title: Flight_BLM_1.0_rep3

description:
Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.
fHB-10

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, spaceflight, replicate 3


title: Ground_BLM_1.0_rep1

status: Public on Jan 20 2017

type: RNA

city: Houston

first: Tao

last: Lu

state: Texas

address: 2101 E NASA Pkwy

department: Radiation Research

country: USA

institute: NASA Johnson Space Center

description:
Gene expression after 3 hours of 1.0 micrg/mlbleomycin treatment.
gHB-07

hyb_protocol: Followed Agilent protocol for SurePrint G3 Human Gene Expression v3 8x60K Microarray Kit (G4851). 50 ng of total RNA was used for RNA amplification and labeling according to the Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.7, using Agilent Labeling Kit along with an Agilent’s RNA Spike-In Kit (Agilent).  The resulting cRNAs were purified using Qiagen RNeasy mini spin columns and measured again on the Nanodrop for yields (1.1 to 1.5 g per sample) and dye incorporation (average 13.2 pmol/g, with 2 of the 15 samples at 7.7 and 9.9 pmol/g). The samples were then fragmented and 0.6 µg of each hybridization mixture was loaded onto the arrays.

scan_protocol: The slides were scanned with Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.5.1.

data_processing: The scanned images were processed with Agilent Feature Extraction Software Version 11.0.1.1 to obtain background subtracted and spatially detrended Processed Signal intensities..

molecule: total RNA

organism: Homo sapiens

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, ground, replicate 1

label_protocol: Single color labeling with Cyanine-3 (Cy3), using Agilent kit and protocol.

growth_protocol: Human fibroblasts AG01522 were cultured at 37ºC in alpha-MEM supplemented with 10% heat-inactivated fetal bovine serum and Penicillin and Streptomycin to conflence.

extract_protocol: Total RNA was extracted using Qiagen miRNeasy Mini kits. RNA quality was verified by Nanodrop Spectophotometer and Agilent Bioanalyzer.

treatment_protocol: After in Space on ISS for three daya, the cells were treated with 1.0 microgram/ml of bleomycin for 3 hours and with no drug control.

tag: cell type

value: fibroblast

tag: gender

value: Male

tag: cell line


title: HDF_CON

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

description: HDF CON.AVG_Signal

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

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

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

label: biotin

source_name: HDF

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

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

value: human diploid fibroblast (HDF)

tag: treated with

value: none (control)


title: epidermis_D94_young_22y

city: Zürich

first: Nicola

last: Zamboni

state: Zurich

address: Auguste-Piccard-Hof 1

department: Institute for Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

hyb_protocol: done by Genomics Services from Miltenyi Biotec

data_processing: Agilent Feature Extraction Software; data processing using LIMMA for R

source_name: human epidermis, inner forearm

label_protocol: Agilent Whole Human Genome Oligo Microarrays 8x60K V2 Kit

extract_protocol: Suction blisters were obtained as described previously from the inner forearms of 28 young (20 to 25 years) and 54 old (aged between 55 and 66 years) healthy female volunteers (Sudel et al Photochem Photobiol 2003). Suction blister roofs were taken and immediately stored at -80°C . For transcriptomics analysis the suction blister epidermis samples were homogenized using a ball mill. RNA was extracted using RNeasy Fibrous Tissue Mini Kit  (Qiagen) according to manufacturer's instructions

treatment_protocol: no treatment

tag: tissue

value: epidermis

value: female

tag: age

tag: group

value: young


title: Ground_Ctrl_rep3

description:
Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.
gHA-04

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, ground, replicate 3


title: Ground_Ctrl_rep2

description:
Gene expression after 3 hours of 1.0 micrg/mlbleomycin treatment.
gHA-03

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, ground, replicate 2


title: Ground_Ctrl_rep1

description:
Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.
gHA-02

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, ground, replicate 1


title: epidermis_D110_young_24y

scan_protocol: done by Genomics Services from Miltenyi Biotec


title: epidermis_D84_old_64y

value: old


title: Flight_BLM_1.0_rep2

description:
Gene expression after 3 hours of 1.0 micrg/mlbleomycin treatment.
fHB-08

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, spaceflight, replicate 2


title: Flight_Ctrl_rep2

description:
Gene expression after 3 hours of 0.0 micrg/mlbleomycin treatment.
fHA-03

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, spaceflight, replicate 2


title: Flight_Ctrl_rep3

description:
Gene expression after 3 hours of 0.1 micrg/mlbleomycin treatment.
fHA-04

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, spaceflight, replicate 3


title: epidermis_D71_old_65y


title: epidermis_D65_old_61y


title: epidermis_D89_young_20y


title: epidermis_D68_old_64y


title: Flight_Ctrl_rep4

description:
Gene expression after 3 hours of 0.1 micrg/mlbleomycin treatment.
fHA-05

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, spaceflight, replicate 4


title: epidermis_D54_young_22y


title: epidermis_D58_old_64y


title: epidermis_D74_young_25y


title: epidermis_D79_old_60y


title: epidermis_D78_old_64y


title: Flight_Ctrl_rep1

description:
Gene expression after 3 hours of 0.0 micrg/mlbleomycin treatment.
fHA-02

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, spaceflight, replicate 1


title: epidermis_D81_young_21y


title: epidermis_D69_young_22y


title: Flight_BLM_1.0_rep1

description:
Gene expression after 3 hours of 1.0 micrg/mlbleomycin treatment.
fHB-07

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, spaceflight, replicate 1


title: epidermis_D49_young_25y


title: epidermis_D51_old_65y


title: epidermis_D35_young_20y


title: epidermis_D64_old_62y


title: epidermis_D48_old_64y


title: epidermis_D24_young_21y


title: epidermis_D67_young_23y


title: epidermis_D47_old_62y


title: epidermis_D43_old_63y


title: epidermis_D42_old_65y


title: epidermis_D20_young_21y


title: epidermis_D21_young_21y


title: epidermis_D40_old_61y


title: epidermis_D45_old_61y


title: epidermis_D19_young_20y


title: epidermis_D18_young_21y


title: epidermis_D33_old_62y


title: epidermis_D91_young_23y


title: epidermis_D17_young_23y


title: epidermis_D31_old_64y


title: epidermis_D14_young_21y


title: epidermis_D26_old_63y


title: epidermis_D15_old_62y


title: epidermis_D11_young_21y


title: epidermis_D13_young_25y


title: Muscle-S

city: Gwangju

first: Kim Ngan

last: Tran

address: 77, Yongbong-ro, Buk-gu

department: Bioenergy and Biomaterials

institute: Chonnam National University, College of Engineering

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

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials; Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP).; Transfer 200μl of hyb solution to each array, then tape holes and parafilm; Hybridize 16 hours at 45° at 60rpm; Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw data were processed with Affymetrix Expression Console Software for background correction and normalization. RMA (Robust Muti-array Average) was used for normalization.

organism: Rattus norvegicus

source_name: Group TS (tail suspension, and irradiation as in group Ct)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Seven-week-old brown rats were housed in polycarbonate cages in a room with controlled temperature (22 ± 2 °C) and a 12 h light/dark cycle. The rats had access to rodent diets and filtered water ad libitum. Rats were divided into 3 groups consisting of six rats each and were treated accordingly. After treatment, rats were anesthetized using diethyl ether and their soleus muscles were isolated and kept at −80 °C. Frozen tissues were ground into powder using a liquid nitrogen-chilled mortar and pestle.

extract_protocol: Total RNA was isolated from individual frozen tissues using Trizol reagent followed instructions of the manufacturer.

treatment_protocol: 3 groups of treatment: 1) Group Ct (continuous irradiation for 2 weeks with a total absorbed dose of 50 mSv); 2) Group TS (tail suspension, and irradiation as in group Ct ); and 3) Group DN (denervation, and irradiation as in group Ct).

tag: strain

value: Brown

value: soleus muscle


title: C57-PBS-21d-5

city: Beijing

first: xiaoxi

last: lv

address: No Jia2, Nanwei road, Xi Cheng district

country: China

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

description:
This is the fifth lung tissue of six PBS instilled mice used in this experiment
C5-1

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing:
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.
All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis. First, high quality expression values (for example, where at least 6 out of 12 samples have values within cut-off, cut-off =100) will be selected for analysis. Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups.

organism: Mus musculus

source_name: PBS instilled, lung

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

value: male

tag: treatment

value: PBS instilled

value: lung


title: C57-PBS-21d-4

description:
This is the fourth lung tissue of six PBS instilled mice used in this experiment
C4-1


title: C57-PBS-21d-2

description:
This is the second lung tissue of six PBS instilled mice used in this experiment
C2-1


title: epidermis_D10_old_66y


title: epidermis_D07_young_23y


title: C57-PBS-21d-6

description:
This is the sixth lung tissue of six PBS instilled mice used in this experiment
C6-1


title: C57-bleo-21d-4

description:
This is the fourth lung tissue of six bleomycin instilled mice used in this experiment
B3-1

source_name: Bleomycin instilled, lung

value: Bleomycin instilled


title: Muscle-D

source_name: Group DN (denervation, and irradiation as in group Ct)


title: Muscle-C

source_name: Group Ct (continuous irradiation for 2 weeks with a total absorbed dose of 50 mSv)


title: WT-C0h

city: Wuhan

first: Hanyan

last: Ye

state: Hubei

address: No. 5, Shizishan street

institute: HuaZhong Agricultural University

description: wild type accession (Huayang) before cold stress

hyb_protocol: cRNA were hybridized for 16 hr at 45℃ on Affymetrix® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Gcos1.4 (GeneChip Operating Software) referring to Affymetrix Statistical Algorithms Description Document.

organism: Oryza sativa

source_name: rice seedlings in four-leaf-stage of Huayang accession

label_protocol: Biotinylated cRNA was prepared according to the technical manual of GeneChip® Expression Analysis.

growth_protocol: Rice seedlings grew in potting soil until they went into 4-leaf stage.

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

treatment_protocol: the 4-leaf-stage seedlings were moved to artificial chamber at a constant 4°C with 14 hours/10 hours of light/darkness, we took the samples before treatment and after 6 hours' treatment.

tag: cultivar

value: Huayang

value: shoot and leaves

tag: developmental stage

value: four-leaf stage

tag: genotype/variation

value: wild type

value: control


title: C57-bleo-21d-6

description:
This is the sixth lung tissue of six bleomycin instilled mice used in this experiment
B5-1


title: C57-bleo-21d-5

description:
This is the fifth lung tissue of six bleomycin instilled mice used in this experiment
B4-1


title: C57-PBS-21d-1

description:
This is the first lung tissue of six PBS instilled mice used in this experiment
C1-1


title: C57-PBS-21d-3

description:
This is the third lung tissue of six PBS instilled mice used in this experiment
C3-1


title: mutant2-C6h

description: osmyb30 homozygous mutant 2 after cold stress for 6 hours

value: osmyb30 homozygous mutant

value: cold stress for 6 hours


title: mutant2-C0h

description: osmyb30 homozygous mutant 2 before cold stress


title: mutant1-C6h

description: osmyb30 homozygous mutant 1 after cold stress for 6 hours


title: C57-bleo-21d-3

description:
This is the third lung tissue of six bleomycin instilled mice used in this experiment
B2-1


title: WT-C6h

description: wild type accession (Huayang) after cold stress for 6 hours


title: mutant1-C0h

description: osmyb30 homozygous mutant 1 before cold stress


title: C57-bleo-21d-2

description:
This is the second lung tissue of six bleomycin instilled mice used in this experiment
B10-1


title: CK-C6h

description: control accession (ZH11) after cold stress for 6 hours

source_name: rice seedlings in four-leaf-stage of ZH11 accession


title: methylated_control

type: genomic

city: Chapel Hill

first: Gary

middle: L

last: Johnson

state: NC

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina School of Medicine

description: Methcontrol

scan_protocol: Illumina HiScan

data_processing:
Methylation fraction (β) values were normalized to Illumina 450K internal controls (90 probe pairs targeting housekeeping genes) and background subtracted according to the manufacturer's protocol using Illumina GenomeStudio v1.8 software.
Genome build: hg19
[450K_betavalues.csv] Linked as supplementary file on Series record.  File includes Illumina GenomeStudio v1.8 output including normalized methylation fraction (β) values, methylation Probe IDs, UCSC CpG island coordinates, and UCSC RefGene Name/Group.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: methylated human WGA (Whole Genome Amplified) control DNA

extract_protocol: Genomic DNA was isolated using Qiagen DNeasy Blood & Tissue kit and bisulfite conversion of genomic DNA was performed using Zymo Research EZ DNA Methylation kit

tag: control vendor

value: Human WGA Methylated & Non-methylated DNA, Zymo Research


title: CK-C0h

description: control accession (ZH11) before cold stress


title: SUM149neg_DMSO_24h

source_name: EpCAM/CD49f negative SUM149 breast carcinoma subpopulation

growth_protocol: culture media: HuMEC supplemented with 5% FBS and Gibco defined HuMEC supplements

value: SUM149 breast carcinoma cell line, EpCAM/CD49f negative subpopulation

value: DMSO


title: SUM149neg_30nMtrametinib_24h

value: 30nM trametinib


title: OE28-C0h

description: OsMYB30 overexpression plant (OE28) before cold stress

value: OsMYB30 overexpression


title: C57-bleo-21d-1

description:
This is the first lung tissue of six bleomycin instilled mice used in this experiment
B1-1


title: OE2-C6h

description: OsMYB30 overexpression plant (OE2) after cold stress for 6 hours


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep4 [mRNA]

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

description:
CD4TGF/atRA_4
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the “Gene Expression Hybridization Kit” (Agilent, 5188-5242). After posthybridization washes (“Wash Buffers 1 and 2 Kit”, Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies), to obtain Processed Signals (resulting from all intra-array pre-processing, including background corrections) corresponding to the transcript levels.

data_processing: For mRNA arrays, we used the already background-corrected gProcessedSignal. For inter-array comparisons, signal intensities were normalized using the 75th percentile. Replicate probes were mean averaged.

source_name: UCB Naïve T cells, activated +IL2 +TGF-beta +atRA, cultured 5 days

label_protocol: Gene expression profiles were obtained using the commercially available Human Whole Genome Oligo Microarray 4x44K slides containing 41,000 distinct probes (Agilent Technologies, G4112F, Palo Alto, CA, USA), according to the manufacturer’s protocol. Cy3-labelled cRNA was generated using the “Quick Amp Labeling Kit, one-color” (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (“One Color RNA Spike-In Kit”, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

growth_protocol: Mononuclear cells from UCB were isolated following centrifugation through Ficoll-Paque PLUS (Amersham Biosciences, Uppsala, Sweden). Isolated cells were washed two times with PBS-ACD 0.5% and used for the negative immunomagnetic selection of naïve CD4+CD25-CD45RA+ T cells using naïve CD4+ T cell isolation Kit II, according to manufacturer’s recommendations (Miltenyi Biotec, Bergisch Gladbach, Germany). Briefly, all UCB cells (except näive CD4+ T cells) were depleted using a mixture of antibodies (anti-human CD8, CD14, CD15, CD16, CD19, CD25, CD34, CD36, CD45RO, CD56, CD123, TRCγ/δ, HLA-DR and Glycophorin A) linked to magnetic microbeads, using magnetic columns and a QuadroMACS magnet (MiltenyiBiotec). Only samples of näive CD4+ T cells with purity above 95%, as determined by flow cytometry (anti-CD4 PE, anti-CD25 FITC and anti-CD45RA APC), were used in this work.

extract_protocol: Naive T cells, CD4TGF/atRA and CD4Med were collected and resuspended in 250ul of PBS, thoroughly mixed with 750ul of Trizol LS reagent (Invitrogen, Carlsbad, CA, USA) and stored at -80ºC. Total RNA was obtained according to manufacturer’s instructions, and RNA was quantified using a NanoVue Spectrophotometer (GE Healthcare) at 260nM. In addition, the quality of RNA samples was evaluated using RNA 6000 Pico Chip using the Agilent 2100 Bioanalyzer instrument (Agilent Technologies, Colorado Springs, CO, USA). Samples with RIN>7 were used in this work.

treatment_protocol: Naïve CD4+CD25-CD45RA+ T cells were activated with anti-human CD2/CD3/CD28 beads (1:2 bead to cells ratio) in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (Hyclone, Logan, UT, USA), L-glutamine (1mM), streptomycin (100 μg/ml) and penicillin (100 U/ml) (Sigma-Aldrich), and 3x10^5 cells/well were plated in 24 well plates. The complete medium was supplemented with IL-2 (50 U/ml), TGF-β1 (5 ng/ml) and atRA (100 nM), a condition referred as CD4TGF/atRA. As a control for comparisons, naïve T cells were similarly activated, but complete medium was supplemented only with IL-2, a condition referred as CD4Med. The cells were stimulated for a total of 5 days.

value: Umbilical cord blood

value: CD4+CD25-CD45RA+ T cells

value: Activated +IL2 +TGF-beta +atRA

tag: time

value: 5 days

tag: rna id


title: epidermis_D38_old_61y

source_name: human epidermis, inner forearm

value: epidermis

value: female

value: old


title: kidney - 3 days carbohydrate-free - animal TS34

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Gene chip hybridization, washing and scanning were carried out according to Affymetrix protocols.

scan_protocol: Scanning was carried out according to Affymetrix protocols

data_processing: Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done via the Robust Multichip Average (RMA) algorithm.

source_name: kidney_3 days carbohydrate-free

label_protocol: RNA was further processed for hybridization to Affymetrix HT MG-430 PM Array Plates at the Microarray Department of the University of Amsterdam, the Netherlands. RNA amplication and labeling were carried out according to Affymetrix protocols

growth_protocol: C57BL/6 male mice 10-12 weeks old (20-25 grams) were obtained from Harlan, the Netherlands. Animals were housed in individually ventilated cages (3-4 animals/cage) under standard conditions. All mice had free access to ad libitum (AL) food and water (acidified with HCl to a pH of 2.4-2.7) except where noted. All experiments were performed with the approval of the appropriate local ethical board.

extract_protocol: For gene expression analysis, total RNA was extracted from frozen kidney tissue using the QIAzol lysis Reagent and miRNAeasy Mini Kit (QIAGEN, Hilden, Germany), as described in the Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program; animal tissues; aqueous phase. RNA was eluted in RNase free water and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Scientific). Subsequently, quality assessment of the RNA was done using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) and RNA kits and reagents belonging to the same manufacturer.

treatment_protocol: Upon arrival, mice were allowed free ad libitum (AL) access to the SDS chow for 7 days. The fasting experiment was done separately, during which mice were randomly divided into a control group (n=5) or 3 days of fasting (n=4). In a subsequent experiment, mice were randomly divided into the following groups: control group SDS (n=4) or two weeks 30% dietary restriction (n=5), control type I (n=5), or  ad libitum access to  control type I (n=5), 3 days of a protein-free (n=5), fat-free (n=4) or  carbohydrate-free diet (n=5).

value: male

tag: animal id

tag: diet

value: 3 days carbohydrate-free

value: kidney


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep3 [mRNA]

description:
CD4TGF/atRA_3
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).

tag: cell type


title: kidney - 3 days carbohydrate-free - animal TS36

tag: gender


title: kidney - 3 days carbohydrate-free - animal TS31


title: unmethylated_control

description: unmethcontrol

source_name: non-methylated human WGA (Whole Genome Amplified) control DNA


title: OE28-C6h

description: OsMYB30 overexpression plant (OE28) after cold stress for 6 hours

value: shoot and leaves

value: four-leaf stage


title: kidney - 3 days carbohydrate-free - animal TS32


title: Tnaive_activated+IL2_5days_rep4 [mRNA]

description:
CD4med_4
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).

source_name: UCB Naïve T cells, activated +IL2, cultured 5 days

value: Activated +IL2


title: kidney - 3 days carbohydrate-free - animal TS35


title: SUM229neg_30nMtrametinib_24h

source_name: EpCAM/CD49f negative SUM229 breast carcinoma subpopulation

growth_protocol: culture media: F12 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone, 10 mM HEPES

tag: cell line

value: SUM229 breast carcinoma cell line, EpCAM/CD49f negative subpopulation


title: SUM149pos_DMSO_24h

source_name: EpCAM/CD49f positive SUM149 breast carcinoma subpopulation

value: SUM149 breast carcinoma cell line, EpCAM/CD49f positive subpopulation

value: DMSO


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep2 [mRNA]

description:
CD4TGF/atRA_2
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).


title: OE2-C0h

description: OsMYB30 overexpression plant (OE2) before cold stress

value: OsMYB30 overexpression

value: control


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep1 [mRNA]

description:
CD4TGF/atRA_1
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).

value: Umbilical cord blood

value: CD4+CD25-CD45RA+ T cells


title: SUM149pos_30nMtrametinib_24h

value: 30nM trametinib


title: kidney - 3 days fat-free - animal TS42

source_name: kidney_3 days fat-free

value: 3 days fat-free


title: kidney - 3 days fat-free - animal TS41


title: kidney - 3 days fat-free - animal TS38


title: SUM229neg_DMSO_24h


title: Tnaive_activated+IL2_5days_rep3 [mRNA]

description:
CD4med_3
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).

value: 5 days


title: Tnaive_activated+IL2_5days_rep2 [mRNA]

description:
CD4med_2
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).


title: SUM229pos_30nMtrametinib_24h

source_name: EpCAM/CD49f positive SUM229 breast carcinoma subpopulation

value: SUM229 breast carcinoma cell line, EpCAM/CD49f positive subpopulation


title: kidney - 3 days fat-free - animal TS37

value: male


title: Tnaive_fresh_0days_rep4 [mRNA]

description:
Naive_4
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection.

source_name: UCB Naïve T cells, Freshly isolated

value: Naïve


title: SUM159_100nMtrametinib_24h

source_name: SUM159 breast carcinoma cell line

growth_protocol: culture media: DMEM/F12 1:1 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone

value: SUM159 breast carcinoma cell line

value: 100nM trametinib


title: SUM229pos_DMSO_24h


title: Tnaive_fresh_0days_rep3 [mRNA]

description:
Naive_3
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection.


title: kidney - 3 days protein-free - animal TS54

source_name: kidney_3 days protein-free

value: 3 days protein-free

value: kidney


title: Tnaive_fresh_0days_rep1 [mRNA]

description:
Naive_1
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection.


title: kidney - 3 days protein-free - animal TS51


title: 28-PLR-NR

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

country: Italy

institute: University of Verona

description: mammary tumor from 12 weeks of age female PyMT/SIRT6 mouse

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: PyMT/SIRT6 mammary tumor

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

growth_protocol: Mice were housed in groups of 4-5 with food and water available ad libitum in light- and temperature-controlled environments. Care of mice was within the procedures approved by animal care and experimentation authorities of the Canton of Geneva, Switzerland

extract_protocol: RNAs were extracted by Qiagen mRNA extract kits (RNeasy plus). Mircoarray analyses were performed by University of Texas Southwestern Medical Center at Dallas microarray Core facility (http://microarray.swmed.edu/) using Illumina Chip Mouse WG-6 v2.0 (Illumina, CA, USA)

treatment_protocol: Mice were sacrificed at 12 weeks of age and tissues were quickly removed, frozen in liquid nitrogen and subsequently stored at –80ºC

value: mammary tumor

value: 12 weeks-old

value: female

tag: strain/genotype


title: Tnaive_activated+IL2_5days_rep1 [mRNA]

description:
CD4med_1
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).

tag: tissue

value: Activated +IL2


title: 22-AL-FR

tag: age


title: SUM159_DMSO_24h

value: DMSO


title: 13-LR-NL

description: mammary tumor from 12 weeks of age female PyMT mouse

source_name: PyMT mammary tumor

value: PyMT


title: kidney - 3 days protein-free - animal TS52


title: kidney - 3 days protein-free - animal TS50


title: kidney - 3 days protein-free - animal TS49


title: Tnaive_fresh_0days_rep2 [mRNA]

description:
Naive_2
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection.

value: Umbilical cord blood

value: CD4+CD25-CD45RA+ T cells


title: kidney - control (type I) - animal TS30

source_name: kidney_control (type I)

value: control (type I)


title: 26-AR-NL


title: kidney - control (type I) - animal TS29


title: 11-PR-FR


title: kidney - control (type I) - animal TS28


title: 9-AL-IR


title: kidney - control (type I) - animal TS27


title: kidney - 2 weeks 30% dietary restriction - animal TS78

source_name: kidney_2 weeks 30% dietary restriction

value: 2 weeks 30% dietary restriction


title: kidney - control (type I) - animal TS26


title: 21-PR-NR


title: P.gingivalis W83 wild strain rep1

city: Shenyang

first: Hongyan

last: Wang

state: Liaoning Province

address: Nanjing North St. 117

department: Department of Periodontology

institute: School of Stomatology, China Medical University

description: Gene expression of P. gingivalis W83 wild strain

hyb_protocol: Hybridization was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Agilent (California, USA), according to the  Agilen’s Expression user’s guide.

scan_protocol: Scanning was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Agilent (California, USA), according to the  Agilen’s Expression user’s guide.

data_processing: Data analysis was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Agilent (California, USA) . The expression data of probes were normalized using quantile normalization and expression data of genes were generated using the Robust Multichip Average (RMA) algorithm.

organism: Porphyromonas gingivalis

source_name: P.gingivalis W83 wild strain, replicate 1

label_protocol: Labeling was performed at the CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Agilent (California, USA) according to the Agilent’s Expression user’s guide.

growth_protocol: Porphyromonas gingivalis strain W83 was grown anaerobically (10% CO2, 10% H2, 80% N2 ) in enriched brain–heart infusion (BHI) broth containing 5% fiber-free sheep blood, 1% vitamin K and hemin, 37℃.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using NucleoSpin® RNA clean-up（MACHEREY-NAGEL，Germany） according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: Porphyromonas gingivalis strain W83 was treated with 6.25ug/mL for 0.5h.


title: kidney - 2 weeks 30% dietary restriction - animal TS77


title: 16-2B-RR-IR


title: P.gingivalis W83 wild strain rep3

source_name: P.gingivalis W83 wild strain, replicate 3


title: P.gingivalis W83 Nal-P-113-treated rep1

description: Gene expression treated with 6.25ug/mL Nal-P-113

source_name: P.gingivalis W83, treated with Nal-P-113, 0.5h


title: kidney - 2 weeks 30% dietary restriction - animal TS76


title: 20-PL-FL


title: 5-1B-N


title: kidney - 2 weeks 30% dietary restriction - animal TS73


title: 6-1B-L


title: kidney - control (SDS) - animal TS56

source_name: kidney_control (SDS)

value: control (SDS)


title: P.gingivalis W83 wild strain rep2

source_name: P.gingivalis W83 wild strain, replicate 2


title: kidney - 2 weeks 30% dietary restriction - animal TS75

value: male


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep3 [miRNA]

description:
CD4TGF/atRA_3
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).

hyb_protocol: The labeled RNA was purified (MicroBioSpin 6, Bio-Rad, 732-6221), hybridized (overnight for 20 hours at 55°C and 20 rpm) and washed (Agilent, 5188-5327) before scanning.

data_processing: For microRNA arrays, the AFE signal used was gTotalGeneSignal (the sum of the total probe signals per microRNA).

source_name: UCB Naïve T cells, activated +IL2 +TGF-beta +atRA, cultured 5 days

label_protocol: Analysis of microRNA expression profile were performed with the same samples used for mRNA microarray, using the commercially available Agilent Human miRNA Microarray 8x15K slides Release 12.0 (Agilent Technologies, G4471A) and miRNA Kit Complete Labeling and Hyb Kit (Agilent Technologies, 5190-0456), according to the manufacturer’s protocol. Briefly, total RNA (100 ng) from each sample were dephosphorylated with Calf Intestine Alkaline Phosphatase (GE Healthcare, Amersham, UK), and linked to a Cyanine 3-labeled nucleotide (Cyanine 3-pCp) using an enzyme T4 RNA ligase (GE Healthcare, E2050Y).

value: Activated +IL2 +TGF-beta +atRA

value: 5 days


title: kidney - control (SDS) - animal TS55


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep4 [miRNA]

description:
CD4TGF/atRA_4
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).


title: 4-LL-NL

description: mammary tumor from a 12 weeks-old female PyMT mouse


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep2 [miRNA]

description:
CD4TGF/atRA_2
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).


title: Tnaive_activated+IL2_5days_rep4 [miRNA]

description:
CD4med_4
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).

source_name: UCB Naïve T cells, activated +IL2, cultured 5 days


title: Tnaive_activated+IL2+TGF-beta+atRA_5days_rep1 [miRNA]

description:
CD4TGF/atRA_1
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml) +TGF-β1 (5 ng/ml) +atRA (100 nM).


title: Tnaive_activated+IL2_5days_rep3 [miRNA]

description:
CD4med_3
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).


title: kidney - control (SDS) - animal TS58


title: kidney - 3 days fasting - animal K343

source_name: kidney_3 days fasting

value: 3 days fasting


title: kidney - 3 days fasting - animal K344


title: Tnaive_activated+IL2_5days_rep2 [miRNA]

description:
CD4med_2
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection, activated with anti-human CD2/CD3/CD28 beads and cultured for 5 days in RPMI 1640, 10% FBS + IL-2 (50 U/ml).


title: kidney - 3 days fasting - animal K339


title: Tnaive_activated+IL2_5days_rep1 [miRNA]


title: Tnaive_fresh_0days_rep4 [miRNA]

description:
Naive_4
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection.

value: Naïve


title: kidney - 3 days fasting - animal K340

value: kidney


title: Tnaive_fresh_0days_rep2 [miRNA]


title: kidney - control (SDS) - animal K350


title: kidney - control (SDS) - animal K349


title: Tnaive_fresh_0days_rep1 [miRNA]


title: kidney - control (SDS) - animal K348


title: kidney - control (SDS) - animal K347


title: Tnaive_fresh_0days_rep3 [miRNA]

description:
Naive_3
Umbilical Cord Blood Naïve CD4+CD25-CD45RA+ T cells, Freshly isolated by negative selection.


title: kidney - control (SDS) - animal K346


title: Salmonella Typhimurium fimZ mutant

city: Taipei

first: Chang

last: Chieh-Hsiang

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

hyb_protocol: The labeled cDNA was then pooled and hybridized to microarrays at 65° C for 17 h.

scan_protocol: Microarrays were scanned with an Agilent microarray scanner at 535 nm for Cy3-CTP and 625 nm for Cy5-CTP.

data_processing: Scanned images were then analyzed by Feature Extraction 10.5.1.1 software (Agilent). Image analysis and normalization software was used to quantify signal and background intensity for each feature and substantially normalized the data by rank-consistent.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: fimZ mutant Salmonella Typhimurium LB5010

label_protocol: The total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.825 μg of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Bacterial cells were cultured on static LB broth.

extract_protocol: Total RNA were harvested in TRIzol reagent and disrupted using the MagNA Lyser System.

treatment_protocol: Bacterial cells were cultured 37C for 48 hr.

tag: strain/background

value: fimZ mutant

tag: culture condition

value: LB static broth

source_name: Wild-type Salmonella Typhimurium LB5010

value: Wild-type


title: Male liver specific Bcl-6 deficient mouse_rep1

status: Public on Jan 19 2017

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai University

description: Gene expression in male knock out mouse liver

hyb_protocol: The labelled cRNA was hybridized to the Agilent Whole Mouse Genome Microarray v2 8×60k following manufacture's protocol.

scan_protocol: Arrays were scanned using Agilent G2565A Microarray Scanner System.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent Technology) using default parameters.

source_name: Male liver specific Bcl-6 deficient mouse_replicate1

label_protocol: Cy3 labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. cRNA was quantified with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissues with Trizol reagents following manufacture's protocol. Extracted RNA quality was checked by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole liver

value: Male

value: 10 to 11 weeks

tag: genotype

value: knock out


title: Male liver specific Bcl-6 deficient mouse_rep2

source_name: Male liver specific Bcl-6 deficient mouse_replicate2


title: Female wild type mouse_rep1

description: Gene expression in female wild type mouse liver

source_name: Female wild type mouse_replicate1

value: Female

value: wild type


title: Female wild type mouse_rep2

source_name: Female wild type mouse_replicate2


title: Male wild type mouse_rep2

description: Gene expression in male wild type mouse liver

source_name: Male wild type mouse_replicate2


title: Male wild type mouse_rep1

source_name: Male wild type mouse_replicate1


title: Female liver specific Bcl-6 deficient mouse_rep2

description: Gene expression in female knock out mouse liver

source_name: Female liver specific Bcl-6 deficient mouse_replicate2


title: NKL positive T-ALL cell line HPB-ALL

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HGU133plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalization of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

source_name: NKL positive T-ALL cell line

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

extract_protocol: Total RNA was extracted using Trizol reagent.

value: HPB-ALL

tag: cell line type

value: T-ALL cell line

tag: nkl status

value: positive


title: NKL negative T-ALL cell line CML-T1

source_name: NKL negative T-ALL cell line

value: negative


title: NKL negative T-ALL cell line MOLT-16


title: Prostate_Selenium_followup_15

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
A210_30_SEPROS_04013_2_HUGENE_1_0_ST_V1.CEL
15,Selenium,Follow-up

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the GeneChip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library Oligo (v1.43.2).

label: Biotin

source_name: Non-malignant prostate tissue, selenium, follow-up

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: The current study is a double-blind, randomized and placebo-controlled trial on the effects of supplemental intake of selenium on gene expression in non-malignant prostate tissue, registered at clinicaltrials.gov with identifier NCT00446901.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Participants were randomly assigned to take 300 µg selenized yeast (Pharma Nord, Denmark) per day or a placebo (Pharma Nord, Denmark) during an intervention period of 5 weeks. Prostate needle biopsies were obtained from the transition zone (ventral region of the left lobe) before and after the intervention during regular prostate needle biopsies series guided by transrectal ultrasound (TRUS) or during radical prostatectomy. Biopsies were directly embedded in Optimal Cutting Temperature (OCT) Compound (Sakura, Finetek Europe) and frozen in liquid nitrogen. Samples were stored at -80°C until further processing. The biopsies embedded in OCT compound were sectioned at -20°C. At least two representative sections of 5 μm were used for histological examinations. The remainder of the biopsy was sectioned at 20 μm and was used for RNA extraction. For the gene expression analyses, biopsies with histological evidence of adenocarcinoma (as assessed by a uropathologist based on the HE-stained slides) were excluded.

tag: participant id

value: Prostate

tag: age of participant (yrs)

tag: intervention

value: Selenium

value: Follow-up

tag: duration of intervention (days)

tag: serum selenium levels (um)


title: Female liver specific Bcl-6 deficient mouse_rep1

source_name: Female liver specific Bcl-6 deficient mouse_replicate1


title: KMS11_TR_48h

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

hyb_protocol: The targets are then hybridized onto GeneChip® Human Transcriptome Array 2.0 (cat # 902162).  They are hybridized at 45C for 16-18 hours.  The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain (cat # 900720).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G.

data_processing: Affymetrix Transcriptome Analysis Console

source_name: MM KMS11 Cell Line

label_protocol: The Affymetrix GeneChip WT Plus Reagent Kit (cat # 703174) is used to convert 100ng of total RNA into biotinylated sense-strand DNA targets.

extract_protocol: RNA extraction was performing using miRvana total RNA isolation kit

tag: agent

value: Myeloma cells


title: NKL negative T-ALL cell line MOLT-14


title: OPM2_TR_48h

source_name: MM OPM2 Cell Line

tag: cell type


title: NKL negative T-ALL cell line SUP-T1


title: NKL negative T-ALL cell line MOLT-4


title: Prostate_Selenium_baseline_15

description:
A210_29_SEPROS_04013_HUGENE_1_0_ST_V1.CEL
15,Selenium,Baseline

source_name: Non-malignant prostate tissue, selenium, baseline

tag: gender

tag: time

value: Baseline


title: KMS11_CNT

tag: cell line


title: Prostate_Selenium_baseline_14

description:
A210_27_SEPROS_04009_HUGENE_1_0_ST_V1.CEL
14,Selenium,Baseline

tag: tissue


title: OPM2_CNT


title: Prostate_Selenium_followup_14

description:
A210_28_SEPROS_04009_2_HUGENE_1_0_ST_V1.CEL
14,Selenium,Follow-up


title: Prostate_Placebo_followup_13

description:
A210_26_SEPROS_04004_2_HUGENE_1_0_ST_V1.CEL
13,Placebo,Follow-up

source_name: Non-malignant prostate tissue, placebo, follow-up

value: Placebo


title: Prostate_Placebo_followup_11

description:
A210_22_SEPROS_04002_2_HUGENE_1_0_ST_V1.CEL
11,Placebo,Follow-up


title: Prostate_Selenium_followup_12

description:
A210_24A_SEPROS_04003_2_HUGENE_1_0_ST_V1.CEL
12,Selenium,Follow-up


title: Prostate_Selenium_baseline_12

description:
A210_23A_SEPROS_04003_HUGENE_1_0_ST_V1.CEL
12,Selenium,Baseline


title: Prostate_Placebo_baseline_11

description:
A210_21_SEPROS_04002_HUGENE_1_0_ST_V1.CEL
11,Placebo,Baseline

source_name: Non-malignant prostate tissue, placebo, baseline


title: Prostate_Selenium_followup_10

description:
A210_20_SEPROS_04001_2_HUGENE_1_0_ST_V1.CEL
10,Selenium,Follow-up


title: Dis V lcb3

city: worcester

first: Eduardo

middle: M

last: Torres

address: 364 Plantation Street, LRB-523

department: Department of Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description: Grown in YEPD at 30 degrees

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

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

data_processing: Agilent Feature Extractor A.7.5.1

organism: Saccharomyces cerevisiae

source_name: disome yeast

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

growth_protocol: Cells grown in YEPD at 30 degrees

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

tag: strain

tag: age

value: day 1

value: whole cells

source_name: wt yeast


title: Dis IV lcb3

description: Grown in YEPD at 30 degrees


title: Prostate_Placebo_baseline_8

description:
A210_15_SEPROS_01211_HUGENE_1_0_ST_V1.CEL
8,Placebo,Baseline

value: Male


title: Prostate_Placebo_baseline_9

description:
A210_17_SEPROS_01219_HUGENE_1_0_ST_V1.CEL
9,Placebo,Baseline


title: Prostate_Selenium_baseline_10

description:
A210_19_SEPROS_04001_HUGENE_1_0_ST_V1.CEL
10,Selenium,Baseline


title: Prostate_Placebo_followup_8

description:
A210_16_SEPROS_01211_2_HUGENE_1_0_ST_V1.CEL
8,Placebo,Follow-up


title: Dis II lcb3

description: Grown in YEPD at 30 degrees


title: Dis VIII lcb3

description: Grown in YEPD at 30 degrees


title: Dis XI lcb3

description: Grown in YEPD at 30 degrees


title: Dis IX lcb3

description: Grown in YEPD at 30 degrees


title: Prostate_Placebo_followup_7

description:
A210_14_SEPROS_01144_2_HUGENE_1_0_ST_V1.CEL
7,Placebo,Follow-up


title: Prostate_Placebo_followup_6

description:
A210_12_SEPROS_01124_2_HUGENE_1_0_ST_V1.CEL
6,Placebo,Follow-up


title: Prostate_Placebo_baseline_13

description:
A210_25_SEPROS_04004_HUGENE_1_0_ST_V1.CEL
13,Placebo,Baseline


title: Dis XIII lcb3

description: Grown in YEPD at 30 degrees


title: Prostate_Selenium_followup_4

description:
A210_08_SEPROS_01122_2_HUGENE_1_0_ST_V1.CEL
4,Selenium,Follow-up


title: Prostate_Placebo_baseline_7

description:
A210_13_SEPROS_01144_HUGENE_1_0_ST_V1.CEL
7,Placebo,Baseline


title: Dis XV lcb3

description: Grown in YEPD at 30 degrees


title: Dis XIV lcb3

description: Grown in YEPD at 30 degrees


title: Prostate_Selenium_baseline_4

description:
A210_07_SEPROS_01122_HUGENE_1_0_ST_V1.CEL
4,Selenium,Baseline


title: Prostate_Selenium_followup_5

description:
A210_10_SEPROS_01123_2_HUGENE_1_0_ST_V1.CEL
5,Selenium,Follow-up


title: Dis I lcb3

description: Grown in YEPD at 30 degrees


title: Prostate_Selenium_followup_3

description:
A210_06_SEPROS_01083_2_HUGENE_1_0_ST_V1.CEL
3,Selenium,Follow-up


title: Prostate_Placebo_baseline_6

description:
A210_11_SEPROS_01124_HUGENE_1_0_ST_V1.CEL
6,Placebo,Baseline


title: Prostate_Selenium_baseline_5

description:
A210_09_SEPROS_01123_HUGENE_1_0_ST_V1.CEL
5,Selenium,Baseline


title: Prostate_Selenium_followup_2

description:
A210_04_SEPROS_01056_2_HUGENE_1_0_ST_V1.CEL
2,Selenium,Follow-up


title: Prostate_Selenium_baseline_2

description:
A210_03_SEPROS_01056_HUGENE_1_0_ST_V1.CEL
2,Selenium,Baseline


title: Prostate_Placebo_followup_9

description:
A210_18_SEPROS_01219_2_HUGENE_1_0_ST_V1.CEL
9,Placebo,Follow-up


title: Prostate_Placebo_followup_1

description:
A210_02_SEPROS_01055_2_HUGENE_1_0_ST_V1.CEL
1,Placebo,Follow-up


title: lcb3

description: Grown in YEPD at 30 degrees

source_name: disome lcb3 yeast


title: Prostate_Selenium_baseline_3

description:
A210_05_SEPROS_01083_HUGENE_1_0_ST_V1.CEL
3,Selenium,Baseline


title: LRH-1 K289R_refed liver, biological rep6

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

institute: Ecole Polytechnique Fédérale de Lausanne

description:
S3m26
Gene expression data of liver in fasted and then refed mice.

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. ~16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner.

data_processing: Samples were analyzed using Affymetrix Expression Console, Graphpad Prism, and Gene Set Enrichment Analysis (Broad Institute).

source_name: Liver refed, K289R

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from Life Technologies (Part Number 4411974) according to manufacturer's protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufacturer's protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

extract_protocol: Total RNA was extracted using TRIZOL (Invitrogen) and purified with the RNeasy cleanup kit for microarray analysis (Qiagen).

treatment_protocol: Mice were fasted for 24h and then refed for 6h before being sacrificed.

tag: strain/background

tag: genotype/variation

value: LRH-1 K289R

value: Liver

tag: treatment

value: Fasted for 24h, then refed for 6h


title: Prostate_Placebo_baseline_1

description:
A210_01_SEPROS_01055_HUGENE_1_0_ST_V1.CEL
1,Placebo,Baseline


title: LRH-1 WT_refed liver, biological rep6

description:
S3m19
Gene expression data of liver in fasted and then refed mice.

source_name: Liver refed, WT

value: WT


title: LRH-1 K289R_refed liver, biological rep2

description:
S3m22
Gene expression data of liver in fasted and then refed mice.


title: LRH-1 K289R_refed liver, biological rep3

description:
S3m23
Gene expression data of liver in fasted and then refed mice.


title: LRH-1 K289R_refed liver, biological rep1

description:
S3m21
Gene expression data of liver in fasted and then refed mice.


title: LRH-1 K289R_refed liver, biological rep4

description:
S3m24
Gene expression data of liver in fasted and then refed mice.


title: LRH-1 WT_refed liver, biological rep3

description:
S3m16
Gene expression data of liver in fasted and then refed mice.


title: LRH-1 WT_refed liver, biological rep1

description:
S3m14
Gene expression data of liver in fasted and then refed mice.


title: LRH-1 WT_refed liver, biological rep5

description:
S3m18
Gene expression data of liver in fasted and then refed mice.


title: Live Bordetella 3

city: New York

first: Gregory

middle: F

last: Sonnenberg

state: NY

address: 413 East 69th Street, Belfer Research Building 512

institute: Weill Cornell Medical College

hyb_protocol: Array was performed at the University of Pennsylvania Microarray core

data_processing:
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: BMDC

growth_protocol: bone marrow cells were cultured in the presence of GM-CSF

extract_protocol: cells were lysed in Trizol

treatment_protocol: cells were treated with live or heat-killed Bordetella

value: live Bordetella


title: LRH-1 K289R_refed liver, biological rep5

description:
S3m25
Gene expression data of liver in fasted and then refed mice.


title: Live Bordetella 2

scan_protocol: Array was performed at the University of Pennsylvania Microarray core


title: Heat-killed Bordetella 2

label_protocol: Array was performed at the University of Pennsylvania Microarray core

value: heat-killed Bordetella


title: LRH-1 WT_refed liver, biological rep2

description:
S3m15
Gene expression data of liver in fasted and then refed mice.


title: PBS 1

value: PBS


title: Heat-killed Bordetella 1


title: LRH-1 WT_refed liver, biological rep4

description:
S3m17
Gene expression data of liver in fasted and then refed mice.


title: PBS 3


title: Heat-killed Bordetella 3


title: PBS 2


title: Live Bordetella 1


title: HD-C#2_NPCs_Replicate 2

city: Singapore

first: Mahmoud

middle: A

last: Pouladi

address: 8A Biomedical Grove, L5 Immunos

department: BMSI

country: Singapore

institute: A*STAR

hyb_protocol: Labelled cRNAs (750 ng) were hybridized onto the Illumina® HumanHT-12-v4 Expression BeadChip at 58°C for 16 h

scan_protocol: Genechips were scanned using a BeadArray Scanner 500GX

data_processing: The images were analyzed using GenomeStudio Gene Expression v 1.9.0 according to the instructions provided by Illumina. Data was analyzed with GeneSpring default guided workflow (i.e. Analysis type = Expression; Illumina Single Colour; Analysis: Biological Significance). Lower cutoff for ‘Present’ call (0.8) and Upper cutoff for ‘Absent’ Call (0.6). Genespring default normalization: Percentile shift (75%);

source_name: NPCs derived from isogenic Control Clone 2

label_protocol: Biotinylated cRNA was prepared from 300 ng of total RNA using the Epicentre TargetAmp Nano-g Biotin-aRNA Labelling kit for Illumina system

extract_protocol: Total RNA was purified from hiPSCs and hiPSC-derived NPCs following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up procedure.

value: hiPSC-derived neural progenitor cells

value: NPCs

tag: disease state


title: HD-C#2_NPCs_Replicate 3


title: HD-C#1_NPCs_Replicate 3

source_name: NPCs derived from isogenic Control Clone 1


title: HD-C#2_NPCs_Replicate 1


title: LuCaP 105CR PCa xenograft tumor

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 105CR PCa xenograft tumor

hyb_protocol: Cy3 and Cy5 probes were combined and hybridized to Agilent 2x400K SurePrint G3 CGH Microarrays and washed following the manufacturer’s specifications.

scan_protocol: Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the CGH_107_Sep09 protocol with default settings. Feature Extraction Grid_GenomicBuild was hg18:NCBI36:Mar2006. Control probes were removed, duplicate probes averaged, and log2 ratios defined as gProcessedSignal/rProcessedSignal.

label_protocol: One microgram of high molecular weight genomic DNA from each sample was labeled by random priming using the Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP.)  A pool of reference normal male DNA (Promega, Part No. G1471) was labeled with Cy5-dUTP following manufacturer's suggest protocols

extract_protocol: Promega, Part No. G1471

value: male

extract_protocol: Flash frozen LuCaP PCa xenograft tissue was histologically evaluated for regions of viable tumor. gDNA was isolated from 15, 10-micron sections from xenografts with ≥80% tumor content. For xenografts with <80% tumor, stroma and necrotic tissue were removed using an 18-guage needle prior to sectioning. Genomic DNA was isolated using the Qiagen QiaAmp DNA Micro kit incorporating RNAse-treatment, according to the manufacturer's specifications. DNA quality was assessed by agarose gel electrophoresis.

value: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice.

tag: ne group

value: CHGA negative group


title: LuCaP 136CR PCa xenograft tumor

description: LuCaP 136CR PCa xenograft tumor

source_name: A pool of reference normal male DNA (Promega, Part No. G1471)


title: Flower pedicel_NAZ_20hr_rep 2

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

description:
Gene expression in flower NAZ after flower removal at 20hr
20h_24_NAZ

hyb_protocol: The labeled cRNA samples were hybridized on to an Solanum lycopersicum Custom 4x180K Array designed by Genotypic Technology Private Limited. (AMADID: 043310).1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: slides were then scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Agilent Feature Extraction software.Feature extracted data was analyzed using GeneSpring GX Version 12 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization

organism: Solanum lycopersicum

source_name: Flower NAZ after flower removal_20hr

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields using Nanodrop-1000 (JH Bio) and specific activity determined based on the concentration of cRNA and dye incorporation.

growth_protocol: Flower bunches of tomato (Solanum lycopersicum c.v. New Yorker) were harvested between 9 and 11 AM from greenhouse in Israel.

extract_protocol: RNA isolation was done using Qiagen method [Qiagen RNeay Plant minikit (Cat. No.74904)] as per the manufacturer protocol with DNAse treatment

treatment_protocol: The control plant New Yorker, flower bunches containing at least two to four fresh open flowers were brought to the laboratory under high-humidity conditions. Senesced flowers and young (unopened) buds were removed, and the stem ends were trimmed. The flowers were immediately sorted by removing all but two or three fresh flowers from each stem. Bunches of five flower stalks were placed in vials with DDW. They were then placed in an observation room under conditions of 20 ± 1°C, 60 ± 10% RH, and 12 h light at intensity of 14 µmol m-2 s-2, provided by cool white fluorescent tubes. Tissue samples were taken from the AZ, of less than 1 mm thickness for each time point, excised less than 0.5 mm from each side of the visible AZ fracture. For non AZ (NAZ) tissues, 2 mm tissues were taken from the pedicel region. All the  tissues were sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal.

tag: cultivar

value: c.v. New Yorker

value: segement of pedicel

tag: nature of the az

value: No change


title: LuCaP 136 PCa xenograft tumor

description: LuCaP 136 PCa xenograft tumor

value: A pool of reference normal male DNA (Promega, Part No. G1471)


title: LuCaP 147CR PCa xenograft tumor

description: LuCaP 147CR PCa xenograft tumor


title: HD-C#1_NPCs_Replicate 2


title: LuCaP 86.2 PCa xenograft tumor

description: LuCaP 86.2 PCa xenograft tumor


title: LuCaP 115 PCa xenograft tumor

description: LuCaP 115 PCa xenograft tumor


title: Flower pedicel_NAZ_20hr_rep 1

description:
Gene expression in flower NAZ after flower removal at 20hr
20h_23_NAZ


title: LuCaP 141 PCa xenograft tumor

description: LuCaP 141 PCa xenograft tumor


title: LuCaP 81 PCa xenograft tumor

description: LuCaP 81 PCa xenograft tumor


title: LuCaP 147 PCa xenograft tumor

description: LuCaP 147 PCa xenograft tumor


title: CAG180_NPCs_Replicate 3

source_name: NPCs derived from ND36999

value: Huntington disease (HD)


title: LuCaP 96CR PCa xenograft tumor

description: LuCaP 96CR PCa xenograft tumor


title: LuCaP 145.2 PCa xenograft tumor

description: LuCaP 145.2 PCa xenograft tumor

value: CHGA positive/ SYP positive/ AR negative group


title: LuCaP 93 PCa xenograft tumor

description: LuCaP 93 PCa xenograft tumor


title: LuCaP 86.2CR PCa xenograft tumor

description: LuCaP 86.2CR PCa xenograft tumor


title: LuCaP 73 PCa xenograft tumor

description: LuCaP 73 PCa xenograft tumor


title: Flower pedicel_NAZ_16hr_rep 2

description:
Gene expression in flower NAZ after flower removal at 16hr
16h_22_NAZ

source_name: Flower NAZ after flower removal_16hr


title: LuCaP 145.1 PCa xenograft tumor

description: LuCaP 145.1 PCa xenograft tumor


title: LuCaP 92 PCa xenograft tumor

description: LuCaP 92 PCa xenograft tumor


title: LuCaP 96 PCa xenograft tumor

description: LuCaP 96 PCa xenograft tumor


title: LuCaP 81CR PCa xenograft tumor

description: LuCaP 81CR PCa xenograft tumor


title: LuCaP 77 PCa xenograft tumor

description: LuCaP 77 PCa xenograft tumor


title: LuCaP 105 PCa xenograft tumor

description: LuCaP 105 PCa xenograft tumor


title: LuCaP 77CR PCa xenograft tumor

description: LuCaP 77CR PCa xenograft tumor


title: LuCaP 78CR PCa xenograft tumor

description: LuCaP 78CR PCa xenograft tumor


title: HD-C#1_NPCs_Replicate 1


title: LuCaP 73CR PCa xenograft tumor

description: LuCaP 73CR PCa xenograft tumor


title: LuCaP 78 PCa xenograft tumor

description: LuCaP 78 PCa xenograft tumor


title: LuCaP 70CR PCa xenograft tumor

description: LuCaP 70CR PCa xenograft tumor


title: CAG180_NPCs_Replicate 1


title: CAG33_NPCs_Replicate 2

source_name: NPCs derived from ND36997

value: Healthy


title: LuCaP 49 PCa xenograft tumor

description: LuCaP 49 PCa xenograft tumor


title: CAG180_NPCs_Replicate 2


title: LuCaP 58 PCa xenograft tumor

description: LuCaP 58 PCa xenograft tumor


title: HD-C#2_iPSCs_Replicate 3

source_name: isogenic Control Clone 2 for ND36999 hiPSCs

value: Human induced pluripotent stem cells

value: iPSCs


title: HD-C#2_iPSCs_Replicate 2


title: LuCaP 147 PCa xenograft tumor, late passage

description: LuCaP 147 PCa xenograft tumor, CHGA negative group, late passage group

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software versions 10.7.3.1 were used to grid and extract the data using the GE2_105_Jan09 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA.

label_protocol: amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Flash frozen LuCaP PCa xenograft tissue was histologically evaluated for regions of viable tumor. RNA was isolated from 15, 10-micron sections from xenografts with ≥80% tumor content. For xenografts with <80% tumor, stroma and necrotic tissue were removed using an 18-guage needle prior to sectioning. RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.) according to the manufacturer's protocol with on-column DNase digestion followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: late


title: HD-C#2_iPSCs_Replicate 1


title: HD-C#1_iPSCs_Replicate 3

source_name: isogenic Control Clone 1 for ND36999 hiPSCs


title: Flower pedicel_NAZ_4hr_rep 2

description:
Gene expression in flower NAZ after flower removal at 4hr
4h_16_NAZ

source_name: Flower NAZ after flower removal_4hr


title: Flower pedicel_NAZ_8hr_rep 1

description:
Gene expression in flower NAZ after flower removal at 8hr
8h_17_NAZ

source_name: Flower NAZ after flower removal_8hr


title: Flower pedicel_NAZ_16hr_rep 1

description:
Gene expression in flower NAZ after flower removal at 16hr
16h_21_NAZ


title: Flower pedicel_NAZ_4hr_rep 1

description:
Gene expression in flower NAZ after flower removal at 4hr
4h_15_NAZ


title: Flower pedicel_NAZ_12hr_rep 1

description:
Gene expression in flower NAZ after flower removal at 12hr
12h_19_NAZ

source_name: Flower NAZ after flower removal_12hr


title: LuCaP 70 PCa xenograft tumor

description: LuCaP 70 PCa xenograft tumor


title: Flower pedicel_NAZ_0hr_rep 2

description:
Gene expression in flower NAZ without flower removal at 0hr
0h_14_NAZ

source_name: Flower NAZ without flower removal_0hr


title: CAG33_NPCs_Replicate 1


title: Flower pedicel_NAZ_8hr_rep 2

description:
Gene expression in flower NAZ after flower removal at 8hr
8h_18_NAZ


title: LuCaP 145.1 PCa xenograft tumor, late passage

description: LuCaP 145.1 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, late passage group


title: LuCaP 35CR PCa xenograft tumor

description: LuCaP 35CR PCa xenograft tumor


title: CAG33_NPCs_Replicate 3


title: HD-C#1_iPSCs_Replicate 2


title: LuCaP 141 PCa xenograft tumor, late passage

description: LuCaP 141 PCa xenograft tumor, CHGA negative group, late passage group


title: Flower pedicel_NAZ_0hr_rep 1

description:
Gene expression in flower NAZ without flower removal at 0hr
0h_13_NAZ


title: HD-C#1_iPSCs_Replicate 1


title: LuCaP 115 PCa xenograft tumor, late passage

description: LuCaP 115 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 105 PCa xenograft tumor, late passage

description: LuCaP 105 PCa xenograft tumor, CHGA negative group, late passage group


title: CAG180_iPSCs_Replicate 3

source_name: hiPSCs derived from HD patient, ND36999


title: LuCaP 145.2 PCa xenograft tumor, late passage

description: LuCaP 145.2 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, late passage group


title: Flower pedicel_AZ_20hr_rep 1

description:
Gene expression in flower AZ after flower removal at 20hr
20h_11_AZ

source_name: Flower AZ after flower removal_20hr

value: Whole flower AZ

value: seperated


title: CAG180_iPSCs_Replicate 2


title: Flower pedicel_NAZ_12hr_rep 2

description:
Gene expression in flower NAZ after flower removal at 12hr
12h_20_NAZ


title: CAG180_iPSCs_Replicate 1


title: LuCaP 23.1CR PCa xenograft tumor

description: LuCaP 23.1CR PCa xenograft tumor


title: CAG33_iPSCs_Replicate 3

source_name: hiPSCs derived from no-HD subject, ND36997


title: LuCaP 96CR PCa xenograft tumor, late passage

description: LuCaP 96CR PCa xenograft tumor, CHGA negative group, late passage group


title: Flower pedicel_AZ_16hr_rep 1

description:
Gene expression in flower AZ after flower removal at 16hr
16h_9_AZ

source_name: Flower AZ after flower removal_16hr

value: Partialy seperated


title: Flower pedicel_AZ_16hr_rep 2

description:
Gene expression in flower AZ after flower removal at 16hr
16h_10_AZ


title: Flower pedicel_AZ_20hr_rep 2

description:
Gene expression in flower AZ after flower removal at 20hr
20h_12_AZ


title: LuCaP 35 PCa xenograft tumor

description: LuCaP 35 PCa xenograft tumor

value: male


title: LuCaP 23.12 PCa xenograft tumor

description: LuCaP 23.12 PCa xenograft tumor

value: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice.


title: LuCaP 92 PCa xenograft tumor, late passage

description: LuCaP 92 PCa xenograft tumor, CHGA negative group, late passage group

value: CHGA negative group


title: LuCaP 23.1 PCa xenograft tumor

description: LuCaP 23.1 PCa xenograft tumor


title: CAG33_iPSCs_Replicate 2


title: Flower pedicel_AZ_12hr_rep 2

description:
Gene expression in flower AZ after flower removal at 12hr
12h_8_AZ

source_name: Flower AZ after flower removal_12hr

value: c.v. New Yorker


title: CAG33_iPSCs_Replicate 1


title: LuCaP 93 PCa xenograft tumor, late passage

description: LuCaP 93 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, late passage group


title: Flower pedicel_AZ_12hr_rep 1

description:
Gene expression in flower AZ after flower removal at 12hr
12h_7_AZ


title: LuCaP 96 PCa xenograft tumor, late passage

description: LuCaP 96 PCa xenograft tumor, CHGA negative group, late passage group


title: Flower pedicel_AZ_8hr_rep 2

description:
Gene expression in flower AZ after flower removal at 8hr
8h_6_AZ

source_name: Flower AZ after flower removal_8hr

value: Attached


title: Flower pedicel_AZ_8hr_rep 1

description:
Gene expression in flower AZ after flower removal at 8hr
8h_5_AZ


title: LuCaP 136 PCa xenograft tumor, late passage

description: LuCaP 136 PCa xenograft tumor, CHGA negative group, late passage group


title: Flower pedicel_AZ_4hr_rep 2

description:
Gene expression in flower AZ after flower removal at 4hr
4h_4_AZ

source_name: Flower AZ after flower removal_4hr


title: Flower pedicel_AZ_4hr_rep 1

description:
Gene expression in flower AZ after flower removal at 4hr
4h_3_AZ


title: Flower pedicel_AZ_0hr_rep 1

description:
Gene expression in flower AZ without flower removal at 0hr
0h_1_AZ

source_name: Flower AZ without flower removal_0hr


title: LuCaP 78 PCa xenograft tumor, late passage

description: LuCaP 78 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 86.2 PCa xenograft tumor, late passage

description: LuCaP 86.2 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 77 PCa xenograft tumor, late passage

description: LuCaP 77 PCa xenograft tumor, CHGA negative group, late passage group


title: Flower pedicel_AZ_0hr_rep 2

description:
Gene expression in flower AZ without flower removal at 0hr
0h_2_AZ


title: LuCaP 81 PCa xenograft tumor, late passage

description: LuCaP 81 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 73 PCa xenograft tumor, late passage

description: LuCaP 73 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 35 PCa xenograft tumor, late passage

description: LuCaP 35 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 70 PCa xenograft tumor, late passage

description: LuCaP 70 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 49 PCa xenograft tumor, late passage

description: LuCaP 49 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, late passage group


title: LuCaP 35CR PCa xenograft tumor, late passage

description: LuCaP 35CR PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 23.1 PCa xenograft tumor, late passage

description: LuCaP 23.1 PCa xenograft tumor, CHGA negative group, late passage group


title: Leaf AZ_96hr_rep 2

description: Leaf AZ after Leaf deblading_96hr_rep 2

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Data extraction from Images was done using Feature Extraction software of Agilent V-10.7.3.1.Feature extracted data was analyzed using GeneSpring GX Version 12 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization

source_name: Leaf AZ after Leaf debladding at 96hr

growth_protocol: Ex plants -Shoots of tomato (Solanum lycopersicum c.v. VF 36) were harvested between 10 and 12 AM from a commercial greenhouse in Israel.

treatment_protocol: Shoots containing at least four to five mature leaves were brought to the laboratory under high-humidity conditions. Senesced leaves and young (unopened) leaves were removed, and the stem ends were trimmed. Bunches of five shoots were placed in vials with DDW. They were then placed in an observation room under conditions of 20 ± 1°C, 60 ± 10% RH, and 12 h light at intensity of 14 µmol m-2 s-2, provided by cool white fluorescent tubes. All the samples except control were treated with 10 ppm of ethylene for 24h after leaf deblading for each treatment. Tissue samples were taken from the leaf AZ, of less than 1 mm thickness for each time point, excised less than 0.5 mm from each side of the visible AZ fracture. The leaf AZ tissue was sampled at five time points (0, 2, 4, 8, and 14 h), following leaf deblading.

value: Whole leaf abscission zone (AZ)

value: Seperated


title: Leaf AZ_24hr_rep 3

description: Leaf AZ after Leaf deblading_24hr_rep 3

source_name: Leaf AZ after Leaf debladding at 24hr


title: LuCaP 23.1CR PCa xenograft tumor, late passage

description: LuCaP 23.1CR PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 23.12 PCa xenograft tumor, late passage

description: LuCaP 23.12 PCa xenograft tumor, CHGA negative group, late passage group


title: Leaf AZ_48hr_rep 1

description: Leaf AZ after Leaf deblading_48hr_rep 1

source_name: Leaf AZ after Leaf debladding at 48hr


title: LuCaP 145.1 PCa xenograft tumor, early passage

description: LuCaP 145.1 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, early passage group

value: early


title: Leaf AZ_48hr_rep 2

description: Leaf AZ after Leaf deblading_48hr_rep 2


title: Leaf AZ_96hr_rep 3

description: Leaf AZ after Leaf deblading_96hr_rep 3


title: LuCaP 147 PCa xenograft tumor, early passage

description: LuCaP 147 PCa xenograft tumor, CHGA negative group, early passage group


title: Leaf AZ_72hr_rep 3

description: Leaf AZ after Leaf deblading_72hr_rep 3

source_name: Leaf AZ after Leaf debladding at 72hr

value: Partially seperated


title: LuCaP 145.2 PCa xenograft tumor, early passage

description: LuCaP 145.2 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, early passage group


title: Leaf AZ_72hr_rep 2

description: Leaf AZ after Leaf deblading_72hr_rep 2


title: LuCaP 58 PCa xenograft tumor, late passage

description: LuCaP 58 PCa xenograft tumor, CHGA negative group, late passage group


title: LuCaP 141 PCa xenograft tumor, early passage

description: LuCaP 141 PCa xenograft tumor, CHGA negative group, early passage group


title: Leaf AZ_24hr_rep 2

description: Leaf AZ after Leaf deblading_24hr_rep 2


title: Leaf AZ_72hr_rep 1

description: Leaf AZ after Leaf deblading_72hr_rep 1


title: Leaf AZ_0hr_tech rep of A3

description: Leaf AZ without Leaf deblading_0hr_tech.rep of A3

source_name: Leaf AZ without Leaf debladding at 0hr


title: Leaf AZ_96hr_rep 1

description: Leaf AZ after Leaf deblading_96hr_rep 1


title: LuCaP 136 PCa xenograft tumor, early passage

description: LuCaP 136 PCa xenograft tumor, CHGA negative group, early passage group


title: Leaf AZ_48hr_rep 3

description: Leaf AZ after Leaf deblading_48hr_rep 3


title: LuCaP 115 PCa xenograft tumor, early passage

description: LuCaP 115 PCa xenograft tumor, CHGA negative group, early passage group


title: Leaf AZ_24hr_rep 1

description: Leaf AZ after Leaf deblading_24hr_rep 1


title: Leaf AZ_0hr_rep 3

description: Leaf AZ without Leaf deblading_0hr_rep 3


title: Leaf AZ_0hr_rep 2

description: Leaf AZ without Leaf deblading_0hr_rep 2


title: LuCaP 96CR PCa xenograft tumor, early passage

description: LuCaP 96CR PCa xenograft tumor, CHGA negative group, early passage group


title: Leaf AZ_0hr_rep 1

description: Leaf AZ without Leaf deblading_0hr_rep 1


title: Flower AZ_14hr_rep 2

description: Flower AZ after flower removal_14hr_rep 2

source_name: flower AZ after flower removal at 14hr

growth_protocol: Flower bunches of tomato (Solanum lycopersicum c.v. VF 36) were harvested between 10 and 12 AM from a commercial greenhouse in Israel.

treatment_protocol: Bunches containing at least two to four fresh open flowers were brought to the laboratory under high-humidity conditions. Senesced flowers and young (unopened) buds were removed, and the stem ends were trimmed. The flowers were immediately sorted by removing all but two or three fresh flowers from each stem. Bunches of five flower stalks were placed in vials with DDW. They were then placed in an observation room under conditions of 20 ± 1°C, 60 ± 10% RH, and 12 h light at intensity of 14 µmol m-2 s-2, provided by cool white fluorescent tubes. Tissue samples were taken from the AZ, of less than 1 mm thickness for each time point, excised less than 0.5 mm from each side of the visible AZ fracture. The AZ tissue was sampled at five time points (0, 2, 4, 8, and 14 h), following flower removal.

tag: tisssue

value: Whole flower abscission zone (AZ)


title: Flower AZ_14hr_rep 3

description: Flower AZ after flower removal_14hr_rep 3


title: LuCaP 92 PCa xenograft tumor, early passage

description: LuCaP 92 PCa xenograft tumor, CHGA negative group, early passage group


title: Flower AZ_14hr_rep 1

description: Flower AZ after flower removal_14hr_rep 1


title: LuCaP 96 PCa xenograft tumor, early passage

description: LuCaP 96 PCa xenograft tumor, CHGA negative group, early passage group


title: Flower AZ_8hr_rep 3

description: Flower AZ after flower removal_8hr_rep 3

source_name: flower AZ after flower removal at 8hr


title: LuCaP 105 PCa xenograft tumor, early passage

description: LuCaP 105 PCa xenograft tumor, CHGA negative group, early passage group


title: Flower AZ_8hr_rep 2

description: Flower AZ after flower removal_8hr_rep 2


title: LuCaP 93 PCa xenograft tumor, early passage

description: LuCaP 93 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, early passage group


title: LuCaP 78 PCa xenograft tumor, early passage

description: LuCaP 78 PCa xenograft tumor, CHGA negative group, early passage group


title: Flower AZ_8hr_rep 1

description: Flower AZ after flower removal_8hr_rep 1


title: Flower AZ_4hr_rep 3

description: Flower AZ after flower removal_4hr_rep 3

source_name: flower AZ after flower removal at 4hr


title: LuCaP 58 PCa xenograft tumor, early passage

description: LuCaP 58 PCa xenograft tumor, CHGA negative group, early passage group


title: LuCaP 86.2 PCa xenograft tumor, early passage

description: LuCaP 86.2 PCa xenograft tumor, CHGA negative group, early passage group


title: LuCaP 73 PCa xenograft tumor, early passage

description: LuCaP 73 PCa xenograft tumor, CHGA negative group, early passage group


title: Flower AZ_4hr_rep 1

description: Flower AZ after flower removal_4hr_rep 1


title: LuCaP 49 PCa xenograft tumor, early passage

description: LuCaP 49 PCa xenograft tumor, CHGA positive/ SYP positive/ AR negative group, early passage group


title: LuCaP 77 PCa xenograft tumor, early passage

description: LuCaP 77 PCa xenograft tumor, CHGA negative group, early passage group


title: PAH patient pericyte 3

city: Stanford

first: Vinicio

last: de Jesus Perez

state: CA

address: Pulmonary and Critical Care Medicine

institute: Stanford University School of Medicine

description: sildenafil, epoprostenol

data_processing: The data were normalised by GenomeStudio, and differential expression detection was implemented by limma package from Bioconductor.

source_name: Lung

growth_protocol: All pericytes were cultured in pericyte medium, supplement with 2% FBS, 10% pen/strep, 10% pericyte growth supplements. Inculate in 37 degree, 5% CO2. Cells were lysised when reached 80% confluency.

extract_protocol: RNA was extracted by QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Qiality control was performed with Thermofisher Nanodrop.

tag: diagnosis

value: pulmonary aterial hypertension (PAH)

value: M

value: pericytes


title: LuCaP 81 PCa xenograft tumor, early passage

description: LuCaP 81 PCa xenograft tumor, CHGA negative group, early passage group

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines


title: Flower AZ_4hr_rep 2

description: Flower AZ after flower removal_4hr_rep 2


title: LuCaP 70 PCa xenograft tumor, early passage

description: LuCaP 70 PCa xenograft tumor, CHGA negative group, early passage group


title: PAH patient pericyte 2

description: sildenalfil, ambrisentan, treprostinil


title: Flower AZ_2hr_rep 3

description: Flower AZ after flower removal_2hr_rep 3

source_name: flower AZ after flower removal at 2hr


title: LuCaP 35CR PCa xenograft tumor, early passage

description: LuCaP 35CR PCa xenograft tumor, CHGA negative group, early passage group


title: Flower AZ_2hr_rep 2

description: Flower AZ after flower removal_2hr_rep 2


title: Flower AZ_2hr_rep 1

description: Flower AZ after flower removal_2hr_rep 1


title: Flower AZ_0hr_rep 3

description: Flower AZ without flower removal_0hr_rep 3

source_name: flower AZ without flower removal at 0hr


title: PAH patient pericyte 1

description: Tadalafil, ambrisentan, treprostinil

value: F


title: LuCaP 23.1CR PCa xenograft tumor, early passage

description: LuCaP 23.1CR PCa xenograft tumor, CHGA negative group, early passage group


title: Control donor pericyte 3

value: healthy (control)


title: Control donor pericyte 2


title: LuCaP 23.12 PCa xenograft tumor, early passage

description: LuCaP 23.12 PCa xenograft tumor, CHGA negative group, early passage group


title: male gonadectomy, adrenal gland, biological rep2

status: Public on Jan 18 2017

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from rat male adrenal gland after gonadectomy

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Affymetrix® Rat Gene 2.1 ST ArrayStrip (48°C/20 h).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: Male adrenal gland obtained form gonadectomized rats

label_protocol: Total RNA (100 ng) from each sample was subjected to two rounds of sense cDNA amplification (Ambion® WT Expression Kit) (Ambion, TX, USA). The obtained cDNA was used for biotin labeling and fragmentation using AffymetrixGeneChip® WT Terminal Labeling and Hybridization kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Adult male and female Wistar rats (12-week-old; body weight: 120-150 g) were obtained from the Laboratory Animals Breeding Center, Department of Toxicology, Poznan University of Medical Sciences, Poznan, Poland. Animals were kept under standardized conditions of light (14:10 h light-dark cycle, illumination onset 06.00) at constant temperature (23 ̊C) with free access to standard food pellets and water. All experiments were carried out between 10-11 am.

extract_protocol: Total RNA was extracted from samples of entire adrenals using TRI Reagent (Sigma, St Louis, MO, USA), and RNeasyMinElute cleanup Kit (Qiagen, Hilden, Germany). The amount of total mRNA was determined from the optical densityat 260 nm, and the RNA purity was estimated using the 260/280 nm absorption ratio (higher than 1.8) (NanoDropspectrophotometer, ThermoScientific, ALAB, Poland). The RNA integrity and quality were checked in a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2

treatment_protocol: Rats were gonadectomized or sham operated under ketamine (100 mg/kg, i.p.) and xylazine (10 mg/kg, i.p.) anesthesia. ORX was performed via scrotal access while OVX by two dorso-lateral incisions. Fourteen days after surgery half of ORX rats was replaced with testosterone (s.c. injection of Testoviron-Depot, Schering AG, Berlin, 5 mg/100 g body weight) while half of OVX animals with estradiol (s.c. injection of Estradiol-Depot, Jenapharm, 0.5 mg/100 g body weight). After 2 weeks (4 weeks post surgery) rats were decapitated. Adrenal glands were collected to RNAlader and stored in -70 ̊C for further analyses.

value: Wistar rat

value: 12 week old

value: adrenal gland

value: Male


title: Control donor pericyte 1


title: Flower AZ_0hr_rep 2

description: Flower AZ without flower removal_0hr_rep 2


title: LuCaP 35 PCa xenograft tumor, early passage

description: LuCaP 35 PCa xenograft tumor, CHGA negative group, early passage group

value: male

value: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice.

value: CHGA negative group


title: LuCaP 23.1 PCa xenograft tumor, early passage

description: LuCaP 23.1 PCa xenograft tumor, CHGA negative group, early passage group


title: male gonadectomy, adrenal gland, biological rep1


title: male control, adrenal gland, biological rep2

description: Gene expression data from rat male adrenal lgand

source_name: Male adrenal gland served as control


title: female gonadectomy+Estrogen, adrenal gland, biological rep5

description: Gene expression data from rat female adrenal gland after gonadectomy with subsequent estrogen suplementation

source_name: Female adrenal gland obtained form gonadectomized rats with estrogen hormone suplementation

value: Female


title: male gonadectomy, adrenal gland, biological rep3


title: male gonadectomy+Testosterone, adrenal gland, biological rep2

description: Gene expression data from rat male adrenal gland after gonadectomy with subsequent testosterone suplementation

source_name: Male adrenal gland obtained form gonadectomized rats withtestosterone hormone suplementation


title: male control, adrenal gland, biological rep4


title: male gonadectomy+Testosterone, adrenal gland, biological rep4


title: male gonadectomy, adrenal gland, biological rep5


title: male control, adrenal gland, biological rep3


title: male gonadectomy+Testosterone, adrenal gland, biological rep5


title: male gonadectomy+Testosterone, adrenal gland, biological rep1


title: male control, adrenal gland, biological rep1


title: female gonadectomy+Estrogen, adrenal gland, biological rep2


title: male gonadectomy+Testosterone, adrenal gland, biological rep3


title: male gonadectomy, adrenal gland, biological rep4


title: male control, adrenal gland, biological rep5


title: Flower AZ_0hr_ tech.rep of A1

description: Flower AZ without flower removal_0hr_technial.rep of A1

value: Attached


title: female gonadectomy+Estrogen, adrenal gland, biological rep1


title: female gonadectomy+Estrogen, adrenal gland, biological rep3


title: female gonadectomy, adrenal gland, biological rep3

description: Gene expression data from rat female adrenal gland after gonadectomy

source_name: Female adrenal gland obtained form gonadectomized rats


title: female gonadectomy, adrenal gland, biological rep5


title: female gonadectomy+Estrogen, adrenal gland, biological rep4


title: female control, adrenal gland, biological rep4

description: Gene expression data from rat female adrenal lgand

source_name: Female adrenal gland served as control


title: female gonadectomy, adrenal gland, biological rep2


title: female control, adrenal gland, biological rep5


title: female gonadectomy, adrenal gland, biological rep4


title: female control, adrenal gland, biological rep3


title: female gonadectomy, adrenal gland, biological rep1


title: female control, adrenal gland, biological rep1


title: female control, adrenal gland, biological rep2