title: lung_adenocarcinoma_DNA (85040001): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070085): MP

status: Public on Feb 25 2014

type: genomic

city: Vancouver

first: Ian

middle: Michael

last: Wilson

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics

country: Canada

institute: British Columbia Cancer Research Centre

description: For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers.  For example, 85040001 is the adenocarcinoma tumor profile that pairs with 85040002.

hyb_protocol: Hybridization was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.

scan_protocol: Scanning was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.

data_processing:
Data processing was performed according to Illumina directions by the Illumina Cspro service center at Oxford University.  Data were normalized using the average setting.  Software was BSGX version 3.2.3.
Beta values (Intensity Ratio Values) represent methylation level of the CpG locus. ß-values were calculated using the ratio of intensities between methylated and unmethylated alleles, i.e., (Intensity of methylated bead type)/(Intensity of methylated bead type + Intensity of unmethylated bead type).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: lung, adenocarcinoma

label_protocol:
Bisulfite conversion and labelling was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
Bisulfite conversion leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine.
Methylated alleles labeled with Cy3, unmethylated labeled with Cy5

growth_protocol: Tissues were excised during surgical ressection for tumor removal.

extract_protocol: Tumour and normal samples were obtained during surgical ressection.  After pathology review, tumors were microdissected to ensure tumor cells comprised 80% of cells extracted.  DNA was extracted using proteinase K digestion, followed by phenol:chloroform extraction and ethanol precipitation.

tag: disease state

value: adenocarcinoma

tag: sample number


title: lung_adenocarcinoma_DNA (85070109): MP


title: lung_adenocarcinoma_DNA (85070093): MP


title: Affymetrix Mouse Gene 1.0 ST Array for CBA DCs

type: RNA

city: Boston

first: Miguel

last: Stadecker

state: MA

address: 150 Harrison Ave

country: USA

institute: Tufts University School of Medicine

hyb_protocol: Samples were hybridized with Mouse Gene 1.0 ST arrays with GeneChip Hybridization Oven 640 per manufacturer's instructions (Affymetrix).

scan_protocol: Scan was carried out with GeneChip Scanner 30007G per manufacturer's instructions (Affymetrix).

data_processing: Expression Console 1.1 software provided was used to confirm robust, comparable gene-level signals from each chip and generate annotated NetAffxCSV files for analysis with Excel.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CBA/J bone marrow-derived dendritic cells

label_protocol: Total RNA was amplified and labeled according to Affymetrix amplification and labeling kit instrustructions (Affymetrix).

growth_protocol: Bone marrow was flushed from femurs and tibias of normal CBA and BL/6 mice. Red blood cells (RBCs) were lysed with Tris ammonium chloride buffer and cells were cultured in complete-RPMI 1640 medium (Lonza) containing 10% FBS (Aleken Biologicals) and GM-CSF-containing supernatant from the J558L transfectant B cell hybridoma. The medium was changed on day 3 and 5 and cells harvested on day 7.

extract_protocol: Total RNA was obtained by Trizol® (Invitrogen) extraction according to the manufacturer’s instructions.

tag: strain

value: CBA/J

tag: cell type

value: mouse BMDC


title: lung_non-malignant_DNA (85070070): MP

source_name: lung, non-malignant

value: control


title: lung_adenocarcinoma_DNA (85070159): MP


title: lung_non-malignant_DNA (85070086): MP


title: lung_non-malignant_DNA (85070082): MP


title: lung_non-malignant_DNA (85070110): MP


title: Affymetrix Mouse Gene 1.0 ST Array for BL6 DCs

source_name: C57BL/6 bone marrow-derived dendritic cells


title: MH_vs_TH

status: Public on Feb 26 2014

city: Hohhot

first: Wei

last: Wang

address: Inner Mongolia Hohhot City Saihan District Zhao Wuda road 306

country: China

institute: College of Life Sciences Chinese Inner Mongolia Agricultural University

description: CNV analysis of MH vs Thoroughbred

hyb_protocol: Hybridization was processing 60h at 42°C in Roche-NimbleGen hybridization system12.

scan_protocol: Arrays were scanned on an Roche-NimbleGen MS200 scanner.

data_processing: Arrays were processed using NimbleScan,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio.

organism: Equus caballus

source_name: MH DNA

label_protocol: The sample labelling was using NimbleGen Dual-Color DNA Labeling Kit (05223547001).

extract_protocol: The genomic DNA was extracted using Promega Genomic DNA Purification Kit (A1620).

treatment_protocol: Blood was directly collected from horse

tag: genotype

value: Wild type

tag: breed

value: Mongolia horse

tag: tissue

value: blood

source_name: TH DNA

value: wild type

value: Thoroughbred


title: VPA 500 mg/kg BW 4 day, sample 004

city: Bilthoven

first: Alexa

last: Vitins

address: P.O. Box 1

country: Netherlands

institute: RIVM

hyb_protocol: According to the Affymetrix Hybridization, Wash and Stain Kit (#901530)

scan_protocol: According to Affymetrix protocols

data_processing: Cell Intensity Files generated for each GeneChip using the Affymetrix GeneChip Command Console (v3.0) software were normalized using the Robust Multichip Average (RMA) algorithm from http://arrayanalysis.org (BiGCaT Maastricht University).  RMA normalized data were transformed to Log2 by arrayanalysis.org for further analysis.  Additionally, the quality of microarray images was inspected visually (http://arrayanalysis.org, BiGCaT Maastricht University).

source_name: Mouse liver after 4 day VPA treatment

label_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

extract_protocol: Upon sacrifice, liver was immediately dissected. Central half of the left lateral lobe was collected in RNA later and kept for a maximum of one week at 4 oC and frozen at -80 oC until use for RNA isolation. RNA was isolated using the RNeasy Mini Kit.

treatment_protocol: Mice treated for 1, 4, 11 days with vehicle or compound by oral gavage

tag: treatment

value: VPA 500 mg/kg BW 4 day

tag: gender

value: male

tag: age

value: 10 weeks

tag: weight

value: liver


title: DP_vs_TH

description: CNV analysis of DP vs Thoroughbred

source_name: DP DNA

value: Debao pony


title: HQ_vs_TH

description: CNV analysis of HQ vs Thoroughbred

source_name: HQ DNA

value: Hequ horse


title: lung_adenocarcinoma_DNA (85050022): aCGH

description: no additional information

hyb_protocol: Hybridization was performed as described previously (Nat Genet. 2004 Mar;36(3):299-303) for 40 hours.

scan_protocol: Slides were scanned at 10uM resolution on a Perkin Elmer ScanArray Express.

data_processing:
Data were extracted from images using SoftWorx Tracker software.  Systematic biases were removed from Log2 ratios (Cy3/Cy5) using CGHNorm (BMC Bioinformatics. 2005 Nov 18;6:274).  Only clones with SD<=0.075 and SNR>3 (for both channels) were used for further work.
VALUEs represent CGHnorm normalized log2 ratios, where bad array spots (not found etc) are blank.  This data has not been filtered for SNR or SD.

label_protocol: Labeling was performed as described previously (Nat Genet. 2004 Mar;36(3):299-303).  Briefly, tumors were labeled with cy3 dUTP using random primers and Klenow fragment.  Diploid reference was labeled with cy5 dUTP.

extract_protocol: Tumour and normal samples were obtained during surgical resection.  After pathology review, tumors were microdissected to ensure tumor cells comprised 80% of cells extracted.  DNA was extracted using proteinase K digestion, followed by phenol:chloroform extraction and ethanol precipitation.

source_name: diploid male reference

tag: reference

value: diploid male gDNA


title: TET 133 mg/kg BW 1 day, sample 096

source_name: Mouse liver after 1 day TET treatment

value: TET 133 mg/kg BW 1 day


title: lung_non-malignant_DNA (85070062): MP


title: VPA 500 mg/kg BW 1 day, sample 095

source_name: Mouse liver after 1 day VPA treatment

value: VPA 500 mg/kg BW 1 day


title: PBS vehicle 1 day, sample 003

source_name: Mouse liver after 1 day PBS vehicle treatment

value: vehicle control for 1 day


title: TET 133 mg/kg BW 11 day, sample 094

source_name: Mouse liver after 11 day TET treatment

value: TET 133 mg/kg BW 11 day


title: TH_vs_TH

description: CNV analysis of TH vs Thoroughbred


title: Pfn1fl/fl:Y129F mouse#6

city: Cleveland

first: Yi

last: Fan

address: 9500 Euclid Avenue

institute: Cleveland Clinic

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Mouse 2.0 ST Arrays (Affymetrix) and scanned at the Case Western Reserve University Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed using Expression console

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the Labeling Kit (Affymetrix).

growth_protocol: Endothelial cells were isolated from mouse glioma tumors in Tie2-Cre,Pfn1fl/fl:Y129F and Pfn1fl/fl:Y129F mice, by using magnetic-activated cell sorting with an anti-CD105 antibody

extract_protocol: RNA was extracted by using TRIzol reagent according to the manufacturer's instructions.

treatment_protocol: Isolated endothelial cells were treated with glioma-conditioned medium for 12 h.

value: tumor-associated endothelial cells


title: PBS vehicle 11 day, sample 002

source_name: Mouse liver after 11 day PBS vehicle treatment

value: vehicle control for 11 day


title: lung_non-malignant_DNA (85070050): MP

value: control


title: lung_adenocarcinoma_DNA (85070053): MP

value: adenocarcinoma


title: lung_adenocarcinoma_DNA (85070069): MP


title: TET vehicle 4 day, sample 088

source_name: Mouse liver after 4 day TET vehicle treatment

value: vehicle control for 4 day TET


title: TET 44 mg/kg BW 11 day, sample 089

value: TET 44 mg/kg BW 11 day


title: AMD 60 mg/kg BW 1 day, sample 001

source_name: Mouse liver after 1 day AMD treatment

value: AMD 60 mg/kg BW 1 day


title: Pfn1fl/fl:Y129F mouse#7


title: lung_adenocarcinoma_DNA (85070049): MP

source_name: lung, adenocarcinoma


title: VPA 500 mg/kg BW 4 day, sample 092

value: VPA 500 mg/kg BW 4 day

value: male


title: lung_adenocarcinoma_DNA (85070061): MP


title: Pfn1fl/fl:Y129F mouse#10


title: Tie2-Cre,Pfn1fl/fl:Y129F mouse#1


title: PBS vehicle 11 day, sample 090

value: 10 weeks

value: liver


title: PBS vehicle 4 day, sample 087

source_name: Mouse liver after 4 day PBS vehicle treatment

value: vehicle control for 4 day


title: lung_non-malignant_DNA (85070054): MP

source_name: lung, non-malignant


title: TET 44 mg/kg BW 11 day, sample 086


title: AMD 20 mg/kg BW 11 day, sample 091

source_name: Mouse liver after 11 day AMD treatment

value: AMD 20 mg/kg BW 11 day


title: Tie2-Cre,Pfn1fl/fl:Y129F mouse#3


title: Tie2-Cre,Pfn1fl/fl:Y129F mouse#4


title: lung_adenocarcinoma_DNA (85070021): MP


title: TET vehicle 4 day, sample 085


title: PBS vehicle 1 day, sample 082


title: AMD 60 mg/kg BW 4 day, sample 093

source_name: Mouse liver after 4 day AMD treatment

value: AMD 60 mg/kg BW 4 day


title: VPA 500 mg/kg BW 1 day, sample 080

value: VPA 500 mg/kg BW 1 day


title: 2966.68 C R 2966.68 V.Txt

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

institute: Laval University

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing: Images were quantified using ArrayPro 6.4 software (Media Cybernetics). Background subtracted, LOESS normalized, data obtained from log2 of processed Red signal/processed Green signal.

organism: Bos taurus

label_protocol:
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).
Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol: Holstein cycling cows were stimulated during 3 days with FSH given at 12 hr intervals, followed by a coasting period (no FSH) of 68 hours (control) or with GnRH antagonist treatment during the whole coasting period (treatment)

extract_protocol: Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturer instructions. RNA was eluted in 11 µl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.

treatment_protocol: Each cow was exposed to 68hrs coasting conditions with at least one month between the control and the treatment. Cumulus-oocyte complexes (COC’s) were collected by ovum pick-up (OPU). The COC’s were then washed three times to remove follicular fluid and were mechanically denuded to remove all the cumulus cells. Oocytes were then washed, collected in small volumes of PBS, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: sample type

value: holstein

tag: time

value: 68 hours

tag: reproductive status

value: 2nd Parity

value: oocyte


title: 2959.68 R 2959.68 C V.Txt


title: VPA 500 mg/kg BW 1 day, sample 079


title: 2966.68 R 2966.68 C V.Txt


title: VPA 500 mg/kg BW 11 day, sample 081

source_name: Mouse liver after 11 day VPA treatment

value: VPA 500 mg/kg BW 11 day


title: 2959.68 C R 2959.68 V.Txt


title: AMD 20 mg/kg BW 11 day, sample 083


title: lung_adenocarcinoma_DNA (85060358): MP

value: adenocarcinoma


title: lung_non-malignant_DNA (85070022): MP

value: control


title: TET 133 mg/kg BW 1 day, sample 084

value: TET 133 mg/kg BW 1 day


title: TET vehicle 11 day, sample 076

source_name: Mouse liver after 11 day TET vehicle treatment

value: vehicle control for 11 day TET


title: VPA 500 mg/kg BW 11 day, sample 078


title: TET vehicle 1 day, sample 077

source_name: Mouse liver after 1 day TET vehicle treatment

value: vehicle control for 1 day TET


title: lung_adenocarcinoma_DNA (85060354): MP


title: 2719.68 R 2719.68 C V.Txt


title: 2719.68 C R 2719.68 V.Txt


title: lung_non-malignant_DNA (85060355): MP


title: TET vehicle 4 day, sample 075

value: vehicle control for 4 day TET

value: male


title: PBS vehicle 11 day, sample 073

value: vehicle control for 11 day

value: 10 weeks

value: liver


title: lung_non-malignant_DNA (85060312): MP


title: lung_non-malignant_DNA (85060359): MP


title: TET 14.8 mg/kg BW 11 day, sample 074

value: TET 14.8 mg/kg BW 11 day


title: Old [F63D28WB]

city: Neuherberg

first: Steffen

last: Sass

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

description: miRNA expression in fibroblasts derived from female breast

hyb_protocol: Labelled cRNA was hybridized to Affymetrix GeneChip miRNA 2.0 Microarrays for 17h at 48 °C, stained by strepatavidin/phycoerythrin conjugate.

scan_protocol: The chips were scanned as described in the manufacturers´ protocol (FlashTag™ Biotin HSR RNA Labeling Kit P/N 703095 Rev. 2).

data_processing: The data were normalized using Robust Multiarray Average (RMA) within the R environment for statistical computing. Non-human miRNAs and miRNAs with intensity below 80 in all age groups were excluded. The GSE55299.txt contains only human miRNAs that passed the expression threshold.

label: Biotin

source_name: female breast

label_protocol: FlashTag Biotin HSR RNA Labeling procedure as recommended by Affymetrix, as start material 1µg RNA was used.

growth_protocol: The cells were grown in DMEM High Glucose + stable Glutamine (EK 2 mM) (PAA #E15-883) + 1 % v/v AA (von PAA # P11-002 1% v/v) + 10 % FCS GOLD (PAA # A15-151)

extract_protocol: The RNA was extracted using the provider's recommendations for the Qiagen miRNeasy kit, the RIN was measured, only high quality RNA (RIN 9-10) was used for hybridisation.

treatment_protocol: The cells were collected from 10cm2 culture dishes using RLT lysis buffer from the Qiagen miRNeasy kit, were stored at -80°C until RNA extraction.

tag: Sex

value: female


title: AMD 6.7 mg/kg BW 11 day, sample 072

value: AMD 6.7 mg/kg BW 11 day


title: Old [F62D45WB]


title: Old [F67D27WB]


title: Old [F64D41WB]


title: Old [F60D44WB]


title: AMD 60 mg/kg BW 4 day, sample 069

value: AMD 60 mg/kg BW 4 day


title: VPA 500 mg/kg BW 4 day, sample 068

source_name: Mouse liver after 4 day VPA treatment

value: VPA 500 mg/kg BW 4 day


title: lung_adenocarcinoma_DNA (85060311): MP


title: VPA 250 mg/kg BW 11 day, sample 067

value: VPA 250 mg/kg BW 11 day


title: AMD 6.7 mg/kg BW 11 day, sample 070


title: VPA 125 mg/kg BW 11 day, sample 071

value: VPA 125 mg/kg BW 11 day


title: Middle age [F49D39WB]


title: Middle age [F42D18WB]


title: AMD 60 mg/kg BW 11 day, sample 062

value: AMD 60 mg/kg BW 11 day


title: AMD 20 mg/kg BW 11 day, sample 066

value: AMD 20 mg/kg BW 11 day


title: Middle age [F43D40WB]


title: AMD 6.7 mg/kg BW 11 day, sample 061


title: TET 133 mg/kg BW 4 day, sample 060

source_name: Mouse liver after 4 day TET treatment

value: TET 133 mg/kg BW 4 day


title: lung_non-malignant_DNA (85060257): MP

value: control


title: lung_adenocarcinoma_DNA (85060251): MP

value: adenocarcinoma


title: Middle age [F41D35WB]


title: lung_adenocarcinoma_DNA (85060256): MP


title: AMD 6.7 mg/kg BW 11 day, sample 059


title: AMD 20 mg/kg BW 11 day, sample 065


title: Middle age [F40D25WB]


title: TET 133 mg/kg BW 1 day, sample 057

source_name: Mouse liver after 1 day TET treatment

value: TET 133 mg/kg BW 1 day


title: lung_non-malignant_DNA (85060252): MP


title: AMD 60 mg/kg BW 1 day, sample 064

value: AMD 60 mg/kg BW 1 day

value: male


title: AMD 20 mg/kg BW 11 day, sample 058

value: 10 weeks


title: VPA 250 mg/kg BW 11 day, sample 055

value: liver


title: Young [F26D29WB]


title: lung_adenocarcinoma_DNA (85060201): MP


title: TET 133 mg/kg BW 4 day, sample 054


title: lung_adenocarcinoma_DNA (85060144): MP


title: VPA 125 mg/kg BW 11 day, sample 056


title: lung_non-malignant_DNA (85060145): MP


title: lung_non-malignant_DNA (85060202): MP


title: lung_non-malignant_DNA (85060069): MP


title: Young [F26D23WB]


title: Young [F21D16WB]


title: Young [F23D31WB]


title: Young [F20D24WB]


title: VPA 250 mg/kg BW 11 day, sample 051


title: TET 133 mg/kg BW 11 day, sample 048

value: TET 133 mg/kg BW 11 day


title: PBS vehicle 1 day, sample 050

source_name: Mouse liver after 1 day PBS vehicle treatment

value: vehicle control for 1 day


title: AMD 60 mg/kg BW 4 day, sample 053


title: VPA 125 mg/kg BW 11 day, sample 046


title: lung_non-malignant_DNA (85050242): MP


title: TET 44 mg/kg BW 11 day, sample 047

source_name: Mouse liver after 11 day TET treatment

value: TET 44 mg/kg BW 11 day


title: TET 44 mg/kg BW 11 day, sample 052


title: VPA 500 mg/kg BW 11 day, sample 049

value: VPA 500 mg/kg BW 11 day


title: TET vehicle 11 day, sample 043

value: vehicle control for 11 day TET


title: lung_adenocarcinoma_DNA (85060068): MP


title: lung_adenocarcinoma_DNA (85050241): MP


title: silicon-treated, infected vs. mock (si,I_si,m), replicate 3

city: Gent

first: Jonas

last: Van Bockhaven

state: Oost-Vlaanderen

address: Coupure-Links 653

department: Crop protection

country: Belgium

institute: Ghent University

description:
raw data: Cy5 intensities from 'infected rep3.txt' (TEST) vs. Cy3 intensities from 'mock rep3.txt' (REFERENCE)
Biological replicate 3 of 3. silicon-treated, infected vs. mock
si,I_si,m (rep3)

hyb_protocol: Agilent Gene Expression  Hybridization Kit (5188-5242); Agilent microarray hybridization chamber user guide version 2.0

scan_protocol: Images were quantified with DNA microarray scanner (G2505B; Agilent Technologies) using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (version 9.5.3.1) was used for background subtraction. All absolute  intensities lower than 100 were discarded. Expander version 6 software was used for quantile normalization.

organism: Oryza sativa

source_name: infected, silicon-treated, rep3

label_protocol: Agilent Low Input Quick Amp Labeling  (5190-2306); Two-Color  Microarray-Based Gene  Expression Analysis  Low Input Quick Amp Labeling Protocol version 6.6

growth_protocol: Oryza sativa (L) Nipponbare seeds were surface sterilized, germinated on wet sterile filter paper and transplanted to a hydroponic system in modified Hoagland solution (Hewitt and Smith, 1974) which was replaced every 7 days. The rice plants were grown in a growth chamber (28°C, 12h/12h light regime) for five weeks until they reached the 7-leaf stage.

extract_protocol: Total RNA was extracted from frozen leaf tissue (100 mg; two youngest, fully developed leaves per plant; samples pooled from 6 individual plants). Kit: Spectrum Plant Total RNA (Sigma-Aldrich).

treatment_protocol: Conidia of Cochliobolus miyabeanus isolate CM988 were suspended in a solution containing 104 conidia ml-1 in 0.5% gelatin and sprayed on the leaves till run off (±1ml plant-1). Uninfected plants were sprayed with a 0.5% gelatin solution. The plants were kept in an dark infection chamber for 18h and transferred to the growth chamber.

value: silicon

tag: infection

value: infected

value: leaf

source_name: mock, silicon-treated, rep3

value: mock


title: TET vehicle 11 day, sample 042


title: PBS vehicle 4 day, sample 044

value: vehicle control for 4 day


title: AMD 60 mg/kg BW 11 day, sample 039

value: AMD 60 mg/kg BW 11 day


title: silicon-treated, infected vs. mock (si,I_si,m), replicate 2

description:
raw data: Cy5 intensities from 'infected rep2.txt' (TEST) vs. Cy3 intensities from 'mock rep2.txt' (REFERENCE)
Biological replicate 2 of 3. silicon-treated, infected vs. mock
si,I_si,m (rep2)

source_name: infected, silicon-treated, rep2

source_name: mock, silicon-treated, rep2


title: lung_non-malignant_DNA (85050223): MP

tag: disease state

value: control


title: PBS vehicle 4 day, sample 040

source_name: Mouse liver after 4 day PBS vehicle treatment


title: AMD 60 mg/kg BW 1 day, sample 045

source_name: Mouse liver after 1 day AMD treatment


title: PBS vehicle 4 day, sample 041


title: TET vehicle 1 day, sample 038

value: vehicle control for 1 day TET


title: lung_non-malignant_DNA (85050208): MP

source_name: lung, non-malignant

tag: sample number


title: lung_adenocarcinoma_DNA (85050207): MP

source_name: lung, adenocarcinoma

value: adenocarcinoma


title: lung_adenocarcinoma_DNA (85050222): MP


title: control, infected vs. mock (co,I_co,m), replicate 3

description:
raw data: Cy3 intensities from 'infected rep3.txt' (TEST) vs. Cy5 intensities from 'mock rep3.txt' (REFERENCE)
Biological replicate 3 of 3. control, infected vs. mock
co,I_co,m (rep3)

source_name: infected, control, rep3

source_name: mock, control, rep3


title: silicon-treated, infected vs. mock (si,I_si,m), replicate 1

description:
raw data: Cy5 intensities from 'infected rep1.txt' (TEST) vs. Cy3 intensities from 'mock rep1.txt' (REFERENCE)
Biological replicate 1 of 3. silicon-treated, infected vs. mock
si,I_si,m (rep1)

source_name: infected, silicon-treated, rep1

source_name: mock, silicon-treated, rep1


title: VPA 250 mg/kg BW 11 day, sample 037

source_name: Mouse liver after 11 day VPA treatment

value: VPA 250 mg/kg BW 11 day

tag: strain

value: male


title: control, infected vs. mock (co,I_co,m), replicate 2

description:
raw data: Cy3 intensities from 'infected rep2.txt' (TEST) vs. Cy5 intensities from 'mock rep2.txt' (REFERENCE)
Biological replicate 2 of 3. control, infected vs. mock
co,I_co,m (rep2)

source_name: infected, control, rep2

source_name: mock, control, rep2


title: lung_non-malignant_DNA (85050168): MP


title: TET 14.8 mg/kg BW 11 day, sample 036

value: TET 14.8 mg/kg BW 11 day

value: 10 weeks

value: liver


title: TET vehicle 4 day, sample 035

source_name: Mouse liver after 4 day TET vehicle treatment

value: vehicle control for 4 day TET


title: control, infected vs. mock (co,I_co,m), replicate 1

description:
raw data: Cy3 intensities from 'infected rep1.txt' (TEST) vs. Cy5 intensities from 'mock rep1.txt' (REFERENCE)
Biological replicate 1 of 3. control, infected vs. mock
co,I_co,m (rep1)

source_name: infected, control, rep1

source_name: mock, control, rep1


title: AMD 60 mg/kg BW 11 day, sample 033

source_name: Mouse liver after 11 day AMD treatment


title: TET vehicle 1 day, sample 034

source_name: Mouse liver after 1 day TET vehicle treatment


title: PBS vehicle 11 day, sample 032

source_name: Mouse liver after 11 day PBS vehicle treatment

value: vehicle control for 11 day


title: AMD 60 mg/kg BW 11 day, sample 031


title: TET 14.8 mg/kg BW 11 day, sample 030

source_name: Mouse liver after 11 day TET treatment


title: VPA 500 mg/kg BW 11 day, sample 028

value: VPA 500 mg/kg BW 11 day


title: VPA 250 mg/kg BW 11 day, sample 029


title: infected, silicon-treated vs. control (si,I_co,I), replicate 3

description:
raw data file: infected rep3.txt
Biological replicate 3 of 3. infected, silicon-treated vs. control
si,I_co,I (rep3)

source_name: infected, silicon-treated, rep3

value: silicon


title: infected, silicon-treated vs. control (si,I_co,I), replicate 2

description:
raw data file: infected rep2.txt
Biological replicate 2 of 3. infected, silicon-treated vs. control
si,I_co,I (rep2)

source_name: infected, silicon-treated, rep2

value: infected


title: lung_adenocarcinoma_DNA (85050167): MP

source_name: lung, adenocarcinoma


title: PBS vehicle 1 day, sample 025

source_name: Mouse liver after 1 day PBS vehicle treatment

value: vehicle control for 1 day


title: infected, silicon-treated vs. control (si,I_co,I), replicate 1

description:
raw data file: infected rep1.txt
Biological replicate 1 of 3. infected, silicon-treated vs. control
si,I_co,I (rep1)

value: leaf


title: lung_non-malignant_DNA (85050148): MP

source_name: lung, non-malignant


title: TET 14.8 mg/kg BW 11 day, sample 024


title: VPA 500 mg/kg BW 1 day, sample 023

source_name: Mouse liver after 1 day VPA treatment

value: VPA 500 mg/kg BW 1 day


title: mock, silicon-treated vs. control (si,m_co,m), replicate 2

description:
raw data file: mock rep2.txt
Biological replicate 2 of 3. mock, silicon-treated vs. control
si,m_co,m (rep2)

source_name: mock, silicon-treated, rep2

value: mock


title: VPA 125 mg/kg BW 11 day, sample 026

source_name: Mouse liver after 11 day VPA treatment

value: VPA 125 mg/kg BW 11 day


title: mock, silicon-treated vs. control (si,m_co,m), replicate 3

description:
raw data file: mock rep3.txt
Biological replicate 3 of 3. mock, silicon-treated vs. control
si,m_co,m (rep3)

source_name: mock, silicon-treated, rep3

source_name: mock, control, rep3

value: control


title: TET vehicle 11 day, sample 022

source_name: Mouse liver after 11 day TET vehicle treatment

value: vehicle control for 11 day TET


title: TET vehicle 1 day, sample 027

value: vehicle control for 1 day TET


title: mock, silicon-treated vs. control (si,m_co,m), replicate 1

description:
raw data file: mock rep1.txt
Biological replicate 1 of 3. mock, silicon-treated vs. control
si,m_co,m (rep1)

source_name: mock, silicon-treated, rep1


title: lung_adenocarcinoma_DNA (85050147): MP

value: adenocarcinoma


title: lung_adenocarcinoma_DNA (85050031): MP


title: lung_non-malignant_DNA (85050141): MP


title: lung_adenocarcinoma_DNA (85050140): MP


title: lung_non-malignant_DNA (85050023): MP


title: lung_non-malignant_DNA (85050032): MP


title: TET 133 mg/kg BW 4 day, sample 021

source_name: Mouse liver after 4 day TET treatment

value: TET 133 mg/kg BW 4 day

value: male


title: PBS vehicle 11 day, sample 020

value: 10 weeks

value: liver


title: TET 14.8 mg/kg BW 11 day, sample 018

value: TET 14.8 mg/kg BW 11 day


title: lung_adenocarcinoma_DNA (85050022): MP


title: RHΔku80 -- replicate 2

city: Stanford

first: Anjali

last: Shastri

state: CA

address: D305 Farichild Building; 299 Campus Drive

department: Microbiology & Biology

institute: Stanford University

description: Gene expression data from RHΔku80-infected RAW 264.7 cells

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C using the Affymetrix GeneAtlas System

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner

data_processing: The data were analyzed using R/Bioconductor and normalized via RMA

source_name: RAW 264.7 RHΔku80-infected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ug total RNA

growth_protocol: Cells were cultured in Dulbecco’s modiﬁed Eagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin, and 100 g/ml streptomycin.

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

treatment_protocol: Cells were plated in 6 well dishes and infected with Toxoplasma parasites at an MOI=3 (or mock infected) for ~24hours

tag: cell line


title: RHΔku80 -- replicate 1


title: mock -- replicate 2

description: Gene expression data from mock-infected RAW 264.7 cells

source_name: RAW 264.7 mock-infected


title: AMD 6.7 mg/kg BW 11 day, sample 015

source_name: Mouse liver after 11 day AMD treatment

value: AMD 6.7 mg/kg BW 11 day


title: AMD 60 mg/kg BW 4 day, sample 017

source_name: Mouse liver after 4 day AMD treatment

value: AMD 60 mg/kg BW 4 day


title: VPA 125 mg/kg BW 11 day, sample 019


title: mock -- replicate 1


title: AMD 60 mg/kg BW 11 day, sample 012

value: AMD 60 mg/kg BW 11 day


title: lung_adenocarcinoma_DNA (85050011): MP

description: For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers.  For example, 85040001 is the adenocarcinoma tumor profile that pairs with 85040002.


title: TET vehicle 11 day, sample 016


title: lung_non-malignant_DNA (85050012): MP


title: TET 133 mg/kg BW 4 day, sample 007


title: lung_adenocarcinoma_DNA (85040040): MP


title: VPA 500 mg/kg BW 4 day, sample 008

source_name: Mouse liver after 4 day VPA treatment

value: VPA 500 mg/kg BW 4 day


title: TET 133 mg/kg BW 1 day, sample 011

source_name: Mouse liver after 1 day TET treatment

value: TET 133 mg/kg BW 1 day


title: TET 133 mg/kg BW 11 day, sample 014

source_name: Mouse liver after 11 day TET treatment

value: TET 133 mg/kg BW 11 day


title: TET 44 mg/kg BW 11 day, sample 010

value: TET 44 mg/kg BW 11 day


title: AMD 60 mg/kg BW 1 day, sample 013

source_name: Mouse liver after 1 day AMD treatment

value: AMD 60 mg/kg BW 1 day


title: lung_non-malignant_DNA (85040002): MP

source_name: lung, non-malignant

value: control


title: lung_non-malignant_DNA (85040041): MP


title: lung_adenocarcinoma_DNA (85040031): MP

source_name: lung, adenocarcinoma


title: small intestine_P6_mutant 5

status: Public on Feb 24 2014

city: Berlin

first: Jingjing

last: Qi

state: Outside the US or Canada

address: Robert-Roessle-str. 10

institute: Max-Delbrueck-Center for Molecular Medicine

description: Biological replicate of mutant

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized with Illumina Genome Studio, data analysis and quality control were carried out using Partek® software.

source_name: small intestine

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA from whole piece of proximal small intestine was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: C57/BL6;129Ola mixed

value: mutant


title: lung_non-malignant_DNA (85040032): MP


title: small intestine_P6_mutant 3

description: Biological replicate of mutant


title: TET 133 mg/kg BW 11 day, sample 009


title: small intestine_P6_mutant 6

description: Biological replicate of mutant


title: small intestine_P6_mutant 2

description: Biological replicate of mutant


title: small intestine_P6_mutant 4

description: Biological replicate of mutant


title: lung_adenocarcinoma_DNA (85040001): MP

value: adenocarcinoma


title: Back skin treated group

city: Madrid

first: Javier

last: Suela

state: M

address: Faraday 7

country: Spain

institute: NIMGenetics

scan_protocol: 3um resolution scanner (Agilent Scanner C) one color system.

data_processing: Feature Extraction 10.7 and GE1 protocol.

source_name: back skin, treated

label_protocol: Agilent One Color Low Input protocol (200 ng per sample).

extract_protocol: RNA was isolated form the back skin and tail epidermis with TriPureTM Isolation Reagent (Roche) and RNeasy Mini kit (QIAGEN). Skin samples were homogenized in cold TriPure using a Polytron. The concentration and purity of RNA extracts were determined using a Nanodrop ND1000 (Nanodrop Technologies), and the integrity was determined based on the RNA Integrity Number (RIN).

treatment_protocol: For photodynamic treatments (PTs), methyl aminolevulinate as topical cream (Metvix®) was used. For tail skin experiments, Metvix® was applied directly on the skin. For back skin treatments, animals were completely shaved. After 2.5 h of incubation in darkness, the dorsal surface of both the back and the tail was irradiated with red light (636 nm) to a total dose of 2.5 or 10 J/cm2 respectively, using a LED lamp (Aktilite®).

value: back skin

value: photodynamic treatment to induce transient ROS production


title: Tail skin control group

source_name: tail skin, control

value: tail skin


title: small intestine_P6_control 6

description: Biological replicate of control


title: small intestine_P6_control 5

description: Biological replicate of control


title: small intestine_P6_control 4

description: Biological replicate of control


title: Tail skin treated group

source_name: tail skin, treated


title: Back skin control group

source_name: back skin, control


title: small intestine_P6_control 1

description: Biological replicate of control


title: small intestine_P6_control 3

description: Biological replicate of control


title: small intestine_P6_control 2

description: Biological replicate of control


title: small intestine_P6_mutant 1

description: Biological replicate of mutant


title: Pnk_S_d6_inf_rep7

city: Victoria

first: Ben

middle: F

last: Koop

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

description:
raw data filenames: 10248_cy5_80_scan2.txt, 10248_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_S_d6_inf_rep7

hyb_protocol: Samples were hybridized to randomized-order cGRASP 4x44k salmonid arrays (Agilent eArray AMADID: 025055) as per manufacturer’s instructions and slides were washed using stabilization solution to minimize ozone-related problems (Agilent; Sutherland et al., 2012). Slides were kept in the dark in a low ozone atmosphere until scanned.

scan_protocol: scanned on a ScanArray Express (Perkin Elmer) at constant PMT settings to produce saturated median values for ~1% of spots (anterior kidney samples: Cy3:80; Cy5:75 -  skin samples: Cy3:80; Cy5:80).

data_processing: Images were quantified using Imagene (v8; BioDiscovery) and poor or empty spots were flagged. Per block, a background correction for all probes was performed by subtracting the block’s average signal median value for negative control spots from each probe. Sample files were then imported into GeneSpring (v11; Agilent). For each species and tissue experiment, (e.g. Atlantic salmon, head kidney) filters were applied to retain probes for which 65% or more of all samples within at least one condition had background-corrected raw expression values  ≥500 in both channels and flag values for each channel as ‘present’. For statistics tests, a probe was deemed differentially expressed if it passed a Benjamini-Hochberg multiple test corrected p-value ≤ 0.05 and fold change ≥ 1.5. In experiments with a time component (e.g. Atlantic or pink salmon head kidney), a 2-way ANOVA was used to detect probes with a significant effect of infection and those with a time-infection interaction effect. Probes with a main effect but no interaction effect were filtered to retain only those that varied by 1.5 fold between control and experimental for at least one of the three time points. Probes with a significant time by infection interaction were filtered at each time point (FC >= 1.5).

organism: Oncorhynchus gorbuscha

label_protocol: Total RNA samples from Trial 3 were randomized and 200ng total RNA of each was reverse transcribed to cDNA and amplified to labelled-cRNA using Low Input Quick Amp labelling kits as per manufacturer’s instructions (Agilent). Reference channel Cy3-cRNA was constructed by combining equimolar cRNA proportions from each species/infection class conditions, and from each condition including at least one representative from each day (n = 19).

growth_protocol: Pink and chum salmon were obtained as swim-up fry from the Quinsam River and Nanaimo River hatcheries, respectively, on Vancouver Island, British Columbia. Atlantic salmon were obtained as parr from a commercial hatchery on Vancouver Island. The fish were reared in 400 L tanks in flowing water that was an equal mixture of aerated freshwater and seawater and were fed a diet of commercial salmon pellets at a daily rate of 1.0% biomass. Seawater was at 10 degrees Celcius and 30‰ salinity  Ovigerous Lepeophtheirus salmonis were collected from adult Atlantic salmon following harvest from a farm near Vancouver Island and transported in ice cold aerated seawater to Nanaimo. Dissected egg strings were incubated in filtered and ultraviolet irradiated seawater at 9.5 ± 1.0 C and 29.5 ± 0.5‰ salinity, with supplemental aeration, as described previously (Jones et al. 2006). Cultured lice were monitored by daily microscopic examination of triplicate samples and an inoculum containing a known number of copepodids was prepared when the ratio of copepodid to nauplius II stages was greatest.

extract_protocol: Total RNA was extracted from fin and kidney samples using Trizol, as per manufacturer’s instructions, and purified using RNeasy spin columns (QIAGEN), by manufacturer’s instructions with the on-column DNase I digestion.  The RNA was quality checked by agarose gel electrophoresis and quantified by spectrometry (NanoDrop-1000).

treatment_protocol: Ten size-matched (approx. 55-70g) individuals from each species were randomly allocated to each of eight tanks. After seven days acclimation, 5014 copepodids (167/fish) were added to each of four tanks using the metomidate hydrochloride (Aquacalm) sedation exposure method described previously (Jones et al. 2006). Two unexposed tanks were treated the same except with the addition of seawater without copepodids. At three, six, nine and 12 dpe, salmon were sampled by initial sedation with 0.5 mg/L metomidate, then a lethal immersion in 200 mg/L MS-222 followed by blunt head trauma, as previously described (Jones et al., 2007). The left pectoral fin and the anterior kidney were rapidly extracted from each fish and placed in liquid nitrogen, then stored at -80 °C until RNA extraction.

tag: exposure

value: inf

tag: day

source_name: pool of samples from all experimental conditions, containing equimolar sample(s) per condition

tag: tag

value: Reference pool


title: Pnk_S_d6_inf_rep8

description:
raw data filenames: 10255_cy5_80_scan2.txt, 10255_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_S_d6_inf_rep8


title: Pnk_S_d6_inf_rep9

description:
raw data filenames: 10260_cy5_80_scan2.txt, 10260_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_S_d6_inf_rep9


title: Pnk_S_d6_inf_rep6

description:
raw data filenames: 10240_cy5_80_scan4.txt, 10240_cy3_80_scan2_s.txt; block for sample in raw data file: Block4
Pnk_S_d6_inf_rep6


title: Pnk_S_d6_con_rep8

description:
raw data filenames: 10248_cy5_80_scan2.txt, 10248_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_S_d6_con_rep8

value: con


title: Pnk_S_d6_con_rep9

description:
raw data filenames: 10255_cy5_80_scan2.txt, 10255_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_S_d6_con_rep9


title: Pnk_S_d6_inf_rep5

description:
raw data filenames: 10236_cy5_80_scan3.txt, 10236_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_S_d6_inf_rep5


title: Pnk_S_d6_inf_rep2

description:
raw data filenames: 10219_cy5_80_scan2.txt, 10219_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_S_d6_inf_rep2


title: Pnk_S_d6_inf_rep3

description:
raw data filenames: 10225_cy5_80_scan2.txt, 10225_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_S_d6_inf_rep3


title: Pnk_S_d6_con_rep6

description:
raw data filenames: 10248_cy5_80_scan2.txt, 10232_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_S_d6_con_rep6


title: Pnk_S_d6_con_rep7

description:
raw data filenames: 10248_cy5_80_scan2.txt, 10248_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_S_d6_con_rep7


title: Pnk_S_d6_con_rep5

description:
raw data filenames: 10225_cy5_80_scan2.txt, 10225_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_S_d6_con_rep5


title: Pnk_S_d6_inf_rep1

description:
raw data filenames: 10033_cy5_80_scan2.txt, 10033_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_S_d6_inf_rep1


title: Pnk_S_d6_inf_rep4

description:
raw data filenames: 10227_cy5_80_scan2.txt, 10227_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_S_d6_inf_rep4


title: Pnk_S_d6_con_rep10

description:
raw data filenames: 10258_cy5_80_scan2.txt, 10258_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_S_d6_con_rep10


title: Pnk_S_d6_con_rep4

description:
raw data filenames: 10221_cy5_80_scan2.txt, 10221_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_S_d6_con_rep4


title: Pnk_S_d6_con_rep3

description:
raw data filenames: 10037_cy5_80_scan2.txt, 10037_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_S_d6_con_rep3


title: Pnk_AK_d9_inf_rep8

description:
raw data filenames: 10252_cy5_70_scan2.txt, 10252_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_inf_rep8


title: Pnk_AK_d9_inf_rep5

description:
raw data filenames: 10246_cy5_70_scan2.txt, 10246_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d9_inf_rep5


title: Pnk_AK_d9_inf_rep7

description:
raw data filenames: 10249_cy5_70_scan2.txt, 10249_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d9_inf_rep7


title: Pnk_S_d6_con_rep1

description:
raw data filenames: 10036_cy5_80_scan2.txt, 10036_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_S_d6_con_rep1


title: Pnk_AK_d9_inf_rep11

description:
raw data filenames: 10262_cy5_70_scan2.txt, 10262_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d9_inf_rep11


title: Pnk_AK_d9_inf_rep9

description:
raw data filenames: 10254_cy5_70_scan2.txt, 10254_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_inf_rep9


title: Pnk_AK_d9_inf_rep6

description:
raw data filenames: 10247_cy5_70_scan2.txt, 10247_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_inf_rep6


title: Pnk_S_d6_con_rep2

description:
raw data filenames: 10036_cy5_80_scan2.txt, 10036_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_S_d6_con_rep2


title: Pnk_AK_d9_inf_rep10

description:
raw data filenames: 10259_cy5_70_scan2.txt, 10259_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d9_inf_rep10


title: Pnk_AK_d9_inf_rep2

description:
raw data filenames: 10217_cy5_70_scan2.txt, 10217_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_inf_rep2


title: Pnk_AK_d9_inf_rep1

description:
raw data filenames: 10035_cy5_70_scan2.txt, 10035_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_inf_rep1


title: Pnk_AK_d9_inf_rep3

description:
raw data filenames: 10223_cy5_70_scan2.txt, 10223_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d9_inf_rep3


title: Pnk_AK_d9_con_rep9

description:
raw data filenames: 10256_cy5_70_scan2.txt, 10256_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_con_rep9


title: Pnk_AK_d9_con_rep10

description:
raw data filenames: 10262_cy5_70_scan2.txt, 10262_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_con_rep10


title: Pnk_AK_d9_con_rep8

description:
raw data filenames: 10253_cy5_70_scan2.txt, 10253_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d9_con_rep8


title: Pnk_AK_d9_con_rep7

description:
raw data filenames: 10249_cy5_70_scan2.txt, 10249_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_con_rep7


title: Pnk_AK_d6_inf_rep7

description:
raw data filenames: 10246_cy5_70_scan2.txt, 10246_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d6_inf_rep7


title: Pnk_AK_d9_con_rep4

description:
raw data filenames: 10223_cy5_70_scan2.txt, 10223_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_con_rep4


title: Pnk_AK_d9_con_rep6

description:
raw data filenames: 10246_cy5_70_scan2.txt, 10246_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_con_rep6


title: Pnk_AK_d6_inf_rep4

description:
raw data filenames: 10241_cy5_70_scan2.txt, 10241_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_inf_rep4


title: Pnk_AK_d9_inf_rep4

description:
raw data filenames: 10241_cy5_70_scan2.txt, 10241_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_inf_rep4


title: Pnk_AK_d9_con_rep5

description:
raw data filenames: 10244_cy5_70_scan2.txt, 10244_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d9_con_rep5


title: Pnk_AK_d6_inf_rep6

description:
raw data filenames: 10245_cy5_70_scan2.txt, 10245_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_inf_rep6


title: Pnk_AK_d6_inf_rep8

description:
raw data filenames: 10253_cy5_70_scan2.txt, 10253_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d6_inf_rep8


title: Pnk_AK_d9_con_rep3

description:
raw data filenames: 10214_cy5_70_scan2.txt, 10214_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d9_con_rep3


title: Pnk_AK_d6_inf_rep5

description:
raw data filenames: 10244_cy5_70_scan2.txt, 10244_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_inf_rep5


title: Pnk_AK_d9_con_rep2

description:
raw data filenames: 10213_cy5_70_scan2.txt, 10213_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_con_rep2


title: Pnk_AK_d6_inf_rep10

description:
raw data filenames: 10259_cy5_70_scan2.txt, 10259_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d6_inf_rep10


title: Pnk_AK_d6_inf_rep3

description:
raw data filenames: 10217_cy5_70_scan2.txt, 10217_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d6_inf_rep3


title: Pnk_AK_d6_inf_rep9

description:
raw data filenames: 10257_cy5_70_scan2.txt, 10257_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_inf_rep9


title: Pnk_AK_d6_inf_rep2

description:
raw data filenames: 10217_cy5_70_scan2.txt, 10217_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d6_inf_rep2


title: Pnk_AK_d9_con_rep1

description:
raw data filenames: 10034_cy5_70_scan2.txt, 10034_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d9_con_rep1


title: Pnk_AK_d6_con_rep6

description:
raw data filenames: 10234_cy5_70_scan2.txt, 10234_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d6_con_rep6


title: Pnk_AK_d6_con_rep8

description:
raw data filenames: 10247_cy5_70_scan2.txt, 10247_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d6_con_rep8


title: Pnk_AK_d6_con_rep5

description:
raw data filenames: 10229_cy5_70_scan2.txt, 10229_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_con_rep5


title: Pnk_AK_d6_con_rep1

description:
raw data filenames: 10213_cy5_70_scan2.txt, 10213_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_con_rep1


title: Pnk_AK_d6_inf_rep1

description:
raw data filenames: 10065_cy5_70_scan2.txt, 10065_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d6_inf_rep1


title: Pnk_AK_d6_con_rep9

description:
raw data filenames: 10259_cy5_70_scan2.txt, 10259_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_con_rep9


title: Pnk_AK_d3_inf_rep10

description:
raw data filenames: 10254_cy5_70_scan2.txt, 10254_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d3_inf_rep10


title: Pnk_AK_d6_con_rep2

description:
raw data filenames: 10215_cy5_70_scan2.txt, 10215_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d6_con_rep2


title: Pnk_AK_d6_con_rep7

description:
raw data filenames: 10237_cy5_70_scan2.txt, 10237_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d6_con_rep7


title: Pnk_AK_d6_con_rep4

description:
raw data filenames: 10223_cy5_70_scan2.txt, 10223_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d6_con_rep4


title: Pnk_AK_d6_con_rep3

description:
raw data filenames: 10216_cy5_70_scan2.txt, 10216_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d6_con_rep3


title: Pnk_AK_d3_inf_rep8

description:
raw data filenames: 10245_cy5_70_scan2.txt, 10245_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d3_inf_rep8


title: Pnk_AK_d3_inf_rep5

description:
raw data filenames: 10235_cy5_70_scan2.txt, 10235_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d3_inf_rep5


title: Pnk_AK_d3_inf_rep7

description:
raw data filenames: 10245_cy5_70_scan2.txt, 10245_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d3_inf_rep7


title: Pnk_AK_d3_con_rep10

description:
raw data filenames: 10262_cy5_70_scan2.txt, 10262_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_con_rep10


title: Pnk_AK_d3_inf_rep1

description:
raw data filenames: 10065_cy5_70_scan2.txt, 10065_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d3_inf_rep1


title: Pnk_AK_d3_inf_rep3

description:
raw data filenames: 10217_cy5_70_scan2.txt, 10217_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_inf_rep3


title: Pnk_AK_d3_inf_rep9

description:
raw data filenames: 10253_cy5_70_scan2.txt, 10253_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d3_inf_rep9


title: Pnk_AK_d3_inf_rep2

description:
raw data filenames: 10213_cy5_70_scan2.txt, 10213_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d3_inf_rep2


title: Pnk_AK_d3_con_rep8

description:
raw data filenames: 10249_cy5_70_scan2.txt, 10249_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_con_rep8


title: Pnk_AK_d3_inf_rep6

description:
raw data filenames: 10244_cy5_70_scan2.txt, 10244_cy3_80_scan2.txt; block for sample in raw data file: Block2
Pnk_AK_d3_inf_rep6


title: Pnk_AK_d3_inf_rep4

description:
raw data filenames: 10226_cy5_70_scan2.txt, 10226_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d3_inf_rep4


title: Pnk_AK_d3_con_rep4

description:
raw data filenames: 10218_cy5_70_scan2.txt, 10218_cy3_80_scan2.txt; block for sample in raw data file: Block4
Pnk_AK_d3_con_rep4


title: Pnk_AK_d3_con_rep6

description:
raw data filenames: 10229_cy5_70_scan2.txt, 10229_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_con_rep6


title: Pnk_AK_d3_con_rep3

description:
raw data filenames: 10218_cy5_70_scan2.txt, 10218_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d3_con_rep3


title: Pnk_AK_d3_con_rep2

description:
raw data filenames: 10216_cy5_70_scan2.txt, 10216_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_con_rep2


title: Pnk_AK_d3_con_rep9

description:
raw data filenames: 10253_cy5_70_scan2.txt, 10253_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d3_con_rep9


title: Pnk_AK_d3_con_rep5

description:
raw data filenames: 10220_cy5_70_scan2.txt, 10220_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_con_rep5


title: Pnk_AK_d3_con_rep1

description:
raw data filenames: 10034_cy5_70_scan2.txt, 10034_cy3_80_scan2.txt; block for sample in raw data file: Block3
Pnk_AK_d3_con_rep1


title: Chm_S_d6_inf_rep7

description:
raw data filenames: 10236_cy5_80_scan3.txt, 10236_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_S_d6_inf_rep7

organism: Oncorhynchus keta


title: Chm_S_d6_inf_rep9

description:
raw data filenames: 10260_cy5_80_scan2.txt, 10260_cy3_80_scan2.txt; block for sample in raw data file: Block2
Chm_S_d6_inf_rep9


title: Chm_S_d6_inf_rep4

description:
raw data filenames: 10221_cy5_80_scan2.txt, 10221_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_inf_rep4


title: Chm_S_d6_inf_rep5

description:
raw data filenames: 10231_cy5_80blk1-3_70blk4_scan2.txt, 10231_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_S_d6_inf_rep5


title: Chm_S_d6_inf_rep8

description:
raw data filenames: 10258_cy5_80_scan2.txt, 10258_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_inf_rep8


title: Chm_S_d6_inf_rep1

description:
raw data filenames: 10033_cy5_80_scan2.txt, 10033_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_S_d6_inf_rep1


title: Chm_S_d6_inf_rep2

description:
raw data filenames: 10219_cy5_80_scan2.txt, 10219_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_S_d6_inf_rep2


title: Chm_S_d6_inf_rep6

description:
raw data filenames: 10236_cy5_80_scan3.txt, 10236_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_S_d6_inf_rep6


title: Chm_S_d6_inf_rep10

description:
raw data filenames: 10260_cy5_80_scan2.txt, 10260_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_inf_rep10


title: Chm_S_d6_con_rep10

description:
raw data filenames: 10255_cy5_80_scan2.txt, 10255_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_con_rep10


title: Chm_S_d6_inf_rep3

description:
raw data filenames: 10221_cy5_80_scan2.txt, 10221_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_S_d6_inf_rep3


title: Chm_S_d6_con_rep8

description:
raw data filenames: 10242_cy5_80_scan2.txt, 10242_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_con_rep8


title: Chm_S_d6_con_rep9

description:
raw data filenames: 10248_cy5_80_scan2.txt, 10248_cy3_80_scan2.txt; block for sample in raw data file: Block2
Chm_S_d6_con_rep9


title: Chm_S_d6_con_rep7

description:
raw data filenames: 10242_cy5_80_scan2.txt, 10242_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_S_d6_con_rep7


title: Chm_S_d6_con_rep4

description:
raw data filenames: 10221_cy5_80_scan2.txt, 10221_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_S_d6_con_rep4


title: Chm_S_d6_con_rep5

description:
raw data filenames: 10225_cy5_80_scan2.txt, 10225_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_con_rep5


title: Chm_S_d6_con_rep1

description:
raw data filenames: 10036_cy5_80_scan2.txt, 10036_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_S_d6_con_rep1


title: Chm_AK_d6_inf_rep8

description:
raw data filenames: 10237_cy5_70_scan2.txt, 10237_cy3_80_scan2.txt; block for sample in raw data file: Block2
Chm_AK_d6_inf_rep8


title: Chm_AK_d6_inf_rep7

description:
raw data filenames: 10231_cy5_80blk1-3_70blk4_scan2.txt, 10231_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_AK_d6_inf_rep7


title: Chm_S_d6_con_rep3

description:
raw data filenames: 10219_cy5_80_scan2.txt, 10219_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_S_d6_con_rep3


title: Chm_AK_d6_inf_rep10

description:
raw data filenames: 10244_cy5_70_scan2.txt, 10244_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_inf_rep10


title: Chm_AK_d6_inf_rep6

description:
raw data filenames: 10226_cy5_70_scan2.txt, 10226_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_inf_rep6


title: Chm_AK_d6_inf_rep4

description:
raw data filenames: 10218_cy5_70_scan2.txt, 10218_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_inf_rep4


title: Chm_AK_d6_inf_rep3

description:
raw data filenames: 10213_cy5_70_scan2.txt, 10213_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_inf_rep3


title: Chm_S_d6_con_rep2

description:
raw data filenames: 10219_cy5_80_scan2.txt, 10219_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_S_d6_con_rep2


title: Chm_S_d6_con_rep6

description:
raw data filenames: 10227_cy5_80_scan2.txt, 10227_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_S_d6_con_rep6


title: Chm_AK_d6_inf_rep5

description:
raw data filenames: 10220_cy5_70_scan2.txt, 10220_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_AK_d6_inf_rep5


title: Chm_AK_d6_inf_rep9

description:
raw data filenames: 10240_cy5_70_scan2.txt, 10240_cy3_80_scan2_ak.txt; block for sample in raw data file: Block1
Chm_AK_d6_inf_rep9


title: Chm_AK_d6_inf_rep1

description:
raw data filenames: 10065_cy5_70_scan2.txt, 10065_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_AK_d6_inf_rep1


title: Chm_AK_d6_con_rep9

description:
raw data filenames: 10252_cy5_70_scan2.txt, 10252_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_con_rep9


title: Chm_AK_d6_inf_rep2

description:
raw data filenames: 10065_cy5_70_scan2.txt, 10065_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_inf_rep2


title: Chm_AK_d6_con_rep10

description:
raw data filenames: 10257_cy5_70_scan2.txt, 10257_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_AK_d6_con_rep10


title: Chm_AK_d6_con_rep6

description:
raw data filenames: 10241_cy5_70_scan2.txt, 10241_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_con_rep6


title: Chm_AK_d6_con_rep8

description:
raw data filenames: 10251_cy5_70_scan2.txt, 10251_cy3_80_scan2.txt; block for sample in raw data file: Block4
Chm_AK_d6_con_rep8


title: Chm_AK_d6_con_rep5

description:
raw data filenames: 10238_cy5_70_scan2.txt, 10238_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_con_rep5


title: Chm_AK_d6_con_rep3

description:
raw data filenames: 10234_cy5_70_scan2.txt, 10234_cy3_80_scan2.txt; block for sample in raw data file: Block2
Chm_AK_d6_con_rep3


title: Chm_AK_d6_con_rep7

description:
raw data filenames: 10249_cy5_70_scan2.txt, 10249_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_AK_d6_con_rep7


title: Chm_AK_d6_con_rep4

description:
raw data filenames: 10238_cy5_70_scan2.txt, 10238_cy3_80_scan2.txt; block for sample in raw data file: Block2
Chm_AK_d6_con_rep4


title: Chm_AK_d6_con_rep1

description:
raw data filenames: 10035_cy5_70_scan2.txt, 10035_cy3_80_scan2.txt; block for sample in raw data file: Block1
Chm_AK_d6_con_rep1


title: Atl_S_d6_inf_rep9

description:
raw data filenames: 10258_cy5_80_scan2.txt, 10258_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_S_d6_inf_rep9

organism: Salmo salar


title: Atl_S_d6_inf_rep8

description:
raw data filenames: 10242_cy5_80_scan2.txt, 10242_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_S_d6_inf_rep8


title: Atl_S_d6_con_rep9

description:
raw data filenames: 10260_cy5_80_scan2.txt, 10260_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_con_rep9


title: Atl_S_d6_inf_rep3

description:
raw data filenames: 10036_cy5_80_scan2.txt, 10036_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_inf_rep3


title: Atl_S_d6_inf_rep5

description:
raw data filenames: 10231_cy5_80blk1-3_70blk4_scan2.txt, 10231_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_S_d6_inf_rep5


title: Atl_S_d6_inf_rep1

description:
raw data filenames: 10033_cy5_80_scan2.txt, 10033_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_inf_rep1


title: Atl_S_d6_inf_rep4

description:
raw data filenames: 10225_cy5_80_scan2.txt, 10225_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_S_d6_inf_rep4


title: Atl_S_d6_con_rep5

description:
raw data filenames: 10232_cy5_80_scan3.txt, 10232_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_S_d6_con_rep5


title: Atl_S_d6_con_rep6

description:
raw data filenames: 10236_cy5_80_scan3.txt, 10236_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_S_d6_con_rep6


title: Chm_AK_d6_con_rep2

description:
raw data filenames: 10214_cy5_70_scan2.txt, 10214_cy3_80_scan2.txt; block for sample in raw data file: Block3
Chm_AK_d6_con_rep2


title: Atl_S_d6_con_rep4

description:
raw data filenames: 10232_cy5_80_scan3.txt, 10232_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_con_rep4


title: Atl_S_d6_con_rep2

description:
raw data filenames: 10037_cy5_80_scan2.txt, 10037_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_S_d6_con_rep2


title: Atl_S_d6_inf_rep2

description:
raw data filenames: 10033_cy5_80_scan2.txt, 10033_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_S_d6_inf_rep2


title: Atl_S_d6_con_rep8

description:
raw data filenames: 10258_cy5_80_scan2.txt, 10258_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_con_rep8


title: Atl_S_d6_inf_rep7

description:
raw data filenames: 10242_cy5_80_scan2.txt, 10242_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_inf_rep7


title: Atl_S_d6_con_rep3

description:
raw data filenames: 10231_cy5_80blk1-3_70blk4_scan2.txt, 10231_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_S_d6_con_rep3


title: Atl_S_d6_inf_rep6

description:
raw data filenames: 10232_cy5_80_scan3.txt, 10232_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_S_d6_inf_rep6


title: Atl_AK_d9_inf_rep7

description:
raw data filenames: 10237_cy5_70_scan2.txt, 10237_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d9_inf_rep7


title: Atl_S_d6_con_rep7

description:
raw data filenames: 10255_cy5_80_scan2.txt, 10255_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_S_d6_con_rep7


title: Atl_AK_d9_inf_rep9

description:
raw data filenames: 10256_cy5_70_scan2.txt, 10256_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d9_inf_rep9


title: Atl_AK_d9_inf_rep8

description:
raw data filenames: 10254_cy5_70_scan2.txt, 10254_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d9_inf_rep8


title: Atl_S_d6_con_rep1

description:
raw data filenames: 10037_cy5_80_scan2.txt, 10037_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_S_d6_con_rep1


title: Atl_AK_d9_inf_rep2

description:
raw data filenames: 10215_cy5_70_scan2.txt, 10215_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d9_inf_rep2


title: Pnk_AK_d3_con_rep7

description:
raw data filenames: 10246_cy5_70_scan2.txt, 10246_cy3_80_scan2.txt; block for sample in raw data file: Block1
Pnk_AK_d3_con_rep7


title: Atl_AK_d9_inf_rep3

description:
raw data filenames: 10215_cy5_70_scan2.txt, 10215_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d9_inf_rep3


title: Atl_AK_d9_inf_rep6

description:
raw data filenames: 10234_cy5_70_scan2.txt, 10234_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d9_inf_rep6


title: Atl_AK_d9_con_rep10

description:
raw data filenames: 10262_cy5_70_scan2.txt, 10262_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d9_con_rep10


title: Atl_AK_d9_inf_rep5

description:
raw data filenames: 10234_cy5_70_scan2.txt, 10234_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d9_inf_rep5


title: Atl_AK_d9_inf_rep1

description:
raw data filenames: 10064_cy5_70_scan2.txt, 10064_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d9_inf_rep1


title: Atl_AK_d9_con_rep9

description:
raw data filenames: 10254_cy5_70_scan2.txt, 10254_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d9_con_rep9


title: Atl_AK_d9_con_rep4

description:
raw data filenames: 10218_cy5_70_scan2.txt, 10218_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d9_con_rep4


title: Atl_AK_d9_con_rep8

description:
raw data filenames: 10252_cy5_70_scan2.txt, 10252_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d9_con_rep8


title: Atl_AK_d9_con_rep6

description:
raw data filenames: 10241_cy5_70_scan2.txt, 10241_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d9_con_rep6


title: Atl_AK_d9_con_rep5

description:
raw data filenames: 10220_cy5_70_scan2.txt, 10220_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d9_con_rep5


title: Atl_AK_d9_con_rep2

description:
raw data filenames: 10064_cy5_70_scan2.txt, 10064_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d9_con_rep2


title: Atl_AK_d9_con_rep3

description:
raw data filenames: 10215_cy5_70_scan2.txt, 10215_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d9_con_rep3


title: Atl_AK_d9_con_rep1

description:
raw data filenames: 10035_cy5_70_scan2.txt, 10035_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d9_con_rep1


title: Atl_AK_d9_con_rep7

description:
raw data filenames: 10251_cy5_70_scan2.txt, 10251_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d9_con_rep7


title: Atl_AK_d6_inf_rep9

description:
raw data filenames: 10251_cy5_70_scan2.txt, 10251_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d6_inf_rep9


title: Atl_AK_d6_inf_rep8

description:
raw data filenames: 10251_cy5_70_scan2.txt, 10251_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d6_inf_rep8


title: Atl_AK_d6_inf_rep7

description:
raw data filenames: 10240_cy5_70_scan2.txt, 10240_cy3_80_scan2_ak.txt; block for sample in raw data file: Block2
Atl_AK_d6_inf_rep7


title: Atl_AK_d6_con_rep8

description:
raw data filenames: 10247_cy5_70_scan2.txt, 10247_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d6_con_rep8


title: Atl_AK_d6_inf_rep6

description:
raw data filenames: 10233_cy5_70_scan2.txt, 10233_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d6_inf_rep6


title: Atl_AK_d6_inf_rep2

description:
raw data filenames: 10223_cy5_70_scan2.txt, 10223_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d6_inf_rep2


title: Atl_AK_d6_inf_rep5

description:
raw data filenames: 10229_cy5_70_scan2.txt, 10229_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d6_inf_rep5


title: Atl_AK_d6_inf_rep10

description:
raw data filenames: 10256_cy5_70_scan2.txt, 10256_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d6_inf_rep10


title: Atl_AK_d6_inf_rep3

description:
raw data filenames: 10226_cy5_70_scan2.txt, 10226_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d6_inf_rep3


title: Atl_AK_d6_inf_rep1

description:
raw data filenames: 10035_cy5_70_scan2.txt, 10035_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d6_inf_rep1


title: Atl_AK_d9_inf_rep4

description:
raw data filenames: 10229_cy5_70_scan2.txt, 10229_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d9_inf_rep4


title: Atl_AK_d6_con_rep9

description:
raw data filenames: 10257_cy5_70_scan2.txt, 10257_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d6_con_rep9


title: Atl_AK_d6_con_rep7

description:
raw data filenames: 10240_cy5_70_scan2.txt, 10240_cy3_80_scan2_ak.txt; block for sample in raw data file: Block3
Atl_AK_d6_con_rep7


title: Atl_AK_d3_inf_rep7

description:
raw data filenames: 10238_cy5_70_scan2.txt, 10238_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d3_inf_rep7


title: Atl_AK_d6_inf_rep4

description:
raw data filenames: 10226_cy5_70_scan2.txt, 10226_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d6_inf_rep4


title: Atl_AK_d6_con_rep2

description:
raw data filenames: 10222_cy5_70_scan2.txt, 10222_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d6_con_rep2


title: Atl_AK_d3_inf_rep8

description:
raw data filenames: 10238_cy5_70_scan2.txt, 10238_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_inf_rep8


title: Atl_AK_d6_con_rep6

description:
raw data filenames: 10235_cy5_70_scan2.txt, 10235_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d6_con_rep6


title: Atl_AK_d6_con_rep3

description:
raw data filenames: 10222_cy5_70_scan2.txt, 10222_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d6_con_rep3


title: Atl_AK_d6_con_rep1

description:
raw data filenames: 10064_cy5_70_scan2.txt, 10064_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d6_con_rep1


title: Atl_AK_d3_inf_rep1

description:
raw data filenames: 10034_cy5_70_scan2.txt, 10034_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_inf_rep1


title: Atl_AK_d3_inf_rep3

description:
raw data filenames: 10216_cy5_70_scan2.txt, 10216_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d3_inf_rep3


title: Atl_AK_d3_inf_rep4

description:
raw data filenames: 10222_cy5_70_scan2.txt, 10222_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_inf_rep4


title: Atl_AK_d3_inf_rep5

description:
raw data filenames: 10233_cy5_70_scan2.txt, 10233_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d3_inf_rep5


title: Atl_AK_d6_con_rep4

description:
raw data filenames: 10222_cy5_70_scan2.txt, 10222_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d6_con_rep4


title: Atl_AK_d3_con_rep8

description:
raw data filenames: 10257_cy5_70_scan2.txt, 10257_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d3_con_rep8


title: Atl_AK_d3_inf_rep6

description:
raw data filenames: 10235_cy5_70_scan2.txt, 10235_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d3_inf_rep6


title: Atl_AK_d3_con_rep9

description:
raw data filenames: 10259_cy5_70_scan2.txt, 10259_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d3_con_rep9


title: Atl_AK_d6_con_rep5

description:
raw data filenames: 10233_cy5_70_scan2.txt, 10233_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d6_con_rep5


title: Atl_AK_d3_con_rep10

description:
raw data filenames: 10216_cy5_70_scan2.txt, 10216_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_con_rep10


title: Atl_AK_d3_con_rep5

description:
raw data filenames: 10237_cy5_70_scan2.txt, 10237_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_con_rep5


title: Atl_AK_d3_con_rep6

description:
raw data filenames: 10245_cy5_70_scan2.txt, 10245_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d3_con_rep6


title: Atl_AK_d3_inf_rep9

description:
raw data filenames: 10252_cy5_70_scan2.txt, 10252_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_inf_rep9


title: Atl_AK_d3_inf_rep2

description:
raw data filenames: 10214_cy5_70_scan2.txt, 10214_cy3_80_scan2.txt; block for sample in raw data file: Block4
Atl_AK_d3_inf_rep2


title: Atl_AK_d3_con_rep7

description:
raw data filenames: 10256_cy5_70_scan2.txt, 10256_cy3_80_scan2.txt; block for sample in raw data file: Block3
Atl_AK_d3_con_rep7


title: Atl_AK_d3_con_rep4

description:
raw data filenames: 10233_cy5_70_scan2.txt, 10233_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d3_con_rep4


title: Atl_AK_d3_con_rep1

description:
raw data filenames: 10034_cy5_70_scan2.txt, 10034_cy3_80_scan2.txt; block for sample in raw data file: Block1
Atl_AK_d3_con_rep1


title: Atl_AK_d3_con_rep2

description:
raw data filenames: 10214_cy5_70_scan2.txt, 10214_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d3_con_rep2


title: Atl_AK_d3_con_rep3

description:
raw data filenames: 10220_cy5_70_scan2.txt, 10220_cy3_80_scan2.txt; block for sample in raw data file: Block2
Atl_AK_d3_con_rep3


title: 15C, 5h, Replicate 3

city: Helsinki

first: Marita

last: Isokallio

address: PO Box 66

country: Finland

institute: University of Helsinki

description: Log ratios were not derived from a single array.

hyb_protocol: Agilent (Agilent Technologies) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments, Westburg, Leusden, The Netherlands) using pixel resolution of 5 µm, line average 2.

data_processing: The 37 °C and 1 h post-shock raw microarray expression data have been previously deposited in the Gene Expression Omnibus under accession number GSE26587. Image analysis with GenePix Pro 6.0, bad spots were manually flagged (flag-value -100). Data preprocessing in R with limma package: background subtraction with normexp and offset 50. Log2-ratio was calculated between wild type 1 h or 5 h after cold shock and wild type before cold shock and normalized with quantile normalization.

organism: Clostridium botulinum

source_name: WT cold shock, 15C, 5h, Replicate 3

label_protocol: A total of 2 µg of each RNA sample was reverse-transcribed into cDNA and simultaneously labeled with fluorescent dyes. In brief, each 30-µl labeling reaction contained 0.2 µg/µl of random hexamers (Invitrogen), 0.01 M DTT (Invitrogen), 1.3 U/µl ribonuclease inhibitor (Invitrogen), 0.5 µM dATP, dTTP and dGTP, 0.2 µM dCTP, 1.7 nmol of Cy-3 or Cy-5 labeled dCTP (GE Healthcare, Pittsburgh, PA), 13 U/µl of SuperScript III reverse transcriptase (Invitrogen), and appropriate buffer (1 x First Strand Buffer, Invitrogen) and was incubated at 46 °C for 3 h. RNA hydrolysis and reaction inactivation were performed by addition of 10 µl of 0.1 M NaOH and 0.5 mM EDTA and incubation at 70 °C for 15 min. The reactions were subsequently neutralized by addition of 10 µl of 0.1 M HCl. The cDNA was purified with QIAquick PCR Purification Kit (Qiagen), with final elution volume of 40 µl. The cDNA concentration of each sample was measured with NanoDrop.

growth_protocol: TPGY, anaerobic, 37 °C, up to OD600=1.0 (5-7 hours), then subjected to temperature downshift to 15 °C and thereafter incubated at 15 °C.

extract_protocol: Five-ml samples from three replicate C. botulinum ATCC 3502 wild type cultures were collected at mid-logarithmic growth phase at 37 °C, and 1 h and 5 h after temperature downshift to 15 °C. The samples were collected into sterile plastic tubes containing ice-cold ethanol-phenol (9:1) solution (Sigma Aldrich, St. Louis, MO, USA), mixed thoroughly, and incubated on ice for 30 min. Cells were harvested by centrifugation (4 °C, 8000 x g) for 5 min. The cell pellets were immediately frozen to -70 °C until RNA extraction. The cell pellets were thawed on ice for 5 min and used for RNA extraction with the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. The cells were lysed with a solution containing 25 mg/ml lysozyme (Sigma Aldrich, St. Louis, MO, USA) and 250 IU/ml mutanolysin (Sigma Aldrich) in Tris-EDTA buffer (pH 8.0, Fluka BioChemica, Buchs, Switzerland) and agitated at 37 °C for 30 min. The final elution volume of RNAse free water was 300 µl. To confirm efficient removal of all genomic DNA, an additional DNase treatment was carried out using the DNA-free Kit (Ambion, Austin, TX, USA) according to manufacturer’s instructions. The RNA yield and purity (A260/A280) were checked using the NanoDrop ND-1000 device (Thermo Fisher Scientific Inc., Waltham, MA, USA). The RNA purity ratio was >2.0 for all samples. Integrity of RNA was confirmed using a miniaturized gel electrophoresis in the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The RNA integrity number was >9.2 for all RNA samples.

value: ATCC 3502, WT

tag: temperature

value: 15 °C

source_name: WT before cold shock, 37C, Replicate 3

value: 37 °C


title: 15C, 1h, Replicate 2

source_name: WT cold shock, 15C, 1h, Replicate 2

source_name: WT before cold shock, 37C, Replicate 2


title: 15C, 1h, Replicate 3

source_name: WT cold shock, 15C, 1h, Replicate 3


title: 15C, 5h, Replicate 2

source_name: WT cold shock, 15C, 5h, Replicate 2


title: 15C, 1h, Replicate 1

source_name: WT cold shock, 15C, 1h, Replicate 1

source_name: WT before cold shock, 37C, Replicate 1


title: High Fat 1

city: Seattle

first: Julia

last: Cui

state: Washington

address: 4225 Roosevelt Way NE Suite # 100

institute: University of Washington

description: high fat diet

hyb_protocol: Affymetrix standard procedure for Mouse Genome 430 2.0 array; GeneChip Hybridization, Wash and stain kit - Affymetrix 900720, 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan; scanning hardware: Affymetrix GeneChip Scanner 3000 7G with Autoloader; scanning software: Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: Gene expression in livers of mice treated with various diets was determined by the Affymetrix Mouse 430 2.0 Gene Expression arrays in the KUMC Microarray Core Facility. To ensure higher quality results in gene expression data from the microarray, we conducted microarrays on 3 mice per diet (27 microarrays in total) giving a biological n=3 per diet, which lends statistical power to increase the confidence of the conclusions drawn from this experiment. Data were preprocessed by the GCRMA package in R and Bioconductor (Gentleman et al., 2004). The expression values were in log2 scale. The gene annotations were generated using the annaffy package. Genes with average probe intensities above log2(100) in at least one diet were selected for follow-up analyses. The LIMMA package (Smyth et al., 2005) was used to determine the differentially expressed genes among various diets, using the AIN-93M-purified diet as control (global method, false discovery rate adjusted, p < 0.05). To determine statistical significance of data values from a gene symbol represented by multiple probes, values were averaged, and then a one-way ANOVA followed by a Dunnett’s multiple comparison test was performed (using AIN-93 purified diet as control).

source_name: liver_High Fat_3 wks

label_protocol: Biotinylated cRNA were prepared using One-cycle target labeling kit according to the standard Affymetrix protocol. 100ng nucleic acid waas used. Label incorporation method: In-vitro Transcription using the GeneChip 3’ IVT Express Kit - Affymetrix 901228;

growth_protocol: Ten-week old male C57BL/6 mice were purchased from Charles River Laboratories, Inc. (Wilmington, MA).  Mice were housed in a temperature-, light-, and humidity-controlled environment. The housing facility at the University of Kansas Medical Center is accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol: RNA was isolated using RNA-Bee RNA Isolation Reagent (Tel-Test Inc., Friendswood, TX) according to the manufacturer’s protocol. RNA concentrations were quantified using a NanoDrop1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) at a wavelength of 260nm. RNA integrity was evaluated by an Agilent 2100 Bioanalyzer at the KUMC Microarray Facilities.

treatment_protocol: Mice (n=3/diet) were fed one of the 9g diets (Harlan Laboratories) for 3 weeks. All mice were euthanized in the morning (8:00–10:00 A.M.) and blood and tissue samples were collected.

value: 10 weeks

tag: gender

value: male

tag: diet

value: High fat diet for 3 wks

tag: tissue

value: liver


title: High Fat 2

description: high fat diet

tag: age


title: 15C, 5h, Replicate 1

source_name: WT cold shock, 15C, 5h, Replicate 1


title: Diet-restriction 1

description: 75% of the diet TD.8604 consumed by ad lib feeding

source_name: liver_Diet-restriction_3 wks

value: diet for 3 wks-restriction


title: Normal Patient PBMC Sample 8

city: Singapore

first: Hui

last: K. Man

address: 11 Hospital Drive

department: Division of Cellular and Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression data from PBMC sample of  healthy patient

hyb_protocol: The final cRNA obtained was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA), a

scan_protocol: standard Affymetrix protocol

data_processing: The data was analysed using Partek Genomics Suite version 6.5. CEL files were imported into Partek and the following algorithms were applied. GCRMA background correction, quantile normalisation, median-polish probeset summarization, log2 transformation and batch effect removal on the hybridization date using partek proprietary batch-effect removal tool.

source_name: PBMC sample from healthy patient

label_protocol: Five micrograms of total RNA were reverse-transcribed and labeled with biotin.

growth_protocol: Patients with primary pancreatic, gastric or HCC were recruited at diagnosis, and patients with chronic hepatitis B were also recruited according to the protocol approved by the Institutional Review Board.  Informed consent was obtained from all subjects before blood samples were collected.  A total of 10 ml of blood was collected into BD Vacutainer® Plus K2EDTA tubes (Becton-Dickinson, USA).

extract_protocol: Total RNA was extracted from PBMC and WBC using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.  Genomic DNA contamination was removed by DNase I digestion (RNase-Free DNase Set, Qiagen, USA) and the DNA was further purified using an RNeasy MinElute Cleanup kit (Qiagen, USA).  Purified RNA was quantified on an ND-1000 Nano-drop Spectrophotometer (Thermo Scientific, USA).

treatment_protocol: Within 6 hours of collection, blood was processed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Sweden).  Ficoll-Paque PLUS is an aqueous solution of density 1.077 + 0.001 g/ml containing 5.7 g Ficoll 400 and 9 g sodium diatrizoate with 0.0231 g calcium disodium ethylenediamintetraacetic acid in every 100 ml.  Residual red blood cells were lysed in 1 ml RBC lysis buffer (Biolegend, USA) for 5 min, and then washed with 10 ml phosphate buffered saline (PBS).  The isolated peripheral blood mononuclear cells (PBMC) were stored at -80 oC.

tag: sample source

value: Whole Blood

tag: cell type

value: PBMC

value: healthy


title: EFA Deficient 3

description: Essential fatty acid deficient diet

source_name: liver_EFA Deficient_3 wks

value: EFA deficient diet for 3 wks


title: EFA Deficient 1

description: Essential fatty acid deficient diet


title: Pancreatic Cancer PBMC Sample 1

description: Gene expression data from PBMC sample of pancreatic cancer patient

source_name: PBMC sample from pancreatic cancer patient

value: pancreatic cancer


title: High Fat 3

description: high fat diet


title: DHA-supplemented 2

description: 7% sunflower oil (low n-3 diet) (Levant et al., 2006)

source_name: liver_DHA-supplemented_3 wks

value: DHA-supplement diet for 3 wks


title: DHA-supplemented 1


title: Diet-restriction 2


title: EFA Deficient 2

description: Essential fatty acid deficient diet


title: Normal Patient PBMC Sample 10


title: Pancreatic Cancer PBMC Sample 3


title: Normal Patient PBMC Sample 7


title: DHA-supplemented 3


title: Diet-restriction 3


title: Pancreatic Cancer PBMC Sample 2


title: Normal Patient PBMC Sample 9


title: Normal Patient PBMC Sample 5


title: Current LAR Diet 3

description: Natural ingredient diet (used in our animal facility) (Lab chow)

source_name: liver_Current LAR Diet_3 wks

value: Current LAR diet for 3 wks


title: Normal Patient PBMC Sample 6


title: Current LAR Diet 2


title: Normal Patient PBMC Sample 3


title: Normal Patient PBMC Sample 4


title: Current LAR Diet 1


title: Normal Patient PBMC Sample 2


title: Normal Patient PBMC Sample 1


title: Atherogenic Rodent 3

description: Also referred to as high-fat, -sucrose, -cholesterol, and -cholic acid (CA) diet

source_name: liver_Atherogenic Rodent_3 wks

value: Atherogenic rodent diet for 3 wks


title: Atherogenic Rodent 1


title: AIN-93M Purified 3

description: Control diet

source_name: liver_AIN-93M Purified_3 wks

value: AIN-93M purified diet for 3 wks


title: AIN-93M Purified 1

description: Control diet


title: Adjusted Calories 1

description: Adjusted Calories Diet (42% from fat), also referred to as high-saturated fat and -sucrose diet (Western diet)

source_name: liver_Adjusted Calories_3 wks

value: Adjusted calories diet for 3 wks


title: Adjusted Calories 3


title: AIN-93M Purified 2

description: Control diet


title: HCC PBMC Sample 6

description: Gene expression data from PBMC sample of  hepatocellular carcinoma patient

source_name: PBMC sample from hepatocellular carcinoma patient

value: hepatocellular carcinoma


title: HCC PBMC Sample 9


title: HCC PBMC Sample 10


title: 60% Fructose 3

description: 60% fructose diet

source_name: liver_60% fructose_3 wks

value: 60% fructose diet for 3 wks


title: 60% Fructose 1

description: 60% fructose diet

value: 10 weeks


title: HCC PBMC Sample 7


title: Atherogenic Rodent 2

value: male


title: HCC PBMC Sample 8


title: HCC PBMC Sample 3


title: Gastric Cancer PBMC Sample 3

description: Gene expression data from PBMC sample of gastric cancer patient

source_name: PBMC sample from gastric cancer patient

value: gastric cancer


title: Gastric Cancer PBMC Sample 2


title: HCC PBMC Sample 2


title: 220/0

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description:
4968481056_K
baseline

hyb_protocol: A total of 750 ng biotinylated cRNA was hybridized (Ambion).

scan_protocol: The BeadChips were scanned according to the protocol described in the Illumina Whole Genome Gene Expression for BeadStation Manual v3.2, Revision A using scanning software BeadScan 3.5.31.

data_processing: Variance stabilization normalization was applied. The statistical software R and Bioconductor libraries lumi and vsn were used.

source_name: whole-blood leukocytes, etanercept, 0hr

label_protocol: Synthesis, amplification and purification of anti-sense RNA was performed using 300 ng of enriched mRNA per sample and  the Illumina TotalPrep RNA Amplification Kit (Ambion/Applied Biosystems) following the Illumina Sentrix Array Matrix expression protocol.

extract_protocol: Total RNA was isolated in accordance with Qiagen protocols for the extraction of PAXgene tube-treated whole blood.

value: whole-blood leukocytes

tag: disease status

tag: treatment

value: etanercept

tag: time

value: 0 hours

tag: individual identifier


title: 220/4

description:
4968481056_L
endotoxin

source_name: whole-blood leukocytes, etanercept, 4hr

value: 4 hours


title: 221/4

description:
4968529052_L
endotoxin

value: healthy


title: 60% Fructose 2

description: 60% fructose diet

value: liver


title: 219/0

description:
4968529052_I
baseline


title: Adjusted Calories 2


title: Gastric Cancer PBMC Sample 1

value: Whole Blood

value: PBMC

tag: disease state


title: HCC PBMC Sample 5


title: 219/4

description:
4968529052_J
endotoxin


title: 221/0

description:
4968529052_K
baseline


title: HCC PBMC Sample 1


title: HCC PBMC Sample 4


title: 218/0

description:
4968481056_I
baseline


title: 218/4

description:
4968481056_J
endotoxin


title: 211/4

description:
4968529052_F
endotoxin

source_name: whole-blood leukocytes, placebo, 4hr

value: placebo


title: 215/0

description:
4968481056_G
baseline


title: 214/0

description:
4968529046_E
baseline


title: 217/4

description:
4968529046_K
endotoxin


title: 214/4

description:
4968529046_F
endotoxin


title: 209/0

description:
4968481056_E
baseline

source_name: whole-blood leukocytes, placebo, 0hr


title: 209/4

description:
4968481056_F
endotoxin


title: 215/4

description:
4968481056_H
endotoxin


title: 217/0

description:
4968529046_J
baseline


title: 216/4

description:
4968529052_H
endotoxin


title: 206/0

description:
4968481056_C
baseline


title: 206/4

description:
4968481056_D
endotoxin


title: 216/0

description:
4968529052_G
baseline


title: 211/0

description:
4968529052_E
baseline


title: 204/0

description:
4968529046_A
baseline


title: 208/4

description:
4968529046_D
endotoxin


title: 208/0

description:
4968529046_C
baseline


title: 204/4

description:
4968529046_B
endotoxin


title: 202/4

description:
4968529052_B
endotoxin


title: 201/0

description:
4968481056_A
baseline


title: Control shRNA (Luc) in LSCs rep1

status: Public on Feb 23 2014

city: Cambridge

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

hyb_protocol: Standard Illumina hybridzation protocol

scan_protocol: BeadArrays were scanned with a BeadArray Reader (Illumina) and expression intensities were calculated with Beadstudio software (Illumina).

data_processing: The samples were analyzed by MouseWG-6 v2.0 Expression beadchip (Illumina). The quality of probe intensities was determined using the beadarray R package from Bioconductor (Dunning et al., 2007)

source_name: Control shRNA (Luc) in LSCs

label_protocol: Standard Illumina protocol

extract_protocol: RNA was isolated using Trizol (Invitrogen).

tag: strain background

tag: genotype/variation

value: Actin-dsRed

value: bone marrow

value: Leukemia stem cells (LSCs)

tag: cell type info

value: [Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi] driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice


title: 202/0

description:
4968529052_A
baseline


title: Csnk1a1 knockdown (Csnk1a1-94 shRNA) in LSCs rep3


title: Control shRNA (Luc) in LSCs rep3


title: 201/4

description:
4968481056_B
endotoxin


title: Csnk1a1 knockdown (Csnk1a1-94 shRNA) in LSCs rep1


title: Csnk1a1 knockdown (Csnk1a1-94 shRNA) in LSCs rep2


title: Control shRNA (Luc) in LSCs rep2


title: 21lp

city: Dresden

first: Astrid

last: Schuller

address: Zellescher Weg 20B

institute: TU-Dresden

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Arabidopsis Genome Oligo Microarrays (4x44K v3, AMADID 15059) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505B , Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 9.5.1.1 ) was used to read out and process the microarray image files.  The final normalized data include 37,685 relevant probes for detection of mRNA; 6,118 IDs marked as 'NA' or 'ignore' and 1,417 controls probes were excluded.

organism: Arabidopsis thaliana

source_name: Hypertrophied host cells with large plasmodia in the cortex area (21 dai)

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Seeds of Arabidopsis thaliana ecotype Col-0 were soaked on wet filter paper in a Petri dish at 8°C for 72 h and sown onto a mixture of peat containing compost and sand (volume ratio 5:2). Plants were grown in a growth chamber at 24°C with 12 h daylight period (100 µmol m-2 s-1) and at 18°C for 12 h in the dark. Air humidity was 60% and the plants were regularly watered with tap water.

extract_protocol: SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol:
After 14 days the plants were inoculated with 2 ml of a resting spore suspension (2x10^6 spores ml-1) of the Plasmodiophora brassicae (single spore isolate) isolate ‘e3’ as described by Fähling et al. (2003) and Graf et al. (2004). Control plants were watered with the corresponding phosphate buffer only (50 mM KH2PO4, pH 5,5 adjusted with 25 % K2HPO4). Brassica rapa L. ssp. pekinensis cv. ‘Granaat’ (ECD-05) was used for propagation of the P. brassicae isolate. The spores were isolated as described by Mithen and Magrath (1992). At defined time points roots were harvested and carefully washed with deionized water. Root material for RNA isolation was instantly frozen in liquid nitrogen whereas root material for paraffin embedding was instantly dissected and fixed.
Tissue fixation and dehydration; Tissue fixation was performed with the HOPE® Reagents (DCS, Innovative Diagnostic Systems, Hamburg, Germany). Transverse sections of the main roots of A. thaliana (< 5 mm3) were immediately submerged in 1,5 ml of ice-cold (0-4°C) HOPE® I and incubated on ice overnight. All following incubation steps were performed with pre-cooled solutions and done at 0-4°C. The next day HOPE® I solution was discarded and staining of the tissue was performed in 85% ethanol with a few crystals of Eosin (Eosin Y disodium salt, Sigma) for 30 min (the Eosin staining facilitated the recovery of the tissue within the cured paraffin wax blocks). After removal of the staining solution dehydration started with incubation in a pre-mixed HOPE® II / acetone solution (1,5 ml acetone (100%) + 1,5 µl HOPE® II) for 2 h. After the HOPE® II / acetone solution was discarded the tissue was incubated in ice-cold pure acetone for 3 h, replacing the acetone during this incubation step several times. Next acetone was replaced by pre-warmed low-melting paraffin (52-54°C) (DCS, Innovative Diagnostic Systems, Hamburg, Germany) and the tissue was incubated at 54°C (60°C) for 1 h. In the next step this paraffin wax was replaced by Paraplast X-Tra (Carl Roth GmbH, Karlsruhe, Germany) and kept at 54°C (60°C) for 1 h while replacing the paraffin once to twice. Then the paraffin wax including the tissue was poured in a mold and with pre-warmed needles the tissue was placed in the desired position at 54°C (60°C). The paraffin wax was cooled down for hardening at room temperature. The embedded tissue was stored until further use at 8°C with silica gel as desiccant.
Sectioning and slide preparation; Every surface of the microtome as well as every instrument that came in contact with the sections (e.g. blade, tweezers etc.) was cleaned with RNaseZAP® (Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany). The paraffin wax block was clamped directly in the “sample holder” of the microtome and sections of 12 – 20 µm were cut, taken off with tweezers and placed on a drop of 75% ethanol pipetted on a PEN-slide (PALM MembraneSlides PEN/NF, Carl Zeiss MicroImaging GmbH, Bernried, Germany). The PEN-slides were placed on a heating plate at 45°C and incubated until the sections get stretched. Excess of ethanol was poured off and the samples were air-dried at room temperature.  A better attachment of the sections onto the PEN-slides was achieved by placing the slides for a few seconds on a heating plate at 60°C until the paraffin started to melt. PEN-slides with mounted sections were stored at 8°C with silica gel as desiccant until Laser Microdissection and Pressure Catapulting (LMPC).
Laser Microdissection and Pressure Catapulting (LMPC) and sample processing for microarray hybridization; Before cells have been collected with Laser Microdissection and Pressure Catapulting (LMPC) paraffin wax was removed by incubation of PEN-slides with tissue sections in fresh xylene for 5-10 min. Slides were then air-dried under a fume hood for a few minutes and mounted at the PALM® MicroBeam system. Cells and tissue area of interest were selected with the PALM® RoboSoftware, microdissected and catapulted into the cap of a collection device (PALM AdhesiveCaps, Carl Zeiss MicroImaging GmbH, Bernried, Germany) located on top of the desired area. For every sample 200 to 300 cells have been collected. For each type of sample the laser focus adjustment was performed individually. For cutting and catapulting the menu “RoboLPC” has been used, with Laser power: 85 – 100, Laser focus: 74 – 79, Cells were lysed directly in the cap of the collection device using 6,4 µl SuperAmp Lysis Buffer  (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instruction and stored at -20°C.

tag: ecotype

tag: infected with

value: Plasmodiophora brassicae

tag: time point

value: 21 days after infection (dai)


title: 14cc

source_name: Central cylinder from control roots (14 dai)

value: none (phosphate buffer only control)

value: 14 days after infection (dai)

value: Central cylinder from control roots