title: X396 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: X398 genomic DNA from whole blood

status: Public on Oct 04 2016

type: genomic

city: Uppsala

first: Åsa

last: Johansson

state: Sweden

address: BMC, Husarg 3

department: IGP

country: Sweden

institute: Uppsala University

description: normal whole blood

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

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

data_processing:
IDAT files were preprocessed and converted into beta value by minfi Bioconductor package
Tab-delimited .txt files reporting normalized (SWAN) Average Beta values are linked as supplementary files on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: phenol:chloroform protocol

tag: gender

value: Male

tag: age

tag: tissue

value: whole blood

tag: disease state

value: normal


title: X404 genomic DNA from whole blood

description: normal whole blood

value: Female


title: X397 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM026 - time: 16 hai - rep1

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description: Two flats (each flat contained 75 doubled-haploid lines + 4 replicates of each parent = 81 cones/flat) plus CI 16137 (as an internal Mla1 allele control) were grown in a completely randomized design in the Arabidopsis Growth Facility in the Bessey Hall Greenhouse at Iowa State University, Ames, IA USA and transferred to a controlled growth chamber after 7 days. Seedlings were inoculated with B. graminis f. sp. hordei isolate 5874 (AVRa1, AVRa6, AVRa12) at 1600 hours US Central Standard Time.  Lights in the growth chamber were “off” from 4 PM to 12 AM and were “on” from 12:01 AM to 3:59 PM CST.  Seedling first leaves were collected and frozen in liquid nitrogen at 16 ad 32 hours after inoculation (HAI).  Five seedlings were harvested, pooled, and placed in liquid nitrogen for each line in the population within a 20 minute period at 16 and 32 HAI. (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

label: biotin

molecule: total RNA

organism: Hordeum vulgare

source_name: tissue (genotype: QxSM026 - time: 16 hai)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Seedlings were grown in a temperature controlled green house (22˚C) for 7 days. Seedlings were then inoculated with B. graminis f. sp. hordei isolate 5874 (AVRa1, AVRa6, AVRa12) at 1600 hours US Central Standard Time and transferred to a growth chamber (18˚C) until tissue collection.  Lights in the growth chamber were “off” from 4 PM to 12 AM and were “on” from 12:01 AM to 3:59 PM CST.

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: genotype

tag: time point

value: 16 hai

tag: agent

value: Blumeria graminis f. sp. hordei

tag: germplasm name

value: Accession # 18793

tag: organism part

tag: cell type

value: vegetative cell ('PO:0020099')

tag: development stage

value: LP.01 one leaf visible ('PO:0007094')

value: 8 days

tag: growth media

value: peat/perlite/soil


title: genotype: QxSM023 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM023 - time: 32 hai)

value: 32 hai

value: Accession # 18792


title: genotype: QxSM028 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM028 - time: 32 hai)

value: Accession # 18794


title: X395 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM026 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM026 - time: 32 hai)


title: genotype: QxSM019 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM019 - time: 32 hai)

value: Accession # 18791


title: X393 genomic DNA from whole blood

description: normal whole blood


title: X394 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM019 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM019 - time: 16 hai)


title: genotype: QxSM023 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM023 - time: 16 hai)


title: X390 genomic DNA from whole blood

description: normal whole blood


title: X389 genomic DNA from whole blood

description: normal whole blood


title: X392 genomic DNA from whole blood

description: normal whole blood


title: X388 genomic DNA from whole blood

description: normal whole blood


title: X387 genomic DNA from whole blood

description: normal whole blood


title: X401 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM017 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM017 - time: 16 hai)

value: Accession # 18789


title: genotype: QxSM018 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM018 - time: 16 hai)

value: Accession # 18790


title: X391 genomic DNA from whole blood

description: normal whole blood

value: Male


title: X386 genomic DNA from whole blood

description: normal whole blood

value: whole blood


title: genotype: QxSM016 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM016 - time: 32 hai)

value: Accession # 18788


title: genotype: QxSM017 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM017 - time: 32 hai)


title: X382 genomic DNA from whole blood

description: normal whole blood

value: Female

value: normal


title: X384 genomic DNA from whole blood

description: normal whole blood


title: X383 genomic DNA from whole blood

description: normal whole blood


title: X385 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM018 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM018 - time: 32 hai)

value: Blumeria graminis f. sp. hordei


title: X380 genomic DNA from whole blood

description: normal whole blood


title: X381 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM015 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM015 - time: 32 hai)

value: Accession # 18787


title: genotype: QxSM016 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM016 - time: 16 hai)

value: 16 hai

value: vegetative cell ('PO:0020099')


title: genotype: QxSM015 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM015 - time: 16 hai)

value: LP.01 one leaf visible ('PO:0007094')

value: 8 days


title: X377 genomic DNA from whole blood

description: normal whole blood


title: X376 genomic DNA from whole blood

description: normal whole blood


title: X375 genomic DNA from whole blood

description: normal whole blood


title: X374 genomic DNA from whole blood

description: normal whole blood


title: X373 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM013 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM013 - time: 32 hai)

value: 32 hai

value: Accession # 18785

value: peat/perlite/soil


title: genotype: QxSM011 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM011 - time: 32 hai)

value: Accession # 18784


title: genotype: QxSM014 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM014 - time: 32 hai)

value: Accession # 18786


title: X371 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: genotype: QxSM014 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM014 - time: 16 hai)


title: X370 genomic DNA from whole blood

description: normal whole blood


title: X369 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM010 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM010 - time: 32 hai)

value: Accession # 18783


title: genotype: QxSM011 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM011 - time: 16 hai)


title: X368 genomic DNA from whole blood

description: normal whole blood

value: Male


title: X366 genomic DNA from whole blood

description: normal whole blood

value: whole blood


title: X367 genomic DNA from whole blood

description: normal whole blood


title: X378 genomic DNA from whole blood

description: normal whole blood


title: X379 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM013 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM013 - time: 16 hai)


title: X365 genomic DNA from whole blood

description: normal whole blood


title: X364 genomic DNA from whole blood

description: normal whole blood


title: X363 genomic DNA from whole blood

description: normal whole blood


title: X372 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM008 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM008 - time: 32 hai)

value: Accession # 18782


title: X362 genomic DNA from whole blood

description: normal whole blood

value: Female


title: genotype: QxSM008 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM008 - time: 16 hai)


title: genotype: QxSM005 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM005 - time: 32 hai)

value: Accession # 18781


title: X361 genomic DNA from whole blood

description: normal whole blood

value: normal


title: genotype: QxSM005 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM005 - time: 16 hai)

value: Blumeria graminis f. sp. hordei


title: X360 genomic DNA from whole blood

description: normal whole blood


title: X359 genomic DNA from whole blood

description: normal whole blood


title: X356 genomic DNA from whole blood

description: normal whole blood


title: X357 genomic DNA from whole blood

description: normal whole blood


title: X354 genomic DNA from whole blood

description: normal whole blood


title: X358 genomic DNA from whole blood

description: normal whole blood


title: X353 genomic DNA from whole blood

description: normal whole blood


title: X352 genomic DNA from whole blood

description: normal whole blood


title: X355 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM003 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM003 - time: 16 hai)

value: 16 hai

value: Accession # 18780


title: X350 genomic DNA from whole blood

description: normal whole blood


title: X351 genomic DNA from whole blood

description: normal whole blood


title: X349 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM010 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM010 - time: 16 hai)

value: vegetative cell ('PO:0020099')

value: LP.01 one leaf visible ('PO:0007094')


title: X348 genomic DNA from whole blood

description: normal whole blood


title: X346 genomic DNA from whole blood

description: normal whole blood


title: X347 genomic DNA from whole blood

description: normal whole blood


title: X344 genomic DNA from whole blood

description: normal whole blood


title: X345 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM002 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM002 - time: 32 hai)

value: 32 hai

value: Accession # 18779

value: 8 days


title: X342 genomic DNA from whole blood

description: normal whole blood


title: X340 genomic DNA from whole blood

description: normal whole blood


title: X339 genomic DNA from whole blood

description: normal whole blood


title: X343 genomic DNA from whole blood

description: normal whole blood


title: X341 genomic DNA from whole blood

description: normal whole blood


title: X337 genomic DNA from whole blood

description: normal whole blood


title: X338 genomic DNA from whole blood

description: normal whole blood


title: X336 genomic DNA from whole blood

description: normal whole blood


title: genotype: SM89010 - time: 32 hai - rep2

source_name: tissue (genotype: SM89010 - time: 32 hai)

value: Accession # 18777

value: peat/perlite/soil


title: genotype: QxSM002 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM002 - time: 16 hai)


title: X335 genomic DNA from whole blood

description: normal whole blood


title: X334 genomic DNA from whole blood

description: normal whole blood


title: X333 genomic DNA from whole blood

description: normal whole blood


title: genotype: QxSM001 - time: 16 hai - rep1

source_name: tissue (genotype: QxSM001 - time: 16 hai)

value: Accession # 18778


title: X332 genomic DNA from whole blood

description: normal whole blood

value: Male


title: X331 genomic DNA from whole blood

description: normal whole blood

value: whole blood


title: genotype: QxSM003 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM003 - time: 32 hai)


title: genotype: SM89010 - time: 32 hai - rep3


title: genotype: SM89010 - time: 32 hai - rep4


title: X329 genomic DNA from whole blood

description: normal whole blood


title: genotype: SM89010 - time: 16 hai - rep4

source_name: tissue (genotype: SM89010 - time: 16 hai)


title: genotype: QxSM001 - time: 32 hai - rep1

source_name: tissue (genotype: QxSM001 - time: 32 hai)


title: X327 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: genotype: SM89010 - time: 16 hai - rep3


title: genotype: SM89010 - time: 16 hai - rep1


title: genotype: SM89010 - time: 32 hai - rep1


title: genotype: Q21861 - time: 32 hai - rep4

source_name: tissue (genotype: Q21861 - time: 32 hai)

value: Accession # 18776


title: X323 genomic DNA from whole blood

description: normal whole blood


title: genotype: SM89010 - time: 16 hai - rep2


title: genotype: Q21861 - time: 32 hai - rep2


title: X325 genomic DNA from whole blood

description: normal whole blood

value: Female


title: genotype: Q21861 - time: 32 hai - rep1


title: X326 genomic DNA from whole blood

description: normal whole blood


title: X320 genomic DNA from whole blood

description: normal whole blood


title: X322 genomic DNA from whole blood

description: normal whole blood


title: genotype: Q21861 - time: 16 hai - rep3

source_name: tissue (genotype: Q21861 - time: 16 hai)


title: X321 genomic DNA from whole blood

description: normal whole blood


title: X316 genomic DNA from whole blood

description: normal whole blood


title: genotype: Q21861 - time: 32 hai - rep3


title: X318 genomic DNA from whole blood

description: normal whole blood


title: X330 genomic DNA from whole blood

description: normal whole blood


title: X311 genomic DNA from whole blood

description: normal whole blood


title: X310 genomic DNA from whole blood

description: normal whole blood


title: X314 genomic DNA from whole blood

description: normal whole blood


title: X312 genomic DNA from whole blood

description: normal whole blood


title: X324 genomic DNA from whole blood

description: normal whole blood


title: X309 genomic DNA from whole blood

description: normal whole blood


title: X308 genomic DNA from whole blood

description: normal whole blood


title: X317 genomic DNA from whole blood

description: normal whole blood


title: X307 genomic DNA from whole blood

description: normal whole blood


title: X301 genomic DNA from whole blood

description: normal whole blood


title: X300 genomic DNA from whole blood

description: normal whole blood


title: X315 genomic DNA from whole blood

description: normal whole blood


title: X303 genomic DNA from whole blood

description: normal whole blood


title: X302 genomic DNA from whole blood

description: normal whole blood


title: X305 genomic DNA from whole blood

description: normal whole blood


title: X304 genomic DNA from whole blood

description: normal whole blood


title: X313 genomic DNA from whole blood

description: normal whole blood


title: X295 genomic DNA from whole blood

description: normal whole blood


title: X294 genomic DNA from whole blood

description: normal whole blood


title: X293 genomic DNA from whole blood

description: normal whole blood


title: X297 genomic DNA from whole blood

description: normal whole blood


title: X298 genomic DNA from whole blood

description: normal whole blood


title: X296 genomic DNA from whole blood

description: normal whole blood


title: X291 genomic DNA from whole blood

description: normal whole blood


title: X288 genomic DNA from whole blood

description: normal whole blood


title: X289 genomic DNA from whole blood

description: normal whole blood


title: X286 genomic DNA from whole blood

description: normal whole blood


title: genotype: Q21861 - time: 16 hai - rep1


title: X306 genomic DNA from whole blood

description: normal whole blood


title: X299 genomic DNA from whole blood

description: normal whole blood


title: X285 genomic DNA from whole blood

description: normal whole blood


title: X283 genomic DNA from whole blood

description: normal whole blood


title: X282 genomic DNA from whole blood

description: normal whole blood


title: X284 genomic DNA from whole blood

description: normal whole blood


title: X280 genomic DNA from whole blood

description: normal whole blood


title: X278 genomic DNA from whole blood

description: normal whole blood


title: X279 genomic DNA from whole blood

description: normal whole blood


title: X281 genomic DNA from whole blood

description: normal whole blood


title: X277 genomic DNA from whole blood

description: normal whole blood


title: X276 genomic DNA from whole blood

description: normal whole blood


title: X274 genomic DNA from whole blood

description: normal whole blood


title: X272 genomic DNA from whole blood

description: normal whole blood


title: X273 genomic DNA from whole blood

description: normal whole blood


title: X292 genomic DNA from whole blood

description: normal whole blood


title: X275 genomic DNA from whole blood

description: normal whole blood


title: X290 genomic DNA from whole blood

description: normal whole blood


title: X271 genomic DNA from whole blood

description: normal whole blood


title: X287 genomic DNA from whole blood

description: normal whole blood


title: X270 genomic DNA from whole blood

description: normal whole blood


title: X265 genomic DNA from whole blood

description: normal whole blood


title: X267 genomic DNA from whole blood

description: normal whole blood


title: X268 genomic DNA from whole blood

description: normal whole blood


title: X266 genomic DNA from whole blood

description: normal whole blood


title: X263 genomic DNA from whole blood

description: normal whole blood


title: X264 genomic DNA from whole blood

description: normal whole blood


title: X260 genomic DNA from whole blood

description: normal whole blood


title: X262 genomic DNA from whole blood

description: normal whole blood


title: X259 genomic DNA from whole blood

description: normal whole blood


title: X256 genomic DNA from whole blood

description: normal whole blood


title: X257 genomic DNA from whole blood

description: normal whole blood


title: X258 genomic DNA from whole blood

description: normal whole blood


title: X254 genomic DNA from whole blood

description: normal whole blood


title: X255 genomic DNA from whole blood

description: normal whole blood


title: X252 genomic DNA from whole blood

description: normal whole blood


title: X253 genomic DNA from whole blood

description: normal whole blood


title: X251 genomic DNA from whole blood

description: normal whole blood


title: X248 genomic DNA from whole blood

description: normal whole blood


title: X250 genomic DNA from whole blood

description: normal whole blood


title: X269 genomic DNA from whole blood

description: normal whole blood


title: X249 genomic DNA from whole blood

description: normal whole blood


title: X247 genomic DNA from whole blood

description: normal whole blood


title: X241 genomic DNA from whole blood

description: normal whole blood


title: X245 genomic DNA from whole blood

description: normal whole blood


title: X246 genomic DNA from whole blood

description: normal whole blood


title: X244 genomic DNA from whole blood

description: normal whole blood


title: X243 genomic DNA from whole blood

description: normal whole blood


title: X242 genomic DNA from whole blood

description: normal whole blood


title: X261 genomic DNA from whole blood

description: normal whole blood


title: X240 genomic DNA from whole blood

description: normal whole blood


title: X239 genomic DNA from whole blood

description: normal whole blood


title: X235 genomic DNA from whole blood

description: normal whole blood


title: X236 genomic DNA from whole blood

description: normal whole blood


title: X238 genomic DNA from whole blood

description: normal whole blood


title: X234 genomic DNA from whole blood

description: normal whole blood


title: X232 genomic DNA from whole blood

description: normal whole blood


title: X233 genomic DNA from whole blood

description: normal whole blood


title: X231 genomic DNA from whole blood

description: normal whole blood


title: X225 genomic DNA from whole blood

description: normal whole blood


title: X230 genomic DNA from whole blood

description: normal whole blood


title: X224 genomic DNA from whole blood

description: normal whole blood


title: X229 genomic DNA from whole blood

description: normal whole blood


title: X223 genomic DNA from whole blood

description: normal whole blood


title: X226 genomic DNA from whole blood

description: normal whole blood


title: X228 genomic DNA from whole blood

description: normal whole blood


title: X222 genomic DNA from whole blood

description: normal whole blood


title: X221 genomic DNA from whole blood

description: normal whole blood


title: X216 genomic DNA from whole blood

description: normal whole blood


title: X237 genomic DNA from whole blood

description: normal whole blood


title: X220 genomic DNA from whole blood

description: normal whole blood


title: X219 genomic DNA from whole blood

description: normal whole blood


title: X218 genomic DNA from whole blood

description: normal whole blood


title: X213 genomic DNA from whole blood

description: normal whole blood


title: X214 genomic DNA from whole blood

description: normal whole blood


title: X215 genomic DNA from whole blood

description: normal whole blood


title: X217 genomic DNA from whole blood

description: normal whole blood


title: X212 genomic DNA from whole blood

description: normal whole blood


title: X211 genomic DNA from whole blood

description: normal whole blood


title: X210 genomic DNA from whole blood

description: normal whole blood


title: X209 genomic DNA from whole blood

description: normal whole blood


title: X208 genomic DNA from whole blood

description: normal whole blood


title: X207 genomic DNA from whole blood

description: normal whole blood


title: X227 genomic DNA from whole blood

description: normal whole blood


title: X328 genomic DNA from whole blood

description: normal whole blood


title: X203 genomic DNA from whole blood

description: normal whole blood


title: X205 genomic DNA from whole blood

description: normal whole blood


title: X204 genomic DNA from whole blood

description: normal whole blood


title: X201 genomic DNA from whole blood

description: normal whole blood


title: X200 genomic DNA from whole blood

description: normal whole blood


title: X199 genomic DNA from whole blood

description: normal whole blood


title: X197 genomic DNA from whole blood

description: normal whole blood


title: X198 genomic DNA from whole blood

description: normal whole blood


title: X192 genomic DNA from whole blood

description: normal whole blood


title: X191 genomic DNA from whole blood

description: normal whole blood


title: X195 genomic DNA from whole blood

description: normal whole blood


title: X196 genomic DNA from whole blood

description: normal whole blood


title: X193 genomic DNA from whole blood

description: normal whole blood


title: X190 genomic DNA from whole blood

description: normal whole blood


title: X188 genomic DNA from whole blood

description: normal whole blood


title: X189 genomic DNA from whole blood

description: normal whole blood


title: X187 genomic DNA from whole blood

description: normal whole blood


title: X186 genomic DNA from whole blood

description: normal whole blood


title: X202 genomic DNA from whole blood

description: normal whole blood


title: X206 genomic DNA from whole blood

description: normal whole blood


title: X185 genomic DNA from whole blood

description: normal whole blood


title: X183 genomic DNA from whole blood

description: normal whole blood


title: X182 genomic DNA from whole blood

description: normal whole blood


title: X319 genomic DNA from whole blood

description: normal whole blood


title: X184 genomic DNA from whole blood

description: normal whole blood


title: X194 genomic DNA from whole blood

description: normal whole blood


title: X180 genomic DNA from whole blood

description: normal whole blood


title: X181 genomic DNA from whole blood

description: normal whole blood


title: X178 genomic DNA from whole blood

description: normal whole blood


title: X177 genomic DNA from whole blood

description: normal whole blood


title: X179 genomic DNA from whole blood

description: normal whole blood


title: X175 genomic DNA from whole blood

description: normal whole blood


title: X173 genomic DNA from whole blood

description: normal whole blood


title: X172 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_48HRS_RNA_A

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

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

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

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

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 1

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

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: MERSCOV004.0P: Cells were infected with a multiplicity of infection of 5 PFU.

tag: time

tag: infection

value: Mock


title: MHAE002_MOCK_48HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 2


title: X171 genomic DNA from whole blood

description: normal whole blood

value: normal


title: X170 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_48HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 4

value: icMERS


title: MHAE002_MOCK_48HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 5


title: MHAE002_MOCK_48HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 4


title: MHAE002_MOCK_48HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 48h, bioreplicate 3


title: MHAE002_icMERS_48HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 5


title: X169 genomic DNA from whole blood

description: normal whole blood


title: X168 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_48HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 3


title: X167 genomic DNA from whole blood

description: normal whole blood


title: X176 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_48HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 2


title: MHAE002_icMERS_48HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 48h, bioreplicate 1


title: X166 genomic DNA from whole blood

description: normal whole blood


title: X165 genomic DNA from whole blood

description: normal whole blood


title: X174 genomic DNA from whole blood

description: normal whole blood


title: X164 genomic DNA from whole blood

description: normal whole blood


title: genotype: Q21861 - time: 16 hai - rep2

value: 16 hai

value: Blumeria graminis f. sp. hordei


title: MHAE002_MOCK_36HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 4


title: genotype: Q21861 - time: 16 hai - rep4

value: vegetative cell ('PO:0020099')


title: X163 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_36HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 3


title: MHAE002_MOCK_36HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 1


title: MHAE002_MOCK_36HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 5


title: X159 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: X158 genomic DNA from whole blood

description: normal whole blood


title: X160 genomic DNA from whole blood

description: normal whole blood


title: X161 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_36HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 36h, bioreplicate 2


title: X157 genomic DNA from whole blood

description: normal whole blood


title: X155 genomic DNA from whole blood

description: normal whole blood


title: X156 genomic DNA from whole blood

description: normal whole blood


title: X154 genomic DNA from whole blood

description: normal whole blood


title: X162 genomic DNA from whole blood

description: normal whole blood


title: X153 genomic DNA from whole blood

description: normal whole blood


title: X152 genomic DNA from whole blood

description: normal whole blood


title: X150 genomic DNA from whole blood

description: normal whole blood


title: X151 genomic DNA from whole blood

description: normal whole blood


title: X149 genomic DNA from whole blood

description: normal whole blood


title: X148 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_36HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 4


title: X146 genomic DNA from whole blood

description: normal whole blood


title: X147 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_36HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 5


title: MHAE002_icMERS_36HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 2


title: MHAE002_MOCK_24HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 5


title: X144 genomic DNA from whole blood

description: normal whole blood


title: X145 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_36HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 1


title: MHAE002_MOCK_24HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 3


title: MHAE002_icMERS_36HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 36h, bioreplicate 3


title: MHAE002_MOCK_24HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 4


title: X142 genomic DNA from whole blood

description: normal whole blood


title: X140 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_24HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 1


title: X139 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_24HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 24h, bioreplicate 2


title: MHAE002_icMERS_24HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 4


title: X137 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_24HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 5


title: X134 genomic DNA from whole blood

description: normal whole blood


title: X133 genomic DNA from whole blood

description: normal whole blood


title: X132 genomic DNA from whole blood

description: normal whole blood


title: X136 genomic DNA from whole blood

description: normal whole blood


title: X135 genomic DNA from whole blood

description: normal whole blood


title: X143 genomic DNA from whole blood

description: normal whole blood


title: X131 genomic DNA from whole blood

description: normal whole blood


title: X130 genomic DNA from whole blood

description: normal whole blood


title: X141 genomic DNA from whole blood

description: normal whole blood


title: X138 genomic DNA from whole blood

description: normal whole blood


title: X129 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_24HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 2


title: X128 genomic DNA from whole blood

description: normal whole blood


title: X127 genomic DNA from whole blood

description: normal whole blood


title: X125 genomic DNA from whole blood

description: normal whole blood


title: X123 genomic DNA from whole blood

description: normal whole blood


title: X122 genomic DNA from whole blood

description: normal whole blood


title: X121 genomic DNA from whole blood

description: normal whole blood


title: X120 genomic DNA from whole blood

description: normal whole blood


title: X119 genomic DNA from whole blood

description: normal whole blood


title: X117 genomic DNA from whole blood

description: normal whole blood


title: X118 genomic DNA from whole blood

description: normal whole blood


title: X115 genomic DNA from whole blood

description: normal whole blood


title: X114 genomic DNA from whole blood

description: normal whole blood


title: X116 genomic DNA from whole blood

description: normal whole blood


title: X113 genomic DNA from whole blood

description: normal whole blood


title: X124 genomic DNA from whole blood

description: normal whole blood


title: X112 genomic DNA from whole blood

description: normal whole blood


title: X126 genomic DNA from whole blood

description: normal whole blood


title: X110 genomic DNA from whole blood

description: normal whole blood


title: X111 genomic DNA from whole blood

description: normal whole blood


title: X109 genomic DNA from whole blood

description: normal whole blood


title: X107 genomic DNA from whole blood

description: normal whole blood


title: X108 genomic DNA from whole blood

description: normal whole blood


title: X106 genomic DNA from whole blood

description: normal whole blood


title: X105 genomic DNA from whole blood

description: normal whole blood


title: X104 genomic DNA from whole blood

description: normal whole blood


title: X103 genomic DNA from whole blood

description: normal whole blood


title: X102 genomic DNA from whole blood

description: normal whole blood


title: X101 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_24HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 1


title: MHAE002_MOCK_12HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 4


title: X100 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: MHAE002_MOCK_12HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 3


title: X98 genomic DNA from whole blood

description: normal whole blood


title: X96 genomic DNA from whole blood

description: normal whole blood


title: X97 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_12HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 2


title: MHAE002_icMERS_12HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 5


title: MHAE002_MOCK_12HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 5


title: MHAE002_MOCK_12HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 1


title: X95 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_24HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 24h, bioreplicate 3


title: X99 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_12HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 1


title: MHAE002_MOCK_0HRS_RNA_D

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 4


title: MHAE002_MOCK_0HRS_RNA_C

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 3


title: MHAE002_icMERS_12HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 4


title: X91 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_12HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 12h, bioreplicate 3


title: X93 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_0HRS_RNA_A

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 1


title: MHAE002_MOCK_12HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 12h, bioreplicate 2


title: MHAE002_icMERS_0HRS_RNA_E

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 5


title: MHAE002_icMERS_0HRS_RNA_A

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 1


title: X88 genomic DNA from whole blood

description: normal whole blood


title: X94 genomic DNA from whole blood

description: normal whole blood


title: X87 genomic DNA from whole blood

description: normal whole blood


title: X89 genomic DNA from whole blood

description: normal whole blood


title: X86 genomic DNA from whole blood

description: normal whole blood


title: X92 genomic DNA from whole blood

description: normal whole blood


title: X85 genomic DNA from whole blood

description: normal whole blood


title: X84 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_MOCK_0HRS_RNA_E

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 5


title: X81 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: X90 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_0HRS_RNA_B

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 2


title: MHAE002_MOCK_0HRS_RNA_B

source_name: Primary human airway epithelial cells, mock-inoculated, 0h, bioreplicate 2


title: X80 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_MOCK_48HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 5

treatment_protocol: MERSCOV002.0P: Cells were infected with a multiplicity of infection of 5 PFU.

value: MOCK


title: X79 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_MOCK_48HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 4


title: MMVE002_MOCK_48HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 1


title: X83 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_icMERS_48HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 4


title: X78 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_icMERS_48HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 5


title: MHAE002_icMERS_0HRS_RNA_C

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 3


title: X82 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_icMERS_48HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 3


title: MMVE002_MOCK_48HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 3


title: X77 genomic DNA from whole blood

description: normal whole blood


title: MHAE002_icMERS_0HRS_RNA_D

source_name: Primary human airway epithelial cells, icMERS-inoculated, 0h, bioreplicate 4


title: MMVE002_icMERS_48HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 2


title: X76 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_MOCK_48HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 2


title: MMVE002_icMERS_48HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 1


title: MMVE002_MOCK_36HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 5


title: X75 genomic DNA from whole blood

description: normal whole blood


title: SSG1_SDC_rep2

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

country: Japan

institute: National Research Institute of Brewing

description: Gene expression data from SSG1 in SDC medium

hyb_protocol: 5 ug of cRNA were hybridized for 4 hr at 45℃ on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Operating Software(GCOS) v1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Saccharomyces cerevisiae

source_name: SSG1 at early-log phase in SDC medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: WT(W303) and SSG1 strains were grown at 25℃ in YPD medium.

extract_protocol: Total RNA were extracted by acid-phenol method and purified by using RNeasy MiniKit (QUIAGEN) following manufacture's instruction.

treatment_protocol: WT(W303) and SSG1 cells pre-grown in SDC(pH 6.0) medium were inoculated in SDC(pH 6.0) for 12 hr until early-log phase (2×10^6 cells/ml).

tag: strain

tag: genotype/variation

value: SSG1-1 mutant


title: MMVE002_MOCK_36HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 4


title: X74 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: SSG1_SDC_rep1


title: MMVE002_MOCK_36HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 3


title: 487 M81

city: Dallas

first: Zhiyu

last: Zhao

state: Texas

address: 5323 Harry Hines Blvd.

department: Children's Medical Center Research Institute

hyb_protocol: The resulting cRNA was then analyzed with the Illumina Human HT12v4.0 Expression Beadchip (Illumina) at the University of Texas Southwestern Medical Center (UTSW) Simmons Cancer Center Genomics Core.

scan_protocol: The arrays were scanned using an Illumina Beadstation 500 BeadArray reader.

data_processing: BeadStudio (Illumina) was used for data analysis.

source_name: patient derived xenograft

label_protocol: 1 µg of total RNA was biotin labeled using the Illumina Total Prep kit (Ambion).

growth_protocol: Melanoma specimens were obtained with informed consent from all patients according to protocols approved by the Institutional Review Board of the University of Michigan Medical School (IRBMED HUM00050754 and HUM00050085) and enzymatically digested. Freshly dissociated melanoma cells were injected subcutaneously into the right flanks of NSG mice.

extract_protocol: Melanomas were surgically excised and homogenized in Trizol (Invitrogen), then frozen at -80°C. After isolation of RNA from Trizol, total RNA from each sample was further purified using RNeasy micro plus kits (Qiagen).

tag: patient id

tag: tissue type

value: tumor (melanoma)


title: melanocytes M849

institute: University of Texas Southwestern Medical Center

value: melanocytes


title: X73 genomic DNA from whole blood

description: normal whole blood

tag: gender

tag: age


title: 487 M85


title: WT_SDC_rep1

description: Gene expression data from W303 in SDC medium

source_name: W303 at early-log phase in SDC medium

value: Wild type


title: WT_SDC_rep2


title: melanocytes M848


title: X72 genomic DNA from whole blood

description: normal whole blood

tag: tissue

tag: disease state


title: MMVE002_MOCK_36HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 2


title: X70 genomic DNA from whole blood

description: normal whole blood


title: melanocytes M830


title: MMVE002_MOCK_36HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 1


title: 715 M1408


title: MMVE002_icMERS_36HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 5


title: MMVE002_icMERS_36HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 4


title: 715 M1402


title: 715 M1404


title: 711 M1388


title: MMVE002_icMERS_36HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 2


title: Cerebellar neuron enriched culture 16days imidacloprid rep6

city: Setagaya-ku

first: Junko

last: Kimura-Kuroda

state: Tokyo

address: 2-1-6, Kamikitazawa

department: Department of Brain Development and Neural Regeneration

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression in imidacloprid-treated cerebellar neuron-enriched culture of neonatal rats at 16 days in vitro

hyb_protocol: Purified and labeled cRNA was hybridized to Whole Rat Gene Expression ver.3 4x44k Microarray　(Agilent Technologies), according to the manufacturer's procedures. Hybridizations were performed for 17 hours at 65°C at 10 rpm in a rotating hybridization oven.

scan_protocol: The hybridized microarray slides were washed and scanned using Agilent SureScan microarray scanner using a scan resolution of 5 μm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v 11.0.1.1 or 11.5.1.1) with set to default for all parameters. After then, quantile normalization and subsequent data processing were performed with using the GeneSpring GX v13.1 software package (Agilent Technologies). To determine the specific effects of nicotine, acetamiprid, and imidacloprid, raw data of each treatment and control were processed and the results were compared by GeneSpring. This semi-series were for imidacloprid treatment, and raw data of control was same as other semi-series of nicotine and acetamiprid. For each probe, the median of the log summarized values from all the samples was calculated and subtracted from each of the samples to get a transformed baseline.

organism: Rattus norvegicus

source_name: Cerebellar neuron-enriched culture

label_protocol: cRNA was synthesized and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies)

growth_protocol: First, the cerebellar cells were cultured in a synthetic culture medium containing 1% fetal bovine serum for 8 days. After then, the neuron-enriched cultures were maintained in a serum-free synthetic medium consisted of Dulbecco's modified Eagle medium/F12 (Gibco, Thermo Fisher Scientific) with 10 μg/ml bovine insulin (Sigma-Aldrich), 100 μg/ml transferrin (Sigma-Aldrich), 30 nM sodium selenite, 5 nM thyroxine, 100 μM putrescine (Sigma-Aldrich), and antibiotics in a humidified incubator with 5% CO2/95% air, at 37°C.

extract_protocol: Total RNA was isolated from cerebellar neuron-enriched cultures at 16 days in vitro using TRizol reagent (Invitrogen, Thermo Fisher Scientific) and Direct-zol RNA Miniprep Kit (ZYMO Research, Irvine, CA, USA) following manufacturer's recommendations. The RNA extracts were analyzed by Nanodrop 2000 (Thermo Fisher Scientific) and RNA quality was determined by the ratios A260/A280 (close to 2) and A260/A230 (more than 2). The quality of RNA was further assessed with a 2100 Bioanalyzer (Agilent Technologies, Valencia, CA, USA).

treatment_protocol: After 2 days in culture, nicotine, acetamiprid, or imidacloprid was added to the cell cultures at a final concentration of 1 μM. Nicotine, acetamiprid, and imidacloprid were dissolved in dimethyl sulfoxide, and their stock solutions (100 mM) were frozen at -30°C immediately prior to use. To exclude effects of vehicle, dimethyl sulfoxide (0.001% final) was added to the media for the control cultures and each of the treatment cultures. One-half of the culture medium was replaced with a fresh medium every 2 days for the 16 days in culture. During medium replacement, nicotine, acetamiprid, or imidacloprid was added to the culture at a final concentration of 1 μM.

value: Sprague-Dawley rat

value: cerebellum

value: 1 day old, neonatal

tag: treatment

value: imidacloprid (1 uM)


title: X68 genomic DNA from whole blood

description: normal whole blood

value: Male

value: whole blood


title: 711 M1390


title: X71 genomic DNA from whole blood

description: normal whole blood


title: X69 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_icMERS_36HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 3


title: Cerebellar neuron enriched culture 16days imidacloprid rep4


title: MMVE002_icMERS_36HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days imidacloprid rep5


title: Cerebellar neuron enriched culture 16days imidacloprid rep3


title: MMVE002_MOCK_24HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 5


title: 667 M1345


title: Cerebellar neuron enriched culture 16days imidacloprid rep2


title: MMVE002_MOCK_24HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 4


title: X66 genomic DNA from whole blood

description: normal whole blood


title: X64 genomic DNA from whole blood

description: normal whole blood


title: X63 genomic DNA from whole blood

description: normal whole blood


title: Cerebellar neuron enriched culture 16days imidacloprid rep1


title: 667 M1224


title: 660 M1312


title: X65 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_MOCK_24HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 3


title: MMVE002_MOCK_24HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 2


title: Cerebellar neuron enriched culture 16days control for imidacloprid rep6

description: Gene expression in control cerebellar neuron-enriched culture of neonatal rats at 16 days in vitro

value: control


title: Cerebellar neuron enriched culture 16days control for imidacloprid rep4


title: X67 genomic DNA from whole blood

description: normal whole blood

value: Female

value: normal


title: Cerebellar neuron enriched culture 16days control for imidacloprid rep3


title: Cerebellar neuron enriched culture 16days control for imidacloprid rep1


title: MMVE002_icMERS_24HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 5

value: icMERS


title: MMVE002_icMERS_24HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 3


title: MMVE002_icMERS_24HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 2


title: MMVE002_icMERS_24HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 4


title: 656 M1293

source_name: patient derived xenograft


title: MMVE002_MOCK_24HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days control for imidacloprid rep5


title: 660 M1344


title: 656 M1246


title: 651 M1160


title: MMVE002_icMERS_24HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days control for imidacloprid rep2


title: 653 M1217


title: X61 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: X59 genomic DNA from whole blood

description: normal whole blood


title: X60 genomic DNA from whole blood

description: normal whole blood


title: X57 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_MOCK_12HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 5


title: Cerebellar neuron enriched culture 16days acetamiprid rep4

description: Gene expression in acetamiprid-treated cerebellar neuron-enriched culture of neonatal rats at 16 days in vitro

data_processing: Data was obtained using the Agilent Feature Extraction software (v 11.0.1.1 or 11.5.1.1) with set to default for all parameters. After then, quantile normalization and subsequent data processing were performed with using the GeneSpring GX v13.1 software package (Agilent Technologies). To determine the specific effects of nicotine, acetamiprid, and imidacloprid, raw data of each treatment and control were processed and the results were compared by GeneSpring. This semi-series were for acetamiprid treatment, and raw data of control was same as other semi-series of nicotine and imidacloprid. For each probe, the median of the log summarized values from all the samples was calculated and subtracted from each of the samples to get a transformed baseline.

value: acetamiprid (1 uM)


title: MMVE002_MOCK_12HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 4


title: MMVE002_MOCK_12HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 3


title: 653 M1252


title: X56 genomic DNA from whole blood

description: normal whole blood


title: Cerebellar neuron enriched culture 16days acetamiprid rep5

source_name: Cerebellar neuron-enriched culture


title: 641 M1251


title: 634 M1128


title: 633 M1240


title: Cerebellar neuron enriched culture 16days acetamiprid rep2


title: MMVE002_MOCK_12HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days acetamiprid rep3


title: MMVE002_MOCK_12HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 2


title: Cerebellar neuron enriched culture 16days acetamiprid rep6


title: Cerebellar neuron enriched culture 16days acetamiprid rep1


title: MMVE002_icMERS_12HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 5


title: Cerebellar neuron enriched culture 16days control for acetamiprid rep6


title: 641 M1215


title: 633 M1297


title: 634 M1303


title: X55 genomic DNA from whole blood

description: normal whole blood


title: X54 genomic DNA from whole blood

description: normal whole blood


title: X58 genomic DNA from whole blood

description: normal whole blood


title: X53 genomic DNA from whole blood

description: normal whole blood


title: X52 genomic DNA from whole blood

description: normal whole blood


title: X51 genomic DNA from whole blood

description: normal whole blood


title: Cerebellar neuron enriched culture 16days control for acetamiprid rep5


title: Cerebellar neuron enriched culture 16days control for acetamiprid rep3


title: MMVE002_icMERS_12HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 4


title: X48 genomic DNA from whole blood

description: normal whole blood


title: 632 M1127


title: 632 M1203


title: X50 genomic DNA from whole blood

description: normal whole blood


title: Cerebellar neuron enriched culture 16days control for acetamiprid rep4


title: MMVE002_icMERS_12HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 3


title: X49 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_icMERS_12HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 2


title: MMVE002_icMERS_12HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 1


title: 631 M1269


title: MMVE002_MOCK_0HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 5


title: 610 M1057


title: X47 genomic DNA from whole blood

description: normal whole blood


title: 631 M1129


title: X46 genomic DNA from whole blood

description: normal whole blood


title: Cerebellar neuron enriched culture 16days nicotine rep5

description: Gene expression in nicotine-treated cerebellar neuron-enriched culture of neonatal rats at 16 days in vitro

data_processing: Data was obtained using the Agilent Feature Extraction software (v 11.0.1.1 or 11.5.1.1) with set to default for all parameters. After then, quantile normalization and subsequent data processing were performed with using the GeneSpring GX v13.1 software package (Agilent Technologies). To determine the specific effects of nicotine, acetamiprid, and imidacloprid, raw data of each treatment and control were processed and the results were compared by GeneSpring. This semi-series were for nicotine treatment, and raw data of control was same as other semi-series of acetamiprid and imidacloprid. For each probe, the median of the log summarized values from all the samples was calculated and subtracted from each of the samples to get a transformed baseline.

value: nicotine (1 uM)


title: Cerebellar neuron enriched culture 16days control for acetamiprid rep1


title: Cerebellar neuron enriched culture 16days control for acetamiprid rep2


title: Cerebellar neuron enriched culture 16days nicotine rep4


title: 625 M1340


title: MMVE002_MOCK_0HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 4

value: MOCK


title: X45 genomic DNA from whole blood

description: normal whole blood


title: MMVE002_MOCK_0HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 2


title: 625 M1155

source_name: patient derived xenograft


title: X44 genomic DNA from whole blood

description: normal whole blood


title: 610 M1026


title: Cerebellar neuron enriched culture 16days nicotine rep6


title: Cerebellar neuron enriched culture 16days nicotine rep2


title: MMVE002_MOCK_0HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 3


title: MMVE002_icMERS_0HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 0h, bioreplicate 5


title: 600 M1163


title: MMVE002_MOCK_0HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days nicotine rep3


title: 600 M1117


title: MMVE002_icMERS_0HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 0h, bioreplicate 4


title: X43 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: X42 genomic DNA from whole blood

description: normal whole blood


title: X41 genomic DNA from whole blood

description: normal whole blood


title: X40 genomic DNA from whole blood

description: normal whole blood


title: X39 genomic DNA from whole blood

description: normal whole blood


title: X38 genomic DNA from whole blood

description: normal whole blood


title: 534 M861


title: MMVE002_icMERS_0HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 0h, bioreplicate 3


title: MMVE002_icMERS_0HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 0h, bioreplicate 2


title: 597 M924


title: Cerebellar neuron enriched culture 16days control for nicotine rep4

source_name: Cerebellar neuron-enriched culture


title: 597 N1039


title: MMVE002_icMERS_0HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 0h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days control for nicotine rep5


title: MFB002_MOCK_48HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 3

treatment_protocol: Cells were infected with a multiplicity of infection of 5 PFU.

value: Mock


title: Cerebellar neuron enriched culture 16days control for nicotine rep6


title: MFB002_MOCK_48HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 5


title: Cerebellar neuron enriched culture 16days control for nicotine rep1


title: MFB002_MOCK_48HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 4


title: X37 genomic DNA from whole blood

description: normal whole blood


title: 534 M893

value: tumor (melanoma)


title: Cerebellar neuron enriched culture 16days control for nicotine rep2


title: Cerebellar neuron enriched culture 16days nicotine rep1


title: 534 M789


title: MFB002_MOCK_48HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 2


title: 530 M768


title: 534 M916


title: X36 genomic DNA from whole blood

description: normal whole blood


title: 530 M300


title: X62 genomic DNA from whole blood

description: normal whole blood


title: X35 genomic DNA from whole blood

description: normal whole blood


title: 530 M856


title: X33 genomic DNA from whole blood

description: normal whole blood


title: X34 genomic DNA from whole blood

description: normal whole blood


title: X32 genomic DNA from whole blood

description: normal whole blood


title: X31 genomic DNA from whole blood

description: normal whole blood


title: X30 genomic DNA from whole blood

description: normal whole blood


title: MFB002_icMERS_48HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 5


title: MFB002_MOCK_48HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 48h, bioreplicate 1


title: Cerebellar neuron enriched culture 16days control for nicotine rep3


title: X28 genomic DNA from whole blood

description: normal whole blood


title: 651 M1157


title: X29 genomic DNA from whole blood

description: normal whole blood


title: 528 M162


title: MFB002_icMERS_48HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 2


title: 526 M828

source_name: patient derived xenograft


title: X26 genomic DNA from whole blood

description: normal whole blood


title: MFB002_icMERS_48HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 1


title: 526 M538


title: 528 M758


title: MFB002_icMERS_48HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 3


title: X25 genomic DNA from whole blood

description: normal whole blood


title: 526 M841


title: 526 M776


title: X27 genomic DNA from whole blood

description: normal whole blood


title: 514 M1190


title: MFB002_MOCK_36HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 4


title: MFB002_MOCK_36HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 5


title: X24 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: 514 M1183


title: 501 M1214


title: MFB002_MOCK_36HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 3


title: X23 genomic DNA from whole blood

description: normal whole blood


title: X22 genomic DNA from whole blood

description: normal whole blood


title: 528 M216


title: MFB002_icMERS_48HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 48h, bioreplicate 4


title: X20 genomic DNA from whole blood

description: normal whole blood


title: X21 genomic DNA from whole blood

description: normal whole blood


title: MFB002_icMERS_36HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 3


title: MFB002_MOCK_36HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 1


title: 499 M181


title: 501 M1291


title: 498 M218


title: 498 M180


title: MFB002_icMERS_36HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 1


title: X16 genomic DNA from whole blood

description: normal whole blood


title: X18 genomic DNA from whole blood

description: normal whole blood


title: MFB002_MOCK_36HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 36h, bioreplicate 2


title: MFB002_icMERS_36HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 4


title: MFB002_icMERS_36HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 5


title: X17 genomic DNA from whole blood

description: normal whole blood


title: 492 M107


title: MFB002_icMERS_36HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 36h, bioreplicate 2


title: 491 M281


title: X19 genomic DNA from whole blood

description: normal whole blood


title: 491 M824


title: MFB002_MOCK_24HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 4


title: 530 M826


title: X14 genomic DNA from whole blood

description: normal whole blood


title: MFB002_MOCK_24HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 2


title: 491 M941

source_name: patient derived xenograft


title: MFB002_MOCK_24HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 5


title: X13 genomic DNA from whole blood

description: normal whole blood


title: MFB002_MOCK_24HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 1


title: X11 genomic DNA from whole blood

description: normal whole blood


title: X9 genomic DNA from whole blood

description: normal whole blood


title: MFB002_icMERS_24HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 5


title: 492 M923


title: 530 M769


title: X15 genomic DNA from whole blood

description: normal whole blood


title: MFB002_MOCK_24HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 24h, bioreplicate 3


title: X8 genomic DNA from whole blood

description: normal whole blood

source_name: whole blood


title: X12 genomic DNA from whole blood

description: normal whole blood


title: X7 genomic DNA from whole blood

description: normal whole blood


title: 487 M757


title: MFB002_icMERS_24HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 4


title: 481 M876


title: MFB002_icMERS_24HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 3


title: X10 genomic DNA from whole blood

description: normal whole blood


title: MFB002_icMERS_24HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 1


title: MFB002_icMERS_24HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 24h, bioreplicate 2


title: MFB002_MOCK_12HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 4


title: X6 genomic DNA from whole blood

description: normal whole blood


title: 405 M888


title: MFB002_MOCK_12HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 5


title: 481 M145


title: MFB002_MOCK_12HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 2


title: X5 genomic DNA from whole blood

description: normal whole blood


title: 405 M919


title: MFB002_MOCK_12HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 3


title: X4 genomic DNA from whole blood

description: normal whole blood


title: Endometrium exposed to oocytes, Animal 2

city: Sheffield

first: Tamer

last: Nafee

address: The Jessop Wing, Tree Root Walk

department: AURDM

country: United Kingdom

institute: University of Sheffield

description: microRNA expression data from endometrium exposed to unfertilised oocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip microRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing:
Preliminary analysis was carried out using Expression Console to confirm that all arrays met the appropriate QC records. From Expression Console, an RMA normalized pivot table was prepared which gave intensity values for all the probe sets of the array. Microarray experiments were carried out according to MIAME guidelines
Qlucore Omics Software version 2.3 (Qlucore AB).  RMA (Robust Multi – array Average) approach 39for normalisation was used and the probe set intensities were log2 transformed.  A paired t-test was used to determine gene expression changes in the endometrium caused by the presence of a pig embryo and p-values were adjusted to control the error rate to <0.05.

organism: Sus scrofa

source_name: Uterine horn, 6 days after buffer injection - Oocytes confirmed

label_protocol: Poly (A) tailing of total RNA samples using 1:500 dilution of ATP Mix, PAP enzyme, 25 mM MnCl2 in 10X reaction buffer incubated at 37 degrees for 15 minutes. FlashTag Biotin HSR Ligation of the tailed RNA samples was performed using T4 DNA Ligase in 5X specific Ligation Mix incubated at 25 degrees for 30 minutes. An ELOSA (Enzyme Linked Oligosorbent Assay) quality control step was performed using 2 uL of each biotin – labelling reaction, positive and negative controls to confirm the validity of the biotin labelling step

growth_protocol: Three sows were laparoscopically inseminated with semen in one oviduct and with diluent in the contra lateral oviduct.  An affymetrix GeneChip miRNA 3.0 microarray was used to compare the microRNA expression profiles of the endometrium exposed to unfertilised oocytes vs developing embryos,

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

treatment_protocol: Whole endometrial homogenates were surgically collected from the tip of both uterine horns after microscopically confirming the presence of day 6 oocytes / blastocysts. Whole endometrial homogenates were surgically collected from the tip of both uterine horns after microscopically confirming the presence of oocytes / blastocysts

value: Endoemtrium


title: 481 M875


title: MFB002_MOCK_12HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 12h, bioreplicate 1


title: 405 M792


title: Endometrium exposed to oocytes, Animal 1


title: Endometrium exposed to embryo, Animal 2

description: microRNA expression data from endometrium exposed to developing pre-implantation embryo

source_name: Uterine horn, 6 days after insemination - Blastocysts confirmed


title: X3 genomic DNA from whole blood

description: normal whole blood


title: X2 genomic DNA from whole blood

description: normal whole blood


title: Endometrium exposed to embryo, Animal 1


title: MFB002_icMERS_12HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 5


title: X1 genomic DNA from whole blood

description: normal whole blood


title: MFB002_icMERS_12HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 4


title: Bats-72

city: Hangzhou

first: Wengong

last: Si

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Zhejiang university

description: We chosed the endogenous 5S rRNA as the endogenous positive control of miRNA microarray.About the negative control,in addition to single-base mismatch probes for the LC Sciences synthetic sequence, two sets of probes were designed: one for the blank control and the other for the nucleic acid sequence probe with no homology to the experimental sample. The expected hybridization signal values of negative control were below or close to the background signal values, and their signal values were already eliminated from the subsequent data analysis.

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: breast cancer

label_protocol: The assy started from 2 to 5 μg total RNA sample were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using the RNAiso plus(Takara biotechnology, Dalian, China ), following the manufacturer's recommended protocol.

value: breast cancer cell

tag: drug sensitivity

value: resistant


title: Bads-200


title: MFB002_icMERS_12HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 3


title: 308 M871

source_name: patient derived xenograft


title: MFB002_icMERS_12HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 2


title: BCap37

value: sensitive


title: MFB002_icMERS_12HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 12h, bioreplicate 1


title: MFB002_MOCK_0HRS_RNA_E

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 5


title: 308 M872


title: 214 M886


title: 214 M887


title: 205 M891


title: 214 M944


title: MFB002_MOCK_0HRS_RNA_C

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 3


title: Anxa2 knockout, biological replicate 3

city: Washington D. C.

first: Jyoti

middle: K.

last: Jaiswal

address: 111 Michigan Av NW

department: Center for Genetic Medicine Research

institute: Children’s National Health System

description: Gene expression data from Anxa2 knockout mouse

hyb_protocol: 15.2 ug of biotinylated cRNA was fragmented and hybridized to Affymetrix Gene-Chips MG 430 2.0 for 16 hours. The arrays were then washed and stained on the Affymetrix Fluidics station 400.

scan_protocol: Arrays were imaged using Hewlett Packard G2500A gene Array scanner according to manufacturer’s protocol

data_processing: The R library affyQCReport was used for quality control. Raw CEL files were normalized using the RMA algorithm from affy library with Mouse4302_Mm_ENSG_v19.0.0 as custom Chip Description File (CDF) from the BRAINARRAY project (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/ensg.asp) (R version 3.1.2)

organism: Mus musculus

source_name: Anxa2 knockout, gastrocnemius skeletal muscle

label_protocol: An aliquot of 250 ng of total high-quality RNA from each sample was used. cDNA and biotinylated cRNA were synthesized using the Affymetrix GeneChip® 3’ IVT Express Target Amplification, Labeling and Control Reagent kit according to manufacturer’s instructions.

extract_protocol: Directly following euthanasia, Gastrocnemius (GSC) muscles from the left hindlimb were directly frozen liquid nitrogen and stored at -80˚C. Total RNA was extracted from frozen GSC muscles using Trizol reagent (Life Technologies, USA) and cleaned up with RNeasy MinElute cleanup kit (Qiagen, USA) according to the manufacturers’ instructions, and then stored at -80oC until use.

tag: genotype

value: Anxa2 knockout

value: skeletal muscle, gastrocnemius

value: 24 weeks

tag: genetic background


title: MFB002_MOCK_0HRS_RNA_D

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 4


title: 205 M890


title: 205 M170


title: Anxa2 knockout, biological replicate 2


title: Anxa2 knockout, biological replicate 4


title: 481 M144


title: MFB002_MOCK_0HRS_RNA_B

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 2


title: P2_Vehicle

city: Columbus

first: Kevin

middle: R

last: Coombes

state: Ohio

address: 340E Lincoln Tower, 1800 Cannon Drive

department: Biomedical Informatics

institute: Ohio State University Wexner Medical Center

description: Gene expression after stimulation with vehicle control

hyb_protocol: The Cy3-labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 033010_D_F_20110314) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data were then quantile normalized using the limma R package.
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 15 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

source_name: pooled primary CLL B-cells

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

growth_protocol: RPMI 1640 media supplemented with 10% fetal bovine serum, 2mM L-glutamine (Invitrogen), 100U/mL penicillin, and 100ug/mL streptomycin (Sigma)

extract_protocol: Trizol extraction followed by Qiagen Rneasy column clean up. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed.

treatment_protocol: 500 ng/mL CD40 ligand stimulaton for 1 hour

tag: day

value: Vehicle

value: primary CLL B-cells


title: CD4+ iNKT-iPSC (#8)

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

description: undifferentiated induced pluripotent stem cells

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

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting.

data_processing: GenomeStudio V2011.1

source_name: induced pluripotent stem cells

extract_protocol: genomic DNA was extracted and purified using QIAamp DNA Mini Kit according to standard instructions. 500 ng of genomic DNA was subjected to bisulfite conversion using EZ DNA Methylation Kit (ZYMO research).

tag: cell type

value: induced pluripotent stem cells


title: MFB002_MOCK_0HRS_RNA_A

source_name: Primary human fibroblasts, mock-inoculated, 0h, bioreplicate 1


title: MFB002_icMERS_0HRS_RNA_E

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 5


title: Wild type, biological replicate 4

description: Gene expression data from wild type mouse

source_name: Wild type, gastrocnemius skeletal muscle

value: wild type


title: CD4+ iNKT-iPSC (#1)


title: P2_CD40

description: Gene expression after stimulation with CD40


title: P1_CD40


title: CD4+ iNKT (Donor A)

description: CD4+ natural killer T cell

source_name: lymphocytes

value: lymphocytes


title: P1_Vehicle


title: 405 M889


title: Anxa2 knockout, biological replicate 1


title: DN iNKT (Donor C)

description: CD4-/CD8- natural killer T cell


title: MFB002_icMERS_0HRS_RNA_B

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 2

value: icMERS


title: Wild type, biological replicate 3


title: SOPH_LL_2

status: Public on Oct 03 2016

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

description: one of two biological replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: growth on sophorose in constant light

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Trichoderma reesei strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% of the indicated carbon source or 1.5 mM sophorose in constant light (LL) or constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

value: wild-type


title: Wild type, biological replicate 2


title: SOPH_DD_2

description: one of two biological replicates

source_name: growth on sophorose in constant darkness


title: Wild type, biological replicate 1


title: MFB002_icMERS_0HRS_RNA_D

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 4


title: SOPH_DD_1

description: one of two biological replicates


title: NB_Vehicle

source_name: pooled normal blood B-cells

value: normal blood B-cells


title: MFB002_icMERS_0HRS_RNA_C

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 3


title: 308 M873

source_name: patient derived xenograft


title: Endometrium exposed to oocytes, Animal 3

source_name: Uterine horn, 6 days after buffer injection - Oocytes confirmed


title: DN iNKT (Donor A)

description: CD4-/CD8- natural killer T cell


title: CD4+ iNKT-iPSC (#2)


title: re-iNKT (#2)

description: re-differentiated natural killer T cell


title: CD4+ iNKT (Donor B)

description: CD4+ natural killer T cell


title: GLU_DD_2

description: one of two biological replicates

source_name: growth on glucose in constant darkness


title: GLU_LL_1

description: one of two biological replicates

source_name: growth on glucose in constant light


title: SOPH_LL_1

description: one of two biological replicates


title: GLU_DD_1

description: one of two biological replicates


title: CEL_LL_1

description: one of two biological replicates

source_name: growth on cellulose in constant light


title: LAC_LL_2

description: one of two biological replicates

source_name: growth on lactose in constant light


title: CEL_LL_2

description: one of two biological replicates


title: GLY_LL_2

description: one of two biological replicates

source_name: growth on glycerol in constant light


title: GLU_LL_2

description: one of two biological replicates


title: MFB002_icMERS_0HRS_RNA_A

source_name: Primary human fibroblasts, icMERS-inoculated, 0hrs, bioreplicate 1


title: DN iNKT (Donor B)

description: CD4-/CD8- natural killer T cell


title: Margins-2

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

hyb_protocol: According to affymetrix instructions

scan_protocol: According to affymetrix instructions

data_processing: Expression calls were derived using the MAS algorithm implemented in R 2.7.2\Bioconductor 2.2. Samples were median normalized to 50.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Leaf margin tissue dissected from mature leaves

label_protocol: According to affymetrix instructions

growth_protocol: Plants were grown in soil under at 23C with 16h light/8h dark cycles

extract_protocol: RNA was extract using Qiagen RNeasy plant mini kit according to manufacturer instructions

treatment_protocol: Leaf magins were manually dissected and immediately flash-frozen in liquid nitrogen

tag: ecotype

value: Ler


title: Margins-1

value: Leaf margin tissue dissected from mature leaves


title: LAC_DD_1

description: one of two biological replicates

source_name: growth on lactose in constant darkness


title: GLY_LL_1

description: one of two biological replicates


title: LAC_DD_2

description: one of two biological replicates


title: NB_CD40


title: GLY_DD_1

description: one of two biological replicates

source_name: growth on glycerol in constant darkness


title: GLY_DD_2

description: one of two biological replicates


title: LAC_LL_1

description: one of two biological replicates


title: CEL_DD_2

description: one of two biological replicates

source_name: growth on cellulose in constant darkness


title: CEL_DD_1

description: one of two biological replicates


title: IFNa-treatment-24hours-4

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

hyb_protocol: The biotin labeled cDNA was hybridized to  the array for 16 hours at 45°C using the GeneChip® Hybridization Oven 640. Washing  and staining with streptavidin-phycoerythrin was performed using the GeneChip®  Hybridization, Wash and Stain Kit, and the GeneChip® Fluidics Station 450.standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute was used for all the experiments

scan_protocol: The biotin labeled cDNA was hybridized to the array for 16 hours at 45°C using the GeneChip® Hybridization Oven 640. Washing and staining with streptavidin-phycoerythrin was performed using the GeneChip®Hybridization, Wash and Stain Kit, and the GeneChip® Fluidics Station 450.  Standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute  was used for all the experiments.

data_processing: Scanned Images were acquired using the GeneChip® Scanner 3000 7G and the GeneChip® Command Console® Software. Normalized and background-corrected, raw probe intensity values  were uploaded to Partek Genomics Suite ver 6.5 (PARTEK Inc, St. Louis, MO) for further analysis.

label_protocol: cRNA was obtained by an in vitro transcription reaction, and was then used as the template for generating 1st strand cDNA. The cDNA  was fragmented and end-labeled with biotin as suggested by the array manufacturer (affymetrix)

growth_protocol: PBMCs were isolated from the blood of healthy human donors by Histopaque®-1077 gradient centrifugation and MDM were isolated as per standard protocols

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen), and was converted to cDNA following the  GeneChip® WT Plus Reagent Kit protocol. Briefly, total RNA (300 ng) was used for 1st and 2nd strand cDNA synthesis.

treatment_protocol: MDMs were  treated with various concentrations of IFNε for 6 hours or 24 h. Un-treated cells were included as controls.

value: MDM

value: IFNa

tag: time


title: Endometrium exposed to embryo, Animal 3

source_name: Uterine horn, 6 days after insemination - Blastocysts confirmed

value: Endoemtrium


title: IFNa-treatment-24hours-2


title: wholebody_VEG_v_rep8

city: Saint-Pée sur Nivelle

first: Viviana

last: Lazzarotto

address: Quartier Ibarron

country: France

institute: INRA

description:
Gene expression after 3 weeks feeding
VEG_V_8

hyb_protocol: Cy3-labelled cRNA sample yields (> 0.825µg cRNA) and specific activity (> 6pmol of Cy3/µg of cRNA) were verified using a NanoDrop ND-1000: 600ng of Cy3-cRNA were fragmented and hybridized on a sub-array, following the LIQA kit instructions. The hybridization reactions were allowed to continue for 17 hours in a rotating hybridization oven (65°C), prior to washing according to the manufacturer’s instructions.

scan_protocol: Slides were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm – 20 bits).

data_processing:
Data were then obtained with the Agilent Feature Extraction software (10.7.1.1), according to the appropriate GE protocol (GE1_107_Sep09). Data were analysed using GeneSpring software (v. 12.6).
Data were scale-normalized using the median value of each array to identify differentially expressed genes between conditions

organism: Oncorhynchus mykiss

source_name: whole-body alevins_3 weeks feeding_VEG-V

label_protocol: Cy3-labelled experimental cRNA samples were generated using the Agilent “One-Color Microarray-based Gene Expression Analysis” (Low Input Quick Amp Labeling-LIQA) kit, according to manufacturer’s instructions. The method uses T7 RNA Polymerase Blend, which simultaneously amplifies target material and incorporates Cyanine 3-CTP (Cy3). For each sample 150ng of total RNA were used to generate fluorescent cRNA. Agilent Spike-In was included in each reaction. After the denaturation step (10 min in circulating bath at 65°C) and cRNA synthesis step (2hr at 40°C), the reactions were incubated at 70°C for 15 min to inactivate the AffinityScript enzyme. To perform the labelling reaction, cRNA samples were each mixed with 6µL of Transcription Master Mix cocktail, containing Cy3-dye, and then incubated at 40°C for two hours. Purification was performed using Quiagen RNeasy mini spin columns, eluting in 30uL of RNase-free water.

extract_protocol: Total RNA was extracted from whole body alevins collected before the first feeding and after three weeks of feeding using the TRIZOL reagent method.

tag: Stage

value: alevins

tag: broodstock group

value: VEG-fed broodstock

tag: time point

value: 3 weeks fed

tag: maternal diet

value: VEG

tag: experimental diet

value: VEG-V

value: whole body


title: IFNa-treatment-24hours-1


title: wholebody_VEG_v_rep7

description:
Gene expression after 3 weeks feeding
VEG_V_7


title: wholebody_VEG_v_rep5

description:
Gene expression after 3 weeks feeding
VEG_V_5


title: wholebody_VEG_v_rep3

description:
Gene expression after 3 weeks feeding
VEG_V_3


title: wholebody_VEG_v_rep2

description:
Gene expression after 3 weeks feeding
VEG_V_2


title: wholebody_VEG_v_rep6

description:
Gene expression after 3 weeks feeding
VEG_V_6


title: wholebody_VEG_v_rep1

description:
Gene expression after 3 weeks feeding
VEG_V_1


title: IFNe-treatment-24hours-4

value: IFNe


title: wholebody_VEG_v_rep4

description:
Gene expression after 3 weeks feeding
VEG_V_4


title: 10 leukocyte DNA from MMC patient

city: Leuven

first: Anne

last: Rochtus

state: Vlaams-Brabant

address: Herestraat 49, Box 911

department: Cardiovascular Sciences

country: Belgium

institute: University of Leuven

description: patient

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

data_processing: BeadStudio software

label: Cy3 and Cy5

source_name: MMC 10

label_protocol: Standard Illumina protocol

extract_protocol: Leukocyte DNA was extracted using standard protocols

value: myelomeningocele

tag: gender

value: M


title: IFNa-treatment-24hours-3


title: 3 leukocyte DNA from healthy control

description: control

source_name: Control 3

value: healthy


title: 5 leukocyte DNA from healthy control

description: control

source_name: Control 5

value: F


title: wholebody_VEG_c_rep8

description:
Gene expression after 3 weeks feeding
VEG_C_8

source_name: whole-body alevins_3 weeks feeding_VEG-C

value: VEG-C


title: 2 leukocyte DNA from healthy control

description: control

source_name: Control 2


title: 1 leukocyte DNA from healthy control

description: control

source_name: Control 1


title: 6 leukocyte DNA from healthy control

description: control

source_name: Control 6


title: 9 leukocyte DNA from MMC patient

description: patient

source_name: MMC 9


title: 6 leukocyte DNA from MMC patient

description: patient

source_name: MMC 6


title: 2 leukocyte DNA from MMC patient

description: patient

source_name: MMC 2


title: 7 leukocyte DNA from MMC patient

description: patient

source_name: MMC 7


title: IFNe-treatment-24hours-2


title: wholebody_VEG_c_rep6

description:
Gene expression after 3 weeks feeding
VEG_C_6


title: IFNa-treatment-6hours-3


title: IFNe-treatment-24hours-1


title: 4 leukocyte DNA from healthy control

description: control

source_name: Control 4


title: wholebody_VEG_c_rep5

description:
Gene expression after 3 weeks feeding
VEG_C_5


title: 8 leukocyte DNA from MMC patient

description: patient

source_name: MMC 8


title: IFNa-treatment-6hours-2


title: 5 leukocyte DNA from MMC patient

description: patient

source_name: MMC 5


title: wholebody_VEG_c_rep4

description:
Gene expression after 3 weeks feeding
VEG_C_4


title: wholebody_VEG_c_rep7

description:
Gene expression after 3 weeks feeding
VEG_C_7


title: 3 leukocyte DNA from MMC patient

description: patient

source_name: MMC 3


title: IFNe-treatment-24hours-3


title: wholebody_VEG_c_rep1

description:
Gene expression after 3 weeks feeding
VEG_C_1


title: wholebody_VEG_c_rep3

description:
Gene expression after 3 weeks feeding
VEG_C_3


title: IFNe-treatment-6hours-4


title: wholebody_VEG_m_rep8

description:
Gene expression after 3 weeks feeding
VEG_M_8

source_name: whole-body alevins_3 weeks feeding_VEG-M

value: VEG-M


title: wholebody_VEG_c_rep2

description:
Gene expression after 3 weeks feeding
VEG_C_2


title: 1 leukocyte DNA from MMC patient

description: patient

source_name: MMC 1


title: 4 leukocyte DNA from MMC patient

description: patient

source_name: MMC 4


title: IFNe-treatment-6hours-2


title: IFNa-treatment-6hours-1


title: IFNe-treatment-6hours-1


title: wholebody_VEG_m_rep6

description:
Gene expression after 3 weeks feeding
VEG_M_6


title: No treatment control-4

source_name: PBMC-no treatment

value: no treatment

value: control


title: No treatment control-3

value: MDM


title: wholebody_VEG_m_rep7

description:
Gene expression after 3 weeks feeding
VEG_M_7


title: wholebody_VEG_m_rep5

description:
Gene expression after 3 weeks feeding
VEG_M_5