title: WCN003_WNVWT_12h_1_microRNA

source_name: Primary cortical neurons, WNVW-inoculated, 12 hour(s), bioreplicate 2, technical replicate 1


title: WCN002_WNVE218A_8h_1_mRNA

status: Public on Apr 04 2015

type: RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

country: USA

institute: PNNL

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

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

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

molecule: total RNA

organism: Mus musculus

source_name: Primary cortical neurons, inoculated with WNVE218A, 8 hour(s), bioreplicate 1, technical replicate 1

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

growth_protocol: Mouse fetal brain was taken from C57Bl/6J mouse embryos at E15. After removing meninges, cortical tissue was dissociated, filtered and plated in neurobasal medium (with B27 supplement, Glutamax and penicillin/streptomycin) at a density of 5 x 105 cells/well in a poly-D-lysine and laminin coated 24-well dish. Three days after plating (D2), cell medium was replaced with fresh medium.

extract_protocol: Total RNA was isolated from Trizol.

treatment_protocol: On day 4, triplicate technical replicates of cortical neurons were mock-inoculated or inoculated with plasmid-derived wild type West Nile virus NY99 clone 382 (WNVWT) or a plasmid-derived isogenic E218A mutant West Nile virus NY99 clone 382 (WNVE218A). After 1 hr of infection at 37oC, virus inoculum was removed. Neurons were then cultured for 0-23 additional hours at 37oC. At 1, 8, 12 and 24 hours after inoculation medium was removed and RNA harvested from adherent neurons using Trizol.

tag: strain

tag: embryonic stage

tag: developmental stage

value: embryo

tag: tissue

value: brain

tag: time

tag: virus


title: WCN002_WNVWT_8h_3_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 8 hour(s), bioreplicate 1, technical replicate 3

value: WNVWT


title: WCN002_WNVE218A_1h_1_mRNA

source_name: Primary cortical neurons, inoculated with WNVE218A, 1 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVWT_1h_2_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 1 hour(s), bioreplicate 1, technical replicate 2


title: WCN002_WNVWT_24h_1_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 24 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVWT_24h_3_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 24 hour(s), bioreplicate 1, technical replicate 3


title: WCN002_WNVWT_12h_2_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 12 hour(s), bioreplicate 1, technical replicate 2


title: WCN002_WNVE218A_1h_3_mRNA

source_name: Primary cortical neurons, inoculated with WNVE218A, 1 hour(s), bioreplicate 1, technical replicate 3


title: WCN002_WNVWT_12h_3_microRNA

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, 500 ng of total RNA from each sample was labeled with Cy3-pCp. Labeled RNA was mixed with 4.5 μL 10 × Blocking Agent and 22.5 μL of 2X Hi-RPM Hybridization Buffer, heated at 100°C for 5 minutes, and then immediately transfered to an ice water bath for 5 minutes. All of the volume of the hybridization sample was dispensed into the gasket slide and assembled to the miRNA expression microarray slide. The slides were incubated for 55°C for 20 hours in an Agilent Hybridization Oven.

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

source_name: Primary cortical neurons, WNVW-inoculated, 12 hour(s), bioreplicate 1, technical replicate 2

label_protocol: Total RNA from each sample was labeled using miRNA Complete Labeling and Hyb Kit (v2.4, Agilent Technologies)


title: WCN003_WNVE218A_12h_2_microRNA

source_name: Primary cortical neurons, WNVE-inoculated, 12 hour(s), bioreplicate 2, technical replicate 2


title: WCN003_WNVWT_12h_2_microRNA

source_name: Primary cortical neurons, WNVW-inoculated, 12 hour(s), bioreplicate 2, technical replicate 2


title: WCN003_mock_1h_3_mRNA

source_name: Primary cortical neurons, mock-inoculated, 1 hour(s), bioreplicate 2, technical replicate 3

value: mockulum


title: WCN003_mock_12h_3_microRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 2, technical replicate 1


title: WCN002_WNVWT_12h_3_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 12 hour(s), bioreplicate 1, technical replicate 3


title: WCN002_WNVWT_8h_1_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 8 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVWT_1h_1_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 1 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_mock_12h_1_mRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVWT_1h_3_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 1 hour(s), bioreplicate 1, technical replicate 3


title: WCN002_WNVWT_24h_2_mRNA

source_name: Primary cortical neurons, inoculated with WNVWT, 24 hour(s), bioreplicate 1, technical replicate 2


title: WCN002_mock_8h_2_mRNA

source_name: Primary cortical neurons, mock-inoculated, 8 hour(s), bioreplicate 1, technical replicate 2


title: WCN003_mock_12h_2_microRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 2, technical replicate 2


title: WCN002_mock_12h_3_microRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 1, technical replicate 2


title: WCN003_mock_12h_1_microRNA


title: WCN002_mock_1h_3_mRNA

source_name: Primary cortical neurons, mock-inoculated, 1 hour(s), bioreplicate 1, technical replicate 3


title: WCN002_WNVE218A_12h_3_microRNA

source_name: Primary cortical neurons, WNVE-inoculated, 12 hour(s), bioreplicate 1, technical replicate 2


title: WCN002_mock_8h_1_mRNA

source_name: Primary cortical neurons, mock-inoculated, 8 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVE218A_12h_2_microRNA

source_name: Primary cortical neurons, WNVE-inoculated, 12 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVE218A_12h_1_microRNA

source_name: Primary cortical neurons, WNVW-inoculated, 12 hour(s), bioreplicate 1, technical replicate 3


title: WCN002_mock_24h_1_mRNA

source_name: Primary cortical neurons, mock-inoculated, 24 hour(s), bioreplicate 1, technical replicate 1


title: MCL001_d3-5-MERS_12hr_3_mRNA

status: Public on Feb 04 2015

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

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). Quantile normalization and data processing performed using GeneSpring GX v11.5 software (Agilent Technologies).

organism: Homo sapiens

source_name: Calu-3 cells, d3-5-MERS treatment, 12 hours, replicate 3

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA using Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies)

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

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

treatment_protocol: Cells were washed twice with PBS and infected with a multiplicity of infection of 5.

value: 12 hours

tag: replicate


title: MCL001_d3-5-MERS_7hr_1_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 7 hours, replicate 1

value: 7 hours


title: WCN002_mock_24h_3_mRNA

source_name: Primary cortical neurons, mock-inoculated, 24 hour(s), bioreplicate 1, technical replicate 3


title: MCL001_d3-5-MERS_12hr_2_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 12 hours, replicate 2


title: MCL001_d3-5-MERS_7hr_2_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 7 hours, replicate 2


title: WCN002_mock_8h_3_mRNA

source_name: Primary cortical neurons, mock-inoculated, 8 hour(s), bioreplicate 1, technical replicate 3


title: Low-grade ESS patient 2, aCGH

status: Public on Mar 31 2015

type: genomic

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

description:
ESSlow9_aCGH
Patient 2 described in this study.
aCGH profile in primary tumor sample.

hyb_protocol: Labeled samples were hybridized to Agilent-029830 4x180K CGH+SNP whole-genome microarrays (G4890A) (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, Santa Clara, CA, USA). aCGH data were analyzed using Agilent Genomic Workbench 7.0.4.0. software (Agilent Technologies, SantaClara, CA, USA). The ADM-2 algorithm was applied to identify DNA copy number aberrations (CNAs). Aberration Filter: (Minimum Number of Probes for Amplification >= 5 AND Minimum Size (Kb) of Region for Amplification >= 1 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25) OR (Minimum Number of Probes for Deletion >= 5 AND Minimum Size (Kb) of Region for Deletion >= 1 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25).

molecule: genomic DNA

source_name: tumor sample, low-grade ESS

label_protocol: 1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to the manufacturer's recommendations. Reference female DNA supplied with the SureTag Complete DNA Labeling Kit (cat. no. 5190-4240, Agilent Technologies, Santa Clara, CA, USA) was used for the aCGH experiments.

extract_protocol: Genomic DNA was extracted from the frozen tumour specimens using the Blood & Tissue DNasy kit with the optional RNase treatment (Qiagen).

value: primary endometrial stromal sarcoma

tag: histosubtype

value: low-grade endometrial stromal tumor

source_name: reference

tag: gender

value: female

tag: sample type

value: reference


title: MCL001_d3-5-MERS_0hr_2_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 0 hours, replicate 2

value: 0 hours


title: MCL001_d3-5-MERS_0hr_1_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 0 hours, replicate 1


title: WCN002_WNVWT_12h_2_microRNA

source_name: Primary cortical neurons, WNVW-inoculated, 12 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_mock_12h_2_microRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 1, technical replicate 1


title: WCN002_WNVWT_12h_1_microRNA


title: WCN002_mock_24h_2_mRNA

source_name: Primary cortical neurons, mock-inoculated, 24 hour(s), bioreplicate 1, technical replicate 2


title: MCL001_d4B-MERS_24hr_1_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 24 hours, replicate 1

value: 24 hours


title: WCN002_mock_1h_2_mRNA

source_name: Primary cortical neurons, mock-inoculated, 1 hour(s), bioreplicate 1, technical replicate 2


title: WCN002_mock_1h_1_mRNA

source_name: Primary cortical neurons, mock-inoculated, 1 hour(s), bioreplicate 1, technical replicate 1


title: MCL001_d4B-MERS_24hr_2_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 24 hours, replicate 2


title: MCL001_d4B-MERS_7hr_3_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 7 hours, replicate 3


title: WCN002_mock_12h_2_mRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 1, technical replicate 2


title: MCL001_d3-5-MERS_24hr_2_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 24 hours, replicate 2


title: Low-grade ESS patient 1, aCGH

description:
ESSlow7_aCGH
Patient 1 described in this study.
aCGH profile in primary tumor sample.


title: MCL001_dNSP16-MERS_7hr_3_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 7 hours, replicate 3


title: MCL001_dNSP16-MERS_12hr_3_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 12 hours, replicate 3


title: MCL001_d3-5-MERS_24hr_3_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 24 hours, replicate 3


title: MCL001_d3-5-MERS_24hr_1_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 24 hours, replicate 1


title: MCL001_dNSP16-MERS_24hr_1_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 24 hours, replicate 1


title: MCL001_dNSP16-MERS_24hr_2_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 24 hours, replicate 2


title: MCL001_d4B-MERS_24hr_3_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 24 hours, replicate 3


title: MCL001_dNSP16-MERS_0hr_2_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 0 hours, replicate 2


title: MCL001_d4B-MERS_12hr_1_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 12 hours, replicate 1


title: MCL001_RFP-MERS_24hr_3_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 24 hours, replicate 3

value: RFP-MERS


title: MCL001_dNSP16-MERS_0hr_1_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 0 hours, replicate 1


title: MCL001_d4B-MERS_7hr_2_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 7 hours, replicate 2


title: MCL001_RFP-MERS_12hr_3_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 12 hours, replicate 3


title: MCL001_RFP-MERS_24hr_2_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 24 hours, replicate 2


title: MCL001_dNSP16-MERS_12hr_1_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 12 hours, replicate 1


title: MCL001_dNSP16-MERS_7hr_2_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 7 hours, replicate 2


title: MCL001_d4B-MERS_0hr_3_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 0 hours, replicate 3


title: MCL001_d4B-MERS_0hr_2_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 0 hours, replicate 2


title: MCL001_dNSP16-MERS_0hr_3_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 0 hours, replicate 3


title: MCL001_RFP-MERS_7hr_2_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 7 hours, replicate 1


title: MCL001_d4B-MERS_12hr_2_mRNA

source_name: Calu-3 cells, d4B-MERS treatment, 12 hours, replicate 2


title: MCL001_dNSP16-MERS_24hr_3_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 24 hours, replicate 3


title: MCL001_icMERS_24hr_1_mRNA

source_name: Calu-3 cells, icMERS treatment, 24 hours, replicate 1

value: icMERS


title: MCL001_dNSP16-MERS_12hr_2_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 12 hours, replicate 2


title: MCL001_icMERS_24hr_3_mRNA


title: WCN002_mock_12h_3_mRNA

source_name: Primary cortical neurons, mock-inoculated, 12 hour(s), bioreplicate 1, technical replicate 3


title: MCL001_dNSP16-MERS_7hr_1_mRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 7 hours, replicate 1


title: MCL001_RFP-MERS_12hr_1_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 12 hours, replicate 1


title: MCL001_icMERS_7hr_2_mRNA

source_name: Calu-3 cells, icMERS treatment, 7 hours, replicate 2


title: MCL001_icMERS_12hr_2_mRNA

source_name: Calu-3 cells, icMERS treatment, 12 hours, replicate 2


title: MCL001_RFP-MERS_0hr_3_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 0 hours, replicate 3


title: MCL001_icMERS_24hr_2_mRNA


title: MCL001_icMERS_0hr_3_mRNA

source_name: Calu-3 cells, icMERS treatment, 0 hours, replicate 3


title: MCL001_RFP-MERS_0hr_2_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 0 hours, replicate 2


title: MCL001_RFP-MERS_0hr_1_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 0 hours, replicate 1


title: MCL001_mock_24hr_3_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 24 hours, replicate 3

value: mock


title: MCL001_icMERS_12hr_3_mRNA

source_name: Calu-3 cells, icMERS treatment, 12 hours, replicate 3


title: MCL001_RFP-MERS_7hr_1_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 7 hours, replicate 2


title: MCL001_icMERS_0hr_1_mRNA

source_name: Calu-3 cells, icMERS treatment, 0 hours, replicate 1


title: MCL001_mock_12hr_2_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 12 hours, replicate 2


title: MCL001_mock_12hr_1_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 12 hours, replicate 1


title: MCL001_mock_7hr_3_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 7 hours, replicate 3


title: MCL001_icMERS_12hr_1_mRNA

source_name: Calu-3 cells, icMERS treatment, 12 hours, replicate 1


title: MCL001_icMERS_7hr_3_mRNA

source_name: Calu-3 cells, icMERS treatment, 7 hours, replicate 3


title: MCL001_icMERS_0hr_2_mRNA

source_name: Calu-3 cells, icMERS treatment, 0 hours, replicate 2


title: MCL001_mock_0hr_1_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 0 hours, replicate 1


title: MCL001_icMERS_7hr_1_mRNA

source_name: Calu-3 cells, icMERS treatment, 7 hours, replicate 1


title: MCL001_d3-5-MERS_0hr_3_mRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 0 hours, replicate 3


title: MCL001_mock_7hr_2_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 7 hours, replicate 2


title: EIHH001_REBOV_24hr_1_mRNA

source_name: IHH cells, REBOV treatment, 24 hours, replicate 1

growth_protocol: IHH cells were maintained in DMEM medium with 5% FCS with L-glut, Anti-Anti, Na Pyruvate, and Non-essential AA

extract_protocol: Cells were scraped into Trizol and total RNA was isolated from the Trizol extract.

treatment_protocol: Cells were infected with wild-type Ebola viruses at a multiplicity of infection of 0.5.

value: REBOV


title: MCL001_mock_0hr_2_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 0 hours, replicate 2


title: EIHH001_REBOV_48hr_2_mRNA

source_name: IHH cells, REBOV treatment, 48 hours, replicate 2

value: 48 hours


title: MCL001_mock_24hr_2_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 24 hours, replicate 3


title: EIHH001_ZEBOV_72hr_2_mRNA

source_name: IHH cells, ZEBOV treatment, 72 hours, replicate 2

value: 72 hours

value: ZEBOV


title: EIHH001_REBOV_72hr_2_mRNA

source_name: IHH cells, REBOV treatment, 72 hours, replicate 2


title: EIHH001_ZEBOV_48hr_3_mRNA

source_name: IHH cells, ZEBOV treatment, 48 hours, replicate 3


title: MCL001_mock_7hr_1_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 7 hours, replicate 1


title: EIHH001_REBOV_24hr_3_mRNA

source_name: IHH cells, REBOV treatment, 24 hours, replicate 3


title: EIHH001_mock_72hr_2_mRNA

source_name: IHH cells, mock treatment (no virus), 72 hours, replicate 2


title: EIHH001_ZEBOV_48hr_2_mRNA

source_name: IHH cells, ZEBOV treatment, 48 hours, replicate 2


title: EIHH001_mock_72hr_1_mRNA

source_name: IHH cells, mock treatment (no virus), 72 hours, replicate 1


title: EIHH001_mock_24hr_2_mRNA

source_name: IHH cells, mock treatment (no virus), 24 hours, replicate 2


title: EIHH001_ZEBOV_48hr_1_mRNA

source_name: IHH cells, ZEBOV treatment, 48 hours, replicate 1


title: EIHH001_REBOV_72hr_3_mRNA

source_name: IHH cells, REBOV treatment, 72 hours, replicate 3


title: MCL001_mock_12hr_3_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 24 hours, replicate 2


title: EIHH001_mock_72hr_3_mRNA

source_name: IHH cells, mock treatment (no virus), 72 hours, replicate 3


title: EIHH001_ZEBOV_72hr_3_mRNA

source_name: IHH cells, ZEBOV treatment, 72 hours, replicate 3


title: EIHH001_REBOV_48hr_1_mRNA

source_name: IHH cells, REBOV treatment, 48 hours, replicate 1


title: MCL001_mock_0hr_3_mRNA

source_name: Calu-3 cells, mock treatment (no virus), 0 hours, replicate 3


title: MCL001_d3-5-MERS_7hr_2_microRNA

hyb_protocol: Human miRNA MicroarraySlide (8x60K, Agilent Technologies)

scan_protocol: Agilent Scanner G2505C

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). Quantile normalization and data processing performed using GeneSpring GX v12.0 software (Agilent Technologies).

source_name: Calu-3 cells, d3-5-MERS treatment, 7 hours, replicate 2


title: EIHH001_mock_48hr_2_mRNA

source_name: IHH cells, mock treatment (no virus), 48 hours, replicate 2


title: MCL001_RFP-MERS_12hr_2_mRNA

source_name: Calu-3 cells, RFP-MERS treatment, 12 hours, replicate 2


title: MCL001_d4B-MERS_12hr_2_microRNA

source_name: Calu-3 cells, d4B-MERS treatment, 12 hours, replicate 2


title: EIHH001_ZEBOV_24hr_2_mRNA

source_name: IHH cells, ZEBOV treatment, 24 hours, replicate 2


title: MCL001_d4B-MERS_12hr_3_microRNA

source_name: Calu-3 cells, d4B-MERS treatment, 12 hours, replicate 3


title: MCL001_d4B-MERS_12hr_1_microRNA

source_name: Calu-3 cells, d4B-MERS treatment, 12 hours, replicate 1


title: EIHH001_mock_48hr_1_mRNA

source_name: IHH cells, mock treatment (no virus), 48 hours, replicate 1


title: EIHH001_mock_24hr_1_mRNA

source_name: IHH cells, mock treatment (no virus), 24 hours, replicate 1


title: EIHH001_mock_48hr_3_mRNA

source_name: IHH cells, mock treatment (no virus), 48 hours, replicate 3


title: MCL001_d3-5-MERS_7hr_1_microRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 7 hours, replicate 1


title: EIHH001_mock_8hr_3_mRNA

source_name: IHH cells, mock treatment (no virus), 8 hours, replicate 3

value: 8 hours


title: EIHH001_ZEBOV_0hr_3_mRNA

source_name: IHH cells, ZEBOV treatment, 0 hours, replicate 3


title: EIHH001_REBOV_8hr_3_mRNA

source_name: IHH cells, REBOV treatment, 8 hours, replicate 3


title: EIHH001_REBOV_24hr_2_mRNA

source_name: IHH cells, REBOV treatment, 24 hours, replicate 2


title: MCL001_d3-5-MERS_12hr_3_microRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 12 hours, replicate 3


title: EIHH001_ZEBOV_24hr_1_mRNA

source_name: IHH cells, ZEBOV treatment, 24 hours, replicate 1


title: EIHH001_ZEBOV_8hr_2_mRNA

source_name: IHH cells, ZEBOV treatment, 8 hours, replicate 2


title: EIHH001_mock_0hr_3_mRNA

source_name: IHH cells, mock treatment (no virus), 0 hours, replicate 3


title: EIHH001_ZEBOV_8hr_1_mRNA

source_name: IHH cells, ZEBOV treatment, 8 hours, replicate 1


title: EIHH001_mock_8hr_2_mRNA

source_name: IHH cells, mock treatment (no virus), 8 hours, replicate 2


title: EIHH001_mock_0hr_1_mRNA

source_name: IHH cells, mock treatment (no virus), 0 hours, replicate 1


title: EIHH001_ZEBOV_0hr_2_mRNA

source_name: IHH cells, ZEBOV treatment, 0 hours, replicate 2


title: EIHH001_REBOV_8hr_1_mRNA

source_name: IHH cells, REBOV treatment, 8 hours, replicate 1


title: EIHH001_REBOV_0hr_2_mRNA

source_name: IHH cells, REBOV treatment, 0 hours, replicate 2


title: MCL001_d3-5-MERS_12hr_1_microRNA

source_name: Calu-3 cells, d3-5-MERS treatment, 12 hours, replicate 1


title: EIHH001_mock_0hr_2_mRNA

source_name: IHH cells, mock treatment (no virus), 0 hours, replicate 2


title: EIHH001_REBOV_0hr_3_mRNA

source_name: IHH cells, REBOV treatment, 0 hours, replicate 3


title: MCL001_dNSP16-MERS_12hr_1_microRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 12 hours, replicate 1


title: MCL001_d4B-MERS_7hr_3_microRNA

source_name: Calu-3 cells, d4B-MERS treatment, 7 hours, replicate 3


title: MCL001_dNSP16-MERS_12hr_3_microRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 12 hours, replicate 3


title: MCL001_dNSP16-MERS_7hr_1_microRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 7 hours, replicate 1


title: MCL001_dNSP16-MERS_7hr_3_microRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 7 hours, replicate 3


title: MCL001_d4B-MERS_7hr_1_microRNA

source_name: Calu-3 cells, d4B-MERS treatment, 7 hours, replicate 1


title: MCL001_dNSP16-MERS_7hr_2_microRNA

source_name: Calu-3 cells, dNSP16-MERS treatment, 7 hours, replicate 2


title: MCL001_FP-MERS_12hr_2_microRNA

source_name: Calu-3 cells, FP-MERS treatment, 12 hours, replicate 2

value: FP-MERS


title: MCL001_FP-MERS_7hr_2_microRNA

source_name: Calu-3 cells, FP-MERS treatment, 7 hours, replicate 2


title: MCL001_FP-MERS_12hr_1_microRNA

source_name: Calu-3 cells, FP-MERS treatment, 12 hours, replicate 1

value: 12 hours


title: MCL001_FP-MERS_7hr_1_microRNA

source_name: Calu-3 cells, FP-MERS treatment, 7 hours, replicate 1

value: 7 hours


title: MCL001_icMERS_7hr_1_microRNA

source_name: Calu-3 cells, icMERS treatment, 7 hours, replicate 1


title: MCL001_mock_12hr_1_microRNA

source_name: Calu-3 cells, mock treatment (no virus), 12 hours, replicate 1


title: MCL001_mock_12hr_2_microRNA

source_name: Calu-3 cells, mock treatment (no virus), 12 hours, replicate 2


title: MCL001_icMERS_12hr_3_microRNA

source_name: Calu-3 cells, icMERS treatment, 12 hours, replicate 3


title: EIHH001_ZEBOV_72hr_1_mRNA

source_name: IHH cells, ZEBOV treatment, 72 hours, replicate 1


title: MCL001_mock_12hr_3_microRNA

source_name: Calu-3 cells, mock treatment (no virus), 12 hours, replicate 3


title: MCL001_mock_7hr_1_microRNA

source_name: Calu-3 cells, mock treatment (no virus), 7 hours, replicate 1


title: MCL001_mock_7hr_3_microRNA

source_name: Calu-3 cells, mock treatment (no virus), 7 hours, replicate 3


title: MCL001_icMERS_7hr_3_microRNA

source_name: Calu-3 cells, icMERS treatment, 7 hours, replicate 3


title: MCL001_FP-MERS_12hr_3_microRNA

source_name: Calu-3 cells, FP-MERS treatment, 12 hours, replicate 3


title: EIHH001_REBOV_72hr_2_microRNA

source_name: IHH cells, REBOV treatment, 72 hours, replicate 2


title: MCL001_icMERS_12hr_2_microRNA

source_name: Calu-3 cells, icMERS treatment, 12 hours, replicate 2


title: MCL001_mock_7hr_2_microRNA

source_name: Calu-3 cells, mock treatment (no virus), 7 hours, replicate 2


title: EIHH001_ZEBOV_72hr_2_microRNA

source_name: IHH cells, ZEBOV treatment, 72 hours, replicate 2


title: EIHH001_ZEBOV_72hr_3_microRNA

source_name: IHH cells, ZEBOV treatment, 72 hours, replicate 3


title: EIHH001_ZEBOV_48hr_3_microRNA

source_name: IHH cells, ZEBOV treatment, 48 hours, replicate 3


title: EIHH001_mock_72hr_1_microRNA

source_name: IHH cells, mock treatment (no virus), 72 hours, replicate 1

value: Mock


title: EIHH001_REBOV_72hr_1_microRNA

source_name: IHH cells, REBOV treatment, 72 hours, replicate 1


title: EIHH001_REBOV_72hr_3_microRNA

source_name: IHH cells, REBOV treatment, 72 hours, replicate 3


title: EIHH001_mock_72hr_3_microRNA

source_name: IHH cells, mock treatment (no virus), 72 hours, replicate 3


title: EIHH001_mock_72hr_2_microRNA

source_name: IHH cells, mock treatment (no virus), 72 hours, replicate 2


title: EIHH001_ZEBOV_72hr_1_microRNA

source_name: IHH cells, ZEBOV treatment, 72 hours, replicate 1


title: EIHH001_mock_24hr_1_microRNA

source_name: IHH cells, mock treatment (no virus), 24 hours, replicate 1


title: EIHH001_mock_24hr_3_microRNA

source_name: IHH cells, mock treatment (no virus), 24 hours, replicate 3


title: EIHH001_ZEBOV_8hr_2_microRNA

source_name: IHH cells, ZEBOV treatment, 8 hours, replicate 2


title: MCL001_FP-MERS_7hr_3_microRNA

source_name: Calu-3 cells, FP-MERS treatment, 7 hours, replicate 3


title: EIHH001_mock_48hr_1_microRNA

source_name: IHH cells, mock treatment (no virus), 48 hours, replicate 1


title: EIHH001_ZEBOV_8hr_1_microRNA

source_name: IHH cells, ZEBOV treatment, 8 hours, replicate 1


title: EIHH001_ZEBOV_48hr_2_microRNA

source_name: IHH cells, ZEBOV treatment, 48 hours, replicate 2


title: EIHH001_REBOV_24hr_1_microRNA

source_name: IHH cells, REBOV treatment, 24 hours, replicate 1


title: EIHH001_REBOV_48hr_3_microRNA

source_name: IHH cells, REBOV treatment, 48 hours, replicate 3


title: EIHH001_ZEBOV_48hr_1_microRNA

source_name: IHH cells, ZEBOV treatment, 48 hours, replicate 1


title: EIHH001_REBOV_48hr_1_microRNA

source_name: IHH cells, REBOV treatment, 48 hours, replicate 1


title: EIHH001_mock_48hr_2_microRNA

source_name: IHH cells, mock treatment (no virus), 48 hours, replicate 2


title: EIHH001_ZEBOV_8hr_3_microRNA

source_name: IHH cells, ZEBOV treatment, 8 hours, replicate 3


title: EIHH001_REBOV_24hr_2_microRNA

source_name: IHH cells, REBOV treatment, 24 hours, replicate 2


title: EIHH001_REBOV_8hr_2_microRNA

source_name: IHH cells, REBOV treatment, 8 hours, replicate 2


title: EIHH001_ZEBOV_24hr_2_microRNA

source_name: IHH cells, ZEBOV treatment, 24 hours, replicate 2


title: EIHH001_REBOV_8hr_3_microRNA

source_name: IHH cells, REBOV treatment, 8 hours, replicate 3


title: EIHH001_ZEBOV_24hr_3_microRNA

source_name: IHH cells, ZEBOV treatment, 24 hours, replicate 3


title: EIHH001_REBOV_8hr_1_microRNA

source_name: IHH cells, REBOV treatment, 8 hours, replicate 1


title: EIHH001_mock_8hr_1_microRNA

source_name: IHH cells, mock treatment (no virus), 8 hours, replicate 1


title: EIHH001_mock_8hr_2_microRNA

source_name: IHH cells, mock treatment (no virus), 8 hours, replicate 2


title: EIHH001_mock_8hr_3_microRNA

source_name: IHH cells, mock treatment (no virus), 8 hours, replicate 3


title: Control_2h_rep3

status: Public on Apr 29 2014

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: California/San Diego

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

description: Gene expression contol 2h pair to T2C-T

hyb_protocol: Total RNA including miRNA (100 ng) was first dephosphorylated with calf intestine alkaline phosphatase (GE healthcare, Amersham, UK), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 to the 3’-ends using T4 RNA ligase (GE healthcare, Amersham, UK). The labeled RNAs were hybridized to Agilent human miRNA microarray (Santa Clara, CA). Design ID(AMADID)=021827. Standard Agilent’s miRNA microarray hybridization protocol

scan_protocol: Standard Agilent scaning protocol

data_processing: standard Agilent Feature Extraction protocol

label_protocol: Total RNA (100 ng) was labelled with pCp-Cy3 using T4 RNA ligase (GE healthcare, Amersham, UK)

growth_protocol: hCMEC/D3 cells were cultured in EGM-2 MV medium (Lonza, Slough Wokingham, UK) and supplemented with the following components obtained from the manufacturer: 0.025 % (v/v) rhEGF, 0.025 % (v/v) VEGF, 0.025 % (v/v) IGF, 0.1 % (v/v) rhFGF, 0.1 % (v/v) gentamycin, 0.1 % (v/v) ascorbic acid, 0.04 % (v/v) hydrocortisone and 2.5 % (v/v) foetal bovine serum (FBS) (hereafter referred to as EGM-2 medium).

extract_protocol: Total RNA of hCMEC/D3 cells were isolated using miRNeasy mini kit (Qiagen, Sussex, UK) according to the manufacturer’s protocols. The quantity (NanoDrop 1000 spectrophotometer) and the quality (2100 Bioanalyzer, RNA 6000 Pico LabChip; Agilent, Palo Alto, CA, USA) of the total RNA were analyzed prior to determination of mRNA levels

treatment_protocol: hCMEC/D3 cells were seeded onto collagen-coated tissue culture plate supplied by Greiner Bio-one (Gloucestershire, UK) and maintained for 72 h after confluence. Culture media was then changed to EGM-2 media without VEGF. Cells were left untreated or treated with TNFα and IFNγ at the concentrations and times indicated for each experiment.

value: Brain endothelium

tag: cell line

tag: treatment

value: control

value: 2 h


title: human NPC ax0014, derived from line 4

status: Public on Sep 12 2014

city: Cambridgeshire

first: Yichen

last: Shi

address: Suite 3, The Science Village Building, Chesterford Research Park, Little Chesterford

country: United Kingdom

institute: Axol Bioscience Limited

description: gene expression data from human NPC ax0014

hyb_protocol: SourceBioscience provided the standard services for hybridization

scan_protocol: SourceBioscience provided the standard services for scanning

data_processing: The data were analyzed with Expression Console and Transcriptome Console using Affymetrix default analysis settings

label: Biotin

source_name: human NPC ax0014, derived from line 4

label_protocol: SourceBioscience provided the standard services for labeling

growth_protocol: human iPSC cells were cultured on E8 medium; human NPCs were induced with NPC induction medium

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted total RNA according to the manufacturer's instructions

value: human NPC ax0014 , derived from line 4


title: Control_2h_rep1

description: Gene expression contol 2h pair to T2A-T


title: Cytokines_24h_rep1

description: Gene expression contol 24h pair to T24C-C

value: 100 ng/ml TNFα and IFNγ


title: Cytokines_24h_rep3

description: Gene expression contol 24h pair to T24F-C


title: Control_2h_rep2

description: Gene expression contol 2h pair to T2F-T


title: Cytokines_24h_rep2

description: Gene expression contol 24h pair to T24E-C


title: human iPSC line 4

description: gene expression data from human iPSC line 4

source_name: human iPSC line 4

growth_protocol: human iPSC cells were cultured on E8 medium; human NPCs were induced with NPC induce medium

value: human iPSC line 4


title: Control_24h_rep1

description: Gene expression contol 24h pair to T24C-T


title: Control_6h_rep3

description: Gene expression contol 6h pair to T6C-T

value: 6 h


title: pre-miR-155 transfected cells Rep3

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol. Using Human Ref8 v3.

scan_protocol: Standard Illumina scanning protocol

data_processing:
The analysis was run using LUMI and LIMMA packages (R Bioconductor).
The data set was filtered before normalisation, removing any probes that were not successfully detected (detection p-value<0.01) in at least one sample. Leaving those probes in would have reduced power due to the multiple testing correction and added noise to the data set.

source_name: hCMEC/D3 cells

label_protocol: Ambion® TotalPrep 96 RNA Amplification kit was used for Illumina arrays

value: pre-miR-155 transfected


title: pre-miR-155 transfected cells Rep2

description: replicate 2


title: scrambled transfected control Rep3

description: replicate 3

value: scrambled transfected


title: scrambled transfected control Rep1

description: replicate 1


title: Cytokines_2h_rep3

description: Gene expression cytokines 2h pair to T2C-C


title: Cytokines_6h_rep2

description: Gene expression contol 6h pair to T6E-C


title: Cytokines_6h_rep1

description: Gene expression contol 6h pair to T6A-C


title: Cytokines_2h_rep1

description: Gene expression cytokines 2h pair to T2A-C


title: Cytokines_6h_rep3

description: Gene expression contol 6h pair to T6C-C


title: Cytokines_2h_rep2

description: Gene expression cytokines 2h pair to T2F-C


title: scrambled transfected control Rep2

description: replicate 2


title: Control_24h_rep2

description: Gene expression contol 24h pair to T24E-T


title: MCL001_d4B-MERS_7hr_2_microRNA

source_name: Calu-3 cells, d4B-MERS treatment, 7 hours, replicate 2


title: pre-miR-155 transfected cells Rep1

description: replicate 1


title: Control_24h_rep3

description: Gene expression contol 24h pair to T24F-T


title: Control_6h_rep1

description: Gene expression contol 6h pair to T6A-T


title: Control_6h_rep2

description: Gene expression contol 6h pair to T6E-T


title: TNFa and IFNg-treated cells Rep1

status: Public on Sep 16 2013

description: replicate 1

data_processing: The analysis was run using LUMI and LIMMA packages (R Bioconductor). The data set was filtered before normalisation, removing any probes that were not successfully detected (detection p-value<0.01) in at least one sample. Leaving those probes in would have reduced power due to the multiple testing correction and added noise to the data set.

value: TNFa and IFNg-treated


title: Unstimulated cells Rep1

description: replicate 1

value: unstimulated


title: TNFa and IFNg-treated cells Rep3

description: replicate 3


title: Unstimulated cells Rep2

description: replicate 2


title: Cell Hypoxia 5

status: Public on Feb 20 2014

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

description:
Parental cell 5 under hypoxia
CellHO5

hyb_protocol: 130ng labeled RNA was hybridized for 18 hr at 48C on GeneChip miRNA 3.0 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(v.6.6) using the RMA normalization method

label: biotin

source_name: Cell Hypoxia Pair 6

label_protocol: 130ng RNA was labeled using the Affymetrix HSR miRNA Flash Tag Biotin kit

growth_protocol: Cells were cultured in RPMI + 1X Pen/Strep, 10% exosome-free FBS (prepared through ultracentrifugation of FBS - 100,000xg for 6h).

extract_protocol: RNA was extracted using the Qiagen miRNEasy kit

treatment_protocol: Cells were incubated in BioSpherix hypoxia chamber under hypoxic conditions (1% O2) or in a Thermo Scientific cell culture incubator under “normoxic” conditions (20% O2), in all cases at 37C and 5% CO2.

tag: oxygen condition

value: hypoxia

tag: sample group

value: Parental cells

tag: sample pair id

value: pair 6


title: Microvesicle Hypoxia 4

description:
Released exosome 4 under hypoxia
MVHO4

source_name: Exosome Normoxia Pair 5

value: Released exosome

value: pair 5


title: Cell Hypoxia 4

description:
Parental cell 4 under hypoxia
CellHO4

source_name: Cell Hypoxia Pair 5


title: TNFa and IFNg-treated cells Rep2

description: replicate 2


title: Unstimulated cells Rep3

description: replicate 3


title: NSCLC cell line SK-1 nsp [SK-13]

status: Public on Dec 10 2014

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. Copy number from the parffin embedded tumor DNA was calculated after filtration of the PCR fragments above 800 Bp to account for DNA degradation
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines, and fresh frozen lung tumors using  the Qiagen AllPrep kit. DNA from lung paraffin embedded tumors was obtained using the RecoverAll kit from Ambion. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: lung carcinoma cell line


title: NSCLC AD (Mexican Mestizo) cell line, nsp [INER-37_3]

description: Hybridized to 250K_Sty


title: HNSCC_primary_9317806

status: Public on Oct 10 2012

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]  Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample_reference_protocol:  A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.

value: male

value: head-neck

tag: tumor type

value: HNSCC

tag: age

tag: location

value: oral cavity

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

source_name: UHR

value: Stratagene Universal human reference cell line (UHR)


title: Microvesicle Hypoxia 5

description:
Released exosome 5 under hypoxia
MVHO5

source_name: Exosome Hypoxia Pair 6


title: HNSCC_primary_9277139

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

tag: gender

value: female

tag: tissue


title: A427 lung adenocarcinoma cell line, nsp [A427_3]

description: Hybridized to 250K_Sty

tag: cell line


title: HNSCC_primary_9115604

tag: sample type


title: HNSCC_primary_8626410


title: HNSCC_primary_9117735


title: HNSCC_primary_9148965


title: HNSCC_primary_9087735


title: HNSCC_primary_9203560


title: HNSCC_primary_8315636


title: high grade serous ovarian cancer_HGSC4

status: Public on Nov 06 2012

city: Boston

first: Zhigang

middle: C

last: Wang

state: MA

address: 450 Brookline Ave SM936A

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
PFSTx: progression free survival (months) from the end of primary platinum/taxol treatment
BPM: BRCA1 promoter methylation
Grade H/L: high grade (grade 2, 3) / low (grade 1) grade

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: initially performed by DFCI microarray core using softwares from Affymetrix. The data for allelic signals in the sample data table were directly exported by dChip software (dChip_2010_1.exe) after the processing the data from cel files.

source_name: high grade serous ovarian cancer

label_protocol: Affymetrix standard protocol

extract_protocol: DNA extracted by proteinase K disgestion-phenochloroform extraction or Qigen DNA extraction kit from ovarian cancer cells enriched from tumor tissues by needle-microdissection or from ascites by affinity enrichment with anti-EPCAM-conjugated beads.

value: ovarian cancer ascites

tag: pathologic subtype

value: Serous

tag: Stage

value: IV

tag: grade h/l

value: H

tag: primary site

value: peritoneal

tag: tso (tumor sample origin)

value: Ascites

tag: residual disease

tag: resistance

tag: progressed

tag: pfstx (months)

tag: floh%

tag: bpm


title: HNSCC_primary_8381278

tag: tumor type

tag: age

tag: location

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade


title: HNSCC_primary_9182292

tag: gender

tag: tissue

tag: hpv

tag: sample type


title: HNSCC_primary_8374909


title: HNSCC_primary_8669602


title: HNSCC_primary_8314552


title: high grade serous ovarian cancer_HGSC6

tag: pathologic subtype

tag: Stage

value: IIIC

tag: grade h/l

tag: primary site

value: Ovarian

tag: tso (tumor sample origin)

tag: residual disease

value: < 1 cm

tag: resistance


title: high grade serous ovarian cancer_HGSC5

tag: age

tag: progressed

tag: pfstx (months)

tag: floh%

tag: bpm


title: HNSCC_primary_9112894

tag: tumor type

tag: location

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade


title: high grade serous ovarian cancer_HGSC3

tag: tissue

tag: pathologic subtype

tag: Stage

tag: grade h/l

value: ovarian


title: high grade serous ovarian cancer_HGSC1

tag: primary site

tag: tso (tumor sample origin)

tag: residual disease

value: < 1cm

tag: resistance


title: HNSCC_primary_8182912

tag: gender

value: male

tag: age

tag: hpv

tag: sample type


title: HNSCC_primary_8284814

value: head-neck

tag: tumor type

tag: location

tag: ct


title: HNSCC_primary_8114877

value: HNSCC

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)


title: HNSCC_primary_8132955

tag: tissue

value: oral cavity

tag: grade


title: high grade serous ovarian cancer_HGSC2

tag: pathologic subtype

tag: Stage

value: III

tag: grade h/l

tag: progressed

tag: pfstx (months)

tag: floh%

tag: bpm


title: HNSCC_primary_7349605

tag: gender

tag: age

tag: hpv

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_8263347

tag: tumor type

tag: location

tag: sample type


title: HNSCC_primary_7362485

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt


title: HNSCC_primary_7197387

tag: tissue

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade


title: HNSCC_primary_7204950

value: female


title: HNSCC_primary_7099041


title: HNSCC_primary_7314810


title: HNSCC_primary_7089214


title: HNSCC_primary_7191525


title: HNSCC_primary_6335402


title: HNSCC_primary_6378210


title: HNSCC_primary_6161400


title: HNSCC_primary_6366477


title: HNSCC_primary_6370423


title: HNSCC_primary_6193547


title: HNSCC_primary_6272093


title: HNSCC_primary_6297176


title: HNSCC_primary_6303650


title: HNSCC_primary_6378598


title: HNSCC_primary_6161491


title: HNSCC_primary_6187102


title: HNSCC_primary_5383051


title: HNSCC_primary_6291885


title: HNSCC_primary_6094227


title: HNSCC_primary_5278218


title: HNSCC_primary_4345020


title: HNSCC_primary_4207912

value: oropharynx


title: HNSCC_primary_4350301


title: HNSCC_primary_4246880


title: HNSCC_primary_4218578


title: HNSCC_primary_5764636


title: HNSCC_primary_4182315


title: HNSCC_primary_3275717


title: HNSCC_primary_5103886


title: HNSCC_primary_3731441


title: HNSCC_primary_4115629


title: HNSCC_primary_3647626


title: HNSCC_primary_3352865


title: HNSCC_primary_3383430


title: HNSCC_primary_3453190


title: HNSCC_primary_3351138


title: HNSCC_primary_4196866


title: HNSCC_primary_3198447


title: HNSCC_primary_2377559


title: HNSCC_primary_2374976


title: HNSCC_primary_2379888


title: HNSCC_primary_3184366


title: HNSCC_primary_3368081


title: HNSCC_primary_2174722


title: HNSCC_primary_2283812


title: HNSCC_primary_5100731


title: HNSCC_primary_2098442


title: HNSCC_primary_2366928


title: HNSCC_primary_6382317


title: HNSCC_primary_2279587


title: HNSCC_primary_1327847


title: HNSCC_primary_1299400


title: HNSCC_primary_1215799


title: HNSCC_primary_1030692


title: HNSCC_primary_312616


title: HNSCC_primary_332479


title: HNSCC_primary_1202178


title: SNU-16

status: Public on Mar 20 2012

city: Cambridge

first: Nicolas

last: Stransky

address: 7 Cambridge center

department: Cancer Program

institute: Broad Institute

description: SNP array data from the CCLE

hyb_protocol: After denaturation, 200ul of sample are injected into a Genome-Wide Human SNP 6.0 array. Arrays are loaded in the GeneChip® Hybridization Oven 640 @ 50 °C temp, rotating arrays @ 60 rpm. Samples are hybridized for 16 to 18 hours.

scan_protocol: Genome-Wide Human SNP Array 6.0 are stained using the GeneChip® Fluidics Station 450 and scanned using the GeneChip® Scanner 3000

data_processing: The raw CEL files were normalized to copy number estimates using a GenePattern pipeline, as described in Cancer Genome Atlas Research Network et al, Nature, 2008, and hg18 Affymetrix probe annotations. Normalized copy number estimates (log2 ratios) were segmented using the Circular Binary Segmentation (CBS) algorithm, followed by median centering of the segment values to a value of zero in each sample.

source_name: ATCC

label_protocol: PCR amplification fragments (200 and 1100 bp) are labeled using terminal deoxynucleotidyl transferase following the Affymetrix GenomeWideSNP_6 protocol

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: DNA was extracted from frozen cell pellets, containing an average cell count of 4.5 million cells, using the Qiagen Gentra Puregene method following the manufacturers recommendations. Samples were quantified using picogreen on a ThermoScientific Varioskan Flash instrument.

tag: primary site

value: stomach

tag: histology

value: carcinoma

tag: histology subtype1


title: HNSCC_primary_349312


title: RERF-GC-1B

description: SNP array data from the CCLE

source_name: HSRRB


title: HNSCC_primary_532965


title: HNSCC_primary_274483


title: KATO III

description: SNP array data from the CCLE

value: adenocarcinoma


title: OCUM-1

description: SNP array data from the CCLE


title: MKN7

description: SNP array data from the CCLE

source_name: RIKEN


title: iHep (4α3)-MEF

status: Public on Jun 28 2011

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

country: Japan

institute: Medical Institute of Bioreguration, Kyushu University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: induced hepatocyte-like cells derived from MEFs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared from cells using an RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: genetic background

tag: cell type


title: iHep (4α1)-MEF

value: induced hepatocyte-like cells derived from MEFs


title: MEF-2

source_name: mouse embryonic fibroblasts

value: embryonic fibroblasts


title: iHep (4α2)-MEF


title: MEF-1


title: MEF-3


title: Allelic status: HCC1937

status: Public on Dec 31 2010

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1937

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Analyzed using dChip with the reference genotypes of sixty individuals obtained from the dChip website

label: standard Affymetrix protocol

source_name: DNA from breast cancer cell line

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

treatment_protocol: standard Affymetrix protocol

tag: cell line

tag: catalog number

value: ATCC# CRL-2336


title: Allelic status: HCC1395

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1395

value: ATCC# CRL-2324


title: Allelic status: HCC2218

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC2218

value: ATCC# CRL-2343


title: Allelic status: HCC1599

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1599

value: ATCC# CRL-2331


title: Gastric primary non-malignant sample 990489N SNP6

status: Public on Feb 10 2012

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

description: Hybridized to SNP6 array

data_processing: Analysis of raw cel files was performed by Affymetrix Genotyping Console 4.0 software. A reference Model File was created based on 98 non-malignant samples (included as Gastric Normal.REF in the submission). Gastric non-malignant samples and tumors samples were then processed separately using this referenece file by median normalization and GC correlation to obtain the CHP files.

extract_protocol: Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.

value: Gastric primary non-malignant tissue


title: Gastric primary non-malignant sample 990068N SNP6

description: Hybridized to SNP6 array


title: Allelic status: HCC1143

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1143

value: ATCC# CRL-2321


title: Allelic status: HCC1008

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1008

value: ATCC# CRL-2320


title: Gastric primary non-malignant sample 980417N SNP6

description: Hybridized to SNP6 array


title: Prognatous_38d_P5

status: Public on Oct 22 2010

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Pool of five (5) heads dissected from prognatous individuas and stored in RNAlater at -20°C

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software. In the Sample Tables, null corresponds to missing spot; empty values correspond to control spots not included in the normalization.

organism: Dicentrarchus labrax

source_name: 38 days old prognathous sea bass heads

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: Extracted according to Qiagen RNeasy MiniKit protocol for tissue samples.

value: whole heads

tag: age

value: 38 days old

tag: condition

value: Deformed (Prognatous)


title: Prognatous_38d_P3


title: Gastric primary non-malignant sample 76629543N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980401N SNP6

description: Hybridized to SNP6 array


title: Allelic status: HCC38

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC38

value: ATCC# CRL-2314


title: Gastric primary non-malignant sample 980319N SNP6

description: Hybridized to SNP6 array


title: Gastric primary tumor sample 980447T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980447T

value: Gastric primary tumor tissue


title: Gastric primary tumor sample 980097T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980097T


title: Gastric primary tumor sample 980437T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980437T


title: Gastric primary tumor sample 2000986T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000986T


title: Gastric primary tumor sample 980401T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980401T


title: Allelic status: BT474

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
BT474

value: ATCC# HTB-20


title: Gastric primary tumor sample 990489T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990489T


title: Allelic status: MCF7

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
MCF7

value: ATCC# HTB-22


title: Gastric primary tumor sample 980417T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980417T


title: Normal_38d_N6

description: Pool of five (5) heads dissected from normal individuas and stored in RNAlater at -20°C

source_name: 38 days old normal sea bass heads

value: Normal


title: Gastric primary tumor sample 980319T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980319T


title: Gastric primary tumor sample 980436T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 980436T


title: Normal_38d_N4


title: Gastric primary non-malignant sample 980447N SNP6

description: Hybridized to SNP6 array


title: Gastric primary tumor sample 76629543T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 76629543T


title: Gastric primary tumor sample 20021007T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 20021007T


title: Gastric primary non-malignant sample 980436N SNP6

description: Hybridized to SNP6 array


title: Gastric primary non-malignant sample 980437N SNP6

description: Hybridized to SNP6 array


title: Normal_38d_N3


title: Gastric primary tumor sample 2000721T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000721T


title: Gastric primary tumor sample 2000085T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 2000085T


title: Gastric primary non-malignant sample 990275N SNP6

description: Hybridized to SNP6 array


title: Gastric primary tumor sample 990275T SNP6

description: Hybridized to SNP6 array

source_name: Gastric primary tumor sample 990275T


title: Gastric primary non-malignant sample 2000085N SNP6

description: Hybridized to SNP6 array


title: Prognatous_38d_P6


title: Prognatous_58d_P5

description: Pool of five (5) jaws dissected from prognatous individuas and stored in RNAlater at -20°C

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

label: Cyanine 3

source_name: 58 days old prognatous sea bass jaws

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

value: Deformed jaw


title: Normal_58d_N3

description: Pool of five (5) jaws dissected from normal individuas and stored in RNAlater at -20°C

source_name: 58 days old normal sea bass jaws

value: Normal jaw


title: Prognatous_58d_P6


title: Prognatous_58d_P7


title: Prognatous_58d_P4


title: Normal_58d_N2


title: Normal_58d_N4


title: Normal_58d_N5


title: brain, hippocampus: 2_CA3 control 7 days_e1_le1

status: Public on Jun 09 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description:
15 subdissected rat hippocampal slice cultures
Treatment, type=time_course, measurement=7.0 d

organism: Rattus norvegicus

source_name: brain, hippocampus


title: colon_INT_T31_snp

status: Public on Aug 27 2009

city: Milano

first: James

middle: F

last: Reid

address: Via Adamello, 16

department: Molecular Genetics of Cancer

institute: Fondazione Istituto FIRC di Oncologia Molecolare

description: Copy number data of sporadic colon cancer patient (INTcartella:9805494, INTistologico:272259I)

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures using Gene ChIP Scanner 3000.

data_processing: Copy number estimates (log-ratios and state) were calculated using Affymetrix v. 1.5.6 CNAT copy-number pipeline. A set of 48 Hapmap samples were used as anun-paired reference set <http://www.affymetrix.com/support/technical/sample_data/500k_data.affx>.  All additional analysis was performed in R/Bioconductor and is available as a reproducible Sweave document from <http://pierotti.group.ifom-ieo-campus.it/suppl/crc.html>.

source_name: Colon, DNA

label_protocol: Standard Affymetrix procedures.

extract_protocol: DNA was extracted using the QIAamp Tissue Extraction kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: gender

value: F

tag: dimension

tag: stage

value: II

tag: status

tag: survival

tag: apc

tag: kras


title: colon_INT_T152_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9930748, INTistologico:293058I)


title: colon_INT_A33_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9806081, INTistologico:272342I)

value: M


title: colon_INT_T3_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9736918, INTistologico:269537I)

value: IV


title: colon_INT_T12_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9804643, INTistologico:270530I)


title: colon_INT_T130_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9918729, INTistologico:289331I)


title: brain, hippocampus: 3_CA3 control 7 days_e1_le1


title: brain, hippocampus: 3_CA1 control 7 days_e1_le1


title: colon_INT_T41_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9810617, INTistologico:273045I)


title: colon_INT_T86_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9904294, INTistologico:284600I)


title: brain, hippocampus: 2_CA1 control 7 days_e1_le1


title: colon_INT_T224_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2023670, INTistologico:302042I)


title: NCI-H727_NSP

status: Public on Mar 25 2009

city: Charlestown

first: Patricia

last: Greninger

department: Center for Molecular Therapeutics

institute: Massachusetts General Hospital Cancer Center

description: Hybridized to 250K_Nsp

hyb_protocol: Labeling and hybridization was performed as described by the 500k assay manual (P/N 701930 Rev. 2)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the Dynamic Model Mapping algorithm) were processed by Bioconductor/PLASQ. PLASQ copy number and segmented copy number are included in Sample table. SNP genotype calls are provided as supplementary text files. Call data in the TXT files corresponding to the raw CEL files were generated using GTYPE ver. 4.0 with the Dynamic Model Mapping Algorithm. The threshold for Allele A, Allele B and Allele AB was 0.33.

source_name: Lung cell line NCI-H727

extract_protocol: Genomic DNA was extracted Qiagen Blood Amp (P/N 51161).

tag: tissue

value: Lung


title: brain, hippocampus: 1_CA1 lesion 7 days_e1_le1


title: NCI-H441_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line NCI-H441

label_protocol: Labeling and hybridization was performed as described by the 500k assay manual (P/N 701930 Rev. 2)


title: brain, hippocampus: 1_CA1 control 7 days_e1_le1


title: PA-TU-8988T_NSP

description: Hybridized to 250K_Nsp

source_name: Pancreas cell line PA-TU-8988T

value: Pancreas


title: SW 1573_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line SW 1573


title: NCI-H2009_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line NCI-H2009


title: SK-LU-1_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line SK-LU-1


title: brain, hippocampus: 1_CA3 lesion 7 days_e1_le1


title: NCI-H460_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line NCI-H460


title: NCI-H358_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line NCI-H358


title: NCI-H23_NSP

description: Hybridized to 250K_Nsp

source_name: Lung:NSCLC cell line NCI-H23


title: HPAF-II_NSP

description: Hybridized to 250K_Nsp

source_name: Pancreas cell line HPAF-II

value: HPAF-II


title: brain, hippocampus: 1_CA3 control 7 days_e1_le1