title: PC9_None_2hr

description: Gene expression after 2hr in PC9 with no treatment

source_name: PC9, 2hr, no treatment


title: PC9_IRS_22hr

status: Public on Jan 01 2014

type: RNA

city: Minato-ku

first: Noriko

last: Gotoh

state: Tokyo

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: Gene expression after 22hr in PC9 treated with gefinitib

hyb_protocol: Hybridization was carried out using the Gene Expression Hybridization Kit (Agilent Technologies), according to the manufacturer’s directions. Briefly, a cRNA sample (1.65 g) was subjected to fragmentation (30 min at 60 °C) and then hybridization on a 44K Agilent Whole Human Genome Oligo Microarray (G4112F) (Agilent Technologies). . RNA samples with an RNA integrity number (RIN) greater than 8 were used for further analysis. Hybridization was carried out on a 44K Agilent Whole Human Genome Oligo Microarray (G41112F) (Agilent Technologies).

scan_protocol: Microarrays were scanned by a dynamic autofocus microarray scanner (Agilent DNA Microarray Scanner, Agilent Technologies) under the default parameters (Green PMT was set to 100%, and the scan resolution was set to 5 um. Feature Extraction Software v9.1 (Agilent Technologies) was used to obtain a raw signal value and a quality flag (Present [P], Marginal [M], or Absent [A]).

data_processing: After aggregating all the scanned signals for the different time points, cell lines, and treatments into a single data matrix, quantile normalization (Bolstad et al., Bioinformatics, 2003) was applied to remove the between-experiment distributional biases due to assay artifacts by forcing the same percentile values on all of the processed data.

molecule: total RNA

organism: Homo sapiens

source_name: PC9, 22hr, gefinitib

label_protocol: RNA samples were labeled using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies) according to the manufacturer’s directions. Briefly, amplification and labeling of total RNA (500 ng) was performed using Cyanine 3-CTP.

growth_protocol: Parental PC9 cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum. For the stablishment of gefitinib-resistance cell line (PC9GR), PC9 cells were treated with growth medium containing gefitinib at the concentrations 0.02-0.1 uM for 14-28 days, 0.005-0.02 uM for 14-28 days, and 0.1 uM for a range of exposure durations, yielding approximately 500 survived clones. Following further treatments of gefitinib and repeated clone refining with the indicated concentrations (0 uM, 0.1 uM and 1 uM), a total of 179 clones were screened out based on MTT assays that verified significant suppression of growth in the cancer populations after 7 days. Among the clones further refined that lacked the MET amplification and the EGFR T790M mutation, PC9GR was isolated as a line demonstrating one of the lowest dose responses and almost the same doubling time to PC9.

extract_protocol: Total RNA was isolated from each sample by TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s directions. The quality of the total RNA was evaluated on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: After 48-hr starvation, each cell line were treated with 100 ng/ml EGF and/or 0.5 uM gefitinib. Cells were harvested at 26 time points during 24 hours.

tag: tissue

value: non-small cell lung cancer cell line

tag: drug response

value: gefitinib-sensitive cell line

tag: cell line

tag: time

tag: treatment

value: gefinitib


title: Tc_94

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The arrays were scanned to a target intensity of 500 by a GeneArray Scanner, and patterns of hybridization were detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The CEL files were generated using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Signal intensities were derived from CEL files and Signal intensity derived from the CEL files, using GCRMA method.

label: biotin

source_name: primary surgical treatment

label_protocol: biotin

growth_protocol: Frozen tissue samples were embedded, and sections were cut and mounted on slides. The slides were stained with H&E to ensure that at least 70% of the cellular content was comprised of epithelial ovarian cancer cells.

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

treatment_protocol: Frozen rissues

value: ovarian cancer cells

tag: tissue subtype

value: clear cell

tag: advanced disease stage

value: stage IV

tag: recurrence status

value: non-recurrence

tag: survival/death

value: death


title: Tc_65

value: stage II

value: recurrence

value: survival


title: SAM_waterdeficit-rewatering_R30

city: Uppsala

first: Clement

last: Lafon-Placette

address: Almas Allé 5

country: Sweden

institute: SLU

description: SAM gene expression after 9 days in moderate watere deficit floowed by 5 days in non-limiting water conditions

hyb_protocol: RNA hybridization was conducted according to Agilent Technologies instructions. Briefly, the labeled cRNAs were fragmented in Fragmentation mix (Agilent Technologies) during 30 min at 60°C, before addition of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies) and loading onto the arrays. The arrays were incubated at 65°C for 17 hours in Agilent hybridization chambers and then wash according to the protocol at room temperature.

scan_protocol: Microarray slides were scanned with G2505C scanner (Agilent Technologies, France) and raw signal data were extracted using Feature Extraction 10.7 software. Reproducibility and reliability of each single microarray was assessed using Quality Control report data (Feature Extraction, Agilent Technologies).

data_processing: One-color transcriptomics data were normalized per chip to the 75th percentile and per probe to medians and were transformed to log values. Data filtering was based on Feature Extraction flag criteria: non outlier population; not saturated, uniform and significant probe signal; probe signal above background. A probe signal was considered as “well above background” if gBGSubSignal was greater than 2.6 gBG_SD. To pass the filtering, a probe needed to pass all flag criteria for all replicates of at least one experimental condition (Control, Water Deficit or Re-irrigation). After this data filtering, 33005 probes were available. To determine if there were genes differentially expressed between experimental conditions, one-way ANOVA and Welch’s t-test were performed with MeV software (Saeed et al., 2003). Statistical tests were considered significant at ** P < 0.01. Benjamini-Hochberg’s correction was used for false positive discovery. Average linkage hierarchical clustering analysis was applied using Pearson correlation.

organism: Populus x canadensis

source_name: SAM, water deficit followed by rewatering, replicate 2

label_protocol: Fluorescent cRNA (complementary RNA) was generated from 600 ng of total RNA according to Agilent Technologies recommendations. Briefly, RNA spike mix, which is a mix of 10 polyadenylated RNAs synthesized in vitro from E1A adenovirus gene, was prepared with One-Color RNA Spike-In Kit (Agilent Technologies, France) to be used as positive control for labeling and data analysis. For each sample, 80 ng of total RNAs were reverse transcribed, followed by T7 RNA polymerase-mediated simultaneous cRNA synthesis and incorporation of cyanine 3-labeled CTP, using Input Quick Amp Labeling Kit, One Color (Agilent Technologies, France). Fluorescent cRNA was purified with RNeasy Mini Kit (Qiagen, France). Quality control of synthesized fluorescent cRNA was based on cRNA and Cy3 concentration measurement as well as cRNA fragments size. For each sample, a yield of 825 ng of cRNA, a specific activity of 6 pmolCy3/gcRNA and a 200-2000 nucleotides fragments size range were chosen as quality thresholds.

growth_protocol: Unrooted dormant stem cuttings of Populus × euramericana (P. deltoides × P. nigra) ‘Carpaccio’ genotype were obtained from INRA nursery (Nancy, France in 2008). Ten-years old mother plants are cut off each spring. Cuttings were 22 cm long and 0.5-2 cm wide and were harvested in February from plants grown in INRA nursery. Unrooted cuttings (20 for 101-74 and 12 for each hybrid) were then stocked 1 month in 2°C cold dark room. Before potting, cuttings soaked in water in vertical position to favor rooting. Rooted cuttings of Populus × euramericana (P. deltoides × P. nigra) ‘Carpaccio’ genotype (6 cuttings per treatment: ‘Control’, ‘Water deficit’ and ‘Re-irrigation’) were planted in 20L pots containing a mixture of peat and sand (50/50, v/v) amended with magnesian chalk (60 g/100 L) and fertilized with a low releasing fertilizer (Nutricote T100, 13/13/13/2, N/P/K/Mg + trace elements). Plants were placed in a greenhouse (Nancy, France in April 2008) exposed to natural daylight (ranging from 350 to 900 μmol m−2 s−1) and where temperature was maintained in the range 19–26 °C with humidity oscillating between 50 and 75%. Plants were watered to field capacity three times a day for 5 weeks, until plant height was between 0.6 and 0.9 m.

extract_protocol: Total RNAs were independently isolated from 3 individual shoot apical meristems (50 mg fresh weight) per treatment using Nucleospin® RNA Plant (Macherey-Nagel, Hoerdt, France). A control PCR was performed on RNA to confirm the absence of genomic DNA in all the total RNAs preparations. Bioanalyzer 2100 (Agilent Technologies, Massy, France) was used to estimate DNA contamination and RNA integrity with RNA Integrity Number (RIN) measurement (RIN threshold of 8).

treatment_protocol: Soil water availability was determined following relative extractable water (REW), which was maintained in the range of 80-86% (minimum-maximum) for the fully watered treatment and 17–23% for the water deficit by controlled watering every morning. A moderate water deficit was applied for 14 days to the cuttings (‘water deficit’) while cuttings in ‘control’ condition remained fully watered. For the ‘Re-irrigation’ treatment, a moderate water deficit was applied for 9 days and for the 5 following days cuttings were fully watered.

value: shoot apical meristem

tag: genotype

value: Carpaccio

tag: age

value: 5 weeks

value: water deficit followed by rewatering


title: Te_84

value: endometrioid


title: CandidautilisWT_YPD5_10.5hr_rep1

city: Yokohama-shi

first: Hideyuki

last: Tamakawa

state: Kanagawa

address: 1-13-5, Fukuura, Kanazawa-ku

department: Central Laboratories for Key Technologies

institute: KIRIN Co., Ltd.

description:
XYLOSE1
Gene expression after 10.5hr in Candida utilis WT cell grown on glucose.

hyb_protocol: 0.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 20 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 20 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Kirin Candida utilis Oligo Microarrays (custom array) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using the one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software Version 9.5.3.1 (Agilent) using default parameters (protocol GE1-QCM_Feb07 and Grid: 022762_D_F_20090126) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using 75% quantile normalization.

organism: Cyberlindnera jadinii

source_name: Candida utilis WT, YPD5, 10.5hr

label_protocol: Five hundred ng of mRNA were labeled using the Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Yeast cells were pre-cultured with shaking at 30°C for 3 days in 50 ml of YPD2 (10 g/L yeast extract, 20 g/L peptone, and 20 g/L glucose). Cells were harvested and inoculated at starting OD600 nm of 0.1 in 50 ml of YPD5 (10 g/L yeast extract, 20 g/L peptone, and 20 g/L glucose) or YPX5 (10 g/L yeast extract, 20 g/L peptone, and 50 g/L xylose), and grown with gentle stirring at 30°C under semi-aerobic conditions (sampling time: 10.5 or 24 hrs, respectively).

extract_protocol: Total RNA was extracted using glass beads and purified using an RNeasy column (Qiagen).

tag: strain

value: wild-type

tag: growth medium

value: glucose


title: Te_78

value: stage I


title: PC9_IRS_23hr

description: Gene expression after 23hr in PC9 treated with gefinitib

source_name: PC9, 23hr, gefinitib

value: non-small cell lung cancer cell line

value: gefitinib-sensitive cell line

value: gefinitib


title: PC9_None_0.5hr

description: Gene expression after 0.5hr in PC9 with no treatment

source_name: PC9, 0.5hr, no treatment

value: no treatment


title: Tc_64

value: ovarian cancer cells

value: clear cell

value: non-recurrence


title: PC9_IRS_21hr

description: Gene expression after 21hr in PC9 treated with gefinitib

source_name: PC9, 21hr, gefinitib


title: SAM_waterdeficit-rewatering_R35

source_name: SAM, water deficit followed by rewatering, replicate 1


title: rice root-200 mM AHX treatment rep 2

city: Shizuoka

first: JAE-HOON

last: CHOI

address: 836 Ohya

department: Graduate School of Science and Technology

institute: Shizuoka University

description: 200 mM AHX treatment rep 2, root

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software (version A.8.4.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

source_name: AHX-treated rice

label_protocol: Cy3-and Cy5-labeled cRNA were prepared from 200 ng total RNA using Low RNA Input Linear Amp Kit (Agilent) according to manufacturer's protocol .

growth_protocol: Seeds of rice (Oryza sativa L. ‘Nipponbare’) were germinated at 28 °C in a sterilized germination tray. The seedlings had been grown for 14 days at 28 °C.

extract_protocol: Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Germinaed rice was treated with AHX or AOH (50 and 200 mM) for 2 weeks in test-tube. After incubation for 2 weeks, rice seedlings were seperated into two parts, shoot and root.

tag: cultivar

value: Nipponbare

value: root

value: 200mM AHX

source_name: control-rice


title: rice root-50 mM AOH treatment rep 2

description: 50 mM AOH treatment rep 2, root

source_name: AOH-treated rice

value: 50mM AOH


title: rice root-200 mM AOH treatment rep 2

description: 200 mM AOH treatment rep 2, root


title: SAM_waterdeficit-rewatering_R25

source_name: SAM, water deficit followed by rewatering, replicate 3

value: shoot apical meristem

value: Carpaccio

value: 5 weeks


title: PC9_None_0hr

description: Gene expression after 0hr in PC9 with no treatment

source_name: PC9, 0hr, no treatment


title: PC9_IRS_20hr

description: Gene expression after 20hr in PC9 treated with gefinitib

source_name: PC9, 20hr, gefinitib


title: Tc_59

value: survival


title: Tc_63


title: Tc_74

value: stage IV

value: recurrence


title: SAM_waterdeficit_S46

description: SAM gene expression after 14 days in moderate watere deficit

source_name: SAM, water deficit, replicate 3

value: water deficit


title: PC9_IRS_19hr

description: Gene expression after 19hr in PC9 treated with gefinitib

source_name: PC9, 19hr, gefinitib

value: non-small cell lung cancer cell line

value: gefitinib-sensitive cell line


title: rice root-200 mM AOH treatment rep 1

description: 200 mM AOH treatment rep 1, root


title: Tc_56

value: stage I


title: rice root-50 mM AHX treatment rep 2

description: 50 mM AHX treatment rep 2, root

value: 50mM AHX


title: Tc_51

value: ovarian cancer cells

value: clear cell

value: stage III


title: Tc_61

value: non-recurrence


title: PC9_IRS_18hr

description: Gene expression after 18hr in PC9 treated with gefinitib

source_name: PC9, 18hr, gefinitib

value: gefinitib


title: SAM_waterdeficit_S38

source_name: SAM, water deficit, replicate 2


title: rice root-50 mM AOH treatment rep 1

description: 50 mM AOH treatment rep 1, root

value: Nipponbare

value: root

value: 50mM AOH


title: SAM_nonlimiting_T116

description: SAM gene expression after 14 days in non-limiting water conditions

source_name: SAM, non-limiting water, replicate 3

value: shoot apical meristem

value: Carpaccio

value: 5 weeks

value: non-limiting water


title: SAM_waterdeficit_S26

source_name: SAM, water deficit, replicate 1

value: water deficit


title: rice root-50 mM AHX treatment rep 1

description: 50 mM AHX treatment rep 1, root


title: SAM_nonlimiting_T69

source_name: SAM, non-limiting water, replicate 2


title: CandidautilisTMS174_YPX5_24hr_rep1

description:
XYLOSE7
Gene expression after 24hr in Candida utilis TMS174 (xylose-fermenting strain) cell grown on xylose.

source_name: Candida utilis TMS174, YPX5, 24hr

value: xylose

value: 24 hr


title: Tc_49

source_name: primary surgical treatment

value: stage I

value: survival


title: PC9_IRS_16hr

description: Gene expression after 16hr in PC9 treated with gefinitib

source_name: PC9, 16hr, gefinitib

value: non-small cell lung cancer cell line

value: gefitinib-sensitive cell line


title: PC9_IRS_15hr

description: Gene expression after 15hr in PC9 treated with gefinitib

source_name: PC9, 15hr, gefinitib


title: rice root200 mM AHX treatment rep 1

description: 200 mM AHX treatment rep 1, root

source_name: AHX-treated rice

value: 200mM AHX


title: SAM_nonlimiting_T22

source_name: SAM, non-limiting water, replicate 1


title: PC9_IRS_17hr

description: Gene expression after 17hr in PC9 treated with gefinitib

source_name: PC9, 17hr, gefinitib


title: Tc_113

value: ovarian cancer cells

value: clear cell

value: stage III

value: non-recurrence


title: Fibroblast_AZA_TSA_Hour_8_rep3

city: Burlington

first: David

middle: E

last: Kerr

state: VT

address: 500 Main Street 205 Terrill Hall

department: Animal Science

country: USA

institute: University of Vermont

description:
Sample name: 448P
Gene expression 8 hours post-LPS

hyb_protocol: Samples were injected into arrays and placed in the Affymetrix Genechip® Hybridization Oven 640 at 45° C and 60 RPM for 16-18 hours overnight.  Arrays were stained using the Affymetrix Genechip® Fluidics Station 450 and scanned with the Affymetrix Genechip® Scanner 3000

scan_protocol: Affymetrix 3000-G7 scanner using GCOS

data_processing: Probe set and sample matrix expression statistics were calculated using the Robust Multichip Average (RMA) method (Irizarry et al., 2003). Sample quality was assessed based on the 3’:5’ ratio, relative log expression (RLE), and normalized unscaled standard error (NUSE).  Principal Component Analysis (PCA) was also used to look for outlier samples that would potentially introduce latent variation into the analysis of differential expression across sample groups.  Linear modeling of sample groups was performed using ANOVA as implemented in Partek Genomic Suites. The magnitude of the response (fold change calculated using the least square mean) and the p-value associated with each probe set and binary comparison were calculated, as well a step-up, adjusted p-value for the purpose of controlling the false discovery rate (FDR).

label: Biotin

organism: Bos taurus

source_name: Fibroblast, AZA-TSA, hour 8

label_protocol: Approximately 4.5ug of cDNA generated using the Ovation Pico WTA System V2 was fragmented and labeled using the Encore Biotin Module from NuGEN.  Efficiency of the biotin labeling reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay

growth_protocol: Dermal fibroblast cultures were maintained in Dulbecco's Modified Eagle Media (DMEM) with 5% FBS, 1x ITS, 1x Penn/Strep antibiotic

extract_protocol: Total RNA was extracted using the 5 Prime PerfectPure RNA Cell Culture Kit per manufacturers instructions.

treatment_protocol: Control cells were maintained in DMEM described in growth protocol. Treated cells were grown in DMEM described in growth protocol, however 4 days prior to extraction were exposed to 10uM 5-aza-2'-deoxycytidine. One day prior to extraction 80nM trichostation-A was added so the final 24 hours of treatment contained both modifiers

tag: cell type

value: Dermal fibroblast

tag: epigenetic modification

value: Demethylated/Hyper-acetylated

tag: agent

value: LPS

value: hour 8


title: Tc_48

tag: tissue

value: recurrence

value: death


title: PC9_IRS_14hr

description: Gene expression after 14hr in PC9 treated with gefinitib

source_name: PC9, 14hr, gefinitib

tag: drug response

value: gefinitib


title: rice shoot-200 mM AHX treatment rep 2

description: 200 mM AHX treatment rep 2, shoot

value: Nipponbare

value: shoot

source_name: control-rice


title: rice shoot-200 mM AOH treatment rep 2

description: 200 mM AOH treatment rep 2, shoot

source_name: AOH-treated rice


title: Fibroblast_AZA_TSA_Hour_4_rep3

description:
Sample name: 444P
Gene expression 4 hours post-LPS

source_name: Fibroblast, AZA-TSA, hour 4

value: hour 4


title: PC9_IRS_13hr

description: Gene expression after 13hr in PC9 treated with gefinitib

source_name: PC9, 13hr, gefinitib

value: non-small cell lung cancer cell line

tag: cell line


title: rice shoot-50 mM AOH treatment rep 2

description: 50 mM AOH treatment rep 2, shoot

value: 50mM AOH


title: rice shoot-200 mM AOH treatment rep 1

description: 200 mM AOH treatment rep 1, shoot

value: 200mM AHX


title: Fibroblast_AZA_TSA_Hour_2_rep3

description:
Sample name: 442P
Gene expression 2 hours post-LPS

source_name: Fibroblast, AZA-TSA, hour 2

tag: time

value: hour 2


title: rice shoot-50 mM AHX treatment rep 2

description: 50 mM AHX treatment rep 2, shoot

tag: treatment

value: 50mM AHX


title: Fibroblast_Control_Hour_8_rep3

description:
Sample name: 448N
Gene expression for fibroblasts 8 hours post-LPS

source_name: Fibroblast, control, hour 8

value: untreated


title: Fibroblast_Control_Hour_4_rep3

description:
Sample name: 444N
Gene expression for fibroblasts 4 hours post-LPS

source_name: Fibroblast, control, hour 4


title: PC9_IRS_11hr

description: Gene expression after 11hr in PC9 treated with gefinitib

source_name: PC9, 11hr, gefinitib

value: gefitinib-sensitive cell line


title: rice shoot-50 mM AOH treatment rep 1

description: 50 mM AOH treatment rep 1, shoot


title: PC9_IRS_12hr

description: Gene expression after 12hr in PC9 treated with gefinitib

source_name: PC9, 12hr, gefinitib


title: rice shoot200 mM AHX treatment rep 1

description: 200 mM AHX treatment rep 1, shoot


title: PC9_IRS_9hr

description: Gene expression after 9hr in PC9 treated with gefinitib

source_name: PC9, 9hr, gefinitib


title: PC9_IRS_10hr

description: Gene expression after 10hr in PC9 treated with gefinitib

source_name: PC9, 10hr, gefinitib


title: Fibroblast_AZA_TSA_Hour_0_rep3

description:
Sample name: 440P
Basal gene expression for fibroblasts following epigenetic modification can be found in this sample.

source_name: Fibroblast, AZA-TSA, hour 0

value: Dermal fibroblast

value: no LPS

value: hour 0


title: Fibroblast_Control_Hour_2_rep3

description:
Sample name: 442N
Gene expression for fibroblasts 2 hours post-LPS

source_name: Fibroblast, control, hour 2

value: LPS


title: PC9_IRS_8hr

description: Gene expression after 8hr in PC9 treated with gefinitib

source_name: PC9, 8hr, gefinitib


title: rice shoot-50 mM AHX treatment rep 1

description: 50 mM AHX treatment rep 1, shoot

source_name: AHX-treated rice


title: Fibroblast_AZA_TSA_Hour_8_rep2

description:
Sample name: 388P
Gene expression 8 hours post-LPS

source_name: Fibroblast, AZA-TSA, hour 8

value: Demethylated/Hyper-acetylated

value: hour 8


title: Fibroblast_Control_Hour_0_rep3

description:
Sample name: 440N
Basal gene expression for fibroblasts can be found in this sample.

source_name: Fibroblast, control, hour 0


title: PC9_IRS_7hr

description: Gene expression after 7hr in PC9 treated with gefinitib

source_name: PC9, 7hr, gefinitib

value: gefinitib


title: SHA-salt_rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

country: China

institute: Huazhong Agricultural University

hyb_protocol: Microarray analysis was performed using Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version). In total 150ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled probe with the help of low RNA input linear amplification/labeling kit  (Agilent technologies) and 1.65µg of Labeled cRNA probes were fragmented using fragmentation buffer (Agilent Technologies) and hybridized to the Arabidopsis arrays according to manufacturer’s instructions.

scan_protocol: The arrays were scanned using the high resolution array scanner (Agilent technologies) with the appropriate settings for the one color gene expression arrays after hybridization.

data_processing:
Array images were acquired with Agilent's dual-laser microarray scanner and signal intensities were extracted from the scanned images with dedicated Agilent Feature Extraction software (Agilent technologies). The outliers and the abnormal features were flagged and the data was normalized using the intra-array percentile shift normalization (threshold of 75 and above) and median based inter-array normalization. The GeneSpring software (Agilent technologies) was used to calculate the intensity ratios and fold changes.
All the genes with a P value below 0.01 and a fold change above 2 were chosen for further analysis.

organism: Arabidopsis

source_name: Sha ecotype,100mM NaCl, replicate 2

growth_protocol: Seeds of Sha and Ler ecotypes were sown in MS plates and grown at 22/18 °C in the growth chamber under a photoperiod of 12h light/12 h dark at 350 μmol m-2s-1 and 70% relative humidity.

extract_protocol: Total RNA was extracted and purified from leaves of at least 30 seedlings per plate for each ecotype and salt combination using QIAGEN-RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to guidelines specified by the manufacturer. Two biological replicates were prepared for each combination. RNA was quantified using a Nanodrop-ND 8000 spectrophotometer (Thermo Fisher Scientific) and RNA quality was assessed by agarose gel analysis and using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol. Samples with the RNA integrity number of 7.5 and above were chosen for further analysis.

treatment_protocol: Ten days after sowing, uniform seedlings of both ecotypes were carefully transferred to MS plates supplemented with 100 mM NaCl. Seedlings in MS plates without salt were used as controls. Plant materials were collected for RNA extraction at 4th days after transfer.

value: leaf

tag: ecotype

value: SHA


title: PC9_IRS_4hr

description: Gene expression after 4hr in PC9 treated with gefinitib

source_name: PC9, 4hr, gefinitib


title: PC9_IRS_5hr

description: Gene expression after 5hr in PC9 treated with gefinitib

source_name: PC9, 5hr, gefinitib


title: SHA-salt_rep1

source_name: Sha ecotype,100mM NaCl, replicate 1

label_protocol: Microarray analysis was performed using Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version). In total 150ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled probe with the help of low RNA input linear amplification/labeling kit  (Agilent technologies) and 1.65µg of Labeled cRNA probes were fragmented using fragmentation buffer (Agilent Technologies) and hybridized to the Arabidopsis arrays according to manufacturer’s instructions.


title: SHA-control_rep1

source_name: Sha ecotype, control, replicate 1


title: PC9_IRS_6hr

description: Gene expression after 6hr in PC9 treated with gefinitib

source_name: PC9, 6hr, gefinitib


title: Fibroblast_Control_Hour_4_rep2

description:
Sample name: 384N
Gene expression for fibroblasts 4 hours post-LPS

source_name: Fibroblast, control, hour 4

value: hour 4


title: SHA-control_rep2

source_name: Sha ecotype, control, replicate 2


title: Fibroblast_Control_Hour_8_rep2

description:
Sample name: 388N
Gene expression for fibroblasts 8 hours post-LPS

source_name: Fibroblast, control, hour 8


title: PC9_IRS_0hr

description: Gene expression after 0hr in PC9 treated with gefinitib

source_name: PC9, 0hr, gefinitib

value: non-small cell lung cancer cell line


title: Fibroblast_Control_Hour_2_rep2

description:
Sample name: 382N
Gene expression for fibroblasts 2 hours post-LPS


title: Fibroblast_AZA_TSA_Hour_2_rep2

description:
Sample name: 382P
Gene expression 2 hours post-LPS

source_name: Fibroblast, AZA-TSA, hour 2


title: Fibroblast_AZA_TSA_Hour_4_rep2

description:
Sample name: 384P
Gene expression 4 hours post-LPS

source_name: Fibroblast, AZA-TSA, hour 4


title: PC9_IRS_2hr

description: Gene expression after 2hr in PC9 treated with gefinitib

source_name: PC9, 2hr, gefinitib


title: PC9_IRS_0.5hr

description: Gene expression after 0.5hr in PC9 treated with gefinitib

source_name: PC9, 0.5hr, gefinitib


title: Ler-salt_rep2

source_name: Ler ecotype,100mM NaCl, replicate 2

value: Ler


title: Ler-control_rep2

source_name: Ler ecotype, control, replicate 2


title: PC9_IRS_3hr

description: Gene expression after 3hr in PC9 treated with gefinitib

source_name: PC9, 3hr, gefinitib


title: Fibroblast_Control_Hour_0_rep2

description:
Sample name: 380N
Basal gene expression for fibroblasts can be found in this sample.

source_name: Fibroblast, control, hour 0


title: Ler-salt_rep1

source_name: Ler ecotype,100mM NaCl, replicate 1


title: PC9_IRS_1hr

description: Gene expression after 1hr in PC9 treated with gefinitib

source_name: PC9, 1hr, gefinitib


title: Fibroblast_AZA_TSA_Hour_8_rep1

description:
Sample name: 348P
Gene expression 8 hours post-LPS

source_name: Fibroblast, AZA-TSA, hour 8


title: Fibroblast_AZA_TSA_Hour_0_rep2

description:
Sample name: 380P
Basal gene expression for fibroblasts following epigenetic modification can be found in this sample.

source_name: Fibroblast, AZA-TSA, hour 0


title: Fibroblast_AZA_TSA_Hour_2_rep1

description:
Sample name: 342P
Gene expression 2 hours post-LPS


title: PC9_EGF_IRS_23hr

description: Gene expression after 23hr in PC9 treated with EGF and gefitinib

source_name: PC9, 23hr, EGF and gefitinib

value: EGF and gefitinib


title: Fibroblast_AZA_TSA_Hour_4_rep1

description:
Sample name: 344P
Gene expression 4 hours post-LPS


title: PC9_EGF_IRS_21hr

description: Gene expression after 21hr in PC9 treated with EGF and gefitinib

source_name: PC9, 21hr, EGF and gefitinib


title: PC9_EGF_IRS_22hr

description: Gene expression after 22hr in PC9 treated with EGF and gefitinib

source_name: PC9, 22hr, EGF and gefitinib


title: Fibroblast_Control_Hour_4_rep1

description:
Sample name: 344N
Gene expression for fibroblasts 4 hours post-LPS

source_name: Fibroblast, control, hour 4


title: PC9_EGF_IRS_18hr

description: Gene expression after 18hr in PC9 treated with EGF and gefitinib

source_name: PC9, 18hr, EGF and gefitinib


title: CLL_Immobilized_rep9

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

hyb_protocol: Cy3-labeled RNA was hybridized to the Whole Human Genome (4x44K) oligo microarray platform (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (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: CLL

label_protocol: GEP was performed using the Whole Human Genome (4x44K) oligo microarray platform (Agilent  Technologies)

growth_protocol: Freshly isolated CLL cells cultured (1 × 107 cells/ml) in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate (Life Technologies, Carlsbad, CA, USA). CLL cells (n = 49/76) were also co-stimulated for 20h with 1 × 107/mL Dynabeads M-450 Epoxy (Life Technologies) coated with 10 μg goat anti-human IgM (immobilized anti-IgM) (SouthernBiotech, Birmingham, AL).27, 28 The coating procedure was done according to the manufacturer's instructions (Life Technologies).

extract_protocol: Total RNA was extracted from purified CLL cells and normal peripheral blood B cells of healthy donors using the TRIZOL Reagent (Life Technologies) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: In selected experiments, CLL cells  co-stimulated with immobilized anti-IgM were cultured in the presence or not of R406 4mM (Axon Medchem, The Netherlands). CLL cells  were also cultured in the presence or not of 7.5 μg/ml phosphorothioate CpG-ODN oligonucleotide 2006 (5′-TCG TCG TTT TGT CGT TTT GTC GTT-3′; CpG-ODN2006) (Life Technologies, CA) for 20 hours, as previously reported.27, 28

value: Peripheral blood

tag: gender

value: male

value: B-CLL

value: co-stimulated with immobilized anti-IgM


title: CLL_Immobilized_rep12


title: CLL_Immobilized_rep15


title: Fibroblast_Control_Hour_8_rep1

description:
Sample name: 348N
Gene expression for fibroblasts 8 hours post-LPS

source_name: Fibroblast, control, hour 8

value: Dermal fibroblast

value: untreated


title: Fibroblast_Control_Hour_2_rep1

description:
Sample name: 342N
Gene expression for fibroblasts 2 hours post-LPS

source_name: Fibroblast, control, hour 2

value: hour 2


title: Fibroblast_AZA_TSA_Hour_0_rep1

description:
Sample name: 340P
Basal gene expression for fibroblasts following epigenetic modification can be found in this sample.

value: no LPS

value: hour 0


title: PC9_EGF_IRS_19hr

description: Gene expression after 19hr in PC9 treated with EGF and gefitinib

source_name: PC9, 19hr, EGF and gefitinib

value: gefitinib-sensitive cell line


title: PC9_EGF_IRS_24hr

description: Gene expression after 24hr in PC9 treated with EGF and gefitinib

source_name: PC9, 24hr, EGF and gefitinib


title: PC9_EGF_IRS_17hr

description: Gene expression after 17hr in PC9 treated with EGF and gefitinib

source_name: PC9, 17hr, EGF and gefitinib


title: PC9_EGF_IRS_16hr

description: Gene expression after 16hr in PC9 treated with EGF and gefitinib

source_name: PC9, 16hr, EGF and gefitinib


title: CLL_Immobilized_rep14


title: CLL_Immobilized_rep8


title: CLL_Immobilized_rep11


title: PC9_EGF_IRS_20hr

description: Gene expression after 20hr in PC9 treated with EGF and gefitinib

source_name: PC9, 20hr, EGF and gefitinib


title: Fibroblast_Control_Hour_0_rep1

description:
Sample name: 340N
Basal gene expression for fibroblasts can be found in this sample.

source_name: Fibroblast, control, hour 0


title: Ler-control_rep1

source_name: Ler ecotype, control, replicate 1


title: CLL_Immobilized_rep16


title: CLL_Immobilized_rep10


title: CLL_Immobilized_rep13


title: CLL_Immobilized_rep7


title: PC9_EGF_IRS_14hr

description: Gene expression after 14hr in PC9 treated with EGF and gefitinib

source_name: PC9, 14hr, EGF and gefitinib


title: PC9_EGF_IRS_13hr

description: Gene expression after 13hr in PC9 treated with EGF and gefitinib

source_name: PC9, 13hr, EGF and gefitinib


title: PC9_EGF_IRS_15hr

description: Gene expression after 15hr in PC9 treated with EGF and gefitinib

source_name: PC9, 15hr, EGF and gefitinib


title: CLL_Immobilized_rep4


title: CLL_Immobilized_rep3


title: PC9_EGF_IRS_7hr

description: Gene expression after 7hr in PC9 treated with EGF and gefitinib

source_name: PC9, 7hr, EGF and gefitinib


title: H56_2

city: Chiba city

first: Naohiko

last: Seki

state: Chiba

address: Inohana1-8-1, Chuo-ku

institute: Chiba University

hyb_protocol: Denature the solution at 95 ℃ for 5 min. Centrifuge at 12,000 g at 4 ℃ for 2 min. Add 30 μL of 20 x salt Buffer to ditch of “Hybridization Chamber”. Slide is capped by “MASTUNAMI Gap Cover Glass (CG00044 or 24*60 25PCS)”. Fill the gap with 45 μL of the solution. Incubate in 56 ℃ water bath for 16-20 hr.

scan_protocol: Scanner; G2505C (Agilent), Software; Agilent Scan Control (Agilent), Green and Red PMT: 100 %, Scan resolution: 10 um

data_processing: Quantification; Feature Extraction 10.7.3.1 (Agilent). Normalization; First, calculate the average ratio (Hy3/Hy5) of replicated spots on each array. Next, calculate the ratio of average ratio (Tumor/Non tumor).

source_name: Hypopharyngeal squamous cell carcinoma No. 56

label_protocol: We used miRCURY LNA microRNA Array Hi-Power Labeling kit.

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

value: Tumor tissue

value: Male

tag: t

tag: n

tag: m

tag: Stage

value: IVA

tag: differentiation

value: well

source_name: H56 pooled sample

tag: pooled sample composition

value: blends equal amounts of each samples


title: H56_1

value: Non tumor tissue

tag: age


title: PC9_EGF_IRS_12hr

description: Gene expression after 12hr in PC9 treated with EGF and gefitinib

source_name: PC9, 12hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: EGF and gefitinib


title: PC9_EGF_IRS_8hr

description: Gene expression after 8hr in PC9 treated with EGF and gefitinib

source_name: PC9, 8hr, EGF and gefitinib


title: CLL_Immobilized_rep1

source_name: CLL

value: Peripheral blood

value: male

tag: cell type


title: CLL_Immobilized_rep6

value: B-CLL

value: co-stimulated with immobilized anti-IgM


title: CLL_Untreated_rep14

value: untreated


title: H44_2

source_name: Hypopharyngeal squamous cell carcinoma No. 44

value: Female

value: poor

source_name: H44 pooled sample


title: CLL_Untreated_rep16


title: PC9_EGF_IRS_11hr

description: Gene expression after 11hr in PC9 treated with EGF and gefitinib

source_name: PC9, 11hr, EGF and gefitinib


title: CLL_Untreated_rep15


title: CLL_Immobilized_rep5


title: PC9_EGF_IRS_9hr

description: Gene expression after 9hr in PC9 treated with EGF and gefitinib

source_name: PC9, 9hr, EGF and gefitinib


title: PC9_EGF_IRS_5hr

description: Gene expression after 5hr in PC9 treated with EGF and gefitinib

source_name: PC9, 5hr, EGF and gefitinib


title: PC9_EGF_IRS_10hr

description: Gene expression after 10hr in PC9 treated with EGF and gefitinib

source_name: PC9, 10hr, EGF and gefitinib


title: CLL_Immobilized_rep2


title: CLL_Untreated_rep13


title: H44_1


title: CLL_Untreated_rep12


title: CLL_Untreated_rep11


title: S100PBP over-expressing FA6 PDAC cell line, rep3

city: London

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

country: United Kingdom

institute: Barts & The London School of Medicine (QMUL)

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Analysis using R/Bioconductor. Data were normalized using GC-RMA.

source_name: FA6 PDAC cells, over-expressing S100PBP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: PDAC cells were grown in DMEM media containing 10% FCS and 1mg/ml G418.

extract_protocol: RNA was extracted using the Total RNA isolation kit (Ambion).

treatment_protocol: Cells were transfected with 1μg DNA (S100PBP and vector-only) using 3μl Fugene 6 transfection reagent (Roche) in order to establish stable S100PBP over-expressing/control cell lines.

value: pancreatic ductal adenocarcinoma cells (PDACs)

value: S100PBP over-expression


title: PC9_EGF_IRS_6hr

description: Gene expression after 6hr in PC9 treated with EGF and gefitinib

source_name: PC9, 6hr, EGF and gefitinib

value: gefitinib-sensitive cell line


title: H42_2

source_name: Hypopharyngeal squamous cell carcinoma No. 42

value: Tumor tissue

value: Male

value: moderate

source_name: H42 pooled sample


title: PC9_EGF_IRS_4hr

description: Gene expression after 4hr in PC9 treated with EGF and gefitinib

source_name: PC9, 4hr, EGF and gefitinib


title: PC9_EGF_IRS_3hr

description: Gene expression after 3hr in PC9 treated with EGF and gefitinib

source_name: PC9, 3hr, EGF and gefitinib


title: CLL_Untreated_rep10


title: H42_1

value: IVA

value: blends equal amounts of each samples


title: S100PBP over-expressing FA6 PDAC cell line, rep2


title: H37_2

source_name: Hypopharyngeal squamous cell carcinoma No. 37

source_name: H37 pooled sample


title: H32_2

source_name: Hypopharyngeal squamous cell carcinoma No. 32

value: IVC

source_name: H32 pooled sample


title: H37_1

value: Non tumor tissue


title: PC9_EGF_IRS_2hr

description: Gene expression after 2hr in PC9 treated with EGF and gefitinib

source_name: PC9, 2hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: EGF and gefitinib


title: H32_1


title: CLL_Untreated_rep8

source_name: CLL

value: Peripheral blood

value: male

value: B-CLL


title: CLL_Untreated_rep6

value: untreated


title: CLL_Untreated_rep7


title: H31_2

source_name: Hypopharyngeal squamous cell carcinoma No. 31

value: Female

source_name: H31 pooled sample


title: Vector only transfected FA6 PDAC cell line, rep3

source_name: FA6 PDAC cells, vector only

value: pancreatic ductal adenocarcinoma cells (PDACs)

value: vector control


title: PC9_EGF_IRS_0.5hr

description: Gene expression after 0.5hr in PC9 treated with EGF and gefitinib

source_name: PC9, 0.5hr, EGF and gefitinib

value: gefitinib-sensitive cell line


title: CLL_Untreated_rep5


title: PC9_EGF_IRS_0hr

description: Gene expression after 0hr in PC9 treated with EGF and gefitinib

source_name: PC9, 0hr, EGF and gefitinib


title: PC9_EGF_24hr

description: Gene expression after 24hr in PC9 treated with EGF

source_name: PC9, 24hr, EGF

value: EGF


title: H31_1


title: Vector only transfected FA6 PDAC cell line, rep1


title: PC9_EGF_23hr

description: Gene expression after 23hr in PC9 treated with EGF

source_name: PC9, 23hr, EGF


title: S100PBP over-expressing FA6 PDAC cell line, rep1

source_name: FA6 PDAC cells, over-expressing S100PBP

value: S100PBP over-expression


title: H23_2

source_name: Hypopharyngeal squamous cell carcinoma No. 23

value: Tumor tissue

value: Male

value: well

source_name: H23 pooled sample


title: CLL_Untreated_rep9


title: MiaPaCa2 PDAC cells transfected with non-targeting control siRNA, rep2

source_name: MiaPaCa2 PDAC cells, non-targeting control siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: PDAC cells were grown in DMEM media containing 10% FCS.

treatment_protocol: Cells were transfected with 10nM targeting or non-targeting siRNA using 8μl INTERFERIN transfection reagent (Polyplus transfection).

value: non-targeting siRNA


title: H23_1

value: Non tumor tissue

value: IVA

value: blends equal amounts of each samples


title: PC9_EGF_IRS_1hr

description: Gene expression after 1hr in PC9 treated with EGF and gefitinib

source_name: PC9, 1hr, EGF and gefitinib

value: non-small cell lung cancer cell line

value: EGF and gefitinib


title: H19_2

source_name: Hypopharyngeal squamous cell carcinoma No. 19

value: poor

source_name: H19 pooled sample


title: Vector only transfected FA6 PDAC cell line, rep2


title: MiaPaCa2 PDAC cells transfected with S100PBP-targeting siRNA, rep1

source_name: MiaPaCa2 PDAC cells, S100PBP-targeting siRNA

value: S100PBP siRNA


title: CLL_Untreated_rep3

value: Peripheral blood

value: male

value: B-CLL

value: untreated


title: CLL_Untreated_rep4


title: PC9_EGF_21hr

description: Gene expression after 21hr in PC9 treated with EGF

source_name: PC9, 21hr, EGF

value: gefitinib-sensitive cell line

value: EGF


title: CLL_Untreated_rep2

source_name: CLL


title: PC9_EGF_20hr

description: Gene expression after 20hr in PC9 treated with EGF

source_name: PC9, 20hr, EGF


title: MiaPaCa2 PDAC cells transfected with non-targeting control siRNA, rep1

value: pancreatic ductal adenocarcinoma cells (PDACs)


title: CLL_Untreated_rep1


title: H19_1

value: Male


title: MiaPaCa2 PDAC cells transfected with S100PBP-targeting siRNA, rep3


title: MiaPaCa2 PDAC cells transfected with S100PBP-targeting siRNA, rep2


title: H12_2

source_name: Hypopharyngeal squamous cell carcinoma No. 12

value: Tumor tissue

source_name: H12 pooled sample


title: PC9_EGF_22hr

description: Gene expression after 22hr in PC9 treated with EGF

source_name: PC9, 22hr, EGF


title: H12_1


title: H09_2

source_name: Hypopharyngeal squamous cell carcinoma No. 09

value: Female

value: well

source_name: H09 pooled sample


title: H03_2

source_name: Hypopharyngeal squamous cell carcinoma No. 03

value: IVA

value: moderate

source_name: H03 pooled sample


title: H09_1

value: Non tumor tissue

value: blends equal amounts of each samples


title: D0 6

city: Stanford

first: Silke

last: Roedder

state: CA

address: 300 Pasteur Dr

department: Pediatric

institute: Stanford University

description:
KT1441_1_26_11
D0 6

hyb_protocol: 1. Mix the following for each target, scaling up volumes if necessary  for hybridization to multiple probe arrays.quilibrate probe array to room temperature immediately before  use.  3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat  block.  4. Meanwhile, wet the array with an appropriate volume of Pre-  Hybridization Mix (see Table 3.2) by filling it through one of the  septa.  5. Incubate the probe array filled with Pre-Hybridization Mix at  45°C for 10 minutes with rotation.  6. Transfer the hybridization cocktail that has been heated at 99°C,  in step 3, to a 45°C heat block for 5 minutes.  7. Spin the hybridization cocktail at maximum speed in a  microcentrifuge for 5 minutes to collect any insoluble material  from the hybridization mixture.  8. Remove the array from the hybridization oven. Vent the array with  a clean pipette tip and extract the Pre-Hybridization Mix from the  array with a micropipettor. Refill the array with the appropriate  volume of the clarified hybridization cocktail, avoiding any  insoluble matter at the bottom of the tube (see Table 3.2).  9. Place probe array into the hybridization oven, set to 45°C.  10. To avoid stress to the motor, load probe arrays in a balanced  configuration around the axis. Rotate at 60 rpm.  11. Hybridize for 16 hours.  During the latter part of the 16-hour hybridization, proceed to  Chapter 4 to prepare reagents for the washing and staining steps  required immediately after completion of hybridization.

scan_protocol: 1. Select Run → Scanner from the menu bar. Alternatively, click  the Start Scan icon in the tool bar.  The Scanner dialog box appears with a drop-down list of  experiments that have not been run.  2. Select the experiment name that corresponds to the probe array to  be scanned.  A previously run experiment can also be selected by using the  Include Scanned Experiments option box. After selecting this  option, previously scanned experiments appear in the drop-down list.  3. By default, for the GeneArray® Scanner only, after selecting the  experiment the number [2] is displayed in the Number of Scans  box to perform the recommended 2X image scan. For the  GeneChip® Scanner 3000, only one scan is required.  4. Once the experiment has been selected, click the Start button.  A dialog box prompts you to load an array into the scanner.  5. If you are using the GeneArray® Scanner, click the Options button  to check for the correct pixel value and wavelength of the laser  beam.  • Pixel value = 3 μm  • Wavelength = 570 nm  If you are using the GeneChip Scanner 3000, pixel resolution and  wavelength are preset and cannot be changed.  6. Open the sample door on the scanner and insert the probe array  into the holder. Do not force the probe array into the holder. Close  the sample door of the scanner. If you are using the GeneChip  Scanner 3000, do not attempt to close the door by hand. The door  closes automatically through the User Interface when start scan is  selected or the scanner goes into stand-by mode.  7. Click OK in the Start Scanner dialog box.  The scanner begins scanning the probe array and acquiring data.  When Scan in Progress is selected from the View menu, the probe  array image appears on the screen as the scan progresses.

data_processing: Dchip MBEI processing, quantile-quantile normalization

source_name: kidney allograft biopsy, baseline, living donor

label_protocol: NuGen FL-Ovation cDNA Biotin Module V2

extract_protocol: kidney allograft biopsy RNA extracted using Trizol.

tag: disease status

value: baseline, living donor


title: Healthy control_4

city: Suita

first: Shinsuke

last: Nakata

address: 2-2-B5, Yamadaoka

department: Metabolic Medicine

institute: Osaka University, Graduate School of Medicine

description: Gene expression in human blood

hyb_protocol: cRNA was hybridized to an Agilent Whole Human Genome Oligo Microarray 44k (Design ID: 014850).

scan_protocol: All procedures from labeling to scanning were performed according to the manufacturer’s instructions.

data_processing: Intensity values for each scanned feature were quantified using Agilent Feature Extraction Software, which performs background subtractions. Normalization was performed using Agilent GeneSpring GX version 11.0.2. (per chip normalization: 75 percentile shift; per gene normalization: median of all samples).

source_name: whole blood, healthy control

label_protocol: Cy3-labeled cRNA was synthesized from 250 ng of total RNA using the Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Blood samples were collected in PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland), incubated and stored according to the manufacturer’s protocol.  Total RNA was extracted using the PAXgene Blood RNA Kit (PreAnalytiX) according to the manufacturer’s protocol.

value: whole blood

value: female

tag: diabetes type


title: PC9_EGF_18hr

description: Gene expression after 18hr in PC9 treated with EGF

source_name: PC9, 18hr, EGF

tag: tissue

value: non-small cell lung cancer cell line


title: PC9_EGF_15hr

description: Gene expression after 15hr in PC9 treated with EGF

source_name: PC9, 15hr, EGF

tag: drug response


title: D0 8

description:
KT575
D0 8


title: Healthy control_3

description: Gene expression in human blood

value: male


title: Healthy control_6

description: Gene expression in human blood


title: Healthy control_5

description: Gene expression in human blood


title: PC9_EGF_16hr

description: Gene expression after 16hr in PC9 treated with EGF

source_name: PC9, 16hr, EGF

tag: cell line


title: D0 7

description:
KT412_02-01-07
D0 7


title: H03_1


title: D0 9

description:
KT609_2_16_09
D0 9


title: D0 5

description:
KT1422_1_26_11
D0 5


title: PC9_EGF_14hr

description: Gene expression after 14hr in PC9 treated with EGF

source_name: PC9, 14hr, EGF

tag: time


title: PC9_EGF_13hr

description: Gene expression after 13hr in PC9 treated with EGF

source_name: PC9, 13hr, EGF

tag: treatment


title: PC9_EGF_19hr

description: Gene expression after 19hr in PC9 treated with EGF

source_name: PC9, 19hr, EGF


title: D0 40

description:
KT819_06-25-07
D0 40


title: SAS_2 (CB-RNA76-13)

data_processing: Quantification; Feature Extraction 10.7.3.1 (Agilent). Normalization; First, calculate the average ratio (Hy3/Hy5) of replicated spots on each array. Next, calculate the ratio of average ratio (wogonin/DMSO).

source_name: SAS 72h after treatment of 10 ug/ml wogonin

tag: agent

value: Wogonin

source_name: SAS pooled sample


title: PC9_EGF_17hr

description: Gene expression after 17hr in PC9 treated with EGF

source_name: PC9, 17hr, EGF

value: gefitinib-sensitive cell line


title: D0 39

description:
KT818_05-25-07
D0 39


title: D0 37

description:
KT814_05-25-07
D0 37


title: Healthy control_2

description: Gene expression in human blood

tag: gender


title: Healthy control_1

description: Gene expression in human blood


title: SAS_1 (CB-RNA76-13)

source_name: SAS 72h after treatment of 0.01 % DMSO

value: Control


title: Classical 1A_5 (2011)

description: Gene expression in human blood

source_name: whole blood, classical type 1A

value: classical type 1A


title: FaDu_2 (CB-RNA76-12)

source_name: FaDu 72h after treatment of 10 ug/ml wogonin

source_name: FaDu pooled sample


title: Classical 1A_4 (2011)

description: Gene expression in human blood


title: FaDu_1 (CB-RNA76-12)

source_name: FaDu 72h after treatment of 0.01 % DMSO


title: D0 38

description:
KT816_06-25-07
D0 38


title: D0 36

description:
KT812_05-25-07
D0 36


title: PC9_EGF_11hr

description: Gene expression after 11hr in PC9 treated with EGF

source_name: PC9, 11hr, EGF

value: EGF


title: Classical 1A_1 (2011)

description: Gene expression in human blood


title: Classical 1A_3 (2011)

description: Gene expression in human blood


title: PC9_EGF_8hr

description: Gene expression after 8hr in PC9 treated with EGF

source_name: PC9, 8hr, EGF


title: PC9_EGF_10hr

description: Gene expression after 10hr in PC9 treated with EGF

source_name: PC9, 10hr, EGF


title: Fulminant_5 (2011)

description: Gene expression in human blood

source_name: whole blood, fulminant

value: fulminant type 1


title: PC9_EGF_9hr

description: Gene expression after 9hr in PC9 treated with EGF

source_name: PC9, 9hr, EGF


title: D0 35

description:
KT801_06-25-07
D0 35

source_name: kidney allograft biopsy, baseline, living donor


title: D0 32

description:
KT781_02-01-07
D0 32


title: PC9_EGF_12hr

description: Gene expression after 12hr in PC9 treated with EGF

source_name: PC9, 12hr, EGF


title: Fulminant_4 (2011)

description: Gene expression in human blood


title: D0 34

description:
KT796_05-25-07
D0 34


title: D0 33

description:
KT783-1_2_16_09
D0 33


title: PC9_EGF_7hr

description: Gene expression after 7hr in PC9 treated with EGF

source_name: PC9, 7hr, EGF


title: Fulminant_3 (2011)

description: Gene expression in human blood


title: Fulminant_1 (2011)

description: Gene expression in human blood


title: D0 30

description:
KT776_05-25-07
D0 30


title: PC9_EGF_4hr

description: Gene expression after 4hr in PC9 treated with EGF

source_name: PC9, 4hr, EGF


title: PC9_EGF_6hr

description: Gene expression after 6hr in PC9 treated with EGF

source_name: PC9, 6hr, EGF


title: Pinellia-leaf-1

city: Hangzhou

first: Bo

last: Wang

state: zhejiang

address: Xiasha

institute: Zhejiang Sci-Tech University

description: total RNAs were size-fractionated using a YM-100 microcon centrifugal filter (Millipore). After the small RNAs (<300 nt) collected were 3′-extended with a poly(A) tail using poly(A) polymerase

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

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

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

organism: Pinellia pedatisecta

source_name: Pinellia  leaf

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: To extract total RNA using mirVana™ miRNA Kit

tag: source

value: cultured in the greenhouse

value: leaf


title: PC9_EGF_3hr

description: Gene expression after 3hr in PC9 treated with EGF

source_name: PC9, 3hr, EGF


title: Fulminant_2 (2011)

description: Gene expression in human blood


title: D0 31

description:
KT778_2_16_09
D0 31


title: Classical 1A_2 (2011)

description: Gene expression in human blood


title: D0 3

description:
KT1018 B_2_24_09
D0 3


title: Classical 1A_4

description: Gene expression in human blood


title: D0 27

description:
KT764_2_16_09
D0 27


title: PC9_EGF_1hr

description: Gene expression after 1hr in PC9 treated with EGF

source_name: PC9, 1hr, EGF


title: PC9_EGF_5hr

description: Gene expression after 5hr in PC9 treated with EGF

source_name: PC9, 5hr, EGF


title: PC9_EGF_0.5hr

description: Gene expression after 0.5hr in PC9 treated with EGF

source_name: PC9, 0.5hr, EGF


title: PC9_EGF_2hr

description: Gene expression after 2hr in PC9 treated with EGF

source_name: PC9, 2hr, EGF


title: Classical 1A_3

description: Gene expression in human blood

source_name: whole blood, classical type 1A


title: Classical 1A_5

description: Gene expression in human blood


title: D0 22

description:
KT736_01-26-07
D0 22


title: D0 26

description:
KT755_02-06-07
D0 26


title: Fulminant_4

description: Gene expression in human blood


title: D0 23

description:
KT738_06-25-07
D0 23


title: PC9_EGF_0hr

description: Gene expression after 0hr in PC9 treated with EGF

source_name: PC9, 0hr, EGF


title: D0 24

description:
KT752_06-25-07
D0 24


title: Classical 1A_2

description: Gene expression in human blood


title: D0 20

description:
KT717_2_16_09
D0 20


title: D0 21

description:
KT730_01-26-07
D0 21


title: Classical 1A_1

description: Gene expression in human blood


title: D0 18

description:
KT707-1_2_16_09
D0 18


title: Fulminant_2

description: Gene expression in human blood


title: Fulminant_3

description: Gene expression in human blood


title: PE_Fgf2_t120h_tech-rep4_Cy5

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: F2-series_Array-CSK3_112:Cy3-PEt72h|Cy5-PEt120h

hyb_protocol: Slides were pre-hybridized (5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 1% (w/v) bovine serum albumin, fraction V (Sigma)) for 45 minutes at 42°C to block the remaining reactive epoxide groups and reduce background signal. Cy3 and Cy5 labelled RNA samples were combined as described in the experimental design and mixed with 2x hybridization mixture to a final concentration of 5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 0.2 \mug/\muL herring sperm DNA (Invitrogen). Target-RNA mix was denatured for 5 minutes at 70°C and incubated at 42°C for 30 minutes. Hybridization was done in a GeneTAC hybridization station (Genomic Solutions) for 16 hours at 42°C with agitation. The arrays were washed at room temperature in 5 successive buffers, i.e., 1x SSC + 0.2% SDS, 0.1x SSC + 0.2% SDS, 1x SSC, 0.1x SSC and 0.001x SSC, each step lasting 4 minutes. The slides were finally pressure-air dried and stored in the dark.

scan_protocol: Slides were scanned using an Agilent G2565BA microarray scanner on a 10 micro m resolution. The resulting images were split into the red and green channels prior to feature extraction with the GenePix Pro 6.1.0.2 (Axon Instruments Inc.) software.

data_processing: Median spot intensities were imported from the genepix results files using the Limma package. Flagged spots were assigned a weight of 0.1, control spots were removed and the remaining data were normalized with lowess (parameters: span = 0.25, iterations = 2) and aquantile transformations using the R/Limma package in Bioconductor

organism: Gallus gallus

source_name: PE, Fgf2, t120h

label_protocol: 1500 ng amplified RNA ( Ambion MessageAmp-II ) wasd labelled with either Cy3 or Cy5 as decribed by 't Hoen PA ( Nucleic Acids Res. 2003 Mar 1;31(5):e20 )

growth_protocol: Embryonic Proepicardia and Epicardium were isolated and grown as described by van den Hoff MJ et al ( Dev Biol. 2001 Dec 1;240(1):61-76 ) and Boudewijn P T et al ( Dev Biol. 2006 Jul 15;295(2):507-22 )

extract_protocol: Total RNA was isolated using Macherey-Nagel nucleospin columns and DnaseI treated. Quantified with the Nanodrop ND1000 and QC with an Agilent nanoChip.

treatment_protocol: PE explant cultures were treated with either U0126+Bmp2, Fgf2 or Fgf2+Vegf as described by Boudewijn P T et al ( Dev Biol. 2006 Jul 15;295(2):507-22 )


title: PE_Fgf2_t0h_tech-rep4_Cy5

description: F2-series_Array-CSK3_111:Cy3-PEt120h|Cy5-PEt0h

source_name: PE, Fgf2, t0h


title: Fulminant_5

description: Gene expression in human blood

source_name: whole blood, fulminant


title: PE_Fgf2_t120h_tech-rep3_Cy3


title: PC3-ERG Rep1

city: Ann Arbor

first: Christopher

last: Maher

state: MI

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

hyb_protocol: According to the manufacturer's protocol

scan_protocol: Scanned on Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software

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

source_name: PC3 cells overexpressing ERG Rep1

value: prostate cancer cell line PC3

tag: genotype/variation

value: ERG overexpression

source_name: PC3 cells overexpressing ERG (lacking ETS domain) Rep1

value: control


title: D0 17

description:
KT690-2_03-20-07
D0 17

source_name: kidney allograft biopsy, baseline, living donor


title: PE_Fgf2_t72h_tech-rep3_Cy5

description: F2-series_Array-CSK3_110:Cy3-PEt120h|Cy5-PEt72h

source_name: PE, Fgf2, t72h


title: PE_Fgf2_t72h_tech-rep4_Cy3


title: PC3-ERG Rep2

source_name: PC3 cells overexpressing ERG Rep2

label_protocol: According to the manufacturer's protocol

source_name: PC3 cells overexpressing ERG (lacking ETS domain) Rep2


title: D0 15

description:
KT650_02-06-07
D0 15


title: IS 4 hours replicate 6

city: MARSEILLE

first: ariane

last: duval-sabatier

address: Faculté Pharmacie 27 bd Jean Moulin

department: Physiopathologie de l'endothélium

country: France

institute: Inserm 608-Université Aix-Marseille

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 110 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 110 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides  (Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using these parameters : protocol GE1_107_Sep09, Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: IS 4 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Agilent Quick Amp Kit, One-Color 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: HUVEC are cultured in EGM2 medium until use

extract_protocol: RNA are extracted from HUVEC using the Kit

treatment_protocol: HUVECs are washed with PBS and incubated with EGM2 containing 1 mM KCl or 1mM Indoxyl sulfate during 4 hours

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: diagnosis

value: chronic kidney disease


title: ExVivoBlood_fasting_61

first: Norikazu

last: Maeda

state: Osaka

department: Graduate School of Medicine

institute: Osaka University

description: Gene expression at 7:30 am before breakfast in human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent whole human genome 4 × 44 K oligo-DNA microarray (Agilent Technologies, Santa Clara, CA). After hybridization, arrays were washed consecutively by using Gene Expression Wash Pack (#5188-5327, Agilent Technologies, Santa Clara, CA).

scan_protocol: After obtaining fluorescence images of the hybridized arrays by using an Agilent DNA Microarray Scanner (Agilent Technologies).

data_processing: The feature intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1.

source_name: Peripheral blood, fasting, VFA 250

label_protocol: 250 ng of total RNA was converted to cDNA, amplified, and labeled with Cy3 labeled CTP using the Quick Amp Labeling kit (#5190-0442, Agilent Technologies, Santa Clara, CA) according to manufacturer's protocol.

extract_protocol: For total RNA isolation, blood sample was collected into PaxGene Blood RNA tubes (PreAnalytiX/QIAGEN Inc., Valensia, CA) at 7:30 am.

value: whole blood

tag: vfa (cm2)


title: D0 13

description:
KT623_2_16_09
D0 13

value: baseline, living donor


title: ExVivoBlood_fasting_56

source_name: Peripheral blood, fasting, VFA 72

value: female


title: ExVivoBlood_fasting_55

source_name: Peripheral blood, fasting, VFA 211

value: male


title: D0 14

description:
KT636_01-24-07
D0 14


title: ExVivoBlood_fasting_49

source_name: Peripheral blood, fasting, VFA 88


title: PE_Fgf2_t120h_tech-rep2_Cy3


title: Fulminant_1

description: Gene expression in human blood


title: D0 16

description:
KT651_02-14-07
D0 16


title: IS 4 hours replicate 7


title: PE_Fgf2_t120h_tech-rep1_Cy5

description: F2-series_Array-CSK3_109:Cy3-PEt0h|Cy5-PEt120h


title: PE_Fgf2_t0h_tech-rep3_Cy3


title: ExVivoBlood_fasting_48

source_name: Peripheral blood, fasting, VFA 158


title: ExVivoBlood_fasting_46

source_name: Peripheral blood, fasting, VFA 204


title: IS 4 hours replicate 3


title: ExVivoBlood_fasting_54

source_name: Peripheral blood, fasting, VFA 82


title: D0 10

description:
KT613_01-26-07
D0 10


title: PE_Fgf2+Vegf_t120h_tech-rep4_Cy3

description: F2V-series_Array-CSK3_102:Cy3-PEt120h|Cy5-PEt0h

source_name: PE, Fgf2+Vegf, t120h


title: IS 4 hours replicate 4


title: IS 4 hours replicate 5


title: ExVivoBlood_fasting_43

source_name: Peripheral blood, fasting, VFA 409


title: IS 4 hours replicate 1


title: PE_Fgf2+Vegf_t0h_tech-rep4_Cy5

source_name: PE, Fgf2+Vegf, t0h


title: D0 11

description:
KT616_06-25-07
D0 11


title: IS 4 hours replicate 2


title: ExVivoBlood_fasting_39

source_name: Peripheral blood, fasting, VFA 274


title: PE_Fgf2_t24h_tech-rep4_Cy5

description: F2-series_Array-CSK3_091:Cy3-PEt72h|Cy5-PEt24h

source_name: PE, Fgf2, t24h


title: STA16*

description:
KT612_02-06-07
STA16*

source_name: kidney allograft biopsy; post transplant

value: no significant abnormalities


title: STA15

description:
KT540_02-06-07
STA15


title: ExVivoBlood_fasting_38

source_name: Peripheral blood, fasting, VFA 132


title: KCl 4 hours replicate 6

source_name: KCl 4 hours


title: PE_Fgf2+Vegf_t120h_tech-rep3_Cy5

description: F2V-series_Array-CSK3_101:Cy3-PEt72h|Cy5-PEt120h


title: D0 1

description:
KT922_01-26-07
D0 1

source_name: kidney allograft biopsy, baseline, living donor


title: PE_Fgf2_t72h_tech-rep2_Cy3

source_name: PE, Fgf2, t72h


title: ExVivoBlood_fasting_42

source_name: Peripheral blood, fasting, VFA 248


title: PE_Fgf2+Vegf_t72h_tech-rep3_Cy3

description: F2V-series_Array-CSK3_099:Cy3-PEt72h|Cy5-PEt24h

source_name: PE, Fgf2+Vegf, t72h


title: KCl 4 hours replicate 7


title: PE_Fgf2+Vegf_t24h_tech-rep4_Cy5

source_name: PE, Fgf2+Vegf, t24h


title: STA13

description:
KT977_06-28-07
STA13


title: STA12

description:
KT929_2_16_09
STA12


title: ExVivoBlood_fasting_35

source_name: Peripheral blood, fasting, VFA 354


title: ExVivoBlood_fasting_34

source_name: Peripheral blood, fasting, VFA 230


title: KCl 4 hours replicate 4


title: ExVivoBlood_fasting_27

source_name: Peripheral blood, fasting, VFA 126


title: STA11

description:
KT860_2_16_09
STA11


title: PE_Fgf2+Vegf_t0h_tech-rep3_Cy3

description: F2V-series_Array-CSK3_098:Cy3-PEt0h|Cy5-PEt120h


title: PE_Fgf2+Vegf_t120h_tech-rep2_Cy5


title: ExVivoBlood_fasting_29

source_name: Peripheral blood, fasting, VFA 386


title: STA10

description:
KT839_06-25-07
STA10


title: KCl 4 hours replicate 5


title: STA8

description:
KT903_2_16_09
STA8


title: KCl 4 hours replicate 2


title: KCl 4 hours replicate 3


title: KCl 4 hours replicate 1


title: PE_Fgf2+Vegf_t72h_tech-rep4_Cy3


title: PE_Fgf2+Vegf_t72h_tech-rep2_Cy5

description: F2V-series_Array-CSK3_096:Cy3-PEt24h|Cy5-PEt72h


title: PE_Fgf2+Vegf_t24h_tech-rep3_Cy3


title: STA6

description:
KT588_02-06-07
STA6


title: STA7

description:
KT889_06-28-07
STA7


title: PE_Fgf2+Vegf_t72h_tech-rep1_Cy5

description: F2V-series_Array-CSK3_095:Cy3-PEt120h|Cy5-PEt72h


title: ExVivoBlood_fasting_22

source_name: Peripheral blood, fasting, VFA 110


title: ExVivoBlood_fasting_21

source_name: Peripheral blood, fasting, VFA 106


title: PE_Fgf2+Vegf_t24h_tech-rep2_Cy3

description: F2V-series_Array-CSK3_094:Cy3-PEt24h|Cy5-PEt0h


title: PE_Fgf2+Vegf_t0h_tech-rep2_Cy5

source_name: PE, Fgf2+Vegf, t0h


title: ExVivoBlood_fasting_19

source_name: Peripheral blood, fasting, VFA 152


title: CRC110_FFPE

city: sendai

first: masahiro

last: inoue

state: miyagi

address: 4-1 seiryo-machi, aobaku

department: department of clinical oncology

institute: tohoku university

hyb_protocol: Labeled cDNA was hybridized to Whole Human Genome 4x44K Microarray (Agilent, Santa Clara, CA, USA).

scan_protocol: Scanning and image analysis were performed using DNA Microarray Scanner (Agilent, Santa Clara, CA, USA). Raw fluorescence intensities were quantified and normalized using Agilent Feature Extraction Software (Agilent, Santa Clara, CA, USA). Data analysis and visualization were performed with GeneSpring GX ver.11.5.1 (Agilent, Santa Clara, CA, USA).

data_processing: Data was normalized by the percentile shift (all samples were normalized to the signal value of 75th percentile of all of probes on the microarray) and the scaling (all genes were normalized to the median of all samples).

source_name: colorectal cancer (CRC), formalin-fixed paraffin-embedded (FFPE) samples

label_protocol: 300ng total RNA was amplified using TransPlex Complete Whole Transcriptome Amplification Kit (Sigma, St Louis, MO, USA). Amplified cDNA was purified using QIAquick PCR Purification Kit (Qiagen, Valencia, CA, USA). 1.5μg cDNA was labeled with Cy-3 dye using Genomic DNA ULS Labeling Kit (Agilent, Santa Clara, CA, USA). Labeled cDNA was assessed by the nanodrop (Thermo Fisher Scientific, Madison, WI, USA) and was confirmed that degree of labeling was 1.5-3.0%.

extract_protocol: 100 patients with advanced or recurrent CRC who underwent the surgical resection from 1998 to 2010 were enrolled in this study. FFPE samples were obtained from resected primary tumor. Two or four unstained thin slice slides (5-10μm thick) were made and tumor tissue was collected by the macrodissection under a Hematoxylin-Eosin stained tissue slide guide. Total RNA was extracted by Absolutely RNA FFPE Kit (Agilent, Santa Clara, CA, USA).

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: Sex

value: M

tag: t

value: ss

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: S

tag: histology

tag: cluster


title: STA5

description:
KT417_02-07-07
STA5

source_name: kidney allograft biopsy; post transplant

tag: disease status


title: ExVivoBlood_fasting_20

source_name: Peripheral blood, fasting, VFA 188

tag: tissue

tag: age


title: CRC109_FFPE

value: F

value: se

value: T


title: PE_Fgf2+Vegf_t120h_tech-rep1_Cy3

source_name: PE, Fgf2+Vegf, t120h


title: STA4

description:
KT905_06-25-07
STA4


title: CRC111_FFPE

value: III

value: A


title: ExVivoBlood_fasting_16

source_name: Peripheral blood, fasting, VFA 168

tag: gender


title: CRC108_FFPE

value: R


title: CRC105_FFPE

value: D


title: CRC106_FFPE


title: CRC107_FFPE

value: a


title: STA1

description:
KT641_06-25-07
STA1


title: ExVivoBlood_fasting_17

source_name: Peripheral blood, fasting, VFA 138

value: whole blood


title: ExVivoBlood_fasting_13

source_name: Peripheral blood, fasting, VFA 208

value: female


title: ExVivoBlood_fasting_18

source_name: Peripheral blood, fasting, VFA 318


title: STA19

description:
KT1239_2_18_09
STA19

value: no significant abnormalities


title: STA20

description:
KT387_02-07-07
STA20


title: PE_Fgf2+Vegf_t24h_tech-rep1_Cy5

description: F2V-series_Array-CSK3_092:Cy3-PEt0h|Cy5-PEt24h

source_name: PE, Fgf2+Vegf, t24h


title: PE_Fgf2_t0h_tech-rep2_Cy5

description: F2-series_Array-CSK3_086:Cy3-PEt24h|Cy5-PEt0h

source_name: PE, Fgf2, t0h


title: ExVivoBlood_fasting_12


title: CRC104_FFPE

value: colorectal cancer


title: ExVivoBlood_fasting_8

source_name: Peripheral blood, fasting, VFA 160

value: male


title: PE_Fgf2_t72h_tech-rep1_Cy5

description: F2-series_Array-CSK3_088:Cy3-PEt24h|Cy5-PEt72h

source_name: PE, Fgf2, t72h


title: ExVivoBlood_fasting_6

source_name: Peripheral blood, fasting, VFA 274


title: PE_Fgf2_t24h_tech-rep3_Cy3

source_name: PE, Fgf2, t24h


title: STA18

description:
KT614_02-06-07
STA18


title: BL5

description:
KT951_02-22-07
BL5

value: borderline acute renal allograft rejection


title: BL6+CNIT

description:
KT559_02-12-07
BL6+CNIT


title: CRC101_FFPE

value: FFPE


title: CRC102_FFPE

value: M

value: ss

value: IV


title: PE_Fgf2+Vegf_t0h_tech-rep1_Cy3


title: PE_Fgf2_t24h_tech-rep1_Cy5

description: F2-series_Array-CSK3_083:Cy3-PEt0h|Cy5-PEt24h


title: PE_Fgf2_t0h_tech-rep1_Cy3


title: BL1

description:
KT673_02-14-07
BL1


title: PE_Fgf2_t24h_tech-rep2_Cy3


title: CRC103_FFPE


title: STA2

description:
KT901_06-28-07
STA2


title: PE_U0126+Bmp2_t24h_tech-rep4_Cy5

description: UB-series_Array-CSK3_082:Cy3-PEt72h|Cy5-PEt24h


title: CRC099_FFPE

value: se


title: ExVivoBlood_fasting_1

source_name: Peripheral blood, fasting, VFA 196


title: CRC100_FFPE


title: WT keratinocytes without irradiation

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description:
Gene expression data from WT keratinocytes without irradiation
Kc-wt-0h-1385C

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. Arrays were washed and stained by streptavidin-phycoerythrin conjugate in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with 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 100.

organism: Mus musculus

source_name: Kc unirradiated

label_protocol: GeneChip 3' IVT Express Labeling Kit was used to prepare biotinylated cRNA according to the standard Affymetrix protocol from 0.2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse primary keratinocytes were isolated from newborn animals and cultured at 37C until irradiated.

extract_protocol: Total RNA was extracted by using Trizol (Invitrogen) and then purified by using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: UVB (75 mJ/cm2) was irradiated to keratinocyte culture. Keratinocytes were incubated at 37C for 4 h after irradiation.

tag: strain

tag: cell type

value: keratinocyte

tag: genotype/variation

value: WT

tag: stress

value: control


title: BL4

description:
KT578_02-14-07
BL4


title: PE_U0126+Bmp2_t72h_tech-rep4_Cy3


title: ExVivoBlood_fasting_37

source_name: Peripheral blood, fasting, VFA 189

tag: vfa (cm2)


title: ARIB5*

description:
KT649_02-22-07
ARIB5*

value: acute renal allograft rejection, ARIB


description:
Gene expression data from WT keratinocytes 4 h after UVB irradiation
Kc-wt-4h-1385D

source_name: Kc UVB-irradiated

value: UVB-irradiated


description:
Gene expression data from p38a-KO keratinocytes 4 h after UVB irradiation
Kc-K14C-4h-1385B


title: CRC098_FFPE

source_name: colorectal cancer (CRC), formalin-fixed paraffin-embedded (FFPE) samples

tag: sample type

tag: sample

tag: Sex

value: III

value: R


title: PE_U0126+Bmp2_t120h_tech-rep4_Cy5

description: UB-series_Array-CSK3_081:Cy3-PEt0h|Cy5-PEt120h


title: ARIB4**

description:
KT1070_02-22-07
ARIB4**

source_name: kidney allograft biopsy; post transplant


title: ARIB3

description:
KT543_01-30-07
ARIB3


description:
Gene expression data from p38a-KO keratinocytes without irradiation
Kc-K14C-0h-1385A


title: CRC093_FFPE

tag: t

value: X

tag: n

tag: m

value: D

value: muc


title: CRC094_FFPE

value: colorectal cancer

tag: Stage

tag: location

tag: histology


title: PE_U0126+Bmp2_t0h_tech-rep4_Cy3


title: MDC 0h rep 3

city: Philadelphia

first: Amaya

middle: I

last: Wolf

state: PA

address: 3601 Spruce street

institute: Wistar Institute

description: Gene expression data from murine mDC

hyb_protocol: Following fragmentation, RNA was hybridized for 16 hours at 45ºC to MOE430v2 gene chip array (Affymetrix).  The microarrays were  washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.  Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: GeneChips were scanned with a Gene Chip 3000 scanner to collect fluorescence signal after excitation at 570 nm.

data_processing: The data were analyzed with Partek Genimics Suite (v6.6). Data were GCRMA-normalized.

source_name: mDC

label_protocol: Biotinylated cRNA were prepared after reverse transcription of 100ng total RNA, a second round of amplification and labeling with the ENZO IVT reaction.

growth_protocol: Spleens from DPE-GFPxRAG transgenic mice s.c. injected with Flt3L-exressing B16F10 cells 12-14 days earlier to expand DC subsets in vivo were sorted based on GFP-CD11bhiCD11chi expression (mDC) and GFP+CD11b-CD11cint (pDC) according to Iparraguirre et al, JLB 2008

extract_protocol: Total RNA was extracted using the RNeasy Mini kit from Qiagen according to manufacturer's instructions.

treatment_protocol: Following sort, pDCs were cultured in medium for 1h prior to RNA extraction; mDCs were processed directly after the sort for RNA extraction.

tag: tissue

value: spleen

value: mDC


title: CRC090_FFPE

value: FFPE

tag: age

value: F

value: si

value: S

tag: cluster


title: CRC097_FFPE

value: M

value: IV


title: MDC 0h rep 2

description: Gene expression data from murine mDC

tag: strain


title: MDC 0h rep 1

description: Gene expression data from murine mDC

value: speen

tag: cell type


title: ARIB2*

description:
KT725_02-14-07
ARIB2*

tag: disease status

value: acute renal allograft rejection, ARIB


title: ARIB1

description:
KT942_02-14-07
ARIB1


title: PDC med1h rep2

description: Gene expression data from murine pDC

source_name: pDC cultured in medium 1h

value: pDC


title: PE_U0126+Bmp2_t0h_tech-rep3_Cy5

description: UB-series_Array-CSK3_080:Cy3-PEt120h|Cy5-PEt0h


title: ARIB6*

description:
KT1045_02-12-07
ARIB6*


title: CRC089_FFPE

value: a


title: ARIA12*

description:
KT1086_02-12-07
ARIA12*

value: acute renal allograft rejection, ARIA


title: PDC med1h rep1

description: Gene expression data from murine pDC


title: PE_U0126+Bmp2_t120h_tech-rep3_Cy3


title: CRC084_FFPE

value: X

value: III

value: R

value: tub


title: PE_U0126+Bmp2_t24h_tech-rep3_Cy3

description: UB-series_Array-CSK3_079:Cy3-PEt24h|Cy5-PEt72h


title: ARIA3

description:
KT863_03-21-07
ARIA3


title: PE_U0126+Bmp2_t72h_tech-rep2_Cy5

description: UB-series_Array-CSK3_078:Cy3-PEt120h|Cy5-PEt72h


title: ARIA11

description:
KT775_02-22-07
ARIA11


title: CRC085_FFPE

value: colorectal cancer

value: se


title: CRC087_FFPE

value: FFPE

value: mp

value: I


title: PE_U0126+Bmp2_t72h_tech-rep3_Cy5


title: FOG-2R3K5A heart, E16.5, biological rep2

city: Cambridge

first: Eric

last: Svensson

address: 220 Massachusetts Avenue

institute: Novartis

description:
5-Mut2
Gene expression data from FOG-2R3K5A hearts at E16.5

hyb_protocol: 10ug of the biotin labeled, fragmented cRNA was hybridized to the MG 430 2.0 array for 16 hours at 45 degrees C and at 60 rpm in the Affymetrix Hybridization Oven 640

scan_protocol: The arrays were washed and stained on a GeneChipFluidics Station 450 (Affymetrix, Inc) and were scanned using a Gene Chip Scanner 3000 7G to extract the .CEL files.

data_processing: The CEL files were analyzied with dChIP version 1.0.0.1 using default settings for normalization and expression.

source_name: FOG-2R3K5A mouse hearts at E16.5

label_protocol: 3 ug of total RNA was processed into dsDNA and cRNA was synthesized. The target was labeled with biotin and prepared according the GeneChip Expression analysis technical manual (Affymetrix, Inc).

growth_protocol: Embryonic mice from double heterozygous crosses were gestated in the mouse facility and the University of Chicago until embryonic day E16.5

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

treatment_protocol: whole hearts were dissected and frozen in liquid nitrogen, then stored at -80C until genotyping was confirmed.

tag: strain background

tag: genotype/variation

value: whole heart

value: embryonic day 16.5


title: CRC083_FFPE

tag: sample type

value: M


title: CRC082_FFPE

tag: sample

value: IV

value: S


title: PE_U0126+Bmp2_t24h_tech-rep2_Cy3

description: UB-series_Array-CSK3_077:Cy3-PEt24h|Cy5-PEt0h


title: FOG-2R3K5A heart, E16.5, biological rep3

description:
6-Mut3
Gene expression data from FOG-2R3K5A hearts at E16.5


title: ARIA4

description:
KT496_01-30-07
ARIA4


title: PE_U0126+Bmp2_t120h_tech-rep1_Cy5

description: UB-series_Array-CSK3_076:Cy3-PEt72h|Cy5-PEt120h


title: ARIA9

description:
KT1100_02-14-07
ARIA9


title: FOG-2R3K5A heart, E16.5, biological rep1

description:
4-Mut1
Gene expression data from FOG-2R3K5A hearts at E16.5


title: PE_U0126+Bmp2_t0h_tech-rep2_Cy5


title: WT heart, E16.5, biological rep2

description:
2-Wt2
Gene expression data from wild-type hearts at E16.5

source_name: wild-type mouse hearts at E16.5

value: Wild-Type


title: ARIA6

description:
KT1043_02-12-07
ARIA6


title: ARIA+GN*

description:
KT979_01-30-07
ARIA+GN*


title: WT heart, E16.5, biological rep3

description:
3-Wt3
Gene expression data from wild-type hearts at E16.5


title: PE_U0126+Bmp2_t120h_tech-rep2_Cy3


title: CRC081_FFPE

tag: Sex

value: ss

value: A


title: CRC080_FFPE

tag: t


title: WT heart, E16.5, biological rep1

description:
1-Wt1
Gene expression data from wild-type hearts at E16.5


title: Z/Edn2 P8 retina, biological rep 4

city: Baltimore

first: Amir

last: Rattner

state: MD

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Affyimetrix GeneChip Scanner 3000 7G according to the manufacturer's instructions

data_processing: RMA normalization using R Bioconductor

source_name: Z/Edn2; Six3-Cre P8 retina

label_protocol: Affymerix 3' IVT Express kit according to the provider's instructions

growth_protocol: Mouse retinas were dissected from P8 mouse pups

extract_protocol: Total RNA extractyed with Trizol and Rnaesy columns (QiaGen)

value: mixed background (mainly C57BL/6 and 129)

value: retina


title: NOLEU_3571

city: Salamanca

first: ROCIO

last: BENITO

address: Campus Unamuno s/n

country: Spain

institute: centro investigacion del cancer

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133 plus 2.0 microarray (Affymetrix).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: Expression value for each probe set was calculated using RMAExpress program that uses RMA (robust multi-array average) algorithm

source_name: healthy donor

label_protocol: Labeling was performed according to protocols from Affymetrix. Briefly, 5000 ng of total RNA was amplified and labeled. These samples were fragmented and combined with array hybridization controls (Affymetrix, Santa Clara, CA, USA) in hybridization buffer. 11 µg of cRNA target were then hybridized with the GeneChip HG_U133 Plus 2.0 array (Affymetrix)

extract_protocol:
Total RNA was extracted from purified cell populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).

tag: source

value: Bone Marrow

tag: tissue type

value: healthy donor


title: PE_U0126+Bmp2_t0h_tech-rep1_Cy3

description: UB-series_Array-CSK3_075:Cy3-PEt0h|Cy5-PEt24h


title: PE_U0126+Bmp2_t72h_tech-rep1_Cy3


title: PE_U0126+Bmp2_t24h_tech-rep1_Cy5


title: CRC078_FFPE

value: colorectal cancer

tag: n

tag: m

tag: Stage

value: T


title: CRC077_FFPE

tag: tissue

value: FFPE

value: a

value: III

tag: location

value: R

tag: histology


title: CRC079_FFPE

tag: age

value: F

value: se

tag: cluster


title: Z/Edn2 P8 retina, biological rep 3

tag: strain


title: Z/Edn2 P8 retina, biological rep 1


title: NOLEU_3564


title: Z/Edn2 P8 retina, biological rep 2


title: CRC075_FFPE

value: M


title: NOLEU_3565


title: NOLEU_3562


title: Control P8 retina, biological rep 4

source_name: Six3-Cre P8 retina

value: Control


title: CRC076_FFPE

value: si

value: IV

value: S


title: lemon, juice sacs, repl. 3

city: Davis

first: Abhaya

middle: M

last: Dandekar

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

hyb_protocol: Standard Affymetrix protocols were followed.

scan_protocol: Used Affymetrix 3000 GeneChip Scanner, and standard Affymetrix protocols were followed.

data_processing: Standard Affymetrix protocol was followed for image processing. For statistical analyses, R statistical software was used. The RMA method (Irizarry et al., 2003) for background subtraction and normalization was used to preprocess raw probe data and produce the gene expression matrix. One-way ANOVA was used to determine which genes were differentially expressed among different groups. P-values from ANOVA were BH adjusted for multiple hypotheses.

organism: Citrus x limon

source_name: Mature juice sacs tissue from lemon

label_protocol: RNA labeling was performed according to instructions in the GeneChip One Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: A modified hot borate method (Wan and Wilkins, 1994) was used to extract RNA from the pooled samples. Tissue was ground in liquid nitrogen and PVP-40 (200 mg) and put into a pre-chilled collection tube with 6-8 mg proteinase K and 10 ml 80ºC XT buffer (ratio 5 ml/g).  Each sample was mixed, incubated on ice for 1 hr, and centrifuged at 10,000-13,000 rpm for 20 min at 4ºC. The supernatant was filtered through sterile miracloth into a clean collection tube and 10 M LiCl was added (volume ratio 1:4). Samples were mixed and incubated on ice overnight. Samples were centrifuged at 13,000 rpm for 20 min at 4ºC, then washed three times with cold 2 M LiCl. The pellet was resuspended in 2 ml 10 mM Tris HCl, pH 7.5, by gentle vortexing and then centrifuged at 13,000 rpm for 10 min at 4ºC. The supernatant was decanted, 200 μl (1/10 vol) K-acetate (pH 5.5) was added, and the sample was incubated on ice for 15 minutes. Samples were centrifuged at 13,000 rpm for 10 min at 4ºC, the supernatant collected, and 5 ml 95% EtOH was added.  Tubes were mixed and incubated at -20ºC overnight, then centrifuged at 13,000 rpm for 30 min at 4ºC. The pellet was washed with 4 ml 70 % EtOH, centrifuged at 13,000 rpm for 5 min at 4ºC, dried at room temperature, and resuspended in suitable volume of DEPC-dH2O. Quantitative and qualitative determination of RNA was performed with gel electrophoresis.

value: juice sacs


title: NOLEU_3557


title: Control P8 retina, biological rep 3

value: mixed background (mainly C57BL/6 and 129)

value: retina


title: NOLEU_3537

value: Bone Marrow

value: healthy donor


title: lemon, juice sacs, repl. 2


title: lemon, juice sacs, repl. 1


title: Krentz-WT12-031811

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: E15.5 ovaries wt rep3

hyb_protocol: hybridized to Affymetrix 430 2.0 microarrays.

scan_protocol: Affymetrix protocol

data_processing: Cel files were normalized using the GC-RMA algorithm as implemented in the Genedata Expressionist Analyst Package.

source_name: E15.5 ovaries wt

label_protocol: Affymetrix protocol

growth_protocol: Ovaries were dissected from E15.5 embryos and placed in RNAlater (Qiagen)

extract_protocol: RNA was prepared using Allprep Micro Kit (Qiagen).

value: ovaries

value: WT


title: NOLEU_3293


title: lemon, flavedo, repl. 2

source_name: Mature flavedo tissue from lemon

value: flavedo


title: CRC072_FFPE

value: colorectal cancer

value: FFPE

value: ss

value: III


title: CRC074_FFPE

value: M

value: se

value: T


title: lemon, albedo, repl. 3

source_name: Mature albedo tissue from lemon

value: albedo


title: lemon, flavedo, repl. 3


title: CRC073_FFPE

value: IV

value: S


title: lemon, flavedo, repl. 1


title: NOLEU_3178


title: Krentz-WT10-031811

description: E15.5 ovaries wt rep1


title: Krentz-WT11-031811

description: E15.5 ovaries wt rep2


title: CRC070_FFPE


title: CRC068_FFPE

value: F

value: a

value: II

value: R


title: CRC071_FFPE

value: D


title: Control P8 retina, biological rep 1

value: mixed background (mainly C57BL/6 and 129)

value: Control

value: retina


title: CRC067_FFPE

value: colorectal cancer

value: FFPE


title: lemon, albedo, repl. 2


title: CRC066_FFPE


title: CML_3364_G2

data_processing: Expression value for each probe set was calculated using RMAExpress program that uses RMA (robust multi-array average) algorithm.

source_name: CML Patient: Treated

value: Bone Marrow

value: tumor, treated


title: Control P8 retina, biological rep 2


title: CML_3647_I2


title: lemon, albedo, repl. 1


title: Krentz-KO2-031811

description: E15.5 ovaries dmrt1 rep2

source_name: E15.5 ovaries dmrt1

value: ovaries

value: dmrt1 knockout


title: grapefruit, juice sacs, repl. 2

organism: Citrus x paradisi

source_name: Mature juice sacs tissue from grapefruit

value: juice sacs


title: CML_3152_E2


title: grapefruit, juice sacs, repl. 3


title: Krentz-KO3-031811

description: E15.5 ovaries dmrt1 rep3


title: CML_3356_H2


title: grapefruit, juice sacs, repl. 1


title: CML_3338_F2


title: CRC064_FFPE

value: M

value: se

value: IV

value: A


title: CRC063_FFPE

value: ss

value: T


title: grapefruit, flavedo, repl. 3

source_name: Mature flavedo tissue from grapefruit

value: flavedo


title: CRC062_FFPE

source_name: colorectal cancer (CRC), formalin-fixed paraffin-embedded (FFPE) samples

value: D


title: CML_2623_B2


title: CML_1989_C2


title: CML_3071_D2


title: Krentz-2238B_WT_11xS6-072109-8

description: E15.5 testes 129Sv wt rep3

source_name: E15.5 testes 129Sv wt

growth_protocol: testes were dissected from P28 embryos and placed in RNAlater (Qiagen)

value: WT

value: testes


title: Krentz-KO1-031811

description: E15.5 ovaries dmrt1 rep1


title: CRC061_FFPE

value: colorectal cancer


title: Krentz-B6-WT2-072109-4

description: E15.5 testes B6 wt rep3

source_name: E15.5 testes B6 wt


title: Krentz-2299A-_-10xB6-072109-2

description: E15.5 testes B6 dmrt1 rep3

source_name: E15.5 testes B6 dmrt1


title: grapefruit, flavedo, repl. 2


title: Krentz-2216C-_-10xB6-072109-3

description: E15.5 testes B6 dmrt1 rep2


title: grapefruit, flavedo, repl. 1


title: CML_3593_I1

source_name: CML Patient: Diagnosis

value: tumor, at diagnosis


title: CML_3305_H1

value: Bone Marrow


title: CML_3284_G1


title: Krentz-2216A_WT_10xB6-072109-6

description: E15.5 testes B6 wt rep2


title: CRC060_FFPE

value: FFPE

value: F

value: S


title: grapefruit, albedo, repl. 2

source_name: Mature albedo tissue from grapefruit

value: albedo


title: Krentz-2201A_WT_10xB6-072109-5

description: E15.5 testes B6 wt rep1


title: Krentz-2201D-_-10xB6-072109-1

description: E15.5 testes B6 dmrt1 rep1

value: dmrt1 knockout


title: grapefruit, albedo, repl. 1


title: CML_3285_F1


title: grapefruit, albedo, repl. 3


title: Krentz-2088A-_-7xS6-072109-10

description: E15.5 testes 129Sv dmrt1 rep3

source_name: E15.5 testes 129Sv dmrt1


title: Valencia, juice sacs, repl. 3

organism: Citrus sinensis

source_name: Mature juice sacs tissue from Valencia orange

tag: cultivar

value: Valencia

value: juice sacs


title: CRC059_FFPE

value: a

value: III

value: R

value: tub


title: CRC057_FFPE

value: M

value: ss

value: A


title: CRC056_FFPE

value: colorectal cancer

value: se

value: IV

value: C


title: CML_3106_E1

value: Bone Marrow

value: tumor, at diagnosis


title: Krentz-2086A-_-7xS6-072109-9

description: E15.5 testes 129Sv dmrt1 rep2

tag: genotype/variation

value: testes


title: CRC058_FFPE

tag: sample type

value: FFPE


title: Valencia, juice sacs, repl. 2

value: Valencia


title: Krentz-2085A-_-7xS6-072109-11

description: E15.5 testes 129Sv dmrt1 rep1

value: dmrt1 knockout


title: CML_1802_C1


title: CML_2574_B1


title: CRC054_FFPE

tag: sample


title: NOLEU_3525

source_name: healthy donor

value: healthy donor


title: CRC053_FFPE

tag: Sex

value: a


title: Valencia, juice sacs, repl. 1

value: juice sacs


title: Krentz-2015A_WT_7xS6-072109-7

description: E15.5 testes 129Sv wt rep2

value: WT


title: CRC052_FFPE

value: F

tag: t

value: III

value: S


title: CML_3007_D1

tag: source


title: Valencia, flavedo, repl. 3

source_name: Mature flavedo tissue from Valencia orange

value: flavedo


title: Valencia, flavedo, repl. 2


title: #483 replicate 3

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description: Gene expression data from #483 T-ALL in vivo

hyb_protocol: amplified, fragmented, biotin labeled cDNA was hybridized for 18 hr at 45C on Mouse Genome 430 2.0 Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

label_protocol: Affymetrix GeneChip 3’ IVT Express Kit

growth_protocol: #483 T-ALL cells were transplanted into 3 sublethally (7.5 Gy) irradiated C57BL6/J mice. 20 days after Tx EGFP+ T-ALL cells were isolated and subjected to Microarray Analysis.

extract_protocol: Qiagen Rneasy Micro Kit according to manufacturers instructions


title: Valencia, albedo, repl. 3

source_name: Mature albedo tissue from Valencia orange

value: albedo


title: Krentz-1946D_WT_11xS6-072109-12

description: E15.5 testes 129Sv wt rep1


title: CRC050_FFPE

value: colorectal cancer

value: ss

value: IV

value: R


title: Valencia, flavedo, repl. 1


title: CRC045_FFPE


title: #483 replicate 2


title: CML_2860_A2

value: Bone Marrow

tag: tissue type

value: tumor, treated


title: #483 replicate 1


title: CRC051_FFPE

value: FFPE

value: si

tag: n

value: A


title: navel, juice sacs, repl. 3

source_name: Mature juice sacs tissue from navel orange

value: Washington Navel


title: Valencia, albedo, repl. 2

value: Valencia


title: Valencia, albedo, repl. 1


title: navel, juice sacs, repl. 2

value: juice sacs