title: VUB02 P59 14.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140218-829023B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140218-829023B_bottom_cy5_female_fused.txt


title: VUB02 P59 14.1

status: Public on Jun 24 2014

type: genomic

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376080B_top_cy5_male_fused.txt
sample_vs_female_reference: 130429-376080B_top_cy5_female_fused.txt

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in BlueFuse Multi 3.1.

molecule: genomic DNA

organism: Homo sapiens

source_name: hESC culture

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

tag: sample

value: Single hESC

tag: assayed molecule

value: Amplified DNA

source_name: female/male reference

value: reference


title: VUB02 P59 13

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376080B_top_cy3_male_fused.txt
sample_vs_female_reference: 130429-376080B_top_cy3_female_fused.txt


title: VUB02 P59 16

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376081B_top_cy5_male_fused.txt
sample_vs_female_reference: 130429-376081B_top_cy5_female_fused.txt


title: VUB02 P59 12

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376078B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130429-376078B_bottom_cy5_female_fused.txt


title: VUB02 P59 11

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376078B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130429-376078B_bottom_cy3_female_fused.txt


title: VUB02 P59 10

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376074B_top_cy3_male_fused.txt
sample_vs_female_reference: 130426-376074B_top_cy3_female_fused.txt


title: VUB02 P59 07

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829020B_top_cy5_male_fused.txt
sample_vs_female_reference: 140204-829020B_top_cy5_female_fused.txt


title: VUB02 P59 08

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376073B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130426-376073B_bottom_cy3_female_fused.txt


title: VUB02 P59 09

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376074B_top_cy5_male_fused.txt
sample_vs_female_reference: 130426-376074B_top_cy5_female_fused.txt


title: CaLY202 vs control replication-2

city: Shanghai

first: xingxing

last: li

address: Guohe Road

country: China

institute: Second Military Medical University

description: Biological replicate 2 of 2. Control Candida albicans, untreated, harvested after several passages.

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. Two hybridizations were performed by using a reversal fluorescent strategy in one test and control and the other hybridization without performing reversal fluorescent.

organism: Candida albicans

source_name: Candida albicans

label_protocol: The genomic DNA was sonicated to generate fragments 50–2000 bp in size,then the DNA fragment was labeled by fluorescent dye (Cy5 and Cy3-dCTP) with random primer and Klenow enzyme.

growth_protocol: Candida albicans cells were propagated in YPD medium.

extract_protocol: For DNA extraction, 200μl of 25:24:1 phenol/chloroform/isoamyl alcohol were added to the cells resuspended in lysis buffer, together with 300 mg of acid-washed glass beads. The mixture was vortexed for 3 minutes before the addition of 200μl of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH8.0). Following a 5 minutes centrifugation at 9300 g and 4℃ for phase separation (Eppendorf centrifuge 5415D), the DNA in the aqueous phase was precipitated with 1 ml ethanol (96%, v/v) at room temperature, resuspended in 400μl of TE containing 60 mg RNaseA (GE healthcare), and incubated at 37℃ for 6 hours, the DNA was precipitated with 40μl of 3 M ammonium acetate and 1 ml of cold absolute ethanol at -20℃ for 15 minutes, followed by a 5 minutes centrifugation at 9300 g at 4℃. The DNA pellet was carefully washed with 1 ml ethanol (70%, v/v), left to dry at room temperature, and resuspended in 50μl of TE buffer. DNA was purified using the PCR Clean-up NucleoSpin Extract Ⅱ Kit (Macherey-Nagel, Germany) according to manufacturer’s directions.

treatment_protocol: strains were grown routinely in YPD medium at 30°C with shaking overnight, diluted to an OD600 of 0.1 in fresh YPD and were allowed to grow to an OD600 of 0.8. Cells were then harvested, flash-frozen and stored at -80°C.

tag: cell type

value: Yeast form cells

tag: strain

value: Candida albicans CaLY202

value: Candida albicans SN152


title: VUB02 P59 04

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376072B_top_cy3_male_fused.txt
sample_vs_female_reference: 130426-376072B_top_cy3_female_fused.txt


title: VUB02 P59 03

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376072B_top_cy5_male_fused.txt
sample_vs_female_reference: 130426-376072B_top_cy5_female_fused.txt


title: VUB02 P59 05

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376073B_top_cy5_male_fused.txt
sample_vs_female_reference: 130426-376073B_top_cy5_female_fused.txt


title: CaLY202 vs control replication-1

description: Biological replicate 1 of 2. Control Candida albicans, untreated, harvested after several passages.


title: VUB02 P59 02.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829161B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140132-829161B_bottom_cy3_female_fused.txt


title: CaLY350 vs control replication-2

value: Candida albicans CaLY350


title: VUB02 P59 06

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376073B_top_cy3_male_fused.txt
sample_vs_female_reference: 130426-376073B_top_cy3_female_fused.txt


title: CaLY188 vs control replication-2

value: Candida albicans CaLY188


title: CaLY350 vs control replication-1


title: CaLY188 vs control replication-1


title: CaLY188 vs control replication-2

type: RNA

molecule: total RNA

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: Total RNA was isolated by the hot phenol method.


title: CaLY188 vs control replication-1


title: VUB02 P59 02.1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376071B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130426-376071B_bottom_cy3_female_fused.txt


title: VUB02 P59 01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376071B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130426-376071B_bottom_cy5_female_fused.txt


title: Amniocyte B 02

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376059B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 1-376059B_bottom_cy3_female_fused.txt

source_name: Cultured Amniocytes

value: Single Amniocyte


title: Activated memory B cells, HIV, S5

city: Bethesda

first: Susan

last: Moir

state: Maryland

address: 9000 Rockville Pike

department: NIAID

country: USA

institute: NIH

description: activated memory B cells

data_processing:
Data were normalized to the housekeeping genes POLRIIA and GAPDH by a comparative delta Ct method. The Ct values from a given sample were converted to delta Ct (dCt) values by subtracting the Cts from the number of PCR cycles (n = 45). To normalize across samples, the mean value of the housekeeping genes POLRIIA and GAPDH was subtracted from the Ct values within each sample.
Differential expression analysis of resting memory B cells versus the other two subsets, namely tissue-like memory B cells and activated memory B cells, was performed using two-sample Wilcoxon test. To correct for multiple testing, false discovery rates (FDR) were estimated using the Benjamini and Hochberg method.
Fold Change worksheet reports Wilcoxon test pvalues by comparing gene expression in 1) resting memory B cells (RM) versus the other two subsets (AM and TLM), and 2) gp140-specific IgG+ B cells from patients with strong pro-resting memory profile versus weak pro-resting memory profile.

label: FAM

source_name: PBMC

label_protocol: cDNA was synthesized, then preamplified with pool of interested genes and analyzed by quantitative real-time PCR (Applied Biosystems 7500 system) using TaqMan Gene Expression Assay.

extract_protocol: Total RNA was extracted with using the RNeasy micro kit with on-column DNA digestion (Qiagen), according to manufacturer specifications.

value: activated memory B cells

tag: gender

value: Male

tag: age

tag: ethnicity

value: African American


title: Amniocyte B 01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376058B_top_cy3_male_fused.txt
sample_vs_female_reference: 1-376058B_top_cy3_female_fused.txt


title: Amniocyte B pooled

description:
Sample assayed against male reference only
sample_vs_male_reference: AmnioB-299067A_top_fused.txt

value: DNA sample Amniocytes

value: Genomic DNA

source_name: male reference


title: Amniocyte A 08

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376060B_top_cy5_male_fused.txt
sample_vs_female_reference: 1-376060B_top_cy5_female_fused.txt


title: Hydra_control_rep5

city: Zagreb

first: Tomislav

last: Domazet-Loso

address: Bijenicka cesta 54

department: Division of Molecluar Biology

country: Croatia

institute: Ruder Boskovic Institute

hyb_protocol: Labeled cRNA samples (13 in total) were hybridized to custom Agilent Gene Expression Microarray 4 x 44k slides for 17 h at 65°C and treated according to the Agilent protocol.

scan_protocol: The microarrays were scanned using the Agilent High Resolution G2565CA Microarray Scanner System.

data_processing: Raw microarray image files were processed and quality checked by Agilent Feature Extraction 10.7.3 Software. Background subtracted signal intensity values that contain correction for multiplicative surface trends (gProcessedSignal) generated by Feature Extraction Software were used for further data analysis. Using a spreadsheet macro we filtered probes that were flagged as non-uniform or as population outliers. This dataset was normalized by 75th percentile normalization procedure as recommended by Agilent.

organism: Hydra oligactis

source_name: polyps, asexual

label_protocol: About 400 ng of total RNA were labeled with Cy3 using the one-color Quick-Amp Labeling Kit (Agilent Technologies, Waldbronn, Germany).

growth_protocol: Experiments were carried out using H. oligactis strain St.-Petersburg. Animals were maintained under constant environmental conditions including culture medium, food, and temperature (18°C) according to standard procedures (1). Oogenesis was induced by lowering the culture temperature to 10°C and depriving animals of food13 for a period of 14. 1) Lenhoff, M. & Dubois, R. A. Y. Mass culture of Hydra: an improved method and its application to other aquatic invertebrates. Lab. Anim. 4, 139–154 (1970).

extract_protocol: Total RNA was isolated from H. oligactis healthy control (six replicates), tumor-bearing polyps (four replicates) and oogenesis-induced polyps (pooled equal ratios of stages 1-7 of oogenesis, three replicates) by TRIzol reagent (Invitrogen) according to manufacturer’s instructions. After chloroform extraction, the aqueous phase was purified on the RNA-binding cartridge of PureLink RNA Mini Kit (Ambion, Life Technologies, Darmstadt, Germany) according to the protocol of the manufacturer. The RNA samples were additionally purified by glycogen-potassium acetate precipitation followed by washing with ice-cold 80% ethanol.

treatment_protocol: None.

tag: Sex

value: female

tag: Stage

value: asexual polyps


title: Amniocyte A 06

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376059B_top_cy5_male_fused.txt
sample_vs_female_reference: 1-376059B_top_cy5_female_fused.txt


title: Amniocyte A 05

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376058B_top_cy5_male_fused.txt
sample_vs_female_reference: 1-376058B_top_cy5_female_fused.txt


title: Hydra_control_rep2


title: Hydra_control_rep1


title: Hydra_female_rep2

source_name: polyps, undergoing oogenesis, mixed stages

value: polyps undergoing oogenesis


title: Hydra_female_rep3


title: Amniocyte A 04

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376064B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130404-376064B_bottom_cy3_female_fused.txt


title: Hydra_control_rep4


title: Hydra_female_rep1


title: Hydra_control_rep3


title: Hydra_control_rep6


title: Amniocyte A 03.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829162B_top_cy5_male_fused.txt
sample_vs_female_reference: 140132-829162B_top_cy5_female_fused.txt


title: Hydra_tumor_rep4

source_name: polyps, tumor-bearing

value: tumor bearing-polyps


title: Amniocyte A 07

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376059B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 1-376059B_bottom_cy5_female_fused.txt

value: Amplified DNA


title: Hydra_tumor_rep1


title: Hydra_tumor_rep3


title: Amniocyte A 02

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376062B_top_cy3_male_fused.txt
sample_vs_female_reference: 130404-376062B_top_cy3_female_fused.txt

value: reference


title: Amniocyte A 03.1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376063B_top_cy3_male_fused.txt
sample_vs_female_reference: 130404-376063B_top_cy3_female_fused.txt


title: Hydra_tumor_rep2


title: KST062

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array.  GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: The data were extracted analyzed with bioconductor (v.2.11) and RMA.

label: biotin

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

extract_protocol: Trizol

tag: strain background

tag: genotype/variation

value: Kras G12D mutation

tag: tissue

value: bone marrow

tag: in vivo treatment with

value: GDC-0941 alone

tag: cell line

value: 5C Resistant


title: KST077

value: 5C Parental


title: Amniocyte A pooled

description:
Sample assayed against male reference only
sample_vs_male_reference: AmnioA-299067A_bottom_fused.txt


title: Amniocyte A 01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376061B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130404-376061B_bottom_cy3_female_fused.txt

value: Single Amniocyte


title: Amniocyte C 02

description:
Sample assayed against male reference only
sample_vs_male_reference: Fibroblasts-092038A_top_fused.txt


title: Amniocyte C 01

description:
Sample assayed against male reference only
sample_vs_male_reference: Fibroblasts-092038A_bottom_fused.txt


title: 35::EVE1Line3.1 repetition 2 Grown at 35 degrees celsius

city: Gainesville

first: Cintia

middle: Leite

last: Ribeiro

state: FL

address: 2033 Mowry Road room 320F

institute: University of Florida

hyb_protocol: Hybridization was performed according to Agilent Two-Color Low Input Quick Amp Labeling Kit v.6.6 protocol

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: The software used to process the data was R and SAS. The raw signals were quantile normalized and log2 tranformed.

organism: Populus tremula x Populus alba

source_name: Line3.1 xylem tissue from lower 5cm of stem

label_protocol: Labeling was performed according to Agilent Two-Color Low Input Quick Amp Labeling Kit v.6.6 protocol

growth_protocol: Samples were collected from 3-month-old Populus from growth-chamber experiments at 25oC and 35oC temperature

extract_protocol: Total RNA extracted using CTAB according to literature

treatment_protocol: 3 independent lines of 35::EVE1 were obtained by stable transformation of Populus genotype 717 using agrobacterium. EVE1 was clonned from Populus trichocarpa

value: lower 5cm of stem

value: 2-month old

tag: growth

value: growth-chamber grown at 35C


title: Wild-type repetition 4 Grown at 35 degrees celsius

source_name: Wild-type xylem tissue from lower 5cm of stem

value: wild type


title: LP7f_d28

city: Erlangen

first: Fabian

last: Fahlbusch

address: Loschgestr. 15

department: Kinder- und Jugendklinik

country: Germany

institute: Universität Erlangen

description: dol: 28 days

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Rat Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

organism: Rattus norvegicus

source_name: Lumbar mammary gland

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

treatment_protocol: Virgin female Wistar rats came from Charles River. Throughout pregnancy the NP rats received 25g/d of Altromin C1000 containing 17.0% protein, while LP animals were fed 25g/d of Altromin C1003 containing 8.8% protein. At birth, litter size was reduced to 6 females in both groups, which were left to suckle for 21 days. During lactation (d1-d21) and after weaning (d21-d28) NP and LP animals were fed a standard chow and tap water ad libitum. At d21 and d28 3 dams were sacrificed under isofluran narcosis. The lumbar mammary gland (4th and 5th pair) were removed and cleared of visible lymph nodes before snap-freezing in liquid nitrogen. Samples were stored at -80°C until further processing. Abbreviations: NP= normal protein diet, LP= low protein diet, dol= day of life.

value: Wistar

tag: diet

value: Low Protein Diet (LP)


title: Wild-type repetition 1 Grown at 35 degrees celsius


title: 35::EVE1Line7.4 repetition 4 Grown at 35 degrees celsius

source_name: Line7.4 xylem tissue from lower 5cm of stem


title: Fibroblast pooled

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130724-829044B_top_cy5_male_fused.txt
sample_vs_female_reference: 130724-829044B_top_cy5_female_fused.txt

source_name: Dermal fibroblast culture

value: DNA sample Dermal Fibroblasts

value: Genomic DNA


title: NP6f_d28

description: dol: 28 days

value: Normal Protein Diet (NP)


title: KST052

value: JW81 Parental


title: 35::EVE1Line9.1 repetition 4 Grown at 25 degrees celsius

source_name: Line9.1 xylem tissue from lower 5cm of stem


title: LP4f_d28

description: dol: 28 days


title: 35::EVE1Line9.1 repetition 3 Grown at 25 degrees celsius


title: KST057

value: JW81 Resistant


title: NP5f_d28

description: dol: 28 days


title: Amniocyte C DNA

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829162B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140132-829162B_bottom_cy3_female_fused.txt

value: DNA sample Amniocytes

value: reference


title: LP6f_d28

description: dol: 28 days


title: KST051

value: Kras G12D mutation

value: bone marrow

value: 4B Resistant


title: 35::EVE1Line3.1 repetition 4 Grown at 35 degrees celsius


title: 35::EVE1 Line3.1 repetition 1 Grown at 35 degrees celsius


title: 35::EVE1Line9.1 repetition 2 Grown at 25 degrees celsius


title: Fibroblast 17.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829160B_top_cy3_male_fused.txt
sample_vs_female_reference: 140132-829160B_top_cy3_female_fused.txt

value: Single Dermal Fibroblast

value: Amplified DNA


title: 35::EVE1Line7.4 repetition 3 Grown at 35 degrees celsius

value: lower 5cm of stem

value: 2-month old


title: KST046

value: 4B Parental


title: KST056


title: NP4f_d28

description: dol: 28 days

value: Wistar


title: LP6a_d21

description: dol: 21 days

value: Low Protein Diet (LP)


title: LP7c_d21

description: dol: 21 days


title: KST041

value: GDC-0941 alone

value: 20M Resistant


title: KST039


title: Fibroblast 17.1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130528-376007B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130528-376007B_bottom_cy5_female_fused.txt


title: LP4a_d21

description: dol: 21 days


title: 35::EVE1Line9.1 repetition 1 Grown at 25 degrees celsius

value: growth-chamber grown at 35C


title: Wild-type repetition 3 Grown at 35 degrees celsius

value: wild type


title: Fibroblast 16

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130528-376007B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130528-376007B_bottom_cy3_female_fused.txt


title: Fibroblast 14

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376070B_top_cy5_male_fused.txt
sample_vs_female_reference: 1-376070B_top_cy5_female_fused.txt


title: Fibroblast 13

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376069B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 1-376069B_bottom_cy5_female_fused.txt


title: Fibroblast 15

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376070B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 1-376070B_bottom_cy5_female_fused.txt


title: Fibroblast 12

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376069B_top_cy3_male_fused.txt
sample_vs_female_reference: 1-376069B_top_cy3_female_fused.txt


title: 35::EVE1Line3.1 repetition 3 Grown at 35 degrees celsius


title: 35::EVE1Line7.4 repetition 1 Grown at 35 degrees celsius


title: Fibroblast 10.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829160B_top_cy5_male_fused.txt
sample_vs_female_reference: 140132-829160B_top_cy5_female_fused.txt


title: Fibroblast 11

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376068B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 1-376068B_bottom_cy3_female_fused.txt


title: KST036


title: NP6a_d21

description: dol: 21 days

value: Normal Protein Diet (NP)


title: BMDMs incubated with apoptotic cell supernatant

city: Sakyo-ku, Kyoto-shi

first: Hiroshi

last: Yamaguchi

state: Kyoto

address: Yoshida

department: Graduate school of medicine

country: Japan

institute: Kyoto University

description: BMDMs-Apoptotic cell supernatant

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The hybridized signals were detected with an Affymetrix Microarray scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: BMDMs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (GeneChip 3' IVT Express kit, Affymetrix).

growth_protocol: mouse BMDMs were incubated with RPMI containing 10%FCS or apoptotic W3 cells supernatant at 37℃ for 1h.

extract_protocol:
mouse BMDMs were washed with PBS once and lysed with QIAGEN Rneasy Buffer RLT.
QIAGEN RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

value: female

value: 8 wks

tag: tissue source

value: bone marraow

value: bone marrow-derived macrophages (BMDMs)

tag: incubated with

value: apoptotic W3 cell supernatant for 1 h


title: 35::EVE1Line3.1 repetition 4 Grown at 25 degrees celsius

value: growth-chamber grown at 25C


title: Wild-type repetition 2 Grown at 25 degrees celsius


title: NP5a_d21

description: dol: 21 days


title: NP4a_d21

description: dol: 21 days


title: KST034

value: Kras G12D mutation

value: bone marrow

value: 20M Parental


title: KST025

value: 10M Resistant


title: Wild-type repetition 2 Grown at 35 degrees celsius

value: lower 5cm of stem

value: 2-month old


title: Fibroblast 10.1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376068B_top_cy3_male_fused.txt
sample_vs_female_reference: 1-376068B_top_cy3_female_fused.txt

tag: sample

value: Single Dermal Fibroblast

tag: assayed molecule

value: Amplified DNA

value: reference


title: KST026

value: 10M Parental


title: KST021

value: 2M Resistant


title: BMDMs incubated with medium

description: BMDMs-Medium

value: female

tag: cell type

value: medium (control)


title: 35::EVE1Line7.4 repetition 2 Grown at 25 degrees celsius


title: KST023


title: KST024

value: GDC-0941 alone


title: KST035


title: Fibroblast 9

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376067B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 1-376067B_bottom_cy5_female_fused.txt


title: 35::EVE1Line9.1 repetition 2 Grown at 35 degrees celsius


title: 35::EVE1Line9.1 repetition 4 Grown at 35 degrees celsius


title: Wild-type repetition 1 Grown at 25 degrees celsius

value: wild type


title: Fibroblast 8

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376067B_top_cy5_male_fused.txt
sample_vs_female_reference: 1-376067B_top_cy5_female_fused.txt


title: KST016


title: KST014


title: 35::EVE1Line7.4 repetition 4 Grown at 25 degrees celsius


title: Fibroblast 4

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376063B_top_cy5_male_fused.txt
sample_vs_female_reference: 130404-376063B_top_cy5_female_fused.txt


title: Fibroblast 5

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376063B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130404-376063B_bottom_cy5_female_fused.txt


title: Fibroblast 3

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376062B_top_cy5_male_fused.txt
sample_vs_female_reference: 130404-376062B_top_cy5_female_fused.txt


title: Fibroblast 7

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376066B_top_cy5_male_fused.txt
sample_vs_female_reference: 1-376066B_top_cy5_female_fused.txt


title: 35::EVE1Line3.1 repetition 3 Grown at 25 degrees celsius


title: Fibroblast 1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829159B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140132-829159B_bottom_cy5_female_fused.txt


title: KST007

value: 73A Resistant


title: KST013


title: Fibroblast 6

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130404-376064B_top_cy5_male_fused.txt
sample_vs_female_reference: 130404-376064B_top_cy5_female_fused.txt


title: Wild-type repetition 4 Grown at 25 degrees celsius

value: growth-chamber grown at 25C


title: 35::EVE1Line7.4 repetition 1 Grown at 25 degrees celsius


title: 35::EVE1Line9.1 repetition 1 Grown at 35 degrees celsius


title: NHS_60min_biological_repl_6

status: Public on Jun 23 2014

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

description: Gene expression of M. catarrhalis after 60 min in 10% NHS in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 6

hyb_protocol: 2 µg of labeled cDNA was applied to 4x72K custom design NimbleGen arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: Raw data was normalized using Arraystar (DNASTAR) software with Quantile RMA normalization.

organism: Moraxella catarrhalis BBH18

source_name: M. catarrhalis incubated in NHS

label_protocol: Total RNA was labeled according to standard Nimblegen gene expression array protocols.

growth_protocol: Independent cultures of M. catarrhalis BBH18 were expanded to mid-log phase (OD620nm, 1.0 to 1.2), washed in 4 volumes PBS-G, and resuspended in 5 volumes PBS-G (Ca2+ and Mg2+).

extract_protocol: Total RNA was isolated using RNeasy columns (Qiagen) for the control (NHS dilution buffer, n = 5) and NHS (n = 6). Contaminating genomic DNA was removed by treatment with Turbo DNase (Ambion).

treatment_protocol: Bacterial suspensions (~6x10^7 CFU/ml) were mixed in a 1:1 ratio with 20% NHS, 20% heat-inactivated NHS (NHS-HI, 30 min at 56°C), or serum dilution buffer (PBS-G (Ca2+ and Mg2+), control) and incubated at 37°C with agitation (200 rpm). Bacterial suspensions were sampled after 60 min exposure and immediately treated with RNAprotect Bacteria Reagent (Qiagen). After 5 min incubation at room temperature and harvesting by centrifugation, pellets were stored at -80°C.

tag: genotype

value: wild-type

tag: genbank


title: Fibroblast 2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 1-376060B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 1-376060B_bottom_cy5_female_fused.txt


title: KST010

value: Kras G12D mutation

value: bone marrow

value: 2M Parental


title: KST005

value: 73A Parental


title: KST006


title: KST008


title: 35::EVE1Line7.4 repetition 3 Grown at 25 degrees celsius

value: lower 5cm of stem

tag: age

value: 2-month old


title: KST002

value: Kras wild type

value: 8633 Resistant


title: NHS_60min_biological_repl_2

description: Gene expression of M. catarrhalis after 60 min in 10% NHS in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 2


title: 35::EVE1Line3.1 repetition 2 Grown at 25 degrees celsius


title: NHS_60min_biological_repl_4

description: Gene expression of M. catarrhalis after 60 min in 10% NHS in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 4


title: NHS_60min_biological_repl_3

description: Gene expression of M. catarrhalis after 60 min in 10% NHS in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 3


title: 35::EVE1 Line3.1 repetition 1 Grown at 25 degrees celsius


title: NHS_60min_biological_repl_5

description: Gene expression of M. catarrhalis after 60 min in 10% NHS in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 5


title: KST001

value: 8633 Parental


title: NHS_60min_biological_repl_1

description: Gene expression of M. catarrhalis after 60 min in 10% NHS in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 1


title: Control_60min_biological_repl_5

description: Gene expression of M. catarrhalis after 60 min in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 5

source_name: M. catarrhalis incubated in NHS dilution buffer


title: Control_60min_biological_repl_2

description: Gene expression of M. catarrhalis after 60 min in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 2


title: Control_60min_biological_repl_3

description: Gene expression of M. catarrhalis after 60 min in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 3


title: Control_60min_biological_repl_4

description: Gene expression of M. catarrhalis after 60 min in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 4


title: Inoculum in sand+DBF from salicylate 1

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description: cells recovered after 1h of inoculation in sand contaminated with dibenzofuran, precultured in salicylate

hyb_protocol: The volume of different samples was adjusted for the hybridization in order to have at least 2 pmol of labelled Cy3 per array on the slide. Sixty ng of labeled cDNA were loaded onto each microarray, hybridized for 17 hours at 65°C, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60°C for 30 minutes) was omitted.

scan_protocol: Microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (G2505), immediately after hybridization using the One-Color microarray -based gene expression analysis protocol provided by Agilent (scan area 61x21.6mm XDRHi:100% XDRLo:10%).

data_processing: Data were normalized by quantile and scaled with the baseline to the median of all samples. All genes were filtered by expression and were retained when the signal intensity was above the 20th percentile in at least one of the samples.

organism: Rhizorhabdus wittichii RW1

source_name: Inoculum in sand+DBF from salicylate

label_protocol: An amount of 2-5 µg of RNA was mixed with 1.25 µl random primers (500 µg/ml; Promega) in a total volume of 12 µl and incubated at 70 °C for 10 min followed by 4 °C for 5 min. Each tube received 13 µl of mastermix containing 0.625 µl Cyanine 3-dCTP (1 mM; Perkin-Elmer), 0.625 µl Superase-In (20 U/µl; Ambion), 1 µl Superscript II (200 U/µl; Invitrogen), 5 µl 5x 1st strand buffer, 2.5 µl DTT (100 mM), 0.25 µl dATP-dGTP-dTTP mixture (10 mM each), 0.125 µl dCTP (5 mM) and 2.875 µl nuclease-free water. Labeled cDNA was produced by incubation at 42 °C for 120 min, followed by 70 °C for 10 min and 4 °C for 5 min. RNA was hydrolyzed under alkaline conditions as follows. After the addition of 2.5 µl 1 M NaOH, samples were heated at 65 °C for 20 min, allowed to cool to room temperature for 10 min and neutralized by the addition of 2.5 µl 3 M Na-acetate (pH 5.2) and 2.5 µl 1 M HCl. The labeled cDNA was then purified using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer’s instructions. The product was eluted in 20 µl EB buffer and quantity and incorporation efficiency were determined using the MICROARRAY function on a NanoDrop spectrophotometer (ThermoFisher Scientific, Waltham, MA).

growth_protocol: S. wittichii RW1 was cultured in phosphate-buffered mineral medium (medium DSM457 from the German Resource Centre for Biological Material, Braunschweig, Germany) with salicylate (5 mM) or DBF as sole carbon source. Liquid batch cultures were incubated at 30°C and with 180 rpm rotary shaking. DBF was dosed as crystals (1.6 g/L) to sterilized medium.

extract_protocol:
Hot-phenol extraction
After 1 h, the cells were extracted from the sand by adding 5 ml of sterile saline solution (0.9%) to the tube and vortexing for 30”, after which the suspension was filtered over a cell strainer of 70 μm pore size to remove sand grains. The filtrate was then immediately filtered over a 0.22 µm Durapore® membrane filter (Merk Millipore, Ireland) by vacuum suction. The filter with the cells was removed, placed in a 2 ml tube containing 0.5 g of acid washed glass beads (Sigma-Aldrich, CH), frozen in liquid nitrogen and stored at -80°C for RNA isolation. For the control treatments the cells were maintained in the resuspension solution (100 µl) for 1 h at 24-26°C. Subsequently, each of the 100 µl control cell suspensions was added to 2 g of dry sand, after which immediately 5 ml saline solution was added to the mixture and vortexed. Cells were re-extracted immediately from the sand as described above and stored for RNA isolation. We used the acid-phenol method modified from Johnson (Johnson et al 2008). Briefly, each 2 ml tube that contained a frozen filter with RW1 cells (from – 80°C) was filled with 250 μl lysis buffer (containing 50 mM sodium acetate, 10 mM EDTA [pH 5.1]), 100 μl 10% sodium dodecyl sulfate and 1.0 ml buffer-equilibrated phenol (pH 4.3) (Aqua-Roti-Phenol, Roth Sochiel, FR). Cells were lysed by heating in a 70°C water bath for 2 min and then subjected to a bead-beating procedure with a FastPrep FP120 (Bio101, Thermo Fisher Scientific, Waltham, MA, USA). This consisted of bead-beating twice for 45 sec at maximum speed (6.0), followed by an incubation in a 70°C water bath for 10 min, and bead-beating twice again. Cellular debris was collected by centrifugation for 3 min at 15,000 × g and 4°C, after which the aqueous phase was transferred to a new nuclease-free microcentrifuge tube. Then, the aqueous phase was extracted twice with 1 volume of phenol-chloroform-isoamyl alcohol (pH 4.3) (25:24:1, vol/vol) and once with 1 volume of chloroform-isoamyl alcohol (24:1, vol/vol) (Sigma-Aldrich, CH). RNA was precipitated by addition of 0.1 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of 100% ethanol, and incubated overnight at –20°C. The precipitate was collected by centrifugation for 30 min at maximum speed and 4°C, washed twice with 80% ethanol, and resuspended in nuclease-free water. Remaining DNA was removed by DNase I treatment using the DNA-free kit (Life technologies, Carlsbad, CA, USA) according to the manufacturer's instructions. An additional round of precipitation with sodium acetate (0.1 vol, 3 M, pH 5.2) and ethanol (2 vols, 100%) was performed and the RNA was finally purified using an RNeasy MinElute cleanup kit (Qiagen, Germany) in a final volume of 20 µl.

treatment_protocol: Dry sandy soil was contaminated with DBF by spraying 10 ml of a dichloromethane/DBF solution (100 mg DBF per ml dichloromethane) on 500 g of sand on aluminium foil. Dichloromethane was allowed to evaporate for 16 h under a chemical hood after which aliquots of 2 g soil were placed in a 15 ml Greiner tube and homogenized by rotary mixing. To measure the immediate genome-wide reaction of RW1 to sand with or without DBF, we inoculated ~108 RW1 cells taken from exponentially growing liquid batch culture per gram sandy soil at 10% moisture content.

tag: growth media

value: Salicylate

tag: environment

value: Sand

tag: growth phase

value: Lag phase


title: Wild-type repetition 3 Grown at 25 degrees celsius

tag: genotype/variation


title: Inoculum in only sand from salicylate 3

description: cells recovered after 1h of inoculation in only sand, precultured in salicylate

source_name: Inoculum in only sand from salicylate


title: Inoculum in sand+DBF from salicylate 3


title: Control salicylate 3

description: cells harvested from salicylate growing cultures

source_name: Control salicylate

value: Liquid


title: Inoculum in sand+DBF from DBF 3 [Hot-phenol extraction]

description: cells recovered after 1h of inoculation in sand contaminated with dibenzofuran, precultured in dibenzofuran

source_name: Inoculum in sand+DBF from DBF

value: dibenzofuran cristals


title: Inoculum in sand+DBF from DBF 1 [Hot-phenol extraction]


title: Inoculum in only sand from salicylate 2


title: Inoculum in sand+DBF from salicylate 2


title: Inoculum in only sand from salicylate 1


title: 35::EVE1Line9.1 repetition 3 Grown at 35 degrees celsius

tag: tissue


title: Control salicylate 2


title: Control salicylate 1


title: Control Dibenzofuran 3

description: cells harvested from dibenzofuran growing cultures

source_name: Control Dibenzofuran


title: Control Dibenzofuran 2


title: Control_60min_biological_repl_1

description: Gene expression of M. catarrhalis after 60 min in PBS-G Mg2+ Ca2+ (NHS dilution buffer), biological replicate 1


title: Exponential cells in liquid culturesin saturated solution of DBF 2

description: Cells growing in exponential phase

extract_protocol:
Hot-phenol extraction
We used the RNA PowerSoil® Total RNA Isolation Kit (Mobio laboratories, Carlsbad, CA, USA). The replicates were maintained at – 80°C until extraction, filters still frozen were broken inside the tube with RNAse-free tweezers to reduce the size of the filters, before following the protocol indicated by the manufacturer. The RNA pellet was resuspended in a final volume of 20 µl to obtain concentrations higher than 500 ng/µl necessary for subsequent labelling.

treatment_protocol: Dry sandy soil was contaminated with DBF by spraying 10 ml of a dichloromethane/DBF solution (100 mg DBF per ml dichloromethane) on 500 g of sand on aluminium foil. Dichloromethane was allowed to evaporate for 16 h under a chemical hood. To measure the global response of RW1 during growth in sandy soil, we inoculated sandy soil microcosms contaminated with DBF (see above) with ~2.5·105 CFU per g. In order to obtain enough cells to extract RNA, we started with 80 microcosms, each with 10 g of sandy soil. After 16 h, 64 microcosms were sacrificed, cells were extracted by adding 15 ml of saline solution, vortexing and filtering as described above. Cells from 16 microcosms were pooled to obtain four replicates for the exponential phase in sand (SAND-DBF-EXPO). 40 h after inoculation we sacrificed the remaining 16 tubes, extracted cells as before and pooled cells from four microcosms together to produce four replicates of stationary phase in sand (SAND-DBF-STAT). As controls for growth in sand we inoculated fourfold replicate batch cultures with RW in liquid medium with DBF crystals. Cells were recovered by filtration at an OD of 0.2-0.3 (LIQ-DBF-EXPO) and at an OD of 0.9-1 (LIQ-DBF-STAT).

value: dibenzofuran saturated solution

value: Exponential phase


title: Inoculum in sand+DBF from DBF 2 [Hot-phenol extraction]


title: Stationaryl cells in sand contaminated with DBF 3

description: Cells recovered after 40h of growth in sand contaminated with dibenzofuran

extract_protocol:
RNA PowerSoil® Total RNA Isolation Kit
We used the RNA PowerSoil® Total RNA Isolation Kit (Mobio laboratories, Carlsbad, CA, USA). The replicates were maintained at – 80°C until extraction, filters still frozen were broken inside the tube with RNAse-free tweezers to reduce the size of the filters, before following the protocol indicated by the manufacturer. The RNA pellet was resuspended in a final volume of 20 µl to obtain concentrations higher than 500 ng/µl necessary for subsequent labelling.

value: Stationary phase


title: Stationaryl cells in sand contaminated with DBF 1


title: Stationaryl cells in sand contaminated with DBF 2


title: Exponential cells in sand contaminated with DBF 3

description: Cells recovered after 16h of growth in sand contaminated with dibenzofuran


title: Exponential cells in liquid culturesin saturated solution of DBF 1

description: Cells growing in exponential phase


title: Control Dibenzofuran 1


title: Stationary cells in liquid cultures with DBF crystals 3

description: cells harvested from dibenzofuran cultures at stationary phase (O.D. 0.9-1)


title: Exponential cells in liquid culturesin saturated solution of DBF 3

description: Cells growing in exponential phase


title: Stationary cells in liquid cultures with DBF crystals 2


title: Stationary cells in liquid cultures with DBF crystals 1


title: Exponential cells in sand contaminated with DBF 2


title: Exponential cells in sand contaminated with DBF 1


title: KST038

tag: strain background

value: Kras G12D mutation

tag: in vivo treatment with

value: GDC-0941 alone

value: 20M Resistant


title: Exponential cells in liquid cultures with DBF crystals 2

description: cells harvested from dibenzofuran cultures at exponential phase (O.D. = 0.2-0.3)


title: Exponential cells in liquid cultures with DBF crystals 1


title: Inoculum in sand+DBF from DBF 1


title: Inoculum in sand+DBF from DBF 3


title: Inoculum in sand+DBF from DBF 2


title: Exponential cells in liquid cultures with DBF crystals 3


title: P53_cKO_3

city: Pullman

first: Kanako

last: Hayashi

state: WA

address: BLS345, 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed in R (2.14.1) using limma (3.10.2) using the neqc function, which does a normexp background correction using negative control probes, quantile normalization using negative and positive control probes and log2 transformation.

source_name: P53 knock-out

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions.

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

treatment_protocol: Female mice were genotyped and necropsied at 2 month of age.  Uterine tissues were homogenized with Trizol reagent at collection and stored at-80C.

value: P53 knock-out; Cdh1+, P53-

value: 2 months

tag: gender

value: female

value: uterus


title: Cdh1_P53_cKO_3

source_name: Cdh1 and P53 double knock-out

value: Cdh1 and P53 double knock-out; Cdh1-, P53-


title: P53_cKO_1


title: Cdh1_cKO_2

source_name: Cdh1 knock-out

value: Cdh1 knock-out; Cdh1-, P53+


title: P53_cKO_2


title: Cdh1_P53_cKO_1


title: Cdh1_cKO_3


title: Cdh1_P53_cKO_2


title: Cdh1_cKO_1


title: CO_1

source_name: wild type

value: wild type; Cdh1+, P53+


title: hMSCs_control_starvation24h_rep3

city: Barakaldo

first: Clara

middle: Isabel

last: Rodriguez

state: Bizkaia

address: Edificio de Anatomía Patológica, planta 2, Hospital Universitario Cruces

country: Spain

institute: BioCruces Research Health Institute

description:
replicate 1
SAMPLE 9B

hyb_protocol: Standard Illumina hybridization protocol (P-ILMN-2)

scan_protocol: Standard Illumina scanning protocol (P-ILMN-1)

data_processing: Expression data was analyzed with the R/Bioconductor statistical computing environment (www.r-project.org, www.bioconductor.org). Using the lumi package, raw expression data were log2 transformed and quantile normalized. For the detection of differentially expressed genes, a linear model was fitted to the microarrays and empirical Bayes moderated t-statistics were calculated using the limma package (Smyth) from Bioconductor.

source_name: Bone marrow, donor 1

label_protocol: TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina System, utilizes an improved linear RNA amplification procedure to produce micrograms amounts of biotin-labeled antisense RNA.

growth_protocol: Human mesenchymal stem cells (hMSCs) were grown in their specific medium (DMEM, Sigma), supplemented with 10% fetal bovine serum (FBS, Sigma) and passed when sub-confluent, every 5 days during 7 passages (during the entire period of cell culture the treatment detailed below was added to culture medium). Then the cells were serum starved for 24 hours. After this, cell pellets were collected in order to perform RNA extraction.

extract_protocol: Total RNA was isolated from hMSCs using High Pure RNA Isolation Kit (Roche) following the manufacturer´s instructions and quantified with NanoDrop 2000 Spectrophotometer (Thermo Fisher).

treatment_protocol: The accumulation of prelamin A mutant protein was induced by treating hMSCs with the HIV protease inhibitor Tipranavir (TPV), or with the vehicle alone, DMSO, during the entire period of the culture. The concentration of TPV used for the experiments was 20 micromolar. The media and treatments were renewed every other day.

tag: protocol

value: control

value: male


title: CO_3


title: ESC-like cells_homologous injection alone

city: Seoul

first: Jeong Mook

last: Lim

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description:
Gene expression data from ESC-like cells derived from teratoma formed by homololous ESCs injection alone
NC-1

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Gene 1.0 ST Arrays at 45˚C for 16 h. After hybridization, the arrays were washed in Affymetrix Fluidics Station 450 and stained with a streptavidin-phycoerythrin complex.

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

data_processing: The intensity obtained from each probe was extracted using Affymetrix GCOS software. All data were processed using a robust multi-array average (RMA) algorithm. The expression values were computed from CEL files by applying RMA model of the probe-specific correction of perfect-match probes.

label: Biotin

source_name: Mouse ESC-like cells_teratoma-derived_homololous injection alone

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

growth_protocol: ESCs and ESCs-like cells were cultured on mitotically-inactivated ICR mouse embryonic fibroblast monolayer under Dulbecco's modified eagle medium supplemented to 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1% (v/v) nonessential amino acids, 1% (v/v) penicillin/streptomycin, 15% FBS, and 1,000 units/ml mouse leukemia inhibitory factor in a 37˚C incubator with 5% CO2. The somatic cells were cultured in the same basal medium supplemented with 10% FBS and 1% (v/v) penicillin/streptomycin. ESC-like cells were derived from the culture of teratoma-dissociated cells under ESC culture medium.

extract_protocol: Total RNA was extacted from the samples using Rneasy Plus Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cultured ESCs and ESC-like cells were harvested by treating 0.25% trypsin-EDTA and washed with PBS two times. Cell pellets were immersed in RNA later and stored at -70˚C until use.

tag: donor strain and cells

value: B6CBAF1 homologous ESCs

tag: recipient strain

tag: transplantation method

value: Subcutaenous injection

value: ESC-like cells derived from teratoma formed by homologous ESCs injection alone


title: ESC-like cells_heterologous injection alone

description:
Gene expression data from ESC-like cells derived from teratoma formed by heterololous ESCs injection alone
NT-1

source_name: Mouse ESC-like cells_teratoma-derived_heterololous injection alone

value: B6CBAF1 heterologous ESCs

value: ESC-like cells derived from teratoma formed by heterologous ESCs injection alone


title: hMSCs_prelaminA_starvation24h_rep3

description:
replicate 1
SAMPLE 10B

value: serum starvation condition


title: CO_2


title: hMSCs_prelaminA_starvation24h_rep1

description:
replicate 1
SAMPLE 2B


title: ESC-like cells_co-injection with somatic cells batch 2

description:
Gene expression data from ESC-like cells derived from teratoma formed by co-injection of heterololous ESCs with homologous somatic cells
MT-2

source_name: Mouse ESC-like cells_teratoma-derived_co-injection with somatic cells batch 2

value: B6CBAF1 heterologous ESCs + B6D2F1 homologous embryonic fibroblasts

value: ESC-like cells derived from teratoma formed by co-injection of heterologous ESCs with homologous somatic cells


title: hMSCs_control_starvation24h_rep2

description:
replicate 2
SAMPLE 3B

source_name: Bone marrow, donor 2


title: hMSCs_control_starvation24h_rep1

description:
replicate 1
SAMPLE 1B


title: ESCs_parental

description:
Gene expression data from parantal ESCs
NMC

source_name: Mouse ESCs_parental

value: parental ESCs


title: ESC-like cells_co-injection with somatic cells batch 1

description:
Gene expression data from ESC-like cells derived from teratoma formed by co-injection of heterololous ESCs with homologous somatic cells
MT-1

source_name: Mouse ESC-like cells_teratoma-derived_co-injection with somatic cells batch 1


title: hMSCs_prelaminA_starvation24h_rep2

description:
replicate 2
SAMPLE 4B


title: FLU00169.day0

city: Kyoto

first: Maiko

last: Narahara

address: 53 Shogoin Kawaharacho, Sakyo-Ku

description: Gene expression in non-stimulated human whole blood

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the GeneSpringGX11 (Agilent).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

source_name: Peripheral blood, non-stimulated

label_protocol: Agilent standard protocol

extract_protocol: PAXgene Blood RNA Kits (QIAGEN, Hilden, Germany) were then used to collect samples of total RNA.

treatment_protocol: Whole blood was collected from each participant when in a non-stimulated state.

value: whole blood


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title: FLU00192.day0


title: FLU00263.day0


title: FLU00289.day0


title: FLU00139.day0


title: FLU00047.day0


title: FLU00110.day0


title: FLU00053.day0


title: FLU00253.day0


title: FLU00262.day0


title: FLU00285.day0


title: FLU00265.day0


title: FLU00155.day0


title: empty vector control +CHX, -N, +DEX, treatment replicate 3

city: New York

first: Ying

last: Li

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: Gene expression profiles from root protoplasts transfected with Empty vector and treated with +CHX, -N, +DEX

hyb_protocol: The labeled cDNA was hybridized, washed and stained on an ATH1-121501 Arabidopsis Genome Array (Affymetrix) using a Hybridization Control Kit (Affymetrix), a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) on a GeneChip Fluidics Station 450.

scan_protocol: The microarrays were scanned using a GeneChip Scanner (Affymetrix).

data_processing: Microarray intensities were normalized using the GCRMA  package. Differentially expressed genes were then determined using multi-way ANOVA.

organism: Arabidopsis thaliana

source_name: Root protoplasts of 10-day-old Arabidopsis Col-0 seedlings

label_protocol: RNA was converted into cDNA, amplified and labeled with Ovation Pico WTA System V2 (NuGEN) and Encore Biotin Module (NuGEN), respectively.

growth_protocol: Roots of 10-day-old Arabidopsis Col-0 seedlings were harvested and treated with cell wall digesting enzymes Cellulase and Macerozyem for 4 h to prepare protoplasts.

extract_protocol: RNA from was extracted from protoplasts using an RNeasy Micro Kit with RNase-free DNaseI Set (QIAGEN) and quantified on a Bioanalyzer RNA Pico Chip (Agilent Technologies)

treatment_protocol: Protoplasts were transfected with pBeaconRFP_GR::bZIP1 plasmid DNA (or pBeaconRFP_GR empty vetor for empty vector control) for 25 minutes and then incubated overnight to allow the transcription and translation of bZIP1. The Protoplast suspensions were then treated sequentially with 1) +/- Nitrogen for 2 h; 2)+/- CHX; 3) +/- DEX at room temperature. Transfected protoplasts were selected by the RFP fluorescent marker.

tag: ecotype

tag: chx treatment

value: CHX treated

tag: nitrogen treatment

value: 20mM KCl

tag: dex treatment

value: 10 µM DEX in Ethanol

tag: vector

value: pBeaconRFP_GR empty vector


title: FLU00144.day0

tag: age


title: FLU00297.day0


title: empty vector control +CHX, +N, -DEX, treatment replicate 3

description: Gene expression profiles from root protoplasts transfected with Empty vector and treated with +CHX, +N,  -DEX

value: 20 mM KNO3 and 20 mM NH4NO3 solution

value: Ethanol alone


title: empty vector control +CHX, -N, -DEX, treatment replicate 3

description: Gene expression profiles from root protoplasts transfected with Empty vector and treated with +CHX, -N, -DEX


title: empty vector control +CHX, -N, -DEX, treatment replicate 2

description: Gene expression profiles from root protoplasts transfected with Empty vector and treated with +CHX, -N,  -DEX


title: FLU00133.day0


title: empty vector control +CHX, +N, -DEX, treatment replicate 2


title: empty vector control +CHX, +N, +DEX, treatment replicate 2

description: Gene expression profiles from root protoplasts transfected with Empty vector and treated with +CHX, +N, +DEX


title: FLU00142.day0


title: empty vector control +CHX, -N, -DEX, treatment replicate 1


title: FLU00044.day0


title: FLU00179.day0

value: male


title: empty vector control +CHX, +N, +DEX, treatment replicate 1


title: -CHX, -N, +DEX, treatment replicate 3

description: Gene expression profiles from transfected root protoplasts treated with -CHX, -N, +DEX

value: Solvent only


title: -CHX, -N, -DEX, treatment replicate 3

description: Gene expression profiles from transfected root protoplasts treated with -CHX, -N,  -DEX


title: -CHX, +N, -DEX, treatment replicate 3

description: Gene expression profiles from transfected root protoplasts treated with -CHX, +N,  -DEX


title: FLU00154.day0


title: FLU00203.day0


title: FLU00123.day0


title: -CHX, -N, +DEX, treatment replicate 2


title: -CHX, +N, -DEX, treatment replicate 2


title: FLU00191.day0


title: FLU00111.day0


title: FLU00035.day0


title: FLU00127.day0


title: FLU00115.day0


title: FLU00150.day0


title: FLU00161.day0


title: FLU00237.day0


title: empty vector control +CHX, +N, +DEX, treatment replicate 3


title: FLU00033.day0


title: -CHX, -N, -DEX, treatment replicate 2


title: empty vector control +CHX, +N, -DEX, treatment replicate 1


title: FLU00223.day0


title: -CHX, -N, +DEX, treatment replicate 1


title: empty vector control +CHX, -N, +DEX, treatment replicate 1


title: -CHX, +N, +DEX, treatment replicate 3

description: Gene expression profiles from transfected root protoplasts treated with -CHX, +N, +DEX


title: -CHX, -N, -DEX, treatment replicate 1


title: -CHX, +N, -DEX, treatment replicate 1


title: FLU00160.day0


title: -CHX, +N, +DEX, treatment replicate 1


title: FLU00077.day0


title: FLU00003.day0


title: FLU00089.day0


title: -CHX, +N, +DEX, treatment replicate 2


title: VEGF group_1

city: Nanjing

first: Li

last: Wu

state: Jiangsu

address: 305 East Zhongshan Road

institute: Jinling Hospital, Nanjing University School of Medicine

description: Gene expression at 21hr after VEGF administration in ischemic mouse brain

hyb_protocol: 5 ug of Cy3-labelled cRNA was fragmented at 60°C for exactly 30 minutes in a reaction volume of 250 μl containing 10 μl 25x Agilent fragmentation buffer and 50 μl 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 μl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8×60K Microarray 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 Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 8×60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: VEGF group, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Agilent's Low Input Quick Amplification 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: Adult male C57BL/6 mice weighing 23 to 25g (7~8 W) were housed in the same environment with 12 h light/dark cycle and relative humidity of 65%. The room temperature was maintained at approximately 25°C by air conditioning throughout all experiments. All animals were fasted overnight before the surgery, but were allowed free access to water.

extract_protocol: Total RNA was extracted from homogenizing brains using TRIzol® Reagent (Invitrogen, Life Technologies, Carlsbad, California, USA) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice in sham group underwent sham surgery; mice in MCAO group underwent transient (90min) middle cerebral artery occlusion (MCAO) surgery and received 1μl vehicle (PBS, 0.01M, pH 7.4) intracerebroventricularly in the right lateral ventricle 3hr after reperfusion; mice in VEGF group underwent 90min MCAO and received 1μl rhVEGF-A165 (10μg/ml, dissolved in 0.01M PBS) in the right lateral ventricle 3hr after reperfusion. Twenty-four hours after reperfusion, mice were sacrificed and brains were collected for microarray.

tag: strain

value: brain

tag: developmental stage

value: middle cerebral artery occlusion (MCAO) model

tag: agent

value: VEGF


title: VEGF group_3

source_name: VEGF group, replicate 3

tag: tissue


title: VEGF group_2

source_name: VEGF group, replicate 2


title: FLU00288.day0


title: MCAO group_2

description: Gene expression at 21hr after vehicle administration in ischemic mouse brain

source_name: MCAO group, replicate 2

value: vehicle


title: +CHX, -N, +DEX, treatment replicate 3, Biorep 2

description: Gene expression profiles from transfected root protoplasts treated with +CHX, -N, +DEX


title: MCAO group_3

source_name: MCAO group, replicate 3


title: +CHX, -N, -DEX, treatment replicate 3, Biorep 1

description: Gene expression profiles from transfected root protoplasts treated with +CHX, -N,  -DEX


title: sham group_3

description: Gene expression in normal mouse brain

source_name: sham group, replicate 3

value: sham surgery


title: FLU00195.day0


title: FLU00106.day0


title: FLU00017.day0


title: sham group_1

description: Gene expression in normal mouse brain

source_name: sham group, replicate 1


title: +CHX, +N, -DEX, treatment replicate 3, Biorep 2

description: Gene expression profiles from transfected root protoplasts treated with +CHX, +N,  -DEX


title: hom_3

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

hyb_protocol: Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix 3000 array scanner.

data_processing: R/Bioconductor was used to apply the PLIER methodology to generate expression values for the combined samples.

source_name: homozygous STEP KO striatum

extract_protocol: Trizol extraction of total RNA was performed.

tag: genotype

value: homozygous STEP KO

value: striatum

tag: treatment

value: naïve

tag: genetic background


title: +CHX, -N, -DEX, treatment replicate 3, Biorep 2


title: hom_4

tag: gender


title: hom_2


title: het_4

source_name: heterozygous STEP KO striatum

value: heterozygous STEP KO


title: +CHX, +N, -DEX, treatment replicate 3, Biorep 1

value: CHX treated


title: sham group_2

description: Gene expression in normal mouse brain

source_name: sham group, replicate 2

tag: protocol


title: +CHX, -N, +DEX, treatment replicate 3, Biorep 1

value: 20mM KCl


title: FLU00243.day0

value: whole blood

value: female


title: FLU00041.day0


title: hom_1


title: het_5


title: +CHX, +N, +DEX, treatment replicate 3, Biorep 2

description: Gene expression profiles from transfected root protoplasts treated with +CHX, +N, +DEX

value: 20 mM KNO3 and 20 mM NH4NO3 solution

value: 10 µM DEX in Ethanol


title: +CHX, +N, +DEX, treatment replicate 3, Biorep 1


title: het_1

value: male


title: het_2


title: FLU00121.day0


title: MCAO group_1

source_name: MCAO group, replicate 1


title: +CHX, -N, -DEX, treatment replicate 2, Biorep 2

value: Ethanol alone


title: wt_4

source_name: wt mouse striatum

value: WT


title: het_3


title: +CHX, -N, -DEX, treatment replicate 2, Biorep 1


title: wt_3


title: FLU00173.day0


title: wt_2


title: FLU00086.day0


title: FLU00224.day0


title: FLU00295.day0


title: +CHX, -N, +DEX, treatment replicate 2, Biorep 1


title: CECT12600

city: Paterna

first: Amparo

last: Gamero

state: Valencia

address: Avda. Agustín Escardino 7

department: Food Biotechnology

institute: IATA-CSIC

description: the dyes indicated in each raw file were the dyes employed for the labelling of the strains.

hyb_protocol: The mixture of the required Cy3 and Cy5 labelled samples was adjusted to 60 μl with hybridization solution (50% formamide, 5X SSC, 0,1% SDS, 100 μg/ml salmon sperm DNA and water) incubated for 1 minute at 95 ºC and centrifuged at 13000 X g for 1 min. The supernatants were applied to microarrays and the hybridizations were allowed to proceed overnight at 65°C.

scan_protocol: Arrays scanned using an Axon GenePix 4100A scanner and GenePix Pro 6.0 software

data_processing: Using Acuity 4.0 software (Molecular Devices Corp., Union City, CA, USA), manually flagged bad spots were eliminated and the local background was subtracted before averaging the replicate features on the array. Log2 intensity ratios (M values) were then Median normalized to correct for differences in genomic DNA labelling efficiency between samples. The relative hybridization signal of each ORF was derived from the average of the two dye-swap hybridizations performed for each strain. The normalized log2 ratio (M value) was considered as a measure of the relative abundance of each ORF relatively to that of the reference strain S288C. Deviations from the 1:1 hybridization ratio were taken as indicative of changes in DNA copy number. Given that the variability usually observed between S. cerevisiae genomes, (either within laboratory strains or natural isolates), is much lower than this estimate (Adams et al. 1992, Carreto et al. 2008), we interpreted statistically significant variations in hybridization signal as ORF deletions or duplications. Data imported from Acuity was manipulated and clustered, using established algorithms implemented in the software program Genesis. Average linkage clustering with centered correlation was used to generate visual representations of clusters.

organism: Saccharomyces uvarum

label_protocol: Approximately 2 μg of these DNAs were labelled with fluorescently-tagged nucleotides (Amersham, Piscataway, NJ, USA), either Cy3-dCTP or Cy-5 dCTP for the reference and the studied strains, using Exo-Klenow Fragment and random primer Mix (Bioprime Array CGH Kit, Invitrogen). Dye-swap hybridizations were performed for each strain. After labeling, the reactions were heatinactivated, the experimental (Cy5 or Cy3-labeled) and reference (Cy3 or Cy5-labeled) DNAs were mixed and purified away from unincorporated label using the MinElute PCR Purification Kit (QUIAGEN). The degree of labeling was determined by measuring the absorbance at 260 nm and at 550 nm for Cy3- labelled DNA or at 260 nm and 650 nm for Cy5-labeled DNA. Samples with a base/dye ratio between 40 and 80 for both Cy3 and Cy5, were routinely obtained.

growth_protocol: Yeast strains were cultivated in 5ml YPD (1% yeast extract, 2% peptone, 2% glucose), at 28 ºC for 24 hours

extract_protocol: DNA was isolated according to standard procedures (Querol et al., 1992). After isolation the DNAs were digested with HinfI (Takara Bio Inc., Japan) and purified with High Pure PCR Product Purification Kit (Roche Molecular Biochemicals, Mannheim, Germany).

organism: Saccharomyces cerevisiae

tag: reference strain


title: IFO1802

organism: Saccharomyces kudriavzevii


title: wt_1


title: FLU00026.day0

description: Gene expression in non-stimulated human whole blood


title: +CHX, +N, +DEX, treatment replicate 2, Biorep 2


title: FLU00164.day0


title: +CHX, +N, -DEX, treatment replicate 2, Biorep 1


title: +CHX, -N, +DEX, treatment replicate 2, Biorep 2


title: +CHX, +N, -DEX, treatment replicate 2, Biorep 2


title: S. uvarum CECT 12600 replicate A, fermentation at 28C

description: Gene expression of S. uvarum CECT12600 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate A

hyb_protocol: A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight.  (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing:
Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found. Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated.
Genes with a two-fold log2 ratio values were considered to be significantly expressed.

source_name: yeast cells from wine fermentation at 28C

label_protocol: 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA). The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.

growth_protocol: Wine fermentations in Tempranillo must at 12C or 28C

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).

tag: growth phase

value: Beginning of stationary phase

value: Lalvin T73


title: S. uvarum CECT 12600 replicate C, fermentation at 28C

description: Gene expression of S. uvarum CECT12600 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate C


title: S. uvarum CECT 12600 replicate B, fermentation at 28C

description: Gene expression of S. uvarum CECT12600 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate B


title: S. kudriavzevii IFO 1802 replicate C, fermentation at 28C

description: Gene expression of S. kudriavzevii IFO 1802 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate C


title: S. kudriavzevii IFO 1802 replicate B, fermentation at 28C

description: Gene expression of S. kudriavzevii IFO 1802 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate B


title: S. kudriavzevii IFO 1802 replicate A, fermentation at 28C

description: Gene expression of S. kudriavzevii IFO 1802 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C . Replicate A


title: FLU00097.day0


title: S. cerevisiae Fermol cryophile replicate B, fermentation at 28C

description: Gene expression of S. cerevisiae Fermol Cryophile with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C . Replicate B

value: Fermol cryophile


title: +CHX, -N, +DEX, treatment replicate 1, Biorep 2

tag: ecotype


title: +CHX, -N, -DEX, treatment replicate 1, Biorep 2

tag: chx treatment


title: S. cerevisiae Fermol cryophile replicate A, fermentation at 28C

description: Gene expression of S. cerevisiae Fermol Cryophile with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate A


title: +CHX, +N, +DEX, treatment replicate 2, Biorep 1

tag: nitrogen treatment


title: +CHX, -N, -DEX, treatment replicate 1, Biorep 1

tag: dex treatment


title: S. cerevisiae Fermol cryophile replicate C, fermentation at 28C

description: Gene expression of S. cerevisiae Fermol Cryophile with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate C


title: +CHX, -N, +DEX, treatment replicate 1, Biorep 1

tag: vector


title: +CHX, +N, -DEX, treatment replicate 1, Biorep 2


title: S. uvarum CECT 12600 replicate C, fermentation at 12C

description: Gene expression of S. uvarum CECT12600 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate C

source_name: yeast cells from wine fermentation at 12C


title: +CHX, +N, +DEX, treatment replicate 1, Biorep 1


title: SPC/c-Raf mouse tumor 60.6 male 14 months

city: Hannover

first: Kishor

middle: Bapu

last: Londhe

state: Niedersachsen

address: Carl-Neuberg-Str. 1

department: Institut für Pharmako- und Toxikogenomikforschung

institute: Medizinische Hochschule Hannover

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) according to manufacturer’s instruction.

scan_protocol: Array scanning was performed with 3000 G7 scanner (Affymetrix) according to the manufacturer's instruction (Affymetrix).

data_processing: CEL files exported from GCOS were uploaded into Biotique XRAY software (v 3.2). The mixed model nested ANOVA method with Quantile normalization was used to define differential gene expression and alternative splicing. For background the pool of predefined GC probes was used and probes found above background level were selected. For gene expression study the genes having a minimum of 2 probesets with each probeset comprising of a minimum of 2 probes per probeset. Genes having differential expression with p<0.05 were considered. The analysis was done at full, extended and core probe levels. For alternative splicing analysis the transcript clusters having fewer than 3 probesets and probesets having fewer than 3 probes were excluded from analysis. The invariant probes were excluded with significance of p<0.001 and the core probes expressed with significance p<0.001 were considered for analysis.

source_name: tumor male

label_protocol: rRNA reduction was done using Ribominus kit (Life technologies, Invitrogen, Carlsbad, California). Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Four samples each for dysplastic and adenocarcinoma stages and 5 samples from healthy non-transgenic lungs were selected for laser micro-dissection. Lung tissue slices of 10µm were prepared using a cryomicrotome (MICROM GmbH, Walldorf, Germany) and fixed over PEN membrane slide (Zeiss GmbH) and stained with Haematoxylin. The desired cells either dysplastic or transgenic (microscopically unaltered, normal) or adenocarcimona or healthy non-transgenic alveolar cells were laser microdissected and collected in an adhesive cap using the LMPC (Laser Micro-dissection Pressure Catapulting) system.

tag: age

value: 14 months

value: SPC/cRaf transgenic

value: lung adenocarcinoma tumor

tag: Sex


title: S. kudriavzevii IFO 1802 replicate B, fermentation at 12C

description: Gene expression of S. kudriavzevii IFO 1802 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate B

tag: strain


title: S. cerevisiae Fermol cryophile replicate B, fermentation at 12C

description: Gene expression of S. cerevisiae Fermol Cryophile with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C . Replicate B


title: SPC/c-Raf mouse tumor 87.3 male 12 months

extract_protocol: Four samples each for dysplastic and adenocarcinoma stages and 5 samples from healthy non-transgenic lungs were selected for laser micro-dissection. Lung tissue slices of 10µm were prepared using a cryomicrotome (MICROM GmbH, Walldorf, Germany) and fixed over PEN membrane slide (Zeiss GmbH) and stained with Haematoxylin. The desired cells either dysplastic or transgenic (microscopically unaltered, normal) or adenocarcimona or healthy non-transgenic alveolar cells were laser microdissected and collected in an adhesive cap using the LMPC (Laser Micro-dissection Pressure Catapulting) system.

value: 12 months


title: SPC/c-Raf mouse tumor 89.7_60.3 male 13 months

value: 13 months


title: +CHX, +N, -DEX, treatment replicate 1, Biorep 1

description: Gene expression profiles from transfected root protoplasts treated with +CHX, +N,  -DEX

value: CHX treated


title: S. cerevisiae Fermol cryophile replicate C, fermentation at 12C

description: Gene expression of S. cerevisiae Fermol Cryophile with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate C


title: SPC/c-Raf mouse tumor 62.4 female 11.5 months

source_name: tumor female

value: 11.5 months


title: LSG excised from Sjögren’s syndrome patient, clinical sample5

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description:
Gene expression data from labial salivary gland biopsy
SS_5

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with Factor Analysis for Robust Microarray Summarization (FARMS), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: labial salivary gland excised from Sjögren’s syndrome patient

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

extract_protocol: Total RNA was isolatedusing Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: The tissues were immersed in RNAlater (Ambion, Austin, USA) immediately after excision, then treated as per the manufacturer's protocols.

value: labial salivary gland

value: Female


title: S. uvarum CECT 12600 replicate A, fermentation at 12C

description: Gene expression of S. uvarum CECT12600 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate A


title: LSG excised from IgG4-related disease patient, clinical sample3

description:
Gene expression data from labial salivary gland biopsy
IgG4RD_3

source_name: labial salivary gland excised from IgG4-related disease patient


title: S. kudriavzevii IFO 1802 replicate C, fermentation at 12C

description: Gene expression of S. kudriavzevii IFO 1802 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate C


title: S. uvarum CECT 12600 replicate B, fermentation at 12C

description: Gene expression of S. uvarum CECT12600 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate B


title: LSG excised from IgG4-related disease patient, clinical sample1

description:
Gene expression data from labial salivary gland biopsy
IgG4RD_1


title: LSG excised from IgG4-related disease patient, clinical sample2

description:
Gene expression data from labial salivary gland biopsy
IgG4RD_2


title: LSG excised from Sjögren’s syndrome patient, clinical sample4

description:
Gene expression data from labial salivary gland biopsy
SS_4


title: LSG excised from IgG4-related disease patient, clinical sample4

description:
Gene expression data from labial salivary gland biopsy
IgG4RD_4


title: S. kudriavzevii IFO 1802 replicate A, fermentation at 12C

description: Gene expression of S. kudriavzevii IFO 1802 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C . Replicate A


title: SPC/c-Raf mouse transgenic unaltered 73.7 male 6 months

source_name: transgenic unaltered male

value: 6 months

value: lung


title: S. cerevisiae Fermol cryophile replicate A, fermentation at 12C

description: Gene expression of S. cerevisiae Fermol Cryophile with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate A


title: SPC/c-Raf mouse transgenic unaltered 65.1 male 6 months

value: male


title: SPC/c-Raf mouse transgenic unaltered 67.3_71.5 male 5 months

value: 5 months


title: non-transgenic mouse 67.4 female 7 months

source_name: non-transgenic female

value: 7 months

value: wild type

value: female


title: SPC/c-Raf mouse transgenic unaltered 73.5 male 6 months


title: LSG excised from Sjögren’s syndrome patient, clinical sample2

description:
Gene expression data from labial salivary gland biopsy
SS_2


title: FUL2_ChIP replicate 1

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

description: Biological replicate 1 of 3 for FUL2 ChIP-chip analysis.

hyb_protocol: Hybridization was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

scan_protocol: Scan was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

data_processing: Data were processed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/dataguide/index.html).

organism: Solanum lycopersicum

source_name: FUL2 ChIP DNA from the ripening tomato fruits

label_protocol: The ChIPed and input (no ChIP) DNAs were amplified using the GenomePlex WGA2 kit (Sigma). The amplified DNAs (1 µg each) were used for the following analysis. Labeling was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

growth_protocol: Tomato fruits were harvested at the ripening stage.

extract_protocol: Chromatin immunoprecipitated (ChIPed) DNA bound by FUL1 and FUL2 was prepared from the ripening tomato fruits basically as previously described (Ito et al., 2008; Fujisawa et al., 2011). Briefly, fruits were sliced and fixed in a vacuum with 1% formaldehyde for 10 min, followed by the addition of 125 mM glycine for 5 min. After rinsed with ice-cold water, the fruit tissue was frozen in liquid nitrogen and powdered by a mortar and pestle. Chromatin was extracted from the lysed nuclei corrected from the powder. The chromatin solution was sonicated for 10 sec twenty times on 10% power (setting 3) using a Sonifier 450 (Branson). The sonicated chromatin suspension was immunoprecipitated with each of anti-FUL1 and anti-FUL2 antibodies. The antibodies (a polyclonal rabbit antibody) we used were custom-made by Nippon Biotest Laboratories inc. (Japan). The anti-FUL1 and anti-FUL2 antibodies that interacted with FUL1/FUL2-DNA complex was corrected with Protein A-Agarose (Santa Cruz Biotechnology). After reverse cross-linking, proteins were digested with proteinase K (Takara biotech, Japan) and DNA fragments were recovered by phenol-chloroform purification and ethanol precipitation.

tag: chip antibodies

value: anti-FUL2 antibody

value: ripening fruit

source_name: Input DNA from the ripening tomato fruits

value: none, input DNA


title: non-transgenic mouse 92.7 female 11 months

description: RMA expression value derived from Expression Console software; core-exon analysis

value: 11 months

tag: tissue


title: LSG excised from Sjögren’s syndrome patient, clinical sample1

description:
Gene expression data from labial salivary gland biopsy
SS_1


title: LSG excised from Sjögren’s syndrome patient, clinical sample3

description:
Gene expression data from labial salivary gland biopsy
SS_3


title: LSG excised from IgG4-related disease patient, clinical sample5

description:
Gene expression data from labial salivary gland biopsy
IgG4RD_5


title: S59RFP, biological replicate 3

first: Mary

last: Baylies

address: 1275 York Avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from sorted cells

hyb_protocol: Following fragmentation, samples were hybridized in the Affy Hybridization Oven 645 and washed in the Affy Fluidics Station 450.

scan_protocol: Gene Chips were scanned using the Affymextrix GeneChip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite Software 8 using Affymetrix default analysis settings and RMA as normalization method.

organism: Drosophila melanogaster

source_name: RFP+ cells from st 13 Drosophila embryos

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

growth_protocol: 2 hour egg collections grown at 25 degrees were aged until stage 13

extract_protocol: RNA was extracted using Trizol LS according to the manufacturer's instructions

treatment_protocol: Embryos were dechorionated, homogenized, washed and fluorescent cells were collected on a Beckton-Dickson FACSAria Cell Sorter

tag: Stage

tag: preparation

value: dechorionated and homogenized embryos

value: somatic mesoderm

tag: transgene

value: slouch-RFP


title: non-transgenic mouse 92.1 male 11 months

source_name: non-transgenic male

tag: genotype


title: twi-actin-GFP, biological replicate 1

description: Gene expression data from sorted cells

source_name: GFP+ cells from st 13 Drosophila embryos


title: apGFP, biological replicate 3

description: Gene expression data from sorted cells

value: apterous-GFP


title: twi-actin-GFP, biological replicate 3

description: Gene expression data from sorted cells


title: twi-actin-GFP, biological replicate 2

description: Gene expression data from sorted cells


title: S59RFP, biological replicate 1

description: Gene expression data from sorted cells


title: S59RFP, biological replicate 2

description: Gene expression data from sorted cells


title: non-transgenic mouse 67.5 female 7 months


title: SPC/cRaf mouse dysplasia 67.3_71.5 male 5 months

source_name: dysplasia male

value: SPC/cRaf transgenic

value: lung dysplastic lesion


title: SPC/cRaf mouse dysplasia 73.5 male 6 months

value: 6 months


title: non-transgenic mouse 65.0 male 7 months

value: lung


title: SPC/cRaf mouse dysplasia 73.7 male 6 months

value: male


title: FUL2_ChIP replicate 3

description: Biological replicate 3 of 3 for FUL2 ChIP-chip analysis. Dye-swap


title: FUL1_ChIP replicate 3

description: Biological replicate 3 of 3 for FUL1 ChIP-chip analysis. Dye-swap

source_name: FUL1 ChIP DNA from the ripening tomato fruits

value: anti-FUL1 antibody


title: apGFP, biological replicate 1

description: Gene expression data from sorted cells