe, Germany), and a supplement containing insulin transferrine sodium (Roche Diagnostics, Mannheim, Germany), Hepes (Biochrom) and essential amino acids (Biochrom).

extract_protocol: RNA was isolated by means of RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Each cell line was grown in T25 flasks and was split twice to get four flasks for analysis. Cells were kept confluent for seven days. Cells were incubated in FBS free medium (substituted with bovine serum albumin) for three days before gene expression assays and analysis of morphologic features to eliminate effects of FBS.

tag: patient age

value: 83 years

tag: gender

value: male

tag: cnv

value: no previous treatment for AMD

value: no ocular comorbidity or complications


title: CNV-RPE-88 rep3

value: classic CNV with greatest linear diameter of 2 optic disc diameters

value: CNV-derived retina pigment epithelial cells


title: hRPE rep3

source_name: Retina pigment epithelial cells

value: Retina pigment epithelial cells


title: CNV-RPE-88 rep1


title: hRPE rep1


title: hRPE rep2


title: hRPE rep4


title: CNV-RPE-69 rep4

description: patient age 84 years, female, classic CNV with a greatest linear diameter of 2.5 optic disc diameters, no previous treatment for AMD, no ocular comorbidity or complications

value: 84 years

value: female


title: First node OPT vs FFP replicate 3

city: Guangzhou

first: Junliang

last: Zhao

address: 29 Jinying Road, Tianhe District

institute: Guangdong Academy of Agricultural Science

description: Biological replicate 3 of 3.

hyb_protocol: Microarray slides were hybridized for 16 hours at 65℃ with hybridization buffer containing two paired labeled samples in final concentration of 5X Denhardt, 3X SSC and 0.2% SDS. After hybridization, the slides were subjected to four-step stringency washes (2X SSC + 0.2% SDS, twice at 42℃ for 4 min; 0.2X SSC, twice at 42℃ for 4 min).

scan_protocol: Microarrays were scanned using Axon 4000B scanner and analyzed by Genepix Pro 6.0 (Axon Instruments, USA).

data_processing: The raw data from microarrays was filtered by Genepix Pro 6.0. Data were further normalized using the Lowess method in Acuity 4.0 (Axon Instruments, USA).

organism: Oryza sativa

source_name: First node

label_protocol: RNA Amplification and cDNA labeling were conducted using cRNA Amplification and Labeling Kit (CapitalBio, China), according to the manufacturer's protocol. cDNA from first node of rice plants by FFP were labeled with Cy3 dye . cDNA from samples of OPT were labeled with Cy5 dye and paired with FFP for microarray assay.

growth_protocol: The field experiment was conducted in the early cropping season of 2012 at Dafeng experimental farm in Guangzhou (23°10′N, 113°20′E, 41m asl), Guangdong province, China. The experiment was laid out in a split-block design with 2 nitrogen management practicetreatment as the main plot and 2 variety treatments as the subplot.

extract_protocol: About 0.1g (fresh weight) samples of first basal internode of YJRZ was taken at 30 days after transplanting. Total RNA was extracted with Trizol reagent (Invitrogen,Carlsbad, CA, USA) and purified with NucleoSpinRNA Clean-up reagent (MACHEREY-NAGEL,Germany). RNA quality and quantity were assessed by formaldehyde denaturing agarose gel electrophoresis and spectrophotometry (Nanodrop-1000, Thermo-Fisher, USA), respectively.

treatment_protocol: Two nitrogen management practice treatments were applied in the main field: the farmers’N-fertilizer management practice (FFP treatment) and optimized nitrogen application approach (OPT treatment). The amount, ratio and timing of split application of nitrogen in FFP treatment was determined based on our surveyon common practice of most farmers in the Pearl River Delta of Guangdong province, China. It’s noteworthy that all nitrogen applications have been completed before panicle initiation. Under OPT treatment,the total nitrogen input was reduced by 20% compared to that of FFP, and the ratio and timing of split application of nitrogen were all adjusted. Strikingly, much nitrogen application was moved backwards, with up to 40% of nitrogen being applied after panicle initiation.

tag: cultivar

value: Yin-Jing-Ruan-Zhan (YJRZ)

value: 30 days after transplanting

tag: nitrogen management

value: Treated by OPT

tag: tissue

value: first node

tag: nitrogren management

value: Treated by FFP

value: First node


title: ARPE-19 rep4


title: CNV-RPE-69 rep1

value: classic CNV with a greatest linear diameter of 2.5 optic disc diameters

tag: status


title: ARPE-19 rep3

tag: cell type


title: CNV-RPE-69 rep3


title: CNV-RPE-69 rep2


title: CNV-RPE-88 rep2


title: Lami_BMDC

city: Osaka

first: Tomotsugu

last: Takano

address: 3-1 Yamadaoka, Suita

department: Research Institute for Microbial Diseases

institute: Osaka University

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 2.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: BMDC, stimulated with 500μg/ml of laminarin, 8H

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain


title: ARPE-19 rep2


title: MDA-MB-231 Cells Control Triplicate1

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: ARPE-19 rep1


title: First node OPT vs FFP replicate 1

description: Biological replicate 1 of 3.

tag: age


title: First node OPT vs FFP replicate 2

description: Biological replicate 2 of 3.


title: none_BMDC

source_name: BMDC, unstimulated, 8H

value: unstimulated, 8H


title: Negative control

first: Nagendra

middle: Kumar

last: Kaushik

state: Nowon-Gu

address: 20 Kwangwoongil, Wolgye Dong 447-1

department: Biophysics

institute: Kwangwoon University

description: cont 2

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a GeneChip Fluidics Station 450 (Affymetrix) and scanned by using a GeneChip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: monocytes

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the double-stranded cDNA template though an IVT (in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: THP-1 cells were maintained in RPMI-1640 medium supplemented with 10% FBS and antimycotic/antibiotics.

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

treatment_protocol: Prior to plasma treatment, THP-1 cells were stimulated with phorbol (100ng/ml) for 2 days and subsequently non-thermal plasma was exposed to 1 min and 3 min to these PMA treated cells.

value: phorbol


title: Lami_MoDC

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST array, washed and stained according to the manufacturer's instructions.

source_name: MoDC, stimulated with 500μg/ml of laminarin, 8H

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

value: male


title: IMM_EPH04P1_hWB_SLE_TRD-000924:31-001_19

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

scan_protocol: Biotin-labeled cRNA was generated from cDNA and used to probe Human Genome U219 array, comprising of 49,293 probe sets and representing more than 20,000 human genes, using the Gene Titan MC instrument (Affymetrix, West Sacramento, CA). All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

data_processing: CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm using the “Affy” package in R with custom CDF from BrainArray.

source_name: Whole blood

label_protocol: Total RNA was treated with DNase I and cleaned up with Qiagen RNeasy MiniElute Cleanup Kit (Cat. # 74204). The RNA concentrations were determined by NanoDrop and RNA quality was evaluated using Experion (Bio-Rad). All target labeling reagents were purchased from Affymetrix (West Sacramento CA). Double-stranded cDNAs were synthesized from 1ug of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

extract_protocol: Total RNA was isolated from the cells with Qiagen PAXgene blood miRNA kit (Cat. # 763134).

treatment_protocol: PAXgene tubes were stored at -20C until processing for RNA extraction. RNA extraction and Affy profiling were performed in four different batches, noted in the experiment design.

tag: disease

value: SLE

value: 2.5 mL of peripheral blood from SLE patients were collected directly into PAXgene tubes


title: THP-1 monocyte treated with phorbol and 3 min plasma

value: phorbol and 3 min non-thermal plasma


title: I_Ovaries_4

city: Berlin

first: Lena

last: Lampe

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Labeling reactions were column purified, dried down using a speed-vac at 45°C and resuspended in blocking and hybridization buffer.

scan_protocol: After scanning at 5 µm resolution with a G2565CA high-resolution laser microarray scanner features were extracted with an image analysis tool version A.11.5.1.1 using the default protocol

data_processing: Microarray data were analysed using the R limma package. All arrays were corrected for background using the normexp function and normalized by quantile normalization. Next, the data of all replicated spots on the array were pooled using the avereps function, which resulted in an elist containing log2 relative expression values

organism: Anopheles gambiae

source_name: mosquito female ovary; 18h post P. falciparum-infected blood meal; replicate 12

label_protocol: An amount of 100 ng total RNA was processed with the miRNA Complete Labeling and Hyb Kit according the supplier’s recommendations. In brief, samples were dephosphorylated with calf intestine alkaline phosphatase and further denatured with DMSO. The sample RNA functioned as acceptor in a T4 RNA ligase mediated reaction with the RNA donor 3’, 5’-cytidine bisphosphate having a single Cy3 label attached to the 3’ phosphate of the nucleotide (Cy3-pCp).

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. Briefly, after phase separation by centrifugation total RNA was purified by silica membrane, eluted with water and stored at -80°C. The total RNA yield was measured by NanoDropND-1000 Spectrophotometer. The integrity of total RNA was assessed with a 2100 Bioanalyzer and a RNA 6000 Nano LabChip kit. Furthermore, the ratio of miRNA fraction to small RNAs from isolated total RNA was monitored by use of the Agilent Small RNA kit.

treatment_protocol: Three-day-old virgin A. gambiae females were fed with either uninfected human blood, P. falciparum-infected blood or 10% sucrose solution. All mosquito groups were kept at 26°C and 80% humidity. At 18 h post feeding, female mosquitoes were dissected on ice to collect head, midgut, ovaries and the abdominal carcass. The latter includes the fat body as well as the cuticle. Per time point and sample, tissues of 15 female mosquitoes were pooled in cold PBS. After sample collection, the PBS was removed and 500 µl TRIzol added to the tissue samples. The tissues were homogenized using steal beads in a Qiagen tissue lyser (8 min of 50 rpm at 4°C) and kept at -80°C until further usage. The experiment was performed in four biological replicates.

tag: Sex

value: Ovary

tag: condition

value: 18h post P. falciparum infection


title: I_Head_4

source_name: mosquito female head; 18h post P. falciparum-infected blood meal; replicate 16

value: female

value: Head


title: IMM_EPE07P1_hWB_SLE_TRD-000942:31-001_13

hyb_protocol: Biotin-labeled cRNA was generated from cDNA and used to probe Human Genome U219 array, comprising of 49,293 probe sets and representing more than 20,000 human genes


title: IMM_EPF03P1_hWB_SLE_TRD-000915:31-001_41


title: I_Carcass_4

source_name: mosquito female carcass; 18h post P. falciparum-infected blood meal; replicate 4

value: Carcass


title: I_Ovaries_1

source_name: mosquito female ovary; 18h post P. falciparum-infected blood meal; replicate 9


title: I_Head_2

source_name: mosquito female head; 18h post P. falciparum-infected blood meal; replicate 14


title: IMM_EPG03P1_hWB_SLE_TRD-000937:31-001_38


title: I_Head_3

source_name: mosquito female head; 18h post P. falciparum-infected blood meal; replicate 15


title: IMM_EPF06P1_hWB_SLE_TRD-000916:31-001_9


title: Positive control

description: cont 1


title: IMM_EPC04P1_hWB_SLE_TRD-000936:31-001_24


title: I_Head_1

source_name: mosquito female head; 18h post P. falciparum-infected blood meal; replicate 13


title: I_Ovaries_2

source_name: mosquito female ovary; 18h post P. falciparum-infected blood meal; replicate 10


title: IMM_EPF01P1_hWB_SLE_TRD-000931:31-001_31


title: IMM_EPG06P1_hWB_SLE_TRD-000922:31-001_6


title: none_MoDC

source_name: MoDC, unstimulated, 8H

tag: treatment


title: I_Carcass_3

source_name: mosquito female carcass; 18h post P. falciparum-infected blood meal; replicate 3


title: I_Ovaries_3

source_name: mosquito female ovary; 18h post P. falciparum-infected blood meal; replicate 11


title: IMM_EPC02P1_hWB_SLE_TRD-000938:31-001_18


title: IMM_EPB02P1_hWB_SLE_TRD-000944:31-001_17


title: IMM_EPA11P1_hWB_SLE_TRD-000644:31-001_71


title: IMM_EPA05P1_hWB_SLE_TRD-000914:31-001_43


title: IMM_EPB12P1_hWB_SLE_TRD-000875:31-001_24


title: I_Carcass_2

source_name: mosquito female carcass; 18h post P. falciparum-infected blood meal; replicate 2


title: UI_Head_2

source_name: mosquito female head; 18h post normal blood meal; replicate 14

value: 18h post blood meal


title: UI_Head_3

source_name: mosquito female head; 18h post normal blood meal; replicate 15


title: I_Carcass_1

source_name: mosquito female carcass; 18h post P. falciparum-infected blood meal; replicate 1


title: UI_Ovaries_4

source_name: mosquito female ovary; 18h post normal blood meal; replicate 12


title: UI_Head_4

source_name: mosquito female head; 18h post normal blood meal; replicate 16


title: UI_Head_1

source_name: mosquito female head; 18h post normal blood meal; replicate 13


title: UI_Ovaries_3

source_name: mosquito female ovary; 18h post normal blood meal; replicate 11


title: UI_Ovaries_2

source_name: mosquito female ovary; 18h post normal blood meal; replicate 10


title: UI_Carcass_4

source_name: mosquito female carcass; 18h post normal blood meal; replicate 4


title: UI_Ovaries_1

source_name: mosquito female ovary; 18h post normal blood meal; replicate 9


title: IMM_EPF01P1_hu WB_SLE_TRD000580-31-001_27

source_name: Whole blood


title: IMM_EPH07P1_hu WB_SLE_TRD000579-31-001_26


title: IMM_EPA08P1_hu WB_SLE_TRD-000522_50


title: IMM_EPB12P1_hu WB_SLE_TRD-000505:31-001_39


title: UI_Carcass_3

source_name: mosquito female carcass; 18h post normal blood meal; replicate 3


title: IMM_EPE11P1_hWB_SLE_TRD-000874:31-001_46


title: IMM_EPF12P1_hu WB_SLE_TRD000578-31-001_25


title: IMM_EPD01P1_hu WB_SLE_TRD-000553:31-001_86


title: IMM_EPB01P1_hWB_SLE_TRD-000645:31-001_79


title: IMM_EPA05P1_hu WB_SLE_TRD-000524_52


title: IMM_EPG07P1_hWB_SLE_TRD-000646:31-001_55


title: UI_Carcass_2

source_name: mosquito female carcass; 18h post normal blood meal; replicate 2


title: UF_Head_3

source_name: mosquito female head; sugarfed; replicate 15

value: sugarfed


title: IMM_EPB06P1_hu WB_SLE_TRD-000521_49


title: UF_Head_4

source_name: mosquito female head; sugarfed; replicate 16


title: UF_Midgut_4

source_name: mosquito female midgut; sugarfed; replicate 8

value: Midgut


title: UF_Ovaries_1

source_name: mosquito female ovary; sugarfed; replicate 9


title: UF_Midgut_3

source_name: mosquito female midgut; sugarfed; replicate 7


title: UF_Ovaries_4

source_name: mosquito female ovary; sugarfed; replicate 12


title: UI_Carcass_1

source_name: mosquito female carcass; 18h post normal blood meal; replicate 1


title: UF_Head_1

source_name: mosquito female head; sugarfed; replicate 13


title: UF_Ovaries_2

source_name: mosquito female ovary; sugarfed; replicate 10


title: UF_Ovaries_3

source_name: mosquito female ovary; sugarfed; replicate 11


title: UF_Head_2

source_name: mosquito female head; sugarfed; replicate 14


title: UF_Midgut_2

source_name: mosquito female midgut; sugarfed; replicate 6


title: IMM_EPA04P1_hu WB_SLE_TRD-000523_51


title: UF_Midgut_1

source_name: mosquito female midgut; sugarfed; replicate 5


title: IMM_EPE04P1_hu WB_SLE_TRD-000550:31-001_83


title: Control -- HuProt Array 362000

type: protein

city: Frederick

first: Jeff

last: Gildersleeve

state: MD

address: 376 Boyles St.

institute: National Cancer Institute

description:
362000
N/A

hyb_protocol: Arrays were blocked with BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000A fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG.  Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

data_processing: First, median pixel intensity of each feature was background subtracted.  Second, signals for features that were saturated at the high photomultipler tube (PMT) setting were calculated by proportionally scaling the value from the low PMT setting according to a correction factor, which was calculated based on mid-intensity signals measured at the high and low PMT settings.  To account for slide-to-slide variations in array processing, microarray data were normalized by median centering based on a reference serum sample analyzed on each slide.  Additionally, a minimum signal of 150 was set as the floor.  Since array features were printed in duplicate and all samples were analyzed on two slides, pre-processing averaged normalized data from 4 technical replicates.  Final data are reported on a log 2 scale.

molecule: protein

organism: unidentified

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti-human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM  (Jackson Immuno, 109-495-043).

extract_protocol: Serum was obtained from peripheral blood samples

tag: antibody concentration [nm]

tag: antibody

value: IgG

label: DyLight 649

value: IgM


title: R02_CNS

source_name: Kidney Cortex

value: Sprague Dawley

value: Male

value: 7 weeks

value: renal cortex

tag: diet

value: Water and Standard Chow


title: UF_Carcass_3

source_name: mosquito female carcass; sugarfed; replicate 3


title: UF_Carcass_2

source_name: mosquito female carcass; sugarfed; replicate 2


title: UF_Carcass_4

source_name: mosquito female carcass; sugarfed; replicate 4


title: Affinity Mature 3F8 -- HuProt Array 361994

description:
361994
Chimeric mouse-human

organism:
Homo sapiens
Mus musculus


title: UF_Carcass_1

source_name: mosquito female carcass; sugarfed; replicate 1

tag: Sex:


title: Germline 3F8 -- HuProt Array 361998

description:
361998
Chimeric mouse-human


title: cervical cancer-without lymph-node metastasis-3

status: Public on Aug 24 2017

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

description:
ZSZ_NS
miRNA expression of cervical cancer tissue without lymph-node metastasis

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: cervical cancer without lymph-node metastasis

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: Six cervical cancer tissues derived from stage I and II patients with (n=3) or without (n=3) lymph node metastasis collected.

tag: subject status

value: cervical cancer stage I-II patient

value: cervical

tag: tissue subtype

value: without lymph-node metastasis


title: Control -- HuProt Array 361996

description:
361996
N/A


title: cervical cancer-without lymph-node metastasis-2

description:
ZJL_NS
miRNA expression of cervical cancer tissue without lymph-node metastasis


title: cervical cancer-with lymph-node metastasis-3

description:
DDW_NS
miRNA expression of cervical cancer tissue with lymph-node metastasis

source_name: cervical cancer with lymph-node metastasis

value: with lymph-node metastasis


title: cervical cancer-with lymph-node metastasis-1

description:
DRW_NS
miRNA expression of cervical cancer tissue with lymph-node metastasis


title: Affinity Mature 3F8 -- HuProt Array 361993

description:
361993
Chimeric mouse-human


title: cervical cancer-with lymph-node metastasis-2

description:
ZCF_NS
miRNA expression of cervical cancer tissue with lymph-node metastasis


title: cervical cancer-without lymph-node metastasis-1

description:
TJH_NS
miRNA expression of cervical cancer tissue without lymph-node metastasis


title: ExVivo_Blood_7Gy_8213

city: Tempe

first: Jia

last: Zeng

state: AZ

address: 1001 S McAllister Ave

department: The Biodesign Institute

institute: Arizona State University

description: Gene expression after 24hr in 7Gy-irradiated macaque blood

hyb_protocol: The cRNA (1.65 μg) was fragmented and hybridized to Agilent’s whole genome microarrays (G4845A, Agilent Technologies) using the Agilent Gene Expression Hybridization Kit.  Human samples were hybridized at 65°C according to Agilent’s standard protocol; however, NHP samples were incubated at 63°C to optimize hybridization of NHP probes on the human whole genome array platform.  The hybridization was performed for 17 hr. with recommended rotation, followed by washing according to Agilent’s instructions.

scan_protocol: Microarray slides were immediately scanned with the Agilent Scanner (G2404B, Agilent Technologies) using the recommended settings.

data_processing: The scanned images were analyzed with Agilent Feature Extraction (v10.7) using default parameters for background correction and flagging of non-uniform features. The human and NHP Agilent microarray data were quantile-normalized with the qnorm function in R, which transformed the quantiles of dataset so that individual data sets had the same distribution.

organism: Macaca mulatta

source_name: Peripheral Blood, 7Gy

label_protocol: Cyanine-3 (Cy3)-labeled (cRNA) was prepared from 200 ng input RNA using Agilent’s One-Color Quick Amp labeling kit (Agilent Technologies) according to manufacturer’s instructions.  After purification of cRNA by RNAeasy column (QIAGEN, Valencia, CA, USA), the cRNA yield and Cy3 dye incorporation was measured with a NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

extract_protocol: White blood cell and differential cell counts were obtained from the cultured blood samples before irradiation and again immediately before RNA extraction at 24 hr. after irradiation (48 hr. post blood collection).  The RNA extraction was done using the 5-Prime PerfectPure™ blood RNA purification kit (5 Prime, Inc., Gaithersburg, MD) as per manufacturer’s recommendations.  Globin mRNA reduction was performed using human GLOBINclearTM (Ambion Inc., Austin, TX) on both human and NHP samples to prepare them for microarray analysis.

treatment_protocol: Peripheral blood (PB) samples were drawn from 9 healthy male and 5 female Chinese rhesus macaques under a protocol approved by the University of Illinois at Chicago IACUC and shipped at 20 ± 2°C for arrival at Columbia University in New York within 24 hr. of blood draw.  In parallel, de-identified human PB samples were collected, under a Columbia University IRB protocol and with written informed consent, from 10 male and 10 female volunteers, into sodium citrate Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ) as used for NHP samples and maintained at 20 ± 2°C overnight to simulate the NHP sample shipping.  PB samples from both NHP and humans were divided into 2 ml aliquots and diluted 1:1 with RPMI 1640 medium (Mediatech, Herndon, VA, USA) supplemented with 10% heat inactivated fetal bovine serum (HyClone, Logan, UT, USA).  These aliquots were exposed to 0, 2, 5, 6 and 7 Gy Cesium-137 gamma rays at 24 hr. after blood draw using a Gammacell-40 137Cs irradiator (AECL, Ottawa, Ontario, Canada) with a dose rate of 0.8 Gy/min, and then placed in a 37°C humidified incubator with 5% CO2 for 24 hr.

value: whole blood

tag: gender

tag: stress

value: ex vivo irradiation

tag: dose


title: ExVivo_Blood_7Gy_8319

tag: tissue

value: Female


title: ExVivo_Blood_7Gy_8316


title: ExVivo_Blood_7Gy_8052


title: ExVivo_Blood_6Gy_8319

description: Gene expression after 24hr in 6Gy-irradiated macaque blood

source_name: Peripheral Blood, 6Gy


title: ExVivo_Blood_7Gy_8317


title: ExVivo_Blood_7Gy_8128


title: ExVivo_Blood_7Gy_8042


title: ExVivo_Blood_7Gy_8321


title: ExVivo_Blood_7Gy_8304


title: ExVivo_Blood_7Gy_8036


title: ExVivo_Blood_6Gy_8316


title: ExVivo_Blood_7Gy_8221


title: ExVivo_Blood_7Gy_8122


title: ExVivo_Blood_7Gy_8222


title: ExVivo_Blood_6Gy_8222


title: ExVivo_Blood_6Gy_8321


title: THP-1 monocyte treated with phorbol and 1 min plasma

source_name: monocytes

tag: cell line

value: phorbol and 1 min non-thermal plasma


title: ExVivo_Blood_6Gy_8213


title: ExVivo_Blood_6Gy_8304


title: ExVivo_Blood_6Gy_8122


title: ExVivo_Blood_6Gy_8317


title: ExVivo_Blood_6Gy_8052


title: ExVivo_Blood_6Gy_8221


title: ExVivo_Blood_6Gy_8226


title: Germline 3F8 -- HuProt Array 361997

description:
361997
Chimeric mouse-human


title: ExVivo_Blood_5Gy_8319

description: Gene expression after 24hr in 5Gy-irradiated macaque blood

source_name: Peripheral Blood, 5Gy


title: ExVivo_Blood_5Gy_8304


title: ExVivo_Blood_6Gy_8128


title: ExVivo_Blood_5Gy_8042


title: ExVivo_Blood_5Gy_8052


title: ExVivo_Blood_5Gy_8036


title: ExVivo_Blood_5Gy_8128


title: ExVivo_Blood_5Gy_8321


title: ExVivo_Blood_5Gy_8226


title: ExVivo_Blood_5Gy_8122


title: ExVivo_Blood_5Gy_8221


title: ExVivo_Blood_2Gy_8316

description: Gene expression after 24hr in 2Gy-irradiated macaque blood

source_name: Peripheral Blood, 2Gy


title: ExVivo_Blood_5Gy_8316


title: ExVivo_Blood_2Gy_8317


title: ExVivo_Blood_6Gy_8042


title: ExVivo_Blood_2Gy_8304


title: ExVivo_Blood_6Gy_8036


title: ExVivo_Blood_2Gy_8321


title: ExVivo_Blood_5Gy_8317


title: ExVivo_Blood_2Gy_8221


title: ExVivo_Blood_2Gy_8226


title: ExVivo_Blood_2Gy_8213


title: ExVivo_Blood_2Gy_8052


title: ExVivo_Blood_2Gy_8042


title: ExVivo_Blood_2Gy_8036


title: ExVivo_Blood_5Gy_8222


title: ExVivo_Blood_2Gy_8128


title: ExVivo_Blood_2Gy_8222


title: ExVivo_Blood_2Gy_8122


title: ExVivo_Blood_0Gy_8321

description: Gene expression after 24hr in 0Gy-irradiated macaque blood

source_name: Peripheral Blood, 0Gy

value: control


title: ExVivo_Blood_0Gy_8319


title: ExVivo_Blood_0Gy_8316


title: ExVivo_Blood_0Gy_8304


title: ExVivo_Blood_0Gy_8317


title: ExVivo_Blood_0Gy_8128


title: ExVivo_Blood_0Gy_8213


title: ExVivo_Blood_0Gy_8222


title: ExVivo_Blood_5Gy_8213


title: ExVivo_Blood_7Gy_U

description: Gene expression after 24hr in 7Gy-irradiated human blood


title: ExVivo_Blood_0Gy_8221


title: ExVivo_Blood_0Gy_8036


title: ExVivo_Blood_0Gy_8226


title: ExVivo_Blood_7Gy_T


title: ExVivo_Blood_0Gy_8042


title: ExVivo_Blood_7Gy_Q


title: ExVivo_Blood_7Gy_R


title: ExVivo_Blood_7Gy_O


title: ExVivo_Blood_0Gy_8052


title: ExVivo_Blood_7Gy_P


title: ExVivo_Blood_7Gy_S


title: ExVivo_Blood_7Gy_E


title: ExVivo_Blood_7Gy_F


title: ExVivo_Blood_7Gy_H


title: ExVivo_Blood_7Gy_N


title: ExVivo_Blood_7Gy_J


title: ExVivo_Blood_7Gy_M


title: ExVivo_Blood_7Gy_G


title: ExVivo_Blood_7Gy_L


title: ExVivo_Blood_7Gy_K


title: ExVivo_Blood_7Gy_C


title: ExVivo_Blood_6Gy_U

description: Gene expression after 24hr in 6Gy-irradiated human blood


title: ExVivo_Blood_7Gy_A


title: ExVivo_Blood_6Gy_L


title: ExVivo_Blood_6Gy_T


title: ExVivo_Blood_6Gy_N


title: ExVivo_Blood_6Gy_M


title: ExVivo_Blood_7Gy_D


title: ExVivo_Blood_6Gy_Q


title: ExVivo_Blood_6Gy_R


title: ExVivo_Blood_6Gy_P


title: ExVivo_Blood_6Gy_H


title: ExVivo_Blood_6Gy_O


title: ExVivo_Blood_5Gy_U

description: Gene expression after 24hr in 5Gy-irradiated human blood


title: ExVivo_Blood_5Gy_T


title: ExVivo_Blood_6Gy_A


title: ExVivo_Blood_6Gy_G


title: ExVivo_Blood_6Gy_E


title: Sample 74_Responder

city: Paris

first: Olivier

last: KOSMIDER

address: 27 Rue du faubourg Saint Jacques

country: France

institute: Institut Cochin

hyb_protocol: Fragmented, labeled cDNA was hybridized to Affymetrix HuGene-2_0-st oligonucleotide microarrays (ThermoFisher Scientific).

scan_protocol: According to manufacturer protocol

data_processing:
Raw expression values were normalized using Robust Multi-array Averaging (RMA) in R.
Genes differentially expressed between responder and non-responder at baseline, and genes differentially expressed after treatment in responder minus those differentially expressed in non-responder were considered for Gene Set Enrichment Analysis (GSEA).

source_name: Bone marrow mononuclear cells

label_protocol: Linear amplification of 20ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labelling System (NuGEN, San Carlos, CA).

growth_protocol: Direct RNA extraction from bone marrow mononuclear cells.

extract_protocol: Mononuclear cells were purified on Ficoll gradient and pellets were conserved in Trizol (ThermoFisher Scientific, Whaltam, MA) before RNA extraction (QIAGEN)

tag: sample type

value: follow up sample

tag: cell type

value: Bone marrow mononuclear cells

tag: response to lenalidomide

value: Responder


title: ExVivo_Blood_6Gy_F


title: ExVivo_Blood_7Gy_B


title: ExVivo_Blood_6Gy_K


title: ExVivo_Blood_6Gy_C


title: ExVivo_Blood_6Gy_S


title: ExVivo_Blood_6Gy_B


title: Sample 71_Non responder

value: Non responder


title: ExVivo_Blood_5Gy_R

value: Male


title: ExVivo_Blood_5Gy_S


title: ExVivo_Blood_6Gy_J


title: ExVivo_Blood_6Gy_D


title: Sample 72_Responder


title: ExVivo_Blood_5Gy_N


title: ExVivo_Blood_5Gy_O


title: Sample 73_Responder


title: ExVivo_Blood_5Gy_Q


title: Sample 70_Non responder


title: Sample 69_Responder


title: Sample 66_Non responder


title: ExVivo_Blood_5Gy_P


title: Sample 68_Responder


title: Sample 67_Responder


title: ExVivo_Blood_5Gy_K


title: ExVivo_Blood_5Gy_H


title: ExVivo_Blood_5Gy_M


title: ExVivo_Blood_5Gy_J


title: Sample 65_Non responder


title: ExVivo_Blood_5Gy_L


title: ExVivo_Blood_5Gy_B


title: Sample 64_Non responder


title: Sample 62_Responder


title: ExVivo_Blood_5Gy_G


title: Sample 61_Responder


title: Sample 63_Non responder


title: ExVivo_Blood_5Gy_D


title: ExVivo_Blood_5Gy_E


title: Sample 60_Non responder


title: Sample 59_Responder


title: ExVivo_Blood_5Gy_C


title: Sample 58_Responder


title: ExVivo_Blood_5Gy_F


title: Sample 55_Non responder


title: Sample 56_Non responder


title: ExVivo_Blood_5Gy_A


title: Sample 53_Non responder


title: ExVivo_Blood_2Gy_U

description: Gene expression after 24hr in 2Gy-irradiated human blood


title: Sample 57_Non responder


title: ExVivo_Blood_2Gy_R


title: ExVivo_Blood_2Gy_S


title: Sample 54_Responder


title: Sample 51_Non responder


title: Sample 52_Responder


title: ExVivo_Blood_2Gy_Q


title: ExVivo_Blood_2Gy_N


title: ExVivo_Blood_2Gy_O


title: Sample 50_Non responder

value: screening sample


title: ExVivo_Blood_2Gy_L


title: ExVivo_Blood_2Gy_P


title: Sample 49_Non responder


title: ExVivo_Blood_2Gy_M


title: ExVivo_Blood_2Gy_J


title: Sample 48_Non responder


title: Sample 45_Responder


title: Sample 43_Non responder


title: Sample 46_Responder


title: ExVivo_Blood_2Gy_G


title: ExVivo_Blood_2Gy_T


title: Sample 44_Responder


title: ExVivo_Blood_2Gy_H


title: ExVivo_Blood_2Gy_F


title: Sample 47_Non responder


title: ExVivo_Blood_2Gy_K


title: Sample 41_Responder


title: ExVivo_Blood_2Gy_B


title: Sample 39_Responder


title: Sample 40_Non responder


title: ExVivo_Blood_2Gy_E


title: Sample 42_Responder


title: ExVivo_Blood_0Gy_P

description: Gene expression after 24hr in 0Gy-irradiated human blood


title: ExVivo_Blood_0Gy_U


title: Sample 34_Non responder


title: Sample 35_Non responder


title: ExVivo_Blood_2Gy_C


title: Sample 32_Non responder


title: Sample 38_Non responder


title: ExVivo_Blood_0Gy_T


title: ExVivo_Blood_2Gy_D


title: ExVivo_Blood_0Gy_Q


title: ExVivo_Blood_0Gy_S


title: ExVivo_Blood_0Gy_N


title: ExVivo_Blood_2Gy_A


title: ExVivo_Blood_0Gy_O


title: Sample 37_Responder


title: Sample 31_Non responder


title: Sample 30_Non responder


title: Sample 36_Responder


title: Sample 29_Responder


title: Sample 33_Responder


title: ExVivo_Blood_0Gy_R


title: Sample 25_Responder


title: ExVivo_Blood_0Gy_M


title: ExVivo_Blood_0Gy_J


title: ExVivo_Blood_0Gy_K


title: Sample 22_Responder


title: ExVivo_Blood_0Gy_F


title: ExVivo_Blood_0Gy_L


title: ExVivo_Blood_0Gy_G


title: ExVivo_Blood_0Gy_H


title: ExVivo_Blood_0Gy_C


title: Sample 20_Responder


title: Sample 19_Non responder


title: Sample 26_Non responder


title: Sample 27_Non responder


title: ExVivo_Blood_0Gy_D


title: Sample 16_Responder


title: Sample 17_Non responder


title: Sample 14_Non responder


title: Sample 24_Non responder


title: Sample 28_Non responder


title: Sample 10_Responder


title: Sample 21_Responder


title: Sample 8_Responder


title: ExVivo_Blood_0Gy_E


title: Sample 7_Non responder


title: ExVivo_Blood_0Gy_B


title: Sample 18_Responder


title: Sample 6_Non responder


title: Sample 23_Responder


title: Sample 12_Non responder


title: ExVivo_Blood_0Gy_A


title: Sample 13_Non responder


title: Sample 5_Responder


title: Sample 11_Non responder


title: Sample 9_Non responder


title: Sample 2_Non responder


title: Sample 15_Responder


title: A549_Bj-2D-B

first: Keyu

last: Wang

address: Fengtai DONG DA Street NO.20

institute: State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: Gene expression data from A549 cells 48h post influenza H1N1(BJ501) infection.

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: A549, 48h post H1N1 infection

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit. This kit can be used to label any RNA sample, including total RNA, severely degraded RNA, plant RNA, and low molecular weight RNA.

growth_protocol: A549 cells were purchased from the ATCC and cultured in DMEM/F-12(1:1) basic(Gibco) supplemented with 10% FBS and 100 units penicillin-streptomycin ml-1 at 37°C in a humidified atmosphere of 5% (v/v) CO2.

treatment_protocol: A549 cells were used to infect with influenza H1N1 virus (BJ501).  A549 cells were washed and incubated with virus at a multiplicity of infection (MOI) of 1 for 1 h with FBS-free medium . After adsorption, the supernatant was aspirated and cells were cultured in medium supplemented with 2% FBS and 100 units penicillin-streptomycin ml-1 at 37°C in a humidified atmosphere of 5% (v/v) CO2 for indicate hours.  12 h with IAV WSN a nd SeV, o r 24 h with MDRV and HSV.

tag: infection

tag: time


title: A549_Bj-1D-A

description: Gene expression data from A549 cells 24h post influenza H1N1(BJ501) infection.

source_name: A549, 24h post H1N1 infection


title: A549_Bj-Ctl-C

description: Gene expression data from A549 cells before influenza H1N1(BJ501) infection.

source_name: A549, non-infected


title: ND or HFD fed C57BL/6J mouse livers

first: Sung-Joon

middle: Joon

last: Lee

address: 145 Anam-Ro, Rm410, East Bldg., College of Life Sci&Biotechnol. Korea University

department: Biotechnology

institute: Korea University

hyb_protocol: Scanned on an Agilent G2565AA scanner.

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

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: ND-fed mouse livers

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: C57BL/6J male mice were maintained under a 12-h light cycle at 21–25°C and a relative humidity of 50%–60% (SPF condition). Mice were fed a normal (ND) or a high-fat diet (HFD) for 4 weeks prior to tissue sampling.

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA from mouse liver and adipose tissues were extracted using RNAiso Plus reagent following manufacturer's instructions. RNA quality was confirmed by Experion RNA gel (Biorad). RNA samples from 10 livers and 10 adipose tissues were combined in ND and HFD groups then used for a single microarray experiment

tag: strain

value: C57BL/6J WT

value: Liver

source_name: HFD-fed mouse livers


title: Sample 1_Responder


title: A549_Bj-2D-A


title: A549_Bj-3D-B

description: Gene expression data from A549 cells 72h post influenza H1N1(BJ501) infection.

source_name: A549, 72h post H1N1 infection


title: A549_Bj-3D-A


title: Sample 3_Responder


title: ND or HFD -fed C57BL/6J mouse adipose tissues

source_name: ND-fed mouse adipose tissues

value: Adipose tissue

source_name: HFD-fed mouse adipose tissues


title: A549_Bj-2D-C


title: A549_Bj-1D-C


title: A549_Bj-Ctl-B


title: A549_Bj-3D-C


title: A549_Bj-Ctl-A


title: Sample 4_Non responder


title: A549_Bj-1D-B


title: SVP[Pfs25]+GLA-LSQ 24 hours [E21_45 24h]

status: Public on Aug 23 2017

city: Stockholm

first: Elizabeth

middle: Anne

last: Thompson

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rhesus Macaque Gene Expression Microarrays v2 (part number G2519F-026806) 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 Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software, and background corrected gProcessed signals were subjected to quantile normalization.

source_name: SVP[Pfs25]+GLA-LSQ 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input One-Color Quick Amp Labeling Kit (Agilent Technologies) 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.

extract_protocol: RNA was prepared using the PAXgene® Blood RNA Kit, PreAnalytiX, Qiagen following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Blood was collected directly into PAXgene® tubes prior to and 24 hours after immunization and stored at -20C until ready for analysis.

value: Whole blood


title: Pfs25-EPA+GLA-LSQ 24 hours [E14_38 24h]

source_name: Pfs25-EPA+GLA-LSQ 24 hours


title: Pfs25-EPA+GLA-LSQ 24 hours [E05_29 24h]


title: SVP[Pfs25]+GLA-LSQ 24 hours [E15_39 24h]


title: Pfs25-EPA+GLA-LSQ 24 hours [E08_32 24h]


title: Pfs25-EPA+GLA-LSQ 24 hours [E20_44 24h]


title: SVP[Pfs25]+GLA-LSQ 24 hours [E24_48 24h]


title: LAN1 RA treated tumor 2

type: genomic

first: Johan

last: Holmberg

address: Nobels väg 3

department: Department of Cell- and Molecular Biology, Ludwig Institute for Cancer Research

institute: Karolinska Institute

description:
RA 1_LAN1
LAN1 cells xenografted and treated
LAN1 tumor R2
SAMPLE RA 1_LAN1

hyb_protocol: Illumina Infinium HD

scan_protocol: Illumina Infinium HD

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Neuroblastoma

label_protocol: Illumina Infinium HD

growth_protocol: Adult female Crl:Nu (Ncr)-Foxn1 nu (nude mice) were injected subcutaneous with 2x10^6 cells in the right flank (day 0) and received daily i.p. injections from day 8 with vehicle (CTRL), Retinoic acid (RA), 5-Aza-deoxycytidine (AZA), or AZA combined with RA (AZA+RA). Tumors were harvested at day 10, day 14 or EP (1000mm3).

extract_protocol: Mice were sacrificed and tumors were dissected and snapfrozen on dry ice and stored at -80C.

treatment_protocol: Adult female Crl:Nu (Ncr)-Foxn1 nu (nude mice) were treated from day 8 with vehicle (DMSO), 10mg/kg/day Retinoic acid (RA), 0.1mg/kg/day 5-Aza-deoxycytidine (AZA), or AZA combined with RA (AZA+RA). Tumors were taken when reaching 1000mm3 (EP)

tag: treatment

value: RA


title: Pfs25-EPA+GLA-LSQ 24 hours [E22_46 24h]


title: SKNAS Aza+RA treated tumor 6

description:
RA/Aza 1_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor AR6
SAMPLE RA/Aza 1_SKNAS

value: SKNAS

value: Aza+RA


title: LAN1 Aza treated tumor 0

description:
Aza 2_LAN1
LAN1 cells xenografted and treated
LAN1 tumor A0
SAMPLE Aza 2_LAN1

value: Aza


title: LAN1 Ctrl (DMSO) treated tumor 4

description:
Ctrl 1_LAN1
LAN1 cells xenografted and treated
LAN1 tumor C4
SAMPLE Ctrl 1_LAN1

value: Ctrl (DMSO)


title: LAN1 Aza+RA treated tumor 4

description:
RA/Aza 1_LAN1
LAN1 cells xenografted and treated
LAN1 tumor AR4
SAMPLE RA/Aza 1_LAN1


title: SVP[Pfs25]+GLA-LSQ 24 hours [E09_33 24h]


title: LAN1 Aza treated tumor 2

description:
Aza 1_LAN1
LAN1 cells xenografted and treated
LAN1 tumor A2
SAMPLE Aza 1_LAN1


title: LAN1 Ctrl (DMSO) treated tumor 2

description:
Ctrl 2_LAN1
LAN1 cells xenografted and treated
LAN1 tumor C2
SAMPLE Ctrl 2_LAN1


title: SVP[Pfs25]+GLA-LSQ 24 hours [E12_36 24h]


title: SKNAS Aza treated tumor 5

description:
Aza 1_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor A5
SAMPLE Aza 1_SKNAS


title: LAN1 Aza+RA treated tumor 0

description:
RA/Aza 3_LAN1
LAN1 cells xenografted and treated
LAN1 tumor AR0
SAMPLE RA/Aza 3_LAN1


title: LAN1 Aza+RA treated tumor 3

description:
RA/Aza 2_LAN1
LAN1 cells xenografted and treated
LAN1 tumor AR3
SAMPLE RA/Aza 2_LAN1


title: SKNAS Aza+RA treated tumor 2

description:
RA/Aza 2_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor AR2
SAMPLE RA/Aza 2_SKNAS


title: SVP[Pfs25]+GLA-LSQ 24 hours [E06_30 24h]


title: SKNAS Ctrl (DMSO) treated tumor 2

description:
Ctrl 2_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor C2
SAMPLE Ctrl 2_SKNAS


title: SVP[Pfs25]+SVP[R848] 24 hours [E03_27 24h]

source_name: SVP[Pfs25]+SVP[R848] 24 hours


title: SVP[Pfs25]+SVP[R848] 24 hours [E01_25 24h]


title: SVP[Pfs25]+SVP[R848] 24 hours [E19_43 24h]


title: SVP[Pfs25]+SVP[R848] 24 hours [E02_26 24h]


title: LAN1 RA treated tumor 3

description:
RA 2_LAN1
LAN1 cells xenografted and treated
LAN1 tumor R3
SAMPLE RA 2_LAN1


title: SVP[Pfs25]+SVP[R848] 24 hours [E11_35 24h]


title: SVP[Pfs25]+SVP[R848] 24 hours [E16_40 24h]


title: SKNAS Aza treated tumor 4

description:
Aza 3_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor A4
SAMPLE Aza 3_SKNAS


title: SKNAS RA treated tumor 0

description:
RA 1_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor R0
SAMPLE RA 1_SKNAS


title: SVP[Pfs25}+SVP[CpG] 24 hours [E10_34 24h]

source_name: SVP[Pfs25}+SVP[CpG] 24 hours


title: Pfs25-EPA+GLA-LSQ Pre-bleed [E22_22 prebleed]

source_name: Pfs25-EPA+GLA-LSQ Pre-bleed


title: SVP[Pfs25}+SVP[CpG] 24 hours [E07_31 24h]


title: SVP[Pfs25}+SVP[CpG] 24 hours [E13_37 24h]


title: SKNAS Aza+RA treated tumor 3

description:
RA/Aza 3_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor AR3
SAMPLE RA/Aza 3_SKNAS


title: SKNAS Aza treated tumor 2

description:
Aza 2_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor A2
SAMPLE Aza 2_SKNAS


title: LAN1 Ctrl (DMSO) treated tumor 0

description:
Ctrl 3_LAN1
LAN1 cells xenografted and treated
LAN1 tumor C0
SAMPLE Ctrl 3_LAN1


title: SVP[Pfs25}+SVP[CpG] 24 hours [E04_28 24h]


title: SVP[Pfs25}+SVP[CpG] 24 hours [E17_41 24h]


title: SKNAS RA treated tumor 2

description:
RA 2_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor R2
SAMPLE RA 2_SKNAS


title: SKNAS Ctrl (DMSO) treated tumor 3

description:
Ctrl 3_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor C3
SAMPLE Ctrl 3_SKNAS


title: Pfs25-EPA+GLA-LSQ Pre-bleed [E20_20 prebleed]


title: SKNAS Ctrl (DMSO) treated tumor 1

description:
Ctrl 1_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor C1
SAMPLE Ctrl 1_SKNAS


title: SKNAS RA treated tumor 3

description:
RA 3_SKNAS
SKNAS cells xenografted and treated
SKNAS tumor R3
SAMPLE RA 3_SKNAS


title: Pfs25-EPA+GLA-LSQ Pre-bleed [E05_5 prebleed]


title: Pfs25-EPA+GLA-LSQ Pre-bleed [E08_8 prebleed]


title: SVP[Pfs25]+GLA-LSQ Pre-bleed [E09_9 prebleed]

source_name: SVP[Pfs25]+GLA-LSQ Pre-bleed


title: SVP[Pfs25]+SVP[R848] Pre-bleed [E16_16 prebleed]

source_name: SVP[Pfs25]+SVP[R848] Pre-bleed


title: SVP[Pfs25]+SVP[R848] Pre-bleed [E11_11 prebleed]


title: SVP[Pfs25]+SVP[R848] Pre-bleed [E03_3 prebleed]


title: SVP[Pfs25]+GLA-LSQ Pre-bleed [E06_6 prebleed]


title: SVP[Pfs25}+SVP[CpG] Pre-bleed [E07_7 prebleed]

source_name: SVP[Pfs25}+SVP[CpG] Pre-bleed


title: SVP[Pfs25]+SVP[R848] Pre-bleed [E19_19 prebleed]


title: SVP[Pfs25]+SVP[R848] Pre-bleed [E02_2 prebleed]


title: SVP[Pfs25}+SVP[CpG] Pre-bleed [E10_10 prebleed]


title: SVP[Pfs25]+GLA-LSQ Pre-bleed [E21_21 prebleed]


title: SVP[Pfs25]+SVP[R848] Pre-bleed [E01_1 prebleed]


title: SVP[Pfs25]+GLA-LSQ Pre-bleed [E24_24 prebleed]


title: SVP[Pfs25]+GLA-LSQ Pre-bleed [E12_12 prebleed]


title: SVP[Pfs25}+SVP[CpG] Pre-bleed [E17_17 prebleed]


title: SVP[Pfs25}+SVP[CpG] Pre-bleed [E13_13 prebleed]


title: cortical neurons_E14.5 electroporated_160810_FACS sorted at E17.5-3

city: Setagaya-ku

first: Chiaki

last: Ohtaka-Maruyama

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Department of brain development and neural regeneration

institute: Tokyo Metropolitan Institute of Medical Science

description: GFP expression plasmids were electroporated in utero at E14.5 and GFP labeled migrating cells were collected at E17.5 by FACS sorting from dissiciated cell mixture of dorsal part of celebral cortex

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Mouse Gene Expression v2 Microarray (G4846A) using Agilent Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Cortical neurons

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng of total RNA using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA was purified from the collected GFP-positive cells using Trizol (Invitrogen) according to the manufacturer’s   protocol.  The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Brains electroporated in utero with GFP plasmids at E14.5  were collected at E15.5, E16.5, and E17.5, respectively.    GFP-positive dorsal cortical areas were dissected out under a dissection microscope with a fluorescent lamp.  The   tissue fragments were treated with 8-10 U/ml papain (Worthington Biochemical) and 10 μg/ml DNase I (TAKARA Bio),   and then triturated by pipetting in 10% FCS/ DMEM.  Dissociated cortical cells were collected by centrifugation (1,000×g   for 5 min), and then re-suspended in HBS at a concentration of 1-2×106 cells/ml.  Dissociated cells were stained with   2 μg/ml propidium iodide (PI) prior to sorting to distinguish dead cells.  The gating parameters were determined using   the side and forward scatters to eliminate debris and aggregated cells, using red fluorescence (633 nm) to eliminate   dead cells, and green fluorescence (488 nm) to separate the positive from negative cells.  Cells prepared from the   brains not electroporated with pCAGGS-EGFP were used as the negative controls.

value: cerebral cortex

tag: age


title: WTOS5H_replicate2

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description:
WT plant leaves, 5 h after Manduca sexta oral secretion treatment
WTOS5HR2

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 platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) 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: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Quantile normalization and log2 transformation was performed for all raw microarray data using the R package “Agi4x44PreProcess”. All probes with signal within 95% confidence interval of the signal of negative control probes were discared from down-stream analysis.  All replicated probes were averaged.

molecule: polyA RNA

organism: Nicotiana attenuata

source_name: WT plant leaves, 5 h after Manduca sexta oral secretion treatment, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type and ir-MYB8 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of M. sexta oral secretion diluted 1/5 (v/v) in water.

value: leaves

tag: genotype

value: wildtype

value: Manduca sexta oral secretion treatment

tag: timepoint

value: 5 h


title: SVP[Pfs25]+GLA-LSQ Pre-bleed [E15_15 prebleed]


title: WTOS5H_replicate3

description:
WT plant leaves, 5 h after Manduca sexta oral secretion treatment
WTOS5HR3

source_name: WT plant leaves, 5 h after Manduca sexta oral secretion treatment, replicate 3


title: WTC5H_replicate2

description:
WT plant leaves, 5 h, not treated
WTC5HR2

source_name: WT plant leaves, 5 h, not treated, replicate 2

value: not treated


title: WTOS5H_replicate1

description:
WT plant leaves, 5 h after Manduca sexta oral secretion treatment
WTOS5HR1

source_name: WT plant leaves, 5 h after Manduca sexta oral secretion treatment, replicate 1


title: WTOS1H_recplicate3

description:
WT plant leaves, 1 h after Manduca sexta oral secretion treatment
WTOS1HR3

source_name: WT plant leaves, 1 h after Manduca sexta oral secretion treatment, replicate 3

value: 1 h


title: WTOS1H_recplicate1

description:
WT plant leaves, 1 h after Manduca sexta oral secretion treatment
WTOS1HR1

source_name: WT plant leaves, 1 h after Manduca sexta oral secretion treatment, replicate 1


title: WTOS1H_recplicate2

description:
WT plant leaves, 1 h after Manduca sexta oral secretion treatment
WTOS1HR2

source_name: WT plant leaves, 1 h after Manduca sexta oral secretion treatment, replicate 2


title: WTC5H_replicate3

description:
WT plant leaves, 5 h, not treated
WTC5HR3

source_name: WT plant leaves, 5 h, not treated, replicate 3


title: WTC5H_replicate1

description:
WT plant leaves, 5 h, not treated
WTC5HR1

source_name: WT plant leaves, 5 h, not treated, replicate 1


title: SVP[Pfs25}+SVP[CpG] Pre-bleed [E04_4 prebleed]


title: cortical neurons_E14.5 electroporated_160810_FACS sorted at E16.5-3

description: GFP expression plasmids were electroporated in utero at E14.5 and GFP labeled migrating cells were collected at E16.5 by FACS sorting from dissiciated cell mixture of dorsal part of celebral cortex


title: cortical neurons_E14.5 electroporated_160810_FACS sorted at E15.5-3

description: GFP expression plasmids were electroporated in utero at E14.5 and GFP labeled migrating cells were collected at E15.5 by FACS sorting from dissiciated cell mixture of dorsal part of celebral cortex


title: cortical neurons_E14.5 electroporated_150623_FACS sorted at E15.5-2


title: WTC1H_replicate3

description:
WT plant leaves, 1 h, not treated
WTC1HR3

source_name: WT plant leaves, 1 h, not treated, replicate 3