title: Lung_treatment_with_Thioredoxin-1_vs_saline

city: Kyoto

first: Naoya

last: Tanabe

address: 54 Shogoin-kawahara-cho, Sakyo-ku

institute: Kyoto University

hyb_protocol: The protocol supplied by TORAY Industries, Inc..

label_protocol: CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

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

treatment_protocol: C57Bl/6 mice were exposed to cigarette smoke, and then poly(I:C) was administered together with an intraperitoneal injection of Thioredoxin-1 or saline. Three days after the poly(I:C) challenge, mice were sacrificed.

value: male

tag: developmental stage

value: adult

value: lung

tag: exposure

value: cigarette smoke and poly(I:C)

value: Saline


title: OVCAR3-533533-R7_Stable_Media_Rep1

status: Public on Sep 01 2013

type: RNA

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Hybridisation was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000

data_processing: CEL files were produced using the Affymetrix® GeneChip® Command Console® Software (AGCC)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: ovarian cancer cell line

label_protocol: Affymetrix GeneChip® WT Terminal Labelling and Hybridization was performed according to the manufacturer’s protocol

growth_protocol: Cells were maintained at 37ºC and 5% CO2 in RPMI 1640 containing 10% (v/v) FCS, 50 U.mL-1 penicillin and 50ug.mL-1 streptomycin. 'Selected' cells were cultured in 4uM PHA-533533.

extract_protocol: Total RNA was extracted from cell pellets using the mirVana RNA Isolation Kit (Life Technologies).

treatment_protocol: Cell pellets were collected from subconfluent cultures, frozen and stored at -80ºC prior to nucleic acid extraction.

tag: cell type

value: Resistant

tag: growth condition


title: Pt13_IL21

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

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

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

tag: patient

tag: disease state

value: CLL

value: CD40-activated CLL cells

tag: agent


title: OVCAR3-533533-R6_Stable_Media_Rep1


title: C98C2R_1 with array type SUNFLOWER from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: The early sowing constitutes an alternative strategy to avoid drought occurring during flowering and post-flowering periods and responsible for decrease in sunflower production. In French cropping system, early sowing is associated to low temperature period and frost during first development stages in sunflower. Knowledge about metabolism of frost acclimation must be performed to supply tools for breeding programs in sunflower. The aim of our experiment is to unravel the transcriptional regulation underpinning frost tolerance in sunflower

hyb_protocol: labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, total RNA  .

growth_protocol: aerial - - Plants were grown in growth chambers from September 6th to October 12th. Tissue collection (leaf) was carried out the 6th of October and the 11th of October. - October 6th, plants C1 and S1, 65% hygrometry, 4°C air temperature, 150 micromol/m-2/s-1 PPFD, in growth chamber; - October 11th, plants C2 and S2, 65% hygrometry, 4°C air temperature, 150 micromol/m-2/s-1 PPFD, in growth chamber.

treatment_protocol: Name:FROST - environmental treatment - frost,temperature,frost:. C1 C2 S1 S2

tag: age

value: 35 day

tag: treatment

value: chamber 1 control condition then frost

tag: tissue

value: leaf


title: Pt11_IL21


title: C98S2R_2 with array type SUNFLOWER from Affymetrix


title: OVCAR3-533533-R5_Stable_Media_Rep1


title: OVCAR3-533533-R1_Stable_Media_Rep1


title: Pt13_CTR

value: CTR


title: C98C1R_2 with array type SUNFLOWER from Affymetrix

value: 30 day


title: C98S2R_1 with array type SUNFLOWER from Affymetrix


title: OVCAR3-533533-R7_Selected_Drug_Rep1


title: OVCAR3-533533-R3_Stable_Media_Rep1


title: Pt11_CTR


title: Pt12_CTR


title: C98C1R_3 with array type SUNFLOWER from Affymetrix


title: Pt12_IL21


title: C98S1R_3 with array type SUNFLOWER from Affymetrix

hyb_protocol: labelled extract quantity: 5ng

value: chamber 2 cold acclimation then frost


title: ChIP InvF-mock 3

type: genomic

city: Heverlee

first: Jos

last: Vanderleyden

address: Kasteelpark Arenberg 20

department: Department of Microbial and Molecular Systems

country: Belgium

hyb_protocol: samples were hybridized by Nimblegen (see http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf)

scan_protocol: arrays were scanned by nimblegen (see http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf)

data_processing: raw data were converted to log values and normalized by polynomial regression; no background correction was performed (all analysis in matlab)

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: ChIP InvF mock sample, biol rep 3

label_protocol: ChIP and mock ChIP enriched DNA fragments were blunted, amplified via ligation mediated (LM) PCR and then labeled by Nimblegen using random nonamers (see http://www.nimblegen.com/products/lit/chip_userguide_v6p1.pdf)

growth_protocol: Strains were cultured under high osmolarity and limited aeration conditions to induce invasion: cultures were grown overnight in 5 ml Luria-Bertani (LB) medium (10 g/l tryptone, 5 g/l yeast extract and 10 g/l NaCl in distilled water) [29], shaking at 60 rpm under an angle at 37°C, diluted 1:100 in 50 ml LB in large test tubes and cultured shaking at 150 rpm upright until an OD595 of 0.4 (1E09 CFU/ml) was reached (ca. 5 hrs).

extract_protocol: ChIP was performed on three invF-M9 (CMPG5819, ChIP samples) and three wildtype cultures (mock ChIP samples). Strains were cultured under high osmolarity and limited aeration conditions to induce invasion [28]: cultures were grown overnight in 5 ml Luria-Bertani (LB) medium (10 g/l tryptone, 5 g/l yeast extract and 10 g/l NaCl in distilled water) [29], shaking at 60 rpm under an angle at 37°C, diluted 1:100 in 50 ml LB in large test tubes and cultured shaking at 150 rpm upright until an OD595 of 0.4 (1E09 CFU/ml) was reached (ca. 5 hrs). Chromatin immunoprecipitation was performed as follows. DNA-binding proteins were cross-linked to their binding sites in vivo by the addition of formaldehyde (1%). After 20 min, cross-linking was quenched by the addition of glycine (125 mM). Cells were harvested from 50 ml of culture by centrifugation, washed twice with phosphate-buffered saline, resuspended in 500 µl of lysis buffer (10 mM Tris pH 8, 20% sucrose, 50 mM NaCl, 10 mM EDTA with 10 mg/ml lysozyme) and incubated at 37°C for 30 min. Following lysis, 500 µl of 2X immunoprecipitation buffer (100 mM Tris pH 8, 300 mM NaCl, 2% NP-40, 1% Na-deoxycholate, 0.2% SDS) were added. Cellular DNA was then sheared by sonication (Labsonic U Braun) to an average size of 500 to 1000 bp. Cell debris were removed by centrifugation and the supernatant was retained as input sample in immunoprecipitation experiments. A 750 µl aliquot of this input sample was incubated with 4 µl of anti-c-Myc monoclonal mouse antibody (M4439 Sigma) for 4 hrs at 4°C on a rotating wheel. Next, 30µl of protein G Dynabeads (Dynal, Invitrogen) were added and the mixture was incubated at 4°C for an additional hour. The beads were collected from each sample with the dedicated magnet and washed twice with 1X immunoprecipitation buffer, twice with wash buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% Na-deoxycholate) and once with TE buffer pH 8. Immunoprecipitated complexes were removed from the beads by treatment with elution buffer (50 mM TrisHCl pH 8, 10 mM EDTA, 1% SDS) at 65°C for 10 min. Cross-links in the eluted complexes were reversed by overnight incubation at 65°C. DNA was purified from the immunoprecipitate by proteinase K treatment and phenol-chloroform-isoamylalcohol (25:24:1) extraction and resuspended in 30 µl TE buffer pH 8. Leftover input sample was used as reference sample after removing cross links and purification.

tag: genotype

value: wildtype

tag: chip antibody

value: anti-Myc

source_name: ChIP InvF reference sample


title: OVCAR3-533533-R5_Selected_Drug_Rep1


title: Pt10_IL21


title: OVCAR3-533533-R6_Selected_Drug_Rep1


title: OVCAR3-533533-R3_Selected_Drug_Rep1


title: Pt10_CTR


title: Malt1 -/- TH1 Cells  48 hours after induction from Naïve T cells Replicate 1

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

description: Malt1 -/- TH1 Induced Cells

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 2011.1)

data_processing: The data were normalised using quantile normalisation in Genespring (version 12.0) followed by median centered normalization

organism: Mus musculus

source_name: Malt1 -/- TH1 Cells

label_protocol: Biotinylated cDNA were prepared with the Illumina 96 RNA prep Kit (LifeTech)

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

tag: genetic background

value: 8-12 weeks

tag: source cell

value: Naïve (CD4+CD62L+) T cells from lymph nodes and spleens

value: Malt1 -/-

value: TH1 cell

tag: time

value: 48 hours

value: induction of differentiation of Naïve T cells


title: ChIP InvF-IP 3

source_name: ChIP InvF IP sample, biol rep 3


title: ChIP InvF-mock 1

source_name: ChIP InvF mock sample, biol rep 1


title: C98C2R_3 with array type SUNFLOWER from Affymetrix


title: ChIP InvF-IP 2

source_name: ChIP InvF IP sample, biol rep 2


title: C98C2R_2 with array type SUNFLOWER from Affymetrix


title: ChIP InvF-mock 2

source_name: ChIP InvF mock sample, biol rep 2


title: OVCAR3_Parental_Media_Rep4

value: Parental


title: ChIP InvF-IP 1

source_name: ChIP InvF IP sample, biol rep 1


title: OVCAR3_Parental_Media_Rep2


title: Pt9_IL21

value: CLL


title: OVCAR3-533533-R1_Selected_Drug_Rep1

value: Resistant


title: Pt8_IL21

value: CD40-activated CLL cells


title: C98S1R_2 with array type SUNFLOWER from Affymetrix


title: OVCAR3_Parental_Media_Rep3


title: Pt8_CTR


title: Pt9_CTR


title: Pt6_IL21


title: OVCAR3_Parental_Media_Rep1


title: Pt7_IL21


title: SAB_3 with array type ATH1 from Affymetrix

description:
arabidopsis thaliana (columbia-0)  - harvest date: 22-06-12
The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.

hyb_protocol: labelled extract quantity: 15ug

organism: Arabidopsis thaliana

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: seedling - - Media: Murashige and Skoog (with Gamborg B5) medium - Temperature: 23ºC - Light: 100 µE

treatment_protocol: no treatment

tag: genotype/variation

value: SAB


title: Pt7_CTR


title: Pt6_CTR


title: C98C1R_1 with array type SUNFLOWER from Affymetrix

value: chamber 1 control condition then frost

value: leaf


title: Coleoptilar_node_rtcs_4d_rep4

city: Bonn

first: Frank

last: Hochholdinger

state: BW

address: Katzenburgweg 1a

department: INRES - Crop Functional Genomics

country: Germany

institute: University of Bonn

description: chip barcode: 251553810479_1_1

hyb_protocol: Cy3-labelled cRNAs were hybridized in “one-color mode” using Agilent´s “Gene Expression Hybridization Kit” for 17 h at 65°C according to the manufacturer´s protocol. After hybridization microarrays were washed twice with Agilent´s “Gene Expression Wash Buffer” 1 and 2 for one minute each at room temperature and 37°C, respectively followed by a brief wash in acetonitrile.

scan_protocol: Scanning of arrays was performed with Agilent´s G2505B DNA Microarray Scanner at 5 micron resolution in the single path scanning mode of the green dye channel at two laser settings (10% and 100% PMT) using Agilent’s “Scan Control software, version A. 7.0.1”.

data_processing: Features were extracted with Agilent's “Feature Extraction 9.5.3 Image Analysis Software” and normalized via the mean intensity feature of the Rosetta Resolver program (Rosetta Biosoftware, Cambridge, MA, USA) after excluding control features and flagged microarray features and trimming the top and bottom 10% of the data. A p-value threshold of 0.01 was applied which was calculated with Agilent's single color error model.

organism: Zea mays

source_name: Coeloptilar node

label_protocol: Cy3-labelled cRNA was synthesized from 100 ng of polyA RNA using the “Quick Amp Labeling Kit One Color” (Agilent, Santa Clara, CA, USA) which generates fluorescent complimentary RNA (cRNA) by simultaneously amplifying target material and incorporating cyanine 3-labeled dCTP via T7 polymerase.

growth_protocol: Seedlings were grown in a plant growth chamber at 26°C, with a 16 h light, 8 h dark program at 60% humidity. Coleoptilar nodes were manually dissected from seedlings and immediately frozen in liquid nitrogen after isolation.

extract_protocol: Total RNA was isolated from approximately 500 mg of frozen coleoptilar nodes per biological replicate via the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). For all samples, polyA RNA was isolated using the “Illustra mRNA Purification Kit” (GE Biosciences, Piscataway, NJ) and analyzed on Agilent’s (Colorado Springs, CO) Bioanalyzer to check for degradation and to determine concentration.

treatment_protocol: For Agilent microarray profiling, coleoptilar nodes of wild-type and rtcs seedlings 0 (t0), 2 (t2), and 4 (t4) days after the emergence of these structures were used. Each coleoptilar node RNA extract (biological replicate) was obtained from a pool of approximately 10 coleoptilar nodes collected from seedlings of a single laboratory AC. For each genotype/stage combination four biological replicates were hybridized.

value: Coeloptilar node

value: rtcs

value: day 4


title: Coleoptilar_node_rtcs_4d_rep3

description: chip barcode: 251553810419_1_2


title: SIZ_2 with array type ATH1 from Affymetrix


title: Pt5_CTR

value: CTR


title: SIZ_1 with array type ATH1 from Affymetrix


title: Coleoptilar_node_rtcs_4d_rep1

description: chip barcode: 251553810418_1_2


title: Coleoptilar_node_rtcs_4d_rep2

description: chip barcode: 251553810419_1_1


title: AB_3 with array type ATH1 from Affymetrix

description:
arabidopsis thaliana (columbia)  - harvest date: 22-06-12
The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.

value: AB


title: AB_2 with array type ATH1 from Affymetrix

description:
arabidopsis thaliana (columbia)  - age: 10day
The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.


title: Coleoptilar_node_WT_4d_rep4

description: chip barcode: 251553810418_1_1

value: wild type


title: Coleoptilar_node_WT_4d_rep3

description: chip barcode: 251553810417_1_2


title: Coleoptilar_node_WT_4d_rep1

description: chip barcode: 251553810416_1_2


title: Coleoptilar_node_rtcs_2d_rep4

description: chip barcode: 251553810416_1_1

value: day 2


title: Pt4_CTR


title: UT0103L [Expression]

city: Ube

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

country: Japan

institute: Yamaguchi University School of Medicine

description: uterine leiomyoma obtained from same case as UT0103M

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Leiomyoma

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with the Ambion WT Expression Kit (Ambion) and Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from tissues using the ISOGEN (NIPPON GENE)

tag: gender

value: Female

value: frozen tissue ofuterine leiomyoma

value: leiomyoma


title: SAB_2 with array type ATH1 from Affymetrix


title: Pt4_IL21


title: SAB_1 with array type ATH1 from Affymetrix


title: Coleoptilar_node_rtcs_2d_rep3

description: chip barcode: 251553810415_1_2

tag: developmental stage


title: Coleoptilar_node_WT_4d_rep2

description: chip barcode: 251553810417_1_1


title: AB_1 with array type ATH1 from Affymetrix


title: Pt3_IL21


title: Pt3_CTR


title: COL_3 with array type ATH1 from Affymetrix

description:
arabidopsis thaliana (columbia_0)  - harvest date: 22-06-12
The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.

value: COL


title: Coleoptilar_node_rtcs_2d_rep2

description: chip barcode: 251553810415_1_1


title: Pt1_IL21

value: CLL


title: UT0101L [Expression]

description: uterine leiomyoma obtained from same case as UT0101M

value: frozen tissue of uterine leiomyoma


title: Pt2_CTR

value: CD40-activated CLL cells


title: UT0102L [Expression]

description: uterine leiomyoma obtained from same case as UT0102M


title: Coleoptilar_node_rtcs_2d_rep1

description: chip barcode: 251553810414_1_2


title: COL_2 with array type ATH1 from Affymetrix


title: Pt2_IL21


title: UT0103M [Expression]

description: myometrium tissue obtained from same case as UT0103L

source_name: Myomet

value: frozen tissue of myometrium with leiomyoma

value: myometrium tissue obtained from uterus with leiomyoma


title: SIZ_3 with array type ATH1 from Affymetrix


title: UT0101M [Expression]

description: myometrium tissue obtained from same case as UT0101L


title: Coleoptilar_node_WT_2d_rep4

description: chip barcode: 251553810414_1_1


title: UT0102M [Expression]

description: myometrium tissue obtained from same case as UT0102L


title: Coleoptilar_node_WT_2d_rep2

description: chip barcode: 251553810413_1_1


title: Coleoptilar_node_WT_2d_rep3

description: chip barcode: 251553810413_1_2


title: Pt1_CTR


title: Pt5_IL21


title: Myomet0103 [Expression]

description: control myometrium tissue to compare with myometrium with leiomyoma

source_name: Control

value: frozen tissue of myometrium without leiomyoma

value: normal myometrium


title: Myomet0102 [Expression]


title: COL_1 with array type ATH1 from Affymetrix


title: Coleoptilar_node_rtcs_0d_rep3

description: chip barcode: 251553810409_1_2

value: Coeloptilar node

value: rtcs

value: day 0


title: Coleoptilar_node_WT_2d_rep1

description: chip barcode: 251553810410_1_2


title: Myomet0101 [Expression]


title: Coleoptilar_node_rtcs_0d_rep4

description: chip barcode: 251553810410_1_1


title: siLRH-1_#3_rep_1

city: London

first: Simak

last: Ali

address: Du Cane Road

department: Department of Surgery & Cancer

country: United Kingdom

institute: Imperial College London

description:
SAMPLE 9
Replicate 1 of 4.

hyb_protocol: Labelled cRNA was hybridised to the Illumina HumanHT-12 V3.0 expression BeadChip according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: BeadChips were scanned using the BeadArray reader.

data_processing: The BeadChiP image data were preprocessed using GenomeStudio (Illumina). The expression data were then log2 transformed and quantile-normalised using Partek Genomics Suite.

source_name: MCF-7 human cell line, siLRH-1_#3

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrep™-96 RNA Amplification Kit for Illumina arrays.

growth_protocol: MCF-7 cells were cultured in DMEM containing 10% FCS.

extract_protocol: Total RNA was extracted using the RNeasy Kit from QIAGEN following manufacturer's instructions.

treatment_protocol: Cells were transfected with double-stranded RNA oligonucleotides using the Lipofectamine RNAiMax reverse transfection method (Invitrogen, UK), according to manufacturer's protocols. Two different siRNAs against LRH-1 were used: ON-TARGETplus siRNA J-003430-07 (siLRH-1_#2) and J-003430-08 (siLRH-1_#3) from Dharmacon. siGENOME Non-targeting siRNA (Dharmacon, cat. no.:D-001210-01) (siControl) was used as negative control. All siRNA experiments used the double-stranded RNA oligonucleotides at a final concentration of 80 nM.

tag: cell line

tag: sirna knockdown


title: siLRH-1_#3_rep_3

description:
SAMPLE 11
Replicate 3 of 4.


title: Coleoptilar_node_WT_0d_rep3

description: chip barcode: 251553810407_1_2


title: siLRH-1_#3_rep_4

description:
SAMPLE 12
Replicate 4 of 4.


title: Exp_ESCC_169

city: beppu

first: sawada

last: genta

address: tsurumihara

institute: kyushu university

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Fluorescence intensities were determined with an Agilent DNA Microarray Scanner.

data_processing: The gene expression profiles (GE) obtained from microarray data were quintile normalized. The batch effect in microarray experiments was also adjusted by an empirical Bayesian approach

source_name: esphageal squamous cell carcinoma

label_protocol: Cyanine (Cy)-labeled cRNA was prepared using T7 linear amplification as described in the Agilent Low RNA Input Fluorescent Linear Amplification Kit Manual (Agilent Technologies).

extract_protocol: Total RNA was extracted with QIAGEN RNeasy minElute Spin Column (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocols.

treatment_protocol: Laser micro-dissection

value: Male

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis

value: positive


title: Coleoptilar_node_rtcs_0d_rep1

description: chip barcode: 251553810408_1_2


title: Exp_ESCC_171

description: matched with exome sequencing sample ESCC_59

value: poor


title: Coleoptilar_node_rtcs_0d_rep2

description: chip barcode: 251553810409_1_1


title: Coleoptilar_node_WT_0d_rep4

description: chip barcode: 251553810408_1_1

value: wild type


title: siLRH-1_#2_rep_4

description:
SAMPLE 8
Replicate 4 of 4.

source_name: MCF-7 human cell line, siLRH-1_#2


title: Exp_ESCC_170

description: matched with exome sequencing sample ESCC_58


title: siLRH-1_#2_rep_3

description:
SAMPLE 7
Replicate 3 of 4.


title: siLRH-1_#2_rep_1

description:
SAMPLE 5
Replicate 1 of 4.


title: Exp_ESCC_167

description: matched with exome sequencing sample ESCC_56

value: Female

value: well

value: negative


title: siLRH-1_#2_rep_2

description:
SAMPLE 6
Replicate 2 of 4.


title: Exp_ESCC_168

description: matched with exome sequencing sample ESCC_57


title: siLRH-1_#3_rep_2

description:
SAMPLE 10
Replicate 2 of 4.


title: IAA 0h rep3

city: WINSTON SALEM

first: Gloria

middle: Kressin

last: Muday

state: North Carolina

address: 1834 Wake Forest Road

department: Biology

country: USA

institute: Wake Forest University

description: 6 day old arabidopsis roots

hyb_protocol: Following fragmentation, 20 ug of labeled cRNA was hybridized for 16 hr at 45 degrees C on the Affymetrix GeneChips. GeneChips were washed and stained using the GeneChip 450 Fluidics Station according to standard Affymetrix operating procedures

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G system according to the standard Affymetrix protocol

data_processing: Raw data were normalized using systematic variation normalization, and the log2 of the signal intensity is reported.

source_name: 6 day old roots placed on auxin medium for < 5 minutes

label_protocol: Approximately 5ug of purified total RNA was processed to produce biotinylated cRNA targets followed by streptavidin-phycoerythrin fluorescent staining according to the standard Affymetrix 3’-IVT labeling protocol

growth_protocol: 6 days of growth in 100 umol/m2sec2 continuous cool white light on a nylon screen (03-100/32; Sefar Filtration) pressed tigghtly against 1xMS 1% sucrose media (pH 5.6)

extract_protocol: Root samples were ground in liquid nitrogen and the RNA was extracted using the Qiagen Plant RNeasy kit.  The RNA was then precipitated from the eluate with isopropanol

treatment_protocol: Nylon mesh with seedlings grown on the surface was transferred to control media or media containing 1 uM IAA at time 0

value: root


title: Coleoptilar_node_WT_0d_rep2

description: chip barcode: 251553810407_1_1


title: siControl_rep_2

description:
SAMPLE 2
Replicate 2 of 4.

source_name: MCF-7 human cell line, siControl

value: siControl


title: siControl_rep_3

description:
SAMPLE 3
Replicate 3 of 4.


title: Exp_ESCC_166

description: matched with exome sequencing sample ESCC_55


title: siControl_rep_4

description:
SAMPLE 4
Replicate 4 of 4.


title: Exp_ESCC_161


title: baseline subject 160

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: Sample 319

hyb_protocol: Biotin-labeled, amplified material was hybridized to Illumina Human-HT-12 v3 BeadChips, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA; 11322355 Rev. A, 11286331 Rev. A).

scan_protocol: Microarrays were scanned on the Illumina Bead Array Reader (Illumina, Inc., San Diego, CA) with default outlier detection according to the manufacturer's instructions and summarized raw probe intensities were exported using Illumina’s GenomeStudio v2011.1 Gene Expression module.

data_processing: Microarray expression analysis was performed in R (http://www.r-project.org/). Summarized raw probe intensities (48,750 probes) were first filtered by an Illumina detection P value of 0.01 in at least 10% of the samples, leaving 14,168 expressed probes for further analysis. Second, each transcript was transformed and normalized through variance stabilization and normalization.  Third, technical batches were adjusted using ComBat (http://jlab.byu.edu/ComBat/Abstract.html) with fixed effects of amplification round.

source_name: whole blood

label_protocol: Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).

value: male

tag: stimulus

value: baseline

tag: status

value: control

tag: bmi


title: array 71

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

country: Denmark

institute: University of Aarhus

hyb_protocol: The labelled and purified reference samples were mixed and divided into aliquots before combining it with a labelled sample. Each of the 91 labelled samples were co-hybridized with an aliquot of the labelled reference sample and a hybridization blocker containing polydA (Invitrogen Corporation, CA, USA) and Yeast tRNA (Invitrogen Corporation, CA, USA) to 55k pig cDNA microarrays (GEO accession: GPL6173) using a Discovery XT hybridisation station (Ventana Discovery Systems, Tucson, AZ, USA). Chip Prep-2 was transferred from 4 ºC to room temperature 1 hour before use. ChipSpread was prepared by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) followed by incubation at room temperature for 1 hour before use. Labels were printed, trimmed and placed on the slides. The Chip Map reagents (Chip Prep-1, -2 and - 3) were mixed by inversion; the caps were removed and the reagents were placed in the Discovery. The slides were placed in the machine and the run was initiated. The slides were covered with 2.5 mL ChipSpread when the message appeared and the machine used app. 1.5 hours for pre-hybridization of the slides. The Chiphybe80 was mixed and 200 µL were added to the sample (<20 µL) followed by careful mixing. The sample mixtures were heated at 90°C for 3 minutes in a PCR machine carefully mixed by pipetting. The "button" on the machine was pressed to prepare the slides for hybridization. When prompted to, the samples were applied to the slides which were hybridized at 48 ºC for 6 hours. Oil was wiped from the backside of the slides using a clean-room napkin and the slides were placed in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, an equal number of slides were placed in two slide-holders and continued in parallel. The slide-holder was transferred to a HTW filled with RiboWash and washed for 2 min with magnetic stirring at 700 rpm. The HTW was refilled with RiboWash and the wash was repeated. The slide-holder was dipped in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). The slide-holder was then transferred to a HTW filled with 2x SSC and washed for 2 min with magnetic stirring at 700 rpm followed by refill of the HTW with 2x SSC and repetition of the wash. The slide-holder was dipped 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and the holder was left submerged in 0.1x SSC. The slides were transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were dried by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = localFeature.

data_processing: Pre-processing, normalisation and statistical analysis were carried in the R computing environment (version 2.6.1 for Windows) using the packages Linear Models for Microarray Analysis (Limma, version 2.12.0, which is part of the Bioconductor project. Log2 transformed ratios of Alexa-647 to Alexa-555 (not background corrected) were normalized within-slide using loess with default parameters in Limma. Genome-wide expression profiles were generated by assessing cDNA clones comparing testis sample RNA.  Microarray clones were ranked according to their ability to distinguish between groups using linear models for Microarray Analysis. Genes expressed at or below P-values of 5 %  after correcting for multiple testing by Benjamini and Hochberg´s false discovery rate method (FDR) were selected to the further process of analysis by ANOVA to select probes differentially regulated over time. Hierarchical clustering was performed in Cluster (Gene Cluster 3.0) by average linkage and modified Pearson equation for uncentered correlation similarity metric.

organism: Sus scrofa

label_protocol: Alexa Flour-labeled cDNA was synthesized from 20 µg of total-RNA using Superscript Plus Direct cDNA Labeling System (Invitrogen) and purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. "Green" spike-in RNA was added to the common reference samples and "red" spike-in RNA was added to the samples

growth_protocol: The  boars were reared and kept in the same farm units under identical management conditions.

extract_protocol: RNeasy 96 Universal Tissue Kit (Qiagen) without DNAse treatment, following the enclosed protocol. Quantities were measured using a NanoDrop ND-1000. (Thermo Scientific/Fischer Scientific, Oslo Norway). Quality was evaluated by capillary electrophoresis with Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano LabChi kit (Agilent Technologies Inc, Santa Clara CA USA).

tag: breed

value: Duroc

value: boar - uncastrated

tag: age

value: approx. 20 weeks

tag: liveweight

value: 84 kg

tag: tissue

value: testis

tag: animal id

tag: mother id

tag: androstenone related blup

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition

source_name: Testis_tissue_reference [pool of total rna from 40 animals]

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

tag: rna amount

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Coleoptilar_node_WT_0d_rep1

description: chip barcode: 251553810406_1_1

value: Coeloptilar node

tag: genotype/variation

value: wild type

tag: developmental stage

value: day 0


title: stimulated subject 160

description: Sample 320

tag: gender

tag: stimulus

value: stimulated

tag: status

tag: bmi


title: Exp_ESCC_163

description: matched with exome sequencing sample ESCC_53

value: Male

tag: age

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis

value: positive


title: siControl_rep_1

description:
SAMPLE 1
Replicate 1 of 4.

tag: cell line

tag: sirna knockdown

value: siControl


title: Exp_ESCC_165

description: matched with exome sequencing sample ESCC_54


title: Exp_ESCC_164


title: Exp_ESCC_160

description: matched with exome sequencing sample ESCC_51

value: Female


title: array 58

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 16 weeks

tag: liveweight

value: 54 kg

tag: tissue

tag: animal id

tag: mother id

tag: androstenone related blup

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: immature


title: Exp_ESCC_159

description: matched with exome sequencing sample ESCC_50

tag: gender

value: well

value: negative


title: array 70

tag: age

value: approx. 14 weeks

value: 38 kg

value: testis

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

tag: rna amount

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 19

value: approx. 3 weeks


title: baseline subject 159

description: Sample 317

value: male

tag: stimulus

value: baseline

tag: status

value: control

tag: bmi


title: Exp_ESCC_158

description: matched with exome sequencing sample ESCC_49

value: Male

tag: his type

tag: depth

tag: lymph node metastasis

value: positive


title: control 0h rep3

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on control medium for <5 minutes

tag: tissue

value: root


title: Exp_ESCC_157

description: matched with exome sequencing sample ESCC_48

value: moderate


title: array 11

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 1 weeks

tag: mother id

tag: androstenone related blup


title: Exp_ESCC_155

description: matched with exome sequencing sample ESCC_47

value: poor


title: stimulated subject 157

description: Sample 314

value: stimulated

value: case


title: baseline subject 157

description: Sample 313


title: baseline subject 158

description: Sample 315


title: Exp_ESCC_156

value: well

value: negative


title: Exp_ESCC_153

description: matched with exome sequencing sample ESCC_45


title: Exp_ESCC_154

description: matched with exome sequencing sample ESCC_46


title: array 66

value: approx. 20 weeks

tag: liveweight

value: 94 kg

value: testis

tag: animal id

tag: plasma-testosterone

value: 4.4 ng/ml

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 28

tag: gender

tag: age

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

tag: rna amount


title: array 53

value: approx. 16 weeks

value: 54 kg

value: immature


title: baseline subject 155

description: Sample 309

value: male

tag: stimulus

value: baseline

tag: status

tag: bmi


title: array 31

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 3 weeks

tag: tissue

tag: mother id


title: stimulated subject 155

description: Sample 310

value: stimulated

value: case


title: Exp_ESCC_150

description: matched with exome sequencing sample ESCC_15

value: Male

tag: his type

value: well

tag: depth

tag: lymph node metastasis

value: negative


title: baseline subject 156

description: Sample 311


title: stimulated subject 156

description: Sample 312


title: Exp_ESCC_151


title: array 54

value: approx. 12 weeks

tag: liveweight

value: 28 kg

value: testis

tag: animal id

tag: androstenone related blup

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

value: missing value


title: array 65

tag: gender

tag: age

value: approx. 16 weeks

value: 49 kg

tag: development of seminiferous tubles

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 79

tag: breed

value: Duroc

value: 52 kg

tag: tissue

value: 8838 androstenone related BLUP:-0.22

value: 0.8 ng/ml

value: transition

tag: rna amount


title: array 47

value: boar - uncastrated

value: 31 kg

tag: mother id

value: immature


title: Exp_ESCC_152

description: matched with exome sequencing sample ESCC_16

value: Male

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis

value: positive


title: stimulated subject 154

description: Sample 308

value: male

tag: stimulus

value: stimulated

tag: status

value: case

tag: bmi


title: baseline subject 154

description: Sample 307

value: baseline


title: stimulated subject 158

description: Sample 316


title: Exp_ESCC_148

description: matched with exome sequencing sample ESCC_14

value: well


title: array 99

value: approx. 27 weeks

tag: liveweight

value: testis

tag: animal id

tag: plasma-testosterone

value: 3.5 ng/ml

tag: plasma-androstenone

tag: fat-androstenone

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Exp_ESCC_149

tag: gender

tag: age


title: array 62

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 16 weeks

value: 49 kg

tag: androstenone related blup

tag: development of seminiferous tubles

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes


title: stimulated subject 153

description: Sample 306


title: Exp_ESCC_145

description: matched with exome sequencing sample ESCC_12

value: Male

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis


title: baseline subject 153

description: Sample 305

value: male

tag: stimulus

tag: status

tag: bmi


title: Exp_ESCC_147

description: matched with exome sequencing sample ESCC_13

value: Female

value: positive


title: stimulated subject 152

description: Sample 304

value: stimulated

value: case


title: baseline subject 152

description: Sample 303

value: baseline


title: Exp_ESCC_144

description: matched with exome sequencing sample ESCC_11

value: negative


title: Exp_ESCC_146

value: poor


title: Exp_ESCC_141

value: well


title: array 89

value: approx. 27 weeks

tag: liveweight

tag: tissue

value: testis

tag: animal id

tag: mother id

tag: plasma-testosterone

value: 2,7 ng/ml

value: mature

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

tag: rna amount


title: stimulated subject 151

description: Sample 302

tag: gender

value: control

tag: age


title: stimulated subject 150

description: Sample 300


title: array 25

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 3 weeks

tag: androstenone related blup

tag: aged week (number of individuals)

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Exp_ESCC_143

description: matched with exome sequencing sample ESCC_10

value: Male

tag: his type

value: moderate

value: positive


title: Exp_ESCC_140

description: matched with exome sequencing sample ESCC_8

tag: depth

value: negative


title: array 98

value: approx. 25 weeks

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes


title: array 64

value: approx. 12 weeks

tag: liveweight

value: 29 kg

tag: tissue

value: immature


title: array 95

value: approx. 27 weeks

value: testis

tag: animal id

tag: mother id


title: array 6

value: approx. 1 weeks

value: calculated to be negative except for one individulal at 20 weeks of age

tag: rna amount


title: stimulated subject 159

description: Sample 318

tag: gender

value: male

tag: stimulus

value: stimulated

tag: status

value: control

tag: bmi


title: baseline subject 150

description: Sample 299

value: baseline

value: case

tag: age


title: baseline subject 149

description: Sample 297


title: baseline subject 151

description: Sample 301


title: Exp_ESCC_138

description: matched with exome sequencing sample ESCC_7

value: Male

tag: his type

tag: lymph node metastasis


title: Exp_ESCC_135

value: poor

tag: depth


title: array 52

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 16 weeks

value: 61 kg

tag: androstenone related blup

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: aged week (number of individuals)

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: baseline subject 147

description: Sample 293


title: stimulated subject 147

description: Sample 294


title: Exp_ESCC_162

description: matched with exome sequencing sample ESCC_52

value: moderate

value: negative


title: baseline subject 148

description: Sample 295


title: Exp_ESCC_137

value: positive


title: Exp_ESCC_134

description: matched with exome sequencing sample ESCC_6


title: stimulated subject 146

description: Sample 292


title: stimulated subject 149

description: Sample 298


title: Exp_ESCC_142

description: matched with exome sequencing sample ESCC_9

value: well


title: array 87

value: approx. 27 weeks

tag: liveweight

tag: tissue

value: testis

tag: animal id

value: 2.0 ng/ml

tag: development of seminiferous tubles

value: mature

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes


title: stimulated subject 148

description: Sample 296

tag: gender

value: male

tag: stimulus

value: stimulated

tag: status

value: control

tag: bmi


title: Exp_ESCC_133

description: matched with exome sequencing sample ESCC_5

value: Male

tag: age

tag: his type

tag: depth

tag: lymph node metastasis


title: array 35

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 3 weeks

tag: mother id

tag: androstenone related blup

tag: rna amount


title: Exp_ESCC_139


title: Exp_ESCC_136

value: Female


title: array 30

value: approx. 1 weeks

tag: tissue

tag: aged week (number of individuals)

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: baseline subject 146

description: Sample 291

value: baseline


title: array 67

value: approx. 20 weeks

tag: liveweight

value: 95 kg

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition


title: array 94

tag: gender

value: approx. 27 weeks

value: testis

value: missing value

value: mature

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes


title: array 61

tag: age

value: approx. 16 weeks

value: 47 kg

value: immature

value: calculated to be negative except for one individulal at 20 weeks of age


title: array 86

value: Duroc

value: boar - uncastrated

value: 80 kg


title: array 56

value: 53 kg

value: 0 ng/ml

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g


title: array 77

value: approx. 20 weeks

value: 79 kg

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: IAA 2h rep1

description: 6 day old arabidopsis roots

source_name: 6 day old roots placed on auxin medium for 2 hours

value: root


title: Exp_ESCC_132

value: Male

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis

value: negative


title: baseline subject 145

description: Sample 289

value: male

tag: stimulus

value: baseline

tag: status

value: control

tag: bmi


title: stimulated subject 145

description: Sample 290

value: stimulated


title: baseline subject 143

description: Sample 285


title: Exp_ESCC_128

description: matched with exome sequencing sample ESCC_4


title: Exp_ESCC_131


title: stimulated subject 142

description: Sample 284


title: baseline subject 144

description: Sample 287


title: baseline subject 141

description: Sample 281


title: Exp_ESCC_129

value: Female


title: array 85

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 27 weeks

tag: tissue

value: testis

tag: mother id

tag: androstenone related blup

value: 2.0 ng/ml

value: mature

tag: aged week (number of individuals)

value: calculated to be negative except for one individulal at 20 weeks of age

tag: rna amount


title: Exp_ESCC_130

value: poor

value: positive


title: array 51

value: approx. 16 weeks

tag: liveweight

value: 66 kg

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: immature

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 78

tag: gender

tag: age

value: approx. 20 weeks

value: 84 kg

value: 5.8 ng/ml

value: transition

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes


title: Exp_ESCC_125

description: matched with exome sequencing sample ESCC_3

value: Male

tag: his type

value: well

tag: depth

tag: lymph node metastasis

value: negative


title: array 92

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 27 weeks

tag: tissue

value: testis

tag: mother id


title: array 5

value: approx. 1 weeks

tag: androstenone related blup

tag: aged week (number of individuals)

value: calculated to be negative except for one individulal at 20 weeks of age

tag: rna amount


title: array 59

value: approx. 16 weeks

tag: liveweight

value: 69 kg

tag: animal id

tag: plasma-testosterone


title: Exp_ESCC_127

value: moderate

value: positive


title: stimulated subject 143

description: Sample 286

value: male

tag: stimulus

value: stimulated

tag: status

value: control

tag: bmi


title: stimulated subject 141

description: Sample 282

tag: gender

tag: age


title: baseline subject 142

description: Sample 283

value: baseline


title: Exp_ESCC_126

value: Male

tag: his type


title: array 60

value: 61 kg

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: immature

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Exp_ESCC_123

description: matched with exome sequencing sample ESCC_1

value: poor

tag: depth

tag: lymph node metastasis


title: Exp_ESCC_122


title: Exp_ESCC_124

description: matched with exome sequencing sample ESCC_2


title: array 63

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 12 weeks

value: 28 kg

tag: tissue

value: testis

tag: mother id

value: 8838 androstenone related BLUP:-0.22

tag: aged week (number of individuals)

tag: rna amount


title: array 15

value: approx. 3 weeks

tag: androstenone related blup

value: calculated to be negative except for one individulal at 20 weeks of age


title: stimulated subject 140

description: Sample 280

value: male

tag: stimulus

value: stimulated

tag: status

tag: bmi


title: stimulated subject 144

description: Sample 288

tag: gender

value: control

tag: age


title: Exp_ESCC_121

value: Female

tag: his type

value: well

value: negative


title: array 27

value: approx. 1 weeks

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g


title: baseline subject 140

description: Sample 279

value: baseline


title: array 18

value: Duroc

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Exp_ESCC_120

value: Male


title: baseline subject 139

description: Sample 277


title: stimulated subject 139

description: Sample 278


title: Exp_ESCC_119

value: moderate

value: positive


title: array 40

value: boar - uncastrated

value: approx. 12 weeks

tag: liveweight

value: 34 kg

value: testis

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: immature


title: Ts5 roots 2hr KNO3 nitrogen treated, biological rep3

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

institute: New York University

description: 3 Ts5 T.CEL

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix ATH1 GeneChip Arabidopsis Whole Genome Array in the Affymetrix Hybridization oven 640 following standard Affymetrix protocols. GeneChips were washed and stained using the 'EukGE-WS2v4_450' protocol in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner according to standard Affymetrix protocols.

data_processing: The data were analyzed with MAS5.0 as normal for Col0 data but with a modification to the normalisation method to enable a subset of probe sequences within each probe set to be excluded for non-Col0 data.  Probe sequences (within probe sets for each gene) whose signal values were not used were those predicted using our bioinformatic analysis not to hybridise non-Col0 RNA on the Col0 Affymetrix microarray due to sequence differences in the non-Col0 ecotypes; these were excluded to give a more accurate signal value for each gene in the non-Col0 ecotypes.  The probe sequences to be excluded were identified per experiment (i.e. an experiment consisted of the three replicate samples, e.g. Kas2 control, or Kas2 treat). Lists of probe sequences within each gene probeset that were not used for normalisation are supplied in text files (one per experiment) together with a key that denotes the probe numbers given in the experiment files to the Affymetrix probe IDs. On average, 10% of all probe sets were analysed with the complete set of 11 elements and a further 70% analysed with 9 or 10 elements. For example, in Kas2C_Probe_Elements_Removed, the first row is 4,1.  4,1 refers to probe number '4'.  The key for which probe number '4' is, is in the 'key' file and it corresponds to the probe name given on row 4. The same key file is used to interpret all of the other files.  The '1' means that the first element of this probeset was excluded from analysis.  The data was analysed within replicate sets, so for replicates 1, 2, and 3 of Kas2 C the same elements were removed. The reasoning for this is that we used all replicates to identify with best accuracy which elements were not hybridising normally.

source_name: 12 day old Arabidopsis Ts5 ecotype roots, 2 hr 5mM KNO3 nitrogen treated

label_protocol: Biotinylated cRNA from all isolated root samples were prepared according to the standard one-cycle Affymetrix protocol from 1 ug total RNA.

growth_protocol: Plants were grown for 12 days in long day (16hr light/8hr dark) 22 oC conditions in a Percival (Percival Scientific).  Plants were grown hydroponically in basal MS containing no nitrogen except 0.5mM ammonium succinate and 3mM sucrose.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to manufacturer's instructions.

treatment_protocol: At dawn on 12th day plants were either nitrogen-treated (KNO3 to 5mM added) or KCl treated (KCl to 5mM added) as a control treatment for 2 hrs. Whole roots were then harvested and frozen using liquid nitrogen.

tag: tissue

value: root

tag: ecotype

tag: agent

value: KNO3 nitrogen

value: 12 day old seedling roots


title: stimulated subject 138

description: Sample 276

value: male

value: stimulated

value: control


title: baseline subject 138

description: Sample 275

value: baseline


title: Ts5 roots 2hr KNO3 nitrogen treated, biological rep2

description: 2 Ts5 T.CEL


title: Exp_ESCC_116

value: poor

tag: depth

tag: lymph node metastasis

value: negative


title: array 72

tag: breed

value: Duroc

value: approx. 20 weeks

value: 92 kg

tag: mother id

tag: androstenone related blup

value: transition

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

tag: rna amount

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 42

tag: gender

value: boar - uncastrated

tag: age

value: approx. 12 weeks

tag: liveweight

value: 31 kg

value: testis

tag: animal id

value: missing value

value: immature


title: Exp_ESCC_118

value: Male

tag: his type

value: well


title: Ts5 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 Ts5 T.CEL

tag: tissue

value: root

value: KNO3 nitrogen

value: 12 day old seedling roots


title: stimulated subject 137

description: Sample 274

value: male

tag: stimulus

value: stimulated

tag: status

value: case

tag: bmi


title: Exp_ESCC_115

value: poor

tag: depth

tag: lymph node metastasis

value: negative


title: Exp_ESCC_117


title: stimulated subject 136

description: Sample 272

value: control


title: baseline subject 137

description: Sample 273

value: baseline


title: Exp_ESCC_113

value: Female

value: moderate

value: positive


title: Exp_ESCC_112


title: baseline subject 135

description: Sample 269


title: array 81

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 20 weeks

value: 87 kg

value: testis

tag: mother id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: baseline subject 136

description: Sample 271

tag: gender

value: male


title: array 74

tag: age

value: 85 kg

tag: androstenone related blup

value: 7.6 ng/ml

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

tag: rna amount


title: Exp_ESCC_111

value: Male

tag: his type

value: well


title: array 21

value: approx. 3 weeks

tag: tissue


title: Ts5 roots 2hr KCl control treated, biological rep1

description: 1 Ts5 C.CEL

source_name: 12 day old Arabidopsis Ts5 ecotype roots, 2 hr 5mM KCl control treated

value: root

tag: ecotype

tag: agent

value: KCl control

value: 12 day old seedling roots


title: stimulated subject 135

description: Sample 270

tag: stimulus

value: stimulated

tag: status

value: control

tag: bmi


title: array 100

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 27 weeks

tag: liveweight

tag: animal id

tag: mother id

tag: plasma-testosterone

tag: plasma-androstenone

value: immature


title: Exp_ESCC_110

tag: gender

tag: age

tag: depth

tag: lymph node metastasis

value: positive


title: array 75

value: approx. 20 weeks

value: testis

tag: androstenone related blup

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

tag: rna amount

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 68

tag: breed

value: 86 kg

tag: tissue

value: 3.4 ng/ml


title: Exp_ESCC_114

value: Male

tag: his type

value: well


title: baseline subject 134

description: Sample 267

value: male

tag: stimulus

value: baseline

tag: status

tag: bmi


title: stimulated subject 134

description: Sample 268

tag: gender

value: stimulated

value: control


title: Exp_ESCC_109

tag: age

value: moderate


title: array 49

value: Duroc

value: boar - uncastrated

value: approx. 12 weeks

tag: liveweight

value: 25 kg

tag: animal id

tag: mother id

tag: plasma-testosterone

tag: plasma-androstenone

value: missing value

value: immature


title: stimulated subject 133

description: Sample 266


title: array 29

value: approx. 1 weeks

value: testis

tag: androstenone related blup

tag: aged week (number of individuals)

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g


title: array 46

value: 34 kg

tag: fat-androstenone

tag: development of seminiferous tubles

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 96

tag: breed

value: approx. 27 weeks

tag: tissue

value: mature

tag: rna amount


title: Exp_ESCC_107

value: Male

tag: his type

value: well

tag: depth

tag: lymph node metastasis

value: positive


title: array 14

value: Duroc

tag: gender

tag: age

value: approx. 3 weeks


title: baseline subject 133

description: Sample 265

value: male

tag: stimulus

value: baseline

tag: status

value: control

tag: bmi


title: SQ8 roots 2hr KNO3 nitrogen treated, biological rep3

description: 3 SQ8 T.CEL

source_name: 12 day old Arabidopsis SQ8 ecotype roots, 2 hr 5mM KNO3 nitrogen treated

value: root

tag: ecotype

tag: agent

value: KNO3 nitrogen

value: 12 day old seedling roots


title: baseline subject 132

description: Sample 263


title: stimulated subject 132

description: Sample 264

value: stimulated


title: Exp_ESCC_104

value: Female

value: moderate


title: Exp_ESCC_106

value: negative


title: stimulated subject 131

description: Sample 262


title: SQ8 roots 2hr KNO3 nitrogen treated, biological rep1

description: 1 SQ8 T.CEL


title: Exp_ESCC_105


title: Exp_ESCC_103


title: baseline subject 131

description: Sample 261


title: array 32

value: boar - uncastrated

value: approx. 1 weeks

value: testis

tag: mother id

tag: androstenone related blup

tag: aged week (number of individuals)

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: stimulated subject 130

description: Sample 260


title: array 69

value: Duroc

value: approx. 20 weeks

tag: liveweight

value: 90 kg

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes


title: Exp_ESCC_102

tag: gender

value: Male

tag: age

tag: his type

value: well

tag: depth

tag: lymph node metastasis

value: positive


title: array 34

tag: breed

value: approx. 3 weeks

tag: tissue

tag: rna amount


title: Exp_ESCC_101

value: poor


title: HTCC1062_Control_Sta_N_rep1

city: Corvallis

first: Daniel

middle: Patrick

last: Smith

state: OR

address: 220 Nash Hall

department: Microbiology Department

institute: Oregon State University

hyb_protocol: 10 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package.

organism: Candidatus Pelagibacter communis

source_name: Carboy 7

label_protocol: RNA was labeled with biotin labeled nucleotides during the in-vitro transcription reaction.

growth_protocol: Artificial seawater media with no additional (Limted) or 20 µM(Control) NH4Cl, 500 µM pyruvate, 10 µM DMSP, 100 µM oxaloacetate, 50 µM phosphate, vitamins, and trace metals. Cells were grown at 16 °C with intermittent light and sparging with air.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 40 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

tag: nh3 availability

value: Control

tag: growth phase

value: Stationary


title: baseline subject 130

description: Sample 259

value: male

tag: stimulus

value: baseline

tag: status

value: control

tag: bmi


title: HTCC1062_Control_Sta_N_rep2

source_name: Carboy 8


title: HTCC1062_Control_Sta_N_rep3

source_name: Carboy 9


title: array 97

value: boar - uncastrated

value: approx. 27 weeks

tag: liveweight

value: testis

tag: animal id

tag: mother id

tag: androstenone related blup

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

value: mature

tag: aged week (number of individuals)

value: calculated to be negative except for one individulal at 20 weeks of age


title: array 13

value: Duroc

tag: gender

tag: age

value: approx. 1 weeks

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: stimulated subject 128

description: Sample 256

value: stimulated


title: baseline subject 128

description: Sample 255


title: baseline subject 129

description: Sample 257


title: stimulated subject 127

description: Sample 254


title: array 76

tag: breed

value: approx. 20 weeks

value: 93 kg

tag: tissue

tag: development of seminiferous tubles

value: transition

tag: rna amount


title: array 7


title: array 93

value: 9.5 ng/ml


title: Exp_ESCC_108

value: Male

tag: his type

value: moderate

tag: depth

tag: lymph node metastasis

value: positive


title: HTCC1062_Control_Exp_N_rep1

tag: nh3 availability

value: Control

tag: growth phase

value: Exponential


title: array 8

value: boar - uncastrated

value: testis

tag: mother id

tag: androstenone related blup


title: HTCC1062_Limited_Sta_N_rep1

source_name: Carboy 4

value: Nitrogen Limited

value: Stationary


title: array 24

value: Duroc

value: approx. 3 weeks

value: calculated to be negative except for one individulal at 20 weeks of age


title: array 50

value: approx. 16 weeks

tag: liveweight

value: 65 kg

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

value: immature

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: baseline subject 127

description: Sample 253

tag: gender

value: male

tag: stimulus

value: baseline

tag: status

value: control

tag: age

tag: bmi


title: HTCC1062_Control_Exp_N_rep3

value: Control


title: HTCC1062_Control_Exp_N_rep2

value: Exponential


title: baseline subject 126

description: Sample 251

value: case


title: stimulated subject 126

description: Sample 252

value: stimulated


title: array 2

tag: breed

value: boar - uncastrated

value: approx. 1 weeks

tag: tissue

value: testis

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

tag: rna amount


title: array 57

value: Duroc

value: 59 kg

tag: mother id

tag: androstenone related blup

tag: development of seminiferous tubles

value: transition


title: stimulated subject 125

description: Sample 250


title: array 16

value: approx. 3 weeks

value: calculated to be negative except for one individulal at 20 weeks of age


title: HTCC1062_Limited_Exp_N_rep2

source_name: Carboy 5

tag: nh3 availability

value: Nitrogen Limited

tag: growth phase


title: HTCC1062_Limited_Exp_N_rep1


title: HTCC1062_Limited_Exp_N_rep3

source_name: Carboy 6


title: baseline subject 125

description: Sample 249


title: stimulated subject 129

description: Sample 258


title: array 20

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: array 36


title: stimulated subject 124

description: Sample 248

value: male


title: array 22


title: 264-31149-E

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

data_processing: quantile normalized and variance transformed using LUMI package in R

source_name: PBMCs

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

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: treatment

value: vehicle (EtOH) + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: stimulated subject 122

description: Sample 244

tag: gender

tag: stimulus

value: control


title: baseline subject 124

description: Sample 247

value: baseline

tag: status

tag: age


title: 263-31149-D

value: dexamethasone + phytohemagglutinin


title: array 43

tag: breed

value: approx. 12 weeks

tag: liveweight

value: 33 kg

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

value: immature


title: array 48

value: boar - uncastrated

value: 34 kg

tag: tissue

value: testis

tag: mother id

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

tag: rna amount


title: array 26

value: Duroc

tag: androstenone related blup


title: array 90

tag: gender

value: approx. 27 weeks

tag: development of seminiferous tubles

value: mature


title: stimulated subject 121

description: Sample 242

tag: stimulus

value: stimulated

tag: status

tag: bmi


title: stimulated subject 123

description: Sample 246

tag: age


title: baseline subject 123

description: Sample 245


title: baseline subject 121

description: Sample 241


title: Col0 roots 2hr KCl control treated, biological rep1

description: 1 Col0 C.CEL

source_name: 12 day old Arabidopsis Col0 ecotype roots, 2 hr 5mM KCl control treated

value: root

tag: ecotype

tag: agent

value: KCl control

value: 12 day old seedling roots


title: baseline subject 122

description: Sample 243

value: male


title: HTCC1062_Limited_Sta_N_rep2

tag: nh3 availability

value: Nitrogen Limited

tag: growth phase

value: Stationary


title: array 3

tag: breed

value: approx. 1 weeks

tag: tissue

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Prim-5_5mM MTBE, bio rep 3

first: Josephine

middle: Ann

last: Bonventre

address: 1011 Agriculture & Life Sciences Building

department: Environmental & Molecular Toxicology

description:
30_HC.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at Prim-5

hyb_protocol: Hybridizations were performed in an Affymetrix GeneChip Hybridization Oven 640, washing and staining on the Affymetrix Fluidics Station 450 using the GCOS software and protocol EukGE-WS2V4_450.

scan_protocol: Scanning on the Affymetrix GeneChip Scanner using GCOS software and according to standard Affymetrix protocols.

data_processing: Agilent Technologies GeneSpring GX software

organism: Danio rerio

source_name: embryo at Prim-5_exposed to 5mM MTBE

label_protocol: Fragmentation and biotinylation: NuGEN Encore™ Biotin Module (p/n 4200-60) according to the manufacturer.

growth_protocol: Embryos were maintained at 25C for the duration of exposure.

extract_protocol: RNA extractions: RNeasy Mini Kit 250 (p/n 74106) with on-column DNase treatment (RNAse-free DNAse set, 50 rxn, p/n 79254); Reverse transcription and amplification: NuGEN WT-Ovation™ Pico System (p/n 3300-60); cDNA cleanup by Zymo Research DNA Clean & Concentrator -25 kit (p/n D4006).

treatment_protocol: Staged (1K cell stage) embryos were randomly assiged to a experimental group consisting of a time point and treatment. Each group consisted of 15 embryos which were pooled for 1 experimental replicate, with three replicates for each experimental group. Treatment with 0.00625, 0.625, 5mM MTBE or control was in a sealed glass vial beginning at approximately 3 hours post fertilization and ending at the assigned time point. Upon completion of the exposure, embryos were snap frozen in liquid nitrogen and stored at -80C until RNA was extracted.

value: whole embryo lysate

tag: genotype

tag: developmental stage

value: Prim-5; ~30hpf

tag: exposed to

value: 5mM MTBE


title: 259-31147-E

tag: treatment

value: vehicle (EtOH) + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: stimulated subject 120

description: Sample 240

tag: gender

value: control


title: array 10

value: Duroc

value: boar - uncastrated

value: testis

tag: mother id

tag: androstenone related blup

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

tag: rna amount


title: 261-31147-D

value: dexamethasone + phytohemagglutinin


title: Prim-5_5mM MTBE, bio rep 2

description:
30_HB.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at Prim-5


title: 257-31146-E


title: Prim-5_0.625mM MTBE, bio rep 3

description:
30_MC.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at Prim-5

source_name: embryo at Prim-5_exposed to 0.625mM MTBE

value: 0.625mM MTBE


title: array 17

tag: age

value: approx. 3 weeks


title: array 88

value: approx. 27 weeks

tag: liveweight

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

value: missing value ug/g

tag: development of seminiferous tubles

value: mature


title: baseline subject 120

description: Sample 239

source_name: whole blood

value: male

tag: stimulus

value: baseline

tag: status

tag: bmi


title: array 82

tag: breed

tag: gender

value: approx. 18 weeks

value: 65 kg

tag: tissue

value: immature

source_name: Testis_tissue_reference [pool of total rna from 40 animals]

value: calculated to be negative except for one individulal at 20 weeks of age

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: 255-31131-E

tag: treatment

value: vehicle (EtOH) + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: 254-31131-D


title: Prim-5_0.625mM MTBE, bio rep 2

description:
30_MB.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at Prim-5

value: whole embryo lysate

tag: genotype

tag: developmental stage

value: Prim-5; ~30hpf

tag: exposed to


title: stimulated subject 119

description: Sample 238

value: stimulated

value: control

tag: age


title: HTCC1062_Limited_Sta_N_rep3

tag: nh3 availability

value: Nitrogen Limited

tag: growth phase

value: Stationary


title: Prim-5_5mM MTBE, bio rep 1

description:
30_HA.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at Prim-5

value: 5mM MTBE


title: baseline subject 119

description: Sample 237


title: 256-31146-D

value: dexamethasone + phytohemagglutinin


title: array 23

value: Duroc

value: boar - uncastrated

value: approx. 1 weeks

value: testis

tag: mother id

tag: androstenone related blup

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

tag: mean steroid levels from phenotypes

tag: rna amount


title: Prim-5_0.00625mM MTBE, bio rep 3

description:
30_LC.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at Prim-5

source_name: embryo at Prim-5_exposed to 0.00625mM MTBE


title: Prim-5_0.625mM MTBE, bio rep 1

description:
30_MA.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at Prim-5

value: 0.625mM MTBE


title: array 80

tag: breed

value: approx. 16 weeks

tag: liveweight

value: 58 kg

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: immature

value: calculated to be negative except for one individulal at 20 weeks of age


title: 250-31100-E

tag: treatment

value: vehicle (EtOH) + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: stimulated subject 118

description: Sample 236

tag: gender

value: male

tag: stimulus

tag: status

tag: age

tag: bmi


title: array 39

value: approx. 12 weeks

value: 39 kg

tag: tissue

tag: mother id

tag: androstenone related blup

value: 2.4 ng/ml

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: baseline subject 118

description: Sample 235

value: baseline

value: control


title: stimulated subject 117

description: Sample 234

value: stimulated


title: 248-31090-E


title: array 83

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 20 weeks

tag: liveweight

value: 70 kg

tag: animal id

value: 8838 androstenone related BLUP:-0.22

value: transition

tag: mean steroid levels from phenotypes

tag: rna amount


title: 246-31029-E

tag: treatment


title: stimulated subject 116

description: Sample 232


title: array 4

value: approx. 1 weeks

value: testis

value: calculated to be negative except for one individulal at 20 weeks of age


title: 247-31090-D

value: dexamethasone + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: Prim-5_Control, bio rep 2

description:
30_CB.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at Prim-5

source_name: embryo at Prim-5_exposed to embryo media

value: whole embryo lysate

tag: genotype

tag: developmental stage

value: Prim-5; ~30hpf

tag: exposed to

value: embryo media (control)


title: baseline subject 117

description: Sample 233

tag: gender

value: male

tag: stimulus

tag: status

tag: age


title: Prim-5_0.00625mM MTBE, bio rep 1

description:
30_LA.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at Prim-5

tag: tissue


title: array 1

tag: mother id

tag: androstenone related blup

tag: aged week (number of individuals)

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: Prim-5_Control, bio rep 3

description:
30_CC.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at Prim-5


title: 252-31100-D


title: array 9

tag: breed

tag: androstenone related blup from individuals


title: PC-3 cells silenced for HIF1-α

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

institute: Fondazione IRCCS Istituto Nazionale Tumori

description:
PC-3 cells silenced for HIF1-α
PC-3_siHIF1-α
5252223019_H

data_processing: Using BeadStudio software v3 and BeadStudio expression analysis module v3.3.8, the summary intensity given by the average bead intensities among all beads belonging to a particular miRNA was calculated along with the detection p-value; data were quantile normalized and exported with neither background nor scale correction. Filtering was performed using BRB-ArrayTools Version: 4.2.0 - ?_2 (June 2011). We excluded signals with detection p-value>0.05, and miRNAs when a) less than 15 % of expression data had at least a 1.2-fold change in either direction from gene's median value or b) Percent of data missing or filtered out exceeded 30%.

source_name: PC-3 cells, derived from prostate adenocarcinoma metastasis

label_protocol: Total RNA (0.4 μg) was polyadenylated and converted to cDNA by standard methods. After PCR amplification, cDNA was fluorescent labelled using Cy3

extract_protocol: Trizol (Life technology), according to the manufacturer's protocol.

tag: cell line

value: silenced for HIF1-α

tag: emt status

value: epithelial


title: PC-3 cells silenced for HIF1-α, then stimulated with the conditioned medium from prostate cancer-associated fibroblasts

description:
PC-3 cells silenced for HIF1-α, then stimulated with the conditioned medium from human prostate cancer-associated fibroblasts (CAF)
PC-3_siHIF1-α+CAF
5252223019_I

tag: treatment


title: Prim-5_Control, bio rep 1

description:
30_CA.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at Prim-5


title: baseline subject 115

description: Sample 229

value: baseline

value: control

tag: bmi


title: stimulated subject 115

description: Sample 230

value: stimulated


title: 241-31025-E

value: vehicle (EtOH) + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: 21-somites_5mM MTBE, bio rep 3

description:
24_HC.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at 21-somites

source_name: embryo at 21-somites_exposed to 5mM MTBE

tag: genotype

tag: developmental stage

value: 21-somites; ~24hpf

value: 5mM MTBE


title: array 84

value: Duroc

tag: gender

value: boar - uncastrated

value: approx. 27 weeks

tag: liveweight

value: testis

tag: animal id

tag: plasma-testosterone

tag: plasma-androstenone

tag: fat-androstenone

tag: development of seminiferous tubles

value: transition

tag: mean steroid levels from phenotypes

tag: rna amount


title: 245-31029-D

value: dexamethasone + phytohemagglutinin


title: 243-31025-D


title: 238-31019-D


title: baseline subject 116

description: Sample 231

value: male

tag: stimulus

tag: status

tag: age


title: PC-3 cells silenced for COX-2

description:
PC-3 cells silenced for COX-2
PC-3_siCOX-2
5252223019_F

tag: cell line

tag: treatment

value: silenced for COX-2

tag: emt status


title: 21-somites_5mM MTBE, bio rep 2

description:
24_HB.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at 21-somites

tag: tissue

value: whole embryo lysate

tag: genotype

tag: exposed to


title: Prim-5_0.00625mM MTBE, bio rep 2

description:
30_LB.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at Prim-5

tag: developmental stage

value: Prim-5; ~30hpf


title: PC-3 cells silenced for COX-2, then stimulated with the conditioned medium from prostate cancer-associated fibroblasts

description:
PC-3 cells silenced for COX-2, then stimulated with the conditioned medium from human prostate cancer-associated fibroblasts (CAF)
PC-3_siCOX-2+CAF
5252223019_G

value: epithelial


title: PC-3 cells stimulated with the conditioned medium from prostate cancer-associated fibroblasts

description:
PC-3 cells stimulated with the conditioned medium from human prostate cancer-associated fibroblasts (CAF)
PC-3_CAF
5252223019_E

value: mesenchymal


title: 239-31019-E

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: PC-3 cells stimulated with the conditioned medium from prostatic fibroblasts, previously activated with IL-6

description:
PC-3 cells stimulated with the conditioned medium from human prostatic fibroblasts (HPF), previously activated with IL-6
PC-3_HPF+IL-6
5252223019_D


title: 21-somites_0.625mM MTBE, bio rep 2

description:
24_MB.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at 21-somites

source_name: embryo at 21-somites_exposed to 0.625mM MTBE

value: 0.625mM MTBE


title: 21-somites_0.625mM MTBE, bio rep 3

description:
24_MC.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at 21-somites


title: 237-31019-B

value: no treatment


title: PC-3 cells stimulated with the conditioned medium from prostatic fibroblasts, previously activated with TGF-β

description:
PC-3 cells stimulated with the conditioned medium from human prostatic fibroblasts (HPF), previously activated with TGF-β
PC-3_HPF+TGF-β
5252223019_C


title: 236-30942-E

value: vehicle (EtOH) + phytohemagglutinin


title: stimulated subject 113

description: Sample 226

tag: gender

value: stimulated

value: case

tag: bmi


title: baseline subject 113

description: Sample 225

value: baseline


title: PC-3 cells stimulated with the conditioned medium from prostatic fibroblasts

description:
PC-3 cells stimulated with the conditioned medium from human prostatic fibroblasts (HPF)
PC-3_HPF
5252223019_B


title: 235-30942-D


title: 21-somites_0.00625mM MTBE, bio rep 3

description:
24_LC.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at 21-somites

source_name: embryo at 21-somites_exposed to 0.00625mM MTBE

value: 21-somites; ~24hpf


title: stimulated subject 114

description: Sample 228

value: control


title: baseline subject 114

description: Sample 227


title: stimulated subject 112

description: Sample 224


title: baseline subject 112

description: Sample 223


title: 232-30925-D


title: 234-30942-B


title: 229-30925-E


title: 231-30925-B


title: 21-somites_0.625mM MTBE, bio rep 1

description:
24_MA.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at 21-somites


title: 21-somites_0.00625mM MTBE, bio rep 2

description:
24_LB.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at 21-somites


title: stimulated subject 111

description: Sample 222


title: 21-somites_0.00625mM MTBE, bio rep 1

description:
24_LA.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at 21-somites


title: Pt1_IL21

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

tag: patient

tag: disease state

value: CLL

tag: cell type

value: CD40-activated CLL cells

tag: agent


title: Pt1_CTR

value: CTR


title: 228-30814-E


title: Unstimulated PC-3 cells

description:
Unstimulated PC-3 cells
PC-3_Unstimulated
5252223019_A

value: Unstimulated


title: Pt13_IL21


title: baseline subject 111

description: Sample 221

value: male

tag: stimulus


title: stimulated subject 110

description: Sample 220

tag: status


title: baseline subject 110

description: Sample 219

tag: age


title: 21-somites_Control, bio rep 2

description:
24_CB.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at 21-somites

source_name: embryo at 21-somites_exposed to embryo media

value: whole embryo lysate

value: embryo media (control)


title: Pt13_CTR


title: 21-somites_Control, bio rep 1

description:
24_CA.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at 21-somites


title: stimulated subject 109

description: Sample 218


title: baseline subject 109

description: Sample 217


title: array 12

tag: breed

value: Duroc

value: boar - uncastrated

value: approx. 1 weeks

value: testis

tag: mother id

tag: androstenone related blup

tag: aged week (number of individuals)

tag: androstenone related blup from individuals

value: calculated to be negative except for one individulal at 20 weeks of age

tag: mean steroid levels from phenotypes

value: plasma testosterone 1.77 (± 0.19) ng/ml, plasma androstenone 13.86 (± 1.81)) ng/ml, androstenone in fat 1.74 (± 0.33) ug/g

tag: rna amount

value: RNA amount was limited and total RNA from another animal was added (Duroc, gender:boar - uncastrated, weight 69 kg, skatol levels low, id=39281)


title: 227-30814-D

tag: treatment

value: dexamethasone + phytohemagglutinin

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)


title: 225-30809-D


title: Pt12_CTR


title: 221-29929-E

value: vehicle (EtOH) + phytohemagglutinin


title: 6-somites_5mM MTBE, bio rep 3

description:
15_HC.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at 6-somites

source_name: embryo at 6-somites_exposed to 5mM MTBE

tag: tissue

tag: genotype

tag: developmental stage

value: 6-somites; ~15hpf

tag: exposed to

value: 5mM MTBE


title: 21-somites_5mM MTBE, bio rep 1

description:
24_HA.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at 21-somites

value: 21-somites; ~24hpf


title: 223-30809-E


title: Pt11_IL21

tag: patient

tag: disease state

value: CLL

tag: cell type

value: CD40-activated CLL cells

tag: agent


title: 220-29929-D


title: 6-somites_5mM MTBE, bio rep 1

description:
15_HA.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at 6-somites


title: stimulated subject 108

description: Sample 216

tag: gender

value: male

tag: stimulus

value: stimulated

tag: status

value: case

tag: age

tag: bmi


title: Pt11_CTR

value: CTR


title: baseline subject 108

description: Sample 215

value: baseline


title: Pt12_IL21


title: 6-somites_0.625mM MTBE, bio rep 3

description:
15_MC.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at 6-somites

source_name: embryo at 6-somites_exposed to 0.625mM MTBE

value: whole embryo lysate

value: 0.625mM MTBE


title: 219-29928-E


title: 6-somites_0.625mM MTBE, bio rep 2

description:
15_MB.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at 6-somites


title: 6-somites_5mM MTBE, bio rep 2

description:
15_HB.CEL
gene expression of zebrafish embryos exposed to 5mM MTBE and collected at 6-somites


title: Pt10_IL21


title: Pt10_CTR


title: Pt9_IL21


title: 218-29928-D


title: stimulated subject 107

description: Sample 214


title: baseline subject 107

description: Sample 213


title: 6-somites_0.00625mM MTBE, bio rep 2

description:
15_LB.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at 6-somites

source_name: embryo at 6-somites_exposed to 0.00625mM MTBE


title: Pt8_IL21


title: 216-29787-D


title: 6-somites_0.625mM MTBE, bio rep 1

description:
15_MA.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at 6-somites


title: 6-somites_0.00625mM MTBE, bio rep 3

description:
15_LC.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at 6-somites


title: Pt8_CTR


title: stimulated subject 105

description: Sample 210


title: stimulated subject 106

description: Sample 212


title: 6-somites_0.00625mM MTBE, bio rep 1

description:
15_LA.CEL
gene expression of zebrafish embryos exposed to 0.00625mM MTBE and collected at 6-somites


title: baseline subject 105

description: Sample 209


title: 6-somites_Control, bio rep 3

description:
15_CC.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at 6-somites

source_name: embryo at 6-somites_exposed to embryo media

value: embryo media (control)


title: 211-29786-D

source_name: PBMCs


title: baseline subject 106

description: Sample 211


title: 209-29784-D


title: 210-29784-E


title: 6-somites_Control, bio rep 2

description:
15_CB.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at 6-somites


title: 21-somites_Control, bio rep 3

description:
24_CC.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at 21-somites


title: Pt9_CTR


title: 214-29787-E


title: baseline subject 104

description: Sample 207


title: stimulated subject 104

description: Sample 208


title: 6-somites_Control, bio rep 1

description:
15_CA.CEL
gene expression of zebrafish embryos exposed to embryo media (control) and collected at 6-somites


title: Pt7_CTR


title: 207-29779-D


title: Pt6_CTR


title: CD4+ T cell of LP

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: IL-10 +/- mouse LPL.

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

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: lamina propria CD4+ T cells, IL-10 +/-

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

extract_protocol: miRNA samples were extracted from cells using the miRNA Isolation kit (Ambion).

treatment_protocol: Single-cell suspensions of lamina propria lymphocytes were prepared by an enzymatic dissociation method using collagenase. CD4+ T cells of SP and LP were isolated by the MACS system (Miltenyi).

tag: background/strain

value: female

value: 10 weeks

value: lamina propria

value: CD4+ T cells


title: Pt7_IL21

first: Loris

last: De Cecco

address: via Venezian 1

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software


title: stimulated subject 103

description: Sample 206


title: stimulated subject 102

description: Sample 204


title: 203-29776-E

value: vehicle (EtOH) + phytohemagglutinin


title: CD4+ T cell of SP

description: IL-10 +/- mouse spleen.

source_name: spleen CD4+ T cells, IL-10 +/-

value: spleen


title: 205-29779-E


title: Pt6_IL21


title: baseline subject 103

description: Sample 205


title: 202-29776-D

value: dexamethasone + phytohemagglutinin


title: baseline subject 102

description: Sample 203


title: 200-29633-D


title: 198-29628-D


title: baseline subject 100

description: Sample 199


title: stimulated subject 101

description: Sample 202


title: baseline subject 101

description: Sample 201


title: 201-29633-E


title: 194-29623-E