title: Sorted epidermal BL LRCs_01

source_name: Skin cells from quadruple transgenic mice harboring K5-tTA, pTRE-H2B-GFP, K14-CreER and Rosa-tdTomato.

tag: cell type


title: YM

status: Public on Sep 01 2016

type: genomic

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Affymetrix Hybridization Protocol Other: Fragmented single-stranded sense DNA were hybridized to the Affymetrix Genome-Wide Human SNP 6.0 array. Arrays were hybridized in the GeneChip Hybridization Oven 645 and stained in the GeneChip Fluidics Station 450.

scan_protocol: Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000-7G (Affymetrix).

data_processing:
Data Processing Protocol
Calculation Method: The Affy SNP datsets were normalized and signal called by Affy GTC (version 4.2.0.26) using CNV analysis with the default parameters.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: YM cell line

label_protocol:
Affymetrix Labeling Protocol
Other: Fragmented PCR products were terminally labeled with biotin according to the manufacturer's protocol.

extract_protocol:
QIAGEN AllPrep DNA/RNA Mini Protocol
Other: Genomic DNA was isolated using QIAGEN AllPrep DNA/RNA Mini Kit.

tag: cell line

value: YM

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)


title: Brain_West Nile Virus_Infected_7days_rep3 [8021x16072]

type: RNA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

hyb_protocol: Hydridized according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

data_processing: nSolver software, background and internal control standardization. Normalization was performed in nsolver with house keeping genes as internal controls

label: nanostring oligonucleotide probe

molecule: total RNA

organism: Mus musculus

source_name: Brain_West Nile Virus_Infected_7days

label_protocol: Labeled according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: Total RNA was extracted using the RiboPure Kit

tag: timepoint(days)

tag: tissue

value: brain

tag: infection

value: West Nile Virus


title: 40_U2OS_3d_HINFP_2

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

description: Gene expression data on 3d day after HINFP siRNA transfection

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: The data were analyzed with RMA method in R.   Probe set data extracted from custom CDF (hugene11sthsensgcdf_18.0.0)

label_protocol: biotin

growth_protocol: cells were cultured in media supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol: RNA was purified from  cells using RNeasy kit (Qiagen)

treatment_protocol: For reverse transfection protocol, cells at 30% confluence were plated in the growth medium into 6-well plates using 15 nM siRNA and 7 µl HiPerFect (Qiagen) in final total volume 2 100 µl.

tag: sirna

value: HINFP

tag: day after sirna treatment

value: Day 3

tag: replica

value: biological rep 2


title: SPECS_1939

description: No additional information.

value: tumor

tag: individual


title: 39_U2OS_3d_HINFP_1

value: biological rep 1


title: SPECS_1864

description: No additional information.


title: Lung_Caudal_HD_HDP41

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

address: 2900 Ricketts Point Rd

institute: USAMRICD

description: Gene expression data from the left caudal lung lobe; exposed to 100 μg/kg vapor HD

hyb_protocol: Labelled RNA was hybridized for 16 hrs at 48 degrees C on Affymetrix Porcine Genome Array GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics.

scan_protocol: GeneChips were scanned using Affymetrix 7G GeneChip Scanner using Affymetrix GeneChip Command Console Scan Control

organism: Sus scrofa

source_name: lung; left caudal; medium HD

label_protocol: 1ug total RNA was to generate cRNA following manufacturer's instructions (Enzo Life Sciences, Plymouth Meeting, PA).

growth_protocol: Animals were housed individually in straw lined pens and were fed standard pig diet and water ad libitum for 5 days prior to the experiment. From 12 hours prior to the experiment, access to food was withdrawn, but water was freely available.

extract_protocol: Following euthanasia (overdose of sodium pentobarbitone, 200 mg/mL i.v.), lung tissue samples from each lobe were stored in RNAlater at -80 deg C until processed. Tissue was homogenized in RLT buffer containing Beta-mercaptoethanol and total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Animals were pre-medicatd and inhalational anesthesia induced. The animals were intubated and exposed to HD vapor for 10 minutes to 60 ug/kg (low) or 100 ug/kg (medium) doses while in the supine position.

value: Lung

tag: gender

value: Female


title: 4011

city: Indianapolis

first: Xiaoming

last: Yin

state: Indiana

address: 350 West 11th street

department: Department of Pathology and Laboratory Medicine

institute: Indiana University School of Medicine

description: The RNA was extracted from one sample

hyb_protocol: For hybridization, 15 to 20 µg of cRNA were fragmented by incubating in a buffer containing 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc at 95°C for 35 minutes.  The fragmented cRNA were then hybridized with a pre-equilibrated Affymetrix mouse chip (U74Av2) at 45°C for 14-16 hours.  After the hybridization cocktails were removed, the chips were then washed in a fluidic station with low-stringency buffer (6x SSPE, 0.01% Tween 20, 0.005% antifoam) for 10 cycles (2 mixes/cycle) and stringent buffer (100 mM MES, 0.1 M NaCl and 0.01% Tween 20) for 4 cycles (15 mixes/cycle), and stained with SAPE (Strepto-avidin Phycoerythrin).  This was followed by incubation with biotinylated mouse anti-avidin antibody, and restained with SAPE.

scan_protocol: The chips were scanned in a HP ChipScanner (Affymetrix Inc, Santa Clara, CA) to detect hybridization signals.

data_processing: The CEL files generated from the microarray scanning were used as the raw data.  Data quality was examined using the RMAExpress program (v.1.0.5) (http://rmaexpress.bmbolstad.com/).  The density distribution along the Log2 scale was comparable among the samples, which indicated that the quality of the assay was acceptable for comparison.  Microarray data from individual mouse livers within each treatment group were then averaged and the averaged values were used for the subsequently comparisons and pathway analysis.  Significance of differential expression was assessed using un-paired t-test.  The threshold for the significant changes was a difference larger than 25% for upregulated genes and larger than 20% for downregulated genes (fold of change >1.25 or <0.8, p<0.05).  Pathway analysis was conducted using the Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics Resources 6.7 (https://david.ncifcrf.gov/), and Gene Set Enrichment Analysis (GSEA 2.1.)(http://software.broadinstitute.org/gsea/index.jsp), for the differentially expressed gene set and the total gene set, respectively.  The pathway database is from the KEGG annotation (http://www.genome.jp/kegg/pathway.html).

source_name: bid KO_Control_6

label_protocol: Biotinylated cRNA was prepared using standard protocol.

extract_protocol: Mouse livers were dissected and RNA was prepared.  In brief, 20 to 50 mg of liver tissues were disrupted in Buffer RLT (provided in Qiagen RNEasy kit), and homogenized.  One volume of ethanol (70%) was then added to the lysate, creating conditions that promote selective binding of RNA to the RNeasy membrane.  The sample was then applied to the RNeasy Mini spin column.  Contaminants were washed away using RW1 wash buffer (provided in the RNEasy kit).  RNA was eluted in RNase-free water. All binding, wash, and elution steps were performed by centrifugation in a micro-centrifuge.

treatment_protocol: Diethylnitrosamine (DEN, C4H10N2O,) was intraperitoneally administrated to wild type and bid-deficient mice at the age of day 15 as previously described (Bai et al, American Journal of Pathology, 166: 1523-1532, 2005).  Wild type mice were in C57Bl/6J background whereas bid-deficient mice had been backcrossed to C57Bl/6J background for at least 12 generations.  Male mice were used because they were susceptible to this model of carcinogenesis.  Untreated control mice in the same genetic background were age and sex-matched. All of the mice were bred in house.  Mice were euthanized by cervical dislocation following anesthesia at an early stage (4-6 months) and at a later stage (10-12 months) following DEN treatment.  Livers were examined and processed.  The treatment of mice were approved by the IACUC of the University of Pittsburgh.

value: Liver

tag: background strain

value: male

tag: genotype

value: bid KO-/-

tag: treament

value: Control

tag: treatment duration (months)


title: 3944

description: The RNA was extracted from one sample


title: 4142

description: The RNA was extracted from one sample

source_name: bid KO_DEN_4

value: DEN


title: Liver_siKeap1-1_rep4

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

description: Gene expression data from mouse liver

hyb_protocol: 15 µg cRNA samples were fragmented at 94 degree Celsius for 35 min in 40 mM Tris/acetate pH 8.1, 100 mM KOAc and 30 mM MgOAc, added to hybridisation buffer and hybridised to Affymetrix GeneChip for 16-18 hours at 45 degree Celsius and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Array Studio (Omicsoft Corp., Cary, NC, USA) using default settings and RMA as normalization method.

label: Biotin

source_name: Mouse liver

label_protocol: Biotin-UPT and -CTP labelled cRNA was transcribed in vitro using Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, NY, NY) and purified by RNeasy cleanup and ethanol precipitation.

extract_protocol: Total RNA was prepared using the Rneasy Mini Kit

treatment_protocol: 8-week-old male C57BL6/J mice were fed ad libitum a western diet consisting of a high-fat diet supplemented with 6% sucrose in the water to induce insulin resistance and hepatic lipid accumulation. All mice were maintained in individually ventilated cages (max. 5 per cage) in an environmentally controlled room with a 12 h light-dark cycle. Body weight was monitored weekly. For siRNA intervention mice were divided into three groups according to equal body weight and fat mass. For a total of 7 weeks each group was weekly injected with 1 mg modified siRNA per kg body weight in PBS of liver-selective Keap1-specific siRNA (group 1: siKeap1-1, group 2: siKeap1-2) or unspecific scrambled control siRNA (group 3: siControl) via the tail vein.

value: liver

tag: strain

tag: treatment


title: 37_U2OS_3d_NPAT_1

description: Gene expression data on 3d day after NPAT siRNA transfection

value: NPAT


title: Brain_West Nile Virus_Infected_4days_rep3 [8021x16072]

source_name: Brain_West Nile Virus_Infected_4days


title: 3785

description: The RNA was extracted from two equally treated samples


title: Brain_West Nile Virus_Infected_7days_rep2 [8021x16072]


title: Brain_West Nile Virus_Infected_7days_rep1 [8021x16072]


title: 36_U2OS_3d_CASP8AP2_2

description: Gene expression data on 3d day after CASP8AP2 siRNA transfection


title: 38_U2OS_3d_NPAT_2


title: 4200

description: The RNA was extracted from one sample

source_name: bid KO_Control_4


title: Lung_Apical_HD_HDP39

description: Gene expression data from the left apical lung lobe; exposed to 100 μg/kg vapor HD

source_name: lung; left apical; medium HD


title: Lung_Apical_HD_HDP42


title: Lung_Median_HD_HDP39

description: Gene expression data from the left median lung lobe; exposed to 100 μg/kg vapor HD

source_name: lung; left median; medium HD


title: 35_U2OS_3d_CASP8AP2_1


title: Brain_West Nile Virus_Infected_4days_rep2 [8021x16072]


title: 34_U2OS_3d_CONT_2

description: Gene expression data on 3d day after control siRNA transfection

value: control


title: Brain_West Nile Virus_Infected_4days_rep1 [8021x16072]

value: brain


title: Brain_Mock_Infected_12Mdays_rep3 [8024x8049]

value: Mock


title: Lung_Median_HD_HDP34


title: Lung_Caudal_HD_HDP34


title: 33_U2OS_3d_CONT_1


title: Lung_Caudal_HD_HDP33

description: Gene expression data from the left caudal lung lobe; exposed to 60 μg/kg vapor HD

source_name: lung; left caudal; low HD


title: 3912

description: The RNA was extracted from one sample


title: 32_RPE_3d_HINFP_2

value: HINFP


title: Lung_Apical_HD_HDP34


title: 3967

description: The RNA was extracted from one sample


title: 31_RPE_3d_HINFP_1

value: Day 3


title: 3913

description: The RNA was extracted from one sample


title: 30_RPE_3d_NPAT_2

value: biological rep 2


title: Brain_West Nile Virus_Infected_12days_rep3 [8024x8049]

source_name: Brain_West Nile Virus_Infected_12days

value: West Nile Virus


title: Lung_Median_HD_HDP33

description: Gene expression data from the left median lung lobe; exposed to 60 μg/kg vapor HD

source_name: lung; left median; low HD


title: 29_RPE_3d_NPAT_1

value: biological rep 1


title: Brain_Mock_Infected_12Mdays_rep2 [8024x8049]


title: 3749

description: The RNA was extracted from one sample


title: 3700

description: The RNA was extracted from one sample


title: 27_RPE_3d_CASP8AP2_1


title: Lung_Median_HD_HDP41

value: Lung


title: Lung_Apical_HD_HDP33

description: Gene expression data from the left apical lung lobe; exposed to 60 μg/kg vapor HD

source_name: lung; left apical; low HD

value: Female


title: Brain_West Nile Virus_Infected_12days_rep2 [8024x8049]


title: Brain_Mock_Infected_12Mdays_rep1 [8024x8049]


title: 26_RPE_3d_CONT_2


title: 3911

description: The RNA was extracted from one sample

value: Liver


title: 3910

description: The RNA was extracted from one sample

value: male


title: Brain_West Nile Virus_Infected_12days_rep1 [8024x8049]


title: 3696

description: The RNA was extracted from one sample


title: Brain_West Nile Virus_Infected_7days_rep3 [8024x8049]


title: Brain_West Nile Virus_Infected_7days_rep1 [8024x8049]


title: 3940

description: The RNA was extracted from one sample


title: Brain_West Nile Virus_Infected_7days_rep2 [8024x8049]


title: Lung_Caudal_HD_HDP32


title: Lung_Median_HD_HDP31


title: 3750

description: The RNA was extracted from one sample


title: Brain_West Nile Virus_Infected_4days_rep3 [8024x8049]


title: 24_U2OS_2d_CASP8AP2_3

description: Gene expression data on 2nd day after CASP8AP2 siRNA transfection

value: Day 2

value: biological rep 3


title: 3937

description: The RNA was extracted from one sample

value: Control


title: 23_U2OS_2d_CASP8AP2_2


title: SLN432

description: No additional information.

value: tumor

tag: cell type

value: ABC DLBCL cells

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)


title: 28_RPE_3d_CASP8AP2_2

tag: cell line


title: 25_RPE_3d_CONT_1

value: control


title: 22_U2OS_2d_CASP8AP2_1


title: 3929

value: DEN


title: Lung_Apical_HD_HDP32


title: Lung_Caudal_HD_HDP31


title: 3748

description: The RNA was extracted from one sample


title: Brain_West Nile Virus_Infected_4days_rep2 [8024x8049]

value: brain


title: Lung_Apical_HD_HDP31


title: Lung_Caudal_HD_HDP44

description: Gene expression data from the left caudal lung lobe; exposed to air

source_name: lung; left caudal; air


title: Brain_West Nile Virus_Infected_4days_rep1 [8024x8049]


title: 20_U2OS_2d_control_2

description: Gene expression data on 2nd day after control siRNA transfection


title: Lung_Median_HD_HDP44

description: Gene expression data from the left median lung lobe; exposed to air

source_name: lung; left median; air


title: Lung_Apical_HD_HDP44

description: Gene expression data from the left apical lung lobe; exposed to air

source_name: lung; left; apical; air


title: 3756


title: 19_U2OS_2d_control_1


title: Brain_Mock_Infected_12Mdays_rep2 [15155x8054]

value: Mock


title: Brain_Mock_Infected_12Mdays_rep3 [15155x8054]


title: 3978


title: 3974


title: Brain_Mock_Infected_12Mdays_rep1 [15155x8054]


title: 18_U2OS_1d_CASP8AP2_3

description: Gene expression data on 1st day after CASP8AP2 siRNA transfection

value: Day 1


title: 17_U2OS_1d_CASP8AP2_2

value: biological rep 2


title: 21_U2OS_2d_control_3


title: Brain_West Nile Virus_Infected_12days_rep3 [15155x8054]

value: West Nile Virus


title: Lung_Caudal_HD_HDP29

value: Lung


title: Lung_Apical_HD_HDP28

source_name: lung; left apical; air

value: Female


title: WT plants treated with water, biological rep3

city: Berkeley

first: Yangnan

last: Gu

state: CA

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A) for 16 hours at 45C with rotation at 60rpm.

scan_protocol: Immediately following hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the GeneChip® FS450 fluidic station and are then scanned on the GeneChip® Scanner 3000 7G Plus where patterns of hybridization are detected.

data_processing: The data were normalized with RMA algorithm using Gene-Spring GX default analysis settings

organism: Arabidopsis thaliana

label_protocol: RNA probes were labelled using MessageAmp Premier RNA Amplification Kit (Ambion)

growth_protocol: Arabidopsis plants were grown on soil (Metro Mix 360) at 22˚C under a 12/12 hr light/dark cycle for 4 weeks

extract_protocol: The RNA was extracted with TRIzol (Ambion)

treatment_protocol: Mature leaves were sprayed with water or 50 uM dexamethasone

tag: cultivar

value: WT

value: mature leaf

tag: age

value: four weeks


title: 14_U2OS_1d_control_2

description: Gene expression data on 1st day after control siRNA transfection


title: WT plants treated with dexamethasone, biological rep2

tag: tissue


title: Lung_Apical_HD_HDP29


title: Lung_Median_HD_HDP29


title: WT plants treated with dexamethasone, biological rep1


title: 13_U2OS_1d_control_1

value: biological rep 1


title: Brain_West Nile Virus_Infected_12days_rep2 [15155x8054]

tag: timepoint(days)

tag: infection


title: Brain_West Nile Virus_Infected_12days_rep1 [15155x8054]


title: Lung_Caudal_HD_HDP28


title: Brain_West Nile Virus_Infected_7days_rep3 [15155x8054]

source_name: Brain_West Nile Virus_Infected_7days


title: Brain_West Nile Virus_Infected_7days_rep2 [15155x8054]


title: Lung_Median_HD_HDP28


title: Brain_West Nile Virus_Infected_7days_rep1 [15155x8054]


title: 12_RPE1_2d_CASP8AP2_3

tag: sirna

tag: day after sirna treatment

value: Day 2

value: biological rep 3


title: 15_U2OS_1d_control_3

tag: replica


title: 11_RPE1_2d_CASP8AP2_2


title: WT plants treated with water, biological rep1


title: KYSE 960

city: Kyoto

first: T

last: Fujiwara

address: 46-29 Yoshida Shimoadachi-cho Sakyo-ku

country: Japan

institute: Kyoto University

hyb_protocol: According to manufacture’s instructions, labeled and fragmented RNA was hybridized on the human Oligo chip 25k for 16 hour at 37˚C.

scan_protocol: Human Oligo chip 25k was scanned using ProScanArray (PerkinElmer).

data_processing: Cut-off value of 2, values under 2 are replaced by 2, and then log 2 transformed.  No further processing

source_name: esophageal squamous cell carcinoma

label_protocol: According to manufacture’s instructions, aminoallyl-cRNA was prepared from 500 ng of total RNA and was labeled with Cy5.

growth_protocol: KYSE cells were maintained in Ham’s F-12/RPMI 1640 containing 2% fetal bovine serum at 37 ˚C in a fully-humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

tag: cell line type

value: esophageal squamous cell carcinoma

value: KYSE 960


title: Brain_West Nile Virus_Infected_4days_rep3 [15155x8054]


title: Brain_West Nile Virus_Infected_4days_rep2 [15155x8054]


title: WT plants treated with dexamethasone, biological rep3


title: 16_U2OS_1d_CASP8AP2_1


title: KYSE 850

value: KYSE 850


title: Brain_West Nile Virus_Infected_4days_rep1 [15155x8054]


title: WT plants treated with water, biological rep2


title: Brain_Mock_Infected_12Mdays_rep3 [8002x3032]


title: Dex:YFP-CPR5-C plants treated with dexamethasone, biological rep3


title: 10_RPE1_2d_CASP8AP2_1


title: KYSE 590

value: KYSE 590


title: Dex:YFP-CPR5-C plants treated with dexamethasone, biological rep2


title: 07_RPE1_2d_control_1

value: control


title: KYSE 890

value: KYSE 890


title: 06_RPE1_1d_CASP8AP2_3

value: Day 1


title: 09_RPE1_2d_control_3


title: KYSE 520

value: KYSE 520


title: Brain_Mock_Infected_12Mdays_rep2 [8002x3032]

value: brain

value: Mock


title: Dex:YFP-CPR5-C plants treated with water, biological rep1


title: Brain_Mock_Infected_12Mdays_rep1 [8002x3032]


title: KYSE 770

value: KYSE 770


title: 08_RPE1_2d_control_2

value: biological rep 2


title: Dex:YFP-CPR5-C plants treated with water, biological rep3

value: mature leaf


title: AvrRpt2 treated rps2 at 10hpi, rep3

growth_protocol: Arabidopsis plants (Columbia-0 and rps2 mutant) were grown on soil (Metro Mix 360) at 22˚C under a 12/12 hr light/dark cycle for 4 weeks

treatment_protocol: Mature leaves were infiltrated with Psm carrying AvrRpt2 at OD 0.01 in 10mM MgSO4 solution

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 10h

value: four weeks


title: AvrRpt2 treated rps2 at 10hpi, rep2


title: KYSE 70

value: KYSE 70


title: 05_RPE1_1d_CASP8AP2_2


title: Lung_Median_HD_HDP32

value: Lung

tag: gender

value: Female


title: Brain_West Nile Virus_Infected_12days_rep2 [8002x3032]

value: West Nile Virus


title: Brain_West Nile Virus_Infected_12days_rep3 [8002x3032]


title: Brain_West Nile Virus_Infected_12days_rep1 [8002x3032]


title: 03_RPE1_1d_control_3

value: biological rep 3


title: Brain_West Nile Virus_Infected_7days_rep3 [8002x3032]


title: 02_RPE1_1d_control_2


title: Brain_West Nile Virus_Infected_7days_rep2 [8002x3032]


title: 01_RPE1_1d_control_1

value: biological rep 1


title: AvrRpt2 treated rps2 at 0hpi, rep2

source_name: rps2 0h_2

tag: genotype

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 0h


title: AvrRpt2 treated rps2 at 0hpi, rep1

source_name: rps2 0h_1


title: Brain_West Nile Virus_Infected_4days_rep3 [8002x3032]


title: Brain_West Nile Virus_Infected_7days_rep1 [8002x3032]


title: Brain_West Nile Virus_Infected_4days_rep2 [8002x3032]


title: 04_RPE1_1d_CASP8AP2_1


title: AvrRpt2 treated rps2 at 10hpi, rep1


title: AvrRpt2 treated Col-0 at 10hpi, rep3

value: WT


title: AvrRpt2 treated Col-0 at 10hpi, rep2


title: AvrRpt2 treated rps2 at 0hpi, rep3

source_name: rps2 0h_3


title: Pcan2_Sp

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

institute: University of Göttingen

hyb_protocol: 600 ng of Cy3 probes were mixed and hybridized to a 180K custom microarray (Agilent Technologies) for 17 hours at 65ºC in Gex Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions, dried by centrifugation.

scan_protocol: Arrays were scanned at 3 mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and the images were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively (Smyth and Speed 2003).

organism: Pinus canariensis

source_name: Cambial cells differentiating to xylem

label_protocol: 200 ng of total RNA was reversely transcribed using T7 promotor primer and the cDNA was converted to aRNA using T7 RNA polimerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP

growth_protocol: Trees were grown in 3:1 (v/v) peat:vermiculite, in 650 ml cone-containers first and 5 liters containers after the first year. At the moment of this study trees were approximately 150 cm high, with a diameter of 2-3 cm.

extract_protocol: Total RNA was isolated from differentiating xylem samples stored at -80ºC, using the CTAB-LiCl precipitation method (Chang et al. 1993), and purified with the RNeasy Plant Mini Kit (Qiagen, CA, USA). Quantity of total RNA for each sample was measured with Nanodrop model ND-1000 (Thermo Scientific, MA, USA), and RNA quality was checked using the Experion Bioanalyzer (Bio-Rad, CA, USA).

value: Vascular cambium

value: 42 months


title: AvrRpt2 treated Col-0 at 10hpi, rep1


title: KYSE 3410

value: esophageal squamous cell carcinoma

value: KYSE 3410


title: HE3-1

source_name: normal epithelium cell

value: normal epithelium cell


title: KYSE 140

value: KYSE 140


title: KYSE 170

value: KYSE 170


title: KYSE 190

value: KYSE 190


title: Pcan3_Sp


title: KYSE 1170

value: KYSE 1170


title: KYSE 1240

value: KYSE 1240


title: KYSE 1190

value: KYSE 1190


title: Pcan1_Sp


title: HEEpic-2


title: Pcan2_Jl

value: 40 months


title: Pcan3_Jl


title: AvrRpt2 treated Col-0 at 6hpi, rep3

source_name: WT 6h_3

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 6h

value: mature leaf

value: four weeks


title: Brain_Mock_Infected_12Mdays_rep2 [8036x18018]

value: brain

value: Mock


title: Brain_West Nile Virus_Infected_12days_rep3 [8036x18018]

value: West Nile Virus


title: Brain_Mock_Infected_12Mdays_rep1 [8036x18018]


title: yeast-sse1-control-rep3

city: Szeged

first: Zoltan

last: Farkas

state: Csongrad

address: Temesvari krt. 62.

country: Hungary

institute: Biological Research Centre

description: Gene expression data from single gene deletion strain without overexpression

hyb_protocol: Samples were hybridized at 45 °C for 16 hours, then standard washing protocol was performed using Affymetrix GeneChip Fluidics Station 450

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

data_processing: The processing and analysis of expression data was performed with the R 3.2.0/Bioconductor 3.1 [R Core Team (2013). Applying the Affimetrix mask file downloaded from http://www.affymetrix.com/support/technical/mask_files.affx repository the probesets corresponding to Schizosaccharomyces pombe ORFs were excluded from the subsequent analysis. The expression data was RMA normalised, the method is implemented in the affy 1.46 package.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae SSE1 deletion backgound, without overexpression

label_protocol: Standard Affymetrix protocol was used to generate and hybridize biotin labeled cRNA. Briefly, 3’IVT Express Kit (Affymetrix) was used for amplifying and labeling 200 ng of total RNA samples

growth_protocol: 3-3 independent colonies per gentotype were inoculated into leucine dropout SC-MSG liquid medium, and were grown until saturation at 30°C. The saturated cultures were diluted and grown to early mid-log phase (OD600=0.6), and 10^7 cells were used to extract total RNA

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

treatment_protocol: No additional treatment for the cells was used. The cellular response against two different internal stress were investigated only

value: yeast cells

tag: genotype/variation

value: SSE1 deletion

value: exponential phase

tag: plasmid

value: empty


title: Brain_West Nile Virus_Infected_12days_rep2 [8036x18018]


title: Brain_West Nile Virus_Infected_12days_rep1 [8036x18018]


title: AvrRpt2 treated Col-0 at 0hpi, rep2

source_name: WT 0h_2

value: WT

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 0h


title: Brain_Mock_Infected_12Mdays_rep3 [8036x18018]


title: AvrRpt2 treated Col-0 at 0hpi, rep1

source_name: WT 0h_1


title: yeast-sse1-yEVenus-rep3

description: Gene expression data from single gene deletion strain with overexpression

source_name: Saccharomyces cerevisiae SSE1 deletion backgound, with overexpression

value: yEVenus multi-copy plasmid


title: yeast-sse1-yEVenus-rep2


title: yeast-sse1-control-rep1


title: Dex:YFP-CPR5-C plants treated with water, biological rep2


title: Pcan2_Jn

value: Vascular cambium

value: 39 months


title: Ameloblastoma Replicate 16

city: Chapel Hill

first: Shijia

last: Hu

state: NC

address: 228 Brauer Hall Campus Box 7450

department: Pediatric Dentistry

institute: University of North Carolina

description: Biological replicate 16 of 17. Microdissected ameloblastoma.

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA (825 ng) from two different samples were hybridized to Agilent Human Whole Genome Oligonucleotide Microarrays.  The hybridized array was then washed and scanned.

scan_protocol: Scanned on an Agilent G2500 Scanner and data was extracted from the scanned image using Feature Extraction version 9.5 (Agilent Technologies).

source_name: Ameloblastoma

label_protocol: The TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies, Madison, WI, USA) was used for the linear amplification process. 5 µg of amplified aRNA from the laser-captured tissue was labeled with the Cy5 dye and hybridized to the arrays with a Cy3-labeled Stratagene Human Universal Reference(Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from the microdissected cells with the PicoPure RNA Isolation kit (Arcturus Bioscience, Santa Clara, CA, USA).

tag: sample condition

value: FFPE

tag: diagnosis

value: Follicular ameloblastoma

tag: recurrence

value: No

source_name: Stratagene Human Universal Reference

tag: type

value: Reference RNA


title: Ameloblastoma Replicate 17

description: Biological replicate 17 of 17. Microdissected ameloblastoma.

data_processing: Feature Extraction version 9.5 (Agilent Technologies)

value: Fresh frozen


title: Dex:YFP-CPR5-C plants treated with dexamethasone, biological rep1

tag: cultivar

value: mature leaf

value: four weeks


title: AvrRpt2 treated Col-0 at 6hpi, rep1

source_name: WT 6h_1

tag: treatment

value: Infiltration of Psm:AvrRpt2 OD 0.01 for 6h

tag: age


title: Pcan1_Jn

tag: tissue


title: yeast-sse1-control-rep2

value: yeast cells


title: Brain_West Nile Virus_Infected_4days_rep1 [8002x3032]

source_name: Brain_West Nile Virus_Infected_4days

tag: timepoint(days)

value: brain

tag: infection

value: West Nile Virus


title: Pcan3_Jn


title: AvrRpt2 treated Col-0 at 0hpi, rep3

source_name: WT 0h_3


title: AvrRpt2 treated Col-0 at 6hpi, rep2

source_name: WT 6h_2


title: Pcan3_My

value: 38 months


title: Pcan2_My


title: Brain_West Nile Virus_Infected_7days_rep3 [8036x18018]

source_name: Brain_West Nile Virus_Infected_7days


title: Pcan1_My


title: Ameloblastoma Replicate 15

description: Biological replicate 15 of 17. Microdissected ameloblastoma.

value: Multicystic Ameloblastoma, plexiform

value: Yes


title: Brain_West Nile Virus_Infected_7days_rep2 [8036x18018]


title: Brain_West Nile Virus_Infected_7days_rep1 [8036x18018]


title: Brain_West Nile Virus_Infected_4days_rep3 [8036x18018]


title: Brain_Mock_Infected_12Mdays_rep3 [3252x8042]

description: 20151230_WNV1_Sample 12_12.RCC

value: Mock


title: yeast-sse1-yEVenus-rep1

value: SSE1 deletion

value: exponential phase

value: yEVenus multi-copy plasmid


title: Brain_West Nile Virus_Infected_4days_rep1 [8036x18018]


title: Brain_Mock_Infected_12Mdays_rep2 [3252x8042]

description: 20151230_WNV1_Sample 11_11.RCC


title: Brain_West Nile Virus_Infected_4days_rep2 [8036x18018]


title: Brain_Mock_Infected_12Mdays_rep1 [3252x8042]

description: 20151230_WNV1_Sample 10_10.RCC


title: Brain_West Nile Virus_Infected_12days_rep3 [3252x8042]

description: 20151230_WNV1_Sample 09_09.RCC

source_name: Brain_West Nile Virus_Infected_12days


title: Brain_West Nile Virus_Infected_12days_rep2 [3252x8042]

description: 20151230_WNV1_Sample 08_08.RCC


title: Ameloblastoma Replicate 11

description: Biological replicate 11 of 17. Microdissected ameloblastoma.

value: FFPE

value: Multicystic ameloblastoma, plexiform


title: Brain_West Nile Virus_Infected_12days_rep1 [3252x8042]

description: 20151230_WNV1_Sample 07_07.RCC


title: Ameloblastoma Replicate 5

description: Biological replicate 5 of 17. Microdissected ameloblastoma.

value: Follicular ameloblastoma

value: No

value: Reference RNA


title: Pcan1_Jl

value: Vascular cambium

value: 40 months


title: Pcan2_Ab

value: 37 months


title: Ameloblastoma Replicate 13

description: Biological replicate 13 of 17. Microdissected ameloblastoma.

value: Plexiform Ameloblastoma


title: Ameloblastoma Replicate 9

description: Biological replicate 9 of 17. Microdissected ameloblastoma.

value: Peripheral Ameloblastoma


title: Ameloblastoma Replicate 14

description: Biological replicate 14 of 17. Microdissected ameloblastoma.


title: Ameloblastoma Replicate 8

description: Biological replicate 8 of 17. Microdissected ameloblastoma.


title: Ameloblastoma Replicate 10

description: Biological replicate 10 of 17. Microdissected ameloblastoma.


title: Pcan2_Mz

value: 36 months


title: Ameloblastoma Replicate 6

description: Biological replicate 6 of 17. Microdissected ameloblastoma.


title: Ameloblastoma Replicate 12

description: Biological replicate 12 of 17. Microdissected ameloblastoma.


title: Ameloblastoma Replicate 4

description: Biological replicate 4 of 17. Microdissected ameloblastoma.

value: Recurrent ameloblastoma


title: Pcan3_Mz


title: Pcan1_Mz


title: Pcan1_Ab


title: Pcan3_Ab


title: Ameloblastoma Replicate 7

description: Biological replicate 7 of 17. Microdissected ameloblastoma.


title: Brain_West Nile Virus_Infected_7days_rep3 [3252x8042]

description: 20151230_WNV1_Sample 06_06.RCC

value: brain

value: West Nile Virus


title: Brain_West Nile Virus_Infected_4days_rep2 [3252x8042]

description: 20151230_WNV1_Sample 02_02.RCC


title: Brain_West Nile Virus_Infected_4days_rep1 [3252x8042]

description: 20151230_WNV1_Sample 01_01.RCC


title: Brain_West Nile Virus_Infected_4days_rep3 [3252x8042]

description: 20151230_WNV1_Sample 03_03.RCC


title: Brain_West Nile Virus_Infected_7days_rep1 [3252x8042]

description: 20151230_WNV1_Sample 04_04.RCC


title: Brain_West Nile Virus_Infected_7days_rep2 [3252x8042]

description: 20151230_WNV1_Sample 05_05.RCC


title: Ameloblastoma Replicate 3

description: Biological replicate 3 of 17. Microdissected ameloblastoma.

value: Yes


title: skeletal musucle_GDE5 overexpression

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: control

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: The mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNAs of skeletal muscles were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Male control and GDE5 Tg mice (12 weeks) were fed control diet.

tag: strain

value: male

value: skeletal muscle

value: control

source_name: GDE5 Tg

value: GDE5 overexpression


title: Ameloblastoma Replicate 1

description: Biological replicate 1 of 17. Microdissected ameloblastoma.

value: Fresh frozen

value: Follicular ameloblastoma


title: Ameloblastoma Replicate 2

description: Biological replicate 2 of 17. Microdissected ameloblastoma.

value: FFPE

value: Cystic ameloblastoma

value: No

value: Reference RNA


title: Submerged culture with xylose rep 1

status: Public on Aug 23 2016

city: La Moilina

first: Marcel

last: Gutiérrez-Correa

address: Av. La Molina

country: Peru

institute: UNALM

description: Gene expression at 72h in submerged

hyb_protocol: 1,65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing 2x Agilent Blocking reagent, 1X fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HI-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Agilent Oligo Microarrays (G2514F, DesignID: 032510) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) + 0.05 % Triton X-102 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) + 0.05% Triton X-102 (Agilent), then cover with ozone barrier (Agilent), and scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%). Tiff 20 bit images were generated.

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Aspergillus niger

source_name: Submerged

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input RNA Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by Illustra RNA column purification (General Electric, USA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Biofilms and submerged cultures were inoculated with Aspergillus niger spores to a final concentration of 10^6 spores/ml. The cultures were incubated for 72 hours at 28 ºC, shaken at 175 rpm.

extract_protocol: RNA was prepared using Qiazol reagent protocol (Qiagen). An additional clean-up was performed using the RNEasy Plant Mini Kit (Qiagen), following the manufacturer’s RNA Clean-up protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For biofilm culture, the inoculation was in flask containing a polyester cloth square and 70ml of distilled water to allow the attachment of spores. After that, polyester cloth square was transferred to flasks containing 70 mL of the culture médium with the appropriate carbon source (lactose, xylose, maltose or glucose) added to a final concentration of 1%. For submerged culture, the  inoculation was directly in the culture médium .Biofilms and submerged cultures were incubated for 72 hours at 28 ºC, shaken at 175 rpm

tag: developmental stage

value: Mycelium

tag: carbon source

value: xylose

tag: growth time


title: Submerged culture with lactose rep 2

description: Gene expression at 72h in submerged

value: lactose


title: Submerged culture with xylose rep 4

description: Gene expression at 72h in submerged


title: Biofilms culture with xylose rep 1

description: Gene expression at 72h in biofilms

source_name: Biofilms


title: Biofilms culture with xylose rep 2

description: Gene expression at 72h in biofilms


title: Biofilms culture with xylose rep 4

description: Gene expression at 72h in biofilms


title: Biofilms culture with lactose rep 4

description: Gene expression at 72h in biofilms


title: Biofilms culture with lactose rep 3

description: Gene expression at 72h in biofilms


title: Biofilms culture with xylose rep 3

description: Gene expression at 72h in biofilms


title: Submerged culture with lactose rep 1

description: Gene expression at 72h in submerged


title: Submerged culture with xylose rep 3

description: Gene expression at 72h in submerged


title: Submerged culture with lactose rep 4

description: Gene expression at 72h in submerged


title: Submerged culture with xylose rep 2

description: Gene expression at 72h in submerged


title: Submerged culture with lactose rep 3

description: Gene expression at 72h in submerged


title: Biofilms culture with lactose rep 1

description: Gene expression at 72h in biofilms


title: Biofilms culture with lactose rep 2

description: Gene expression at 72h in biofilms


title: Submerged culture with maltose rep 4

description: Gene expression at 72h in submerged

value: maltose


title: Biofilms culture with maltose rep 3

description: Gene expression at 72h in biofilms


title: Submerged culture with maltose rep 3

description: Gene expression at 72h in submerged


title: Biofilms culture with maltose rep 2

description: Gene expression at 72h in biofilms


title: Submerged culture with maltose rep 1

description: Gene expression at 72h in submerged


title: Biofilms culture with maltose rep 1

description: Gene expression at 72h in biofilms


title: Submerged culture with glucose rep 3

description: Gene expression at 72h in submerged

value: glucose


title: Biofilms culture with glucose rep 4

description: Gene expression at 72h in biofilms


title: Biofilm culture with glucose rep 3

description: Gene expression at 72h in biofilms


title: Biofilm culture with glucose rep 2

description: Gene expression at 72h in biofilms


title: Submerged culture with glucose rep 2

description: Gene expression at 72h in submerged


title: Submerged culture with glucose rep 1

description: Gene expression at 72h in submerged


title: Submerged culture with glucose rep 4

description: Gene expression at 72h in submerged


title: Biofilms culture with maltose rep 4

description: Gene expression at 72h in biofilms


title: BnTR1_42_rep3

status: Public on Aug 19 2016

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

description: E. coli cells transformed with pET-28a-BnTR1 were incubated at 37°C for 1 hour, in total of three biological repeats, and this is the third one.

hyb_protocol: Hybridization was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

scan_protocol: Scanning was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

data_processing: Raw data were normalized (quantile method), merged and filtered by Feature Extraction Software (Agilent Technologies Inc.). For the sibiling probes (multiple probes to one gene), we used the median indensity for representation.

organism: Escherichia coli

source_name: BnTR1, 42°C, replicate 3

label_protocol: Labeling was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.

growth_protocol: E. coli Rosetta cells transformed with pET-28a or pET-28a-BnTR1 (OD600nm = 0.6) were induced with 0.1 mM IPTG at 37°C for 1 hour.

extract_protocol: Collected cells were lysed using Trizol (Invitrogen), and total RNA was isolated using phenol-chloroform and precipitated with ice cold isopropanol. Then the precipitations were further washed with 70% ethanol and dissolved in RNase-free water. Genomic DNA was removed using RNase-free DNase I. RNA samples were further purified using RNeasy Mini Kits (Qiagen). RNA concentration and quality were determined using A Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA) and agarose gel electrophoresis. The isolated RNA was stored at −80°C before use.

treatment_protocol: E. coli cells with or without BnTR1 were transferred and incubated at 37°C and 42°C for 1 hour, respectively

tag: culture temperature

tag: vector


title: EmptyVector_37_rep3

description: E. coli cells transformed with pET-28a were incubated at 37°C for 1 hour, in total of three biological repeats, and this is the third one.

source_name: Emplty Vector, 37°C, replicate 3


title: Control sample 9

status: Public on Jul 22 2016

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

country: Spain

institute: Clinica Universidad de Navarra

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Bone marrow

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: not provided

value: Healthy

tag: cell type

value: Plasma cells


title: EmptyVector_42_rep3

description: E. coli cells transformed with pET-28a were incubated at 42°C for 1 hour, in total of three biological repeats, and this is the third one.

source_name: Emplty Vector, 42°C, replicate 3


title: Submerged culture with maltose rep 2

description: Gene expression at 72h in submerged


title: EmptyVector_37_rep2

description: E. coli cells transformed with pET-28a were incubated at 37°C for 1 hour, in total of three biological repeats, and this is the second one.

source_name: Emplty Vector, 37°C, replicate 2


title: BnTR1_42_rep2

description: E. coli cells transformed with pET-28a-BnTR1 were incubated at 42°C for 1 hour, in total of three biological repeats, and this is the second one.

source_name: BnTR1, 42°C, replicate 2


title: BnTR1_37_rep1

description: E. coli cells transformed with pET-28a-BnTR1 were incubated at 37°C for 1 hour, in total of three biological repeats, and this is the first one.

source_name: BnTR1, 37°C, replicate 1


title: EmptyVector_42_rep2

description: E. coli cells transformed with pET-28a were incubated at 42°C for 1 hour, in total of three biological repeats, and this is the second one.

source_name: Emplty Vector, 42°C, replicate 2


title: BnTR1_37_rep3

source_name: BnTR1, 37°C, replicate 3


title: EmptyVector_42_rep1

description: E. coli cells transformed with pET-28a were incubated at 42°C for 1 hour, in total of three biological repeats, and this is the first one.

source_name: Emplty Vector, 42°C, replicate 1


title: Biofilm culture with glucose rep 1

description: Gene expression at 72h in biofilms


title: BnTR1_42_rep1

description: E. coli cells transformed with pET-28a-BnTR1 were incubated at 42°C for 1 hour, in total of three biological repeats, and this is the first one.

source_name: BnTR1, 42°C, replicate 1


title: BnTR1_37_rep2

description: E. coli cells transformed with pET-28a-BnTR1 were incubated at 37°C for 1 hour, in total of three biological repeats, and this is the second one.

source_name: BnTR1, 37°C, replicate 2


title: EmptyVector_37_rep1

description: E. coli cells transformed with pET-28a were incubated at 37°C for 1 hour, in total of three biological repeats, and this is the first one.

source_name: Emplty Vector, 37°C, replicate 1


title: Control sample 12


title: Age- and sex-matched unaffected control iPSC-derived neurons from NN1 (clone 0B1)

status: Public on Jul 01 2016

first: Owen

last: Rennert

address: 10 Center Drive, MSC 1255, Building 10, Room 1C-250

department: NICHD

institute: National Institutes of Health

description: Gene expression data from age- and sex-matched unaffected control iPSC-derived neural culture NN1

hyb_protocol: cDNA was hybridization at 45C overnight. Wash and staining was performed by GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned by GeneChip Scanner 3000 7G controlled AGCC Scan Control (Affymetrix)

data_processing: Microarray data were analyzed by Partek Genomics Suite 6.6 with quantile normalization and RMA background correction. A batch effect due to scan date was removed before student T-test analysis for differentially expressed genes between autistic and their unaffected siblings' iPSC-derived neurons.

label_protocol: cDNA was labeled by biotin using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Fibroblast culture was maintained in alpha MEM medium containing 15% FBS. iPSC/hESC culture was maintained on Matrigel with mTeSR1 medium. iPSC-derived neural culture was maintained in Neurobasal medium containing 1% N2, 2% B27 (without Retinoic acid), 1% GlutaMax, 1% Antibiotics, BDNF (10ng/ml), GDNF (10ng/ml), IGF-1 (10ng/ml), and cAMP (1μM, Sigma) (All neurotrophic factors were from Peprotech).

extract_protocol: Total RNA was extracted by Trizol and purified by Direct-zol RNA MiniPrep (Zymo Research). RNA integrity was assessed by BioAnalyzer.

value: iPSC-derived neuron

tag: disease type

value: Normal

tag: donor id

tag: donor age

tag: donor sex

value: Male

tag: batch


title: Age- and sex-matched unaffected control iPSC-derived neurons from NN1 (clone 004)


title: Control sample 4

tag: diagnosis


title: Unaffected sibling control iPSC-derived neurons from AN2 (clone 0B4)

description: Gene expression data from unaffected sibling control iPSC-derived neural culture AN2


title: Control sample 5


title: Unaffected sibling control iPSC-derived neurons from AN2 (clone 001)


title: Age- and sex-matched unaffected control iPSC-derived neurons from NN2 (clone 0B3)

description: Gene expression data from age- and sex-matched unaffected control iPSC-derived neural culture NN2


title: Unaffected sibling control iPSC-derived neurons from AN3 (clone CT2)

description: Gene expression data from unaffected sibling control iPSC-derived neural culture AN3


title: Control sample 10


title: Unaffected sibling control iPSC-derived neurons from AN1 (clone 0B8)

description: Gene expression data from unaffected sibling control iPSC-derived neural culture AN1


title: Unaffected sibling control iPSC-derived neurons from AN1 (clone 0B2)


title: Autistic iPSC-derived neurons from AA1 (clone 008)

description: Gene expression data from autistic iPSC-derived neural culture AA1

source_name: Autistic iPSC-derived neurons

value: ASD


title: Autistic iPSC-derived neurons from AA2 (clone 007)

description: Gene expression data from autistic iPSC-derived neural culture AA2


title: Autistic iPSC-derived neurons from AA2 (clone 001)


title: Autistic iPSC-derived neurons from AA1 (clone 001)


title: Unaffected sibling control iPSC-derived NPC from AN3 (clone CT2)

description: Gene expression from unaffected sibling control neural progenitor cell (NPC) culture  AN3

value: iPSC-derived NPC


title: Age- and sex-matched unaffected control iPSC-derived NPC from NN2 (clone 0B3)

description: Gene expression from age- and sex-matched unaffected control neural progenitor cell (NPC) culture  NN2


title: Autistic iPSC-derived neurons from AA3 (clone MP1)

description: Gene expression data from autistic iPSC-derived neural culture AA3


title: Age- and sex-matched unaffected control iPSC-derived NPC from NN1 (clone 004)

description: Gene expression from age- and sex-matched unaffected control neural progenitor cell (NPC) culture  NN1


title: Age- and sex-matched unaffected control iPSC-derived NPC from NN1 (clone 0B1)


title: Unaffected sibling control iPSC-derived NPC from AN1 (clone 0B2)

description: Gene expression from unaffected sibling control neural progenitor cell (NPC) culture  AN1


title: Autistic iPSC-derived NPC from AA2 (clone 001)

description: Gene expression from autistic neural progenitor cell (NPC) culture  AA2

source_name: Autistic iPSC-derived NPC


title: Autistic iPSC-derived NPC from AA1 (clone 001)

description: Gene expression from autistic neural progenitor cell (NPC) culture  AA1


title: Autistic iPSC-derived NPC from AA3 (clone MP1)

description: Gene expression from autistic neural progenitor cell (NPC) culture  AA3


title: Unaffected sibling control iPSC-derived NPC from AN1 (clone 0B8)


title: Unaffected sibling control iPSC-derived NPC from AN2 (clone 0B4)

description: Gene expression from unaffected sibling control neural progenitor cell (NPC) culture  AN2


title: Autistic iPSC-derived NPC from AA2 (clone 007)


title: Autistic iPSC-derived NPC from AA1 (clone 008)


title: Age- and sex-matched unaffected control iPSC from NN2 (clone 0B3)

description: Gene expression data from age- and sex-matched unaffected control induced pluripotent stem cell (iPSC) culture NN2

value: iPSC


title: Unaffected sibling control iPSC-derived NPC from AN2 (clone 001)


title: Age- and sex-matched unaffected control iPSC from NN1 (clone 0B1)

description: Gene expression data from age- and sex-matched unaffected control induced pluripotent stem cell (iPSC) culture NN1


title: Age- and sex-matched unaffected control iPSC from NN1 (clone 004)


title: Unaffected sibling control iPSC from AN2 (clone 0B4)

description: Gene expression data from unaffected sibling control induced pluripotent stem cell (iPSC) culture AN2

source_name: Unaffected sibling control iPSC


title: Unaffected sibling control iPSC from AN3 (clone CT2)

description: Gene expression data from unaffected sibling control induced pluripotent stem cell (iPSC) culture AN3


title: Unaffected sibling control iPSC from AN1 (clone 0B8)

description: Gene expression data from unaffected sibling control induced pluripotent stem cell (iPSC) culture AN1


title: Unaffected sibling control iPSC from AN1 (clone 0B2)


title: Autistic iPSC from AA3 (clone MP1)

description: Gene expression data from autistic induced pluripotent stem cell (iPSC) culture AA3

source_name: Autistic iPSC


title: Autistic iPSC from AA2 (clone 007)

description: Gene expression data from autistic induced pluripotent stem cell (iPSC) culture AA2


title: Autistic iPSC from AA2 (clone 001)


title: Unaffected sibling control iPSC from AN2 (clone 001)

description: Gene expression data from unaffected sibling control induced pluripotetn stem cell (iPSC) culture AN2


title: Age- and sex-matched unaffected healthy donor fibroblast NN2 rep2

description: Gene expression data from age- and sex-matched unaffected healthy donor skin fibroblast culture NN2

source_name: Age- and sex-matched unaffected control fibroblast

value: Fibroblast


title: Normal female hESC E53 rep2

description: Gene expression data from normal female human embryonic stem cell (hESC) ESI-053

source_name: WT hESC

value: hESC

value: WT

value: embryonic

value: Female

tag: cell line


title: Normal female hESC C2 rep2

description: Gene expression data from normal female human embryonic stem cell (hESC) CT2


title: Normal female hESC E53 rep1


title: Unaffected sibling control donor fibroblast AN2 rep2

description: Gene expression data from unaffected sibling control donor skin fibroblast culture AN2

source_name: Unaffected sibling control fibroblast


title: Unaffected sibling control donor fibroblast AN3 rep2

description: Gene expression data from unaffected sibling control donor skin fibroblast culture AN3


title: Unaffected sibling control donor fibroblast AN2 rep1


title: Autistic donor fibroblast AA1 rep2

description: Gene expression data from autistic donor skin fibroblast culture AA1

source_name: Autistic fibroblast


title: Age- and sex-matched unaffected healthy donor fibroblast NN1 rep1

description: Gene expression data from age- and sex-matched unaffected healthy donor skin fibroblast culture NN1


title: Autistic donor fibroblast AA1 rep1


title: Autistic iPSC from AA1 (clone 001)

description: Gene expression data from autistic induced pluripotent stem cell (iPSC) culture AA1


title: Unaffected sibling control donor fibroblast AN3 rep1


title: Autistic donor fibroblast AA3 rep1

description: Gene expression data from autistic donor skin fibroblast culture AA3


title: Autistic iPSC from AA1 (clone 008)


title: Autistic donor fibroblast AA2 rep2

description: Gene expression data from autistic donor skin fibroblast culture AA2


title: Autistic donor fibroblast AA3 rep2


title: Unaffected sibling control donor fibroblast AN1 rep2

description: Gene expression data from unaffected sibling control donor skin fibroblast culture AN1


title: Age- and sex-matched unaffected healthy donor fibroblast NN2 rep1


title: Age- and sex-matched unaffected healthy donor fibroblast NN1 rep2


title: Autistic donor fibroblast AA2 rep1


title: Unaffected sibling control donor fibroblast AN1 rep1


title: Melmet 5 treated with vemurafenib Set3

status: Public on Aug 01 2015

city: Oslo

first: Lina

last: Prasmickaite

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

description: replicate 1

hyb_protocol: A total of 750ng of biotin-labeled cRNA was hybridized followingstandard Illumina protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw microarray data was preprocessed and quantile normalized in Illumina Genome Studio v2011.1 at transcript level. The data was imported into J-Express v2012 (www.molmine.com) and log2-transformed

source_name: Melanoma cell line Melmet 5

label_protocol: standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit In short, 500ng of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: Total RNA was isolated using the TRI Reagent® (Invitrogen, Carlsbad, CA) using the manufacturer protocol. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer

tag: treatment

value: vemurafenib

tag: cancer type

value: Melanoma

tag: growing conditions

value: mono-cultures

tag: tissue origin

value: Metastases lymph node


title: dmc1-rec8delta_ssDNA_5h_rep1

status: Public on Aug 06 2015

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
rec8delta_rep1
ssDNA enrichment

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the marrray package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

source_name: meiotic time point 0h ssDNA enrichment

label_protocol: 1.5 μg of ssDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated at the indicated timepoints.

extract_protocol: To isolate ssDNA, ~109 cells were fixed in 70% ethanol at –20°C. Cells were spheroplasted in sorbitol buffer (1M sorbitol, 1% beta-mercaptoethanol, 0.2 mg/ml zymolyase 100T, 0.1M EDTA, pH 7.4), lysed in NDS (0.6% SDS, 300mM EDTA, 10mM Tris.HCl, pH 9.5). DNA deproteinated with proteinase K (0.25mg/ml; Roche) at 50°C, twice phenol extracted, treated with RNase A, and stored in TE (1mM EDTA, 10mM Tris.HCl, pH 7.5) at 4°C. 25 μg DNA were digested to completion with EcoRI (New England Biolabs). ssDNA was enriched by batch absorption to BND cellulose. Briefly, a 50% slurry of BND-cellulose was equilibrated in NET (1M NaCl, 10mM Tris, pH 7.6, 1mM EDTA). Digested DNA was adjusted to 1M NaCl and ssDNA was incubated with a 500 μl bed volume of BND-cellulose for 5 minutes. Resin was washed with five bed volumes of NET. ssDNA was eluted five times with 600 μl NET + 1.8% caffeine. DNA was precipitated and concentrated for microarray analysis.

tag: strain

tag: genotype

value: dmc1 delta; rec8 delta

source_name: meiotic time point 5h ssDNA enrichment


title: Melmet 5 fraction treated with vemurafenib Set3

description: replicate 3

value: Melmet 5 fraction vemurafenib

value: Co-cultures


title: Normal female hESC C2 rep1

city: Bethesda


title: dmc1-rec8delta_ssDNA_5h_rep2

description:
rec8delta_rep2
ssDNA enrichment


title: Melmet 5 ctr Set3

description: replicate 3

value: control


title: Melmet 5 fraction control Set3

description: replicate 2

value: Melmet5 fraction control


title: Melmet 5 fraction treated with vemurafenib Set2

description: replicate 2


title: Melmet 5 treated with vemurafenib Set2

description: replicate 3


title: Melmet 5 fraction control Set2

description: replicate 1


title: Melmet 5 fraction control Set1

description: replicate 3


title: Melmet 5 fraction treated with vemurafenib Set1

description: replicate 1


title: DS 3

status: Public on Jul 24 2015

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Data was normalised and VST transformed using lumi

source_name: HMEC

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

growth_protocol: Normal finite life span HMECs were obtained from reduction mammoplasty tissue of a 21-year-old individual, specimen 184, and were cultured as previously described (Garbe et al., 2009). Independent cultures were serially passaged from passage 6 (early proliferating, EP cells) through to deep senescence (DS cells). DS cultures underwent no further expansion upon at least two serial passages. The DS cells in our experiments displayed the key characteristics of cellular senescence. All experiments were done on three individual cultures of EP and DS cells, passaged from single progenitor plates.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc).

treatment_protocol: HMECs were transfected with 60nM siGLO siRNA (Dharmacon) in 384-well or 6-well plates using Dharmafect3 (Dharmacon)

tag: Sex

value: F

tag: cell stage

value: deep senescenc


title: Melmet 5 treated with vemurafenib Set1

description: replicate 2


title: HUVEC_HRG_24hr_1

status: Public on Mar 12 2015

city: Uppsala

first: Lena

last: Claesson-Welsh

state: Uppsala

address: Dag Hammarskjölds v 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

hyb_protocol: GeneChip® ST Arrays ( GeneChip® Human Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: GeneChip® Scanner 3000 7G

data_processing: The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method first suggested by Li and Wong in 2001 (1,2). Subsequent analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). In order to search for the differentially expressed genes between X and the Y groups an empirical Bayes moderated t-test was then applied (3), using the ‘limma’ package (4). To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg (5).

source_name: HUVEC 24hrs HRG

label_protocol: Amplified and biotinylated sense-strand cDNA were generated from the entire expressed genome according to the Ambion WT Expression Kit( P/N 4425209 Rev B 05/2009) and Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 3, Affymetrix Inc., Santa Clara, CA)

growth_protocol: Early passage HUVECs were cultured in complete MV2 medium.

extract_protocol: Qiagen RNA easy Kit

treatment_protocol: Cell media was removed and replace with MV2 media with 1% FCS with HRG (1 ug/ml) or PBS.

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: DS 2


title: EP 3

value: early proliferating


title: X714_PAF_2

status: Public on Mar 11 2015

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

description: PAF from patient2

hyb_protocol: Biotin-labeled sense-strand cDNA were hybridized for 16 hours at 45C on GeneChip with GeneChip Hybridization Oven 640 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were obtained by Affymetrix GeneChip Command Console.　Data were normalized by the RMA (Robust Multi-array Average) procedure in R package.

source_name: PAF

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

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: Total RNA was extracted.

tag: individual

value: PAF


title: HUVEC_Basal_24hr_2

source_name: HUVEC 24hrs Basal

tag: cell type


title: HUVEC_Basal_24hr_1


title: GEA5_GF00_PAF_4

description: PAF from patient4


title: HUVEC_HRG_6hr_2

source_name: HUVEC 6hrs HRG


title: GEA5_GF20_nonPAF_4

description: non PAF from patient4

source_name: nonPAF

value: nonPAF


title: HUVEC_Basal_6hr_1

source_name: HUVEC 6hrs Basal


title: HUVEC_HRG_24hr_2


title: EP 2


title: EP 1


title: X1423_nonPAF_3

description: non PAF from patient3


title: HUVEC_Basal_6hr_2


title: X565_PAF_1

description: PAF from patient1


title: Melmet 5 ctr Set2

description: replicate 2


title: X718_nonPAF_2

description: non PAF from patient2


title: X1420_PAF_3

description: PAF from patient3


title: HUVEC_HRG_6hr_1


title: Melmet 5 ctr Set1

description: replicate 1


title: X1040_nonPAF_1

description: non PAF from patient1


title: Cell line 2108

status: Public on Mar 01 2015

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: No additional information.

hyb_protocol: Affymetrix Hybridization Protocol Other: cDNAs were fragmented and hybridized to the GeneChip Human Gene 1.0 ST Arrays. The arrays were washed and stained in a Fluidics Station 450 (Affymetrix).

scan_protocol: Affymetrix Scanning Protocol Other: Scanning was carried out with the GeneChip Scanner 3000 and image analysis with the Affymetrix GeneChip Command Console Scan Control.

data_processing:
Partek Data Processing Protocol
Calculation Method: Expression data were normalized using the RMA algorithm, http://www.partek.com/ (Partek Inc., St. Louis, MO). Data were log-transformed (base 2) for parametric analysis. All analyses were performed using Partek Genomic Suite. Principal component analysis (PCA) was applied for visualization based on the complete data set. Class comparison was based on ANOVA encompassing variations related to batch effect and other hidden variables. Heat maps are presented based on Partek visualization programs. The functional interpretation of gene signature was executed using Ingenuity Pathways Analysis (IPA) tools 3.0 (http://www.ingenuity.com ).

source_name: Cell line 2108

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from mRNA (Affymetrix WT Terminal Labeling Kit).

extract_protocol:
Extraction Protocol
Other: Total RNA from melanoma cell lines and patients' melanoma metastases was extracted using miRNeasy minikit (Qiagen). RNA quality and quantity was estimated using Nanodrop (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). First- and second-strand cDNA were synthesized from 300 ng of total RNA according to manufacturer's instructions (Ambion WT Expression Kit).

tag: disease state

value: metastic melanoma


title: Cell line 62428

description: No additional information.

source_name: Cell line 62428


title: Cell line 2139

description: No additional information.

source_name: Cell line 2139


title: Cell line 62438

description: No additional information.

source_name: Cell line 62438


title: Cell line A375

description: No additional information.

source_name: Cell line A375


title: Cell line 1936

description: No additional information.

source_name: Cell line 1936


title: Cell line 1962

description: No additional information.

source_name: Cell line 1962


title: Cell line 1858w

description: No additional information.

source_name: Cell line 1858w


title: Cell line 2035 R

description: No additional information.

source_name: Cell line 2035 R


title: Cell line 1858m

description: No additional information.

source_name: Cell line 1858m


title: Cell line 1195

description: No additional information.

source_name: Cell line 1195


title: Cell line 1290p54

description: No additional information.

source_name: Cell line 1290p54


title: Cell line 1102

description: No additional information.

source_name: Cell line 1102


title: Cell line 1182

description: No additional information.

source_name: Cell line 1182


title: Cell line 526

description: No additional information.

source_name: Cell line 526


title: Cell line 261I6p - repeat 1

description: No additional information.

source_name: Cell line 261I6p


title: Cell line 146III6p - repeat 1

description: No additional information.

source_name: Cell line 146III6p


title: Cell line 201II8p - repeat 1

description: No additional information.

source_name: Cell line 201II8p


title: Cell line 261II7p

description: No additional information.

source_name: Cell line 261II7p


title: Cell line 1938

description: No additional information.

source_name: Cell line 1938


title: Cell line 888

description: No additional information.

source_name: Cell line 888


title: Cell line 140V5p - repeat 1

description: No additional information.

source_name: Cell line 140V5p


title: Cell line 1993

description: No additional information.

source_name: Cell line 1993


title: Cell line 261IV7p

description: No additional information.

source_name: Cell line 261IV7p


title: Cell line 1290p14

description: No additional information.

source_name: Cell line 1290p14


title: Cell line 938

description: No additional information.

source_name: Cell line 938


title: Cell line 146I6p - repeat 1

description: No additional information.

source_name: Cell line 146I6p


title: Cell line 1858f

description: No additional information.

source_name: Cell line 1858f


title: Cell line 201I5p - repeat 1

description: No additional information.

source_name: Cell line 201I5p


title: Cell line 146II6p - repeat 1

description: No additional information.

source_name: Cell line 146II6p


title: Cell line 22202 - repeat 1

description: No additional information.

source_name: Cell line 22202


title: Cell line 140IV6p - repeat 1

description: No additional information.

source_name: Cell line 140IV6p


title: Cell line 29999 - repeat 1

description: No additional information.

source_name: Cell line 29999


title: Cell line 10999 - repeat 1

description: No additional information.

source_name: Cell line 10999


title: Cell line 18599 - repeat 1

description: No additional information.

source_name: Cell line 18599


title: Cell line 29999 - repeat 2

description: No additional information.


title: Cell line 22202 - repeat 2

description: No additional information.


title: Cell line 2086

description: No additional information.

source_name: Cell line 2086


title: Cell line 10999 - repeat 2

description: No additional information.


title: Cell line 3104

description: No additional information.

source_name: Cell line 3104


title: Cell line 261I6p - repeat 2

description: No additional information.

source_name: Cell line 261I6p


title: Cell line 18599 - repeat 2

description: No additional information.


title: Cell line 3107

description: No additional information.

source_name: Cell line 3107


title: Cell line 3025

description: No additional information.

source_name: Cell line 3025


title: Cell line 140V5p - repeat 2

description: No additional information.

source_name: Cell line 140V5p


title: Cell line 146II6p - repeat 2

description: No additional information.


title: Cell line 2297

description: No additional information.

source_name: Cell line 2297


title: Cell line 2195

description: No additional information.

source_name: Cell line 2195


title: Cell line 201I5p - repeat 2

description: No additional information.


title: Cell line 146III6p - repeat 2

description: No additional information.

source_name: Cell line 146III6p


title: Cell line 146I6p - repeat 2

description: No additional information.

source_name: Cell line 146I6p


title: Cell line 201II8p - repeat 2

description: No additional information.

source_name: Cell line 201II8p


title: Cell line 2744

description: No additional information.

source_name: Cell line 2744


title: Cell line 2492

description: No additional information.

source_name: Cell line 2492


title: Cell line 2458

description: No additional information.

source_name: Cell line 2458


title: Cell line 2448

description: No additional information.

source_name: Cell line 2448


title: Cell line 2427

description: No additional information.

source_name: Cell line 2427


title: Cell line 2523

description: No additional information.

source_name: Cell line 2523


title: Cell line 140IV6p - repeat 2

description: No additional information.

source_name: Cell line 140IV6p


title: Cell line 2224

description: No additional information.

source_name: Cell line 2224


title: Cell line 2075

description: No additional information.

source_name: Cell line 2075


title: Cell line 1866

description: No additional information.

source_name: Cell line 1866


title: Cell line 2035

description: No additional information.

source_name: Cell line 2035


title: Cell line 2805

description: No additional information.

source_name: Cell line 2805


title: TGFB1+TAK1,biological rep2

status: Public on Feb 26 2015

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomcis Suite using the RMA normalization method

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: Gingival fibroblasts were grown in DMEM 10% FBS until 40-60% confluence and then in DMEM 0.5% FBS overnight prior to treatment

extract_protocol: TRIZOL was used to extract RNA

treatment_protocol: Cells were pre-treated with DMSO or 400 nM (5Z)-7-Oxozeanol for 45 minutes prior to treatment with or without TGFβ1 (4 ng/ml, R&D systems) for 6 hours

value: gingival fibroblast

value: TBFB1 + 5Z-7-Oxozeanol


title: DMSO,biological rep2

source_name: DMSO,biological

value: DMSO


title: Cell line 2155

description: No additional information.

source_name: Cell line 2155


title: TAK1,biological rep2


title: TAK1,biological rep1


title: TGFB1+TAK1,biological rep1


title: DMSO, biological rep1

source_name: DMSO, biological


title: Day 11 CD19 BBz, biological rep 3

status: Public on Jan 14 2015

city: Philadelphia

first: Carl

last: June

state: Pennsylvania

address: 3400 civic center blvd STRC 421 8-123

department: Department of Pathology

institute: University of Pennsylvania

description:
Day 11 sample expressing CD19 BBz CAR
D11ND306BB

hyb_protocol: cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 1.0ST GeneChips

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Data was process with Partek Genomics Suite, normalized with RMA.

label_protocol: Samples were biotinylated by terminal transferase end labeling

growth_protocol: T cells grown in R10 media from stimulation to rest down.

extract_protocol: Samples were collected, pelletedand snap frozen in liquid nitrogen.  RNA was isolated with Qiagen microRNA kit.

treatment_protocol: Cells were transduced with lentivirus on day 1 post stimulation.

value: CD4+ T cells

tag: car transduction status

value: CD19 CD8a 4-1BB CD3z


title: TGFB1,biological rep1


title: TGFB1,biological rep2


title: Day 11 cMet IgG4, biological rep 2

description:
Day 11 sample expressing cMet CAR
D11ND340LL

value: cMet IgG4 CD28 CD3z


title: Day 11 CD19 28z, biological rep 3

description:
Day 11 sample expressing CD19 28z CAR
D11ND30619

value: CD19 CD8a CD28 CD3z


title: Day 11 cMet IgG4, biological rep 3

description:
Day 11 sample expressing cMet CAR
D11ND306LL


title: Day 11 CD19 28z, biological rep 1

description:
Day 11 sample expressing CD19 28z CAR
D11ND25619


title: Day 11 cMet IgG4, biological rep 1

description:
Day 11 sample expressing cMet CAR
D11ND256LL


title: Day 11 CD19 BBz, biological rep 1

description:
Day 11 sample expressing CD19 BBz CAR
D11ND256BB


title: Day 11 untransduced, biological rep 3

description:
Day 11 sample untransduced
D11ND306m

value: Untransduced


title: Day 11 CD19 28z, biological rep 2

description:
Day 11 sample expressing CD19 28z CAR
D11ND34019


title: Day 11 untransduced, biological rep 2

description:
Day 11 sample untransduced
D11ND340m


title: Day 6 CD19 28z, biological rep 3

description:
Day 6 sample expressing CD19 28z CAR
D6ND30619


title: Day 11 untransduced, biological rep 1

description:
Day 11 sample untransduced
D11ND256m


title: Day 24 cMet IgG4, biological rep 1

description:
Day 24 sample expressing cMet CAR
D24ND256LL


title: Day 6 untransduced, biological rep 3

description:
Day 6 sample untransduced
D6ND306m


title: Day 24 cMet IgG4, biological rep 3

description:
Day 24 sample expressing cMet CAR
D24ND306LL


title: Day 24 cMet IgG4, biological rep 2

description:
Day 24 sample expressing cMet CAR
D24ND340LL


title: Day 11 CD19 BBz, biological rep 2

description:
Day 11 sample expressing CD19 BBz CAR
D11ND340BB


title: Day 6 CD19 BBz, biological rep 3

description:
Day 6 sample expressing CD19 BBz CAR
D6ND306BB


title: Day 6 CD19 BBz, biological rep 2

description:
Day 6 sample expressing CD19 BBz CAR
D6ND340BB


title: Day 6 CD19 28z, biological rep 1

description:
Day 6 sample expressing CD19 28z CAR
D6ND25619


title: Day 6 CD19 28z, biological rep 2

description:
Day 6 sample expressing CD19 28z CAR
D6ND34019


title: Day 6 cMet IgG4, biological rep 3

description:
Day 6 sample expressing cMet CAR
D6ND306LL


title: Day 6 untransduced, biological rep 2

description:
Day 6 sample untransduced
D6ND340m


title: Prestimulation, biological rep 3

description:
Prior to bead stimulation
D0ND306

value: Prestimulation


title: Prestimulation, biological rep 1

description:
Prior to bead stimulation
D0ND256


title: Day 6 CD19 BBz, biological rep 1

description:
Day 6 sample expressing CD19 BBz CAR
D6ND256BB


title: Day 6 cMet IgG4, biological rep 1

description:
Day 6 sample expressing cMet CAR
D6ND256LL


title: Day 6 untransduced, biological rep 1

description:
Day 6 sample untransduced
D6ND256m


title: Day 6 cMet IgG4, biological rep 2

description:
Day 6 sample expressing cMet CAR
D6ND340LL


title: Prestimulation, biological rep 2

description:
Prior to bead stimulation
D0ND340


title: Radiation+cigarette_smoke_extract_24h_rep1

status: Public on Dec 31 2014

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description:
Sample 43
Biological replicate 1 of 3.

hyb_protocol: Hybridization and washes were performed on an Affymetrix® GeneChip™ Fluidics Station 450 instrument using protocols provided by Affymetrix®. This work was performed as a commercial service by a shared genomic facility of the University at Buffalo, Buffalo, NY.

scan_protocol: Arrays were scanned on an Affymetrix® GeneChip™ Scanner 3000 instrument using protocols provided by Affymetrix®. This work was performed as a commercial service by a shared genomic facility of the University at Buffalo, Buffalo, NY.

data_processing: Raw data for all 54 arrays (in .CEL files) was processed together using Affymetrix® Power Tools (version 1.15.0) on Mac OS X 10.6.8. Briefly, background signals were adjusted using the 'rma' method. Array data was then quantile normalized and median polish summarized. All arrays appeared to have yielded data of good quality as assessed using criteria suggested by Affymetrix®.

source_name: NCI-H460, radiation and cigarette smoke extract, 24 hr

label_protocol: The WT Expression kit from Ambion® (Austin, TX) was used to generate sense-strand complementary DNA (cDNA) from 100 ng total RNA. The cDNA was fragmented and labeled with biotin as per protocols provided with the GeneChip™ WT Terminal Labeling and Hybridization kit (Affymetrix®). This work was performed as a commercial service by a shared genomic facility of the University at Buffalo, Buffalo, NY.

growth_protocol: 3x10e5 NCI-H460 cells, at passage number 9 after procurement from ATCC® (Manassas, VA) and maintained in RPMI-1640 medium (Life Technologies®, Grand Island, NY) with 10% fetal bovine serum (Atlanta Biologicals®, Lawrenceville, GA) at 37 ºC under 5% carbon dioxide, were seeded per well of 6-well tissue culture dishes. After 24 hours, the culture medium was replaced with that without serum and cells were grown for another 24 hours.

extract_protocol: Total RNA was extracted from -80 ºC-frozen cell-pellets using the Total RNA Purification kit (catalog# 37500, Norgen-Biotek®, Thorold, ON, Canada) following the kit manufacturer's guidelines. The kit uses silicon carbide spin-columns. On-column DNase I treatment was performed to reduce contaminating genomic DNA. RNA eluted from the columns was treated on-column with DNase I again as per the manufacturer's guidelines provided with the RNase-Free DNase I kit (Norgen-Biotek®). Absorbance at 260 nm and electrophoresis on Bioanalyzer™ 2100 (Agilent®, Austin, TX) was used to estimate RNA concentration and quality.

treatment_protocol: Nictoine (5 uM; Sigma®, Saint Louis, MO) or cigarette smoke extract (5 uM nicotine-equivalent) was added to the culture media, and after 2 hours, cells were irradiated with one dose of 6 Gy ionizing radiation (cesium-137 source), or cisplatin (1 uM; Sigma®) was added to the culture medium. All treatments were performed concurrently using a total of nine 6-well cuture plates. After another 2 or 24 hours, cells were harvested by scraping into the culture medium, spun down, washed in 10 ml phosphate-buffered saline, and collected as cell-pellets after another round of centrifugation at room temperature. The total 54 cell-pellets were stored frozen at -80 ºC until RNA extraction.

value: human lung large cell carcinoma cells

value: radiation and cigarette smoke extract

tag: timepoint

value: 24 hours


title: Cisplatin_24h_rep2

description:
Sample 47
Biological replicate 2 of 3.

source_name: NCI-H460, cisplatin, 24 hr

value: cisplatin


title: Radiation_24h_rep3

description:
Sample 39
Biological replicate 3 of 3.

source_name: NCI-H460, radiation, 24 hr

value: radiation


title: Cisplatin_24h_rep1

description:
Sample 46
Biological replicate 1 of 3.


title: Cisplatin+nicotine_24h_rep3

description:
Sample 51
Biological replicate 3 of 3.

source_name: NCI-H460, cisplatin and nicotine, 24 hr

value: cisplatin and nicotine


title: Radiation+nicotine_24h_rep1

description:
Sample 40
Biological replicate 1 of 3.

source_name: NCI-H460, radiation and nicotine, 24 hr

value: radiation and nicotine


title: Radiation_24h_rep2

description:
Sample 38
Biological replicate 2 of 3.


title: Cisplatin+nicotine_24h_rep1

description:
Sample 49
Biological replicate 1 of 3.


title: Cisplatin+cigarette_smoke_extract_24h_rep2

description:
Sample 53
Biological replicate 2 of 3.

source_name: NCI-H460, cisplatin and cigarette smoke extract, 24 hr

value: cisplatin and cigarette smoke extract


title: Radiation_24h_rep1

description:
Sample 37
Biological replicate 1 of 3.


title: Radiation+cigarette_smoke_extract_24h_rep3

description:
Sample 45
Biological replicate 3 of 3.


title: Radiation+nicotine_24h_rep2

description:
Sample 41
Biological replicate 2 of 3.


title: Cisplatin_24h_rep3

description:
Sample 48
Biological replicate 3 of 3.


title: Radiation+nicotine_24h_rep3

description:
Sample 42
Biological replicate 3 of 3.


title: Cisplatin+cigarette_smoke_extract_24h_rep3

description:
Sample 54
Biological replicate 3 of 3.


title: Radiation+cigarette_smoke_extract_24h_rep2

description:
Sample 44
Biological replicate 2 of 3.


title: Cisplatin+cigarette_smoke_extract_24h_rep1

description:
Sample 52
Biological replicate 1 of 3.


title: Cisplatin+nicotine_24h_rep2

description:
Sample 50
Biological replicate 2 of 3.


title: Cigarette_smoke_extract_24h_rep2

description:
Sample 35
Biological replicate 2 of 3.

source_name: NCI-H460, cigarette smoke extract, 24 hr

value: cigarette smoke extract


title: Cigarette_smoke_extract_24h_rep1

description:
Sample 34
Biological replicate 1 of 3.


title: Control_24h_rep3

description:
Sample 30
Biological replicate 3 of 3.

source_name: NCI-H460, control, 24 hr

value: control (none)


title: Nicotine_24h_rep3

description:
Sample 33
Biological replicate 3 of 3.

source_name: NCI-H460, nicotine, 24 hr

value: nicotine


title: Nicotine_24h_rep2

description:
Sample 32
Biological replicate 2 of 3.


title: Cisplatin+cigarette_smoke_extract_2h_rep3

description:
Sample 27
Biological replicate 3 of 3.

source_name: NCI-H460, cisplatin and cigarette smoke extract, 2 hr

value: 2 hours


title: Control_24h_rep1

description:
Sample 28
Biological replicate 1 of 3.


title: Control_24h_rep2

description:
Sample 29
Biological replicate 2 of 3.


title: Cisplatin+cigarette_smoke_extract_2h_rep2

description:
Sample 26
Biological replicate 2 of 3.


title: Cigarette_smoke_extract_24h_rep3

description:
Sample 36
Biological replicate 3 of 3.


title: Cisplatin+cigarette_smoke_extract_2h_rep1

description:
Sample 25
Biological replicate 1 of 3.


title: Nicotine_24h_rep1

description:
Sample 31
Biological replicate 1 of 3.


title: Cisplatin+nicotine_2h_rep3

description:
Sample 24
Biological replicate 3 of 3.

source_name: NCI-H460, cisplatin and nicotine, 2 hr


title: Cisplatin+nicotine_2h_rep2

description:
Sample 23
Biological replicate 2 of 3.


title: Radiation_2h_rep3

description:
Sample 12
Biological replicate 3 of 3.

source_name: NCI-H460, radiation, 2 hr


title: Radiation+nicotine_2h_rep3

description:
Sample 15
Biological replicate 3 of 3.

source_name: NCI-H460, radiation and nicotine, 2 hr


title: Radiation+nicotine_2h_rep2

description:
Sample 14
Biological replicate 2 of 3.


title: Radiation+nicotine_2h_rep1

description:
Sample 13
Biological replicate 1 of 3.


title: Radiation+cigarette_smoke_extract_2h_rep3

description:
Sample 18
Biological replicate 3 of 3.

source_name: NCI-H460, radiation and cigarette smoke extract, 2 hr


title: Cisplatin_2h_rep3

description:
Sample 21
Biological replicate 3 of 3.

source_name: NCI-H460, cisplatin, 2 hr


title: Cisplatin_2h_rep2

description:
Sample 20
Biological replicate 2 of 3.


title: Nicotine_2h_rep1

description:
Sample 4
Biological replicate 1 of 3.

source_name: NCI-H460, nicotine, 2 hr


title: Radiation_2h_rep1

description:
Sample 10
Biological replicate 1 of 3.


title: Radiation+cigarette_smoke_extract_2h_rep1

description:
Sample 16
Biological replicate 1 of 3.


title: Control_2h_rep3

description:
Sample 3
Biological replicate 3 of 3.

source_name: NCI-H460, control, 2 hr


title: Cisplatin+nicotine_2h_rep1

description:
Sample 22
Biological replicate 1 of 3.


title: Cisplatin_2h_rep1

description:
Sample 19
Biological replicate 1 of 3.


title: Nicotine_2h_rep2

description:
Sample 5
Biological replicate 2 of 3.


title: Cigarette_smoke_extract_2h_rep3

description:
Sample 9
Biological replicate 3 of 3.

source_name: NCI-H460, cigarette smoke extract, 2 hr


title: Radiation+cigarette_smoke_extract_2h_rep2

description:
Sample 17
Biological replicate 2 of 3.


title: Nicotine_2h_rep3

description:
Sample 6
Biological replicate 3 of 3.


title: Cigarette_smoke_extract_2h_rep1

description:
Sample 7
Biological replicate 1 of 3.


title: Cigarette_smoke_extract_2h_rep2

description:
Sample 8
Biological replicate 2 of 3.


title: Radiation_2h_rep2

description:
Sample 11
Biological replicate 2 of 3.


title: Control_2h_rep1

description:
Sample 1
Biological replicate 1 of 3.


title: human macrophages (si HIF-2alpha) 16h 20 ng/ml IL-10, 4h 1% oxygen [12N3]

status: Public on Nov 30 2014

city: Frankfurt

first: Nathalie

last: Dehne

address: Theodor-Stern-Kai 7

department: Faculty of Medicine, Institute of Biochemestry I

institute: Goethe-University Frankfurt

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label_protocol: Samples were labelled with Ambion WT Expression Kit washed and stained using the HWS Kit (Affymetrix).

growth_protocol: primary human leukocytes were isloated from Buffy-coated blood using Leucosept tubes and LSM 1077. Cells were differentiated to macrophages by addition of human serum to RPMI medium containing pencecilin/steptomycin for 5 days.

extract_protocol: total RNA was isolated using Quiagen RNeasy Kit, RNA was amplified using Ambion WT Expression Kit

treatment_protocol: primary human macrophages were petreated with or without IL-10 (20ng/ml) for 16h and aditionally 4h under 21% or 1% oxygen. RNA was isolated using the Quiagen RNeasy Micro Kit.

value: macrophages


title: Control_2h_rep2

description:
Sample 2
Biological replicate 2 of 3.


title: human macrophages (si HIF-2alpha) 16h 20 ng/ml IL-10, 4h 1% oxygen [12N2]


title: A549_mock_input_rep2 [HuGene-1_0]

status: Public on Dec 23 2014

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: Adherent human lung cancer cell line (ATCC CCL-185)

hyb_protocol: Between 0.6 and 3.0 µg fragmented and labeled DNA was hybridized to an Affymetrix Human Gene 1.1 ST Array. Hybridization and washing was performed according to the instructions of the manufacturer.

scan_protocol: Scanning was performed on an Affymetrix GeneTitan® system.

data_processing: Normalization was done using the RMA algorithm with the Affymetrix GeneChip Expression Console Software

label_protocol: 2 µg RNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by terminal labeling with biotin using the “WT Terminal Labeling Kit” (Affymetrix, Inc., Santa Clara, CA, USA) according to the instructions of the manufacturer.

growth_protocol: Adherent monolayers, maintained in DMEM supplemented with 10% fetal calf serum at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was extrated using TRIzol according to the manufacturer's instructions (Life Technologies).

treatment_protocol: Cells were mock-infected and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 30h.

tag: cell origin

value: lung epithelial cell


title: A549_Ad5_input_rep1 [HuGene-1_0]

treatment_protocol: Cells were infected with human adenovirus 5 at an MOI of 30 TCID50/cell and maintained at 37°C in a humidified atmosphere containing 5% CO2 for 30h.


title: A549_mock_input_rep1 [HuGene-1_0]


title: human macrophages (si HIF-1alpha) 16h 20 ng/ml IL-10, 4h 1% oxygen [11N2]


title: human macrophages (si HIF-1alpha) 16h 20 ng/ml IL-10, 4h 1% oxygen [11N3]


title: A549_Ad5_input_rep2 [HuGene-1_0]


title: human macrophages (si HIF-2alpha) 16h 20 ng/ml IL-10, 4h 1% oxygen [12N1]


title: human macrophages (si HIF-1alpha) 16h 20 ng/ml IL-10, 4h 1% oxygen [11N1]


title: human macrophages (si control) 16h without treatment, 4h 1% oxygen [7N1]


title: human macrophages (si HIF-2alpha) 16h 20 ng/ml IL-10, 4h 21% oxygen [6N1]


title: human macrophages (si control) 16h without treatment, 4h 1% oxygen [7N2]


title: human macrophages (si HIF-1alpha) 16h 20 ng/ml IL-10, 4h 21% oxygen [5N2]


title: human macrophages (si HIF-1alpha) 16h 20 ng/ml IL-10, 4h 21% oxygen [5N3]


title: human macrophages (si HIF-1alpha) 16h 20 ng/ml IL-10, 4h 21% oxygen [5N1]


title: human macrophages (si control) 16h 20 ng/ml IL-10, 4h 1% oxygen [10N1]


title: human macrophages (si HIF-2alpha) 16h without treatment, 4h 1% oxygen [9N3]


title: human macrophages (si control) 16h without treatment, 4h 1% oxygen [7N3]


title: human macrophages (si control) 16h 20 ng/ml IL-10, 4h 1% oxygen [10N3]


title: human macrophages (si HIF-2alpha) 16h 20 ng/ml IL-10, 4h 21% oxygen [6N2]


title: human macrophages (si HIF-2alpha) 16h without treatment, 4h 1% oxygen [9N1]


title: human macrophages (si HIF-2alpha) 16h 20 ng/ml IL-10, 4h 21% oxygen [6N3]


title: human macrophages (si HIF-1alpha) 16h without treatment, 4h 1% oxygen [8N2]


title: human macrophages (si HIF-2alpha) 16h without treatment, 4h 1% oxygen [9N2]


title: human macrophages (si control) 16h 20 ng/ml IL-10, 4h 21% oxygen [4N3]


title: human macrophages (si control) 16h 20 ng/ml IL-10, 4h 1% oxygen [10N2]


title: human macrophages (si HIF-1alpha) 16h without treatment, 4h 1% oxygen [8N3]


title: human macrophages (si HIF-2alpha) 16h without treatment, 4h 21% oxygen [3N1]


title: human macrophages (si control) 16h 20 ng/ml IL-10, 4h 21% oxygen [4N1]


title: human macrophages (si HIF-1alpha) 16h without treatment, 4h 1% oxygen [8N1]


title: human macrophages (si control) 16h 20 ng/ml IL-10, 4h 21% oxygen [4N2]


title: human macrophages (si HIF-1alpha) 16h without treatment, 4h 21% oxygen [2N3]


title: human macrophages (si HIF-2alpha) 16h without treatment, 4h 21% oxygen [3N2]


title: human macrophages (si HIF-1alpha) 16h without treatment, 4h 21% oxygen [2N2]


title: human macrophages (si control) 16h without treatment, 4h 21% oxygen [1N2]


title: human macrophages (si control) 16h without treatment, 4h 21% oxygen [1N3]


title: human macrophages (si HIF-2alpha) 16h without treatment, 4h 21% oxygen [3N3]


title: siYAP RNA #1 transfected, biological rep 4

status: Public on Oct 17 2014

first: Zhewei

last: Shen

state: PA

address: BRB II/III Rm 527, 421 Curie Blvd.,

hyb_protocol: standard Affymetrix protocol, performed by Penn Genomic Analysis Core

data_processing:
standard Affymetrix protocol, conducted by Penn Bioinformatics Core and Dr. John Tobias
Expression level of genes in RISC-free or siYAP treated HUVEC

source_name: Human umbilical vein endothelial cell

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were cultured in culture dishes pre-coated with 0.1% gelatin with commercial EGM2 media from Lonza

extract_protocol: Qiagen miRNeasy kit was used for extraction

treatment_protocol: siRNA was synthesized as duplex by Life Technology and transfected directly using Invitrogen RNAiMAX. All steps were conducted according to the included vendor protocol.

value: siYAP RNA #1 transfected

value: Primary cell line


title: siYAP RNA #1 transfected, biological rep 2

scan_protocol: standard Affymetrix protocol, performed by Penn Genomic Analysis Core


title: human macrophages (si HIF-1alpha) 16h without treatment, 4h 21% oxygen [2N1]


title: RISC-free control transfected, biological rep 2

value: RISC-free control transfected


title: siYAP RNA #1 transfected, biological rep 1


title: RISC-free control transfected, biological rep 3


title: RISC-free control transfected, biological rep 4


title: siYAP RNA #2 transfected, biological rep 1

value: siYAP RNA #2 transfected


title: siYAP RNA #2 transfected, biological rep 4


title: siYAP RNA #2 transfected, biological rep 3


title: siYAP RNA #1 transfected, biological rep 3