title: HRG 04h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0004h00m00s.r01

source_name: 6KR HRG 04h00m Rep1

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

tag: cell type

tag: disease

tag: derived from metastatic site

tag: age

tag: gender


title: HRG 06h00m Rep2

status: Public on Dec 01 2014

type: RNA

city: Yokohama

first: Mariko

last: Okada-Hatakeyama

state: KANAGAWA

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0006h00m00s.r02

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: The data were analyzed with GeneChip Operating System (GCOS) (ver.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The Single-Array Expression Analysis function was used and the trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 6KR HRG 06h00m Rep2

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: cell line

tag: tissue

value: mammary gland; breast

value: epithelial

value: adenocarcinoma

value: pleural effusion

value: 69 years adult

value: female

tag: ethnicity

value: Caucasian

tag: agent

value: HRG

tag: time


title: subject 203, group C, stimulation B, time 0 days 8659387160_F

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

department: Jenner Institute

country: United Kingdom

institute: University of Oxford

hyb_protocol: Illumina HT-12 v4 kit according to manufacturer's instructions

scan_protocol: Illumina iScan machine scanned to produce summary idat files. Idat files read by genome studio with no correction or background subtraction

data_processing: Data processing done in R using the following packages: limma (excluding probes with detection p value >0.05 in all samples) and normalising with neqc using the control probes.

source_name: PBMC

label_protocol: Ambion Illumina Totalprep  and Illumina chip kits according to manufacturer's instructions

extract_protocol: Qiagen RNeasy kit according to instructions including DNase I digest

treatment_protocol: PBMC extracted in and cryopreserved. PBMC thawed and rested overnight with benzonase then counted on a casy counter and 1-2 million cells stimulated with R10 media alone (U) or with 1-4 million cfu of SSI BCG (B) for 12 hours. PBMC pelleted and frozen in 350uL Qiagen RLT buffer containing beta-mercaptoethanol.

value: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: ArthrospiraPCC8005_control5000Gy-1

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Arthrospira sp. PCC8005 control condition non-irradiated for 5000Gy

hyb_protocol: Hybridization mixture with 2µg Cy3-labeled cDNA was subsequently prepared. Samples were hybridized to Arthrospira_ HX12 array (Nimblegen) for 18 hours at 42 ºC.

scan_protocol: The arrays were washed and scanned in a Roche-Nimblegen MS 200 scanner. Raw data files (Pair and XYS files) were obtained from images using DEVA software (Roche-Nimblegen).

data_processing: Raw data were pre-processed using the “Oligo” package (version 1.24) in BioConductor (version 2.12 / R version 3.0.1) as follows: i) background correction based on the Robust Multichip Aver-age (RMA) convolution model (Irizarry et al., 2003), ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), and iii) summarization of multiple probe intensities for each probe set to one expression value per gene using the median polish approach (Irizarry et al., 2003). To test for differential expression between the different irradiated conditions and the reference conditions (no irradiation) the Bayesian adjusted t-statistics was used as implemented in the “LIMMA” package (version 2.18.0)(Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini & Hochberg, 1995). Transcripts were considered significantly differentially expressed when the corresponding adjusted p-value was lower than 0.05 and their absolute FC was equal or larger than 2 for upregulated genes, and equal or miner than 0.5 for the down regulated ones. Gene annotation was curated manually.

organism: Limnospira indica PCC 8005

label_protocol: RNA extracts and the new designed Arthrospira HX12 arrays (Nimblegen) microarray chips were provided to IRBB in Barcelona. cDNA library preparation and amplification were performed from 25 ng total RNA using the Complete Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich), according to the instructions of the manufacturer, with 17 cycles of amplification, resulting in microgram quantities of cDNA. Labelling and hybridization of the cDNA onto the microarray, were performed according to Roche-Nimblegen expression guide v5p1. For each sample, 1µg cDNA was labelled by Cy3 nonamers primers and Klenow polymerization.

growth_protocol: The strain of Arthrospira sp. PCC 8005 was obtained from Pasteur Culture Collection. Three in-dependent cultures (n=3) were used for irradiation. They were grown separately on a rotatory shaker in an incubator at 30°C (Binder KBW 400), in 500 ml Zarrouk medium (Zarrouk) to mid-exponential corresponding to an OD750 ~1. Cultures were illuminated with a photon flux density of ~ 42 µE m -2 s-1 provided by three Osram daylight tubes. The cultures were then divided at 50 ml/flask into thirty vented cell culture flasks (CELLSTAR® Filter Cap Cell Culture Flasks) which were also divided into two parts as controls and samples for irradiation

extract_protocol: Due to the high exopolysaccharide and secondary metabolites content of Arthrospira, that inter-fers with the yield and quality of extracted RNA, the RNA extraction procedure had to be opti-mized. In total, 30 ml of irradiated and control Arthrospira cultures were centrifuged 20 min at 10000 g. Cell pellets were frozen immediately at -80°C, until analysis (ca. 5 days). The breakage of the cells was done by applying a heat shock procedure. Cells resuspended in Trizol (Invitro-gen), were incubated at 95°C for 5 min and then submerged immediately on ice for additional 5 min. Next, the released RNA was separated from the cell debris by centrifugation (Eppendorf) at (10000 g, 10 min) at 4°C. RNA purification was performed using the Direct-zol RNA miniprep 2050 from (Zymosearch) following the manufacturer's instructions. RNA samples (150 µg) were then treated 30 min at 37°C using DNAse (TURBO DNA-free™, Ambion) following the manu-facturer's instructions. The RNA was concentrated using RNA Clean & Concentrator™-25 (Zy-mosearch). RNA quatity and purity was assessed by spectrophotometric analysis using NanoDrop ND-1000 Spectrophotometer (Thermo scientific). The quality and integrity of RNA was assessed using the Bioanalyzer 2100 (Agilent) according to manufacturer's instructions.  It is worthwhile to mention, that the Bioanalyser RNA profiles for Arthrospira are however different from standard profiles obtained for most other bacteria, as the rRNA profile for Arthrospira  contains 3 fragments (3 peaks) instead of 2, representing 16S and 23S rRNA, as has also been reported with Nostoc punctiforme (Pinto et al., 2009).

treatment_protocol: The irradiation was performed using RITA facility at the Belgian Reactor N°2 (BR2) (Supple-mentary Figure 1). The irradiation was done in dark, inside a closed canister, surrounded by four sources of 60Co gamma rays (Energy of 1.33 Mev and 1.17 Mev). Different doses of gamma rays were given at a constant dose rate of 527 Gy/h. “Scheme 1 supplementary file” illustrate the dif-ferent tested doses and the occurred irradiation time. The temperature inside the irradiation canis-ter was automatically monitored and ranged between 26-27°C. The time required for irradiation was dose-dependent and so respective controls were kept at the same conditions as irradiated samples. All analyses were performed immediately (i.e. within 1 hour) after irradiation.

tag: treatment

value: 0 Gy


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_26

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Gene expression data from PBMCs isolated from whole blood.

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays (Freeman et al. in BMC Biol 2012, 10:90). Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 was performed according to Affymetrix protocols.

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor. Then, normalized probeset data were transformed by RMA algorithm.

organism: Sus scrofa

source_name: PBMC, HR, day 28

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer's protocol. After DNaseI treatment, the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Vaccination, 1 ml (30 IU) of tetanus toxoid (Equilis Tetanus-Vaccine).

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

value: male

value: tetanus vaccination

tag: sampling time point

value: day 28

tag: pig identifier


title: subject 228, group C, stimulation B, time 0 days 8670586019_H

tag: cell type


title: ArthrospiraPCC8005_control3200Gy-1

description: Arthrospira sp. PCC8005 control condition non-irradiated for 3200Gy


title: ArthrospiraPCC8005_control3200Gy-2

source_name: Arthrospira sp. PCC8005 control condition non-irradiated for 3200Gy


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_24

source_name: PBMC, LR, day 28

value: low-reactive


title: HRG 03h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0003h00m00s.r02

source_name: 6KR HRG 03h00m Rep2

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

tag: age

tag: gender


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_22


title: subject 202, group C, stimulation U, time 7 days 8670586019_F

tag: time (days)

value: U


title: subject 227, group C, stimulation B, time 7 days 8670586019_G

tag: stimulation


title: HRG 02h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0002h00m00s.r02

source_name: 6KR HRG 02h00m Rep2

tag: tissue

value: pleural effusion

value: 69 years adult

value: female

tag: ethnicity

value: Caucasian

tag: agent

value: HRG

tag: time


title: HRG 03h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0003h00m00s.r01

source_name: 6KR HRG 03h00m Rep1


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_21

tag: breed

value: German Landrace

tag: treatment


title: HRG 02h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090529.hgu133plus.MCF7E1_6KR.HRG_0905.0002h00m00s.r01

source_name: 6KR HRG 02h00m Rep1


title: N2 on idr-1 RNAi replicate 2

city: New Delhi

first: Arnab

last: Mukhopadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description: Gene expression of idr-1 RNAi treated N2 worms at L4 stage

hyb_protocol: Standard Agilent procedures

scan_protocol: Standard Agilent procedures

data_processing: Feature Extraction Software 9.1 (Agilent)

organism: Caenorhabditis elegans

source_name: whole organism total RNA isolated, idr-1 RNAi treated, replicate-2

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

growth_protocol: RNAi plates were prepared by supplementing Nematode Growth Media (NGM) media with 100 µg/ml ampicillin and 2 mM IPTG. RNAi bacteria were grown overnight at 37°C in LB media supplemented with 100 µg/ml ampicillin and 12.5 µg/ml tetracycline. The next day, the cultures were diluted (1:50) in LB containing 100 µg/ml ampicillin and grown at 37°C until an OD600 of 0.9. The bacterial pellets were resuspended in 1X PBS (phosphate-buffered saline) containing 1 mM IPTG. About 200 µl of the bacterial suspension was seeded onto the RNAi plates. The seeded plates were dried at RT for 2-3 days and stored at 4°C till further use.

extract_protocol: RNA was isolated using Trizol (Invitrogen, USA).  Briefly, worms grown on vector or RNAi of interest were washed off the plates with M9 buffer. Then, 0.3 ml of Trizol reagent was added and the worms lysed by vigorous vortexing. RNA was purified by phenol:chloroform:isoamylalcohol extraction and ethanol precipitation. The concentration and the purity of the RNA were determined using Bioanalyzer (Agilent, USA). Alternatively, the quality of the ribosomal 28 S and 18 S on an agarose gel was used as a measure of integrity and the absorbance at 260/280 nm was used to determine quantity.

treatment_protocol: Strains for RNA isolation were initially grown on E. coli OP50. Gravid adult worms were bleached and the eggs were hatched on plates containing respective RNAi bacteria. For sample collection L4 staged worms were washed off the plates with M9 buffer.

tag: larvae stage

value: L4 stage


title: subject 228, group C, stimulation U, time 7 days 8670586019_E

value: PBMC

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_20

tag: cell type

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

value: male

value: tetanus vaccination

tag: sampling time point

tag: pig identifier


title: HRG 01h30m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.HRG_0905.0001h30m00s.r02

source_name: 6KR HRG 01h30m Rep2

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

tag: disease

tag: derived from metastatic site

tag: age

tag: gender


title: N2 on control RNAi replicate 2

description: Gene expression of control RNAi treated N2 worms at L4 stage

source_name: whole organism total RNA isolated, Control RNAi treated, replicate-2


title: subject 222, group C, stimulation U, time 2 days 8670586019_C

tag: time (days)

tag: stimulation


title: subject 225, group C, stimulation U, time 2 days 8670586019_D


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_18

tag: breed

value: low-reactive

tag: treatment

value: day 28


title: subject 223, group C, stimulation U, time 2 days 8670586019_A

value: U

tag: group


title: HRG 01h30m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.HRG_0905.0001h30m00s.r01

source_name: 6KR HRG 01h30m Rep1

tag: tissue

value: epithelial

value: adenocarcinoma

value: pleural effusion

value: 69 years adult

tag: ethnicity

tag: agent

tag: time


title: subject 224, group C, stimulation U, time 14 days 8670586019_B

tag: cell type

tag: volunteer

tag: bcg quantity (pcr)


title: N2 on control RNAi replicate 1

source_name: whole organism total RNA isolated, Control RNAi treated, replicate-1

tag: larvae stage


title: N2 on idr-1 RNAi replicate 1

source_name: whole organism total RNA isolated, idr-1 RNAi treated, replicate-1


title: Rescue 02

city: Brussels

first: benjamin

last: beck

address: route de Lennik 808

institute: ULB

description: Rescue 1363

hyb_protocol: The microarrays have been performed by facilities (IRB FGC Barcelona)

organism: Mus musculus

source_name: FACS sorted tumor epithelial cells Twist1/p53 cKO 02

growth_protocol: DMBA/TPA induced skin tumors

extract_protocol: Qiagen RNA purification microkit

treatment_protocol: TAM 5x2mg

tag: genotype/variation

value: 5x 2mg TAMOXIFEN

tag: isolation

value: FACS

tag: staining

value: Epcam+/Lin-/DAPI-

value: tumor epithelial cells


title: HRG 01h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.HRG_0905.0001h00m00s.r02

source_name: 6KR HRG 01h00m Rep2

tag: cell line

tag: disease

tag: derived from metastatic site

tag: age

tag: gender

value: female

value: Caucasian

value: HRG


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_15

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

tag: Sex

value: male

tag: treatment

value: tetanus vaccination

tag: sampling time point

tag: pig identifier


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_17

tag: cell type

value: high-reactive

value: day 28


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_19


title: Rescue 01

description: Rescue 1362

scan_protocol: The microarrays have been performed by facilities (IRB FGC Barcelona)

source_name: FACS sorted tumor epithelial cells Twist1/p53 cKO 01


title: subject 225, group C, stimulation B, time 14 days 8659387174_L

source_name: PBMC

value: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: CTRL Rescue 01

description: CTRL 1364

data_processing: The microarrays have been performed by facilities (IRB FGC Barcelona)

source_name: FACS sorted tumor epithelial cells CTRL from Rescue 01

tag: genotype/variation

tag: isolation

tag: staining


title: subject 235, group C, stimulation B, time 14 days 8659387174_K


title: HRG 01h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.HRG_0905.0001h00m00s.r01

source_name: 6KR HRG 01h00m Rep1

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

tag: tissue

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

value: pleural effusion

tag: age

value: 69 years adult

tag: ethnicity

tag: agent

tag: time


title: HRG 00h30m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.HRG_0905.0000h30m00s.r02

source_name: 6KR HRG 00h30m Rep2

tag: cell type

tag: gender

value: female

value: Caucasian


title: CTRL Rescue 02

description: CTRL 1365

source_name: FACS sorted tumor epithelial cells CTRL from Rescue 02

label_protocol: The microarrays have been performed by facilities (IRB FGC Barcelona)

tag: treatment

value: 5x 2mg TAMOXIFEN

value: FACS

value: Epcam+/Lin-/DAPI-

value: tumor epithelial cells


title: HRG 00h30m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.HRG_0905.0000h30m00s.r01

source_name: 6KR HRG 00h30m Rep1

value: HRG


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_23

source_name: PBMC, HR, day 28

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

value: tetanus vaccination

tag: sampling time point

value: day 28

tag: pig identifier


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_16

source_name: PBMC, LR, day 28

value: low-reactive


title: subject 203, group C, stimulation B, time 14 days 8659387174_J

value: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: EGF 08h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.EGF_0905.0008h00m00s.r02

source_name: 6KR EGF 08h00m Rep2

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

tag: tissue

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

value: pleural effusion

tag: age

value: 69 years adult

value: EGF


title: subject 204, group C, stimulation B, time 7 days 8659387174_H

tag: cell type


title: subject 227, group C, stimulation U, time 0 days 8659387174_E

value: U


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_13

value: German Landrace

value: male

tag: treatment


title: EGF 04h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.EGF_0905.0004h00m00s.r02

source_name: 6KR EGF 04h00m Rep2

tag: gender

value: female

tag: ethnicity

value: Caucasian

tag: agent

tag: time


title: subject 228, group C, stimulation U, time 14 days 8659387174_F


title: EGF 08h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.EGF_0905.0008h00m00s.r01

source_name: 6KR EGF 08h00m Rep1


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_12

description: Gene expression data from PBMCs isolated from whole blood.

tag: breed

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

value: tetanus vaccination

tag: sampling time point

value: day 28

tag: pig identifier


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_14

value: low-reactive


title: BrafCa/Ca Soft Tissue Sarcoma 1

city: Durham

first: Jeffrey

last: Mito

state: NC

country: USA

institute: Duke University Medical Center

description: Primary sarcoma

hyb_protocol: Following fragmentation, cRNA is hybridized for 16 hours at 45c on  Mouse genome 430A 2.0 arrays and underwent automated washing and staining on the fluidics station.

scan_protocol: Genechips were scanned using the GeneChip Scanner 3000 7g

data_processing: All data was analyzed using the RMA algorithm was used to normalize data.

source_name: Primary soft tissue sarcoma generated from conditional alleles of Braf and p53

label_protocol: Biotynlated cRNA was generated using Ambion messageAmp premier kit, per manufacturer's protocol

growth_protocol: Tumors were generated in BrafCa;p53Flox/Flox mice by injection with an Adenovirus expressing Cre-recombinase as described previously (Kirsch DG, et al. Nat. Med 2007).

extract_protocol: TRIzol extraction of total RNA per manufacturer's protocol followed by RNA purification using the Qiagen Rneasy kit, per manufacturer's protocol

tag: genotype

value: Braf Ca/Ca; p53 Fl/Fl

value: muscle


title: BrafCa/Ca Soft Tissue Sarcoma 3

description: Primary sarcoma


title: BrafCa/Ca Soft Tissue Sarcoma 2

description: Primary sarcoma


title: EGF 06h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.EGF_0905.0006h00m00s.r02

source_name: 6KR EGF 06h00m Rep2

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

value: epithelial


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_10


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_11


title: subject 203, group C, stimulation B, time 7 days 8659387174_G

value: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_09

value: German Landrace

tag: cell type

tag: treatment


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_08

value: male


title: EGF 04h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.EGF_0905.0004h00m00s.r01

source_name: 6KR EGF 04h00m Rep1

tag: tissue

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

value: pleural effusion

tag: age

value: 69 years adult

tag: gender

value: female

tag: ethnicity

value: EGF


title: BrafCa/+ Soft Tissue Sarcoma 1

description: Primary sarcoma

value: Braf Ca/+; p53 Fl/Fl


title: subject 227, group C, stimulation U, time 2 days 8659387174_D

value: U


title: EGF 06h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090528.hgu133plus.MCF7E1_6KR.EGF_0905.0006h00m00s.r01

source_name: 6KR EGF 06h00m Rep1

value: Caucasian

tag: agent

tag: time


title: BrafCa/+ Normal Muscle

description: Normal Muscle from non-tumor bearing limb

source_name: Normal Muscle isolated from non-tumor bearing hind limb

tag: genotype

value: muscle


title: BrafCa/Ca Soft Tissue Sarcoma 5

description: Primary sarcoma

value: Braf Ca/Ca; p53 Fl/Fl


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_07

tag: breed

value: peripheral blood mononuclear cells

tag: temperament group

value: low-reactive

tag: Sex

value: tetanus vaccination

tag: sampling time point

value: day 28

tag: pig identifier


title: subject 225, group C, stimulation U, time 7 days 8659387174_A

value: PBMC

tag: time (days)

tag: stimulation

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: EGF 03h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0003h00m00s.r02

source_name: 6KR EGF 03h00m Rep2

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

tag: tissue

value: mammary gland; breast

tag: cell type

value: epithelial

tag: disease

tag: derived from metastatic site


title: EGF 03h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0003h00m00s.r01

source_name: 6KR EGF 03h00m Rep1

value: adenocarcinoma

value: pleural effusion

tag: age

value: 69 years adult

tag: gender

tag: ethnicity

tag: agent

tag: time


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_05

tag: breed

value: German Landrace

tag: temperament group

tag: Sex

value: female

tag: treatment

tag: sampling time point


title: subject 204, group C, stimulation B, time 14 days 8659387155_L

source_name: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group

tag: volunteer


title: aox1a:rpoTmp MLD stressed rep 3

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

description: Gene expression from Arabidopsis leaves of 4-week old aox1a:rpoTmp mutant plants, 4 d after moderate light and drought (MLD) stress.

hyb_protocol: Following fragmentation, aRNA was hybridized, washed and stained as per manufacterers' instructions.

scan_protocol: GeneChips were scanned using the approved Affymetrix scanner.

data_processing: Data was first analyzed with Gene expression console (MAS 5.0) to determine presence/absence (i.e. above background) expression. Only probesets present in 2 or more replicates were retained. Partek Genomics Suite (v6.5) was used to carry out GC-RMA normalisation of data and this was used for further analysis.

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves from 4-week old aox1a:rpoTmp mutant plants, 4 d after moderate light and drought (MLD) stress.

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

growth_protocol: Arabidopsis plants were grown for 4/5/6-7 weeks at 22°C for 16 h at 100 μE m-2 s 1 light conditions and 8 h of dark (standard conditions).

extract_protocol: Total RNA was extraced using the Qiagen Rneasy Plant RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: 4-week-old plants (aox1a and WT), 5 week old rpoTmp mutant lines and 6 to 7 week old aox1a:rpoTmp plants that were grown under standard conditions (with watering every 2 d) were then transferred to either moderate light conditions (approximately 350 μE m-2 s-1) with no water (starting 4 d prior to transfer to ensure that soil was dry) (MLD) or maintained in normal growth conditions (untreated).

tag: tissue

value: leaf

tag: genotype

value: aox1a:rpoTmp mutant

value: 4-week old plants


title: subject 222, group C, stimulation U, time 14 days 8659387174_B

tag: cell type

value: U

tag: bcg quantity (pcr)


title: subject 217, group C, stimulation U, time 0 days 8659387174_C


title: aox1a:rpoTmp MLD stressed rep 2

tag: age


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_03

value: peripheral blood mononuclear cells

value: high-reactive

value: male

value: tetanus vaccination

tag: pig identifier


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_06

value: day 28


title: subject 235, group C, stimulation B, time 7 days 8659387155_J

value: PBMC

value: C


title: WT(Col0), MLD stressed (control for aox1a:rpoTmp) rep 2

description: Gene expression from Arabidopsis leaves of 4-week old WT (Col0) plants, 4 d after moderate light and drought (MLD) stress. Control for aox1a:rpoTmp plants.

source_name: Arabidopsis leaves from 4-week old WT (Col0) plants, 4 d after moderate light and drought (MLD) stress. Control for aox1a:rpoTmp plants.


title: aox1a:rpoTmp MLD stressed rep 1


title: EGF 01h30m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0001h30m00s.r01

source_name: 6KR EGF 01h30m Rep1

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

tag: gender

tag: ethnicity

value: Caucasian

tag: agent

value: EGF


title: subject 224, group C, stimulation B, time 2 days 8659387155_K

value: B


title: EGF 02h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0002h00m00s.r01

source_name: 6KR EGF 02h00m Rep1

value: pleural effusion

value: 69 years adult

value: female

tag: time


title: EGF 01h30m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0001h30m00s.r02

source_name: 6KR EGF 01h30m Rep2


title: EGF 02h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0002h00m00s.r02

source_name: 6KR EGF 02h00m Rep2


title: BrafCa/Ca Normal Muscle

value: Braf Ca/Ca; p53 Fl/Fl

value: muscle


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_01

source_name: PBMC, HR, day 28

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

tag: treatment

tag: sampling time point


title: subject 234, group C, stimulation B, time 7 days 8659387155_I

value: PBMC

tag: time (days)

tag: stimulation

tag: group

tag: volunteer


title: PBMC response to tetanus toxoid, HR, day 28, Phenomics_04

tag: cell type

value: tetanus vaccination

value: day 28

tag: pig identifier


title: WT(Col0), MLD stressed (control for aox1a:rpoTmp) rep 1

tag: tissue

value: leaf

tag: genotype

tag: age

value: 4-week old plants


title: EGF 01h00m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0001h00m00s.r01

source_name: 6KR EGF 01h00m Rep1

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

tag: gender

tag: ethnicity


title: PBMC response to tetanus toxoid, LR, day 28, Phenomics_02

source_name: PBMC, LR, day 28

tag: breed

tag: temperament group

value: low-reactive

tag: Sex


title: aox1a:rpoTmp untreated rep 3

description: Gene expression from Arabidopsis leaves of 4-week old aox1a:rpoTmp mutant plants, 4 d after continued growth in standard (UT) conditions.

source_name: Arabidopsis leaves from 4-week old aox1a:rpoTmp mutant plants, 4 d after continued growth in standard (UT) conditions.

value: aox1a:rpoTmp mutant

value: 5-week old plants


title: EGF 01h00m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0001h00m00s.r02

source_name: 6KR EGF 01h00m Rep2

value: pleural effusion

value: 69 years adult

value: female

value: Caucasian

tag: agent

value: EGF

tag: time


title: aox1a:rpoTmp untreated rep 2


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_48

source_name: PBMC, HR, day 14

value: German Landrace

value: peripheral blood mononuclear cells

value: high-reactive

value: male

tag: treatment

tag: sampling time point

value: day 14


title: subject 228, group C, stimulation B, time 2 days 8659387155_H

tag: cell type

value: PBMC

tag: time (days)

tag: stimulation

value: B

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: subject 234, group C, stimulation U, time 14 days 8659387155_F

value: U


title: subject 217, group C, stimulation B, time 14 days 8659387155_G


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_45

source_name: PBMC, LR, day 14

value: low-reactive

value: tetanus vaccination

tag: pig identifier


title: EGF 00h30m Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0000h30m00s.r01

source_name: 6KR EGF 00h30m Rep1

tag: cell line

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

tag: tissue

value: mammary gland; breast

value: epithelial

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

tag: age


title: EGF 00h30m Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.EGF_0905.0000h30m00s.r02

source_name: 6KR EGF 00h30m Rep2

value: pleural effusion

value: 69 years adult

tag: gender

value: female

tag: ethnicity

value: Caucasian


title: aox1a:rpoTmp untreated rep 1

value: leaf

tag: genotype

value: aox1a:rpoTmp mutant

value: 5-week old plants


title: subject 202, group C, stimulation U, time 14 days 8659387155_E

value: PBMC


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_43

description: Gene expression data from PBMCs isolated from whole blood.

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

tag: treatment

value: day 14


title: WT(Col0), untreated (control for aox1a:rpoTmp) rep 2

description: Gene expression from Arabidopsis leaves of 4-week old WT (Col0) plants, 4 d after continued growth in standard (UT) conditions. Control for aox1a:rpoTmp plants.

source_name: Arabidopsis leaves from 4-week old WT (Col0) plants, 4 d after continued growth in standard (UT) conditions. Control for aox1a:rpoTmp plants.


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_41

tag: cell type

value: low-reactive

value: tetanus vaccination

tag: sampling time point


title: WT(Col0), MLD stressed (control for aox1a:rpoTmp) rep 3

value: 4-week old plants


title: Control Rep2

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.Ctr001_0905.0000h00m00s.r02

source_name: 6KR no treated 00h00m Rep2

value: 6KR-EGFR expressing MCF7 (Originally, wild-type MCF7 was obtained from ATCC (American Type Culture Collection)

value: mammary gland; breast

value: epithelial

tag: agent

value: control (untreated)

tag: time


title: subject 223, group C, stimulation U, time 0 days 8659387155_D

source_name: PBMC

tag: time (days)

tag: stimulation

value: U

tag: group

value: C

tag: volunteer

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_44

value: female

tag: pig identifier


title: Femoral_258 restenotic lesion from 122

city: Kuopio

first: Einari

last: Aavik

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Gene expression data from restenotic lesion

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) 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: Femoral artery atherectomy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Expression 3'- Amplification for IVT Labeling kit, Affymetrix).

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

tag: age

tag: gender

value: male

tag: tissue

value: restenotic lesion


title: Femoral_239 restenotic lesion from 28


title: WT(Col0), untreated (control for aox1a:rpoTmp) rep 3

value: leaf

tag: genotype

value: 5-week old plants


title: Control Rep1

description:
From early to late gene expression (30min to 8hour) induced by growth hormone stimulation.
090526.hgu133plus.MCF7E1_6KR.Ctr001_0905.0000h00m00s.r01

source_name: 6KR no treated 00h00m Rep1

tag: cell line

tag: disease

value: adenocarcinoma

tag: derived from metastatic site

value: pleural effusion

value: 69 years adult

tag: ethnicity

value: Caucasian


title: subject 225, group C, stimulation U, time 0 days 8659387155_C

tag: cell type

value: PBMC


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_39

tag: breed

value: German Landrace

value: peripheral blood mononuclear cells

tag: temperament group

value: high-reactive

tag: Sex

tag: treatment

value: tetanus vaccination

tag: sampling time point

value: day 14


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_40


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_42


title: WT(Col0), untreated (control for rpoTmp) rep 3

description: Gene expression from Arabidopsis leaves of 4-week old WT (Col0) plants, 4 d after continued growth in standard (UT) conditions. Control for rpoTmp plants.

source_name: Arabidopsis leaves from 4-week old WT (Col0) plants, 4 d after continued growth in standard (UT) conditions. Control for rpoTmp plants.

value: 4-week old plants


title: Femoral_206 restenotic lesion from 21


title: subject 217, group C, stimulation U, time 7 days 8659387155_A

tag: time (days)

tag: stimulation

value: U

tag: group

value: C

tag: volunteer


title: WT(Col0), untreated (control for rpoTmp) rep 1

tag: age


title: WT(Col0), untreated (control for aox1a:rpoTmp) rep 1

tag: tissue


title: subject 234, group C, stimulation B, time 2 days 8659387174_I

value: B

tag: bcg quantity (pcr)


title: BrafCa/+ Soft Tissue Sarcoma 2

description: Primary sarcoma

source_name: Primary soft tissue sarcoma generated from conditional alleles of Braf and p53

tag: genotype

value: Braf Ca/+; p53 Fl/Fl

value: muscle


title: Femoral_159 restenotic lesion from 50

tag: gender

value: female

value: restenotic lesion


title: Femoral_195 restenotic lesion from 79

value: male


title: subject 223, group C, stimulation B, time 7 days 8659387151_L


title: subject 202, group C, stimulation U, time 0 days 8659387155_B


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_38

tag: pig identifier


title: subject 204, group C, stimulation B, time 0 days 8659387151_K


title: WT(Col0), untreated (control for rpoTmp) rep 2

value: leaf


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_37

value: low-reactive


title: WT(Col0), MLD stressed (control for rpoTmp) rep 1

description: Gene expression from Arabidopsis leaves of 4-week old WT (Col0) plants, 4 d after moderate light and drought (MLD) stress. Control for rpoTmp plants.

source_name: Arabidopsis leaves from 4-week old WT (Col0) plants, 4 d after moderate light and drought (MLD) stress. Control for rpoTmp plants.


title: WT(Col0), MLD stressed (control for rpoTmp) rep 2


title: WT(Col0), MLD stressed (control for rpoTmp) rep 3


title: subject 202, group C, stimulation B, time 2 days 8659387151_I

value: PBMC


title: rpoTmp(line 2) untreated rep 2

description: Gene expression from Arabidopsis leaves of 4-week old rpoTmp mutant plants (line 2), 4 d after continued growth in standard (UT) conditions.

source_name: Arabidopsis leaves from 4-week old rpoTmp mutant plants (line 2), 4 d after continued growth in standard (UT) conditions.

value: rpoTmp mutant

value: 5-week old plants


title: Femoral_79 primary lesion

description: Gene expression data from primary atherosclerotic lesion

value: primary atherosclerotic lesion


title: rpoTmp(line 2) MLD stressed rep 2

description: Gene expression from Arabidopsis leaves of 4-week old rpoTmp mutant plants (line 2), 4 d after moderate light and drought (MLD) stress.

source_name: Arabidopsis leaves from 4-week old rpoTmp mutant plants (line 2), 4 d after moderate light and drought (MLD) stress.


title: subject 222, group C, stimulation B, time 7 days 8659387151_G


title: Femoral_21 primary lesion


title: Femoral_50 primary lesion


title: subject 203, group C, stimulation B, time 2 days 8659387151_H


title: subject 203, group C, stimulation U, time 0 days 8659387151_F


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_36

value: German Landrace

value: peripheral blood mononuclear cells

value: tetanus vaccination


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_33

value: day 14


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_35

value: high-reactive


title: rpoTmp(line 2) untreated rep 1


title: subject 222, group C, stimulation U, time 0 days 8659387151_E

value: U

value: C


title: PC-3_cultured in spheroid

city: Tokyo

first: Tetsuo

last: Mashima

address: 3-8-31, Ariake,Koto-ku

institute: JFCR

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: Human prostate cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The cell line was cultured in vitro in 10cm dishes until 80-90% confluency and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: no treatment.

tag: cell line

tag: culture condition

value: spheroid  culture conditions


title: rpoTmp(line 2) MLD stressed rep 1


title: PC-3_cultured in 2D

value: normal 2D conditions


title: Femoral_28 primary lesion

value: female


title: subject 217, group C, stimulation U, time 2 days 8659387151_C

tag: cell type


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_32

tag: breed

tag: temperament group


title: subject 235, group C, stimulation U, time 2 days 8659387151_D


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_31

tag: Sex

tag: treatment


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_34

tag: sampling time point


title: PC-3_expressing shTRIB1-2

tag: genotype/variation

value: TRIB1 depletion


title: rpoTmp(line 1) untreated rep 2

description: Gene expression from Arabidopsis leaves of 4-week old rpoTmp mutant plants (line 1), 4 d after continued growth in standard (UT) conditions.

source_name: Arabidopsis leaves from 4-week old rpoTmp mutant plants (line 1), 4 d after continued growth in standard (UT) conditions.

value: leaf


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_30

value: low-reactive


title: subject 224, group C, stimulation U, time 7 days 8659387151_B

value: PBMC

tag: time (days)

tag: stimulation

tag: group


title: WT(Col0), untreated (control for aox1a) rep 3

description: Gene expression from Arabidopsis leaves of 4-week old WT (Col0) plants, 4 d after continued growth in standard (UT) conditions. Control for aox1a plants.

source_name: Arabidopsis leaves from 4-week old WT (Col0) plants, 4 d after continued growth in standard (UT) conditions. Control for aox1a plants.

tag: tissue

tag: age

value: 4-week old plants


title: PC-3_expressing shGFP

value: control


title: subject 227, group C, stimulation U, time 14 days 8659387151_A

tag: volunteer

tag: bcg quantity (pcr)


title: rpoTmp(line 1) MLD stressed rep 2

description: Gene expression from Arabidopsis leaves of 4-week old rpoTmp mutant plants (line 1), 4 d after moderate light and drought (MLD) stress.

source_name: Arabidopsis leaves from 4-week old rpoTmp mutant plants (line 1), 4 d after moderate light and drought (MLD) stress.

tag: genotype

value: rpoTmp mutant

value: 5-week old plants


title: subject 219, group A, stimulation B, time 7 days 9235792101_L

value: B

value: A


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_29

source_name: PBMC, HR, day 14

value: German Landrace

value: peripheral blood mononuclear cells

value: tetanus vaccination

value: day 14

tag: pig identifier


title: rpoTmp(line 1) untreated rep 1


title: rpoTmp(line 1) MLD stressed rep 1


title: subject 251, group A, stimulation B, time 7 days 9235792101_J


title: PC-3_expressing shTRIB1-1

tag: cell line


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_27

tag: cell type

value: high-reactive

value: male


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_26

tag: breed


title: WT(Col0), untreated (control for aox1a) rep 1


title: BreastCancer_EndocrineResistant_Biopsy_R61_mRNA

city: Cambridge

first: Alexey

middle: A

last: Larionov

state: Cambridgeshire

address: Box 238, Lv 6 Addenbrooke's Treatment Centre, Cambridge BioMedical Campus

department: School of Clinical Medicine

institute: The University of Cambridge

hyb_protocol: Modifyed Illumina hybridization protocol adapted to the NuGen amplification and labelling procedure.  The hybridization temperature was reduced to account for weaker cDNA-cDNA pairing strength as described in J.D.Heath et al.: Nugen's WT-ovation FFPE system coupled with a novel labelling protocol enables genome-wide gene expression profiling of FFPE samples on the illumina beadarray platform (Illumina Application Note # 2. NuGEN Technologies, Inc: p. M01069_FFPE_IllumApp Note2_ 10/07a)

scan_protocol: Standard Illumina scanning protocol

data_processing: Non-processed data were exported from Genome Studio; then data were normalised using background correction, variance-stabilisoing transformation and quantile normalisation as implemented in default settings of lumiExpresso() function from lumi R-package.

source_name: Clinical biopsy of breast cancer taken at the time of endocrine resistance

label_protocol: RNA was amplified using NuGen WT-Ovation FFPE kit v2 and biotinilated according to the NuGen procedure approved by Illumina for use with their mRNA micrioarrays, as described in J.D.Heath et al.: Nugen's WT-ovation FFPE system coupled with a novel labelling protocol enables genome-wide gene expression profiling of FFPE samples on the illumina beadarray platform (Illumina Application Note # 2. NuGEN Technologies, Inc: p. M01069_FFPE_IllumApp Note2_ 10/07a)

extract_protocol: RNA was extracted using miRNEasy Qiagen kits, followed by DNase treatment in accordance with the manufactirer's recommendations. Quality control was performed with NanoDrop and Agilent Bioanalyser.

value: Clinical biopsy of breast cancer


title: subject 246, group A, stimulation B, time 0 days 9235792101_I


title: subject 213, group A, stimulation B, time 14 days 9235792101_K


title: subject 242, group A, stimulation B, time 7 days 9235792101_H


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_28

source_name: PBMC, LR, day 14

tag: temperament group


title: BreastCancer_EndocrineResistant_Biopsy_R85_mRNA


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_24

tag: Sex

value: female


title: BreastCancer_EndocrineResistant_Biopsy_R16_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R98_mRNA


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_25

tag: treatment


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_23

tag: sampling time point


title: WT(Col0), untreated (control for aox1a) rep 2

value: leaf


title: BreastCancer_EndocrineResistant_Biopsy_R86_mRNA


title: WT(Col0), MLD stressed (control for aox1a) rep 3

description: Gene expression from Arabidopsis leaves of 4-week old WT (Col0) plants, 4 d after moderate light and drought (MLD) stress. Control for aox1a plants.

source_name: Arabidopsis leaves from 4-week old WT (Col0) plants, 4 d after moderate light and drought (MLD) stress. Control for aox1a plants.


title: WT(Col0), MLD stressed (control for aox1a) rep 2


title: WT(Col0), MLD stressed (control for aox1a) rep 1


title: aox1a(line 2) untreated rep 1

description: Gene expression from Arabidopsis leaves of 4-week old aox1a mutant plants (line 2), 4 d after continued growth in standard (UT) conditions.

source_name: Arabidopsis leaves from 4-week old aox1a mutant plants (line 2), 4 d after continued growth in standard (UT) conditions.

value: aox1a mutant


title: subject 246, group A, stimulation U, time 7 days 9235792101_F

source_name: PBMC

value: PBMC

value: U


title: subject 237, group A, stimulation B, time 7 days 9235792101_G


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_21

value: low-reactive


title: BreastCancer_EndocrineResistant_Biopsy_R97_mRNA


title: subject 220, group C, stimulation U, time 7 days 9235792101_E

value: C


title: aox1a(line 2) MLD stressed rep 1

description: Gene expression from Arabidopsis leaves of 4-week old aox1a mutant plants (line 2), 4 d after moderate light and drought (MLD) stress.

source_name: Arabidopsis leaves from 4-week old aox1a mutant plants (line 2), 4 d after moderate light and drought (MLD) stress.

value: 4-week old plants


title: aox1a(line 2) untreated rep 2


title: BreastCancer_EndocrineResistant_Biopsy_R75_mRNA


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_19


title: subject 219, group A, stimulation U, time 2 days 9235792101_D


title: BreastCancer_EndocrineResistant_Biopsy_R51_mRNA


title: aox1a(line 2) MLD stressed rep 2


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_22


title: subject 250, group A, stimulation U, time 7 days 9235792101_B


title: subject 250, group A, stimulation U, time 0 days 9235792101_C


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_17


title: BreastCancer_EndocrineResistant_Biopsy_R79_mRNA


title: subject 237, group A, stimulation U, time 2 days 9235792101_A


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_18


title: BreastCancer_EndocrineResistant_Biopsy_R45_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R77_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R64_mRNA


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_20


title: BreastCancer_EndocrineResistant_Biopsy_R54_mRNA


title: subject 220, group C, stimulation B, time 14 days 9235792083_L

value: B


title: aox1a(line 1) untreated rep 2

description: Gene expression from Arabidopsis leaves of 4-week old aox1a mutant plants (line 1), 4 d after continued growth in standard (UT) conditions.

source_name: Arabidopsis leaves from 4-week old aox1a mutant plants (line 1), 4 d after continued growth in standard (UT) conditions.


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_15

description: Gene expression data from PBMCs isolated from whole blood.


title: aox1a(line 1) untreated rep 1


title: BreastCancer_EndocrineResistant_Biopsy_R07_mRNA


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_16


title: aox1a(line 1) MLD stressed rep 2

description: Gene expression from Arabidopsis leaves of 4-week old aox1a mutant plants (line 1), 4 d after moderate light and drought (MLD) stress.

source_name: Arabidopsis leaves from 4-week old aox1a mutant plants (line 1), 4 d after moderate light and drought (MLD) stress.


title: subject 213, group A, stimulation B, time 2 days 9235792083_K

value: A


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_14

value: German Landrace


title: aox1a(line 1) MLD stressed rep 1


title: BreastCancer_EndocrineResistant_Biopsy_R92_mRNA


title: WT seedlings, biological replicate 2

city: Ciudad de Buenos Aires

first: Pablo

last: Cerdan

address: Avda Patricias Argentinas 435

country: Argentina

institute: Leloir Institute Foundation

description: Gene expression data from 10d-old seedlings

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

source_name: Arabidopsis seedlings at floral induction stage

label_protocol: Biotinylated cRNA labelling was made from 5 ug total RNA according to Affymetrix protocols

extract_protocol: Total RNA was prepared using Qiagen RNeasy Plant Mini Kit according to the manufacturer's instructions.

value: Whole seedlings (leaves + roots)

value: wild type

tag: cultivar

value: Columbia

value: 10 days-old seedlings


title: subject 237, group A, stimulation B, time 14 days 9235792083_I

tag: time (days)


title: BreastCancer_EndocrineResistant_Biopsy_R02_mRNA


title: subject 258, group A, stimulation B, time 14 days 9235792083_J

tag: stimulation


title: BreastCancer_EndocrineResistant_Biopsy_R32_mRNA


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_13

value: peripheral blood mononuclear cells

value: high-reactive

value: male

value: tetanus vaccination

value: day 14


title: WT seedlings, biological replicate 1


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_10


title: WT seedlings, biological replicate 3


title: subject 220, group C, stimulation B, time 0 days 9235792083_H

value: PBMC

tag: group


title: subject 213, group A, stimulation B, time 0 days 9235792083_G


title: BreastCancer_EndocrineResistant_Biopsy_R89_mRNA

tag: tissue

value: Clinical biopsy of breast cancer


title: subject 242, group A, stimulation U, time 14 days 9235792083_E

value: U


title: BreastCancer_EndocrineResistant_Biopsy_R59_mRNA


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_11

value: low-reactive


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_09


title: gis5 seedlings, biological replicate 3

tag: age


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_12


title: subject 212, group A, stimulation U, time 14 days 9235792083_D

tag: volunteer


title: BreastCancer_EndocrineResistant_Biopsy_R88_mRNA


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_08


title: subject 251, group A, stimulation U, time 0 days 9235792083_C

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_06

value: female


title: BreastCancer_EndocrineResistant_Biopsy_R83_mRNA


title: gis5 seedlings, biological replicate 1

tag: genotype


title: subject 231, group A, stimulation B, time 2 days 9235792078_L

value: B


title: subject 210, group A, stimulation B, time 2 days 9235792078_J

value: A


title: BreastCancer_EndocrineResistant_Biopsy_R34_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R47_mRNA


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_04

value: German Landrace

tag: pig identifier


title: gis5 seedlings, biological replicate 2

value: Whole seedlings (leaves + roots)


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_03


title: BreastCancer_EndocrineResistant_Biopsy_R78_mRNA


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_07


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_02


title: subject 212, group A, stimulation U, time 0 days 9235792083_B


title: subject 231, group A, stimulation B, time 14 days 9235792078_I


title: subject 231, group A, stimulation U, time 0 days 9235792083_A


title: BreastCancer_EndocrineResistant_Biopsy_R31_mRNA


title: subject 212, group A, stimulation B, time 7 days 9235792078_H


title: BreastCancer_EndocrineResistant_Biopsy_R13_mRNA


title: PBMC response to tetanus toxoid, LR, day 14, Phenomics_05


title: BreastCancer_EndocrineResistant_Biopsy_R67_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R42_mRNA


title: subject 237, group A, stimulation U, time 0 days 9235792078_C


title: PBMC response to tetanus toxoid, HR, day 14, Phenomics_01


title: PBMC response to tetanus toxoid, day 0, Phenomics_48

source_name: PBMC, HR, day 0

value: day 0


title: PBMC response to tetanus toxoid, day 0, Phenomics_46

source_name: PBMC, LR, day 0


title: BreastCancer_EndocrineResistant_Biopsy_R82_mRNA


title: subject 219, group A, stimulation U, time 0 days 9235792078_A


title: subject 242, group A, stimulation U, time 2 days 9235792078_D


title: subject 213, group A, stimulation B, time 7 days 9235792078_G


title: PBMC response to tetanus toxoid, day 0, Phenomics_47


title: BreastCancer_EndocrineResistant_Biopsy_R81_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_43


title: BreastCancer_EndocrineResistant_Biopsy_R53_mRNA


title: subject 246, group A, stimulation U, time 2 days 9235792078_B


title: PBMC response to tetanus toxoid, day 0, Phenomics_45


title: PBMC response to tetanus toxoid, day 0, Phenomics_44


title: BreastCancer_EndocrineResistant_Biopsy_R80_mRNA


title: subject 212, group A, stimulation B, time 2 days 9235792074_K


title: BreastCancer_EndocrineResistant_Biopsy_R76_mRNA


title: subject 210, group A, stimulation B, time 0 days 9235792074_I


title: subject 210, group A, stimulation B, time 14 days 9235792074_J


title: BreastCancer_EndocrineResistant_Biopsy_R74_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_42


title: subject 242, group A, stimulation B, time 0 days 9235792074_G


title: PBMC response to tetanus toxoid, day 0, Phenomics_41


title: BreastCancer_EndocrineResistant_Biopsy_R73_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_39


title: PBMC response to tetanus toxoid, day 0, Phenomics_40


title: BreastCancer_EndocrineResistant_Biopsy_R68_mRNA


title: subject 219, group A, stimulation U, time 14 days 9235792074_D


title: PBMC response to tetanus toxoid, day 0, Phenomics_38


title: BreastCancer_EndocrineResistant_Biopsy_R43_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R65_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R71_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R60_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_37


title: subject 251, group A, stimulation U, time 14 days 9235792074_C


title: PBMC response to tetanus toxoid, day 0, Phenomics_36


title: subject 220, group C, stimulation U, time 2 days 9235792074_A

value: C


title: BreastCancer_EndocrineResistant_Biopsy_R70_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_35


title: subject 219, group A, stimulation U, time 7 days 8803836002_L


title: BreastCancer_EndocrineResistant_Biopsy_R41_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_34


title: BreastCancer_EndocrineResistant_Biopsy_R69_mRNA


title: PA080_8764_090423

type: genomic

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

description: Hybridized to SNP6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: BioDiscovery Nexus Copy Number 6.0 and default settings and SNP Rank segmentation, human genome version GRCh37/hg19 and default HAPMAP-based reference file.

label: Biotin

molecule: genomic DNA

source_name: colon cancer primary tumour tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: QIAamp DNA mini kit.

value: colon cancer

tag: Stage

value: MSS


title: subject 258, group A, stimulation U, time 2 days 9235792074_E

tag: cell type


title: subject 213, group A, stimulation U, time 14 days 8803836002_K


title: PA080_94_090621

description: Hybridized to SNP6.0 array

value: MSI-L


title: subject 251, group A, stimulation U, time 7 days 8803836002_J


title: PA080_6930_090423

description: Hybridized to SNP6.0 array


title: PA080_7_111123

description: Hybridized to SNP6.0 array

value: MSI-H


title: PA080_7422_090303

description: Hybridized to SNP6.0 array


title: PA080_668_090319

description: Hybridized to SNP6.0 array


title: subject 258, group A, stimulation U, time 0 days 9235792074_B


title: PA080_6289_090304

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_32

tag: breed

value: peripheral blood mononuclear cells

value: tetanus vaccination


title: PBMC response to tetanus toxoid, day 0, Phenomics_31

tag: temperament group


title: PA080_68_090621

description: Hybridized to SNP6.0 array


title: BreastCancer_EndocrineResistant_Biopsy_R35_mRNA


title: PA080_8528_090423

description: Hybridized to SNP6.0 array


title: subject 246, group A, stimulation U, time 0 days 8803836002_I

value: PBMC


title: PA080_55_090621

description: Hybridized to SNP6.0 array


title: subject 237, group A, stimulation U, time 7 days 8803836002_G


title: BreastCancer_EndocrineResistant_Biopsy_R15_mRNA

value: Clinical biopsy of breast cancer


title: PA080_6484_090319

description: Hybridized to SNP6.0 array


title: subject 242, group A, stimulation U, time 7 days 8803836002_H

value: U


title: PA080_57_090621

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_33

value: low-reactive

tag: Sex


title: PBMC response to tetanus toxoid, day 0, Phenomics_29

value: high-reactive

value: female

tag: treatment


title: BreastCancer_EndocrineResistant_Biopsy_R08_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R29_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R18_mRNA


title: PA080_51_111209

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_26

value: male

tag: sampling time point


title: PA080_8585_090318

description: Hybridized to SNP6.0 array


title: BreastCancer_EndocrineResistant_Biopsy_R04_mRNA


title: PA080_53_120816

description: Hybridized to SNP6.0 array


title: subject 220, group C, stimulation B, time 7 days 8803836002_E

value: B


title: BreastCancer_EndocrineResistant_Biopsy_R40_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_30

value: German Landrace


title: subject 250, group A, stimulation B, time 0 days 8803836002_C

value: A


title: PBMC response to tetanus toxoid, day 0, Phenomics_27

value: day 0


title: subject 246, group A, stimulation B, time 7 days 8803836002_F


title: PBMC response to tetanus toxoid, day 0, Phenomics_25


title: PA080_5_120816

description: Hybridized to SNP6.0 array

value: colon cancer


title: subject 219, group A, stimulation B, time 2 days 8803836002_D


title: PBMC response to tetanus toxoid, day 0, Phenomics_28


title: PA080_47_111123

description: Hybridized to SNP6.0 array

value: MSS


title: subject 250, group A, stimulation B, time 7 days 8803836002_B


title: BreastCancer_EndocrineResistant_Biopsy_R44_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R06_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R33_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_24


title: PBMC response to tetanus toxoid, day 0, Phenomics_23


title: subject 213, group A, stimulation U, time 2 days 8803836001_K


title: subject 237, group A, stimulation B, time 2 days 8803836002_A


title: BreastCancer_EndocrineResistant_Biopsy_R46_mRNA


title: PA080_5126_090303

description: Hybridized to SNP6.0 array


title: PA080_49_111206

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_21


title: PBMC response to tetanus toxoid, day 0, Phenomics_22


title: PA080_47_090618

description: Hybridized to SNP6.0 array


title: subject 237, group A, stimulation U, time 14 days 8803836001_I


title: subject 258, group A, stimulation U, time 14 days 8803836001_J


title: BreastCancer_EndocrineResistant_Biopsy_R48_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R72_mRNA


title: PA080_4440_090303

description: Hybridized to SNP6.0 array


title: BreastCancer_EndocrineResistant_Biopsy_R14_mRNA


title: PA080_45_111220

description: Hybridized to SNP6.0 array


title: subject 213, group A, stimulation U, time 0 days 8803836001_G


title: BreastCancer_EndocrineResistant_Biopsy_R01_mRNA


title: subject 242, group A, stimulation B, time 14 days 8803836001_E


title: PBMC response to tetanus toxoid, day 0, Phenomics_17


title: PA080_9_111214

description: Hybridized to SNP6.0 array


title: BreastCancer_EndocrineResistant_Biopsy_R56_mRNA


title: BreastCancer_EndocrineResistant_Biopsy_R62_mRNA


title: PBMC response to tetanus toxoid, day 0, Phenomics_18


title: PA080_5374_090304

description: Hybridized to SNP6.0 array


title: subject 231, group A, stimulation B, time 7 days 8803836001_F


title: PBMC response to tetanus toxoid, day 0, Phenomics_19


title: PBMC response to tetanus toxoid, day 0, Phenomics_16


title: subject 220, group C, stimulation U, time 0 days 8803836001_H

value: C


title: PBMC response to tetanus toxoid, day 0, Phenomics_20


title: PA080_43_111123

description: Hybridized to SNP6.0 array


title: IPF Patient 6

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

description: SAMPLE 12556

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio

label_protocol: Standard Illumina Protocol

growth_protocol: IPF fibroblasts were outgrown from lung tissue obtained by surgical lung biopsy of patients with IPF.  All segments were confirmed histologically to show the characteristic histopathologic pattern termed usual interstitial pneumonia.  Control fibroblasts were cultured from histologically normal regions of lung from age-matched patients undergoing resection for lung nodules.

extract_protocol: Genomic DNA was extracted using Qiagen Dneasy kit; 1 microgram DNA was bisulfite converted using Zymo Research EZ DNA Methylation kit

treatment_protocol: Fibroblasts were cultured and examined at passages 4-5.

tag: disease

value: idiopathic pulmonary fibrosis


title: subject 251, group A, stimulation B, time 0 days 8803836001_C

tag: time (days)


title: IPF Patient 5

description: SAMPLE 12555


title: PBMC response to tetanus toxoid, day 0, Phenomics_15

value: peripheral blood mononuclear cells


title: subject 212, group A, stimulation B, time 14 days 8803836001_D

tag: stimulation


title: PA080_4263_090311

description: Hybridized to SNP6.0 array

value: MSI-H


title: PBMC response to tetanus toxoid, day 0, Phenomics_14

value: tetanus vaccination


title: IPF Patient 4

description: SAMPLE 12554


title: IPF Patient 3

description: SAMPLE 12553


title: subject 231, group A, stimulation B, time 0 days 8803836001_A

value: PBMC

tag: group


title: subject 212, group A, stimulation B, time 0 days 8803836001_B


title: PBMC response to tetanus toxoid, day 0, Phenomics_12


title: IPF Patient 2

description: SAMPLE 12552


title: PBMC response to tetanus toxoid, day 0, Phenomics_11


title: PA080_37_120816

description: Hybridized to SNP6.0 array

tag: tissue


title: subject 231, group A, stimulation U, time 2 days 8803828068_L

value: U


title: subject 210, group A, stimulation U, time 2 days 8803828068_J


title: PA080_39_111206

description: Hybridized to SNP6.0 array

value: MSI-L


title: PBMC response to tetanus toxoid, day 0, Phenomics_13

value: high-reactive


title: PA080_3949_090311

description: Hybridized to SNP6.0 array


title: PA080_3850_090213

description: Hybridized to SNP6.0 array


title: Control Patient 2

description: SAMPLE 12545

value: Unaffected


title: subject 212, group A, stimulation U, time 7 days 8803828068_H


title: PA080_336_120322

description: Hybridized to SNP6.0 array


title: subject 231, group A, stimulation U, time 14 days 8803828068_I


title: IPF Patient 1

description: SAMPLE 12551


title: Control Patient 3

description: SAMPLE 12547


title: PBMC response to tetanus toxoid, day 0, Phenomics_08

value: low-reactive

value: male


title: PA080_33_120816

description: Hybridized to SNP6.0 array


title: subject 250, group A, stimulation U, time 2 days 8803828068_K


title: PA080_353_090621

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_10

value: German Landrace


title: subject 213, group A, stimulation U, time 7 days 8803828068_G

value: A


title: PA080_3003_090319

description: Hybridized to SNP6.0 array


title: Commercial Cell Line 2

description: SAMPLE 12540

tag: cell line


title: Commercial Cell Line 3

description: SAMPLE 12542


title: PA080_313_090621

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_06

value: female

value: day 0


title: Control Patient 1

description: SAMPLE 12543


title: Commercial Cell Line 1

description: SAMPLE 12539


title: PA080_3_111206

description: Hybridized to SNP6.0 array

value: colon cancer

value: MSS


title: PBMC response to tetanus toxoid, day 0, Phenomics_03


title: subject 242, group A, stimulation B, time 2 days 8803828068_D

value: B

tag: volunteer


title: PA080_31_111214

description: Hybridized to SNP6.0 array


title: PBMC response to tetanus toxoid, day 0, Phenomics_09

value: peripheral blood mononuclear cells


title: subject 251, group A, stimulation B, time 2 days 8803828068_E

tag: bcg quantity (pcr)


title: PBMC response to tetanus toxoid, day 0, Phenomics_04


title: subject 258, group A, stimulation B, time 7 days 8803828068_F


title: control_K

city: Parkville

last: Saffery

state: Victoria

address: Flemington Rd

department: Cancer, Disease and Developmental Epigenetics

institute: Murdoch Children's Research Institute

hyb_protocol: Bisulphite-converted DNA was hybridized as per manufacturer's instructions at AGRF (www.agrf.org.au)

scan_protocol: Scanned as per manufacturer's instructions at AGRF (www.agrf.org.au)

data_processing: Raw data extracted from Illumina BeadStudio software

label: Cy5 and Cy3

source_name: normal colon

label_protocol: Illumina protocol

extract_protocol: DNA was extracted from all tissue using DNeasy 96 Blood and Tissue kits according  to the manufacturer’s instructions (Qiagen, Hilden, Germany).

value: normal

tag: gender


title: hyperplastic_polyp_tissue_I

source_name: hyperplastic polyposis syndrome

value: hyperplastic polyposis syndrome

value: F

value: Sigmoid colon

value: SSA

value: KRAS


title: PBMC response to tetanus toxoid, day 0, Phenomics_02

value: tetanus vaccination

tag: pig identifier


title: hyperplastic_polyp_tissue_H

value: M

value: Transverse colon

value: MVHP

value: BRAF


title: PBMC response to tetanus toxoid, day 0, Phenomics_07

value: German Landrace

value: low-reactive

value: male


title: subject 246, group A, stimulation B, time 2 days 8803828068_B

value: PBMC

value: A


title: PA080_35_111209

description: Hybridized to SNP6.0 array

value: colon cancer

tag: Stage

value: MSS


title: PA080_296_090621

description: Hybridized to SNP6.0 array


title: PA080_270_090621

description: Hybridized to SNP6.0 array

value: MSI-H


title: subject 237, group A, stimulation B, time 0 days 8803828068_C

tag: cell type

value: B


title: PA080_289_090621

description: Hybridized to SNP6.0 array


title: PA080_27_111214

description: Hybridized to SNP6.0 array


title: hyperplastic_polyp_tissue_G

value: hyperplastic polyposis syndrome

value: F

value: FDR


title: subject 210, group A, stimulation U, time 7 days 8803801060_L

value: U


title: subject 219, group A, stimulation B, time 0 days 8803828068_A


title: PA080_25_111214

description: Hybridized to SNP6.0 array


title: subject 210, group A, stimulation U, time 14 days 8803801060_J


title: PA080_278_090621

description: Hybridized to SNP6.0 array


title: subject 212, group A, stimulation U, time 2 days 8803801060_K


title: control_F

value: normal


title: PA080_262_090621

description: Hybridized to SNP6.0 array


title: hyperplastic_polyp_tissue_C

value: Splenic flexure


title: control_D


title: PA080_269_090618

description: Hybridized to SNP6.0 array


title: hyperplastic_polyp_tissue_E

value: Descending colon

value: SSA


title: subject 210, group A, stimulation U, time 0 days 8803801060_I


title: PA080_235_120322

description: Hybridized to SNP6.0 array


title: hyperplastic_polyp_tissue_A

value: Ascending colon

value: BRAF


title: control_B


title: hyperplastic_polyp_tissue_G2

value: Transverse colon

value: WT


title: subject 242, group A, stimulation U, time 0 days 8803801060_G

value: PBMC

value: A


title: subject 251, group A, stimulation B, time 14 days 8803801060_C


title: subject 246, group A, stimulation B, time 14 days 8803801060_F


title: hyperplastic_polyp_tissue_L2

value: M

value: SDR

value: MVHP


title: subject 258, group A, stimulation B, time 0 days 8803801060_B

value: B


title: hyperplastic_polyp_tissue_C2

value: hyperplastic polyposis syndrome

value: F


title: PA080_241_090621

description: Hybridized to SNP6.0 array

value: colon cancer

value: MSS


title: hyperplastic_polyp_tissue_B2

value: MP


title: hyperplastic_polyp_tissue_A2

value: HP/SSA

value: KRAS


title: Neural precursors, midbrain precursors 2, rep2 (gene level)

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

institute: UCL Institute of Neurology

description:
A653_768
Neural precursors, midbrain precursors 2.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Data were processed using Partek Genomics Suite v6.6. Arrays were preprocessed using RMA quantile normalization with GC background correction. Gene-level summary signals were generated by calculating the Winsorized mean of expression values of all probe sets annotated to a transcript.

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.na30.hg19.probeset_core.mps
Core exons were used in the analysis.
Transcript assignments were based on genome build hg19.

source_name: Neural precursors

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

growth_protocol:
hESCs: CDM+FGF2(10ng/ml) + Insulin (10ng/ml) + Activin (10ng/ml).
Neural precursors: CDM (Day0-8), FGF2(10ng/ml; Day 8-16), FGF8(200ng/ml) + puromorphamine (1µM) from Day 16-24.
hESC-derived neurons: DMEM(HG)+ B27(2%)+BDNF(10ng/ml)+GDNF(10ng/ml).

extract_protocol: Total RNA was extracted from all cell samples using the RNeasy kit (Qiagen), from fetal samples using TRIzol (Invitrogen) and from adult substantia nigra using the miRNeasy kit (Qiagen). cDNA synthesis and amplification was performed using the Ambion®WT Expression Kit (Ambion).

value: neural precursors


title: H9-2

city: Taipei

first: Kang-Yu

last: Tai

address: Yonglin Biomedical Engineering Hall, No.49, Fanglan Rd.

department: Genome and Systems Biology Degree Program

country: Taiwan

institute: National Taiwan University

description:
MEG3-OFF
6247231044_L

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Quantile normalization were carried out using commercial microarray analysis software,

source_name: hESC

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

growth_protocol: ReproCELL primate and human ES Cell culture medium on MEF;

extract_protocol: Total RNA from the cells were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen)

tag: esc cell lines


title: Neural precursors, neural precursors 1, rep2 (gene level)

description:
A653_727
Neural precursors, neural precursors 1.


title: H9-1

description:
MEG3-OFF
6247231044_K


title: Neural precursors, neural precursors 2, rep1 (gene level)

description:
A653_748
Neural precursors, neural precursors 2.


title: NTU1-9

description:
MEG3-OFF
6247231044_J


title: Neural precursors, midbrain precursors 1, rep1 (gene level)

description:
A653_703
Neural precursors, midbrain precursors 1.


title: subject 220, group C, stimulation B, time 2 days 8803801060_A

value: C


title: PA080_23_111214

description: Hybridized to SNP6.0 array


title: subject 250, group A, stimulation U, time 14 days 8803801060_H

value: U


title: NTU1-7

description:
MEG3-OFF
6247231044_H


title: NTU1-6

description:
MEG3-OFF
6247231044_G


title: TMNK-1 mock 48h, replicate 3

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

description: Gene expression data from cells after 48h of culture

hyb_protocol: Following fragmentation, 3.5mg of fragmented and labeled ss-DNA were hybridized for 16h at 45C with 60rpm rotation on GeneChip® Human Gene 2.0 ST Array per protocol (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).   GeneChips were washed and stained in the Affymetrix Fluidics Station 450 per protocol (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

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

data_processing: Partek Genomics Suite v6.6 was used to import and process these data using quantile normalization and RMA background correction adjusting for GC content.  Only those probes with log2 expression greater than 3 in at least one sample (19,549 out of 53,617 total) were used for subsequent statistical analysis.

source_name: Immortalized human liver sinusoidal endothelial cell

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix)

growth_protocol: Cell lines were plated at density of 1x10^6 cells/ml to create confluent monolayer and were then cultured for 48h

extract_protocol: Extraction of RNA was performed using QIAgen RNeasy Kit according to manufacturers protocol

treatment_protocol: No treatment (mock)

tag: media type

value: DMEM media, 10% FBS, 1% penicillin/streptomycin


title: hESC, rep5 (gene level)

description:
A653_1476
hESC.

value: hESC


title: NTU1-8

description:
MEG3-OFF
6247231044_I


title: hESC, rep4 (gene level)

description:
A653_1475
hESC.


title: PA080_23_090618

description: Hybridized to SNP6.0 array

value: MSI-H


title: PA080_201_111209

description: Hybridized to SNP6.0 array


title: hESC, rep3 (gene level)

description:
A653_1474
hESC.


title: TMNK-1 mock 48h, replicate 2

value: Immortalized human liver sinusoidal endothelial cell


title: TMNK-1 mock 48h, replicate 1


title: EB

description:
MEG3-ON  EB
6247231044_E


title: PA080_203_111220

description: Hybridized to SNP6.0 array


title: hESC, rep2 (gene level)

description:
A653_717
hESC.


title: HMEC mock 48h, replicate 3

source_name: Immortalized human microvascular endothelial cell

value: HMEC

value: MCDB131 media, 10% FBS, 10mg/ml EGF, 100mg/ml Hydrocortisone, 20% L-Glutamine


title: NTU1-5

description:
MEG3-OFF
6247231044_F


title: hESC, rep1 (gene level)

description:
A653_691
hESC.


title: PA080_19835_090407

description: Hybridized to SNP6.0 array


title: NTU1-4

description:
MEG3-ON
6247231044_D


title: PA080_231_090618

description: Hybridized to SNP6.0 array


title: HMEC mock 48h, replicate 2

value: Immortalized human microvascular endothelial cell


title: PA080_195_111206

description: Hybridized to SNP6.0 array


title: PA080_201_090618

description: Hybridized to SNP6.0 array


title: HMEC mock 48h, replicate 1


title: PA080_197_111214

description: Hybridized to SNP6.0 array


title: NTU1-2

description:
MEG3-ON
6247231044_B


title: PA080_20510_090311

description: Hybridized to SNP6.0 array


title: PA080_19_111214

description: Hybridized to SNP6.0 array


title: hESC-derived neurons, rep2 (gene level)

description:
A653_716
hESC-derived neurons.

source_name: hESC-derived neurons

value: hESC-derived neurons


title: NTU1-1

description:
MEG3-ON
6247231044_A


title: PA080_189_111220

description: Hybridized to SNP6.0 array

value: MSI-L


title: PA080_20061_090311

description: Hybridized to SNP6.0 array

value: colon cancer


title: hESC-derived neurons, rep3 (gene level)

description:
A653_731
hESC-derived neurons.


title: NTU1-3

description:
MEG3-ON
6247231044_C


title: PA080_187_090621

description: Hybridized to SNP6.0 array

value: MSS


title: linc00467 siRNA transfected

city: Randwick, Sydney

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre UNSW

institute: Children's Cancer Institute Australia

description:
Gene expression data from neuroblastoma cells knocking-down of lncMycN
BE(2)-C neuroblastoma cells were cultured in Roswell Park Memorial Institute Medium (RPMI) 1640 supplemented with 10% fetal calf serum and 1% L-glutamine.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome HuGene-2_0-st Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing:
Images were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
Results were further analysed in R (http://www.r-project.org/) with bioconductor package (http://www.bioconductor.org/).

source_name: neuroblasotma BE(2)-C cells transfected with linc00467 siRNA

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

treatment_protocol: BE(2)-C cells were transfected with control siRNA or linc00467 siRNA for 48 hours.

value: peripheral nervous system tumour cell

tag: genotype

value: MYCN-amplified neuroblastoma cells

value: linc00467 siRNA


title: PA080_18366_090814

description: Hybridized to SNP6.0 array


title: PA080_195_090621

description: Hybridized to SNP6.0 array


title: hESC-derived neurons, rep1 (gene level)

description:
A653_713
hESC-derived neurons.


title: PA080_185_111123

description: Hybridized to SNP6.0 array


title: siControl.sub [IV C-S]

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description: IV C-S

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and lowess normalised.

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

growth_protocol: MCF7 cells were grown in DMEM 10% FBS under standard cell culture conditions.

extract_protocol: Total RNA was extracted using TRIAZOL reagent. Subpolysomal and polysomal RNA was extracted using Guanidine HCl-ethanol precipitation, followed by LiCl precipitation. All samples were then repurified using miRNeasy kit (Qiagen).

treatment_protocol: Control ON-TARGETplus Non-targeting Pool and ON-TARGETplus SMART pool siRNAs targeting eIF4A1 were transfected into cells according to manufacturer's instructions (Thermo Scientific). DharmaFECT1 Transfection Reagent was used.


title: Seedlings-120min-rep1

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

description: Biological replicate 1 of 3

hyb_protocol: Hybridization was performed using the NCode™ miRNA Labeling System (Invitrogen, Cat#MIRLS-20), according to the manufracturer´s instructions

scan_protocol: Hybridized arrays were scanned with a GenePix 4200A scanner (Axon Instruments, Forster City, California, United States) as previously described (Wellmer et al., 2004; Wellmer et al., 2006).

data_processing: Averages of three biological replicates of normalized values were taken to calculate the expression ratios (Elicitor vs. Mock) using Rosetta Resolver Biosoftware (www.rosettabio.com) were further adjusted for multi-hypothesis testing using the Benjamini & Hochberg procedure

source_name: Control seedlings 120min

label_protocol: Probe labeling was performed using the NCode™ miRNA Labeling System (Invitrogen, Cat#MIRLS-20), according to the manufracturer´s instructions

growth_protocol: Arabidopsis Col O seedlings were grown for 15 days on MSO plates + vitamins, on filter papers, under 12h/12h light/dark regime, in a climate chamber set to 21°C.

extract_protocol: RNA was extracted using  MIRVANA kit (Ambiont)

treatment_protocol: Arabidopsis seedlings were then treated either with liquid solution of Fusarium oxysporum 247 elicitors (final concentration 300μg/ml), or with mock (H2O)

tag: ecotype

value: seedlings

tag: treated with

value: H2O (mock)

tag: time after treatment (min)

tag: molecule subtype

value: small RNA

source_name: Elicitor seedlings 120min

value: F. oxysporum 247 elicitors


title: PA080_193_111123

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 016/10 (gene level)

description:
A653_1291
Adult control substantia nigra.

source_name: Control adult substantia nigra

value: substantia nigra

tag: developmental stage

value: adult


title: Seedlings-60min-rep3

description: Biological replicate 3 of 3

source_name: Control seedlings 60min

value: H2O (mock control)

source_name: Elicitor seedlings 60min


title: control siRNA transfected

description:
Gene expression data from control neuroblastoma cells
BE(2)-C neuroblastoma cells were cultured in Roswell Park Memorial Institute Medium (RPMI) 1640 supplemented with 10% fetal calf serum and 1% L-glutamine.

source_name: control neuroblastoma BE(2)-C cells

tag: treatment

value: control siRNA


title: Seedlings-120min-rep3

description: Biological replicate 3 of 3

tag: tissue


title: Adult control substantia nigra, 013/10 (gene level)

description:
A653_1441
Adult control substantia nigra.


title: Seedlings-120min-rep2

description: Biological replicate 2 of 3


title: sieIF4AI.poly [II A-P]

description: II A-P

tag: cell line


title: PA080_187_111209

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 015/10 (gene level)

description:
A653_1142
Adult control substantia nigra.


title: sieIF4AI.sub [II A-S]

description: II A-S


title: Seedlings-60min-rep2

description: Biological replicate 2 of 3


title: siControl.total [III C-tot]

description: III C-tot


title: Adult control substantia nigra, 032/10 (gene level)

description:
A653_1346
Adult control substantia nigra.


title: siControl.total [I C-tot]

description: I C-tot


title: Adult control substantia nigra, 025/10 (gene level)

description:
A653_1090
Adult control substantia nigra.


title: Seedlings-60min-rep1

description: Biological replicate 1 of 3


title: PA080_184_090621

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 024/10 (gene level)

description:
A653_1031
Adult control substantia nigra.


title: PA080_175_111220

description: Hybridized to SNP6.0 array


title: PA080_181_111206

description: Hybridized to SNP6.0 array


title: sieIF4AI.poly [I A-P]

description: I A-P


title: Adult control substantia nigra, 001/10 (gene level)

description:
A653_974
Adult control substantia nigra.


title: sieIF4AI.total [IV A-tot]

description: IV A-tot


title: PA080_183_111214

description: Hybridized to SNP6.0 array


title: Seedlings-30min-rep3

description: Biological replicate 3 of 3

source_name: Control seedlings 30min

source_name: Elicitor seedlings 30min


title: siControl.poly [IV C-P]

description: IV C-P


title: Seedlings-30min-rep2

description: Biological replicate 2 of 3


title: Adult control substantia nigra, 010/10 (gene level)

description:
A653_964
Adult control substantia nigra.


title: Seedlings-30min-rep1

description: Biological replicate 1 of 3


title: Adult control substantia nigra, 006/10 (gene level)

description:
A653_950
Adult control substantia nigra.


title: Seedlings-5min-rep3

description: Biological replicate 3 of 3

source_name: Control seedlings 5min

source_name: Elicitor seedlings 5min


title: sieIF4AI.total [I A-tot]

description: I A-tot


title: sieIF4AI.total [III A-tot]

description: III A-tot


title: Adult control substantia nigra, 012/10 (gene level)

description:
A653_917
Adult control substantia nigra.


title: Adult control substantia nigra, 007/10 (gene level)

description:
A653_890
Adult control substantia nigra.


title: siControl.sub [I C-S]

description: I C-S


title: sieIF4AI.total [II A-tot]

description: II A-tot


title: Seedlings-5min-rep1

description: Biological replicate 1 of 3


title: Adult control substantia nigra, 008/10 (gene level)

description:
A653_883
Adult control substantia nigra.


title: PA080_178_090814

description: Hybridized to SNP6.0 array

source_name: colon cancer primary tumour tissue


title: PA080_17271_090423

description: Hybridized to SNP6.0 array


title: siControl.poly [I C-P]

description: I C-P


title: siControl.sub [II C-S]

description: II C-S


title: Adult control substantia nigra, 003/10 (gene level)

description:
A653_875
Adult control substantia nigra.


title: siControl.total [IV C-tot]

description: IV C-tot


title: PA080_17075_090319

description: Hybridized to SNP6.0 array


title: WP3ΔlexA-20℃-rep5

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

description:
8211 WP3cy5-lexAcy3.LSR
WP3ΔlexA cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1 M DTT, 1 μl 10 mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40 mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model
2 raw data files, each with 3 spots per probe/gene, each spot is a techinical replicate for a total of 6 replicates

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) shaking at  220 rpm at 20°C

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

value: WP3 cells were cultured at 20℃ in 2216E medium

value: delta lexA

value: wild type


title: Adult control substantia nigra, 011/10 (gene level)

description:
A653_874
Adult control substantia nigra.


title: WP3ΔlexA-20℃-rep6


title: PA080_171_111206

description: Hybridized to SNP6.0 array


title: PA080_18_090621

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 036/09 (gene level)

description:
A653_794
Adult control substantia nigra.


title: Seedlings-5min-rep2

description: Biological replicate 2 of 3


title: siControl.poly [II C-P]

description: II C-P


title: WP3ΔlexA-20℃-rep2

description:
9790 WP3cy3-lexAcy5.LSR
WP3ΔlexA cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3


title: Adult control substantia nigra, 022/08 (gene level)

description:
A653_772
Adult control substantia nigra.


title: WP3ΔlexA-20℃-rep1


title: PA080_169_111123

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 027/09 (gene level)

description:
A653_762
Adult control substantia nigra.


title: sieIF4AI.poly [IV A-P]

description: IV A-P


title: siControl.poly [III C-P]

description: III C-P


title: WP3ΔlexA-20℃-rep3


title: Adult control substantia nigra, 034/09 (gene level)

description:
A653_800
Adult control substantia nigra.


title: sieIF4AI.sub [III A-S]

description: III A-S


title: PA080_165_111206

description: Hybridized to SNP6.0 array

value: MSI-H


title: PA080_16538_090423

description: Hybridized to SNP6.0 array

value: colon cancer


title: PA080_17_111209

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 035/09 (gene level)

description:
A653_719
Adult control substantia nigra.