title: WAT_HFD-S_1

city: Gothenburg

first: Leif

last: Väremo

address: Kemivägen 10

department: Biology and Biological Engineering

institute: Chalmers University of Technology

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

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

data_processing: The data was processed with quantile normalization, pm-only for background correction, iterative PLIER algorithm for expresion index calculation

source_name: white adipose tissue, diet

label_protocol: 1000 picograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA from the entire expressed transcriptome according to the Nugen Technologies, Inc. protocols Ovation® Pico WTA System V2 (M01224v2) and Encore Biotine Module (M01111v5)

growth_protocol: 15 week old male C57BL/6 mice were fed one out of three diets (low fat diet [LFD], high fat diet rich in saturated fatty acids [HFD-S], high fat diet rich in polyunsaturated fatty acids [HFD-P]) for eighet weeks before the organs included in the study were harvested and analysed with microarray.

extract_protocol: Total RNA from SKM (gastrocnemius), BMC, WAT (retroperitoneal),  BAT (intrascapular), SPL and LIV were isolated using the RNeasy Lipid Tissue Mini kit (BMC, WAT, BAT, SPL LIV; Qiagen Nordic, Sweden) or the RNeasy Fibrous Tissue Mini (SKM; Qiagen) according to the manufacturer’s instruction. Total RNA concentration was measured by NanoDrop (Thermo Fisher Scientific, Gothenburg, Sweden). The quality of the RNA was evaluated by RNA 6000 Nano LabChip for Agilent 2100 Bioanalyzer (Agilent Technologies, Sweden). The RNA was labeled and hybridized to GeneChip® Mouse Gene 1 x ST arrays (Affymetrix, Santa Clara, CA, USA) at the genomics core facility, Swegene Centre for Integrative Biology at Lund University, Sweden.

treatment_protocol: Diet for eight weeks; either low fat diet, high fat diet rich in saturated fatty acids or high fat diet rich in polyunsaturated fatty acids.

value: white adipose tissue

tag: diet

value: hig fat diet rich in polyunsaturated fatty acids


title: WAT_HFD-P_3

status: Public on May 12 2016

type: RNA

country: Sweden

label: biotin

molecule: total RNA

organism: Mus musculus

tag: gender

value: Male

tag: strain

tag: tissue

value: hig fat diet rich in saturated fatty acids


title: WAT_HFD-P_1


title: Bxpc-3_untreated control_24 hr_rep2

city: Shanghai

first: Shuheng

last: Jiang

address: #800, Dongchuan Road

country: China

institute: Shanghai Cancer Institute

description: Gene expression data from  untreated Bxpc-3 pancreatic cancer cell lines

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

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

data_processing: Expression signals were calculated using the Agilent Feature Extraction software (version 10.7.3.1 Agilent Technologies, Santa Clara, CA).

organism: Homo sapiens

source_name: Bxpc-3 Pancreatic Cancer Cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Bxpc-3 cells were maintained in RPMI-1640 medium with 2 mM glutamine, 5 mM glucose supplemented with 1%  penicillin, and streptomycin and tested for mycoplasma contamination.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were serum-starved for 24 hr and then stimulated with 10 μM 5-HT (Sigma) for another 24 hr.

tag: cell line

tag: treatment

value: Bxpc-3 treatment group, untreated control


title: prostate_cancer_primary_71 (GBX.PCA71)

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two [x] 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

treatment_protocol: Not Applicable

tag: pathologic gleason score

tag: age

tag: pathologic stage

tag: preoperative psa

value: prostate cancer


title: prostate_cancer_primary_67 (GBX.PCA67)


title: WAT_HFD-S_2


title: WAT_HFD-S_3


title: Bxpc-3_untreated control_24 hr_rep3


title: Bxpc-3_5-HT treated_24 hr_rep3

description: Gene expression data from 5-HT treated Bxpc-3 pancreatic cancer cell lines

value: Bxpc-3 treatment group, 5-HT treated 24 hr


title: prostate_cancer_primary_65 (GBX.PCA65)


title: WAT_HFD-P_4


title: WAT_HFD-P_2


title: WAT_HFD-S_4


title: prostate_cancer_primary_61 (GBX.PCA61)


title: WAT_LFD_3

value: low fat diet


title: WAT_LFD_4


title: prostate_cancer_primary_58 (GBX.PCA58)


title: SPL_HFD-S_4

source_name: spleen, diet

value: spleen


title: WAT_LFD_2


title: prostate_cancer_primary_55 (GBX.PCA55)


title: SPL_HFD-S_3


title: prostate_cancer_primary_52 (GBX.PCA52)


title: prostate_cancer_primary_36 (GBX.PCA36)


title: SPL_HFD-S_2


title: prostate_cancer_primary_32 (GBX.PCA32)


title: prostate_cancer_primary_41 (GBX.PCA41)


title: prostate_cancer_primary_28 (GBX.PCA28)


title: prostate_cancer_primary_25 (GBX.PCA25)


title: prostate_cancer_primary_27 (GBX.PCA27)


title: prostate_cancer_primary_11 (GBX.PCA11)


title: prostate_cancer_primary_20 (GBX.PCA20)


title: prostate_cancer_primary_9 (GBX.PCA9)


title: SPL_HFD-P_2


title: SPL_HFD-P_4


title: prostate_cancer_primary_354 (GBX.PCA354)


title: prostate_cancer_primary_352 (GBX.PCA352)


title: prostate_cancer_primary_355 (GBX.PCA355)


title: WAT_LFD_1


title: SPL_HFD-P_1


title: SPL_HFD-S_1


title: SPL_LFD_4


title: prostate_cancer_primary_349 (GBX.PCA349)


title: MUS_HFD-S_4

source_name: skeletal muscle, diet

value: skeletal muscle


title: SPL_HFD-P_3


title: MUS_HFD-S_3


title: SPL_LFD_2


title: prostate_cancer_primary_346 (GBX.PCA346)


title: SPL_LFD_1


title: prostate_cancer_primary_344 (GBX.PCA344)


title: prostate_cancer_primary_343 (GBX.PCA343)


title: MUS_HFD-S_1


title: FF_liver_3hr_PMI

status: Public on May 13 2016

city: Kasugai

first: Masatoshi

last: Ichihara

state: Aichi

address: 1200 Matsumoto-cho

country: Japan

institute: Chubu University

hyb_protocol: The biotin-labeled aRNAs from FF tissues and fragmented DNA from FFPE tissues were hybridized with the array strips at 45°C for 16 h. After hybridization, the strips were washed and stained in the GeneAtlas Fluidics Station using the GeneAtlas Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The intensity of each hybridized probe was measured using the GeneAtlas Imaging Station.

data_processing: The obtained CEL files were normalized and summarized using the robust multiarray average (RMA) method with Expression Console software (Affymetrix).

source_name: FF mouse liver at 3hr in the postmortem interval

label_protocol: Comparative analysis of gene expression profiles was performed using the MG-430 PM Array Strips and the Affymetrix GeneAtlas microarray system (Affymetrix, Santa Clara, CA, USA), according to the manufacturer's instructions. For RNA samples from FF tissues, the corresponding amplified and biotin-labeled antisense RNA (aRNA) was synthesized using a GeneChip 3'IVT Express kit (Affymetrix). The resulting aRNA was fragmented as described by the manufacturer. On the other hand, for RNA samples from FFPE tissues, the corresponding amplified and biotin-labeled DNA fragments were generated using the WT-Ovation FFPE RNA Amplification System V2 (NuGEN, San Carlos, CA, USA) followed by the Encore Biotin Module (NuGEN) according to the manufacturers’ protocols.

extract_protocol: Excised livers and brains were first immersed in RNAlater (Ambion, Austin, TX, USA) and cryopreserved (FF samples). Total RNA was isolated with the RNeasy Mini Kit (Qiagen, Hilden, Germany) from these FF samples. In addition to FF samples, we fixed excised livers and brains with 10% formalin for 24 h and then embedded in paraffin (FFPE samples). FFPE samples were stored at room temperature for 7 d and were then cut into 10-μm wide slices, followed by extraction of RNA using RNeasy FFPE Kit (Qiagen).

value: male

value: 10 weeks

value: BALB/c

value: liver

tag: preservation

value: FF


title: prostate_cancer_primary_350 (GBX.PCA350)


title: prostate_cancer_primary_339 (GBX.PCA339)


title: MUS_HFD-P_3


title: prostate_cancer_primary_338 (GBX.PCA338)


title: prostate_cancer_primary_348 (GBX.PCA348)


title: MUS_LFD_4


title: MUS_HFD-S_2


title: prostate_cancer_primary_336 (GBX.PCA336)


title: MUS_HFD-P_1


title: prostate_cancer_primary_334 (GBX.PCA334)


title: MUS_LFD_2


title: MUS_LFD_3


title: prostate_cancer_primary_337 (GBX.PCA337)


title: MUS_HFD-P_2


title: MUS_HFD-P_4


title: LIV_HFD-S_6

source_name: liver, diet


title: LIV_HFD-S_7


title: LIV_HFD-P_4


title: MUS_LFD_1


title: prostate_cancer_primary_333 (GBX.PCA333)


title: LIV_HFD-S_4


title: prostate_cancer_primary_332 (GBX.PCA332)


title: prostate_cancer_primary_331 (GBX.PCA331)


title: prostate_cancer_primary_330 (GBX.PCA330)


title: prostate_cancer_primary_326 (GBX.PCA326)


title: LIV_HFD-S_5


title: prostate_cancer_primary_324 (GBX.PCA324)


title: LIV_HFD-P_2


title: prostate_cancer_primary_323 (GBX.PCA323)


title: prostate_cancer_primary_321 (GBX.PCA321)


title: prostate_cancer_primary_320 (GBX.PCA320)


title: LIV_LFD_6


title: prostate_cancer_primary_319 (GBX.PCA319)


title: LIV_LFD_5


title: LIV_HFD-S_3


title: LIV_HFD-P_1


title: prostate_cancer_primary_317 (GBX.PCA317)


title: prostate_cancer_primary_314 (GBX.PCA314)


title: LIV_HFD-P_3


title: LIV_LFD_4


title: LIV_LFD_3


title: prostate_cancer_primary_313 (GBX.PCA313)


title: LIV_LFD_1


title: prostate_cancer_primary_327 (GBX.PCA327)


title: prostate_cancer_primary_312 (GBX.PCA312)


title: BMC_HFD-S_3

source_name: bone marrow cells, diet

value: bone marrow cells


title: prostate_cancer_primary_311 (GBX.PCA311)


title: prostate_cancer_primary_310 (GBX.PCA310)


title: BMC_HFD-P_4


title: BMC_HFD-P_2


title: prostate_cancer_primary_309 (GBX.PCA309)


title: BMC_HFD-S_4


title: prostate_cancer_primary_306 (GBX.PCA306)


title: prostate_cancer_primary_305 (GBX.PCA305)


title: BMC_HFD-P_1


title: prostate_cancer_primary_307 (GBX.PCA307)


title: prostate_cancer_primary_304 (GBX.PCA304)


title: prostate_cancer_primary_303 (GBX.PCA303)


title: BMC_HFD-S_1


title: prostate_cancer_primary_302 (GBX.PCA302)


title: prostate_cancer_primary_301 (GBX.PCA301)


title: prostate_cancer_primary_300 (GBX.PCA300)


title: BMC_LFD_2


title: BMC_LFD_3


title: BMC_LFD_4


title: BMC_LFD_1


title: BAT_HFD-S_4

source_name: brown adipose tissue, diet

value: brown adipose tissue


title: BMC_HFD-S_2


title: prostate_cancer_primary_70 (GBX.PCA70)


title: BMC_HFD-P_3


title: prostate_cancer_primary_297 (GBX.PCA297)


title: BAT_HFD-P_3


title: BAT_HFD-S_3


title: BAT_HFD-P_4


title: BAT_HFD-S_1


title: BAT_HFD-S_2


title: prostate_cancer_primary_295 (GBX.PCA295)


title: prostate_cancer_primary_294 (GBX.PCA294)


title: prostate_cancer_primary_296 (GBX.PCA296)


title: prostate_cancer_primary_291 (GBX.PCA291)


title: prostate_cancer_primary_292 (GBX.PCA292)


title: BAT_HFD-P_2


title: prostate_cancer_primary_290 (GBX.PCA290)


title: prostate_cancer_primary_299 (GBX.PCA299)


title: BAT_LFD_4


title: prostate_cancer_primary_287 (GBX.PCA287)


title: BAT_HFD-P_1


title: prostate_cancer_primary_285 (GBX.PCA285)


title: prostate_cancer_primary_286 (GBX.PCA286)


title: BAT_LFD_1


title: NM_3

city: Yokohama

first: Jing-Ru

last: Li

state: Kanagawa

address: 1-7-22 Suehiro-cho,

department: Devision of Genomic Technology

institute: RIKEN Center for Life Science Technologies,

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi package in R

source_name: Negative control siRNA transfected plus mock-gene lentivirus transduced.

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

growth_protocol: Normal human skin fibroblast cells, NB1RGB, were provided by RIKEN Bioresource Center (#RCB0222, Tsukuba, Japan) and were cultured in 10% fetal bovine serum supplemented with minimum essential medium alpha (MEMα, Wako, Japan) at 5% CO2 and 37°C. One day after transduction with lentivirus, the medium was changed into the monocyte medium, consisting of RPMI1640 (Wako, Japan) and 20 ng/ml rhM-CSF(Wako, Japan), 20 ng/ml IL-4 (Wako, Japan), 1 mM sodium pyruvate, 50 µM ß-mercaptoethanol, and 10% fetal bovine serum

extract_protocol: RNA was isolated using NucleoSpin® kit (Macherey-Nagel, Germany) according to the user manual

tag: cell type

value: fibroblast


title: prostate_cancer_primary_283 (GBX.PCA283)


title: prostate_cancer_primary_282 (GBX.PCA282)


title: BAT_LFD_2


title: prostate_cancer_primary_280 (GBX.PCA280)


title: prostate_cancer_primary_281 (GBX.PCA281)


title: prostate_cancer_primary_279 (GBX.PCA279)


title: prostate_cancer_primary_277 (GBX.PCA277)


title: prostate_cancer_primary_289 (GBX.PCA289)


title: prostate_cancer_primary_276 (GBX.PCA276)


title: NM_2

description: replicate 2


title: prostate_cancer_primary_275 (GBX.PCA275)


title: BAT_LFD_3


title: PT_155_Follicular

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

country: USA

institute: Northwestern University

data_processing: The data were normalised by Ingenuity

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

extract_protocol: Total RNA was isolated from 30 mg of frozen tissue using the RNeasy Fibrous Tissue Mini Kit (Qiagen) according to manufacturer protocols. Quality control was performed with Agilent Bioanalyser.

value: endocervix

tag: phases of the menstrual cycle

value: Follicular


title: PT_152_Follicular


title: PT_H122_Follicular


title: PT_128_Luteal

value: Luteal


title: PT_127_Luteal


title: PT_123A_Luteal


title: PT_141_Follicular


title: prostate_cancer_primary_273 (GBX.PCA273)


title: PT_1A_Follicular


title: prostate_cancer_primary_274 (GBX.PCA274)


title: PT_121_Follicular


title: prostate_cancer_primary_270 (GBX.PCA270)


title: prostate_cancer_primary_272 (GBX.PCA272)


title: PT_119_Follicular


title: PT_142_Follicular


title: prostate_cancer_primary_271 (GBX.PCA271)


title: prostate_cancer_primary_269 (GBX.PCA269)


title: prostate_cancer_primary_268 (GBX.PCA268)


title: NM_1

description: replicate 1


title: PT_118_Luteal


title: prostate_cancer_primary_264 (GBX.PCA264)


title: prostate_cancer_primary_265 (GBX.PCA265)


title: prostate_cancer_primary_263 (GBX.PCA263)


title: prostate_cancer_primary_255 (GBX.PCA255)


title: prostate_cancer_primary_254 (GBX.PCA254)


title: prostate_cancer_primary_261 (GBX.PCA261)


title: prostate_cancer_primary_253 (GBX.PCA253)


title: prostate_cancer_primary_249 (GBX.PCA249)


title: prostate_cancer_primary_250 (GBX.PCA250)


title: prostate_cancer_primary_252 (GBX.PCA252)


title: prostate_cancer_primary_251 (GBX.PCA251)


title: prostate_cancer_primary_247 (GBX.PCA247)


title: prostate_cancer_primary_245 (GBX.PCA245)


title: prostate_cancer_primary_244 (GBX.PCA244)


title: prostate_cancer_primary_243 (GBX.PCA243)


title: prostate_cancer_primary_240 (GBX.PCA240)


title: prostate_cancer_primary_238 (GBX.PCA238)


title: prostate_cancer_primary_242 (GBX.PCA242)


title: prostate_cancer_primary_239 (GBX.PCA239)


title: prostate_cancer_primary_241 (GBX.PCA241)


title: prostate_cancer_primary_235 (GBX.PCA235)


title: prostate_cancer_primary_231 (GBX.PCA231)


title: prostate_cancer_primary_227 (GBX.PCA227)


title: prostate_cancer_primary_233 (GBX.PCA233)


title: prostate_cancer_primary_234 (GBX.PCA234)


title: prostate_cancer_primary_225 (GBX.PCA225)


title: prostate_cancer_primary_230 (GBX.PCA230)


title: prostate_cancer_primary_347 (GBX.PCA347)


title: prostate_cancer_primary_222 (GBX.PCA222)


title: prostate_cancer_primary_217 (GBX.PCA217)


title: prostate_cancer_primary_223 (GBX.PCA223)


title: prostate_cancer_primary_216 (GBX.PCA216)


title: prostate_cancer_primary_221 (GBX.PCA221)


title: prostate_cancer_primary_212 (GBX.PCA212)


title: prostate_cancer_primary_211 (GBX.PCA211)


title: prostate_cancer_primary_215 (GBX.PCA215)


title: prostate_cancer_primary_204 (GBX.PCA204)


title: prostate_cancer_primary_206 (GBX.PCA206)


title: prostate_cancer_primary_207 (GBX.PCA207)


title: prostate_cancer_primary_203 (GBX.PCA203)


title: prostate_cancer_primary_202 (GBX.PCA202)


title: prostate_cancer_primary_201 (GBX.PCA201)


title: prostate_cancer_primary_197 (GBX.PCA197)


title: prostate_cancer_primary_195 (GBX.PCA195)


title: prostate_cancer_primary_226 (GBX.PCA226)


title: prostate_cancer_primary_196 (GBX.PCA196)


title: prostate_cancer_primary_198 (GBX.PCA198)


title: prostate_cancer_primary_200 (GBX.PCA200)


title: prostate_cancer_primary_189 (GBX.PCA189)


title: prostate_cancer_primary_190 (GBX.PCA190)


title: prostate_cancer_primary_199 (GBX.PCA199)


title: prostate_cancer_primary_187 (GBX.PCA187)


title: prostate_cancer_primary_194 (GBX.PCA194)


title: prostate_cancer_primary_193 (GBX.PCA193)


title: prostate_cancer_primary_186 (GBX.PCA186)


title: prostate_cancer_primary_184 (GBX.PCA184)


title: prostate_cancer_primary_210 (GBX.PCA210)


title: prostate_cancer_primary_185 (GBX.PCA185)


title: prostate_cancer_primary_181 (GBX.PCA181)


title: prostate_cancer_primary_179 (GBX.PCA179)


title: prostate_cancer_primary_180 (GBX.PCA180)


title: prostate_cancer_primary_177 (GBX.PCA177)


title: prostate_cancer_primary_176 (GBX.PCA176)


title: prostate_cancer_primary_175 (GBX.PCA175)


title: prostate_cancer_primary_188 (GBX.PCA188)


title: prostate_cancer_primary_173 (GBX.PCA173)


title: prostate_cancer_primary_172 (GBX.PCA172)


title: prostate_cancer_primary_183 (GBX.PCA183)


title: prostate_cancer_primary_171 (GBX.PCA171)


title: prostate_cancer_primary_169 (GBX.PCA169)


title: prostate_cancer_primary_170 (GBX.PCA170)


title: prostate_cancer_primary_168 (GBX.PCA168)


title: prostate_cancer_primary_163 (GBX.PCA163)


title: prostate_cancer_primary_161 (GBX.PCA161)


title: prostate_cancer_primary_162 (GBX.PCA162)


title: prostate_cancer_primary_154 (GBX.PCA154)


title: prostate_cancer_primary_151 (GBX.PCA151)


title: prostate_cancer_primary_165 (GBX.PCA165)


title: prostate_cancer_primary_146 (GBX.PCA146)


title: prostate_cancer_primary_147 (GBX.PCA147)


title: prostate_cancer_primary_148 (GBX.PCA148)


title: prostate_cancer_primary_145 (GBX.PCA145)


title: prostate_cancer_primary_160 (GBX.PCA160)


title: prostate_cancer_primary_152 (GBX.PCA152)


title: prostate_cancer_primary_141 (GBX.PCA141)


title: prostate_cancer_primary_136 (GBX.PCA136)


title: prostate_cancer_primary_138 (GBX.PCA138)


title: prostate_cancer_primary_137 (GBX.PCA137)


title: prostate_cancer_primary_132 (GBX.PCA132)


title: prostate_cancer_primary_144 (GBX.PCA144)


title: prostate_cancer_primary_140 (GBX.PCA140)


title: prostate_cancer_primary_135 (GBX.PCA135)


title: prostate_cancer_primary_159 (GBX.PCA159)


title: prostate_cancer_primary_166 (GBX.PCA166)


title: prostate_cancer_primary_129 (GBX.PCA129)


title: prostate_cancer_primary_134 (GBX.PCA134)


title: prostate_cancer_primary_128 (GBX.PCA128)


title: prostate_cancer_primary_127 (GBX.PCA127)


title: prostate_cancer_primary_126 (GBX.PCA126)


title: prostate_cancer_primary_125 (GBX.PCA125)


title: prostate_cancer_primary_123 (GBX.PCA123)


title: prostate_cancer_primary_116 (GBX.PCA116)


title: prostate_cancer_primary_121 (GBX.PCA121)


title: prostate_cancer_primary_118 (GBX.PCA118)


title: prostate_cancer_primary_114 (GBX.PCA114)


title: prostate_cancer_primary_117 (GBX.PCA117)


title: prostate_cancer_primary_131 (GBX.PCA131)


title: prostate_cancer_primary_109 (GBX.PCA109)


title: prostate_cancer_primary_115 (GBX.PCA115)


title: prostate_cancer_primary_113 (GBX.PCA113)


title: prostate_cancer_primary_111 (GBX.PCA111)


title: prostate_cancer_primary_110 (GBX.PCA110)


title: prostate_cancer_primary_104 (GBX.PCA104)


title: prostate_cancer_primary_107 (GBX.PCA107)


title: prostate_cancer_primary_108 (GBX.PCA108)


title: prostate_cancer_primary_99 (GBX.PCA99)


title: prostate_cancer_primary_139 (GBX.PCA139)


title: prostate_cancer_primary_96 (GBX.PCA96)


title: prostate_cancer_primary_92 (GBX.PCA92)


title: prostate_cancer_primary_100 (GBX.PCA100)


title: prostate_cancer_primary_94 (GBX.PCA94)


title: prostate_cancer_primary_112 (GBX.PCA112)


title: prostate_cancer_primary_89 (GBX.PCA89)


title: prostate_cancer_primary_88 (GBX.PCA88)


title: prostate_cancer_primary_87 (GBX.PCA87)


title: prostate_cancer_primary_122 (GBX.PCA122)


title: prostate_cancer_primary_120 (GBX.PCA120)


title: prostate_cancer_primary_86 (GBX.PCA86)


title: prostate_cancer_primary_82 (GBX.PCA82)


title: prostate_cancer_primary_85 (GBX.PCA85)


title: prostate_cancer_primary_79 (GBX.PCA79)


title: prostate_cancer_primary_78 (GBX.PCA78)


title: prostate_cancer_primary_95 (GBX.PCA95)


title: prostate_cancer_primary_76 (GBX.PCA76)


title: prostate_cancer_primary_105 (GBX.PCA105)


title: prostate_cancer_primary_84 (GBX.PCA84)


title: prostate_cancer_primary_72 (GBX.PCA72)


title: prostate_cancer_primary_64 (GBX.PCA64)


title: prostate_cancer_primary_91 (GBX.PCA91)


title: prostate_cancer_primary_62 (GBX.PCA62)


title: prostate_cancer_primary_59 (GBX.PCA59)


title: prostate_cancer_primary_60 (GBX.PCA60)


title: prostate_cancer_primary_63 (GBX.PCA63)


title: prostate_cancer_primary_57 (GBX.PCA57)


title: prostate_cancer_primary_56 (GBX.PCA56)


title: prostate_cancer_primary_54 (GBX.PCA54)


title: prostate_cancer_primary_66 (GBX.PCA66)


title: prostate_cancer_primary_69 (GBX.PCA69)


title: prostate_cancer_primary_53 (GBX.PCA53)


title: prostate_cancer_primary_51 (GBX.PCA51)


title: prostate_cancer_primary_50 (GBX.PCA50)


title: prostate_cancer_primary_81 (GBX.PCA81)


title: prostate_cancer_primary_49 (GBX.PCA49)


title: prostate_cancer_primary_68 (GBX.PCA68)


title: prostate_cancer_primary_46 (GBX.PCA46)


title: prostate_cancer_primary_48 (GBX.PCA48)


title: prostate_cancer_primary_44 (GBX.PCA44)


title: M2-BMDMs_WT_replicate2

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description: Gene expression in wild-type BMDMs stimulated with IL-4 for 6hrs, replicate2

hyb_protocol: Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner.

data_processing: The data were normalized by percentile shift and filtered by flag, using GeneSpring GX software (Silicon Genetics).

source_name: BMDMs, WT, IL-4, 6hrs, replicate2

label_protocol: RNA samples were labeled with Cy3 using the Quick Amp Labeling kit (Agilent) according to the manufacturer's protocol.

growth_protocol: Bone marrow cells were cultured in DMEM supplemented with 10% fetal bovine serum, M-CSF, and Antibiotic-Antimycotic. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2 for 7 days.

extract_protocol: Total RNA was extracted from BMDMs using RNeasy Micro kit (Qiagen).

treatment_protocol: BMDMs are untreated, or treated with M1-stimuli (LPS and IFNg) or with M2-stimuli (IL-4) for 6 hours.

value: Female

value: 8 weeks

value: BMDM

tag: genotype/variation

value: WT

value: M2-stimuli (IL-4)


title: prostate_cancer_primary_47 (GBX.PCA47)

value: prostate cancer


title: prostate_cancer_primary_39 (GBX.PCA39)


title: prostate_cancer_primary_45 (GBX.PCA45)


title: prostate_cancer_primary_43 (GBX.PCA43)


title: M2-BMDMs_WT_replicate1

description: Gene expression in wild-type BMDMs stimulated with IL-4 for 6hrs, replicate1

source_name: BMDMs, WT, IL-4, 6hrs, replicate1

value: Male


title: prostate_cancer_primary_38 (GBX.PCA38)


title: prostate_cancer_primary_37 (GBX.PCA37)


title: prostate_cancer_primary_40 (GBX.PCA40)


title: prostate_cancer_primary_34 (GBX.PCA34)


title: prostate_cancer_primary_35 (GBX.PCA35)


title: prostate_cancer_primary_33 (GBX.PCA33)


title: prostate_cancer_primary_42 (GBX.PCA42)


title: prostate_cancer_primary_31 (GBX.PCA31)


title: M1-BMDMs_Keap1CKO_replicate1

description: Gene expression in Keap1-deficient BMDMs　stimulated with LPS and IFNg for 6hrs, replicate1

source_name: BMDMs, Keap1CKO, LPS and IFNg, 6hrs, replicate1

value: Keap1 CKO

value: M1-stimuli (LPS and IFNg)


title: M2-BMDMs_Keap1CKO_replicate2

description: Gene expression in Keap1-deficient BMDMs　stimulated with IL-4 for 6hrs, replicate2

source_name: BMDMs, Keap1CKO, IL-4, 6hrs, replicate2


title: M1-BMDMs_WT_replicate2

description: Gene expression in wild-type BMDMs stimulated with LPS and IFNg for 6hrs, replicate2

source_name: BMDMs, WT, LPS and IFNg, 6hrs, replicate2


title: M2-BMDMs_Keap1CKO_replicate1

description: Gene expression in Keap1-deficient BMDMs　stimulated with IL-4 for 6hrs, replicate1

source_name: BMDMs, Keap1CKO, IL-4, 6hrs, replicate1


title: M1-BMDMs_WT_replicate1

description: Gene expression in wild-type BMDMs stimulated with LPS and IFNg for 6hrs, replicate1

source_name: BMDMs, WT, LPS and IFNg, 6hrs, replicate1


title: prostate_cancer_primary_30 (GBX.PCA30)


title: BMDMs_Keap1CKO_replicate2

description: Gene expression in Keap1-deficient BMDMs, replicate2

source_name: BMDMs, Keap1CKO, replicate2


title: BMDMs_WT_replicate2

description: Gene expression in wild-type BMDMs, replicate2

source_name: BMDMs, WT, replicate2


title: M1-BMDMs_Keap1CKO_replicate2

description: Gene expression in Keap1-deficient BMDMs　stimulated with LPS and IFNg for 6hrs, replicate2

source_name: BMDMs, Keap1CKO, LPS and IFNg, 6hrs, replicate2


title: prostate_cancer_primary_29 (GBX.PCA29)

source_name: FFPE prostate cancer


title: prostate_cancer_primary_26 (GBX.PCA26)


title: prostate_cancer_primary_24 (GBX.PCA24)


title: BMDMs_WT_replicate1

description: Gene expression in wild-type BMDMs, replicate1

source_name: BMDMs, WT, replicate1


title: prostate_cancer_primary_15 (GBX.PCA15)


title: prostate_cancer_primary_17 (GBX.PCA17)


title: prostate_cancer_primary_22 (GBX.PCA22)


title: prostate_cancer_primary_21 (GBX.PCA21)


title: prostate_cancer_primary_19 (GBX.PCA19)


title: prostate_cancer_primary_23 (GBX.PCA23)


title: prostate_cancer_primary_14 (GBX.PCA14)


title: prostate_cancer_primary_16 (GBX.PCA16)


title: prostate_cancer_primary_12 (GBX.PCA12)


title: prostate_cancer_primary_13 (GBX.PCA13)


title: prostate_cancer_primary_10 (GBX.PCA10)


title: prostate_cancer_primary_18 (GBX.PCA18)


title: prostate_cancer_primary_8 (GBX.PCA8)


title: prostate_cancer_primary_7 (GBX.PCA7)


title: prostate_cancer_primary_6 (GBX.PCA6)


title: prostate_cancer_primary_5 (GBX.PCA5)


title: prostate_cancer_primary_4 (GBX.PCA4)


title: prostate_cancer_primary_3 (GBX.PCA3)


title: prostate_cancer_primary_1 (GBX.PCA1)


title: prostate_cancer_primary_2 (GBX.PCA2)


title: BMDMs_Keap1CKO_replicate1

description: Gene expression in Keap1-deficient BMDMs, replicate1

source_name: BMDMs, Keap1CKO, replicate1


title: DAM1_Cy3

type: genomic

city: Amsterdam

first: Marc

last: Hogenbirk

address: Plesmanlaan

country: Netherlands

institute: Netherlands Cancer Institute

description:
processed data file names: HG18_Economy_01_HX1_INT.txt; HG18_Economy_01_HX1_RAT.txt
Adenosine Methylated DNA regions
DamID samples

hyb_protocol: The Cy3/Cy5 pooled samples were hybridized according to the manufacture protocol (Nimblegen Arrays User guide: Chip-chip analysis v2.0) using Nimblegen hybrization kit LS   (p/n 05583934001) in a TECAN 4800 hybridization station (Tecan, Switzerland) with the following modifications.  Brielfy,  the volume of the Cy5/Cy3 pooled  samples was adjusted to 60ul with nuclease free water (Ambion, AM9937) and 60ul of 2x hybridization buffer,  24ul of hybridization component A and 2,4ul of alignment oligo was added.  After  16 hours of hybridization,  the slides were automatically washed with the Nimblegen kit was buffers I, II and III and dried with Nitrogen

scan_protocol: Slides were scanned using a Agilent microarrays scanner (Model G2505C) on a 2 micron resolution at 100% and 50% PMT using Scan Control software (Version A.8.1.3).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4
scaled, intensity values (INT files) and log2 (AIDDam/Damt) ratio (RAT files)

molecule: genomic DNA

source_name: Ramos

label_protocol: DamID samples were labeled according to Nimblegen manufacture protocol using the Nimblegen Arrays User guide: Chip-chip analysis v2.0. Briefly,  1500ng of amplified methylated DNA was labeled for 12 hours using Klenow reaction with incorporation of Cy5 or Cy3-dye labeled random nonamers, followed by an isopropanol precipitation and ethanol cleanup. The labeled fraction was air-dried using a vacuum concentrator (Eppendorf 5301) and dissolved in 25 ul of nuclease free water (Ambion, AM9937). Following quantification using UV/Vis on a ND-1000 (Thermo Fisher Scientific Inc.) , 60ug of labeled Dam-fusion and 60 ug of Dam-only methylated fragments were  pooled  and hybridized  on Nimblegen HG18_Economy_HX1 arrays 2.1M arrays.

growth_protocol: Cell culture

extract_protocol: Qiagen minelute DNA isolation kit, for details see manufacturers protocol.

treatment_protocol: DamID (Vogel et al 2007)

value: Ramos GC B


title: AIDDAM1_Cy5


title: sciatic nerve_8 month old_replicate 8

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: Affymetrix Expression Console, RMA normalization

organism: Rattus norvegicus

source_name: 8 month old rat sciatic nerve

label_protocol: Illumina TotalPrep-96

growth_protocol: Animals were housed by two in standard type 4 cages with ad libitum access to food and water on a 12 hour light/dark cycle at a temperature between 20-24°C and a relative humidity between 50-60%.

extract_protocol: RNA was extracted with the Qiagen miRNeasy kit according to the manufacturer's instructions.

treatment_protocol: Rats were sacrificed by exsanguination under isoflurane anesthesia and about 1cm of sciatic and radial nerves were dissected out from the mid-tight or arm region and frozen in liquid nitrogen.

value: male

value: 8 months

value: Wistar

value: sciatic nerve

tag: animal id


title: radial nerve_8 month old_replicate 6

value: radial neve


title: sciatic nerve_8 month old_replicate 7


title: radial nerve_8 month old_replicate 7

source_name: 8 month old rat radial nerve


title: sciatic nerve_8 month old_replicate 6


title: U937_P8_ex2_1

city: Freiburg

first: Michael

last: Lübbert

address: Hugstetter Str. 55

country: Germany

institute: Medical Center - University of Freiburg

hyb_protocol: according to manufacturer (Illumina)

scan_protocol: according to manufacturer (Illumina)

data_processing: Raw data was normalised and prepared with a custome R-script which is published with the paper.

label: Cy5 and Cy3

label_protocol: according to manufacturer (Illumina)

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 1% penicillin/streptamycin and 10% fetal calf serum.

extract_protocol: Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen) and bisulfite converted

treatment_protocol: Cells were treated with 3x24h pulses of 5-aza-2´-deoxycytidine, alone or in combination with the HDACi panobinostat (Pano) or valproic acid (VPA). HDACi was added with the last pulse of DAC for 24h.


title: TrxB2-DUC_DTT__atc_rep3

city: NEW YORK

first: Kan

last: Lin

state: New York

address: 413 East 69th Street

department: Microbiology and Immunology

institute: Weill Cornell Medical College

hyb_protocol: The One Color Cy3-labeled samples were initially mix with fragmentation mix consisting of 10X blocking Agent, nuclease free water, and 25X fragmentation buffer and incubated at 60 °C for 30minutes to fragment the cRNA. After incubation, 2X Hybridization Buffer was added to each sample to stop fragmentation reaction. The samples were hybridized to a custom-designed Mtb microarray for 17 hours at 65°C in a rotating hybridization oven. At the end of 17 hours the slides were taken out, dissembled in GE Wash Buffer 1, transferred to rack with clean GE Wash buffer 1 and mixed for 1-2 min at room temperature. Then the rack containing the hybridized slides was transferred to prewarmed (37°C) Wash Buffer 2 and stirred for 1 min. Finally, the rack containing the washed hybridized slides was slowly taken out of dish and allowed to air dry for 10-15 seconds.

scan_protocol: Each 8X15 hybridized slide was placed in slide holder and covered with ozone-barrier slide cover. The slides were immediately scanned in Agilent Sure Scan Microarray B Scanner using Protocol for One-Color Microarray Gene Expression. Once scanning was complete, the data was extracted using Agilent feature extraction software version 9.5.1.

data_processing: The raw data were extracted with Feature Extraction using Agilent default analysis settings.

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb,TrxB2-DUC,DTT 2mM,atc 800 ng/ml, 24hr, replicate3

label_protocol: 100 ng RNA was used for labeling with a Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer's instructions

growth_protocol: Mtb was grown in Middlebrook 7H9 medium with 0.2% glycerol, 0.05% Tween-80, 0.5% BSA, 0.2% dextrose, and 0.085% NaCl.

extract_protocol: Cultures were mixed with 1:1 ratio with GTC buffer containing guanidinium thiocyanate (4 M), sodium lauryl sulfate (0.5%), trisodium citrate (25 mM), and 2-mercaptoethanol (0.1 M) and pelleted by centrifugation. Bacterial RNA was isolated as previously described (Goodsmith, N. et al. PLoS Pathog 2015 Feb;11(2):e1004645).

treatment_protocol: Atc was added to TrxB2-DUC culture to a final concentration of 800ng/ml and DTT was added to a final concentration of 2mM when the culture OD reached 0.5~0.6. Control group was not treated.

tag: genotype

value: DTT 2mM, atc 800 ng/ml


title: radial nerve_8 month old_replicate 8


title: sciatic nerve_8 month old_replicate 5


title: sciatic nerve_8 month old_replicate 4


title: radial nerve_8 month old_replicate 5


title: radial nerve_8 month old_replicate 4


title: TrxB2-DUC_DTT__atc_rep2

source_name: Mtb,TrxB2-DUC,DTT 2mM,atc 800 ng/ml, 24hr, replicate2


title: sciatic nerve_8 month old_replicate 3


title: radial nerve_8 month old_replicate 3


title: sciatic nerve_8 month old_replicate 2


title: radial nerve_8 month old_replicate 2


title: U937_V1_ex2_2


title: U937_P8_ex2_2


title: U937_D50V1_ex2_2


title: U937_V1_ex2_3


title: TrxB2-DUC_DTT__atc_rep1

source_name: Mtb,TrxB2-DUC,DTT 2mM,atc 800 ng/ml, 24hr, replicate1


title: sciatic nerve_8 month old_replicate 1


title: U937_P8_ex2_3


title: U937_D50P8_ex2_1


title: TrxB2-DUC_atc_rep2

source_name: Mtb,TrxB2-DUC,atc 800 ng/ml, 24hr, replicate2

value: atc 800 ng/ml


title: radial nerve_24 month old_replicate 8

source_name: 24 month old rat radial nerve

value: 24 months


title: radial nerve_8 month old_replicate 1


title: sciatic nerve_24 month old_replicate 7

source_name: 24 month old rat sciatic nerve


title: sciatic nerve_24 month old_replicate 8


title: sciatic nerve_24 month old_replicate 6


title: U937_ctrl_ex2_3

value: ctrl


title: TrxB2-DUC_atc_rep1

source_name: Mtb,TrxB2-DUC,atc 800 ng/ml, 24hr, replicate1


title: TrxB2-DUC_DTT_rep3

source_name: Mtb,TrxB2-DUC,DTT 2mM, 24hr, replicate3

value: DTT 2mM


title: U937_D50V1_ex2_1


title: U937_D50_ex2_3


title: U937_D50_ex2_2


title: U937_D50P8_ex2_3


title: U937_V1_ex2_1


title: radial nerve_24 month old_replicate 5


title: sciatic nerve_24 month old_replicate 5


title: radial nerve_24 month old_replicate 7


title: radial nerve_24 month old_replicate 6


title: TrxB2-DUC_DTT_rep2

source_name: Mtb,TrxB2-DUC,DTT 2mM, 24hr, replicate2


title: U937_D50P8_ex2_2


title: U937_D50V1_ex2_3


title: TrxB2-DUC_rep3

value: no treatment


title: sciatic nerve_24 month old_replicate 3


title: U937_ctrl_ex2_2


title: TrxB2-DUC_DTT_rep1

source_name: Mtb,TrxB2-DUC,DTT 2mM, 24hr, replicate1


title: U937_D50_ex2_1


title: radial nerve_24 month old_replicate 3


title: radial nerve_24 month old_replicate 4


title: sciatic nerve_24 month old_replicate 4


title: TrxB2-DUC_rep1


title: TrxB2-DUC_no atc_rep5

source_name: Mtb,TrxB2-DUC,no atc treatment, replicate5

extract_protocol: Cultures were mixed at a 1:1 ratio with GTC buffer containing guanidinium thiocyanate (4 M), sodium lauryl sulfate (0.5%), trisodium citrate (25 mM), and 2-mercaptoethanol (0.1 M) and pelleted by centrifugation. Bacterial RNA was isolated as previously described (Goodsmith, N. et al. PLoS Pathog 2015 Feb;11(2):e1004645).

treatment_protocol: Atc was added to TrxB2-DUC culture at a final concentration of 400ng/ml when the culture OD reached 0.5~0.6. Control group was not treated with atc.

value: no atc


title: TrxB2-DUC_atc_rep3

source_name: Mtb,TrxB2-DUC,atc 800 ng/ml, 24hr, replicate3


title: radial nerve_24 month old_replicate 2


title: TrxB2-DUC_no atc_rep1

source_name: Mtb,TrxB2-DUC,no atc treatment, replicate1


title: TrxB2-DUC_no atc_rep3

source_name: Mtb,TrxB2-DUC,no atc treatment, replicate3


title: sciatic nerve_24 month old_replicate 2


title: TrxB2-DUC_no atc_rep2

source_name: Mtb,TrxB2-DUC,no atc treatment, replicate2


title: TrxB2-DUC_atc_24hr_rep1

source_name: Mtb,TrxB2-DUC,atc 400 ng/ml, 24hr, replicate1

value: atc 400 ng/ml


title: TrxB2-DUC_atc_24hr_rep2

source_name: Mtb,TrxB2-DUC,atc 400 ng/ml, 24hr, replicate2


title: TrxB2-DUC_atc_24hr_rep3

source_name: Mtb,TrxB2-DUC,atc 400 ng/ml, 24hr, replicate3


title: radial nerve_24 month old_replicate 1


title: sciatic nerve_24 month old_replicate 1


title: U937_ctrl_ex2_1


title: TrxB2-DUC_no atc_rep4

source_name: Mtb,TrxB2-DUC,no atc treatment, replicate4


title: TrxB2-DUC_rep2


title: TrxB2-TetON-tetO-WT_no atc_120hr

source_name: Mtb,TrxB2-TetON-tetO-WT, no atc, 120 hr

treatment_protocol: TrxB2-TetON-tetO-WT was grown in 7H9 medium containing 400 ng/ml atc, until the culture OD reached 0.5~0.6. Then Mtb was washed with 7H9 medium 3 times and suspended in 7H9 medium with or without atc.


title: TrxB2-DUC_atc_6hr_rep3

source_name: Mtb,TrxB2-DUC,atc 400 ng/ml, 6hr, replicate3


title: TrxB2-DUC_atc_6hr_rep1

source_name: Mtb,TrxB2-DUC,atc 400 ng/ml, 6hr, replicate1


title: TrxB2-DUC_atc_6hr_rep2

source_name: Mtb,TrxB2-DUC,atc 400 ng/ml, 6hr, replicate2


title: MGG11_adherent_miRNA

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

institute: ETH Zürich

hyb_protocol: Hybridization was performed at 55 °C for 20 hours while rotating with subsequent washes.

scan_protocol: Scanning was performed using high dynamic range settings on an Agilent microarray scanner. Agilent Feature Extraction Software v 10.7.3.1 was used to extract the data.

data_processing: limma_3.24.15 on R 3.2.0 were used for cyclic-loess normalization on log transformed data

label: Cyanine 3-pCp

source_name: MGG11 adherent cells

label_protocol: 100ng total RNA of each sample were labeled according to the Agilent miRNA Complete Labeling and Hybridization Kit.

growth_protocol: Differentiated glioma cells medium (DMEM + 10% FCS)

extract_protocol: Exiqon Total RNA extraction kit, on column DNASE treatment (Qiagen)

value: glioma cell line

tag: tumor state

value: adherent


title: MGG11_sphere_miRNA

source_name: MGG11 sphere cells

growth_protocol: Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems).

value: sphere


title: TrxB2-TetON-tetO-WT_no atc_24hr

source_name: Mtb,TrxB2-TetON-tetO-WT, no atc, 24 hr


title: TrxB2-TetON-tetO-WT_no atc_48hr

source_name: Mtb,TrxB2-TetON-tetO-WT, no atc, 48 hr


title: TrxB2-TetON-tetO-WT_atc_72hr

source_name: Mtb,TrxB2-TetON-tetO-WT,atc 400 ng/ml, 72 hr


title: TrxB2-TetON-tetO-WT_atc_120hr

source_name: Mtb,TrxB2-TetON-tetO-WT,atc 400 ng/ml, 120 hr


title: TrxB2-TetON-tetO-WT_atc_48hr

source_name: Mtb,TrxB2-TetON-tetO-WT,atc 400 ng/ml, 48 hr


title: MGG8_sphere_miRNA

source_name: MGG8 sphere cells


title: TrxB2-TetON-tetO-WT_no atc_72hr

source_name: Mtb,TrxB2-TetON-tetO-WT, no atc, 72 hr


title: MGG4_adherent_miRNA

source_name: MGG4 adherent cells


title: MGG4_sphere_miRNA

source_name: MGG4 sphere cells


title: MGG8_adherent_miRNA

source_name: MGG8 adherent cells


title: TrxB2-TetON-tetO-WT_atc_24hr

source_name: Mtb,TrxB2-TetON-tetO-WT,atc 400 ng/ml, 24 hr


title: TrxB2-TetON-tetO-WT_atc_0hr

source_name: Mtb,TrxB2-TetON-tetO-WT,atc 400 ng/ml, 0 hr


title: Ambion_control_rep1

city: Detroit

first: Joshua

last: Stevens

state: MICHIGAN (MI)

address: 540 E. Canfield St.

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

hyb_protocol: RNAs were hybridized to Illumina WG-8 v2 arrays (Chip IDs: 1787466094 & 1714478097) according to manufacture's protocol

scan_protocol: Scanning procedures were carried out according to manufacturer’s recommendations (Illumina, Wallingford).

data_processing: Microarrays were also analyzed using GeneSpring GX (Agilent Technologies). In this analysis, expression values were normalized using a percentile shift. Raw signals were thresholded to 1.0 with a percentile target of 75. Values were then baselined to the median of all samples. All entities that were flagged as present were retained. Retained values were analyzed using ANOVA with post hoc Tukey’s HSD and Storey curve fitting for multiple testing corrections

source_name: Ambion reference RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina)

growth_protocol: cells were grown in DMEM with 1mg/ml glucose, 10% fetal bovine serum, and1% penicillin, streptomycin, and fungizone solution

extract_protocol: Cells were lysed at room temperature in trizol for 30 minutes, phenol chloroform extracted, and the RNA from the upper aqueous phase was precipitated with ice cold ethanol

treatment_protocol: Treated cells were treated with 1.0ug/ml doxorubicin for two two weeks prior to harvest

tag: reference

value: Ambion reference RNA


title: 041_Pd109+dox_rep2

value: MDAH-041 cells


title: 041_Pd109_rep2


title: Illumina_control_rep1

source_name: Illumina reference RNA

value: Illumina reference RNA


title: 041_Pd54_rep1


title: U937P8_3

hyb_protocol: according to manufacturer (Affymetrix)

scan_protocol: according to manufacturer (Affymetrix)

data_processing: CEL files were imported including control and interrogating probes, pre-background adjustment was set to adjust for GC Content and probe sequence, and RMA background correction was performed. Arrays were normalized using Quantile normalization and probe set summarization was done using Median Polish. Probe values were log2 transformed.

label_protocol: according to manufacturer (Affymetrix)

extract_protocol: RNA was isolated using TRIZOL with subsequent purification on the RNeasy MinElute Spin Column (Qiagen).


title: 041_Pd109_rep1


title: 041_Pd54_rep2


title: 041_Pd25_rep2


title: U937P8_2


title: 041_Pd17_rep2


title: Ambion_control_rep2


title: 041_Pd7_rep2


title: 041_Pd109+dox_rep1


title: Illumina_control_rep2


title: U937P8_1


title: 041_Pd25_rep1


title: 041_Pd7_rep1


title: 041_Pd17_rep1


title: Unstable MDAH-041 clone 2 Rep 2

source_name: Unstable MDAH-041 clone 2 Rep 2

value: Unstable MDAH-041 clone 2


title: U937V1_1


title: CCL-110 Rep 2

source_name: CCL-110 Rep 2


title: U937D50V1_2


title: U937V1_2


title: U937D50P8_2


title: U937D50P8_1


title: Stable MDAH clone Rep 2

source_name: Stable MDAH clone Rep 2

value: Stable MDAH clone


title: U937D50_3


title: CCL-110 Rep 1

source_name: CCL-110 Rep 1


title: U937D50_2


title: Stable MDAH-041 subclone treated with doxorubicin to induce instability rep 2


title: U937V1_3


title: U937ctrl_3


title: U937ctrl_2


title: Tan065 Rep 1

source_name: Tan065 Rep 1


title: AIDDAM2_CY3

description:
processed data file names: HG18_Economy_02_HX1_INT.txt; HG18_Economy_02_HX1_RAT.txt
Adenosine Methylated DNA regions
DamID samples

source_name: Ramos

value: Ramos GC B


title: DAM2_CY5


title: U937D50_1


title: Tan065 Rep 2

source_name: Tan065 Rep 2


title: Stable MDAH-041 subclone treated with doxorubicin to induce instability rep 1


title: Stable MDAH clone Rep 1

source_name: Stable MDAH clone Rep 1


title: Unstable MDAH-041 clone 2 Rep 1

source_name: Unstable MDAH-041 clone 2 Rep 1


title: c6 PBL

status: Public on May 11 2016

type: SRA

city: Aurora

first: Jill

last: Slansky

address: 12800 East 19th Ave

institute: Univ Colorado Som

description:
total RNA via single cell analysis
TCR specific primers were used in single cell emulsion droplets to amplify only TCRs from single CD8 T cells lysed within the droplets

library_source: transcriptomic

data_processing:
Paired reads were joined following the reverse complementation of the Read 1 sequences to create a 500bp total length read with the C regions on the ends and the V regions in the center
Paired reads were then clipped from either end using the overlap sequence used to joined the alpha and beta TCR moelcules within the emulsion droplet during PCR amplification and overlap extension, generating an alpha and beta file with shared cluster IDs
Sequences were then processed using CompleteTCR to 1.) identify the V, J, and CDR3, 2.) to pair the reads using the cluster IDs, and 3.) compute frequency values for individual read pairs
Genome_build: IMGT TCR database
Supplementary_files_format_and_content: All processed files contain the identified TCR pairs and frequencies for each pair.  The sample tissue as well as the patient ID are included in the file names for simplicity

source_name: peripheral blood lymphocytes

extract_protocol:
No extraction of RNA was performed, rather single cells were lysed within an emulsion droplet and RT-PCR was performed using TCR specific primers
PCR amplicons were generated using primers containing the Read1, Read2, and Bridge priming sites as well as Illumina indicies (Read 2 side) and custom indicies on the Read 1 side
amplicon sequencing following RT-PCR of a specific gene(s)

treatment_protocol: CD8+ T cells were selected from bulk samples using a positive selection kit.  CD* T cells were incubated overnight in 10U/ml of IL-2 prior to emulsion RT-PCR sequencing

tag: illumina read 2 barcode

value: 5' - CGTGAT - 3'

tag: custom read 1 barcode

tag: cell type isolated

value: CD8+ T cells


title: U937ctrl_1

tag: cell line


title: Unstable MDAH-041 clone 1 Rep 1

source_name: Unstable MDAH-041 clone 1 Rep 1

value: Unstable MDAH-041 clone 1


title: OsisHESC, SF1 siRNA 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: cRNA samples were hybridized to an Agilent Technologies Human Gene Expression 8x60K Microarray Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters. Each sample represents one channel of a dual-channel array.

data_processing: Expression arrays were processed using BioConductor (one color arrays, Quantile normalization). Also we used combat algorithm [Johnson et al. 2007, Biostatistics 8(1):118-127] for batch correcting the dataset by patient (as the “batch” variable).

source_name: OsisHESC, SF1 siRNA

label_protocol: The cRNA labeling was performed according to Protocol from Agilent Technologies Inc. (Santa Clara, CA) using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer's protocol.

growth_protocol: Stromal fibroblast cells were isolated from ovarian endometriomas and healthy proliferative phase endometrial biopsies under a human subject protocol approved by the Institutional Review Board of Baylor College of Medicine. Endometriosis HESC (OsisHESC) and healthy HESC cultures were established. The stromal cells were subsequently cultured in HESC media (DMEM F12, 10% fetal bovine serum, antibiotic-antimycotic, HEPES and NaHCO3).

extract_protocol: RNA was isolated using the RNAeasy Mini kit (QIAGEN) as per manufacterer’s instructions.

treatment_protocol: For microarray analysis, OsisHESC from three different patients were grown to approximately 70% confluence and subsequently transfected with 60nM scrambled, non-targeting (siNT), NR5A1-targeting (siSF1) siRNA (ON-TARGETplus, Thermo Scientific, Waltham, MA) using Lipofectamine RNAiMax lipid (Life Technologies, Carlsbad, CA) per the manufacturer’s instructions.  After 48 hours of transfection exposure cells were harvested.

value: human endometriotic stromal fibroblast


title: c4 PBL

value: 5' - TGGTCA - 3'

value: 5' - TGCANNNNNN - 3'


title: OsisHESC, SF1 siRNA 3


title: OsisHESC, Non-targeting siRNA 3

source_name: OsisHESC, Non-targeting siRNA


title: OsisHESC, SF1 siRNA 1


title: OsisHESC, Non-targeting siRNA 2


title: U937D50P8_3

tag: treatment


title: U937D50V1_1


title: p20 PBL

value: 5' - GCCTAA - 3'

value: 5' - GTACNNNNNNNN - 3'


title: c2 PBL


title: c3 PBL

value: 5' - ACGTNNNN - 3'


title: p20 LNR

source_name: sentinel lymph node

tag: sentinel ln tumor invasion

value: yes


title: c1 PBL

value: 5' - GATCGC -3'


title: p20 tumorR

source_name: breast tumor

tag: tumor stage

value: IA


title: p20 tumorL


title: Unstable MDAH-041 clone 1 Rep 2

source_name: Unstable MDAH-041 clone 1 Rep 2


title: p19 tumor

value: IIIA

value: 5' - ACATCG - 3'


title: p19 PBL


title: p17 LN

value: no


title: p19 LN


title: p18 tumor

value: IIA


title: c5 PBL


title: p17 tumor


title: p17 PBL


title: p16 LN


title: p20 LNL


title: p16 PBL


title: p16 tumor


title: p15 tumor

value: IV


title: p14 LN


title: p14 PBL


title: p14 tumor


title: p13 tumor


title: p11 PBL


title: p11 tumor


title: p10 Normal

source_name: non-cancerous breast tissue


title: p13 PBL


title: p10 LN


title: p18 PBL

value: 5' - CGTGAT - 3'


title: p10 tumor

value: CD8+ T cells


title: p9 tumor

value: 5' - ATCATC - 3'


title: p8 LN


title: p10 PBL


title: p8 tumor


title: p9 PBL


title: p7 PBL


title: p8 PBL


title: p9 Normal


title: p15 PBL


title: p7 tumor


title: p6 tumor


title: p5 PBL


title: p5 LN


title: U937D50V1_3


title: p5 Normal


title: p5 tumor


title: p4 PBL


title: p12 tumor


title: p12 PBL


title: p3 LN


title: p3 PBL


title: p3 tumor

value: IIB


title: p2 tumor


title: p2 PBL


title: p1 LN


title: p1 PBL


title: p1 tumor


title: p6 PBL


title: OsisHESC, Non-targeting siRNA 1

value: human endometriotic stromal fibroblast


title: Patient_258_Post-treatment

city: SYRACUSE

first: Mira

last: Krendel

address: 505 Irving Ave

institute: Upstate Medical University

description: MeDIP DNA sample from blood monocytes of patient after CPAP treatment

hyb_protocol: According to Affymetrix standard protocols.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
GCOS 1.3 software (Affymetrix) was used to produce .CEL files. Data were analyzed using the Partek Genomic Suite Software (PGS) (St. Louis, MO).
Signals were adjusted according to probe sequence and background corrected using the Robust Multiarray method (RMA) . Model-based analysis of tiling-arrays (MAT) was used to identify regions of differential cirDNA modification by combining adjacent probes showing significant differences between the groups. A sliding windows of 500 bp was set, according to the average size of the fragments produced in the amplicon preparation step.

source_name: monocyte DNA from patient after CPAP treatment

growth_protocol: The patient population included in this study consisted of 6 adult patients (1 male and 5 female) diagnosed with severe OSA (indicated by a apnea-hypopnea index (AHI) pre-treatment > 30 events/hour total sleep time.

extract_protocol: For each patient, blood was collected by venipuncture in the fasting state within 1 hour from awakening before start receiving PAP treatment (PRE- group), as well as after 3 months of treatment (POST-group). Peripheral blood mononuclear cells (PBMCs) were isolated using gradient centrifugation and the CD14+ monocytes fraction was isolated using the Milteny Biotec MACS magnetic cell separation system. DNA was isolated from the isolated CD14+ monocytes using the DNeasy kit (Qiagen, Valencia, CA), according to manufacturer’s instructions. DNA was quantified and quality assessed by absorbance measurement using Nanodrop (Thermo Scientific, Wilmington, DE) and DNA integrity was verified by agarose gel electrophoresis. Isolated DNA was stored at -20 ⁰C until use. DNA methylation profiles before and after treatment for the patients exhibiting the highest POST/PRE AHI rations (n=6) were assessed using a MeDIP-chip strategy.  First, 1.5 µg of fragmented DNA was immunoprecipitated using an antibody against 5-methylcytosine (Eurogentec-AnaSpec, Inc. Freemont, CA) following the MeDIP protocol. Immunoprecipitated DNA was amplified using an adaptor mediated PCR strategy, as described elsewhere and subsequently fragmented, biotin-labeled, and hybridized on Affymetrix GeneChip Human Promoter Array 1.0R (Affymetrix, Santa Clara, CA) and scanned, according to manufacturer’s protocol.

treatment_protocol: All patients were clinically evaluated by sleep specialists and received PAP treatment. AHI indices before and after treatment were determined by overnight polysomnography.  Adherence to the treatment was monitored using smart card technology embedded in the PAP machines (average adherence among the complete patient cohort: 5.45 ± 1.37 days/week used; 88.9 ± 15.3 % of days used, with 67.7 ± 25.0 % of days used > 4 hours/night).

value: CPAP treatment

tag: tissue

value: blood monocytes

tag: Sex

value: Female


title: Patient_236_Post-treatment

label_protocol: According to Affymetrix standard protocols.


title: Patient_235_Post-treatment

value: Male


title: Patient_238_Post-treatment


title: Patient_226_Post-treatment


title: p4 tumor

value: 5' - TGGTCA - 3'

value: 5' - GTACNNNNNNNN - 3'


title: Patient_258_Pre-treatment

description: MeDIP DNA sample from blood monocytes of patient before CPAP treatment

source_name: monocyte DNA from patient before CPAP treatment

value: No treatment


title: Patient_224_Post-treatment


title: Patient_238_Pre-treatment


title: Patient_236_Pre-treatment


title: Patient_224_Pre-treatment


title: Patient_226_Pre-treatment


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700039

city: Boston

first: Laura

middle: M

last: Cox

state: MA

address: 77 Avenue Louis Pasteur

department: Neurology

institute: Brigham and Women's Hospital

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

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

data_processing: nSolver software, background and internal control standardization

source_name: Monocytes, Blood

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

growth_protocol: Not applicable

extract_protocol: Norgen Bioteck Total RNA Purification kit.  https://norgenbiotek.com/sites/default/files/resources/Total-RNA-Purification-Kit-Insert-PI17200-32-M14.pdf

treatment_protocol: Not applicable

tag: age

value: female

value: Monocyte

tag: group

value: Copaxone


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700070

tag: cell type


title: normal kidney 4

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

hyb_protocol: The mRNA expression profile was determined using Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software and GeneSpring Software of Agilent. Data was quantil normalized.

source_name: normal kidney 3

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the PicoRNA kit (Agilent) on a Bioanalyzer2100.

value: normal kidney


title: Cap37int_alcohologenesis_rep3

city: Toulouse

first: Philippe

last: Soucaille

address: 135 avenue de Rangueil

country: France

institute: INSA Toulouse

hyb_protocol: Hybridization followed a one-color microarray-based gene expression analysis protocol (Agilent)

scan_protocol: The slides were scanned using a Tecan MS200 scanner.

data_processing: The scanned slides were analyzed using Feature Extraction V.11.5.1.1.

organism: Clostridium acetobutylicum ATCC 824

source_name: Chemostat culture

label_protocol: The RNAs were labeled with a Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: The culture conditions described previously by Vasconcelos et al. (Vasconcelos I, et al. J Bacteriol. 1994; 176, 1443-1450.) and Girbal et al. (Girbal L, Soucaille P.  J Bacteriol. 1995; 176,6433-6438.) were used for the phosphate-limited continuous culture of C. acetobutylicum, fed with a constant total carbon amount of 995 mM. The cultures were maintained under acidogenesis (pH 6.3, 995 mM of carbon from glucose), solventogenesis (pH 4.4, 995 mM of carbon from glucose) and alcohologenesis (pH 6.3, 498 mM of carbon from glucose and 498 mM of carbon from glycerol).

extract_protocol: RNA was extracted using an RNeasy Midi kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions with supplementation of DNase treatment using RNase-Free DNase Set (Qiagen). RNA quantity and quality evaluations were performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France) and a NanoDrop ND-1000 spectrophotometer (Labtech France, Paris, France) at 260 nm and 280 nm.

treatment_protocol: Immediately frozen in liquid nitrogen

tag: genotype/variation

value: Cap0037::int alcohologenesis


title: Patient_235_Pre-treatment


title: Cap37int_solventogenesis_rep1

value: Cap0037::int solventogenesis


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700031

value: male


title: Cap37int_acidogenesis_rep2

value: Cap0037::int acidogenesis


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700050


title: normal kidney 3

source_name: normal kidney 2

label_protocol: The mRNA expression profile was determined using Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray according to the manufacturers recommendations


title: normal kidney 2

source_name: normal kidney 4


title: Cap37int_solventogenesis_rep2


title: Cap37int_solventogenesis_rep3


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700081


title: Cap37int_alcohologenesis_rep2


title: Cap37int_acidogenesis_rep1


title: Cap37int_acidogenesis_rep3


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700040


title: FHMLiver_12d_Untreated control_Rep_5

city: St Paul

first: Anthony

last: Schroeder

address: 1985 Lower Buford Cir # 173

institute: University of Minnesota

description:
Control_5
Gene expression after 12 d of exposure to well (control) water

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity between 9 and 14 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions.  Following the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized onto custom designed fathead minnow (60K oligonucleotide) arrays for 17 hours at 65°C in a rotating hybridization oven.  Following hybridization, microarrays were washed 1 minute at room temperature in GE Wash Buffer 1 (Agilent), 1 minute at 37°C  in GE wash buffer 2 (Agilent), 30 seconds with acetonitrile, and dired with stabilization and drying solution (Agilent)

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200 AL scanner at PMT gain level 420 using default setting (Scan resolution 5 um, One channel-green, Laser power 100%).

data_processing: Data were resolved from microarray images using Feature Extraction software v10.7 (Agilent) using default parameters. Extracted raw data were imported into GeneSpring GX 12.6 (Agilent) and all data subjected to the default normalization procedure for Agilent one-color microarray data.  Statistical analysis was performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA followed by for Tukey's post hoc comparisions to identify significant differential gene expression between the untreated control and treated fish.

organism: Pimephales promelas

source_name: liver_12d_Untreated control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by  RNeasy column purfication (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer.

extract_protocol: Total RNA was extracted from the randomly chosen fathead minnow livers (6-7 per treatment) using the Rneasy Kit (Qiagen) following the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was checked using a Agilent 2100 Bioanalyzer.

treatment_protocol: Two groups of 10 male fathead minnows were subjected to two or three treatments (exposure to water from upstream (Chisago only), downstream, or  wastewater treatment plant effluent outfall) from two locations (Chisago and North Branch) along St. Croix River).  The control group consisted of fish exposed to well water.

value: Reproductively mature 7-month old

tag: gender

tag: exposed to

value: well water (untreated control)

value: liver


title: Cap37int_alcohologenesis_rep1


title: Monocyte-MultipleSclerosisTreatedInteferon-E700036

value: Interferon


title: FHMLiver_12d_Untreated control_Rep_4

description:
Control_4
Gene expression after 12 d of exposure to well (control) water


title: FHMLiver_12d_North Branch Effluent_Rep_5

description:
NB_EFF_5
Gene expression after 12 d of exposure to stream water near final effluent of North Branch WWTP

source_name: liver_12d_North Branch_effluent

value: wastewater treatment plant effluent outfall

tag: location

value: North Branch along St. Croix River


title: Monocyte-MultipleSclerosisTreatedInteferon-E700048


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700034


title: FHMLiver_12d_Untreated control_Rep_7

description:
Control_7
Gene expression after 12 d of exposure to well (control) water


title: Monocyte-MultipleSclerosisTreatedCopaxone-E700064


title: FHMLiver_12d_North Branch Effluent_Rep_6

description:
NB_EFF_6
Gene expression after 12 d of exposure to stream water near final effluent of North Branch WWTP


title: Monocyte-MultipleSclerosisTreatedInteferon-E700056


title: FHMLiver_12d_Untreated control_Rep_6

description:
Control_6
Gene expression after 12 d of exposure to well (control) water


title: normal kidney 1

source_name: normal kidney 1


title: Monocyte-MultipleSclerosisUntreated-E700014

value: Untreated


title: FHMLiver_12d_Untreated control_Rep_3

description:
Control_3
Gene expression after 12 d of exposure to well (control) water


title: Monocyte-MultipleSclerosisUntreated-E700021


title: FHMLiver_12d_North Branch Effluent_Rep_3

description:
NB_EFF_3
Gene expression after 12 d of exposure to stream water near final effluent of North Branch WWTP


title: FHMLiver_12d_North Branch Effluent_Rep_4

description:
NB_EFF_4
Gene expression after 12 d of exposure to stream water near final effluent of North Branch WWTP


title: FHMLiver_12d_North Branch DS_Rep_4

description:
NB_DS_4
Gene expression after 12 d of exposure to water downstream of North Branch effluent

source_name: liver_12d_North Branch_downstream site

value: water from downstream


title: FHMLiver_12d_North Branch Effluent_Rep_1

description:
NB_EFF_1
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: FHMLiver_12d_North Branch DS_Rep_5

description:
NB_DS_5
Gene expression after 12 d of exposure to water downstream of North Branch effluent


title: FHMLiver_12d_Untreated control_Rep_1

description:
Control_1
Gene expression after 12 d of exposure to well (control) water


title: FHMLiver_12d_North Branch Effluent_Rep_2

description:
NB_EFF_2
Gene expression after 12 d of exposure to stream water near final effluent of North Branch WWTP


title: Monocyte-MultipleSclerosisUntreated-E700033


title: Monocyte-MultipleSclerosisUntreated-E700053


title: Monocyte-Control-IGTB195

value: Control


title: Monocyte-Control-IGTB1245


title: Monocyte-Control-IGTB1441

value: female


title: Monocyte-MultipleSclerosisUntreated-E700019

value: Monocyte


title: FHMLiver_12d_North Branch DS_Rep_6

description:
NB_DS_6
Gene expression after 12 d of exposure to water downstream of North Branch effluent


title: Monocyte-MultipleSclerosisUntreated-E700029


title: Monocyte-Control-IGTB295


title: Monocyte-Control-IGTB529


title: FHMLiver_12d_North Branch DS_Rep_3

description:
NB_DS_3
Gene expression after 12 d of exposure to water downstream of North Branch effluent


title: FHMLiver_12d_North Branch DS_Rep_2

description:
NB_DS_2
Gene expression after 12 d of exposure to water downstream of North Branch effluent


title: FHMLiver_12d_Chisago US_Rep_5

description:
Chisago_US_5
Gene expression after 12 d of exposure to water upstream of Chisago effluent

source_name: liver_12d_Chisago_upstream site

value: water from upstream

value: Chisago along St. Croix River


title: FHMLiver_12d_Chisago US_Rep_7

description:
Chisago_US_7
Gene expression after 12 d of exposure to water upstream of Chisago effluent


title: FHMLiver_12d_Chisago US_Rep_6

description:
Chisago_US_6
Gene expression after 12 d of exposure to water upstream of Chisago effluent


title: FHMLiver_12d_Chisago US_Rep_4

description:
Chisago_US_4
Gene expression after 12 d of exposure to water upstream of Chisago effluent


title: FHMLiver_12d_Chisago US_Rep_2

description:
Chisago_US_2
Gene expression after 12 d of exposure to water upstream of Chisago effluent


title: Monocyte-Control-IGTB713


title: FHMLiver_12d_Chisago US_Rep_1

description:
Chisago_US_1
Gene expression after 12 d of exposure to water upstream of Chisago effluent


title: wilms tissue 4

source_name: wilms tissue 55

value: blastemal WT


title: Monocyte-Control-IGTB257


title: Monocyte-Control-IGTB1165


title: Monocyte-Control-IGTB1718


title: Monocyte-Control-IGTB1419


title: Monocyte-Control-IGTB57


title: Monocyte-Control-IGTB374


title: FHMLiver_12d_Untreated control_Rep_2

description:
Control_2
Gene expression after 12 d of exposure to well (control) water


title: FHMLiver_12d_North Branch DS_Rep_1

description:
NB_DS_1
Gene expression after 12 d of exposure to water downstream of North Branch effluent


title: FHMLiver_12d_Chisago US_Rep_3

description:
Chisago_US_3
Gene expression after 12 d of exposure to water upstream of Chisago effluent


title: FHMLiver_12d_Chisago Effluent_Rep_4

description:
Chisago_EFF_4
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: FHMLiver_12d_Chisago Effluent_Rep_3

description:
Chisago_EFF_3
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: FHMLiver_12d_Chisago Effluent_Rep_5

description:
Chisago_EFF_5
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: Monocyte-Control-IGTB1487


title: FHMLiver_12d_Chisago DS_Rep_7

description:
Chisago_DS_7
Gene expression after 12 d of exposure to water downstream of Chisago effluent

source_name: liver_12d_Chisago_downstream site


title: FHMLiver_12d_Chisago Effluent_Rep_2

description:
Chisago_EFF_2
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: FHMLiver_12d_Chisago Effluent_Rep_6

description:
Chisago_EFF_6
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: FHMLiver_12d_Chisago Effluent_Rep_7

description:
Chisago_EFF_7
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: Monocyte-Control-IGTB811


title: FHMLiver_12d_Chisago DS_Rep_6

description:
Chisago_DS_6
Gene expression after 12 d of exposure to water downstream of Chisago effluent


title: Monocyte-Control-IGTB1577


title: FHMLiver_12d_Chisago Effluent_Rep_1

description:
Chisago_EFF_1
Gene expression after 12 d of exposure to stream water near final effluent of Chisago WWTP


title: Monocyte-Control-IGTB578


title: Tcell-MultipleSclerosisTreatedCopaxone-E700040

source_name: T cells, Blood

value: Tcell

value: Copaxone


title: Tcell-MultipleSclerosisTreatedCopaxone-E700050

value: male


title: Tcell-MultipleSclerosisTreatedCopaxone-E700031


title: Tcell-MultipleSclerosisTreatedCopaxone-E700064


title: Tcell-MultipleSclerosisTreatedCopaxone-E700070


title: Tcell-MultipleSclerosisTreatedCopaxone-E700034


title: Tcell-MultipleSclerosisTreatedCopaxone-E700039


title: Tcell-MultipleSclerosisTreatedInteferon-E700036


title: FHMLiver_12d_Chisago DS_Rep_5

description:
Chisago_DS_5
Gene expression after 12 d of exposure to water downstream of Chisago effluent

value: Reproductively mature 7-month old


title: FHMLiver_12d_Chisago DS_Rep_4

description:
Chisago_DS_4
Gene expression after 12 d of exposure to water downstream of Chisago effluent


title: FHMLiver_12d_Chisago DS_Rep_3

description:
Chisago_DS_3
Gene expression after 12 d of exposure to water downstream of Chisago effluent


title: Tcell-MultipleSclerosisUntreated-E700014


title: Tcell-MultipleSclerosisTreatedInteferon-E700048


title: Tcell-MultipleSclerosisTreatedInteferon-E700056


title: FHMLiver_12d_Chisago DS_Rep_1

description:
Chisago_DS_1
Gene expression after 12 d of exposure to water downstream of Chisago effluent


title: C3H10T1/2 cells overexpressing Venus

city: Bunkyo-ku

first: Ryo

last: Nakamichi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

institute: Tokyo Medical and Dental University

description: Gene expression data from C3H10T1/2 overexpressd Venus

hyb_protocol: The cRNAs were hydrolyzed and hybridized to the GeneChip (R) Mouse Genome 430 2.0 array (Affymetrix).

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

data_processing: The data were analyzed with Robust Multi-chip Average using Affymetrix default analysis settings and global scaling as normalization method.

source_name: C3H10T1/2 cells overexpressing Venus RNA

label_protocol: Total RNA (200 ng) was reverse-transcribed and biotinylated using the GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: C3H10T1/2 cells were grown in α-minimum essential medium with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol: ISOGEN (Nippongene) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Venus or Venus-Mkx were overexpressed in C3H10T1/2 cells by using retrovirus.

tag: overexpression

value: Venus


title: Tcell-MultipleSclerosisUntreated-E700021


title: C3H10T1/2 cells

description: Gene expression data from C3H10T1/2

source_name: C3H10T1/2 cells RNA

value: control


title: Tcell-MultipleSclerosisTreatedCopaxone-E700081


title: Tcell-MultipleSclerosisUntreated-E700026


title: Tcell-MultipleSclerosisUntreated-E700019


title: Tcell-MultipleSclerosisUntreated-E700033


title: Tcell-MultipleSclerosisUntreated-E700053


title: Monocyte-Control-IGTB515


title: Tcell-MultipleSclerosisUntreated-E700029


title: Tcell-Control-IGTB1245


title: Tcell-Control-IGTB1443


title: FHMLiver_12d_Chisago DS_Rep_2

description:
Chisago_DS_2
Gene expression after 12 d of exposure to water downstream of Chisago effluent

value: liver


description: Gene expression data from C3H10T1/2 overexpressd Venus-Mkx

source_name: C3H10T1/2 cells overexpressing Venus-Mkx RNA

value: Venus-Mkx


title: Tcell-Control-IGTB0529


title: Tcell-Control-IGTB0496


title: Smad4flox/floxMerCreMer Stra8−/−_E14.5_Female2

city: Mishima

first: Quan

last: Wu

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

description: Gene expression in Smad4 Stra8 double mutant

hyb_protocol: 1.65 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100ul of mixture was used hybridize with Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207). Averaged and normalized intensities were processed from raw data in text files with R packages: Agi4x44PreProcess and mgug4122a.db.  For the background correction, “half” method was used and for normalization “quantile” method was used. MeanSignal was chosen for foreground and BGMedianSignal was chosen for background.

source_name: E14.5 embryonic gonad

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Tamoxifen was injected at E9.5 and E10.5 into pregnant mice, and samples were harvested at E14.5.

extract_protocol: Total RNA was extracted with RNeasy mini kit (QIAGEN, Valencia, CA) according to the manufacture's protocol

treatment_protocol: Embryonic gonads were disected in ice-cold PBS and were stored at -80 degree until total RNA extraction.

value: Embryonic gonad

value: Female

tag: developmental stage

tag: background

value: mixed


title: Smad4flox/floxMerCreMer Stra8−/−_E14.5_Female1


title: Tcell-Control-IGTB0374

value: Control


title: Smad4flox/floxMerCreMer Stra8−/−_E14.5_Female3


title: Smad4flox/floxMerCreMer Stra8+/−_E14.5_Female2

description: Gene expression in Smad4 single mutant


title: Smad4flox/floxMerCreMer Stra8+/−_E14.5_Female3

description: Gene expression in Smad4 single mutant


title: COS conditions rep 6

city: Montreal

first: R. Thomas

last: Jagoe

state: Quebec

address: Jewish General Hospital, 3755 Cote Ste Catherine

department: Medicine

institute: McGill University

description: Biological replicate 6 of 6: COS culture conditions vs STD

hyb_protocol: Performed on fully-automated enclosed hybridisation station (Tecan HS400Pro). Samples were injected manually then co-hybridised (56 degrees C x 16 hrs) then washed and dried automatically prior to scanning

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Two-colour images were analysed using Spot software (CSIRO, 2007) and mean signal intensity for each spot was determined after background correction and Loess print-tip (within-array) normalisation of the log2 ratio  (FlexArray, Genome Quebec, McGill University).
Normalized log2 ratio (Hy3/Hy5)

label_protocol: 2µg total RNA from each experimental sample was covalently 3’-labeled with a single Hy3 (test) or Hy5 (reference) fluorophore per molecule using the Hi-Power Labeling kit (Exiqon, Woburn MA)

growth_protocol: C2C12 myoblasts (ATCC) less than 10 passages grown in high-glucose DMEM (Gibco) with 10% FBS (invitrogen) seeded on 0.15% gelatin-coated 6-well plates at at 2.2 x 10^6 cells per well, grown to 80% confluence and differentiated in medium containing 10% horse serum.  All initial cultures were performed in standard tissue culture conditions (21% O2, 5% CO2, humidified incubator at 37C)

extract_protocol: RNA was extracted using the miRNeasy mini protocol (Qiagen) as per the manufacturer's instructions

treatment_protocol: All treatments started day 5 post differentiation including transfer to new culture conditions (COS) and/or treatment with additional soluble agents. All media and treatments were changed every 24hrs prior to harvesting cells (D5-D7).

value: Myotubes

value: COS culture conditions day 5-8 post differentiation:4% O2, low-frequency (1Hz/0.1Hz for 18h/6h respectively) biphasic 5ms square-wave electrical stimulation, and daily TNF-α (20 pg/ml; R&D systems) and IL-6 (100 pg/ml; R&D systems)

value: STD culture conditions:21% O2


title: Smad4Flox/Flox Stra8+/-_E14.5_Female_3

description: Gene expression in female


title: COS conditions rep 5

description: Biological replicate 5 of 6: COS culture conditions vs STD


title: Self-self (DexCTL) rep 4

description: Biological replicate 4 of 4 for self-self hybridisation experiment

value: Dex (Dexamethasone 1µM) Day 5-8 in STD conditions


title: Smad4Flox/+ StellaMerCreMer Stra8+/-_E14.5_Male_2

description: Gene expression in male

value: Male


title: Tcell-Control-IGTB0369

value: female

value: Tcell


title: Self-self (COS) rep 3

description: Biological replicate 3 of 4 for self-self hybridisation experiment


title: Tcell-Control-IGTB0195


title: Tcell-Control-IGTB1441


title: DNA_YearDay137B

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

description:
YD137B
whole genomic DNA extracted from seawater
DNA_YearDay137B_rep1
DNA_YearDay137B_rep2

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing:
Quality control was employed to remove noise by eliminating features in which the Cy3 signal was not at least twice the value of the control probes.
Cy3/Cy5 fluorescence intensities were standardized to the highest Cy3/Cy5 fluorescence across the each probe set (normalized fluorescence ratio; FRN) The 12 probesets are as follows: Chloro_NR, Chloro_rbcL, Cyano_hnat, Cyano_narB, Cyano_rbcL, Diatom_NR, Diatom_rbcL, Distant_Chromo_rbcL, EukNrt2, Hapto_rcbL, NDNH_rbcL, Non_Diatom_NR

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard (20-mer) + 70-mer

label_protocol: The genomic DNA was fragmented by digestion with Hinf1, and labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from the filters using  AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).

tag: molecule type

value: 70-mer probe conjugated to the 20-mer standard DNA

organism: seawater metagenome

source_name: seawater

value: North Atlantic Bloom Experiment (NAB08) spring 2008


title: DNA_YearDay139

description:
YD139
whole genomic DNA extracted from seawater
DNA_YearDay139_rep1
DNA_YearDay139_rep2


title: Smad4Flox/+ StellaMerCreMer Stra8+/-_E14.5_Male_3

description: Gene expression in male


title: Tcell-Control-IGTB0295


title: Tcell-Control-IGTB1487


title: Tcell-Control-IGTB0257


title: DNA_YearDay137A

description:
YD137A
whole genomic DNA extracted from seawater
DNA_YearDay137A_rep1
DNA_YearDay137A_rep2


title: DNA_YearDay134B

description:
YD134B
whole genomic DNA extracted from seawater
DNA_YearDay134B_rep1
DNA_YearDay134B_rep2


title: Self-self (CTL) rep 2b

description: Biological replicate 2 of 4, technical replicate 2 of 2 for self-self hybridisation experiment


title: Smad4Flox/+ StellaMerCreMer Stra8+/-_E14.5_Female_1

description: Gene expression in female


title: Smad4Flox/+ Stra8+/-_E14.5_Female_2

description: Gene expression in female


title: Smad4flox/floxMerCreMer Stra8+/−_E14.5_Female1

description: Gene expression in Smad4 single mutant


title: Smad4Flox/+ StellaMerCreMer Stra8+/-_E14.5_Male_1

description: Gene expression in male


title: Tcell-Control-IGTB0057


title: Self-self (CTL) rep 1

description: Biological replicate 1 of 4 for self-self hybridisation


title: Self-self (CTL) rep 2a

description: Biological replicate 2 of 4, technical replicate 1 of 2 for self-self hybridisation experiment


title: COS conditions rep 4

description: Biological replicate 4 of 6: COS culture conditions vs STD


title: Tcell-Control-IGTB0578


title: DNA_YearDay132

description:
YD132
whole genomic DNA extracted from seawater
DNA_YearDay132_rep1
DNA_YearDay132_rep2


title: Tcell-Control-IGTB1419


title: DNA_YearDay131B

description:
YD131B
whole genomic DNA extracted from seawater
DNA_YearDay131B_rep1
DNA_YearDay131B_rep2


title: Dex and COS conditions rep 2

description: Biological replicate 2 of 2: Dex treatment under COS conditions vs COS conditions

value: DEX+COS culture conditions day 5-8 post differentiation:4% O2, low-frequency (1Hz/0.1Hz for 18h/6h respectively) biphasic 5ms square-wave electrical stimulation, and daily TNF-α (20 pg/ml; R&D systems) and IL-6 (100 pg/ml; R&D systems) + daily Dexamethasone (1µM)


title: COS conditions rep 3

description: Biological replicate 3 of 6: COS culture conditions vs STD


title: Tcell-Control-IGTB1165

value: male


title: Tcell-Control-IGTB1577


title: DNA_YearDay129

description:
YD129
whole genomic DNA extracted from seawater
DNA_YearDay129_rep1
DNA_YearDay129_rep2


title: DNA_YearDay128

description:
YD128
whole genomic DNA extracted from seawater
DNA_YearDay128_rep1
DNA_YearDay128_rep2


title: Tcell-Control-IGTB0713


title: COS conditions rep 2

description: Biological replicate 2 of 6: COS culture conditions vs STD


title: melanoma cells, concentration 1 treatment

city: Sarajevo

first: Lejla

last: Pojskic

address: Zmaja od Bosne 8

country: Bosnia and Herzegovina

institute: Institute for Genetic Engineering and Biotechnology

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLPO, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., treated/non-treated cells) ratios.

label: SYBR Green

label_protocol: RT2 First strand kit (Qiagen  GmbH, Hilden, Germany) was used for generation of cDNA for  further genetic analysis according to manufacturer’s protocol (RT2  Profiler PCR Array Handbook, Qiagen N. V., Venlo, Limburg,  Netherlands).

growth_protocol: The Human Caucasian melanoma cell line (GR-M) was obtained  from Culture Collections, Public Health England, London, UK  (Cat. No. 95032301). Cell line was cultured in RPMI 1640  (Gibco-Invitrogen, Grand Island, NY) with L-glutamine  supplemented with 10% of fetal bovine serum (FBS) and  100 units/ml penicillin, 100 mg/ml streptomycin (Sigma-Aldrich,  St. Louis, MO). T-25 flasks (NUNC, Rochester, NY) with vented  caps were used as a culture dishes and cultures were maintained in  CO2 incubator (EC 160, Nuve, Ankara, Turkey) at 37  C in a  5%CO2 atmosphere with 95% humidity.

extract_protocol: RNA was extracted from harvested  cells using RNA isolation kit (QIAGEN GmbH, Hilden,  Germany).

treatment_protocol: Cell cultures were treated  with K2(B3O3F4OH) in concentrations of 0.025 mg/ml and  0.25 mg/ml at 70% of confluence. Cells were exposed to  K2(B3O3F4OH) for 48 h.

value: K2(B3O3F4OH) treatment with 1mM


title: COS conditions rep 1

description: Biological replicate: 1 of 6: COS culture conditions vs STD


title: melanoma cells, concentration 2 treatment

description: Test

source_name: Human Caucasian melanoma cell line (GR-M)

value: K2(B3O3F4OH) treatment with 0,1mM


title: Tcell-Control-IGTB0515


title: DNA_YearDay127

description:
YD127
whole genomic DNA extracted from seawater
DNA_YearDay127_rep1
DNA_YearDay127_rep2


title: non-treated melanoma cells

description: Control

value: negative control


title: DNA_YearDay134A

description:
YD134A
whole genomic DNA extracted from seawater
DNA_YearDay134A_rep1
DNA_YearDay134A_rep2


title: DNA_YearDay126

description:
YD126
whole genomic DNA extracted from seawater
DNA_YearDay126_rep1
DNA_YearDay126_rep2


title: DNA_YearDay125

description:
YD125
whole genomic DNA extracted from seawater
DNA_YearDay125_rep1
DNA_YearDay125_rep2


title: DNA_YearDay131A

description:
YD131A
whole genomic DNA extracted from seawater
DNA_YearDay131A_rep1
DNA_YearDay131A_rep2


title: Tcell-Control-IGTB1718


title: Tcell-Control-IGTB0811


title: Dex and COS conditions rep 1

description: Biological replicate 1 of 2: Dex treatment under COS conditions vs COS conditions


title: CY499 97

status: Public on May 10 2016

city: Stanford

first: Fiona

last: Strouts

state: CA

address: Campus Drive

institute: Stanford

description: CY499 97

hyb_protocol: reference URL : http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.8.pdf Hybridization method : 8 ug of Cy5-labeled amplified RNA and 5 ug of Cy3-labeled Universal Human Reference aRNA (Stratagene) were hybridized to Human Exonic Evidence Based Oligonucleotide (HEEBO) microarrays. Dye-labeled RNA was fragmented and then mixed with 250 ?l 2_ Hi-RPM Hybridization Buffer (Agilent Technologies) and hybridized to the microarrays at 65?C for 14 hours using the hybridization gasket slides and microarray hybridization chamber (Agilent Technologies).

scan_protocol: Scan Power : 100 PMT Volts : 554 Pixel Size : 10 Laser on time : 194130 Laser Power : 3.11 Scan Date : 2012-11-07 Scan Temperature : 33.25 Scan Time : 17:35:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 700, 4430

source_name: Stratagene Human Universal Reference aa aRNA, NuGEN amplified, 5ug of pooled Alexa Fluor 3 labeled

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol: Extraction method : Human Universal Reference RNA (Stratagene)

tag: reference sample name

source_name: PAXGene NHP aRNA, 8ug, EpiC amplified, Cy5 lab, spiked dop control

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol:
Extraction method : PreAnalytiX PAXgene Blood RNA Kit
Amplification method : Epicentre TargetAmp Aminoallyl aRNA Amp Kit

treatment_protocol:
Vaccine Route : SC
Treatment : Virus
Treatment group : 6
Vaccine Dose : Single
Day : 97

tag: test sample name

tag: time point (days)


title: CY499 95

description: CY499 95

scan_protocol: Scan Power : 100 PMT Volts : 528 Pixel Size : 10 Laser on time : 195015 Laser Power : 3.09 Scan Date : 2012-11-12 Scan Temperature : 31.36 Scan Time : 17:07:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 640, 5080

value: Human Universal Reference RNA (Stratagene)

treatment_protocol:
Vaccine Route : SC
Treatment : Virus
Treatment group : 6
Vaccine Dose : Single
Day : 95


title: CY509R 1

description: CY509R 1

scan_protocol: Scan Power : 100 PMT Volts : 566 Pixel Size : 10 Laser on time : 192641 Laser Power : 3.11 Scan Date : 2012-11-03 Scan Temperature : 32.49 Scan Time : 20:38:43 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 760, 4440

treatment_protocol:
Vaccine Route : ID
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : 1


title: CY499 93

description: CY499 93

scan_protocol: Scan Power : 100 PMT Volts : 547 Pixel Size : 10 Laser on time : 194995 Laser Power : 3.10 Scan Date : 2012-11-12 Scan Temperature : 31.09 Scan Time : 16:46:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : SC
Treatment : Virus
Treatment group : 6
Vaccine Dose : Single
Day : 93


title: CY509R 3

description: CY509R 3

scan_protocol: Scan Power : 100 PMT Volts : 554 Pixel Size : 10 Laser on time : 192668 Laser Power : 3.11 Scan Date : 2012-11-03 Scan Temperature : 32.58 Scan Time : 21:06:11 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : 3


title: CY499 1

description: CY499 1

scan_protocol: Scan Power : 100 PMT Volts : 556 Pixel Size : 10 Laser on time : 193965 Laser Power : 3.11 Scan Date : 2012-11-07 Scan Temperature : 32.58 Scan Time : 14:49:39 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 440, 5360


title: CY488 D97

description: CY488 D97

scan_protocol: Scan Power : 100 PMT Volts : 517 Pixel Size : 10 Laser on time : 189049 Laser Power : 3.10 Scan Date : 2012-09-20 Scan Temperature : 33.74 Scan Time : 17:27:34 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 640, 4800


title: CY509R -2

description: CY509R -2

scan_protocol: Scan Power : 100 PMT Volts : 547 Pixel Size : 10 Laser on time : 192082 Laser Power : 3.09 Scan Date : 2012-11-02 Scan Temperature : 31.03 Scan Time : 13:15:52 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 520, 4640

treatment_protocol:
Vaccine Route : ID
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : -2


title: CY509R 7

description: CY509R 7

scan_protocol: Scan Power : 100 PMT Volts : 543 Pixel Size : 10 Laser on time : 192726 Laser Power : 3.10 Scan Date : 2012-11-03 Scan Temperature : 32.77 Scan Time : 22:04:41 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : 7


title: CY499 -11

description: CY499 -11

scan_protocol: Scan Power : 100 PMT Volts : 514 Pixel Size : 10 Laser on time : 194972 Laser Power : 3.10 Scan Date : 2012-11-12 Scan Temperature : 30.69 Scan Time : 16:23:54 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : -11


title: CY499 88

description: CY499 88

scan_protocol: Scan Power : 100 PMT Volts : 523 Pixel Size : 10 Laser on time : 194049 Laser Power : 3.10 Scan Date : 2012-11-07 Scan Temperature : 33.10 Scan Time : 16:14:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 840, 5020

treatment_protocol:
Vaccine Route : SC
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : 88


title: CY488 D95

description: CY488 D95

scan_protocol: Scan Power : 100 PMT Volts : 513 Pixel Size : 10 Laser on time : 189028 Laser Power : 3.10 Scan Date : 2012-09-20 Scan Temperature : 33.71 Scan Time : 17:06:35 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0


title: CY509R 5

description: CY509R 5

scan_protocol: Scan Power : 100 PMT Volts : 557 Pixel Size : 10 Laser on time : 192699 Laser Power : 3.10 Scan Date : 2012-11-03 Scan Temperature : 32.71 Scan Time : 21:37:51 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

treatment_protocol:
Vaccine Route : ID
Treatment : Placebo
Treatment group : 6
Vaccine Dose : Single
Day : 5


title: CY509R -11

description: CY509R -11

scan_protocol: Scan Power : 100 PMT Volts : 580 Pixel Size : 10 Laser on time : 192581 Laser Power : 3.10 Scan Date : 2012-11-03 Scan Temperature : 32.37 Scan Time : 19:39:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0