title: Compound 33, 40 min rep2

city: Montreal

first: Andre

last: Nantel

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: Compound 33, 40 min

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was isolated from duplicate independent biological samples using the RNeasy mini kit (Qiagen). Briefly, frozen cells were thawed out in RNeasy buffer RLT at a ratio of 3:1 [vol/vol] buffer/pellet. Resuspended cells were divided into 1 ml aliquots in 2 ml screw cap microcentrifuge tubes containing 0.6 ml of 0.5 mm diameter acid-washed glass beads. Samples were homogenized 6 times, for 5 minutes each, in a BeadBeater set at maximum speed.

treatment_protocol: An overnight culture of C. albicans grown in YPD at 37˚C was diluted to 0.1 OD600 and grown at 37˚C to exponential phase (0.4–0.5 OD600).  After the incubation period, compounds were added at concentrations that caused a 50% reduction in CFU after a 3.5-hour incubation compared to DMSO (0.75 µg/ml for compound 13 and 3 µg/ml for compound 33).  Samples were collected at 0, 20, 40 and 60 minutes.  The cells were pelleted, supernatant was removed, and the cell pellet was flash frozen with liquid nitrogen.  Samples were stored at -80˚C until processed for RNA isolation.

value: compoUnd 33

tag: time

value: 40 min

source_name: Untreated cells, 60 min

value: Untreated

value: 60 min


title: sh control + TGFb, replicate 2

status: Public on May 01 2012

type: RNA

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

country: Spain

institute: IBMB

description: dissected out  from  embrionic cerebral cortex (E12.5). Cells are stably transfected with a random shRNA.

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 110%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

molecule: total RNA

organism: Mus musculus

source_name: sh control + TGFb

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

tag: cell type

value: neural stem cells

tag: knockdown

value: control

tag: treatment

value: TGFb

tag: age


title: Compound 33, 40 min rep1

state: QC

country: Canada

value: Compound 33


title: Compound 33, 60 min rep1

source_name: Compound 33, 60 min


title: Compound 33, 60 min rep2


title: Compound 33, 20 min rep2

source_name: Compound 33, 20 min

value: 20 min


title: T=0 control 33 rep2

source_name: Untreated cells, 0 min

value: 0 min


title: Compound 33, 20 min rep1


title: Compound 13, 60 min rep1

source_name: Compound 13, 60 min

value: Compound 13


title: T=0 control 13 rep1


title: T=0 control 13 rep2


title: Compound 13, 20 min rep2

source_name: Compound 13, 20 min

value: compoUnd 13


title: Compound 13, 40 min rep2

source_name: Compound 13, 40 min


title: Compound 13, 40 min rep1


title: T=0 control 33 rep1


title: Compound 13, 20 min rep1


title: OS223 REPLICATE 18

city: Arlington

first: Sealy

last: Hambright

state: TX

address: 701 S. Nedderman Dr.

department: Biology

country: USA

institute: UT Arlington

description: OS223 aRNA

hyb_protocol: Anti-sense RNA from strains OS223, OS195, OS185, and OS155 were used for the assay. Two different strains were simultaneously hybridized per slide in a competitive two-color scheme for each possible pairwise comparison excluding self. Each 60 µl hybridization reaction contained approximately 2 µg aRNA per strain, oppositely labeled with either Alexa-Flour 555 or Alexa-Flour 647 dyes. The aRNA solution was contained on the slide using 25 X 40 mm LifterSlips (Thermo Scientific, Waltham, MA). Slides were then statically incubated at 50⁰C for 18 hours in single-slide rubber hybridization chambers (CamLab, Cambridge, U.K.).

scan_protocol: Three biological replicates were used per strain comparison, allowing for 18 hybridizations to be performed, using a loop design format. In addition, dye swaps hybridizations were performed for all biological replicates for a total of 36 slide hybridizations. Slides were scanned at a 30-µm resolution using a Genepix 4200A scanner (Axon Instruments, Sunnyvale, CA).

data_processing: Overall expression was analyzed using the Genespring GX11 software (Agilent technologies, Santa Clara, CA), with foreground-background signal intensities imported separately per channel in a one color format. The data set including 36 slides, representing 72 samples, was normalized by applying a quantile algorithm, then Log2 transformed to a threshold of 1.0. Normalized signal intensities were filtered using an upper cutoff of 95% and lower cutoff of 10% per channel, keeping all entities falling within that range in at least half of the samples.

label: Alexa Flour-555

organism: Shewanella baltica OS223

source_name: OS223 aRNA

label_protocol: aRNA was synthesized using Ambions MessageAmp II kit. aRNA was indirectly labeled with Alexa Flour 555 and 647 dyes.

growth_protocol: Grown separately at 25C in defined media with glucose as sole C source. Grown to OD 0.400 (exponential phase) at 600nm for total RNA extraction.

extract_protocol: Total RNA was extracted using Ambions RiboPure bacterial RNA kit. mRNA was enriched using Ambions MICROBExpress kit.

treatment_protocol: All strains were treated exactly the same to assess baseline transcriptional variation.

tag: strain


title: OS223 REPLICATE 8

description: OS223 aRNA


title: OS223 REPLICATE 17

description: OS223 aRNA

label: Alexa Flour-647


title: Compound 13, 60 min rep2


title: OS223 REPLICATE 6

description: OS223 aRNA


title: OS223 REPLICATE 2

description: OS223 aRNA


title: OS223 REPLICATE 7

description: OS223 aRNA


title: OS223 REPLICATE 5

description: OS223 aRNA


title: OS223 REPLICATE 4

description: OS223 aRNA


title: OS223 REPLICATE 3

description: OS223 aRNA


title: OS223 REPLICATE 15

description: OS223 aRNA


title: OS223 REPLICATE 14

description: OS223 aRNA


title: OS223 REPLICATE 9

description: OS223 aRNA


title: OS223 REPLICATE 13

description: OS223 aRNA


title: OS223 REPLICATE 11

description: OS223 aRNA


title: OS223 REPLICATE 10

description: OS223 aRNA


title: OS223 REPLICATE 12

description: OS223 aRNA


title: OS223 REPLICATE 16

description: OS223 aRNA


title: OS195 REPLICATE 5

description: OS195 aRNA

organism: Shewanella baltica OS195

source_name: OS195 aRNA


title: OS195 REPLICATE 7

description: OS195 aRNA


title: OS195 REPLICATE 4

description: OS195 aRNA


title: OS195 REPLICATE 18

description: OS195 aRNA


title: OS223 REPLICATE 1

description: OS223 aRNA


title: OS195 REPLICATE 15

description: OS195 aRNA


title: OS185 REPLICATE 4

description: OS185 aRNA

organism: Shewanella baltica OS185

source_name: OS185 aRNA


title: OS195 REPLICATE 11

description: OS195 aRNA


title: OS195 REPLICATE 16

description: OS195 aRNA


title: OS195 REPLICATE 12

description: OS195 aRNA


title: OS195 REPLICATE 3

description: OS195 aRNA


title: OS185 REPLICATE 6

description: OS185 aRNA


title: OS195 REPLICATE 17

description: OS195 aRNA


title: OS195 REPLICATE 9

description: OS195 aRNA


title: OS195 REPLICATE 8

description: OS195 aRNA


title: OS185 REPLICATE 8

description: OS185 aRNA


title: OS185 REPLICATE 9

description: OS185 aRNA


title: OS195 REPLICATE 10

description: OS195 aRNA


title: OS195 REPLICATE 14

description: OS195 aRNA


title: OS195 REPLICATE 13

description: OS195 aRNA


title: OS185 REPLICATE 3

description: OS185 aRNA


title: OS185 REPLICATE 2

description: OS185 aRNA


title: OS195 REPLICATE 1

description: OS195 aRNA


title: OS195 REPLICATE 2

description: OS195 aRNA


title: OS185 REPLICATE 16

description: OS185 aRNA


title: OS185 REPLICATE 17

description: OS185 aRNA


title: OS195 REPLICATE 6

description: OS195 aRNA


title: OS185 REPLICATE 5

description: OS185 aRNA


title: OS185 REPLICATE 7

description: OS185 aRNA


title: OS185 REPLICATE 11

description: OS185 aRNA


title: OS155 REPLICATE 7

description: OS155 aRNA

organism: Shewanella baltica OS155

source_name: OS155 aRNA


title: OS155 REPLICATE 8

description: OS155 aRNA


title: OS155 REPLICATE 9

description: OS155 aRNA


title: OS185 REPLICATE 1

description: OS185 aRNA


title: OS185 REPLICATE 18

description: OS185 aRNA


title: OS155 REPLICATE 11

description: OS155 aRNA


title: OS185 REPLICATE 13

description: OS185 aRNA


title: OS155 REPLICATE 10

description: OS155 aRNA


title: OS155 REPLICATE 13

description: OS155 aRNA


title: OS155 REPLICATE 1

description: OS155 aRNA


title: OS155 REPLICATE 16

description: OS155 aRNA


title: OS185 REPLICATE 10

description: OS185 aRNA


title: OS155 REPLICATE 5

description: OS155 aRNA


title: OS155 REPLICATE 12

description: OS155 aRNA


title: OS185 REPLICATE 12

description: OS185 aRNA


title: OS185 REPLICATE 14

description: OS185 aRNA


title: OS155 REPLICATE 14

description: OS155 aRNA


title: OS155 REPLICATE 18

description: OS155 aRNA


title: OS185 REPLICATE 15

description: OS185 aRNA


title: OS155 REPLICATE 3

description: OS155 aRNA


title: OS155 REPLICATE 17

description: OS155 aRNA


title: OS155 REPLICATE 15

description: OS155 aRNA


title: OS155 REPLICATE 4

description: OS155 aRNA


title: OS155 REPLICATE 6

description: OS155 aRNA


title: OS155 REPLICATE 2

description: OS155 aRNA


title: WG0041985-DNA_H03_RM3863

type: genomic

city: Toronto

first: Ekaterina

last: Rogaeva

address: 6 Queen’s Park Crescent West

institute: Tanz Centre for Neurodegenerative Diseases

hyb_protocol: Samples were applied to beadchips and the loaded beadchips were incubated overnight in the Illumina Hybridization oven. Unhybridized and non-specifically hybridized DNA was washed away, and beadchips were prepared for staining and extension.

scan_protocol: The beadchips were scanned on the Illumina BeadArray Reader using default settings.

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: 750ng of DNA was denatured and neutralized before amplification. The denatured DNA was isothermally amplified in an overnight step, and the amplified product was them enzymatically fragmented (i.e. End-point fragmentation), precipitated with isopropanol, collected by centrifugation at 4 degrees celciums, and resuspended in hybridization buffer. C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled.

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.

tag: qc status

value: Passed QC

value: Blood

tag: disease status

value: Unaffected


title: WG0041985-DNA_H04_6982

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

value: Failed QC

value: Other phenotype


title: WG0041985-DNA_H05_3342


title: WG0041985-DNA_H02_RX1218


title: WG0041985-DNA_F04_NY0026

value: AD


title: WG0041985-DNA_C06_3578


title: WG0041985-DNA_H01_RM5850


title: WG0041985-DNA_E01_RM3552


title: WG0041985-DNA_E04_RM3843


title: WG0041985-DNA_D05_3332


title: WG0041985-DNA_G06_3656


title: WG0041985-DNA_E05_3333


title: WG0041985-DNA_D04_RM4270


title: WG0041985-DNA_D03_RM4225


title: WG0041985-DNA_E03_RM4228


title: WG0041985-DNA_G03_RM3754


title: WG0041985-DNA_G02_RX1244


title: WG0041985-DNA_F05_3336


title: WG0041985-DNA_D06_3579


title: WG0041985-DNA_G04_4626


title: WG0041985-DNA_F02_RX0849


title: WG0041985-DNA_E06_3580


title: WG0041985-DNA_F03_RM2208


title: WG0041985-DNA_D01_RM8073


title: WG0041985-DNA_G05_3338


title: WG0041985-DNA_G01_RX0750


title: WG0041985-DNA_D02_RM4261


title: WG0041985-DNA_E02_RM8129


title: WG0041985-DNA_F06_3581


title: WG0041985-DNA_F01_RX0715


title: WG0041985-DNA_C05_3331


title: WG0041985-DNA_B05_6985


title: WG0041985-DNA_C03_RM0147


title: WG0041985-DNA_C02_RM0129


title: WG0041985-DNA_B06_3381


title: WG0041984-DNA_H09_RX0745


title: WG0041985-DNA_B04_RM8333


title: WG0041985-DNA_B03_NY2227


title: WG0041984-DNA_H03_RX0462


title: WG0041985-DNA_A03_RM6668


title: WG0041985-DNA_A02_RX0842


title: WG0041984-DNA_H12_RX0821


title: WG0041985-DNA_A04_RM3615


title: WG0041985-DNA_C01_RM0115


title: WG0041984-DNA_H07_RX1196


title: WG0041984-DNA_H10_RX0961


title: WG0041985-DNA_A05_6984


title: WG0041984-DNA_H08_RM6316


title: WG0041984-DNA_H04_RM6272


title: WG0041985-DNA_C04_RX0341


title: WG0041984-DNA_G12_RX0436


title: WG0041985-DNA_B02_NY2161


title: WG0041984-DNA_H05_RX0495


title: WG0041984-DNA_H01_RM6358


title: WG0041985-DNA_A06_3443


title: WG0041984-DNA_H06_RX0450


title: WG0041984-DNA_G09_RM4013


title: WG0041984-DNA_H02_RM6100


title: WG0041984-DNA_G11_RM6453


title: WG0041984-DNA_G07_RX0580


title: WG0041984-DNA_G10_RX0951


title: WG0041984-DNA_G03_RX1212


title: WG0041984-DNA_G04_RX0938


title: WG0041984-DNA_F12_RX0444


title: WG0041984-DNA_F07_RX1179


title: WG0041984-DNA_G05_RM6021


title: WG0041984-DNA_G08_RM6391


title: WG0041984-DNA_F08_RM8334


title: WG0041984-DNA_E12_RX0332


title: WG0041984-DNA_F09_RX0879


title: WG0041984-DNA_F04_RX0463


title: WG0041984-DNA_F06_RM6520


title: WG0041984-DNA_G06_RM6127


title: WG0041984-DNA_F11_RM5706


title: WG0041984-DNA_E11_RX0448


title: WG0041984-DNA_E09_RX0531


title: WG0041984-DNA_F03_RX1007


title: WG0041984-DNA_F10_RM4058


title: WG0041984-DNA_F05_RX0464


title: WG0041984-DNA_G02_RM6734


title: WG0041984-DNA_F01_RX0848


title: WG0041984-DNA_E10_RX0524


title: WG0041984-DNA_F02_RX0460


title: WG0041984-DNA_E07_RX0986


title: WG0041984-DNA_E08_RX0720


title: WG0041984-DNA_E05_RX0846


title: WG0041984-DNA_E06_RX1240


title: WG0041984-DNA_E03_RM5492


title: WG0041984-DNA_E02_RM5351


title: WG0041984-DNA_D12_RX0873


title: WG0041984-DNA_D10_RM2104


title: WG0041984-DNA_E04_RM6240


title: WG0041984-DNA_D11_RM5607


title: WG0041984-DNA_D09_RM4200


title: WG0041984-DNA_D07_RX0978


title: WG0041984-DNA_E01_RM5413


title: WG0041984-DNA_D04_RX0277


title: WG0041984-DNA_D06_RX0885


title: WG0041984-DNA_D03_RX0790


title: WG0041984-DNA_C12_RM4306


title: WG0041984-DNA_D01_RM5379


title: WG0041984-DNA_D02_RM5603


title: WG0041984-DNA_C04_RX0469


title: WG0041984-DNA_C11_RX0733


title: WG0041984-DNA_D05_RX0575


title: WG0041984-DNA_C08_RM2189


title: WG0041984-DNA_C09_NY2332


title: WG0041984-DNA_C06_RM8199


title: WG0041984-DNA_C01_RX0572


title: WG0041984-DNA_C07_RM6540


title: WG0041984-DNA_C03_RX0697


title: WG0041984-DNA_B12_RM8149


title: WG0041984-DNA_C10_RM4112


title: WG0041984-DNA_D08_RX0507


title: WG0041984-DNA_B08_NY2331


title: WG0041984-DNA_B11_RM0082


title: WG0041984-DNA_C02_RX0244


title: WG0041984-DNA_B06_RX0509


title: WG0041984-DNA_B10_RM6569


title: WG0041984-DNA_A09_RX0528


title: WG0041984-DNA_A06_RX0242


title: WG0041984-DNA_B02_RX1015


title: WG0041984-DNA_B03_RM3743


title: WG0041984-DNA_A05_RX0429


title: WG0041984-DNA_B01_RX0261


title: WG0041984-DNA_A10_RM5467


title: WG0041984-DNA_A11_NY0607


title: WG0041984-DNA_A08_RX0982


title: WG0041983-DNA_H12_RX0709


title: WG0041983-DNA_H09_RX0900


title: WG0041984-DNA_B04_RX0440


title: WG0041984-DNA_A02_RX0282


title: WG0041984-DNA_A04_RM6132


title: WG0041983-DNA_H11_RM3731


title: WG0041983-DNA_H10_RM8120


title: WG0041984-DNA_C05_RM4303


title: WG0041983-DNA_H07_RX0362


title: WG0041983-DNA_H08_RX0425


title: WG0041984-DNA_A07_NY2231


title: WG0041983-DNA_H06_RM5643


title: WG0041984-DNA_B05_RX1160


title: WG0041983-DNA_H05_RM6235


title: WG0041983-DNA_H04_RM6017


title: WG0041984-DNA_A03_RX0483


title: WG0041983-DNA_H03_RM5383


title: WG0041984-DNA_B09_NY1383


title: WG0041983-DNA_H02_RM4280


title: WG0041983-DNA_H01_RX1077


title: WG0041983-DNA_G12_RX0301


title: WG0041983-DNA_G06_RX1217


title: WG0041983-DNA_G10_RM8026


title: WG0041984-DNA_B07_RM3663


title: WG0041983-DNA_G07_RX0808


title: WG0041983-DNA_G11_RM6375


title: WG0041983-DNA_G09_RX0290


title: WG0041983-DNA_G04_RM5390


title: WG0041983-DNA_G08_RM5592


title: WG0041983-DNA_G01_RM6534


title: WG0041983-DNA_F12_RM6408


title: WG0041983-DNA_F10_RM6630


title: WG0041983-DNA_F08_RX1010


title: WG0041983-DNA_F06_RM5780


title: WG0041983-DNA_F11_RX0489


title: WG0041983-DNA_F04_RX1129


title: WG0041983-DNA_E11_RM6503


title: WG0041983-DNA_G02_RM6636


title: WG0041983-DNA_F09_RX0479


title: WG0041983-DNA_F02_RM6002


title: WG0041983-DNA_F07_RM8249


title: WG0041983-DNA_F01_RM6254


title: WG0041983-DNA_E08_RM8034


title: WG0041983-DNA_G05_RM5395


title: WG0041983-DNA_E07_RM2090


title: WG0041983-DNA_E09_RX0539


title: WG0041983-DNA_E10_RM6573


title: WG0041983-DNA_G03_RM5068


title: WG0041983-DNA_E12_RM5989


title: WG0041983-DNA_F05_RM6725


title: WG0041983-DNA_E06_RM1620


title: WG0041983-DNA_F03_RX0711


title: WG0041983-DNA_E05_RX0291


title: WG0041983-DNA_E03_RM8167


title: WG0041983-DNA_E02_RX0721


title: WG0041983-DNA_E04_RX0447


title: WG0041983-DNA_D10_RM5714


title: WG0041983-DNA_E01_RM5839


title: WG0041983-DNA_D09_RX0823


title: WG0041983-DNA_D11_RX0746


title: WG0041983-DNA_D12_RX1048


title: WG0041983-DNA_D08_RX0228


title: WG0041983-DNA_D05_RM1989


title: WG0041983-DNA_C12_RM6498


title: WG0041983-DNA_D06_RM4153


title: WG0041983-DNA_D03_RX0348


title: WG0041983-DNA_C07_RX0983


title: WG0041983-DNA_D02_RM5355


title: WG0041983-DNA_D04_RM8106


title: WG0041983-DNA_C11_RX0457


title: WG0041983-DNA_C08_RM6374


title: WG0041983-DNA_D07_RM4146


title: WG0041983-DNA_C02_RM5596


title: WG0041983-DNA_C06_RX0274


title: WG0041983-DNA_C05_RM8354


title: WG0041983-DNA_B12_RX1125


title: WG0041983-DNA_C10_RX0736


title: WG0041983-DNA_C09_RX0832


title: WG0041983-DNA_C03_RM5308


title: WG0041983-DNA_B10_RX0742


title: WG0041983-DNA_B11_RX1014


title: WG0041983-DNA_C01_RX0734


title: WG0041983-DNA_B08_RX0441


title: WG0041983-DNA_C04_RM4251


title: WG0041983-DNA_B06_RM6144


title: WG0041983-DNA_D01_RM5282


title: WG0041983-DNA_B07_RX0424


title: WG0041983-DNA_B05_RX0280


title: WG0041983-DNA_B01_RX1166


title: WG0041983-DNA_B03_RX0506


title: WG0041983-DNA_B02_RM4117


title: WG0041983-DNA_B04_RM5614


title: WG0041983-DNA_B09_RX0230


title: WG0041983-DNA_A12_RM8086


title: WG0041983-DNA_A10_RM8275


title: WG0041983-DNA_A08_RM5553


title: WG0041983-DNA_A09_RX0485


title: WG0041983-DNA_A06_RX0466


title: WG0041916-DNA_H02_NY1628


title: WG0041983-DNA_A07_RM6117


title: WG0041983-DNA_A05_RX1057


title: WG0041916-DNA_H09_NY2122


title: WG0041983-DNA_A02_RM8014


title: WG0041983-DNA_A11_RM4169


title: WG0041916-DNA_H04_NY1704


title: WG0041916-DNA_H05_NY1870


title: WG0041916-DNA_H10_NY2235


title: WG0041916-DNA_H01_NY1602


title: WG0041916-DNA_H03_NY1652


title: WG0041983-DNA_A04_RM5574


title: WG0041983-DNA_A03_RX0724


title: WG0041916-DNA_G08_NY2080


title: WG0041916-DNA_G11_NY2306


title: WG0041916-DNA_G04_NY1794


title: WG0041916-DNA_G05_NY1854


title: WG0041916-DNA_H08_NY2088


title: WG0041916-DNA_G02_NY1632


title: WG0041916-DNA_F11_NY2294


title: WG0041916-DNA_G03_NY1647


title: WG0041916-DNA_G12_NY2402


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title: WG0041916-DNA_D05_NY1770


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title: WG0041916-DNA_C04_NY2083


title: WG0041916-DNA_C05_NY1810


title: WG0041916-DNA_B09_NY2092


title: WG0041916-DNA_C01_NY1592


title: WG0041916-DNA_B10_NY2134


title: WG0041916-DNA_C02_NY1614


title: WG0041916-DNA_B06_NY1873


title: WG0041916-DNA_B03_NY1631


title: WG0041916-DNA_B04_NY1684


title: WG0041916-DNA_B02_NY1613


title: WG0041916-DNA_B05_NY1728


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title: WG0041916-DNA_A10_NY2126


title: WG0041916-DNA_B01_NY1587


title: WG0041916-DNA_A04_NY1649


title: WG0041916-DNA_A03_NY2204


title: WG0041916-DNA_A05_NY1725


title: WG0041916-DNA_B08_NY2045


title: WG0041916-DNA_A02_NY1600


title: WG0041915-DNA_H11_NY1914


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title: WG0041916-DNA_A09_NY2086


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title: WG0041915-DNA_G12_NY1546


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value: Unknown


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title: WG0041911-DNA_E03_RM5086


title: WG0041911-DNA_D05_RM6512


title: WG0041911-DNA_D08_RM6536


title: WG0041911-DNA_C12_RM0623


title: WG0041911-DNA_D06_RM6582


title: WG0041911-DNA_C10_RM6475


title: WG0041911-DNA_C08_RM6489


title: WG0041911-DNA_D02_RM6491


title: WG0041911-DNA_C07_RX0478


title: WG0041911-DNA_F06_RM5972


title: WG0041911-DNA_C06_RM6332


title: WG0041911-DNA_C05_RM6264


title: WG0041911-DNA_D04_RM6455


title: WG0041911-DNA_D03_RM6440


title: WG0041911-DNA_C04_RM6428


title: WG0041911-DNA_B11_RM6353


title: WG0041911-DNA_C11_RM6588


title: WG0041911-DNA_C01_RM6183


title: WG0041911-DNA_C09_RM6404


title: WG0041911-DNA_D12_RM6082


title: WG0041911-DNA_C03_RM6259


title: WG0041911-DNA_C02_RM6237


title: WG0041911-DNA_B06_RM6303


title: WG0041911-DNA_B08_RM6308


title: WG0041911-DNA_B10_RM6326


title: WG0041911-DNA_B09_RM6443


title: WG0041911-DNA_D07_RM6486


title: WG0041911-DNA_B04_RX0423


title: WG0041911-DNA_B07_RM3584


title: WG0041911-DNA_B12_RM6722


title: WG0041911-DNA_D01_RM6449


title: WG0041911-DNA_B05_RM3658


title: WG0041911-DNA_B02_RM6614


title: WG0041911-DNA_B03_RX0259


title: WG0041911-DNA_A06_RM5867


title: WG0041911-DNA_A11_RM6275


title: WG0041911-DNA_A10_RM5679


title: WG0041911-DNA_B01_RX0380


title: WG0041911-DNA_A04_RM6141


title: WG0041911-DNA_A02_RM6151


title: WG0041911-DNA_A05_RM6173


title: WG0041911-DNA_A07_RM6310


title: WG0041910-DNA_H12_RM4299


title: WG0041910-DNA_H11_RM5940


title: WG0041910-DNA_H09_RM6092


title: WG0041911-DNA_A08_RM6346


title: WG0041910-DNA_H10_RM6136


title: WG0041910-DNA_H07_RM6048


title: WG0041910-DNA_H06_RM6161


title: WG0041911-DNA_A09_RM5906


title: WG0041911-DNA_A03_RM6160


title: WG0041910-DNA_H08_RM6047


title: WG0041910-DNA_H02_RM6036


title: WG0041910-DNA_H04_RM6873


title: WG0041910-DNA_H05_RM5844


title: WG0041910-DNA_H01_RM6045


title: WG0041910-DNA_G12_RM6029


title: WG0041910-DNA_G09_RM5898


title: WG0041910-DNA_H03_RM5799


title: WG0041910-DNA_G10_RM5732


title: WG0041910-DNA_G08_RM5580


title: 3D7_76

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

hyb_protocol: Used NimbleGen's standard CGH hybridization protocol (http://www.nimblegen.com/products/lit/lit.html) with the following modification: used 1x Denhardt's Solution in place of sample tracking control

scan_protocol: Arrays were scanned at 2um on a NimbleGen MS200 scanner with autogain per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)

data_processing: Arrays were processed using NimbleScan v2.5 per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html). The .bases files were created from scanned images using NimbleGen’s NimbleScan software (Analysis -> Reports -> Sequencing Bases ). These files contain the same information as NimbleGen .pair files but the probes have been collated by SNP locus. Due to this enhanced organization and readability, we use the .bases file instead of the .pair file as our raw data. We do not attempt to normalize between samples or across an entire image within one sample and directly use these intensity values in our secondary analysis, so no processed data is provided.

organism: Plasmodium falciparum

source_name: 3D7 DNA

label_protocol: Used NimbleGen's standard labeling protocol (http://www.nimblegen.com/products/lit/lit.html) with the following modification: used a custom 65% AT random nonamer mix from TriLink Biotechnologies

extract_protocol: Phenol-chloroform extraction (Moll et al. 2008. Methods in Malaria Research. MR4/ATCC.)


title: WG0041910-DNA_G11_RM6075


title: WG0041910-DNA_G06_RM5859


title: WG0041910-DNA_G05_RM5984


title: WG0041910-DNA_G04_RM5863


title: 3D7_75


title: 3D7_74


title: WG0041910-DNA_G02_RM5816


title: WG0041910-DNA_G07_RM5303


title: 3D7_73


title: WG0041910-DNA_F11_RM5399


title: WG0041910-DNA_F10_RM8015


title: 3D7_72


title: 3D7_71


title: WG0041910-DNA_F09_RX1088


title: 3D7_70


title: WG0041910-DNA_G03_RM5744


title: 3D7_68


title: 3D7_69


title: 3D7_67


title: WG0041910-DNA_E11_RM4061


title: WG0041910-DNA_F08_RM4049


title: WG0041910-DNA_F04_RM4235


title: WG0041910-DNA_F12_RM5593


title: 3D7_66


title: 3D7_65


title: WG0041910-DNA_F06_RM8388


title: WG0041910-DNA_F07_RM1992


title: 3D7_64


title: WG0041910-DNA_F02_RM3819


title: WG0041910-DNA_E08_RX0262


title: WG0041910-DNA_E09_RM4141


title: 3D7_63


title: 3D7_62


title: 3D7_61


title: 3D7_60


title: WG0041910-DNA_F05_RM2133


title: WG0041910-DNA_E12_RX1094


title: 3D7_59


title: WG0041910-DNA_F03_RM4101


title: 3D7_57


title: 3D7_58


title: 3D7_56


title: WG0041910-DNA_E05_RM4092


title: 3D7_55


title: WG0041910-DNA_E02_RM3722


title: WG0041910-DNA_E07_RM4060


title: 3D7_54


title: 3D7_53


title: WG0041910-DNA_D12_RM3503


title: WG0041910-DNA_G01_RM5674


title: WG0041910-DNA_E04_RM4248


title: WG0041910-DNA_D10_RX0319


title: WG0041910-DNA_E06_RM8121


title: 3D7_51


title: 3D7_52


title: WG0041910-DNA_D07_RM1833


title: WG0041910-DNA_D08_RM4266


title: WG0041910-DNA_E01_RM3827


title: WG0041910-DNA_D09_RM3872


title: WG0041910-DNA_E03_RM4319


title: 3D7_50


title: 3D7_47


title: WG0041910-DNA_D06_RM3760


title: 3D7_46


title: 3D7_48


title: 3D7_45


title: 3D7_49


title: 3D7_44


title: WG0041910-DNA_D05_RM8216


title: 3D7_42


title: WG0041910-DNA_D03_RM4236


title: WG0041910-DNA_D04_RX1023


title: 3D7_43


title: 3D7_41


title: WG0041910-DNA_D02_RM2183


title: 3D7_40


title: WG0041910-DNA_D01_RM3534


title: WG0041910-DNA_C11_RM3510


title: 3D7_38


title: 3D7_37


title: 3D7_39


title: WG0041910-DNA_C07_RM4074


title: 3D7_36


title: WG0041910-DNA_C09_RM3796


title: WG0041910-DNA_C10_RM3816


title: 3D7_35


title: 3D7_34


title: WG0041910-DNA_C12_RM8277


title: WG0041910-DNA_C06_RM4213


title: WG0041910-DNA_C05_RM3823


title: 3D7_32


title: 3D7_31


title: WG0041910-DNA_C04_RM1504


title: 3D7_30


title: WG0041910-DNA_C08_RM3642


title: 3D7_29


title: 3D7_33


title: 3D7_28


title: WG0041910-DNA_C03_RM3898


title: WG0041910-DNA_B09_RM1462


title: 3D7_27


title: WG0041910-DNA_C02_RM3790


title: 3D7_26


title: WG0041910-DNA_B12_RX0248


title: WG0041910-DNA_B11_RM1472


title: WG0041910-DNA_B10_RM4067


title: WG0041910-DNA_B04_RM8098


title: WG0041910-DNA_B07_RM4063


title: WG0041910-DNA_D11_RM2148


title: 3D7_24


title: 3D7_25


title: 3D7_21


title: 3D7_22


title: WG0041910-DNA_B03_RM1427


title: WG0041910-DNA_B05_RM4036


title: 3D7_20


title: 3D7_19


title: WG0041910-DNA_A07_RX1101


title: 3D7_18


title: 3D7_17


title: 3D7_23


title: WG0041910-DNA_A09_RM4166


title: WG0041910-DNA_A10_RX0347


title: WG0041910-DNA_B06_RM4162


title: 3D7_15


title: 3D7_14


title: WG0041910-DNA_A03_RM5124


title: 3D7_16


title: WG0041910-DNA_A02_RX0763


title: WG0041910-DNA_A08_RM3802


title: WG0041910-DNA_A05_RM3861


title: 3D7_13


title: WG0041910-DNA_B01_RM4173


title: 3D7_12


title: 3D7_11


title: 3D7_10


title: WG0041910-DNA_C01_RM3572


title: WG0041910-DNA_B08_RM3897


title: 3D7_9


title: 3D7_8


title: WG0041909-DNA_H10_RM3845


title: 3D7_7


title: WG0041909-DNA_H11_RM3882


title: 3D7_5


title: WG0041909-DNA_H09_RM6319


title: WG0041910-DNA_B02_RX0312


title: WG0041909-DNA_H08_RM4269


title: 3D7_6


title: 3D7_3


title: WG0041910-DNA_A11_RX0843


title: WG0041909-DNA_H06_RM4129


title: 3D7_4


title: WG0041909-DNA_H05_RM4000


title: Thailand M1321

source_name: Thailand M1321 DNA

value: Thailand M1321


title: WG0041909-DNA_H07_RM3764


title: WG0041909-DNA_H03_RM0573


title: 3D7_1


title: Thailand M1320

source_name: Thailand M1320 DNA

value: Thailand M1320


title: WG0041910-DNA_A06_RM1335


title: 3D7_2


title: Thailand M1319

source_name: Thailand M1319 DNA

value: Thailand M1319


title: Thailand M1317

source_name: Thailand M1317 DNA

value: Thailand M1317


title: WG0041909-DNA_H02_RM3763


title: WG0041910-DNA_A04_RM8052


title: WG0041909-DNA_G12_RM8270


title: Thailand M1316

source_name: Thailand M1316 DNA

value: Thailand M1316


title: Thailand M1256

source_name: Thailand M1256 DNA

value: Thailand M1256


title: Thailand M1255

source_name: Thailand M1255 DNA

value: Thailand M1255


title: WG0041909-DNA_H04_RM0588


title: Thailand M1242

source_name: Thailand M1242 DNA

value: Thailand M1242


title: WG0041909-DNA_H12_RX0474


title: Thailand M1237

source_name: Thailand M1237 DNA

value: Thailand M1237


title: WG0041909-DNA_H01_RM1175


title: Thailand M1236

source_name: Thailand M1236 DNA

value: Thailand M1236


title: WG0041909-DNA_G09_RM8116


title: WG0041909-DNA_G10_RM8131


title: Thailand M1231

source_name: Thailand M1231 DNA

value: Thailand M1231


title: WG0041909-DNA_G11_RM8214

value: Passed QC

value: Blood


title: Thailand M1226

source_name: Thailand M1226 DNA

value: Thailand M1226


title: WG0041909-DNA_G03_RM6623

value: Unaffected


title: Thailand M1218

source_name: Thailand M1218 DNA

value: Thailand M1218


title: WG0041909-DNA_G06_RM6712


title: WG0041909-DNA_G08_RM8278


title: WG0041909-DNA_G07_RM6871

value: Failed QC

value: AD


title: Thailand M1217

source_name: Thailand M1217 DNA

value: Thailand M1217


title: Thailand M1199

source_name: Thailand M1199 DNA

value: Thailand M1199


title: WG0041909-DNA_G04_RX1050

source_name: Blood


title: WG0041909-DNA_G02_RX0501


title: Thailand M1197

source_name: Thailand M1197 DNA

value: Thailand M1197


title: Thailand M1196

source_name: Thailand M1196 DNA

value: Thailand M1196


title: Thailand M1188

source_name: Thailand M1188 DNA

value: Thailand M1188


title: Thailand M1186

source_name: Thailand M1186 DNA

value: Thailand M1186


title: Thailand M1176

source_name: Thailand M1176 DNA

value: Thailand M1176


title: Thailand M1163

source_name: Thailand M1163 DNA

value: Thailand M1163


title: Thailand M1161

source_name: Thailand M1161 DNA

value: Thailand M1161


title: WG0041909-DNA_F11_RM6080


title: WG0041909-DNA_F10_RM6598


title: WG0041909-DNA_F12_RM0527


title: Thailand M1126

source_name: Thailand M1126 DNA

value: Thailand M1126


title: Thailand M1125

source_name: Thailand M1125 DNA

value: Thailand M1125


title: Thailand M1111

source_name: Thailand M1111 DNA

value: Thailabd M1111


title: WG0041909-DNA_F08_RM5947

value: Blood


title: WG0041909-DNA_F07_RM6014

value: Passed QC


title: Thailand M1094

source_name: Thailand M1094 DNA

value: Thailand M1094


title: WG0041909-DNA_F03_RM8288

value: Failed QC

value: Unaffected


title: Thailand M1069

source_name: Thailand M1069 DNA

value: Thailand M1069


title: WG0041909-DNA_F01_RM4159

value: AD


title: Thailand M1064

source_name: Thailand M1064 DNA

value: Thailand M1064


title: WG0041909-DNA_G01_RM8159


title: WG0041909-DNA_F04_RM0414


title: WG0041909-DNA_F09_RM5864


title: Thailand M1050

source_name: Thailand M1050 DNA

value: Thailand M1050


title: WG0041909-DNA_F06_RM5190


title: WG0041909-DNA_G05_RM8290


title: WG0041909-DNA_F02_RM3851

value: Unknown


title: WG0041909-DNA_F05_RX0819


title: Thailand M978

source_name: Thailand M978 DNA

value: Thailand M978


title: Thailand M965

source_name: Thailand M965 DNA

value: Thailand M965


title: Thailand M935

source_name: Thailand M935 DNA

value: Thailand M935


title: WG0041909-DNA_E11_RM8082

source_name: Blood


title: Thailand M934

source_name: Thailand M934 DNA

value: Thailand M934


title: WG0041909-DNA_E12_RM3617


title: Thailand M928

source_name: Thailand M928 DNA

value: Thailand M928


title: Laos BMT592

source_name: Laos BMT592 DNA

value: Laos BMT592


title: WG0041909-DNA_E05_RM6595


title: WG0041909-DNA_E04_RM5960


title: WG0041909-DNA_E09_RM3837


title: Laos BMT579

source_name: Laos BMT579 DNA

value: Laos BMT579


title: WG0041909-DNA_E07_RM5505

value: Blood


title: Laos BMT559

source_name: Laos BMT559 DNA

value: Laos BMT559


title: Laos BMT552

source_name: Laos BMT552 DNA

value: Laos BMT552


title: WG0041909-DNA_E02_RM6042

value: Failed QC


title: Laos BMT553

source_name: Laos BMT553 DNA

value: Laos BMT553


title: WG0041909-DNA_D09_RM6405

value: Passed QC

value: Unaffected


title: Laos BMT549

source_name: Laos BMT549 DNA

value: Laos BMT549


title: WG0041909-DNA_D12_RM5446


title: Laos BMT545

source_name: Laos BMT545 DNA

value: Laos BMT545


title: Laos BMT544

source_name: Laos BMT544 DNA

value: Laos BMT544


title: WG0041909-DNA_E01_RM5761

value: AD


title: WG0041909-DNA_E10_RM8054


title: WG0041909-DNA_D11_RM5251


title: Laos BMT510

source_name: Laos BMT510 DNA

value: Laos BMT510


title: WG0041909-DNA_D10_RM5045


title: Laos BMT509

source_name: Laos BMT509 DNA

value: Laos BMT509


title: Laos BMT587

source_name: Laos BMT587 DNA

value: Laos BMT587


title: WG0041909-DNA_D08_RM5325


title: WG0041909-DNA_E06_RM6085


title: Laos BMT487

source_name: Laos BMT487 DNA

value: Laos BMT487


title: Laos BMT476

source_name: Laos BMT476 DNA

value: Laos BMT476


title: WG0041909-DNA_E03_RM5299


title: Laos BMT474

source_name: Laos BMT474 DNA

value: Laos BMT474


title: WG0041909-DNA_D07_RX0526

source_name: Blood

value: Blood


title: Laos BMT491

source_name: Laos BMT491 DNA

value: Laos BMT491


title: Laos BMT461

source_name: Laos BMT461 DNA

value: Laos BMT461


title: WG0041909-DNA_D06_RM6513


title: Laos BMT455

source_name: Laos BMT455 DNA

value: Laos BMT455


title: Laos BMT452

source_name: Laos BMT452 DNA

value: Laos BMT452


title: WG0041909-DNA_D05_RM5701

value: Failed QC


title: Laos BMT444

source_name: Laos BMT444 DNA

value: Laos BMT444


title: WG0041909-DNA_C11_RM5858

value: Passed QC

value: Unaffected


title: Laos BMT126

source_name: Laos BMT126 DNA

value: Laos BMT126


title: WG0041909-DNA_D04_RM5617

value: AD


title: Laos BMT122

source_name: Laos BMT122 DNA

value: Laos BMT122


title: WG0041909-DNA_D02_RM6067


title: Laos BMT076

source_name: Laos BMT076 DNA

value: Laos BMT076


title: WG0041909-DNA_C06_RM6732


title: WG0041909-DNA_D03_RM5426


title: WG0041909-DNA_C09_RM6044


title: Laos BMT068

source_name: Laos BMT068 DNA

value: Laos BMT068


title: Laos BMT063

source_name: Laos BMT063 DNA

value: Laos BMT063


title: WG0041909-DNA_C12_RM5657


title: WG0041909-DNA_C10_RM6488


title: Laos BMT058

source_name: Laos BMT058 DNA

value: Laos BMT058


title: WG0041909-DNA_D01_RM5005


title: WG0041909-DNA_C03_RM5326


title: Laos BMT055

source_name: Laos BMT055 DNA

value: Laos BMT055


title: WG0041909-DNA_E08_RM3714

value: Blood


title: Cambodia CAM31

source_name: Cambodia CAM31 DNA

value: Cambodia CAM31


title: WG0041909-DNA_C05_RM5041


title: Cambodia CAM30

source_name: Cambodia CAM30 DNA

value: Cambodia CAM30


title: Cambodia CAM32

source_name: Cambodia CAM32 DNA

value: Cambodia CAM32


title: WG0041909-DNA_C07_RM5588


title: WG0041909-DNA_C02_RM5442


title: Cambodia CAM29

source_name: Cambodia CAM29 DNA

value: Cambodia CAM29


title: Cambodia CAM27

source_name: Cambodia CAM27 DNA

value: Cambodia CAM27


title: WG0041909-DNA_B12_RM6033

source_name: Blood

value: Failed QC


title: Cambodia CAM26

source_name: Cambodia CAM26 DNA

value: Cambodia CAM26


title: WG0041909-DNA_B09_RM5131


title: WG0041909-DNA_C01_RM5066

value: Passed QC


title: Cambodia CAM25

source_name: Cambodia CAM25 DNA

value: Cambodia CAM25


title: Laos BMT060

source_name: Laos BMT060 DNA

value: Laos BMT060


title: Cambodia CAM24

source_name: Cambodia CAM24 DNA

value: Cambodia CAM24


title: WG0041909-DNA_B10_RM6565

value: Unaffected


title: Cambodia CAM23

source_name: Cambodia CAM23 DNA

value: Cambodia CAM23


title: Cambodia CAM22

source_name: Cambodia CAM22 DNA

value: Cambodia CAM22


title: WG0041909-DNA_B06_RX0635


title: Cambodia CAM21

source_name: Cambodia CAM21 DNA

value: Cambodia CAM21


title: WG0041909-DNA_B03_RM6243


title: Cambodia CAM20

source_name: Cambodia CAM20 DNA

value: Cambodia CAM20


title: WG0041909-DNA_B04_RM5493

value: Blood

value: AD


title: Cambodia CAM19

source_name: Cambodia CAM19 DNA

value: Cambodia CAM19


title: WG0041909-DNA_B08_RM5099


title: Cambodia CAM18

source_name: Cambodia CAM18 DNA

value: Cambodia CAM18


title: WG0041909-DNA_B02_RM5416


title: Cambodia CAM16

source_name: Cambodia CAM16 DNA

value: Cambodia CAM16


title: WG0041909-DNA_A09_RM5635


title: WG0041909-DNA_B01_RM6784


title: Cambodia CAM15

source_name: Cambodia CAM15 DNA

value: Cambodia CAM15


title: WG0041909-DNA_B05_RM6745


title: WG0041909-DNA_A11_RM6370

value: Failed QC


title: Cambodia CAM14

source_name: Cambodia CAM14 DNA

value: Cambodia CAM14


title: WG0041909-DNA_B07_RM5368

value: Passed QC


title: WG0041909-DNA_A08_RM5757


title: Cambodia CAM13

source_name: Cambodia CAM13 DNA

value: Cambodia CAM13


title: Cambodia CAM12

source_name: Cambodia CAM12 DNA

value: Cambodia CAM12


title: Cambodia CAM11

source_name: Cambodia CAM11 DNA

value: Cambodia CAM11


title: Rana sierrae-Liver- infected-late-rep3

city: Berkeley

first: Thomas

last: Poorten

state: CA

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

description:
Sample name: 15, L, I, 2, Liver
Raw data file: 426764A12_liver_pmt900_635.xys

hyb_protocol: An 18-hour hybridization was conducted at 42 degrees in a Nimblegen Hybridization System 4 chamber (NimbleGen, Madison, WI)

scan_protocol: The chips were scanned on an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) using GenePix Pro v6.1 software (Molecular Devices, Sunnyvale, CA). For scanning, the PMT gain was adjusted for optimal saturation. The final PMT gain used was 750 for the spleen chip, 750 for the 2 skin chips, and 900 for the 2 liver chips.

data_processing: Each tissue type (skin, liver, and spleen) was analyzed separately.  Using the R package oligo, each array was background corrected and normalized using the quantile normalization procedure. Each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure [33-35]. The median polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed.

organism: Rana sierrae

source_name: Rana sierrae-Liver- infected-late

label_protocol: cDNAs were fluorescently labeled with Cy5 from TRILink BioTechnologies (TRILink BioTechnologies, San Diego, CA) using the standard Nimblegen Gene Expression Analysis v3.2 protocol

growth_protocol: Experimental animals were reared in the lab from wild-caught egg masses, so development and metamorphosis occurred in lab conditions without exposure to Bd.  Prior to the experiment the frogs were housed communally, but for the experiement they were each kept in individual tanks.  The frogs were kept in a room maintained at 18 degrees C with 12:12 light:dark photoperiod.  The frogs were fed crickets twice per week ad libitum with a water change.

extract_protocol: Total RNA was extracted using a routine Trizol/Chloroform protocol.

treatment_protocol: For each species, half of the experimental frogs (chosen by coin toss) were designated as controls and half were inoculated with Bd. Bd inoculum was prepared by growing Sierra-Nevada Bd on 1% agar, 1% tryptone plates for 2 weeks. The Bd isolate used was maintained in the lab for approximately one year (~four passages) prior to the experiment. Chytrid plates were flooded with water and agitated for zoospore release. Frogs in the exposed group were held overnight (~12 hours) in a 100mL water-bath inoculation with >106 zoospores per treatment. Exposures were repeated for three days. Frogs in the control group were handled identically but received only sham inoculations (no Bd exposure).

value: late

tag: tissue

value: Liver

value: infected

tag: population source

value: ebbets


title: Cambodia CAM9

source_name: Cambodia CAM9 DNA

value: Cambodia CAM9


title: Rana muscosa-Liver- control-early-rep3

description:
Sample name: 5, E, C, 1, Liver
Raw data file: 426764A11_liver_pmt900_635.xys

organism: Rana muscosa

source_name: Rana muscosa-Liver- control-early

value: early

value: control


title: Cambodia CAM10

source_name: Cambodia CAM10 DNA

value: Cambodia CAM10


title: WG0041909-DNA_A03_RM0708

source_name: Blood

value: Blood

value: Unaffected


title: WG0041909-DNA_A04_RM5105

value: AD


title: Cambodia CAM7

source_name: Cambodia CAM7 DNA

value: Cambodia CAM7


title: WG0041909-DNA_A06_RM6345


title: Cambodia CAM8

source_name: Cambodia CAM8 DNA

value: Cambodia CAM8


title: WG0041909-DNA_A07_RM5583

value: Passed QC


title: WG0041909-DNA_C04_RM6389

value: Failed QC


title: WG0041908-DNA_H10_RM6049


title: Rana muscosa-Liver- infected-late-rep3

description:
Sample name: 20, L, I, 1, Liver
Raw data file: 426764A10_liver_pmt900_635.xys

source_name: Rana muscosa-Liver- infected-late


title: Cambodia CAM6

source_name: Cambodia CAM6 DNA

value: Cambodia CAM6


title: Cambodia CAM5

source_name: Cambodia CAM5 DNA

value: Cambodia CAM5


title: WG0041909-DNA_A02_RM6197


title: Cambodia CAM3

source_name: Cambodia CAM3 DNA

value: Cambodia CAM3


title: WG0041908-DNA_H11_RM5037


title: Rana muscosa-Liver- infected-early-rep3

description:
Sample name: 11, E, I, 1, Liver
Raw data file: 426764A08_liver_pmt900_635.xys

source_name: Rana muscosa-Liver- infected-early

value: Liver


title: WG0041909-DNA_A05_RM6716


title: Rana sierrae-Liver- control-late-rep3

description:
Sample name: 23, L, C, 2, Liver
Raw data file: 426764A09_liver_pmt900_635.xys

source_name: Rana sierrae-Liver- control-late

value: late


title: Cambodia CAM2

source_name: Cambodia CAM2 DNA

value: Cambodia CAM2


title: Rana muscosa-Liver- control-early-rep2

description:
Sample name: 6, E, C, 1, Liver
Raw data file: 426764A07_liver_pmt900_635.xys


title: WG0041908-DNA_H12_RM5273


title: WG0041909-DNA_A10_RM5638


title: P29-BPD-2, miRNA

city: Rochester

first: Jie

last: Dong

state: MN

address: 200 1st SW

department: Thoracic Surgery

institute: Mayo Clinic

description:
Real-time PCR.
microRNA expression from BPD lung at postnatal day 29.

hyb_protocol: Not applicable.

scan_protocol: Quantitative 384-well TaqMan Low Density Array real-time PCR was run on the ABI PRISM 7900 System using the TaqMan Universal PCR Master Mix.

data_processing: Raw miRNA array data was analyzed using RQ manager software on the ABI system. All undetectable data and the data with CT values greater than 35 were treated as 35. Normalized CT was calculated by comparing each miRNA value to that of small nuclear U6 RNA. The U6 RNA is a common internal control for each microRNA array card. The copy number of miRNAs in each cell (assuming each cell contains 30 pg of total RNA) was calculated from a formula 10(40-CT)/ 3.34/22 that was estimated using synthetic lin-4 miRNA.

label: FAM

source_name: lung, P29, BPD

label_protocol: miRNA was Reverse Transcribed to cDNA using the Megaplex TM RT Rodent Primers Pool and the TaqMan MicroRNA Reverse Transcription Kit.

growth_protocol: Time-pregnant mice were maintained on an ad libitium diet of standard chow and water. Within 12 hr of birth, pups were pooled and then randomized into four experimental groups: mice would be exposed to either hyperoxic (80%) or room air conditions for either 14 or 29 days. Nursing dams were rotated between exposure groups every 24 hours to prevent oxygen toxicity in the dams and mitigate maternal effects between the experimental groups.

extract_protocol: The mirVana miRNA Isolation Kit (Ambion) was used for miRNA isolation according to manufacturer's instructions.

treatment_protocol: Lungs were isolated by manual dissection with the aid of a dissecting microscope where necessary. Lungs were washed twice with PBS before total RNA extraction.

value: ICR

value: lung

value: postnatal day 29

value: hyperoxia

tag: disease state


title: Rana sierrae-Liver- control-late-rep2

description:
Sample name: 24, L, C, 2, Liver
Raw data file: 426764A06_liver_pmt900_635.xys

value: control

value: ebbets


title: WG0041908-DNA_H08_RM6552

value: Blood

value: Unaffected


title: P29-BPD-1, miRNA


title: P29-WT-2, miRNA

description:
Real-time PCR.
microRNA expression from WT lung at postnatal day 29.

source_name: lung, P29, WT

value: room air

value: normal


title: Rana sierrae-Liver- infected-early-rep3

description:
Sample name: 8, E, I, 2, Liver
Raw data file: 426764A05_liver_pmt900_635.xys

source_name: Rana sierrae-Liver- infected-early

value: early

value: infected


title: WG0041908-DNA_H07_RM6767

value: Passed QC


title: WG0041908-DNA_H04_RM6068

value: Failed QC

value: AD


title: WG0041908-DNA_H06_RM5354


title: Cambodia CAM1

source_name: Cambodia CAM1 DNA

value: Cambodia CAM1


title: WG0041908-DNA_H02_RM5600


title: P14-BPD-2, miRNA

description:
Real-time PCR.
microRNA expression from BPD lung at postnatal day 14.

source_name: lung, P14, BPD

value: postnatal day 14


title: Rana muscosa-Liver- infected-late-rep2

description:
Sample name: 18, L, I, 1, Liver
Raw data file: 426764A04_liver_pmt900_635.xys

value: late

value: Liver


title: P29-BPD-3, miRNA

value: ICR

value: lung

value: postnatal day 29


title: WG0041908-DNA_H09_RM1759


title: WG0041908-DNA_H03_RX1146


title: P14-BPD-3, miRNA

value: hyperoxia


title: P29-WT-1, miRNA


title: P14-BPD-1, miRNA


title: WG0041908-DNA_G10_RX0893

value: Blood


title: WG0041908-DNA_H01_RX0486

value: Unaffected


title: P14-WT-2, miRNA

description:
Real-time PCR.
microRNA expression from WT lung at postnatal day 14.

source_name: lung, P14, WT

value: room air


title: P14-WT-1, miRNA

value: normal


title: WG0041908-DNA_G09_RX0845


title: Rana sierrae-Liver- control-early-rep3

description:
Sample name: 1, E, C, 2, Liver
Raw data file: 426764A03_liver_pmt900_635.xys

source_name: Rana sierrae-Liver- control-early

value: early

value: control

value: ebbets


title: Rana muscosa-Liver- control-early-rep1

description:
Sample name: 4, E, C, 1, Liver
Raw data file: 426547A11_liver_pmt900_635.xys

source_name: Rana muscosa-Liver- control-early


title: Rana muscosa-Liver- control-late-rep3

description:
Sample name: 28, L, C, 1, Liver
Raw data file: 426764A02_liver_pmt900_635.xys

source_name: Rana muscosa-Liver- control-late


title: Rana muscosa-Liver- infected-early-rep2

description:
Sample name: 12, E, I, 1, Liver
Raw data file: 426764A01_liver_pmt900_635.xys

value: infected


title: WG0041908-DNA_G11_RM5531

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

source_name: Blood

value: Passed QC


title: WG0041908-DNA_H05_RX0477


title: WG0041908-DNA_G12_RX1108

value: AD


title: Rana sierrae-Liver- infected-early-rep2

description:
Sample name: 7, E, I, 2, Liver
Raw data file: 426547A12_liver_pmt900_635.xys


title: Rana muscosa-Liver- control-late-rep2

description:
Sample name: 26, L, C, 1, Liver
Raw data file: 426547A10_liver_pmt900_635.xys


title: WG0041908-DNA_G08_RM5565

value: Failed QC


title: Rana sierrae-Liver- infected-late-rep2

description:
Sample name: 16, L, I, 2, Liver
Raw data file: 426547A09_liver_pmt900_635.xys

source_name: Rana sierrae-Liver- infected-late

value: late


title: WG0041908-DNA_G06_RM6747


title: WG0041908-DNA_G07_RX0744


title: Rana muscosa-Liver- control-late-rep1

description:
Sample name: 27, L, C, 1, Liver
Raw data file: 426547A06_liver_pmt900_635.xys

value: Liver


title: Rana sierrae-Liver- control-early-rep1

description:
Sample name: 3, E, C, 2, Liver
Raw data file: 426547A07_liver_pmt900_635.xys


title: Rana muscosa-Liver- infected-early-rep1

description:
Sample name: 10, E, I, 1, Liver
Raw data file: 426547A04_liver_pmt900_635.xys


title: WG0041908-DNA_G05_RM5062


title: Rana sierrae-Liver- infected-early-rep1

description:
Sample name: 9, E, I, 2, Liver
Raw data file: 426547A05_liver_pmt900_635.xys


title: Rana sierrae-Liver- infected-late-rep1

description:
Sample name: 17, L, I, 2, Liver
Raw data file: 426547A02_liver_pmt900_635.xys


title: Rana sierrae-Liver- control-late-rep1

description:
Sample name: 21, L, C, 2, Liver
Raw data file: 426547A01_liver_pmt900_635.xys


title: Rana muscosa-Liver- infected-late-rep1

description:
Sample name: 19, L, I, 1, Liver
Raw data file: 426547A03_liver_pmt900_635.xys

source_name: Rana muscosa-Liver- infected-late


title: WG0041908-DNA_G04_RM6737


title: Rana muscosa-Skin- infected-late-rep3

description:
Sample name: 20, L, I, 1, Skin
Raw data file: 426867A12_skin_pmt750_635.xys

source_name: Rana muscosa-Skin- infected-late

value: Skin


title: Rana sierrae-Liver- control-early-rep2

description:
Sample name: 2, E, C, 2, Liver
Raw data file: 426547A08_liver_pmt900_635.xys


title: Rana sierrae-Skin- infected-early-rep3

description:
Sample name: 8, E, I, 2, Skin
Raw data file: 426867A11_skin_pmt750_635.xys

source_name: Rana sierrae-Skin- infected-early


title: WG0041908-DNA_G03_RM6030


title: Rana sierrae-Skin- control-late-rep3

description:
Sample name: 21, L, C, 2, Skin
Raw data file: 426867A10_skin_pmt750_635.xys

source_name: Rana sierrae-Skin- control-late


title: Cambodia CAM4

source_name: Cambodia CAM4 DNA

value: Cambodia CAM4


title: Rana sierrae-Skin- infected-late-rep3

description:
Sample name: 16, L, I, 2, Skin
Raw data file: 426867A08_skin_pmt750_635.xys

source_name: Rana sierrae-Skin- infected-late


title: Rana muscosa-Skin- infected-early-rep3

description:
Sample name: 11, E, I, 1, Skin
Raw data file: 426867A07_skin_pmt750_635.xys

source_name: Rana muscosa-Skin- infected-early


title: Rana sierrae-Skin- control-early-rep3

description:
Sample name: 2, E, C, 2, Skin
Raw data file: 426867A09_skin_pmt750_635.xys

source_name: Rana sierrae-Skin- control-early


title: Rana sierrae-Skin- infected-late-rep2

description:
Sample name: 17, L, I, 2, Skin
Raw data file: 426867A05_skin_pmt750_635.xys


title: WG0041908-DNA_G01_RM6549

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled


title: Rana sierrae-Skin- control-early-rep2

description:
Sample name: 3, E, C, 2, Skin
Raw data file: 426867A06_skin_pmt750_635.xys


title: pre-miR-106b replicate 3

city: Bethesda

first: Robert

middle: Scott

last: Hudson

state: MD

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

description: Gene expression data from LNCaP cells transfected with pre-miR oligos

hyb_protocol: GeneChip® Human Genome U133A 2.0 (Affymetrix Inc., Santa Clara, CA) arrays were used following standard Affymetrix procedures as outlined in the Affymetrix technical manual. GeneChips® were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips® were scanned using the Affymetrix GeneChip ® Scanner Scanner 3000

data_processing: Microarray data (CEL files) were normalized using RMA and MAS.5 filtered for  genes with their detection calls as “P” or “M” within at least 3 samples.

label: biotin

source_name: Prostate cancer LNCaP cells

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

growth_protocol: Cells were plated in six-well plates at 2.5x105 cells per well, allowed to grow for 48-72 hours and then switched to antibiotic free media before being transfected.

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen, Carlsbad, CA) as directed by the manufacturer. The quantity and quality of RNA was assessed with a Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Pre-miRNA and control oligonucleotides (Ambion, Austin, TX) at 30-nM final concentration were transfected using Lipofectamine 2000 (Invitrogen, Carlsbad, CA), as directed by the manufacturer. Briefly, cells were plated in six-well plates at 2.5X10^5 cells per well, grown for 48-72 hr, and then switched to antibiotic free media prior to transfection. Next, 1.5 µl oligos at 50µM and 4 µl Lipofectamine 2000 were added individually to 250 µl of Opti-MEM (Invitrogen) and then combined and incubated for at least 20 minutes, before being added to cells (2.5 ml media in total). Cells were collected at 24 hr for microarray studies.

tag: cell line

value: LNCaP

tag: oligo transfection

tag: batch


title: WG0041908-DNA_F11_RM6125


title: Rana sierrae-Skin- control-late-rep2

description:
Sample name: 23, L, C, 2, Skin
Raw data file: 426867A04_skin_pmt750_635.xys


title: pre-miR-106b replicate 2


title: WG0041908-DNA_F10_RM6116


title: pre-miR-control replicate 2

value: pre-miR-control


title: pre-miR-106b replicate 1


title: WG0041908-DNA_F08_RM5793

value: Blood


title: WG0041908-DNA_F03_RM5089


title: Rana muscosa-Skin- control-late-rep3

description:
Sample name: 26, L, C, 1, Skin
Raw data file: 426867A03_skin_pmt750_635.xys

source_name: Rana muscosa-Skin- control-late


title: WG0041908-DNA_F06_RM5885


title: pre-miR-control replicate 3


title: WG0041908-DNA_E12_RM6000

value: Unaffected


title: WG0041908-DNA_F05_RM5567


title: WG0041908-DNA_F02_RM5764


title: WG0041908-DNA_G02_RM6699


title: Rana muscosa-Skin- control-early-rep3

description:
Sample name: 5, E, C, 1, Skin
Raw data file: 426867A02_skin_pmt750_635.xys

source_name: Rana muscosa-Skin- control-early


title: WG0041908-DNA_F04_RM5959


title: pre-miR-control replicate 1


title: PDEF+ rep2

city: Buffalo

first: Ashwani

last: Sood

state: New York

address: Elm & Carlton Streets

department: Immunology

institute: Roswell Park Cancer Institute

description: Biological Replicate of PDEF (+)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Set Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Gene Chip Operating Software (GCOS) and downstream analysis was done using Partek Genomics Suite.

source_name: PDEF +

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: shRNA plasmid trasnfected MCF-7 cells and control vector plasmid transfected MCF-7 cells were grown in Dulbecco's modified eagle medium supplemented with 10% fetal bovine serum at 37oC in a humidified CO2 incubator.

extract_protocol: Trizol extraction of total RNA was performed.


title: Rana muscosa-Skin- infected-early-rep2

description:
Sample name: 12, E, I, 1, Skin
Raw data file: 426867A01_skin_pmt750_635.xys


title: WG0041908-DNA_E11_RM6603


title: WG0041908-DNA_F12_RX0168


title: prostate RNA 114

city: Boston

first: Kathryn

last: Penney

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

description: Refer to the Illumina DASL Assay System Manual

hyb_protocol: stamdard the Illumina DASL Assay

scan_protocol: stamdard the Illumina DASL Assay

data_processing:
For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene
Gleason category: 1=Gleason ≥8, 0=Gleason ≤6; value=Normalized signal intensity

label: Cy3, Cy5

source_name: primary prostate cancer

label_protocol: stamdard the Illumina DASL Assay

extract_protocol: Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen)

value: primary prostate cancer tumor

tag: gleason category


title: WG0041908-DNA_E07_RM6515


title: PDEF- rep2

description: Biological Replicate of PDEF (-)

source_name: PDEF -

value: PDEF


title: PDEF+ rep1


title: Rana sierrae-Skin- infected-late-rep1

description:
Sample name: 15, L, I, 2, Skin
Raw data file: 426808A12_skin_pmt750_635.xys


title: PDEF- rep1


title: wild type E0, biological rep3

city: Beijing

first: Tingjian

last: Chen

address: One Tsinghua Garden Road

department: Department of Chemical Engineering

country: China

institute: Tsinghua University

description: Gene expression data from cells in log phase under ethanol stress

hyb_protocol: E. coli genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) were used for hybridization, and arrays were run in triplicate with biological replicates to allow for statistical confidence in differential gene expression

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Data were analyzed using GeneChip Operating Software Version 1.4 (Affymetrix)

organism: Escherichia coli

source_name: Cells in log phase under ethanol stress

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol

growth_protocol: Cells were grown at 37°C in Luria-Bertani (LB) medium containing 50 μg/ml ampicillin overnight, then diluted at a ratio of 1:100 into LB medium containing 1.5% (v/v) ethanol and 50 μg/ml ampicillin, and grown at 37°C.

extract_protocol: Total RNA was isolated from the cells stored in liquid nitrogen using TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and RNeasy MinElute Cleanup Kits (Qiagen, Valencia, CA, USA)

treatment_protocol: The cells were centrifuged when they reached the log phase, and then rapidly chilled and stored in liquid nitrogen until used for the DNA microarray assay

tag: genotype

value: wild type IrrE


title: Rana sierrae-Skin- infected-early-rep2

description:
Sample name: 7, E, I, 2, Skin
Raw data file: 426808A11_skin_pmt750_635.xys

value: early


title: wild type E0, biological rep2


title: WG0041908-DNA_F01_RX0481

source_name: Blood


title: Rana muscosa-Skin- infected-early-rep1

description:
Sample name: 10, E, I, 1, Skin
Raw data file: 426808A10_skin_pmt750_635.xys


title: wild type E0, biological rep1


title: mutant E1, biological rep3

value: ethanol-tolerant mutant E1 of IrrE


title: WG0041908-DNA_F09_RM6115


title: Rana muscosa-Skin- infected-late-rep2

description:
Sample name: 18, L, I, 1, Skin
Raw data file: 426808A09_skin_pmt750_635.xys

value: infected


title: mutant E1, biological rep1


title: mutant E1, biological rep2


title: Rana sierrae-Skin- control-late-rep1

description:
Sample name: 22, L, C, 2, Skin
Raw data file: 426808A08_skin_pmt750_635.xys

value: control

value: ebbets


title: ila1_biological rep2

first: Baocai

last: Zhang

state: Beijng

address: Beichen west road

department: Center for Genome Biology

institute: Institute of Genetics and Developmental Biology, CAS

description: mutant ila1 lamina joint at tiller stage

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing:
The data analysis were performed with Affymetrix GeneChip Operating Software (Version 1.4).
CapitalBio Molecule Annotation System (V3.0)-cacluated signal intensity

organism: Oryza sativa Japonica Group

source_name: lamina joint at tiller stage

extract_protocol: The TRIzol method as suggest by Affymetrix.

tag: cultivar

value: Japonica

value: Lamina joint

tag: genotype/variation

value: mutant ila1


title: WG0041908-DNA_E06_RM6381

value: Failed QC

tag: cell type

value: AD


title: WG0041908-DNA_F07_RM5765


title: ila1_biological rep1


title: ZH11_biological rep1

description: ZH11 lamina joint at tiller stage


title: ZH11_biological rep2

description: ZH11 lamina joint at tiller stage


title: Rana sierrae-Skin- infected-early-rep1

description:
Sample name: 9, E, I, 2, Skin
Raw data file: 426808A06_skin_pmt750_635.xys

value: Skin


title: wild-type (untreated) vs. TMX-/- (LPS/GalN-treated)_liver_24 h

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNA was isolated from liver samples using miRNeasy kit (QIAGEN).

treatment_protocol: Mice were injected intraperitoneally with a combination of 3 ng LPS and 10 mg D-(+)-galactosamine, and liver samples were collected 24 h post-injection.

tag: gender

value: female

value: wild-type

value: untreated

value: TMX-/-

value: LPS/GalN treated for 24 h


title: Rana muscosa-Skin- infected-late-rep1

description:
Sample name: 19, L, I, 1, Skin
Raw data file: 426808A07_skin_pmt750_635.xys

value: late

tag: treatment


title: WG0041908-DNA_E10_RX0522

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

value: Passed QC

value: Blood

value: Unaffected


title: WG0041908-DNA_E04_RM6499


title: wild-type (untreated) vs. TMX-/- (untreated)_liver_24 h


title: WG0041908-DNA_E08_RM6487


title: wild-type (untreated) vs. wild-type (LPS/GalN-treated)_liver_24 h


title: Challenge Sample (0Gy + 2Gy) at 8h; biological repl. C

first: Bahram

last: Parvin

state: Ca

institute: Lawrence Berkeley National Laboratory

description:
total RNA (ribosomal RNA removed)
0_2Gy_8h_C_(HuGene-1_0-st-v1).CEL

hyb_protocol: The fragmented, biotinylated ssDNA probes (5.5ug) were hybridized in a volume of 220ul at 45°C for 16 hours to Affymetrix high density Human Junction Arrays. The arrays were washed and stained with streptavidinphycoerythrin (SAPE, final concentration 10 μg/ml). Signal amplification was performed using a biotinylated anti-streptavidin antibody.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip® Scanner 3000 7G scanner with an autoloader, according to the Affymetrix GeneChip® WT Sense Target Labeling Assay protocol for the GeneChip Human Gene 1.0 ST Array.

data_processing: Robust multi-array analysis (RMA) was performed to normalize data collected from the different samples through R bioconductor (v.2.13.0). Samples were examined for quality control using the NUSE protocol.

source_name: Challenge Sample (0Gy + 2Gy) at 8h

label_protocol: Double-stranded cDNA was synthesized with random hexamers tagged with a T7 promoter sequence and used as a template in the presence of T7 RNA polymerase to produce cRNA. In the second cycle of cDNA synthesis, random hexamers were used to reverse transcribe cRNA from the first cycle, producing single-stranded DNA (ssDNA) in the sense orientation. The ssDNA was fragmented by the uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 which recognizes the dUTP incorporated in the ssDNA during the second-cycle, first-strand reverse transcription reaction and breaks the DNA strand. The fragmented ssDNA was labeled with terminal deoxynucleotidyl transferase and a DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Primary fetal human lung fibroplasts WI-38 (Coriell; AG06814) were cultured under physiological oxygen condition (3% O2 and 10% CO2) in DMEM medium with 10 % serum.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. An initial step to remove ribosomal RNA was used to minimize background and to increase detection sensitivity and specificity.  Ribosomal RNA subtraction was conducted using a protocol that was modified by Affymetrix for the RiboMinus Transcriptome Kit (Invitrogen).

treatment_protocol: Cells were exposed to a challenging dose of 2 Gy of X-rays (160 kVp) 4 hours after receiving a sham exposure (0 Gy) or an adaptive dose of 0.1 Gy.

value: Primary fetal human lung fibroplasts  (TP53 proficient)

tag: age

value: 12 FW


title: Rana muscosa-Skin- control-late-rep1

description:
Sample name: 27, L, C, 1, Skin
Raw data file: 426808A04_skin_pmt750_635.xys

value: control


title: Rana muscosa-Skin- control-late-rep2

description:
Sample name: 25, L, C, 1, Skin
Raw data file: 426808A05_skin_pmt750_635.xys


title: WG0041908-DNA_D12_RM8048


title: WG0041908-DNA_E09_RX0517


title: WG0041908-DNA_E01_RM5327


title: Challenge Sample (0Gy + 2Gy) at 8h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0_2Gy_8h_B_(HuGene-1_0-st-v1).CEL


title: Challenge Sample (0Gy + 2Gy) at 8h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0_2Gy_8h_A_(HuGene-1_0-st-v1).CEL


title: WG0041908-DNA_E02_RX0473


title: Rana sierrae-Skin- control-early-rep1

description:
Sample name: 1, E, C, 2, Skin
Raw data file: 426808A03_skin_pmt750_635.xys

value: early

value: ebbets


title: Challenge Sample (0Gy + 2Gy) at 4h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0_2Gy_4h_B_(HuGene-1_0-st-v1).CEL

source_name: Challenge Sample (0Gy + 2Gy) at 4h


title: Challenge Sample (0Gy + 2Gy) at 4h; biological repl. C

description:
total RNA (ribosomal RNA removed)
0_2Gy_4h_C_(HuGene-1_0-st-v1).CEL


title: Challenge Sample (0Gy + 2Gy) at 4h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0_2Gy_4h_A_(HuGene-1_0-st-v1).CEL


title: WG0041908-DNA_E05_RX0437


title: Rana muscosa-Skin- control-early-rep2

description:
Sample name: 4, E, C, 1, Skin
Raw data file: 426808A02_skin_pmt750_635.xys


title: Challenge Sample (0Gy + 2Gy) at 2h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0_2Gy_2h_B_(HuGene-1_0-st-v1).CEL

source_name: Challenge Sample (0Gy + 2Gy) at 2h


title: Challenge Sample (0Gy + 2Gy) at 2h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0_2Gy_2h_A_(HuGene-1_0-st-v1).CEL


title: Challenge Sample (0Gy + 2Gy) at 1h; biological repl. C

description:
total RNA (ribosomal RNA removed)
0_2Gy_1h_C_(HuGene-1_0-st-v1).CEL

source_name: Challenge Sample (0Gy + 2Gy) at 1h


title: Rana muscosa-Skin- control-early-rep1

description:
Sample name: 6, E, C, 1, Skin
Raw data file: 426808A01_skin_pmt750_635.xys


title: WG0041908-DNA_D10_RX0071


title: Rana muscosa-Spleen- control-late-rep2

description:
Sample name: 25, L, C, 1, Spleen
Raw data file: 426508A11_spleen_pmt850_635.xys

source_name: Rana muscosa-Spleen- control-late

value: Spleen


title: Challenge Sample (0Gy + 2Gy) at 1h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0_2Gy_1h_A_(HuGene-1_0-st-v1).CEL


title: Challenge Sample (0Gy + 2Gy) at 1h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0_2Gy_1h_B_(HuGene-1_0-st-v1).CEL


title: Rana sierrae-Spleen- control-early-rep2

description:
Sample name: 1, E, C, 2, Spleen
Raw data file: 426508A12_spleen_pmt850_635.xys

source_name: Rana sierrae-Spleen- control-early


title: WG0041908-DNA_D11_RM5346

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

value: Failed QC


title: Adaptive Sample (0.1Gy + 2Gy) at 8h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_8h_B_(HuGene-1_0-st-v1).CEL

source_name: Adaptive Sample (0.1Gy + 2Gy) at 8h


title: Rana sierrae-Spleen- control-early-rep1

description:
Sample name: 3, E, C, 2, Spleen
Raw data file: 426508A10_spleen_pmt850_635.xys


title: Adaptive Sample (0.1Gy + 2Gy) at 4h; biological repl. C

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_4h_C_(HuGene-1_0-st-v1).CEL

source_name: Adaptive Sample (0.1Gy + 2Gy) at 4h


title: Rana muscosa-Spleen- infected-late-rep2

description:
Sample name: 18, L, I, 1, Spleen
Raw data file: 426508A09_spleen_pmt850_635.xys

source_name: Rana muscosa-Spleen- infected-late

value: infected


title: Adaptive Sample (0.1Gy + 2Gy) at 8h; biological repl. C

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_8h_C_(HuGene-1_0-st-v1).CEL


title: Adaptive Sample (0.1Gy + 2Gy) at 4h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_4h_A_(HuGene-1_0-st-v1).CEL


title: WG0041908-DNA_D07_RM5324


title: Rana muscosa-Spleen- infected-late-rep1

description:
Sample name: 19, L, I, 1, Spleen
Raw data file: 426508A08_spleen_pmt850_635.xys


title: WG0041908-DNA_D08_RM5563


title: Adaptive Sample (0.1Gy + 2Gy) at 2h; biological repl. C

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_2h_C_(HuGene-1_0-st-v1).CEL

source_name: Adaptive Sample (0.1Gy + 2Gy) at 2h


title: Adaptive Sample (0.1Gy + 2Gy) at 4h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_4h_B_(HuGene-1_0-st-v1).CEL


title: Adaptive Sample (0.1Gy + 2Gy) at 2h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_2h_B_(HuGene-1_0-st-v1).CEL


title: Adaptive Sample (0.1Gy + 2Gy) at 8h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_8h_A_(HuGene-1_0-st-v1).CEL


title: Adaptive Sample (0.1Gy + 2Gy) at 1h; biological repl. C

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_1h_C_(HuGene-1_0-st-v1).CEL

source_name: Adaptive Sample (0.1Gy + 2Gy) at 1h


title: Adaptive Sample (0.1Gy + 2Gy) at 2h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_2h_A_(HuGene-1_0-st-v1).CEL


title: WG0041908-DNA_E03_RX0318

value: AD


title: Rana muscosa-Spleen- control-early-rep2

description:
Sample name: 5, E, C, 1, Spleen
Raw data file: 426508A07_spleen_pmt850_635.xys

source_name: Rana muscosa-Spleen- control-early


title: WG0041908-DNA_D09_RM5601


title: WG0041908-DNA_D06_RX1097


title: Adaptive Sample (0.1Gy + 2Gy) at 1h; biological repl. B

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_1h_B_(HuGene-1_0-st-v1).CEL


title: WG0041908-DNA_D02_RM6266


title: Rana sierrae-Spleen- infected-early-rep2

description:
Sample name: 7, E, I, 2, Spleen
Raw data file: 426508A05_spleen_pmt850_635.xys

source_name: Rana sierrae-Spleen- infected-early


title: Baseline (0Gy + 0Gy) at 0h

description:
total RNA (ribosomal RNA removed)
0_0Gy_0h_A_(HuGene-1_0-st-v1).CEL

source_name: Baseline (0Gy + 0Gy) at 0h


title: Adaptive Sample (0.1Gy + 2Gy) at 1h; biological repl. A

description:
total RNA (ribosomal RNA removed)
0.1_2Gy_1h_A_(HuGene-1_0-st-v1).CEL


title: Rana sierrae-Spleen- infected-early-rep1

description:
Sample name: 9, E, I, 2, Spleen
Raw data file: 426508A02_spleen_pmt850_635.xys


title: Rana muscosa-Spleen- control-early-rep1

description:
Sample name: 4, E, C, 1, Spleen
Raw data file: 426508A06_spleen_pmt850_635.xys


title: Rana muscosa-Spleen- infected-early-rep1

description:
Sample name: 11, E, I, 1, Spleen
Raw data file: 426508A01_spleen_pmt850_635.xys

source_name: Rana muscosa-Spleen- infected-early


title: Rana muscosa-Spleen- infected-early-rep2

description:
Sample name: 12, E, I, 1, Spleen
Raw data file: 426508A04_spleen_pmt850_635.xys


title: 7_control (for BCC)

city: Bochum

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

country: Germany

institute: Ruhr-University Bochum

hyb_protocol: Labeled miRNA samples  were  hybridized  at  55°C  for  20hrs  on  separate  Human  miRNA  Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays  were  washed  with  increasing  stringency  using  Gene  Expression Wash Buffers  (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile (Sigma-Aldich, St.Louis, USA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner.

data_processing: Fluorescent signal intensities were extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer's instructions.

source_name: skin biopsy

label_protocol: For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The  spiked  total  RNA  was  treated  with  alkaline  calf  intestine  phosphatase  (CIP).  The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer's instructions.

extract_protocol: miRNAs was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer's protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA).

treatment_protocol: All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation.

value: male

tag: tissue origin

value: skin

value: adjacent non-lesional tissue (intraindividual control)


title: control EpiSCs in N2B27 + Activin + Fgf stimulated with GCSF for 3 hours replicate 2

city: Cambridge

first: Jose

last: Silva

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge, centre for stem cell research

hyb_protocol: standard Illumina Hybridisation protocol

scan_protocol: standard protocol Bead array Reader from Illumina

data_processing: The data were loaded into the R package lumi (Du, P., Kibbe, W. A. & Lin, S. M. lumi: a pipeline for processing Illumina microarray. Bioinformatics 24, 1547-1548 (2008)). A given probe needed to abide to the Illumina detection p-value of 0.01 in at least one of the samples. If failing this probe was excluded from analysis to prevent noise. Subsequently the data was transformed using variance stabilisation (Lin, S. M., Du, P., Huber, W. & Kibbe, W. A. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36, e11 (2008)) and then normalised using quantile normalisation.

source_name: control EpiSCs in N2B27+Activin+Fgf stimulated with GCSF for 3 hours replicate 1

label_protocol: Ambion's Illumina TotalPrep-96 RNA Amplification protocol  for the amplification and labelling

extract_protocol: Qiagen RNeasy kit

tag: strain

value: EpiSC


title: control EpiSCs in N2B27 + Activin + Fgf stimulated with GCSF for 3 hours replicate 3

value: N2B27+Activin+Fgf stimulated with GCSF for 3 hours


title: control EpiSCs in N2B27 + Activin + Fgf stimulated with GCSF for 3 hours replicate 1


title: 6_control (for BCC)


title: WG0041908-DNA_C11_RM6242

description: C and G nucleotides are biotin labeled; A and T nucleotides are dinitrophenyl labeled

source_name: Blood

tag: qc status

value: Passed QC

tag: disease status


title: WG0041908-DNA_C12_RM8047

value: Blood


title: 5_control (for BCC)

value: female

tag: tissue


title: Rana muscosa-Spleen- control-late-rep1

description:
Sample name: 26, L, C, 1, Spleen
Raw data file: 426508A03_spleen_pmt850_635.xys

value: late

tag: population source


title: GY118F EpiSCs in N2B27 + Activin + Fgf stimulated with GCSF for 3 hours replicate 1

source_name: GY118F EpiSCs in N2B27+Activin+Fgf stimulated with GCSF for 3 hours replicate 2

tag: transgene


title: GY118F EpiSCs in N2B27 + Activin + Fgf stimulated with GCSF for 3 hours replicate 2

source_name: GY118F EpiSCs in N2B27+Activin+Fgf stimulated with GCSF for 3 hours replicate 3


title: 4_control (for BCC)


title: WG0041908-DNA_D05_RX1185

value: Unaffected


title: Baseline (0Gy + 0Gy) at 4h

description:
total RNA (ribosomal RNA removed)
0_0Gy_4h_(HuGene-1_0-st-v1).CEL

source_name: Baseline (0Gy + 0Gy) at 4h

tag: cell line

value: Primary fetal human lung fibroplasts  (TP53 proficient)

value: 12 FW


title: Control EpiSCs in N2B27 + Activin + Fgf replicate nr. 3

source_name: Control EpiSCs in N2B27+Activin+Fgf replicate nr. 3


title: 3_control (for BCC)


title: WG0041908-DNA_C08_RM5986


title: WG0041908-DNA_D04_RM6524


title: 2_control (for BCC)


title: WG0041908-DNA_C09_RX0825


title: Control EpiSCs in N2B27 + Activin + Fgf replicate nr. 1

source_name: Control EpiSCs in N2B27+Activin+Fgf replicate nr. 1


title: Control EpiSCs in N2B27 + Activin + Fgf replicate nr. 2

source_name: Control EpiSCs in N2B27+Activin+Fgf replicate nr. 2


title: GY118F EpiSCs in N2B27 + Activin + Fgf replicate nr. 2

source_name: GY118F EpiSCs in N2B27+Activin+Fgf replicate nr. 2


title: GY118F EpiSCs in N2B27 + Activin + Fgf replicate nr. 3

source_name: GY118F EpiSCs in N2B27+Activin+Fgf replicate nr. 3


title: WG0041908-DNA_D03_RM6283


title: WG0041908-DNA_C06_RM6219


title: WG0041908-DNA_C07_RM6104


title: 1_control (for BCC)


title: WG0041908-DNA_C10_RM6452


title: time (hrs)-24 + 2.66

hyb_protocol: Illumina Hybridisation protocol

scan_protocol: Bead array Reader from Illumina

source_name: GY118F iPS cells derived and maintained in N2B27 plus GCSF from which GCSF was withdrawn for 24 hours and to which subsequently GCSF was added back for 2 hours and 40 minutes

tag: origin

value: adult neural stem cells

value: iPSC


title: WG0041908-DNA_C05_RM5812


title: 6_BCC

source_name: BCC biopsy

value: Basal cell carcinoma (BCC)


title: time (hrs) -12 + 2.66

source_name: GY118F iPS cells derived and maintained in N2B27 plus GCSF from which GCSF was withdrawn for 12 hours and to which subsequently GCSF was added back for 2 hours and 40 minutes


title: time (hrs) -24

source_name: GY118F iPS cells derived and maintained in N2B27 plus GCSF from which GCSF was withdrawn for 24 hours


title: GY118F EpiSCs in N2B27 + Activin + Fgf replicate nr. 1

source_name: GY118F EpiSCs in N2B27+Activin+Fgf replicate nr. 1


title: 7_BCC


title: time (hrs) -12

source_name: GY118F iPS cells derived and maintained in N2B27 plus GCSF from which GCSF was withdrawn for 12 hours


title: 5_BCC


title: miR-206 KO; mdx-3

city: Dallas

first: Ning

last: Liu

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Mus musculus skeletal muscle

label_protocol: Cy3-labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genetic background

value: 3 months

value: tibialis anterior muscle

value: miR-206 KO, mdx


title: time (hrs) - 0

source_name: GY118F iPS cells derived and maintained in N2B27 plus GCSF


title: 3_BCC

value: skin


title: 4_BCC

value: male


title: miR-206 KO; mdx-2

description: replicate 1

tag: genotype


title: mdx-3

description: replicate 1

value: mdx


title: WG0041908-DNA_C02_RX0417

source_name: Blood


title: mdx-2

description: replicate 1


title: 2_BCC


title: mdx-1

description: replicate 1


title: WG0041908-DNA_B12_RM5927


title: WG0041908-DNA_C01_RM5067


title: hippocampus adult Sedentary no. 23

city: Urbana

first: Rachel

middle: Ann

last: Kohman

state: IL

address: 405 N Mathew

department: Psychology

institute: University of Illinois

source_name: hippocampus from adult sedentary

label_protocol: Biotinylated cRNA was prepared with the AMIL1791 Illumina® TotalPrep™ RNA Amplification Kit.

growth_protocol: Mice were weaned at the age of 4 weeks, and afterwards supplied with standard nutrition until sacrification.

extract_protocol: Animals were sacrificed by rapid decapitation without anesthesia. Hippocampal samples were dissected on a chilled glass dish and immediately placed into RNAlater solution (Qiagen, Valencia, CA) and stored at -20ºC until RNA isolation. Hippocampal samples were homogenized and RNA purified with the RNeasy Mini kit (Qiagen, Valencia, CA), then quantified and assessed for purity using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and an Agilent 2100 bioanalyzer.

treatment_protocol: Mice were individually housing with or without a running wheel for 8 weeks.

value: Male

value: BALB/c

value: 3.5 months-old

tag: exercise condition

value: Sedentary

value: hippocampus