title: 8th leaf stage of Mo17

city: wuhan

first: shaopeng

last: zhang

address: No.1,Shizishan Street · Hongshan District

institute: Huangzhong agricultural university

description: Analysis used shoot apex RNA of mock-inoculated Mo17 at the 8th leaf stage as control samples for comparison to the inoculated Mo17 taken at the 8th leaf stage

hyb_protocol: Each microarray was hybridized with a mix of 3 mg of Cy3-labeled target and 3 mg of Cy5-labeled target resuspended in 60 mL of 13 hybridization buffer (50% formamide, 53 SSC, 0.1% SDS, 0.4 mg mL21 tDNA, and 0.2 mg mL21 salmon sperm DNA).Hybridizations were carried out overnight at 42 C in a SlideBooster hybridization station (Advalytix).

scan_protocol: After slide washing (most stringent wash for 5min in 0.053 SSC at room temperature), slides were immediately scanned on a ScanArray 4000XL scanner (Perkin-Elmer).

data_processing: Statistical analyses for the microarray experiment were performed using BioConductor limma package of R software (http://www.r-project.org). We read the intensity data into an RGList object in R, associated the gene name with each spot by reading the GenePix array list (GAL) file, and normalized the M-values within and between each array. Empirical Bayes statistics were applied to identify differentially expressed genes for each sample group

organism: Zea mays subsp. mays

source_name: RNA of Mo17 shoot apex at the 8th leaf stage (mock-inoculated control)

label_protocol: The incorporated amino-allyl dUTP was then labeled by covalent binding with activated dye esters using Cy5 Mon-Reactive Dye Pack and Cy3 Mon-Reactive Dye Pack (GE Healthcare).

growth_protocol: Seeds of Mo17 were sterilized by soaking in 75% alcohol for 5 min, and then soaked in water for 12 h before sowing in sterilized sand for germination at 25°C in the dark. Basidiospores of S. reilianum were cultured from a single colony grown on YEPS medium (2% w/v tryptone, 1% w/v yeast extract, 2% w/v sucrose, and 2% w/v agar) at 28°C in the dark. Each single colony was grown in potato dextrose broth for 2 days at 24°C in the dark with shaking. Approximately 0.5 ml of each culture was centrifuged and resuspended in 0.1 ml water. For mating assays, two different single colony isolates were mixed together and incubated in PD medium for 1 day at 24°C in the dark with shaking. The hyphae were stained with DAPI (4′, 6′-diamidino-2-phenylindole) to visualize nuclei to detect dikaryotic hyphae. Two compatible mating-type isolates were selected.

extract_protocol: At each growth stage, we collected shoot apexes for RNA extraction from 10 control and 10 S. reilianum-infected plants. The 10 apexes were pooled for extraction. RNA from three independent experiments was extracted with Trizol (Invitrogen) and DNA was removed using the RNase-free DNase set (Fermentas). RNA quantity and quality were assessed by a Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and by agarose gel electrophoresis

treatment_protocol: Two compatible mating-type isolates were cultured in 20 ml PD medium for 2 days at 28°C in the dark with shaking at 200 rpm. After microscopic examination, suspension cultures of two isolates were mixed and incubated in 100 ml PD medium for 1 day at 28°C in the dark with 200 rpm shaking until the optical density at 600 nm reached 0.5–1.0. The culture was then applied to radicle roots and injected into the mesocotyl of budding seeds of maize. The inoculated seedlings were kept in a growth chamber for 6 days under a 14-h light/10-h dark photoperiod (24/20°C) and 20% relative humidity before transplanting into a field.

value: shoot

source_name: RNA of Mo17 shoot apex at the 8th leaf stage (S. reilianum-infected)


title: Wild Type Mice fed Low fat diet 3

status: Public on Jan 29 2013

type: RNA

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

country: USA

institute: Beth Israel Deaconess Medical Center

description: Wild Type Mice fed Low fat diet

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained using Standard protocol.

scan_protocol: Affymetrix High-throughtput scanner standard protocol

data_processing: Data was normalized by a robust multi-chip analysis (RMA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: Affymetrix standard methods were applied using the high throughput protocal for PM arrays

extract_protocol: total RNA was extracted using Trizol Protocol.

tag: genotype

value: Wild Type

tag: treatment

value: Low fat diet

tag: gender

value: male

tag: tissue

value: liver


title: PML Knockout Mice fed High Fat Diet 2

description: PML Knockout Mice fed High Fat Diet

value: PML Knockout

value: High Fat Diet


title: PML Knockout Mice fed High Fat Diet 3

description: PML Knockout Mice fed High Fat Diet


title: AS1_2

city: Frederick

first: Xiaolin

last: Wu

state: MD

address: 8560 Progress Drive, C3001

department: Cancer Research Technology Program

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on Affymetrix GeneChip scanner 3000 7G.

data_processing: Data were collected using Affymetrix AGCC software and then analyzed using RMA normalization in the Exon workflow of Partek Genomic Suite software.

organism: Homo sapiens

source_name: MALAT1 depleted WI38 cells

label_protocol: Total RNA (100 ng) was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Human diploid fibroblasts [WI38] were grown in DMEM with high glucose, 10% fetal bovine serum and 1% NEA.

extract_protocol: Cells treated with control and MALAT1-AS oligos were collected and RNA was isolated using All-Prep DNA/RNA isolation kit [Qiagen] according to manufacturer's instructions.

treatment_protocol: WI38 cells were treated with control and MALAT1- antisense oligonucleotides at a final concentration of 100nM, two times with a gap of 24hrs using Lipofectamine RNAimax [Invitrogen] according to manufacturer's instructions.

tag: cell line

tag: cell type

value: lung fibroblast

tag: genotype/variation


title: AS2_1


title: AS1_1


title: Expression data of 102 Rad

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Soute 5.0 (Scaling target 500), PerChip & PerGene normalized

source_name: Patient 102 Rad

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Rectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

value: Rectal Cancer

tag: response to preoperative chemoradiotherapy

value: Non-responder


title: Ctr_1

source_name: control WI38 cells

value: Control-antisenseOligo


title: Tumor sample 112 (SNP)

type: genomic

city: Birmingham

first: Theresa

middle: V

last: Strong

state: AL

address: 1530 3rd Avenue South

department: Medicine

institute: University of Alabama at Birmingham

hyb_protocol: Samples were hybridized for 16-18 hr and washed and stained on the GeneChip fluidics station 450 using the appropriate fluidics protocol.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 7G.

data_processing:
Genotyping Console 3.02 was used for data processing and GeneChip quality control.  Data quality control and data analysis was performed using Partek GS 6.4.  SNP calls were made using Birdseed V-2.  The following criteria were applied for quality control parameters:  Contrast QC>0.4, QC call rate >86%, SNP call rate >97% and MAPD<0.4.  Copy number calls of SNP 6.0 data were determined using a Hidden Markov Model and a minimum criterion of 50 markers was used to identify significant CNAs.

The CNA data are available as supplementary files of the GSE26232 record.

label: bioitin

molecule: genomic DNA

source_name: Genomic DNA isolated from breast of subject 112

label_protocol: Samples were end labeled using terminal deoxynucleotidyl transferase according to the Affymetrix protocol.

extract_protocol: Genomic DNA was isolated with phenol extraction according to the standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).

value: female

tag: age

value: breast (tumor)

tag: tumor grade

tag: race

value: African-American

tag: diagnosis

value: invasive lobular carcinoma

tag: subtype

value: luminal A

tag: estrogen receptor

value: positive

tag: progesterone receptor

value: equivocal


title: Th17

first: CASEY

middle: T

last: WEAVER

state: Alabama

address: 845 19th Street South

department: Pathology

description: Gene expression data from Th17 cells.

hyb_protocol: The arrays were hybridized overnight per Affymetrix protocol at 45C, and then washed, stained, and scanned the next day.

scan_protocol: GeneChips were scanned on an Affymetrix 3000 7G scanner with an autoloader.

data_processing: The data were analyzed using GeneSpring GX version 11.0.2 software using Affymetrix Exon Expression default settings using RMA16.

source_name: B6.Cg-Tg(TcraTcrb)425Cbn/J (OT-II TCR transgenic), Th17 cells

label_protocol: cRNA was generated by standard methods (Affymetrix), followed by ssDNA fragmentation, end label biotinylation and preparation of hybridization cocktail.

growth_protocol: Naïve OT-II-Tg CD4+ T cells (CD4+CD25-CD62LhighCD44low) were sorted by flow cytometry and activated by Ova peptide in the presence of T-cell-depleted splenic APC derived from Il23a-/- mice in RPMI medium containing 10% FCS.

extract_protocol: OT-II-Tg CD4 Th0, Th22 & Th17 cells grown under specific conditions were purified by MACS after 60 hours of culture, and DNase-free RNA was isolated from collected cells for microarray analysis.

treatment_protocol: Naïve OT-II-Tg CD4+ T cells were stimulated in the presence of IL-6 alone (Th22), under IL-6 + TGFβ (Th17) or without cytokines (Th0).

tag: strain

value: splenic naïve CD4+ T cells

tag: t-helper cell subset


title: Ctr_2


title: 6th leaf stage of Mo17

country: China

description: Analysis used shoot apex RNA of mock-inoculated Mo17 at the 6th leaf stage as control samples for comparison to the inoculated Mo17 taken at the 6th leaf stage

source_name: RNA of Mo17 shoot apex at the 6th leaf stage (mock-inoculated control)

value: shoot

source_name: RNA of Mo17 shoot apex at the 6th leaf stage (S. reilianum-infected)


title: AS2_2


title: Tumor sample 121 (SNP)

source_name: Genomic DNA isolated from breast of subject 121

value: European-American

value: invasive mammary carcinoma with ductal features

value: negative


title: Tumor sample 116, rep1 (SNP)

source_name: Genomic DNA isolated from breast of subject 116

value: invasive ductal carcinoma with focal mucinous features

value: luminal B


title: Tumor sample 115 (SNP)

source_name: Genomic DNA isolated from breast of subject 115

value: invasive ductal carcinoma

value: basal


title: Platelets from Smad4 −/− mice

city: Shanghai

first: Junling

last: Liu

address: No.280 Chongqing Road

institute: Shanghai Jiaotong University

description: Gene expression in platelets from Smad4 knock out mice

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: Platelet

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Mice carrying Smad4 gene flanked by loxP recognition sites (Smad4f/f) 7 were crossed with transgenic mice carrying Cre recombinase under the control of the PF4 promoter (PF4-Cre) 8 to generate mice with conditional Magakaryocyte/platelet specific Smad4 deficiency.

extract_protocol: Total RNA was extracted and purified using mirVanaTM  PARISTM (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Mice were genotyped by PCR, and Smad4 deficiency in platelets was confirmed by Western blotting.

value: platelets

tag: genotype

value: Smad4 −/−


title: Wild Type Mice fed Low fat diet 1

description: Wild Type Mice fed Low fat diet

value: Wild Type

tag: treatment

value: Low fat diet

value: male

value: liver


title: Muscle_OXPAT

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

organism: Rattus norvegicus

source_name: Tibialis anterior muscle, 8 days after electroporation with expression vector of OXPAT (Plin5), pool of 6 animals

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Eight-week old male Wistar rats were purchased from Charles River (Wilmington, Massachusetts, USA). Rats were housed individually on a 12:12 h light-dark cycle (light from 7:00 am to 7:00  pm), at room temperature (21–22 °C). Rats had free access to water and prior to the diet intervention they received standard laboratory chow.

extract_protocol: Total RNA was prepared from tibialis anterior muscle using the RNeasy kit for fibrous tissue (Qiagen). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). Equal amounts of RNA from n=6 rats per group were pooled and analysed by microarray.

treatment_protocol: At the start of the experiment rats were fed a high fat diet (45% energy from fat, D01060502, Research Diets, New Brunswick, NJ) for the duration of the 3-week intervention. Two weeks after the start of the diet intervention, overexpression of Plin5 (OXPAT) or Plin2 (ADRP) in either the right or left tibialis anterior (TA) muscle of the rat was accomplished by an in vivo DNA electrotransfer technique to achieve overexpression of PLIN5 or PLIN2 in one leg; the contralateral TA served as a sham-electroporated internal control. Plin5 or Plin2 was electroporated randomly in the left or the right TA. DNA electroporation was performed under isoflurane anaesthesia. TA muscles were transcutaneously injected with either 150 μg (2 μg/μl) pcDNA3.1-CMV-Plin5, pENTR-CMV-Plin2, or pcDNA3.1-empty vector in 0.9% sterile saline. Within 15 seconds after the last injection 5 electric pulses were applied by two stainless steel plate electrodes placed at the ventral and dorsal side of the leg. One high voltage pulse of 800 V/cm and four low voltage pulses of 80 V/cm at 1 Hz were generated by an ECM 830 electroporator (BTX, San Diego, CA, USA). Rats were killed 8 days post-electroporation. TA muscles were quickly dissected and rapidly frozen in melting isopentane for further analyses.

value: Wistar

tag: gender

value: 11 wk

value: tibialis anterior muscle

value: expression vector of OXPAT (Plin5)


title: Th22

description: Gene expression data from Th22 cells.

source_name: B6.Cg-Tg(TcraTcrb)425Cbn/J (OT-II TCR transgenic), Th22 cells

value: splenic naïve CD4+ T cells


title: Platelets from Smad4 f/f mice

description: Gene expression in platelets from wildtype mice, control

value: Smad4 f/f


title: Muscle_EmptyVector

source_name: Tibialis anterior muscle, 8 days after electroporation with empty expression vector (control), pool of 6 animals

tag: tissue

value: empty (control) expression vector


title: Muscle_ADRP

source_name: Tibialis anterior muscle, 8 days after electroporation with expression vector of ADRP (Plin2), pool of 6 animals

value: expression vector of ADRP (Plin2)


title: 2nd leaf stage of Mo17

description: Analysis used shoot apex RNA of mock-inoculated Mo17 at the 2nd leaf stage as control samples for comparison to the inoculated Mo17 taken at the 2nd leaf stage

source_name: RNA of Mo17 shoot apex at the 2nd leaf stage (mock-inoculated control)

value: shoot

source_name: RNA of Mo17 shoot apex at the 2nd leaf stage (S. reilianum-infected)


title: Th0

description: Gene expression data from Th0 cells.

source_name: B6.Cg-Tg(TcraTcrb)425Cbn/J (OT-II TCR transgenic), Th0 cells


title: R3R4 replicate 3

status: Public on Jan 28 2013

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

hyb_protocol: Double stranded cDNA and biotin-labeled cRNA were synthesized and purified according to the recommended Illumina protocol using a TotalPrep RNA Amplification kit (Applied Biosystems). Samples of 400ng of total RNA were reverse transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled via incorporation of biotin-16-UTP.

scan_protocol: BeadChips were scanned on the Illumina iScan at the Yale Center for Genome Analysis.

data_processing: Data were made positive by adding an offset to remove negative values, log2 transformed, and subjected to the VST variance-stabilizing transformation, then quantile normalized using procedures in the R 2.13 bioconductor lumi 2.4.0 package.

source_name: R3/R4 Erythroid cells

label_protocol: Double stranded cDNA and biotin-labeledcRNA were synthesized and purified according tothe recommended Illumina protocol using aTotalPrep RNA Amplification kit (Invitrogen).

growth_protocol: Human CD34+-selected stem and progenitor cells were obtained from the Yale Center for Excellence in Molecular Hematology. To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668. Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured  for 9 to 14 days in StemSpan SF expansion medium which contains human transferrin (200 ng/ml) and insulin (10 ng/ml) (StemSpan 09650) and was supplemented with estradiol (1 micromolar), dexamethasone (1 micromolar),  Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml). FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)

extract_protocol: RNA was prepared using the Qiagen RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: R3/R4 Erythroid cells


title: R3R4 replicate 4


title: CD34 replicate 3

source_name: CD34+ progenitor cells

value: CD34+ progenitor cells


title: R3R4 replicate 1


title: R3R4 replicate 9

growth_protocol: Human CD34+-selected stem and progenitor cells were obtained from the Yale Center for Excellence in Molecular Hematology. To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668.  Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured in StemSpan SF expansion medium (StemSpan 09650) with estradiol (100 ng/ml), dexamethasone (10 ng/ml), human transferrin (200 ng/ml), insulin (10 ng/ml), Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml) for 9 to 14 days. FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)


title: 4th leaf stage of Mo17

description: Analysis used shoot apex RNA of mock-inoculated Mo17 at the 4th leaf stage as control samples for comparison to the inoculated Mo17 taken at the 4th leaf stage

source_name: RNA of Mo17 shoot apex at the 4th leaf stage (mock-inoculated control)

source_name: RNA of Mo17 shoot apex at the 4th leaf stage (S. reilianum-infected)


title: TB08 683 GOJT3

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

country: United Kingdom

institute: University of Cambridge

description: Samples were prepared at Hutchison/MRC Research Centre and the arrays were run at Microarray Resource Centre, University of Cambridge, UK.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing: GenomeStudio v2010.1.

source_name: Snap frozen surgical resection specimen

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted from snap frozen tissue using phenol/chloroform and bisulfite converted.

value: Gastro-esophageal junctional tumor (adenocarcinoma)


title: TB08 381 GOJT3


title: R3R4 replicate 5


title: TB08 528 GOJT2


title: CD34 replicate 2


title: TB08 11345 GOJT2


title: R3R4 replicate 6


title: CD34 replicate 1


title: TB08 567 GOJT1


title: R3R4 replicate 8


title: R3R4 replicate 2


title: TB08 171 GOJT2


title: TB06 0002 TO

value: Esophageal adenocarcinoma


title: TB08 871 GOJT2


title: TB08 1094 GOJT2


title: d36


title: TB03 372 OT


title: d128


title: R3R4 replicate 7


title: d004


title: d160


title: Tumor sample 104 (SNP)

source_name: Genomic DNA isolated from breast of subject 104

value: female

value: breast (tumor)

value: European-American

value: invasive ductal carcinoma & associated ductal carcinoma in situ

value: basal

value: negative


title: Normal (SNP)

description: AF

source_name: Geomic DNA isolated from peripheral blood of normal reference

value: peripheral blood

value: African-American


title: d5


title: d70


title: d14


title: d51


title: d157


title: d18


title: AH0204.27042009A

source_name: Snap frozen endoscopic biopsy

value: Duodenum


title: d19


title: ad0162.09032006c

value: Barrett's esophagus


title: ahm0883.23072009e


title: ahm0184.17112008f


title: ahm0343.12012009b


title: d9


title: ahm0608.20082009b


title: UCL05-139


title: AHM0846.11052009A


title: AHM0343.04102007D


title: ahn00184.15112005b


title: AHM0498.13092007F


title: ahm0320.18122008c


title: UCL05-1326


title: ahn0081.10092009c


title: UCL05-174


title: d141


title: ahm0878.13072009


title: UCL03-1024


title: AHM0295.10092007B


title: d52


title: UCL02-391


title: UCL04-3935


title: UCL04-1204


title: UCL02-291


title: UCL03-990


title: UCL03-575


title: PsOEt-24-NL

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

description: O_NL_Time0 in GSE11903 (GSM300832)

hyb_protocol: Procedure used standard Affymetrix protocol.

data_processing: Scans were imported into Rosetta Resolver and pre-processed using the 'Resolver Affymetrix Rosetta Intensity Profile Builder (saves reporters)' pipeline

source_name: Non-lesional skin biopsy from psoriasis patient, Pre-dose

label_protocol: Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

extract_protocol: Total RNA extraction.

tag: tissue type

value: Non-lesional skin

tag: time

value: Pre-dose


title: PsOEt-24-Week 4

description: O_LS_Wk4 in GSE11903 (GSM300836)

scan_protocol: Procedure used standard Affymetrix protocol.

source_name: Lesional skin biopsy from psoriasis patient, Week4_etanercept

value: Lesional skin


title: PsOEt-22-NL

description: M_NL_Time0 in GSE11903 (GSM300820)


title: PsOEt-22-Week 1

description: M_LS_Wk1 in GSE11903 (GSM300822)

source_name: Lesional skin biopsy from psoriasis patient, Week1_etanercept


title: PsOEt-23-Week 4

description: N_LS_Wk4 in GSE11903 (GSM300830)


title: PsOEt-24-Week 2

description: O_LS_Wk2 in GSE11903 (GSM300835)

source_name: Lesional skin biopsy from psoriasis patient, Week2_etanercept


title: PsOEt-22-LS

description: M_LS_Time0 in GSE11903 (GSM300821)

source_name: Lesional skin biopsy from psoriasis patient, Pre-dose


title: PsOEt-22-Week 12

description: M_LS_Wk12 in GSE11903 (GSM300825)

source_name: Lesional skin biopsy from psoriasis patient, Week12_etanercept


title: PsOEt-21-Week 12

description: L_LS_Wk12 in GSE11903 (GSM300819)


title: PsOEt-22-Week 4

description: M_LS_Wk4 in GSE11903 (GSM300824)


title: PsOEt-23-Week 1

description: N_LS_Wk1 in GSE11903 (GSM300828)


title: PsOEt-21-Week 2

description: L_LS_Wk2 in GSE11903 (GSM300817)


title: PsOEt-24-LS

description: O_LS_Time0 in GSE11903 (GSM300833)


title: PsOEt-21-LS

description: L_LS_Time0 in GSE11903 (GSM300815)


title: PsOEt-24-Week 1

description: O_LS_Wk1 in GSE11903 (GSM300834)


title: PsOEt-20-Week 1

description: K_LS_Wk1 in GSE11903 (GSM300811)


title: PsOEt-23-Week 2

description: N_LS_Wk2 in GSE11903 (GSM300829)


title: PsOEt-23-Week 12

description: N_LS_Wk12 in GSE11903 (GSM300831)


title: PsOEt-21-Week 1

description: L_LS_Wk1 in GSE11903 (GSM300816)


title: PsOEt-22-Week 2

description: M_LS_Wk2 in GSE11903 (GSM300823)


title: PsOEt-23-LS

description: N_LS_Time0 in GSE11903 (GSM300827)


title: PsOEt-21-NL

description: L_NL_Time0 in GSE11903 (GSM300814)


title: PsOEt-19-Week 12

description: J_LS_Wk12 in GSE11903 (GSM300808)


title: PsOEt-20-LS

description: K_LS_Time0 in GSE11903 (GSM300810)


title: PsOEt-20-Week 2

description: K_LS_Wk2 in GSE11903 (GSM300812)


title: PsOEt-20-NL

description: K_NL_Time0 in GSE11903 (GSM300809)


title: PsOEt-23-NL

description: N_NL_Time0 in GSE11903 (GSM300826)


title: PsOEt-19-Week 4

description: J_LS_Wk4 in GSE11903 (GSM300807)


title: PsOEt-19-Week 2

description: J_LS_Wk2 in GSE11903 (GSM300806)


title: PsOEt-24-Week 12

description: O_LS_Wk12 in GSE11903 (GSM300837)


title: PsOEt-18-LS

description: I_LS_Time0 in GSE11903 (GSM300798)


title: PsOEt-19-LS

description: J_LS_Time0 in GSE11903 (GSM300804)


title: PsOEt-18-Week 12

description: I_LS_Wk12 in GSE11903 (GSM300802)


title: PsOEt-18-Week 4

description: I_LS_Wk4 in GSE11903 (GSM300801)


title: PsOEt-17-Week 4

description: H_LS_Wk4 in GSE11903 (GSM300795)


title: PsOEt-19-NL

description: J_NL_Time0 in GSE11903 (GSM300803)


title: PsOEt-17-Week 12

description: H_LS_Wk12 in GSE11903 (GSM300796)


title: PsOEt-18-Week 2

description: I_LS_Wk2 in GSE11903 (GSM300800)


title: PsOEt-19-Week 1

description: J_LS_Wk1 in GSE11903 (GSM300805)


title: PsOEt-14-Week 2

description: E_LS_Wk2 in GSE11903 (GSM300776)


title: PsOEt-18-NL

description: I_NL_Time0 in GSE11903 (GSM300797)


title: PsOEt-18-Week 1

description: I_LS_Wk1 in GSE11903 (GSM300799)


title: PsOEt-17-LS

description: H_LS_Time0 in GSE11903 (GSM300792)


title: PsOEt-15-NL

description: F_NL_Time0 in GSE11903 (GSM300779)


title: PsOEt-17-Week 1

description: H_LS_Wk1 in GSE11903 (GSM300793)


title: PsOEt-16-Week 2

description: G_LS_Wk2 in GSE11903 (GSM300788)


title: PsOEt-16-Week 4

description: G_LS_Wk4 in GSE11903 (GSM300789)


title: PsOEt-14-Week 4

description: E_LS_Wk4 in GSE11903 (GSM300777)


title: PsOEt-16-LS

description: G_LS_Time0 in GSE11903 (GSM300786)


title: PsOEt-16-Week 12

description: G_LS_Wk12 in GSE11903 (GSM300790)


title: PsOEt-16-NL

description: G_NL_Time0 in GSE11903 (GSM300785)


title: PsOEt-14-Week 1

description: E_LS_Wk1 in GSE11903 (GSM300775)


title: PsOEt-15-Week 1

description: F_LS_Wk1 in GSE11903 (GSM300781)


title: PsOEt-15-Week 2

description: F_LS_Wk2 in GSE11903 (GSM300782)


title: PsOEt-16-Week 1

description: G_LS_Wk1 in GSE11903 (GSM300787)


title: PsOEt-17-Week 2

description: H_LS_Wk2 in GSE11903 (GSM300794)


title: PsOEt-15-LS

description: F_LS_Time0 in GSE11903 (GSM300780)


title: PsOEt-17-NL

description: H_NL_Time0 in GSE11903 (GSM300791)


title: PsOEt-15-Week 4

description: F_LS_Wk4 in GSE11903 (GSM300783)


title: PsOEt-13-Week 4

description: D_LS_Wk4 in GSE11903 (GSM300771)


title: PsOEt-13-NL

description: D_NL_Time0 in GSE11903 (GSM300767)


title: PsOEt-13-Week 2

description: D_LS_Wk2 in GSE11903 (GSM300770)


title: PsOEt-11-Week 1

description: B_LS_Wk1 in GSE11903 (GSM300757)


title: PsOEt-12-NL

description: C_NL_Time0 in GSE11903 (GSM300761)


title: PsOEt-14-NL

description: E_NL_Time0 in GSE11903 (GSM300773)


title: PsOEt-10-Week 1

description: A_LS_Wk1 in GSE11903 (GSM300751)


title: PsOEt-12-Week 4

description: C_LS_Wk4 in GSE11903 (GSM300765)


title: PsOEt-12-Week 2

description: C_LS_Wk2 in GSE11903 (GSM300764)


title: PsOEt-13-LS

description: D_LS_Time0 in GSE11903 (GSM300768)


title: PsOEt-12-Week 1

description: C_LS_Wk1 in GSE11903 (GSM300763)


title: PsOEt-13-Week 1

description: D_LS_Wk1 in GSE11903 (GSM300769)


title: PsOEt-10-LS

description: A_LS_Time0 in GSE11903 (GSM300750)


title: PsOEt-10-Week 4

description: A_LS_Wk4 in GSE11903 (GSM300753)


title: PsOEt-11-Week 4

description: B_LS_Wk4 in GSE11903 (GSM300759)


title: PsOEt-10-Week 2

description: A_LS_Wk2 in GSE11903 (GSM300752)


title: PsOEt-12-LS

description: C_LS_Time0 in GSE11903 (GSM300762)


title: PsOEt-11-Week 2

description: B_LS_Wk2 in GSE11903 (GSM300758)


title: PsOEt-11-LS

description: B_LS_Time0 in GSE11903 (GSM300756)


title: PsOEt-11-NL

description: B_NL_Time0 in GSE11903 (GSM300755)


title: PsOEt-14-LS

description: E_LS_Time0 in GSE11903 (GSM300774)


title: PsOEt-10-NL

description: A_NL_Time0 in GSE11903 (GSM300749)


title: mMSC-BM-wt#2

city: Armilla

first: Alberto

last: Labarga

state: Granada

address: Av. Innovacion 1

country: Spain

institute: Experimental Serendipity S.L.

description:
252800514714_S01_GE1_107_Sep09_1_4
Mouse MSCs from bone marrow (BM), wild type.
Duplicate#2

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).

data_processing: Background correction was performed using limma normexp and between array normalization using quantile normalization using R. Primary data was examined using GeneSpring 11.0 software (Silicon Genetics, Redwood City, CA). Gene expression in the control and experimental groups was compared using Student's t test and a Benjamini Hochberg multi-testing correction. Only genes satisfying the threshold of P value < 0.05 and a fold change expression >2 were included and assigned as significant. Analysis of pathways significantly altered by p53 or Rbp53 deficiency was performed using the Ingenuity Pathway software 8.0 (IPA; Ingenuity Systems, Inc., Redwood City, CA).

source_name: BM-MSCs of WT mice

label_protocol: Total RNA samples were labeled with Cy3 using the Agilent Low Input Quick Amp Labeling Kit following the manufacturer's instructions (Agilent Technologies, CA).

growth_protocol: RbloxP/loxPp53loxP/loxP BM-MSCs and ASCs were induced to differentiate towards the osteogenic lineage for 10 days using the Osteogenic MSCs Differentiation BulletKit (Lonza). Following this treatment, Rb and p53 mutant MSCs were generated by excision of the LoxP-flanked sequences by infection of all MSC cultures with adenoviral vectors expressing the Cre-recombinase gene under the control of the CMV promoter (Ad-CMV-Cre). WT and the osteogenic-primed p53-/- Rb-/- mMSCs (FVB background) from BM or fat (ASCs), as well as tumor cell lines derived from the ostoegenic-primed p53-/-Rb-/- BM-MSC cultures, were maintained in complete MSC growth medium (DMEM-Advanced, 10% FBS, 1% Pen/Strep and 1% Glutamax). Only cells between passages 2 and 5 were used for gene expression analysis.

extract_protocol: Duplicate independent cultures of primary (WT, and osteogenic-primed Rb-/-p53-/-) ASCs and BM-MSCs and tumoral (TRbp53-10D) BM-MSCs were collected during exponential cell growth and stabilized in RNAlater (Ambion, Austin, TX) solution until RNA extraction. RNA was isolated using the Agilent Total RNA Isolation Kit (Agilent Technologies, Palo Alto, CA), and its quality was checked in the Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment.

tag: strain/background

value: FVB

tag: genotype/variation

value: WT

tag: cell type

value: mesenchymal stem cells (MSCs) from bone marrow (BM-MSCs)

tag: tumor

value: non-tumorigenic


title: mASC-Rb-/-p53-/-Osteo-10#2

description:
252800514714_S01_GE1_107_Sep09_2_2
Mouse MSCs from fat (ASCs) differentiated to the osteogenic lineage for 10 days, Rb-/-p53-/-.
Duplicate#2

source_name: ASCs of Rb-/-p53-/- mice differentiated to the osteogenic lineage for 10 days

value: Rb p53 double-knockout

value: mesenchymal stem cells (MSCs) from adipose (ASCs) differentiated to osteogenic lineage for 10 days


title: Tumor-mMSC-BM-Rb-/-p53-/-Osteo-10#1

description:
252800514715_S01_GE1_107_Sep09_1_1
Tumor obtained upon s.c. inoculation of mouse MSCs from BM differentiated to the osteogenic lineage for 10 days, Rb-/-p53-/-.
Duplicate#1

source_name: Tumor obtained upon s.c. inoculation of BM-MSCs of Rb-/-p53-/- mice differentiated to the osteogenic lineage for 10 days

value: tumor cell line derived from mesenchymal stem cells (MSCs) from bone marrow (BM-MSCs) differentiated to osteogenic lineage for 10 days

value: tumorigenic


title: mMSC-BM-Rb-/-p53-/-Osteo-10#1

description:
252800514714_S01_GE1_107_Sep09_2_3
Mouse MSCs from BM differentiated to the osteogenic lineage for 10 days, Rb-/-p53-/-.
Duplicate#1

source_name: BM-MSCs of Rb-/-p53-/- mice differentiated to the osteogenic lineage for 10 days

value: mesenchymal stem cells (MSCs) from bone marrow (BM-MSCs) differentiated to osteogenic lineage for 10 days


title: Tumor-mMSC-BM-Rb-/-p53-/-Osteo-10#2

description:
252800514715_S01_GE1_107_Sep09_1_2
Tumor obtained upon s.c. inoculation of mouse MSCs from BM differentiated to the osteogenic lineage for 10 days, Rb-/-p53-/-.
Duplicate#2


title: mMSC-BM-Rb-/-p53-/-Osteo-10#2

description:
252800514714_S01_GE1_107_Sep09_2_4
Mouse MSCs from BM differentiated to the osteogenic lineage for 10 days, Rb-/-p53-/-.
Duplicate#2


title: iDCs-2day-rep3, miRNA expression

city: kunming

last: Zhao

address: Eastern Jiaochang road,32#

institute: Kunming institute of zoology.CAS

description: miRNA expression of monocyte derive iDCs after stimulation of GM-CSF and rhIL-4 for 2 days

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent Technologies). GeneView data were also analyzed by Feature Extraction Software.

source_name: iDCs, rep3

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from buffy coat by centrifugation at 2200rpm for 20min on lymphocyte separation medium. The phase containing white cells was removed and washed in RPMI-1640.CD14+ monocytes were separated with CD14+ microbeads and a magnetic separation column over a magnetic field (Miltenyi Biotec) according to the manufacture’s protocol. Eluted cells were washed thoroughly to remove the nonspecific binding to the beads. Purified monocytes were used as dendritic cell (DCs) precursors and were cultured in six-well plate in RPMI-1640 medium supplemented weih 10% heat inactivated fetal bovine serum (FBS), 2mM L-glutamine, 1Mm sodium pyruvate, 100U/mL penicillin and 100μg/mL streptomycin at 1 × 106 cells/mL at 37℃ in a 5% CO2 humidified incubator for different days.

extract_protocol: microRNA samples were isolated from precursor, iDCs and mDCs using the  mirVana RNA isolation kit according to the manufacturer’s protocol (Ambion). The microRNA quality, concentration, and integrity were analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: To generate immature DC (iDCs), monocytes were cultured for 1-6 days in the presence of 1000U/mL GM-CSF and 500 U/mL rhIL-4, followed by additional 1-2 days stimulation with 10ng/mL TNF-α, 10ng/mL IL-1β, 10ng/mL IL-6 and 10μg/mL PGE2 to get fully differentiated and matured DCs (mDCs). Medium exchange was performed every 2 days with fresh cytokine cocktails.

tag: developmental stage

value: monocyte derived immature DCs


title: mDCs-4day-rep2, miRNA expression

description: miRNA expression of monocyte derive mDCs after differentiation with GM-CSF and rhIL-4 for 2 days and then maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days.

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

source_name: mDCs, rep2

value: monocyte derived mature DCs


title: mDCs-4day-rep1, miRNA expression

source_name: mDCs, rep1

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


title: mDCs-4day-rep3, miRNA expression

source_name: mDCs, rep3


title: precursor-0day-rep3, miRNA expression

description: miRNA expression of monocytes purified from PBMCs

source_name: monocytes, rep3

value: monocytes from PBMC


title: iDCs-2day-rep1, miRNA expression

source_name: iDCs, rep1


title: iDCs-2day-rep2, miRNA expression

source_name: iDCs, rep2


title: precursor-0day-rep2, miRNA expression

source_name: monocytes, rep2


title: mASC-Rb-/-p53-/-Osteo-10#1

description:
252800514714_S01_GE1_107_Sep09_2_1
Mouse MSCs from fat (ASCs) differentiated to the osteogenic lineage for 10 days, Rb-/-p53-/-.
Duplicate#1


title: precursor-0day-rep1, miRNA expression

source_name: monocytes, rep1


title: mMSC-BM-wt#1

description:
252800514714_S01_GE1_107_Sep09_1_3
Mouse MSCs from bone marrow (BM), wild type.
Duplicate#1


title: mASC-wt#2

description:
252800514714_S01_GE1_107_Sep09_1_2
Mouse MSCs from fat (ASCs), wild type.
Duplicate#2

source_name: ASCs of WT mice

value: mesenchymal stem cells (MSCs) from adipose (ASCs)


title: mDCs-4day-rep1, gene expression

description: gene expression of monocyte derive mDCs after differentiation with GM-CSF and rhIL-4 for 2 days and then maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days.

hyb_protocol: According to the Agilent Whole Human Genome Microarray (4x44K) Protocol (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent Technologies). Data were also analyzed by  Feature Extraction Software.

extract_protocol: Total RNA samples were isolated from precursor, iDCs and mDCs using the QIAGEN RNAeasy mini kit according to the manufacturer’s protocol (QIAGEN). The RNA quality, concentration, and integrity were analyzed  by electrophoresis.


title: iDCs-2day-rep1, gene expression

description: gene expression of monocyte derive iDCs after stimulation of GM-CSF and rhIL-4 for 2 days

scan_protocol: According to the Agilent Whole Human Genome Microarray (4x44K) Protocol (Agilent Technologies).


title: precursor-0day-rep1, gene expression

description: gene expression of monocytes purified from PBMCs

label_protocol: According to the Agilent Whole Human Genome Microarray (4x44K) Protocol (Agilent Technologies).


title: iDCs-2day-rep3, gene expression


title: mDCs-4day-rep2, gene expression


title: precursor-0day-rep3, gene expression


title: mASC-wt#1

description:
252800514714_S01_GE1_107_Sep09_1_1
Mouse MSCs from fat (ASCs), wild type.
Duplicate#1


title: iDCs-2day-rep2, gene expression


title: precursor-0day-rep2, gene expression


title: control biological rep3

first: Laurence

middle: G

last: Rahme

address: 50 Blosson St, Thier 340

department: Surgery

institute: Massachusetts General Hospital

description: Gene expression data from mouse without 2-AA treatment

hyb_protocol: cRNA was hybridized onto MOE430A oligonucleotide arrays (Affymetrix, CA, USA)

scan_protocol: MOE430A oligonucleotide arrays (Affymetrix, CA, USA) according to to the Affymetrix protocol

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.

source_name: mouse without 2-AA treatment

label_protocol: Biotinylated cRNA was generated with 10 µg of total cellular RNA according to the protocol outlined by Affymetrix Inc.

extract_protocol: Trizol® isolation method  for RNA extraction.

treatment_protocol: Mice were injected intra-peritoneally (IP) with 100µl of 2-AA (6.75 mg /kg mice), and mouse skeletal muscle was analyzed 4 days post 2-AA treatment.

value: gastrocnemius muscles


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 14, biological rep2

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: Gene expression data from ferret lung on Day 14 after infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using Expression Console Version 1.1 (Affymetrix) default analysis settings.

organism: Mustela putorius furo

source_name: Ferret

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

treatment_protocol: Intranasal infection of ferrets with 10^6 EID50 A/California/07/2009 (H1N1) was performed.  On Day 0 (before infection), Day 3, 5, 7 and 14 (post infection ), ferrets were euthanized and lymph nodes were excised and put in RNAlater (Ambion, Austin, TX) immediately.

value: lymph nodes

tag: infection (virus strain)

value: A/California/07/2009 (H1N1)

tag: time point

value: Day 14


title: 2-AA treatment biological rep2

description: Gene expression data from 2-AA treated mouse

source_name: 2-AA treated mouse for 4 days


title: 2-AA treatment biological rep3


title: 2-AA treatment biological rep1


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 7, biological rep3

description: Gene expression data from ferret lung on Day 7 after infection

value: Day 7


title: mDCs-4day-rep3, gene expression


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 14, biological rep3


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 5, biological rep1

description: Gene expression data from ferret lung on Day 5 after infection

value: Day 5


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 3, biological rep1

description: Gene expression data from ferret lung on Day 3 after infection

value: Day 3


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 5, biological rep3


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 7, biological rep2


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 3, biological rep3


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 3, biological rep2


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 5, biological rep2


title: Ferret lymph nodes, uninfected, on Day 0, biological rep2

description: Gene expression data from ferret lung before infection

value: N/A; Uninfected

value: Day 0


title: Ferret lymph nodes, uninfected, on Day 0, biological rep3


title: Ferret lymph nodes, uninfected, on Day 0, biological rep1


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 7, biological rep1


title: control biological rep2


title: control biological rep1


title: Islets-C57BL6-6wk-5

city: St. Louis

first: Javier

middle: A

last: Carrero

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

hyb_protocol: GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
Expression Console for Quality Control, robust multi-array analysis with quantile normalization for normalization of data, Combat for batch effect correction.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.probeset.csv

source_name: Islets of Langerhans

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay

growth_protocol: Specific pathogen-free barrier animal facility.

extract_protocol: Ambion RNAqueous.

treatment_protocol: None.

value: islets of langerhans

tag: age


title: Islets-C57BL6-6wk-6


title: Islets-C57BL6-6wk-3


title: Islets-C57BL6-6wk-2


title: Lgr5-sorted cells 2

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description: biological replicate 2 of 2

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Ratios are given in log10.

source_name: Lgr5-sorted cells after CCl4 treatment for 6 days

label_protocol: 1µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: liver cultures were grown from single Lgr5 isolated cells and cultured in the media described in Sato et al (Nature 2009) with some modifications. For complete culture description, see accompaning material and methods

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: liver organoids were cultured in either expansion or differentiation conditions according to the materials and methods

value: Lgr5-sorted cells

source_name: mouse reference RNA (Stratagene)

value: mouse reference RNA (Stratagene)


title: Islets-C57BL6-6wk-4


title: Liver 2

description: biological replicate 2 of 2

source_name: Whole liver tissue

value: Liver


title: Islets-B6g7-6wk-4


title: Islets-B6g7-6wk-5


title: Ferret lymph nodes with A/California/07/2009 (H1N1) on Day 14, biological rep1


title: Islets-B6g7-6wk-6


title: Sorted duct 2

description: biological replicate 2 of 2

source_name: Ductal cells sorted for Mic1-1c3

value: Ductal cells


title: Islets-C57BL6-6wk-1


title: Hepatocytes 2

description: biological replicate 2 of 2

source_name: Hepatocytes fraction after liver isolation

value: Hepatocytes


title: Islets-B6g7-6wk-1


title: Islets-B6g7-6wk-3


title: Islets-B6g7-6wk-2


title: BEAS-2B cells_10 μM symplostatin 5 + 4% NaOAc treatment_3 h_rep2

city: Gainesville

first: Lilibeth

last: Salvador

state: Fl

address: 1600 SW Archer Road

department: Medicinal Chemistry

institute: University of Florida

hyb_protocol: The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned using a GeneChip 7G Scanner.

data_processing: Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software.  The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.

label: Biotin

source_name: Bronchial epithelial cells, treated with 10 μM symplostatin 5 and 4% NaOAc for 3 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).

growth_protocol: Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C.  All culture plates and flasks were coated with collagen before use.

extract_protocol: RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit

treatment_protocol: A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.

value: Bronchial epithelial cells

value: treated with 10 μM symplostatin 5 (prepared in DMSO) and 4% NaOAc for 3 h


title: BEAS-2B cells_10 μM symplostatin 5 + 4% NaOAc treatment_3 h_rep1


title: Liver 1

description: biological replicate 1 of 2


title: BEAS-2B cells_10 μM symplostatin 5 + 100 nM human neutrophil elastase treatment_3 h_rep1

source_name: Bronchial epithelial cells, treated with 10 μM symplostatin 5 and 100 nM elastase for 3 h

value: treated with 10 μM symplostatin 5 (prepared in DMSO) and 100 nM elastase (prepared in 4% NaOAc) for 3 h


title: Lgr5-sorted cells 1

description: biological replicate 1 of 2


title: Islets-NODRAG-6wk-5


title: BEAS-2B cells_10 μM symplostatin 5 + 100 nM human neutrophil elastase treatment_3 h_rep2


title: BEAS-2B cells_DMSO+100 nM human neutrophil elastase treatment_3 h_rep1

source_name: Bronchial epithelial cells, treated with 1% DMSO and 100 nM elastase for 3 h

value: treated with 1% DMSO and 100 nM elastase (prepared in 4% NaOAc) for 3 h


title: Hepatocytes 1

description: biological replicate 1 of 2


title: BEAS-2B cells_DMSO+100 nM human neutrophil elastase treatment_3 h_rep2


title: Sorted duct 1

description: biological replicate 1 of 2


title: Islets-NODRAG-6wk-4


title: BEAS-2B cells_DMSO+4% NaOAc treatment_3 h_rep1

source_name: Bronchial epithelial cells, treated with 1% DMSO and 4% NaOAc for 3 h


title: Islets-NODRAG-6wk-2


title: CCl4 Liver1 day3

description: biological replicate 1 of 2

source_name: liver tissue after CCl4 treatment for 3days


title: Islets-NODRAG-2wk-5


title: CCl4 Liver2 day3

description: biological replicate 2 of 2


title: Islets-NODRAG-2wk-6


title: Islets-NODRAG-6wk-1


title: Islets-NODRAG-6wk-6


title: CCl4 Liver2 day13

description: biological replicate 2 of 2

source_name: liver tissue after CCl4 treatment for 13days


title: Islets-NODRAG-6wk-3


title: A549 TIMP-2 day 21 tumor

city: BETHESDA

first: DIMITRA

last: BOURBOULIA

address: 8717 GROVEMONT CIRCLE

department: RADIATION ONCOLOGY BRANCH

institute: NIH

description:
tumor day 21 post injection
gene expression data from A549 TIMP-2 control xenograft tumors (pool of 6)

scan_protocol: Wash/stain/scan of the microarray is carried out under strictly controlled conditions with the Affymetrix Fluidics Station and Scanner.

data_processing: The array data were processed using the R/Bioconductor Statistical Package.

source_name: Tumor xenograft of A549 cells transfected with TIMP-2 injected into NOD-SCID mice.

label_protocol: About 100 ng of total RNA samples are reverse transcribed and labeled by biotin.  If the labeling reaction is successful and passes labeling QC, samples are hybridized overnight to Affymetrix GeneChip microarrays.

growth_protocol: cells were cultured for 48hrs to 80% confluency.

extract_protocol: FOR CELL LINES: Total RNA from three independent exponential growth phase cell cultures of A549 EV, TIMP-2 and Ala+TIMP-2 was isolated using the RNAeasy kit (Qiagen). FOR TUMORS: Equal amounts of RNA (500ng) from six tumors per group were pooled into one sample and used to perform microarray analysis in tumor xenografts.

treatment_protocol: No treatment

tag: parental cell line

tag: transfection

value: tumor xenograft

tag: host

value: NOD-SCID mouse


title: Islets-NODRAG-2wk-3

tag: strain


title: Islets-NOD-DBX-2

value: NOD


title: Islets-NOD-DBX-1


title: Islets-NOD-18wk-3


title: Islets-NOD-18wk-2


title: Adult Pancreas 2

description: biological replicate 2 of 2

source_name: Pancreas from wildtype mice

value: Pancreas


title: Islets-NODRAG-2wk-1


title: A549 Ala+TIMP-2, biological rep 3

description:
transfected cell line
gene expression data from Ala+TIMP-2 overexpressing a549 cells

hyb_protocol: If the labeling reaction is successful and passes labeling QC, samples are hybridized overnight to Affymetrix GeneChip microarrays.

source_name: A549 cells transfected with human cDNA Ala+TIMP-2

tag: cell line


title: Islets-NOD-DBX-3


title: A549 EV control day 21 tumor

description:
tumor day 21 post injection
gene expression data from A549 EV control xenograft tumors (pool of 6)

source_name: Tumor xenograft of A549 cells transfected with EV control injected into NOD-SCID mice.

value: EV control


title: Islets-NOD-18wk-1


title: A549 Ala+TIMP-2 day 21 tumor

description:
tumor day 21 post injection
gene expression data from A549 Ala+TIMP-2 control xenograft tumors (pool of 6)

source_name: Tumor xenograft of A549 cells transfected with Ala+TIMP-2 injected into NOD-SCID mice.


title: Adult Pancreas 1

description: biological replicate 1 of 2


title: DM_Liver organoid

description: no biological replicates

source_name: Liver organoids cultured in differentiation medium

value: Liver organoids


title: A549 Ala+TIMP-2, biological rep 1


title: Islets-NODRAG-2wk-4

source_name: Islets of Langerhans


title: Islets-NODRAG-2wk-2


title: A549 Ala+TIMP-2, biological rep 2


title: Islets-NOD-12wk-1


title: Islets-NOD-12wk-3


title: Islets-NOD-8wk-6


title: A549 TIMP-2, biological rep 2

description:
transfected cell line
gene expression data from TIMP-2 overexpressing A549 cells

source_name: A549 cells transfected with human cDNA TIMP-2


title: Adult liver 1

description: biological replicate 1 of 2

source_name: Liver from wildtype mice

source_name: mouse reference RNA (Stratagene)


title: Islets-NOD-12wk-2


title: Adult liver 2

description: biological replicate 2 of 2


title: A549 TIMP-2, biological rep 3


title: EM1_Liver organoid

description: biological replicate 1 of 2

source_name: Liver organoids cultured in expansion medium


title: Brown adipose tissue 2

description: biological replicate 2 of 3

source_name: Brown adipose tissue from wildtype mice

value: Brown adipose tissue


title: EM2_Liver organoid

description: biological replicate 2 of 2


title: Brown adipose tissue 3

description: biological replicate 3 of 3


title: A549 EV control, biological rep 3

description:
transfected cell line
gene expression data from A549 EV control

source_name: A549 cells transfected with EV control


title: A549 EV control, biological rep 2


title: A549 TIMP-2, biological rep 1


title: Islets-NOD-8wk-3

value: islets of langerhans


title: Islets-NOD-8wk-4


title: A549 EV control, biological rep 1


title: Islets-NOD-8wk-2


title: White adipose tissue 3

description: biological replicate 3 of 3

source_name: White adipose tissue from wildtype mice

value: White adipose tissue


title: Brown adipose tissue 1

description: biological replicate 1 of 3

value: mouse reference RNA (Stratagene)


title: BEAS-2B cells_DMSO+4% NaOAc treatment_3 h_rep2

source_name: Bronchial epithelial cells, treated with 1% DMSO and 4% NaOAc for 3 h

tag: treatment


title: Islets-NOD-8wk-5

tag: tissue


title: Skin-Psoriasis-45803-LS

source_name: Lesional skin biopsy from psoriasis patient

extract_protocol: The frozen biopsy was homogenized using a TissueRuptor and RNA extracted using the mirVana™ kit with on-column DNase treatment

tag: tissue type

value: Lesional skin

tag: gender

value: Male


title: Skin-Psoriasis-45803-NL

source_name: Non-lesional skin biopsy from psoriasis patient

value: Non-lesional skin


title: White adipose tissue 2

description: biological replicate 2 of 3


title: Islets-NOD-8wk-1


title: Skin-Psoriasis-45798-NL


title: Muscle 1

description: biological replicate 1 of 3

source_name: Muscle from wildtype mice

value: Muscle


title: Muscle 3

description: biological replicate 3 of 3


title: Skin-Psoriasis-45807-NL

value: Female


title: Muscle 2

description: biological replicate 2 of 3


title: Islets-NOD-6wk-4


title: White adipose tissue 1

description: biological replicate 1 of 3


title: Skin-Psoriasis-45807-LS


title: Islets-NOD-6wk-5


title: Islets-NOD-6wk-1


title: Skin-Psoriasis-45808-NL


title: Skin-Psoriasis-45798-LS


title: Islets-NOD-6wk-6


title: Skin-Psoriasis-45808-LS


title: Islets-NOD-4wk-6


title: Skin-Psoriasis-45802-LS


title: Skin-Psoriasis-45801-LS


title: Islets-NOD-4wk-2


title: Islets-NOD-4wk-3


title: Islets-NOD-6wk-3


title: Islets-NOD-4wk-5


title: Skin-Psoriasis-45799-NL


title: Skin-Psoriasis-45799-LS


title: Islets-NOD-4wk-4


title: Skin-Psoriasis-45801-NL


title: Skin-Psoriasis-45802-NL


title: Islets-NOD-6wk-2


title: Skin-Psoriasis-45800-NL


title: Islets-NOD-2wk-6


title: Islets-NOD-2wk-5


title: Islets-NOD-2wk-2


title: Islets-NOD-2wk-4


title: Islets-NOD-4wk-1


title: Skin-Psoriasis-43618-LS


title: 6751

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Mice used in hybridization IDs 6750-6753 are littermates and backcrossed for > 12 generations in C57Bl/6

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 14 pmol; Cy5 label: 10 pmol) was hybridised on Agilent arrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.1.1.1)

data_processing: The Agilent processed signal values (i.e., features gProcessedSignal and rProcessedSignal from Agilent Feature Extraction v10.1.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3 intensities) were computed and in case of multiple probes for the same Agilent ID, log-intensities were averaged. Control probes were remove prior to analysis.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Hippocampi and cortices were dissected from WT and Nxf7 KO male mice. RNA was extracted with Trizol according to the manufacturers' instructions (Invitrogen), DNaseI-treated for 30 min at 37°C and purified on an RNAeasy column (Qiagen). RNA concentration and integrity was assessed using a Bioanalyser 2100 (Agilent).

value: male

value: 28 days

value: hippocampus

tag: genotype

value: Nxf7-knockout (KO)

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

value: wild type (WT)


title: 6752


title: Skin-Psoriasis-40041-NL


title: 9209

description: Mice used in hybridization IDs 9206-9209 are littermates and backcrossed for > 12 generations in C57Bl/6

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: The Agilent processed signal values (i.e., features gProcessedSignal and rProcessedSignal from Agilent Feature Extraction v10.7.3.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3 intensities) were computed and in case of multiple probes for the same Agilent ID, log-intensities were averaged. Control probes were remove prior to analysis.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 500 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

value: cortex

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 500 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).


title: Skin-Psoriasis-38326-NL


title: 6753


title: 9208


title: Islets-NOD-2wk-3

value: NOD


title: Skin-Psoriasis-43618-NL


title: Skin-Psoriasis-40041-LS


title: 9206


title: Skin-Psoriasis-43617-NL


title: Skin-Psoriasis-43617-LS


title: Skin-Psoriasis-43616-LS


title: CCl4 Liver1 day13

description: biological replicate 1 of 2

source_name: liver tissue after CCl4 treatment for 13days

value: Liver


title: Skin-Psoriasis-42949-NL


title: 6750


title: Islets-NOD-2wk-1


title: Skin-Psoriasis-42949-LS


title: Skin-Psoriasis-38326-LS


title: Skin-Psoriasis-43616-NL


title: 9207


title: mutant 11-104A4 complemented at 40oC rep2

status: Public on Jan 27 2013

city: Tampa

first: Elena

middle: S

last: Suvorova

address: 3720 Spectrum Blvd

institute: University of South Florida

description: gene expression data from mutant 11-104A4 complemented with cosmid TOXOV53 grown 32h at resticted temperature

hyb_protocol: Fragmented cRNA (5μg) was hybridized to the Toxoplasma gondii Affymetrix microarray according to standard hybridization protocols (ToxoGeneChip: http://ancillary.toxodb.org/docs/Array-Tutorial.html).

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

data_processing: Hybridization data was preprocessed with Robust Multi-array Average (RMA) and normalized using per chip and per gene median polishing and analyzed using the software package GeneSpring GX (Agilent Technologies).  t-Test was run in order to identify genes with significantly greater than random variation in RNA abundance across the data grouped by temperature and mutant type.  Variances were calculated using cross-gene error model, with a p-value cutoff 0.1, and multiple testing correction: Benjamini and Hochberg False Discovery Rate.

organism: Toxoplasma gondii

source_name: mutant 11-104A4 complemented with TOXOV53 grown for 32h at 40oC

label_protocol: A total of 500ng starting RNA was used to produce biotinilated cRNA using the Affymetrix One-Cycle Kit (Affymetrix).

growth_protocol: Toxoplasma gonidii mutant 11-104A4 was grown in HFF monolayers for 16h at 34oC, then was either left at 34oC for another 32h or shifted to 40oC. Mutant 11-104A4 complemented with TOXOV53 was similarly analyzed at 40oC.

extract_protocol: RNA was extracted from parasites using the RNeasy kit with β-mercaptoethanol and DNase I treatment (Qiagen).   RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Parasites were separated by filtration and collected by centrifugation.

value: tachyzoite

tag: genotype/variation

value: mutant 11-104A4

tag: complementation

value: complemented with cosmid TOXOV53

tag: growth temperature

value: restricted temperature


title: Skin-Psoriasis-45800-LS

value: Lesional skin


title: mutant 11-104A4 at 34oC rep2

description: gene expression data from mutant 11-104A4 grown 32h at permissive temperature

source_name: mutant 11-104A4 grown for 32h at 34oC

tag: developmental stage

value: permissive temperature


title: mutant 11-104A4 at 34oC rep1


title: mutant 11-104A4 at 40oC rep2

description: gene expression data from mutant 11-104A4 grown 32h at resticted temperature

source_name: mutant 11-104A4 grown for 32h at 40oC


title: mutant 11-104A4 at 40oC rep1


title: Replicate Resting Day 7 CD4 T cells restimulated on plate-bound anti-CD3 and CD28 antibodies for 18 hours

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: Cy3-labelled RNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent UCSF custom 8x15K miRNA arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters)

source_name: activated mouse CD4 T cells

label_protocol: Total RNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers protocol

extract_protocol: RNA was extracted using Trizol reagent and standard protocol.

treatment_protocol: CD4 T cells were isolated from mouse spleen and lymph nodes using CD4-coated magnetic beads. Cells were activated on plate-bound anti-CD3 and CD28 antibodies for indicated times.

tag: cell type

value: CD4 T cells

value: spleen/lymph nodes

value: 6-8 weeks


title: mutant 11-104A4 complemented at 40oC rep1


title: CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 65 hours, off stimulation, rested in IL-2 until day 7

value: activated on plate-bound anti-CD3 and CD28 antibodies 65 hours, taken off stimulation and rested in IL-2 containing media until day 7


title: Replicate CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 65 hours


title: Replicate CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 42 hours


title: CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 65 hours


title: Replicate CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 24 hours


title: Tumor-mMSC-BM-p53-/-#1

description:
US82003505_251486833247_S01_GE1_107_Sep09_1_1
Triplicate #1

hyb_protocol: Triplicated samples were hybridized with the Whole Mouse Genome Microarray (G4122F) following the manufacturer's instructions (Agilent Technologies, CA).

source_name: Tumor obtained upon s.c. inoculation of BM-MSCs of p53-/- mice

label_protocol: Total RNA samples were labeled with Cy3 using the Quick-Amp Labeling kit following the manufacturer's instructions (Agilent Technologies, CA).

growth_protocol: WT, p53-/- and p53-/- Rb-/- mMSCs (FVB background) from BM (BM-MSCs) or adipose tissue (ASCs), as well as tumor cell lines derived from p53-/- and p53-/-Rb-/- BM-MSC and ASC cultures, were maintained in complete MSC growth medium (DMEM-Advanced, 10% FBS, 1% Pen/Strep and 1% Glutamax). Only cells between passages 5 and 15 were used for gene expression analysis.

extract_protocol: Triplicate independent cultures of primary (WT, p53-/- and Rb-/-p53-/-) and tumoral (Tp53 and TRbp53) ASC and BM-MSCs were collected during exponential cell growth and stabilized in RNAlater (Ambion, Austin, TX) solution until RNA extraction. RNA was isolated using the Agilent Total RNA Isolation Kit (Agilent Technologies, Palo Alto, CA), and its quality was checked in the Agilent 2100 Bioanalyzer.

tag: strain/background

value: FVB

value: p53 knockout

value: tumor cell line derived from mesenchymal stem cells (MSCs) from bone marrow (BM-MSCs)

tag: tumor

value: tumorigenic


title: CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 24 hours

tag: age


title: Tumor-mASC-p53-/-#2

description:
US82003505_251486833246_S02_GE1_107_Sep09_1_3
Triplicate #2

source_name: Tumor obtained upon s.c. inoculation of ASCs of p53-/- mice

value: tumor cell line derived from mesenchymal stem cells (MSCs) from adipose (ASCs)


title: Resting Day 7 CD4 T cells restimulated on plate-bound anti-CD3 and CD28 antibodies for 18 hours


title: Tumor-mMSC-BM-p53-/-#3

description:
US82003505_251486833247_S01_GE1_107_Sep09_1_3
Triplicate #3


title: mASC-Rb-/-p53-/-#3

description:
US82003505_251486833244_S01_GE1_107_Sep09_1_3
Triplicate #3

source_name: ASCs of Rb-/-p53-/- mice

value: Rb p53 double-knockout

value: mesenchymal stem cells (MSCs) from adipose (ASCs)


title: Tumor-mMSC-BM-p53-/-#2

description:
US82003505_251486833247_S01_GE1_107_Sep09_1_2
Triplicate #2


title: mASC-p53-/-#3

description:
US82003505_251486830012_S01_GE1_107_Sep09_1_3
Triplicate #3

source_name: ASCs of p53-/- mice


title: mASC-Rb-/-p53-/-#1

description:
US82003505_251486829914_S01_GE1_107_Sep09_1_3
Triplicate #1


title: mASC-Rb-/-p53-/-#2

description:
US82003505_251486829915_S01_GE1_107_Sep09_1_3
Triplicate #2


title: Tumor-mASC-Rb-/-p53-/-#1

description:
US82003505_251486829914_S01_GE1_107_Sep09_1_4
Triplicate #1

source_name: Tumor obtained upon s.c. inoculation of ASCs of Rb-/-p53-/- mice


title: Tumor-mASC-p53-/-#1

description:
US82003505_251486833247_S01_GE1_107_Sep09_1_4
Triplicate #1


title: Tumor-mASC-p53-/-#3

description:
US82003505_251486833246_S02_GE1_107_Sep09_1_4
Triplicate #3


title: Tumor-mASC-Rb-/-p53-/-#2

description:
US82003505_251486833244_S01_GE1_107_Sep09_1_4
Triplicate #2


title: Tumor-mASC-Rb-/-p53-/-#3

description:
US82003505_251486829915_S01_GE1_107_Sep09_1_4
Triplicate #3


title: mASC-WT#3

description:
US82003505_251486830012_S01_GE1_107_Sep09_1_1
Triplicate #3

source_name: ASCs of WT mice

value: WT

value: non-tumorigenic


title: mASC-p53-/-#1

description:
US82003505_251486830010_S01_GE1_107_Sep09_1_3
Triplicate #1


title: CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 42 hours


title: mASC-p53-/-#2

description:
US82003505_251486830011_S01_GE1_107_Sep09_1_3
Triplicate #2


title: Replicate CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 12 hours


title: CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 12 hours


title: Replicate CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 6 hours


title: CD4 T cells activated on plate-bound anti-CD3 and CD28 antibodies 6 hours


title: Naïve CD4 T cells from spleen and lymph nodes


title: Replicate naïve CD4 T cells from spleen and lymph nodes


title: mMSC-BM-Rb-/-p53-/-#1

description:
US82003505_251486829914_S01_GE1_107_Sep09_1_2
Triplicate #1

source_name: BM-MSCs of Rb-/-p53-/- mice

value: mesenchymal stem cells (MSCs) from bone marrow (BM-MSCs)


title: mMSC-BM-Rb-/-p53-/-#2

description:
US82003505_251486833244_S01_GE1_107_Sep09_1_2
Triplicate #2


title: AtT20 cell_48hr_control_rep3

city: Sendai

first: Akiko

last: Saito-Hakoda

address: 2-1, Seiryo-machi, Aoba-ku

department: Molecular Endocrinology

institute: Tohoku University Graduate School of Medicine

description: Gene expression  in AtT20 cells (control)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Advanced Flag Improt Setting:
Feature is not positive and significant :Not detected
Feature is not uniform: compromised
Feature is not above background: Not detected
Feature is Saturated : compromised
Feature is a population outliler?compromised
Normalization Options:
Threshold raw signal to 1.0
Normalization algorithm : Percentile Shift
Percentile target: 75(%)
Baseline Options:
Do not perform baseline transformation.

source_name: AtT20 cell, 48hr, control, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using a Low Input Quick-AMP labeling kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: AtT20 cells were grown with Dulbecco's modified Eagle medium (DMEM) supplemented with 10 % fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin. Cells were cultured in a humidified incubator at 37 C with 5 % CO2.

extract_protocol: Total RNAs were isolated using NucleoSpin RNA II (TaKaRa Bio, Ohtsu, Japan) according to the manufacturer’s instructions. Samples were treated with DNase before the experiments in order to remove any contaminant DNA. The RNA was quantified by a Nanodrop 2000 (Thermo Scientific). The quality of the RNA for microarray was evaluated by an Agilent BioAnalyzer 2100. RNA samples with RIN (RNA integrity number) >8.0 and A260/A280 of approximately 2.0 were used for the gene expression analysis.

treatment_protocol: AtT20 cells grown to 50 % confluence in regular medium in 12-multiwell plates were incubated either without or with an RXR agonist HX630 at 10 μM in DMEM supplemented with 1 % stripped FBS media for 48 hr.

value: murine pituitary corticotroph tumor cells (AtT20 cell)

tag: agent

value: control


title: AtT20 cell_48hr_HX630 10μM_rep1

description: Gene expression  in AtT20 cells treated with HX630 at 10 μM for 48 hr

source_name: AtT20 cell, 48hr, HX630 μM, replicate 1


title: AtT20 cell_48hr_HX630 10μM_rep2

source_name: AtT20 cell, 48hr, HX630 μM, replicate 2


title: mASC-WT#2

description:
US82003505_251486830011_S01_GE1_107_Sep09_1_1
Triplicate #2


title: mMSC-BM-p53-/-#2

description:
US82003505_251486833246_S01_GE1_107_Sep09_1_1
Triplicate #2

source_name: BM-MSCs of p53-/- mice


title: mASC-WT#1

description:
US82003505_251486830010_S01_GE1_107_Sep09_1_1
Triplicate #1


title: Tumor-mMSC-BM-Rb-/-p53-/-#1

description:
US82003505_251486833245_S01_GE1_107_Sep09_1_1
Triplicate #1

source_name: Tumor obtained upon s.c. inoculation of BM-MSCs of Rb-/-p53-/- mice


title: AtT20 cell_48hr_HX630 10μM_rep4

source_name: AtT20 cell, 48hr, HX630 μM, replicate 4


title: AtT20 cell_48hr_control_rep1

source_name: AtT20 cell, 48hr, control, replicate 1


title: Tumor-mMSC-BM-Rb-/-p53-/-#2

description:
US82003505_251486833245_S01_GE1_107_Sep09_1_2
Triplicate #2


title: Tumor-mMSC-BM-Rb-/-p53-/-#3

description:
US82003505_251486833245_S01_GE1_107_Sep09_1_3
Triplicate #3


title: mMSC-BM-WT#2

description:
US82003505_251486833244_S01_GE1_107_Sep09_1_1
Triplicate #2

source_name: BM-MSCs of WT mice


title: AtT20 cell_48hr_HX630 10μM_rep3

source_name: AtT20 cell, 48hr, HX630 μM, replicate 3


title: mMSC-BM-Rb-/-p53-/-#3

description:
US82003505_251486829915_S01_GE1_107_Sep09_1_2
Triplicate #3


title: mMSC-BM-p53-/-#3

description:
US82003505_251486833246_S01_GE1_107_Sep09_1_2
Triplicate #3


title: mMSC-BM-p53-/-#1

description:
US82003505_251486833245_S01_GE1_107_Sep09_1_4
Triplicate #1


title: AtT20 cell_48hr_control_rep4

source_name: AtT20 cell, 48hr, control, replicate 4


title: mMSC-BM-WT#3

description:
US82003505_251486829915_S01_GE1_107_Sep09_1_1
Triplicate #3


title: IGROV1- proliferating-rep1

status: Public on Jan 26 2013

city: Melbourne

first: Karen

middle: Elizabeth

last: Sheppard

state: Victoria

address: St Andrews Place

department: Research

country: Australia

institute: Perter MacCallum Cancer Centre

hyb_protocol: Hybridization was for 16hrs andaccording to the standard Affymetrix protocol

scan_protocol: GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using standard Fluidics Protocol ((Fluidics protocol FS450_007)). GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: The data was  gc-rma normalised using the R Bioconductor package affy.

source_name: IGROV1- proliferating

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Ovarian cancer cell lines were plated and harvested when 50-80% confluent.    RNA was extracted and hybridized on Affymetrix microarrays. At least 3 biological repeats were performed for each cell line.

extract_protocol: QIAgen Rneasy was used to extract RNA

value: Exponentially proliferating ovarian cancer cells


title: AtT20 cell_48hr_control_rep2

source_name: AtT20 cell, 48hr, control, replicate 2


title: siControl TNF [MO156_HuST]

city: Rehovot

first: Tomer

last: Cooks

address: 250 Herzel

country: Israel

institute: WIS

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: PANC1, sicontrol, TNFa (0.5 ng/ml, 24 hrs)

label_protocol: RNA ( 10μg) was labeled and hybridized to Affymetrix GeneChip Human Exon 1.0 ST arrays

growth_protocol: PANC1 cells were were maintained at 37°C in a standard 5% CO2 humidified incubator

extract_protocol: RNA was isolated with a NucleoSpin RNA II kit (Macherey-Nagel).

treatment_protocol: 0.5 ng/ ml of TNFa was added and 24 hours later cells were harvested

value: Epithelial cancer cell


title: sip53 TNF [MO161_HuST]

hyb_protocol: According to Affymetrix standard protocols

source_name: PANC1, sip53, TNFa (0.5 ng/ml, 24 hrs)


title: mMSC-BM-WT#1

description:
US82003505_251486829914_S01_GE1_107_Sep09_1_1
Triplicate #1


title: sip53 [MO155_HuST]

source_name: PANC1, sip53, no treatment


title: sip53 TNF [MO157_HuST]


title: siControl [MO158_HuST]

source_name: PANC1, sicontrol, no treatment


title: sip53 [MO159_HuST]


title: VFP-0129_G7_DF [HG-Focus]

city: silver spring

first: peifang

last: sun

address: 503 robert grant ave

institute: Naval Medical Research Center

hyb_protocol: The biotin-labeled and fragmented cRNA was hybridized to the HUGeneFL GeneChip array (Affymetrix) or to the TEST 3 array as described previously. Briefly, a 220-ml hybridization solution consisting of 1 M NaCl, 10 mM Tris (pH 7.6), 0.005% Triton X-100, 50 pM control Oligo B2 (59-bioGTCAAGATGCTACCGTTCAG-39) (Affymetrix), control cRNA cocktail (Bio B [150 pM], Bio C [500 pM], Bio D [2.5 nM], and Cre X [10 nM]; American Type Tissue Collection [Manassas, VA] and Lofstrand Laboratories [Gaithersburg, MD]), herring sperm DNA (0.1 mg/ml), and fragmented labeled sample cRNA (0.05 mg/ml) was heated to 95°C for 35 min, cooled to 40°C, and clarified by centrifugation. Hybridization was at 42°C in a rotisserie hybridization oven (model 320; Affymetrix) at 60 rpm or 16 hr. Following hybridization, the gene chip arrays were washed 10 times at 25°C with 63 SSPE-T buffer (1 M NaCl, 0.006 M EDTA, and 0.06 M Na3PO4) and 0.005% Triton X-100 (pH 7.6), using the automated fluidics station protocol. Gene chip arrays were incubated at 50°C in 0.53 SSPE-T and 0.005% Triton X-100 for 20 min at 60 rpm in the rotisserie oven. Gene chip arrays were stained for 15 min at room temperature and at 60 rpm, with streptavidin–phycoerythrin (Molecular probes, Eugene, OR) stain solution at a final concentration of 10 mg/ml in 63SSPE-T buffer and acetylated bovine serum albumin (1.0 mg/ml; Sigma).

scan_protocol: Gene chip arrays were washed twice at room temperature with 63 SSPE-T buffer. Gene chip arrays were scanned with an HP GeneArray scanner (Hewlett-Packard, Santa Clara, CA) controlled by GeneChip 3.1 software (Affymetrix).

data_processing:
Gene chips with a scaling factor >50 on dChip software (2005 version) were eliminated from further analysis [PMID 12803996 and 20078211]. Gene chips were also examined by QA/QC functions built in the Partek software according to the company’s User’s Manual. Affymetrix CEL files were imported to Partek Genomics Suite Version 6.6 (Partek). Gene chips that failed by QC metrics and appeared as outliers on Principal Component Analysis (PCA) were eliminated for further analysis. CEL files were normalized at the probe level using the Robust Multi-chip Average (RMA) method built into in Partek Genomic Suite software. RMA is a method of normalization of microarray data that leverages gene expression assessments made on Affymetrix gene chips. For each probeset, the technique generates an estimated value for the probe and chip effects that result in the overall pattern of probe set values observed in the data set. RMA is comprised of 3 calculation applications that address background correction, normalization of quantiles, and median polish summarization. Gene expression data were expressed as log2 values. Data sets from the two gene chip platforms were first normalized individually and further analyzed independently.
Differentially expressed genes were analyzed using analysis of variance (ANOVA) built in the Partek software. Multi-way ANOVA was chosen based on the number of factors contributing to chip data variation. The following factors were taken in consideration as variation factors: subject #, scan date (date the gene chip experiment was done and the chip image was taken), infecting serotype, illness day (days of illness when sample was taken), and disease severity (samples associated with DF or DHF category). Genes considered being significant only by chance were defined by the false discovery rate (FDR≥5%) and were excluded from further analysis. In this study, genes with fold change of >2 or <-2 and a p value plus a FDR < 5% were counted to be significant. Heatmap and principal component analysis were used to visualize the most informative trends by showing the predominant gradients in the data set.

label_protocol:
Double-stranded cDNA was synthesized in two steps with the SuperScript Choice system (GIBCO-BRL, Rockville, MD) and the reverse transcription primer T7-(dt)24 (59-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(T)24-39] (Genset, La Jolla, CA). First-strand synthesis was carried out in a 20-ml reaction. Approximately 5 mg of total RNA or 1.0 mg of poly(A) RNA was annealed to 7 mg of T7-(dt)24 primer at 70°C for 10 min. Reverse transcription was carried out at 37°C for 1 hr in a final concentration of 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol(DTT), dATP, dCTP, dGTP, and dTTP (500 mM each), and SuperScript II reverse transcriptase (20,000 to 30,000 U/ml) and the reaction was terminated by placing the tube on ice. Second strand synthesis was carried out in 150 ml incorporating the entire 20-ml first-strand reaction mixture and the 130-ml second strand reaction mixture for a final concentration of 25 mM Tris-HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 10 mM (NH4)2SO4, 0.15 mM b-NAD1, dATP, dCTP, dGTP, and dTTP (250 mM each), 1.2 mM DTT, DNA ligase (65 U/ml), DNA polymerase I (250 U/ml), and RNase H (13 U/ml). The mixture was incubated at 16°C for 2 hr, whereupon 2 ml of T4 DNA polymerase at 5 U/ml was added and the incubation continued at 16°C for 5 min. To terminate the reaction, 10 ml of 0.5 M EDTA was added. The cDNA was purified with phenol–chloroform–isoamyl alcohol (24:23:1) saturated with 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA (Ambion, Austin, TX). The purified cDNA was precipitated with 5 M ammonium acetate and absolute ethanol at 220°C for 20 min. The pellet was resuspended in 7–9 ml of RNase-free water to achieve a final concentration of between 0.25 and 0.65 mg/ml.
Synthesis of biotin-labeled cRNA was carried out by in vitro transcription using the MEGAscript T7 in vitro transcription kit (Ambion). In accordance with the manufacturer’s instructions, 0.4–1.0 mg of double-stranded cDNA was placed into a 20-ml reaction mix, at room temperature, containing Ambion 13 reaction buffer and enzyme mix (proprietary). The labeling mix consisted of 7.5 mM ATP, 7.5 mM GTP, 5.6 mM UTP and 1.9 mM biotinylated UTP (Enzo Diagnostics, Farmingdale, NY), and 5.6 mM CTP and 1.9 mM biotinylated CTP (Enzo Diagnostics). The reaction was incubated at 37°C for 5 hr. The biotin-labeled cRNA was purified with RNeasy spin columns (Qiagen,Valencia, CA) according to the manufacturer’s protocol. The biotin-labeled cRNA was fragmented in a 40-ml reaction mixture containing 40 mM Tris–acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate, incubated at 94°C for 35 min, and then put on ice.

growth_protocol:
Peripheral blood mononuclear cells (PBMCs) were separated using Ficoll-paque according to manufacturer's instruction
Cells were frozen in 10%  dimethyl sulfoxide (DMSO) in -70  ͦC until use.

extract_protocol: The DMSO-cryopreserved cells were resuspended in 1 ml of TRI Reagent (Molecular Research Center, Woodlands, TX). The mixture was vortexed for 15 sec and allowed to stand at room temperature for 10 min. The manufacturer’s instructions for the preparation of total RNA were followed.

tag: patient no.

tag: Stage

tag: infecting serotype

tag: phase

value: Convalenscent

tag: severity

value: DF (dengue fever)

tag: fever days or defervescent (df) days

value: c

tag: scan date


title: VFP-0142_G0_DF [HG-Focus]

value: Early Acute


title: VFP-0145_G5_DF [HG-Focus]

value: Late Acute


title: VFP-0145_G2_DF [HG-Focus]


title: VFP-0117_G7_DF [HG-Focus]


title: VFP-0144_G2_DF [HG-Focus]


title: VFP-0142_G7_DF [HG-Focus]


title: VFP-0145_G7_DF [HG-Focus]


title: VFP-0144_G5_DF [HG-Focus]


title: VFP-0029_G1_DF [HG-Focus]


title: VFP-0113_G7_DF [HG-Focus]


title: VFP-0117_G4_DF [HG-Focus]


title: VFP-0129_G1_DF [HG-Focus]


title: VFP-0129_G4_DF [HG-Focus]


title: VFP-0113_G2_DF [HG-Focus]


title: VFP-0003_G7_DF [HG-Focus]


title: VFP-0144_G7_DF [HG-Focus]


title: VFP-0111_G7_DF [HG-Focus]


title: siControl [MO154_HuST]

tag: cell line


title: VFP-0117_G6_DF [HG-Focus]


title: VFP-0142_G3_DF [HG-Focus]


title: VFP-0111_G6_DF [HG-Focus]


title: VFP-0105_G7_DF [HG-Focus]


title: VFP-0104_G7_DF [HG-Focus]


title: VFP-0104_G6_DF [HG-Focus]


title: VFP-0101_G7_DF [HG-Focus]


title: VFP-0104_G3_DF [HG-Focus]


title: VFP-0105_G4_DF [HG-Focus]


title: VFP-0111_G4_DF [HG-Focus]


title: VFP-0113_G6_DF [HG-Focus]


title: VFP-0105_G3_DF [HG-Focus]


title: VFP-0090_G7_DF [HG-Focus]


title: VFP-0082_G7_DF [HG-Focus]


title: VFP-0083_G2_DF [HG-Focus]


title: VFP-0090_G2_DF [HG-Focus]


title: VFP-0083_G5_DF [HG-Focus]


title: VFP-0090_G5_DF [HG-Focus]


title: VFP-0082_G4_DF [HG-Focus]


title: VFP-0082_G5_DF [HG-Focus]


title: VFP-0087_G3_DF [HG-Focus]


title: VFP-0081_G7_DF [HG-Focus]


title: VFP-0101_G3_DF [HG-Focus]


title: VFP-0085_G5_DF [HG-Focus]


title: VFP-0085_G3_DF [HG-Focus]


title: VFP-0087_G5_DF [HG-Focus]


title: VFP-0087_G7_DF [HG-Focus]


title: VFP-0101_G4_DF [HG-Focus]


title: VFP-0085_G7_DF [HG-Focus]


title: VFP-0075_G7_DF [HG-Focus]


title: VFP-0081_G6_DF [HG-Focus]


title: VFP-0081_G2_DF [HG-Focus]


title: VFP-0075_G5_DF [HG-Focus]


title: VFP-0075_G2_DF [HG-Focus]


title: VFP-0083_G7_DF [HG-Focus]


title: VFP-0070_G7_DF [HG-Focus]


title: VFP-0070_G2_DF [HG-Focus]


title: VFP-0064_G6_DF [HG-Focus]


title: VFP-0070_G4_DF [HG-Focus]


title: VFP-0064_G7_DF [HG-Focus]


title: VFP-0064_G5_DF [HG-Focus]


title: VFP-0064_G4_DF [HG-Focus]


title: VFP-0064_G2_DF [HG-Focus]


title: VFP-0057_G7_DF [HG-Focus]


title: VFP-0057_G3_DF [HG-Focus]


title: VFP-0060_G3_DHF [HG-Focus]

value: DHF (dengue hemorrhagic fever)


title: VFP-0057_G6_DF [HG-Focus]


title: VFP-0064_G3_DF [HG-Focus]


title: VFP-0056_G2_DF [HG-Focus]


title: VFP-0056_G3_DF [HG-Focus]


title: VFP-0056_G4_DF [HG-Focus]


title: VFP-0057_G2_DF [HG-Focus]


title: VFP-0056_G5_DF [HG-Focus]


title: VFP-0060_G4_DHF [HG-Focus]


title: VFP-0057_G1_DF [HG-Focus]


title: VFP-0063_G3_DF [HG-Focus]


title: VFP-0060_G7_DHF [HG-Focus]


title: VFP-0063_G5_DF [HG-Focus]


title: VFP-0057_G4_DF [HG-Focus]


title: VFP-0056_G7_DF [HG-Focus]


title: VFP-0056_G6_DF [HG-Focus]


title: VFP-0063_G7_DF [HG-Focus]


title: VFP-0053_G7_DF [HG-Focus]


title: VFP-0045_G5_DF [HG-Focus]


title: VFP-0045_G7_DF [HG-Focus]


title: VFP-0045_G4_DF [HG-Focus]


title: VFP-0041_G4_DF [HG-Focus]


title: VFP-0047_G7_DHF [HG-Focus]


title: VFP-0053_G3_DF [HG-Focus]


title: VFP-0047_G4_DHF [HG-Focus]


title: VFP-0053_G4_DF [HG-Focus]


title: VFP-0041_G7_DF [HG-Focus]


title: VFP-0041_G5_DF [HG-Focus]


title: VFP-0041_G6(1)_DF [HG-Focus]


title: VFP-0034_G3_DF [HG-Focus]


title: VFP-0037_G7_DF [HG-Focus]


title: VFP-0041_G3_DF [HG-Focus]


title: VFP-0039_G2_DF [HG-Focus]


title: VFP-0039_G5_DF [HG-Focus]


title: VFP-0033_G7_DF [HG-Focus]


title: VFP-0040_G2_DF [HG-Focus]


title: VFP-0039_G7_DF [HG-Focus]


title: VFP-0037_G4_DF [HG-Focus]


title: VFP-0037_G6_DF [HG-Focus]


title: VFP-0040_G4_DF [HG-Focus]


title: VFP-0033_G2_DF [HG-Focus]


title: VFP-0040_G6_DF [HG-Focus]


title: VFP-0034_G6_DF [HG-Focus]


title: VFP-0033_G5_DF [HG-Focus]


title: VFP-0034_G7_DF [HG-Focus]


title: VFP-0041_G6(2)_DF [HG-Focus]


title: VFP-0047_G5_DHF [HG-Focus]


title: VFP-0031_G7_DF [HG-Focus]


title: VFP-0031_G5_DF [HG-Focus]


title: VFP-0030_G7_DF [HG-Focus]


title: VFP-0031_G4_DF [HG-Focus]


title: VFP-0027_G6_DF [HG-Focus]


title: VFP-0029_G7_DF [HG-Focus]


title: VFP-0026_G2_DF [HG-Focus]


title: VFP-0026_G7_DF [HG-Focus]


title: VFP-0029_G6_DF [HG-Focus]


title: VFP-0027_G7_DF [HG-Focus]


title: VFP-0030_G5_DF [HG-Focus]


title: VFP-0026_G6_DF [HG-Focus]


title: VFP-0023_G3_DF [HG-Focus]


title: VFP-0025_G7_DF [HG-Focus]


title: VFP-0023_G7_DF [HG-Focus]


title: VFP-0023_G6_DF [HG-Focus]


title: VFP-0022_G7_DF [HG-Focus]


title: VFP-0022_G4_DF [HG-Focus]


title: VFP-0025_G4_DF [HG-Focus]


title: VFP-0021_G7_DF [HG-Focus]


title: VFP-0022_G6_DF [HG-Focus]


title: VFP-0020_G5_DF [HG-Focus]


title: VFP-0027_G2_DF [HG-Focus]


title: VFP-0017_G3_DF [HG-Focus]


title: VFP-0020_G6_DF [HG-Focus]


title: VFP-0025_G6_DF [HG-Focus]


title: VFP-0020_G4_DF [HG-Focus]


title: VFP-0021_G2_DF [HG-Focus]


title: VFP-0030_G2_DF [HG-Focus]


title: VFP-0017_G7_DF [HG-Focus]


title: VFP-0021_G6_DF [HG-Focus]


title: VFP-0017_G1_DF [HG-Focus]


title: VFP-0015_G7_DF [HG-Focus]


title: VFP-0014_G4_DF [HG-Focus]


title: VFP-0013_G7_DF [HG-Focus]


title: VFP-0013_G5_DF [HG-Focus]


title: VFP-0013_G4_DF [HG-Focus]


title: VFP-0013_G6_DF [HG-Focus]


title: VFP-0015_G4_DF [HG-Focus]


title: VFP-0014_G7_DF [HG-Focus]


title: VFP-0014_G5_DF [HG-Focus]


title: VFP-0013_G2_DF [HG-Focus]


title: VFP-0012_G5_DF [HG-Focus]


title: VFP-0012_G7_DF [HG-Focus]


title: VFP-0013_G3_DF [HG-Focus]


title: VFP-0012_G3_DF [HG-Focus]


title: VFP-0012_G0_DF [HG-Focus]


title: VFP-0008_G6_DF [HG-Focus]


title: VFP-0008_G7_DF [HG-Focus]


title: VFP-0012_G1_DF [HG-Focus]


title: VFP-0011_G4_DHF [HG-Focus]


title: VFP-0011_G6_DHF [HG-Focus]


title: VFP-0012_G2_DF [HG-Focus]


title: VFP-0015_G6_DF [HG-Focus]


title: VFP-0011_G7_DHF [HG-Focus]


title: VFP-0003_G3_DF [HG-Focus]


title: VFP-0008_G5_DF [HG-Focus]


title: VFP-0003_G2_DF [HG-Focus]


title: Hippocampus rep1

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description:
SAMPLE 6
tissue sample taken from adult donor killed in road accident.

hyb_protocol: RNA was quantified using Nanodrop and quality was checked by Agilent Total RNA 6000 chip. 400 ng of total RNA was amplified by Illumina® TotalPrep™ RNA Amplification Kit (Ambion). Amplified RNA was hybridized with HumanHT-12 gene expression array (Illumina)  according to Illumina protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: Data aquisition and analysis were done by GenomeStudio software (Illumina) using gene expression module (GSGX v.1.8).

source_name: hippocampus tissue

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion).

growth_protocol: Cells were grown on DMEM/F12 medium containing 10% fetal calf serum (Invitrogen) at 37°C and 5% CO2. Hippocampus sample was obtained postmortem and stored in RNAlater at -70°C.

extract_protocol: Total  RNA was extracted from samples  with Trizol reagent according to manufacture instruction.

tag: tissue

value: hippocampus


title: NGP127 rep1

description: SAMPLE 6

source_name: cell line

value: neuroblastoma cells


title: HepG2 rep1

description: SAMPLE 4

value: hepatocarcinoma cells


title: A549 rep1

description: SAMPLE 3

value: lung carcinoma cells