title: 38w Ath HF+BCAA-2

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

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

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method on core dataset.

source_name: 38w Ath HF+BCAA

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

extract_protocol: Total RNA was isolated from frozen liver tissue samples using a High Pure RNA Tissue Kit (Roche Applied Science, Indianapolis, IN) according to the manufacturer’s protocol.

treatment_protocol: Ath & HF diet mice were generated as described previously. 5 Male C57BL/6J mice were maintained in a pathogen-free animal facility under a standard 12-h/12-h light/dark cycle. After weaning at week 8, male mice were divided randomly into 3 groups and each group was given one of the following diets for 30 or 60 weeks: (i) basal diet, (ii) Ath & HF diet, or (iii) Ath & HF diet supplemented with 3% BCAA. Mice were killed at week 38 to analyze the progression of hepatic fibrosis or at week 68 to analyze the development of hepatic tumors.

tag: gender

value: Male


title: 38w Ath HF+BCAA-3

status: Public on Jun 12 2017

type: RNA

country: Japan

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain


title: 68w Ath HF+BCAA-1

source_name: 68w Ath HF+BCAA


title: 68w Ath HF-2

source_name: 68w Ath HF


title: A5633_Unt-4B

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that did not have detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

source_name: Unt

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: RAW264.7 cells were maintained in DMEM, 10%FBS, 20mM Hepes, and 2mM glutamine by standard procedures.

extract_protocol: RNA was purified by Qiagen RNAeasy kit

treatment_protocol: RAW264.7 cells were treated with individual TLR ligands (100 ng/mL LPS, 1 μM P3C, and 1 μM R848 for stimulation of TLR4, TLR2, and TLR7, respectively) for either 1, 2 or 4 h. LPS was from Alexis Biochemicals, Salmonella minnesota R595 TLRgrade, ALX-581-008-L002. R848 was from Enzo Life Sciences Inc. Pam3CSK4 was from Invivogen, San Diego, CA.

tag: ligand

value: Untreated

tag: ligand concentration

value: Zero

tag: incubation time

tag: experimental replicate

value: B

tag: cell type

value: Macrophage

tag: cell line


title: 68w Ath HF+BCAA-2


title: A5622_Unt-2B


title: 68w Ath HF+BCAA-3


title: ML01_PFC-Ctrl1

city: bethesda

first: abdel

last: elkahloun

address: 50 south dr

institute: nih

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

source_name: Home caged animal

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse MoGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 200 ng of total RNA was used for labeling with the Ambion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652). After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Mice were socialy defeated or home caged.

tag: tissue

value: prefrontal cortex

tag: genotype/variation

value: wild type

tag: protocol

value: Home caged animal


title: A5623_LPS-4B

source_name: LPS

value: LPS

value: 100 ng/mL


title: 38w Ath HF-1

source_name: 38w Ath HF


title: A5626_R848-4B

value: 1 μM


title: 68w Ath HF-1


title: A5625_P3C-4B


title: 38w Ath HF-3


title: 38w Ath HF-2


title: 38w basal diet-3

source_name: 38w basal diet


title: 38w basal diet-2


title: 38w Ath HF+BCAA-1


title: A5614_P3C-2B


title: 68w Ath HF-3


title: A5612_LPS-2B


title: A5615_R848-2B


title: 38w basal diet-1


title: A5611_Unt-1B


title: A5590_LPS-4A

value: A


title: A5589_Unt-2A


title: A5581_P3C-2A


title: A5600_Unt-4A


title: A5578_Unt-1A


title: A5593_R848-4A


title: A5582_R848-2A


title: A5571_R848-1A


title: A5592_P3C-4A


title: A5604_R848-1B


title: A5579_LPS-2A


title: HT1080_CTRL_RES

city: Candiolo

first: ymera

last: pignochino

address: str provinciale 142

country: Italy

institute: IRCCS Candiolo cancer center

hyb_protocol: Entire amount of fluorescent cDNA was hybridized on HumanHT-12_V4 beadchip for 18 hours. Array washes were performed using wash buffer

scan_protocol: Hybridized Beadchips were scanned using Illumina HiScan. Raw data were analyzed by Illumina GenomeStudio software version V2011.1

data_processing: Data were are Normalized with loess normalization from the lumi packages

organism: Homo sapiens

source_name: Fibrosarcoma Cell Line

label_protocol: Fuorescent cDNA were obtained using the Human Whole-Genome DASL HT Assay kit Illumina

growth_protocol: cells grown in monolayer using RPMI10% FBS medium 37°C 5%CO2

extract_protocol: RNA extraction was performed using mirneasy from quiagen. RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies)

treatment_protocol: 24 hour exposure to 0.125 nM trabectedin, or 1.25 uM olaparib, or their combination, or left untreated (in RPMI10%FBS)

tag: sample type

value: Untreated Cells


title: SW684_OLA_RES

value: 24 hours olaparib treated cells


title: SW684_Combo_RES

value: 24 hours combination treated cells


title: A5568_LPS-1A


title: SW684_TRAB_RES

value: 24 hours trabectedin treated cells


title: HT1080_OLA_RES


title: A5601_LPS-1B


title: HT1080_TRAB_RES


title: SW684_CTRL_RES


title: DMR_TRAB_SENS

source_name: Uterine Leiomyosarcoma Cell Line

value: DMR


title: SJSA1_CTRL_SENS

source_name: Osteosarcoma Cell Line


title: DMR_OLA_SENS


title: SJSA1_OLA_SENS


title: SJSA1_TRAB_SENS


title: DMR_Combo_SENS


title: A5603_P3C-1B


title: HT1080_Combo_RES


title: SJSA1_Combo_SENS


title: A5570_P3C-1A


title: DMR_CTRL_SENS


title: 402.91_Combo_SENS

source_name: Myxoid Liposarcoma Cell Line


title: 402.91_OLA_SENS


title: 402.91_TRAB_SENS


title: TC106_OLA_SENS

source_name: Ewing sarcoma Cell Line


title: TC106_Combo_SENS


title: TC106_TRAB_SENS


title: TC106_CTRL_SENS


title: 402.91_CTRL_SENS


title: BT549_stimulated_B

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

scan_protocol: Standard Illumina scanning protocol

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

source_name: BT549 stimulated

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: treatment

value: stimulated with wound healing fluids

tag: replicate


title: BT549_stimulated_A


title: SUM 149_stimulated_A

source_name: SUM 149 stimulated

value: SUM 149


title: BT549_ctr_B

source_name: BT549 ctr

value: un-stimulated


title: BT549_ctr_A


title: SUM 149_stimulated_B

value: B


title: MDA-MB-157_ctr_A

source_name: MDA-MB-157 ctr


title: MDA-MB-157_stimulated_B

source_name: MDA-MB-157 stimulated


title: MDA-MB-231_ctr_A

source_name: MDA-MB-231 ctr


title: MDA-MB-157_ctr_B


title: MDA-MB-468_stimulated_B

source_name: MDA-MB-468 stimulated


title: 14 miRNA

city: Beijing

first: Fan

middle: Li

last: juan

state: Beijing

address: 11th Xizhimen south street,Xicheng district

department: Reproductive medical Center

country: China

institute: Peking University Peoples' Hospital

description:
Gene expression without treatment
254606410487_1-4

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: human endometrium

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease

value: Control

value: female

tag: age

value: Endometrium

tag: collect time

value: Window of implantation


title: MDA-MB-157_stimulated_A


title: MDA-MB-468_stimulated_A


title: 15 miRNA

description:
Gene expression without treatment
254606410487_2-4

tag: gender


title: 13 miRNA

description:
Gene expression without treatment
254606410487_2-3


title: SUM 149_ctr_B

source_name: SUM 149 ctr


title: MDA-MB-231_stimulated_A

source_name: MDA-MB-231 stimulated


title: MDA-MB-231_stimulated_B


title: MDA-MB-468_ctr_B

source_name: MDA-MB-468 ctr


title: SUM 149_ctr_A


title: MDA-MB-231_ctr_B


title: 5 miRNA

description:
Gene expression without treatment
254606411001_1-3

value: RIF (recurrent implantation failure)


title: MDA-MB-468_ctr_A


title: 4 miRNA

description:
Gene expression without treatment
254606411001_2-2


title: 6 miRNA

description:
Gene expression without treatment
254606411001_2-3


title: 9 miRNA

description:
Gene expression without treatment
254606410487_2-1


title: 11 miRNA

description:
Gene expression without treatment
254606410487_2-2


title: 7 miRNA

description:
Gene expression without treatment
254606411001_1-4


title: 12 miRNA

description:
Gene expression without treatment
254606410487_1-3


title: 2 miRNA

description:
Gene expression without treatment
254606411001_2-1


title: 3 miRNA

description:
Gene expression without treatment
254606411001_1-2


title: LNCaP_DHT_2hr

city: Washington, DC

first: Shu

last: Yang

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

institute: GEORGE WASHINGTON UNIV

description: LncRNA expression after 2 hr DHT treatment in LNCaP cells.

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data.

source_name: LNCaP cell, 2 hr, 10 nM DHT

label_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: LNCaP cells were cultured in phonel-red free RPMI 1640 supplemented with 5% charcoal-stripped fetal bovine serum for 72hr.

extract_protocol: Total RNA of samples was isolated by using TRIzol (Invitrogen) and the RNeasy mini kit (QIAGEN). Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: After hormone starvation, LNCaP were treated with 10 nM DHT for 0 and 2 hr.

value: LNCaP


title: control_S9_A4

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

data_processing: quantile normalization

source_name: CD4+ T cells polarized towards Th30

extract_protocol: After another 48 hours, cells were harvested and the gene expression analysis was performed using the SurePrint G3 Human GE 8x60k Microarray kit (Aglient Technologies, Palo Alto, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Naïve CD4+ T cells were isolated by buffy coat using MACS negative sorting. 5 million naïve CD4+ T cells were transfected with 200 mM scramble control siRNAs (Dharmacon, Lafayette, CO, USA ) or 500mM ON-TARGETplus SMARTpool siRNAs targeting each candidate gene (Dharmacon, Lafayette, CO, USA ) by a nucleofectorTM II Device (Lonza Ltd., Basel, Switzerland). After 4 hours, cells were polarized towards Th2 direction by plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), IL-4 (10 ng/mL) and anti-IL-12 (5 ug/mL) in the presence of IL-2 (17 ng/mL).

tag: subject

tag: array


title: USF2_siRNA_S9_A3

hyb_protocol: according to the manufacturer’s instructions

source_name: CD4+ T cells polarized towards Th25


title: MESSA

type: genomic

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

hyb_protocol: labeled DNA was cleaned-up and hybridized using the Agilent-030587 CCMC CGH plus SNP 180k Microarray platform. Each test DNA sample (Cy5) was hybridized with a reference DNA (Cy3) from Homo sapiens (Agilent).

scan_protocol: Slides were scanned using the Agilent G2505C Microarray Scanner

data_processing: Agilent Genomic Workbench 7.0.4

molecule: genomic DNA

source_name: MESSA

label_protocol: Comparative genomic hybridization using aCGH microarrays wad carried out using the enzymatic labeling method. Digestion, labeling, hybridization, washing and slide scanning were performed following the manufacturers protocols (Agilent Technologies). Briefly, 750ng of samples and control DNA in a total volume of 10.1uL were digested with restriction enzymes and labeled with Cy3 and Cy5.

growth_protocol: TC-106 RPMI 10%FBS, 402.91 RPMI 10%FBS, DMR RPMI10%FBS, sjsa-1 RPMI10%FBS, HT1080 EMEM 10%FBS, SW684 Leibovitz 10%FBS, MESSA mcCoy's 10%FBS, MESSA-DX5 mcCoy's 10%FBS

extract_protocol: Qiagen DNA mini Kit

treatment_protocol: standard culture condition in RPMI 10% FBS fror all cell lines but for HT1080 (EMEM) MESSA and MESSA -DX5 (McCoy's)

value: Uterine sarcoma cell line

value: MESSA

source_name: Agilent Euro Female

value: Agilent Reference DNA


title: LNCaP_DHT_0hr

description: LncRNA expression after 0 hr DHT treatment in LNCaP cells.

source_name: LNCaP cell, 0 hr, 10 nM DHT


title: HIS1_siRNA_S9_A4

scan_protocol: according to the manufacturer’s instructions

source_name: CD4+ T cells polarized towards Th32


title: SW684

value: Fibrosarcoma cell line

source_name: Agilent Euro Male


title: COPEB_siRNA_S9_A4

source_name: CD4+ T cells polarized towards Th31

label_protocol: according to the manufacturer’s instructions


title: HT1080


title: HIS1_siRNA_S7_A3

source_name: CD4+ T cells polarized towards Th22


title: SJSA1

value: Osteosarcoma cell lines


title: MESSA-DX5

value: Uterine sarcoma cell line (multidrug-resistant)


title: CBL_siRNA_S9_A3

source_name: CD4+ T cells polarized towards Th24


title: atra_rep3

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

hyb_protocol: Equal amounts of Cy3 labeled target were hybridized to Agilent whole human genome 4x44K arrays. Hybridizations were performed according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned by the Agilent Scanner G2505C

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 (Agilent).

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent)

growth_protocol: Human breast cancer cells T47D were purchased from ATCC and cultured in DMEM with FBS.

extract_protocol: Total RNA was extracted by Rneasy mini kit followed by Dnase I treatment.

treatment_protocol: Cells were treated with ATRA (S4-6) or vehicle (S1-3) for 24 hrs

tag: gender source

value: human breast cancer cells

tag: treated with

value: all-trans retinoic acid (ATRA) for 24hrs


title: control_S8_A4

source_name: CD4+ T cells polarized towards Th26


title: atra_rep2


title: CBL_siRNA_S8_A4

source_name: CD4+ T cells polarized towards Th27


title: USF2_siRNA_S7_A3

source_name: CD4+ T cells polarized towards Th20


title: COPEB_siRNA_S8_A4

source_name: CD4+ T cells polarized towards Th29


title: control 2

source_name: CD4+ T cells polarized towards Th23

value: control


title: HIS1_siRNA_S6_A2

source_name: CD4+ T cells polarized towards Th17


title: CBL_siRNA_S7_A3

source_name: CD4+ T cells polarized towards Th19


title: vehicle_rep3

value: vehicle for 24hrs


title: atra_rep1


title: 402.91

value: Myxoid liposarcoma cell line


title: USF2_siRNA_S8_A4

source_name: CD4+ T cells polarized towards Th28


title: DMR

source_name: DMR

value: Soft tissue sarcoma cell line

value: DMR


title: control_S7_A3

source_name: CD4+ T cells polarized towards Th18


title: COPEB_siRNA_S7_A3

source_name: CD4+ T cells polarized towards Th21


title: TC106

value: Ewing's sarcoma cell line


title: vehicle_rep2

value: female


title: HIS1_siRNA_S5_A2

source_name: CD4+ T cells polarized towards Th14


title: COPEB_siRNA_S6_A2

source_name: CD4+ T cells polarized towards Th16


title: COPEB_siRNA_S5_A2

source_name: CD4+ T cells polarized towards Th13


title: control_S6_A2

source_name: CD4+ T cells polarized towards Th15


title: CBL_siRNA_S5_A2

source_name: CD4+ T cells polarized towards Th11


title: USF2_siRNA_S4_A1

source_name: CD4+ T cells polarized towards Th4


title: CBL_siRNA_S6_A1

source_name: CD4+ T cells polarized towards Th8


title: USF2_siRNA_S5_A2

source_name: CD4+ T cells polarized towards Th12


title: USF2_siRNA_S6_A1

source_name: CD4+ T cells polarized towards Th9


title: HIS1_siRNA_S4_A1

source_name: CD4+ T cells polarized towards Th6


title: COPEB_siRNA_S4_A1

source_name: CD4+ T cells polarized towards Th5


title: control_S5_A2

source_name: CD4+ T cells polarized towards Th10


title: SW620 GCNT3 vs. NoORF R2

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CARRETERA DE CANTOBLANCO

department: BIOINFORMATICS

country: Spain

institute: IMDEA FOOD

description: Biological replicate 2 of 3.

hyb_protocol: The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes. Slides were Sure Print G3 Agilent 4x44K Human V2 (G4852A-026652).

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Loess intra-array normalization and quantile interarray normalization using LIMMA.

source_name: SW620 NoORF CRC Cells

label_protocol: Total RNA (200 ng) was amplified using Two Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). Preparation of probes and hybridization were performed as described in Two-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies. Briefly, for each hybridization, 825 ng of Cy3 probes and 825 ng of Cy5 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease-free water in a 25 ul reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with 25 ul of 2x Hybridization Buffer.

growth_protocol: SW620 cells were grown in DMEM medium.

extract_protocol: RNeasy Mini Kit (Qiagen, Germantown, MD, USA) was used following manufacturer's conditions to obtain total RNA from SW620 cultured cells. Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Plasmid selection was performed by adding 2 μg/ml puromycin.

value: SW620 (ATCC® CCL-227™)

value: colorectal carcinoma (CRC) cell line

tag: stable expression

value: No ORF

source_name: SW620 GCNT3 CRC Cells


title: control_S4_A1

source_name: CD4+ T cells polarized towards Th2


title: SW620 GCNT3 vs. NoORF R3

description: Biological replicate 3 of 3.

tag: cell type


title: CBL_siRNA_S4_A1

source_name: CD4+ T cells polarized towards Th3


title: vehicle_rep1

tag: cell line


title: control 1

source_name: CD4+ T cells polarized towards Th7


title: SW620 GCNT3 vs. NoORF R1

description: Biological replicate 1 of 3.


title: SCC25_HNSCC_CTX_rep1_CTXSurival7.61

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

data_processing: fRMA normalization with R/Bioconductor package fRMA v1.7.2.

source_name: Total RNA for HNSCC cell line SCC25 100 nM cetuximab (24 hr)

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: HNSCC

tag: 7 day cetuximab cell survival rate

value: 100 nM cetuximab (24 hr)


title: SCC1_HNSCC_CTX_rep3_CTXSurival29.44

source_name: Total RNA for HNSCC cell line SCC1 100 nM cetuximab (24 hr)


title: SQ20B_HNSCC_CTX_rep2_CTXSurival28.65

source_name: Total RNA for HNSCC cell line SQ20B 100 nM cetuximab (24 hr)


title: SCC25_HNSCC_CTX_rep2_CTXSurival7.61


title: SQ20B_HNSCC_CTX_rep3_CTXSurival28.65


title: SCC25_HNSCC_CTX_rep3_CTXSurival7.61


title: SQ20B_HNSCC_CTX_rep1_CTXSurival28.65


title: SCC1_HNSCC_CTX_rep2_CTXSurival29.44


title: SCC1_HNSCC_CTX_rep1_CTXSurival29.44


title: SCC61_HNSCC_CTX_rep2_CTXSurival40.16

source_name: Total RNA for HNSCC cell line SCC61 100 nM cetuximab (24 hr)


title: SCC090_HNSCC_CTX_rep3_CTXSurival39.07

source_name: Total RNA for HNSCC cell line SCC090 100 nM cetuximab (24 hr)


title: SCC1, batch M

hyb_protocol: The fragmented and labeled single strand cDNA was then hybridized to Human U133 Plus 2 array following Nugen recommended procedure at 45C for 18 hrs with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA.  The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Command Console (AGCC) 4.1 software from Affymetrix, using the standard default settings.

data_processing: CEL files are read in with the R/Bioconductor package affy. Gene expression data is normalized with the R/Bioconductor package fRMA (v1.16.0).

label_protocol: Samples were labeled with Nugen Affymetrix IVT express or Nugen Ovation RNA v2 as indicated under the label column of sample characteristics using standard manufacturer protocols.

extract_protocol: Total RNA was extracted from each transduced cells using Qiagen RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer's protocol.

tag: sirna

tag: batch

value: M


title: SCC090_HNSCC_CTX_rep2_CTXSurival39.07


title: PI_SC, batch M

value: Scramble


title: SCC047_HNSCC_CTX_rep2_CTXSurival31.2

source_name: Total RNA for HNSCC cell line SCC047 100 nM cetuximab (24 hr)


title: 93VU147T_HNSCC_CTX_rep3_CTXSurival35.57

source_name: Total RNA for HNSCC cell line 93VU147T 100 nM cetuximab (24 hr)


title: SCC25, batch M


title: PI3K_AFT, batch M

description: HaCaT-PIK3CA treated with Afatinib (10nM)

value: Afatinib (10nM)


title: SCC047_HNSCC_CTX_rep3_CTXSurival31.2


title: 93VU147T_HNSCC_CTX_rep1_CTXSurival35.57


title: PI3K_CTX, batch M

description: HaCaT-PIK3CA treated with Cetuximab (100nM)

value: Cetuximab (100nM)


title: PI3K_GFT, batch M

description: HaCaT-PIK3CA treated with Gefitinib (100nM)

value: Gefitinib (100nM)


title: PI3K_ctrl, batch M

description: HaCaT-PIK3CA Control (PBS)

source_name: HaCaT-PIK3CA Control (PBS)

value: Control


title: SCC047_HNSCC_CTX_rep1_CTXSurival31.2


title: Fadu Control, batch P

description: FaDu Control (PBS)

source_name: FaDu Control (PBS)

value: Fadu

value: P


title: 93VU147T_HNSCC_CTX_rep2_CTXSurival35.57


title: SCC61_HNSCC_CTX_rep3_CTXSurival40.16


title: SCC090_HNSCC_CTX_rep1_CTXSurival39.07


title: SCC61_HNSCC_CTX_rep1_CTXSurival40.16


title: PI_KD, batch M

value: EGFR


title: C12_0.5 vs DMSO_0.5 2

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Acinetobacter baumannii

label_protocol: Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)

growth_protocol: 50 ng of DNase treated RNA was obtained from cultures in exponential growth phase media (optical density of 0.5 at 600 nm) after incubating an hour with N-(3-Oxo-dodecanoyl) homoserine lactone

extract_protocol: Total RNA extracted using High Pure RNA Isolation Kit (Roche)  following manufacturer's instructions

treatment_protocol: The cultures were treated with N-(3-Oxo-dodecanoyl) homoserine lactone, at a final concentration of 10µM during an hour and with the solvent DMSO as negative control.

value: C12 Treatment

value: DMSO Control


title: Rif5C vs WtC

city: Barcelona

first: Jesús

last: Aranda

address: Facultat de Biociències, Plaza Cívica, s/n

department: Departament de Genètica i Microbiologia

institute: Universitat Autònoma de Barcelona

scan_protocol: Two-Color Microarray-Based Prokaryote Analysis 1.4

source_name: ATCC 17978 derivative spontaneous mutant Rif5

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

growth_protocol: A. baumannii ATCC 17978 wild-type strain was grown in Luria Bertani (LB) medium and incubated at 37ºC with shaking at 180 rpm.

extract_protocol: Total RNA was extracted using an RNeasy mini kit (Qiagen). DNA contaminants were removed from the RNA by digestion with DNase Turbo (Ambion).

treatment_protocol: All strains were grown until the mid-exponential growth phase (OD600=0.6) was reached

tag: strain

tag: genotype

value: spontaneous mutant Rif5

source_name: ATCC 17978 wild-type

value: wild-type


title: DMSO_0.5 vs C12_0.5 1

tag: treatment


title: WtD vs Rif5D

value: wildtype


title: MO_SC, batch M

description: HaCaT-Mock

source_name: HaCaT-Mock

value: HaCaT-Mock


title: Mock_CTX, batch M

description: HaCaT-Mock treated with Cetuximab (100nM)


title: Mock_GTF, batch M

description: HaCaT-Mock treated with Gefitinib (100nM)


title: DMSO_0.5 vs C12_0.5 2


title: MO_KD, batch M

description: HaCaT-Mock


title: HRAS_ctrl, batch M

description: HaCaT-HRAS Control (PBS)

source_name: HaCaT-HRAS Control (PBS)

value: HaCaT-HRAS


title: Mock_ATF, batch M

description: HaCaT-Mock treated with Afatinib (10nM)

source_name: HaCaT-Mock treated with Afatinib (10nM)


title: HRAS_GFT, batch M

description: HaCaT-HRAS treated with Gefitinib (100nM)


title: HRAS_AFT, batch M

description: HaCaT-HRAS treated with Afatinib (10nM)

source_name: HaCaT-HRAS treated with Afatinib (10nM)


title: C12_0.5 vs DMSO_0.5 1


title: HR_SC, batch M

description: HaCaT-HRAS

source_name: HaCaT-HRAS


title: HR_KD, batch M

description: HaCaT-HRAS


title: HRAS_CTX, batch M

description: HaCaT-HRAS treated with Cetuximab (100nM)


title: Rif5A vs Rif8A

source_name: ATCC 17978 derivative spontaneous mutant Rif8

value: spontaneous mutant Rif8


title: Rif8B vs Rif5B


title: MCF-7_Treated with L7 tomato fruit extract rep.1

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

description: Gene expression data from MCF_7 breast cancer cells (24 day incubation)

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human . GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix GeneChip® PrimeView™ Human  expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

source_name: MCF-7 cells

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf)

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum, 2% glutamine, 1% penicillin and 1% streptomycin stock solutions. Cells were incubated at 37°C/ 95% air/ 5% CO2 and the media was changed every two days.

extract_protocol: Cells were washed 3 times using PBS  and total RNA was collected from adherent tissue culture cells using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: No special treatments before harvesting were carried out.

value: MCF-7 cells treated with L7 tomato fruit extract  (1µg/ml)


title: MCF-7_Treated with L6 tomato fruit extract rep.2

value: MCF-7 cells treated with L6 tomato fruit extract  (1µg/ml)


title: MCF-7_Treated with L6 tomato fruit extract rep.1


title: MCF-7_negative control (non-treated) rep.1

value: MCF-7 cells non-treated


title: FADU, batch M

description: FaDu

source_name: FaDu

value: FaDu

value: M


title: EGFR_GFT, batch M

description: HaCaT-EGFR treated with Gefitinib (100nM)

value: HaCaT-EGFR

value: Gefitinib (100nM)


title: MCF-7_negative control (non-treated) rep.2


title: MCF-7_Treated with L7 tomato fruit extract rep.2

value: MCF-7 cells treated with L7  tomato fruit extract (1µg/ml)


title: EGFR_CTX, batch M

description: HaCaT-EGFR treated with Cetuximab (100nM)

value: Cetuximab (100nM)


title: HACAT, batch M

description: HaCaT-Parent

source_name: HaCaT-Parent

value: HaCaT-Parent


title: EGFR_AFT, batch M

description: HaCaT-EGFR treated with Afatinib (10nM)

source_name: HaCaT-EGFR treated with Afatinib (10nM)

value: Afatinib (10nM)


title: MCF-7_Treated with WT tomato fruit extract rep.2

value: MCF-7 cells treated with WT tomato fruit extract  (1µg/ml)


title: EG_SC, batch M

description: HaCaT-EGFR

source_name: HaCaT-EGFR

value: Scramble


title: Primary_Colorectal_Tumor_F535 (PrimeView)

city: Salamanca

first: Jose

middle: María

last: Sayagués

state: Salamanca

address: Campus Miguel de Unamuno

department: Department of Medicine

institute: Cancer Research Center (IBMCC-CSIC/USAL)

hyb_protocol: Total RNA (100-1000 ng) from both tumoral and non-tumoral colorectal tissues was hybridized to the Affymetrix PimeView Human Gene Expression following the instructions of the manufacturer

scan_protocol: Fluorescence signals were detected using the GeneChip Scanner 3000 7G (Affymetrix) and data stored as .CEL files

data_processing:
Raw data was normalized with the Robust Multi-array Average (RMA) algorithm, which included sequential background correction, intra- and inter-microarray well normalization, probe set summarization and calculation of expression signals
Quantile normalized gene level expression values from Affymetrix Expression Console

source_name: Rectum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA

growth_protocol: Not applicable

extract_protocol: Sample preparation was performed as described in the Affymetrix GeneChip Expression Analysis Manual (Santa Clara, CA, USA). Briefly, each frozen tissue (≥0.3 g) was crushed to powder at cryogenic temperatures and homogeneized in Trizol (Life Technologies Inc, Rockville, MD). Total RNA was then extracted using the miRNeasy mini kit according to the instructions of the manufacturer (Qiagen, Valencia, CA)

treatment_protocol: Not applicable

tag: disease state

value: Primary Colorectal Tumor

tag: ptnm

tag: metastasis

value: Metachronous

tag: Sex

value: Male


title: PI3K_SC_CTX1, batch E

source_name: HaCaT-PIK3CA treated with Cetuximab (100nM)

value: E


title: PI3K_SC_GFT1, batch E

source_name: HaCaT-PIK3CA treated with Gefitinib (100nM)


title: Primary_Colorectal_Tumor_F545 (PrimeView)

tag: age


title: Mock_GFT2, batch E

source_name: HaCaT-Mock treated with Gefitinib (100nM)

value: HaCaT-Mock


title: HRAS_SC_GFT1, batch E

source_name: HaCaT-HRAS treated with Gefitinib (100nM)

value: HaCaT-HRAS


title: Primary_Colorectal_Tumor_F530 (PrimeView)


title: Primary_Colorectal_Tumor_7657 (PrimeView)


title: Primary_Colorectal_Tumor_F544 (PrimeView)

value: Synchronous

value: Female


title: Mock_AFT2, batch E

description: HaCaT-Mock treated with Afatinib (10nM)


title: Mock_CTX2, batch E

source_name: HaCaT-Mock treated with Cetuximab (100nM)


title: Primary_Colorectal_Tumor_7135 (PrimeView)

source_name: Left colon


title: PI3K_SC_CO2, batch E

description: HaCaT-PIK3CA Control (PBS)

source_name: HaCaT-PIK3CA Control (PBS)

value: Control


title: Primary_Colorectal_Tumor_7196 (PrimeView)


title: MCF-7_Treated with WT tomato fruit extract rep.1


title: HRAS_SC_CTX1, batch E

source_name: HaCaT-HRAS treated with Cetuximab (100nM)


title: Primary_Colorectal_Tumor_7104 (PrimeView)


title: Primary_Colorectal_Tumor_6967 (PrimeView)

source_name: Right colon


title: HRAS_SC_AFT1, batch E

description: HaCaT-HRAS treated with Afatinib (10nM)

source_name: HaCaT-HRAS treated with Afatinib (10nM)


title: Primary_Colorectal_Tumor_7108 (PrimeView)


title: Primary_Colorectal_Tumor_7013 (PrimeView)


title: Primary_Colorectal_Tumor_F033 (PrimeView)


title: Mock_Ctrl3, batch E

description: HaCaT-Mock Control (PBS)

source_name: HaCaT-Mock Control (PBS)


title: Primary_Colorectal_Tumor_7164 (PrimeView)


title: EG_KD, batch M

description: HaCaT-EGFR

value: HaCaT-EGFR

value: EGFR

value: M


title: HRAS_SC_CO2, batch E

description: HaCaT-HRAS Control (PBS)

source_name: HaCaT-HRAS Control (PBS)


title: Primary_Colorectal_Tumor_6905 (PrimeView)


title: PI3K_SC_AFT1, batch E

source_name: HaCaT-PIK3CA treated with Afatinib (10nM)


title: Primary_Colorectal_Tumor_7194 (PrimeView)


title: Primary_Colorectal_Tumor_6753 (PrimeView)


title: EGFR_SC_CX1, batch E

source_name: HaCaT-EGFR treated with Cetuximab (100nM)

value: Cetuximab (100nM)


title: EGFR_SC_AFT1, batch E

description: HaCaT-EGFR treated with Afatinib (10nM)

source_name: HaCaT-EGFR treated with Afatinib (10nM)


title: Primary_Colorectal_Tumor_6804 (PrimeView)


title: Primary_Colorectal_Tumor_6391 (PrimeView)


title: Primary_Colorectal_Tumor_6382 (PrimeView)


title: EGFR_SC_GFT1, batch E

source_name: HaCaT-EGFR treated with Gefitinib (100nM)

value: Gefitinib (100nM)


title: PIKD2, batch J

value: J


title: SCC25, batch J


title: PISC2, batch J


title: Primary_Colorectal_Tumor_6602 (PrimeView)

source_name: Rectum


title: Primary_Colorectal_Tumor_6383 (PrimeView)


title: FvB-saline-1

city: Paris

first: Capucine

last: TROLLET

address: GH Pitie Salpetriere Bat Babinski 47 bd de l'hopital

country: France

institute: Myology Research Center UMRS974 INSERM

description: Gene expression from AAV injected tibialis anterior muscle

hyb_protocol: Prior to hybridization, the arrays were registered on GeneChip® Command Console® Software (AGCC) (Affymetrix, Santa Clara, CA). After the overnight hybridization, the arrays were washed and stained using the GeneChip® Hybridization on a Fluidics 450 station (Affymetrix, Santa Clara, CA)

scan_protocol: scanned using the AGCC scan control software (Affymetrix, Santa Clara, CA).

data_processing: The raw data “cel” files were analyzed using Bioconductor (R software). Raw signal intensities were quantile normalized with oligo package and differential expression analysis was performed using the limma package 69. Principal component analysis was performed using prcomp function and rgl package.

source_name: tibialis anterior muscle

label_protocol: Ninety ng of total RNA per sample was further processed using the GeneChip® WT PLUS Reagent Kit for whole transcript expression profiling (Affymetrix, Santa Clara, CA). The sense strand single stranded (ss) cDNA was purified, fragmented, labeled using DNA labeled reagent

growth_protocol: tibialis anterior muscles were excised from tendon to tendon

extract_protocol: Total RNA was extracted from skeletal muscles using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA quality and purity was determined using a ND-1000 NanoDrop spectrophotometer (NanoDrop Technologies). Quality control was performed on total RNA extracted from mouse muscles using a Nanodrop and Bioanalyzer (Agilent technologies, Santa Clara, CA). RNA quality and purity was determined using a ND-1000 NanoDrop spectrophotometer (NanoDrop Technologies) followed by Quality Control analysis (Agilent 2100 Bioanalyzer, Eukaryote Total RNA Nano assay, Agilent RNA 6000 Nano Kit, Agilent RNA Nano LabChip) to determine the RNA integrity number (RIN, 28S/18S ratio).

treatment_protocol: muscles frozen in liquid nitrogen-cooled-isopentane

tag: gender

value: male

value: FvB

value: 28-30 weeks old


title: Primary_Colorectal_Tumor_6349 (PrimeView)

value: Primary Colorectal Tumor


title: PIKD1, batch J


title: PISC1, batch J

value: Scramble


title: PI3KGFT1, batch J

source_name: HaCaT-PIK3CA treated with Gefitinib (100nM)


title: A17-shRNA3X-4


title: SCC1, batch J


title: EGFR_SC_CO2, batch E

description: HaCaT-EGFR Control (PBS)

source_name: HaCaT-EGFR Control (PBS)

value: E


title: FvB-saline-3


title: Colorectal_liver_metastasis_F544 (PrimeView)

source_name: Liver

value: Colorectal liver metastasis


title: Colorectal_liver_metastasis_F545 (PrimeView)

value: Metachronous

value: Male


title: A17-shRNA3X+optPAB-4


title: FvB-saline-2


title: A17-saline-2


title: A17-shRNA3X+optPAB-3


title: Colorectal_liver_metastasis_F535 (PrimeView)


title: PI3KSCCO1, batch J

description: HaCaT-PIK3CA Control (PBS)


title: Primary_Colorectal_Tumor_6346 (PrimeView)

value: Synchronous


title: A17-shRNA3X-3


title: Colorectal_liver_metastasis_F530 (PrimeView)


title: Colorectal_liver_metastasis_7657 (PrimeView)


title: Colorectal_liver_metastasis_F033 (PrimeView)


title: PI3KCTX1, batch J

source_name: HaCaT-PIK3CA treated with Cetuximab (100nM)


title: Colorectal_liver_metastasis_7104 (PrimeView)


title: A17-shRNA3X+optPAB-2


title: PI3KCTX2, batch J


title: PI3KCtnl2, batch J

description: HaCaT-PIK3CA Control (PBS)

value: Control


title: A17-optPAB-3


title: Colorectal_liver_metastasis_7164 (PrimeView)


title: A17-shRNA3X+optPAB-1


title: Colorectal_liver_metastasis_7196 (PrimeView)

value: Female


title: A17-saline-1


title: PI3KAPT2, batch J

value: Afatinib (10nM)


title: A17-optPAB-2


title: Colorectal_liver_metastasis_7013 (PrimeView)


title: A17-shRNA3X-2


title: MOSC1, batch J

description: HaCaT-Mock

source_name: HaCaT-Mock

value: HaCaT-Mock


title: PI3KCtnl1, batch J

description: HaCaT-PIK3CA Control (PBS)

source_name: HaCaT-PIK3CA Control (PBS)


title: MOKD2, batch J

description: HaCaT-Mock

value: EGFR


title: MOKD1, batch J

description: HaCaT-Mock


title: PI3KAFT1, batch J


title: MOSC2, batch J

description: HaCaT-Mock


title: A17-optPAB-1


title: Colorectal_liver_metastasis_7108 (PrimeView)


title: Colorectal_liver_metastasis_6753 (PrimeView)


title: Colorectal_liver_metastasis_6602 (PrimeView)


title: A17-shRNA3X-1


title: Primary_Colorectal_Tumor_F545 (miRNA-3)

hyb_protocol: Total RNA (100-1000 ng) from both tumoral and non-tumoral colorectal tissues was hybridized to the Affymetrix mir3.0 array following the instructions of the manufacturer

label_protocol: 1.0 ug of total RNA was labeled using the Flash Tag Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays according to the manufacturer's instructions.


title: Primary_Colorectal_Tumor_F530 (miRNA-3)


title: Primary_Colorectal_Tumor_F544 (miRNA-3)


title: MockSCCX1, batch J

source_name: HaCaT-Mock treated with Cetuximab (100nM)

value: Cetuximab (100nM)


title: Colorectal_liver_metastasis_6391 (PrimeView)


title: Primary_Colorectal_Tumor_F535 (miRNA-3)


title: MOCKSCGF1, batch J

source_name: HaCaT-Mock treated with Gefitinib (100nM)

value: Gefitinib (100nM)

value: J


title: Colorectal_liver_metastasis_6967 (PrimeView)


title: Non-tumoral_colorectal_tissue_F545 (PrimeView)

source_name: Normal mucosa

value: normal

value: Not Applicable


title: Colorectal_liver_metastasis_6346 (PrimeView)


title: MOCKSCCO1, batch J

description: HaCaT-Mock Control (PBS)

source_name: HaCaT-Mock Control (PBS)


title: Primary_Colorectal_Tumor_7196 (miRNA-3)

source_name: Left colon

value: Primary Colorectal Tumor


title: MOCKCTX1, batch J


title: Colorectal_liver_metastasis_6382 (PrimeView)


title: Primary_Colorectal_Tumor_F033 (miRNA-3)


title: Non-tumoral_colorectal_tissue_F259 (PrimeView)


title: Colorectal_liver_metastasis_6349 (PrimeView)


title: MOCKCtnl2, batch J

description: HaCaT-Mock Control (PBS)


title: Colorectal_liver_metastasis_6383 (PrimeView)


title: Primary_Colorectal_Tumor_7164 (miRNA-3)


title: HRSC2, batch J

description: HaCaT-HRAS

source_name: HaCaT-HRAS

value: HaCaT-HRAS

value: Scramble


title: MOCKGFT1, batch J


title: Non-tumoral_colorectal_tissue_6391 (PrimeView)


title: HRSC1, batch J

description: HaCaT-HRAS


title: MOCKAFT1, batch J

description: HaCaT-Mock treated with Afatinib (10nM)

source_name: HaCaT-Mock treated with Afatinib (10nM)


title: Primary_Colorectal_Tumor_7194 (miRNA-3)

source_name: Right colon


title: Primary_Colorectal_Tumor_7657 (miRNA-3)


title: MOCKSCAF1, batch J

description: HaCaT-Mock treated with Afatinib (10nM)


title: Non-tumoral_colorectal_tissue_F251 (PrimeView)


title: Non-tumoral_colorectal_tissue_F260 (PrimeView)


title: MOCKCtnl1, batch J

description: HaCaT-Mock Control (PBS)


title: Primary_Colorectal_Tumor_7135 (miRNA-3)


title: Non-tumoral_colorectal_tissue_F258 (PrimeView)


title: Primary_Colorectal_Tumor_7013 (miRNA-3)


title: Primary_Colorectal_Tumor_6967 (miRNA-3)


title: Primary_Colorectal_Tumor_7108 (miRNA-3)


title: Non-tumoral_colorectal_tissue_F253 (PrimeView)


title: Primary_Colorectal_Tumor_7104 (miRNA-3)


title: HRKD1, batch J

description: HaCaT-HRAS


title: HRKD2, batch J

description: HaCaT-HRAS


title: HRASGFT2, batch J

source_name: HaCaT-HRAS treated with Gefitinib (100nM)


title: HRASSCCO1, batch J

description: HaCaT-HRAS Control (PBS)

source_name: HaCaT-HRAS Control (PBS)


title: HRASGFT1, batch J


title: Non-tumoral_colorectal_tissue_F254 (PrimeView)


title: Non-tumoral_colorectal_tissue_F249 (PrimeView)


title: Primary_Colorectal_Tumor_6753 (miRNA-3)


title: Primary_Colorectal_Tumor_6905 (miRNA-3)


title: Primary_Colorectal_Tumor_6804 (miRNA-3)

source_name: Rectum


title: HRASCTX1, batch J

source_name: HaCaT-HRAS treated with Cetuximab (100nM)


title: Primary_Colorectal_Tumor_6391 (miRNA-3)


title: HRASCtnl2, batch J

description: HaCaT-HRAS Control (PBS)


title: HRASCTX2, batch J


title: Primary_Colorectal_Tumor_6382 (miRNA-3)


title: Primary_Colorectal_Tumor_6602 (miRNA-3)


title: HRASAFT2, batch J

description: HaCaT-HRAS treated with Afatinib (10nM)

source_name: HaCaT-HRAS treated with Afatinib (10nM)


title: Primary_Colorectal_Tumor_6346 (miRNA-3)


title: EGSC1, batch J

description: HaCaT-EGFR

source_name: HaCaT-EGFR

value: HaCaT-EGFR


title: HRASCtnl1, batch J

description: HaCaT-HRAS Control (PBS)


title: EGSC2, batch J

description: HaCaT-EGFR


title: Primary_Colorectal_Tumor_6383 (miRNA-3)

value: Metachronous


title: MAF x_22

hyb_protocol: 1.65 µg Cy3 labeled cRNA from each sample was hybridized to Agilent SurePrint G3 Human GE v2 8x60K slides. The microarray slides were hybridized for 17 hours at 65°C in a rotating oven.

scan_protocol: After washing according to the manufacturer’s instructions, the slides were analyzed using the Agilent Microarray scanner 2505C with default settings for all parameters.

data_processing: Gene expression data was obtained with Agilent`s feature extraction software (version 10.7.3.1), and next quantile normalized

source_name: CD4+ T cells polarized towards Th2 cells

label_protocol: The expression profiling 200 ng of total RNA from each sample was labeled with Cy3 and transcribed to cRNA using the Agilent Quick Amp Labeling Kit, one color. The labeled cRNA was purified with the RNEasy Mini Kit from Qiagen. The labeling efficiency was assessed using the NanoDrop ND-1000 UV-Vis Spectrophotometer.

extract_protocol: For microarray experiments the cells were harvested at 24h of polarization and lysed in 600 ll Qiazol.

treatment_protocol: Human Naïve CD4+ T cells were isolated from fresh buffy coats with Miltenyis Naïve CD4+ T Cell Isolation Kit II, according to the manufacturer’s instructions. Cells were either transfected in a cuvette with 600nM human on target plus SMART pool against MAF, MYB and GATA3 (ThermoFisherScientific Inc, USA), non-targeting siRNA (ThermoFisherScientific Inc) or with transfection buffer using the Amaxa transfection program U-014. Five hours after the nucleofection cells were washed, activated and polarized towards TH2 for or 24h. The cells were activated with platebound anti-CD3 (500 ng/ml), 500 ng/ml soluble anti-CD28, 5 µg/ml anti-IL-12, 10 ng/ml IL-4 and 17 ng/ml IL-2 (R&D Systems).

tag: subject


title: GATA3 x_23


title: Colorectal_liver_metastasis_F033 (miRNA-3)

source_name: Liver

value: Colorectal liver metastasis

value: Male


title: MOCK x_24


title: HRASAFT1, batch J

description: HaCaT-HRAS treated with Afatinib (10nM)


title: Colorectal_liver_metastasis_F535 (miRNA-3)


title: Colorectal_liver_metastasis_F545 (miRNA-3)


title: EGFRSCCO1, batch J

description: HaCaT-EGFR Control (PBS)

source_name: HaCaT-EGFR Control (PBS)

value: Control


title: Colorectal_liver_metastasis_F530 (miRNA-3)


title: EGKD2, batch J

description: HaCaT-EGFR


title: Colorectal_liver_metastasis_F544 (miRNA-3)

value: Synchronous

value: Female


title: MYB x_21


title: EGKD1, batch J

description: HaCaT-EGFR


title: Primary_Colorectal_Tumor_6349 (miRNA-3)


title: MOCK x_20


title: EGFRGFT2, batch J

source_name: HaCaT-EGFR treated with Gefitinib (100nM)


title: Colorectal_liver_metastasis_7164 (miRNA-3)


title: Colorectal_liver_metastasis_7657 (miRNA-3)


title: EGFRGFT1, batch J


title: GATA3 x_19


title: EGFRCTX2, batch J

source_name: HaCaT-EGFR treated with Cetuximab (100nM)


title: Colorectal_liver_metastasis_7196 (miRNA-3)


title: EGFRCTX1, batch J


title: MAF x_18


title: MYB x_17


title: Colorectal_liver_metastasis_7108 (miRNA-3)


title: Colorectal_liver_metastasis_7104 (miRNA-3)


title: EGFRCtnl2, batch J

description: HaCaT-EGFR Control (PBS)


title: Colorectal_liver_metastasis_7013 (miRNA-3)


title: GATA3 x_15


title: Colorectal_liver_metastasis_6391 (miRNA-3)


title: MYB x_13


title: Colorectal_liver_metastasis_6967 (miRNA-3)


title: EGFRAFT2, batch J

description: HaCaT-EGFR treated with Afatinib (10nM)

source_name: HaCaT-EGFR treated with Afatinib (10nM)

value: Afatinib (10nM)


title: EGFRCtnl1, batch J

description: HaCaT-EGFR Control (PBS)


title: GATA3 x_11


title: MAF MOCK2 x_8


title: MOCK x_16


title: MOCK x_12


title: EGFRAFT1, batch J

description: HaCaT-EGFR treated with Afatinib (10nM)


title: Colorectal_liver_metastasis_6602 (miRNA-3)


title: Colorectal_liver_metastasis_6383 (miRNA-3)


title: Colorectal_liver_metastasis_6382 (miRNA-3)


title: MAF x_14


title: Colorectal_liver_metastasis_6753 (miRNA-3)


title: OE-SZ19-rep1

first: Akira

last: Sawa

address: 600 North Wolfe St.

department: Psychiatry and Behavioral Sciences

institute: Johns Hopkins University School of Medicine

hyb_protocol: Biotin-labeled cRNA were hybridized to HG-U133 Plus 2.0 GeneChips in accordance with the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Data analysis was performed using Partek Genomics Suite (version 6.5) and R ver 3.1.1.

source_name: OE schizophrenia

label_protocol: Biotin-labeled cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen).

tag: group

value: Patient

value: M

tag: race

value: AA

tag: education

tag: smoking

value: n

tag: tissue

value: OE


title: MYB x_9


title: OE-SZ18-rep1

value: y


title: MAF x_10


title: Colorectal_liver_metastasis_6349 (miRNA-3)


title: Colorectal_liver_metastasis_6346 (miRNA-3)


title: OE-SZ20-rep1

value: F


title: Non-tumoral_colorectal_tissue_F545 (miRNA-3)

source_name: Normal mucosa

value: normal

value: Not Applicable


title: MAF NON2 x_7


title: Non-tumoral_colorectal_tissue_F260 (miRNA-3)


title: OE-SZ17-rep1

value: Cauc


title: OE-SZ15-rep1


title: MAF MOCK x_6


title: OE-SZ16-rep1


title: Non-tumoral_colorectal_tissue_F259 (miRNA-3)


title: OE-SZ14-rep2


title: MAF NON x_5


title: GATA3 MOCK x_4


title: Non-tumoral_colorectal_tissue_F258 (miRNA-3)


title: OE-SZ14-rep1


title: OE-SZ13-rep1


title: GATA3 NON x_3


title: OE-SZ10-rep1


title: Non-tumoral_colorectal_tissue_F253 (miRNA-3)


title: MYB MOCK x_2


title: OE-SZ11-rep1


title: Non-tumoral_colorectal_tissue_F251 (miRNA-3)


title: Non-tumoral_colorectal_tissue_F249 (miRNA-3)


title: MYB NON x_1


title: Non-tumoral_colorectal_tissue_F254 (miRNA-3)


title: OE-SZ8-rep1


title: OE-SZ6-rep1


title: OE-SZ7-rep1


title: MCF7_shATM3_Spheres

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: Standard cell line derived from primary breast carcinoma.

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to Agilent 8x60K whole human genome oligonucleotide microarrays (Grid ID 039494), at 65°C for 17 hours using Agilent's Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.7 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09).

data_processing: The gProcessedSignal data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, which is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in log2 scale. Then, differential gene lists were obtained from filtered data using Microsoft Excel. Differentially expressed genes were identified by a combination of 1-tail T test and fold-change ratio.

source_name: MCF7 mammospheres, shATM#3

label_protocol: 200ng of poly A+ RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Input Linear Amplification Kit and purified with Qiagen's RNeasy mini spin columns.

growth_protocol: Human breast cancer cell lines MCF-7 and MCF-7-HER2 (overexpressing HER2 gene) were cultured in RPMI-1640 containing 2 mM L-glutamine and supplemented with 10% HyClone* Fetal Bovine Serum (Invitrogen) at 37°C in a CO2 incubator (5%).

extract_protocol: Undifferentiated cells were collected for RNA extraction and microarray analysis. Total RNA was extracted using Trizol (Invitrogen) and DNase treated by Qiagen columns. Quality and integrity of each sample were checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with an RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: ATM gene was silenced with an interference protocol. The shATM construct, generously provided by Y. Lerenthal and Y. Shiloh, had the following sequence: shATM construct (#1 position 912 5'-GACTTTGGCTGTCAACTTTCG-3') and shATM (#3 position 8538 5' GGA GCG CAC CAT CTT CTT C 3') shRNA and control shGFP 5'- GGAGCGCACCATCTTCTTC-3' (Biton et al. 2006). ATM was silenced in MCF7 and MCF7-HER2 cells by lentivirus-mediated expression of short-hairpin RNA using lentiviruses produced in HEK 293T cells by cotransfecting pSIN18.cPPT.RNAi. p.EGFP.WPRE lentiviral vector with targeting sequences together with respective plasmids encoding for gag-pol and VSV-G proteins. Viral supernatant was collected 48 h post-transfection, filtered through a 0.45 μm pore size filter and added to the cells (MCF7 and MCF7-HER2 breast cancer cell lines) in the presence of 2 μg/ml polybrene. For microarray experiments, to avoid off targets effects, we decide to use mRNA extracted from a biological triplicate of MCF7 and MCF7-HER2 cells grown as mammospheres (Spheres) and infected with lentivirus expressing two different RNA interference targeting ATM (shATM#1 and shATM#3) and two control RNA interference (shGFP and pSin18 empty vector (pvl)).

tag: cell line

tag: cell type

value: breast cancer cell line

tag: transgenic

value: infected with lentivirus expressing shATM#3

tag: sample type

value: ATM silencing

value: female


title: MCF7_HER2_shATM3_Spheres

source_name: MCF7_HER2 mammospheres, shATM#3

value: HER2 receptor overexpression

tag: treatment

value: HER2, ATM silencing


title: Non-tumoral_colorectal_tissue_6391 (miRNA-3)

tag: disease state

value: Female


title: OE-SZ4-rep1

value: Patient


title: OE-SZ5-rep1

value: M


title: MCF7_shGFP_Spheres, rep2

source_name: MCF7 mammospheres, shGFP

value: infected with lentivirus expressing shGFP

value: control


title: MCF7_HER2_shATM1_Spheres, rep2

source_name: MCF7_HER2 mammospheres, shATM#1

value: infected with lentivirus expressing shATM#1


title: MCF7_HER2_shGFP_Spheres, rep2

source_name: MCF7_HER2 mammospheres, shGFP


title: OE-SZ3-rep1

value: y

value: OE


title: OE-SZ2-rep1

value: AA


title: MCF7_shGFP_Spheres, rep1


title: cisplatin 10µM_72H_3

city: Düsseldorf

first: Ana-Maria

last: Florea

state: NRW

address: Moorenstr. 5

department: Neuropathology

country: Germany

institute: University Düsseldorf

hyb_protocol: Affymetrix chip hybridizations were performed at the Center for Biological and Medical Research (BMFZ) at Heinrich Heine University Düsseldorf using a GeneChip Hybridization Oven 645 and a GeneChip® Scanner 3000 7G.

scan_protocol: GeneChip® Scanner 3000 7G

data_processing: Bioinformatic evaluation of the microarray data was done with the R framework for statistical computing. The dataset was normalized and log2-transformed using the robust multi-array average (RMA) method implemented in the affy package. Differential expression of mRNA was assessed by computing the moderated t-statistics using the LIMMA package. The resulting p-values were corrected for multiple testing by controlling the false discovery rate. An mRNA was considered as being differentially expressed when the corrected p-value was below 0.05.

source_name: treated 10µM Cisplatin/72h

label_protocol: RNA quality was determined using the Agilent Bioanalyzer and the Eukaryote Total RNA Nano Chip (Agilent Technologies, Hayward, CA, USA). The RNA integrity number (RIN) was measured as 9.9-10. The Affymetrix HuGene 2.0 ST and WT plus reagent kit (Affymetrix, Santa Clara, California, United States) was used following the provider’s recommendation with a start material of 100ng of total RNA.

growth_protocol: The SH-SY5Y (ATCC® CRL2266™), neuroblastoma cell line was obtained from American Type Culture Collection (ATCC, Manassas, Virginia). The cells were maintained in culture as recommended by the provider. SH-SY5Y cells were grown in DMEM/F12 medium supplemented with 10% (v/v) heat inactivated fetal bovine se-rum (FBS), penicillin (0.1lU) and streptomycin (100μg/mL). The cells were cultured under sterile conditions and were grown in a humidified incubator at 37°C with 95% O2 and 5% CO2.

extract_protocol: For extraction of RNA and DNA we used the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the provider’s protocol. Extracted RNA was kept at -80°C.

treatment_protocol: Three samples of  SH-SY5Y cells and four samples of 72h treated SH-SY5Y neuroblastoma cell line with 10µM CDDP for 72h were subjected to Affymetrix chip analyses.

value: neuroblastoma

value: treated 10µM Cisplatin/72h


title: MCF7_shATM1_Spheres, rep2

source_name: MCF7 mammospheres, shATM#1

value: breast cancer cell line


title: cisplatin 10µM_72H_4


title: MCF7_HER2_shGFP_Spheres, rep1


title: OE-C22-rep2

source_name: OE control

value: Control


title: control 3

source_name: control


title: control 2


title: cisplatin 10µM_72H_2


title: MCF7_HER2_shATM1_Spheres, rep1


title: OE-SZ1-rep1

value: Cauc

value: n


title: MCF7_HER2_pvl_Spheres

source_name: MCF7_HER2 mammospheres, pSin18 empty vector

value: HER2 receptor overexpression

value: infected with lentivirus expressing pSin18 empty vector (pvl)

value: female


title: cisplatin 10µM_72H_1


title: OE-C22-rep1


title: OE-C18-rep1

value: F


title: MCF7_shATM1_Spheres, rep1

value: ATM silencing


title: OE-C19-rep1


title: OE-C17-rep1


title: MCF7_pvl_Spheres

source_name: MCF7 mammospheres, pSin18 empty vector


title: control 1


title: H2009_Control sh 2

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

institute: Center for Applied Medical Research (CIMA)

description:
Gene expression data from H2009 cells
H2009_GFP2

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Affymetrix HuGene-2_0-st chip with bioconductor cdf (hugene20stv1cdf); The data were normalized with Bioconductor software using RMA algorithm.

source_name: H2009_GFP shRNA

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cells were grown in RPMI164 medium supplemented with 10% FBS and 1% antibiotics

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: H2009 cells were infected with lentivirus carrying a FOSL1 or a control (GFP) shRNA for 2 days. Then, cells were selected for 3 days using 5ug/ml puromycin. After that, cells were counted and plated at a density of 600,000 cells/well (6-well plate) for 24h.

value: mutant KRAS lung adenocarcinoma cells

tag: infected with

value: lentivirus carrying a GFP shRNA


title: OE-C16-rep1

value: M


title: H2009_Control sh 3

description:
Gene expression data from H2009 cells
H2009_GFP3


title: MeT-5A_PBS_48h

city: Tokyo

last: Yokoi

state: Tokyo-to

address: 5-1-1 Tsukiji, Chuo-ku

department: Group for Research of Molecular Functions and Targets

institute: National Cancer Center　Research Institute

description: Gene expression after 48hr in PBS-treated MeT-5A

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2600D Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: To perform mRNA microarray, 5x104 MeT-5A cells were cultured in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1 % antibiotic–antimycotic solution (AA, Invitrogen) at 37°C in 5% CO2

extract_protocol: Total RNA was extracted from MeT-5A treated with EVs using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The EVs from five types of cells (ES-2 cells, A2780 cells, SKOV3 cells, HOSE1 cells and HOSE2 cells) were added to MeT-5A cells with two types of EV concentration (10 mg or 30 mg). Total mRNAs were extracted by the MeT-5A cells 12 h or 48 h after treatment with EVs.

value: PBS

tag: time point

tag: dose


title: H2009_Control sh 1

description:
Gene expression data from H2009 cells
H2009_GFP1


title: OE-C15-rep1

tag: age

value: OE


title: MeT-5A_SKOV3_EV_30mg_48h

description: Gene expression after 48hr in 30mg of SKOV3 EV-treated MeT-5A

value: EVs from SKOV3


title: MeT-5A_SKOV3_EV_30mg_12h

description: Gene expression after 12hr in 30mg of SKOV3 EV-treated MeT-5A


title: OE-C14-rep1

tag: gender

value: AA


title: H2009_FOSL1 sh1 3

description:
Gene expression data from FOSL1 depleted H2009 cells
H2009_Fosl1_sh3_3

source_name: H2009_FOSL1 shRNA

value: lentivirus carrying a FOSL1 shRNA


title: MeT-5A_SKOV3_EV_10mg_12h

description: Gene expression after 12hr in 10mg of SKOV3 EV-treated MeT-5A


title: OE-C13-rep1


title: MeT-5A_A2780-EV_30mg_48h

description: Gene expression after 48hr in 30mg of A2780 EV-treated MeT-5A

value: EVs from A2780


title: OE-C12-rep1

value: Control

value: y


title: MeT-5A_SKOV3_EV_10mg_48h

description: Gene expression after 48hr in 10mg of SKOV3 EV-treated MeT-5A


title: H2009_FOSL1 sh1 2

description:
Gene expression data from FOSL1 depleted H2009 cells
H2009_Fosl1_sh3_2


title: OE-C11-rep1


title: MeT-5A_A2780-EV_30mg_12h

description: Gene expression after 12hr in 30mg of A2780 EV-treated MeT-5A


title: OE-C9-rep1

value: n


title: OE-C10-rep1

value: Cauc


title: MeT-5A_PBS_12h

description: Gene expression after 12hr in PBS-treated MeT-5A


title: OE-C5-rep1


title: MeT-5A_A2780-EV_10mg_48h

description: Gene expression after 48hr in 10mg of A2780 EV-treated MeT-5A


title: OE-C4-rep1


title: H2009_FOSL1 sh1 1

description:
Gene expression data from FOSL1 depleted H2009 cells
H2009_Fosl1_sh3_32


title: OE-C8-rep1


title: MeT-5A_ES-2-EV_30mg_48h

description: Gene expression after 48hr in 30mg of ES-2 EV-treated MeT-5A

value: EVs from ES-2


title: MeT-5A_ES-2-EV_30mg_12h

description: Gene expression after 12hr in 30mg of ES-2 EV-treated MeT-5A


title: MeT-5A_ES-2-EV_10mg_48h

description: Gene expression after 48hr in 10mg of ES-2 EV-treated MeT-5A


title: MeT-5A_A2780-EV_10mg_12h

description: Gene expression after 12hr in 10mg of A2780 EV-treated MeT-5A


title: OE-C3-rep1


title: OE-C2-rep1


title: OE-C1-rep1


title: MeT-5A_HOSE2-EV_30mg_48h

description: Gene expression after 48hr in 30mg of HOSE2 EV-treated MeT-5A

value: EVs from HOSE2


title: MeT-5A_HOSE1-EV_30mg_12h

description: Gene expression after 12hr in 30mg of HOSE1 EV-treated MeT-5A

value: EVs from HOSE1


title: MeT-5A_ES-2-EV_10mg_12h

description: Gene expression after 12hr in 10mg of ES-2 EV-treated MeT-5A


title: paired_LB-SZ19-rep1

source_name: paired lymphoblast schizophrenia

value: Patient

value: Yes

value: lymphoblast


title: paired_LB-SZ20-rep1

value: F

value: No


title: paired_LB-SZ21-rep1


title: paired_LB-SZ16-rep1

value: M


title: paired_LB-SZ15-rep1


title: MeT-5A_HOSE2-EV_10mg_48h

description: Gene expression after 48hr in 10mg of HOSE2 EV-treated MeT-5A


title: MeT-5A_HOSE1-EV_30mg_48h

description: Gene expression after 48hr in 30mg of HOSE1 EV-treated MeT-5A


title: paired_LB-SZ18-rep1


title: mimic Neg CTR exp3

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: mimic Neg CTR CD34+ cells

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: Cord Blood CD34+ cells

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments.  Briefly, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in 24-well plates at 5 x 10^5/mL in Iscove modified Dulbecco's medium (IMDM; Euroclone) containing 20% Human Serum (Bio-Whittaker), stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Electroporation program on CD34+ cells was based on a previously published protocol (Norfo R et al, Blood, 2014), optimized to be performed on the 4D-Nucleofector™ System (Lonza, Basel, Switzerland; http://www.lonza.com). Briefly, each sample was electroporated twice, once every 24h, with mirVanaTM miRNA mimics (Thermo Fisher Scientific Inc) starting from the day after CD34+ cells purification. For each electroporation, 4x10^5 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza), containing 3 µg (0,21 nmol) of mirVanaTM miR-494-3p miRNA mimic (mimic miR-494), and pulsed with the program DS112. To exclude nonspecific effects caused by interfering RNA nucleofection, a sample transfected with mirVana miRNA mimic Negative Control #1 (mimic Neg CTR) was included. After each transfection, CD34+ cells were transferred into pre-warmed fresh medium in 24-well plates (Euroclone) and maintained in the same culture conditions as described above.    For liquid culture differentiation assays, 24 hours after the last nucleofection CD34+ cells were plated (5 x 10^5/mL) in IMDM added with 20% BIT 9500 serum substitute (bovine serum albumin, insulin, and transferrin; StemCell Technologies), in order to set up a multilineage cell culture (SCF, 50 ng/mL; Flt3L, 50 ng/mL; TPO, 20 ng/mL; IL-3, 10 ng/mL; IL-6, 10 ng/mL; all cytokines from Miltenyi) (Bianchi E et al Blood 2010). We set up megakaryocyte unilineage cultures by seeding 5×105 cells/mL in IMDM with the addition of 20% BIT and THPO 100 ng/mL (Miltenyi Biotec) (Guglielmelli P et al, Blood, 2009)

value: mimic Neg CTR

tag: experiment

value: Cord Blood


title: MeT-5A_HOSE1-EV_10mg_48h

description: Gene expression after 48hr in 10mg of HOSE1 EV-treated MeT-5A


title: paired_LB-SZ14-rep1

tag: group


title: paired_LB-SZ17-rep1

tag: race


title: paired_LB-SZ13-rep1

tag: education


title: mimic Neg CTR exp2

description: mimic Neg CTR CD34+ cells


title: MeT-5A_HOSE1-EV_10mg_12h

description: Gene expression after 12hr in 10mg of HOSE1 EV-treated MeT-5A


title: Treatment with Lactoferrin-based product_SL143

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

institute: Biópolis SL

description: Gene expression data from C. elegans (strain N2) at young adult stage

hyb_protocol: Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA).

data_processing:
GeneChip Operating Software supplied by Affymetrix was used to perform gene expression analysis. Four samples of control fed conditions and four samples of treated conditions were statistically analysed. Raw data obtained from Affymetrix arrays were background corrected using RMA methodology. Intensity signal was standardized across arrays via quantile normalization algorithm. The difference between treated samples and controls was statistically tested using limma moderate t-statistic. Aiming to control the false disocvery rate, p-values were corrected for multiple testing using Benjamini and Hochberg method.
A table of RMA signals is linked to the Series record.  The ID column lists worm base identifiers; the IDs column lists the corresponding Affymetrix probeset IDs found in GPL200.

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans at young adult stage

label_protocol: Gene expression analysis was performed according to the Affymetrix-recommended protocol using Affymetrix C.Elegans Genome Array. GeneChips containing probes for over 22,500 transcripts. Total RNA (300 ng per sample) was biotin- labeled using the Affymetrix GeneChip 3' IVT express protocol

growth_protocol: C. elegans was cultured in Nematode Growth Medium (NGM) as standard diet. Nematodes were age-synchronized by isolating eggs from gravid adults. Embryos were incubated in the corresponding agar plates at 20ºC for 3 days (until reach young adult stage)

extract_protocol: Worms from each fed condition (NGM or Lactoferrin-based product) were collected with M9 buffer and disrupted by sonication (3 pulses at 10W, 20s/pulse). RNA was isolated with a comercial kit (RNAsy Kit, Qiagen)

treatment_protocol: Treated nematodes were cultured in NGM plates supplemented with 150 µL of a Lactoferrin-based product and incubated at 20ºC from egg to young adult stage.

tag: strain

tag: agent

value: Lactoferrin-based product


title: Treatment with Lactoferrin-based product_SL141


title: paired_LB-SZ7-rep1

tag: smoking


title: mimic Neg CTR exp1

description: mimic Neg CTR CD34+ cells

tag: tissue


title: mimic miR-494 exp2

description: mimic miR-494 CD34+ cells

value: mimic miR-494


title: paired_LB-SZ12-rep1

value: AA

tag: cell type


title: paired_LB-SZ6-rep1

value: y


title: paired_LB-SZ10-rep1


title: mimic miR-494 exp1

description: mimic miR-494 CD34+ cells


title: paired_LB-SZ5-rep1


title: Treatment with Lactoferrin-based product_SL139


title: mimic miR-494 exp3

description: mimic miR-494 CD34+ cells


title: NGM_SL142

value: control


title: paired_LB-SZ9-rep1

value: n


title: paired_LB-SZ4-rep1


title: NGM_SL138


title: Treatment with Lactoferrin-based product_SL137


title: NGM_SL140


title: NGM_SL136


title: paired_LB-SZ3-rep1

value: Cauc


title: paired_LB-C20-rep1

source_name: paired lymphoblast control

value: Control


title: paired_LB-SZ1-rep1


title: paired_LB-SZ2-rep1


title: paired_LB-C21-rep1


title: paired_LB-C19-rep1


title: paired_LB-C17-rep1


title: paired_LB-C22-rep1


title: paired_LB-C18-rep1


title: Rela-/-Relb-/-Rel-/- untreated replicate 1

city: New Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Marg

department: Infection and immunity

country: India

institute: National Institute of Immunology

description: SAMPLE 9

hyb_protocol: illumina standard direct hybridization protocol

scan_protocol: By using illumina Bead Array Reader version 3.7.9.27572

data_processing: The raw data was extracted from illumina's Genome studio software and the same used to check the quality of data. The data were normalized using quantile normalisation method.

source_name: Mouse embryonic fibroblasts

label_protocol: Biotinylated cRNA were prepared with TargetAmpTM- Nano labelling Kit for illumina Expression Beadchip

growth_protocol: Mouse embryonic fibroblasts were cultured in complete DMEM media with 10% BCS and passaged by trypsinizing every third day.

extract_protocol: Total RNA was isolated using  RNeasy Kit (QIAGEN) and on column DNase digestion was performed according to manufacturer protocol. Quality control was performed using Agilent Bioanalyzer.

treatment_protocol: Mouse embryonic fibroblasts were treated at 90% confluency with recombinant tumor necrosis factor (10 ng/ml)

value: Mouse embryonic fibroblasts

tag: genotype

value: Rela-/-Relb-/-Rel-/-

value: untreated


title: paired_LB-C13-rep1

value: Yes

value: lymphoblast


title: paired_LB-C12-rep1


title: Rela-/-Relb-/-Rel-/- 6h TNF replicate 2

description: SAMPLE 12

tag: treatment

value: TNF


title: Rela-/-Relb-/-Rel-/- untreated replicate 2

description: SAMPLE 10


title: paired_LB-C11-rep1

value: M


title: paired_LB-C15-rep1

value: No


title: Rela-/-Nfkb2-/- untreated replicate 2

description: SAMPLE 6


title: Rela-/-Relb-/-Rel-/- 6h TNF replicate 1

description: SAMPLE 11


title: paired_LB-C14-rep1


title: Rela-/-Nfkb2-/- 6h TNF replicate 2

description: SAMPLE 8


title: Rela-/-Nfkb2-/- 6h TNF replicate 1

description: SAMPLE 7


title: paired_LB-C16-rep1


title: WT 6h TNF replicate 1

description: SAMPLE 3

value: WT


title: Rela-/-Nfkb2-/- untreated replicate 1

description: SAMPLE 5


title: WT 6h TNF replicate 2

description: SAMPLE 4


title: paired_LB-C9-rep1


title: paired_LB-C10-rep1


title: paired_LB-C5-rep1


title: paired_LB-C8-rep1


title: WT untreated replicate 1

description: SAMPLE 1


title: -20°C eWAT,biological rep2

city: Jinan

first: Xiaoyan

last: Yang

address: 107 West Wenhua Road

institute: Shandong University Qilu Hospital

description: Gene expression data from mice epididymal adipose tissue exposed to -20°C

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Mouse Exon 1.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix Expression Console default analysis settings and global scaling as normalization method. Normalized signal intensities were transformed to the log base 2 scale.

source_name: epididymal adipose tissue from mice exposed to -20°C

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.

growth_protocol: Epididymal adipose tissue from mice exposed to 30°C, 4°C, -10°C and -20°C.

extract_protocol: All samples were prepared using Trizol. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Epididymal adipose tissue was washed by cold RNase-free normal saline, quickly dissected and put in liquid nitrogen when sacrificing the mice. Tissues were stored in -80°C until RNA extraction.

value: epididymal adipose tissue


title: paired_LB-C4-rep1


title: -20°C eWAT,biological rep3


title: paired_LB-C2-rep1

value: F


title: -20°C eWAT,biological rep1


title: paired_LB-SZ11-rep1

value: Patient

value: AA


title: Olive oil 10 min replicate 3

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

institute: ICTAN-CSIC

description: Biological replicate 3 of 3

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60 ºC for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65ºC, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned. Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GLP5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

scan_protocol: Images from Cy3 and HyPer5 channels were captured with a GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA, respectively. The ratio of each probe (M) was defined as log [Cy3 intensity/HyPer5 intensity] where HyPer5 is the wild type. Fold change (FC) is defined as 2M. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5

organism: Lactiplantibacillus plantarum

source_name: Treated cells: Experimental

label_protocol: Fluorescently labelled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen): 20 ug of total RNA was transformed to cDNA with SuperscriptTM III Reverse Transcriptase using anchored oligo(dT)20 primers, and including aminoallyl-modified nucleotides. After cDNA purification, the Cy3 and HyPer5 fluorescent dyes (Amersham Biosciences) were coupled to the aminoallyl-modified first-strand cDNA. Purification of Cy3- and HyPer5-labeled cDNA probes was carried out with the CyScribe GFX Purification Kit.

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS to an OD600 ≈ 0.8-0.9, then one pair of the culture was centrifuged at 9,000 x g for 5 min at 20 ºC and cells washed  twice in 100 mM phosphate buffer pH 7.0.

extract_protocol: For RNA extraction the celular pellet was mixed with 2 mL of quenching buffer (60% methanol, 66.7 mM HEPES, pH 6.5, -40 ºC) . Following quenching, the cells were pelleted by centrifugation at 9,000 x g for 10 min at -10 ºC, transferred to a screw cap tube containing an extraction mixture (500 uL 1:4 chloroform-acid phenol, 30uL of 10% SDS, 30uL Na-acetate 3M pH 5.2, 400uL Tris-EDTA buffer [10 mM Tris(hydroxymethyl)amino methane, 1 mM EDTA] pH 7.4, 15 mg of polyvinylpoly-pyrrolidone, and 500 mg of 75-150um glass beads). The cells were broken under frozen conditions in the Mini-BeadBeather (BIOSPEC Products, INC.) using three treatments of 4600 rpm for 40 seconds cycles (and chilled on dry ice for 60 seconds between cycles). The suspension was then centrifuged at 4 ºC at 10,000 x g for 2 min. Two extractions with 500 uL of chloroform were performed, and the supernatant containing the RNA was separated by centrifugation.  The sample was immediately frozen in liquid nitrogen, and stored at -80 ºC. NanoDrop ND-1000 instrument was used for quantification of RNA. Continued with the QUIAGEN RNA isolation kit. Two treatments with DNase I (Ambion) were applied and the absence of genomic DNA was confirmed by PCR.

treatment_protocol: Washed cells were suspended in 0.5 mL of 100 mM phosphate buffer pH 7.0 and then exposed to 0.5 mL of olive oil (final olive oil concentration 50 %) by vortex-shaking during 10 minutes. After exposure cells were centrifuged and RNA extracted and purified.

tag: compound

value: Olive oil 50%

value: without olive oil

source_name: Untreated cells: Control


title: paired_LB-C3-rep1

value: Cauc

value: n


title: Olive oil 10 min replicate 2

description: Biological replicate 2 of 3


title: Olive oil 10 min replicate 1

description: Biological replicate 1 of 3


title: paired_LB-C1-rep1

value: Control


title: -10°C eWAT,biological rep1

description: Gene expression data from mice epididymal adipose tissue exposed to -10°C

source_name: epididymal adipose tissue from mice exposed to -10°C


title: non-paired_LB-SZ17-rep1

source_name: non-paired lymphoblast schizophrenia

value: y


title: -10°C eWAT,biological rep3


title: -10°C eWAT,biological rep2


title: WT untreated replicate 2

description: SAMPLE 2

value: Mouse embryonic fibroblasts

value: untreated


title: 4°C eWAT,biological rep1

description: Gene expression data from mice epididymal adipose tissue exposed to 4°C

source_name: epididymal adipose tissue from mice exposed to 4°C


title: 30°C eWAT,biological rep1

description: Gene expression data from mice epididymal adipose tissue exposed to 30°C

source_name: epididymal adipose tissue from mice exposed to 30°C


title: non-paired_LB-SZ14-rep1

value: lymphoblast


title: 30°C eWAT,biological rep2


title: 4°C eWAT,biological rep2


title: non-paired_LB-SZ11-rep1


title: non-paired_LB-SZ12-rep1


title: non-paired_LB-SZ15-rep1


title: non-paired_LB-SZ19-rep1


title: non-paired_LB-SZ18-rep1


title: non-paired_LB-SZ13-rep1


title: 4°C eWAT,biological rep3


title: 30°C eWAT,biological rep3


title: non-paired_LB-SZ9-rep1


title: non-paired_LB-SZ6-rep1

value: Asian


title: non-paired_LB-SZ8-rep1


title: Rag1 mutant zebrafish_PolyIC_rep4

city: Leiden

first: Monica

last: Varela

address: Einsteinweg 55

department: ASH

country: Netherlands

institute: Leiden University

hyb_protocol: Each amplified and labelled sample was briefly hybridized at 65 °C for 17 hours following manufacturer instructions.

scan_protocol: Microarray slides were scanned with Agilent Technologies Scanner model G2505B.

data_processing: Spot intensities and other quality control features were extracted with the Feature Extraction software version 10.4.0.0 (Agilent). The results for the fluorescence intensity data and quality annotations were imported into GeneSpring GX version 12.6 (Agilent Technologies). All of the control features (including the positive and negative controls and the landing lights) were excluded from subsequent analyses. Normalization was then carried out by a percentile shift at the 75th percentile. Entities with an expression between the 20 and 95th percentile in the raw data were retained and used in subsequent analyses.

organism: Danio rerio

source_name: Kidney Rag1 mutant Adult Zebrafish Poly I:C 24 hours post-stimulation

label_protocol: Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit according to manufacturer's instructions.

extract_protocol: RNA was extracted with TRIzol reagent (Life Technologies, Madrid, Spain) following the TRIzol manufacturer’s specifications in combination with the RNeasy Mini Kit (Qiagen, Madrid), and preserved at -80 ºC until use. After DNase I treatment, RNA quality was assessed with the Agilent 2100 Bioanalyzer and kept frozen at -80 °C until all of the experiments could be hybridized and processed simultaneously.

treatment_protocol: Wild type and Rag1 mutant fish were intraperitoneally injected with PBS or 10 μg of pure Poly I:C (Sigma). 4 biological replicates per treatment (PBS and Poly I:C) were taken. For each biological replicate, 4 kidneys from 4 different fish were pooled after 24 hours post injection and conserved at -80ºC until use.

tag: genotype/variation

value: Rag1 mutant

tag: treament

value: PolyIC

value: Kidney

tag: immune-stimulation

value: Stimulated


title: non-paired_LB-SZ3-rep1

tag: age

value: F

value: No


title: non-paired_LB-SZ7-rep1

value: Patient

tag: gender

value: M


title: Wild type zebrafish_PolyIC_rep4

source_name: Kidney Wild type Adult Zebrafish Poly I:C 24 hours post-stimulation

value: Wild type


title: non-paired_LB-C21-rep1

source_name: non-paired lymphoblast control

value: Cauc


title: non-paired_LB-SZ4-rep1

value: AA


title: Rag1 mutant zebrafish_PolyIC_rep3


title: non-paired_LB-C22-rep1

value: Control

value: n


title: non-paired_LB-SZ5-rep1


title: Rag1 mutant zebrafish_PBS_rep4

source_name: Kidney Rag1 mutant Adult Zebrafish PBS 24 hours post-stimulation

value: PBS

value: Normal


title: Rag1 mutant zebrafish_PolyIC_rep2


title: non-paired_LB-C20-rep1

value: lymphoblast


title: Rag1 mutant zebrafish_PBS_rep3


title: Rag1 mutant zebrafish_PBS_rep1


title: non-paired_LB-SZ2-rep1


title: Rag1 mutant zebrafish_PolyIC_rep1


title: Wild type zebrafish_PolyIC_rep2


title: Wild type zebrafish_PolyIC_rep3


title: Rag1 mutant zebrafish_PBS_rep2


title: non-paired_LB-C17-rep1


title: non-paired_LB-C19-rep1


title: Wild type zebrafish_PBS_rep3

source_name: Kidney Wild type Adult Zebrafish PBS 24 hours post-stimulation


title: Wild type zebrafish_PolyIC_rep1


title: Wild type zebrafish_PBS_rep4


title: non-paired_LB-C16-rep2


title: non-paired_LB-C18-rep1

value: y


title: Wild type zebrafish_PBS_rep2


title: Wild type zebrafish_PBS_rep1


title: 8_K1Cre_female_243

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

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

data_processing: The data were normalized by percentile shift and filtered by flag, using GeneSpring GX software (Silicon Genetics).

source_name: Kidney_K1Cre (Control)_female

label_protocol: RNA samples were labeled with Cy3 using the Quick Amp Labeling kit (Agilent) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from kidneys using Sepazol-RNA I Super G RNA extraction kit (Nakalai).

tag: strain background

value: Mixed (with contributions from 129Sv/J and C57BL/6J strains)

value: K1Cre (Keap1+/-::Nrf2Flox/Flox::K5-Cre)

value: female

value: 8 weeks

value: kidney


title: non-paired_LB-C14-rep1

city: Baltimore

tag: group

value: No


title: non-paired_LB-C16-rep1

tag: race


title: 6_NEKO_male_239

value: NEKO (Keap1-/-::Nrf2Flox/Flox::K5-Cre)

value: male


title: non-paired_LB-C11-rep2


title: OsHOX24-overexpression seedlings, drought stress, rep1

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

description: Gene expression data from drought stress treated OsHOX24 overexpression rice seedlings

hyb_protocol: Following fragmentation, 3.5 ug of labelled 2nd cycle ss-cDNA were hybridized for 17 h at 45 degree celsius on GeneChip whole target expression array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 as per FS450_0002 fluidics protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were imported into Genespring software and probe summarization and normalization was performed using RMA algorithm

organism: Oryza sativa

source_name: Rice seedlings

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® 3' IVT PLUS Reagent Kit User Manual, Affymetrix)

growth_protocol: Wild-type and transgenic rice seedlings were grown in hydroponics system (trays) containing Yoshida medium, at 28±1 degree celsius for three weeks, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark

extract_protocol: Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions

treatment_protocol: For control conditions and drought stress treatment, seedlings were kept in RO water and dried between folds of tissue paper at 28 ± 1 degree celsius for 3 h, respectively

value: OsHOX24 overexpressed

tag: stress

value: drought

tag: ecotype

value: Pusa Basmati 1

value: Seedlings

value: Three week old


title: non-paired_LB-C13-rep1

value: Control

value: M

value: Cauc

tag: education

value: n


title: non-paired_LB-C12-rep1

tag: smoking

value: y

value: lymphoblast


title: non-paired_LB-C15-rep1

value: AA


title: non-paired_LB-C10-rep2


title: Wild-type seedlings, drought stress, rep3

description: Gene expression data from drought stress treated wild-type rice seedlings

value: wild type

tag: tissue


title: OsHOX24-overexpression seedlings, drought stress, rep3


title: Wild-type seedlings, drought stress, rep1


title: OsHOX24-overexpression seedlings, drought stress, rep2


title: 7_K1Cre_male_241

source_name: Kidney_K1Cre (Control)_male

value: Mixed (with contributions from 129Sv/J and C57BL/6J strains)

value: K1Cre (Keap1+/-::Nrf2Flox/Flox::K5-Cre)

value: 8 weeks

value: kidney


title: non-paired_LB-C7-rep1

value: No

tag: cell type


title: 1_K1_female_232

value: K1 (Keap1+/-::Nrf2Flox/Flox)

value: female


title: OsHOX24-overexpression seedlings, control, rep3

description: Gene expression data from control OsHOX24 overexpression rice seedlings

value: OsHOX24 overexpressed

value: Pusa Basmati 1

value: Seedlings


title: OsHOX24-overexpression seedlings, control, rep2

value: Three week old


title: 5_NEKO_male_238

value: NEKO (Keap1-/-::Nrf2Flox/Flox::K5-Cre)

value: male


title: non-paired_LB-C9-rep1

value: Control

value: F

value: n


title: non-paired_LB-C11-rep1

value: AA

value: lymphoblast


title: 2_NEKO_female_233

value: Mixed (with contributions from 129Sv/J and C57BL/6J strains)


title: Wild-type seedlings, drought stress, rep2

value: wild type

value: drought


title: 4_K1Cre_male_235

value: K1Cre (Keap1+/-::Nrf2Flox/Flox::K5-Cre)

value: 8 weeks

value: kidney


title: non-paired_LB-C10-rep1

value: M

value: No


title: 3_NEKO_female_234

value: female


title: non-paired_LB-C8-rep1


title: COPD 7

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: 3901 Rainbow Blvd.

department: Internal Medicine

institute: University of Kansas Medical Center

description:
COPD lung parenchyma tissue
C.7

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
The data was analyzed through Illumina's GenomeStudio methylation module (v1.9.0).
Unmethylated and methylated signal intensities in series supplementary file

label: Cy3 and Cy5

source_name: COPD lung tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Lung tissues were collected snap frozen and stored at -80 °C. Genomic DNA was extracted from lung tissue. Briefly, 1 ?g genomic DNA was bisulfite-converted using EZ DNA Methylation Kit (Zymo Research, Irvine, CA). The bisulfite-converted DNA samples were assayed using Infinium HumanMethylation450 BeadChip array from Illumina (San Diego, CA) following the manufacturer’s instructions.

value: lung parenchyma

tag: Sex

tag: pack years

tag: fev%

tag: fev/fvc%


title: non-paired_LB-C5-rep1


title: COPD 8

description:
COPD lung parenchyma tissue
C.8


title: OsHOX24-overexpression seedlings, control, rep1

tag: genotype/variation

value: OsHOX24 overexpressed

value: Pusa Basmati 1

value: Seedlings

value: Three week old


title: Wild-type seedlings, control, rep1

description: Gene expression data from control wild-type rice seedlings


title: Wild-type seedlings, control, rep3


title: COPD 6

description:
COPD lung parenchyma tissue
C.6


title: Wild-type seedlings, control, rep2


title: non-paired_LB-C4-rep1

value: Control

value: Other

value: n


title: COPD 3

description:
COPD lung parenchyma tissue
C.3


title: COPD 5

description:
COPD lung parenchyma tissue
C.5


title: Smoker 8

description:
Smoker lung parenchyma tissue
S.8

source_name: Smoker lung tissue