title: lung_tumor_resection_Y20


title: DCs ID78 non-infected rep_1

status: Public on Dec 06 2011

type: RNA

city: Montreal

first: luis

last: Barreiro

state: Quebec

address: 3175 Chemin de la Côte Sainte-Catherine

country: Canada

institute: luis

hyb_protocol: As recommended by Illumina.

scan_protocol: As recommended by Illumina.

data_processing: Bioconductor software package lumi. The data provided is log2 transformed.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human dendritic cells

label_protocol: As recommended by Illumina.

growth_protocol: Blood monocytes were purified from PBMCs by positive selection with magnetic CD14 MicroBeads. In order to derive dendritic cells, monocytes were cultured for 5 days in RPMI 1640  supplemented with 10% heat-inactivated FCS , L-glutamina, GM-CSF (20 ng/ml; Immunotools), and IL-4 (20 ng/ml; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.

extract_protocol: Total RNA was extracted from the non-infected DCs and the MTB-infected DCs using the miRNeasy kit (Qiagen).

treatment_protocol: We infected DCs with an MTB strain expressing green-fluorescent protein (H37Rv)

tag: gender

value: Male

tag: sample

tag: infection status

value: non-infected

tag: replicate


title: lung_tumor_resection_Y22

type: genomic

city: Boston

first: Yen-Tsung

last: Huang

address: 665 Huntington Avenue

country: USA

institute: Harvard School of Public Health

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: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. The data table contains the normalized expression values produced by that algorithm.

label: biotin

molecule: genomic DNA

source_name: lung tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumor tissue from non-small cell lung cancer patients at surgery using the Promega Qiagen DNA Extraction Kit. DNA quality and quantity was assessed using OD measure and agarose gel electrophoresis.

tag: smoking packyears

tag: Stage

tag: histology


title: lung_tumor_resection_Y21


title: DCs ID78 MTB-infected rep_1

value: MTB-infected


title: DCs ID80 MTB-infected rep_1


title: DCs ID77 MTB-infected rep_1


title: DCs ID77 non-infected rep_1


title: lung_tumor_resection_Y19


title: DCs ID80 non-infected rep_1


title: lung_tumor_resection_1121T


title: lung_tumor_resection_Y18


title: DCs ID75 non-infected rep_1


title: lung_tumor_resection_Y17


title: lung_tumor_resection_Y16


title: lung_tumor_resection_Y13


title: DCs ID88 MTB-infected rep_2


title: DCs ID75 MTB-infected rep_1


title: lung_tumor_resection_Y12


title: lung_tumor_resection_Y11


title: DCs ID91 MTB-infected rep_2


title: DCs ID90 MTB-infected rep_2


title: lung_tumor_resection_Y10


title: DCs ID90 non-infected rep_2


title: lung_tumor_resection_Y09


title: DCs ID87 MTB-infected rep_2


title: lung_tumor_resection_Y08


title: DCs ID91 MTB-infected rep_1


title: DCs ID91 non-infected rep_2


title: DCs ID87 non-infected rep_2


title: lung_tumor_resection_Y15


title: lung_tumor_resection_Y05


title: lung_tumor_resection_Y07


title: DCs ID90 non-infected rep_1


title: DCs ID88 non-infected rep_2


title: DCs ID91 non-infected rep_1


title: lung_tumor_resection_Y06


title: DCs ID68 MTB-infected rep_2


title: lung_tumor_resection_Y01


title: DCs ID90 MTB-infected rep_1


title: lung_tumor_resection_Y04


title: DCs ID68 non-infected rep_2


title: lung_tumor_resection_5254T


title: lung_tumor_resection_4554T


title: DCs ID59 non-infected rep_2


title: DCs ID81 MTB-infected rep_1


title: DCs ID57 MTB-infected rep_2


title: DCs ID59 MTB-infected rep_2


title: lung_tumor_resection_3011T


title: lung_tumor_resection_0311T


title: lung_tumor_resection_2370T


title: lung_tumor_resection_1820T


title: DCs ID20 MTB-infected rep_2


title: DCs ID20 non-infected rep_2


title: DCs ID54 MTB-infected rep_2


title: DCs ID30 non-infected rep_2


title: DCs ID55 MTB-infected rep_2


title: lung_tumor_resection_4454T


title: DCs ID29 non-infected rep_2


title: DCs ID57 non-infected rep_2


title: DCs ID54 non-infected rep_2


title: DCs ID55 non-infected rep_2


title: lung_tumor_resection_1674T


title: DCs ID29 MTB-infected rep_2


title: DCs ID30 MTB-infected rep_2


title: DCs ID28 MTB-infected rep_2


title: lung_tumor_resection_4040T


title: lung_tumor_resection_3372T


title: lung_tumor_resection_3312T


title: lung_tumor_resection_1541T


title: DCs ID28 non-infected rep_2


title: lung_tumor_resection_3293T


title: lung_tumor_resection_3147T


title: lung_tumor_resection_3441T


title: lung_tumor_resection_3365T


title: lung_tumor_resection_3451T


title: DCs ID27 non-infected rep_2


title: lung_tumor_resection_4349T


title: DCs ID52 MTB-infected rep_2


title: lung_tumor_resection_3222T


title: lung_tumor_resection_3242T


title: DCs ID53 non-infected rep_2


title: DCs ID25 non-infected rep_2


title: lung_tumor_resection_0880T


title: DCs ID25 MTB-infected rep_2


title: DCs ID26 MTB-infected rep_2


title: lung_tumor_resection_1650T


title: DCs ID27 MTB-infected rep_2


title: DCs ID26 non-infected rep_2


title: DCs ID52 non-infected rep_2


title: DCs ID50 MTB-infected rep_2


title: lung_tumor_resection_DB404


title: lung_tumor_resection_DB502


title: DCs ID51 MTB-infected rep_2


title: lung_tumor_resection_1398T


title: DCs ID51 non-infected rep_2


title: DCs ID50 non-infected rep_2


title: lung_tumor_resection_1489T


title: DCs ID49 MTB-infected rep_2


title: lung_tumor_resection_1166T


title: lung_tumor_resection_DB430


title: DCs ID47 MTB-infected rep_2


title: lung_tumor_resection_DB560


title: lung_tumor_resection_DB384


title: DCs ID49 non-infected rep_2


title: lung_tumor_resection_DB142


title: DCs ID40 MTB-infected rep_2


title: lung_tumor_resection_DB372


title: lung_tumor_resection_DB140


title: lung_tumor_resection_DB134


title: lung_tumor_resection_4728T


title: lung_tumor_resection_DB276


title: lung_tumor_resection_DB262


title: DCs ID53 MTB-infected rep_2


title: DCs ID40 non-infected rep_2


title: DCs ID47 non-infected rep_2


title: DCs ID39 MTB-infected rep_2


title: lung_tumor_resection_5239T


title: DCs ID38 non-infected rep_2


title: DCs ID39 non-infected rep_2


title: lung_tumor_resection_4559T


title: DCs ID38 MTB-infected rep_2


title: lung_tumor_resection_4638T


title: lung_tumor_resection_5267T


title: lung_tumor_resection_3403T


title: lung_tumor_resection_3387T


title: DCs ID33 non-infected rep_2


title: DCs ID32 non-infected rep_2


title: DCs ID32 MTB-infected rep_2


title: DCs ID31 MTB-infected rep_2


title: lung_tumor_resection_3308T


title: lung_tumor_resection_3367T


title: DCs ID12 MTB-infected rep_2


title: DCs ID13 MTB-infected rep_2


title: DCs ID13 non-infected rep_2


title: DCs ID31 non-infected rep_2


title: DCs ID33 MTB-infected rep_2


title: lung_tumor_resection_3174T


title: DCs ID12 non-infected rep_2


title: DCs ID11 non-infected rep_2


title: lung_tumor_resection_3259T


title: lung_tumor_resection_2495T


title: DCs ID10 MTB-infected rep_2


title: lung_tumor_resection_1728T


title: lung_tumor_resection_3265T


title: lung_tumor_resection_1640T


title: lung_tumor_resection_1705T


title: DCs ID10 non-infected rep_2


title: lung_tumor_resection_3304T


title: lung_tumor_resection_2280T


title: DCs ID8 MTB-infected rep_2


title: DCs ID8 non-infected rep_2


title: DCs ID24 non-infected rep_2


title: DCs ID23 MTB-infected rep_2


title: DCs ID24 MTB-infected rep_2


title: DCs ID9 MTB-infected rep_2


title: lung_tumor_resection_1228T


title: lung_tumor_resection_0670T


title: lung_tumor_resection_1379T


title: lung_tumor_resection_1467T


title: DCs ID23 non-infected rep_2


title: lung_tumor_resection_DB476


title: lung_tumor_resection_DB556


title: lung_tumor_resection_DB434


title: lung_tumor_resection_0006T


title: lung_tumor_resection_DB442


title: DCs ID17 MTB-infected rep_2


title: lung_tumor_resection_DB538


title: lung_tumor_resection_DB406


title: lung_tumor_resection_DB480


title: lung_tumor_resection_1629T


title: DCs ID22 MTB-infected rep_2


title: DCs ID16 MTB-infected rep_2


title: DCs ID17 non-infected rep_2


title: lung_tumor_resection_DB370


title: DCs ID11 MTB-infected rep_2


title: lung_tumor_resection_DB350


title: DCs ID16 non-infected rep_2


title: lung_tumor_resection_DB362


title: lung_tumor_resection_DB352


title: DCs ID46 MTB-infected rep_2


title: DCs ID45 MTB-infected rep_2


title: lung_tumor_resection_DB328


title: DCs ID14 non-infected rep_2


title: DCs ID45 non-infected rep_2


title: DCs ID44 MTB-infected rep_2


title: lung_tumor_resection_DB330


title: lung_tumor_resection_DB310


title: lung_tumor_resection_DB316


title: DCs ID44 non-infected rep_2


title: DCs ID43 MTB-infected rep_2


title: DCs ID9 non-infected rep_2


title: DCs ID22 non-infected rep_2


title: DCs ID46 non-infected rep_2


title: DCs ID43 non-infected rep_2


title: lung_tumor_resection_DB294


title: lung_tumor_resection_DB246


title: lung_tumor_resection_DB240


title: lung_tumor_resection_DB266


title: lung_tumor_resection_DB260


title: DCs ID42 MTB-infected rep_2


title: DCs ID41 MTB-infected rep_2


title: lung_tumor_resection_DB230


title: lung_tumor_resection_DB224


title: DCs ID41 non-infected rep_2


title: DCs ID68 MTB-infected rep_1


title: lung_tumor_resection_DB208


title: lung_tumor_resection_DB206


title: lung_tumor_resection_DB264


title: DCs ID68 non-infected rep_1


title: lung_tumor_resection_DB176


title: DCs ID59 non-infected rep_1


title: DCs ID42 non-infected rep_2


title: DCs ID57 MTB-infected rep_1


title: DCs ID59 MTB-infected rep_1


title: lung_tumor_resection_DB018


title: DCs ID57 non-infected rep_1


title: lung_tumor_resection_5295T


title: lung_tumor_resection_DB094


title: lung_tumor_resection_5245T


title: lung_tumor_resection_DB186


title: lung_tumor_resection_DB116


title: lung_tumor_resection_5271T


title: lung_tumor_resection_5150T


title: lung_tumor_resection_DB118


title: DCs ID20 non-infected rep_1


title: DCs ID55 non-infected rep_1


title: lung_tumor_resection_5133T


title: DCs ID20 MTB-infected rep_1


title: lung_tumor_resection_4696T


title: lung_tumor_resection_5098T


title: DCs ID14 MTB-infected rep_2


title: lung_tumor_resection_4676T


title: lung_tumor_resection_5210T


title: DCs ID52 MTB-infected rep_1


title: DCs ID54 MTB-infected rep_1


title: lung_tumor_resection_4648T


title: DCs ID53 non-infected rep_1


title: DCs ID53 MTB-infected rep_1


title: DCs ID54 non-infected rep_1


title: lung_tumor_resection_4516T


title: lung_tumor_resection_3477T


title: lung_tumor_resection_3624T


title: DCs ID55 MTB-infected rep_1


title: lung_tumor_resection_3484T


title: DCs ID52 non-infected rep_1


title: lung_tumor_resection_3466T


title: lung_tumor_resection_3426T


title: lung_tumor_resection_3414T


title: lung_tumor_resection_4378T


title: lung_tumor_resection_4684T


title: lung_tumor_resection_3504T


title: lung_tumor_resection_3450T


title: lung_tumor_resection_4480T


title: lung_tumor_resection_3469T


title: DCs ID51 non-infected rep_1


title: lung_tumor_resection_3445T


title: DCs ID50 MTB-infected rep_1


title: lung_tumor_resection_5196T


title: DCs ID51 MTB-infected rep_1


title: DCs ID50 non-infected rep_1


title: DCs ID49 non-infected rep_1


title: lung_tumor_resection_3453T


title: lung_tumor_resection_4576T


title: DCs ID49 MTB-infected rep_1


title: DCs ID47 MTB-infected rep_1


title: lung_tumor_resection_3408T


title: lung_tumor_resection_3316T


title: lung_tumor_resection_3290T


title: lung_tumor_resection_3313T


title: DCs ID46 MTB-infected rep_1


title: lung_tumor_resection_3303T


title: DCs ID47 non-infected rep_1


title: lung_tumor_resection_3364T


title: lung_tumor_resection_3280T


title: lung_tumor_resection_3363T


title: lung_tumor_resection_3281T


title: lung_tumor_resection_3309T


title: DCs ID46 non-infected rep_1


title: lung_tumor_resection_3061T


title: lung_tumor_resection_3228T


title: lung_tumor_resection_3233T


title: lung_tumor_resection_3276T


title: lung_tumor_resection_3256T


title: DCs ID45 MTB-infected rep_1


title: lung_tumor_resection_3052T


title: lung_tumor_resection_3195T


title: DCs ID45 non-infected rep_1


title: lung_tumor_resection_2915T


title: lung_tumor_resection_2708T


title: lung_tumor_resection_2707T


title: DCs ID43 non-infected rep_1


title: DCs ID44 non-infected rep_1


title: lung_tumor_resection_2705T


title: lung_tumor_resection_3277T


title: DCs ID42 MTB-infected rep_1


title: DCs ID42 non-infected rep_1


title: DCs ID41 MTB-infected rep_1


title: lung_tumor_resection_2446T


title: DCs ID40 MTB-infected rep_1


title: DCs ID40 non-infected rep_1


title: lung_tumor_resection_2482T


title: DCs ID39 non-infected rep_1


title: lung_tumor_resection_2627T


title: DCs ID41 non-infected rep_1


title: lung_tumor_resection_2388T


title: DCs ID39 MTB-infected rep_1


title: DCs ID43 MTB-infected rep_1


title: lung_tumor_resection_2368T


title: lung_tumor_resection_2259T


title: lung_tumor_resection_2529T


title: lung_tumor_resection_3402T


title: lung_tumor_resection_2292T


title: lung_tumor_resection_2330T


title: lung_tumor_resection_2336T


title: DCs ID38 non-infected rep_1


title: DCs ID33 MTB-infected rep_1


title: DCs ID38 MTB-infected rep_1


title: DCs ID33 non-infected rep_1


title: lung_tumor_resection_2249T


title: lung_tumor_resection_2285T


title: lung_tumor_resection_1963T


title: lung_tumor_resection_2177T


title: lung_tumor_resection_1861T


title: lung_tumor_resection_2233T


title: DCs ID44 MTB-infected rep_1


title: DCs ID30 MTB-infected rep_1


title: PRB25847

city: South San Francisco

first: Yuting

last: Sun

state: CA

address: 1 DNA way

department: Research Oncology

institute: Genentech

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133P 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Notreatment

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

growth_protocol: The LuCaP35 tumors were inoculated subcutaneously in NOD/SCID mice, and grew for ~1 month.

extract_protocol: Qiagen Rneasy kit used for the extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Surgical castration or sham control were performed on mice with matched tumor sizes.  Tumors were harvested 4 weeks post castration.

tag: strain

value: NOD/SCID

tag: tumor type

tag: disease type

value: Prostate cancer


title: DCs ID32 MTB-infected rep_1


title: DCs ID32 non-infected rep_1


title: DCs ID28 MTB-infected rep_1


title: DCs ID31 MTB-infected rep_1


title: PRB25849


title: DCs ID29 MTB-infected rep_1


title: PRB25854

source_name: Castration


title: lung_tumor_resection_1793T


title: DCs ID28 non-infected rep_1


title: PRB25850


title: DCs ID29 non-infected rep_1


title: PRB25848


title: DCs ID27 MTB-infected rep_1


title: DCs ID30 non-infected rep_1


title: lung_tumor_resection_1805T


title: lung_tumor_resection_1777T


title: PRB25845


title: lung_tumor_resection_1720T


title: lung_tumor_resection_1676T


title: lung_tumor_resection_1817T


title: lung_tumor_resection_1852T


title: lung_tumor_resection_1654T


title: DCs ID27 non-infected rep_1


title: lung_tumor_resection_1771T


title: PRB25853


title: PRB25852


title: PRB25851


title: DCs ID26 MTB-infected rep_1


title: lung_tumor_resection_1601T


title: lung_tumor_resection_1636T


title: DCs ID25 non-infected rep_1


title: DCs ID24 MTB-infected rep_1


title: lung_tumor_resection_1543T


title: DCs ID24 non-infected rep_1


title: DCs ID26 non-infected rep_1


title: lung_tumor_resection_1516T


title: PRB25846


title: DCs ID23 MTB-infected rep_1


title: DCs ID25 MTB-infected rep_1


title: lung_tumor_resection_1384T


title: lung_tumor_resection_1399T


title: PRB28975

hyb_protocol: Cyanine-5 dye was then incorporated through an IVT reaction using the Quick Amp Labeling kit (Agilent Technologies). 750 ng of each Cyanine-5 labeled test sample was pooled with Cyanine-3 labeled Universal Mouse Reference (Stratagene) and hybridized onto Agilent’s Whole Mouse Genome 4x44K arrays as described in the manufacturer’s protocol.

scan_protocol: GeneChip scanner 3000.

data_processing: Agilent's Feature Extraction software 10.7

organism: Mus musculus

source_name: Mouse prostate non-stem cells

label_protocol: Quick Amp Labeling kit

growth_protocol: Cells were isolated directly from the prostate tissue of BL6 mice

extract_protocol: PicoPure RNA isolation kit. The samples were amplifed using Message Amp II aRNA Amplification kit before labeling.

treatment_protocol: The isolated primary cells were sorted by immunoflurescent staining and FACS.

tag: tissue type

value: prostate

tag: facs

tag: cell type

value: non-stem cell

source_name: Universal Mouse Reference (Stratagene)

tag: reference

value: Universal Mouse Reference (Stratagene)


title: DCs ID23 non-infected rep_1


title: Met28_5M

city: San Francisco

first: Terence

last: Friedlander

address: 1450 3rd Street

department: Hemotology-Oncology

institute: UCSF

description: metastatic prostate cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2. Average Beta and Unmethylated and methylated signal intensities are provided.

label: Cy5 and Cy3

source_name: genomic DNA from metastatic prostate cancer

label_protocol: DNA was bisulfite-converted using the EZ DNA Methylation Kit (Zymo) then processed per standard Illumina protocol

extract_protocol: Tumors were removed within 2 hours of death in a rapid autopsy. A single pathologist sectioned 15 tissue slices at 15-um from areas with extensive tumor involvement. DNA was extracted with a Wizard Genomic DNA Isolation kit (Promega) and purified by phenol/chloroform extraction. All DNAs were of sufficient quality and quantity for genomic analysis by gel chromatography and UV-Vis spectrophotometery.

tag: tissue

value: metastatic prostate cancer

value: Soft Tissue Metastasis


title: DCs ID22 MTB-infected rep_1


title: DCs ID22 non-infected rep_1


title: lung_tumor_resection_1418T


title: PRB28974


title: lung_tumor_resection_1300T


title: PRB28971


title: Met25_46M

description: metastatic prostate cancer


title: Met26_38M

description: metastatic prostate cancer


title: PRB28970


title: Met24_6M

description: metastatic prostate cancer

value: Liver Metastasis


title: PRB28969


title: Met28_41M

description: metastatic prostate cancer


title: PRB28959

source_name: Mouse prostate stem cells

value: stem cell


title: lung_tumor_resection_1293T


title: DCs ID17 MTB-infected rep_1


title: DCs ID17 non-infected rep_1


title: lung_tumor_resection_1295T


title: Met13_21M

description: metastatic prostate cancer


title: PRB28968


title: lung_tumor_resection_1294T


title: DCs ID16 MTB-infected rep_1


title: PRB28956


title: lung_tumor_resection_1292T


title: lung_tumor_resection_1276T


title: lung_tumor_resection_1184T


title: DCs ID14 MTB-infected rep_1


title: PRB28955


title: DCs ID16 non-infected rep_1


title: Met22_62M

description: metastatic prostate cancer


title: Met3_81M

description: metastatic prostate cancer


title: Met20_6M

description: metastatic prostate cancer


title: DCs ID14 non-infected rep_1


title: DCs ID12 MTB-infected rep_1


title: Met6_9M

description: metastatic prostate cancer


title: Met18_6M

description: metastatic prostate cancer


title: lung_tumor_resection_1183T


title: lung_tumor_resection_1162T


title: lung_tumor_resection_1003T


title: DCs ID12 non-infected rep_1


title: lung_tumor_resection_1098T


title: DCs ID13 MTB-infected rep_1


title: Met12_6M

description: metastatic prostate cancer


title: lung_tumor_resection_1165T


title: lung_tumor_resection_0944T


title: Met28_41M [aCGH]

description:
genomic DNA from metastatic prostate cancer
Cy3=Metastatic Prostate Tumor from Rapid Autopsy, Cy5=Pooled Male Genomic DNA

hyb_protocol: Labelled tumor and normal DNA were combined together and with hybridization buffer (Agilent Oligo aCGH Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1)

data_processing: CN data was mapped to the human genome sequence hg18 freeze and log2 intensity ratios were segmented using circular binary segmentation (CBS) to translate noisy intensity measurements into regions of equal CN (UCSF Biostatistic Core)

source_name: Soft Tissue Metastasis

label_protocol: 500 ng of tumor genomic DNA were labeled with Cy-3 and 500 ng normal reference DNA labelled with Cy-5 along with 5X Buffer, 10X dNTP and Exo-Klenow enzyme, incubated at 37C for 2 hr and 65C for 10 min. All reagents from the Agilent Genomic DNA Labeling Kit PLUS

extract_protocol: DNA was extracted with a Wizard Genomic DNA Isolation kit (Promega) and purified by phenol/chloroform extraction

source_name: Pooled genomic DNA from healthy anonymous donors


title: Met29_23M

description: metastatic prostate cancer


title: DCs ID13 non-infected rep_1


title: Met29_23M [aCGH]


title: lung_tumor_resection_0882T


title: DCs ID11 non-infected rep_1


title: Met10_36M

description: metastatic prostate cancer


title: Met28_5M [aCGH]


title: DCs ID11 MTB-infected rep_1


title: Tcf1-/+ ETP thymocyte, biological rep3

city: Cambridge

first: Jiangwen

last: Zhang

state: MA

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

description: Gene expression data from mouse ETP stage Tcf1-/+ thymocytes.

hyb_protocol: 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with affy bioconductor package.

source_name: mouse DN1 stage thymocytes, Lin-CD44+CD25-kit+.

label_protocol: Average yield from 1000 cells was 3 ng of total RNA. The RNA was amplified using Ovation Pico WTA System (NuGen, San Carlos, CA). Labeling, fragmentation and hybridization to Mouse Genome 430 2.0 Arrays were done according to the manufacturer's instructions (Affymetrix Inc., Santa Clara, CA).

growth_protocol: Tcf1-/- and Tcf1-/+ strains were bred and housed under pathogen-free conditions

extract_protocol: Extraction of total RNA was performed using Arcturus PicoPure RNA Isolation kit (Life Technologies, Foster City, CA) according to the manufacturer's instructions.

treatment_protocol: Mice were sacrificed at 10 weeks of age

value: thymus

tag: genotype

tag: age

value: DN1 thymocyte, 10 weeks

tag: genotype/variation

value: wild type

tag: background strain


title: Met17_18M

description: metastatic prostate cancer

tag: gender


title: Met3_81M [aCGH]

source_name: Liver Metastasis


title: Met26_38M [aCGH]


title: lung_tumor_resection_0135T


title: DCs ID9 MTB-infected rep_1

tag: sample

tag: infection status

tag: replicate


title: DCs ID10 MTB-infected rep_1


title: DCs ID10 non-infected rep_1


title: Tcf1-/+ ETP thymocyte, biological rep1


title: Tcf1-/- ETP thymocyte, biological rep1

description: Gene expression data from mouse ETP stage thymocytes with ablation of Tcf1.


title: DCs ID9 non-infected rep_1


title: Tcf1-/- ETP thymocyte, biological rep2


title: Tcf1-/- ETP thymocyte, biological rep3


title: 350562

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
6-TCP1-mir129-M3 vs. 5-TCP1-mirCTL-M3
Date:2009/07/16

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion protocol.

extract_protocol: Other

tag: cell line

value: papillary thyroid carcinoma

tag: transfection

tag: label

tag: extract

tag: subject

value: negative pre-miRNA


title: 350131

description:
1-TCP1-mirCTL-M1 vs. 2-TCP1-miR129-M1
Date:2009/07/16


title: 350491

description:
5-TCP1-mirCTL-M3 vs. 6-TCP1-mir129-M3
Date:2009/07/16


title: Met18_6M [aCGH]

value: Male


title: 350497

description:
4-TCP1-miR129-M2 vs. 3-TCP1-mirCTL-M2
Date:2009/07/16


title: 350493

description:
2-TCP1-miR129-M1 vs. 1-TCP1-mirCTL-M1
Date:2009/07/16


title: 350489

description:
3-TCP1-mirCTL-M2 vs. 4-TCP1-miR129-M2
Date:2009/07/16


title: Met6_9M [aCGH]


title: Met24_6M [aCGH]


title: DCs ID8 MTB-infected rep_1


title: DCs ID8 non-infected rep_1

value: non-infected


title: DCs ID7 MTB-infected rep_1

value: MTB-infected


title: Met20_6M [aCGH]


title: Met17_18M [aCGH]


title: KL_10_SAP-Tfh-like

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cRNAs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: biotin-streptavidin

source_name: Primary CD4+ T cells

label_protocol: 500 ng of total RNA was used for labeling with the Illumina total prep kit.  The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: Wildtype and SAP-deficient OT-II naïve CD4+CD44loCD62L+CD25- T cells were purified by cell sorting.  Cells were cultured for 3.5 days in the presence of OVA peptide and T-depleted mitomycin C-treated splenocytes in IMDM media, under Tfh-like polarizing conditions (αIFNγ (XMG1.2), αIL-12 (C17.8), αIL-4 (11B11, 10 µg/ml), αTGF-β (1D11, 20 µg/ml), IL-6 (100 ng/ml), IL-21 (50 ng/ml).

extract_protocol: RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).

tag: strain

value: SAP-deficient TCR transgenic OT-II

value: spleen and lymph nodes

value: SAP-deficient in vitro generated Tfh-like cells


title: Met25_46M [aCGH]


title: Met13_21M [aCGH]


title: Met12_6M [aCGH]


title: RD cell line replicate 3

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

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

scan_protocol: BeadChips were scanned on the Illumina iScan

data_processing: Data were made positive by adding an offset to remove negative values, log2 transformed, and subjected to the VST variance-stabilizing transformation, then quantile normalized using procedures in the R bioconductor lumi 1.14 package.

source_name: RD rhabdomyosarcoma cell line

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

growth_protocol: K562 (erythroid), HeLa (cervical cancer) and RD cells (muscle, rhabdomyosarcoma) were maintained in RPMI 1640 medium with 10% fetal calf serum. SH-SY5Y cells (neural, neuroblastoma) were maintained in a 1:1 mixture of DMEM and Ham’s F12 media with 10% fetal calf serum.

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

value: RD


title: KL_11_SAP-Tfh-like

tag: cell type


title: DCs ID7 non-infected rep_1


title: Tcf1-/+ ETP thymocyte, biological rep2


title: Met22_62M [aCGH]


title: Kidney_CSAP_rep2

city: Cordoba

first: German

middle: Alexis

last: Gonzalez

state: Cordoba

address: Av. Armada Argentina 3555

department: School of Engineering

country: Argentina

institute: Catholic University of Cordoba

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 1,0 ST Rat Cartage, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R/Bioconductor using RMA as normalization method

organism: Rattus norvegicus

source_name: kidney, choline-supplemented, diet supplemented with fish oil

label_protocol: The cRNA were prepared according to Ambion WT Expression Kit manual Cat Nº 4411973

growth_protocol: Animals were individually housed in suspended wire-bottomed cages in an air conditioned room (25 ± 1 °C) and were exposed to light/darkness periods of 12:00/12:00 hours. Body weight was recorded daily. Animals handling followed the Guide for the Use and Care of Laboratory Animals of the American Physiological Society (Bethesda, MD, USA).

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

treatment_protocol: Wistar, male weanling rats from the Animal Facility of the Centre of Experimental and Applied Pathology were divided into 4 groups and fed with the following diets: 1- Choline-deficient diet with vegetable oils as lipids (corn and hydrogenated oils); 2- Choline-supplemented diet with vegetable oils as lipids; 3- Choline-deficient diet with menhaden oil as lipid; and 4- Choline supplemented diet with menhaden oil as lipid. Animals were sacrificed after 6 days of receiving the experimental diets. Animals were anesthetized with sodium pentobarbital (40 mg/kg).

value: Wistar

value: male

value: kidney


title: DCs ID6 MTB-infected rep_1


title: Met10_36M [aCGH]


title: K.L_08_WT-Tfh-like

value: WT TCR transgenic OT-II

value: WT in vitro generated Tfh-like cells


title: Kidney_CSAP_rep1


title: KL_12_SAP-Tfh-like


title: RD cell line replicate 2


title: DCs ID5 MTB-infected rep_1


title: Kidney_CSAM_rep2

source_name: kidney, choline-supplemented, diet supplemented with corn oil


title: Kidney_CDAP_rep2

source_name: kidney, choline-deficient, diet supplemented with fish oil


title: RD cell line replicate 1


title: K.L_07_WT-Tfh-like


title: K.L_09_WT-Tfh-like


title: K562 cell line replicate 1

source_name: K562 erythroleukemia cell line


title: Kidney_CSAM_rep1


title: DCs ID4 MTB-infected rep_1

source_name: Human dendritic cells


title: Kidney_CDAP_rep1


title: DCs ID5 non-infected rep_1


title: DCs ID4 non-infected rep_1


title: Kidney_CDAMSN_rep2

source_name: kidney, choline-deficient, diet supplemented with corn oil


title: SY5Y cell line replicate 3

source_name: SH-SY5Y neuroblastoma cell line


title: Kidney_CDAMSN_rep1


title: K562 cell line replicate 3


title: K562 cell line replicate 2


title: DCs ID6 non-infected rep_1


title: DCs ID3 non-infected rep_1


title: HeLa cell line replicate 3

source_name: HeLa cervical cancer cell line

value: HeLa


title: Kidney_CDAMCN_rep2

source_name: kidney, choline-deficient, diet supplemented with corn oil, necrotic


title: DCs ID3 MTB-infected rep_1


title: DCs ID2 MTB-infected rep_1


title: HeLa cell line replicate 1


title: Resist Mo_inf_12h_rep3

status: Public on Dec 05 2011

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 12h E infected

hyb_protocol: Prior to hybridization, the microarrays were denatured by exposing to steam from boiling water for three seconds, UV cross-linked and then immersed in pre-hybridization buffer [5X sodium chloride, sodium citrate buffer (SSC), 0.1% sodium dodecyl sulfate (SDS) (Ambion, Austin, TX), 1% bovine serum albumin (BSA)] at 42ºC for a minimum of 45 min.  The arrays were then washed four times in RNase-, DNase-free, distilled water, immersed in 100% isopropanol for 10 seconds, and dried by centrifugation. Slides were hybridized at 42ºC for approximately 40 hours in a dark, humid chamber (Corning, Corning, NY), washed for 10 min at 42ºC with low stringency buffer [1 X SSC, 0.2% SDS] and then washed twice for 5-min each wash in a higher stringency buffer [0.1 X SSC, 0.2% SDS and 0.1 X SSC] at room temperature with agitation.

scan_protocol: Immediately after washing, the slides were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). Scans were performed using the autoscan feature with the percent saturated pixels set at 0.03%

data_processing: The spots representing genes on the arrays were adjusted for background and normalized to internal controls using image analysis software (GenePix Pro 6.0; Axon Instruments, Inc.). Spots with fluorescent signal values below background were disregarded in all analyses. Initially, arrays were normalized against bovine reference RNA. Data was analyzed using GeneSifter (VizX Labs, Seattle, WA) and a combinatorial statistical approach as follows: data were normalized by mean and then combined, Student’s t test was performed with a cutoff value of 0.05, and pairwise comparisons were made with a fold-change cutoff of 1.5 or 2-fold. Computational hierarchical cluster analysis, analysis of variance (ANOVA), and principal component analysis (PCA) were performed using Spotfire DecisionSite 8.2 (Spotfire, Inc., Somerville, MA), after normalization by mean.

organism: Bos taurus

source_name: Monocytes-derived macrophages, resistant, infected w/ B. abortus S2308, 12 h post-infection

label_protocol: Briefly, cDNA from bovine experimental samples (i.e. from infected and control loops)  and cDNA generated from the bovine reference RNA sample were co-hybridized to a custom 13K bovine 70-mer oligoarray. The cDNA was reverse-transcribed using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA) and labeled with amino-allyl-UTP (Ambion, Austin, TX).  Cy3 and Cy5 dye esters were covalently linked to the amino-allyl group by incubating the samples with the dye esters in 0.1M sodium carbonate buffer.

extract_protocol: Supernatant from the monocyte-derived macrophages cultures was taken out and cells rinsed once with cold PBS at 4 and 12 h p.i. One ml of Tri-reagent® (Ambion, Austin, TX) was added to each flask and RNA extracted using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion) with 1% RNAse inhibitor (Promega, Madison, WI). Genomic DNA was removed by RNase free - DNAse I treatment (Ambion) according to the manufacturer’s instructions, and samples were stored at -80ºC until used.

tag: resistance

value: Naturally resistant to Brucellosis

value: monocytes-derived macrophage

tag: culture type

value: Primary cell culture

source_name: Bovine reference RNA

treatment_protocol: Fresh bovine brain and cerebellum were collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.

value: brain cortex and cerebellum


title: Resist Mo_Inf_12h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 12h A infected

tag: tissue


title: Resist Mo_Inf_12h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 12h B infected


title: Suscept Mo_Inf_12h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 12h A infected

source_name: Monocytes-derived macrophages, susceptible, infected w/ B. abortus S2308, 12 h post-infection

value: female

value: Naturally susceptible to Brucellosis


title: L. mono untreated vs CMPD-treated

city: Ithaca

first: M.

middle: Elizabeth

last: Palmer

state: NY

address: 415 Stocking Hall

department: Food Science

institute: Cornell University

description: Expression profiles were measured for 4 independent biological replicates. Array data were analyzed using a one way ANOVA model to compare differences between strains, and a two way ANOVA model to identify genes regulated by L. mono untreated and L. mono treated.

hyb_protocol: Microarray slide blocking was performed prior to hybridization. Slides were immersed in blocking solution (1% BSA, 5X SSC, 0.1% SDS) at 42°C. After 1 h, the slides were washed for 5 min in 0.1x SSC twice, followed by 30 sec in deionized water and then dried by centrifugation. For the strains to be compared, labeled cDNAs were combined and dried, then suspended in 50μl of hybridization buffer (5X SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 0.06 μg/μl salmon sperm DNA in DEPC-treated water). Samples were vortexed for 1 min and denatured at 95°C for 5 min (repeated twice), followed by a brief centrifugation, then applied to the slides using mSeries LifterSlips™ (Erie Scientific). Following overnight hybridization at 42°C, the slides were washed in 2X SSC+0.1% SDS (5 min, 42˚C), with subsequent 5-min washes at room temperature in 2X SSC+0.1% SDS, 2X SSC, and 0.2X SSC, followed by final rinse in deionized water. Slides were dried by centrifugation.

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis.

organism: Listeria monocytogenes 10403S

source_name: untreated

label_protocol: cDNA was synthesized from purified total RNA and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA Labeling System according to the manufacturer's protocol with following modifications. 6 μg total RNA was combined with 3μg random primers, incubated at 70°C for 10 min. Following a 5 min on ice, 6 μl 5X First-Strand buffer, 1.5 μl 0.1M dithiothreitol (DTT), 1.5 μl dNTP mix containing aminoallyl-dATP and aminohexyl-dTTP, 1 μl RNaseOUT and 2 μl SuperScript III Reverse Transcriptase were added to the reaction tube. The reverse transcription reaction was carried out at 42ºC overnight. Remaining RNA was hydrolyzed by addition of 15 μl 1N NaOH (70ºC for 10 min) and then neutralized with 15 μl 1N HCl. Each cDNA sample was purified with the QIAquick PCR purification kit (Qiagen) using RNase-free water for the final elution step. cDNA samples were dried in a SpeedVac until reduced to ~3 μl. Each cDNA sample was combined with 2X Coupling Buffer and then added to a vial of DMSO-suspended CyTM Dye (GE Healthcare) and the dye coupling reaction was carried out at room temperature for 1h. Labeled cDNA samples were purified with the QIAquick PCR purification kit with an additional 35% Guanidine-HCl wash step and a final elution step in RNase-free water. Purified, labeled cDNA was quantified with UV spectrophotometer readings at wavelengths appropriate to determine the frequency of incorporation (FOI), which is defined as the number of labeled nucleotides incorporated per 1,000 nucleotides of cDNA. cDNA samples with FOIs between 20-50 were used for microarray hybridization.

growth_protocol: Cells were grown in BHI broth at 37°C with shaking (250 rpm; Series 25 Incubator Shaker, New Brunswick Scientific) unless otherwise indicated. All optical density measurements (OD) were made with a model DU640 spectrophotometer (Beckman). L. monocytogenes 10403S was streaked onto brain heart infusion (BHI) agar from –80°C glycerol stock cultures followed by incubation at 37°C for 24 h. A single colony was subsequently inoculated into a tube containing 5 ml BHI broth and grown overnight. 50 μl of this overnight culture was then added to a tube of 5 ml fresh, pre-warmed BHI broth and grown to logarithmic phase (OD600=0.4), then diluted 1:100 in fresh, pre-warmed BHI broth (50 μl into 5 ml broth). After growth to OD600=0.4, NaCl was added (to achieve a final concentration of 0.3M NaCl). After incubation at 37°C for 10 min with shaking, a 2X volume of RNAProtect Bacteria Reagent (Qiagen) were added to cells to stabilize RNA, vortexed, and incubated at room temperature for 5 min. Cells were then pelleted by centrifugation at 5000 rpm for 5 min (Avanti J-25 Centrifuge, Beckman). Supernatant was removed and cell pellets were stored at -80°C until RNA isolation.

extract_protocol: RNA was extracted and DNase treated using Ambion RiboPureTM -Bacteria Kit (Ambion, Austin, TX) according to the manufacturer’s instructions. Total nucleic acid concentrations and purity was assessed using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA quality was analyzed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA) and only RNA of excellent integrity (RNA integrity number of ≥8) was used.

source_name: treated with CMPD

growth_protocol: Cells were grown in BHI broth at 37°C with shaking (250 rpm; Series 25 Incubator Shaker, New Brunswick Scientific) unless otherwise indicated. All optical density measurements (OD) were made with a model DU640 spectrophotometer (Beckman). L. monocytogenes 10403S was streaked onto brain heart infusion (BHI) agar from –80°C glycerol stock cultures followed by incubation at 37°C for 24 h. A single colony was subsequently inoculated into a tube containing 5 ml BHI broth and grown overnight. 50 μl of this overnight culture was then added to a tube of 5 ml fresh, pre-warmed BHI broth and grown to logarithmic phase (OD600=0.4), then diluted 1:100 in fresh, pre-warmed BHI broth (50 μl into 5 ml broth). After growth to OD600=0.4, 64uM of CMPD and NaCl were added (to achieve a final concentration of 0.3M NaCl). After incubation at 37°C for 10 min with shaking, a 2X volume of RNAProtect Bacteria Reagent (Qiagen) were added to cells to stabilize RNA, vortexed, and incubated at room temperature for 5 min. Cells were then pelleted by centrifugation at 5000 rpm for 5 min (Avanti J-25 Centrifuge, Beckman). Supernatant was removed and cell pellets were stored at -80°C until RNA isolation.


title: Suscept Mo_Inf_12h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 12h B infected


title: HeLa cell line replicate 2


title: Suscept Mo_Co_12h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 12h A control

source_name: Monocytes-derived macrophages, susceptible, not infected (control), 12 h


title: Resist Mo_Co12h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 12h E control

source_name: Monocytes-derived macrophages, resistant, not infected (control), 12 h

extract_protocol:
Supernatant from the monocyte-derived macrophages cultures was taken out and cells rinsed once with cold PBS at 4 and 12 h p.i. One ml of Tri-reagent® (Ambion, Austin, TX) was added to each flask and RNA extracted using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion) with 1% RNAse inhibitor (Promega, Madison, WI). Genomic DNA was removed by RNase free - DNAse I treatment (Ambion) according to the manufacturer’s instructions, and samples were stored at -80ºC until used.
Supernatant from the monocyte-derived macrophages cultures was taken out and cells rinsed once with cold PBS at 4 and 12 h p.i. One ml of Tri-reagent® (Ambion, Austin, TX) was added to each flask and RNA extracted using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion) with 1% RNAse inhibitor (Promega, Madison, WI). Genomic DNA was removed by RNase free - DNAse I treatment (Ambion) according to the manufacturer’s instructions, and samples were stored at -80ºC until used.

treatment_protocol:
Fresh bovine brain and cerebellum were collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.
Fresh bovine brain and cerebellum were collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: Kidney_CDAMCN_rep1


title: Suscept Mo_Co_12h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 12h B control


title: DCs ID2 non-infected rep_1

value: Male

value: non-infected


title: 8542_Untreated_24hr_1

city: Worcester

first: Matthew

middle: J

last: Simmons

address: 364 Plantation St

department: Cancer Biology

institute: UMASS Medical School

description: 8542 Untreated.cel

hyb_protocol: Following fragmentation, cRNA were hybridized to Affymetrix Mouse Genome 430A_2.0 chip. 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: Analyses were performed using BRB-ArrayTools developed by Dr. Richard Simon and BRB-ArrayTools Development Team.

source_name: mouse mammary tumor derived cell line

label_protocol: Samples were processed and labeled with the Affymetrix 3’ IVT Express Kit with biotin according to the standard Affymetrix protocol from 5ug of total RNA.

growth_protocol: Cells were maintained in DMEM/F12 1:1 media supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 µg/ml). Cells were maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol: Cells were collected by scraping and total RNA was isolated using Trizol (Invitrogen), followed by further purifification using the RNAeasy Mini kit (Qiagen)

treatment_protocol: Cells were left untreated or treated with  2 ug/ml doxycycline for 24 hours.

value: Primary mammary tumor

value: mouse mammary tumor derived cell line 8542

tag: agent

value: Untreated

tag: intracellular domain of notch1 (icn1) status

value: On


title: 8542_Dox_24hr_1

description: 8542 Dox.cel

value: doxycycline

value: Off


title: Suscept Mo_Co_12h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 12h C control


title: Resist Mo_Co_12h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 12h B control

value: male


title: Suscept Mo_Inf_4h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 4h E infected

source_name: Monocytes-derived macrophages, susceptible, infected w/ B. abortus S2308, 4 h post-infection


title: Resist Mo_Co_12h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 12h A control


title: 8534_Untreated_24hr_1

description: 8534 Untreated.cel

value: mouse mammary tumor derived cell line 8534


title: 8534_Dox_24hr_1

description: 8534 Dox.cel


title: Suscept Mo_Co_4h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 4h D control

source_name: Monocytes-derived macrophages, susceptible, not infected (control), 4 h


title: SY5Y cell line replicate 1


title: Suscept Mo_Inf_4h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 4h A infected


title: Suscept Mo_Co_4h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 4h A control


title: patched tumors rep2

city: SAN DIEGO

first: Alexey

middle: M

last: Eroshkin

state: California

address: Alexey Eroshkin, 3803 Ruette San Raphael

department: Bioinformatics Core

institute: SBPMDI

hyb_protocol: As recommended by Affymetrix

scan_protocol: Using standard protocols

data_processing: Microarray data were preprocessed using robust multichip analysis (RMA) in Partek Genomics Suite 6.5 (Partek, Inc.). Result is log2 transformed normalized data.

source_name: patched tumors

label_protocol: As suggested by Affymetrix

extract_protocol: To isolate cerebellar stem cells, Prominin1+, Lineage-negative (Lin–) cells were FACS-sorted from cerebella of 5-7-day-old WT mice. Tumor cells were isolated by enzymatic dissociation of cerebella from adult tumor-bearing mice. All cells were snap-frozen in liquid nitrogen. RNA was isolated using the RNAqueous kit (Ambion), and was labeled and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

tag: genotype/variation

value: Ptch1 mutant

tag: age

value: Adult

tag: cell source

value: patched tumors


title: Resist Mo_inf_4h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 4h F infected

source_name: Monocytes-derived macrophages, resistant, infected w/ B. abortus S2308, 4 h post-infection

tag: gender

value: Naturally resistant to Brucellosis

value: monocytes-derived macrophage

value: Primary cell culture


title: progenitor-derived tumors rep5

source_name: progenitor-derived tumors

value: progenitor-derived tumors

value: Myc/DNp53-infected Prom1+ cells


title: patched tumors rep1


title: progenitor-derived tumors rep2


title: patched tumors rep3


title: Resist Mo_Inf_4h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 4h D infected

value: brain cortex and cerebellum


title: Resist Mo_Co_4h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 4h F control

source_name: Monocytes-derived macrophages, resistant, not infected (control), 4 h


title: Resist Mo_Inf_4h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 4h A infected


title: Resist Mo_Co_4h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 4h D control


title: SY5Y cell line replicate 2

source_name: SH-SY5Y neuroblastoma cell line


title: stem cell-derived tumors rep5

source_name: stem cell-derived tumors

value: tumor-bearing mice

value: stem cell-derived tumors

value: Myc/DNp53-infected Prom1+Lin- cells


title: stem cell-derived tumors rep4


title: Resist Mo_Co_4h_rep1

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

R 4h A control


title: stem cell-derived tumors rep3


title: stem cell-derived tumors rep2


title: Replication timing of FM01 myoblasts

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description: Note that across .pair files, all of the design names end in "_HG18_WG_CGH_v3.1_HX3" so the 719690 meaningful probes in each of the .pair files are identical. The different numbers at the beginning of the design name refer to the date it was created by NimbleGen. The only difference is that some of the designs from different dates have different random control probes.

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 1.1 kb across the human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of FM01 myoblasts

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: disease status

value: FSHD

value: F

value: myoblasts

tag: sample type

value: early replication intermediate

source_name: Late-replicating DNA of FM01 myoblasts

value: late replication intermediate


title: stem cell-derived tumors rep1


title: Replication timing of CM1 myoblasts

source_name: Early-replicating DNA of CM1 myoblasts

value: control

value: M

source_name: Late-replicating DNA of CM1 myoblasts


title: PAX2 shRNA 15839  puromycin stable TOV21G cell line

city: Houston

first: Kwong-Kwok

last: Wong

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

description: Gene expression data from PAX2 shRNA15839  puromycin stable TOV21G cell line

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix GeneChip U133A Plus 2.0 arrays according to manufacturer's instructions.

scan_protocol: Slides were scanned using the Affymetrix 7G scanner, and CEL files generated using Expression Console software

data_processing: All CEL files were imported into dChip2010, normalized with invariant set with TOV21G_PAX2_15841 as baseline, and expression values were obtained using Model-based expression with PM signal only

source_name: PAX2 knockdown cell

label_protocol: The GeneChip® 3’ IVT Express Kit was used to synthesize first-strand cDNA from total RNA by revderse transcription. The cDNA was then converted into a double-stranded DNA template for transcription. Biotin-congugated nucleotide (cRNA) was then generated by In vitro transcription.  synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA  template for transcription. In vitro transcription synthesizes aRNA and incorporates a  biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA). The  aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic  phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for  hybridization onto GeneChip 3’ expression arrays.

growth_protocol: All cells were grown in Roswell Park Memorial Institute-1640 (RPMI-1640) with 10% fetal bovine serum and 1% penicillin/streptomycin in 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted from cell culture using RNEasy Kit

treatment_protocol: MISSION TRC shRNA Lentiviral Particles (Sigma-Aldrich, MO, USA) targeting various regions of PAX2 (shRNA 15839, CCGGCGTCTCTTCCATCAACAGAATCTCGAGATTCTGTTGATGGAAGAGACGTTTTT; shRNA 15840, CCGGCCCAAAGTGGTGGACAAGATTCTCGAGAATCTTGTCCACCACTTTGGGTTTTT; shRNA 15841, CCGGGATGAAGTCAAGTCGAGTCTACTCGAGTAGACTCGACTTGACTTCATCTTTTT) were used to transduce the parental ovarian cancer cell lines that expressed PAX2. The control lentivirus PLKO-puro (no insert sequence) (Sigma-Aldrich, MO, USA) and shRNA non-target control (insert sequence: CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT) (Sigma-Aldrich, MO, USA) were used as negative controls. Puromycin was used to select transfected cells. After stable knockdown, western blot and real-time reverse transcription polymerase chain reaction (RT-PCR) were used to confirm the efficacy of PAX2 knockdown.

tag: treatment

value: PAX2 knockdown

tag: cell line


title: Replication timing of CM4 myoblasts

source_name: Early-replicating DNA of CM4 myoblasts

source_name: Late-replicating DNA of CM4 myoblasts


title: Suscept Mo_Inf_4h_rep2

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 4h D infected

value: female

value: Naturally susceptible to Brucellosis

source_name: Bovine reference RNA


title: PAX2 shRNA 15841  puromycin stable TOV21G cell line

description: Gene expression data from PAX2 shRNA15841  puromycin stable TOV21G cell line


title: Suscept Mo_Inf_12h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 12h C infected

source_name: Monocytes-derived macrophages, susceptible, infected w/ B. abortus S2308, 12 h post-infection

value: monocytes-derived macrophage

value: Primary cell culture


title: PAX2 shRNA 15840  puromycin stable TOV21G cell line

description: Gene expression data from PAX2 shRNA15840  puromycin stable TOV21G cell line


title: IGFBP2 silencing - experiment 3A

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: We compared the transcription profiles of IGFBP2 silencing cells (RH36) by microarray competitive hybridization against siCONTROL cells.

hyb_protocol: Ranges along 350 and 300 pico-moles and 2.7 and 3.0 µg of aRNA labeled with Cy3 and Cy5 were co-precipitated with the ammonium acetate and ethanol. Pellet was resuspended in 110 µl with the hybridization solution composed by SSC 5X, SDS 0.1%, Formamide 25% and salmon sperm purified DNA 100 ng/µl and carried out in an automatic hybridization station (ArrayBooster, Advalytix) at 48° C for 30 hours in the competitive hybridization. Microarray slides, before hybridization, have been blocked with the pre-hybridization solution (SSC 5X, SDS 0.1%, salmon sperm purified DNA 100 ng/ul and Denhardt's solution 5X) for 6 hours at 48° C. After the hybridization slides were washed at room temperature with 1X SSC 0.2% SDS for 4 minutes one time; 0.1X SSC 0.2% SDS for 4 minutes one time; 0.2X SSC for 3 minutes two times each with new solution and 0.1X SSC for 3 minutes one time. Slides were dried centrifuging 1 minute at 800 X g at 20° C.

scan_protocol: After stringent washings, fluorescence left in the microarray slides were read with the ScanArray LITE confocal laser scanner (PerkinElmer) with 5 µm resolution. The scans images were quantified with ScanArray Express (PerkinElmer) software using the fixed circle method.

data_processing:
Fluorescence intensity was determined with the ScanArray Express software (PerkinElmer) using fixed circle method and median spot intensity background subtracted was normalized with MIDAS tool (from TIGR TM4 suite; Saeed et al., 2003) using sequentially global mean normalization and local mean normalization (LOWESS) methods. Lowess normalization was performed without distinguishing between different sub-arrays.
From this analysis were included only the array positions containing a 70-mer oligonucleotides. The generated normalized matrix was loaded in to TIGR MeV software.

source_name: RH36 treated with siRNA pool for IGFBP2 target gene (test)

label_protocol: Label protocol Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer.  1ug of total RNA for each of three siRNA experiments (siIGFBP2-1,2,3) was linearly amplified with with the MessageAmp™ aRNA amplification kit (Ambion). 5ug of the amplified RNA (aRNA) have been dried for 12 hours using a Heto Lyolab 3000 freeze-dryer (Heto-Holten A/S) and coupled with Cy5 post-labeling dye (Amersham, GE Healthcare). Coupling was performed for 45 minutes at room temperature. Unincorporated dyes were eliminated using MEGAclear™ Kit (Ambion). Labeled aRNA was eluted in ultraPURE™ distilled water DNase, RNase Free (Gibco) and quantized in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

growth_protocol: DMEM + 10% Fetal Calf Serum (FCS).

extract_protocol:
Total RNA was extracted with TRIzol method (Invitrogen). The procedure was:
1. Addition of chloroform  0.2ml/1ml Trizol and shake for 1 minute;
2. Leave in ice for 15 minutes and then centrifuge at 4º C for 20 minutes at 14,000 X g;
3 Transfer the supernatant to 1.5 ml microfuge non-stick tubes and add an equal volume of isopropanol to precipitate the RNA;
4. Incubate at 4º C for 20 minutes and centrifuge at 4º C for 20 minutes at 14,000 X g;
5. Discard the supernatant and wash with ethanol 75% centrifuging for 15 minutes at 4º C at 14,000 X g;
6. Pellet was resuspended in ultraPURE™ distilled water DNase, RNase Free (Gibco).

treatment_protocol: RH36 cells at 50-70% confluent status were transfected with pool siRNA for target gene IGFBP2 (siIGFBP2)  using Dharmafect 3 transfection reagent following the manufacturer’s instructions (Dharmacon, Thermo Scientific, Lafayette, CO). After 48 hours from transfection the cells were harvested with TRIzol (Invitrogen) for total RNA extraction. The  efficacy of the knockdown of the gene was evaluated at mRNA or protein level by RT-PCR and western blot.

value: rhabdomyosarcoma cell line

tag: sirna transfection

value: IGFBP2 transcript was silenced with siRNA pool (Darmachon)

source_name: RH36 treated with siRNA pool for non-targeting gene (Reference)

label_protocol: Label protocol Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer.  1ug of total RNA for pool of three siRNA experiments with non-targeting siRNA was linearly amplified with with the MessageAmp™ aRNA amplification kit (Ambion). 5ug of the amplified RNA (aRNA) have been dried for 12 hours using a Heto Lyolab 3000 freeze-dryer (Heto-Holten A/S) and coupled with Cy5 post-labeling dye (Amersham, GE Healthcare). Coupling was performed for 45 minutes at room temperature. Unincorporated dyes were eliminated using MEGAclear™ Kit (Ambion). Labeled aRNA was eluted in ultraPURE™ distilled water DNase, RNase Free (Gibco) and quantized in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: RH36 cells at 50-70% confluent status were transfected with non-targeting siRNA pool (siCONTROL) using Dharmafect 3 transfection reagent following the manufacturer’s instructions (Dharmacon, Thermo Scientific, Lafayette, CO). After 48 hours from transfection the cells were harvested with TRIzol (Invitrogen) for total RNA extraction. The  efficacy of the knockdown of the gene was evaluated at mRNA or protein level by RT-PCR and western blot.

value: treated with siRNA pool for non-targeting gene (Dharmacon)


title: IGFBP2 silencing - experiment 2B (Technical replicate)


title: progenitor-derived tumors rep3

value: Adult

value: progenitor-derived tumors

value: Myc/DNp53-infected Prom1+ cells


title: IGFBP2 silencing - experiment 3B (Technical replicate)


title: Replication timing of FM7 myoblasts

source_name: Early-replicating DNA of FM7 myoblasts

value: FSHD

value: F

source_name: Late-replicating DNA of FM7 myoblasts


title: progenitor-derived tumors rep4

source_name: progenitor-derived tumors


description: Gene expression data fromPLKO-1 vector control puromycin stable TOV21G cell line

source_name: non-target shRNA control

value: non-target control


title: IGFBP2 silencing - experiment 2A


title: IGFBP2 silencing - experiment 1B (Technical replicate)


title: HCT15 cell line, 5aza treated

status: Public on Dec 04 2011

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Gene expression profile of surgically resected material

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Normalization was performed by robust multi-array average (RMA) method under R 2.6.2 statistical software with affy package from BioConductor. The normalization procedure was separately performed for each data set of clinical samples, HT29 cells, and HCT15 cells. The normalized gene expression levels were presented as log2-transformed values by RMA.

source_name: HCT15 cell line

label_protocol: cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Cells were treated with 0.5 uM 5-aza-2'-deoxycytidine (Sigma Aldrich, St Louis, MO) for 72 hours.

value: colorectal cancer cell line

tag: treatment group

value: 5aza treated


title: parental TOV21G cell line

description: Gene expression data from parental TOV21G cell line

source_name: Parental cells

value: control


title: HCT15 cell line, control

treatment_protocol: Cells were left untreated (control).


title: Replication timing of CM5 myoblasts

source_name: Early-replicating DNA of CM5 myoblasts

value: M

value: myoblasts

value: early replication intermediate

source_name: Late-replicating DNA of CM5 myoblasts

value: late replication intermediate


title: FceRla KO mHRF

city: Tokyo

first: Kenji

last: Matsumoto

address: 2-10-1 Okura, Setagaya-ku

department: Allergy and Immunology

institute: National Research Institute for Child Health and Development

description:
FceRa-/- mHRF-His
Raw data file:
US80503145_252800510859_S01_GE1_107_Sep09_2_4.txt

hyb_protocol: Standard hybridization

scan_protocol: Agilent Technologies Scanner G2505C, and Scanner Control Sofware ver 8.0

data_processing: Per Chip, per gene normalization using median value was performed by GeneSpring GX11

source_name: Lung chellenged with HRF

growth_protocol: Whole lung was homogenized and total RNA was wxtracted using

extract_protocol: RNeasy Total RNA Mini Kit (Qiagen)

treatment_protocol: intranasal administration of mouse histamine-releasing factor

tag: strain

value: FceRIa-/-

value: Whole lung

tag: stress

value: HRF


title: IGFBP2 silencing - experiment 1A

tag: cell type

value: rhabdomyosarcoma cell line

value: IGFBP2 transcript was silenced with siRNA pool (Darmachon)

value: treated with siRNA pool for non-targeting gene (Dharmacon)


title: FcRg KO mHRF

description:
FcRg-/- mHRF-His
Raw data file:
US80503145_252800510859_S01_GE1_107_Sep09_1_4.txt

value: FcRg-/-


title: FcRg KO PBS

description:
FcRg-/- PBS
Raw data file:
US80503145_252800510859_S01_GE1_107_Sep09_1_3.txt

source_name: Lung chellenged with PBS

value: PBS


title: HT29 cell line, 5aza treated

source_name: HT29 cell line


title: Replication timing of FM1 myoblasts

source_name: Early-replicating DNA of FM1 myoblasts

value: FSHD

source_name: Late-replicating DNA of FM1 myoblasts


title: FceRla KO PBS

description:
FcRla-/- PBS
Raw data file:
US80503145_252800510859_S01_GE1_107_Sep09_2_3.txt


title: blood, normal, biological rep2

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description:
Gene expression data.
normal_2

hyb_protocol: Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.

data_processing: Data was RMA processed in R with the Affy package.

source_name: blood

label_protocol: Single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).

growth_protocol: Experiments were performed with material in the peripheral blood and at the site of coronary occlusion obtained from 4 patients undergoing primary percutaneous coronary intervention (PCI) for ACS, presenting clinically as ST-segment elevation myocardial infarctions (STEMI). Immediately after diagnostic angiography and identification of the culprit lesion, the presence of total coronary occlusion and angiographic signs of an occluding thrombus, the culprit coronary artery was intubated with a 6 F Medtronic guiding catheter and wired with a 0.014 inch guide wire. Prior to any subsequent interventional procedures, thrombi were removed from the site of coronary occlusion with an aspiration catheter (Export™XT6F Aspiration Catheter, Medronic Inc., Minneapolis, MN, USA) and immediately immersed in phosphate-buffered saline (PBS) containing vials. In parallel, arterial blood was sampled from the aorta and stored in vials. In addition, peripheral blood from healthy controls was obtained in a similar manner. Peripheral blood leukocytes (PBL) were treated in a similar fashion and mRNA was extracted from both cells.

extract_protocol: Total RNA of freshly isolated thrombi and corresponding peripheral blood leukocytes was isolated using the commercially available QIAGEN RNeasy Mini Kit (QIAGEN) in accordance with the manufacturer’s recommendations.

tag: disease state

value: normal

value: blood

value: leukocytes


title: HT29 cell line, control

tag: tissue

value: colorectal cancer cell line

value: control


title: blood, normal, biological rep4

description:
Gene expression data.
normal_4


title: Replication timing of FM5 myoblasts

source_name: Early-replicating DNA of FM5 myoblasts

value: M

value: myoblasts

source_name: Late-replicating DNA of FM5 myoblasts


title: Suscept Mo_Co_4h_rep3

description:
Reference RNA is a mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

S 4h E control

source_name: Monocytes-derived macrophages, susceptible, not infected (control), 4 h

value: female

tag: resistance

value: Naturally susceptible to Brucellosis

value: monocytes-derived macrophage

tag: culture type

value: Primary cell culture

source_name: Bovine reference RNA

value: brain cortex and cerebellum


title: PDGF-BB treated replicate 1

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description:
Data from S17 cells treated with 100ng/ml PDGF-BB for 72h
SAMPLE 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C.

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

data_processing: Rma normalized in R

source_name: S17 cell_100ng/ml PDGF-BB for 72h

label_protocol: Biotinylated cRNA was prepared according to the instructions of the manufacturer.

growth_protocol: SC S17 growing in 10-cm dishes were trypsinized in 0.25% trypsin solution and resuspended with MEM containing 2% FBS.

extract_protocol: Qiagen Rneasy

treatment_protocol: 100ng/ml PDGF-BB for 72h

value: Stromal cell


title: WT mHRF

description:
B6 mHRF-His
Raw data file:
US80503145_252800510859_S01_GE1_107_Sep09_1_2.txt

tag: genotype/variation

value: wild type

value: Whole lung

value: HRF


title: blood, normal, biological rep3

description:
Gene expression data.
normal_3


title: WT PBS

description:
B6 PBS
Raw data file:
US80503145_252800510859_S01_GE1_107_Sep09_1_1.txt

value: PBS


title: PDGF-BB treated replicate 3

description:
Data from S17 cells treated with 100ng/ml PDGF-BB for 72h
SAMPLE 6


title: blood vessel, infarction, biological rep4

description:
Gene expression data.
infarction_4

source_name: blood vessel after myocardial infarction

value: myocardial infarction

value: blood vessel


title: Control replicate 3

description:
Data from control S17 cells
SAMPLE 3

source_name: S17 cell control

treatment_protocol: control


title: blood vessel, infarction, biological rep3

description:
Gene expression data.
infarction_3

value: leukocytes


title: patched tumors rep4

source_name: patched tumors

value: Ptch1 mutant

tag: age

value: Adult

value: patched tumors


title: Control replicate 2

description:
Data from control S17 cells
SAMPLE 2


title: blood, normal, biological rep1

description:
Gene expression data.
normal_1

value: normal

value: blood


title: Control replicate 1

description:
Data from control S17 cells
SAMPLE 1


title: blood vessel, infarction, biological rep2

description:
Gene expression data.
infarction_2


title: Diffuse-type Gastric Cancer Replicate 3

description: Biological replicate 3 of 3. Gastric cancer vs. normal gastric mucosal tissues.

hyb_protocol: Hybridization and signal detection of Mouse GE 4x44K v2 Microarray (G4122F, Agilent) was performed following the manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2539A scanner.

data_processing: Gene expression data were acquired by Feature Extraction Software version 9.5.3 (Agilent) and were then transformed into log2 ratio of Cy5 / Cy3 for each gene. Probes that were marked as present in all three samples were used.

source_name: Diffuse-type gastric cancer

label_protocol: Using 250 ng of total RNA, cRNA was prepared using Low RNA Input Fluorescent Linear Amplification Kit PLUS, Two-Color (Agilent), and labeled with Cy5 for three independent mouse DGC samples and Cy3 for a pool of five normal gastric mucosal samples.

extract_protocol: Five normal gastric mucosae, from which stromas were removed mechanically in 30 mM EDTA-2Na, and three primary gastric cancers were obtained from Atp4b-Cre-;Cdh1loxP/loxP;Trp53loxP/loxP and Atp4b-Cre+;Cdh1loxP/loxP;Trp53loxP/loxP mice at 12 months, respectively. Total RNA from the tissues was isolated with TRIzol Reagent (Invitrogen, Carlsbad, CA). Contaminant DNA was removed by digestion with RNase-free DNase using DNA-free Kit (Applied Biosystems, Carlsbad, CA). Integrity of obtained RNA was assessed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples were confirmed to have an RNA Integrity Number (RIN) greater than 7.

value: 12 months

source_name: pooled normal gastric mucosal tissues


title: blood vessel, infarction, biological rep1

description:
Gene expression data.
infarction_1


title: treatment: Rbaal VIGS - rep1

status: Public on Dec 03 2011

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Virus treated barley leaf 7 (counted from the base) with Rbaal silencing construct

hyb_protocol: Affy Barley1 hyb

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: leaf (treatment: Rbaal VIGS)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  16 h photoperiod, light intensity 250 µmol-2 s-1  Environmental Conditions:  Conviron growth room, flourescent lighting

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: germplasm name

tag: organism part

tag: development stage

value: PO:0007101 LP.09 nine leaves visible

value: 42 days

tag: growth media

value: peat/perlite/soil

value: Rbaal VIGS


title: progenitor-derived tumors rep1

source_name: progenitor-derived tumors

tag: cell source

value: progenitor-derived tumors

value: Myc/DNp53-infected Prom1+ cells


title: treatment: Rbaal VIGS - rep3

description: treatment=Rbaal VIGS rep 3

tag: treatment


title: treatment: Co-silencing (Rbaal + PDS) - rep3

description: treatment=Co-silencing rep 3

source_name: leaf (treatment: Co-silencing (Rbaal + PDS))

value: Co-silencing (Rbaal + PDS)


title: treatment: Empty Virus (no inserted plant sequences) - rep1

description: Virus treated barley leaf 7 (counted from the base) without silencing construct

source_name: leaf (treatment: Empty Virus (no inserted plant sequences))


title: treatment: Co-silencing (Rbaal + PDS) - rep2

description: treatment=Co-silencing rep 2


title: Diffuse-type Gastric Cancer Replicate 2

description: Biological replicate 2 of 3. Gastric cancer vs. normal gastric mucosal tissues.


title: treatment: Rbaal VIGS - rep2

description: treatment=Rbaal VIGS rep 2


title: treatment: Co-silencing (Rbaal + PDS) - rep1

description: Virus treated barley leaf 7 (counted from the base) with both Rbaal and PDS silencing constructs


title: treatment: Empty Virus (no inserted plant sequences) - rep3

description: treatment=Empty Virus rep 3


title: treatment: Untreated Control - rep2

description: treatment=Untreated Control rep 2

source_name: leaf (treatment: Untreated Control)

value: untreated control


title: treatment: Empty Virus (no inserted plant sequences) - rep2

description: treatment=Empty Virus rep 2


title: treatment: Untreated Control - rep3

description: treatment=Untreated Control rep 3


title: treatment: Untreated Control - rep1

description: Untreated control barley leaf 7 (counted from the base)


title: Diffuse-type Gastric Cancer Replicate 1

description: Biological replicate 1 of 3. Gastric cancer vs. normal gastric mucosal tissues.


title: lola_isoform_K_(ORC4)_rep4

city: Bethesda

first: Edward

last: Giniger

state: MD

department: NINDS

institute: NIH

hyb_protocol: Hybridization was performed using the Fred Hutchinson Cancer Research Center Genomics Resources standard protocol. Briefly, experimental and control labeled cDNA targets were co-hybridized to microarrays for 16 hrs at 63°C and sequentially washed at room temperature in 1 x SSC and 0.03% SDS for 2 min, 1 x SSC for 2 min, 0.2 x SSC with agitation for 20 min, and 0.05 x SSC with agitation for 10 min.  Arrays were immediately centrifuged until dry.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).  Image analysis was performed using GenePix Pro 6.0.

data_processing: LOESS normalized, no background correction, scaled by median absolute deviation, all performed using limma package (Author, Gordon Smyth) within R statistical language.

organism: Drosophila melanogaster

source_name: lola C4-/- embryos, 10-12 hours after egg laying

label_protocol: First-strand cDNA synthesis and labeling were performed using the Fred Hutchinson Cancer Research Center Genomics Resources standard protocol. In brief, each total RNA sample (20-30 μg) was reverse transcribed using SuperScript II (Invitrogen) with aa-dUTP/dNTPs incorporation. The resulting cDNAs were subsequently coupled to either Cy3 or Cy5 fluorophores (GE Healthcare Bio-Sciences Corp., Piscataway, NJ).

growth_protocol: Embryos were collected for 2 hours at 25C on grape juice agar plates and incubated an additional 6 hours at 25C in a moist chamber. Embryos of the desired genotype were then hand-sorted with a fluorescent dissecting microscope based on positive GFP expression in the CNS. Sorted embryos were returned to 25C and allowed to develop until 10.0 hours after the end of egg collection. lola mutant and control embryos were collected concurrently.

extract_protocol: Experimental and control total RNA samples were extracted with Trizol (Invitrogen) per manufacturer’s instructions. Final RNA pellet was rinsed twice with 75% ethanol, air-dried 10 minutes, resuspended in 20μl RNase-free water at 60o and stored at -70o. Each RNA sample for microarrays was 20-30 μg of total RNA, derived from ~300 embryos.

treatment_protocol: Collected embryos were dechorionated with 50% bleach, rinsed once with 0.1 M Na phosphate pH 7.2; 0.3% Triton X-100, and rinsed twice with sterile water.

value: w1118; lolaORC4 sca-GAL4/lolaORC4 UAS-tau-eGFP

tag: developmental stage

value: embryonic, 10-12 hours after egg laying

source_name: ctrl embryos 10-12 hours after egg laying

value: w1118; sca-GAL4/UAS-tau-eGFP (control)


title: lola_isoform_K_(ORC4)_rep2


title: lola_isoform_K_(ORC4)_rep5


title: lola_isoform_K_(ORC4)_rep1


title: lola_isoform_K_(ORC4)_rep3


title: lola_null_(ORE76)_rep7

source_name: lola E76-/- embryos, 10-12 hours after egg laying

value: w1118; lolaORE76 sca-GAL4/lolaORE76 UAS-tau-eGFP


title: lola_null_(ORE76)_rep5


title: Potato leaves, control Vs. salt-treated, day3, rep3

city: Belvaux

first: Danièle

last: Evers

address: 41, rue du Brill

department: EVA

country: Luxembourg

institute: CRP-Gabriel Lippmann

hyb_protocol: Probe hybridization was performed according to the TIGR protocol. Probes were precipitated during 1 h at  80°C. After centrifugation at 16000×g at 4°C during 20 min, the probes were washed with cold 75% EtOH, dried, resuspended in 60 µL hybridization buffer (5X SSC, 50% formamide, 0.1% SDS) and finally denatured at 95°C for 3 min. Hybridization in individual chambers was done at 42°C during 16 h. Cy5-labelled cDNAs of salt-treated plants were hybridized versus Cy3-labelled cDNAs of control plants. Two slides were performed with a dye-swap (inverted labelling). Slides were washed and dried by centrifugation at 30×g during 5 min. The TIGR 10K potato microarrays containing 15,264 cDNAs repeated twice (http://www.jcvi.org/potato/sol_ma_microarrays.shtml) were used for the experiments.

scan_protocol: Slides were scanned using a Professional 4200A microarray scanner (Molecular Devices Corporation, Union City, CA, USA). Two laser channels were used (532 nm and 635 nm) at different settings for the photomultiplier tube (PMT gain). The two PMT gains were automatically adjusted with the Genepix® Pro 6.0 software (Molecular Devices Corporation, Union City, CA, USA) to reach a global intensity ratio close to 1 with pixel saturation equal to 0.001%. Spots with a diameter smaller than 60 µm, spots with a signal intensity below background intensity plus two standard deviations were discarded from further analysis. MA plots (log ratio (stress/control) versus mean (log(stress),log(control))) were performed to check the quality of the arrays.

data_processing: To analyze gpr files generated by Genepix® Pro 6.0 software, data were imported into Acuity 4.0 software (Molecular Devices Corporation, Union City, CA, USA) and normalized with the print-tip Lowess method. A “one sample t-test” was first performed for the four slides. In order to retain spots with repeatable results, only probes with a p-value below 0.05 were selected. As a second step, probes with a log ratio below -0.5 and above 0.5 were selected to generate the final list.

organism: Solanum tuberosum

source_name: Potato leaves, control, day3

label_protocol: Labelling of 15 µg RNA per sample was performed following the TIGR protocol. Reverse transcription was performed using Superscript II kit (Invitrogen) during 2 hours. The reaction was stopped by addition of 10 µL 0.5 M EDTA. Untranscribed RNA was degraded by addition of 10 µL 1 M NaOH and incubation at 65°C during 15 min. Sixty microliters of 1 M Tris-HCl were added for neutralization. aa-cDNA purification was performed using the QIAquick PCR purification kit (Qiagen, Leusden, The Netherlands). Washing steps were performed using 500 µL of 5 mM KPO4 pH=8.5, 80% EtOH solution and elution was done using two times 30 µL of 4 mM KPO4 pH=8.5 (final volume 60 µL). Precipitation of aa-cDNA was performed during 1 hour at 80°C. After centrifugation at 16000×g during 20 min, the pellet was washed using cold 75% EtOH and vacuum-dried for 10 min. The pellet was solubilized in 4.5 µL daily-prepared 0.1 M Na2CO3. A volume of 4.5 µL of dye (previously resuspended in DMSO following manufacturer instructions) was then added and the labelling reaction took place during 1 h at room temperature. To remove uncoupled dye, the QIAquick PCR purification kit was used and the elution was performed twice with supplied elution buffer EB (final volume of 65 µL). Cyanine incorporation was controlled by measuring the absorbance at 260 nm (cDNA), 550 nm (Cy3) and 650 nm (Cy5), followed by an adjustment of the Cy3- and Cy5-coupled cDNA quantities.

growth_protocol: After in vitro multiplication, plantlets of a Solanum tuberosum Cv. Désirée were transferred for acclimatization in a 13-cm diameter pot with 0.25 dm3 of 3:1 soil:sand mixture during 2 months before salt exposure. The culture room parameters were set at 21°C/18°C (day/night), 12 hours daylight and a light intensity of 40 μmol.m-2.s-1.

extract_protocol: The first and second leaves were sampled after 3 days on two different sets of plants. Leaves were immediately frozen in liquid nitrogen before being stored at -80°C. For each treatment, four biological replicates were sampled. Total RNA was extracted from 100 mg of frozen leaves with the RNeasy Plant Mini Kit (Qiagen, Leusden, The Netherlands) including DNase treatment, following the manufacturer’s instructions. Quality control was performed with the RNA Nano assay using a 2100 Bioanalyzer (Agilent Technologies, Diegem, Belgium). RNA samples with a RIN (RNA integrity number adapted to plant rRNA profiles) lower than 7 were excluded from the experiment. RNA purity and concentration were measured by the absorbance at 260 nm and 280 nm using a DU800 spectrophotometer (Beckman Coulter, Villepinte, France).

treatment_protocol: Salt treatment was started at day 0 by watering the plants with 75 mL of 150 mM NaCl solution while the control plants were watered with the same amount of tap water.

tag: cultivar

value: Desirée

value: leaves

value: water control

tag: treatment duration

value: 3 days

source_name: Potato leaves, salt-treated, day3

value: salt


title: Potato leaves, control Vs. salt-treated, day3, rep4


title: Potato leaves, control Vs. salt-treated, day3, rep2


title: lola_null_(ORE76)_rep6

tag: strain


title: PDGF-BB treated replicate 2

description:
Data from S17 cells treated with 100ng/ml PDGF-BB for 72h
SAMPLE 5

tag: cell line

tag: cell type

value: Stromal cell


title: lola_isoform_K_(ORC4)_rep7


title: lola_null_(ORE76)_rep4


title: Potato leaves, control Vs. salt-treated, day3, rep1

tag: tissue


title: lola_null_(ORE76)_rep2


title: 7226 | IgG | IFN-low [Intel]

status: Public on Dec 02 2011

type: other

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

description: IgG

hyb_protocol: Serum was diluted 1:250 from stocks (maintained at -80 deg. C. in) in PBS + 0.5% Tween 20 (Sigma-Aldrich, St. Louis, MO) and 2.5% fetal calf serum (Omega Scientific, Tarzana CA). Post primary incubation, washed arrays were incubated with 0.375ug/ml Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA)

scan_protocol: Arrays were scanned using an Axon digital scanning system (Molecular Devices, Sunnyvale, CA)

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

molecule: other

source_name: systemic lupus erythematosus

tag: interferon signature category

value: IFN-low


title: 7227 | IgG | IFN-low [Intel]

description: IgG


title: 7235 | IgG | IFN-low [Intel]

description: IgG


title: 7228 | IgG | IFN-low [Intel]

description: IgG


title: 7241 | IgG | IFN-low [Intel]

description: IgG


title: 7245 | IgG | IFN-low [Intel]

description: IgG


title: 7243 | IgG | IFN-low [Intel]

description: IgG


title: 7252 | IgG | IFN-low [Intel]

description: IgG


title: 7251 | IgG | IFN-low [Intel]

description: IgG


title: 7247 | IgG | IFN-low [Intel]

description: IgG


title: lola_null_(ORE76)_rep3


title: Potato leaves, control Vs. cold-treated, day3, rep2

hyb_protocol: Probe hybridization was performed according to the TIGR protocol. Probes were precipitated during 1 h at  80°C. After centrifugation at 16000×g at 4°C during 20 min, the probes were washed with cold 75% EtOH, dried, resuspended in 60 µL hybridization buffer (5X SSC, 50% formamide, 0.1% SDS) and finally denatured at 95°C for 3 min. Hybridization in individual chambers was done at 42°C during 16 h. Cy5-labelled cDNAs of cold-treated plants were hybridized versus Cy3-labelled cDNAs of control plants. Slides were washed and dried by centrifugation at 30×g during 5 min. The TIGR 10K potato microarrays containing 15,264 cDNAs repeated twice (http://www.jcvi.org/potato/sol_ma_microarrays.shtml) were used for the experiments.

source_name: Potato leaves, cold treated, day3

growth_protocol: After in vitro multiplication, plantlets of a Solanum tuberosum Cv. Desirée were transferred for acclimatization in a 13-cm diameter pot with 0.25 dm3 of 3:1 soil:sand mixture during 2 months before cold exposure (4°C). The culture room parameters were set at 21°C/18°C (day/night), 12 hours daylight and a light intensity of 40 μmol.m-2.s-1.

treatment_protocol: Cold treatment was started at day 0 by decreasing the temperature to 4°C while the control plants grew at 20°C.

value: cold exposure

value: control temperature


title: Potato leaves, control Vs. cold-treated, day3, rep3


title: Potato leaves, control Vs. cold-treated, day3, rep4


title: lola_null_(ORE76)_rep1


title: 7225 | IgG | IFN-high [Intel]

description: IgG

value: IFN-high


title: 7254 | IgG | IFN-low [Intel]

description: IgG


title: 7232 | IgG | IFN-high [Intel]

description: IgG


title: 7231 | IgG | IFN-high [Intel]

description: IgG


title: 7230 | IgG | IFN-low [Intel]

description: IgG


title: 7234 | IgG | IFN-high [Intel]

description: IgG


title: 7229 | IgG | IFN-high [Intel]

description: IgG


title: 7249 | IgG | IFN-low [Utz]

description: IgG

hyb_protocol: Serum was diluted 1:250 from stocks (maintained at -80 deg. C. in) in PBS + 0.5% Tween 20 (Sigma-Aldrich, St. Louis, MO) and 2.5% fetal calf serum (Omega Scientific, Tarzana CA). Post primary incubation, washed arrays were incubated with 0.375ug/ml Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA).

value: IFN low


title: 7226 | IgG | IFN-low [Utz]

description: IgG


title: 7253 | IgG | IFN-low [Intel]

description: IgG


title: 7235 | IgG | IFN-low [Utz]

description: IgG


title: 7227 | IgG | IFN-low [Utz]

description: IgG


title: 7230 | IgG | IFN-low [Utz]

description: IgG


title: 7240 | IgG | IFN-high [Intel]

description: IgG


title: 7239 | IgG | IFN-high [Intel]

description: IgG


title: 7236 | IgG | IFN-high [Intel]

description: IgG


title: 7237 | IgG | IFN-high [Intel]

description: IgG


title: 7243 | IgG | IFN-low [Utz]

description: IgG


title: 7238 | IgG | IFN-low [Intel]

description: IgG


title: 7233 | IgG | IFN-high [Intel]

description: IgG


title: 7244 | IgG | IFN-high [Intel]

description: IgG


title: 7242 | IgG | IFN-high [Intel]

description: IgG


title: 7246 | IgG | IFN-high [Intel]

description: IgG


title: 7245 | IgG | IFN-low [Utz]

description: IgG


title: 7249 | IgG | IFN-low [Intel]

description: IgG


title: 7251 | IgG | IFN-low [Utz]

description: IgG


title: 7228 | IgG | IFN-low [Utz]

description: IgG


title: 7248 | IgG | IFN-high [Intel]

description: IgG


title: 7241 | IgG | IFN-low [Utz]

description: IgG


title: 7247 | IgG | IFN-low [Utz]

description: IgG


description: Gene expression data from non-target shRNA  puromycin stable TOV21G cell line

source_name: vector control

value: vector control


title: 7250 | IgG | IFN-high [Intel]

description: IgG


title: 7253 | IgG | IFN-low [Utz]

description: IgG


title: Potato leaves, control Vs. cold-treated, day3, rep1


title: 7254 | IgG | IFN-low [Utz]

description: IgG


title: 7252 | IgG | IFN-low [Utz]

description: IgG


title: 7229 | IgG | IFN-high [Utz]

description: IgG

value: IFN high


title: 7225 | IgG | IFN-high [Utz]

description: IgG


title: 7236 | IgG | IFN-high [Utz]

description: IgG


title: 7233 | IgG | IFN-high [Utz]

description: IgG


title: 7231 | IgG | IFN-high [Utz]

description: IgG


title: 7237 | IgG | IFN-high [Utz]

description: IgG


title: 7232 | IgG | IFN-high [Utz]

description: IgG


title: 7234 | IgG | IFN-high [Utz]

description: IgG


title: ECRG4 set: T193

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

institute: Institut Paoli-Calmettes

description: Primary breast tumor

hyb_protocol: see Affymetrix standard protocols (www.affymetrix.com)

data_processing: RMA using a quantile normalization (R package affy, v 1.20.0)

source_name: human breast cancer tumors

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

value: positive


title: ECRG4 set: T194

description: Primary breast tumor

scan_protocol: see Affymetrix standard protocols (www.affymetrix.com)

value: negative


title: 7239 | IgG | IFN-high [Utz]

description: IgG


title: ECRG4 set: T189

description: Primary breast tumor

label_protocol: see Affymetrix standard protocols (www.affymetrix.com)


title: ECRG4 set: T186

description: Primary breast tumor


title: ECRG4 set: T178

description: Primary breast tumor


title: ECRG4 set: T196

description: Primary breast tumor


title: 7238 | IgG | IFN-low  [Utz]

description: IgG


title: ECRG4 set: T190

description: Primary breast tumor