title: SW620-3

city: Xiamen

first: Wei

last: Yan

address: Hubin South Road 201

institute: Xiamen University

description: Exiqon’s miRCURY LNA™ microRNA Array, 7th gen - hsa, mmu & rno

hyb_protocol: miRNA array hybridization by Kits and Reagents:2×Hybridization buffer,Phalanx Hyb. Assembly,miRCURYTM Array and .Wash buffer kit (Cat #208021, Exiqon).

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: a) The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.  b) We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)-/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.  c) After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.  d) Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.   e) You can find the detail information in miRNA Expression Profiling Data.

source_name: human colorectal cancer cell line

label_protocol: Exiqon’s miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon)

growth_protocol: SW480 and SW620 cell lines were obtained from American Type Culture Collection (ATCC, Manassas, VA) and were maintained in RPMI (Invitrogen) containing 10% FBS (Invitrogen) and penicillin G-streptomycin (Invitrogen).

extract_protocol: Total RNA extraction was performed using TRIzol reagent (Invitrogen, Carlsbad, CA).Purification by RNasey Mini Kit(Qiagen p/n 74104).RNA quantification and quality control by NanoDrop ND-1000 and Denaturing Agarose Gel electrophoresis

treatment_protocol: Collect logarithmic growth phase cells of SW480 and SW620 from three independent experiments.


title: om_6427

status: Public on Aug 01 2016

type: genomic

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description: Female adipose tissue.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K BeadChip using standard Illumina protocol.

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

data_processing:
Quantile normalization was applied, followed by BMIQ normalization. Batch effects were checked and removed from the dataset.
Data was normalized and analyzed using GenomeStudio software, R packages and Qlucore software.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: obese female, omental adipose tissue, insulin sensitive

label_protocol: Standard Illumina protocol for Human Methylation 450K DNA Analysis BeadChip.

extract_protocol: Genomic DNA was prepared from adipose tissue using the QIAamp DNA Mini kit (cat no. 51304, Qiagen, Hilden, Germany).

tag: tissue

value: omental adipose tissue

tag: gender

value: female

tag: phenotype

value: obese

tag: disease state

value: no systemic insulin resistance

tag: insulin resistance

value: sensitive

tag: individual identifier


title: SW620-2

type: RNA

country: China

molecule: total RNA

tag: cell line


title: om_6436

description: Female adipose tissue.


title: 24h Tacrolimus 4

city: Vienna

first: Constantin

last: Aschauer

address: Waehringer Gürtel 18-20, 1090 Wien

country: Austria

institute: Medical University of Vienna

hyb_protocol: Protocols for RNA extraction, RNA labeling, hybridization and washing of microarrays can   Be found on our website (http://www.meduniwien.ac.at/nephrogene/)

scan_protocol: Affymetrix GeneChip Scanner 7G Plus

data_processing:
The oligo R package was used for pre-processing and normalization of expression data (RMAnormalized in log2 scale)
the TIGR MultiExperimentViewer was used in order to identify differentially regulated transcripts

label: biotin

source_name: human mesangial cells-in vitro_Tacrolimus

growth_protocol: cultured in MCDB-131 media (Gibco-invitrogen), supplemented with 10% FBS, 100U penicillin/ml 100ug/ml streptomycin and 2mmol L-Glutamine (all supplied from Gibco-Invitrogen) at 37°C in humid atmosphere with 5%CO2 in air

extract_protocol: Trizol and chloroform reagent was used to purify RNA

treatment_protocol: cultured in serum free media and FK 506 (Abcam) dissolved in DMSO (Sigma) in a final concentration of 1 µM for 24h

value: human mesangial cells

tag: treated with

value: FK 506 dissolved in DMSO in 1 µM final conc. for 24h


title: SW620-1


title: 24h Tacrolimus 3

label_protocol: Protocols for RNA extraction, RNA labeling, hybridization and washing of microarrays can   Be found on our website (http://www.meduniwien.ac.at/nephrogene/)


title: 24h Tacrolimus 2


title: om_6408

description: Female adipose tissue.


title: MEF-V, biological rep1

city: Bethesda

first: Yuri

last: Postnikov

state: MD

address: 37 Convent Dr

country: USA

institute: NIH

description: Gene expression data from mouse embryonic fibroblasts

hyb_protocol: Biotininylated probes were hybridized to Affymetrix Mouse Gene 1.0 ST arrays using Affymetrix Fluidics Station.

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

data_processing: Data were analyzed by BRB Array Tools, GeneSpring GX 12.6 (Agilent Technologies) and Partek Genomics Suite 6.5 software

organism: Mus musculus

source_name: Mouse embryonic fibroblasts expressing empty expression vector (MEF-V)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: SV40-immortalized mouse embryonic fibroblast (ATCC) cell lines were maintained in Dulbecco's modified Eagle's medium, supplemented with 10% fetal calf serum, at 37˚C and 5% CO2.

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

treatment_protocol: Cells were harvested by trypsinization

value: embryonic fibroblasts

value: SV40-immortalized (ATCC, CRL-2907)

tag: vector

value: empty expression vector (MEF-V)


title: SW480-3


title: PS3

city: Guangzhou

first: Zhaofeng

last: Huang

state: Guangdong

address: 74# zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

description: MeDIP-ChIP human sperm DNA after density selection

hyb_protocol: hybridized to NimbleGen Human DNA Methylation 3x720K Promoter Plus CpG Island Arrays, which is a multiplex slide with 3 identical arrays per Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA). For array hybridization, Roche NimbleGen's Human Promoter plus CpG Island array was used, which is a 3x720k format array design containing 27,728 CpG Islands and all well-characterized Promoter regions (from about -2,440bp to +610bp of the TSSs) totally covered by ~720,000 probes.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner.

data_processing: Raw data was extracted as pair files by NimbleScan software. We perform Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample.

source_name: MeDIP DNA from subject 3 sperm sample after selection

label_protocol: The purified DNA was quantified using a nanodrop ND-1000. For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

growth_protocol: no culture

extract_protocol: Genomic DNA (gDNA) was extracted from 6 Cell samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA). The purified gDNA was then quantified and quality assessed by nanodrop ND-1000. Genomic DNA of each sample was sonicated to ~200 – 1000 bp with a Bioruptor sonicator (Diagenode) on “Low” mode for 10 cycles of 30 seconds “ON” & 30 seconds “OFF”. The gDNA and each sheared DNA were aragrose analyzed. 1 μg of sonicated genomic DNA was used for immunoprecipitation using a mouse monoclonal anti-5-methylcytosine antibody (Diagenode). For this, DNA was heat-denatured at 94 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4 °C with rocking agitation in 400 μL immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 200 μL of anti-mouse IgG magnetic beads were added and incubated for an additional 2 hours at 4 °C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. MeDIP DNA were purified using Qiagen MinElute columns (Qiagen)Immunoprecipitation of methylated DNA was performed using BiomagTM magnetic beads coupled mouse monoclonal antibody against 5-methylcytidine. The immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation. The MeDIP-enriched DNA was amplified using a WGA kit from Sigma-Aldrich (GenomePlex® Complete Whole Genome Amplification (WGA2) kit). The amplified DNA samples were then purified with QIAquick PCR purification kit (Qiagen).

treatment_protocol: sperm after selection

tag: sample type

value: MeDIP DNA

tag: cell type

value: sperm

source_name: Input DNA from subject 3 sperm sample after selection

value: none, input DNA


title: om_6304

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin resistant

value: systemic insulin resistance

value: resistant


title: om_6424

description: Female adipose tissue.


title: 24h Tacrolimus 1


title: om_6426

description: Female adipose tissue.


title: S3

description: MeDIP-ChIP human sperm DNA without selection

source_name: MeDIP DNA from subject 3 sperm sample before selection

treatment_protocol: sperm before selection

source_name: Input DNA from subject 3 sperm sample before selection


title: om_6409

description: Female adipose tissue.


title: PS2

source_name: MeDIP DNA from subject 2 sperm sample after selection

source_name: Input DNA from subject 2 sperm sample after selection


title: om_6302

description: Female adipose tissue.


title: om_6295

description: Female adipose tissue.


title: SW480-1


title: om_6268

description: Female adipose tissue.


title: om_6272

description: Female adipose tissue.


title: S1

source_name: MeDIP DNA from subject 1 sperm sample before selection

source_name: Input DNA from subject 1 sperm sample before selection


title: PAO1 Untreated biological rep3

city: Cork

first: Fergal

last: O'Gara

address: UCC, Western Rd

department: Microbiology Dept, Univerisity College Cork

country: Ireland

institute: BIOMERIT Research Centre

description: Gene expression data from P. aeruginosa grown not in the presence of bile.

hyb_protocol: The labelled cDNA was hybridization to the Pseudomonas aeruginosa Affymetrix GeneChip Genome Array, which was subsequently washed and scanned.

scan_protocol: GeneChips were then scanned.

data_processing: The data were analyzed with Affymetrix' GeneChip Operating Software (GCOS).

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 Untreated

label_protocol: Biotinylated cDNA was prepared from 10 ug total RNA.

growth_protocol: Three independent cultures of P. aeruginosa strain PAO1 were grown shaking from OD600nm 0.025 to 0.8 at 37 °C.

extract_protocol: Subsequently 500 μl of culture was treated with 1 ml of RNAProtect Bacteria Reagent (Qiagen). Total RNA was extracted using the RNAeasy kit (Qiagen) according to the manufacturer's instructions. To ensure DNA free RNA, the total RNA was DNase treated using TURBO DNase (Ambion).

treatment_protocol: P. aeruginosa strain PAO1 were exposed to 0.3% (w/v) complex bile (Sigma).

tag: agent


title: PAO1 Treated with bile biological rep2

description: Gene expression data from P. aeruginosa grown in the presence of bile.

source_name: PAO1 Treated with bile

value: bile


title: S2

source_name: MeDIP DNA from subject 2 sperm sample before selection

source_name: Input DNA from subject 2 sperm sample before selection


title: om_6290

description: Female adipose tissue.


title: PAO1 Treated with bile biological rep3


title: om_6401

description: Female adipose tissue.


title: PAO1 Treated with bile biological rep1


title: om_6247

description: Female adipose tissue.


title: om_6285

description: Female adipose tissue.


title: PAO1 Untreated biological rep2


title: SW480-2

source_name: human colorectal cancer cell line


title: om_6221

description: Female adipose tissue.


title: om_6220

description: Female adipose tissue.


title: om_6232

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin sensitive


title: om_6217

description: Female adipose tissue.


title: T47D-PD2

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
PD replicate 2
9992405092_K

hyb_protocol: Standard Illumina Human HT-12 V4.0 expression beadchip hybridization protocol

scan_protocol: Standard Ilumina scanning protocol using Illumina HiScan scanner.

data_processing: Data were background subtracted and quantile normalized among arrays and log2 transformed and analysis were preformed using R/Bioconductor packages

source_name: T47D PD

label_protocol: RNA was labeled with biotin using the Illumina Total PrepKit from Ambion.

growth_protocol: Cells were grown in DMEM+10%FBS

extract_protocol: RNA was extracted using the QIAGEN kit and manufacturer's protocol was followed. Experion RNA analysis System (Bio-Rad)were used for quality control

treatment_protocol: MCF7, T47D cells were treated with DMSO/ PD-0332991

tag: treatment

value: PD


title: PAO1 Untreated biological rep1

description: Gene expression data from P. aeruginosa  grown not in the presence of bile.


title: T47D-ctrl3

description:
control replicate 3
9992405092_I

source_name: T47D control

value: Control


title: T47D-PD3

description:
PD replicate 3
9992405092_L


title: om_6230

description: Female adipose tissue.

value: omental adipose tissue

value: female


title: om_6212

description: Female adipose tissue.

value: obese

value: no systemic insulin resistance


title: T47D-ctrl2

description:
control replicate 2
9992405092_H


title: T47D-ctrl1

description:
control replicate 1
9992405092_G


title: PC-9_Erlotinib_miR371_precursor_#3 (SAM9259254)

city: South San Francisco

first: Richard

last: Bourgon

state: CA

address: 1 DNA Way, MS 93

department: Bioinformatics & Computational Biology

institute: Genentech, Inc.

hyb_protocol: 12.5 micrograms of cRNA was fragmented and hybridized to Human Genome 133 Plus 2.0 arrays at 45 degrees C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained using Affymetrix HWS kit using their Fluidics station and then scanned on GeneChip scanner 3000.

data_processing: Gene expression data were background corrected and quantile normalized using the rma function in the affy package from Bioconductor.

source_name: PC-9 cell line, treated with Erlotinib, transfected with miR371 precursor

label_protocol: Preparation of cRNA was done using Affymetrix 3' IVT Express kit and protocol provided by Affymetrix. Briefly, 0.5 ug of total RNA was converted into double-stranded cDNA and used to generate biotin labeled cRNA which was then purified.

growth_protocol: Each cell line was plated in 10cm plates and cultured to 80% confluency.

extract_protocol: Cells were washed with 1X PBS and total RNA was extracted using RNeasy kit from Qiagen as per the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO or 2uM erlotinib for 24 hours after cells reached 80% confluency.

value: Erlotinib for 24hrs

tag: transfection

value: miR371 precursor


title: om_6207

description: Female adipose tissue.


title: PS1

source_name: MeDIP DNA from subject 1 sperm sample after selection

source_name: Input DNA from subject 1 sperm sample after selection


title: T47D-PD1

description:
PD replicate 1
9992405092_J


title: MCF7-PD3

description:
PD replicate 3
9992405092_F

source_name: MCF7 PD


title: MCF7-PD2

description:
PD replicate 2
9992405092_E


title: PC-9_Erlotinib_miR371_precursor_#1 (SAM9259252)


title: MCF7-PD1

description:
PD replicate 1
9992405092_D


title: PC-9_Erlotinib_GFP_vector_#2 (SAM9259244)

source_name: PC-9 cell line, treated with Erlotinib, transfected with GFP vector

value: GFP vector


title: om_6200

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin resistant


title: PC-9_Erlotinib_GFP_vector_#3 (SAM9259245)


title: MCF7-ctrl1

description:
control replicate 1
9992405092_A

source_name: MCF7 control


title: PC-9_DMSO_miR371_precursor_#3 (SAM9259242)

source_name: PC-9 cell line, treated with DMSO, transfected with miR371 precursor

value: DMSO


title: MCF7-ctrl2

description:
control replicate 2
9992405092_B


title: om_6160

description: Female adipose tissue.


title: MCF7-ctrl3

description:
control replicate 3
9992405092_C


title: PC-9_Erlotinib_GFP_vector_#1 (SAM9259243)


title: PC-9_DMSO_miR371_precursor_#2 (SAM9259241)


title: om_6144

description: Female adipose tissue.

value: sensitive


title: PC-9_DMSO_miR371_precursor_#1 (SAM9259240)


title: om_6156

description: Female adipose tissue.


title: PC-9_Erlotinib_miR371_precursor_#2 (SAM9259253)


title: PC-9_DMSO_GFP_vector_#2 (SAM9259232)

source_name: PC-9 cell line, treated with DMSO, transfected with GFP vector


title: om_6149

description: Female adipose tissue.


title: PC-9_DMSO_GFP_vector_#1 (SAM9259231)


title: om_6199

description: Female adipose tissue.


title: U87_NT_2

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (Hiscan array scanner)

data_processing: Output from BeadStudio were processed using beadarray bioconductor package. Raw data was quantile normalized and log2 transformed using normaliseIllumina function.

source_name: cell line

label_protocol: target probes were labelled with biotin using TargetAmp Nano labelling kit.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 100 u/ml penicillin and 100 g/ml streptomycin.

extract_protocol: RNA extraction was done by QIAGEN RNeasy Mini Kit.

value: non-targeting siRNA


title: U87_siBCL6_2

value: BCL6 siRNA


title: PC-9_erlotinib_DTP_GFP_VECTOR_#3 (SAM630853)

growth_protocol: 1 million cells for each cell line were plated in 15cm plates and cultured for 3 days for DMSO treated cells and 9 days for DTPs. Fresh media was replaced every 3 days.

extract_protocol: DMSO treated cells were harvested upon reaching 100% confluency on day 3. DTPs were harvested on day 10 after 9 days of erlotinib treatment. Cells were washed with 1X PBS and total RNA was extracted using RNA isolation kit from Exiqon as per the manufacturer's instructions.

treatment_protocol: Cells were treated with 2uM erlotinib after cells reached 80% confluency after initial plating. Media containing fresh drug was replaced every 3 days for 9 days.

value: Erlotinib for 9 days

value: DTP


title: U87_NT_1


title: om_6145

description: Female adipose tissue.

value: systemic insulin resistance

value: resistant


title: om_6125

description: Female adipose tissue.


title: om_6113

description: Female adipose tissue.


title: om_6094

description: Female adipose tissue.


title: om_6123

description: Female adipose tissue.


title: om_6102

description: Female adipose tissue.


title: om_6155

description: Female adipose tissue.


title: Fetal lung #2

city: Lund

first: Sara

last: Rolandsson Enes

address: BMC, C12

department: EMV

institute: Lund University

description: Fetal lung

scan_protocol: Standard Illumina iScan N240 scanning protocol scan setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

source_name: Cultured mesenchymal stromal cell (MSC), passage 3

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: RNeasy mini kit (Qiagen)

value: No

value: healthy

value: Lung


title: Rotenone

city: Shinagawa-ku

first: Sonoko

last: Atsumi

state: Tokyo

address: 3-14-23 Kamiosaki

country: Japan

institute: Institute of Microbial Chemistry (BIKAKEN)

description: Sample 3

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of four samples were normalized by quantile algorithm with Bioconductor.

source_name: NIH3T3/EGFRvIII, Rotenone treated

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: 3D culture

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: ON treatment

value: NIH3T3 cell line stably expressing EGFRvIII

tag: growth protocol

value: 3D culture

value: Rotenone


title: PC-9_erlotinib_DTP_GFP_VECTOR_#1 (SAM630851)


title: Fetal lung #3

description: Fetal lung


title: Healthy bone marrow aspirate #3

description: Bone marrow aspirates

value: Bone marrow


title: om_6107

description: Female adipose tissue.

value: omental adipose tissue

value: female

value: obese

value: no systemic insulin resistance


title: Ertredin

description: Sample 2

source_name: NIH3T3/EGFRvIII, Ertedin treated

value: Ertredin


title: PC-9_DMSO_GFP_vector_#3 (SAM9259233)

value: DMSO

value: GFP vector


title: U87_siBCL6_1

value: BCL6 siRNA


title: PC-9_erlotinib_DTP_GFP_VECTOR_#2 (SAM630852)

value: Erlotinib for 9 days

value: DTP


title: om_6086

description: Female adipose tissue.

value: systemic insulin resistance

value: resistant


title: Healthy bone marrow aspirate #2

description: Bone marrow aspirates

value: No

value: healthy


title: Fetal lung #1

description: Fetal lung

value: Lung


title: PC-9_GFP_VECTOR_#2 (SAM630849)

value: parental


title: AG1478

description: Sample 4

source_name: NIH3T3/EGFRvIII, AG1478 treated

value: NIH3T3 cell line stably expressing EGFRvIII

value: 3D culture


title: PC-9_GFP_VECTOR_#3 (SAM630850)


title: Lung-transplanted with BOS #2

description: Lung-transplanted BOS

value: bronchiolitis obliterans syndrome

value: Distal lung biopsies


title: control

description: Sample 1

source_name: NIH3T3/EGFRvIII, control

value: control


title: Lung-transplanted with BOS #1

description: Lung-transplanted BOS


title: om_6085

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin sensitive

value: omental adipose tissue

value: female

value: obese

value: no systemic insulin resistance

value: sensitive


title: om_6091

description: Female adipose tissue.


title: om_6093

description: Female adipose tissue.


title: Lung-transplanted with BOS #3

description: Lung-transplanted BOS


title: Healthy bone marrow aspirate #1

description: Bone marrow aspirates

value: Bone marrow


title: PC-9_GFP_VECTOR_#1 (SAM630848)

value: DMSO

value: GFP vector


title: wild type infected replicate D

city: Gainesville

first: Zsolt

last: Toth

state: FL

institute: University of Florida

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization approach was performed with Partek Genomics Suite software (v.6.6).

source_name: SLK_WT KSHV_infected

label_protocol: standard Affymetrix protocol

growth_protocol: standard cell culture

extract_protocol: Trizol followed by Rneasy column purification

treatment_protocol: SLK cells were infected with KSHV virus for 72 hours. Uninfected cells and these infected cells were collected in Trizol.

value: SLK

tag: infected with

value: wild type Kaposi's sarcoma-associated herpesvirus (KSHV)

tag: time point

value: 72 hrs post-infection (hpi)


title: LANA KO infected replicate E

source_name: SLK_LANA KO KSHV_infected

value: LANA knockout (KO) Kaposi's sarcoma-associated herpesvirus (KSHV)


title: om_6084

description: Female adipose tissue.

tag: tissue

value: systemic insulin resistance

value: resistant


title: LANA KO infected replicate F


title: Lung-transplanted no BOS #2

description: Lung-transplanted No BOS

value: No

value: No BOS or good outcome recipients have a FEV1 >90% of baseline


title: wild type infected replicate C


title: Uninfected replicate A

value: none (uninfected)


title: Uninfected replicate B


title: om_6083

description: Female adipose tissue.

value: omental adipose tissue

tag: gender


title: Lung-transplanted no BOS #3

description: Lung-transplanted No BOS

value: Distal lung biopsies


title: om_6072

description: Female adipose tissue.

value: female

tag: phenotype

value: obese


title: om_6080

description: Female adipose tissue.

tag: disease state


title: om_6073

description: Female adipose tissue.

tag: insulin resistance


title: Th1 activated rep3

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

country: United Kingdom

institute: University of Leicester

hyb_protocol: Fragmented cRNA (15 ug) was hybridized to GeneChip arrays at 45°C for 18 hours. GeneChips were washed and stained on the GeneChip fluidics station 450 (Affymetrix)

scan_protocol: GeneChips were scanned on the GeneChip scanner 3000

data_processing: The data were analysed in Partek Genomics Suite 6.6 using the gene expression workflow. RMA algorithm, quantile normalisation.

source_name: Day 28 Th1 cells, activated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5ug total RNA

growth_protocol: Cells were cultured for 28 days with weekly restimulation with anti-CD3/anti-CD28

extract_protocol: Total RNA was extracted using TRIzol according to manufacturers instructions

treatment_protocol: Cells were either resting or activated for 4 hours with PMA/Ionomycin

value: Female

tag: donor

value: C

value: Activated


title: Lung-transplanted no BOS #1

description: Lung-transplanted No BOS


title: Control.3_MCF7

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: MCF7 cell_control

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell line


title: Th2 activated rep3

source_name: Day 28 Th2 cells, activated


title: om_6070

description: Female adipose tissue.

tag: individual identifier


title: Th2 resting rep3

source_name: Day 28 Th2 cells, resting

value: Resting


title: Th1 resting rep3

source_name: Day 28 Th1 cells, resting


title: mimic.miR500.1_MCF7

source_name: MCF7 cell_mimic.miR500


title: mimic.miR500.2_MCF7


title: Th2 activated rep2

value: B


title: om_6055

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin resistant


title: Th2 resting rep2


title: Th1 activated rep2


title: Control.1_MCF7


title: Control.2_MCF7


title: mimic.miR500.3_MB231

source_name: MDA-MB-231 cell_mimic.miR500


title: mimic.miR500.2_MB231


title: om_6051

description: Female adipose tissue.


title: om_6037

description: Female adipose tissue.


title: om_6040

description: Female adipose tissue.


title: om_6039

description: Female adipose tissue.

value: no systemic insulin resistance

value: sensitive


title: om_6036

description: Female adipose tissue.


title: Th2 activated rep1

value: Male

value: A


title: Control.3_MB231

source_name: MDA-MB-231 cell_control


title: Th1 resting rep1


title: Th1 activated rep1


title: Control.1_MB231


title: mimic.miR500.3_MCF7


title: Th1 resting rep2


title: mimic.miR500.1_MB231


title: Th2 resting rep1


title: om_6032

description: Female adipose tissue.

value: systemic insulin resistance

value: resistant


title: om_5999

description: Female adipose tissue.


title: om_6000

description: Female adipose tissue.


title: Control.2_MB231


title: om_6028

description: Female adipose tissue.


title: om_6025

description: Female adipose tissue.


title: om_5991

description: Female adipose tissue.


title: panicles of ZH11 plants_high temperature

first: Hai

last: Zhou

address: Wushan

department: College of Life Sciences

institute: South China Agricultural University

description: Gene expression data from young panicles from microspore mother cell to meiosis of ZH11 plants grown at high temperature.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix rice Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

organism: Oryza sativa Japonica Group

source_name: Young panicles from microspore mother cell to meiosis of ZH11 plants grown at high temperature.

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

growth_protocol: Rice plants were grown in the growth cabinet at day average temperatures (DAT) of 23°C or 28°C.

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Young panicles from microspore mother cell to meiosis of rice were ground into a fine power in liquid nitrogen and placed in the Trizol solution(Invitrogen).

tag: line

tag: genotype/variation

value: Wild-type


title: panicles of Os02g12290iL1 plants_low temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of Os02g12290iL1 plants grown at low temperature.

source_name: Young panicles from microspore mother cell to meiosis of Os02g12290iL1 plants grown at low temperature.

value: knockdown of Os02g12290 by RNA interference (RNAi)


title: panicles of Os02g12290iL1 plants_high temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of Os02g12290iL1 plants grown at high temperature.

source_name: Young panicles from microspore mother cell to meiosis of Os02g12290iL1 plants grown at high temperature.


title: panicles of AnS-1 plants_low temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of AnS-1 plants grown at low temperature.

organism: Oryza sativa Indica Group

source_name: Young panicles from microspore mother cell to meiosis of AnS-1 plants grown at low temperature.

value: TGMS mutain


title: panicles of ZH11 plants_low temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of ZH11 plants grown at low temperature.

source_name: Young panicles from microspore mother cell to meiosis of ZH11 plants grown at low temperature.


title: panicles of AnN plants_high temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of AnN plants grown at high temperature.

source_name: Young panicles from microspore mother cell to meiosis of AnN plants grown at high temperature.

value: AnN


title: panicles of AnS-1 plants_high temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of AnS-1 plants grown at high temperature.

source_name: Young panicles from microspore mother cell to meiosis of AnS-1 plants grown at high temperature.


title: high-isoflavone soybean diet, bio rep5

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

description: normalized by SuperNORM data service

hyb_protocol: GeneChip® Hybridization Oven 640 (Affymetrix)

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix）

data_processing: The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model.

organism: Rattus norvegicus

source_name: SD rat liver, male

label_protocol: GeneChip® 3' IVT Express Kit

growth_protocol: Male Sprague-Dawley rats were obtained from Charles River Japan (Kanagawa, Japan) at 4 week of age. Animals were housed individually in a room with a controlled temperature (20-22ºC), humidity (55-65%), and 12-h-light/-dark cycle. During their adaptation to the conditions, rats were fed a commercial non-purified diet (Type NMF; Oriental Yeast Co., Tokyo, Japan) for 5 days. Rats were allowed free access to diet and water.

extract_protocol: Acid guanidinium thiocyanate-phenol-chloroform extraction

treatment_protocol: Animals were randomly divided into 4 groups and fed an experimental diet for 21 days. The experimental diets were as follows: a diet containing 200 g/kg casein (Cas) ;a diet containing two proteins derived equally from casein and Fukuyutaka (conventional cultiver soybean) (F10); a diet containing two proteins derived from casein and Yukipirika (hihg-isoflavone soybean) in the proportion of three parts to one (Y05); a diet containing two proteins derived equally from casein and Yukipirika (Y10).

value: liver

tag: strain

value: Male Sprague-Dawley rats

tag: age

value: 4 weeks of age

tag: diet

value: rats were adapted to the condition for 5 days and fed high-isoflavone soybean diet for 21 days


title: om_6047

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin sensitive

value: omental adipose tissue

value: female

value: obese


title: panicles of AnN plants_low temperature

description: Gene expression data from young panicles from microspore mother cell to meiosis of AnN plants grown at low temperature.

source_name: Young panicles from microspore mother cell to meiosis of AnN plants grown at low temperature.


title: om_5876

description: Female adipose tissue.


title: om_5987

description: Female adipose tissue.


title: high-isoflavone soybean diet, bio rep4

description: normalized by SuperNORM data service


title: high-isoflavone soybean diet, bio rep2

description: normalized by SuperNORM data service


title: om_5859

description: Female adipose tissue.

value: no systemic insulin resistance


title: high-isoflavone soybean diet, bio rep1

description: normalized by SuperNORM data service


title: casein+high-isoflavone soybean diet, bio rep5

description: normalized by SuperNORM data service

value: rats were adapted to the condition for 5 days and fed casein+high-isoflavone soybean diet for 21 days


title: om_5857

description: Female adipose tissue.

value: sensitive


title: casein+high-isoflavone soybean diet, bio rep4

description: normalized by SuperNORM data service


title: om_5811

description: Female adipose tissue.


title: casein+high-isoflavone soybean diet, bio rep3

description: normalized by SuperNORM data service


title: om_5985

description: Female adipose tissue.


title: casein+high-isoflavone soybean diet, bio rep1

description: normalized by SuperNORM data service


title: om_5810

description: Female adipose tissue.


title: om_5861

description: Female adipose tissue.


title: conventional cultiver soybean diet, bio rep3

description: normalized by SuperNORM data service

value: rats were adapted to the condition for 5 days and fed conventional cultiver soybean diet for 21 days


title: om_5803

description: Female adipose tissue.


title: casein+high-isoflavone soybean diet, bio rep2

description: normalized by SuperNORM data service


title: conventional cultiver soybean diet, bio rep5

description: normalized by SuperNORM data service


title: conventional cultiver soybean diet, bio rep2

description: normalized by SuperNORM data service


title: conventional cultiver soybean diet, bio rep4

description: normalized by SuperNORM data service


title: om_5849

description: Female adipose tissue.


title: om_5794

description: Female adipose tissue.


title: high-isoflavone soybean diet, bio rep3

description: normalized by SuperNORM data service


title: om_5829

description: Female adipose tissue.


title: conventional cultiver soybean diet, bio rep1

description: normalized by SuperNORM data service


title: casein diet, bio rep5

description: normalized by SuperNORM data service

value: rats were adapted to the condition for 5 days and fed casein diet for 21 days


title: bl_6455

source_name: obese female, peripheral blood mononuclear cells, insulin resistant

extract_protocol: Genomic DNA was prepared from PBMCs using the QIAamp DNA Mini kit (cat no. 51304, Qiagen, Hilden, Germany).

tag: cell type

value: peripheral blood mononuclear cells

value: systemic insulin resistance

value: resistant


title: om_5834

description: Female adipose tissue.

extract_protocol: Genomic DNA was prepared from adipose tissue using the QIAamp DNA Mini kit (cat no. 51304, Qiagen, Hilden, Germany).


title: casein diet, bio rep3

description: normalized by SuperNORM data service


title: bl_6443


title: casein diet, bio rep2

description: normalized by SuperNORM data service


title: bl_6453

source_name: obese female, peripheral blood mononuclear cells, insulin sensitive


title: bl_6446


title: om_5828

description: Female adipose tissue.


title: casein diet, bio rep4

description: normalized by SuperNORM data service


title: bl_6466


title: casein diet, bio rep1

description: normalized by SuperNORM data service


title: bl_6436


title: bl_6444


title: SCR:PIF1/pifQ over pifQ replicate 3

city: Daejeon

first: Keunhwa

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

description: Biological replicate 3 of 3

hyb_protocol: Each 850ng of cyanine 3-labeled and cyanine 5-labeled cRNA target were mixed and the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent Arabidopsis (V4) GE 4X 44K Microarray. The arrays hybridized at 65oC for 17 h using Agilent Hybridization oven(Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology, USA)

data_processing: Background correction was performed using the normexp method in LIMMA and intensity data were normalized using LOWESS method

organism: Arabidopsis thaliana

label_protocol: Total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions Briefly, each 25ng total RNA was and T7 promoter primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 10min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours. Amplified and labeled cRNA was purified on RNase mini column (Qiagen) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Seeds were surface sterilized, plated on a half-strength Murashige and Skoog (1/2MS) medium containing 0.8% phytoagar without sucrose, and imbibed for 3 days at 4º C. The plates were irradiated with white light (60 μmol∙m−2∙s−1) for 6 hours and then incubated for 2.5 days in the dark.

extract_protocol: Total RNAs were isolated from seeds using Spectrum Plant Total RNA Kit (Sigma, www.sigma-aldrich.com), according to the manufacturer's instructions.

value: etiolated seedlings

source_name: pifQ mutant

value: pifQ mutant


title: SCR:PIF1/pifQ over pifQ replicate 2

description: Biological replicate 2 of 3


title: SCR:PIF1/pifQ over pifQ replicate 1

description: Biological replicate 1 of 3


title: pDCIS14

city: Duesseldorf

first: Silke

last: Schultz

address: Merowingerplatz 1A

department: Department of Obstetrics and Gynaecology

country: Germany

institute: University Hospital Duesseldorf

scan_protocol: Illumina BeadStation 500 scanner protocol

data_processing: quantile normalized by Illumina GenomeStudio software procedure

source_name: breast cancer

label_protocol: two colour Cy3-Cy5-biotin labelling

extract_protocol: total RNA was extracted using the Roche High Pure miRNA isolation Kit. Quality control was performed with Agilent Bioanalyser.

value: FFPE breast cancer

value: pure DCIS

tag: tissue donor

value: Patient 30


title: bl_6427

first: Ingrid

institute: Karolinska Institute

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

data_processing:
Quantile normalization was applied, followed by BMIQ normalization. Batch effects were checked and removed from the dataset.
Data was normalized and analyzed using GenomeStudio software, R packages and Qlucore software.

label_protocol: Standard Illumina protocol for Human Methylation 450K DNA Analysis BeadChip.


title: bl_6426


title: pDCIS13

value: Patient 29


title: pDCIS10

value: Patient 26


title: bl_6424

value: female


title: pDCIS12

value: Patient 28


title: pDCIS11

value: Patient 27


title: pDCIS7

value: Patient 23


title: bl_6285

value: obese

value: no systemic insulin resistance

value: sensitive


title: pDCIS8

value: Patient 24


title: bl_6302

value: peripheral blood mononuclear cells

value: systemic insulin resistance


title: bl_6304

value: resistant


title: bl_6401


title: bl_6408


title: pDCIS2

value: Patient 18


title: pDCIS5

value: FFPE breast cancer

value: Patient 21


title: bl_6272


title: bl_6295


title: bl_6268


title: pDCIS1

value: pure DCIS

value: Patient 17


title: pDCIS4

value: Patient 20


title: pDCIS3

value: Patient 19


title: pDCIS9

value: Patient 25


title: bl_6230

value: female


title: bl_6217


title: IDC 14

value: IDC

value: Patient 14


title: bl_6409

value: obese

value: no systemic insulin resistance


title: bl_6232

value: sensitive


title: pDCIS6

value: Patient 22


title: bl_6221

value: peripheral blood mononuclear cells

value: systemic insulin resistance


title: bl_6247

value: resistant


title: DCIS 13

value: FFPE breast cancer

value: DCIS

value: Patient 13


title: bl_6290


title: DCIS 12

value: Patient 12


title: bl_6220


title: bl_6276


title: bl_6200


title: IDC 12


title: bl_6207


title: DCIS 14


title: bl_6212


title: IDC 11

value: Patient 11


title: IDC9

value: Patient 9


title: DCIS 10

value: Patient 10


title: bl_6155

value: female


title: bl_6156


title: DCIS 11


title: DCIS 9


title: IDC 8

value: IDC

value: Patient 8


title: DCIS 7

value: Patient 7


title: bl_6199

value: obese


title: IDC 7


title: IDC 6

value: Patient 6


title: DCIS 8


title: IDC 10


title: bl_6160


title: IDC 13


title: DCIS 6


title: bl_6145


title: bl_6125


title: bl_6144

value: no systemic insulin resistance

value: sensitive


title: bl_6107

value: peripheral blood mononuclear cells


title: bl_6113


title: 7964427089_L: BB42

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description:
Gender: male=0; female=1.
Age: years at diagnosis
Site of primary: oral cavity=0; oropharynx=1; hypopharynx=2; larynx=3.
Stage of T at first diagnosis according to AJCC 8th edition
Grading  according to WHO: well differentiated=1; moderately differentiated=2; scarcely differentiated=3.
Radiotherapy (RT) prior to recurrence: No=0; Yes=1.
Progression Free Survival (PFS): Long (>12 months); Short(<5 months).

hyb_protocol: Illumina WG-DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Patient with Short Progression Free Survival

label_protocol: Illumina WG-DASL protocol

extract_protocol: RNA was extracted with Rneasy FFPE kit following manufacturer's instructions.

tag: diagnosis

value: Head and neck squamous cell carcinoma (HNSCC)

tag: site of primary

tag: Stage

tag: grading

tag: rt

tag: pfs

value: SHORT

tag: primary vs rec/met

value: primary tumour


title: IDC 5

tag: tissue

value: FFPE breast cancer

tag: disease state

value: Patient 5


title: bl_6102

city: Huddinge

last: Dahlman

address: Hälsovägen 7

tag: gender

tag: phenotype

tag: insulin resistance

tag: individual identifier


title: bl_6123

value: systemic insulin resistance

value: resistant


title: IDC 4

value: Patient 4


title: 7964427089_K: BB41

tag: age


title: DCIS 4

value: DCIS


title: bl_6093

value: female


title: DCIS 5


title: 7964427089_J: AY54

source_name: Patient with Long Progression Free Survival

value: LONG


title: 7964427089_I: BB39


title: 7964427089_H: BB38


title: bl_6085


title: bl_6094


title: bl_6080


title: bl_6086


title: 7964427089_G: BB37


title: bl_6083


title: DCIS 3

value: Patient 3


title: bl_6091

value: obese


title: bl_6084


title: IDC 3

value: IDC


title: 7964427089_F: BB36


title: IDC 2

value: Patient 2


title: bl_6149

value: no systemic insulin resistance

value: sensitive


title: bl_6073

value: peripheral blood mononuclear cells


title: bl_6072


title: bl_6070


title: 7964427089_E: BB35

value: Head and neck squamous cell carcinoma (HNSCC)

value: SHORT


title: DCIS 2

value: FFPE breast cancer


title: IDC 1


title: DCIS 1

value: Patient 1


title: bl_6051

value: systemic insulin resistance


title: bl_6055

value: resistant


title: LTAD siSOCS2 DHT

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from LTAD cells  treated with DHT 10 nM 48h after siSOCS2 transfection.

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS.  LTAD cells were cultured in phenol red free RPMI containing 10% charcoal/dextran treated FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using RNeasy (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or DHT (10 nM).

tag: cell line

value: LTAD

value: prostate cancer

tag: sirna

tag: ligand

value: DHT 10 nM


title: bl_6039

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K BeadChip using standard Illumina protocol.

tag: cell type

value: female


title: bl_6047


title: LTAD siSOCS2-AS1 DHT

description: Gene expression data from LTAD cells  treated with DHT 10 nM 48h after siSOCS2-AS1 transfection.


title: 7964427082_L: AY52

tag: diagnosis

tag: site of primary

value: primary tumour


title: 7964427082_J: BA92

tag: Stage

tag: grading


title: LTAD siSOCS2 Et

description: Gene expression data from LTAD cells treated with vehicle (ethanol) 48h after siSOCS2 transfection.

value: Vehicle


title: bl_6036

value: obese


title: LTAD siNC Et

description: Gene expression data from LTAD cells treated with vehicle (ethanol) 48h after siControl transfection.

value: Control


title: LTAD siNC DHT

description: Gene expression data from LTAD cells treated with DHT 10 nM 48h after siControl transfection.


title: 7964427089_B: BA93

tag: rt

tag: pfs

value: LONG


title: bl_6032


title: LNCaP siSOCS2 Et

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) 48h after siSOCS2 transfection.

value: LNCaP


title: 7964427082_K: BA96

tag: primary vs rec/met


title: LNCaP siSOCS2 DHT

description: Gene expression data from LNCaP cells  treated with DHT 10 nM 48h after siSOCS2 transfection.


title: 7964427082_G: BA89


title: LTAD siSOCS2-AS1 Et

description: Gene expression data from LTAD cells treated with vehicle (ethanol) 48h after siSOCS2-AS1 transfection.


title: 7964427082_I: BB40

value: recurrence/metastasis


title: bl_6037

value: peripheral blood mononuclear cells

tag: disease state


title: bl_6040

tag: gender


title: 7964427089_A: BA95

value: Head and neck squamous cell carcinoma (HNSCC)


title: 7964427082_F: BA88

value: SHORT


title: 7964427082_H: BA90


title: bl_6028

tag: phenotype


title: 7964427082_B: BA84


title: 7964427082_E: BA86


title: LNCaP siSOCS2-AS1 DHT

description: Gene expression data from LNCaP cells  treated with DHT 10 nM 48h after siSOCS2-AS1 transfection.


title: bl_6000

value: no systemic insulin resistance

tag: insulin resistance

value: sensitive


title: 7964427073_L: AY49


title: LNCaP siNC Et

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) 48h after siControl transfection.


title: LNCaP siNC DHT

description: Gene expression data from LNCaP cells treated with DHT 10 nM 48h after siControl transfection.


title: 7964427082_A: AY50


title: Calu-6 cells transfected with LAPTM4B-specific  siRNA 3

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Gene expression of Calu-6 cells transfected with siRNA against the LAPTM4B gene- biological replicate 3

hyb_protocol: 2.5 ug of fragmented and labeled cDNA, was generated using the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99 degrees Celcius for 5 minutes, cooled to 45 degrees Celsius for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 uL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45 degrees Celcius with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 system.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files)

data_processing: Raw expression data were normalized and summarized using the Robust Multichip Analysis (RMA) method along with log2 transformation using the integrated BRB-Array Tools software developed by Dr. Richard Simon and the BRB-Array Tools development team.

source_name: Calu-6 lung cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Affymetrix).

growth_protocol: Calu-6 cells were cultured with DMEM/F12, with or without 10% FBS, in a humidified incubator with 5% CO2

extract_protocol: Total RNA was isolated 48 hours following switching cell culture medium (72 hours following transfection) using the RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with control or LAPTM4B-specific siRNA (siRNA from Dharmacon) using Lipofectamine RNAiMAX reagent from Life Technologies according to the manufacturer's instructions. One day following transfection, cells were incubated in serum-containing medium or switched to culture medium with 0% FBS.

tag: type of sirna

value: siRNA against LAPTM4B

tag: replicate

value: Biological replicate 3

tag: serum level in cell culture medium following transfection

value: 10% FBS


title: hCG-6h sample#2

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

description: Cumulus cells at 7h after the ovulatory signals

hyb_protocol: Fragmented and biotin-labeled cDNA from each sample were then hybridized to Affymetrix Mouse 430v2 Arrays for 16 h at 45°C.  Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix)

scan_protocol: The arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).

data_processing:
After the post-hybridization staining and washing, the arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).   Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, summarization based on a multi-array model fit robustly using the median polish algorithm, and sketch-quantile normalization. For this experiment, one pairwise comparison was used to statistically resolve gene expression differences between Type levels using the R/maanova analysis package40 (Wu et al. 2003).  Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimate of variance components from within the R/maanova package40-41.  Statistical significance levels of the pairwise comparison wase calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method42.  Differentially expressed genes are declared at an FDR q-value threshold of 0.05.
Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, summarization based on a multi-array model fit robustly using the median polish algorithm, and sketch-quantile normalization.

source_name: cumulus cells at 6-h of hCG priming

label_protocol: RNA samples were  subjected to cDNA synthesis and amplification using the Nugen Ovation Pico WTA System (NuGEN Technologies, Inc, San Carlos, CA). The resulting cDNAs were then fragmented and biotin-labeled using the Encore™ Biotin Module (NuGEN Technologies, Inc).

growth_protocol: 21-day old female mice were primed with eCG (5IU/mouse) for 46 hours to stimulate follicle development, and then mice were either primed with or without 5IU/mouse of hCG for 6 h (designated as hCG-6h and hCG-0h, respectively).  Cumulus cells from 50 COCs were then collected into 1.5 ml centrifuge tube and re-suspended in 350 µl of RLT buffer (Qiagen, Valencia, CA).  After brief vortexing, the the lysate was snap frozen in liquid nitrogen and temporarily stored at -80°C until RNA isolation.   Three sets of hCG-0h and hCG-6h samples were collected and employed for microarray study.   Medium used for oocyte isolation was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma). Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 µM to prevent the GV-stage oocytes from undergoing maturation during the process of culture.

extract_protocol: Total RNA was extracted from COCs using the RNAeasy micro kit purchased from Qiagen (Valencia, CA) according to the manufacturer's instruction. The quality and quantity of RNA were measured by the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) according to supplied protocols (Invitrogen, Carlsbad, CA).

treatment_protocol: no additional treatments were carried out

tag: cell

value: cumulus cells

tag: genotype

value: Wildtype

tag: age

value: Isolated from 23-d WT-mice primed with eCG for 46h, followed by hCG 6h


title: hCG-6h sample#1

description: Cumulus cells at 6h after the ovulatory signals


title: bl_6025

tag: cell type

value: female

tag: individual identifier


title: hCG-0h sample#3

description: Cumulus cells before the ovulatory signals

source_name: cumulus cells at 0-h of hCG priming

value: Isolated from 23-d WT-mice primed with eCG for 46h


title: hCG-6h sample#3

description: Cumulus cells at 8h after the ovulatory signals


title: bl_5999

value: obese


title: bl_5987

value: systemic insulin resistance

value: resistant


title: bl_5991


title: bl_5876


title: bl_5985


title: hCG-0h sample#1


title: hCG-0h sample#2


title: bl_5861


title: LNCaP siSOCS2-AS1 Et

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) 48h after siSOCS2-AS1 transfection.

tag: cell line

value: LNCaP

value: prostate cancer

tag: sirna

tag: ligand

value: Vehicle


title: Calu-6 cells transfected with scrambled siRNA 3

description: Gene expression of Calu-6 cells transfected with control siRNA-biological replicate 3

value: control scrambled siRNA


title: 7964427073_K: AY46

description:
Gender: male=0; female=1.
Age: years at diagnosis
Site of primary: oral cavity=0; oropharynx=1; hypopharynx=2; larynx=3.
Stage of T at first diagnosis according to AJCC 8th edition
Grading  according to WHO: well differentiated=1; moderately differentiated=2; scarcely differentiated=3.
Radiotherapy (RT) prior to recurrence: No=0; Yes=1.
Progression Free Survival (PFS): Long (>12 months); Short(<5 months).

tag: diagnosis

value: Head and neck squamous cell carcinoma (HNSCC)

tag: site of primary

tag: Stage

tag: grading

tag: rt

tag: pfs

value: LONG

value: recurrence/metastasis


title: Calu-6 cells transfected with scrambled siRNA 2

description: Gene expression of Calu-6 cells transfected with control siRNA-biological replicate 2

tag: type of sirna

value: Biological replicate 2


title: Calu-6 cells transfected with LAPTM4B-specific  siRNA 1

description: Gene expression of Calu-6 cells transfected with siRNA against the LAPTM4B gene- biological replicate 1

value: siRNA against LAPTM4B

tag: replicate

value: Biological replicate 1

value: 10% FBS


title: 7964427073_E: BA21

tag: gender

tag: primary vs rec/met


title: bl_5857

value: peripheral blood mononuclear cells

tag: phenotype

tag: disease state

value: no systemic insulin resistance

tag: insulin resistance

value: sensitive


title: 7964427073_G: BA24

tag: age

value: SHORT

value: primary tumour


title: 7964427073_F: BA22


title: RPE TAA day 30 bio rep2

city: Davis

first: Zeljka

last: Smit-McBride

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

description: Gene expression data at day 30 from the eyes intravitreally injected with TAA at day 0

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX 11 using RMA algorhitm as analysis and normalization method.

source_name: RPE TAA treatment day 30

label_protocol: Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 0.100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were 2 months old, kept at normal 12/12 light/dark conditions, feed ad libitum

treatment_protocol: Animals were sacrificed within CO2 chamber, eyes were enucleated, disected, retinal tissue was removed and quicky immersed into 300ul RNALater. Samples were stored in RNALater at -20C till the total RNA isolation step.

tag: strain

value: males

tag: organ

value: eye

tag: tissue

value: RPE/choroid

tag: treatment

value: TAA

tag: day


title: bl_5859

tag: cell type

value: female

value: obese

tag: individual identifier


title: 7964427073_I: BA26

tag: diagnosis

value: Head and neck squamous cell carcinoma (HNSCC)

tag: site of primary

tag: Stage

tag: grading

tag: rt


title: bl_5849

tag: gender


title: RPE TAA day 30 bio rep3


title: Calu-6 cells transfected with LAPTM4B-specific  siRNA 2

description: Gene expression of Calu-6 cells transfected with siRNA against the LAPTM4B gene- biological replicate 2

tag: cell line

tag: type of sirna

tag: replicate

tag: serum level in cell culture medium following transfection


title: bl_5834

tag: phenotype

tag: disease state

value: systemic insulin resistance

tag: insulin resistance

value: resistant


title: 7964427073_H: BA25

tag: age

tag: pfs

tag: primary vs rec/met


title: bl_5829

tag: cell type

tag: individual identifier


title: Serum starved Calu-6 cells transfected with LAPTM4B-specific  siRNA 3

description: Gene expression of serum starved Calu-6 cells transfected with siRNA against the LAPTM4B gene- biological replicate 3

value: siRNA against LAPTM4B

value: Biological replicate 3

value: 0% FBS


title: 7964427073_C: BA19

tag: diagnosis

tag: site of primary


title: bl_5810

value: peripheral blood mononuclear cells


title: 7964427073_D: BA20

tag: Stage

tag: grading


title: bl_5828

tag: gender

value: no systemic insulin resistance


title: Serum starved Calu-6 cells transfected with LAPTM4B-specific  siRNA 2

description: Gene expression of serum starved Calu-6 cells transfected with siRNA against the LAPTM4B gene- biological replicate 2

tag: cell line

value: Biological replicate 2


title: 7964427073_B: BA18

tag: rt

value: SHORT


title: Calu-6 cells transfected with scrambled siRNA 1

description: Gene expression of Calu-6 cells transfected with control siRNA-biological replicate 1

tag: type of sirna

value: control scrambled siRNA

tag: replicate

value: Biological replicate 1

value: 10% FBS


title: bl_5803

tag: phenotype

value: sensitive


title: RPE DEX day 30 bio rep2

description: Gene expression data at day 30 from the eyes intravitreally injected with DEX at day 0

source_name: RPE DEX treatment day 30

tag: strain

value: males

tag: organ

value: eye

tag: tissue

value: RPE/choroid

tag: treatment

value: DEX

tag: day


title: Serum starved Calu-6 cells transfected with scrambled siRNA 3

description: Gene expression of serum starved Calu-6 cells transfected with control siRNA-biological replicate 3

tag: serum level in cell culture medium following transfection


title: RPE DEX day 30 bio rep3


title: 7964427070_L: BA16

value: Head and neck squamous cell carcinoma (HNSCC)

tag: age

tag: pfs

value: LONG

tag: primary vs rec/met

value: primary tumour


title: 7964427073_A: BA17

tag: diagnosis

tag: site of primary

tag: Stage

value: recurrence/metastasis


title: Serum starved Calu-6 cells transfected with LAPTM4B-specific  siRNA 1

description: Gene expression of serum starved Calu-6 cells transfected with siRNA against the LAPTM4B gene- biological replicate 1

tag: cell line

value: siRNA against LAPTM4B

value: 0% FBS


title: RPE DEX day 30 bio rep1

tag: gender


title: transgenic CA1 /ischemia, biological rep3

city: Durham

first: Wei

last: Yang

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

description: Gene expression data from SUMO-KD ischemia mouse brain

hyb_protocol: The cRNA were hybridized  on  Affymetrix  GeneChip Mouse Genome 430A 2.0 in  Affymetrix  GeneChip hybridization oven 645, and were washed in Affymetrix GeneChip®  Fluidics Station 450 s/Ambion, Austin, TX).

scan_protocol: GeneChips wre scanned using Affymetrix GeneChip® Scanner 7G.

data_processing: The data were analyzed with Partek Genomics Suite 6.6. Robust multi-chip analysis (RMA) normalization was done on the entire data set.

source_name: CA1 sample from SUMO-KD transgenic mouse brain in ischemia group

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion) from total RNA

growth_protocol: After 10 minutes global cerebral ischemia and 3 hours reperfusion, the CA1 subfields of hippocampus were carefully dissected out for RNA prepareation.  Each sample was pooled from 2 mouse brains.

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

treatment_protocol: The CA1 tissue samples were snap frozen in liqquid nitrogen and kept at -80 until use.

tag: genotype

value: SUMO-KD

tag: group

value: ischemia


title: 7964427070_I: AY53

tag: grading

tag: rt


title: RPE TAA day 30 bio rep1

tag: strain

tag: organ

value: TAA


title: RPE BSS day 30 bio rep2

description: Gene expression data at day 30 from the eyes intravitreally injected with BSS at day 0

source_name: RPE BSS control day 30

tag: tissue

tag: treatment

value: BSS control


title: Serum starved Calu-6 cells transfected with scrambled siRNA 2

description: Gene expression of serum starved Calu-6 cells transfected with control siRNA-biological replicate 2

tag: type of sirna

value: control scrambled siRNA

tag: replicate

value: Biological replicate 2

tag: serum level in cell culture medium following transfection


title: 7964427070_K: BA15

tag: age

tag: pfs

value: SHORT

tag: primary vs rec/met


title: RPE BSS day 30 bio rep3

value: males

tag: day


title: RPE TAA day 7 bio rep3

description: Gene expression data at day 7 from the eyes intravitreally injected with TAA at day 0

source_name: RPE TAA treatment day 7

value: eye


title: bl_5811

tag: cell type

value: peripheral blood mononuclear cells

value: female

tag: phenotype

value: obese

tag: disease state

value: no systemic insulin resistance

tag: insulin resistance

value: sensitive

tag: individual identifier


title: M+A2

city: Barcelona

first: Andrés

middle: Michael

last: Ciudad

state: Barcelona

address: Joan XXIII sn

department: Pharmacology and chemical therapeutics

country: Spain

institute: University of Barcelona

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
GeneSpring Software (RMA normalization)
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: anterior striata, mephedrone + ethanol

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

extract_protocol: Samples were extracted from the scull of the animal, dissected and immediately frozen on dry ice; total RNA extracted by means of QUIAGEN mini lipid kit;  cDNA synthesis and amplification was performed using the cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: CPP 10-day protocol. Drugs were administered 15 minutes before animals were placed in the drug-paired compartment.

value: Swiss CD-1

tag: gender

value: male

value: adolescent

value: anterior striata


title: RPE BSS day 30 bio rep1

tag: strain

value: RPE/choroid


title: transgenic  CA1 /sham, biological rep2

description: Gene expression data from SUMO-KD sham mouse brain

source_name: CA1 sample from SUMO-KD transgenic mouse brain in sham group

tag: genotype

value: SUMO-KD

tag: group

value: sham


title: transgenic  CA1 /ischemia, biological rep2

value: ischemia


title: 7964427070_F: BA83

tag: diagnosis

value: Head and neck squamous cell carcinoma (HNSCC)

tag: site of primary

tag: Stage

tag: grading

tag: rt

value: recurrence/metastasis


title: transgenic CA1 /sham, biological rep1


title: RPE TAA day 7 bio rep2

value: males

tag: organ

tag: tissue

tag: treatment

value: TAA


title: RPE TAA day 7 bio rep1

value: eye

tag: day


title: M+A3

tag: age


title: M+A1


title: 7964427070_C: AY47

tag: pfs

value: LONG

tag: primary vs rec/met

value: primary tumour


title: 7964427070_E: BA82

value: SHORT


title: bl_5794

tag: cell type

value: peripheral blood mononuclear cells

value: female

tag: phenotype

value: obese

tag: disease state

value: no systemic insulin resistance

tag: insulin resistance

value: sensitive

tag: individual identifier


title: 7964427070_D: AY48

tag: diagnosis

tag: gender


title: transgenic  CA1 /sham, biological rep3

tag: genotype

tag: group


title: MEF 3

source_name: anterior striata, mephedrone

tag: strain

value: Swiss CD-1

value: male

value: adolescent

value: anterior striata


title: MEF 1


title: MEF 2


title: RPE DEX day 7 bio rep2

description: Gene expression data at day 7 from the eyes intravitreally injected with DEX at day 0

source_name: RPE DEX treatment day 7

tag: organ

value: RPE/choroid

value: DEX


title: RPE DEX day 7 bio rep3

value: males

tag: tissue


title: 7964427070_B: BA81

description:
Gender: male=0; female=1.
Age: years at diagnosis
Site of primary: oral cavity=0; oropharynx=1; hypopharynx=2; larynx=3.
Stage of T at first diagnosis according to AJCC 8th edition
Grading  according to WHO: well differentiated=1; moderately differentiated=2; scarcely differentiated=3.
Radiotherapy (RT) prior to recurrence: No=0; Yes=1.
Progression Free Survival (PFS): Long (>12 months); Short(<5 months).

value: Head and neck squamous cell carcinoma (HNSCC)

tag: site of primary

tag: Stage

tag: grading

tag: rt


title: Wild-type CA1 /ischemia, biological rep3

description: Gene expression data from wild-type ischemia mouse brain

source_name: CA1 sample from wild-type mouse brain in ischemia group

value: wild-type

value: ischemia


title: Wild-type CA1 /ischemia, biological rep1


title: RPE BSS day 7 bio rep3

description: Gene expression data at day 7 from the eyes intravitreally injected with BSS at day 0

source_name: RPE BSS control day 7

value: eye

tag: treatment

value: BSS control

tag: day


title: Serum starved Calu-6 cells transfected with scrambled siRNA 1

description: Gene expression of serum starved Calu-6 cells transfected with control siRNA-biological replicate 1

tag: cell line

tag: type of sirna

value: control scrambled siRNA

tag: replicate

value: Biological replicate 1

tag: serum level in cell culture medium following transfection

value: 0% FBS


title: genomic DNA from ctrl cells

city: Hachioji

first: Kenji

last: Onda

department: Clinical Pharmacology

institute: Tokyo University of Pharmacy and Life Sciences

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 iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011.1,  Methylation Modulev1.9.0

label: Cy5 and Cy3

source_name: Leukemic cells

label_protocol: Standard Illumina Protocol

growth_protocol: F-36p cells were cultured in RPMI-1640 supplemented with 5% inactivated FBS and 5 ng/ml IL-3.

extract_protocol: Genomic DNA was extracted from F-36P using NucleoSpin Tissue kit according to instructions

treatment_protocol: F-36P cells were treated by AS2S2 for 72 h

value: control

tag: cell type

value: leukemic cells


title: ALCOHOL 2

source_name: anterior striata, ethanol

value: Swiss CD-1

tag: gender

tag: age


title: Wild-type CA1 /ischemia, biological rep2

tag: genotype

tag: group


title: Wild-type CA1 /sham, biological rep3

description: Gene expression data from wild-type sham mouse brain

source_name: CA1 sample from wild-type mouse brain in sham group

value: sham


title: genomic DNA from cells treated with 4uM As2S2

value: 4uM As2S2

value: male


title: 7964427070_A: AY45

source_name: Patient with Long Progression Free Survival

tag: diagnosis

tag: pfs

value: LONG

tag: primary vs rec/met

value: primary tumour


title: RPE DEX day 7 bio rep1

tag: strain

value: males

tag: organ

tag: tissue

value: RPE/choroid

value: DEX


title: genomic DNA from cells treated with 2uM As2S2

description: Sample2_As2S2_low (2uM)

tag: treatment

value: 2uM As2S2


title: ALCOHOL 1

value: adolescent

value: anterior striata


title: ALCOHOL 3


title: Sample 13573 rep 3 vs PETRA rep 3

city: A Coruña

first: Margarita

last: Poza

address: As Xubias

department: Microbiology

institute: Fundacion Prof Novoa Santos-Insituto de Investigacion Biomedica

hyb_protocol: Microarrays where 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 v. 1.3 (Agilent)

growth_protocol: All samples were grown in LB media except the INF sample that was extracted from lungs.

extract_protocol: Total RNA was extracted using the RNAeasy Kit and the Minelute Kit (both from Qiagen)

treatment_protocol: Cells were separated by centrifugation and washed prior to RNA extraction.

value: over-expressing small RNA 13573

source_name: PETRA 3

value: With empty vector


title: SF2

source_name: anterior striata, saline


title: RPE BSS day 7 bio rep1

value: eye

value: BSS control

tag: day


title: RPE BSS day 7 bio rep2


title: Wild-type CA1 /sham, biological rep2

value: wild-type


title: Sample 13573 rep 1 vs PETRA rep 1

source_name: PETRA 1


title: SF1

value: Swiss CD-1


title: Knock-out rep 3 vs Infected rep 2

source_name: KO 3

value: Knock-out

source_name: INF 2

value: recovered from infected mice


title: W4 Neurons at Day 16 VPA 2 [mRNA]

city: Baltimore

first: Lena

last: Smirnova PhD

address: 615 North Wolfe St

department: School of Public Health

institute: The Johns Hopkins University

description:
W4 ND16 VPA 2
gene expression data from neurally differentiated W4 mES cells after exposure to VPA

hyb_protocol: Labeled single-stranded DNA (5.5 μg) was combined with hybridization and spike controls and hybridized with a pre-equilibrated Affymetrix chip for 16–18 h.

scan_protocol: Following hybridization, arrays were washed and stained with a streptavidin phycoerythrin conjugate using an automated GeneChip® Fluidics Station 450. They were then scanned with a GeneChip® Scanner 3000 using a 570-nm excitation wavelength laser

data_processing:
Microarray quality control assessment and data acquisition were performed with the GeneChip® Operating Software (Affymetrix). Normalization among the different microarray data files was performed by robust multiarray analysis inside the Partek 6.5 software. Unsupervised hierarchical clustering analysis and a principal component analysis were performed with the Partek software to establish non-forced groups of samples. Differential expression was determined by using t statistics. False discovery rates were determined by following the Benjamini-Hochberg procedure. Data were expressed as mean ± S.D. Student's t test was done to determine the statistical significance of the pairwise comparisons.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv

source_name: neurally differentiated mES cells line W4, VPA

label_protocol: Amplified and biotinylated sense strand DNA was generated from total RNA according to the Affymetrix whole transcript sense target labeling assay

growth_protocol: mES cells line W4 were cultivated upto 16 days in F12-DMEM/Neurobasal medium supplemented with B27, N2, bFGF, Laminin, BSA, insulin and β-mercaptoethanol on PLO-coated 6-well plates in order to induce neural differentiation.

extract_protocol: After 16 days of treatment and differentiation RNA was extracted using Trizol reagent according to manufacturer's protocol.

treatment_protocol: mES cells were treated with sub-toxic concentrations of developmental neurotoxicant, VPA (300uM), during 16 days of neural differentiation. As a control cells were incubated to PBS. Medium was exchanged every second day.

tag: cell line

value: mouse embryonic stem cell line W4

tag: toxicant treatment

value: VPA (300uM)


title: Infected rep 1 vs wild type

source_name: INF 1

value: Wild type


title: Wild-type CA1 /sham, biological rep1

value: sham


title: PETRA rep 2 vs sample 13573 rep 2

source_name: PETRA 2


title: Wild type vs knock-out rep 2

source_name: KO 2


title: W4 Neurons at  Day 16 VPA 3 [mRNA]

description:
W4 ND16 VPA 3
gene expression data from neurally differentiated W4 mES cells after exposure to VPA


title: W4 Neurons at Day 16 VPA 1 [mRNA]

description:
W4 ND16 VPA 1
gene expression data from neurally differentiated W4 mES cells after exposure to VPA


title: W4 Neurons at Day 16 PBS 3 [mRNA]

description:
W4 ND16 PBS 3
gene expression data from neurally differentiated W4 mES cells

source_name: neurally differentiated mES cells line W4, PBS (solvent control)

value: control (PBS)


title: conidia_keratin_rep2

city: RIBEIRAO PRETO

first: Tamires

middle: Aparecida

last: Bitencourt

state: SP

address: AV COSTABILE ROMANO 2221

department: BIOTECNOLOGY

country: Brazil

institute: UNAERP

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA ( specific activity >9pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume  of 55uL, containing 25x Agilent fragmentation buffer and 10x Blocking Agent following manufacture's instructions.

scan_protocol: Slides were scanned immediately after washing on Agilent DNA Microarray scanner using one color  scan setting for 1x44K  array slides ( Scan area 61x21.6mm, scan resolution 10uM, Dye channerl was set to Green, and Green PMT was set to 100%)

data_processing: The scanned  images were analysed with Agilent Feature Extraction version 10.5 using default parameters to obtain background subtracted and spatially detrended  Processed Signal intensities

organism: Trichophyton rubrum

source_name: Conidia growth on Cove's Medium

label_protocol: Cyanine-3 (Cy-3) labeled cRNA was prepared from 75ng RNA using  the Agilent Low input Amplification Kit (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction, followed by purification with RNAspin Mini Isolation Kit ( GE Healthcare).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Illusta RNAspin Mini RNA Isolation Kit (GE Healthcare) following manufacture's recommendation. The RNA integrity was measured by microfluidic electrophoresis using Agilent 6000 RNA Nano chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: 2.6 106 conidia/mL were inoculated in Cove's medium with glucose and nitrate ( control), in Cove's medium with 0.25% elastin, and in Cove's medium with 0.5% keratin and incubated for 24h, 36h and 72 h

tag: medium

value: Medium with 0.5%  of keratin for 24h, 36h and 72h


title: Knock-out rep 1 vs wild type

source_name: KO 1


title: conidia_elastin_rep2

value: Medium with 0.25% of elastin for 24h, 36h and 72h


title: Wild type vs infected rep 3

source_name: INF 3


title: W4 Neurons at Day 16 PBS 1 [mRNA]

description:
W4 ND16 PBS 1
gene expression data from neurally differentiated W4 mES cells


title: W4 Neurons at Day 16 PBS 2 [mRNA]

description:
W4 ND16 PBS 2
gene expression data from neurally differentiated W4 mES cells


title: conidia_elastin_rep1


title: conidia_control_rep2

value: Glucose and Nitrate for 24h, 36h, 72h


title: MHAE001_MOCK_48HRS_RNA_B

status: Public on Jun 21 2016

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

description: mRNA

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 x Blocking Agent and 2.2 μl of 25 x Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 100μ l of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: Primary human airway epithelial cells, mock-inoculated, 48h

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

treatment_protocol: MERSCOV004.0P: Cells were infected with a multiplicity of infection of 5 PFU.

value: primary airway epithelial cells

tag: virus infection

value: MOCK

tag: time (post-infection)


title: MHAE001_MOCK_48HRS_RNA_D

description: mRNA

tag: cell type


title: MHAE001_MOCK_48HRS_RNA_A

description: mRNA


title: conidia_keratin_rep1


title: MHAE001_icMERS_48HRS_RNA_E

description: mRNA

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h

value: MERS-coronavirus (icMERS)


title: MHAE001_icMERS_48HRS_RNA_C

description: mRNA


title: transgenic CA1 /ischemia, biological rep1

description: Gene expression data from SUMO-KD ischemia mouse brain

source_name: CA1 sample from SUMO-KD transgenic mouse brain in ischemia group

value: SUMO-KD

value: ischemia


title: conidia_control_rep1


title: MHAE001_icMERS_48HRS_RNA_D

description: mRNA


title: MHAE001_icMERS_48HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_48HRS_RNA_C

description: mRNA


title: MHAE001_MOCK_36HRS_RNA_D

description: mRNA

source_name: Primary human airway epithelial cells, mock-inoculated, 36h


title: MHAE001_MOCK_36HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_36HRS_RNA_E

description: mRNA


title: MHAE001_icMERS_36HRS_RNA_C

description: mRNA

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h


title: MHAE001_icMERS_36HRS_RNA_E

description: mRNA


title: MHAE001_icMERS_48HRS_RNA_A

description: mRNA


title: MHAE001_MOCK_36HRS_RNA_A

description: mRNA


title: MHAE001_MOCK_36HRS_RNA_C

description: mRNA


title: MHAE001_icMERS_36HRS_RNA_D

description: mRNA


title: MHAE001_icMERS_36HRS_RNA_A

description: mRNA


title: MHAE001_MOCK_24HRS_RNA_E

description: mRNA

source_name: Primary human airway epithelial cells, mock-inoculated, 24h


title: MHAE001_MOCK_48HRS_RNA_E

description: mRNA


title: MHAE001_MOCK_24HRS_RNA_D

description: mRNA


title: MHAE001_MOCK_24HRS_RNA_A

description: mRNA


title: MHAE001_MOCK_12HRS_RNA_D

description: mRNA

source_name: Primary human airway epithelial cells, mock-inoculated, 12h


title: MHAE001_icMERS_36HRS_RNA_B

description: mRNA


title: MHAE001_icMERS_24HRS_RNA_D

description: mRNA

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h


title: MHAE001_MOCK_12HRS_RNA_E

description: mRNA


title: MHAE001_MOCK_12HRS_RNA_C

description: mRNA


title: MHAE001_MOCK_24HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_24HRS_RNA_C

description: mRNA


title: MHAE001_icMERS_12HRS_RNA_E

description: mRNA

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h


title: MHAE001_icMERS_24HRS_RNA_E

description: mRNA


title: MHAE001_icMERS_24HRS_RNA_A

description: mRNA


title: MHAE001_icMERS_24HRS_RNA_C

description: mRNA


title: MHAE001_MOCK_12HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_0HRS_RNA_D

description: mRNA

source_name: Primary human airway epithelial cells, mock-inoculated, 0h


title: MHAE001_icMERS_12HRS_RNA_C

description: mRNA


title: MHAE001_icMERS_12HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_0HRS_RNA_E

description: mRNA


title: MHAE001_icMERS_12HRS_RNA_D

description: mRNA


title: MHAE001_MOCK_0HRS_RNA_A

description: mRNA


title: MHAE001_MOCK_0HRS_RNA_B

description: mRNA


title: MHAE001_icMERS_12HRS_RNA_A

description: mRNA


title: MHAE001_icMERS_0HRS_RNA_E

description: mRNA

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h


title: MHAE001_MOCK_0HRS_RNA_C

description: mRNA


title: MHAE001_icMERS_0HRS_RNA_C

description: mRNA


title: MHAE001_icMERS_0HRS_RNA_D

description: mRNA


title: MHAE001_MOCK_36HRS_microRNA_C

status: Public on Jun 09 2016

description: microRNA

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 x Blocking Agent and 2.2 μl of 25 x Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 x GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

label_protocol: Total RNA was labeled according to Agilent's Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.


title: MHAE001_icMERS_0HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_36HRS_microRNA_B

description: microRNA


title: MHAE001_MOCK_36HRS_microRNA_D

description: microRNA


title: MHAE001_icMERS_24HRS_RNA_B

description: mRNA


title: MHAE001_MOCK_36HRS_microRNA_E

description: microRNA


title: MHAE001_MOCK_36HRS_microRNA_A

description: microRNA


title: MHAE001_icMERS_36HRS_microRNA_D

description: microRNA


title: MHAE001_icMERS_36HRS_microRNA_C

description: microRNA


title: MHAE001_icMERS_36HRS_microRNA_B

description: microRNA


title: MHAE001_icMERS_36HRS_microRNA_A

description: microRNA


title: MHAE001_MOCK_12HRS_RNA_A

description: mRNA


title: MHAE001_icMERS_24HRS_microRNA_C

description: microRNA


title: MHAE001_MOCK_24HRS_microRNA_E

description: microRNA


title: MHAE001_icMERS_24HRS_microRNA_D

description: microRNA


title: MHAE001_icMERS_24HRS_microRNA_E

description: microRNA


title: SF3

source_name: anterior striata, saline

tag: gender

value: male

tag: age

value: adolescent

value: anterior striata


title: MHAE001_icMERS_24HRS_microRNA_A

description: microRNA


title: MHAE001_MOCK_12HRS_microRNA_E

description: microRNA


title: MHAE001_icMERS_24HRS_microRNA_B

description: microRNA


title: MHAE001_MOCK_24HRS_microRNA_C

description: microRNA


title: MHAE001_MOCK_24HRS_microRNA_D

description: microRNA


title: MHAE001_MOCK_12HRS_microRNA_C

description: microRNA


title: MHAE001_MOCK_24HRS_microRNA_B

description: microRNA


title: MHAE001_MOCK_12HRS_microRNA_B

description: microRNA


title: MHAE001_MOCK_12HRS_microRNA_A

description: microRNA


title: MHAE001_icMERS_36HRS_microRNA_E

description: microRNA


title: MHAE001_icMERS_12HRS_microRNA_A

description: microRNA


title: MHAE001_icMERS_12HRS_microRNA_B

description: microRNA


title: MHAE001_icMERS_12HRS_microRNA_D

description: microRNA


title: ICL104_Cal04_48hr_RNA_3

status: Public on May 26 2016

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

growth_protocol: SCL002.0P: Maintenance, Plating, and Virus Infection of Calu-3 cells

extract_protocol: TCL001.0P: Preparation of Samples from Calu-3 cells for Isolation of RNA

treatment_protocol: Cells were infected with an MOI of 3. After infection, wash and replace with 2 ml of DMEM-F12 + .3% BSA and 1 ug/ml TPCK-trypsin.

tag: virus

value: wild-type pandemic H1N1 (A/California/04/2009); Cal04

tag: time


title: ICL104_Cal04_48hr_RNA_2


title: MHAE001_icMERS_0HRS_RNA_A

description: mRNA


title: ICL104_Cal04_48hr_RNA_4


title: ICL104_Cal04_48hr_RNA_5


title: ICL104_Mock_48hr_RNA_5

value: Mock


title: ICL104_Mock_48hr_RNA_4


title: ICL104_Cal04_48hr_RNA_1


title: ICL104_Cal04_36hr_RNA_3


title: ICL104_Cal04_36hr_RNA_5


title: ICL104_Mock_48hr_RNA_3


title: ICL104_Mock_36hr_RNA_1


title: ICL104_Mock_36hr_RNA_3


title: ICL104_Mock_48hr_RNA_2


title: ICL104_Cal04_24hr_RNA_5


title: ICL104_Mock_36hr_RNA_2


title: ICL104_Mock_36hr_RNA_4


title: ICL104_Cal04_24hr_RNA_4


title: ICL104_Mock_48hr_RNA_1


title: ICL104_Cal04_24hr_RNA_1


title: ICL104_Mock_24hr_RNA_2


title: ICL104_Mock_24hr_RNA_1


title: ICL104_Mock_24hr_RNA_5


title: ICL104_Cal04_12hr_RNA_5


title: ICL104_Mock_36hr_RNA_5


title: ICL104_Cal04_36hr_RNA_2


title: ICL104_Mock_24hr_RNA_4


title: ICL104_Cal04_24hr_RNA_2


title: ICL104_Cal04_36hr_RNA_1


title: ICL104_Cal04_12hr_RNA_2


title: ICL104_Mock_12hr_RNA_4


title: ICL104_Cal04_7hr_RNA_3


title: ICL104_Mock_12hr_RNA_2


title: ICL104_Mock_12hr_RNA_3


title: ICL104_Mock_7hr_RNA_3


title: ICL104_Cal04_12hr_RNA_4


title: ICL104_Cal04_7hr_RNA_1


title: ICL104_Cal04_7hr_RNA_5


title: ICL104_Cal04_7hr_RNA_2


title: ICL104_Cal04_7hr_RNA_4


title: ICL104_Cal04_12hr_RNA_1


title: ICL104_Mock_12hr_RNA_5


title: ICL104_Mock_7hr_RNA_5


title: ICL104_Mock_7hr_RNA_2


title: ICL104_Mock_12hr_RNA_1


title: ICL104_Cal04_0hr_RNA_3


title: ICL104_Mock_7hr_RNA_1


title: ICL104_Cal04_0hr_RNA_4


title: ICL104_Cal04_0hr_RNA_5


title: ICL104_Cal04_12hr_RNA_3


title: ICL104_Mock_0hr_RNA_5


title: ICL104_Mock_7hr_RNA_4


title: MHAE001_icMERS_12HRS_microRNA_E

description: microRNA


title: ICL104_Mock_0hr_RNA_4


title: ICL104_Mock_0hr_RNA_3


title: ICL104_Mock_0hr_RNA_1


title: ICL104_Mock_0hr_RNA_2


title: ICL104_Cal04_0hr_RNA_2


title: splenic cells, control

status: Public on May 09 2016

city: Tokyo

first: Makoto

last: Ishii

address: 35 Shinanomachi Shinjyuku

department: Division of Pulmonary Medicine Department of Medicine

institute: Keio University School of Medicine

description: Gene expression after sham treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: splenic cells, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: splenic cells

tag: agent

value: control


title: EHUH001_mucin_48h_4_RNA

status: Public on May 07 2016

source_name: Huh cells, mucin-inoculated, 48h, bioreplicate 4

growth_protocol: Cells and virus were grown on 10% FBS DMEM supplemented with L-glut, Pen/Strep, nonessential amino acids and sodium pyruvate.

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: Cells were infected with a multiplicity of infection of 3.

value: Huh

value: mucin


title: EHUH001_ssGP_48h_3_RNA

source_name: Huh cells, ssGP-inoculated, 48h, bioreplicate 3

value: ssGP


title: EHUH001_wild_48h_2_RNA

source_name: Huh cells, wild-inoculated, 48h, bioreplicate 2

value: wild


title: splenic cells, clarithromycin-treated

description: Gene expression after clarithromycin treatment

source_name: splenic cells, clarithromycin-treated

value: clarithromycin


title: EHUH001_wild_48h_3_RNA

source_name: Huh cells, wild-inoculated, 48h, bioreplicate 3


title: EHUH001_wild_48h_4_RNA

source_name: Huh cells, wild-inoculated, 48h, bioreplicate 4


title: EHUH001_wild_48h_5_RNA

source_name: Huh cells, wild-inoculated, 48h, bioreplicate 5


title: EHUH001_mucin_48h_1_RNA

source_name: Huh cells, mucin-inoculated, 48h, bioreplicate 1


title: EHUH001_wild_48h_1_RNA

source_name: Huh cells, wild-inoculated, 48h, bioreplicate 1


title: EHUH001_ssGP_48h_1_RNA

source_name: Huh cells, ssGP-inoculated, 48h, bioreplicate 1


title: EHUH001_ssGP_48h_2_RNA

source_name: Huh cells, ssGP-inoculated, 48h, bioreplicate 2


title: EHUH001_mucin_48h_5_RNA

source_name: Huh cells, mucin-inoculated, 48h, bioreplicate 5


title: EHUH001_mock_48h_3_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 3

value: mock


title: EHUH001_mock_48h_4_RNA

source_name: Huh cells, mock-inoculated, 48h, bioreplicate 4


title: EHUH001_mucin_48h_2_RNA

source_name: Huh cells, mucin-inoculated, 48h, bioreplicate 2