title: P38 inhibitor + PAH mixture_4h biological rep 1

city: Aurora

first: Alison

middle: Kendall

last: Bauer

state: CO

address: 12850 E. Montview Blvd.; Rm 3125

department: Environmental and Occupational Health

institute: University of Colorado Denver

hyb_protocol: 3.5ug of fragmented and biotinylated ss-cDNA was hybridizised to the Affymetrix Mouse Gene 2.0 ST arrays in the GeneChip Hybridization Oven 640 with rotation at 60 rpm for 16 hours at 45°C.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: Partek Genomics Suite 6.6 software was used to normalize the data. The CEL file data was RMA normalized and log 2 transformed.

source_name: P38 inhibitor + PAH mixture_4h, C10

label_protocol: 150 ng total RNA was processed according to the UserGuide GeneChip® WT PLUS Reagent Kit Rev3 protocol.  Biotinylated cRNA was prepared using the Affymetrix TdT and biotinylated labeling reagents.

growth_protocol: C10 cells were cultured in CMRL 1066 containing 10% FBS and 1% glutamate in a humidified atmosphere at 37 C, 5% CO2 , and 95% air.  Following confluence, C10s underwent complete serum deprivation for 24 h in normal growth medium. Cells were then treated with PAH or vehicle (DMSO) directly to the plate from a stock solution.

extract_protocol: Total RNA was extracted from C10 cells using  Macherey-Nagel NucleoSpin RNA II kit . Total RNA was quality tested using an Agilent Tapestation Bioanalyzer (Agilent) and only those samples passing with a RIN of 7 or higher were used.

treatment_protocol: C10 cells were treated with a 1:1 ratio PAH mixture (1-methlyanthracene:fluoranthene; 20uM each) for 4 or 8 hr time points.

tag: cell line

value: non-tumorigenic alveolar type II cell line C10

tag: tissue of origin

value: lung

value: P38 inhibitor + PAH mixture

value: 5uM + 40uM

tag: replicate


title: PAH Mixture_4h biological rep 3

status: Public on Jul 11 2017

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: PAH Mixture_4h, C10

tag: agent

value: PAH Mixture

tag: dose

tag: time


title: P38 inhibitor + PAH mixture_4h biological rep 3


title: PAH Mixture_8h biological rep 3

source_name: PAH Mixture_8h, C10


title: P38 inhibitor + PAH mixture_8h biological rep 1

source_name: P38 inhibitor + PAH mixture_8h, C10


title: P38 inhibitor + PAH mixture_8h biological rep 2


title: PAH Mixture_8h biological rep 2


title: PAH Mixture_8h biological rep 1


title: P38 inhibitor + PAH mixture_4h biological rep 2


title: P38 inhibitor + PAH mixture_8h biological rep 3


title: Fluoranthene biological rep 3

source_name: Fluoranthene, C10

value: Fluoranthene


title: PAH Mixture_4h biological rep 1


title: liver biopsy 5

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 5.5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Homo sapiens

source_name: NASH liver baseline

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Clean-up RNA with DNAse treatment were performed with Rneasy microkit Qiagen according to the manufacturer's instructions

tag: sample name

value: patient 5

tag: liver status

value: NASH

tag: type of intervention

value: Diet

value: baseline

tag: age

tag: gender

value: female

tag: scan date

tag: tissue

value: liver biopsy


title: Fluoranthene biological rep 2


title: PAH Mixture_4h biological rep 2


title: DMSO control biological rep 3

source_name: DMSO control, C10

value: DMSO

value: control


title: Liverbiopsy_SIVpositive_2

city: Madison

first: Brian

middle: P

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

description: r2267_Liver_08262014_(RheGene-1_0-st).CEL(normalized)

hyb_protocol: Following fragmentation and labeling 3.0 ug of ss cDNA was hybridized to the Affymetrix  Rhesus Gene 1.0  ST  array  according to manufacturer protocols for each sample.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G with   Autoloader.  Scanner serial #50208130.

data_processing: Raw data for hepatic transcript expression were exported from the Affymetrix platform and analyzed by GeneSpring GX (Agilent). Data were normalized by the Robust Multi-chip Average (RMA) method (molmine.com).  For liver tissue, gene expression was compared between SIV-infected and non-infected macaques using a moderated t-statistic  with > 2-fold difference in expression and P ≤ 0.005 as thresholds for significance. Microarray probe sets that had signal intensities lower than 100 in both SIV and control groups were excluded, resulting in 26,353 data rows.

organism: Macaca mulatta

label_protocol: Biotinylated ss cDNA was prepared from 1.5  ng of total RNA using the Affymetrix GeneChip® WT Pico kit.

growth_protocol: Male Rhesus macaques (Macaca mulatta) were obtained through the Wisconsin National Primate Research Center. All macaques were screened prior to inclusion in the study with a physical exam, CBC, and serum biochemical panel.All animals were fed a fixed formula global primate diet (Teklad, Harlan Laboratories, Madison WI), and no animals had a history of prior TMP/SMX exposure.

extract_protocol: Total RNA was extracted by homogenizing liver samples in TRIzol (Ambion) according to manufacturer’s protocol. RNA pellets were resolubilized in RNase free water and were treated with 2U DNase I (Ambion) at 37°C for 30 min, followed by inactivation with EDTA (5mM) and heating at 75°C for 10 min. RNase inhibitor (Applied Biosystems) was added to a final concentration of 1U/µl. RNA integrity was accessed by Agilent 2100 BioAnalyzer, and quantified by NanoDrop ND-1000 (ThermoFisher). RNA was stored at -80°C until preparation for arrays.

treatment_protocol: Male Rhesus macaques (Macaca mulatta) chronically infected with SIVmac239, along with age and sex-matched uninfected controls, were obtained through the Wisconsin National Primate Research Center. Animals were studied during chronic infection, at least 10 weeks after inoculation.  Infected animals also had a CD4+ count and viral load performed prior to sampling.

value: male

tag: siv status

value: SIV positive

tag: body weight

tag: cd4 count

tag: viral load copies/ml

tag: wbc count

tag: hematocrit

tag: platlets

tag: months post infection

value: liver


title: Liverbiopsy_SIVpositive_1

description: r2353_Liver_08262014_(RheGene-1_0-st).CEL(normalized)


title: Liverbiopsy_SIVpositive_3

description: r98016_Liver_08262014_(RheGene-1_0-st).CEL(normalized)


title: DMSO control biological rep 1

tag: cell line

value: non-tumorigenic alveolar type II cell line C10

tag: tissue of origin

tag: agent

tag: dose

tag: replicate


title: DMSO control biological rep 2

value: lung

tag: time


title: Liverbiopsy_SIVnegative_1

description: r2252_Liver_08262014_(RheGene-1_0-st).CEL(normalized)

tag: gender

value: SIV negative

tag: age


title: Striatum Nestin THAP1 KO (7 STR KO)

status: Public on Jul 10 2017

city: Bethesda

first: Ravindran

last: Kumaran

state: MD

address: 35 Lincoln Drive

institute: NIH

description: 7 STR KO

hyb_protocol: Standard Illumina hybridizaion protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadStudio software suite: Cubic spline normalization with background subtraction on a per brain region basis to generate expression values for each gene.

source_name: Striatum Nestin THAP1 KO

label_protocol: RNA was amplified using the Illumina TotalPrep RNA amplification kit, resulting in biotin labeled cRNA.

extract_protocol: Frozen tissue were homogenized in TriZol reagent and RNA was extracted according to the Invitrogen TriZol protocol.

tag: tissue

value: Brain

tag: tissue region

value: Striatum

tag: genotype/variation

value: THAP1 KO


title: Fluoranthene biological rep 1

value: Fluoranthene


title: Liverbiopsy_SIVnegative_3

description: r5090_Liver_08262014_(RheGene-1_0-st).CEL(normalized)

tag: siv status

tag: body weight


title: Liverbiopsy_SIVnegative_2

description: r99070_Liver_08262014_(RheGene-1_0-st).CEL(normalized)

tag: wbc count


title: Striatum Nestin THAP1 KO (8 STR KO)

description: 8 STR KO


title: Striatum Nestin THAP1 KO (5 STR KO)

description: 5 STR KO


title: Striatum Nestin THAP1 KO (6 STR KO)

description: 6 STR KO


title: Striatum Nestin Con (1 STR Con)

description: 1 STR Con

source_name: Striatum Nestin Con


title: Striatum Nestin Con (3 STR Con)

description: 3 STR Con


title: Striatum Nestin Con (4 STR Con)

description: 4 STR Con


title: Cortex Nestin THAP1 KO (16 CTX KO)

description: 16 CTX KO

source_name: Cortex Nestin THAP1 KO

value: Cortex


title: Cortex Nestin THAP1 KO (14 CTX KO)

description: 14 CTX KO


title: Striatum Nestin Con (2 STR Con)

description: 2 STR Con


title: Cortex Nestin THAP1 KO (13 CTX KO)

description: 13 CTX KO


title: Cortex Nestin THAP1 KO (15 CTX KO)

description: 15 CTX KO


title: liver biopsy 36 (66)

source_name: no NASH liver follow-up

tag: sample name

value: patient 36 (66)

tag: liver status

value: no NASH

tag: type of intervention

value: Diet

value: follow-up

tag: scan date


title: Cortex Nestin Con (11 CTX Con)

description: 11 CTX Con

source_name: Cortex Nestin Con


title: Cortex Nestin Con (12 CTX Con)

description: 12 CTX Con


title: Cortex Nestin Con (9 CTX Con)

description: 9 CTX Con


title: Cerebellum Nestin THAP1 KO (23 CB KO)

description: 23 CB KO

source_name: Cerebellum Nestin THAP1 KO

value: Cerebellum


title: Cerebellum Nestin Con (19 CB Con)

description: 19 CB Con

source_name: Cerebellum Nestin Con

value: control


title: Cerebellum Nestin THAP1 KO (22 CB KO)

description: 22 CB KO


title: Exposed replicate 2

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Gene expression data from hippocampus Exp2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with R bioconductor. MAS5.0 was used for background correction and samples were median normalized. Welch's t-test was used in order to identify differentially expressed genes between the exposed and sham group.

source_name: exposed to mobile phone radiation.

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

growth_protocol: C57BL/6 adult mice were exposed to mobile phone radiation for 2 hours and hippocampal regions were extracted 6 hours post exposure.

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

treatment_protocol: C57BL/6 adult mice were exposed to GSM 1800 MHz at an average electric field intensity of 11 Volt per meter.

value: Hippocampus

tag: strain

value: adult


title: Cortex Nestin Con (10 CTX Con)

description: 10 CTX Con


title: Cerebellum Nestin Con (18 CB Con)

description: 18 CB Con


title: Cerebellum Nestin Con (20 CB Con)

description: 20 CB Con


title: Cerebellum Nestin THAP1 KO (21 CB KO)

description: 21 CB KO


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient206 (miRNA)

city: Milan

first: Luca

last: Roz

address: Via Venezian 1

department: Experimental Oncology and Molecular Medicine

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description:
miRNA expression of lung fibroblasts primary culture
253575810013_1-4

hyb_protocol: Hybridization for 20 h at 55°C.

scan_protocol: Scanned at 2 mm resolution using an Agilent DNA microarray scanner. The resulting images were analyzed using Agilent's Feature Extraction software v10.7.

data_processing: One to 4 different probes can target each miRNA and each probe is spotted 10 to 40 times on the array. The total gene signal for each miRNA was obtained by summing the probe signals derived with the Agilent Feature Extraction software. Each probe was defined as detected if its value is greater than 3 times its standard error, and each miRNA was defined as detected if at least one of the probes was detected. Only human (“hsa”) miRNAs  were selected for downstream analyses. Data were log2 transformed and quantile normalized.

label_protocol: One μg of RNA was labeled and processed according to the manufacturer’s recommended protocol.

growth_protocol: Clinical specimens were obtained from a consecutive series of consenting patients. The protocol was approved by the Internal Review and the Ethics Boards of the Fondazione IRCCS, Istituto Nazionale dei Tumori (Milan, Italy). Tissue fragments from  lung tumors (or normal lungs) were finely minced using a scalpel blade, enzymatically digested for 1h at 37 °C with collagenase IV (5mg/ml) in serum-free DMEM F12 and filtered through a 100µm cell strainer. Red blood cells were removed using 1X Lysing Buffer. Primary fibroblasts cell lines were obtained from dissociated tissues by culturing suspensions in RPMI medium with 10% serum.

extract_protocol: Total RNA from cells was extracted using TRIzol® reagent (Life Technologies) according to the manufacturer’s instructions.

tag: individual

value: Patient 206

tag: culture

value: primary culture of patient-derived lung fibroblasts

tag: culture generated from

value: Male

tag: smoking  (1=current, 0=never, former >24 months)

tag: copd (gold score)


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient226 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810013_1-3

value: Patient 226

tag: gender

value: Female

tag: age


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient206 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810013_2-1

value: Cancer Tissue


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient206 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810013_2-2

value: Normal Tissue_Proximal To Cancer Lesion


title: Sham exposed 2

description: Gene expression data from hippocampus SE2

source_name: sham-exposed to mobile phone radiation.

tag: tissue


title: Cerebellum Nestin Con (17 CB Con)

description: 17 CB Con

value: Brain

tag: tissue region

tag: genotype/variation


title: Cerebellum Nestin THAP1 KO (24 CB KO)

description: 24 CB KO

value: THAP1 KO


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient226 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810013_1-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient226 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810013_1-2


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient221 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_2-2

value: Patient 221


title: Sham exposed 1

description: Gene expression data from hippocampus SE1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient228 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_1-4

value: Patient 228


title: Exposed replicate 1

description: Gene expression data from hippocampus Exp1


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient167 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_1-2

value: Patient 167


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Sample 1_Patient208 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_2-3

value: Patient 208


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient208 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_2-4


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient167 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_1-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient194 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_1-4

value: Patient 194


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient221 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_2-3


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient153 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_1-3

value: Patient 153


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient193 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_2-3

value: Patient 193


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient168 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_1-2

value: Patient 168


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient176 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_1-1

value: Patient 176


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient193 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_2-4

value: primary culture of patient-derived lung fibroblasts


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient228 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_2-1

value: Male


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient193 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_2-2


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient167 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810011_1-3


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient176 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_1-3


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient176 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_1-4


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient208 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_2-2


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Sample 2_Patient208 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810010_2-1


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient095 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_2-3

value: Patient 095


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient095 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_2-4

value: Female


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient201 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_1-1

value: Patient 201


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient203 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_2-2

value: Patient 203


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient201 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_1-2

value: Cancer Tissue


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient190 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_1-2

value: Patient 190


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient163 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_1-4

value: Patient 163


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient158 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_1-3

value: Patient 158


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient201 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810009_2-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient203 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_2-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient220 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_2-4

value: Patient 220


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient190 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810008_1-1


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient220 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_2-3


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient160 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_2-2

value: Patient 160

value: Normal Tissue_Proximal To Cancer Lesion


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient160 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_2-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient205 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_1-3

value: Patient 205


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient160 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_1-4


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient205 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_1-2


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient205 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810007_1-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient200 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_2-3

value: Patient 200


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient109 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_2-4

value: Patient 109


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient107 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_1-4

value: Patient 107


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient109 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_2-2

value: primary culture of patient-derived lung fibroblasts


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient107 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_1-2


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient200 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_1-3

value: Male


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient177 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_2-3

value: Patient 177


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient177 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_1-1

value: Female


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient154 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_2-4

value: Patient 154


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient166 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_1-3

value: Patient 166


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient154 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_2-2


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient158 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_1-2


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Proximal To Cancer Lesion_Patient166 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_1-1


title: Lung Fibroblasts_Primary Culture_Normal Tissue_Distant From Cancer Lesion_Patient200 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810005_2-1


title: Lung Fibroblasts_Primary Culture_Cancer Tissue_Patient166 (miRNA)

description:
miRNA expression of lung fibroblasts primary culture
253575810004_2-1

value: Cancer Tissue


title: Plasmid ID: pTH11173 - Assay ID: 11379 (ME layout)

type: protein

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the higher-quality scan was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: The 8-mer Z-scores were calculated as the average of normalized intensities of probes (i.e. probe Z-scores) that contained the 8-mer.

molecule: protein

organism: Schizophyllum commune

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

tag: plasmid

tag: expressed protein

value: GST-tagged C2H2 zinc finger transcription factor

tag: uniprot id

tag: array design

value: ME layout


title: Plasmid ID: pTH11153 - Assay ID: 11404 (ME layout)

label_protocol: Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.


title: Plasmid ID: pTH11153 - Assay ID: 11326 (HK layout)

value: HK layout


title: Plasmid ID: pTH11164 - Assay ID: 11386 (HK layout)

organism: Batrachochytrium dendrobatidis


title: Plasmid ID: pTH11165 - Assay ID: 11371 (ME layout)

organism: Physcomitrium patens


title: Plasmid ID: pTH11159 - Assay ID: 11381 (HK layout)


title: Plasmid ID: pTH11160 - Assay ID: 11382 (HK layout)

organism: Arabidopsis thaliana


title: Plasmid ID: pTH11165 - Assay ID: 11387 (HK layout)


title: Plasmid ID: pTH11173 - Assay ID: 11395 (HK layout)


title: Plasmid ID: pTH11160 - Assay ID: 11366 (ME layout)


title: Plasmid ID: pTH11151 - Assay ID: 11402 (ME layout)

organism: Histoplasma capsulatum


title: Plasmid ID: pTH11164 - Assay ID: 11370 (ME layout)


title: Plasmid ID: pTH11152 - Assay ID: 11403 (ME layout)


title: Plasmid ID: pTH11171 - Assay ID: 11377 (ME layout)


title: Plasmid ID: pTH11150 - Assay ID: 11323 (HK layout)


title: Plasmid ID: pTH11151 - Assay ID: 11324 (HK layout)


title: Plasmid ID: pTH11152 - Assay ID: 11325 (HK layout)


title: Plasmid ID: pTH11149 - Assay ID: 11400 (ME layout)


title: Plasmid ID: pTH11159 - Assay ID: 11365 (ME layout)


title: Plasmid ID: pTH11149 - Assay ID: 11322 (HK layout)


title: Plasmid ID: pTH11141 - Assay ID: 11314 (HK layout)


title: Plasmid ID: pTH10262 - Assay ID: 11213 (HK layout)

organism: Toxoplasma gondii


title: Plasmid ID: pTH11141 - Assay ID: 11298 (ME layout)


title: Plasmid ID: pTH10263 - Assay ID: 11214 (HK layout)

organism: Dictyostelium discoideum


title: Plasmid ID: pTH11171 - Assay ID: 11393 (HK layout)


title: Plasmid ID: pTH11150 - Assay ID: 11401 (ME layout)


title: Plasmid ID: pTH11139 - Assay ID: 11312 (HK layout)


title: Plasmid ID: pTH11139 - Assay ID: 11296 (ME layout)


title: Plasmid ID: pTH10259 - Assay ID: 11210 (HK layout)

organism: Schizosaccharomyces pombe


title: Plasmid ID: pTH10262 - Assay ID: 11197 (ME layout)


title: Plasmid ID: pTH10257 - Assay ID: 11192 (ME layout)


title: Plasmid ID: pTH10257 - Assay ID: 11208 (HK layout)


title: Plasmid ID: pTH10252 - Assay ID: 11188 (ME layout)

organism: Neurospora crassa


title: Plasmid ID: pTH10259 - Assay ID: 11194 (ME layout)


title: Plasmid ID: pTH10263 - Assay ID: 11198 (ME layout)


title: Plasmid ID: pTH10255 - Assay ID: 11190 (ME layout)


title: Plasmid ID: pTH10256 - Assay ID: 11191 (ME layout)


title: Plasmid ID: pTH10252 - Assay ID: 11204 (HK layout)


title: Plasmid ID: pTH10255 - Assay ID: 11206 (HK layout)


title: Plasmid ID: pTH10242 - Assay ID: 11125 (ME layout)


title: Plasmid ID: pTH10242 - Assay ID: 11141 (HK layout)


title: Plasmid ID: pTH10256 - Assay ID: 11207 (HK layout)


title: Plasmid ID: pTH10237 - Assay ID: 11017 (HK layout)

organism: Puccinia graminis


title: Plasmid ID: pTH10245 - Assay ID: 11235 (ME layout)


title: Plasmid ID: pTH10239 - Assay ID: 11019 (HK layout)


title: Plasmid ID: pTH10244 - Assay ID: 11149 (HK layout)


title: Plasmid ID: pTH10238 - Assay ID: 11018 (HK layout)


title: Plasmid ID: pTH10237 - Assay ID: 11001 (ME layout)


title: Plasmid ID: pTH10245 - Assay ID: 11251 (HK layout)


title: Plasmid ID: pTH10239 - Assay ID: 11003 (ME layout)


title: Plasmid ID: pTH10244 - Assay ID: 11133 (ME layout)


title: Plasmid ID: pTH10236 - Assay ID: 11016 (HK layout)


title: Plasmid ID: pTH10238 - Assay ID: 11002 (ME layout)


title: Plasmid ID: pTH10236 - Assay ID: 11000 (ME layout)


title: Plasmid ID: pTH10235 - Assay ID: 10999 (ME layout)


title: Plasmid ID: pTH10234 - Assay ID: 10998 (ME layout)


title: Plasmid ID: pTH10235 - Assay ID: 11015 (HK layout)


title: Plasmid ID: pTH10233 - Assay ID: 10991 (HK layout)


title: Plasmid ID: pTH10233 - Assay ID: 11007 (ME layout)


title: Plasmid ID: pTH10232 - Assay ID: 11006 (ME layout)


title: Plasmid ID: pTH10234 - Assay ID: 11014 (HK layout)


title: Plasmid ID: pTH10231 - Assay ID: 10750 (HK layout)

organism: Rhizopus delemar


title: Plasmid ID: pTH10230 - Assay ID: 10749 (HK layout)


title: Plasmid ID: pTH10229 - Assay ID: 10748 (HK layout)


title: Plasmid ID: pTH10228 - Assay ID: 10747 (HK layout)


title: Plasmid ID: pTH10231 - Assay ID: 10734 (ME layout)


title: Plasmid ID: pTH10227 - Assay ID: 10746 (HK layout)


title: Plasmid ID: pTH10225 - Assay ID: 10744 (HK layout)


title: Plasmid ID: pTH10230 - Assay ID: 10733 (ME layout)


title: Plasmid ID: pTH10229 - Assay ID: 10732 (ME layout)


title: Plasmid ID: pTH10217 - Assay ID: 10736 (HK layout)


title: Plasmid ID: pTH10220 - Assay ID: 10739 (HK layout)


title: Plasmid ID: pTH10232 - Assay ID: 10990 (HK layout)


title: Plasmid ID: pTH10221 - Assay ID: 10740 (HK layout)


title: Plasmid ID: pTH10223 - Assay ID: 10742 (HK layout)


title: Plasmid ID: pTH10225 - Assay ID: 10728 (ME layout)


title: Plasmid ID: pTH10227 - Assay ID: 10730 (ME layout)


title: Plasmid ID: pTH10224 - Assay ID: 10743 (HK layout)


title: Plasmid ID: pTH10221 - Assay ID: 10724 (ME layout)


title: Plasmid ID: pTH10228 - Assay ID: 10731 (ME layout)


title: Plasmid ID: pTH10220 - Assay ID: 10723 (ME layout)


title: Plasmid ID: pTH10223 - Assay ID: 10726 (ME layout)


title: Plasmid ID: pTH10224 - Assay ID: 10727 (ME layout)


title: Plasmid ID: pTH10219 - Assay ID: 10738 (HK layout)


title: Plasmid ID: pTH10219 - Assay ID: 10722 (ME layout)


city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

description:
Monocyte-derived DC vaccine #4 of patient 220 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124625

hyb_protocol: Samples were hybridized according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used with dafault settings for processed signals. Data were first Lowess normalized with BRB. Genes not passing quality criteria (flag, signal intensity, presence across the dataset) were filtered. Batch effect due to different hybridizations spanning across 2 years was removed with Partek.

source_name: monocyte derived DC, test RNA

label_protocol: Test RNA and Universal Reference RNA (Stratagene) were amplified and labeled according to the Two-color Microarray-based Gene Expression Analysis (quick Amp Labeling) protocol from Agilent Version 5.7

growth_protocol: Cryopreserved elutriated Monocytes were thawed and cultured with GMCSF (1000 IU/ml) and IL4 (1000 IU/ml) for 3 days to obtain immature dendritic cells. On day 2 KLH was added to culture, while on day 3 to induce maturation LPS (30 ng/ml) and IFNg (1000 IU/ml) were added to the culture. 24 h later cells were harvested and pulsed for 2 h with TARP peptides. 20 million of cells were infused to patient whereas remaing cells were used for RNA isolation

extract_protocol: Total RNA extracted using miRNeasy kit from Qiagen

tag: patient #

tag: vaccine lot #

tag: hybridization batch

tag: cell type

value: monocyte derived DC

source_name: Universal Human Reference RNA

tag: reference source

value: Stratagene Catalog #740000


title: Plasmid ID: pTH10217 - Assay ID: 10720 (ME layout)


description:
Monocyte-derived DC vaccine #5 of patient 218 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124623


description:
Monocyte-derived DC vaccine #2 of patient 220 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124624


description:
Monocyte-derived DC vaccine #2 of patient 217 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124619


description:
Monocyte-derived DC vaccine #4 of patient 217 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124620


description:
Monocyte-derived DC vaccine #1 of patient 218 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124621


description:
Monocyte-derived DC vaccine #3 of patient 218 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124622


description:
Monocyte-derived DC vaccine #1 of patient 220 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124604


description:
Monocyte-derived DC vaccine #3 of patient 220 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124605


description:
Monocyte-derived DC vaccine #1 of patient 217 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124599


description:
Monocyte-derived DC vaccine #4 of patient 215 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124615


description:
Monocyte-derived DC vaccine #5 of patient 220 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124606


description:
Monocyte-derived DC vaccine #2 of patient 218 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124602


description:
Monocyte-derived DC vaccine #3 of patient 215 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124595


description:
Monocyte-derived DC vaccine #4 of patient 218 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124603


description:
Monocyte-derived DC vaccine #1 of patient 215 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124594


description:
Monocyte-derived DC vaccine #4 of patient 216 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124618


description:
Monocyte-derived DC vaccine #3 of patient 205 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117108


description:
Monocyte-derived DC vaccine #1 of patient 212 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117109


title: Monocyte-derived DC vaccine #2 of patient 216 (124616)

description:
Monocyte-derived DC vaccine #2 of patient 216 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124616


description:
Monocyte-derived DC vaccine #5 of patient 215 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124596


description:
Monocyte-derived DC vaccine #3 of patient 217 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124600


description:
Monocyte-derived DC vaccine #3 of patient 216 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124598


title: Monocyte-derived DC vaccine #2 of patient 216 (124617)

description:
Monocyte-derived DC vaccine #2 of patient 216 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124617


description:
Monocyte-derived DC vaccine #1 of patient 216 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124597


description:
Monocyte-derived DC vaccine #4 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117107


description:
Monocyte-derived DC vaccine #7 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117105


description:
Monocyte-derived DC vaccine #2 of patient 214 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117106


description:
Monocyte-derived DC vaccine #2 of patient 210 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117110


description:
Monocyte-derived DC vaccine #5 of patient 217 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124601


description:
Monocyte-derived DC vaccine #2 of patient 215 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
124614


description:
Monocyte-derived DC vaccine #4 of patient 207 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117104


description:
Monocyte-derived DC vaccine #1 of patient 211 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117097


description:
Monocyte-derived DC vaccine #2 of patient 212 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117090


description:
Monocyte-derived DC vaccine #4 of patient 201 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117098


description:
Monocyte-derived DC vaccine #5 of patient 204 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117101


description:
Monocyte-derived DC vaccine #4 of patient 211 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117102


description:
Monocyte-derived DC vaccine #4 of patient 214 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117089


description:
Monocyte-derived DC vaccine #5 of patient 203 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117081


description:
Monocyte-derived DC vaccine #2 of patient 201 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117096


description:
Monocyte-derived DC vaccine #6 of patient 206 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117088


description:
Monocyte-derived DC vaccine #4 of patient 204 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117092


description:
Monocyte-derived DC vaccine #1 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117100


description:
Monocyte-derived DC vaccine #3 of patient 203 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117084


description:
Monocyte-derived DC vaccine #6 of patient 205 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117087


description:
Monocyte-derived DC vaccine #2 of patient 202 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117076


description:
Monocyte-derived DC vaccine #1 of patient 205 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117083


description:
Monocyte-derived DC vaccine #3 of patient 201 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117075


description:
Monocyte-derived DC vaccine #5 of patient 211 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117085


description:
Monocyte-derived DC vaccine #5 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117070


description:
Monocyte-derived DC vaccine #2 of patient 204 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117095


description:
Monocyte-derived DC vaccine #2 of patient 205 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117073


description:
Monocyte-derived DC vaccine #6 of patient 203 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117067


description:
Monocyte-derived DC vaccine #2 of patient 206 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117079


description:
Monocyte-derived DC vaccine #3 of patient 214 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117066


description:
Monocyte-derived DC vaccine #1 of patient 204 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117099


description:
Monocyte-derived DC vaccine #2 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117077


description:
Monocyte-derived DC vaccine #1 of patient 203 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117082


description:
Monocyte-derived DC vaccine #2 of patient 203 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117069


description:
Monocyte-derived DC vaccine #1 of patient 207 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117068


description:
Monocyte-derived DC vaccine #5 of patient 205 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117080


description:
Monocyte-derived DC vaccine #2 of patient 207 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116981


description:
Monocyte-derived DC vaccine #4 of patient 203 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116985


description:
Monocyte-derived DC vaccine #5 of patient 214 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116976


description:
Monocyte-derived DC vaccine #4 of patient 212 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116983


description:
Monocyte-derived DC vaccine #5 of patient 210 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116978


description:
Monocyte-derived DC vaccine #3 of patient 206 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117074


description:
Monocyte-derived DC vaccine #3 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117064


description:
Monocyte-derived DC vaccine #1 of patient 202 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116984


description:
Monocyte-derived DC vaccine #1 of patient 214 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116968


description:
Monocyte-derived DC vaccine #5 of patient 201 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116965


description:
Monocyte-derived DC vaccine #6 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116967


description:
Monocyte-derived DC vaccine #4 of patient 210 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117063


description:
Monocyte-derived DC vaccine #3 of patient 207 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116960


description:
Monocyte-derived DC vaccine #1 of patient 210 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116961


description:
Monocyte-derived DC vaccine #6 of patient 201 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116969


description:
Monocyte-derived DC vaccine #4 of patient 202 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116953


description:
Monocyte-derived DC vaccine #2 of patient 208 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116957


description:
Monocyte-derived DC vaccine #4 of patient 206 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116970


description:
Monocyte-derived DC vaccine #5 of patient 206 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116949


description:
Monocyte-derived DC vaccine #1 of patient 206 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116964


description:
Monocyte-derived DC vaccine #5 of patient 207 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
117065


description:
Monocyte-derived DC vaccine #1 of patient 201 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116948


description:
Monocyte-derived DC vaccine #3 of patient 210 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116956


description:
Monocyte-derived DC vaccine #3 of patient 204 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116959


description:
Monocyte-derived DC vaccine #3 of patient 202 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116954


description:
Monocyte-derived DC vaccine #8 of patient 209 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116962


description:
Monocyte-derived DC vaccine #3 of patient 211 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116947


description:
Monocyte-derived DC vaccine #3 of patient 212 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116944


description:
Monocyte-derived DC vaccine #2 of patient 211 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116943


title: F86

city: Mexico

first: Blanca

middle: E

last: Castro

state: Mexico City

address: Cuauhtemoc 330

country: Mexico

institute: CMNSXXI

hyb_protocol: The sample with hybridization cocktail was incubated at 99°C and 45°C for 5 minutes respectively.  Finally a total of 130ul of sample labeled and prepared were injected in a new GeneChip® miRNA 4.0 array and hybridized at 48°C for 16-18 hours.

scan_protocol: Every sample was washed in the GeneChip® Fluidics Station 450 following FS450-0002 protocol and array fluorescence was measured by the GeneChip ® Scanner 3000 7G.

data_processing: Raw data from .CEL files were analyzed using Affymetrix® Expression ConsoleTM software to normalize fluorescence signals and to obtain the quality control data. To adjust background signal a Robust Multichip Analysis (RMA) was carried out and once completed we observed that the values of spike_in-control probes comply the quality standards established by the manufacturer.

source_name: Retinoblastoma

label_protocol: Total RNA was tailing and biotinylated using Affymetrix Flash-tag biotin microarray (Affymetrtix, USA) for miRNAs and spike-in controls probes were added. Poli-A tailing  on end 3’ was carried out at 37°C in 15ul reaction volume contained 1x reaction buffer, MnCl2 25mM, 1ul of 1:50 ATP mix and 1ul of phosphatidic acid phosphatase (PAP) polymerase. The biotin was added to this poli-A tails at 25°C adding 4ul of ligation mix containing biotin and 2ul of T4 DNA ligase making a total of 21ul then 2.5ul of stop solution was added. An Enzyme Linked Oligosorbent (ELOSA) was performed to confirm previous biotin labeling process. 2ul from sample were used to detect spike control oligos by colorimetric reaction revealed with HRP and measured UV absorbance. Every sample which absorbance is 1.5nm more than negative control is considered as successfully labeled and tailed.

growth_protocol: 12 Rb from enucleated patients with no chemotherapy history were maintained in BSF 12% complemented RPMI medium for a week and collected in lysis buffered reagent. All samples came from patients of Children Hospital of Mexico “Federico Gomez” and Pediatric Hospital “Silvestre Frenk Freund” of Mexican Social Security Institute in Mexico City.

extract_protocol: Total RNA was extracter from each sample using TRIzol reagent and was suspended in nuclease free water and stored at -70°C.

tag: disease state

value: Retinoblastoma

tag: Sex

value: female

tag: type

value: unilateral


description:
Monocyte-derived DC vaccine #6 of patient 204 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116946


title: F77

value: male

value: bilateral


title: F78


title: F66


description:
Monocyte-derived DC vaccine #4 of patient 205 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116945


title: F85


title: F73


title: F56


title: F122


title: F54


title: Day 5 effector P14 polysome RNA replicate 2

city: Atlanta

first: Koichi

last: Araki

state: GA

address: 1510 Clifton Rd

department: Department of Microbiology and Immunology

institute: Emory University School of Medicine

hyb_protocol: Hybridization was performed at Dana-Farber Cancer Institute.

scan_protocol: Scan was performed at Dana-Farber Cancer Institute.

data_processing: Data were preprocessed and normalized with robust multichip averaging in GenePattern (Broad Institute).

source_name: Day 5 effector P14 polysome RNA

label_protocol: RNA was ampified and labeled by Ovation Pico WTA System V2 (Nugen) according to the manufacturer's instructions.

growth_protocol: P14 transgenic CD8 T cells specific for GP33 epitope of lymphocytic choriomeningitis virus (LCMV) were adoptively transferred into B6 mice, followed by LCMV Armstrong infection. Day 5 effector, day 8 effector, and memory (day 40~60 post infection) P14 CD8 T cells were purified from the LCMV-infected mice. Naive P14 CD8 T cells were directly purified from P14 transgenic mice. Total and polysome-associated (3 or more ribosomes) mRNAs were isolated from these purified P14 cells, and microarray analyses were performed.

extract_protocol: Trizol extraction of total RNA and polysome-associated RNA was performed according to the manufacturer's instructions. RNA was treated by DNase, followed by column-purification of RNA.

tag: gender

tag: host strain background

value: Spleen

value: effector P14 CD8 T cells at day 5 after LCMV infection (clonal expansion phase)

tag: molecule subtype

value: Polysome-associated RNA


title: F189


title: Day 8 effector P14 polysome RNA replicate 1

source_name: Day 8 effector P14 polysome RNA

tag: tissue

value: effector P14 CD8 T cells at day 8 after LCMV infection (peak of CD8 T cell response)


title: Day 8 effector P14 polysome RNA replicate 3


title: F50


title: Day 8 effector P14 polysome RNA replicate 2


title: Naive P14 polysome RNA replicate 2

source_name: Naive P14 polysome RNA

tag: strain

value: P14 transgenic mice

value: naive P14 CD8 T cells


title: Day 5 effector P14 total RNA replicate 3

source_name: Day 5 effector P14 total RNA

value: Total RNA


description:
Monocyte-derived DC vaccine #1 of patient 208 cohybridized with Universal Human Reference RNA on Agilent Platform GPL4133
116951


title: Day 8 effector P14 total RNA replicate 3

source_name: Day 8 effector P14 total RNA


title: F-1


title: Day 5 effector P14 total RNA replicate 2


title: Naive P14 polysome RNA replicate 3


title: Day 5 effector P14 polysome RNA replicate 3


title: Day 8 effector P14 total RNA replicate 2


title: Day 8 effector P14 total RNA replicate 1


title: Day 5 effector P14 polysome RNA replicate 1


title: Naive P14 total RNA replicate 2

source_name: Naive P14 total RNA


title: Day 5 effector P14 total RNA replicate 1


title: Naive P14 total RNA replicate 3


title: Naive P14 total RNA replicate 1


title: Naive P14 polysome RNA replicate 1


title: WRΔA26 infected BMDM at 2hr-replicate 3

status: Public on Jul 09 2017

city: Taipei

first: Wen

last: Chang

address: 128 Sec 2 Academia Rd, Nankang

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WRΔA26 2hr-rep3

hyb_protocol: Agilent Gene Expression Hybridization Kits and wash kit were  used for hybridization according to the manufacturer’s instruction.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using the AgilentG3_GX_2 Color scan protocol for 8x60K high densitiy Micorarray Formats (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Red and Green PMT is set to 100%, the resulting file is a 20 bit tiff image).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used to quanitify the image intensity , background subtraction and LOWESS normalization (Gene spring v. 14.5).

source_name: WRΔA26 infected D8-BMDM cells

label_protocol: 10 µg of total RNA were primed with  anchored Oligo-(dT) at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase, and 10mM dNTP including amino-allyl-dUTP. (SuperScript Indirect cDNA Labeling System, Invitrogen).  After reaction, add 10μL 0.5M EDTA and 10μL 1N NaOH, incubate at 70℃ for 15 min to hydrolysis RNA followed by neutralization with addition of 25μL 1M HEPES pH 7.4. Then purified using QIAquick(Qaigen) kit, aa-cDNA was eluted from column with 60 μl 0.1M NaHCO3 pH 9.0.  The elute was added into a tube containing  Alexa 555 or Alexa 647 NHS ester. Coupled the dye at room temperature in the dark for 60-90 min.  The reaction was stopped by adding 15 μl of 4 M NH2OH-HCl in the dark for 15 min. Labeled cDNA was purified through QIAquick column.

growth_protocol: Bone marrow cells were flushed out of mouse femurs and tibias of C57BL/6 mice of 6-10 weeks old, treated with ACK lysis buffer (150mM NH4C ,10mM KHCO3 and 0.1mM EDTA) to remove red blood cells. These cells were then plated in 100mm non-TC petri dishes containing Dubelcco’s modified Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 1% Penicillin and Streptomycin (Gibco), 2mM L-glutamine (Gibco), 1mM sodium pyruvate (Sigma) and 10% L929-condition medium. Cell cultures were replenished with fresh medium every three days and BMDM purity was determined at day 7.

extract_protocol: Infected and Mock-treated BMDM cells were lysed in 4M-guanidine thiocynate and subjected to high-speed centrifugation in a SW60 Ti rotor (Beckman) at 37,000rpm (14,000 xg) through a dense cushion of cesium chloride (5.7M) for 12hrs at 25°C. Following centrifugation, RNA pellets were then resuspended in 3M sodium acetate and absolute ethanol and precipitated for 1hr at -80°C. RNA pellet was then centrifuged and resuspended in DEPC water.

treatment_protocol: BMDM cells were then reseeded at day 7 in BMDM growth medium plus 10ng/ml recombinant M-CSF (Perprotech Inc) for overnight. On day of treatment, BMDM cells were infected with WT-WR and WRΔA26 virions at moi=20 PFU/cell and harvested at 1, 2, 4 and 8 hours p.i..

value: BMDM

tag: infection

tag: time

tag: age

value: 6 weeks

value: Female

source_name: Mock infected BMDM

value: mock


title: WRΔA26 infected BMDM at 8hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WRΔA26 8hr-rep3


title: WRΔA26 infected BMDM at 8hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WRΔA26 8hr-rep2


title: WRΔA26 infected BMDM at 4hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WRΔA26 4hr-rep3


title: WT-WR infected BMDM at 2hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WT-WR 2hr-rep3

source_name: WT-WR infected D8-BMDM cells

value: WT-WR


title: WRΔA26 infected BMDM at 2hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WRΔA26 2hr-rep2


title: WT-WR infected BMDM at 8hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WT-WR 8hr-rep3


title: WRΔA26 infected BMDM at 4hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WRΔA26 4hr-rep2


title: WRΔA26 infected BMDM at 1hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WRΔA26 1hr-rep3


title: WRΔA26 infected BMDM at 1hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WRΔA26 1hr-rep2


title: WT-WR infected BMDM at 4hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WT-WR 4hr-rep2


title: WT-WR infected BMDM at 4hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WT-WR 4hr-rep3


title: WT-WR infected BMDM at 1hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WT-WR 1hr-rep2


title: WRΔA26 infected BMDM at 2hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WRΔA26 2hr-rep1


title: WRΔA26 infected BMDM at 8hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WRΔA26 8hr-rep1


title: WRΔA26 infected BMDM at 4hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WRΔA26 4hr-rep1


title: WT-WR infected BMDM at 2hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WT-WR 2hr-rep2


title: WT-WR infected BMDM at 1hr-replicate 3

description:
Biological replicate 3 of 3. Uninfected BMDM cells.
WT-WR 1hr-rep3


title: WT-WR infected BMDM at 8hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WT-WR 8hr-rep1


title: WT-WR infected BMDM at 4hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WT-WR 4hr-rep1


title: MMC1 vs MMC25

city: Barcelona

first: Francisco Jose

last: Pérez-Cano

state: Catalunya

address: Edifici B, 3a planta,  Av. Joan XXIII s/n

department: Departament de Fisiologia-Farmàcia

country: Spain

institute: Universitat de Barcelona

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

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

organism: Rattus norvegicus

source_name: Reference diet

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: At the end of the nutritional intervention, a 5 mm piece of the middle of the colon was collected from all animals in aseptic conditions in RNAlater® and kept at 4 ºC overnight before storing at -20 ºC for further gene expression analysis by microarray.

extract_protocol: The RNA was isolated by the RNeasy Mini Kit following the manufacturer's recommendations and quantified with a NanoDrop spectrophoyometer and NanoDrop IVD-1000 v.3.1.2 software. The agilent 2100 Bioanalyzer with the RNA 600 LabChip kit was used to provide an RNA integrity number for each sample.

treatment_protocol: Tissue samples were transfered into lysing matrix tubes containing an appopriate buffer  and were homogenized in a FastPrep® instrument for 30 s. Lysate were centrifuged for 3 min at 12.000 g to aliminate excess tissue debris.

value: Colon

tag: rat strain

value: Wistar

value: Six week old

tag: dietary intervention

value: Reference diet

source_name: Inulin diet

value: Inulin diet


title: MMC38 vs MMC32

source_name: Cocoa fiber diet

value: Cocoa fiber diet


title: MMC14 vs MMC17

source_name: Cocoa diet

value: Cocoa diet


title: WT-WR infected BMDM at 8hr-replicate 2

description:
Biological replicate 2 of 3. Uninfected BMDM cells.
WT-WR 8hr-rep2


title: WT-WR infected BMDM at 1hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WT-WR 1hr-rep1


title: MMC19 vs MMC13


title: WT-WR infected BMDM at 2hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WT-WR 2hr-rep1


title: MMC31 vs MMC3


title: MMC30 vs MMC24


title: MMC4 vs MMC11


title: Day 31

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: SAMPLE 9

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Fluidics Protocol FS450_0007).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console

source_name: differentiated and expanded stem cells

label_protocol: 100ng of total RNA were amplified and labeled with biotin  according to the protocol described in the GeneChip Whole Transcript (WT) Sense Target Labeling Assay User Manual.

growth_protocol: CD34+ stem cells at a density of 10^5 cells/ml were expanded for 10 days in basal expansion medium (GBGM) supplemented with high doses of stem cell factor (SCF), interleukin-7 (IL-7); thrombopoetin (TPO) and FMS-like tyrosine kinase 3 ligand (Flt3L; all factors at a concentration of 25 ng/mL; CellGro®, CellGenix GmbH, Freiburg, Germany) and low doses of granulocyte colony-stimulating factor (G-CSF, 250 pg/mL; Stemcell Technologies, Vancouver, Canada), granulocyte- macrophage colony-stimulating factor (GM-CSF, 10 pg/mL; Stemcell Technologies) and IL-6 (50 pg/mL; CellGenix GmbH)

treatment_protocol: At day 10, TPO was replaced with IL-15 (20 ng/mL; CellGro®, CellGenix GmbH) and at day 14, Flt3L with IL-2 (1.000 U/mL; Chiron Corporation, Emeryville, CA, USA).

value: umbilical cord blood stem cells

value: CD34+ stem cells

tag: time point

value: Day 31


title: Day 35

description: SAMPLE 10

value: Day 35


title: Day 24

description: SAMPLE 6

value: Day 24


title: MMC10 vs MMC2


title: WRΔA26 infected BMDM at 1hr-replicate 1

description:
Biological replicate 1 of 3. Uninfected BMDM cells.
WRΔA26 1hr-rep1

value: BMDM


title: Day 27

description: SAMPLE 7

value: Day 27


title: Day 22

description: SAMPLE 5

value: Day 22


title: Day 20

description: SAMPLE 4

value: Day 20


title: Day 29

description: SAMPLE 8

value: Day 29


title: Day 17

description: SAMPLE 3

value: Day 17


title: Day 15

description: SAMPLE 2

value: Day 15


title: mTECS FVB

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: mouse Epithelial Trachea Cells, FVB mouse strain

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.

source_name: mTECS FVB

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

growth_protocol: Not applicable

extract_protocol: Trizol followed by RNAeasy spin columns

treatment_protocol: Not applicable

value: FVB

value: Epithelial Trachea Cells


title: Day 10

description: SAMPLE 1

source_name: undifferentiated expanded stem cells

value: Day 10


title: POS5

status: Public on Jul 08 2017

city: Castellón

first: Josep

middle: A

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

hyb_protocol: Each sample (1.65 µg) was hybridized to the Custom Seabass Oligo Microarray Kit (Agilent p/n G2509F-064054) at 65 ºC for 17 h using Agilent GE hybridization kit

scan_protocol: Arrays were scanned with Agilent scanner G2505B

data_processing: Spot intensities and other quality control features were extracted with Agilent Feature Extraction software version 11.5.1.1, and was further analyzed, including percentile shift normalization, one-way ANOVA, principal components analysis and k-means clustering of differentially expressed genes, by means of GeneSpring GX 12.6.1 software (Agilent)

organism: Dicentrarchus labrax

source_name: Posterior intestine

label_protocol: Total RNA (100 ng) from each individual sample was amplified and Cy3-labeled with Agilent One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling kit) along with Agilent One-color RNA SpikeIn kit. After labeling, cRNA was purified with RNeasy mini spin columns (Qiagen)

extract_protocol: Total RNA from target tissues was isolated with the the Ambion MagMax-96 for Microarray kit

tag: intestine section

value: Posterior intestine


title: POS1


title: MED4

source_name: Middle intestine

value: Middle intestine


title: POS4


title: POS6


title: MED2


title: POS3


title: POS7


title: POS8


title: MED1


title: MED3


title: MED7


title: POS2


title: MED6


title: MED5


title: ANT5

source_name: Anterior intestine

value: Anterior intestine


title: ANT8


title: ANT2


title: ANT4


title: Foreskin Dermal fibroblasts from 5 month old patient treated with GC4419

city: Iowa City

first: Kranti

last: Mapuskar

state: Iowa

address: 500 Newton Road

department: Radiation Oncology

institute: University of Iowa

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control ratios: normalized gene expression (2^(- Delta Ct)) in the Test Sample divided the normalized gene expression (2^(- Delta Ct)) in the Control Sample
Fold-Regulation represents fold-change results in a biologically meaningful way. Fold-change values greater than one indicate a positive- or an up-regulation, and the fold-regulation is equal to the fold-change for values > 1. For Fold-change values < 1, values have been transformed to -1/VALUE.

label: SYBR Green

source_name: Foreskin

label_protocol: PCR assays were performed using the Mitochondria Energy Metabolism PCR array panel from Qiagen (PAHS008Z) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: foreskin

tag: cell type

value: primary dermal fibroblasts

value: 5 months


title: Dermal fibroblasts from a 78 years old patient treated with GC4419

description: Test

source_name: Arm skin

value: arm

value: 78 years


title: ANT6


title: ANT3


title: ANT7


title: ANT1


title: genomic DNA from  replicates UC188

status: Public on Jul 07 2017

type: genomic

city: Hefei

first: Fusheng

last: Zhou

address: No 96 Meishan Road, Hefei, China

country: China

institute: Anhui Medical University

description: Normal skin sample

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: replicates UC188

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from skin samples using Omega bio-tek system (D3396-02) according to standard instructions

value: Female

value: Skin

value: Normal


title: genomic DNA from  normal skin sample 177

description: Normal skin sample

source_name: normal skin sample 177


title: genomic DNA from  normal skin sample 171

description: Normal skin sample

source_name: normal skin sample 171


title: genomic DNA from  normal skin sample 176

description: Normal skin sample

source_name: normal skin sample 176


title: genomic DNA from  normal skin sample 183

description: Normal skin sample

source_name: normal skin sample 183


title: genomic DNA from  normal skin sample 163

description: Normal skin sample

source_name: normal skin sample 163

value: Male


title: genomic DNA from  normal skin sample 187

description: Normal skin sample

source_name: normal skin sample 187


title: genomic DNA from  normal skin sample 184

description: Normal skin sample

source_name: normal skin sample 184


title: genomic DNA from  normal skin sample 175

description: Normal skin sample

source_name: normal skin sample 175


title: genomic DNA from  normal skin sample 155

description: Normal skin sample

source_name: normal skin sample 155


title: genomic DNA from  normal skin sample 157

description: Normal skin sample

source_name: normal skin sample 157


title: genomic DNA from  normal skin sample 185

description: Normal skin sample

source_name: normal skin sample 185


title: genomic DNA from  normal skin sample 188

description: Normal skin sample

source_name: normal skin sample 188


title: genomic DNA from  normal skin sample 181

description: Normal skin sample

source_name: normal skin sample 181


title: genomic DNA from  normal skin sample 170

description: Normal skin sample

source_name: normal skin sample 170


title: genomic DNA from  normal skin sample 162

description: Normal skin sample

source_name: normal skin sample 162


title: genomic DNA from  normal skin sample 150

description: Normal skin sample

source_name: normal skin sample 150


title: genomic DNA from  normal skin sample 191

description: Normal skin sample

source_name: normal skin sample 191


title: genomic DNA from  normal skin sample 151

description: Normal skin sample

source_name: normal skin sample 151


title: genomic DNA from  normal skin sample 164

description: Normal skin sample

source_name: normal skin sample 164


title: genomic DNA from  normal skin sample 166

description: Normal skin sample

source_name: normal skin sample 166


title: genomic DNA from  normal skin sample 152

description: Normal skin sample

source_name: normal skin sample 152


title: genomic DNA from  normal skin sample 142

description: Normal skin sample

source_name: normal skin sample 142


title: genomic DNA from  normal skin sample 179

description: Normal skin sample

source_name: normal skin sample 179


title: genomic DNA from  normal skin sample 167

description: Normal skin sample

source_name: normal skin sample 167


title: genomic DNA from  normal skin sample 145

description: Normal skin sample

source_name: normal skin sample 145


title: genomic DNA from  normal skin sample 161

description: Normal skin sample

source_name: normal skin sample 161


title: genomic DNA from  normal skin sample 147

description: Normal skin sample

source_name: normal skin sample 147


title: genomic DNA from  normal skin sample 143

description: Normal skin sample

source_name: normal skin sample 143


title: genomic DNA from  replicates UC185

description: Normal skin sample

source_name: replicates UC185


title: genomic DNA from  normal skin sample 134

description: Normal skin sample

source_name: normal skin sample 134


title: genomic DNA from  normal skin sample 136

description: Normal skin sample

source_name: normal skin sample 136


title: genomic DNA from  normal skin sample 131

description: Normal skin sample

source_name: normal skin sample 131


title: genomic DNA from  normal skin sample 132

description: Normal skin sample

source_name: normal skin sample 132


title: genomic DNA from  normal skin sample 114

description: Normal skin sample

source_name: normal skin sample 114


title: genomic DNA from  normal skin sample 133

description: Normal skin sample

source_name: normal skin sample 133


title: genomic DNA from  normal skin sample 115

description: Normal skin sample

source_name: normal skin sample 115


title: genomic DNA from  normal skin sample 124

description: Normal skin sample

source_name: normal skin sample 124


title: genomic DNA from  normal skin sample 126

description: Normal skin sample

source_name: normal skin sample 126


title: genomic DNA from  normal skin sample 122

description: Normal skin sample

source_name: normal skin sample 122


title: genomic DNA from  normal skin sample 121

description: Normal skin sample

source_name: normal skin sample 121


title: genomic DNA from  normal skin sample 128

description: Normal skin sample

source_name: normal skin sample 128


title: genomic DNA from  normal skin sample 127

description: Normal skin sample

source_name: normal skin sample 127


title: genomic DNA from  normal skin sample 113

description: Normal skin sample

source_name: normal skin sample 113


title: genomic DNA from  normal skin sample 107

description: Normal skin sample

source_name: normal skin sample 107


title: genomic DNA from  normal skin sample 120

description: Normal skin sample

source_name: normal skin sample 120


title: genomic DNA from  normal skin sample 116

description: Normal skin sample

source_name: normal skin sample 116


title: genomic DNA from  normal skin sample 112

description: Normal skin sample

source_name: normal skin sample 112


title: genomic DNA from  normal skin sample 108

description: Normal skin sample

source_name: normal skin sample 108


title: genomic DNA from  normal skin sample 125

description: Normal skin sample

source_name: normal skin sample 125


title: genomic DNA from  normal skin sample 105

description: Normal skin sample

source_name: normal skin sample 105


title: genomic DNA from  normal skin sample 102

description: Normal skin sample

source_name: normal skin sample 102


title: genomic DNA from  normal skin sample 109

description: Normal skin sample

source_name: normal skin sample 109


title: genomic DNA from  normal skin sample 101

description: Normal skin sample

source_name: normal skin sample 101


title: genomic DNA from  normal skin sample 103

description: Normal skin sample

source_name: normal skin sample 103


title: genomic DNA from  normal skin sample 110

description: Normal skin sample

source_name: normal skin sample 110


title: genomic DNA from  normal skin sample 100

description: Normal skin sample

source_name: normal skin sample 100


title: genomic DNA from  normal skin sample 098

description: Normal skin sample

source_name: normal skin sample 098


title: genomic DNA from  normal skin sample 119

description: Normal skin sample

source_name: normal skin sample 119


title: genomic DNA from  normal skin sample 111

description: Normal skin sample

source_name: normal skin sample 111


title: genomic DNA from  normal skin sample 099

description: Normal skin sample

source_name: normal skin sample 099


title: genomic DNA from  normal skin sample 106

description: Normal skin sample

source_name: normal skin sample 106


title: genomic DNA from  normal skin sample 104

description: Normal skin sample

source_name: normal skin sample 104


title: genomic DNA from  normal skin sample 067

description: Normal skin sample

source_name: normal skin sample 067


title: genomic DNA from  psoriatic skin sample 208

description: psoriatic skin sample

source_name: psoriatic skin sample 208

value: Psoriasis


title: genomic DNA from  psoriatic skin sample 209

description: psoriatic skin sample

source_name: psoriatic skin sample 209


title: genomic DNA from  psoriatic skin sample 207

description: psoriatic skin sample

source_name: psoriatic skin sample 207


title: genomic DNA from  psoriatic skin sample 199

description: psoriatic skin sample

source_name: psoriatic skin sample 199


title: genomic DNA from  psoriatic skin sample 206

description: psoriatic skin sample

source_name: psoriatic skin sample 206


title: genomic DNA from  psoriatic skin sample 202

description: psoriatic skin sample

source_name: psoriatic skin sample 202


title: genomic DNA from  psoriatic skin sample 194

description: psoriatic skin sample

source_name: psoriatic skin sample 194


title: genomic DNA from  psoriatic skin sample 204

description: psoriatic skin sample

source_name: psoriatic skin sample 204


title: genomic DNA from  psoriatic skin sample 196

description: psoriatic skin sample

source_name: psoriatic skin sample 196


title: genomic DNA from  psoriatic skin sample 210

description: psoriatic skin sample

source_name: psoriatic skin sample 210


title: genomic DNA from  psoriatic skin sample 201

description: psoriatic skin sample

source_name: psoriatic skin sample 201


title: genomic DNA from  psoriatic skin sample 211

description: psoriatic skin sample

source_name: psoriatic skin sample 211


title: genomic DNA from  psoriatic skin sample 193

description: psoriatic skin sample

source_name: psoriatic skin sample 193


title: genomic DNA from  psoriatic skin sample 192

description: psoriatic skin sample

source_name: psoriatic skin sample 192


title: genomic DNA from  psoriatic skin sample 197

description: psoriatic skin sample

source_name: psoriatic skin sample 197


title: genomic DNA from  psoriatic skin sample 200

description: psoriatic skin sample

source_name: psoriatic skin sample 200


title: genomic DNA from  psoriatic skin sample 190

description: psoriatic skin sample

source_name: psoriatic skin sample 190


title: CD34+-EC aggregates 8hours with soluble VEGF rep2

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

hyb_protocol: Labeled miRNA was hybridized onto Agilent's Human miRNA Microarrays V3, Release 12.0 (P/N G4471A-021827) annotated against the Sanger miRBASE 12.0 database of miRNAs according to the manufacturer's instructions.

scan_protocol: The microarrays were scanned by an Agilent B Scanner (G2565BA). Agilent Feature Extraction Image Analysis Sofware (Version 10.7.3.1) was used to obtain fluorescence intensities from raw microarray image files.

data_processing: The raw data were analyzed using BRB-ArrayTools v3.4.0 developed by Dr. Richard Simon and BRB-ArrayTools development team. This analysis generates a median normalized dataset that is subjected to a statistical study and clustering using MeV software. The differentially expressed miRNAs obtained from MeV were used to calculate the M-value and Fold-change variation. It was considered as differentially expressed miRNA a variation equal or higher than 2 fold between the different conditions.

source_name: Human CD34+ endothelial cell aggregates

label_protocol: Agilent miRNA complete labeling and hyb kit (p/n 5190-0456) was used according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Valencia, CA). The efficiency of cRNA synyhesis and dye incorporation was measured using NanoDrop ND1000 spectrophotometer.

growth_protocol: Human CD34+ endothelial cells were expanded in 1% (w/v) gelatin-coated T75 flasks (BD Falcon) in EGM-2 medium (Lonza). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2 and medium was refreshed every other day.

extract_protocol: Total RNA was isolated using the absolutely RNA miRNA kit (400814, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. RNA quality was assessed by an Agilent 2100 Bioanalyser (G2943CA), using an Agilent RNA 6000 Nano kit (5067-1511).

treatment_protocol: EC aggregates with defined cell numbers were formed as reported elsewhere. Briefly, confluent CD34+-derived EC cultures (passage 4) were trypsinized and suspended in serum reduced EGM-2 (1%, v/v, FBS) medium without VEGF that contains 20% (w/v) methocel. The methocel solution was prepared by dissolving carboxymethylcellulose (6 g) in M-200 basal medium (500 mL). After centrifugation, the gel-like supernatant was used for experiments. Cells suspended in methocel solution (10,000 cells per 30 µL of methocel solution) were seeded into nonadhesive bacteriological dishes (Greiner, Frickenhausen, Germany; in drops of 30 µL) in the absence (soluble VEGF group and cell control group) or presence of microparticles (VEGF-conjugated microparticles and blank microparticles) and cultured at 37ºC (5% CO2, 95% humidity) for 12 h. Under these conditions, suspended ECs formed spontaneous aggregates.

tag: cells

value: Endothelial cells

tag: passage number

value: Passage 5

tag: treatment

value: 8 hours treatment with soluble VEGF


title: genomic DNA from  psoriatic skin sample 184

description: psoriatic skin sample

source_name: psoriatic skin sample 184

tag: disease state


title: genomic DNA from  psoriatic skin sample 185

description: psoriatic skin sample

source_name: psoriatic skin sample 185

tag: gender


title: genomic DNA from  psoriatic skin sample 188

description: psoriatic skin sample

source_name: psoriatic skin sample 188


title: genomic DNA from  psoriatic skin sample 195

description: psoriatic skin sample

source_name: psoriatic skin sample 195


title: CD34+-EC aggregates 2hours with soluble VEGF rep3

value: 2 hours treatment with soluble VEGF


title: genomic DNA from  psoriatic skin sample 205

description: psoriatic skin sample

source_name: psoriatic skin sample 205


title: genomic DNA from  psoriatic skin sample 175

description: psoriatic skin sample

source_name: psoriatic skin sample 175


title: genomic DNA from  psoriatic skin sample 179

description: psoriatic skin sample

source_name: psoriatic skin sample 179


title: CD34+-EC aggregates 8hours with soluble VEGF rep1


title: CD34+-EC aggregates 2hours with soluble VEGF rep2


title: genomic DNA from  psoriatic skin sample 191

description: psoriatic skin sample

source_name: psoriatic skin sample 191


title: genomic DNA from  psoriatic skin sample 174

description: psoriatic skin sample

source_name: psoriatic skin sample 174


title: genomic DNA from  psoriatic skin sample 177

description: psoriatic skin sample

source_name: psoriatic skin sample 177


title: CD34+-EC aggregates 2hours with soluble VEGF rep1


title: genomic DNA from  psoriatic skin sample 172

description: psoriatic skin sample

source_name: psoriatic skin sample 172


title: genomic DNA from  psoriatic skin sample 187

description: psoriatic skin sample

source_name: psoriatic skin sample 187


title: genomic DNA from  psoriatic skin sample 173

description: psoriatic skin sample

source_name: psoriatic skin sample 173


title: CD34+-EC aggregates 8hours with VEGF-conjugated microparticles rep2

value: 8 hours treatment with VEGF-conjugated microparticles


title: CD34+-EC aggregates 8hours with VEGF-conjugatedmicroparticles rep1


title: genomic DNA from  psoriatic skin sample 171

description: psoriatic skin sample

source_name: psoriatic skin sample 171


title: genomic DNA from  psoriatic skin sample 170

description: psoriatic skin sample

source_name: psoriatic skin sample 170


title: CD34+-EC aggregates 2hours with VEGF-conjugated microparticles rep2

value: 2 hours treatment with VEGF-conjugated microparticles


title: genomic DNA from  psoriatic skin sample 176

description: psoriatic skin sample

source_name: psoriatic skin sample 176


title: CD34+-EC aggregates 2hours with VEGF-conjugated microparticles rep1

source_name: Human CD34+ endothelial cell aggregates


title: genomic DNA from  psoriatic skin sample 168

description: psoriatic skin sample

source_name: psoriatic skin sample 168


title: CD34+-EC aggregates 2hours with VEGF-conjugated microparticles rep3


title: CD34+-EC aggregates 2hours without treatment rep3

value: 2 hours without treatment


title: genomic DNA from  psoriatic skin sample 169

description: psoriatic skin sample

source_name: psoriatic skin sample 169


title: CD34+-EC aggregates 2hours without treatment rep2


title: CD34+-EC aggregates 2hours without treatment rep1


title: CD34+-EC aggregates 2hours with blank microparticles rep3

value: 2 hours treatment with blank microparticles


title: genomic DNA from  psoriatic skin sample 166

description: psoriatic skin sample

source_name: psoriatic skin sample 166


title: CD34+-EC aggregates 2hours with blank microparticles rep2


title: CD34+-EC aggregates 2hours with blank microparticles rep1


title: genomic DNA from  psoriatic skin sample 165

description: psoriatic skin sample

source_name: psoriatic skin sample 165


title: genomic DNA from  psoriatic skin sample 164

description: psoriatic skin sample

source_name: psoriatic skin sample 164


title: genomic DNA from  psoriatic skin sample 161

description: psoriatic skin sample

source_name: psoriatic skin sample 161


title: genomic DNA from  psoriatic skin sample 163

description: psoriatic skin sample

source_name: psoriatic skin sample 163


title: PS18_NS whole blood cells_non-stimulated_rep15

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

institute: McGill University Health Centre

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with lumi in R. Probes with Detection P val < 0.05 in at least 3 samples were kept for analysis.

source_name: whole blood cells,non-stimulated

label_protocol: The 102 RNA samples were labelled using the Illumina TotalPrep RNA Amplification Kit from Ambion

extract_protocol: Total RNA was then extracted employing a modified protocol of the LeukoLOCK RNA extraction kit (Ambion, CA, USA) and cleaned with the RNAeasy kit (Qiagen, Germany)

value: male

tag: duration of stimulation

tag: dose


title: genomic DNA from  psoriatic skin sample 141

description: psoriatic skin sample

source_name: psoriatic skin sample 141

tag: tissue


title: genomic DNA from  psoriatic skin sample 139

description: psoriatic skin sample

source_name: psoriatic skin sample 139


title: PS20_NS whole blood cells_non-stimulated_rep17

value: female


title: PS19_NS whole blood cells_non-stimulated_rep16


title: PS17_NS whole blood cells_non-stimulated_rep14


title: PS21_NS whole blood cells_non-stimulated_rep18


title: genomic DNA from  psoriatic skin sample 143

description: psoriatic skin sample

source_name: psoriatic skin sample 143


title: genomic DNA from  psoriatic skin sample 167

description: psoriatic skin sample

source_name: psoriatic skin sample 167


title: PS16_NS whole blood cells_non-stimulated_rep13


title: genomic DNA from  psoriatic skin sample 140

description: psoriatic skin sample

source_name: psoriatic skin sample 140


title: PS15_NS whole blood cells_non-stimulated_rep12


title: genomic DNA from  psoriatic skin sample 136

description: psoriatic skin sample

source_name: psoriatic skin sample 136


title: genomic DNA from  psoriatic skin sample 138

description: psoriatic skin sample

source_name: psoriatic skin sample 138


title: PS13_NS whole blood cells_non-stimulated_rep4


title: genomic DNA from  psoriatic skin sample 129

description: psoriatic skin sample

source_name: psoriatic skin sample 129


title: genomic DNA from  psoriatic skin sample 137

description: psoriatic skin sample

source_name: psoriatic skin sample 137


title: genomic DNA from  psoriatic skin sample 135

description: psoriatic skin sample

source_name: psoriatic skin sample 135


title: PS11_NS whole blood cells_non-stimulated_rep3


title: genomic DNA from  psoriatic skin sample 133

description: psoriatic skin sample

source_name: psoriatic skin sample 133


title: genomic DNA from  psoriatic skin sample 128

description: psoriatic skin sample

source_name: psoriatic skin sample 128


title: PS6_NS whole blood cells_non-stimulated_rep8


title: PS8_NS whole blood cells_non-stimulated_rep10


title: genomic DNA from  psoriatic skin sample 125

description: psoriatic skin sample

source_name: psoriatic skin sample 125


title: PS7_NS whole blood cells_non-stimulated_rep9


title: genomic DNA from  psoriatic skin sample 134

description: psoriatic skin sample

source_name: psoriatic skin sample 134


title: genomic DNA from  psoriatic skin sample 123

description: psoriatic skin sample

source_name: psoriatic skin sample 123


title: PS3_NS whole blood cells_non-stimulated_rep6


title: genomic DNA from  psoriatic skin sample 121

description: psoriatic skin sample

source_name: psoriatic skin sample 121


title: PS5_NS whole blood cells_non-stimulated_rep7

source_name: whole blood cells,non-stimulated


title: PS9_NS whole blood cells_non-stimulated_rep11


title: PS2_NS whole blood cells_non-stimulated_rep5


title: PS10_NS whole blood cells_non-stimulated_rep2


title: genomic DNA from  psoriatic skin sample 120

description: psoriatic skin sample

source_name: psoriatic skin sample 120


title: PS1_NS whole blood cells_non-stimulated_rep1


title: genomic DNA from  psoriatic skin sample 142

description: psoriatic skin sample

source_name: psoriatic skin sample 142


title: genomic DNA from  psoriatic skin sample 122

description: psoriatic skin sample

source_name: psoriatic skin sample 122


title: genomic DNA from  psoriatic skin sample 132

description: psoriatic skin sample

source_name: psoriatic skin sample 132


title: PS63 whole blood cells_stimulated_rep1

source_name: whole blood cells,stimulated


title: PS62 whole blood cells_stimulated_rep1


title: PS61_NS whole blood cells_non-stimulated_rep49


title: genomic DNA from  psoriatic skin sample 117

description: psoriatic skin sample

source_name: psoriatic skin sample 117


title: genomic DNA from  psoriatic skin sample 127

description: psoriatic skin sample

source_name: psoriatic skin sample 127


title: genomic DNA from  psoriatic skin sample 124

description: psoriatic skin sample

source_name: psoriatic skin sample 124


title: PS61 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 119

description: psoriatic skin sample

source_name: psoriatic skin sample 119


title: genomic DNA from  psoriatic skin sample 116

description: psoriatic skin sample

source_name: psoriatic skin sample 116


title: PS60 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 114

description: psoriatic skin sample

source_name: psoriatic skin sample 114


title: genomic DNA from  psoriatic skin sample 118

description: psoriatic skin sample

source_name: psoriatic skin sample 118


title: genomic DNA from  psoriatic skin sample 109

description: psoriatic skin sample

source_name: psoriatic skin sample 109


title: PS58_NS whole blood cells_non-stimulated_rep46


title: genomic DNA from  psoriatic skin sample 115

description: psoriatic skin sample

source_name: psoriatic skin sample 115


title: genomic DNA from  psoriatic skin sample 113

description: psoriatic skin sample

source_name: psoriatic skin sample 113


title: PS59 whole blood cells_stimulated_rep1


title: PS56 whole blood cells_stimulated_rep1


title: PS52 whole blood cells_stimulated_rep1


title: PS50 whole blood cells_stimulated_rep1


title: PS53 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 108

description: psoriatic skin sample

source_name: psoriatic skin sample 108


title: PS49 whole blood cells_stimulated_rep1


title: PS54 whole blood cells_stimulated_rep1


title: PS45 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 107

description: psoriatic skin sample

source_name: psoriatic skin sample 107


title: PS46 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 103

description: psoriatic skin sample

source_name: psoriatic skin sample 103


title: genomic DNA from  psoriatic skin sample 106

description: psoriatic skin sample

source_name: psoriatic skin sample 106


title: PS44 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 102

description: psoriatic skin sample

source_name: psoriatic skin sample 102


title: PS43 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 104

description: psoriatic skin sample

source_name: psoriatic skin sample 104


title: genomic DNA from  psoriatic skin sample 111

description: psoriatic skin sample

source_name: psoriatic skin sample 111


title: genomic DNA from  psoriatic skin sample 101

description: psoriatic skin sample

source_name: psoriatic skin sample 101


title: PS42 whole blood cells_stimulated_rep1

source_name: whole blood cells,stimulated


title: PS40 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 099

description: psoriatic skin sample

source_name: psoriatic skin sample 099


title: PS38 whole blood cells_stimulated_rep1


title: PS41 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 100

description: psoriatic skin sample

source_name: psoriatic skin sample 100


title: genomic DNA from  psoriatic skin sample 094

description: psoriatic skin sample

source_name: psoriatic skin sample 094


title: genomic DNA from  psoriatic skin sample 095

description: psoriatic skin sample

source_name: psoriatic skin sample 095


title: genomic DNA from  psoriatic skin sample 097

description: psoriatic skin sample

source_name: psoriatic skin sample 097


title: PS37 whole blood cells_stimulated_rep1


title: PS35 whole blood cells_stimulated_rep1


title: PS36 whole blood cells_stimulated_rep1


title: PS34 whole blood cells_stimulated_rep1


title: PS29 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 093

description: psoriatic skin sample

source_name: psoriatic skin sample 093


title: PS30 whole blood cells_stimulated_rep1


title: PS28 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 096

description: psoriatic skin sample

source_name: psoriatic skin sample 096


title: genomic DNA from  psoriatic skin sample 089

description: psoriatic skin sample

source_name: psoriatic skin sample 089


title: genomic DNA from  psoriatic skin sample 105

description: psoriatic skin sample

source_name: psoriatic skin sample 105


title: genomic DNA from  psoriatic skin sample 090

description: psoriatic skin sample

source_name: psoriatic skin sample 090


title: genomic DNA from  psoriatic skin sample 087

description: psoriatic skin sample

source_name: psoriatic skin sample 087


title: genomic DNA from  psoriatic skin sample 091

description: psoriatic skin sample

source_name: psoriatic skin sample 091


title: genomic DNA from  psoriatic skin sample 088

description: psoriatic skin sample

source_name: psoriatic skin sample 088


title: PS26 whole blood cells_stimulated_rep1


title: PS33 whole blood cells_stimulated_rep1


title: PS24 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 084

description: psoriatic skin sample

source_name: psoriatic skin sample 084


title: genomic DNA from  psoriatic skin sample 086

description: psoriatic skin sample

source_name: psoriatic skin sample 086


title: PS23 whole blood cells_stimulated_rep1


title: colorectal cancer cell line, V9P

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

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

data_processing:
Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Received from INSERM, R. Hamelin, Paris

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

growth_protocol: Grown in medium according to supplier recommendations with added fetal bovine serum, antibiotics Streptomycin and Penicillin, along with amino acid L-glutamine.

extract_protocol: Total RNA was isolated from cell pellets using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

tag: cell line

tag: sample type

value: colorectal cancer cell line


title: PS27 whole blood cells_stimulated_rep1

source_name: whole blood cells,stimulated


title: colorectal cancer cell line, WiDr

source_name: ATCC(Supplier ID CCL-218)

value: WiDr


title: PS22 whole blood cells_stimulated_rep1


title: genomic DNA from  psoriatic skin sample 082

description: psoriatic skin sample

source_name: psoriatic skin sample 082

value: Female


title: genomic DNA from  psoriatic skin sample 092

description: psoriatic skin sample

source_name: psoriatic skin sample 092

value: Skin