title: Dad 1

status: Public on Sep 30 2014

type: genomic

city: London

first: Christina

middle: A

last: Castellani

state: Ontario

address: Biological and Geological Sciences Building

department: Biology

country: Canada

institute: The University of Western Ontario

description: Processed at ArrayStar

hyb_protocol: The total input and immunoprecipitated DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively, and hybridized to NimbleGen Human DNA Methylation 3x720K Promoter Plus CpG Island Arrays

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner

data_processing: Data was processed using Partek Genomics Suite

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: Immunoprecipitation of methylated DNA was performed using BiomagTM magnetic beads coupled mouse monoclonal antibody against 5-methylcytidine. The immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation.

extract_protocol: DNA was extracted from whole blood using the 5 Prime Perfect Pure DNA Blood Kit (Gaithersburg, MD, USA), following the manufacturer’s protocol

tag: disease state

value: Unaffected


title: Mom 1

description: Processed at ArrayStar


title: Mom 3

description: Processed at ArrayStar


title: Mom 2

description: Processed at ArrayStar


title: Unaffected 1

description: Processed at ArrayStar


title: Affected 1

description: Processed at ArrayStar

value: Schizophrenia


title: Affected 2

description: Processed at ArrayStar


title: Unaffected 2

description: Processed at ArrayStar


title: JHB.16.D.rep4

type: RNA

city: Notre Dame

first: David

middle: W

last: Severson

state: IN

address: 44 Galvin Life Sciences

department: Biological Sciences

country: USA

institute: University of Notre Dame

hyb_protocol: Hybridization was performed by the University of Notre Dame Genomics Core facility using the NimbleGen Hybridization kit following the standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning (2 μm resolution) was performed by the University of Notre Dame Genomics Core facility following the standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Culex quinquefasciatus

source_name: whole pupae (pool of 10)

label_protocol: Labeling was performed by the University of Notre Dame Genomics Core facility using the NimbleGen labeling kit following the standard operating protocol. See www.nimblegen.com.

growth_protocol: All samples were reared to the pupa stage at 25°C, with a light/dark cycle of 16 h/8 h. Beef liver powder slurry was provided ad libitum

extract_protocol: Total RNA was extracted using RNeasy Mini and Qiashredder kits (Qiagen). RNA concentrations were measured using the Nanodrop ND-2000 (ThermoScientific), and RNA quality was assessed using the Bioanalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies).

treatment_protocol: On the day of the larva-pupa molt, pupae were collected and placed either back in 25°C; 16 h/8 h (ND) or 18°C; 8 h/16 h (D). Samples were collected 8, 16, and 24 hours later. Pools of 10 were used for total RNA extraction.

tag: time point (hours post-exposure)

tag: condition

value: diapause-inducing (18°C; 8 h light/16 h dark)

tag: biological replicate

tag: strain

value: Johannesburg


title: SB.24.D.rep4

organism: Culex pipiens

value: South Bend


title: JHB.16.ND.rep4

value: non-diapause (25°C; 16 h light/8 h dark)


title: SB.16.ND.rep4


title: SB.24.ND.rep4


title: SB.8.D.rep4


title: JHB.8.D.rep4


title: SB.8.ND.rep4


title: JHB.24.D.rep4


title: JHB.8.ND.rep4


title: JHB.24.ND.rep3


title: JHB.24.D.rep3


title: SB.16.D.rep4


title: VIISSSH04

city: Berkeley

first: Yvette

middle: M

last: Piceno

state: CA

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

description: Microbial-community DNA extracted from coral samples (mucus, tissue, and skeleton) was used to examine the bacterial diversity associated with this coral.

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
CEL files were converted to CELa files and then processed using proprietary software (PhyCA).
Data are provide as intensity values scaled to internal standards.

label: biotin

organism: mixed sample

source_name: bacterial colonies with normal pigmentation, associated with coral samples

label_protocol: TDT enzyme (Promega; Madison, WI) and GeneChip Labeling Reagent (Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

extract_protocol: DNA was extracted using the MoBion PowerPlant DNA Isolation Kit with modifications (see publication)

treatment_protocol: see publication for definitions of healthy or dark spot tissue

value: Virgin Islands National Park

value: Healthy


title: VIISSSH05


title: VIISSSH03


title: JHB.24.ND.rep4


title: VIISSSH02


title: VIISSSH01


title: SB.24.D.rep3


title: VIISSSD10

source_name: bacterial colonies with dark spot lesions, associated with coral samples

value: Dark spot


title: VIISSSD09


title: JHB.16.ND.rep3


title: VIISSSD07


title: SB.24.ND.rep3


title: VIISSSD08


title: DRTOSSH04

value: Dry Tortugas National Park


title: SB.16.ND.rep3


title: JHB.16.D.rep3


title: DRTOSSH06


title: DRTOSSH01


title: DRTOSSH03


title: VIISSSD06


title: DRTOSSD10


title: DRTOSSD08


title: SB.16.D.rep3


title: SB.8.D.rep3


title: SB.8.ND.rep3


title: JHB.8.D.rep3


title: DRTOSSD07


title: JHB.16.D.rep2


title: SB.16.ND.rep2


title: SB.24.ND.rep2


title: JHB.24.D.rep1


title: JHB.24.D.rep2


title: JHB.24.ND.rep1


title: JHB.8.ND.rep3


title: JHB.8.D.rep2


title: SB.24.D.rep2


title: JHB.8.ND.rep2


title: SB.8.D.rep2


title: SB.8.ND.rep2


title: JHB.16.ND.rep2


title: CD34+ cells transduced with retroviral vectors expressing c-KIT(N822K), rep2

city: Munich

first: Christian

last: Wichmann

address: Marchioninistr. 15

country: Germany

institute: LMU

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the Hybridization Oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendations.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution.

data_processing:
Scanned image files were visually inspected for artifacts and then analyzed. Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09.
The microarray data analysis consists of the following steps: 1. between-array normalization, 2. global clustering and PCA-analysis, 3. fitting the data to a linear model, 4. detection of differential gene expression and 5. over-representation analysis of differentially expressed genes.

source_name: CD34+ peripheral blood, vector encoding c-KIT(N822K)

label_protocol: 500 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendations. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: CD34+ cells were cultured as described in Mulloy et al., 2002 & 2003.

extract_protocol: Extraction of nucleic acids was carried out using TRIZOL (Invitrogen, Carlsbad, CA) following standard procedures.

treatment_protocol: CD34+ cells were transduced with retroviral vectors encoding c-KIT(N822K) or mock control vectors and FACS selected prior to analysis.

tag: donor disease status

value: healthy

tag: donor developmental stage

value: adult

tag: cell type

value: CD34+ hematopoietic progenitor cells

tag: retroviral vector


title: CD34+ cells transduced with mock control retroviral vectors, rep2

source_name: CD34+ peripheral blood, mock control vector

value: MSCV-ires-GFP


title: JHB.24.ND.rep2


title: CD34+ cells transduced with mock control retroviral vectors, rep1


title: SB.16.D.rep2


title: SB.24.ND.rep1


title: SB.24.D.rep1


title: Fear30 4

city: Atlanta

first: Brian

middle: George

last: Dias

state: GA

address: 954 Gatewood Rd NE

department: Psychiatry and Behavioral Sciences

institute: Emory University

hyb_protocol: https://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA-microRNA-Array-6th-gen-hsa-mmu-rno-manual.pdf (see manufacturer's protocol for more detail)

scan_protocol: Images were acquired using an Agilent array scanner and spot signals were processed (default background subtraction) and quantified using GenePix Pro 4.1.

data_processing: Intensities within arrays were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm as implemented in the Comprehensive R-based Microarray Analysis web front end (CARMAweb 1.4). The log2 values of the difference between the sample and reference signals were used for hierarchical clustering.

organism: Mus musculus

source_name: Amygdala tissue, 30 mins after auditory fear conditioning

label_protocol: A reference pool of RNA was made from mixing equal amount of total RNA from the individual animals. 500 ng of total RNA from each sample and reference pool were labelled with miRCURY™ Hy3™ and Hy5™ fluorescent label (Exiqon, Denmark). The Hy3™-labeled samples and a Hy5™-labeled reference pool RNA samples were mixed pair-wise and hybridized to the miRCURY™ LNA array (6th gen - hsa, mmu & rno) (Exiqon, Denmark) according to manufacturer's protocol for Maui hybridisation chamber.

extract_protocol: 30 minutes after conditioning, Fear30 animals were rapidly decapitated and brains fresh frozen on dry ice. The same was done for the Control group. Brains were punched on a freezing microtome using a 1mm punch, and bilateral amygdala tissue were collected from each animal. miRNA and RNA were extracted from the brain punches using the Qiagen miRNeasy Kit.

treatment_protocol: Adult male mice were either left in their home cage (Control) or subjected to auditory fear conditioning (Fear) using 5 Tone+Shock pairings (6kHz tone, 0.6mA shock).

tag: treatment

value: fear

tag: tissue

value: Brain Amygdala

tag: gender

value: male

tag: age

tag: genetic background


title: Fear30 1


title: Fear30 3


title: Fear30 2


title: 552454A03

city: Dallas

first: Duojia

last: Pan

state: Texas

address: 6001 Forest Park

department: Physiology

institute: UT Southwestern Medical Center

description: DNA methylation

hyb_protocol: Hybridization were done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 100128_HG19_MKF_HELP_ChIP

scan_protocol: Standard NimbleGen protocol.

data_processing: HELP package in R from Bioconductor

source_name: HBEC3 DNMT1-RFTS, MspI

label_protocol: Labeling was done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 100128_HG19_MKF_HELP_ChIP

growth_protocol: normal HBEC3 culture condition

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the HELP protocol

tag: cell line

tag: genotype/variation

source_name: HBEC3 DNMT1-RFTS, HpaII


title: 552454A02

description: DNA methylation

source_name: HBEC3 DNMT1, MspI

source_name: HBEC3 DNMT1, HpaII


title: Control 4

source_name: Amygdala tissue, Home Cage

value: control


title: Control 3


title: CD34+ cells transduced with retroviral vectors expressing c-KIT(N822K), rep1


title: Control 2


title: Control 1


title: 552454A01

description: DNA methylation

source_name: HBEC3 Vector, MspI

value: Vector

source_name: HBEC3 Vector, HpaII


title: SB.16.ND.rep1


title: JHB.16.D.rep1

value: diapause-inducing (18°C; 8 h light/16 h dark)


title: JHB.16.ND.rep1

value: Johannesburg


title: SB.16.D.rep1

value: South Bend


title: JHB.8.ND.rep1

value: non-diapause (25°C; 16 h light/8 h dark)


title: Hypoxia EXP3

city: Toronto

first: Cindy

last: Yao

address: 661 University Avenue, Suite 510

institute: OICR

description:
Hypoxia
20121018_Elizabeth_6_06

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: miRNAs with counts equal or lower than the negative controls were discarded from the analysis. miRNA counts were normalized to housekeeping gene RPLP0 and averaged for 3 independent experiments.

label: nanoString probe

source_name: Transformed mammary epithelial cell line (HMLER)_Hypoxia

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

growth_protocol: Human mammary epithelial (HMLER) cells were grown in serum free DME/F12 (1:1) media supplemented with 10 ng/ml hEGF, 0.5 ug/ml hydrocortisone, and 10 ug/ml insulin (as previously described by Elenbaas et al., 2001).  In vitro experiments were conducted with 60-80% confluent cultures.

extract_protocol: Total RNA was isolated using TRI reagent (Sigma)

treatment_protocol: Cells were exposed to hypoxia (1% O2) for 7 days,  transduced with lentivirus to stably knockdown DICER or stimulated with 2.5 ng/ml TFGB1 for 12 days.  For hypoxic exposure cells were transferred into a HypOxygen H35 workstation. The atmosphere in the chamber consisted of 5% H2, 5% CO2, the desired % O2, and residual N2.  Knockdown was achieved using a lentiviral shRNA construct directed against DICER (TRCN0000051258) or GFP as control (TRCN0000072181).

value: HMLER

value: Immortalized and transformed human mammary epithelial cells by introduction of SV40 large-T antigen, telomerase catalytic subunit, and H-Ras oncoprotein

value: Female


title: Hypoxia EXP2

description:
Hypoxia
20121018_Elizabeth_5_05


title: shDICER EXP1

description:
DICER knockdown
20121018_Elizabeth_7_07

source_name: Transformed mammary epithelial cell line (HMLER)_shDICER


title: TGFB1 EXP2

description:
TGFB1 stimulation
20121018_Elizabeth_11_11

source_name: Transformed mammary epithelial cell line (HMLER)_TGFB2


title: shDICER EXP3

description:
DICER knockdown
20121018_Elizabeth_9_09


title: Hypoxia EXP1

description:
Hypoxia
20121018_Elizabeth_4_04


title: JHB.8.D.rep1


title: TGFB1 EXP1

description:
TGFB1 stimulation
20121018_Elizabeth_10_10

source_name: Transformed mammary epithelial cell line (HMLER)_TGFB1


title: TGFB1 EXP3

description:
TGFB1 stimulation
20121018_Elizabeth_12_12

source_name: Transformed mammary epithelial cell line (HMLER)_TGFB3


title: shDICER EXP2

description:
DICER knockdown
20121018_Elizabeth_8_08


title: SB.8.D.rep1

source_name: whole pupae (pool of 10)


title: OSCC25T

city: Waurnponds

first: sivapriya

last: pavuluri

state: VIC

address: 75, Pigdons Road

department: School of Medicine

country: Australia

institute: Deakin University

hyb_protocol: microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450

scan_protocol: Genechip scanner 3000 7G

data_processing: The input files were normalized with full quantile normalization (Irizarry et al 2003).  For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points.  Next, the 818,005 probes were manipulated into the analysis values as follows.  Probes with GC count less than 6 and greater than 17 were excluded from the analysis.  Probe scores were then transformed by taking the Base-2 Logarithm of 0 plus the probe score.  Background CorrectionExon arrays do not use individual mis-match probes.  Background is established from a pool of probes designed for that purpose.  Background probes are stratified by CG content and are defined in the HumanGene10ST_antigenomic.bgp file.  BGP files can also be downloaded from www.affymetrix.com.  Each probe score was corrected for background by subtracting the median expression score of background probes with similar GC content.    Probe-set Presence/Absence and the Removal of Non-expressed Probe-setsNon-expressed probes can cause tests for alternative splicing to find false positives (because they cause 'non-parallel' expression patterns across the gene).  A probe-set is judged to be expressed above background if for any group: Integral from T0 to Infinity of the standard normal distribution < Significance (0.05) Where: T0 = Sqr(GroupSize) (T - P) / Sqr(Pvar), GroupSize = Number of CEL files in the group, T = Average of probe scores in probe-set, P = Average of Background probes averages of GC content, and Pvar = Sum of Background probe variances / (Number of probes in probe-set)^2,Hence we test that the average of probe-sets in a group is greater than the average expression of background probes of similar gc content as the probe-set probes as the center of background for the probe-set and derive its dispersion from the background probe-set variance.

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual

growth_protocol: Tumor samples and the surrounding normal margins were collected from the oral squamous cell carcinoma (OSCC) patients. The tissues collected were immediately placed in RNA later solution (Qiagen) and further stored at -80⁰C till further use.

extract_protocol: Total RNA was extracted from the tissues using Qiagen Rneasy mini kit according to manufacturers protocol.

treatment_protocol: not applicable

tag: uid

tag: filenumber

value: late stage OSCC

value: tumor

tag: tumor stage

value: III


title: OSCC15T

tag: disease state


title: OSCC27T

value: IV


title: Aerobic EXP2

description:
Aerobic
20121018_Elizabeth_2_02

source_name: Transformed mammary epithelial cell line (HMLER)_Aerobic


title: Aerobic EXP1

description:
Aerobic
20121018_Elizabeth_1_01


title: Aerobic EXP3

description:
Aerobic
20121018_Elizabeth_3_03


title: SB.8.ND.rep1

tag: time point (hours post-exposure)

tag: condition

tag: biological replicate


title: OSCC5T


title: OSCC10T


title: OSCC9T


title: OSCC4T


title: pLKO.1_empty_vector_3

description:
empty vector
20120712_wouter_I_09

label: nanostring probe

source_name: MCF7 cell line_pLKO.1_empty_vector_3

growth_protocol: MCF7 cells were grown in DME/F12 (1:1) media supplemented with 10% FBS.  In vitro experiments were conducted with 60-80% confluent cultures.

treatment_protocol: Cells were exposed to anoxia (<0.02% O2) for 16 hours or transduced with lentivirus to stably knockdown DICER.  For hypoxic exposure cells were transferred into a HypOxygen H35 workstation. The atmosphere in the chamber consisted of 5% H2, 5% CO2, the desired % O2, and residual N2.  Knockdown was achieved using a lentiviral shRNA construct directed against DICER (TRCN0000051258) or pLKO.1 empty vector as control

value: breast adenocarcinoma; derived from metastatic site:pleural effusion


title: shDICER_1

description:
DICER knockdown
20120712_wouter_J_10

source_name: MCF7 cell line_shDICER_1


title: shDICER_3

description:
DICER knockdown
20120712_wouter_L_12

source_name: MCF7 cell line_shDICER_3


title: shDICER_2

description:
DICER knockdown
20120712_wouter_K_11

source_name: MCF7 cell line_shDICER_2


title: pLKO.1_empty_vector_2

description:
empty vector
20120712_wouter_H_08

source_name: MCF7 cell line_pLKO.1_empty_vector_2


title: OSCC7T


title: Exp3_Hyp

description:
hypoxia
20120712_wouter_F_06

source_name: MCF7 cell line_Exp3_Hyp


title: pLKO.1_empty_vector_1

description:
empty vector
20120712_wouter_G_07

source_name: MCF7 cell line_pLKO.1_empty_vector_1


title: OSCC15N

value: surrounding normal margins


title: Exp2_Hyp

description:
hypoxia
20120712_wouter_D_04

source_name: MCF7 cell line_Exp2_Hyp


title: Exp3_Norm

description:
normal oxygen
20120712_wouter_E_05

source_name: MCF7 cell line_Exp3_Norm


title: OSCC29T


title: OSCC3T


title: Exp2_Norm

description:
normal oxygen
20120712_wouter_C_03

source_name: MCF7 cell line_Exp2_Norm


title: Exp1_Hyp

description:
hypoxia
20120712_wouter_B_02

source_name: MCF7 cell line_Exp1_Hyp


title: OSCC10N


title: Exp1_Norm

description:
normal oxygen
20120712_wouter_A_01

source_name: MCF7 cell line_Exp1_Norm


title: OSCC9N


title: EPCdEC of the second donor at passage 4 was subcultured to passage 7

city: Shinjuku-ku

first: Kumiko

last: Saeki

state: Tokyo

address: 1-21-1 Toyama

department: Department of disease control

country: Japan

institute: National Center for Global Health and Medicine

hyb_protocol: Samples were hybridized according to the Affymetrix standard protocol.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Normalized expression signal data was generated at the exon level using Affymetrix's Expression Console by RMA.

source_name: Human adult bone marrow mononuclear cell-derived endothelial progenitor outgrowth cells (EPOCs): lot B112057, BioChain Institute, Inc., Hayward, CA

label_protocol: Samples were labeled according to the Affymetrix standard protocol.

growth_protocol: Vascular endothelia cells were cultured on 0.1% gelatin-coated plates using EGM®-2 BulletKit (Lonza Group Ltd. Basel, Switzerland) . Cells were subcultured at split ratios of 1:2 ~ 1:3 twice a week.

extract_protocol: Total RNAs were isolated by using TRIzoL® Reagent (Life Technologies, Inc., Grand Island, NY).

value: vascular endothelical cells


title: EPCdEC of the first donor at passage 12

source_name: Human adult bone marrow mononuclear cell-derived endothelial progenitor outgrowth cells (EPOCs): lot B112054, BioChain Institute, Inc., Hayward, CA


title: OSCC3N


title: OSCC4N


title: Control_DMSO

city: Ikoma

first: Ryo

last: Nasuno

address: 8916-5, Takayama-cho

institute: Nara Institute of Science and Technology

hyb_protocol: Labeled cRNA dissoleved in hybridization buffer was incubated on Yeast (S. cerevisiae) Genome Oligo Microarray (4 x 44K) for 17 hr.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent). Raw intensity values were normalized to the 50 percentile shift and then submitted to a baseline correction based on the median of the control samples. The normalized data were used to calculate 'log2 sample/control' ratio (included in the 'complete_data.txt').

organism: Saccharomyces cerevisiae

label_protocol: cDNA was synthesized using total RNA as a template, and then cRNA was synthesized from cDNA by in vitro transcription. cRNA was labeled during that by Cy3.

growth_protocol: Synthetic dextrose (SD) minimal medium up to log phase (OD600 = 1)

extract_protocol: Cells were disrupted by multi-beads shocker using 0.5 mm glass beads, and total RNA was prepared using the RNeasy Mini Kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Add SNAP dissolved in DMSO into cells suspended in SD medium

tag: strain

tag: treated with

value: DMSO


title: OSCC19N


title: SNAP_10min

source_name: S288C_SNAP for 10 min

value: SNAP for 10 min


title: VEC generated from adult bone marrow-derived EPC (EPCdEC) of the first donor at passage 4 was subcultured to passage 7

tag: cell type


title: SNAP_60min

source_name: S288C_SNAP for 60 min

value: SNAP for 60 min


title: SNAP_30min

source_name: S288C_SNAP for 30 min

value: SNAP for 30 min


title: CD66Low cells Replicate2

city: Bangalore

first: Chitra

last: Pattabiraman

state: Karntaka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

hyb_protocol: Slides: Human 4x44K Array AMADID: 025085, Agilent’s In situ Hybridzation kit 5188-5242

scan_protocol: Agilent Technologies Scanner G2505C US90403632,  Scan_NumChannels (1), Scan_MicronsPerPixelX(5),Scan_MicronsPerPixelY(5), Agilent FE Version 10.7.3.1, Grid- 025085_D_F_20090818, Background Detrend,On(FeatNCRange, LoPass), Multiplicative Detrend True

data_processing: The normalization was done using GeneSpring GX Version 11.5 using the recommended Per Chip and Per Gene Normalization: Normalize to specific samples CD66Low vs CD66High.Percentile Shift Normalization- Percentile shift normalization is a global normalization, where the locations of all the spot intensitiesin an array are adjusted. This normalization takes each column in an experiment independently, and computes the percentile of the expression values for this array, across all spots (where n has a range from 0-100 and n=50 is the median). It subtracts this value from the expression value of each entity.

source_name: CIN612 9E_CD66_low

label_protocol: Agilent’s Quick-Amp labeling Kit (p/n5190-0442), T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis)

growth_protocol: CIN612 9E cells were cultured on MitomycinC treated feeder cells (NIH3T3 J2) in Emedia supplemented with EGF

extract_protocol: Qiagen’s RNeasy minikit Cat#74104

treatment_protocol: Pluriselect Universal Mouse S beads (Pluriselect) were conjugated to the CD66 antibody(BD Pharmigen, 551354) and sorting was performed according to the manufacturer's instructions.

value: CIN612 9E

tag: tissue origin

value: cervical precancer

tag: cd66 expression

value: Low


title: G2_P470_Ch3+5

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

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

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

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

organism: Macaca mulatta

source_name: Macaca mulatta_Blood_SIVgp96 + gp120

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

growth_protocol: 36 Indian-origin outbred, young adult, male and female rhesus macaques divided into thre vaccination groups of 12 animals each. Groups were balanced for Mamu-A*01 (three in each group), Mamu-B*08 (one in each group), and for susceptible and resistant TRIM5α alleles. There were no Mamu-B*17+ animals.

extract_protocol: RNA was extracted from the PAXgene tubes using Qiagen PAXgene Blood RNeasy Mini kits and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: The prime group (PG) received Gp96 SIV Ig vaccine 292 cells that were transfected with plasmids encoding gp96-Ig, SIVmac251 rev-tat-nef, Gag and gp160 (35). They were injected intraperitoneally with 107 irradiated gp96SIVIg vaccine cells in HBSS, which secrete 10 μg of gp96SIVIg per 24 h. For the prime-boost group (PBG), 100 μg of rSIVgp120 protein was added to the vaccine cells. The control group received 292-gp96 Ig cells not transfected with SIV antigens. After a 32-week vaccination phase, which consisted of priming in weeks 0, 6, and 25 and (for the PBG only) additional boosts in weeks 6 and 25, all animals were subject to up to seven weekly low-dose intrarectal challenges starting at 33-week with SIVmac251 at a dosage of 120 TCID50. Whenever an animal had detectable viral load (>50 copies/ml of plasma) at 5 days post challenge, it was considered viremic, further challenges were suspended, and only viral load screening continued on a weekly basis. Whole blood samples (preserved in PAXgene tubes) were collected 2 weeks prior to the first prime, 1 week after the first prime, 2 weeks before and 1 week after the third prime, 1 week before the first challenge, for newly infected animals five days into the corresponding study week and from viremic animals four days into the study week (also denoted as challenge 2 and challenge 3)

tag: tissue

value: Blood

tag: treatment

value: SIVgp96 + gp120


title: RPEshp

city: NEW YORK

first: Shaheen

last: Kabir

state: NY

address: 1230 York Ave

institute: Rockefeller University

description:
SAMPLE 24
no replicate

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalized using percentile shift in Genespring v12.6

label_protocol: Ambion MessageAmp kit

extract_protocol: RNA was extracted with QIAGEN Rneasy Columns as per manufacturer's instructions.

tag: clone

value: parental

tag: genotype

value: Wild type


title: RPE25

description:
SAMPLE 22
no replicate

tag: cell line

value: Knockout


title: HT-KO-21A

description:
SAMPLE 19
replicate 1


title: HT-KO-21B

description:
SAMPLE 20
replicate 2


title: G2_P470_Ch2+5


title: RPE30

description:
SAMPLE 23
no replicate


title: HT-KO-8A

description:
SAMPLE 17
replicate 1


title: G2_P442_Wk26


title: G2_P442_Wk32


title: HT-WT-2A

description:
SAMPLE 13
replicate 1


title: HT-KO-8B

description:
SAMPLE 18
replicate 2


title: HT-WT-9A

description:
SAMPLE 15
replicate 1


title: HT-WT-2B

description:
SAMPLE 14
replicate 2


title: CD66Low cells Replicate1

value: High


title: CD66High cells Replicate1

source_name: CIN612 9E_CD66_high


title: G2_P442_Wk-2_3


title: G2_P470_Ch1+5


title: CD66High cells Replicate2


title: RPE23

description:
SAMPLE 21
no replicate


title: HT-WT-9B

description:
SAMPLE 16
replicate 2


title: G2_P442_Wk-2_2


title: HC-KO-21B

description:
SAMPLE 10
replicate 2


title: HC-KO-28B

description:
SAMPLE 12
replicate 2


title: HC-KO-28A

description:
SAMPLE 11
replicate 1


title: G2_P442_Wk23


title: G2_P442_Wk-2


title: G2_P442_Wk1


title: HC-KO-21A

description:
SAMPLE 9
replicate 1


title: G2_P442_Ch1+5


title: G2_P440_Wk26


title: G2_P440_Wk1


title: G2_P442_Ch3+5


title: G2_P439_Wk1


title: HC-KO-10B

description:
SAMPLE 8
replicate 2


title: G2_P439_Wk23


title: G2_P440_Wk26_2


title: HC-WT-20B

description:
SAMPLE 4
replicate 2


title: G2_P440_Wk-2


title: G2_P440_Ch1+5


title: G2_P440_Wk23


title: HC-WT-15B

description:
SAMPLE 2
replicate 2


title: G2_P439_Wk-2


title: HC-WT-23A

description:
SAMPLE 5
replicate 1


title: HC-WT-20A

description:
SAMPLE 3
replicate 1


title: HC-WT-23B

description:
SAMPLE 6
replicate 2


title: G2_P439_Wk26


title: G2_P440_Ch2+5


title: G2_P439_Wk32


title: G2_P430_Wk23


title: G2_P439_Ch3+4


title: hDFCs induced by hDPCs-CM

city: Seoul

first: Su Jin

last: Park

address: 101 Daehagro, Chongro-gu

department: Department of Oral Histology-Developmental Biology

country: South Korea

institute: Seoul National University

description: replicate 1

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip

scan_protocol: Array were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina Gene

source_name: hDFCs in osteogenic medium with hDPCs-CM

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: Cell were grown in DMEM medium supplemented with 100IU/ml penicillin, 100 ug/ml streptomycin (Gibco BRL, Carlsbad, CA), and 10% Fetal Bovine Serum (Gibco BRL) at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol: Total RNAs were isolated using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) to hDFCs treated with or without hDPCs-CM samples.

treatment_protocol: When hDFCs reached 80-90% confluence, the cells were induced by osteogenic differentiation medium with or without hDPCs-CM for day 7

value: Human Dental Follicle

value: induced by hDPCs-CM


title: G2_P430_Wk26


title: G2_P430_Ch1+5


title: G2_P429_Wk32


title: G2_P439_Ch1+5


title: HC-WT-15A

description:
SAMPLE 1
replicate 1


title: hDFCs control

description: replicate 1

source_name: hDFCs in osteogenic medium

value: control


title: G2_P429_Wk23


title: G2_P430_Wk-2


title: G2_P429_Ch2+5


title: G2_P421_Wk-2


title: G2_P421_Wk1


title: G2_P430_Wk1


title: G2_P421_Wk26


title: G2_P429_Wk26


title: G1_P511_Wk23_2

source_name: Macaca mulatta_Blood_SIVgp96


title: G2_P429_Wk-2


title: G1_P511_Wk-2


title: G2_P429_Ch3+5


title: G1_P511_Wk23


title: G1_P511_Ch1+5


title: G2_P421_Wk32


title: G2_P421_Wk23


title: G1_P511_Wk32


title: G2_P429_Wk1


title: G1_P510_Wk32


title: G1_P511_Wk1


title: G1_P510_Wk26


title: G1_P510_Wk1_3


title: G1_P510_Ch1+5


title: G1_P510_Wk1


title: G1_P472_Wk23


title: G1_P472_Wk26


title: G1_P510_Wk1_2


title: G1_P444_Wk-2


title: G1_P472_Wk1


title: G1_P471_Wk26


title: G1_P471_Wk-2_2


title: G1_P444_Wk23


title: G1_P444_Wk32


title: G1_P444_Ch1+5


title: G1_P510_Wk-2


title: G1_P471_Wk23


title: G1_P428_Wk23


title: G1_P472_Wk-2


title: G1_P444_Wk32_2


title: G1_P444_Wk26


title: G1_P471_Wk1


title: G1_P444_Wk1


title: G1_P471_Wk-2


title: G1_P510_Wk23


title: G1_P428_Wk-2


title: G1_P428_Wk32


title: G1_P427_Wk23


title: G1_P444_Wk32_3


title: G1_P428_Ch1+5


title: G1_P428_Wk1


title: G1_P427_Wk32


title: G1_P427_Wk26


title: G1_P427_Wk-2


title: G1_P426_Wk26_3


title: G1_P426_Wk-2


title: G1_P426_Wk1


title: G1_P427_Wk1


title: G1_P423_Wk32


title: G1_P423_Wk26


title: G1_P426_Ch1+5


title: G1_P426_Wk26_2


title: G1_P426_Wk26


title: G1_P426_Wk23


title: G1_P423_Wk-2


title: G1_P423_Wk23_2


title: G1_P423_Wk1


title: G1_P423_Wk-2_2


title: G1_P423_Ch1+5


title: G1_P423_Wk23


title: G1_P422_Wk32


title: G1_P422_Wk1


title: G1_P422_Wk23


title: G1_P422_Ch1+5


title: G1_P419_Wk-2


title: G1_P422_Wk26


title: G1_P417_Wk23


title: G1_P419_Wk23


title: G1_P417_Wk26


title: G1_P422_Wk-2


title: G3_P509_Wk32

source_name: Macaca mulatta_Blood_mockgp96


title: G1_P419_Wk32


title: Normal tissue from patient 819

city: HANGZHOU

first: wang

last: jianguo

state: ZHEJIANG

address: 79 Qingchun Road

department: Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine

country: China

institute: zhejiang university

description: raw file name: US10313827_253831410035_S01_GE2_107_Sep09_1_4

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent G2565CA scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.7.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

source_name: Adjacent Normal tissue from patient 819

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-2000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: gender

value: Female

tag: histological type of adjacent normal tissue

value: liver tissue


title: G1_P419_Wk1


title: G1_P419_Wk26


title: Cancer tissue from patient 819

source_name: Cancer tissue from patient 819

tag: tumor stage

value: moderately differentiated

tag: age

tag: afp

tag: distant metastasis

value: no

tag: lymph node metastasis

tag: vascular invasion

tag: tumor size (centimeters)

tag: prognosis

value: Death


title: Normal tissue from patient 929

description: raw file name: US10313827_253831410035_S01_GE2_107_Sep09_1_3

source_name: Adjacent Normal tissue from patient 929

value: male


title: G1_P417_Wk-2


title: Cancer tissue from patient 929

source_name: Cancer tissue from patient 929

value: Survival


title: Cancer tissue from patient 959

description: raw file name: US10313827_253831410035_S01_GE2_107_Sep09_1_2

source_name: Cancer tissue from patient 959


title: Normal tissue from patient 1046

description: raw file name: US10313827_253831410035_S01_GE2_107_Sep09_1_1

source_name: Adjacent Normal tissue from patient 1046


title: HC-KO-10A

description:
SAMPLE 7
replicate 1


title: G1_P417_Wk1


title: G3_P509_Wk23_2


title: Non-celiac/non-inflamed patient_11

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

description: CONTROL

data_processing:
Housekeeping gene RPLPO was simultaneously quantified and used as an endogenous control of input RNA (Life Technologies)
Relative expression in each sample was calculated using the accurate Ct method and normalized to the average expression value of the 15 control samples
Fold Change worksheet reports DEBUT/TTO, DEBUT/CONTROL and TTO/CONTROL ratios

label: Taqman Gene Expression assays

source_name: Intestinal biopsy

label_protocol:
RNA was normalized to 8 ng/ul and converted to cDNA using the AffinityScript cDNA Synthesis kit (Agilent Technologies) following manufacturer´s protocol
Specific Target Amplification (STA) was performed
Gene expression analyses were performed using Fluidigm Biomark 48.48 dynamic arrays and commercially available TaqMan Gene Expression assays

growth_protocol: Samples stored in liquid nitrogen untill RNA extraction

extract_protocol: NucleoSpin microRNA kit following manufacturer´s instructions for total RNA

tag: disease state

value: Non-inflamed mucosa


title: Non-celiac/non-inflamed patient_14

description: CONTROL


title: G3_P509_Wk23_3

value: Blood


title: Non-celiac/non-inflamed patient_12

description: CONTROL


title: Cancer tissue from patient 1046

source_name: Cancer tissue from patient 1046


title: G3_P509_Wk-2


title: G3_P509_Wk23


title: Normal tissue from patient 959

source_name: Adjacent Normal tissue from patient 959


title: G3_P509_Wk1_2


title: G3_P509_Wk26


title: Non-celiac/non-inflamed patient_10

description: CONTROL


title: Non-celiac/non-inflamed patient_9

description: CONTROL


title: G3_P509_Wk1


title: G3_P508_Wk23


title: G3_P508_Wk32


title: Non-celiac/non-inflamed patient_8

description: CONTROL


title: Cancer tissue from patient 796

description: raw file name: US10313827_253831410020_S01_GE2_107_Sep09_1_1

source_name: Cancer tissue from patient 796


title: G3_P508_Wk-2


title: G3_P474_Wk32


title: Non-celiac/non-inflamed patient_6

description: CONTROL


title: Non-celiac/non-inflamed patient_7

description: CONTROL


title: mouse hepatic angiosarcoma cell line, biological replicate 3

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: The Hybridization, Wash and Stain Kit (Affymetrix) was used to hybridize all samples for 17 hours at 45°C in Affymetrix hybridization oven 645. The arrays were washed and stained on Fluidics station 450 using wash protocol FS450_0007 (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.

data_processing: Microarray data were preprocessed using standard RMA algorithm as implemented in the OLIGO package of Bioconductor libraries of R statistical environment.

source_name: hepatic angiosarcoma cell line

label_protocol: 250 ng of total RNA was reverse transcribed and biotinylated with the whole-transcript Expression Kit (Ambion) and whole-transcript Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: MxCre Notch1 lox/lox mice or Notch 1 lox/lox wildtype (WT) mice on a C57Bl/6 background were injected with 300ug of polyiosinic-polycytidylic acid at the age of 4 weeks at day 0, 3, and 6 to induce Cre expression for deletion of the loxP-flanked exon encoding the signal peptide of Notch 1 as previously described. Mice were euthanised by CO2 inhalation and liver samples were collected and snap-frozen for RNA extraction. For the establishment of angiosarcoma (AS) cell lines, hepatic endothelial cells were isolated from Notch1 knockout (KO) mice harbouring a visible AS. Longterm culturing of the primary cells selected malignant AS cells based on their atypical growth capacity and eventually lead to a uniform cell population.

extract_protocol: Total RNA was extracted from the PHH using Qiazol reagent and miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction

tag: background strain

tag: genotype/variation

value: Notch1 knockout


title: high fat diet, replicate 2

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

description: NMRI mice were fed with standard diet (3.3% fat) and water ad libitum until the age of 40 days. Then the higher fat diet (18% fat) was fed for 8 days. Age matched animals on normal fat diet (3.3% fat) were used as control. After 8 days, animals were sacrificed and gonadal fat was taken and shock frozen in liquid nitrogen. For microarray analyses, three fat fed and three normal fed male NMRI mice were used, and the RNA from gonadal fat pads was extracted and pooled for both conditions. 100 µg RNA from each pool was reverse transcribed, labeled and used for microarray analysis according to standard protocols in duplicates with mouse expression arrays.

hyb_protocol: Hybridization protocol following fragmentation, biotinilated RNA were hybridized 16hrs at 45° C with rotation (60rpm) into individual Affymetrix Gene Mouse Arrays 1.0 ST. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) according to GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual (Affymetrix) instructions.

scan_protocol: Microarrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix) and quality control was evaluated by Affymetrix software (Expression ConsoleTM).

data_processing: Computation of the RMA (Robust Multichip Average) expression measure (log2) in R as described in Irizarry et al Biostatistics (2003) including background adjustment and quantile normalization.

source_name: gonadal fat pads RNA of three overfed (18% fat) male NMRI mice, replicate 2

label_protocol: Labeling protocol was carried out with 300 ng of purified RNA, with biotin, according to Affymetrix Gene Mouse Arrays 1.0 ST protocol.

growth_protocol: male NMRI mice were housed and bred at the mouse facility of the FBN, Dummerstorf, Germany. Mice were housed in a semi-barrier system. Air was exchanged 12 times per hour and coarsely filtered. The room temperature was between 22.4 and 22.7° C, humidity between 50 and 60% and a 12L:12D light cycle was applied. NMRI mice were fed with standard rodent diet (V1534-000 with 3.3% fat; Ssniff, Soest, Germany) and water ad libitum until the age of 40 days

extract_protocol: For RNA isolation from gonadal fad pads, RNeasy® Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) was used. Tissue pieces of 30-50 mg were cut, immediately placed into 1 ml of QIAzol Lysis reagent, homogenized for 20 seconds using a rotor-stator homogenizer and further treated according to the manufacturer’s protocol. RNA was pooled for both conditions.

treatment_protocol: The fat diet (FD; 18% fat; C1057, Altromin, Lage, Germany) was given to experimental animals for 8 days ad libitum. Age matched animals on normal fat diet (ND; 3.3% fat; V1534-000, Ssniff, Soest, Germany) were used as control. After 8 days, animals were sacrificed and gonadal fat was taken and shock frozen in liquid nitrogen.

tag: strain

value: NMRI mice

tag: Sex

value: 48 days

tag: tissue

value: gonadal fat pads

tag: diet

value: 18% fat


title: G3_P508_Wk1

tag: treatment


title: G3_P474_Wk26


title: high fat diet, replicate 1

source_name: gonadal fat pads RNA of three overfed (18% fat) male NMRI mice, replicate 1


title: normal fat diet, replicate 1

source_name: gonadal fat pads RNA of three normal fed (3.3% fat) male NMRI mice, replicate 1


title: G1_P428_Wk26


title: G3_P474_Wk23


title: Normal tissue from patient 796

source_name: Adjacent Normal tissue from patient 796

tag: gender

tag: histological type of adjacent normal tissue


title: mouse hepatic angiosarcoma cell line, biological replicate 1


title: mouse hepatic angiosarcoma cell line, biological replicate 2


title: Non-celiac/non-inflamed patient_5

description: CONTROL


title: mouse liver sample, KO strain, biological replicate 1

source_name: liver


title: mouse liver sample, WT strain, biological replicate 3

value: Notch1 wild type


title: mouse liver sample, KO strain, biological replicate 2


title: mouse liver sample, KO strain, biological replicate 3


title: G3_P508_Wk26

source_name: Macaca mulatta_Blood_mockgp96


title: G3_P474_Wk-2


title: Non-celiac/non-inflamed patient_3

description: CONTROL


title: Non-celiac/non-inflamed patient_4

description: CONTROL


title: mouse liver sample, WT strain, biological replicate 1


title: Non-celiac/non-inflamed patient_1

description: CONTROL


title: Non-celiac/non-inflamed patient_2

description: CONTROL


title: G3_P474_Wk1


title: mouse liver sample, WT strain, biological replicate 2


title: Treated celiac patient_15

description: TTO


title: G3_P473_Wk26


title: G3_P473_Wk-2


title: normal fat diet, replicate 2

source_name: gonadal fat pads RNA of three normal fed (3.3% fat) male NMRI mice, replicate 2

tag: age


title: WFat_CT56

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Intensity values normalized using Affymetrix Expression Console software (GC-RMA).

source_name: white adipose

label_protocol: not provided

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for one week. Mice were then transferred to complete darkness prior to collection. Collection began at CT18. Mice were housed in light-tight boxes for the duration of the experiment.

extract_protocol: Organ samples were homogenized in Trizol reagent (Invitrogen) using a Tissuelyser (Qiagen). RNA was extracted using RNeasy columns (Qiagen) as per manufacturer’s protocol, then pooled from three mice for each organ and time point.

value: white adipose


title: WFat_CT60


title: WFat_CT50


title: G3_P473_Wk1


title: WFat_CT54


title: G3_P473_Wk23


title: Treated celiac patient_14

description: TTO


title: WFat_CT62


title: WFat_CT48


title: WFat_CT52


title: WFat_CT42


title: WFat_CT64


title: Treated celiac patient_13

description: TTO


title: WFat_CT44


title: Treated celiac patient_12

description: TTO


title: WFat_CT58


title: WFat_CT46


title: G3_P441_Wk32


title: Treated celiac patient_11

description: TTO


title: G3_P441_Wk26


title: Treated celiac patient_10

description: TTO


title: Treated celiac patient_9

description: TTO


title: WFat_CT38


title: WFat_CT32


title: WFat_CT40


title: Non-celiac/non-inflamed patient_15

description: CONTROL


title: G3_P441_Wk23


title: WFat_CT36


title: G3_P473_Wk32


title: G3_P441_Wk-2


title: WFat_CT26


title: WFat_CT20


title: WFat_CT30


title: Treated celiac patient_8

description: TTO


title: WFat_CT34


title: G3_P441_Wk-2_3


title: Treated celiac patient_7

description: TTO


title: WFat_CT22


title: WFat_CT28


title: G3_P441_Wk1_3


title: G3_P441_Wk-2_2


title: Non-celiac/non-inflamed patient_13

description: CONTROL


title: WFat_CT24


title: Treated celiac patient_6

description: TTO


title: Mus_CT62

source_name: skeletal muscle

value: skeletal muscle


title: Treated celiac patient_5

description: TTO


title: Mus_CT60


title: Mus_CT64


title: G3_P441_Wk1_2


title: G3_P441_Wk1


title: Treated celiac patient_4

description: TTO


title: WFat_CT18


title: G3_P438_Wk32


title: Mus_CT54


title: Mus_CT52


title: Treated celiac patient_3

description: TTO


title: Mus_CT56


title: Treated celiac patient_2

description: TTO


title: G3_P438_Wk26


title: Mus_CT50


title: Treated celiac patient_1

description: TTO


title: Active celiac patient_15

description: DEBUT

value: Inflamed mucosa


title: G3_P438_Wk23_2


title: Mus_CT58


title: Mus_CT46


title: Mus_CT44


title: G3_P438_Wk23


title: G3_P438_Wk-2


title: Mus_CT42


title: Mus_CT40


title: Mus_CT38


title: Active celiac patient_14

description: DEBUT


title: Active celiac patient_13

description: DEBUT


title: Mus_CT34


title: G3_P438_Wk1


title: Mus_CT30


title: Mus_CT32


title: Mus_CT36


title: Active celiac patient_12

description: DEBUT


title: Mus_CT48


title: Mus_CT28


title: G3_P433_Wk26


title: G3_P433_Wk32


title: Mus_CT22


title: Mus_CT26


title: Mus_CT24


title: Active celiac patient_11

description: DEBUT


title: G3_P433_Wk23


title: Mus_CT20


title: Active celiac patient_10

description: DEBUT


title: Active celiac patient_9

description: DEBUT


title: Active celiac patient_7

description: DEBUT


title: Active celiac patient_8

description: DEBUT


title: Active celiac patient_6

description: DEBUT


title: G3_P433_Wk1


title: G3_P432_Wk32


title: G3_P433_Wk-2


title: G3_P432_Wk26


title: Active celiac patient_5

description: DEBUT


title: Lun_CT62

source_name: lung

value: lung


title: G3_P432_Wk23


title: Lun_CT58


title: Lun_CT52


title: Lun_CT64


title: Active celiac patient_4

description: DEBUT


title: Lun_CT60


title: Mus_CT18


title: G3_P432_Wk1


title: Lun_CT50


title: Lun_CT46


title: Lun_CT54


title: Lun_CT42


title: Lun_CT44


title: Lun_CT40


title: Lun_CT56


title: Lun_CT48


title: G3_P425_Wk26


title: Active celiac patient_2

description: DEBUT


title: Active celiac patient_1

description: DEBUT


title: G3_P432_Wk-2


title: Lun_CT38


title: Lun_CT34


title: G3_P425_Wk23


title: Lun_CT36


title: Active celiac patient_3

description: DEBUT


title: Lun_CT26


title: G3_P425_Wk1


title: Lun_CT24


title: G3_P424_Wk32


title: Lun_CT28


title: ECs generated from  umbilical cord-derived endothelial progenitor cells at passage 4 was subcultured to passage 7

description: endothelial cells generated from human umbilical cord-derived endothelial progenitor cells at passage 4 was subcultured to passage 7

data_processing: Normalized expression signal data was generated at the gene level using Affymetrix's Expression Console by RMA.

source_name: Human cord blood-derived EPOCs: lot B205115, BioChain Institute, Inc.

tag: cell type

value: vascular endothelical cells


title: Lun_CT32


title: G3_P425_Wk-2


description: EPCdEC of the second donor at passage 4 was subcultured to passage 7

source_name: Human adult bone marrow mononuclear cell-derived endothelial progenitor outgrowth cells (EPOCs): lot B112057, BioChain Institute, Inc., Hayward, CA


title: Lun_CT30


title: Lun_CT22


title: EPCdEC of the first donor at passage 4 purchased as a distinct pacakge a half year later was subcultured to passage 7

source_name: Human adult bone marrow mononuclear cell-derived endothelial progenitor outgrowth cells (EPOCs): lot B112054, BioChain Institute, Inc., Hayward, CA


title: Lun_CT18


title: EPCdEC of the first donor at passage 12

description: EPCdEC of the first donor at passage 12


title: G3_P424_Wk-2_2


title: Liv_CT58

value: liver


title: G3_P424_Wk23


title: Liv_CT56


title: G3_P424_Wk26


title: Lun_CT20


title: Liv_CT54


title: G3_P424_Wk-2


title: Liv_CT64


title: Liv_CT62


title: Liv_CT52


title: Liv_CT60


title: Liv_CT48


title: human dermal microvascular endothelial cells

source_name: HMVEC purchased from Dainippon Sumitomo Pharma Co., Ltd. (Osaka Japan)


title: G3_P420_Wk32


title: Liv_CT50


title: G3_P420_Wk26


title: G3_P424_Wk1


title: Liv_CT42


title: Liv_CT46


description: VEC generated from adult human bone marrow-derived EPC (EPCdEC) of the first donor at passage 4 was subcultured to passage 7


title: human umbilical vein endothelial cells

description: human umbilical vein endothelial cells

source_name: HUVEC purchased from Dainippon Sumitomo Pharma Co., Ltd. (Osaka Japan)


title: G3_P420_Wk23


title: Liv_CT44


title: Liv_CT32


title: Liv_CT40


title: human aortic endothelial cells

description: human aortic endothelial cells

source_name: HAEC purchased from Dainippon Sumitomo Pharma Co., Ltd. (Osaka Japan)


title: Liv_CT34


title: Liv_CT28


title: Liv_CT30


title: G3_P420_Wk1


title: G3_P420_Wk-2


title: G3_P418_Wk32


title: K5140_Root_Salt_2

city: Urrbrae

first: Sam

last: Henderson

state: South Australia

address: Hartley Grove

institute: University of Adeladie

hyb_protocol: Hybridisations were performed at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia) using custom 8 x 60K gene expression microarrays from Agilent, and using methods recommended by Agilent.

scan_protocol: Image scanning was performed at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia) using methods as recommended by Agilent.

data_processing: Scanned images were analysed with Feature Extraction Software 10.7.3 (Agilent Technologies, Santa Clara, California, USA) and the Cy3 median signal intensities for each spot on the arrays were imported into R for further processing. The data was log(2) transformed and quantile normalized. Since the microarray hybridizations were performed at different dates we observed batch effects which we corrected for with the ComBat package (Johnson et al., 2007). Differentially expressed genes were identified using the Linear Model for Microarray Data (LIMMA) package (Smyth, 2004), and the Benjamini and Hochberg correction method was applied to account for multiple testing (Benjamini & Hochberg, 1995).

organism: Vitis x champinii x Vitis riparia

source_name: K51-40, Total Root, 50 mM chloride

label_protocol: Single colour labelling was performed at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia) using reagents, kits and protocols as recommended by Agilent.

growth_protocol: Pot-grown grapevines of K51-40 (Vitis champinii X Vitis riparia), 140 Ruggeri (Vitis berlandieri X Vitis rupestris) and Cabernet Sauvignon (Vits vinifera) were established from cuttings and maintained in a glasshouse as described previously (Gong et al., 2011). Grapevines were watered daily with tap water that contained 3.2 mM Cl–. Vines were given fortnightly applications via fertigation of Megamix Plus (Rutec Pty. Ltd., Tamworth, New South Wales) and Iron Sodium EDTA (concentration 42.6 g/L), 25 mLs per 250 L. Typical analysis of this solution was macro elements in mM: K, Na, Ca, Mg and Cl, respectively, 1.3, 2.4, 1.5, 1.1 and 2.7, and micro elements in μM: Fe, B, respectively, 25.2 and 3. Mature leaves were excised from grapevines and the petioles were dipped in a hormone gel containing 1.5 g.l-1 IBA (Clonex, Growth Technology, O’Connor, Western Australia) and then placed in propagation trays containing vermiculite and perlite at a 1:1 ratio (Australian Vermiculite and Perlite Pty Ltd, Campbellfield, Victoria, Australia). The propagation trays (33 × 28 cm x 5.5 cm deep) were placed on heat beds (30 ºC) (Heat ’n’ Grow by Thermofilm, Springvale, Victoria, Australia) in a mini-shadehouse within the glasshouse. To maintain high humidity, the mini-shadehouse was covered with 90 % shadecloth and the leaves were misted with fine sprays for 1 min every hour during the day from 7 am to 7 pm. After approximately 3 weeks, rooted-leaves were transferred to aerated hydroponics tanks containing modified Hoagland Solution (Hoagland & Arnon, 1950) containing the following nutrients (mM) for a two-week pre-treatment period: KNO3, 1.0; Ca(NO3)2·4H2O, 1.0; MgSO4·7H2O, 0.4; KH2PO4, 0.2; H3BO3, 4.6×10-2; MnCl2·4H2O, 9.1×10-3; ZnSO4·7H2O, 7.6×10-4; CuSO4·5H2O, 3.2×10-4; Na2MoO4·2H2O, 2.4×10-4; EDTA-Fe-Na, 7.1×10-2 (pH 6.5).

extract_protocol: Frozen roots were ground to a fine powder in liquid nitrogen using a mortar and pestle. RNA was extracted using the Spectrum Plant Total RNA Kit (Sigma, St. Louis, Missouri, USA) following the manufacturer’s recommended protocol. RNA was DNase I treated with Turbo DNA-free (Life Technologies, Carlsbad, California, USA) for 1 hour at 37 oC to remove any contaminating genomic DNA. RNA was then precipitated at minus 80 oC overnight in 5 volumes of 100 % ethanol (v/v) and 1/10 volumes of 3 M NaOAC. After ethanol precipitation, RNA was resuspended in nuclease free water and analysed on a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA). Only RNA samples with 260/280 and 260/230 absorbance ratios greater than 1.8 were used. RNA integrity was measured on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, California, USA).

treatment_protocol: Following pre-treatment, 16 rooted-leaves of K51-40, 140 Ruggeri and Cabernet Sauvignon were subjected to nutrient solution only (control) or to 50 mM Cl– (Na+: Ca2+: Mg2+ = 6:1:1) in nutrient solution for 4 days. At harvest, the rooted-leaves of each genotype were washed in de-ionised water, blotted dry with paper towel, weighed, then separated into lamina, petiole and roots. Fresh weights of all plant parts were also obtained. Separate root samples were taken for RNA extraction.

value: whole roots

tag: plant material

value: rooted leaves


title: Liv_CT36


title: Liv_CT38


title: K5140_Root_Salt_1


title: K5140_Root_Salt_3


title: Liv_CT24


title: G3_P418_Wk26_3


title: Liv_CT22


title: G3_P418_Wk26


title: 140Ruggeri_Root_Salt_3

organism: Vitis cinerea var. helleri x Vitis rupestris

source_name: 140 Ruggeri, Total Root, 50 mM chloride


title: 140Ruggeri_Root_Salt_2


title: K5140_Root_Salt_4


title: Liv_CT20


title: Liv_CT26


title: G3_P418_Wk26_2


title: Kid_CT64

source_name: kidney

value: kidney


title: Kid_CT60


title: Kid_CT58


title: G3_P418_Wk23


title: Kid_CT54


title: CabernetSauvignon_Root_Salt_4

organism: Vitis vinifera

source_name: Cabernet Sauvignon, Total Root, 50 mM chloride


title: Kid_CT56


title: Kid_CT48


title: CabernetSauvignon_Root_Salt_3


title: Kid_CT44


title: Kid_CT46


title: Liv_CT18


title: Kid_CT42


title: Kid_CT50


title: K5140_Root_Control_4

source_name: K51-40, Total Root, 0 mM chloride


title: Kid_CT62


title: K5140_Root_Control_3


title: G3_P418_Wk-2


title: Kid_CT38


title: Kid_CT36


title: 140Ruggeri_Root_Salt_1


title: G3_P418_Wk1_3


title: CabernetSauvignon_Root_Salt_2


title: Kid_CT52


title: G3_P418_Wk1_2


title: CabernetSauvignon_Root_Salt_1


title: G2_P507_Wk26

source_name: Macaca mulatta_Blood_SIVgp96 + gp120

value: SIVgp96 + gp120


title: G3_P418_Wk1

source_name: Macaca mulatta_Blood_mockgp96

value: Blood


title: Kid_CT40


title: G2_P507_Wk32


title: Kid_CT30


title: Kid_CT34


title: G2_P507_Wk23


title: K5140_Root_Control_2


title: G2_P507_Wk-2


title: Kid_CT32


title: G2_P507_Wk1


title: Kid_CT26


title: Kid_CT24


title: Kid_CT28


title: Kid_CT20


title: Kid_CT22


title: Kid_CT18


title: 140Ruggeri_Root_Control_2

source_name: 140 Ruggeri, Total Root, 0 mM chloride


title: Hyp_CT64

source_name: hypothalamus

value: hypothalamus


title: G2_P506_Wk32_3


title: Hyp_CT62


title: G2_P507_Ch1+5


title: 140Ruggeri_Root_Control_1


title: 140Ruggeri_Root_Control_3


title: Hyp_CT60


title: K5140_Root_Control_1


title: G2_P506_Wk32_2


title: CabernetSauvignon_Root_Control_3

source_name: Cabernet Sauvignon, Total Root, 0 mM chloride


title: Hyp_CT58


title: Hyp_CT56


title: CabernetSauvignon_Root_Control_4


title: Hyp_CT52


title: G2_P506_Wk32


title: G2_P506_Wk26


title: G2_P506_Wk23_2


title: Hyp_CT46


title: Hyp_CT48


title: Hyp_CT54


title: CabernetSauvignon_Root_Control_1


title: Hyp_CT42


title: Hyp_CT44


title: Hyp_CT50


title: CabernetSauvignon_Root_Control_2


title: Hyp_CT36


title: G2_P506_Ch1+5


title: G2_P506_Wk23


title: Hyp_CT34


title: G2_P505_Wk32_2


title: Hyp_CT30


title: Hyp_CT32


title: Hyp_CT40


title: Hyp_CT38


title: G2_P505_Wk26


title: Hyp_CT22


title: Hyp_CT28


title: Hyp_CT24


title: G2_P506_Wk1


title: Hyp_CT26


title: Hyp_CT18


title: G2_P505_Wk23


title: Hyp_CT20


title: Hrt_CT64

source_name: heart

value: heart


title: Hrt_CT60


title: Hrt_CT62


title: G2_P505_Wk32


title: G2_P505_Ch3+5


title: G2_P505_Wk1


title: G2_P504_Wk32


title: Hrt_CT54


title: Hrt_CT56


title: Hrt_CT48


title: Hrt_CT52


title: Hrt_CT50


title: Hrt_CT58


title: G2_P504_Wk23


title: Hrt_CT38


title: G2_P504_Wk26


title: Hrt_CT42


title: Hrt_CT40


title: G2_P504_Wk-2


title: G2_P505_Wk-2


title: Hrt_CT36


title: G2_P504_Ch1+5


title: G2_P504_Wk1


title: Hrt_CT46


title: Hrt_CT34


title: Hrt_CT28


title: Hrt_CT26


title: Hrt_CT30


title: Hrt_CT32


title: Hrt_CT22


title: G2_P475_Wk32


title: Hrt_CT20


title: Hrt_CT24


title: G2_P475_Wk26


title: G2_P475_Wk-2


title: G2_P475_Ch2+5


title: G2_P475_Wk1


title: Hrt_CT18


title: Cer_CT64

source_name: cerebellum

value: cerebellum


title: Cer_CT60


title: Cer_CT62


title: G2_P475_Wk23


title: G2_P470_Wk26


title: G2_P475_Ch1+5


title: Cer_CT52


title: Cer_CT48


title: Cer_CT58


title: Cer_CT56


title: Cer_CT38


title: Cer_CT50


title: Cer_CT44


title: Cer_CT46


title: G2_P470_Wk23


title: Cer_CT42


title: G2_P470_Wk1


title: Cer_CT34


title: G2_P470_Wk-2


title: Cer_CT36


title: Cer_CT32


title: Cer_CT24


title: Cer_CT26


title: Cer_CT28


title: Responder_PAC3_CardB

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

data_processing:
The normalization and all the data analysis were performed with R2.15 Bioconductor 2.10
For the normalization it was used the platform normalizer MammU6.
Fold_Change.txt reports ΔΔCt for each statitistical contrast (ΔΔCt = test deltaCt - reference deltaCt).

label: FAM

source_name: MRCC patient_sunitinib_responder

label_protocol: 350ng of total RNA from each patient was first reverse-transcribed using a stem-loop RT Megaplex Primer Pool and the Taqman MicroRNA Reverse Transcription Kit (Applied Biosystem). cDNAs were preamplified with the TaqMan Preamp Master Mix kit and Megaplex Preamp Primer Human pools. Expression of 667 human mature miRNAs and 6 endogenous controls was profiled using TLDA microfluidic cards A and B (Applied Biosystem) on a 7900HT Fast real time system.

extract_protocol: Total RNA was extracted with the RecoverAllTM Total Nucleic Acid Isolation Kit (Ambion).

treatment_protocol: Tumor confirmed by pathologist tissues samples were formalin-fixed and paraffin-embedded (FFPE). Blocks were sliced into 10µm sections.

tag: disease

value: metastatic renal-cell carcinoma (MRCC)

tag: response to sunitinib treatment

value: responder (sensitive)

tag: patient status

value: Patient with clinical benefit after sunitinib treatment

value: 4 unstained sections of FFPE tumor tissue from MRCC patient before treatment


title: Responder_PAC4_CardB


title: Non responder_PAC5_CardB

source_name: MRCC patient_sunitinib_non-responder

value: non-responder (resistant)

value: Patient with clear cancer progression after sunitinib treatment


title: Responder_PAC1_CardB


title: Non responder_PAC2_CardB


title: Non responder_PAC6_CardB


title: Cer_CT40


title: BFat_CT64

source_name: brown adipose

value: brown adipose


title: Cer_CT22


title: BFat_CT62


title: Cer_CT30


title: BFat_CT60


title: Cer_CT18


title: BFat_CT58


title: Cer_CT54


title: 35S::KLU, biological replicate 3

city: Gent

first: Hannes

last: Claeys

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB-UGent

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Data was processed with Robust Multichip Average (RMA) (background correction, normalization, and summarization) as implemented in BioConductor (Irizarry et al., 2003a; Irizarry et al., 2003b; Gentleman et al., 2004).
Absolute expression values log2 transformed in the RMA procedure

organism: Arabidopsis thaliana

label_protocol: Standard Affymetrix protocol

growth_protocol: Plants were grown on 1/2 MS medium under 16 h light (80µm/m2/s)/8 h dark cycle at 21°C

extract_protocol: RNeasy plant mini kit (Qiagen), according to manufacturer protocol

tag: ecotype

value: Shoot

tag: developmental stage

value: Stage 1.03

tag: genotype


title: BFat_CT54


title: BFat_CT56


title: 35S::KLU, biological replicate 2


title: BFat_CT52


title: 35S::KLU, biological replicate 1


title: BFat_CT50


title: WT, biological replicate 3

value: WT


title: BFat_CT46


title: BFat_CT48


title: BFat_CT44


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep4

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Plants were grown in a controlled 20°C glasshouse prior to VIGS treatment.  Twelve days after VIGS treatment, half of the plants in each replication were challenged with the compatible Bgh isolate 5874.  Top halves of seedling third leaves (about 10 cm) from each split-plot experimental unit were harvested into liquid N2 at 32 hours after inoculation (HAI).  RNA was isolated for GeneChip hybridization from the 32-HAI samples. (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Hordeum vulgare

source_name: tissue (genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248])

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Plants were grown in a controlled 20°C glasshouse prior to VIGS treatment.  Twelve days after VIGS treatment, half of the plants in each replication were challenged with the compatible Bgh isolate 5874.

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: Accession #16097

tag: organism part

value: vegetative cell ('PO:0020099')

tag: development stage

value: 3 leaf fully expanded ('PO:0001053')

value: 21 days

tag: growth media

value: peat/perlite/soil


title: BFat_CT42

tag: strain

tag: tissue


title: WT, biological replicate 2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep4

source_name: tissue (genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00)


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep5


title: WT, biological replicate 1


title: BFat_CT40


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep3


title: Cer_CT20


title: GO5; 8h after switch to ambient CO2 concentrations; biological rep 3

city: Düsseldorf

first: Veronica

last: Maurino

address: Universitätsstrasse 1

department: Plant Molecular Physiology and Biotechnology

institute: Heinrich-Heine-University

description: hyb13023.CEL; G05_8h_a3

hyb_protocol: Following fragmentation, cRNAs were hybridized on Genechip Arabidopsis ATH1 Genome Arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/) at the VIB Microarray Facility (Leuven, Belgium)

scan_protocol: GeneChips were scanned according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/) at the VIB Microarray Facility (Leuven, Belgium)

data_processing: Raw data (CEL files) were processed with the statistical algorithm Robust Multiarray Average (gcRMA) with the affy package of R (v.2.15.0)/Bioconductor

source_name: GO5_8h after switch to ambient CO2 conc.

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3'IVT Express Kit

growth_protocol: Columbia-0 (Col-0, wild type), catalase-deficient Salk plants  (10-15% of wild-type catalase activity; cat2-2; N576998; (Queval et  al., 2007)) and A. thaliana plants expressing glycolate oxidase in  chloroplasts (GO5 plants; (Fahnenstich et al., 2008)) were grown in  soil under a 16h light/8h dark regime at photosynthetically active  photon flux densities (PPFD) of 75 µmol quanta m-2 s-1 at 22°C  day/18°C night temperatures and a CO2 concentration of 3,000 ppm.

extract_protocol: Total RNA was extracted whole rozettes (2 plants/biolocal rep) using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Invitrogen).

treatment_protocol: After three weeks of growth, plants were transferred to ambient CO2  concentration (380 ppm) and the same PPFD. Whole rosettes were  harvested at 0h and 8h after transfer. Control samples were harvested  at 8 h from plants continuously maintained in high CO2.

tag: genotype/variation

value: expressing glycolate oxidase in chloroplasts (GO 5)

tag: harvested at

value: 3 weeks

value: 2 whole rosettes


title: GO5; 0h after switch to ambient CO2 concentrations; biological rep 3

description: hyb13022.CEL; G05_0h_3

source_name: GO5_0h after switch to ambient CO2 conc.

tag: age


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep5

tag: cell type


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep1


title: BFat_CT38


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep3


title: BFat_CT36


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep2


title: BFat_CT34


title: GO5; harvested at 8h, continiously maintained in high CO2; biological rep 3

description: hyb13024.CEL; G05_8h_c3

source_name: GO5_harvested at 8h, continiously maintained in high CO2

value: 8h, continiously maintained in high CO2


title: Hrt_CT44

value: heart


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep1


title: BFat_CT32


title: BFat_CT28


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep5

source_name: tissue (genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control))


title: cat2-2; harvested at 8h, continiously maintained in high CO2; biological rep 3

description: hyb13021.CEL; cat_8h_c3

source_name: cat2-2_harvested at 8h, continiously maintained in high CO2

value: catalase-deficient Salk plants (cat2-2)


title: BFat_CT30


title: cat2-2; 8h after switch to ambient CO2 concentrations; biological rep 3

description: hyb13020.CEL; cat_8h_a3

source_name: cat2-2_8h after switch to ambient CO2 conc.


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep4


title: BFat_CT26


title: cat2-2; 0h after switch to ambient CO2 concentrations; biological rep 3

description: hyb13019.CEL; cat_0h_3

source_name: cat2-2_0h after switch to ambient CO2 conc.


title: BFat_CT24


title: WT; 8h after switch to ambient CO2 concentrations; biological rep 3

description: hyb13017.CEL; Col_8h_a3

source_name: WT_8h after switch to ambient CO2 conc.

value: Columbia-0 (Col-0, wild type)


title: GO5; harvested at 8h, continiously maintained in high CO2; biological rep 2

description: hyb13015.CEL; G05_8h_c2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep1


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep3


title: BFat_CT18


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep2


title: GO5; 0h after switch to ambient CO2 concentrations; biological rep 2

description: hyb13013.CEL; G05_0h_2


title: WT; 0h after switch to ambient CO2 concentrations; biological rep 3

description: hyb13016.CEL; Col0_0h_3

source_name: WT_0h after switch to ambient CO2 conc.


title: BFat_CT22


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep5

source_name: tissue (genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248])


title: cat2-2; harvested at 8h, continiously maintained in high CO2; biological rep 2

description: hyb13012.CEL; cat_8h_c2


title: BFat_CT20


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep4


title: GO5; 8h after switch to ambient CO2 concentrations; biological rep 2

description: hyb13014.CEL; G05_8h_a2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep2


title: Bstm_CT64

source_name: brainstem

value: brainstem


title: cat2-2; 8h after switch to ambient CO2 concentrations; biological rep 2

description: hyb13011.CEL; cat_8h_a2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep3


title: TBI zebrafish_control

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

description:
Gene expression in no TBI-injured zebrafish
Brain control

hyb_protocol: The fragmented labeled cRNA was then hybridized to oligo microarray at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA),  image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Danio rerio

source_name: TBI-injured zebrafish, 0dpi, control

label_protocol: 1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's recommendations. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

treatment_protocol: Each fish was intraperitoneally injected with 1×108 C. albicans cells suspended in 10μL sterile 1× phosphate-buffered saline (PBS)

value: brain

tag: gender

value: male

value: 1 year

tag: collection date


title: Bstm_CT62


title: Bstm_CT60


title: WT; harvested at 8h, continiously maintained in high CO2; biological rep 3

description: hyb13018.CEL; Col_8h_c3

source_name: WT_harvested at 8h, continiously maintained in high CO2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep4

source_name: tissue (genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00)


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep5


title: Bstm_CT56


title: TBI zebrafish_28dpi

description:
Gene expression after 28dpi in TBI-injured zebrafish
Brain 28 dpa

source_name: TBI-injured zebrafish, 28dpi


title: WT; harvested at 8h, continiously maintained in high CO2; biological rep 2

description: hyb13009.CEL; Col_8h_c2


title: TBI zebrafish_21dpi

description:
Gene expression after 21dpi in TBI-injured zebrafish
Brain 21 dpa

source_name: TBI-injured zebrafish, 21dpi


title: Bstm_CT58


title: GO5; 0h after switch to ambient CO2 concentrations; biological rep 1

description: hyb13004.CEL; G05_0h_1


title: cat2-2; 0h after switch to ambient CO2 concentrations; biological rep 2

description: hyb13010.CEL; cat_0h_2


title: WT; 8h after switch to ambient CO2 concentrations; biological rep 2

description: hyb13008.CEL; Col_8h_a2


title: TBI zebrafish_3dpi

description:
Gene expression after 3dpi in TBI-injured zebrafish
Brain 3 dpa

source_name: TBI-injured zebrafish, 3dpi


title: TBI zebrafish_15dpi

description:
Gene expression after 15dpi in TBI-injured zebrafish
Brain 15 dpa

source_name: TBI-injured zebrafish, 15dpi


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep1


title: GO5; harvested at 8h, continiously maintained in high CO2; biological rep 1

description: hyb13006.CEL; G05_8h_c1


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep3


title: TBI zebrafish_6dpi

description:
Gene expression after 6dpi in TBI-injured zebrafish
Brain 6 dpa

source_name: TBI-injured zebrafish, 6dpi


title: GO5; 8h after switch to ambient CO2 concentrations; biological rep 1

description: hyb13005.CEL; G05_8h_a1

source_name: GO5_8h after switch to ambient CO2 conc.


title: Bstm_CT54


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep5

source_name: tissue (genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control))


title: TBI zebrafish_1dpi

description:
Gene expression after 1dpi in TBI-injured zebrafish
Brain 1 dpa

source_name: TBI-injured zebrafish, 1dpi


title: Bstm_CT52


title: Bstm_CT50


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep2


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep1


title: WT; 0h after switch to ambient CO2 concentrations; biological rep 2

description: hyb13007.CEL; Col0_0h_2


title: Bstm_CT48


title: TBI zebrafish_10dpi

description:
Gene expression after 10dpi in TBI-injured zebrafish
Brain 10 dpa

source_name: TBI-injured zebrafish, 10dpi


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep4


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep3


title: cat2-2; harvested at 8h, continiously maintained in high CO2; biological rep 1

description: hyb13003.CEL; cat_8h_c1

source_name: cat2-2_harvested at 8h, continiously maintained in high CO2


title: TBI zebrafish_0.25dpi

description:
Gene expression after 0.25dpi in TBI-injured zebrafish
Brain 6 hours

source_name: TBI-injured zebrafish, 0.25dpi


title: cat2-2; 0h after switch to ambient CO2 concentrations; biological rep 1

description: hyb13001.CEL; cat_0h_1

source_name: cat2-2_0h after switch to ambient CO2 conc.


title: Bstm_CT44


title: STING tumor DNA III

city: Chicago

first: Seng-Ryong

last: Woo

state: Illinois

address: 929 E 57th street

department: Pathology

institute: University of Chicago

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G and CEL.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and dChip software using Affymetrix default analysis settings and global scaling as normalization method. The genes scored as "absent" or with signal intensity <100 were first filtered out.

source_name: STING knock out BMDCs tumor-derived DNA stimulation

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

growth_protocol: Bone marrow derived dendritic cells were generated by culturing bone marrow cells in the presence of GM-CSF for 9-12 days.

extract_protocol: Total RNA was isolated with Rneasy kit (Qiagen) using manufacture`s instruction.

treatment_protocol: BMDCs were stimulated with tumor-derived DNA using Lipofectamin for 7 hours.

tag: strain background

value: STING knockout

value: bone marrow derived dendritic cells (BMDCs)

tag: stimulated with

value: purified tumor-cell derived DNA


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep2

value: Accession #16097

value: vegetative cell ('PO:0020099')

value: 3 leaf fully expanded ('PO:0001053')


title: WT; 0h after switch to ambient CO2 concentrations; biological rep 1

description: hyb12998.CEL; Col0_0h_1

source_name: WT_0h after switch to ambient CO2 conc.


title: WT; 8h after switch to ambient CO2 concentrations; biological rep 1

description: hyb12999.CEL; Col_8h_a1

source_name: WT_8h after switch to ambient CO2 conc.


title: WT tumor DNA III

source_name: WT BMDCs tumor-derived DNA stimulation

value: wild type


title: Bstm_CT46

source_name: brainstem


title: WT; harvested at 8h, continiously maintained in high CO2; biological rep 1

description: hyb13000.CEL; Col_8h_c1

source_name: WT_harvested at 8h, continiously maintained in high CO2

value: 3 weeks


title: Bstm_CT38


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep5

source_name: tissue (genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248])

value: Accession #16552

value: 21 days

value: peat/perlite/soil


title: Bstm_CT40


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep4


title: WT media III

source_name: WT BMDCs no stimulation

value: none (unstimulated control)


title: cat2-2; 8h after switch to ambient CO2 concentrations; biological rep 1

description: hyb13002.CEL; cat_8h_a1

source_name: cat2-2_8h after switch to ambient CO2 conc.

value: catalase-deficient Salk plants (cat2-2)

value: 2 whole rosettes


title: genotype: HOR11358 (Mla9) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep1


title: spx1,spx2 resupplied Pi 4h, biological rep2

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

description: Gene expression data from spx1,spx2 plants grown in Pi-lacking medium an resupplied with Pi for 4 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Each microarray was scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, 2006). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003).

source_name: spx1,spx2 plants grown phosphate-lacking medium and resupplied with Pi for 4 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

extract_protocol: Trizol extraction of total RNA and cleanup with RNeasy (Qiagen), according to the manufacturers's instructions.

value: seedlings

value: 7 days

value: spx1,spx2 double mutant


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep2


title: STING tumor DNA II

value: STING knockout


title: Bstm_CT32

value: brainstem


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep3


title: Bstm_CT36


title: WT tumor DNA II

value: bone marrow derived dendritic cells (BMDCs)

value: purified tumor-cell derived DNA


title: WT media II


title: spx1,spx2 resupplied Pi 4h, biological rep3


title: STING tumor DNA

description: W3-STING tDNA


title: Bstm_CT34


title: Bstm_CT30


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:Bln1[248] - rep1

value: vegetative cell ('PO:0020099')


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep4

source_name: tissue (genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00)

value: 3 leaf fully expanded ('PO:0001053')


title: WT tumor DNA

description: W2-129 tDNA

value: wild type


title: spx1,spx2 complete, biological rep3

description: Gene expression data from spx1,spx2 plants grown in complete medium


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep5


title: spx1,spx2 resupplied Pi 4h, biological rep1


title: WT media

description: W1-129 media


title: spx1,spx2 no Pi, biological rep2

description: Gene expression data from spx1,spx2 plants grown in phosphate-lacking medium

source_name: spx1,spx2 plants grown phosphate-lacking medium


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep3


title: spx1,spx2 no Pi, biological rep1


title: Bstm_CT24


title: spx1,spx2 no Pi, biological rep3


title: Bstm_CT26


title: Day7 recover

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data from cell culture

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring GX 7.3.1 using Affymetrix default analysis settings and normalized to day1 control

source_name: SCp2 cells treated with MMP3 for 4d and allowed to recover in MMP3-free media for 3d

label_protocol: This project used the Affymetrix Mouse 430 2.0 GeneChip 200 ng of total RNA was used as input

growth_protocol: Cells were grown in DMEM+2% FCS

extract_protocol: Phenol/Chloroform

treatment_protocol: Treatment with MMP3

value: mammary gland

tag: treatment

value: Balb/c


title: Day5 recover

description: Gene expression data from cell culture

source_name: SCp2 cells treated with MMP3 for 4d and allowed to recover in MMP3-free media for 1d


title: spx1,spx2 complete, biological rep1

source_name: spx1,spx2 plants grown in complete medium


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep2

value: Accession #16552

value: 21 days


title: Bstm_CT28


title: Day4 MMP3

description: Gene expression data from cell culture

source_name: SCp2 cells treated with MMP3 for 4d

value: MMP3 for 4d


title: Bstm_CT20


title: Day6 recover

description: Gene expression data from cell culture

source_name: SCp2 cells treated with MMP3 for 4d and allowed to recover in MMP3-free media for 2d


title: spx1,spx2 complete, biological rep2


title: Day3 MMP3

description: Gene expression data from cell culture

source_name: SCp2 cells treated with MMP3 for 3d

value: MMP3 for 3d


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep4

source_name: tissue (genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control))

value: peat/perlite/soil


title: WT resupplied Pi 4h, biological rep3

description: Gene expression data from WT plants grown in Pi-lacking medium an resupplied with Pi for 4 h

source_name: Col-0 plants grown phosphate-lacking medium and resupplied with Pi for 4 h

value: seedlings

value: wild-type Col-0


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep5


title: Bstm_CT22


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: BSMV:00 - rep1


title: WT resupplied Pi 4h, biological rep2

value: 7 days


title: Day2 MMP3

description: Gene expression data from cell culture

source_name: SCp2 cells treated with MMP3 for 2d

value: MMP3 for 2d


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep3


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep2


title: Day1 MMP3

description: Gene expression data from cell culture

source_name: SCp2 cells treated with MMP3 for 1d

value: MMP3 for 1d


title: genotype: Clansman (Mla13) - treatedoruntreated: Non-Inoc. - treatment: Mock (Buffer Control) - rep1


title: WT no Pi, biological rep3

description: Gene expression data from WT plants grown in phosphate-lacking medium

source_name: Col-0 plants grown phosphate-lacking medium


title: Bstm_CT18

source_name: brainstem

value: brainstem


title: WT no Pi, biological rep2


title: Aor_CT60

source_name: aorta

value: aorta


title: Aor_CT58


title: WT resupplied Pi 4h, biological rep1


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep4

source_name: tissue (genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248])

value: vegetative cell ('PO:0020099')


title: Aor_CT64


title: Aor_CT62


title: Liver_WT_PCN_Rep3

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

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

label: Biotin

label_protocol: Standard Affymetrix procedures

growth_protocol: Adult male wild-type mice and PXR-KO mice were maintained on standard laboratory chow and were allowed food and water ad libitum.

extract_protocol: Total RNA was extracted and transcribed to cDNA

treatment_protocol: Portions of the livers were rapidly snap-frozen in liquid nitrogen and stored at -70°C until analysis.

value: Wildtype

tag: Sex

value: Male

value: Liver

tag: compound

value: Pregnenolone carbonitrile

tag: route

value: IP

tag: dose

value: 400 mg/kg


title: Aor_CT56


title: WT complete, biological rep2

description: Gene expression data from WT plants grown in complete medium

source_name: Col-0 plants grown in complete medium

tag: genotype


title: WT complete, biological rep3


title: Liver_WT_PCN_Rep4


title: Aor_CT54


title: Day1 control

description: Gene expression data from cell culture

source_name: Untreated SCp2 cells

value: mammary gland

value: untreated

value: Balb/c


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep2

tag: germplasm name

value: Accession #16552

tag: organism part

tag: development stage

value: 3 leaf fully expanded ('PO:0001053')

value: 21 days

tag: growth media

value: peat/perlite/soil


title: Liver_WT_Vehicle_Rep4

tag: tissue

value: vehicle

value: 0 mg/kg


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep5

tag: age


title: Liver_WT_PCN_Rep1


title: WT no Pi, biological rep1

value: seedlings

value: 7 days

value: wild-type Col-0


title: Aor_CT52

tag: strain

value: aorta


title: WT complete, biological rep1


title: Liver_WT_PCN_Rep2

value: Wildtype

value: Male

value: Liver


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep3

tag: cell type

value: vegetative cell ('PO:0020099')


title: Liver_WT_Vehicle_Rep2

value: IP


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep5

source_name: tissue (genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00)


title: Aor_CT48


title: Aor_CT46


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep3


title: Liver_WT_Vehicle_Rep1


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep4


title: Liver_WT_Vehicle_Rep3


title: Bstm_CT42

value: brainstem


title: Aor_CT50


title: Aor_CT44


title: Liver_PXR KO_PCN_Rep4

source_name: Liver_PXR KO_PCN

value: Pxr knockout

value: Pregnenolone carbonitrile

value: 400 mg/kg


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep2

value: Accession #16552

value: 3 leaf fully expanded ('PO:0001053')

value: 21 days


title: TotalRNA_24h_5000 nM 11-KT

city: Leipzig

first: Eva

last: Fetter

address: Permoserstraße 15

department: Bioanalytical Ecotoxicology

institute: UFZ-Helmholtz Centre for Environmental Research

description: Exposure with 11-ketotestosterone started at 96hpf

hyb_protocol: Hybridization was performed with Gene Expression Hybridization Kit (5188-5242) from Agilent according to the manufacturer instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

source_name: Pool of 50 embryo_homogenate_24h_5000 nM 11-KT

label_protocol: Labelling was performed with LowInput QuickAmp Kit One-Color (5190-2305) from Agilent according to the manufacturer instructions

growth_protocol: Embryos were kept in an incubator at 26°C with complete daily renewal of the embryonic media and a light cycle of 12:12 hours light:dark.

extract_protocol: Total RNA was isolated from 50 embryos using phase-lock tubes (5Prime GmbH, Hamburg) and Trizol (Invitrogen, Darmstadt) according to the manufacturer’s instructions. RNA was further purified using RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls and 11 concentrations of 11-ketotestosterone ranging from 0.05-5000 nM.

tag: developmental stage

value: 120 hpf

value: OBI_established from local breader stock


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:Bln1[248] - rep1

description: Plants were grown in a controlled 20°C glasshouse prior to VIGS treatment.  Twelve days after VIGS treatment, half of the plants in each replication were challenged with the compatible Bgh isolate 5874.  Top halves of seedling third leaves (about 10 cm) from each split-plot experimental unit were harvested into liquid N2 at 32 hours after inoculation (HAI).  RNA was isolated for GeneChip hybridization from the 32-HAI samples. (May still include original submitter created erros/discrepancies)

value: peat/perlite/soil


title: Liver_PXR KO_PCN_Rep3


title: TotalRNA_24h_500 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_500 nM 11-KT


title: Aor_CT40


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: BSMV:00 - rep1


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep5

source_name: tissue (genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control))


title: TotalRNA_24h_1500 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_1500 nM 11-KT


title: Aor_CT42


title: Liver_PXR KO_PCN_Rep2


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep4


title: Aor_CT38


title: Aor_CT36


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep3


title: TotalRNA_24h_50 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_50 nM 11-KT


title: Liver_PXR KO_PCN_Rep1


title: TotalRNA_24h_150 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_150 nM 11-KT


title: TotalRNA_24h_15 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_15 nM 11-KT


title: Liver_PXR KO_Vehicle_Rep4

source_name: Liver_PXR KO_Vehicle

value: Vehicle

value: 0 mg/kg


title: Liver_PXR KO_Vehicle_Rep3


title: Liver_PXR KO_Vehicle_Rep2


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep2


title: Aor_CT30

value: aorta


title: TotalRNA_24h_5 nM  11-KT

source_name: Pool of 50 embryo_homogenate_24h_5 nM  11-KT


title: Aor_CT28


title: TotalRNA_24h_1.5 nM  11-KT

source_name: Pool of 50 embryo_homogenate_24h_1.5 nM  11-KT


title: Aor_CT34


title: Aor_CT26


title: Aor_CT32


title: TotalRNA_24h_0.15 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_0.15 nM 11-KT


title: genotype: Clansman (Mla13) - treatedoruntreated: Inoc. w/ Bgh 5874 - treatment: Mock (Buffer Control) - rep1