title: 400 ppm rotenone liver at day 1, biological rep3


title: Control liver at day 14, biological rep4

status: Public on Jan 02 2017

type: RNA

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

hyb_protocol: Following fragmentation, 5.2 µg of biotin-labeled single-stranded copyDNA (ss-cDNA) was hybridized for 16 hr at 45C on a GeneChip® Rat Transcriptome Array 1.0. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 using the FS450_001 protocol.

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

data_processing: Intensity values in CEL file data were first adjusted using GCCN correction to normalize the signal distribution based on the specific GC count, and then with the SST-algorithm, to expand the dynamic range of the intensity signals. Both of these algorithms are implemented in the Affymetrix® APT tool, running on an UNIX background. Further processing and quality control of the adjusted CEL files were performed with the Robust Multichip Analysis (RMA) algorithm, all implemented in the software Refiner Array (Genedata Expressionist®, current version 9), including background removal, normalization and then summarization of intensity values, to obtain a single intensity value for a transcript ID.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Control liver at day 14

label_protocol: Biotin-labeled single-stranded copyDNA (ss-cDNA) was prepared according to the standard Affymetrix protocol from 300 ng high quality total liver RNA (GeneChip® WT Plus Reagent Kit Version1).

growth_protocol: All animal experiments were performed according to the German guidelines for care and use of laboratory animals and are approved by the State Agency for Nature, Environment and Consumer Protection North Rhine-Westphalia in Germany (LANUV). Male RccHan Wistar rats at the age of 7-8 weeks were purchased from Harlan laboratories BV (Horst, Netherlands). Animals were housed under controlled standard conditions in groups with 2 or 3 animals per cage in makrolon cages type IV, with a 12h light-dark cycle at 22 ± 2°C. Standard rodent chow pellets and water were provided ad libitum.

extract_protocol: On days  1, 3 or 14  rats were euthanized and blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from liver (70 mg) using the RNeasy Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

treatment_protocol: Male RccHan Wistar rats (7-8 weeks old) were randomly assigned to the vehicle or treatment group (n=5). 400 ppm rotenone (Sigma Aldrich, Steinheim, Germany) was administered in the diet for 1, 3 or 14 consecutive days. Control groups received untreated food.

tag: strain

value: Wistar (RccHan:WIST)

tag: gender

value: male

tag: age

value: 7-8 weeks

tag: treated with

value: none (untreated control)

tag: tissue

value: liver


title: Control liver at day 3, biological rep3

source_name: Control liver at day 3


title: Control liver at day 14, biological rep1


title: 400 ppm rotenone liver at day 14, biological rep1

source_name: 400 ppm rotenone liver at day 14

value: 400 ppm rotenone for 14 days


title: 400 ppm rotenone liver at day 3, biological rep3

source_name: 400 ppm rotenone liver at day 3

value: 400 ppm rotenone for 3 days


title: 400 ppm rotenone liver at day 1, biological rep2

source_name: 400 ppm rotenone liver at day 1

value: 400 ppm rotenone for 1 day


title: 400 ppm rotenone liver at day 1, biological rep4


title: Control liver at day 3, biological rep4


title: control [A2483-40]

city: Kongens Lyngby

first: David Adrian

last: Ewald

address: Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

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

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

data_processing:
The normalization and summarization was carried out in R, using:
- rma {affy}
- normalize.quantiles.robust {preprocessCore}
Versions: preprocessCore_1.32.0 ; affy_1.48.0

organism: Mus musculus

source_name: control

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

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

value: skin, dorsal, control

tag: condition

value: NN

tag: treatment

value: no treatment

tag: Sex

value: female


title: control [A2483-39]


title: Control liver at day 14, biological rep3


title: 400 ppm rotenone liver at day 3, biological rep4


title: Control liver at day 3, biological rep2


title: Control liver at day 1, biological rep3

source_name: Control liver at day 1


title: Control liver at day 3, biological rep1


title: Control liver at day 1, biological rep4


title: OVA-ODT 24h [A2483-31]

source_name: OVA-ODT 24h

value: skin, dorsal, OVA-ODT 24h

value: LS

value: OVA-ODT treated, sampling 24h after the last sensitization


title: 400 ppm rotenone liver at day 3, biological rep1


title: control [A2483-38]


title: 400 ppm rotenone heart at day 14, biological rep1

source_name: 400 ppm rotenone heart at day 14

label_protocol: Biotin-labeled single-stranded copyDNA (ss-cDNA) was prepared according to the standard Affymetrix protocol from 300 ng high quality total heart RNA (GeneChip® WT Plus Reagent Kit Version1).

extract_protocol: On days  1, 3 or 14  rats were euthanized and blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from from heart (left ventricle apex, 30 mg), using the RNeasy Fibrous Tissue Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

value: heart


title: OVA-ODT 24h [A2483-29]


title: 800R.NH4NO3_rep2

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

country: Spain

institute: Universidad Pública de Navarra

description: Gene expression after 5 weeks CO2 tratment. Sample collected 4h from the beginning of the light period

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. For this study, the significant difference in gene expression was Q value < 0.05 and log2 fold change > 0.5.

organism: Arabidopsis thaliana

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana, Columbia 0 ecotype (col 0) plants grown under hydroponic conditions.

extract_protocol: Total RNA was isolated according to Liao et al.(2004).

tag: ecotype

value: Columbia 0

value: root


title: Control liver at day 1, biological rep1

value: Wistar (RccHan:WIST)

value: male


title: 400 ppm rotenone heart at day 14, biological rep4

value: 7-8 weeks


title: NC/Nga(-mite) [A2483-23]

source_name: NC/Nga(-mite)

value: skin, ear, control

value: NN/NL

tag: genotype

value: NC/Nga(-mite)


title: 400 ppm rotenone heart at day 3, biological rep3

source_name: 400 ppm rotenone heart at day 3

value: 400 ppm rotenone for 3 days


title: OVA-ODT 24h [A2483-30]


title: 400 ppm rotenone heart at day 14, biological rep2

value: 400 ppm rotenone for 14 days


title: NC/Nga(-mite) [A2483-24]


title: 400 ppm rotenone heart at day 1, biological rep3

source_name: 400 ppm rotenone heart at day 1

value: 400 ppm rotenone for 1 day


title: 400 ppm rotenone heart at day 14, biological rep3


title: 400 ppm rotenone heart at day 1, biological rep4


title: NC/Nga(-mite) [A2483-22]


title: 400 ppm rotenone heart at day 3, biological rep4


title: NC/Nga(+mite) [A2483-18]

source_name: NC/Nga(+mite)

value: skin, ear, NC/NGA(+mite)

value: NC/Nga(+mite)


title: NC/Nga(-mite) [A2483-21]


title: NC/Nga(-mite) [A2483-25]


title: NC/Nga(+mite) [A2483-20]


title: 400 ppm rotenone heart at day 3, biological rep1


title: Control heart at day 14, biological rep4

source_name: Control heart at day 14

value: none (untreated control)


title: 400 ppm rotenone heart at day 1, biological rep2


title: 400 ppm rotenone heart at day 3, biological rep2


title: NC/Nga(+mite) [A2483-19]

value: LS


title: NC/Nga(+mite) [A2483-17]


title: C57BL/6NCrSlc [A2483-15]

value: NN

value: female


title: C57BL/6NCrSlc [A2483-14]


title: 400 ppm rotenone heart at day 1, biological rep1

value: heart


title: NC/Nga(+mite) [A2483-16]


title: C57BL/6NCrSlc [A2483-13]


title: C57BL/6NCrSlc [A2483-12]


title: Control heart at day 14, biological rep1


title: Control heart at day 14, biological rep2


title: filaggrin mutaion [A2483-09]

source_name: filaggrin mutation

value: skin, ear, FLG mut

value: filaggrin mutation


title: filaggrin mutaion [A2483-08]


title: filaggrin mutaion [A2483-07]


title: Control heart at day 3, biological rep4

source_name: Control heart at day 3

value: Wistar (RccHan:WIST)

value: male


title: Flaky tail(B6 back) [A2483-05]

source_name: Flaky tail(B6 back)

value: skin, back, Flaky tail

value: Flaky tail(B6 back)


title: Control heart at day 3, biological rep3

value: 7-8 weeks


title: Flaky tail(B6 back) [A2483-04]


title: filaggrin mutaion [A2483-06]


title: filaggrin mutaion [A2483-10]


title: Control heart at day 1, biological rep2

source_name: Control heart at day 1


title: Control heart at day 3, biological rep2


title: Flaky tail(B6 back) [A2483-03]


title: Flaky tail(B6 back) [A2483-01]


title: 400 ppm rotenone brain stem at day 14, biological rep1

source_name: 400 ppm rotenone brain stem at day 14

label_protocol: Biotin-labeled single-stranded copyDNA (ss-cDNA) was prepared according to the standard Affymetrix protocol from 300 ng high quality total brain stem RNA (GeneChip® WT Plus Reagent Kit Version1).

extract_protocol: On days  1, 3 or 14  rats were euthanized and blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from brain stem (70 mg) using the RNeasy Lipid Tissue Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

value: brain stem


title: C7M2FT

city: Toronto

first: David

last: Kaplan

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

hyb_protocol: cRNA were fragment and hybridized to gene ships according to manufacturers protocol (Affymetrix). The GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using a laser scanner

data_processing: Gene expression analyses were completed using R (v3.2.0).

organism: Homo sapiens

source_name: Cultured NB Met model

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 nanogram total RNA

growth_protocol: SK-N-AS cells or sublines were cultured in high glucose DMEM media (Invitrogen) containing 10% FBS, 1% non-essential amino acids (Invitrogen) and 1% pen/strep (Invitrogen).

extract_protocol: RNA was isolated using the Ribopure kit (Invitrogen) according to the manufacturer’s instructions.

tag: sample type

value: neuroblastoma metastatic model

tag: culture

value: In vitro isolate


title: Control heart at day 3, biological rep1


title: Control heart at day 1, biological rep4


title: 400 ppm rotenone brain stem at day 14, biological rep4

value: 400 ppm rotenone for 14 days


title: C57BL/6NCrSlc [A2483-11]

value: skin, ear, control


title: SKNASTR

source_name: Cultured NB Primary model

value: neuroblastoma primary model


title: Control heart at day 1, biological rep1

value: none (untreated control)


title: Flaky tail(B6 back) [A2483-02]

value: LS


title: 400 ppm rotenone brain stem at day 14, biological rep3


title: Control heart at day 1, biological rep3


title: 400 ppm rotenone brain stem at day 3, biological rep4

source_name: 400 ppm rotenone brain stem at day 3

value: 400 ppm rotenone for 3 days


title: 400 ppm rotenone brain stem at day 14, biological rep2


title: Control liver at day 1, biological rep2

source_name: Control liver at day 1

value: liver


title: Control heart at day 14, biological rep3

value: heart


title: 400 ppm rotenone brain stem at day 3, biological rep3


title: C2M4AG


title: C3M1jaw


title: 400 ppm rotenone brain stem at day 3, biological rep1


title: Control brain stem at day 14, biological rep4

source_name: Control brain stem at day 14


title: C21M3FT


title: C7M2AG


title: 400 ppm rotenone brain stem at day 1, biological rep3

source_name: 400 ppm rotenone brain stem at day 1

value: 400 ppm rotenone for 1 day


title: 400 ppm rotenone brain stem at day 1, biological rep4

value: Wistar (RccHan:WIST)


title: C18M4Brain


title: C1M4AG


title: C2M3FT


title: C21M4Brain


title: Control brain stem at day 14, biological rep2

value: male


title: C21M1Brain


title: C7M1jaw


title: C21M3Brain


title: C10M2FT


title: 400 ppm rotenone brain stem at day 3, biological rep2


title: Control brain stem at day 3, biological rep4

source_name: Control brain stem at day 3


title: C18M3Brain


title: C21M2Brain


title: 400 ppm rotenone brain stem at day 1, biological rep2


title: Control brain stem at day 14, biological rep3


title: Control brain stem at day 3, biological rep3


title: 400 ppm rotenone brain stem at day 1, biological rep1


title: Control brain stem at day 3, biological rep2


title: Control brain stem at day 14, biological rep1


title: MINO

city: Nantes

last: CHIRON

address: 8 quai Moncousu

country: France

institute: CRCNA

description: Gene expression data

hyb_protocol: Biotinylated cRNA was amplified with a double in vitro transcription and hybridized to the human U133 2.0 plus GeneChips, according to the manu- facturer’s instructions (Affymetrix, Santa Clara, CA, USA)

scan_protocol: Fluorescence intensities were quantified and analyzed using the GCOS software

data_processing: Gene expression data were normalized with the MAS5 algorithm and analyzed with our bioinformatics platforms: RAGE (http://rage.montp.inserm.fr/)

source_name: MCL cell line 11

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% FCS and 2mM glutamine

extract_protocol: RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany)

value: Mantle cell lymphoma

tag: cell line

value: MINO


title: DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 24h replicate 3

city: Xi'an

first: Bei

last: Han

state: Shaanxi

address: NO 76 Yanta West Road

department: School of Public Health

country: China

institute: Xi'an Jiaotong University

description:
Biological replicate 3 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 24h culture cells
D3vsC3; D-3vsC-3:cy5ByCy3Signal(normalized)

hyb_protocol: The labelled DNA was dissolved into hybridization buffer (2×GEx Hyb buffer (HI-RPM), Agilent In Situ Hybridization Kit; 25% formamide) at 45°C overnight. After hybridization, the slides were washed in 0.2% SDS and 2× SSC at 42°C for 5min, then washed in 0.2× SSC at room temperature for 5min. Finally the slides were drying for microarray scan.

scan_protocol: Scanned on an Agilent G2565CA scanner

data_processing: Quantile normalized,background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Clostridium beijerinckii NCIMB 8052

source_name: collected the whole fermentation cells_P2 with CaCO3 at 24h

label_protocol: The Crystal Core® cDNA amplified RNA labelling kit (CapitalBio, Beijing, China) were used as the protocol. 1 µg of total RNA were primed with 1 µl of 100 µM T7 Oligo (dT) DNA primer at 70°C for 10 min to get the 1st strand cDNA, then transcribed into cRNA at 37°C for 4 h in the presence of T7 enzyme Mix, and the 2µg of cRNA were reversed transcribed into cDNA at 25°C for 10min,  37°C for 1.5 h in the presence of 1.5 µl CbcScript II RTase (CapitalBio) with 4µl Random Primer; and 1 µg of cDNA,100 µM each dATP, dTTP, dGTP, with 25 µM dCTP Cy3-label (Cy5-label) were used for labeling by 4µl Random Primer and1.2 µl Klenow Fragment .

growth_protocol: DG-8052 cells were grown at P2 medium/ P2 meidum with 4g/L CaCO3 in anaerobic chamber at 35 °C.

extract_protocol: Total cellular RNA was extracted from homogenized cells using RiboPureTM RNA Purification Kit, bacteria (Ambion®, Life Technologies, Inc., US) according to the manufacturer’s instructions.

value: degenerated strain

tag: culture media

value: P2 medium with 4g/L CaCO3

tag: culture duration

value: 24 hrs

value: P2 medium


title: DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 24h replicate 2

description:
Biological replicate 2 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 24h culture cells
D2vsC2; D-2vsC-2:cy5ByCy3Signal(normalized)

source_name: collected the whole fermentation cells_P2


title: Control brain stem at day 3, biological rep1

value: 7-8 weeks

value: brain stem


title: DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 24h replicate 1

description:
Biological replicate 1 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 24h culture cells
D1vsC1; D-1vsC-1:cy5ByCy3Signal(normalized)


title: Z138

description: Gene expression data

source_name: MCL cell line 10

label_protocol: Biotinylated cRNA was amplified with a double in vitro transcription and hybridized to the human U133 2.0 plus GeneChips, according to the manu- facturer’s instructions (Affymetrix, Santa Clara, CA, USA)


title: E. coli ATCC 25922 Ser83Leu+QnrS replicate 2

status: Public on Jan 01 2017

city: Seville

first: Jose Manuel

last: Rodriguez Martinez

address: Snchez Pizjuan SN

institute: University of Seville

description: Biological replicate 2 of 2. 1 hour of exposition to 1 mg/L of ciprofloxacin

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli ATCC 25922

source_name: Exponential cells (DO600=0,4)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: E. coli ATCC 25922 (wild-type) and EC14, EC19, EC24 (LLQR) isogenic strains were tested to evaluate the global response to relevant fix concentration of ciprofloxacin (1 mg/L, breakpoint for reduced susceptibility according to CLSI). All of them were susceptible to quinolones according to CLSI breakpoints. (CLSI, n.d.) Cultures were started from single colonies and grown overnight in 25 ml of LB. These cell were diluted 1:100 and growth to cell concentration of 4x108 cells/ml (OD600 nm=0.4, exponential phase) for treatment. Three biological replicates per genotype were incubated at 1 mg/L of ciprofloxacin during 60 minutes (that means 250xMIC for E. coli ATCC 25922, 8xMIC for EC14, 2xMIC for EC19 and 1xMIC for EC24). Approximately 109 cells (2 ml) were taken for RNA isolation.

extract_protocol: RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Biological replicates per genotype were incubated at 1 mg/L of ciprofloxacin during 60 minutes (that means 250xMIC for E. coli ATCC 25922, 8xMIC for EC14, 2xMIC for EC19 and 1xMIC for EC24).

tag: substrain

tag: genotype/variation

value: Ser83Leu substitution in GyrA and coding for QnrS1


title: DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 12h replicate 3

description:
Biological replicate 3 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 12h culture cells
B3vsA3; B-3vsA-3:cy5ByCy3Signal(normalized)

source_name: collected the whole fermentation cells_P2 with CaCO3 at 12h

tag: strain

value: 12 hrs


title: E. coli ATCC 25922 marR deletion+QnrS replicate 1

description: Biological replicate 1 of 2. 1 hour of exposition to 1 mg/L of ciprofloxacin

value: marR deletion and coding for QnrS1


title: NTS1

description: Gene expression data

source_name: MCL cell line 1


title: MAVER

description: Gene expression data

source_name: MCL cell line 7

value: MAVER


title: DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 12h replicate 2

description:
Biological replicate 2 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 12h culture cells
B2vsA2; B-2vsA-2:cy5ByCy3Signal(normalized)


title: E. coli ATCC 25922 QnrS replicate 1

value: coding for QnrS1


title: Granta-519

description: Gene expression data

source_name: MCL cell line 4


title: REC1

description: Gene expression data

source_name: MCL cell line 8


title: E. coli ATCC 25922 QnrS replicate 2


title: Control brain stem at day 1, biological rep4

source_name: Control brain stem at day 1

tag: gender

value: none (untreated control)


title: JVM2

description: Gene expression data

source_name: MCL cell line 6


title: Wild-type E. coli ATCC 25922 replicate 1

description: Biological control replicate 1 of 2. 1 hour of exposition to 1 mg/L of ciprofloxacin

value: wild-type


title: JEKO

description: Gene expression data

source_name: MCL cell line 5

value: JEKO


title: Wild-type E. coli ATCC 25922 replicate 2

description: Biological control replicate 2 of 2. 1 hour of exposition to 1 mg/L of ciprofloxacin


title: UPN1

description: Gene expression data

source_name: MCL cell line 9


title: E. coli ATCC 25922 Ser83Leu+QnrS replicate 1


title: NTS3

description: Gene expression data

source_name: MCL cell line 3


title: E. coli ATCC 25922 marR deletion+QnrS replicate 2


title: Control brain stem at day 1, biological rep1

value: Wistar (RccHan:WIST)

value: male

tag: age


title: DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 12h replicate 1

description:
Biological replicate 1 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 12h culture cells
B1vsA1; B-1vsA-1:cy5ByCy3Signal(normalized)


title: ADX-PSL ZT22

city: Fukuoka

first: Satoru

last: Koyanagi

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

country: Japan

institute: Kyushu University

description: Gene expression in spinal cord of ADX-PSL mice at ZT22 after 7days nerve injury

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray 4x44K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Spinal cord of ADX-PSL mice at ZT22

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

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: Spinal cord

value: ICR


title: NTS2

description: Gene expression data

source_name: MCL cell line 2

value: Mantle cell lymphoma


title: Control brain stem at day 1, biological rep3

tag: treated with


title: Control brain stem at day 1, biological rep2

tag: tissue


title: ADX-PSL ZT10

description: Gene expression in spinal cord of ADX-PSL mice at ZT10 after 7days nerve injury

source_name: Spinal cord of ADX-PSL mice at ZT10


title: Sham-PSL ZT22

description: Gene expression in spinal cord of sham-PSL mice at ZT22 after 7days nerve injury

source_name: Spinal cord of sham-PSL mice at ZT22


title: Sham-PSL ZT10

description: Gene expression in spinal cord of sham-PSL mice at ZT10 after 7days nerve injury

source_name: Spinal cord of sham-PSL mice at ZT10


title: TN_W2

city: Lisboa

first: Margarida

last: Rocheta

address: Tapada da ajuda

country: Portugal

institute: Instituto Superior de Agronomia

hyb_protocol: Microarrays hybridization were performed according to the Affymetrix GeneChip® expression Analysis Technical Manual.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Scanned arrays were analyzed first with Affymetrix MAS 5.0 software to obtain Absent/Present calls and for subsequent analysis with DNA-Chip Analyzer (dChip) Version Release (Apr 15, 2005) (http://www.dchip.org, Wong Lab, Harvard).

organism: Vitis vinifera

source_name: Water stress - irrigation withdrawn until ψleaf= -0.9 Mpa, biological rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Plants were transplanted to pots filled with soil placed in the greenhouse under 200 µmol m-2 s-1 light intensity, 16h light / 8h dark photoperiod, temperature of 25ºC day / 23ºC night and irrigation when necessary with nutrient solution [53]. When plants were about 50 to 60 cm high, with 6 to 8 expanded leaves, stresses were applied to groups of six plants,

extract_protocol: Total RNA from leaves was extracted through the method described by Reid et al.

treatment_protocol: Vitis vinifera L. varieties Touriga Nacional and Trincadeira shoots were collected in the field during the winter pruning season. Collected shoots were disinfected with 2g L-1 fungicide (mixture of ciprodinil and fludioxonil), wrapped in absorbent paper and placed at 4ºC for circa two months. Then they were placed in distilled water under controlled conditions (25ºC, 50 mmol m-2 s-1) for two weeks upon which they had developed roots and a few new leaves.

tag: variety

value: Touriga Nacional

value: leaves from greenhouse grown plants


title: TR_L1

source_name: Light stress, 1 hour at 2000µmolm2s-1, biological rep1

value: Trincadeira


title: TR_L2

source_name: Light stress, 1 hour at 2000µmolm2s-1, biological rep2


title: FTR_C3

source_name: Field control, biological rep3

value: leaves from field grown plants


title: TN_C3

source_name: Control, biological rep3


title: TN_C1

source_name: Control, biological rep1


title: TN_L1


title: TN_W3

source_name: Water stress - irrigation withdrawn until ψleaf= -0.9 Mpa, biological rep3


title: TR_L3

source_name: Light stress, 1 hour at 2000µmolm2s-1, biological rep3


title: TR_H2

source_name: Heat stress - 1h at 42ºC, biological rep2


title: FTR_S3

source_name: Field stress, biological rep3


title: TR_H3

source_name: Heat stress - 1h at 42ºC, biological rep3


title: TN_H3


title: TN_H2


title: FTR_S2

source_name: Field stress, biological rep2


title: TR_C2

source_name: Control, biological rep2


title: TR_C1


title: TN_L3


title: TR_C3


title: TR_W1

source_name: Water stress - irrigation withdrawn until ψleaf= -0.9 Mpa, biological rep1


title: TR_H1

source_name: Heat stress - 1h at 42ºC, biological rep1


title: TN_H1


title: TN_W1


title: TN_C2


title: TN_L2


title: FTR_S1

source_name: Field stress, biological rep1


title: FTR_C2

source_name: Field control, biological rep2


title: TR_W3


title: TR_W2

source_name: Water stress - irrigation withdrawn until ψleaf= -0.9 Mpa, biological rep2


title: FTR_C1

source_name: Field control, biological rep1


title: FTN_C3


title: FTN_S1


title: R6/2-LNA-SCB-repl-4

city: Barcelona

first: Eulalia

last: Marti

address: Dr. Aiguader 88

institute: Centre for Genomic Regulation

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

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

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The mouse dissected striatum was placed immediately in Qiazol solution from Qiagen, followed by RNA extraction with the miRNeasy kit (Qiagen) as indicated by the manufacturer.

value: striatum brain tissue

value: 11 weeks old


title: FTN_S2


title: R6/2-LNA-CTG-repl-5


title: R6/2-LNA-CTG-repl-2


title: R6/2-LNA-SCB-repl-2


title: FTN_C2


title: FTN_S3


title: Kidney_5dnorUDCAPrefeeding_3w_CommonBileDuctLigation_179

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 4.0.)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files. Data Pre-Processing and Filtering (Partek Genomics Suite, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization).

label: Biotin

label_protocol: Affymetrix WT PLUS Reagent Kit  P/N 703147 Rev3, (Cat No. 902280); Lot: 4248402

extract_protocol: Isolation of total RNA was performed using TRIzol reagent (Life Technologies; Carlsbad, CA; Cat No 15596018). RNA was quantified spectrophotometrically at 260 and 280 nm.

value: kidney


title: MiRNAs expression in bone marrow T cells of AA patient C

city: Jinan

first: Yuan-xin

last: Sun

address: 107 Wenhuaxi Rd

institute: Qilu hospital, Shandong University

description: MiRNAs expression data in bone marrow T cells of AA patient C

hyb_protocol: Biotin-labeled sample was hybridized for 16 hr at 48℃ on miRNA Array. MiRNA Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: MiRNA Chips were scanned using the Affymetrix Scanner 3000 7G.

data_processing: The signal values obtained were analyzed with Affymetrix miRNA Expression Console.

source_name: bone marrow T cells of AA patient C

label_protocol: Tailed RNA and FlashTag ligation mix biotin were mixed and incubated according to the protocol of FlashTag Biotin RNA labeling Kit for Affymetrix GeneChip miRNA Arrays (Genisphere).

treatment_protocol: cell sorting protocol: Bone marrow mononuclear cells were obtained by aspiration of the iliac crest of patients and healthy donors and prepared with the use of lymphocyte separation medium. CD3+ cells were positively selected from three SAA patients and three healthy controls by means of immunomagnetic activated cell sorting system (Miltenyi, Bergisch Gladbach, Germany), according to the manufacturer’s instruction. Purity of CD3+ cells was 93% to 97% by flow cytometry analysis.

tag: subject status

value: Acquired aplastic anemia (AA) patient

tag: subject id

value: Patient-C

value: bone marrow

tag: cell type

value: CD3+ T cells


title: MiRNAs expression in bone marrow T cells of healthy control D

description: MiRNAs expression data in bone marrow T cells of healthy control D

value: healthy control

value: Control-D


title: Wild-type-LNA-SCB-repl-4

value: male

tag: genotype

value: wild-type


title: R6/2-LNA-SCB-repl-1


title: R6/2-LNA-SCB-repl-5


title: R6/2-LNA-SCB-repl-3


title: R6/2-LNA-CTG-repl-3


title: Wild-type-LNA-SCB-repl-1


title: R6/2-LNA-CTG-repl-4


title: Wild-type-LNA-SCB-repl-2


title: MiRNAs expression in bone marrow T cells of AA patient G

description: MiRNAs expression data in bone marrow T cells of AA patient G

source_name: bone marrow T cells of AA patient G

value: Patient-G


title: Wild-type-LNA-SCB-repl-5


title: MiRNAs expression in bone marrow T cells of AA patient B

description: MiRNAs expression data in bone marrow T cells of AA patient B

source_name: bone marrow T cells of AA patient B

value: Patient-B


title: FTN_C1

value: Touriga Nacional


title: R6/2-LNA-CTG-repl-1


title: Kidney_5dnorUDCAPrefeeding_3w_CommonBileDuctLigation_172


title: MiRNAs expression in bone marrow T cells of healthy control E

description: MiRNAs expression data in bone marrow T cells of healthy control E

value: Control-E


title: Kidney_5dnorUDCAPrefeeding_3w_CommonBileDuctLigation_175


title: Wild-type-LNA-SCB-repl-3


title: Kidney_3w_CommonBileDuctLigation_170

source_name: 3w cBDL


title: Kidney_3w_CommonBileDuctLigation_164


title: Kidney_3w_Sham_operation_160

source_name: 3w SHAM


title: 5F shLUC SMER 1

city: Boston

first: Melissa

last: Kinney

state: MA

address: 1 Blackfan Circle

country: USA

institute: Boston Children's Hospital

description: 5F shLUC replicate A

hyb_protocol: Hybridization cocktails were prepared by combining the fragmented, biotin-labeled cDNA with hybridization cocktail (Affymetrix Hybridization, Wash, and Stain Kit)

scan_protocol: The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000

data_processing: Microarray signal intensities were RMA-summarized and quantile normalized

source_name: CD34-5F HSPCs

label_protocol: The cDNAs were fragmented and labeled using a Nugen Encore Biotin Module

growth_protocol: CD34-5F cells. Human induced pluripotent stem cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Doxycycline was added at 2 μg/ml (Sigma). CD34-5F cells were transduced with lentiviral vectors with shRNAs for Luciferase (control) or ATG5. To initiate differentiation, shRNA-transduced CD34-5F cells were cultured in SFEM progenitor medium without Dox for 2 days. DMSO or SMER28 was added for 72 hours before RNA extraction. 2) CD34+ cord blood progenitors (AllCells) were transduced with lentiviral vectors with shRNAs for Luciferase (control) and RPS19 for 24 hours. Virus was washed off and GFP+ cells were isolated by flow sorting after 24 hours. Cells were cultured in SFEM progenitor medium for 72 hours with DMSO or SMER28 (50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.RNA samples (up to 50 ng) were processed using a Nugen PICO WTA System V2 kit.

treatment_protocol: CB CD34+ progenitors transduced with shLUC or shRPS19 (2 days of culture) were treated with DMSO or SMER28 (10 μM) for 72 hours in expansion conditions. CD34-5F cells transduced with shLUC or shATG5 were cultured without Dox for 2 days and treated with DMSO or SMER28 for 72 hours. For both cell types, RNA was isolated from sorted GFP+ cells (positive for shRNA) after a total of 5 days in culture.

tag: treatment


title: 5F shLUC DMSO 2

description: 5F shLUC replicate B

value: DMSO


title: Kidney_3w_CommonBileDuctLigation_165


title: 5F shLUC SMER 2

description: 5F shLUC replicate B


title: 5F shATG5 SMER 2

description: 5F shATG5 replicate B


title: 5F shATG5 DMSO 2

description: 5F shATG5 replicate B


title: 5F shATG5 SMER 1

description: 5F shATG5 replicate A


title: Kidney_3w_Sham_operation_159


title: Kidney_3w_Sham_operation_158


title: CB shRPS19 DMSO 2

description: shRPS19 replicate 2

source_name: Cord blood CD34+


title: BT-549_Mimic 4-3

city: Aurora

first: Jennifer

middle: K

last: Richer

state: CO

address: Mail Stop 8104, RC1N 5th Floor P18-5127, 12800 E. 19th Ave.

department: Pathology

institute: University of Colorado Anschutz Medical Campus

description: Gene expression data from miR-150-5p mimic transfected cells

hyb_protocol: One ug of biotinylated RNA from each sample was hybridized onto Affymetrix® GeneChip Mouse Transcriptome Array 1.0 according to the manufacturer's recommendations.

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

data_processing: CEL files were normalized using robust multiarray analysis (RMA). Values are log2 scale.

source_name: miR-150-5p mimic transfected_BT-549

label_protocol: One ug of total RNA from each sample was labelled with FlashTag Biotin RNA Labeling kit (Genisphere, Hatfield, PA, USA).

growth_protocol: BT-549 cell were grown in RPMI-1640 supplemented with 10% FBS.

treatment_protocol: Mature miR-150-5p (miRNA mimic) or non-specific negative control (NC) (Ambion, Austin, TX, USA) at a concentration of 50 nM were incubated with Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) in culture medium per the manufacturer's instructions before addition to cells. Mock transfection using just lipofectamine without added RNA was also used as a negative control. Cells were incubated at 37°C for 24 hrs before replacement of medium. Transfected cells were then harvested for RNA and protein at 72 hours.

value: breast cancer cell line

tag: transfected with

value: miR-150-5p mimic

tag: time point

value: 72 hours post transfection


title: CB shLUC DMSO 2

description: shLUC replicate 2


title: 5F shATG5 DMSO 1

description: 5F shATG5 replicate A


title: 5F shLUC DMSO 1

description: 5F shLUC replicate A


title: CB shLUC SMER 2

description: shLUC replicate 2


title: CB shRPS19 SMER 1

description: shRPS19 replicate 1


title: CB shRPS19 DMSO 1

description: shRPS19 replicate 1


title: CB shLUC DMSO 1

description: shLUC replicate 1


title: MiRNAs expression in bone marrow T cells of healthy control F

description: MiRNAs expression data in bone marrow T cells of healthy control F

value: Control-F


title: BT-549_Mimic 4-2

tag: cell line


title: CB shRPS19 SMER 2

description: shRPS19 replicate 2


title: BT-549_NC 3-3

description: Gene expression data from negative control transfected cells

source_name: negative control transfected_BT-549

value: negative control


title: BT-549_Mimic 4-1


title: BT-549_NC 3-2


title: BT-549_NC 3-1


title: CB shLUC SMER 1

description: shLUC replicate 1


title: BT-549_Mock 2-3

description: Gene expression data from mock transfected cells

source_name: mock transfected_BT-549

value: mock


title: BT-549_Mock 2-1


title: BT-549_Mock 2-2


title: ZR-75-1_Mimic 4-3

source_name: miR-150-5p mimic transfected_ZR-75-1

growth_protocol: ZR-75-1 cell were grown in RPMI-1640 supplemented with 10% FBS.

treatment_protocol: Mature miR-150-5p (miRNA mimic) or non-specific negative control (NC) (Ambion, Austin, TX, USA) at a concentration of 50 nM were incubated with Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) in culture medium per the manufacturer's instructions before addition to cells. Mock transfection using just lipofectamine without added RNA was also used as a negative control. Cells were incubated at 37°C for 24 hrs before replacement of medium. Transfected cells were then harvested for RNA and protein at 48 hours.

value: 48 hours post transfection


title: ZR-75-1_Mimic 4-2


title: ZR-75-1_Mimic 4-1


title: ZR-75-1_NC 3-1

source_name: negative control transfected_ZR-75-1


title: ZR-75-1_NC 3-3


title: ZR-75-1_Mock 2-3

source_name: mock transfected_ZR-75-1


title: ZR-75-1_Mock 2-2


title: PC-3 RWDD4 clone #17

city: Bethesda

first: Jean

last: Winter

state: MD

address: 50 South Driver

department: NHGRI

institute: NIH

description: Gene expression data from prostate cancer cells lines

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to The Affymetrix Human GeneChip® 2.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

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

data_processing: Data was processed via Partek and normalized using RMA.

source_name: Prostate Cancer cell line

label_protocol: Labeling performed using GeneChip® WT Terminal Labeling and Controls Kit according to manufacturer's protocol.

growth_protocol: PC-3 cells were incubated in 5% CO2 at 37 °C.

extract_protocol: Total RNA was isolated from cells using QIAGEN RNeasy Mini Kit with on-column DNaseI digestion.

treatment_protocol: not applicable

tag: overexpressed gene


title: PC-3 RWDD4 clone #6


title: PC-3 RWDD4 clone #24


title: PC-3 control clone #5

value: control


title: ZR-75-1_NC 3-2


title: PC-3 control clone #4


title: PC-3 CENPU clone #4

value: CENPU


title: PC-3 control clone #2


title: PC-3 CENPU clone #5


title: HTC116-miR1966OE-2

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);   Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Genomics Suite, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization)

growth_protocol: HCT116 cells were cultured in McCoy’s 5A modified Medium (w/o L-Glutamine, 2,2g/L sodium bicarbonate). Growth media contained 10% foetal bovine serum (FBS) gold (Biochrome, Austria) and antibiotics (50 units per ml of penicillin, 50μg/ml of streptomycin). Cells were incubated in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol: miRNeasy

value: overexpressing miR-196b


title: PC-3 control clone #3 (RWDD4 study)


title: PC-3 control clone #4 (RWDD4 study)


title: PC-3 control clone #3


title: ZR-75-1_Mock 2-1


title: PC-3 RWDD4 clone #5


title: PC-3 control clone #1


title: PC-3 CENPU clone #7


title: PC-3 CENPU clone #13


title: PC-3 control clone #2 (RWDD4 study)


title: PC-3 CENPU clone #1


title: HTC116-miR1966OE-3


title: PC-3 control clone #5 (RWDD4 study)


title: HTC116-miR1966OE-1


title: Bel HG only

city: Hong Kong

first: Kin Wah

last: Lee

address: 21 Sassoon Road

institute: The University of Hong Kong

hyb_protocol: standard Affymetrix protocol: Service by the Centre for Genomic Sciences, The University of Hong Kong

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method

growth_protocol: BEL7402 HCC cells grown in the presence or absence of 10ng/ml hepatocyte growth factor (HGF)

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


title: HTC116-CoOE-3

value: empty vector control


title: D.rerio_Grbeta-beclo-experiment: GRbeta/beclo_4

city: Leiden

first: Marcel

last: Schaaf

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description:
Sample 1322
Biological replicate 4 of 4: GRbeta/beclo

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Twenty larvae per treatment group were collected in 1 ml of TRIZOL® Reagent (Invitrogen) and stored at -80°C. Larvae were homogenized in TRIZOL® and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Wild type and Tg(hsp70:Gal4, UAS:EGFP-grbeta) embryos were heat-shocked at 1 and 2 dpf at 37°C for 2.5 hours. At 3 dpf, larvae were treated with 25 microM beclomethasone or vehicle (0.05 % DMSO) for 6 hours.  Per treatment group, 20 larvae were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. Four individual experiments were performed, yielding quadruplicate samples per treatment group.

tag: sample type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study.

source_name: Tg(hsp70:Gal4, UAS:EGFP-grbeta), beclomethasone-treated 3dpf larvae. RNA isolated from 20 larvae.

value: Tg(hsp70:Gal4, UAS:EGFP-grbeta)


title: D.rerio_Grbeta-beclo-experiment: GRbeta/veh_4

description:
Sample 1321
Biological replicate 4 of 4: GRbeta/veh

source_name: Tg(hsp70:Gal4, UAS:EGFP-grbeta), vehicle-treated 3dpf larvae. RNA isolated from 20 larvae.


title: D.rerio_Grbeta-beclo-experiment: GRbeta/veh_3

description:
Sample 1305
Biological replicate 3 of 4: GRbeta/veh


title: Bel HGF10

scan_protocol: standard Affymetrix protocol: Service by the Centre for Genomic Sciences, The University of Hong Kong

value: 10ng/ml hepatocyte growth factor (


title: HTC116-CoOE-1

tag: genotype/variation


title: D.rerio_Grbeta-beclo-experiment: con/veh_4

description:
Sample 1319
Biological replicate 4 of 4: con/veh

source_name: Control (wild type), vehicle-treated 3dpf larvae. RNA isolated from 20 larvae.

value: Control (wild type)


title: HTC116-CoOE-2


title: D.rerio_Grbeta-beclo-experiment: con/beclo_4

description:
Sample 1320
Biological replicate 4 of 4: con/beclo

source_name: Control (wild type), beclomethasone-treated 3dpf larvae. RNA isolated from 20 larvae.


title: D.rerio_Grbeta-beclo-experiment: GRbeta/beclo_3

description:
Sample 1306
Biological replicate 3 of 4: GRbeta/beclo


title: D.rerio_Grbeta-beclo-experiment: con/beclo_3

description:
Sample 1304
Biological replicate 3 of 4: con/beclo


title: CL1-0_ mock-overexpressing cells

city: Taipei

first: Jin-Yuan

last: Shih

address: #7, Chung-Shan South Road,

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

description: micrRNA expression data from the mock-overexpressing cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: lung cancer cell line

label_protocol: cy3-labled cRNA were prepared according to the standard Illumina's proven DASL assay from 200ng total RNA

growth_protocol: Cells were cultured in RPMI-1640 medium  with 10% fetal bovine serum (FBS), 100 u/ml penicillin and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: Slug-overexpressing and mock-overexpressing cells were selected with 500ug/ml G418 (geneticin; Life Technologies) for one month.

tag: disease state

value: lung adenocacinoma

tag: phenotype

value: mock-overexpressing cells


title: D.rerio_Grbeta-beclo-experiment: GRbeta/veh_2

description:
Sample 1289
Biological replicate 2 of 4: GRbeta/veh


title: D.rerio_Grbeta-beclo-experiment: con/beclo_2

description:
Sample 1288
Biological replicate 2 of 4: con/beclo


title: D.rerio_Grbeta-beclo-experiment: con/veh_1

description:
Sample 1263
Biological replicate 1 of 4: con/veh


title: D.rerio_Grbeta-beclo-experiment: GRbeta/veh_1

description:
Sample 1265
Biological replicate 1 of 4: GRbeta/veh


title: D.rerio_Grbeta-beclo-experiment: GRbeta/beclo_1

description:
Sample 1266
Biological replicate 1 of 4: GRbeta/beclo


title: D.rerio_Grbeta-beclo-experiment: GRbeta/beclo_2

description:
Sample 1290
Biological replicate 2 of 4: GRbeta/beclo


title: CL1-0_ Slug-overexpressing cells

description: micrRNA expression data from the Slug-overexpressing cells

value: Slug-overexpressing cells


title: D.rerio_Grbeta-beclo-experiment: con/veh_2

description:
Sample 1287
Biological replicate 2 of 4: con/veh


title: D.rerio_Grbeta-beclo-experiment: con/veh_3

description:
Sample 1303
Biological replicate 3 of 4: con/veh


title: D.rerio_Grbeta-beclo-experiment: con/beclo_1

description:
Sample 1264
Biological replicate 1 of 4: con/beclo


title: D3 Mouse 55

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: Lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Male MutaTMMouse, aged ~12 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung was removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections using Trizol reagent (Invitrogen) and further purified using the Direct-zol RNA MiniPrep kit according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of the coal tar extract dissolved in olive oil were selected to dose the animals: 1.3 mg BaP equivalents/kg-bw/day, 2.5 mg BaP equivalents/kg-bw/day, and 5.1 mg BaP equivalents/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

tag: strain

value: MutaTMMouse

value: Lung

tag: time

value: 28 + 3 days

tag: gender

value: Male

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: D1 Mouse 43

tag: tissue


title: D0 Mouse 36


title: D3 Mouse 52


title: D2 Mouse 49


title: D2 Mouse 47


title: D2 Mouse 48


title: D0 Mouse 5

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of the 8PAH mixture dissolved in olive oil were selected to dose the animals: 15 mg BaP equivalents/kg-bw/day, 30 mg BaP equivalents/kg-bw/day, and 60 mg BaP equivalents/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.


title: D2 Mouse 50


title: D2 Mouse 30


title: D0 Mouse 4


title: D3 Mouse 54


title: D0 Mouse 37


title: D1 Mouse 24


title: D3 Mouse 35.1


title: D1 Mouse 41


title: D0 Mouse 38


title: D1 Mouse 42


title: D0 Mouse 39


title: D3 Mouse 51


title: D1 Mouse 45


title: D0 Mouse 40


title: D2 Mouse 46


title: D3 Mouse 34


title: D2 Mouse 23


title: D3 Mouse 35.2


title: D1 Mouse 44


title: D3 Mouse 53


title: D2 Mouse 29


title: D1 Mouse 25


title: D0 Mouse 2


title: D0 Mouse 3


title: D3 Mouse 32


title: D2 Mouse 28


title: D3 Mouse 18

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of the 4PAH mixture dissolved in olive oil were selected to dose the animals: 12.5 mg BaP equivalents/kg-bw/day, 25 mg BaP equivalents/kg-bw/day, and 50 mg BaP equivalents/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.


title: D0 Mouse 1


title: D1 Mouse 10


title: D2 Mouse 26


title: D1 Mouse 22


title: D3 Mouse 20


title: D0 Mouse 2


title: D1 Mouse 7


title: D1 Mouse 21


title: D3 Mouse 16


title: D1 Mouse 9


title: D3 Mouse 31


title: D0 Mouse 4


title: D2 Mouse 13


title: D0 Mouse 3


title: D2 Mouse 12


title: Liver Late  Infected 1

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

description:
Liver tissue collected after 18h from the infected group
Liver - RNA pooled from 3 mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8 x 60K array slides. Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Host gene expression by One – color microarray based exon analysis was performed using the mice microarray slide (8X60K : Agilent - 028005). Total RNA (100 ng) was labeled with Low Input Quick Amp WT Labeling Kit as per manufacturers instructions. RNA samples were pooled (6 mice from each group were divided into two pools of three to pool the RNA and run as duplicates) for labeling. The quality check of the labeled cRNA was performed using NanoDrop and the yield and specific activity were estimated.

extract_protocol: RNA isolation from the tissues was performed using QIAGEN RNeasy® Microarray Tissue Mini Kit as per standard protocol.  The purity and concentration of total RNA extracted was checked using Nanodrop spectrophotometer by using 1 µl of total RNA against nuclease free water as blank to determine the absorbance ratio 260/280 nm. The quality check of the isolated RNA was performed in Agilent 2100 Bioanalyzer as per standard protocol using the Agilent RNA 6000 Nano Kit. The extracted RNA was found to be of good quality, having RNA integrity number (RIN) greater than 7.

treatment_protocol: Three groups of 6 mice each including one control and two infected groups were used in the study. Group 1 and Group 2 were infected with 1.67 ×103 cfu of P. multocida at a volume of 0.1ml inoculum to each mouse, intraperitoneally and sacrificed humanely at onset of clinical signs (termed Onset – 6 h) and at later stages of infection (termed Late - 18 h), respectively. Tissues - lung, liver and spleen were collected aseptically at both the time points. Group 3, kept as control was injected with 0.1 ml of PBS and respective tissues were collected aseptically after 18 h. The tissues were collected in RNase free 1.5 ml centrifuge tube containing 0.5 ml RNAlater to prevent degradation of RNA and stored at -80 ºC

value: liver

tag: Sex

value: Swiss Albino

tag: age

value: 6 - 8 wks

tag: infection status

value: infected with Pasteurella multocida


title: Liver Late  Infected 2

description:
Liver tissue collected after 18h from the infected group
Liver - RNA pooled Other 3 mice


title: D2 Mouse 15


title: D3 Mouse 17


title: D1 Mouse 6


title: Lung Late  Infected 2

description:
Lung tissue collected after 18h from the infected group
Lung - RNA pooled Other 3 mice

value: lung


title: D2 Mouse 11


title: D0 Mouse 1


title: D2 Mouse 14


title: D0 Mouse 5


title: Lung Late  Infected 1

description:
Lung tissue collected after 18h from the infected group
Lung - RNA pooled from 3 mice


title: Lung Onset  Infected 2

description:
Lung tissue collected after 6h from the infected group
Lung - RNA pooled Other 3 mice

value: 6 h


title: Spleen Late  Infected 1

description:
Spleen tissue collected after 18h from the infected group
Spleen - RNA pooled Ofrom 3 mice

value: spleen


title: Liver Control 2

description:
Liver tissue collected after 18h from the control group
Liver - RNA pooled Other 3 mice

value: control (not infected)


title: Lung Control 2

description:
Lung tissue collected after 18h from the control group
Lung - RNA pooled Other 3 mice


title: Liver Onset  Infected 1

description:
Liver tissue collected after 6h from the infected group
Liver - RNA pooled from 3 mice


title: Spleen Onset Infected 1

description:
Spleen tissue collected after 6h from the infected group
Spleen - RNA pooled from 3 mice


title: Spleen Onset Infected 2

description:
Spleen tissue collected after 6h from the infected group
Spleen - RNA pooled Other 3 mice


title: Lung Onset  Infected 1

description:
Lung tissue collected after 6h from the infected group
Lung - RNA pooled from 3 mice

value: lungSw


title: Spleen Control 2

description:
Spleen tissue collected after 18h from the control group
Spleen - RNA pooled Other 3 mice


title: PGN-319_1 Data from Strain KDP315

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

description: Deficient mutant of PGN-0319 constructed from P. gingivalis ATCC 33277.

hyb_protocol: 1. Fragmentation of Cy3 labeled cRNA was carried out at 60°C for 30 min.  2. Stop fragmentation.  3. Hybridization was performed at 65°C for 17 h with agitation in Hybrioven.

scan_protocol: Scanned by Agilent Technologies Microarray Scanner.

data_processing: Normalization (Per Chip: Normalize to 75 percentile) was used GeneSpring GX software.

organism: Porphyromonas gingivalis ATCC 33277

source_name: Microorganism frequently isolated from lesion of chronic periodontitis

label_protocol: Cy3 label with Input Quick-Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: P. gingivalis cells grown to an OD660 of 0.6-0.8 in brain heart infusion broth (Becton Dickinson Sparks, MD) supplemented with 0.5% yeast extract, 5 µg/ml menadione and 0.5 µg /ml hemin at 37°C under anaerobic condition.

extract_protocol: TRIzol reagent (Invitorogen, Carlsbad, CA)

value: PGN_0319::ermF ermAM, Emr


title: Spleen Late  Infected 2

description:
Spleen tissue collected after 18h from the infected group
Spleen - RNA pooled Other 3 mice


title: Liver Control 1

description:
Liver tissue collected after 18h from the control group
Liver - RNA pooled from 3 mice


title: Liver Onset  Infected 2

description:
Liver tissue collected after 6h from the infected group
Liver - RNA pooled Other 3 mice


title: Pg33277_2 Data from Strain ATCC33277

description: Wild type

value: Wild type


title: Lung Control 1

description:
Lung tissue collected after 18h from the control group
Lung - RNA pooled from 3 mice


title: Spleen Control 1

description:
Spleen tissue collected after 18h from the control group
Spleen - RNA pooled from 3 mice


title: SKM1_D120

type: genomic

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

description: Hybridized to Cytoscan 750K Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.

data_processing: CEL files, generated by AGCC Viewer. CYCHP, generated by Chromosome Analysis Suite (all provided by Affymetrix); CYCHP provide data for copy number and absence of heterozigosity analysis.

molecule: genomic DNA

source_name: Cell line_SKM-1

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: The human MDS/AML cell lines F-36P, MOLM-13, OHN-GM, SKK-1, SKM-1 were cultured in RPMI-1640 supplemented with either 10% (MOLM-13 and SKK-1) or 20% fetal bovine serum (F-36P, OHN-GM and SKM-1) at 37ºC in 5% CO2. Granulocyte/macrophage colony-stimulating factor (GM-CSF) was added to F-36P cell line (1ng/mL) and to OHN-GM cell line (10ng/mL).

extract_protocol: Genomic DNA was extracted with AllPrep DNA/RNA/Protein Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: MDS/AML


title: F36P_D119

description: Hybridized to Cytoscan 750K Array

source_name: Cell line_F-36P


title: PGN-319_2 Data from Strain KDP315


title: SKK1_D117

description: Hybridized to Cytoscan 750K Array

source_name: Cell line_SKK-1


title: OHNGM_D118

description: Hybridized to Cytoscan 750K Array

source_name: Cell line_OHN-GM

value: OHN-GM


title: Pg33277_1 Data from Strain ATCC33277

description: Wild type


title: 36 pbc aih

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned  on iScan

data_processing:
no data processing was applied
Thus the 'Matrix_signal_intensities.txt' file contains theta values from unprocessed file.

source_name: primary biliary cirrhosis

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA).

extract_protocol: Genomic DNA was extracted from whole blood treated with EDTA using a QIAamp DNA Mini Kit

tag: clinical condition

value: primary biliary cirrhosis

tag: age of onset

value: blood


title: 28 pbc n/n n/p


title: 35 psc aih

source_name: primary sclerosing cholangitis

value: primary sclerosing cholangitis


title: 34 psc k

source_name: primary sclerosing cholangitis_female

value: female


title: FFPE DNA-Breast Cancer, Tissue Core 20 vs. Female Ref DNA

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description: Reference DNA samples have been fragmented to an average size of 500bp (matching the average size of DNA samples extracted from FFPE specimens) with Covaris S220x system prior to labeling and hybridization

hyb_protocol: Array CGH was performed on oligonucleotide-based SurePrint G3 Human CGH 4x180K microarray slides (design code: 022060) according the protocol provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.3, March 2014). Following the hybridization, the slides were washed sequentially: twice for 2:30 min in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technologies) at room temperature, twice for 30 sec min in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technologies) at 37◦C. Washed slides were immersed in acetonitrile to remove all remaining traces of the wash buffers.

scan_protocol: Scanned on an Agilent G2565CA scanner (Dye channel: R+G; Scan resolution: 2.5µm, double pass; Tiff file dynamic range: 16 Bit; Red PMT gain: 100%; Green PMT gain: 100%; No XDR)

data_processing:
Microarray TIFF image files were processed with the Agilent Genomic Feature Extraction Software (version 10.7.3.1). The resulting text files were imported and analyzed with Agilent Genomic Workbench Software (version 6.5.0.18 Lite). Aberrant regions were recognized using ADM-2 algorithm with threshold set to 7.0. Threshold of the centralization algorithm was set to 6.0 and bin size of 10. To avoid false positive calls, aberration filters were applied to define the minimum log2 ratio (minimum average absolute log2 ratio = 0.25) and the minimum number of probes in an aberrant interval (minProbes = 25).
log2 ratio = Normalized log2 ratios (Cy5/Cy3) representing test/reference. The log2 ratios were obtained using the Agilent Genomic Workbench 6.5.0.18; Average log2 value of a genomic interval = average log2 ratios calculated for entire aberrant genomic intervals (0 indicates balance copy number state)

source_name: Tissues specimen of primary FFPE breast cancer

label_protocol: DNA samples were labeled using  Agilent SureTag DNA Labeling Kit (Cat #: 5190-3400) following instruction provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis v7.3, March 2014). Slight modifications to the original protocol were introduced - i.e.  restiriction digestion with AluI and RsaI was omitted.

extract_protocol: Genomic DNA were isolated out of formalin-fixed, paraffin-embedded (FFPE) tissue specimens using the QIAamp DNA FFPE Tissue Kit (Qiagen) following the instructions published by the manufacturer (QIAamp DNA FFPE Tissue Handbook 06/2012). FFPE tissue specimens were excised from primary breast tumors using a sterile disposable biopsy punch (1.5mm diameter), excess paraffin was removed, residual tissue was manually minced using sterile scalpel blades before starting the DNA isolation. Following the DNA extraction DNA, DNA yield were quantified spectrophotometrically and the average size of extracted DNA molecules was assessed on 1.5% agarose gel supplemented with ethidium bromide. Reference DNA samples were extracted using the DNeasy blood and tissue Kit (Qiagen) from mononuclear cells obtained from peripheral blood following gradient centrifugation in 65% percoll soultion. DNA extraction was conducted following the protocol provided by the manufacturer (DNeasy Blood & Tissue Handbook 07/2006). High-molecular weight DNA in reference samples was sheared using Covaris S220x system down to approximately 500 bp (size matching the average fragments size of DNA in test samples) following guidelines provided by the manufacturer (microTUBE AFA fiber snap-cap 130µl tubes, peak incident power  - 105W, duty factor - 5%, cycles per burst - 200, treatment time - 80s, Temperature 7 oC. Following the average DNA fragments size was assessed on 1.5% agarose gel supplemente with ethidium bromide.

value: clinical sample

value: tumor sample

tag: diagnosis

value: breast cancer

source_name: Mononuclear cells enriched (gradient centrifugation in Percoll 65) from peripheral blood of a healthy donor_DNeasy Blood & Tissue Kit

value: Clinical sample

value: peripheral blood

value: mononuclear cells

value: healthy donor


title: FFPE DNA-Breast Cancer, Tissue Core 41 vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core B vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core 84 vs. Female Ref DNA


title: 32 psc m

source_name: primary sclerosing cholangitis_male

value: male


title: 29 psc m


title: 30 psc m


title: 31 psc m


title: 27 pbc n/n k

source_name: primary biliary cirrhosis_female


title: 33 psc k


title: FFPE DNA-Breast Cancer, Tissue Core D vs. Female Ref DNA


title: 23 pbc p/n k


title: MOLM3_D116

description: Hybridized to Cytoscan 750K Array

source_name: Cell line_MOLM-13

tag: cell line


title: 20 pbc p/n k


title: FFPE DNA-Breast Cancer, Tissue Core 45 vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core 72 vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core A vs. Female Ref DNA


title: 19 pbc p/n k


title: 17 pbc p/n k


title: 18 pbc p/n k


title: 10 pbc p/p k


title: 15 pbc p/n k


title: 14 pbc p/p k


title: 9 pbc p/p k


title: 21 pbc p/n k


title: FFPE DNA-Breast Cancer, Tissue Core 44 vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core C vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core 34H vs. Female Ref DNA


title: FFPE DNA-Breast Cancer, Tissue Core 44H vs. Female Ref DNA


title: 8 pbc p/p k


title: 7 pbc p/p k


title: 5 pbc p/p k


title: 6 pbc p/p k


title: 4 pbc p/p k


title: 1 pbc p/p k


title: 3 pbc p/p k


title: 80 m/ z

source_name: control for inflammatory bowel diseases_male

value: control for inflammatory bowel diseases


title: 79 m/ z


title: 77 m/ z


title: 75 m/ z


title: 76 m/ z


title: 74 k/ z

source_name: control for inflammatory bowel diseases_female


title: 2 pbc p/p k


title: 71 k/ z


title: 68 k/ z


title: 78 m/ z


title: 61 k/ z


title: 70 k/ z


title: 64 k/ z


title: 69 k/ z


title: 65 k/ z


title: 60 k/ z


title: 63 k/ z


title: 66 k/ z


title: 52 m/ z


title: 58 m/ z


title: 51 m/ z


title: 25 pbc n/p k


title: 59 m/ z


title: 62 k/ z


title: 55 m/ z


title: 50 wzjg a/m

value: ulcerative colitis

value: adult (>18years)


title: 49 wzjg a/m


title: 56 m/ z


title: 48 wzjg a/m


title: 73 k/ z


title: 47 wzjg a/m


title: 72 k/ z


title: 67 k/ z


title: 46 wzjg a/m


title: 45 wzjg a/m


title: 54 m/ z


title: 43 wzjga/k


title: 44 wzjg a/k


title: 53 m/ z


title: 40 clc a/m

source_name: Crohn’s disease_male_adult (>18years)

value: Crohn’s disease


title: 42 wzjga/k


title: 39 clc a/m


title: 33 clc a/k

source_name: Crohn’s disease_female_adult (>18years)


title: 38 clc a/m


title: 57 m/ z


title: 36 clc a/k


title: 37 clc a/m


title: 32 clc a/k


title: 30 wzjg y/m

value: young (<19years)


title: 34 clc a/k


title: 31 wzjg y/m


title: 29 wzjg y/m


title: 26 wzjg y/m


title: 28 wzjg y/m


title: 24 wzjg y/k


title: 22 wzjg y/k


title: 41 wzjg a/k


title: 25 wzjg y/m


title: 27 wzjg y/m


title: 35 clc a/k


title: 23 wzjg y/k


title: 21 wzjg y/k


title: 20 wzjg y/k


title: 18 wzjg y/k


title: 15 clc y/m

source_name: Crohn’s disease_male_young (<19years)


title: 16 clc y/m


title: 14 clc y/m


title: 13 clc y/m


title: 12 clc y/m


title: 11 clc y/m


title: 9 clc y/m


title: 8 clc y/m


title: 4 clc y/k

source_name: Crohn’s disease_female_young (<19years)


title: 2 clc y/k


title: 5 clc y/k


title: 6 clc y/k


title: 19 wzjg y/k


title: 3 clc y/k


title: 7 clc y/k


title: 10 clc y/m


title: 1 clc y/k


title: CMK11-5 DMSO rep3

city: Fujisawa

first: Yoshinori

last: Ishikawa

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: Oncology Drug Discovery Unit

institute: Takeda Pharmaceutical Company Ltd.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

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

extract_protocol: RNA was purified with extracted with QIAGEN RNeasy mini kit with DNase I treatment with  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Treatment with test article or DMSO for 24 hours

tag: treatment

value: DMSO

value: AML cell line


title: CMK11-5 T-3775440 rep1

tag: sample type


title: HEL92.1.7 T-3775440 rep2


title: CMK11-5 T-3775440 rep2


title: CMK11-5 DMSO rep1


title: HEL92.1.7 DMSO rep1


title: HEL92.1.7 T-3775440 rep3


title: KD_rep1 (I)

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

description: RNAs isolated from ZIP7-KD hMSCs

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Control probes were excluded before data processing. Scanned signal intensity (gMedianSignal) was log2-transformed. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011b).

label: Cyanine 3-CTP

source_name: ZIP7-KD hMSCs

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Human mesenchymal stem cells were purchased (Lonza), and maintained in DMEM medium (Gibco) with 10% FBS and antibiotics, at 37 °C.

extract_protocol: Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

treatment_protocol: siRNA transfection was performed with ON-TARGETplus SMARTpool siRNA (Life Technologies) using Lipofectamine RNAimax (Life Technologies) according to the manufacturer’s instructions.

value: Human mesenchymal stem cells (hMSCs)

tag: genotype/variation


title: CMK11-5 T-3775440 rep3


title: HEL92.1.7 DMSO rep2


title: HEL92.1.7 DMSO rep3


title: GIST-T1 cells with control molecule 2

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: gene expression in GIST-T1 cells transfected with a control molecule (replicate 2)

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: GIST-T1 cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Thermo Fisher Scientific).

treatment_protocol: GIST-T1 cells (3.0E+6 cells) were transfected with 100 pmol of a miR-186 mirVana miRNA inhibitor (Thermo Fisher Scientific) or a mirVana miRNA inhibitor Negative Control #1 (Thermo Fisher Scientific) using a Cell Line Nucleofector kit L (Lonza) and a Nucleofector device (Lonza) according to manufacturer's instruction. Forty-eight hours after transfection, total RNA was extracted.

tag: transfection

value: control molecule


title: KD_rep2 (I)

description: RNAs isolated from ZIP7-KD hMSCs


title: CMK11-5 DMSO rep2


title: GIST-T1 cells with miR-186_inhibitor_1

description: gene expression in GIST-T1 cells transfected with a miR-186 inhibitor molecule (replicate 1)

value: miR-186 inhibitor


title: WT_rep2 (I)

description: RNAs isolated from WT hMSCs

source_name: WT hMSCs

value: WT


title: HEL92.1.7 T-3775440 rep1


title: GIST-T1 cells with miR-186_inhibitor_2

description: gene expression in GIST-T1 cells transfected with a miR-186 inhibitor molecule (replicate 2)


title: GIST-T1 cells with control molecule 1

description: gene expression in GIST-T1 cells transfected with a control molecule (replicate 1)


title: Non Responder - sample 78

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from CRC patients at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: Arrays were scanned using the Agilent Scanner G2505B

data_processing: The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] "Agi4x44PreProcess" (intra-array[Multiplicatively Detrended] and inter-array [Quantile] normalization).

source_name: Pre Treatment biopsies

label_protocol: Agilent Whole Human Genome GE44K microarray platform was used. Standard Agilent RNA extraction and hybridization protocols were used.

growth_protocol: No growth protocols were used

extract_protocol: RNA was extracted by phenol/chloroform extraction (TRIzol; Invitrogen) prior to further purification by column chromatography (RNeasy Mini kit; Qiagen). RNA integrity was then assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: Pre CRT research biopsies (2-3 mm3) were collected during the initial diagnostic endoscopy, immediately frozen and stored in a liquid nitrogen tank.

value: CRC sample

tag: disease state

value: Rectal cancer

tag: name

value: Male

tag: class

value: Non Responder


title: Non Responder - sample 79


title: Responder - sample 76

value: Responder


title: Non Responder - sample 72


title: Non Responder - sample 77


title: Non Responder - sample 80

value: Female


title: Non Responder - sample 75


title: Non Responder - sample 73


title: WT_rep1 (I)

description: RNAs isolated from WT hMSCs


title: Responder - sample 74


title: Responder - sample 68


title: Non Responder - sample 69


title: Responder - sample 70


title: Responder - sample 66


title: Responder - sample 63


title: Non Responder - sample 71


title: sd_13_20

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: limited SSc sample

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Agilent scanner

data_processing: Images were quantified using Feature Extraction Software

source_name: Sample: Human Tissue Biopsy

label_protocol: 25ng of total RNA was reversed transcribed using Agilent Low Input Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

value: SSc patient 3mm forearm skin punch biopsy

value: Systemic sclerosis

tag: gender

value: F

source_name: Universal Human Reference

tag: reference

value: Universal Human Reference


title: Responder - sample 65

tag: tissue

tag: Sex


title: sd_13_22

description: limited SSc sample


title: Non Responder - sample 62

tag: age


title: sd_13_08

description: limited SSc sample


title: Non Responder - sample 64


title: sd_13_06

description: limited SSc sample


title: sd_12_84

description: limited SSc sample

value: M


title: Responder - sample 56


title: sd_12_98

description: limited SSc sample


title: Non Responder - sample 61


title: sd_12_7

description: limited SSc sample


title: Non Responder - sample 58


title: sd_12_8

description: limited SSc sample


title: Non Responder - sample 59


title: Non Responder - sample 57


title: sd_12_76

description: limited SSc sample


title: sd_12_93

description: limited SSc sample


title: sd_12_6

description: limited SSc sample


title: Non Responder - sample 55


title: Responder - sample 60


title: sd_12_4

description: limited SSc sample


title: Responder - sample 53


title: Responder - sample 51


title: sd_12_3

description: limited SSc sample


title: sd_12_57

description: limited SSc sample


title: sd_12_27

description: limited SSc sample


title: Responder - sample 50


title: Non Responder - sample 49


title: Responder - sample 67


title: Non Responder - sample 48


title: sd_12_19

description: limited SSc sample


title: sd_12_31

description: limited SSc sample


title: CK-0 h-rep2

city: Beijing

first: weiqiang

last: zhang

address: No 2 Yuanmingyuan Xi Lu, Haidian District

institute: China Agricultural University

description: Gene expression data.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: GeneChip Operating Software (GCOS1.4, Affymetrix), dChip 2008 (Li C, 2001aLi C, 2001b), and MAS 5.0.

organism: Zea mays

source_name: The internodes meristem not ethephon or normal-water sprayed treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Sterilized seeds of maize (Zea mays) were sown in a greenhouse (temperature, 28°C day/20°C night; 16 h photoperiod; 40% relative humidity) at China Agricultural University, Beijing.

treatment_protocol: At the jointing stage (8 leaves), 600 mg/L ethephon was sprayed on 100 seedlings served as the treatment group, and a normal-water sprayed on another 100 seedlings served as the control group, respectively.

value: internodes meristem


title: CK-0 h-rep1

description: Gene expression data.


title: Responder - sample 43


title: CK-48 h-rep3

description: Gene expression data.

source_name: The internodes meristem after normal-water sprayed treatment 2 day (48 h)


title: Non Responder - sample 45


title: Non Responder - sample 47


title: Non Responder - sample 52


title: sd_12_18

description: limited SSc sample


title: sd_12_20

description: limited SSc sample


title: sd_11_40

description: limited SSc sample


title: sd_12_17

description: limited SSc sample


title: CK-0 h-rep3

description: Gene expression data.


title: sd_12_1

description: limited SSc sample


title: Non Responder - sample 46


title: sd_12_102

description: limited SSc sample


title: Responder - sample 44


title: Eth-48 h-rep3

description: Gene expression data.

source_name: The internodes meristem after ethephon sprayed treatment 2 day (48 h)


title: WP3-salt shock 90 min-rep5

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
raw data file: Salt90min-cy3+Salt0min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy5 and WP3 cDNA-salt shock 90 min  was labled with Cy3

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
For every microarray slide, there are 16416 spots, which were divided into 48 blocks. For every block, there are 18 columns and 19 rows. 16416=48*18*19.  There are 3 spots for a single gene on a single microarray slide, thus we get 3 ratios of the expression level of this gene in 2 samples (rep1, rep2 and rep3).  As dye-swaps were performed (label cDNA with different fluorecent dye), we can get another 3 ratios of the expression level of this gene in 2 samples (rep4, rep5 and rep6).
The replicate spots on the array were printed in the same row in adjacent columns.  Replicate number was assigned to the spots in ascending column order. For example, WP00027 is printed  in block 1, row 2, columns 13, 14 and 15. Replicate 1/4 is column 13, 2/5 is column 14 and replicate 3/6 is column 15.
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model.  Microarray spots with P values <0.01 in the T-test and log2 ratio>1 or <-1 were regarded as differentially expressed genes.

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were treated with 12% (w/v) NaCl for 90 min.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: culture protocol

value: WP3 cells were cultured at 20°C in 2216E medium

source_name: WP3 cells at mid-exponential phase and were treated with 12% (w/v) NaCl for 90 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were treated with 12% (w/v) NaCl for 90 min


title: WP3-salt shock 90 min-rep4


title: Eth-48 h-rep2

description: Gene expression data.


title: CK-48 h-rep1

description: Gene expression data.


title: WP3-salt shock 90 min-rep3

description:
raw data file: Salt0min-cy3+Salt90min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-salt shock 90 min  was labled with Cy5


title: WP3-salt shock 90 min-rep6


title: CK-48 h-rep2

description: Gene expression data.


title: CK-24 h-rep1

description: Gene expression data.

source_name: The internodes meristem after normal-water sprayed treatment 1 day (24 h)


title: Eth-24 h-rep3

description: Gene expression data.

source_name: The internodes meristem after ethephon sprayed treatment 1 day (24 h)


title: WP3-salt shock 90 min-rep2


title: WP3-salt shock 60 min-rep6

description:
raw data file: Salt60min-cy3+Salt0min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy5 and WP3 cDNA-salt shock 60 min  was labled with Cy3

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were treated with 12% (w/v) NaCl for 60 min.

source_name: WP3 cells at mid-exponential phase and were treated with 12% (w/v) NaCl for 60 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were treated with 12% (w/v) NaCl for 60 min


title: WP3-salt shock 60 min-rep3

description:
raw data file: Salt0min-cy3+Salt60min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-salt shock 60 min  was labled with Cy5


title: WP3-salt shock 60 min-rep4


title: WP3-salt shock 60 min-rep5


title: Eth-48 h-rep1

description: Gene expression data.


title: WP3-salt shock 60 min-rep2


title: CK-24 h-rep2

description: Gene expression data.


title: Eth-24 h-rep2

description: Gene expression data.


title: WP3-salt shock 60 min-rep1


title: WP3-salt shock 30 min-rep3

description:
raw data file: Salt0min-cy3+Salt30min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-salt shock 30 min  was labled with Cy5

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were treated with 12% (w/v) NaCl for 30 min.

source_name: WP3 cells at mid-exponential phase and were treated with 12% (w/v) NaCl for 30 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were treated with 12% (w/v) NaCl for 30 min


title: WP3-salt shock 30 min-rep4

description:
raw data file: Salt30min-cy3+Salt0min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy5 and WP3 cDNA-salt shock 30 min  was labled with Cy3


title: CK-24 h-rep3

description: Gene expression data.


title: Eth-24 h-rep1

description: Gene expression data.


title: WP3-salt shock 30 min-rep6


title: WP3-salt shock 30 min-rep5


title: WP3-salt shock 90 min-rep1


title: WP3-salt shock 30 min-rep2


title: Sample_56

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalizeed using quantile method and logged
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

source_name: Adjacent tissue matching RCC

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: Adjacent tissue matching RCC

tag: status

value: NO-CKD

value: Medulla


title: Sample_58

value: CKD


title: Sample_54


title: Sample_55

value: Cortex


title: Sample_57


title: Sample_53


title: Sample_52


title: Sample_49


title: Sample_51


title: Sample_48


title: WP3-salt shock 30 min-rep1


title: Sample_46


title: Sample_39

source_name: Healty Kidney Donor

value: Healty Kidney Donor


title: Sample_47


title: Sample_42


title: Sample_44


title: Sample_45


title: Sample_37


title: Sample_50


title: Sample_36


title: Sample_40


title: Sample_38


title: Sample_35


title: Sample_34


title: Sample_33


title: Sample_32


title: sd_12_59

description: limited SSc sample


title: Sample_43


title: Sample_30


title: Sample_31


title: Sample_29


title: Sample_41


title: Sample_27


title: Sample_26


title: Sample_28


title: Sample_25


title: Sample_24


title: Sample_23


title: Sample_22


title: Sample_21


title: Sample_19


title: Sample_20


title: Sample_18


title: Sample_16


title: Sample_15


title: Sample_14


title: Sample_11


title: Sample_12


title: Sample_13


title: Sample_09


title: Sample_10


title: Sample_08


title: Sample_07


title: Sample_05


title: Sample_04


title: Sample_06


title: Sample_03


title: Sample_02


title: Sample_01


title: Sample_17


title: Responder - sample 54

value: CRC sample

value: Rectal cancer

value: Male

value: Responder