title: line E9 root tissue grown in normal condition, biological rep1


title: line E9 root tissue grown in phosphorus deficiency and drought stress, biological rep1

status: Public on Apr 28 2016

type: RNA

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Agilent gene expression array data of 4 x180k format 60-mer oligonucleotide probes designed against the S.lycopersicum cv. Heinz 1706 build 2.4 (annotation 2.5) genome

hyb_protocol: 200 ng of RNA was used for cDNA synthesis and Cy3-labelling using the Low Input Quick Amp Labeling Kit for One-Color Microarray-Based Gene Expression Agilent analysis. 1.65 µg of linearly amplified and labelled cDNA was hybridized for 17 h at 65°C in an oven with a rotating platform (see manufacturer's web site at http://www.agilent.com/).

scan_protocol: Arrays were imaged using an MS200 microarray scanner using only the 480 nm laser using the autogain feature of the NimbleScan software.

data_processing: Image (tiff) files were imported into the Agilent Feature Extraction software for quality control assessment, grid alignment and expression value extraction at the probe and transcript leve. The Robust Multichip Average (RMA) algorithm was used to normalize the data, taking outlier probes into account, and to summarize expression at the transcript level using median polish (Irizarry et al. 2003). This was used to output log2 normalized gene expression levels (see Matrix).

molecule: total RNA

organism: Solanum lycopersicum x Solanum pimpinellifolium

source_name: plant root tissue

label_protocol: RNA was labelled with the Cy3 dye according to Agilent Technologies; One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (see manufacturer's web site at http://www.agilent.com/).

growth_protocol: The E9 and L5 line rootstocks were grafted to Boludo scion and were grown in medium grade perlite in glasshouse conditions at 22°C for 29 days.

extract_protocol: Approximately 0.5 g of root tissue was sampled midway between the base of the plant and the base of the pot by removing a handful of root/perlite material during the time period 10:00 and 11:00 h GMT (dawn was at 05:48 h). Perlite was washed from the roots with tap water (sampling process taking approximately 90 seconds) and then the roots were frozen in liquid nitrogen. Total RNA samples, using three biological replicates per treatment, were extracted using the Spectrum™ Plant Total RNA Kit (Sigma) including on–column DNase digestion.

treatment_protocol: For the control treatment, plants were irrigated daily to pot capacity with Hoagland’s solution containing 1 mM H3PO4 (control treatment with excess phosphorus). For the drought and low phosphorus multi-stress treatment, plants were initially irrigated to pot capacity with Hoagland’s solution containing no added H3PO4 for a period of 19 days after transplanting (to deplete phosphorus in the transplanted peat block); then, for the subsequent 10 days, the pots were irrigated to 70% of pot capacity with Hoagland’s solution containing a low H3PO4 concentration (10 µM) to provide the drought and low phosphorus treatment.

tag: line

value: E9 NIL

tag: organ and cell type

value: root tissue


title: line E9 root tissue grown in normal condition, biological rep2


title: Wy_3d_3

status: Public on Apr 27 2016

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Starting with 5 μg of totalRNA with a 28S/18S rRNA peak ratio >1.7, biotin-labeled cRNA  samples for hybridization on Affymetrix GeneChip RAE230A arrays were prepared accord- ing to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis 701194 Rev.1). This protocol includes the use of the SuperScript Choice System (Invitro- gen Life Technologies) for cDNA synthesis and the ENZO RNA Transcript Labeling Kit (Affymetrix Inc.) for in vitro transcription. The cRNA (15 μg) was then fragmented in buffer supplied with the Cleanup Module and hybridized for 16 h at 45°C. The microarrays were washed and stained with streptavidin-phycoerythrin (SAPE, Molecular Probes) on the Affymetrix Fluidics Station 400 including an amplification step according to the manufacturer’s instructions.

scan_protocol: The fluorescent images of the GeneChips were captured with the Affymetrix GeneChip Scanner 3000.

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

label: biotin

organism: Rattus norvegicus

source_name: liver, Wy-14643, 3 days, 60 mg/kg

label_protocol: Biotin-labeled cRNA samples for hybridization on Affymetrix GeneChip RAE230A arrays were prepared according to the protocol supplied with the GeneChip Sample Cleanup module (Affymetrix Inc., Santa Clara, CA).

growth_protocol: Male Wistar Hanover rats (Crl:WI[Gl/BRL/Han]IGS BR) from Charles River Laboratories, Inc. (Raleigh, NC) were maintained on certified rodent chow (Certified Rodent Diet 5200; Purina Mills, St. Louis, MO) ad libitum in individual suspended stainless steel wire-mesh cages. The animals were kept under controlled temperature (18–26°C), humidity (30–70%), and lighting (12 h light/dark cycle) and were acclimated for a minimum of 6 days.

extract_protocol: Frozen liver sections were grinded in a Mixer Mill MM 200 (Retsch GmbH and Co. KG, Haan, Germany) using precooled stainless steel balls. After adjusting the volume to 1ml with RLT lysis buffer, total RNA was isolated using Qiagen RNAeasy spin column kits, including a DNase digestion step according to the manufacturer’s instructions. A volume of lysate corresponding to 7mg of tissue was loaded RNeasy spin column. The final product was quality controlled by gel analysis using RNA 6000 Nano chips on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Only samples with a peak area ratio >2.0 of 28S to 18S rRNA were used. RNA concentrations were determined with Ribogreen (Molecular Probes, Eugene, OR).

treatment_protocol: Animals (8–10 weeks old) were assigned to dose groups (five rats/group) by weight using a weight stratification-based computer program. Substances were administered by gastric gavage for up to 14 days (in a volume of 5 ml/kg body weight/day) based on the group mean weekly body weight for each dose group.

tag: strain

value: Crl:WI[Gl/BRL/Han]IGS BR

tag: tissue

value: liver

value: Wy

tag: group

value: 3 days

value: 60 mg/kg


title: line E9 root tissue grown in phosphorus deficiency and drought stress, biological rep4


title: Wy_1d_2

source_name: liver, Wy-14643, 1 day, 60 mg/kg

value: 1 day


title: Wy_3d_1


title: line E9 root tissue grown in phosphorus deficiency and drought stress, biological rep3


title: Wy_1d_3


title: Wy_3d_2


title: TAA_7d_3

source_name: liver, Thioacetamid, 7 days, 19.2 mg/kg

value: TAA

value: Thioacetamid

value: 7 days


title: TAA_7d_2


title: sev-GAL4>UAS-GFP_1

city: Varanasi

first: Subhash

middle: C

last: Lakhotia

state: UP

address: Cytogenetics Lab

department: Zoology

country: India

institute: Banaras Hindu UNiversity

description: Gene Expression data from 16-17 hr APF whole pupa expressing GFP under sevenless GAL4 driver,used as control

hyb_protocol: Following fragmentation, 12 µg of cRNA samples were hybridized for 16 hr at 45°C on Drosophila Genome 2.0 microarray chips for 3’ IVT array . GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Summary of the expression levels for each gene in the four genotypes was obtained from the Expression Console software and Affymetrix Transcription analysis console.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster 16-17 hr old pupae

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (Affymetrix GeneChip Expression Analysis Technical Manual using the GeneChip 3’ IVT Plus Reagent Kit).

growth_protocol: 0-1 hr APF stage of sev-GAL4>UAS-GFP, sev-GAL4>Ras1V12, sev-GAL4>Ras1V12 hsrω-RNAi and sev-GAL4>Ras1V12 EP3037 pupae were collected and kept at 24°C and allowed to age for 16-17 hr.

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

treatment_protocol: 16-17 hr APF sev-GAL4>UAS-GFP, sev-GAL4>Ras1V12, sev-GAL4>Ras1V12 hsrω-RNAi and sev-GAL4>Ras1V12 EP3037 pupae were dissected in 1X PBS to remove the pupal case while all the internal tissues were placed on ice in the TriReagent solution (Sigma Aldrich) for RNA extraction.

value: Pupa without pupal case

tag: genotype

tag: age

value: 16-17 hr APF


title: Wy_1d_1


title: TAA_3d_1

source_name: liver, Thioacetamid, 3 days, 19.2 mg/kg


title: TAA_7d_1


title: TAA_3d_2


title: Sal_1J_48h_1

source_name: liver, Vehicle (0.9% physiological saline), 48 hrs, 0 mg/kg

value: Sal

value: Vehicle (0.9% physiological saline)

value: 48 hrs

value: 0 mg/kg


title: Sal_1J_48h_3


title: TAA_3d_3


title: Sal_1J_6h_3

source_name: liver, Vehicle (0.9% physiological saline), 6 hrs, 0 mg/kg

value: 6 hrs


title: Sal_1J_24h_2

source_name: liver, Vehicle (0.9% physiological saline), 24 hrs, 0 mg/kg

value: 24 hrs


title: Sal_1J_48h_2

value: Crl:WI[Gl/BRL/Han]IGS BR


title: Sal_1J_6h_2

value: liver


title: Prop_7d_3

source_name: liver, Propranolol, 7 days, 40 mg/kg

value: Prop

value: Propranolol

value: 40 mg/kg


title: Sal_1J_12h_3

source_name: liver, Vehicle (0.9% physiological saline), 12 hrs, 0 mg/kg

value: 12 hrs


title: Sal_1J_12h_1


title: Prop_7d_1


title: Prop_7d_2


title: Sal_1J_24h_1


title: Sal_1J_12h_2


title: Sal_1J_24h_3


title: Prop_3d_3

source_name: liver, Propranolol, 3 days, 40 mg/kg

value: 3 days


title: Prop_3d_2


title: Prop_1d_3

source_name: liver, Propranolol, 1 day, 40 mg/kg

value: 1 day


title: Prop_3d_1


title: Prop_14d_2

source_name: liver, Propranolol, 14 days, 40 mg/kg

value: 14 days


title: Praz_7d_3

source_name: liver, Prazosin, 7 days, 1 mg/kg

value: Praz

value: Prazosin

value: 7 days

value: 1 mg/kg


title: Prop_14d_3


title: Prop_14d_1


title: Praz_7d_1


title: Prop_1d_2


title: Praz_3d_1

source_name: liver, Prazosin, 3 days, 1 mg/kg


title: Praz_7d_2


title: Prop_1d_1


title: Praz_1d_1

source_name: liver, Prazosin, 1 day, 1 mg/kg


title: PB_7d_2

source_name: liver, Phenobarbital, 7 days, 80 mg/kg

value: PB

value: Phenobarbital

value: 80 mg/kg


title: Praz_3d_3


title: Praz_14d_1

source_name: liver, Prazosin, 14 days, 1 mg/kg


title: Praz_3d_2


title: Sal_1J_6h_1

value: Sal

value: Vehicle (0.9% physiological saline)

value: 6 hrs

value: 0 mg/kg


title: PB_3d_1

source_name: liver, Phenobarbital, 3 days, 80 mg/kg

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver


title: PBO_3d_2

source_name: liver, Piperonyl-butoxide, 3 days, 1200 mg/kg

value: PBO

value: Piperonyl-butoxide


title: Praz_14d_2


title: PB_7d_3


title: PBO_1d_3

source_name: liver, Piperonyl-butoxide, 1 day, 1200 mg/kg

value: 1 day


title: Praz_1d_2


title: Praz_1d_3


title: PB_7d_1


title: PBO_3d_1

value: 3 days


title: PBO_3d_3


title: PBO_1d_1


title: Praz_14d_3

value: Praz

value: 14 days


title: PB_3d_2


title: PB_3d_3


title: PBO_1d_2


title: NPip_7d_2

source_name: liver, N-Nitrosopiperidine, 7 days, 20 mg/kg

value: NPip

value: N-Nitrosopiperidine

value: 7 days

value: 20 mg/kg


title: NPip_7d_3


title: PB_1d_1

source_name: liver, Phenobarbital, 1 day, 80 mg/kg

value: PB

value: Phenobarbital

value: 80 mg/kg


title: PB_1d_3


title: PB_14d_3

source_name: liver, Phenobarbital, 14 days, 80 mg/kg


title: NPip_7d_1


title: PB_14d_1


title: NPip_3d_1

source_name: liver, N-Nitrosopiperidine, 3 days, 20 mg/kg


title: NPip_3d_3


title: NPip_14d_2

source_name: liver, N-Nitrosopiperidine, 14 days, 20 mg/kg


title: PB_14d_2


title: NPip_14d_1


title: NPip_14d_3


title: NNM_3d_2

source_name: liver, N-Nitrososmorpholine, 3 days, 3.5 mg/kg

value: NNM

value: N-Nitrososmorpholine

value: 3.5 mg/kg


title: NNM_7d_3

source_name: liver, N-Nitrososmorpholine, 7 days, 3.5 mg/kg

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver


title: NPip_3d_2


title: NPip_1d_1

source_name: liver, N-Nitrosopiperidine, 1 day, 20 mg/kg


title: NNK_14d_2

source_name: liver, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone , 14 days, 20 mg/kg

value: NNK


title: NPip_1d_2

value: 1 day


title: NNM_7d_1


title: NNK_7d_2

source_name: liver, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone , 7 days, 20 mg/kg


title: NNK_7d_3


title: NNK_14d_1


title: Nif_7d_3

source_name: liver, Nifedipine, 7 days, 3 mg/kg

value: Nif

value: Nifedipine

value: 3 mg/kg


title: NNM_3d_1

value: 3 days


title: NPip_1d_3

value: NPip

value: N-Nitrosopiperidine


title: NNM_7d_2

value: 7 days


title: NNM_3d_3


title: Nif_7d_2


title: NNK_7d_1

value: 20 mg/kg


title: Nif_3d_3

source_name: liver, Nifedipine, 3 days, 3 mg/kg


title: NNK_14d_3

value: 14 days


title: PB_1d_2

value: PB

value: Phenobarbital

value: 80 mg/kg


title: Nif_1d_3

source_name: liver, Nifedipine, 1 day, 3 mg/kg


title: Nif_1d_2


title: Nif_3d_1


title: Nif_7d_1


title: Nif_14d_3

source_name: liver, Nifedipine, 14 days, 3 mg/kg


title: Nif_3d_2


title: MPy_7d_3

source_name: liver, Methapyrilene HCl, 7 days, 60 mg/kg

value: MPy

value: Methapyrilene HCl

value: 60 mg/kg


title: Nif_14d_1

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver


title: MPy_3d_1

source_name: liver, Methapyrilene HCl, 3 days, 60 mg/kg


title: MPy_3d_3


title: MPy_3d_2


title: MDA_1d_1

source_name: liver, Methylendianiline, 1 day, 50 mg/kg

value: MDA

value: Methylendianiline

value: 1 day

value: 50 mg/kg


title: Nif_14d_2

value: Nif

value: Nifedipine

value: 3 mg/kg


title: Mcarb_7d_3

source_name: liver, Methylcarbamate, 7 days, 400 mg/kg

value: Mcarb

value: Methylcarbamate

value: 7 days

value: 400 mg/kg


title: MDA_7d_1

source_name: liver, Methylendianiline, 7 days, 50 mg/kg


title: MDA_3d_2

source_name: liver, Methylendianiline, 3 days, 50 mg/kg

value: 3 days


title: MPy_7d_1

value: MPy


title: MDA_1d_3


title: MDA_14d_3

source_name: liver, Methylendianiline, 14 days, 50 mg/kg

value: 14 days


title: MDA_3d_3


title: MDA_1d_2


title: MDA_3d_1


title: MDA_14d_1


title: Nif_1d_1


title: MPy_7d_2

value: Methapyrilene HCl

value: 60 mg/kg


title: Mcarb_3d_3

source_name: liver, Methylcarbamate, 3 days, 400 mg/kg

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver


title: Mcarb_7d_1


title: Mcarb_3d_2


title: Mcarb_3d_1


title: Mcarb_1d_3

source_name: liver, Methylcarbamate, 1 day, 400 mg/kg


title: Mcarb_7d_2


title: MDA_7d_2

value: MDA

value: Methylendianiline


title: MDA_14d_2

value: 50 mg/kg


title: Mcarb_1d_1

value: 1 day


title: Mcarb_14d_3

source_name: liver, Methylcarbamate, 14 days, 400 mg/kg


title: Mcarb_1d_2


title: Mcarb_14d_2


title: MDA_7d_3


title: Ibup_7d_2

source_name: liver, Ibuprofen, 7 days, 94 mg/kg

value: Ibup

value: Ibuprofen

value: 94 mg/kg


title: Ibup_14d_2

source_name: liver, Ibuprofen, 14 days, 94 mg/kg


title: Ibup_7d_3


title: Ibup_1d_3

source_name: liver, Ibuprofen, 1 day, 94 mg/kg


title: ETH_7d_3

source_name: liver, Ethionine, 7 days, 200 mg/kg

value: ETH

value: Ethionine

value: 200 mg/kg


title: Ibup_3d_2

source_name: liver, Ibuprofen, 3 days, 94 mg/kg

value: 3 days


title: ETH_1d_2

source_name: liver, Ethionine, 1 day, 200 mg/kg


title: Ibup_1d_2


title: Ibup_7d_1

value: 7 days


title: Ibup_3d_3


title: Ibup_1d_1


title: Ibup_3d_1


title: ETH_7d_2


title: ETH_7d_1


title: Mcarb_14d_1

value: Mcarb

value: Methylcarbamate

value: 14 days

value: 400 mg/kg


title: Ibup_14d_1

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver


title: ETH_14d_1

source_name: liver, Ethionine, 14 days, 200 mg/kg


title: ETH_3d_1

source_name: liver, Ethionine, 3 days, 200 mg/kg


title: Ibup_14d_3


title: ETH_1d_3


title: ETH_3d_3


title: ETH_14d_3


title: ETH_3d_2


title: DMN_7d_3

source_name: liver, Dimethylnitrosamine, 7 days, 4 mg/kg

value: DMN

value: Dimethylnitrosamine

value: 4 mg/kg


title: DMN_3d_3

source_name: liver, Dimethylnitrosamine, 3 days, 4 mg/kg


title: ETH_14d_2


title: ETH_1d_1

value: 1 day


title: DMN_7d_1


title: DMN_3d_1


title: DMN_3d_2


title: DHEA_7d_2

source_name: liver, Dehydroepiandrosterone, 7 days, 600 mg/kg

value: DHEA

value: Dehydroepiandrosterone

value: 600 mg/kg


title: DHEA_7d_3


title: DHEA_3d_2

source_name: liver, Dehydroepiandrosterone, 3 days, 600 mg/kg


title: DHEA_1d_2

source_name: liver, Dehydroepiandrosterone, 1 day, 600 mg/kg


title: DHEA_7d_1


title: DMN_7d_2


title: DHEA_1d_1


title: DHEA_14d_2

source_name: liver, Dehydroepiandrosterone, 14 days, 600 mg/kg


title: DHEA_14d_3


title: DHEA_14d_1


title: DHEA_3d_3


title: DHEA_3d_1


title: DCB_3d_2

source_name: liver, 1,4-Dichlorobenzene, 3 days, 300 mg/kg

value: DCB

value: 300 mg/kg


title: DES_3d_2

source_name: liver, Diethyl-stilbestrol, 3 days, 10 mg/kg

value: DES

value: Diethyl-stilbestrol

value: 3 days

value: 10 mg/kg


title: DES_3d_3


title: DCB_1d_3

source_name: liver, 1,4-Dichlorobenzene, 1 day, 300 mg/kg


title: DCB_3d_3


title: DCB_7d_1

source_name: liver, 1,4-Dichlorobenzene, 7 days, 300 mg/kg

value: 7 days


title: DCB_1d_2


title: DES_1d_1

source_name: liver, Diethyl-stilbestrol, 1 day, 10 mg/kg


title: DHEA_1d_3


title: DES_1d_2


title: DCB_7d_2


title: DCB_14d_3

source_name: liver, 1,4-Dichlorobenzene, 14 days, 300 mg/kg

value: 14 days


title: DCB_7d_3

value: Crl:WI[Gl/BRL/Han]IGS BR


title: DES_3d_1

value: liver


title: CPA_7d_3

source_name: liver, Cyproterone acetate, 7 days, 100 mg/kg

value: CPA

value: Cyproterone acetate

value: 100 mg/kg


title: DCB_14d_1


title: CPA_7d_2


title: DCB_14d_2


title: DCB_3d_1


title: CPA_3d_3

source_name: liver, Cyproterone acetate, 3 days, 100 mg/kg


title: CPA_14d_1

source_name: liver, Cyproterone acetate, 14 days, 100 mg/kg


title: CPA_1d_3

source_name: liver, Cyproterone acetate, 1 day, 100 mg/kg

value: 1 day


title: CPA_3d_1


title: CPA_7d_1


title: DCB_1d_1


title: CPA_1d_1


title: CO_1M_7d_1

source_name: liver, Vehicle (Corn oil), 7 days, 0 mg/kg

value: CO

value: Vehicle (Corn oil)

value: 0 mg/kg


title: CPA_14d_2


title: CPA_14d_3


title: CO_1M_1d_2

source_name: liver, Vehicle (Corn oil), 1 day, 0 mg/kg


title: CO_1M_3d_3

source_name: liver, Vehicle (Corn oil), 3 days, 0 mg/kg


title: CO_1M_14d_2

source_name: liver, Vehicle (Corn oil), 14 days, 0 mg/kg


title: CO_1M_7d_2


title: CO_1M_14d_3


title: CPA_1d_2


title: CO_1M_7d_3


title: CO_1C_7d_1


title: CO_1M_1d_3


title: CO_1M_3d_1


title: CO_1C_3d_1


title: CO_1A_7d_3


title: CO_1A_7d_2


title: CO_1C_7d_3


title: CO_1M_3d_2


title: CO_1C_3d_3


title: CO_1A_7d_1


title: CO_1M_1d_1


title: CO_1M_14d_1


title: CO_1A_3d_3


title: CO_1A_3d_2


title: CO_1A_1d_3


title: CO_1C_3d_2


title: CO_1A_1d_2


title: CO_1A_14d_2


title: CMC_1O_3d_2

source_name: liver, Vehicle (Carboxymethylcellulose), 3 days, 0 mg/kg

value: CMC

value: Vehicle (Carboxymethylcellulose)


title: CMC_1O_7d_1

source_name: liver, Vehicle (Carboxymethylcellulose), 7 days, 0 mg/kg


title: CO_1A_3d_1


title: CO_1A_14d_3


title: CMC_1O_1d_1

source_name: liver, Vehicle (Carboxymethylcellulose), 1 day, 0 mg/kg


title: CMC_1O_7d_3


title: CMC_1O_7d_2


title: CO_1A_1d_1


title: CMC_1O_14d_2

source_name: liver, Vehicle (Carboxymethylcellulose), 14 days, 0 mg/kg


title: CMC_1O_3d_3


title: CMC_1O_14d_3


title: CMC_1O_1d_2


title: CO_1A_14d_1


title: CMC_1O_3d_1


title: CMC_1N_1d_3


title: CMC_1N_3d_2


title: CMC_1N_7d_3


title: CMC_1N_1d_2


title: CMC_1N_7d_2


title: CMC_1N_3d_3


title: CMC_1N_3d_1


title: CMC_1N_7d_1


title: CMC_1N_14d_2


title: CMC_1H_7d_3


title: CMC_1O_14d_1


title: CMC_1N_14d_3


title: CMC_1H_7d_1


title: CMC_1H_3d_4


title: CMC_1H_3d_3


title: CMC_1H_3d_1


title: CMC_1H_1d_4


title: CMC_1N_14d_1


title: CMC_1H_7d_2


title: CMC_1H_1d_2


title: CMC_1H_1d_3


title: CMC_1H_14d_3


title: CMC_1F_7d_6


title: CMC_1H_14d_2


title: CMC_1H_14d_1


title: CMC_1F_7d_2


title: CMC_1H_1d_1


title: CMC_1F_7d_3


title: CMC_1F_3d_3


title: CMC_1F_7d_4


title: CMC_1F_7d_5


title: CMC_1F_3d_1


title: CMC_1F_3d_2


title: CMC_1H_3d_2


title: CMC_1N_1d_1


title: CMC_1F_1d_3


title: CMC_1F_7d_1


title: CMC_1F_1d_2


title: CMC_1F_1d_1


title: CPA_3d_2


title: CMC_1F_14d_3


title: CMC_1F_14d_6


title: CMC_1F_14d_4


title: CMC_1D_7d_4


title: CMC_1D_7d_6


title: CMC_1F_14d_2


title: CMC_1F_14d_5


title: CMC_1F_14d_1


title: CMC_1D_7d_5


title: Sample_33

city: Leiden

first: Nils

last: Bomer

state: Zuid-Holland

address: Post zone S-05-P, P.O. box 9600

department: Molecular Epidemiology

country: Netherlands

institute: LUMC

description:
cartilage_mRNA
9239303024_E

hyb_protocol: Standard Illumina hybridization protocol with Ambion TotalPrep-96 RNA amplification kit.

scan_protocol: Slides were scanned with the Illumina Beadscanner 500GX.

data_processing: Raw data were prepared with GenomeStudio Software (Gene Expression module v1.0), without normalization, background substraction, or imputation of missing data. Subsequently, quality control was performed in R statistical programming language using the lumi-package, and data were prepared for analysis by applying robust spline normalization (RSN) and variance-stabilizing transformation (vst).

organism: Mus musculus

source_name: articular cartilage

label_protocol: To perform cDNA synthesis, amplification, biotin labeling, and hybridization onto the microarrays the Ambion TotalPrep-96 RNA amplification kit was used according to the manufacturer's protocol.

growth_protocol: Dio2-/--mice were backcrossed onto the C57Bl/6 background. In the experiments reported here, mice were in the 6th generation of backcrossing. All animals were littermates and were caged together and housed in the same facility. Mice were group housed in standard mouse cages with sawdust as bedding material and under conventional laboratory conditions; constant room temperature (22 +/- 2 °C), humidity level (55 +/- 5 %), a 12-h light:12-h dark cycle (lights on at 8 AM) and standard food (Sniff, Soest, Germany) and water available ad libitum.

extract_protocol: RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit following the manufacturer's recommendations. Quality control was performed with the 2100 Bioanalyser (Agilent).

treatment_protocol: Male Dio2-/-- and wild-type-mice were subjected to a forced treadmill-running regimen on a four lane modular treadmill (Columbus Instruments, Columbus, OH, USA). These mice ran for 3 weeks 1 hour/day, 5 days/week, at a speed of 11 m/min and with an inclination of 5°.

tag: genotype/variation

value: Dio2-/- knockout

tag: challenge

value: run

value: cartilage

tag: Sex

value: male


title: Sample_25

description:
cartilage_mRNA
9239550016_F


title: Sample_24

description:
cartilage_mRNA
9239550016_E


title: Sample_31

description:
cartilage_mRNA
9239303019_E

value: wildtype


title: Sample_34

description:
cartilage_mRNA
9239303024_F


title: Sample_32

description:
cartilage_mRNA
9239303024_D


title: CMC_1D_3d_4

value: 3 days


title: CMC_1O_1d_3

value: Crl:WI[Gl/BRL/Han]IGS BR


title: CMC_1D_7d_1

value: liver

value: 7 days


title: Sample_23

description:
cartilage_mRNA
9239550016_D


title: CMC_1D_7d_3


title: CMC_1D_3d_5


title: Sample_29

description:
cartilage_mRNA
9239303019_C


title: CMC_1D_3d_2


title: CMC_1D_7d_2


title: CO_1C_7d_2


title: Sample_30

description:
cartilage_mRNA
9239303019_D


title: Sample_19

description:
cartilage_mRNA
9239550006_F

value: norun


title: CMC_1D_3d_3


title: CMC_1D_3d_6


title: CMC_1D_3d_1


title: Sample_16

description:
cartilage_mRNA
9239550006_D


title: CMC_1D_1d_3


title: Sample_27

description:
cartilage_mRNA
9239303025_F


title: Sample_21

description:
cartilage_mRNA
9239303025_D


title: Sample_20

description:
cartilage_mRNA
9239303025_C


title: CMC_1D_14d_1

value: 14 days


title: CMC_1D_1d_1

value: 1 day


title: CMC_1D_1d_2


title: Sample_15

description:
cartilage_mRNA
9239303047_E


title: Sample_12

description:
cartilage_mRNA
9239303047_C


title: CMC_1D_14d_3


title: Sample_35

description:
cartilage_mRNA
9239303047_F


title: CMC_1B_3d_2


title: CMC_1B_7d_1


title: Sample_22

description:
cartilage_mRNA
9239303025_E


title: CMC_1D_14d_2


title: CMC_1B_7d_3


title: Sample_14

description:
cartilage_mRNA
9239303047_D


title: CMC_1B_1d_3


title: Sample_17

description:
cartilage_mRNA
9239550006_E


title: CMC_1B_3d_3


title: Mon_3

city: Yokohama

first: Jing-Ru

last: Li

state: Kanagawa

address: 1-7-22 Suehiro-cho,

department: Devision of Genomic Technology

country: Japan

institute: RIKEN Center for Life Science Technologies,

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi package in R

organism: Homo sapiens

source_name: monocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion kit for Illumina arrays

growth_protocol: Normal human skin fibroblast cells, NB1RGB, were provided by RIKEN Bioresource Center (#RCB0222, Tsukuba, Japan) and were cultured in 10% fetal bovine serum supplemented with minimum essential medium alpha (MEMα, Wako, Japan) at 5% CO2 and 37°C. One day after transduction with lentivirus, the medium was changed into the monocyte medium, consisting of RPMI1640 (Wako, Japan) and 20 ng/ml rhM-CSF(Wako, Japan), 20 ng/ml IL-4 (Wako, Japan), 1 mM sodium pyruvate, 50 µM ß-mercaptoethanol, and 10% fetal bovine serum

extract_protocol: RNA was isolated using NucleoSpin® kit (Macherey-Nagel, Germany) according to the user manual

tag: cell type

value: monocyte


title: CMC_1B_1d_2


title: KDOE_3

description: replicate 3

source_name: Overepxressed SPI1, MNDA, CEBPA, IRF8 1 day after Knocking down PRRX1, OSR1, LHX9, TWIST2

value: fibroblast


title: Mon_2

description: replicate 2


title: Mon_1

description: replicate 1


title: KDOE_2

description: replicate 2


title: CMC_1B_7d_2

value: 0 mg/kg


title: KDOE_1

description: replicate 1


title: KD-only_3

description: replicate 3

source_name: Knocked down PRRX1, OSR1, LHX9, TWIST2


title: CMC_1B_14d_2

value: CMC


title: Clon_7d_3

source_name: liver, Clonidine, 7 days, 0.1 mg/kg

value: Clon

value: Clonidine

value: 0.1 mg/kg


title: CMC_1B_14d_3

value: Vehicle (Carboxymethylcellulose)


title: OE-only_2

description: replicate 2

source_name: Overepxressed SPI1, MNDA, CEBPA, IRF8


title: Clon_3d_1

source_name: liver, Clonidine, 3 days, 0.1 mg/kg


title: KD-only_1

description: replicate 1


title: Clon_7d_1


title: Clon_3d_2


title: FIB_3

description: replicate 3

source_name: fibroblasts


title: CMC_1B_14d_1


title: Clon_7d_2


title: CMC_1B_1d_1


title: FIB_2

description: replicate 2


title: OE-only_1

description: replicate 1


title: KD-only_2

description: replicate 2


title: FIB_1

description: replicate 1


title: OE-only_3

description: replicate 3


title: Clon_3d_3


title: Clon_1d_1

source_name: liver, Clonidine, 1 day, 0.1 mg/kg


title: Clon_1d_3


title: HCC1395_siCtrl_rep2

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

data_processing: GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.9 was used and cubic spline normalization was applied to the data.

source_name: control siRNA

label_protocol: Standard labeling protocol with biotin wirh Cy3-streptavidin

growth_protocol: Human cell lines MDA-MB-468 (p53 R273H), HCC-1395 (p53 R175H),  were cultured in DMEM medium (Sigma) supplemented with 10% FCS (ECS0180L, Euroclone), and antibiotics (DE17-602E, Lonza). Human cell BT-549 (p53 R249S) were cultured in RPMI medium (Sigma) supplemented with 10% FBS and antibiotics. Human cell SUM-149 (p53 M237I) cells were cultured in DMEM:F12 Ham’s medium 1:1, supplemented with 10% FCS and antibiotics.

extract_protocol: RNA was extracted with Qiazol reagent (Qiagen), following the protocol provided by the manufacturer. RNA integrity was checked by formaldehyde agarose gel electrophoresis. Purity and concentration were determined on a Nanodrop spectrophotometer.

treatment_protocol: All cells lines were transfected at 50-70% confluence two times with 24h interval (to increase efficiency of silencing), with 50 nM siRNA oligonucleotides using Lipofectamine RNAiMax (Invitrogen), following manufacturer’s instructions. After 48 hr of the second silencing, cells were processed.

tag: cell line


title: HCC1395_siCtrl_rep1


title: Clon_14d_3

source_name: liver, Clonidine, 14 days, 0.1 mg/kg


title: ERRγfl/fl mouse pancreatic islets infected with adenovirus Cre, technical replicate 2

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

country: USA

institute: Salk Institute

description: technical replicate 2

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using GeneSpring GX with normalizations  set to the 75th percentile, and per-gene normalizations to the median and specific samples.

source_name: pancreatic islets

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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

value: ERRγ KO

value: pancreatic islets

tag: genetic background


title: Clon_14d_2


title: HCC1395_siTP53_rep2

source_name: p53 siRNA


title: Clon_1d_2


title: Clon_14d_1


title: CIDB_7d_3

source_name: liver, C.I Direct Black, 7 days, 146 mg/kg

value: CIDB

value: C.I Direct Black

value: 146 mg/kg


title: CMC_1B_3d_1

source_name: liver, Vehicle (Carboxymethylcellulose), 3 days, 0 mg/kg

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver

value: 3 days


title: HCC1395_siTP53_rep3


title: HCC1395_siCtrl_rep3


title: HCC1395_siTP53_rep1


title: CIDB_3d_2

source_name: liver, C.I Direct Black, 3 days, 146 mg/kg


title: CIDB_3d_3


title: CIDB_7d_1

value: 7 days


title: ERRγfl/fl mouse pancreatic islets infected with adenovirus Cre, technical replicate 1

description: technical replicate 1


title: SUM149_siCtrl_rep2


title: CIDB_7d_2


title: ERRγfl/fl mouse pancreatic islets infected with adenovirus EGFP, technical replicate 1

description: technical replicate 1

value: wild-type


title: CIDB_3d_1


title: ERRγfl/fl mouse pancreatic islets infected with adenovirus EGFP, technical replicate 2

description: technical replicate 2


title: CFX_7d_2

source_name: liver, Cefuroxime, 7 days, 250 mg/kg

value: CFX

value: Cefuroxime

value: 250 mg/kg


title: SUM149_siCtrl_rep3


title: CFX_3d_1

source_name: liver, Cefuroxime, 3 days, 250 mg/kg


title: CFX_3d_3


title: CFX_1d_3

source_name: liver, Cefuroxime, 1 day, 250 mg/kg

value: 1 day


title: SUM149_siCtrl_rep1


title: SUM149_siTP53_rep1


title: SUM149_siTP53_rep3


title: CFX_7d_1


title: SUM149_siTP53_rep2


title: CFX_1d_2


title: CFX_1d_1


title: 2667: Saliva-preterm-rep35

type: genomic

city: Edinburgh

first: James

last: Boardman

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

institute: University of Edinburgh

hyb_protocol: Bisulphite conversion of 500ng input DNA was carried out using the EZ DNA Methylation Kit (Zymo Research, Freiburg, Germany). Four microlitres of bisulphite-converted DNA was processed using the Infinium HD Assay for Methylation. This was performed using the Illumina Methylation 450k beadchip and Infinium chemistry (Illumina, Inc., San Diego, CA, USA)

scan_protocol: The arrays were imaged on the Illumina HiScan platform

data_processing:
GenomeStudio Analysis software (version 2011.1). Polymorphic, nonspecific, and unreliable probes were filtered out. Background was subtracted with the methylumi package ('noob' method), beta values were normalised with the BMIQ method (Teschendorff et all 2013)
Unmethylated and methylated signal intensities in supplementary file

label: Cy5 and Cy3

molecule: genomic DNA

source_name: saliva, preterm

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA OG-575 kit was used for sampling of saliva (DNAGenotek Inc, Kanata, Canada). DNA was extracted using an alcohol precipitation technique as per manufacturer’s instructions, and was rehydrated in TE 0.5. Gel electrophoresis was used to qualify DNA extraction and Qubit® 2.0 Fluorometer was utilised for quantification of DNA concentration.

value: saliva

tag: pregancy

value: preterm

tag: gender

value: M

tag: pmabirth

tag: pmascan

tag: chorio

value: No

tag: steroids

value: Yes

tag: tpndays

tag: los


title: 6127: Saliva-preterm-rep36

tag: tissue


title: CFX_14d_1

source_name: liver, Cefuroxime, 14 days, 250 mg/kg

tag: strain

tag: group

value: 14 days


title: AlAl_7d_3

source_name: liver, Allyl alcohol, 7 days, 36 mg/kg

value: AlAl

value: Allyl alcohol

value: 36 mg/kg


title: CFX_14d_2

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver


title: BT549_siCtrl_rep3


title: AlAl_7d_2

value: 7 days


title: 6134: Saliva-preterm-rep34


title: BT549_siTP53_rep3


title: AlAl_3d_3

source_name: liver, Allyl alcohol, 3 days, 36 mg/kg

value: 3 days


title: BT549_siCtrl_rep2


title: 2914: Saliva-preterm-rep33


title: BT549_siCtrl_rep1


title: 6036: Saliva-preterm-rep32

value: F


title: AlAl_1d_3

source_name: liver, Allyl alcohol, 1 day, 36 mg/kg


title: 7006: Saliva-preterm-rep31


title: 2680: Saliva-preterm-rep29


title: 2666: Saliva-preterm-rep30


title: AlAl_14d_1

source_name: liver, Allyl alcohol, 14 days, 36 mg/kg


title: AlAl_3d_1


title: AlAl_14d_3


title: BT549_siTP53_rep2


title: 6013: Saliva-preterm-rep28


title: MDAMB468_siCtrl_rep3


title: AlAl_1d_2


title: CFX_3d_2

value: CFX

value: Cefuroxime


title: CFX_14d_3

value: 250 mg/kg


title: CFX_7d_3


title: AlAl_14d_2


title: AB1_7d_3

source_name: liver, Aflatoxin B1, 7 days, 0.24 mg/kg

value: Aflatoxin B1


title: AlAl_1d_1

value: 1 day


title: AlAl_3d_2


title: MDAMB468_siCtrl_rep2

source_name: control siRNA


title: AB1_7d_2


title: BT549_siTP53_rep1


title: MDAMB468_siCtrl_rep1


title: MDAMB468_siTP53_rep3


title: 6126: Saliva-preterm-rep27

value: saliva

value: preterm


title: 2783: Saliva-preterm-rep26

value: M

value: Yes


title: AB1_3d_2

source_name: liver, Aflatoxin B1, 3 days, 0.24 mg/kg


title: AB1_7d_1


title: AB1_3d_3


title: Aap_6h_2

source_name: liver, Acetaminophen, 6 hrs, 4250 mg/kg

value: Aap

value: Acetaminophen

value: 6 hrs


title: Aap_6h_3

value: Crl:WI[Gl/BRL/Han]IGS BR


title: 2618: Saliva-preterm-rep24

value: No


title: 6073: Saliva-preterm-rep25


title: MDAMB468_siTP53_rep2

source_name: p53 siRNA


title: Aap_24h_1

source_name: liver, Acetaminophen, 24 hrs, 4250 mg/kg

value: liver

value: 24 hrs


title: Aap_48h_2

source_name: liver, Acetaminophen, 48 hrs, 4250 mg/kg

value: 48 hrs


title: Aap_48h_1


title: Aap_6h_1


title: AB1_3d_1

value: 3 days


title: Aap_48h_3


title: Aap_12h_2

source_name: liver, Acetaminophen, 12 hrs, 4250 mg/kg

value: 12 hrs


title: Aap_24h_3


title: 6017: Saliva-preterm-rep23

value: F


title: Aap_24h_2


title: 6133: Saliva-preterm-rep22


title: Aap_12h_1


title: AA_7d_3

source_name: liver, Acetamide, 7 days, 3000 mg/kg

value: AA

value: Acetamide

value: 7 days


title: 6069: Saliva-preterm-rep19

value: saliva

value: preterm


title: 2956: Saliva-preterm-rep21

value: Yes


title: 2913: Saliva-preterm-rep20

value: M


title: AlAl_7d_1

value: AlAl

value: Allyl alcohol

value: 36 mg/kg


title: 2981: Saliva-preterm-rep17

value: No


title: MDAMB468_siTP53_rep1


title: 2910: Saliva-preterm-rep18


title: AA_1d_3

source_name: liver, Acetamide, 1 day, 3000 mg/kg

value: Crl:WI[Gl/BRL/Han]IGS BR

value: liver

value: 1 day


title: 2717: Saliva-preterm-rep16


title: AA_14d_3

source_name: liver, Acetamide, 14 days, 3000 mg/kg

value: 14 days


title: AA_7d_1


title: AA_7d_2


title: AA_1d_1


title: AA_3d_2

source_name: liver, Acetamide, 3 days, 3000 mg/kg

value: 3 days


title: AA_3d_3


title: AA_1d_2


title: AA_3d_1


title: AA_14d_1


title: 6130: Saliva-preterm-rep15

source_name: saliva, preterm


title: Aap_12h_3

value: Aap

value: Acetaminophen

value: 12 hrs


title: 3-MC_7d_2

source_name: liver, 3-Methylcholanthrene, 7 days, 25 mg/kg

value: 7 days

value: 25 mg/kg


title: 6076: Saliva-preterm-rep13

value: saliva

value: preterm

value: F


title: 3-MC_3d_1

source_name: liver, 3-Methylcholanthrene, 3 days, 25 mg/kg


title: 3-MC_1d_3

source_name: liver, 3-Methylcholanthrene, 1 day, 25 mg/kg


title: 3-MC_3d_3


title: 2685: Saliva-preterm-rep12

value: M

value: Yes


title: 3-MC_1d_2


title: 3-MC_14d_2

source_name: liver, 3-Methylcholanthrene, 14 days, 25 mg/kg


title: 3-MC_3d_2


title: 6131: Saliva-preterm-rep14


title: 6108: Saliva-preterm-rep11


title: 3-MC_7d_1


title: 3-MC_7d_3


title: 2-NF_7d_3

source_name: liver, 2-Nitrofluorene, 7 days, 44 mg/kg

value: 44 mg/kg


title: 3-MC_14d_3


title: 6090: Saliva-preterm-rep8

value: No


title: 2-NF_7d_2

value: Crl:WI[Gl/BRL/Han]IGS BR


title: AA_14d_2

value: liver

value: AA

value: Acetamide


title: 3-MC_14d_1

value: 14 days


title: 2-NF_3d_3

source_name: liver, 2-Nitrofluorene, 3 days, 44 mg/kg

value: 3 days


title: 3-MC_1d_1

value: 1 day


title: 2-NF_3d_2


title: 2-NF_7d_1


title: 2-AAF_7d_2

source_name: liver, 2-Acetylaminofluorene, 7 days, 1.2 mg/kg

value: 1.2 mg/kg


title: 2-NF_3d_1


title: 2982: Saliva-preterm-rep7


title: 2-AAF_7d_3

value: 7 days


title: 2-AAF_7d_1


title: 2926: Saliva-preterm-rep5


title: 2691: Saliva-preterm-rep3


title: 2-AAF_1d_3

source_name: liver, 2-Acetylaminofluorene, 1 day, 1.2 mg/kg


title: 2-AAF_3d_3

source_name: liver, 2-Acetylaminofluorene, 3 days, 1.2 mg/kg


title: 2-AAF_3d_2


title: 2-AAF_1d_2


title: 2-AAF_3d_1


title: 2966: Saliva-preterm-rep10


title: 2-AAF_1d_1


title: 2939: Saliva-preterm-rep9


title: 2908: Saliva-preterm-rep4


title: 2891: Saliva-preterm-rep6


title: 2962: Saliva-preterm-rep2


title: 2866: Saliva-full_term-rep35

source_name: saliva, full term


title: 2-AAF_14d_1

source_name: liver, 2-Acetylaminofluorene, 14 days, 1.2 mg/kg


title: 2-AAF_14d_2


title: 2963: Saliva-preterm-rep1


title: 2-AAF_14d_3


title: 2736: Saliva-full_term-rep36


title: Atp8b1 G308V/G308V_14M_23_male

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix's Expression Console (Version 1.2) software using the RMA method which incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm. For this experiment, six pairwise comparisons were used to statistically resolve gene expression differences between sample groups using the R/maanova analysis package. Specifically, differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova. Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value.

source_name: Lung, Atp8b1, male, 14 M

label_protocol: One hundred microgram of total RNA was converted to cDNA, amplified and labeled with biotin using the Ambion Message Amp Premier RNA Amplification kit (Life Technologies, Grand Island, NY) as per manufacturer’s protocol.

extract_protocol: Trizol extraction and RNeasy kit (Qiagen) were performed according to the manufacturer's instructions for extraction of total RNA.

tag: strain/background

tag: genotype/variation

value: male

tag: age

value: lung


title: 2396: Saliva-full_term-rep34

value: saliva


title: Atp8b1 G308V/G308V_14M_22_male

tag: Sex


title: 4248: Saliva-full_term-rep33

value: F


title: 2488: Saliva-full_term-rep32

value: M


title: B6_14M_18_male

source_name: Lung, C57BL/6J, male, 14 M

value: wild-type


title: 2406: Saliva-full_term-rep31


title: B6_14M_13_female

source_name: Lung, C57BL/6J, female, 14 M

value: female


title: Atp8b1 G308V/G308V_14M_21_female

source_name: Lung, Atp8b1, female, 14 M


title: Atp8b1 G308V/G308V_14M_20a_female


title: B6_14M_15_female


title: B6_14M_17_male


title: B6_14M_16a_male


title: B6_14M_14_female


title: Atp8b1 G308V/G308V_14M_19_female


title: Atp8b1 G308V/G308V_7_9 wk_12_male

source_name: Lung, Atp8b1, male, 7-9 wk


title: Atp8b1 G308V/G308V_7_9 wk_10_male


title: Atp8b1 G308V/G308V_7_9 wk_11_male


title: Atp8b1 G308V/G308V_7_9 wk_8_female

source_name: Lung, Atp8b1, female, 7-9 wk


title: 2743: Saliva-full_term-rep30


title: 2307: Saliva-full_term-rep27


title: 2368: Saliva-full_term-rep29


title: 2763: Saliva-full_term-rep26


title: Atp8b1 G308V/G308V_7_9 wk_9a_female


title: Atp8b1 G308V/G308V_7_9 wk_7_female


title: B6_7_9 wk_3 male

source_name: Lung, C57BL/6J, male, 7-9 wk


title: 2865: Saliva-full_term-rep28


title: 2767: Saliva-full_term-rep23


title: B6_7_9 wk_5_male


title: B6_7_9 wk_4 male


title: Atp8b1 G308V/G308V_14M_24_male


title: 2740: Saliva-full_term-rep25


title: 2778: Saliva-full_term-rep22


title: B6_7_9 wk_1 male


title: 2761: Saliva-full_term-rep24


title: Control vs transgenic in cryolesioned mice [WTC148 vs TC110]

city: Bellaterra

first: Luis

last: Pardo

state: Barcelona

address: Campus UAB Edificio M

country: Spain

institute: Universitat Autónoma de Barcelona

description: WTC148 vs TC110

hyb_protocol: The samples were hybridized in the SurePrint G3 Microarray slides according to the manufacturer's protocol. We used a loop design in which each sample was hybridized four times, and balanced with respect to the use of Cy3 and Cy5 in the samples.

scan_protocol: The microarray slides were scanned using the Agilent microarray scanner (G2565CA), and the resulting images were extracted with Agilent Feature Extraction Software (version 10.7).

data_processing:
Background correction was performed using the normexp method (offset = 10) implemented in the Bioconductor LIMMA package to adjust local median (M) background estimates. Background-corrected intensity data were normalized using the loess method to remove the bias within each array.  A-values quantile normalization (Aquantile) was used to remove the bias between arrays. Two-color arrays were analyzed independently. To make both arrays comparable, we used Intraspot Correlation to re-scale the M and A-values to have equal variances in each array. Finally, the statistical linear model in LIMMA was applied to the resulting data to determine the target genes differentially expressed between the experimental groups

LogFC results (available on Series record): Data resulting from apply the statistical linear model in LIMMA to the normalized signal intensities of each slide, in order to determine the target genes differentially expressed between the experimental groups. Estimated coefficients for the comparisons WTC-WT; TC-T; TC-WTC, T-WT and statistics by the empirical Bayes method are shown. The T-WT comparison did not present differences in gene expression and is not included in these results.

source_name: WT_cryolesion_right hemisphere cortex

label_protocol: The samples were labeled for Cy5 or Cy3 using the Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: Animals were maintained under standard laboratory conditions and used at 5-7 months old.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen). The concentration was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific), and the RNA quality with theAgilent 2100 Bioanalyzer

treatment_protocol: A focal cryoinjury was carried out on the surface of the brain by applying a dry ice pellet for 30 seconds. Animals where sacrified 3 days post lesion

tag: strain background

value: wild type

value: 5-7 months

value: right hemisphere cortex

tag: condition

value: after a focal cryolesion (C)

value: GFA2-tTa/TetO-VP16-CREB; overexpressing a constitutively active form of CREB in astrocytes (VP16-CREB)


title: 2454: Saliva-full_term-rep21

tag: pregancy


title: 2818: Saliva-full_term-rep17

tag: gender


title: 2531: Saliva-full_term-rep18


title: Control vs transgenic in cryolesioned mice [WTC126 vs TC124]

description: WTC126 vs TC124

source_name: transgenic_normal (control)_right hemisphere cortex

value: normal (control)


title: Transgenic vs control in cryolesioned mice [TC129 vs WTC135]

description: TC129 vs WTC135


title: 2466: Saliva-full_term-rep16


title: WT vs transgenic in control mice [WT156 vs T133]

description: WT156 vs T133

source_name: WT_normal (control)_right hemisphere cortex


title: 2885: Saliva-full_term-rep19


title: nuc_acc_male_low_loneliness 24

city: Stony Brook

first: Turhan

last: Canli

state: NY

address: Dept. of Psychology

department: Psychology

institute: Stony Brook University

description: mRNA expression

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).

scan_protocol: Hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs for which at least 20 out of 26 samples had flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: nucleus accumbens

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA was isolated from frozen nucleus accumbens tissue using TRI Reagent (Sigma-Aldrich) followed by clean-up using the RNeasy kit (Qiagen). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Each individual’s sample was then prepared for the Arraystar Human LncRNA Array v2.0.

treatment_protocol: At autopsy, the brainstem was removed and the brain hemisected. One hemisphere was cut into 1cm slabs in a plexiglass jig, put into individual freezer bags, placed on a metal plate, and put into a -80o freezer. This tissue was the source of the gene-expression studies. A  complete neuropathologic evaluation was performed that included the determination of pathologic AD by NIA-Reagan criteria as  described elsewhere (Schneider JA, Arvanitakis Z, Bang W, Bennett DA. Mixed brain pathologies account for most dementia cases in community-dwelling older persons. Neurology. 2007;69(24):2197-204).

tag: loneliness group

value: low

tag: loneliness score at baseline

tag: age at baseline

tag: global cognition at last visit (scaled)

tag: reagan ad score


title: B6_7_9 wk_2 male


title: Cryolesion vs control in WT mice [WTC116 vs WT111]

description: WTC116 vs WT111


title: nuc_acc_male_high_loneliness 25

description: mRNA expression

value: high


title: nuc_acc_male_high_loneliness 26

description: mRNA expression


title: Control vs cryolesion in transgenic mice [T151 vs TC113]

description: T151 vs TC113


title: Transgenic cryolesion vs WT control  [TC122 vs WT141]

description: TC122 vs WT141


title: Cryolesion vs control in transgenic mice [TC107 vs T132]

description: TC107 vs T132


title: Transgenic vs WT in control mice [T115 vs WT155]

description: T115 vs WT155


title: Transgenic vs WT in control mice [T136 vs WT142  ]

description: T136 vs WT142


title: 7005: Saliva-full_term-rep11

tag: pmabirth

tag: pmascan

tag: chorio

value: No

tag: steroids

tag: tpndays

tag: los


title: 7002: Saliva-full_term-rep14

tag: tissue


title: 2776: Saliva-full_term-rep20


title: nuc_acc_male_high_loneliness 22

description: mRNA expression


title: control vs cryolesion in WT mice [WT144 vs WTC125]

description: WT144 vs WTC125

tag: genotype/variation

tag: age

tag: strain


title: nuc_acc_male_low_loneliness 23

description: mRNA expression


title: 4270: Saliva-full_term-rep12

tag: pregancy


title: 7007: Saliva-full_term-rep8

tag: gender


title: 7008: Saliva-full_term-rep7


title: nuc_acc_male_low_loneliness 21

description: mRNA expression

tag: loneliness group


title: nuc_acc_male_high_loneliness 19

description: mRNA expression

tag: loneliness score at baseline


title: nuc_acc_male_low_loneliness 20

description: mRNA expression

tag: age at baseline


title: nuc_acc_male_low_loneliness 15

description: mRNA expression

tag: global cognition at last visit (scaled)


title: nuc_acc_male_high_loneliness 16

description: mRNA expression

tag: reagan ad score


title: YO20mg_4

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

institute: Gifu University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 μl containing 1x Blocking Agent and 1x Fragmentation Buffer. On completion of the fragmentation reaction, 2x Hybridization Buffer HI-RPM solution was added to the fragmentation mixture containing 0.6 μg of Cy3-labelled cRNA and hybridized for 17 h, at 65C and 10 rpm. After hybridization, microarrays were washed according to Quick Amp Labeling Kit Protocol (Agilent).

scan_protocol: The hybridized microarray slides were washed according to the manufacturer’s instructions and were scanned with an Agilent DNA Microarray Scanner (#G2565CA, Agilent Technologies, CA, USA) at a resolution of 5 μm.

data_processing: These data were normalized by the quantile methods using Excel.

organism: Saccharomyces cerevisiae

source_name: Y2O3-treatment_20 mg, 8h, replicate4

label_protocol: The cDNA was synthesized by Quick Amp Labeling Kit (Agilent) using 0.5 μg total RNA as a template. Cyanine-3 (Cy3) labeled cRNA was prepared from cDNA using the T7 RNA polymerase. Cy3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN, Hilden, Germany), and checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: These yeast cells were grown in YPD medium (1.0% yeast extract, 2.0% peptone ; Becton, Dickinson and Co., NJ, USA, and 2.0% glucose, if necessary 1.5% agar; Wako Pure Chemical Industries, Ltd, Osaka, Japan) at 30°C for 8 h.

extract_protocol: The yeast cells after stressed were collected by centrifugation of 15,000 rpm for 1.0 min at 4°C. RNA extraction conformed according to partially modified manufacture protocol of Fast RNA ® Pro Red Kit (MP Biomedicals, CA, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After yeast cells were grown for 6 h (exponentially growing cells) at 30℃, 5 mg of YCl3・6H2O (Wako Pure Chemical Industries, Osaka, Japan) or 3 mg, 20 mg of Y2O3 nanoparticle (CIK NanoTek Corporation, Tokyo, Japan) were exposed to yeast cells, and these yeast cells were further incubated for 2h.


title: 7004: Saliva-full_term-rep10

tag: pmabirth


title: nuc_acc_male_low_loneliness 14

description: mRNA expression


title: 7009: Saliva-full_term-rep6

tag: pmascan


title: 4269: Saliva-full_term-rep9


title: nuc_acc_male_high_loneliness 17

description: mRNA expression


title: YO20mg_3

source_name: Y2O3-treatment_20 mg, 8h, replicate3


title: YO20mg_1

source_name: Y2O3-treatment_20 mg, 8h, replicate1


title: nuc_acc_fem_low_loneliness 13

description: mRNA expression


title: nuc_acc_fem_high_loneliness 12

description: mRNA expression


title: YO20mg_2

source_name: Y2O3-treatment_20 mg, 8h, replicate2


title: C_2_4

source_name: non-treatment_nov09, 8h, replicate4


title: nuc_acc_fem_low_loneliness 9

description: mRNA expression


title: 4227: Saliva-full_term-rep5

source_name: saliva, full term


title: 2449: Saliva-full_term-rep15


title: C_2_3

source_name: non-treatment_nov09, 8h, replicate3


title: 4285: Saliva-full_term-rep13


title: 4239: Saliva-full_term-rep4


title: YO3mg_4

source_name: Y2O3-treatment_3 mg, 8h, replicate4


title: 4249: Saliva-full_term-rep3


title: nuc_acc_fem_high_loneliness 7

description: mRNA expression


title: C_2_1

source_name: non-treatment_nov09, 8h, replicate1


title: nuc_acc_fem_low_loneliness 10

description: mRNA expression


title: 4220: Saliva-full_term-rep1


title: 4229: Saliva-full_term-rep2


title: nuc_acc_fem_low_loneliness 8

description: mRNA expression


title: YCl5mg_4

source_name: YCl-treatment, 8h, replicate4


title: YO3mg_2

source_name: Y2O3-treatment_3 mg, 8h, replicate2


title: YO3mg_1

source_name: Y2O3-treatment_3 mg, 8h, replicate1


title: YCl5mg_3

source_name: YCl-treatment, 8h, replicate3


title: nuc_acc_male_high_loneliness 18

description: mRNA expression


title: YCl5mg_1

source_name: YCl-treatment, 8h, replicate1


title: YCl5mg_2

source_name: YCl-treatment, 8h, replicate2


title: C_1_3

source_name: non-treatment_sep09, 8h, replicate3


title: nuc_acc_fem_high_loneliness 5

description: mRNA expression

source_name: nucleus accumbens


title: nuc_acc_fem_high_loneliness 4

description: mRNA expression


title: C_1_4

source_name: non-treatment_sep09, 8h, replicate4


title: MSC 7d 100 μg/mL iron oxide nanoparticles rep3

city: Nanjing

first: Qiwei

last: Wang

address: NO.87 Dingjiaqiao

country: China

institute: Southeast University

description: Gene expression after 7days cultured mesenchymal stem cells

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

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

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

source_name: MensenchymalStemcells,7d, 100 μg/mL iron oxide nanoparticles

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

extract_protocol: RNA was prepared using the RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Huam bone marrow-derived mesenchymal stem cells were exposed to iron oxide nanoparticles, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: bone marrow

tag: Sex

tag: treatment

value: 100 μg/mL iron oxide nanoparticles


title: C_1_2

source_name: non-treatment_sep09, 8h, replicate2


title: MSC 7d 100 μg/mL iron oxide nanoparticles rep1

value: male


title: C_1_1

source_name: non-treatment_sep09, 8h, replicate1


title: nuc_acc_fem_low_loneliness 1

description: mRNA expression


title: nuc_acc_fem_high_loneliness 3

description: mRNA expression


title: nuc_acc_fem_low_loneliness 2

description: mRNA expression


title: MSC 7d untreated rep3

description: Gene expression after 9days expose to iron oxide nanoparticles in mesenchymal stem cells

source_name: MensenchymalStemcells,7d, untreated

value: untreated


title: nuc_acc_fem_low_loneliness 6

description: mRNA expression


title: MSC 7d 100 μg/mL iron oxide nanoparticles rep2


title: HFD NiPKO biological rep. 2

status: Public on Apr 26 2016

first: Christoph

last: Handschin

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

hyb_protocol: Following fragmentation, 4.25 ug of DNA were hybridized for 17 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed at the Life Sciences Training Facility of the University of Basel, using the PARTEK Software Suite and Bioconductor.

source_name: kidney, HFD, NiPKO mice

label_protocol: Sense target biotin labeling according to the  Mouse 2.0 ST Whole Gene Array from Affymetrix

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

value: Kidney

tag: genotype

value: PGC-1alpha knockout


title: Primitive erythroid progenitors from 5-FU-treated ESAM-KO mice

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Lin- FCgRII/III-/Lo CD41Lo c-Kit+ Sca1- endoglin+ CD150+ cells sorted from 5-FU-treated ESAM-KO mice.

hyb_protocol: After labeling, the labeled 2 ug of each cDNA sample was then hybridized on Agilent-039494 SurePrint G3 Human GE 8x60K v2 Microarray at 65°C for 17 h with rotation in the dark. Hybridization was performed using a Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer's instructions. Slides were washed in GE washing buffer.

scan_protocol: Slides were scanned with an Agilent Microarray Scanner G2505C.

data_processing: Agilent Feature Extraction software (Version 10.10.1.1) was used to convert images into gene expression data. Raw data were imported into GeneSpring GX 11.0 (Agilent Technologies) for database management and quality control. This normalized data without the threshold raw signal and the global normalization algorithm was used for identifying differentially expressed genes.

label_protocol: Twenty nanogram of total RNA was reverse transcribed into double strand cDNAs by using an Ovation® Pico WTA System V2 (NuGen) following manufacturer's protocol. Resulting cDNAs were subsequently used for in vitro transcription by DNA polymerase and labeled with cyanine-3 using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA samples from sorted cells were isolated using RNeasy Mini Kit (Qiagen, Venlo, Netherlands).

treatment_protocol: WT and ESAM-KO mice were treated with single 5-FU injection (120 mg/kg), and all mice were sacrificed 8 days after treatment. Bone marrow cells obtained from femora and tibiae were stained with FITC- anti-Lin Abs in combination with PE-anti-CD150, PerCPCy5.5-anti-c-Kit, APC-anti-endoglin, PE-Cy7-anti-Sca1, APC-Cy7-anti-FCgRII/III, and biotinylated anti-CD41 Abs. Subsequent to staining with SAv-PE-TR, Lin- FCgRII/III-/Lo CD41Lo c-Kit+ Sca1- endoglin+ CD150+ cells were sorted with FACSAria (BD Bioscience).

value: ESAM-KO

tag: cell type


title: HFD NiPKO biological rep. 4

tag: tissue


title: MSC 7d untreated rep2

description: Gene expression after 8days expose to iron oxide nanoparticles in mesenchymal stem cells


title: HFD NiPKO biological rep. 3


title: MSC 7d untreated rep1

description: Gene expression after 7days expose to iron oxide nanoparticles in mesenchymal stem cells


title: Primitive erythroid progenitors from 5-FU-treated WT mice

description: Lin- FCgRII/III-/Lo CD41Lo c-Kit+ Sca1- endoglin+ CD150+ cells sorted from 5-FU-treated WT mice.

tag: genotype/variation


title: HFD NiPKO biological rep. 1


title: HFD CTRL biological rep. 4

source_name: kidney, HFD, CTRL mice

value: control


title: HFD CTRL biological rep. 3


title: Oa_SEL_19

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description: Blood samples were aseptically collected in Paxgene blood collection tubes, allowed to rest for 2 hours at room temperature, then stored at –20 °C till the extraction process.

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software.
Normalized with quantile method; NA (or blank) corresponds to probes not considered for the normalization step; null corresponds to missing data from analysis and/or probes (genes) that didn't pass the filtering step.

organism: Ovis aries

source_name: Sheep, Ovis aries, female, 12-24 m old, treated (SEL 1.40 mg/animal/day)

label_protocol: Amplification and labelling was done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: RNA from blood samples was isolated using Paxgene RNA extraction kit, according to manufacturer's instruction. Isolated RNA was purified using Qiagen RNeasy Mini Kit protocol.

value: Blood

value: female

tag: age

value: 12-24 months


title: Chow NiPKO biological rep. 2

source_name: kidney, chow diet, NiPKO mice


title: Oa_SEL_17


title: HFD CTRL biological rep. 1


title: nuc_acc_fem_high_loneliness 11

description: mRNA expression


title: Chow NiPKO biological rep. 4


title: HFD CTRL biological rep. 2


title: Oa_SEL_20


title: Chow NiPKO biological rep. 3


title: C_2_2

source_name: non-treatment_nov09, 8h, replicate2

tag: strain


title: Oa_SEL_15


title: Oa_SEL_18


title: Chow CTRL biological rep. 3

source_name: kidney, chow diet, CTRL mice


title: Chow NiPKO biological rep. 1


title: Chow CTRL biological rep. 4


title: Oa_SEL_13


title: Oa_SEL_16


title: Chow CTRL biological rep. 2


title: Oa_SEL_14


title: Oa_SEL_7

source_name: Sheep, Ovis aries, female, 12-24 m old, untreated control


title: Oa_SEL_12


title: Oa_SEL_8


title: Chow CTRL biological rep. 1


title: S61

city: Taipei

first: Chen

middle: Shih

last: Wen

address: Changde St.

department: Graduate Institute of Oral Biology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Agilent Technologies G2505C scanner (635nm power 100  PMT 0 ; 532nm power n/a, PMT n/a ) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: Transient transfection and established stable clone cells. The S61 plasmids construct vectors were transiently transfected into DLD1 and SAS cells by lipofectamin2000 transfection reagents (invitrogen, Carlsbad, California). Briefly, 3 ug of plasmids DNA was mixed with 4.5 ug of transfection reagents. The transfection protocol was performed according to the manufacturer’s instructions (invitrogen) and checked by western blot analysis. After 24 hr of transfection, the cells were plated in fresh media with 10% fetal calf serum and 3 ug/mL puromycin. The resistant clones were selected and cultured.

tag: cell line

tag: transfection


title: Oa_SEL_11


title: Oa_SEL_9


title: Neo

value: Neo


title: Oa_SEL_1


title: YO3mg_3

source_name: Y2O3-treatment_3 mg, 8h, replicate3


title: Oa_SEL_10


title: Oa_SEL_5


title: MedicagoLeaf_Phosphate_rep3b

city: Göteborg

first: Cornelia

last: Spetea

address: Carl Scottbergsgata 22B

department: Biological and Environmental Sciences

institute: Gothenburg University

description:
Pi3b
Gene expression in leaves of 4 weeks old M. truncatula P fertilized plants

hyb_protocol: Labelled cRNA was purified, fragmented and hybridized on Agilent Medicago Oligoarrays (8x60k) at 65°C under rotation in a hybridization oven. Array slides were washed with Gene Expression Wash Buffers prior to drying.

scan_protocol: After washing, slides were  scanned with the G2565BA DNA microarray Scanner (Agilent Technologies)

data_processing: Scanned imaged were analyzed with the Agilent feature extraction Software Version 7.2.  Resulting raw data were normalized (75 Quantile, median to baseline of all samples)

organism: Medicago truncatula

source_name: Leaf_Phopshate fertilized

label_protocol: Total RNA was used to synthesize cyanine 3-labelled using Low Input Quick Amp Labeling according to Agilent One-Color Gene Expression protocol.

growth_protocol: The plants were grown in a CLF PlantMaster chamber (Plant Climatics, Wertingen, Germany) using a daily cycle of 16 h of light (400 μmol photons m-2 s-1) at 25°C and 8 h of dark at 19°C, and at relative humidity of 40%. Plants were watered once per week with a modified Long Ashton Nutrient Solution (Hewitt, 1966), containing twice the amount of nitrate and no phosphate.

extract_protocol: Total RNA was extracted from leaves of M. truncatula plants using E.Z.N.A. plant RNA kit Standard protocol following manufacturer’s instructions (Omega Bio-Tek, Norcross, GA, USA). Quality of RNA preparations was verified using the Agilent 2200 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Control plants: Mock inoculated with soil containing leek roots, Mycorrhized plants: Inoculated with soil containing leek roots and the AM fungi Rhizophagus irregularis, Phosphate fertilized plants:  Mock inoculated with soil cointainnig leek roots and watered each week with 5 mM NaH2PO4.

value: 4 weeks

value: leaf

tag: treatment group

value: Phosphate fertilized plants


title: MedicagoLeaf_Phosphate_rep2a

description:
Pi2a
Gene expression in leaves of 4 weeks old M. truncatula P fertilized plants


title: MedicagoLeaf_Phosphate_rep2b

description:
Pi2b
Gene expression in leaves of 4 weeks old M. truncatula P fertilized plants


title: MedicagoLeaf_Phosphate_rep1b

description:
Pi1b
Gene expression in leaves of 4 weeks old M. truncatula P fertilized plants


title: Oa_SEL_6


title: MedicagoLeaf_Mycorrhized_rep3b

description:
AM3b
Gene expression in leaves of 4 weeks old M. truncatula mycorrhized plants

value: Mycorrhized plants


title: Oa_SEL_4


title: Oa_SEL_2


title: MedicagoLeaf_Phosphate_rep1a

description:
Pi1a
Gene expression in leaves of 4 weeks old M. truncatula P fertilized plants


title: MedicagoLeaf_Mycorrhized_rep1b

description:
AM1b
Gene expression in leaves of 4 weeks old M. truncatula mycorrhized plants


title: MedicagoLeaf_Mycorrhized_rep2

description:
AM2
Gene expression in leaves of 4 weeks old M. truncatula mycorrhized plants


title: Oa_SEL_3


title: MedicagoLeaf_Control_rep3a

description:
NAM3a
Gene expression in leaves of 4 weeks old M. truncatula control plants

value: Control plants


title: MedicagoLeaf_Phosphate_rep3a

description:
Pi3a
Gene expression in leaves of 4 weeks old M. truncatula P fertilized plants


title: MedicagoLeaf_Control_rep1

description:
NAM1
Gene expression in leaves of 4 weeks old M. truncatula control plants


title: #115-F5 neg

city: Silver Spring

first: Mate

last: Tolnay

state: MD

address: 10903 New Hampshire Ave.

department: Office of Biological Product

institute: FDA/CDER

description: gene expression on sort purified cells

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: Microarrays were scanned with an Agilent G2505 C High-Resolution Scanner, and raw intensity signals were extracted using Agilent Feature Extraction software.

data_processing: Raw data were analyzed using Rosetta Resolver software, which uses an error model to account for error due to random factors and systematic biases.  Raw data were normalized using median scaling (without flagged and control data).

source_name: FCRL5-/CD21-/lo/CD27- cells from donor #115

label_protocol: Amplification, Cy3 labeling, hybridization, washing, and scanning were performed according to Agilent manufacturer protocols by Phalanx Biotech Group (San Diego, CA).  Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: Total RNA was prepared using RNeasy Micro kit from Qiagen (74004).  RNA quality and integrity were determined using an Agilent 2100 Bioanalyzer.  All RNA samples had RIN values greater than 8.0.

treatment_protocol: PBMC from leukapheresis of healthy donors were obtained by Ficoll-Hypaque centrifugation, and B cells were then isolated from PBMC by negative magnetic bead-based selection using B cell enrichment cocktail (StemCell Technologies). Cells were then stained with CD27-APC, CD19-APC-Cy7, CD21-PE-cy7 and FCRL5-PE, and sorted by flow cytometry to get the FCRL5- and FCRL5+ tissue-like memory B cells (CD21-/lo/CD27-/CD19+).

value: blood

tag: cell isolation

value: sort purified

tag: cell markers

value: B cells


title: #112-F5 pos

description: gene expression on sort purified cells

source_name: FCRL5+/CD21-/lo/CD27- cells from donor #112


title: MedicagoLeaf_Mycorrhized_rep1a

description:
AM1a
Gene expression in leaves of 4 weeks old M. truncatula mycorrhized plants


title: MedicagoLeaf_Control_rep3b

description:
NAM3b
Gene expression in leaves of 4 weeks old M. truncatula control plants


title: #116-F5 neg

description: gene expression on sort purified cells

source_name: FCRL5-/CD21-/lo/CD27- cells from donor #116


title: #116-F5 pos

description: gene expression on sort purified cells

source_name: FCRL5+/CD21-/lo/CD27- cells from donor #116


title: MedicagoLeaf_Control_rep2b

description:
NAM2b
Gene expression in leaves of 4 weeks old M. truncatula control plants


title: #112-F5 neg

description: gene expression on sort purified cells

source_name: FCRL5-/CD21-/lo/CD27- cells from donor #112


title: MedicagoLeaf_Mycorrhized_rep3a

description:
AM3a
Gene expression in leaves of 4 weeks old M. truncatula mycorrhized plants


title: MedicagoLeaf_Control_rep2a

description:
NAM2a
Gene expression in leaves of 4 weeks old M. truncatula control plants


title: #115-F5 pos

description: gene expression on sort purified cells

source_name: FCRL5+/CD21-/lo/CD27- cells from donor #115


title: chorioamnion_gbs covR_rep3

city: Seattle

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 transformed, using the oligo package of Bioconductor

label: Cy3 fluorescent label

organism: Macaca nemestrina

source_name: chorioamnion gbs covR treated

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Cynomolgus Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissue samples using the Qiagen RNeasy kit, following the manufacturer's recommendations. Quality and quantity were assessed using an Agilent 2100 Bioanalyzer, and NanoDrop 8000 spectrophotometer, respectively.

tag: gender

tag: origin

value: lower uterus

value: chorioamnion

value: gbs covR


title: Gemcitabine Resistant Panc1 (Panc1-GR1)

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: MicroRNA data expression from gemcitabine-resistant Panc1 cell clones

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments. 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

source_name: Panc1 human pancreatic cancer cell line, gemcitabine resistant

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) with antibiotics and incubated at 37 C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated from parental Panc1 and gemcitabine resistance Panc1 cell lines using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: GEM-resistant cells were generated by exposure to gradually increasing concentrations of the reagent for 2 months. Parental Panc1cells (Panc1-P) were exposed to GEM at an initial concentration of 2 ng/ml. When the cells adapted, the GEM concentration was increased. The final GEM concentration was 30 ng/ml. Using this process, we successfully generated GEM-resistant cells. Limiting the dilution of the established cells allowed the cloning of the GEM-resistant Panc1cells, and the three independent clones (Panc1-GRs: Panc1-GR1, -GR2, and –GR3) were used in the present experiments.

value: Gemcitabine resistant Panc1 derivative generated from the parental Panc1 line by consecutive treatments with 30ng/ml gemcitabine over a period of 2 months


title: chorioamnion_saline_rep3

source_name: chorioamnion saline treated

value: saline


title: Parental Panc1 (Panc1-Pt)

description: MicroRNA data expression from parental Panc1 cell clones

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

source_name: Panc1 human pancreatic cancer cell line

value: Panc1 without gemcitabine treatment


title: chorioamnion_gbs covR_rep4

value: female


title: chorioamnion_gbs covR_rep2


title: chorioamnion_saline_rep1


title: chorioamnion_gbs covR_rep5


title: chorioamnion_saline_rep4


title: chorioamnion_gbs covR_rep1


title: chorioamnion_saline_rep2


title: day 4_rep2

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data of embryonic bodies

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: Embryonic Stem Cells

growth_protocol: Embryoid Bodies (Ebs) were generated by plating R1 mouse ES cells into 6cm low cell binding dishes as a single cell suspension (35000cells/ml) in 5ml of mES growth medium without Lif and incubating them fo 3 or 4 days.

extract_protocol: RNA was prepared with RNeasy Mini kit (Qiagen)

treatment_protocol: Four days old Ebs where treated for the next 3 or 4 days with 2uM RA (Retinoic Acid, Sigma R2625). Day of RA addition corresponds to the sample name day 0.  Three days RA treatment corresponds to the sample name day3. Four days RA tratment corresponds to the sample name day4.

value: embryonic stem cells

value: Day 4 - After the addition of retinoic acid


title: chorioamnion_saline_rep5


title: day 0_rep2

hyb_protocol: According to Affymetrix standard protocols

value: Day 0 - Before the addition of retinoic acid


title: chorioamnion_gbs dcovRdcylE_rep5

source_name: chorioamnion gbs dcovRdcylE treated

value: gbs dcovRdcylE


title: day 3_rep2

label_protocol: According to Affymetrix standard protocols

value: Day 3 - After the addition of retinoic acid


title: chorioamnion_gbs dcovRdcylE_rep4


title: chorioamnion_gbs dcovRdcylE_rep3


title: Gemcitabine Resistant Panc1 (Panc1-GR1)

description: mRNA data expression from gemcitabine-resistant Panc1 cell clones

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) with antibiotics and incubated at 37°C in a humidified incubator with 5% CO2.

treatment_protocol: GEM-resistant cells were generated by exposure to gradually increasing concentrations of the reagent for 2 months.  Parental Panc1 cells (Panc1-P) were exposed to GEM at an initial concentration of 2 ng/ml.  When the cells adapted, the GEM concentration was increased.  The final GEM concentration was 30 ng/ml.  Using this process, we successfully generated GEM-resistant cells.  Limiting the dilution of the established cells allowed the cloning of the GEM-resistant Panc1 cells, and the three independent clones (Panc1-GRs: Panc1-GR1, -GR2, and –GR3) were used in the present experiments.


title: chorioamnion_gbs dcovRdcylE_rep1


title: day 4_rep1


title: chorioamnion_gbs dcovRdcylE_rep2


title: Parental Panc1 (Panc1-Pt)

description: mRNA data expression from parental Panc1 cell clones


title: day 0_rep1


title: day 3_rep1


title: mouse normal liver tissue, biological rep1

status: Public on Apr 25 2016

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

description: Gene expression data from Oil-treated Balb/c mice liver at 6 weeks

hyb_protocol: Following fragmentation, double-stranded cDNA were hybridized for 16 hr at 45℃ on Affymetrix Mouse Gene ST 1.0 array (Affymetrix, SantaClara, CA, USA). GeneChips were washed and stained in the GeneChip2 Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G.

data_processing: Tiff images generated by the GeneChip2 Scanner 3000 7G were processed by the Genepix 6 microarray analysis software (Molecular Devices). Gene array analysis was performed according to the manufacturer’s instructions (GeneChip 430 2.0 and 230 2.0; Affymetrix, Santa Clara, CA).

source_name: Oil-treated liver at 6 weeks, biological rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA ( The Ambion® WT Expression Kit  For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 2009, Affymetrix).

growth_protocol: All Balb/c mice aged at 8 weeks obtained from institute of laboratory animal sciences, CAMS & PUMC (Beijing , China), weighting about 20g. Mice were maintained in a 12-h light/dark cycle at 22- 25°C with free access to food and water. All protocols were approved by the Ethical Committee of Tianjin Medical University.

treatment_protocol: After acclimatization for one week, the hepatic fibrosis mice model was produced by administration of carbon tetrachloride (CCl4, Sigma-Aldrich, St. Louis, MO, USA) for 6 weeks, while the control Balb/c mice treated with oil for 6 weeks.

value: Male

value: Balb/c

value: liver


title: mouse fibrotic liver tissue, biological rep5

description: Gene expression data from CCl4-induced Balb/c mice liver fibrosis at 6 weeks

source_name: CCl4-induced liver fibrosis at 6 weeks, biological rep5


title: mouse fibrotic liver tissue, biological rep4

source_name: CCl4-induced liver fibrosis at 6 weeks, biological rep4


title: mouse normal liver tissue, biological rep3

source_name: Oil-treated liver at 6 weeks, biological rep3


title: mouse normal liver tissue, biological rep2

source_name: Oil-treated liver at 6 weeks, biological rep2


title: mouse fibrotic liver tissue, biological rep1

source_name: CCl4-induced liver fibrosis at 6 weeks, biological rep1


title: Rapid Progression Patient 67

city: Göttingen

first: Raquel

last: Pinho

address: Waldweg 33

country: Germany

institute: Universität Medizin Göttingen

description: Gene expression data for Parkinson's Disease patient with rapid disease progression

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The  expression data was summarized and normalized using Probe Logarithmic Intensity ERror estimation (PLIER) method through Expression Console software (Affymetrix Inc) on all the platform Perfect Match (PM) probes, composed of 49,386 probe sets. Quality control parameters of the microarrays included 3’ to 5’ ratio, labeling matrices, PM mean and polyA spike mean and probe cell intensity.

source_name: whole blood sample

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA isolation was performed using PAXgene Blood RNA Kit.RNA quality was monitored using a Bioanalyzer (Agilent Tecnologies) and determined based on the RNA Integrity Number (RIN) package.

value: whole blood

value: Female

tag: clinical classification

value: Rapid progression Parkinson's Disease patient

tag: updrs-mds3.12 score

tag: age at examination (years)


title: mouse normal liver tissue, biological rep5

source_name: Oil-treated liver at 6 weeks, biological rep5


title: mouse fibrotic liver tissue, biological rep2

source_name: CCl4-induced liver fibrosis at 6 weeks, biological rep2


title: mouse normal liver tissue, biological rep4

source_name: Oil-treated liver at 6 weeks, biological rep4


title: Slow Progression Patient 62

description: Gene expression data for Parkinson's Disease patient with slow disease progression

value: Slow progression Parkinson's Disease patient


title: Slow Progression Patient 60


title: Slow Progression Patient 69


title: Rapid Progression Patient 61


title: Rapid Progression Patient 63


title: Rapid Progression Patient 58


title: Slow Progression Patient 59


title: Slow Progression Patient 66


title: mouse fibrotic liver tissue, biological rep3

source_name: CCl4-induced liver fibrosis at 6 weeks, biological rep3


title: Slow Progression Patient 64


title: Slow Progression Patient 65


title: Rapid Progression Patient 70


title: T20

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

description:
Renal Gene Expression
Total RNA incl. miRNA

hyb_protocol: For each sample 1.65 ug cRNA was fragmented and hybridized to an Agilent Human Whole Genome 44K oligoarray for 17 hours at 65oC.

scan_protocol: Arrays were washed and scanned at 5 um using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), and signal intensity data was extracted using Agilent Feature Extraction software (v10.5.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: Kidney Biopsy

label_protocol: From each biopsy 200 ng of total RNA was used to generate Cyanine 3 (Cy3) labelled cRNA for hybridization to Agilent oligonucleotide microarrays according to the Agilent One-Color Microarray protocol (Agilent Technologies, Santa Clara, CA, USA). Briefly, first and second strands of cDNA were generated containing a T7 RNA polymerase promoter using the Agilent Quick Amp Kit. A T7 RNA polymerase synthesized cRNA and incorporated Cy3-labelled CTP. Labelled cRNA was purified on Qiagen RNeasy columns and the final cRNA concentration and labeling efficiency were determined using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, USA).

extract_protocol:
[biopsy protocol]: Renal wedge biopsies were stored in RNALater (Quiagen) immediately after removal
Total RNA was isolated using miRNeasy (Quiagen) following the manufacturers protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer, and only samples with a A260/280 ratio of >1.6 were used.

tag: donor death

value: Cerebrovascular

tag: last donor creatinine

value: kidney


title: T21

value: male


title: TA_CB_P53_MYC_HT_AKT_A_TUMOR (Mouse xenograph from hNSC transduced with MYC, dominant-negative TP53, hTERT, and AKT)

city: La Jolla

first: Pablo

last: Tamayo

address: 3855 Health Sciences Drive MC 0658

department: Moores Cancer Center

institute: UCSD

description: Mouse xenograph tumor from hNSC transduced with MYC, dominant-negative TP53, hTERT, and AKT

hyb_protocol: Standard hyb protocol for U133 plus PM HT Human Array

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator).

source_name: xenograft

label_protocol: RNA was assessed for quality and integrity using a Bioanalyzer (Agilent Technologies) and samples had a RNA Integrity Number score of higher than 8.2 (51).

growth_protocol: The human cerebellar neural stem cells were derived as described in Lopez WO, Nikkhah G, Kahlert UD, Maciaczyk D, Bogiel T, Moellers S, et al. Clinical neurotransplantation protocol for Huntington's and Parkinson's disease. Restorative neurology and neuroscience. 2013;31:579-95.Human neural stem and progenitor cells were obtained from first  trimester human fetal autopsy specimens in concordance with German law  and Ethics Board evaluation. The study was also approved by the Johns  Hopkins Institutional Review Board. The cells were obtained by  dissecting the cerebellar anlage and culturing as neurospheres.

extract_protocol: RNA was extracted from cells and xenograft tumors using TRIZOL according to manufacturer’s directions

treatment_protocol: Cells were transduced using lentiviral and retroviral vectors.  The  R248W-TP53 plasmid (Addgene plasmid 16437) and MYC plasmid (Addgene  plasmid 17758) were subcloned into pWPI  (Addgene 12254) as described in Mao XG, Hutt-Cabezas M, Orr BA, Weingart M, Taylor I, Rajan AK, et al. LIN28A facilitates the transformation of human neural stem cells and promotes glioblastoma tumorigenesis through a pro-invasive genetic program. Oncotarget. 2013;4:1050-64.   For hTERT, Addgene plasmid 12245 was used.  The SV40 plasmid is described in Raabe EH, Lim KS, Kim JM, Meeker A, Mao XG, Nikkhah G, et al. BRAF activation induces transformation and then senescence in human neural stem cells: a pilocytic astrocytoma model. Clin Cancer Res. 2011;17:3590-9.  For constitutively active AKT, the retroviral Addgene plasmid 15294 was used.   Lentivirus was produced by transfecting 293T cells with VSV-G envelope plasmid, Δ8.9 gag/pol plasmid and the plasmid containing the gene of interest as described using Fugene (Roche) per manufacturer’s instruction.  Retrovirus was produced by transfecting 293T-GP cells with VSV-G plasmid and the plasmid containing the gene of interest using Fugene.  In both cases, 24 hours post transfection, 293T cells were switched to EGF-FGF media and the supernatant was collected at 48 and 72h.   The collected supernatant was filtered with a 0.45 micron filter and stored at -80C until use.      Cerebellar neural stem cells were dissociated using Accutase (Sigma) and gentle tituration, then incubated with viral MYC; SV40; or MYC, hTERT and DN-p53 viral supernatants for 24 hours.  After approximately one week in culture, spheres were identified and individually placed into wells of a 24-well plates.  Expression of the introduced oncogenes was verified by western blot and qPCR.  Cells successfully transduced with MYC, hTERT and DN-p53 were then incubated with AKT viral supernatant for 24 hours.  The cells were then placed under puromycin selection for 72hours, following which sub-clones were generated as described above.

tag: tissue type

value: mouse xenograft


title: Slow Progression Patient 56

tag: tissue


title: Slow Progression Patient 57


title: TA_CB (Human cerebellar neural stem cells control hNSC)

value: Human cerebellar neural stem cells


title: TA_CB_P53_MYC_hT_AKT (hNSC transduced with MYC, dominant-negative TP53, hTERT, and AKT)

value: human cerebellar neural stem cells


title: Rapid Progression Patient 54


title: TA_CB_P53_MYC_HT_AKT_B_TUMOR (Mouse xenograph from hNSC transduced with MYC, dominant-negative TP53, hTERT, and AKT)

description: Mouse xenograph tumor from human cerebellar neural stem cells transduced with MYC, dominant-negative TP53, hTERT, and AKT


title: KO 72h O3 Replicate 4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 72hr ozone exposure in MBL knockout lungs

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Knockout right lung, ozone, 72 hr

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: NA.

extract_protocol: Total whole lung RNA extracted using the Qiagen Mini RNA plus isolation kit according to manufacturers instructions and quality control performed using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA), samples that passed QC were transcribed to cRNA

treatment_protocol: Mice were exposed to filtered air or ozone (0.3ppm) for 24, 48, or 72 hours. Lungs were harvested after exposures and snap-frozen prior to analysis.

value: lung

value: 7 weeks

tag: genotype

value: MBL knockout

tag: route

value: Continuous whole body inhalation

tag: agent

value: ozone

tag: dose

value: 0.3 ppm

tag: time of exposure

value: 72 hour


title: V01

tag: age

value: Trauma


title: KO 72h O3 Replicate 3


title: KO 72h air Replicate 2

description: Gene expression after 72hr air exposure in MBL knockout lungs

source_name: Knockout right lung, air, 72 hr

value: 0 ppm


title: WT 72h O3 Replicate 3

description: Gene expression after 72hr ozone exposure in wildtype lungs

source_name: Wildtype right lung, ozone, 72 hr

value: Wildtype


title: TA_CB_p53_MYC (hNSC transduced with MYC, dominant-negative TP53)


title: V11

value: female


title: Slow Progression Patient 53

value: whole blood

value: Male

value: Slow progression Parkinson's Disease patient


title: KO 72h air Replicate 1

value: male


title: Rapid Progression Patient 55

value: Female

value: Rapid progression Parkinson's Disease patient


title: I36

value: Cerebrovascular

value: kidney


title: I04


title: T15


title: T23


title: Slow Progression Patient 52


title: KO 72h O3 Replicate 2

value: lung

value: 7 weeks

value: MBL knockout


title: WT 72h O3 Replicate 2

value: Continuous whole body inhalation

value: ozone

value: 0.3 ppm


title: KO 72h O3 Replicate 1

value: 72 hour


title: Rapid Progression Patient 52


title: TA_CB_p53_MYC_hT (hNSC transduced with MYC, dominant-negative TP53, hTERT)

value: Human cerebellar neural stem cells


title: WT 72h O3 Replicate 4

value: Wildtype


title: Rapid Progression Patient 50

value: whole blood


title: WT 72h air Replicate 3

description: Gene expression after 72hr air exposure in wildtype lungs

source_name: Wildtype right lung, air, 72 hr

value: 0 ppm


title: WT 72h O3 Replicate 1


title: I41

value: female


title: I21

value: male

value: Trauma


title: WT 72h air Replicate 2


title: WT 72h air Replicate 1


title: KO 48h O3 Replicate 4

description: Gene expression after 48hr ozone exposure in MBL knockout lungs

source_name: Knockout right lung, ozone, 48 hr

value: 48 hour


title: KO 48h O3 Replicate 1


title: KO 48h air Replicate 3

description: Gene expression after 48hr air exposure in MBL knockout lungs

source_name: Knockout right lung, air, 48 hr


title: Slow Progression Patient 49

value: Female

value: Slow progression Parkinson's Disease patient


title: KO 48h O3 Replicate 2

value: lung


title: Slow Progression Patient 48

value: Male


title: Slow Progression Patient 44


title: Rapid Progression Patient 45

value: Rapid progression Parkinson's Disease patient


title: KO 48h O3 Replicate 3

value: 7 weeks

value: MBL knockout

value: Continuous whole body inhalation


title: WT 48h O3 Replicate 1

description: Gene expression after 48hr ozone exposure in wildtype lungs

source_name: Wildtype right lung, ozone, 48 hr

value: ozone

value: 0.3 ppm


title: Rapid Progression Patient 47


title: WT 48h O3 Replicate 3

value: Wildtype


title: I24

value: Cerebrovascular

value: kidney


title: KO 48h air Replicate 2

value: 0 ppm


title: WT 48h O3 Replicate 2

value: male


title: I54


title: WT 48h O3 Replicate 4


title: I15

value: female


title: KO 48h air Replicate 1

value: 48 hour


title: I01


title: Rapid Progression Patient 46

value: whole blood

value: Female


title: I26

value: Trauma


title: T09


title: Slow Progression Patient 43

value: Slow progression Parkinson's Disease patient


title: I25


title: WT 48h air Replicate 3

description: Gene expression after 48hr air exposure in wildtype lungs

source_name: Wildtype right lung, air, 48 hr

value: lung


title: KO  24h O3 Replicate 1

description: Gene expression after 24hr ozone exposure in MBL knockout lungs

source_name: Knockout right lung, ozone, 24 hr

value: 7 weeks

value: 24 hour


title: KO  24h O3 Replicate 3

value: MBL knockout

value: Continuous whole body inhalation


title: I52


title: WT 48h air Replicate 2

value: ozone


title: I34


title: Rapid Progression Patient 42

value: Rapid progression Parkinson's Disease patient


title: KO  24h O3 Replicate 2

value: 0.3 ppm


title: Rapid Progression Patient 39

value: Male


title: KO  24h Air Replicate 3

description: Gene expression after 24hr air exposure in MBL knockout lungs

source_name: Knockout right lung, air, 24 hr

value: 0 ppm


title: I30

value: Cerebrovascular

value: kidney


title: WT 48h air Replicate 1

value: male

value: Wildtype

value: 48 hour


title: Rapid Progression Patient 37

source_name: whole blood sample

value: whole blood


title: Rapid Progression Patient 36


title: I47

value: Trauma


title: KO  24h Air Replicate 2

value: lung


title: Slow Progression Patient 40

value: Female

value: Slow progression Parkinson's Disease patient


title: WT  24h O3 Replicate 2

description: Gene expression after 24hr ozone exposure in wildtype lungs

source_name: Wildtype right lung, ozone, 24 hr

value: 7 weeks

value: 24 hour


title: WT  24h O3 Replicate 1

value: Continuous whole body inhalation

value: ozone


title: WT  24h Air Replicate 1

description: Gene expression after 24hr air exposure in wildtype lungs

source_name: Wildtype right lung, air, 24 hr


title: WT  24h Air Replicate 2


title: KO  24h Air Replicate 1

value: MBL knockout


title: I29