title: tg_0909

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from murine SHOX-transgenic pooled fore- and hindlimbs at stage E12.5

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of mouse430_2 -type from Affymetrix. A Custom CDF Version 13 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: tg_E12.5 pooled fore- and hindlimb tissue

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

growth_protocol: murine embryonic fore- and hindlimb tissue was dissected at stage E12.5

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen) according to the manufacturer's instructions, following homogenization using a PT1300 D polytron (Kinematica). DNA was hydrolyzed using the RNAse-free DNAse Kit (Qiagen). Samples from embryonic limbs (E12.5) of the same genotype (wildtype and SHOX transgene) were pooled.

treatment_protocol: Tissue was stored at -80°C until RNA preparation

value: SHOX transgene

value: pooled fore- and hindlimb tissue


title: tg_0309

status: Public on Aug 13 2014

type: RNA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype/variation

tag: tissue

tag: age


title: 0nM_rep1

city: Barcelona

first: José

last: Portugal

address: Parc Cientific de Barcelona, Baldiri Reixac, 10

department: Molecular Genomics

country: Spain

institute: Instituto de Biologia Molecular  de Barcelona-CSIC

description: Gene expression after no treatment with DIG-MSK

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).  Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: cells, 0 nM, replicate 1

label_protocol: One-Color Microarray-Based Eukaryote Analysis Fair Play III Labeling v. 1.3 (Agilent)

growth_protocol: A2780 cells were maintained in RPMI 1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies), 100 U/ml penicillin, 100 g/ml streptomycin and 2 mM sodium pyruvate at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: RNA was isolated using the UltraspecRNA reagent (Biotecx) following the manufacturer's recommendations. RNA was digested with RNAse-free DNAse I (Roche Diagnostics) in the presence of RNasin (Promega), phenol extracted and precipitated, and the pellet was dissolved in RNAse-free water. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells sub-cultured at a density of 2.5 x 104 cells/ml were incubated with either 8 nM or 80 nM DIG-MSK at 37 °C for 24 h.

tag: treatment

value: none (contol)

tag: cell line


title: 80nM_rep3

description: Gene expression after treatment with 80 nM DIG-MSK

source_name: cells, 80 nM, replicate 3

value: 80 nM DIG-MSK


title: MCF10A_hsa-miR-1-3p_1

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All data were imported and normalized using the Base server (http://base.thep.lu.se).

source_name: MCF10A, hsa-miR-1-3p mimic

label_protocol: Standard Illumina labeling protocol

growth_protocol: All cell lines were purchased from ATCC and used at low passage numbers. Cells were cultured as reported previously (Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10: 515-52).

extract_protocol: RNA was extracted with TRIZOL (Life Technologies) according to the manufacturer's instructions. RNA quantity and quality were assessed with NanoDrop ND 1000 spectrophotometer (NanoDrop Tech) and LabChip GX (Perkin Elmer) respectively before loading the samples on a HumanHT-12 v3.0.

treatment_protocol: Transfections were performed with Lipofectamine 2000 (Life Technologies) following the manufacturer’s instructions. All oligonucleotides and miRNA mimics were transfected at 100 nM unless stated otherwise. Antisense oligonucleotides contained 2’ O-methyl modifications and were from IDT DNA Technologies. Non-targeting siRNA control was from Thermo Scientific. All miRNA mimics were purchased from Qiagen; the customized mimics corresponding to the mature sequence of miR-4728-3p (25 nt) and a 25 nt control.

tag: cell type

value: human mammary epithelial cells

tag: transfected with

value: hsa-miR-1-3p mimic


title: 0nM_rep3

source_name: cells, 0 nM, replicate 3

value: none (control)


title: 8nM_rep3

description: Gene expression after treatment with 8 nM DIG-MSK

source_name: cells, 8 nM, replicate 3

value: 8 nM DIG-MSK


title: 80nM_rep1

source_name: cells, 80 nM, replicate 1


title: Normal myometrium rep1

status: Public on Aug 14 2014

city: Jinan

first: Zhaojian

last: Liu

state: Shandong

address: 44# Wenhua xi Road

department: Cell Biology

country: China

institute: Shandong University

description: Expression profiling data from normal myometrium

hyb_protocol: The labeled cRNAs were hybridized onto the Human lncRNA Array v2.0 (8 x 60K, Arraystar) using agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: uterine normal myometrium

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's protocol,followed by RNA easy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -80C

extract_protocol: For RNA extraction, RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Cryopulverization of tissue using the Biopulverizer and then homogenization using the Mini-Bead-Beater-16 before RNA extraction

tag: gender

value: female

value: uterine normal myometrium


title: 8nM_rep1

source_name: cells, 8 nM, replicate 1


title: wt_0309

description: Gene expression data from murine wildtype pooled fore- and hindlimbs at stage E12.5

source_name: wt_E12.5 pooled fore- and hindlimb tissue

value: wildtype


title: MCF10A_hsa-miR-1-3p_ctrl_1

source_name: MCF10A, non-targeting control

value: non-targeting control


title: MCF10A_hsa-miR-1-3p_ctrl_4


title: wt_0909


title: 0nM_rep2

source_name: cells, 0 nM, replicate 2


title: Cdkn2a-/- Eµ-Myc B cell at t=48, biological replicate 2

city: Los Angeles

first: Colin

last: Flinders

address: 2250 Alcazar St. CSC-140

department: Biological Chemistry

country: USA

institute: University of California, Los Angeles

hyb_protocol: Following fragmentation, 5.2 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 1.0 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: Data was quantified and processed with robust multi-array average using the justRMA function of the 1.40.0 affy R package (RMA). Expression values were log2 transformed. Probe sets were annotated using the Affymettrix MoGene-1_0-st-v1.na33.2.mm9.probeset.csv file.

source_name: B cells treated with 750nM Mafosfamide at t=48

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

growth_protocol: Eµ-Myc cells were seeded at a concentration of 2e5 cells/mL in 50mL in t175 flasks containing 4e5 irradiated Cdkn2a-/- mouse embyronic fiborblasts.

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini kit (Cat. No. 74104).

treatment_protocol: At t=0, mafosfamide was added to t175 flasks to a final concentration of 750nM.

tag: strain background

value: Eµ-Myc; Cdkn2a-/-

value: Eµ-Myc B-cells

tag: treated with

value: 750nM Mafosfamide for 48hrs


title: Cdkn2a-/- Eµ-Myc B cell R500 750nM, biological replicate 1

source_name: Dose escalated resistant line R500, treated with 750nM Mafosfamide

value: Dose escalated resistant line R500

value: 750nM Mafosfamide for 24hrs


title: Cdkn2a-/- Eµ-Myc B cell at t=24, biological replicate 3

source_name: B cells treated with 750nM Mafosfamide at t=24


title: NF-YC KD ES cells 96hr, replicate 1

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Cells transfected with NF-YC siRNA

hyb_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org).  Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.

source_name: E14Tg2a ES Cells

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

growth_protocol: Mouse ES cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). For siRNA transfection experiments, passage 20-35 cells were cultured in M15 medium: DMEM (Invitrogen) supplemented with 15% FBS (vol/vol), 10 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Invitrogen), 1× EmbryoMax nucleosides (Millipore), and 1U per ml of ESGRO mLIF (Millipore)

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen)

value: embryonic stem cells


title: Cdkn2a-/- Eµ-Myc B cell at t=48, biological replicate 4


title: Cdkn2a-/- Eµ-Myc B cell R4000 0nM, biological replicate 1

source_name: Dose escalated resistant line R4000

value: Dose escalated resistant line R4000


title: Cdkn2a-/- Eµ-Myc B cell R500 0nM, biological replicate 1

source_name: Dose escalated resistant line R500


title: Cdkn2a-/- Eµ-Myc B cell at t=48, biological replicate 5


title: Cdkn2a-/- Eµ-Myc B cell at t=24, biological replicate 4


title: Cdkn2a-/- Eµ-Myc B cell R1000 0nM, biological replicate 1

source_name: Dose escalated resistant line R1000

value: Dose escalated resistant line R1000


title: Cdkn2a-/- Eµ-Myc B cell at t=48, biological replicate 3


title: Cdkn2a-/- Eµ-Myc B cell at t=48, biological replicate 1


title: Cdkn2a-/- Eµ-Myc B cell R4000 750nM, biological replicate 1

source_name: Dose escalated resistant line R4000, treated with 750nM Mafosfamide


title: Cdkn2a-/- Eµ-Myc B cell at t=12, biological replicate 4

source_name: B cells treated with 750nM Mafosfamide at t=12

value: 750nM Mafosfamide for 12hrs


title: Cdkn2a-/- Eµ-Myc B cell R1000 750nM, biological replicate 1

source_name: Dose escalated resistant line R1000, treated with 750nM Mafosfamide


title: Cdkn2a-/- Eµ-Myc B cell at t=24, biological replicate 2


title: Cdkn2a-/- Eµ-Myc B cell R100 0nM, biological replicate 1

source_name: Dose escalated resistant line R100

value: Dose escalated resistant line R100


title: Cdkn2a-/- Eµ-Myc B cell at t=12, biological replicate 1


title: Cdkn2a-/- Eµ-Myc B cell at t=12, biological replicate 3


title: Cdkn2a-/- Eµ-Myc B cell at t=24, biological replicate 1


title: Cdkn2a-/- Eµ-Myc B cell at t=6, biological replicate 3

source_name: B cells treated with 750nM Mafosfamide at t=6

value: 750nM Mafosfamide for 6hr


title: Cdkn2a-/- Eµ-Myc B cell at t=6, biological replicate 4


title: Cdkn2a-/- Eµ-Myc B cell at t=6, biological replicate 1


title: Longterm_HCC1954-SKBR3_pPRAS_T246

type: protein

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center

description:
rabbit monoclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files

hyb_protocol: Arrays were blocked using 50% Odyssey Blocking Puffer (LI-COR) in PBS. Primary antibodies were applied at a dilution of 1:300 and visualized by the application of Alexa680-labeled secondary antibodies (1:8000). Slides were washed with PBST between the incubation steps. Prior to scanning, arrays were wash once with MilliQ.

scan_protocol: Arrays were scanned using the Odyssey Infrared Imaging System (LI-COR), and signal intensities were determined using the GenePix Pro 5.0 analysis software.

data_processing:
Each biological sample was printed in triplicate on the array. One array was stained with Fast Green FCF to account for the total protein amount, a normalization factor for each spot was calculated, and antibody signals of each spot were normalized.
On-slide total protein quantification based on staining with Fast Green FCF served as basis for normalization of the signals derived from antibody incubation. A spot specific normalization factor was calculated by dividing the spot specific signal intensity by the mean of the signal intensities of all spots on this slide. The raw signal intensity of each spot was than divided by the normalization factor.

label: Alexa Fluor 680

molecule: protein

growth_protocol: Cells were seeded in 6-well plates, cultivated for 24h prior to addition of the inhibitors.

extract_protocol: Medium was replaced by ice-cold PBS, transferred on ice, and cells were harvested manually by scraping in M-PER lysis buffer (Pierce, Bonn, Germany) containing protease inhibitor Complete Mini and phosphatase inhibitor PhosSTOP (Roche, Mannheim, Germany). Cells were lyzed for 20 min on an end-over-end shaker and lysates were cleared at 16,000 x g by centrifugation.

treatment_protocol: The inhibitors trastuzumab (10 ng/µL), pertuzumab (10 ng/µL), and erlotinib (1 µM) (Roche, Penzberg, Germany) were added to cells in full growth medium either alone (erlotinib) or in combinations. After inhibition medium was removed and ice-cold PBS was added to the plates.

tag: protein target

value: phospho-PRAS

tag: phospho site

tag: antibody id


title: Longterm_HCC1954-SKBR3_PTEN_none

description:
rabbit polyclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files

value: total-PTEN


title: Cdkn2a-/- Eµ-Myc B cell at t=6, biological replicate 2


title: Longterm_HCC1954-SKBR3_pNFkB_S536

value: phospho-NFkB


title: Longterm_HCC1954-SKBR3_pGSK3alpha/beta_Y279Y216

value: Epitomics 2309-1


title: Longterm_HCC1954-SKBR3_pTSC2_T1462


title: Longterm_HCC1954-SKBR3_p53_none

description:
mouse monoclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files


title: Longterm_HCC1954-SKBR3_pERBB2_Y1248

value: Millipore 06-229


title: Longterm_HCC1954-SKBR3_pFoxO1/3a_T24T32


title: Longterm_HCC1954-SKBR3_pp70S6K_T389


title: Cdkn2a-/- Eµ-Myc B cell at t=0, biological replicate 5

source_name: B cells at t=0

value: none (untreated control)


title: Cdkn2a-/- Eµ-Myc B cell at t=12, biological replicate 2

value: Eµ-Myc; Cdkn2a-/-


title: Cdkn2a-/- Eµ-Myc B cell at t=0, biological replicate 4

value: Eµ-Myc B-cells


title: Longterm_HCC1954-SKBR3_pERBB3_Y1289


title: Longterm_HCC1954-SKBR3_pp38_T180Y182


title: Longterm_HCC1954-SKBR3_CyclinD1_none


title: Cdkn2a-/- Eµ-Myc B cell at t=0, biological replicate 1


title: Cdkn2a-/- Eµ-Myc B cell at t=0, biological replicate 3


title: Longterm_HCC1954-SKBR3_CyclinB1_none


title: Longterm_HCC1954-SKBR3_pcJUN_S63

value: phospho-cJUN


title: Longterm_HCC1954-SKBR3_BAX_none

value: total-BAX


title: Longterm_HCC1954-SKBR3_pcRAF_S338

value: phospho-cRAF


title: Longterm_HCC1954-SKBR3_pAKT_S473

value: phospho-AKT


title: Longterm_HCC1954-SKBR3_pERBB1_Y1173


title: Longterm_HCC1954-SKBR3_pERK1/2_T202Y204


title: Cdkn2a-/- Eµ-Myc B cell at t=0, biological replicate 2


title: Normal myometrium rep2

source_name: uterine normal myometrium

value: female

value: uterine normal myometrium


title: Mutant (fenofibrate, starting in young adulthood, 1% DMSO), biological replicate 3

city: Philadelphia

first: Shana

middle: Erin

last: McCormack

state: PA

address: 34th and Civic Center Boulevard, Suite 11NW30

department: Pediatrics, Division of Diabetes and Endocrinology

institute: Children's Hospital of Philadelphia

description: Gene expression data from mutant C. elegans (treated with fenofibrate beginning in young adulthood)

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

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

data_processing: Custom library file was downloaded from BRAINARRAY, which regrouped original probes to unique ENTREZ gene IDs. RMA method was used to summarize and normalize probe-level data into gene-level data

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Revision 5, Affymetrix).

growth_protocol: C. elegans were grown on NGM agar 10 cm plates spread with standard OP50 E. coli.  Synchrony was obtained by bleaching gravid adults, plating the recovered eggs on unspread NGM plates overnight, after which L1-stage arrested animals were transferred to NGM plates spread with standard OP50 E. coli.

extract_protocol: Trizol reagent was used according to the manufacturer's instructions to extract total RNA from aliquots of 500 to 1,000 sorted adult worms

treatment_protocol: Worms were treated either beginning in development or for 24 hours in young adulthood as indicated. Untreated worms were treated with vehicle only. 4 replicates of 1000 adult worms each were collected.

tag: genotype

value: gas-1 (fc21) ETC Complex missense mutation (allele = K09A9.5)

tag: treatment (drug name)

value: Drug:fenofibrate (14 microM)

tag: treatment (drug or buffer control timing)

value: beginning in young adulthood

tag: buffer

value: 1% DMSO

tag: age at rna isolation

value: young adult

tag: batch number


title: Mutant (rosiglitazone, starting in young adulthood, 1% DMSO), biological replicate 2

description: Gene expression data from mutant C. elegans (treated with rosiglitazone beginning in young adulthood)

value: Drug:rosiglitazone (5 mM)


title: Mutant (fenofibrate, starting in young adulthood, 1% DMSO), biological replicate 2


title: Mutant (fenofibrate, starting in L1 larval stage, 1% DMSO), biological replicate 1

description: Gene expression data from mutant C. elegans (treated with fenofibrate beginning in L1 larval stage)

value: beginning in L1 larval stage


title: Mutant (fenofibrate, starting in young adulthood, 1% DMSO), biological replicate 4


title: Mutant (rosiglitazone, starting in young adulthood, 1% DMSO), biological replicate 1


title: Mutant (fenofibrate, starting in L1 larval stage, 1% DMSO), biological replicate 2


title: MCF10A_miR-4728-3p_ctrl_5

value: human mammary epithelial cells

value: ctrl_siRNA (non-targeting control)


title: Mutant (fenofibrate, starting in L1 larval stage, 1% DMSO), biological replicate 4


title: Mutant (fenofibrate, starting in L1 larval stage, 1% DMSO), biological replicate 3


title: Mutant (rosiglitazone, starting in young adulthood, 1% DMSO), biological replicate 4


title: Mutant (rosiglitazone, starting in young adulthood, 1% DMSO), biological replicate 3


title: MCF10A_miR-4728-3p_ctrl_4


title: MCF10A_miR-4728-3p_ctrl_6


title: MCF10A_miR-4728-3p_ctrl_3


title: MCF10A_miR-4728-3p_6

value: hsa-miR-4728-3p mimic


title: Mutant (rosiglitazone, starting in L1 larval stage, 1% DMSO), biological replicate 3

description: Gene expression data from mutant C. elegans (treated with rosiglitazone beginning in L1 larval stage)


title: MCF10A_miR-4728-3p_ctrl_2


title: Mutant (rosiglitazone, starting in L1 larval stage, 1% DMSO), biological replicate 4


title: Mutant (resveratrol, starting in development, 1% DMSO), biological replicate 3

description: Gene expression data from mutant C. elegans (treated with resveratrol beginning in development)

value: Drug:resveratrol (50 microM)


title: Mutant (resveratrol, starting in young adulthood, 1% DMSO), biological replicate 4

description: Gene expression data from mutant C. elegans (treated with resveratrol beginning in young adulthood)


title: Mutant (fenofibrate, starting in young adulthood, 1% DMSO), biological replicate 1


title: Mutant (resveratrol, starting in young adulthood, 1% DMSO), biological replicate 2


title: Mutant (rosiglitazone, starting in L1 larval stage, 1% DMSO), biological replicate 1


title: Mutant (resveratrol, starting in development, 1% DMSO), biological replicate 4


title: MCF10A_miR-4728-3p_ctrl_1


title: Mutant (resveratrol, starting in young adulthood, 1% DMSO), biological replicate 3


title: Mutant (resveratrol, starting in young adulthood, 1% DMSO), biological replicate 1


title: Mutant (rosiglitazone, starting in L1 larval stage, 1% DMSO), biological replicate 2


title: Mutant (resveratrol, starting in development, 1% DMSO), biological replicate 1


title: Mutant (NA starting in young adulthood, S-basal), biological replicate 3

description: Gene expression data from mutant C. elegans (treated with nicotinic acid beginning in young adulthood)

value: Drug:nicotinic acid (1 mM)

value: S-basal


title: Mutant (resveratrol, starting in development, 1% DMSO), biological replicate 2


title: MCF10A_miR-4728-3p_5


title: MCF10A_miR-4728-3p_4


title: Mutant (NA starting in young adulthood, S-basal), biological replicate 4


title: MCF10A_miR-4728-3p_3


title: Mutant (NA starting in young adulthood, S-basal), biological replicate 1


title: Mutant (NA starting in young adulthood, S-basal), biological replicate 2


title: Mutant (untreated, 1% DMSO since young L1 larval stage), biological replicate 2

description: Gene expression data from mutant C. elegans (1% DMSO since L1 larval stage, control for treatment with resveratrol, rosiglitazone, or fenofibrate since L1 larval stage)


title: Mutant (untreated, 1% DMSO since young L1 larval stage), biological replicate 4


title: Mutant (untreated, 1% DMSO since young L1 larval stage), biological replicate 1


title: Mutant (untreated, 1% DMSO since young L1 larval stage), biological replicate 3


title: Mutant (untreated, 1% DMSO since young adulthood), biological replicate 4

description: Gene expression data from mutant C. elegans (1% DMSO since young adulthood, control for treatment with resveratrol, rosiglitazone, or fenofibrate since young adulthood)


title: Mutant (NA starting in L1 larval stage, S-basal), biological replicate 1

description: Gene expression data from mutant C. elegans (treated with nicotinic acid beginning in development)


title: Mutant (NA starting in L1 larval stage, S-basal), biological replicate 4


title: Non-Responders to the Novel Mitochonrial Inhibitor CPI-613 rep3

city: Winston-Salem

first: Jeff

last: Chou

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

hyb_protocol: 10 ug biotinylated cRNA was hybridized to the Affymetrix Gene Atlas U219 Human Genome array strips according to current Affymetrix protocols.

scan_protocol: The arrays were washed and scanned according to standard Affymetrix GeneAtlas instructions using the GeneAtlas scanner and software control(GeneAtlas Instrument Control (GAIC) v. 1.0.6.).

data_processing: Raw data (CEL files) were generated using Affymetrix AGCC software and quantile normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Affymetrix controls were examined to evaluate hybridization quality using Partek Genomics Suite software (Partek Inc.).

label: Biotin

source_name: human peripheral blood mononuclear cells

label_protocol: 250 ng total RNA was amplified and labeled according to the Affymetrix 3’-IVT labeling protocol.

extract_protocol: Total RNA was isolated from peripheral blood mononuclear cells using the RiboPure-Blood Kit (Life Technologies (AM1928)).

value: blood mononuclear cells

tag: age

tag: diagnosis

value: AML

value: M


title: MCF10A_miR-4728-3p_1

tag: cell line


title: Mutant (untreated, 1% DMSO since young adulthood), biological replicate 2


title: Shortterm_SKBR3_pmTOR_S2448

description:
rabbit polyclonal
rabbit polyclonal

growth_protocol: Cells were seeded in 6-well plates, cultivated for 24h, and serum-starved for additional 24h.

treatment_protocol: The inhibitors trastuzumab (10 ng/µL), pertuzumab (10 ng/µL), and erlotinib (1 µM) (Roche, Penzberg, Germany) were added to cells in starvation medium either alone or in combinations 1 h prior to stimulation with EGF or HRG (5 nM) for 0, 4, 8, 12, 16, 20, 30, 40, 50 and 60 min. After stimulation, medium was removed and ice-cold PBS was added to the plates.

value: phospho-mTOR


title: Responders to the Novel Mitochonrial Inhibitor CPI-613 rep4

tag: cell type

value: MDS


title: Mutant (NA starting in L1 larval stage, S-basal), biological replicate 3

value: gas-1 (fc21) ETC Complex missense mutation (allele = K09A9.5)


title: Shortterm_SKBR3_pp70S6K_T389

description:
mouse monoclonal
rabbit polyclonal


title: Shortterm_SKBR3_pERBB3_Y1289

description:
rabbit monoclonal
rabbit polyclonal


title: Cdkn2a-/- Eµ-Myc B cell at t=24, biological replicate 5

tag: genotype/variation

value: Eµ-Myc; Cdkn2a-/-

value: Eµ-Myc B-cells

value: 750nM Mafosfamide for 24hrs


title: Responders to the Novel Mitochonrial Inhibitor CPI-613 rep1

tag: gender

value: F


title: Mutant (NA starting in L1 larval stage, S-basal), biological replicate 2

value: beginning in L1 larval stage

value: young adult


title: Shortterm_SKBR3_pPLCgamma_S1248

description:
rabbit polyclonal
rabbit monoclonal

value: phospho-PLCgamma


title: Responders to the Novel Mitochonrial Inhibitor CPI-613 rep3


title: MCF10A_miR-4728-3p_2

value: human mammary epithelial cells

tag: transfected with

value: hsa-miR-4728-3p mimic


title: Non-Responders to the Novel Mitochonrial Inhibitor CPI-613 rep4


title: Responders to the Novel Mitochonrial Inhibitor CPI-613 rep2


title: Shortterm_SKBR3_pPKCalpha_S657Y658

description:
rabbit polyclonal
rabbit polyclonal

value: phospho-PKCalpha

value: Abcam ab23513


title: Mutant (untreated, 1% DMSO since young adulthood), biological replicate 3

value: beginning in young adulthood

value: 1% DMSO


title: Shortterm_SKBR3_pMEK1/2_S217S221

description:
rabbit polyclonal
rabbit polyclonal

value: Sigma M7683


title: Non-Responders to the Novel Mitochonrial Inhibitor CPI-613 rep1

value: blood mononuclear cells

value: AML

value: M


title: Longterm_BT474_pTSC2_T1462


title: Longterm_BT474_pp70S6K_T389


title: Longterm_BT474_pPRAS_T246

value: phospho-PRAS


title: Longterm_BT474_p53_none


title: Longterm_BT474_pp38_T180Y182


title: Non-Responders to the Novel Mitochonrial Inhibitor CPI-613 rep2


title: Wildtype (untreated, 1% DMSO starting at L1 larval stage), biological replicate 4

description: Gene expression data from wild-type C. elegans (1 % DMSO since L1 larval stage, control for treatment with resveratrol, rosiglitazone, or fenofibrate since L1 larval stage)

value: N2 Bristol (wild-type)


title: Longterm_BT474_pFoxO1/3a_T24T32


title: Wildtype (untreated, 1% DMSO starting at L1 larval stage), biological replicate 1


title: Longterm_BT474_pGSK3alpha/beta_Y279Y216

value: Epitomics 2309-1


title: Wildtype (untreated, 1% DMSO starting at L1 larval stage), biological replicate 2


title: Longterm_BT474_pNFkB_S536

value: phospho-NFkB


title: Longterm_BT474_pERBB3_Y1289


title: Longterm_BT474_PTEN_none

value: total-PTEN


title: Wildtype (untreated, 1% DMSO starting at L1 larval stage), biological replicate 3

value: beginning in L1 larval stage

value: young adult


title: Longterm_BT474_pERBB2_Y1248

value: Millipore 06-229


title: Mutant (untreated, 1% DMSO since young adulthood), biological replicate 1

value: gas-1 (fc21) ETC Complex missense mutation (allele = K09A9.5)


title: Mutant (untreated, S-basal since L1 larval stage), biological replicate 4

description: Gene expression data from mutant C. elegans (S-basal since L1 larval stage, control for nicotinic acid treatment)

value: S-basal


title: Wildtype (untreated, 1% DMSO since young adulthood), biological replicate 2

description: Gene expression data from wild-type C. elegans (1 % DMSO since young adulthood, control for treatment with resveratrol, rosiglitazone, or fenofibrate since young adulthood)


title: Longterm_BT474_pERBB1_Y1173


title: Wildtype (untreated, 1% DMSO since young adulthood), biological replicate 1


title: Longterm_BT474_CyclinD1_none


title: Shortterm_HCC1954_pERBB3_Y1289


title: Mutant (untreated, S-basal since L1 larval stage), biological replicate 2


title: Wildtype (untreated, 1% DMSO since young adulthood), biological replicate 3


title: Wildtype (untreated, 1% DMSO since young adulthood), biological replicate 4


title: Shortterm_HCC1954_pPDK1_S241


title: Mutant (untreated, S-basal since L1 larval stage), biological replicate 3


title: Shortterm_HCC1954_pmTOR_S2448

value: phospho-mTOR


title: Mutant (untreated, S-basal since L1 larval stage), biological replicate 1


title: Mutant (untreated, S-basal since young adulthood), biological replicate 3

description: Gene expression data from mutant C. elegans (S-basal since young adulthood, control for nicotinic acid treatment)

value: beginning in young adulthood


title: Longterm_BT474_pcRAF_S338

description:
rabbit monoclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files

value: phospho-cRAF


title: Longterm_BT474_pcJUN_S63

value: phospho-cJUN


title: Shortterm_HCC1954_pPLCgamma_S1248

description:
rabbit polyclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files

value: phospho-PLCgamma


title: Mutant (untreated, S-basal since young adulthood), biological replicate 4


title: Longterm_BT474_BAX_none

value: total-BAX


title: Shortterm_HCC1954_pMEK1/2_S217S221

value: Sigma M7683


title: Shortterm_HCC1954_pERBB2_Y1248


title: Longterm_BT474_pRPS6_S235S236


title: Longterm_BT474_pRB_S807S811

value: phospho-RB


title: Shortterm_HCC1954_pPKCalpha_S657Y658

value: phospho-PKCalpha

value: Abcam ab23513


title: Mutant (untreated, S-basal since young adulthood), biological replicate 2


title: Mutant (untreated, S-basal since young adulthood), biological replicate 1


title: Longterm_BT474_CyclinB1_none

description:
mouse monoclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files


title: Wildtype (untreated, S-basal since L1 larval stage), biological replicate 4

description: Gene expression data from wild-type C. elegans (S-basal since L1 larval stage, control for nicotinic acid treatment since L1 larval stage)

value: N2 Bristol (wild-type)


title: Shortterm_SKBR3_pERBB2_Y1248


title: Shortterm_SKBR3_pERBB1_Y1068


title: Longterm_BT474_pAKT_S473

value: phospho-AKT


title: Longterm_BT474_pERK1/2_T202Y204


title: Wildtype (untreated, S-basal since L1 larval stage), biological replicate 3

value: beginning in L1 larval stage


title: Wildtype (untreated, S-basal since L1 larval stage), biological replicate 1

value: young adult


title: Wildtype (untreated, S-basal since young adulthood), biological replicate 4

description: Gene expression data from wild-type C. elegans (S-basal since young adulthood, control for nicotinic acid treatment since young adulthood)


title: Shortterm_HCC1954_pERBB1_Y1068


title: Wildtype (untreated, S-basal since L1 larval stage), biological replicate 2


title: Shortterm_SKBR3_pPDK1_S241


title: Wildtype (untreated, S-basal since young adulthood), biological replicate 3


title: Wildtype (untreated, S-basal since young adulthood), biological replicate 2


title: Shortterm_SKBR3_pERK1/2_T202Y204


title: Shortterm_HCC1954_pp70S6K_T389


title: Wildtype (untreated, S-basal since young adulthood), biological replicate 1


title: Shortterm_BT474_pERBB3_Y1289

description: rabbit monoclonal

hyb_protocol: Arrays were blocked using Odyssey Blocking Puffer (LI-COR). Primary antibodies were applied at a dilution of 1:350 or 1:1400 and visualized by the application of Alexa680-labeled secondary antibodies (1:8000). After washing and rinsing the slides in ddH2O, slides were dried at room temperature protected from light.

growth_protocol: Cells were seeded in 6-well plates and serum-starved for 24h.

extract_protocol: Medium was replaced by ice-cold PBS, transferred on ice, and cells were harvested by scraping in M-PER lysis buffer (Pierce, Bonn, Germany) containing protease inhibitor Complete Mini and phosphatase inhibitor PhosSTOP (Roche, Mannheim, Germany). Cells were lyzed for 20 min on an end-over-end shaker and lysates were cleared at 13,000 rpm for 10 min by centrifugation.


title: Shortterm_BT474_pERBB2_Y1221Y1222

description: rabbit monoclonal


title: Shortterm_BT474_pMEK1/2_S217S221

description: rabbit polyclonal


title: Shortterm_BT474_pPKCalpha_S657Y658

description: rabbit polyclonal

value: Abcam ab23513, Millipore 06-822


title: Shortterm_BT474_pPLCgamma_S1248

description: rabbit polyclonal


title: Shortterm_BT474_pERBB1_Y1086

description: rabbit polyclonal


title: Shortterm_BT474_pAKT_S473


title: Shortterm_BT474_pp70S6K_T389


title: Shortterm_BT474_pERK1/2_T202Y204

description:
mouse and rabbit monoclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files


title: Orange Root, Biological Rep 1

city: Madison

first: Megan

last: Bowman

state: WI

address: 1575 Linden Drive

department: Plant Breeding and Plant Genetics

institute: University of Wisconsin-Madison

hyb_protocol: aRNA fragmentation reactions were setup targeting 16 µg at 400ng/µl. Agarose gel analysis of fragmented and non-fragmented anti-sense RNA (aRNA) was run on 2% agarose gel to verify fragmented product sizes. 10 µg of aRNA was then hybridized to the Medicago GeneChip (Affymetrix) array using the hybridization cocktail prepared according to the protocol described in the Expression Analysis Technical Manual with Specific Protocols for Using the GeneChip® (Affymetrix). Arrays were hybridized over night at 45°C for 16 hours in Affymetrix 640 Hybridization oven (Affymetrix). The Medicago Affymetrix GeneChips were processed on the Affymetrix 450 Fluidics station using the standard protocol for the Medicago array.

scan_protocol: GeneChips were then scanned using the Affymetrix GC3000 scanner.

data_processing: Subsequent data were extracted from the scanned images using the Affymetrix Expression Console version 1.1 software.

organism: Daucus carota

source_name: Daucus carota orange storage root, 11 weeks post planting

label_protocol: RNA for each pooled sample and was concentrated using a Vacufuge plus and then labeled for microarray hybridization using the MessageAmp™ Premier IVT kit.

growth_protocol: Storage root tissues from two near isogenic recombinant inbred lines were grown in greenhouse conditions and harvested at 11 weeks post planting flash frozen in liquid nitrogen, followed by storage at -80C.

extract_protocol: Total RNA was extracted using the Trizol RNA Plus Kit according to the manufacturer's instructions.

treatment_protocol: Root tissue was harvested at 11 weeks. Orange storage root color was visibly detected and carotenoids were quantified by HPLC in B8788. No carotenoid pigmentation was detected in B8788 by HPLC.

tag: tissue

value: storage root

tag: color

value: orange


title: normal colonic mucosa sample AUS2_077_p1966_NM

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

hyb_protocol: Samples were hybridized onto GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: For analysis at the exon level, raw data were processed (using a custom-made cdf-file; HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) and analyzed for alternative splicing with the FIRMA algorithm (aroma.affymetrix). For gene-level analysis, raw data were processed with the RMA procedure using Expression Console (Affymetrix; gene-core analysis).

source_name: Normal colonic mucosa from colorectal cancer patient

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from <100 mg tissue biopsies using the Ambion RiboPure kit (Life Technologies), according to the manufacturer's protocol.

value: normal colonic mucosa biopsy

tag: tumor stage

tag: msi-status


title: normal colonic mucosa sample AUS2_035_p1834_NM


title: normal colonic mucosa sample AUS2_045_p1835_NM


title: normal colonic mucosa sample AUS2_074_p1837_NM


title: Orange Root, Biological Rep 3

tag: genotype


title: SKBR3_pAKT_S473

description:
rabbit polyclonal
There are several sub-arrays on one slide. Each sub-array is incubated with one specific antibody, but one slide with 2 or 3 sub-arrays is stained with Fast Green FCF. Therefore, the number or rows differ between the antibody-files and the FCF-files.

extract_protocol: Medium was replaced by ice-cold PBS, transferred on ice, and cells were harvested manually by scraping in M-PER lysis buffer (Pierce, Bonn, Germany) containing protease inhibitor Complete Mini and phosphatase inhibitor PhosSTOP (Roche, Mannheim, Germany). Cells were lyzed for 20 min on an end-over-end shaker and lysates were cleared at 16,000 x g by centrifugation.

treatment_protocol: The inhibitors trastuzumab (10 ng/µL), pertuzumab (10 ng/µL), and erlotinib (1 µM) (Roche, Penzberg, Germany) were added to cells in starvation medium either alone or in combinations 1 h prior to stimulation with EGF or HRG (5 nM) for 0, 4, 8, 12, 16, 20, 30, 40, 50 and 60 min. After stimulation, medium was removed and ice-cold PBS was added to the plates.

tag: protein target

tag: phospho site

tag: antibody id


title: normal colonic mucosa sample AUS2_131_p1844_NM


title: White Root, Biological Rep 2

source_name: Daucus carota white storage root, 11 weeks post planting

value: white


title: Orange Root, Biological Rep 2


title: normal colonic mucosa sample AUS2_107_p1841_NM


title: CO.55

status: Public on Aug 12 2014

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

institute: IBIS

description:
SAMPLE 38
test

data_processing:
Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .
Matrix non-normalized 'Card A' and Matrix non-normalized 'Card B' are linked as supplementary files on the Series record. Cycle threshold (Ct) values were calculated with the SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. (Applied Biosystems)
Matrix normalized 'Card A' and Matrix normalized 'Card B' are linked as supplementary files on the Series record.  Expression of target miRNAs was normalized in relation to expression of MammU6.

label: FAM

source_name: Tumor tissue

label_protocol: FAM.

extract_protocol: Total RNA, containing small RNA, was extracted from tumor tissue samples by mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.

tag: disease state

value: advanced colorectal cancer

tag: chemotherapy response

value: Responder


title: CO.53

description:
SAMPLE 37
test


title: White Root, Biological Rep 1


title: CO.49

description:
SAMPLE 36
test

value: Non-responder


title: CO.48

description:
SAMPLE 35
test


title: CO.57

description:
SAMPLE 39
test


title: White Root, Biological Rep 3


title: CO.34

description:
SAMPLE 30
test


title: CO.39

description:
SAMPLE 32
test


title: CO.47

description:
SAMPLE 34
test


title: Human rituximab-resistant l Raji/R cell line

city: Nanning

first: Fang

middle: Mei

last: Pan

state: Guangxi

address: No.71, Hedi Road

department: Chemotherapy

institute: Tumor Hospital of Guangxi Medical University

description: Gene expression data from the rituximab-resistant Raji/R cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212,Affymetrix, Santa Clara, CA,US) and Command Console Software 3.1 (Affymetrix, Santa Clara,CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies,Santa Clara, CA, US).

source_name: Human Raji cells treated with rituximab

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

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

value: Raji

value: Burkitt’s lymphoma


title: CO.35

description:
SAMPLE 31
test


title: CO.31

description:
SAMPLE 27
test


title: CO.33

description:
SAMPLE 29
test


title: CO.32

description:
SAMPLE 28
test


title: CO.30

description:
SAMPLE 26
test


title: Human rituximab-resistant l Jeko-1/R cell line

description: Gene expression data from the rituximab-resistant Jeko-1/R cell line

source_name: Human Jeko-1 cells treated with rituximab

value: mantle cell lymphoma


title: Human parental Jeko-1 cell line

description: Gene expression data from the parental Jeko-1 cell line

source_name: Human Jeko-1 cells without rituximab treatment


title: CO.28

description:
SAMPLE 24
test


title: CO.27

description:
SAMPLE 23
test


title: Human parental Raji cell line

description: Gene expression data from the parental Raji cell line

source_name: Human Raji cells without rituximab treatment


title: CO.26

description:
SAMPLE 22
test


title: CO.43

description:
SAMPLE 33
test


title: CO.22

description:
SAMPLE 20
test


title: CO.25

description:
SAMPLE 21
test


title: CO.21

description:
SAMPLE 19
test


title: CO.20

description:
SAMPLE 18
test


title: CO.19

description:
SAMPLE 17
test


title: reference vs BH_Salt-2

city: Suwon

first: seokyung

last: yoon

address: Onjeong-ro

country: South Korea

institute: KFRI

hyb_protocol: After checking labeling efficiency, each 750ng of cyanine 3-labeled and cyanine 5-labeled cRNA target were mixed and the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent Mouse whole genome 44K microarray. The arrays hybridized at 65oC for 17 h using Agilent Hybridization oven(Agilent Technology, USA). The hybridized miroarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction. Then normalization for Agilent one-color method was performed, which is  LOWESS and Per Gene: Normalize to median.

organism: Populus alba x Populus glandulosa

source_name: reference RNA

label_protocol: Each 0.2 ug total RNA was mixed T7 promoter primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 65 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was preformed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours. Amplified and labeled cRNA was purified on RNase mini column (Qiagen) according to the manufacturer’s protocol.

growth_protocol: Hybrid poplar (Populus alba × P. glandulosa) was chosen for this research. The plants were acclimated in soil and grown for 6 weeks in controlled conditions in a growth room (16 h light; light intensity, 150 μmol m-2sec-1; 24°C).

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

treatment_protocol: Plants with a height of about 15 cm were separately exposed to either drought or salt stress. For drought treatment, 6-week-old plants were subjected to progressive drought by withholding of water. Fully expanded leaves were collected after 9 days of treatment, and then subjected to RNA extraction. For salt treatment, 6-week-old plants were transferred to a container of 150 mM NaCl, and then treated with the salt solution for up to 72 h. Fully expanded leaves were collected after 24 h of treatment, and then subjected to RNA extraction. For control samples, leaves of plants were immediately collected before drought and salt treatments. At the time of harvest, leaves of plants (n = 3) were immediately frozen in liquid nitrogen and stored at −70°C.

tag: plant

value: pooling RNA from 18 popular samples

source_name: BH_Salt-treated popular

value: BH_Salt-treated popular


title: CO.29

description:
SAMPLE 25
test


title: reference vs BH_Dry-4

source_name: BH_Day-treated popular

value: BH_Day-treated popular


title: reference vs BH_Salt-4


title: reference vs BH_Notreat-2

source_name: BH_Notreated popular

value: BH_Notreated popular


title: CO.18

description:
SAMPLE 16
test


title: CO.16

description:
SAMPLE 15
test


title: reference vs BH_Dry-2


title: CO.15

description:
SAMPLE 14
test


title: reference vs BH_Notreat-4


title: Shortterm_BT474_pmTOR_S2481

description: rabbit polyclonal

value: phospho-mTOR

value: Millipore 09-343


title: MTECs_ALId2vd7_rep3

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: post-ALI MTECs: day 2 versus day 7, replicate #3

hyb_protocol: Two hybridizations were carried out in a sequential manner. The primary hybridization was performed by adding cDNA to the microarray which was incubated at 63 °C for 16-20 h. A second hybridization was carried out using the Cy3 and Cy5 labeled fluorescent dendrimers (Genisphere) which contain oligos complementary to the capture sequence in the dT primers.

scan_protocol: Slides were scanned immediately after hybridization in a PerkinElmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence. Each slide was scanned twice at constant laser power with two different PMT settings. Each scan was exported in GenePix format. The scans at both settings were combined using functional regression estimators to enhance detection of differential expression (see PMID 19058173).

data_processing: Microarray normalization and statistical analysis is performed using packages from the Bioconductor project executed in the R programming environment (PMID 15461798). Scans at both settings were combined using functional regression estimators generating a single dataset for each array (PMID 19058173). Within array normalization was performed using the robustspline method, and between arrays normalization was performed using the Aquantile method as implemented in the LIMMA package (PMID 16646809). Differential expression was assessed using linear models and empirical Bayes moderated F statistics, also using the LIMMA package, using a single model for time course data (PMID 15738394). As interpretation of microarray data is improved through the use of multiple annotation sources (PMID 20089164), probes were annotated using the manufacturer’s annotation files (http://alizadehlab.stanford.edu/heebo.html), annotations from ReMOAT (PMID 19923232), AILUN (PMID 17971777), AceView (PMID 16925834), and Ensembl (PMID 20459806) databases. Differences in gene expression were considered significant if P < 0.05 after adjustment for multiple testing (Benjamini & Hochberg, J Roy Statist Soc Ser B. 1995;57(1):289-300.), limiting the false discovery rate to <5%. Visualization and plotting was performed using DecisionSite for Functional Genomics (TIBCO Spotfire). Microarray data were deposited in GEO (Accession numbers pending). We performed visualization and plotting using TIBCO Spotfire DecisionSite for Functional Genomics (TIBCO Spotfire, Somerville, MA, USA).

source_name: post-ALI MTECs: day 2, replicate #3

label_protocol: From total RNA, first strand cDNA was generated by fluorophore/dendrimer specific oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900 kit (Genisphere). The 3DNA dT primers bear a capture sequence on the 5′ end that during hybridization binds Genisphere dendrimers labeled with either Cy3 or Cy5 dye in a sequence dependent fashion. Each sample was split in half, and labeled with each dye separately, creating technical replicates for each condition.

growth_protocol: Primary-culture mouse tracheal epithelial cells (mTECs) were established on Transwell membranes using air-liquid interface (ALI) conditions as described previously (You et al, AJP Lung, 2002, PMID 12388377)

extract_protocol: Total RNA was isolated using RNeasy micro kit (Qiagen, Valencia, CA)

value: tracheal epithelial cell

tag: culture conditions

value: cells were cultured at air-liquid interface (ALI)

tag: time (postali_day)

tag: strain

value: Male

source_name: post-ALI MTECs: day 7, replicate #3


title: MTECs_ALId7vd0_rep3

description: post-ALI MTECs: day 7 versus day 0, replicate #3

tag: cell type

source_name: post-ALI MTECs: day 0, replicate #3


title: CO.13

description:
SAMPLE 12
test


title: MTECs_ALId7vd0_rep2

description: post-ALI MTECs: day 7 versus day 0, replicate #2

source_name: post-ALI MTECs: day 7, replicate #2

tag: gender

source_name: post-ALI MTECs: day 0, replicate #2


title: MTECs_ALId0vd2_rep3

description: post-ALI MTECs: day 0 versus day 2, replicate #3


title: CO.10

description:
SAMPLE 9
test


title: MTECs_ALId0vd2_rep2

description: post-ALI MTECs: day 0 versus day 2, replicate #2

source_name: post-ALI MTECs: day 2, replicate #2


title: CO.8

description:
SAMPLE 8
test


title: T47D I3C (3)

city: Houston

first: Khandan

last: Keyomarsi

state: Tx

address: 1515 Holcombe Blvd. Unit 66

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

description: Illumina HT-12 v4 expression arrays

hyb_protocol: Illumina beadarray hybridization protocol for gene expression profiling. Performed by The Genomics Core Facility at MD Anderson Cancer according to manufactures instructions.

scan_protocol: Image acquisition performed by The Genomics Core Facility at MD Anderson Cancer according to manufactures instructions.

data_processing: Raw signal intensities were obtained using the Beadstudio analysis software from Illumina.Raw signal intensities were obtained using the Beadstudio analysis software from Illumina and imported into the lumi Bioconductor package (R version 2.15 and Bioconductor version 2.11). The lumi package was used to perform quality control, We used the robust spline normalization (RSN) algorithm to normalize between arrays. This algorithm combines the features of quantile and loess normalization, is designed to normalize the variance-stabilized data.

source_name: ER-positve, Luminal, I3C-Sensitive Breast Cancer Cell Line

label_protocol: TargetAmp - Nano Labeling Kit for Illumina Expression BeadChip.

growth_protocol: All cell lines were maintained in a humidified tissue culture incubator at 37ºC and 6.5% CO2. All cell lines were obtained from ATCC and were routinely authenticated and tested for mycoplasma contamination using the MycoAlert assay kit (Lonza). The culture media was a-MEM supplemented with 10% fetal calf serum (Atlanta Biological), 0.01M HEPES, 2 mM L-glutamine, and 0.01 mg/mL of ciprofloxacin, 0.1 mM non-essential amino acids and 1 mM sodium pyruvate.

extract_protocol: Total RNA was extracted from 2 x106 cells using the RNAeasy kit (Qiagen) and subjected to on column DNase I (NEB) digestion (all performed according to manufactures instructions). RNA integrity was confirmed using an Agilent Technologies Bioanalyzer 2100.

treatment_protocol: Microarray analysis was performed on three I3C sensitive cell lines (luminal ERa-positive: MCF-7, ZR751, and T47D) and three I3C insensitive cell lines (non-luminal ERa-negative: MDA-MB-231, MDA-MB-436, and MDA-MB-157) treated in triplicate with either 200 micromolar I3C or an equivalent volume of DMSO for 24 hours.

tag: treatment

tag: concentration i3c

value: 200 micromolar

value: breast cancer

tag: cell line


title: T47D I3C (1)

description: Illumina HT-12 v4 expression arrays

tag: tissue


title: CO.7

description:
SAMPLE 7
test

value: advanced colorectal cancer


title: MTECs_ALId2vd7_rep2

description: post-ALI MTECs: day 2 versus day 7, replicate #2


title: CO.12

description:
SAMPLE 11
test


title: CO.14

description:
SAMPLE 13
test


title: MTECs_ALId2vd7_rep1

description: post-ALI MTECs: day 2 versus day 7, replicate #1

source_name: post-ALI MTECs: day 2, replicate #1

source_name: post-ALI MTECs: day 7, replicate #1


title: CO.5

description:
SAMPLE 5
test

source_name: Tumor tissue


title: MTECs_ALId7vd0_rep1

description: post-ALI MTECs: day 7 versus day 0, replicate #1

source_name: post-ALI MTECs: day 0, replicate #1


title: CO.6

description:
SAMPLE 6
test

value: Responder


title: CO.4

description:
SAMPLE 4
test


title: MTECs_ALId0vd2_rep1

description: post-ALI MTECs: day 0 versus day 2, replicate #1


title: T47D I3C (2)

description: Illumina HT-12 v4 expression arrays


title: CO.3

description:
SAMPLE 3
test

value: Non-responder


title: MCF-7 I3C (2)

description: Illumina HT-12 v4 expression arrays


title: T47D DMSO (1)

description: Illumina HT-12 v4 expression arrays

value: DMSO

value: 0 micromolar


title: T47D DMSO (3)

description: Illumina HT-12 v4 expression arrays


title: CO.2

description:
SAMPLE 2
test


title: MCF-7 I3C (1)

description: Illumina HT-12 v4 expression arrays


title: MCF-7 DMSO (1)

description: Illumina HT-12 v4 expression arrays


title: MCF-7 I3C (3)

description: Illumina HT-12 v4 expression arrays


title: MCF-7 DMSO (3)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-231 I3C

description: Illumina HT-12 v4 expression arrays

source_name: ER-negative, Basal I3C-Insensitive Breast Cancer Cell Line


title: MCF-7 DMSO (2)

description: Illumina HT-12 v4 expression arrays


title: CO.1

description:
SAMPLE 1
test


title: MDA-MB-231 DMSO (3)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-231 DMSO (2)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId3_Scr_shRNA_rep3_TH3

description:
d3.Scr.r3.TH3
ALI day 3, Scrambled Control shRNA, replicate 3, sample #3

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: Quantile normalized data generated in BeadStudio 3.0 (Illumina, San Diego, CA) were adjusted first for negative numbers by adding a small constant to all signal values. Data were then Log2-transformed. Data were then Log2-transformed. Probes not detected on at least one array (detection value p<0.05) were excluded from further analysis. Differential expression was detected using using linear models and empirical Bayes moderated F statistics, as implemented in the LIMMA package (PMID 16646809) in the Bioconductor project executed in the R programming environment (PMID 15461798). Differences in gene expression were considered significant if P < 0.05 after adjustment for multiple testing (Benjamini & Hochberg, J Roy Statist Soc Ser B. 1995;57(1):289-300.), limiting the false discovery rate to <5%. Visualization and plotting was performed using DecisionSite for Functional Genomics (TIBCO Spotfire).

label_protocol: Biotinylated aRNA were prepared using the Illumina TotalPrep Kit (Ambion) per manufacturer's protocol.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Lentivirus-mediated shRNA transduction of mTEC was performed as previously described (Horani, et al, 2012 & 2013, PMIDs 23040496 & 23713995)

tag: shRNA

value: Scr shRNA


title: MDA-MB-157 I3C (1)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId3_Myb_shRNA_rep3_TH6

description:
d3.Myb.r3.TH6
ALI day 3, Myb shRNA, replicate 3, sample #6

value: Myb shRNA


title: MDA-MB-157 DMSO (3)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-231 DMSO (1)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-157 I3C (2)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-231 I3C (1)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId9_Scr_shRNA_rep2_TH8

description:
d9.Scr.r2.TH8
ALI day 9, Scrambled Control shRNA, replicate 2, sample #8


title: MTECs_ALId9_Scr_shRNA_rep3_TH9

description:
d9.Scr.r3.TH9
ALI day 9, Scrambled Control shRNA, replicate 3, sample #9


title: MTECs_ALId9_Myb_shRNA_rep3_TH12

description:
d9.Myb.r3.TH12
ALI day 9, Myb shRNA, replicate 3, sample #12


title: MDA-MB-157 DMSO (1)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-157 I3C (3)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId3_Myb_shRNA_rep1_TH4

description:
d3.Myb.r1.TH4
ALI day 3, Myb shRNA, replicate 1, sample #4


title: MDA-MB-436 I3C (3)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId3_Scr_shRNA_rep1_TH1

description:
d3.Scr.r1.TH1
ALI day 3, Scrambled Control shRNA, replicate 1, sample #1


title: MTECs_ALId9_Scr_shRNA_rep1_TH7

description:
d9.Scr.r1.TH7
ALI day 9, Scrambled Control shRNA, replicate 1, sample #7


title: MDA-MB-436 I3C (2)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-157 DMSO(2)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId9_Myb_shRNA_rep1_TH10

description:
d9.Myb.r1.TH10
ALI day 9, Myb shRNA, replicate 1, sample #10


title: MTECs_ALId3_Myb_shRNA_rep2_TH5

description:
d3.Myb.r2.TH5
ALI day 3, Myb shRNA, replicate 2, sample #5


title: MDA-MB-436 I3C (1)

description: Illumina HT-12 v4 expression arrays


title: PRED treated C7H2 cells, exp3

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: Gene expression profile of 6 hours 7.0e-7M prednisolone treated C7H2 T-ALL cells, experiment 3.

hyb_protocol: Target samples were hybridized to Human HuGene 1.0 ST microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the GCRMA method (option GSB.adjust set to FALSE), for probe set summarization the robust methods from the affyPLM package were used. For transcript probe set definition a custom CDF package was used, that was based on a complete re-alignment of the Exon microarray oligo-probes and annotation to Ensembl version 74.

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: T-ALL CCRF-CEM-C7H2 cells were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity.

extract_protocol: Total cell RNA was extracted using the TRIZOL protocol, and RNA quantity and integrity determined by optical density measurements and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively. Two hundred and fifty ng of high quality RNA was processed using the Ambion Affymetrix GeneChip WT Expression Kit.

treatment_protocol: Cells were treated in 3 independent experiments for 6 hours either with 1.0e-7M dexamethasone, 7.0e-7M prednisolone (both synthetic GCs) or 0.1% ethanol as empty carrier control.

value: childhood acute lymphoblastic leukemia cells (chALL)

value: prednisolone

tag: concentration


title: DEX treated C7H2 cells, exp3

description: Gene expression profile of 6 hours 1.0e-7M dexamethasone treated C7H2 T-ALL cells, experiment 3.

value: dexamethasone


title: EtOH treated C7H2 cells, exp3

description: Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, experiment 3.

value: ethanol


title: MTECs_ALId3_Scr_shRNA_rep2_TH2

description:
d3.Scr.r2.TH2
ALI day 3, Scrambled Control shRNA, replicate 2, sample #2


title: DEX treated C7H2 cells, exp2

description: Gene expression profile of 6 hours 1.0e-7M dexamethasone treated C7H2 T-ALL cells, experiment 2.


title: ZR75-1 DMSO (3)

description: Illumina HT-12 v4 expression arrays


title: ZR75-1 DMSO (2)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-436 DMSO (2)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-436 DMSO (1)

description: Illumina HT-12 v4 expression arrays


title: ZR75-1 I3C (3)

description: Illumina HT-12 v4 expression arrays


title: MTECs_ALId9_Myb_shRNA_rep2_TH11

description:
d9.Myb.r2.TH11
ALI day 9, Myb shRNA, replicate 2, sample #11


title: PRED treated C7H2 cells, exp2

description: Gene expression profile of 6 hours 7.0e-7M prednisolone treated C7H2 T-ALL cells, experiment 2.


title: ZR75-1 I3C (1)

description: Illumina HT-12 v4 expression arrays


title: ZR75-1 I3C (2)

description: Illumina HT-12 v4 expression arrays


title: ZR75-1 DMSO (1)

description: Illumina HT-12 v4 expression arrays


title: MDA-MB-436 DMSO (3)

description: Illumina HT-12 v4 expression arrays


title: HT1197 eIF3a knock-down cells, experiment 3

description: eIF3a knock-down cells, experiment 3.

hyb_protocol: Following RNA purification, 20 μg of cRNA were fragmented at 95° using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to the GeneChips (Human Genome 133 plus 2.0).

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: Data preprocessing was performed in R using Bioconductor's (version 2.15.1) GCRMA package (version 2.28.0).

source_name: eIF3a knock-down cells, experiment 3

label_protocol: 500 ng total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: HT1197 cells were grown under standard culture conditions.

extract_protocol: RNA was extracted using TRI-reagent (Sigma) according to manufacturer's protocol.

treatment_protocol: HT1197 cells with a construct containing an shRNA against eIF3a were either treated for 72 hours with doxycycline (resulting in the eIF3a knock-down) or kept in culture for 72 hours without additional treatment (control samples).

value: Urinary Bladder Cancer (UBC)

tag: group

value: eIF3a knock-down

tag: experiment

value: doxycyclin


title: EtOH treated C7H2 cells, exp2

description: Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, experiment 2.


title: EtOH treated C7H2 cells, exp1

description: Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, experiment 1.


title: 8.0e-6M Solu-dacortin treated C7H2 cells, expA3

description: Gene expression profile of 6 hours 8.0e-6M Solu-dacortin (prednisolone 21-(sodium succinate)) treated C7H2 T-ALL cells, experiment A3.

extract_protocol: Total cell RNA was extracted using the TRIZOL protocol, and RNA quantity and integrity determined by optical density measurements and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively. Two hundred and fifty ng of high quality RNA was processed using the Ambion Affymetrix GeneChip WT Expression Kit. For the 3 GeneChips for 8.0e-6M Solu-dacortin treatment the Affymetrix 3' IVT Expression Kit was used for cRNA cleanup, instead of components from the Affymetrix GeneChip WT Expression Kit.

tag: treated with

value: Solu-dacortin (prednisolone)


title: HT1197 control cells, experiment 3

description: control cells, experiment 3.

source_name: control cells, experiment 3

value: CTRL


title: T47D DMSO (2)

description: Illumina HT-12 v4 expression arrays

value: breast cancer


title: CO.11

description:
SAMPLE 10
test

tag: disease state

value: advanced colorectal cancer


title: PRED treated C7H2 cells, exp1

description: Gene expression profile of 6 hours 7.0e-7M prednisolone treated C7H2 T-ALL cells, experiment 1.


title: 8.0e-6M Solu-dacortin treated C7H2 cells, expA2

description: Gene expression profile of 6 hours 8.0e-6M Solu-dacortin (prednisolone 21-(sodium succinate)) treated C7H2 T-ALL cells, experiment A2.


title: 4.0e-6M Solu-dacortin treated C7H2 cells, expA3

description: Gene expression profile of 6 hours 4.0e-6M Solu-dacortin (prednisolone 21-(sodium succinate)) treated C7H2 T-ALL cells, experiment A3.


title: DEX treated C7H2 cells, exp1

description: Gene expression profile of 6 hours 1.0e-7M dexamethasone treated C7H2 T-ALL cells, experiment 1.


title: 8.0e-6M Solu-dacortin treated C7H2 cells, expA1

description: Gene expression profile of 6 hours 8.0e-6M Solu-dacortin (prednisolone 21-(sodium succinate)) treated C7H2 T-ALL cells, experiment A1.


title: HT1197 eIF3a knock-down cells, experiment 2

description: eIF3a knock-down cells, experiment 2.

source_name: eIF3a knock-down cells, experiment 2


title: WT-2

first: Wayne

middle: W

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.12). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's test. Only data with a false discovery rate (FDR) adjusted p-value <0.05 and at least 2x differential expression were included in the analysis. Data underwent z-score transformation for display.

source_name: Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: genotype/variation

value: Foxp3cre control


title: WT-3


title: HT1197 control cells, experiment 2

description: control cells, experiment 2.

source_name: control cells, experiment 2


title: DEX treated C7H2 cells, expA3

description: Gene expression profile of 6 hours 1.0e-7M dexamethasone treated C7H2 T-ALL cells, experiment A3.


title: P300-3


title: MDA-MB-231 I3C (2)

description: Illumina HT-12 v4 expression arrays

value: 200 micromolar


title: EtOH treated C7H2 cells, expA3

description: Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, experiment A3.


title: WT-1


title: HT1197 control cells, experiment 1

description: control cells, experiment 1.

source_name: control cells, experiment 1


title: P300-1


title: P300-2


title: CBP-3


title: HT1197 eIF3a knock-down cells, experiment 1

description: eIF3a knock-down cells, experiment 1.

source_name: eIF3a knock-down cells, experiment 1


title: DEX treated C7H2 cells, expA2

description: Gene expression profile of 6 hours 1.0e-7M dexamethasone treated C7H2 T-ALL cells, experiment A2.


title: CBP-2


title: 4.0e-6M Solu-dacortin treated C7H2 cells, expA2

description: Gene expression profile of 6 hours 4.0e-6M Solu-dacortin (prednisolone 21-(sodium succinate)) treated C7H2 T-ALL cells, experiment A2.


title: CBP-1


title: 4.0e-6M Solu-dacortin treated C7H2 cells, expA1

description: Gene expression profile of 6 hours 4.0e-6M Solu-dacortin (prednisolone 21-(sodium succinate)) treated C7H2 T-ALL cells, experiment A1.


title: EtOH treated C7H2 cells, expA1

description: Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, experiment A1.


title: EtOH treated C7H2 cells, expA2

description: Gene expression profile of 6 hours ethanol treated C7H2 T-ALL cells, experiment A2.


title: Tcacao_endophyte_inoculated_Leaf_T14_rep4

city: Panama

first: Luis

last: Mejia

address: Roosvelt Ave. Tupper Building – 401

department: Smithsonian Tropical Research Institute

country: Panama

institute: Smithsonian Institution

hyb_protocol: Hybridizations were performed by the Pennsylvania State University Core Genomics Faciliy, according to published facility protocols (http://www.huck.psu.edu/facilities/genomics-up/protocols/nimblegen-protocols).

scan_protocol: Arrays were scanned with an Axon GenePix 4000B scanner.

data_processing: Data was preprocessed with the robust multiarray analysis (RMA) method and normalized using quantile normalization

organism: Theobroma cacao

source_name: Theobroma cacao leaf inoculated with fungal endophyte Colletotrichum tropicale strain 5101

label_protocol: One µg of total RNA was amplified using mRNA amplification kit (Amino Allyl MessageAmp II™, Ambion, Austin, TX) prior to labeling and hybridization. aRNA was dye coupled with Cy3 or Cy5 (GE Health Care #RPN5661) and subsequently purified according to manufacturer’s instructions.

growth_protocol: Theobroma cacao seedlings used in this experiment were grown in Percival growth chambers (model I35LL, 115 volts, 1/4 Hp, series: 8503122.16, Percival Scientific, Inc., Perry IA) with 12/12 h light/dark photoperiod and temperatures of 30ºC and 26ºC respectively.

extract_protocol: Total RNA was extracted as in Verica et al. Plant Cell Rep. 23(6):404)

treatment_protocol: Seedlings were inoculated one time by spraying conidia (asexual spores) suspended in water (10^6 spore/ml) of the endophytic fungus Colletotrichum tropicale, as in Mejia et al. 46(1):4) to treated seedlings. Three un-inoculated T. cacao leaves (E-) were collected at time 0, just prior to inoculation, and four T. cacao leaves inoculated with C. tropicale (E+) were collected at 3, 7, and 14 dpi, each leaf from a different plant. Collected leaves were placed in RNA stabilizing solution RNAlater until RNA was extracted.

tag: genotype

value: leaf

tag: time

value: 14 dpi


title: Tcacao_endophyte_inoculated_Leaf_T7_rep2

value: inoculated with fungal endophyte Colletotrichum tropicale strain 5101

value: 7 dpi


title: Tcacao_endophyte_inoculated_Leaf_T14_rep2


title: Tcacao_endophyte_inoculated_Leaf_T7_rep3


title: Tcacao_endophyte_inoculated_Leaf_T14_rep1


title: TgCRND8_Day80_biological_rep4

city: Toronto

first: Peter

last: St George-Hyslop

state: Ontario

address: 6 Queen’s Park Crescent West

country: Canada

institute: Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto

description:
TG80_4
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 80d

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C  on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Arrays are scanned using a GeneArray Scanner.

data_processing: The data were analyzed with Biocondoctor packages on R statistical software.

label_protocol: The total RNA was reverse transcribed using a T7-promoter coupled oligo(d)T primer (GeneChip T7-Oligo(d)T Promoter Primer Kit, Affymetrix). After the second-strand cDNA synthesis, an in vitro transcription (IVT) reaction was performed using an Enzo BioArray High Yield RNA transcript labeling kit (Affymetrix).

extract_protocol: The frozen mice brains were treated with RNAlater ICE (Ambion) to stabilized RNA, and then cut into the three parts; olfactory bulb, forebrain and cerebellum & brainstem. The RNA samples (forebrain) were extracted using TRIzol (Invitorogen) followed by secondary clean-up using RNAeasy Mini column (QIAGEN) to avoid genomic DNA contamination.

tag: genetic background

value: TgCRND8 transgenic mouse

tag: transgene

value: APPSwe/Ind

tag: age

value: 80 days

value: forebrain


title: Tcacao_endophyte_inoculated_Leaf_T7_rep4


title: Control_Day70_biological_rep4

description:
L70_4
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 70d

value: non-transgenic littermate mouse

value: 70 days


title: DEX treated C7H2 cells, expA1

description: Gene expression profile of 6 hours 1.0e-7M dexamethasone treated C7H2 T-ALL cells, experiment A1.

tag: cell type

value: childhood acute lymphoblastic leukemia cells (chALL)

value: dexamethasone


title: Control_Day150_biological_rep3

description:
L150_3
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 150d

value: 150 days


title: TgCRND8_Day150_biological_rep4

description:
TG150_4
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 150d


title: TgCRND8_Day70_biological_rep4

description:
TG70_4
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 70d


title: Control_Day150_biological_rep4

description:
L150_4
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 150d


title: Control_Day80_biological_rep4

description:
L80_4
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 80d


title: Tcacao_endophyte_inoculated_Leaf_T3_rep2

tag: treatment

value: 3 dpi


title: Tcacao_endophyte_inoculated_Leaf_T14_rep3


title: Tcacao_endophyte_inoculated_Leaf_T3_rep1


title: Tcacao_uninoculated_Leaf_T0_rep3

source_name: Theobroma cacao leaf Control un-inoculated

value: un-inoculated control

value: 0 dpi


title: Tcacao_endophyte_inoculated_Leaf_T3_rep4


title: Tcacao_endophyte_inoculated_Leaf_T7_rep1


title: Control_Day80_biological_rep3

description:
L80_3
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 80d


title: Tcacao_endophyte_inoculated_Leaf_T3_rep3


title: Control_Day150_biological_rep2

description:
L150_2
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 150d


title: TgCRND8_Day80_biological_rep3

description:
TG80_3
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 80d


title: 2 Gy (BMMSC)

city: Minneapolis

first: susanta

middle: k

last: hui

state: MN

address: 420 Delaware Street SE

department: Therapeutic Radiology

institute: University of Minnesota

description:
Test
SAMPLE 4

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
The fold_change.txt reports Fold_change 1 = test/control (i.e., 2 Gy (ESMSC)/0 Gy (ESMSC)) ratios and Fold_change 2 = test/control (i.e., 2 Gy (BMMSC)/0 Gy (BMMSC)) ratios.

label: SYBR Green

source_name: BMMSC

label_protocol: PCR assays were performed using human bone marrow mesenchymal stem cells, human embryonic stem cells, and human Wnt signaling pathway PCR assay panel (SA Biosciences) following the Manufacturer’s instructions. Reverse transcription was performed withthe same amount of total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Max3000P, Strategene) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit according to th emanufactures instruction

treatment_protocol: X-ray beams at 2Gy or 0Gy were irradiated 4 hours before extracting RNA.

value: bone marrow mesenchymal stem cells (BMMSC)

tag: stimulation

value: 2 Gy irradiation

value: 4 hours


title: TgCRND8_Day70_biological_rep3

description:
TG70_3
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 70d


title: Tcacao_uninoculated_Leaf_T0_rep2

value: leaf


title: Control_Day70_biological_rep3

description:
L70_3
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 70d


title: TgCRND8_Day150_biological_rep2

description:
TG150_2
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 150d


title: 0 Gy (BMMSC)

description:
Control
SAMPLE 3

value: none (no radiation)


title: 2 Gy (ESMSC)

description:
Test
SAMPLE 2

source_name: ESMSC

value: embryonic mesenchymal stem cells (ESMSC)


title: TgCRND8_Day80_biological_rep2

description:
TG80_2
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 80d

value: TgCRND8 transgenic mouse

value: APPSwe/Ind


title: 0 Gy (ESMSC)

description:
Control
SAMPLE 1


title: Tcacao_uninoculated_Leaf_T0_rep1


title: TgCRND8_Day150_biological_rep1

description:
TG150_1
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 150d

value: forebrain


title: Control_Day70_biological_rep2

description:
L70_2
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 70d

value: non-transgenic littermate mouse


title: Control_Day150_biological_rep1

description:
L150_1
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 150d


title: 5497 - 2mo Lkb1 KO 2

first: Jinsheng

last: Yu

address: 660 S. Euclid Ave.

department: Genetics

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio (v2010)

source_name: Pooled RNA extracted from 3 sciatic nerves. Each nerve was dissected from different mouse.

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

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

tag: strain

value: mixed FVB/C57BL/6

value: mouse sciatic nerve

value: LKB1-SCKO mutant


title: 5491 - 2mo mixed Ctrl 2

description: replicate 2

tag: tissue

value: control


title: Control_Day80_biological_rep1

description:
L80_1
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 80d

value: 80 days


title: Control_Day80_biological_rep2

description:
L80_2
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 80d


title: TgCRND8_Day70_biological_rep2

description:
TG70_2
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 70d

value: 70 days


title: TgCRND8_Day80_biological_rep1

description:
TG80_1
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 80d


title: TgCRND8_Day150_biological_rep3

description:
TG150_3
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 150d

value: 150 days


title: 5490 - 2mo mixed Ctrl 1

description: replicate 1


title: 5496 - 2mo Lkb1 KO 1

description: replicate 1


title: TgCRND8_Day70_biological_rep1

description:
TG70_1
Gene expression data from a forebrain sample of a transgenic mouse model of Alzheiemr's disease (TgCRND8) at the age of 70d


title: Control_Day70_biological_rep1

description:
L70_1
Gene expression data from a forebrain sample of a non-transgenic littermate mouse at the age of 70d


title: Kainate-induced status epilepticus, Scrambled ODN,14B

city: Irvine

first: Shawn

last: McClelland

state: CA

address: 19182 Jamboree

department: Anatomy & Neurobiology

institute: UC Irvine

description: male adult rats

data_processing: The data were normalised using Genomestudio across Illumina standards

organism: Rattus norvegicus

source_name: Rat CA1 hippocampus

extract_protocol: RNA was extracted with array grade total RNA isolation kit from SABiosciences. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Rats were injected with either saline or Kainate (to induce status epilepticus), 3 hours after status epilepticus was abrogated oligodeoxynucleotides (Scrambled or hcn1 NRSE sequence) were infused ICV

tag: injection

value: Kainate

tag: odn

value: Scrambled


title: Outer hair cells-1 month-0

city: Omaha

first: David

last: He

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

description:
Whole genome transcriptome expression in the outer hair cells at the age of one month of CBA/J mice
OHC-0

hyb_protocol: The transcriptome profile of the two cell populations was determined by GeneChip microarray analysis (Affymetrix, Santa Clare, CA, USA). Synthesis of cDNA, hybridization to chips, and washes were performed according to the manufacture’s protocol.

scan_protocol: GeneChips were scanned at 3 µm density with a GeneArray Scanner (Affymetrix).

data_processing: The data was normalized by Affy program “Expression Console”.  Mean fluorescence signal intensity for each probe was quartile normalized. The average of three mean signals for each gene probe was normalized to that for an added control oligonucleotide. Each gene probe was assessed for expression based on a Wilcoxon Rank-Sum test of the gene probe set signals compared to the distribution of signals from the background.

source_name: Mouse cochlea at the age of one month

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Amplification and synthesis of cDNA were completed using the NuGEN Ovation Pico WTA System V2.

growth_protocol: CBA/J mice were used at the age of 25-35 days.

extract_protocol: Total RNA from approximately 2,000 IHCs and OHCs separately suspended in RNALater were extracted and purified using the Qiagen miRNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: The basilar membrane together with the organ of Corti was isolated and transferred to an enzymatic digestion medium in a small Petri dish. The enzymatic digestion medium contained 1 ml L-15 and 1 mg Collegene IV (Sigma). After 5 min incubation at room temperature, the tissue was transferred to a small plastic chamber (0.8 ml in volume) containing enzyme-free culture medium (Leibovitz's L-15, 7.35 pH, 300 mOsm). Hair cells were separated after gentle trituration of the tissue with a small pipette.

value: CBA/J

value: outer hair cells in the cochlea

value: 25-35 days old


title: Kainate-induced status epilepticus, Scrambled ODN,8B

description: male adult rats


title: Inner hair cells-1 month-2

description:
Whole genome transcriptome expression in the inner hair cells at the age of one month of CBA/J mice
IHC-2

data_processing:
The data was normalized by Affy program “Expression Console”.  Mean fluorescence signal intensity for each probe was quartile normalized. The average of three mean signals for each gene probe was normalized to that for an added control oligonucleotide. Each gene probe was assessed for expression based on a Wilcoxon Rank-Sum test of the gene probe set signals compared to the distribution of signals from the background.
Please note that 18,240 transcripts (out of total 41,345 mouse RefSeq transcripts included in the microarray) were examined after excluding control sequences and judiciously setting a cutoff for background. Of those, 16,647 and 17,711 transcripts were considered "expressed" in IHCs and OHCs, respectively, and 16,117 transcripts were expressed in both cell populations ('HC-Transcriptomes.xlsx' available on Series record).

value: inner hair cells in the cochlea


title: Kainate-induced status epilepticus, Scrambled ODN,13B

description: male adult rats


title: Inner hair cells-1 month-3

description:
Whole genome transcriptome expression in the inner hair cells at the age of one month of CBA/J mice
IHC-3


title: Kainate-induced status epilepticus, NRSE ODN,6B

description: male adult rats

value: NRSE


title: Kainate-induced status epilepticus, NRSE ODN,17B

description: male adult rats


title: Outer hair cells-1 month-2

description:
Whole genome transcriptome expression in the outer hair cells at the age of one month of CBA/J mice
OHC-2


title: Kainate-induced status epilepticus, NRSE ODN,15B

description: male adult rats


title: Control, Scrambled ODN,10B

description: male adult rat

value: Saline


title: Kainate-induced status epilepticus, NRSE ODN,19B

description: male adult rats


title: Control, Scrambled ODN,2B

description: male adult rat


title: Outer hair cells-1 month-3

description:
Whole genome transcriptome expression in the outer hair cells at the age of one month of CBA/J mice
OHC-3


title: Kainate-induced status epilepticus, Scrambled ODN,8

description: male adult rat


title: Inner hair cells-1 month-1

description:
Whole genome transcriptome expression in the inner hair cells at the age of one month of CBA/J mice
IHC-1


title: Outer hair cells-1 month-1

description:
Whole genome transcriptome expression in the outer hair cells at the age of one month of CBA/J mice
OHC-1


title: Kainate-induced status epilepticus, Scrambled ODN,14

description: male adult rat


title: Control, Scrambled ODN,1B

description: male adult rat


title: Kainate-induced status epilepticus, Scrambled ODN,13

description: male adult rat


title: Control, Scrambled ODN,9B

description: male adult rat


title: Kainate-induced status epilepticus, NRSE ODN,15

description: KA+NRSE n=4 male adult rats


title: Kainate-induced status epilepticus, NRSE ODN,17

description: KA+NRSE n=4 male adult rats


title: Control, Scrambled ODN,10

description: male adult rat


title: Kainate-induced status epilepticus, NRSE ODN,6

description: KA+NRSE n=4 male adult rats


title: Kainate-induced status epilepticus, NRSE ODN,19

description: KA+NRSE n=4 male adult rats


title: Normal 15, control tissue

city: Aurora

first: Stephen

middle: C

last: Dreskin

state: CO

department: Division of Allergy and Clinical Immunology, Department of Medicine

institute: University of Colorado Denver

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Affy GCS3000.

data_processing: Hybridization intensities were quantified and normalized across all arrays using the RMA algorithm with GC adjust available as an array processing tool on Partek® Genomics Suite™ 6.5 software (St. Louis, MS).

source_name: tissue biopsy of normal skin from healthy control

label_protocol: Standard Affymetrix procedures.

growth_protocol: Not applicable.

value: normal skin

tag: urticaria status

value: non-afffected

tag: patient


title: Control, Scrambled ODN,1

description: male adult rat


title: Normal 12, control tissue


title: Normal 14, control tissue


title: Normal 13, control tissue


title: Control, Scrambled ODN,9

description: male adult rat


title: Patient 8, control tissue

source_name: tissue biopsy of non-lesional skin from CIU patient

value: non-lesional skin

value: affected


title: Control, Scrambled ODN,2

description: male adult rat


title: PBMC genomic DNA_Control11

type: genomic

first: Patrick

last: McGowan

address: 1265 Military Trail

department: Biological Sciences

institute: University of Toronto Scarborough

description:
PBMC genomic DNA from Control subject 11
7985#WG0153568-DNA#B11#G00216

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Illumina Genome Studio; the non_normalized.txt contains unmethylated (A) and methylated (B) signal intensities.

molecule: genomic DNA

source_name: Control PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Omega EZNA Tissue DNA Kit; Qiagen MinElute Reaction Cleanup Kit; Genome Quebec sample processing protocols

tag: gender

value: female

tag: subject id

value: Control subject 11

value: Control

value: peripheral blood mononuclear cells (PBMC)


title: Patient 7, lesion tissue

source_name: tissue biopsy of urticaria lesion from CIU patient

value: lesional skin


title: Normal 11, control tissue


title: PBMC genomic DNA_Control12

description:
PBMC genomic DNA from Control subject 12
7985#WG0153568-DNA#B12#G00143

value: Control subject 12

tag: disease state


title: Patient 6, control tissue


title: Patient 6, lesion tissue


title: Patient 7, control tissue


title: PBMC genomic DNA_Control10

description:
PBMC genomic DNA from Control subject 10
7985#WG0153568-DNA#B10#G00199

value: Control subject 10


title: PBMC genomic DNA_Control8

description:
PBMC genomic DNA from Control subject 8
7985#WG0153568-DNA#B08#G00208

value: Control subject 8


title: PBMC genomic DNA_CFS11

description:
PBMC genomic DNA from CFS subject 11
7985#WG0153568-DNA#B05#G00121

source_name: CFS PBMC

value: CFS subject 11

value: Chronic Fatigue Syndrome (CFS)


title: Patient 4, control tissue


title: PBMC genomic DNA_Control9

description:
PBMC genomic DNA from Control subject 9
7985#WG0153568-DNA#B09#G00150

value: Control subject 9


title: Patient 3, control tissue


title: Patient 4, lesion tissue


title: Patient 2, control tissue


title: prostate cancer sample P542

city: Porto

first: Manuel

middle: R.

last: Teixeira

address: Rua Dr. António Bernardino de Almeida

department: Department of Genetics

country: Portugal

institute: Portuguese Oncology Institute-Porto

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

data_processing: Raw data was pre-processed at the gene level using the RMA approach implemented in Expression Console (Affymetrix; gene-core analysis).

source_name: Primary prostate cancer sample

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue samples using TRIzol (Invitrogen by Life Technologies, Carlsbad, CA, U.S.A.)

value: Primary prostate cancer biopsy

tag: ets rearrangement

value: ETV1 rearrangement


title: PBMC genomic DNA_CFS7

description:
PBMC genomic DNA from CFS subject 7
7985#WG0153568-DNA#B01#G00021

value: CFS subject 7


title: Patient 3, lesion tissue

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


title: PBMC genomic DNA_Control5

description:
PBMC genomic DNA from Control subject 5
7985#WG0153568-DNA#A11#G00135

value: Control subject 5


title: PBMC genomic DNA_Control6

description:
PBMC genomic DNA from Control subject 6
7985#WG0153568-DNA#A12#G00213

value: Control subject 6


title: PBMC genomic DNA_CFS10

description:
PBMC genomic DNA from CFS subject 10
7985#WG0153568-DNA#B04#G00030

value: CFS subject 10


title: prostate cancer sample P525


title: Patient 2, lesion tissue

value: affected


title: Patient 1, control tissue

value: non-lesional skin


title: PBMC genomic DNA_Control7

description:
PBMC genomic DNA from Control subject 7
7985#WG0153568-DNA#B07#G00162

value: female

value: Control subject 7

value: Control


title: PBMC genomic DNA_CFS8

description:
PBMC genomic DNA from CFS subject 8
7985#WG0153568-DNA#B02#G00059

value: CFS subject 8

value: peripheral blood mononuclear cells (PBMC)


title: prostate cancer sample P522

value: ETV4 rearrangement


title: PBMC genomic DNA_CFS9

description:
PBMC genomic DNA from CFS subject 9
7985#WG0153568-DNA#B03#G00054

value: CFS subject 9


title: PBMC genomic DNA_Control2

description:
PBMC genomic DNA from Control subject 2
7985#WG0153568-DNA#A08#G00140

value: Control subject 2


title: PBMC genomic DNA_Control4

description:
PBMC genomic DNA from Control subject 4
7985#WG0153568-DNA#A10#G00212

value: Control subject 4


title: PBMC genomic DNA_Control3

description:
PBMC genomic DNA from Control subject 3
7985#WG0153568-DNA#A09#G00158

value: Control subject 3


title: PBMC genomic DNA_CFS12

description:
PBMC genomic DNA from CFS subject 12
7985#WG0153568-DNA#B06#G00113

value: CFS subject 12

value: Chronic Fatigue Syndrome (CFS)


title: prostate cancer sample P488

value: Primary prostate cancer biopsy

value: ETV1 rearrangement


title: prostate cancer sample P499


title: Patient 1, lesion tissue

value: lesional skin


title: Control Visceral fat

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

description: Gene expression data

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® Human Gene 1.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 12.5. RMA16 algorithm was used for normalization

source_name: Control Visceral fat

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion). For cDNA fragmentation and labeling Affymetrix WT Terminal Labeling kit (Affymetrix) was used.

extract_protocol: TriZol reagent (Life Technologies)

value: Visceral fat


title: PBMC genomic DNA_CFS4

description:
PBMC genomic DNA from CFS subject 4
7985#WG0153568-DNA#A04#G00042

value: CFS subject 4


title: prostate cancer sample P487

value: ERG rearrangement


title: prostate cancer sample P470

value: No ETS rearrangement


title: PBMC genomic DNA_CFS5

description:
PBMC genomic DNA from CFS subject 5
7985#WG0153568-DNA#A05#G00080

value: female

value: CFS subject 5


title: PBMC genomic DNA_Control1

description:
PBMC genomic DNA from Control subject 1
7985#WG0153568-DNA#A07#G00211

value: Control subject 1

value: Control

value: peripheral blood mononuclear cells (PBMC)