title: D2_Chondrogenic hMSC_TGF-b_PTHrP_L_1w

city: Goyang

first: Jong-Min

address: 814 Siksa-dong

department: College of Medicine

country: South Korea

institute: Dongguk University

description: miRNA

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Donor2-hMSC, after condrogenic induction, +TGF-b-3w, +PTHrP-last 1w

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: hMSCs are generally isolated from bone marrow aspirates harvested from the superior iliac crest of the pelvis in humans. The marrow sample is fractionated on a density gradient solution. Then the cells are plated at densities ranging from 1 × 104 cells/cm2 to 0.4 × 106 cells/cm2. Cells are generally cultured in a DMEM/F12 media in the presence of 10% FBS and 1% streptomycin/penicillin, in 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from the chondrogenic-cell pellets and the monolayer cultured hMSCs using TriZol reagent (Invitrogen) according to manufecturer' instruction.

treatment_protocol: hMSC cell pellets were cultured in chondrogenic medium (CM; DMEM/F12-high glucose, 1.25 mg/ml BSA, 1 mM sodium pyruvate, 1% ITS, 50 mM L-ascobate, 50 mM L-proline, 100 nM dexamethasone, 1% penicillin/streptomycin) containing 10 ng/ml TGF-β3 for 3 weeks. PTHrP stimuli were maintained during all 3 weeks, only during the last week of the 3-week cultivation, or not at all.

tag: tissue

value: Bone marrow

value: female


title: 37868702

status: Public on Dec 01 2016

type: genomic

city: Rockville

first: Rose

last: Yang

state: MD

address: 9609 Medical Center Dr

department: Division of Cancer Epidemiology and Genetics

country: USA

institute: National Cancer Institute

hyb_protocol: The reference sample was a pool of six male individuals (Promega, Madison, WI) provided by Nimblegen. 2.5 μg of test and reference DNA were labeled with Cy3 and Cy5 respectively and co-hybridized to the array slides. The intensity of the two fluorescent dyes that reflects chromosomal imbalances between test and reference samples was extracted using NimbleScan software, and SignalMap™ was employed to visualize the array-CGH data. The Cy3 and Cy5 signal intensities on each array were normalized to one another using the qspline normalization. The log2 ratio was then created for each probe and was used as input to the segment-calling algorithm (SegMNT) to identify copy number changes and breakpoints. The hybridization, normalization, window-averaging, and segmentation analyses were performed by Nimblegen.

molecule: genomic DNA

organism: Homo sapiens

source_name: Germline DNA from Blood

extract_protocol: Standard DNA extraction protocol

tag: affection status (melanoma)

value: Affected

tag: age

tag: gender

value: M

tag: cdkn2a mutation status

value: Positive

tag: sample type

value: Pooled from 6 healthy individuals


title: 37947602

data_processing: The Cy3 and Cy5 signal intensities on each array were normalized to one another using the qspline normalization. The log2 ratio was then created for each probe and was used as input to the segment-calling algorithm (SegMNT) to identify copy number changes and breakpoints.

label_protocol: 2.5 μg of test and reference DNA were labeled with Cy3 and Cy5 respectively and co-hybridized to the array slides. The intensity of the two fluorescent dyes that reflects chromosomal imbalances between test and reference samples was extracted using NimbleScan software, and SignalMap™ was employed to visualize the array-CGH data.

value: F


title: 37996502

scan_protocol: The intensity of the two fluorescent dyes that reflects chromosomal imbalances between test and reference samples was extracted using NimbleScan software, and SignalMap™ was employed to visualize the array-CGH data.


title: 37994002

value: Unaffected

value: Negative


title: D2_Chondrogenic hMSC_TGF-b_PTHrP_3w

type: RNA

last: Lee

description: miRNA

molecule: total RNA

source_name: Donor2-hMSC, after condrogenic induction, +TGF-b-3w, +PTHrP-3w


title: mRNA_OE-SSZ1Δire1Δscj1-rep1

city: Zhenjiang

first: Huang

last: Guoping

state: Jiangsu province

address: Xuefu Road 301#

department: Institute of Life Sciences

country: China

institute: Jiangsu University

hyb_protocol: 600ng of labeled cRNA was hybridized onto Agilent SurePrint G3 GE 8x60K Microarray for 17 hours at 65°C, 10 rpm in Agilent hybridization oven.

scan_protocol: After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37°C before scanning on Agilent High Resolution Microarray Scanner (C-model).

data_processing:
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The raw data were imported into GeneSpring GX 13.0 (Agilent Technologies) for the analysis. Source technology Agilent.SingleColor.31120 was used and saccharomyces cerevisiae was chosen as source organism.
After removed control probes, filtered on flags[detected], and filtered on expression (20.0-673749.438) with entities where at least 100 percent of samples in any 1 out of 3 conditions have values within cut-off, retained values were analyzed using one-way ANOVA with corrected p-value cut-off 0.05 and multiple testing corrections by the Benjamini and Hochberg method (Benjamini and Hochberg, 1995) to correct false discovery rate, and asymptotic P value computation was performed to determine differential expression of genes.

label: cyanine 3-CTP

organism: Saccharomyces cerevisiae

label_protocol: 100 ng of total RNA was labeled with Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) following manufacturer instruction (One-Color Microarray-Based Gene Expression, Analysis Low Input Quick Amp Labeling, version 6.5). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.

growth_protocol: Cultures of samples were grown to an OD600 of 0.2-0.3 at 30 °C in synthetic media with shaking at 200 rpm.

extract_protocol: Total RNA of samples was extracted by using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells of samples were harvested from cultures with a concentration of less than 0.3 OD/mL.

tag: growth phase

value: early log phase

tag: genotype

value: OE SSZ1Δire1Δscj1


title: D1_Chondrogenic hMSC_TGF-b_PTHrP_3w

description: miRNA

source_name: Donor1-hMSC, after condrogenic induction, +TGF-b-3w, +PTHrP-3w

value: male


title: 38824302


title: D1_Chondrogenic hMSC_TGF-b_only

description: miRNA

source_name: Donor1-hMSC, after condrogenic induction, +TGF-b-3w


title: 37926602


title: 37996402


title: mRNA_OE-SSZ1Δire1-rep2

value: OE SSZ1Δire1


title: 37991102


title: 37924402


title: 37927202


title: 37897002


title: D1_Chondrogenic hMSC_TGF-b_PTHrP_L_1w

description: miRNA

source_name: Donor1-hMSC, after condrogenic induction, +TGF-b-3w, +PTHrP-last 1w


title: D2_Undifferentiated hMSC

description: miRNA

source_name: Donor2-hMSC, before condrogenic induction


title: D2_Chondrogenic hMSC_TGF-b_only

description: miRNA

source_name: Donor2-hMSC, after condrogenic induction, +TGF-b-3w


title: 37991002


title: 37928902

value: Unknown


title: D1_Undifferentiated hMSC

description: miRNA

source_name: Donor1-hMSC, before condrogenic induction


title: 37937402


title: 37895502


title: 37894902


title: 37878002


title: 37974002


title: RERF-GC-1B

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

description: Short tandem repeat (STR) analysis verified identical and authentic on November 2014.

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 40 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 8.0 in DNA Analytics. To detect amplifications and deletions, we set the values of parameters for aberration filters as: minimum number of probes in region 4, minimum absolute average log2ratio for region 2, maximum number of aberrant regions 100000, and percentage penetrance per feature 0.

source_name: Established cell line from human gastric cancer tissue

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: standard proteinase K-digestion method

tag: cell line

tag: differentiation

value: unknown

tag: provider

value: JCRB

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: AZ521

source_name: human peripheral blood mononuclear cells of 8 healthy donors


title: HSC59

value: Signet ring cell

value: Kazuyoshi, Yanagihara


title: HSC60


title: HSC39


title: JR-St

value: JR-St

value: IBL


title: HSC43


title: TGBC11TKB

value: RIKEN


title: HSC58


title: 37947102

value: Affected

value: Positive

value: Pooled from 6 healthy individuals


title: 37972602

value: F

value: Negative


title: 37991302


title: SNU668

value: KCLB


title: NCC-StC-K140

value: male


title: 37815702


title: SNU601


title: v2 aCGH GSY505

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86571.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: Agilent Feature Extraction

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

label_protocol: not provided

extract_protocol: not provided

tag: test

source_name: 165 ng HaeIII-cut genomic DNA of GSY505

tag: strain

tag: type

value: Brewing contaminant


title: v2 aCGH GSY312

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86573.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA of GSY312

value: Lager beer - commercially produced strain


title: v2 aCGH GSY205

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86575.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY205

value: Cider


title: 37972502

value: Unaffected


title: KE97

value: Signet ring cell

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: v2 aCGH GSY2232

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85750.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2232

value: Wine - commercially produced strain


title: KatoIII

value: KatoIII

value: JCRB


title: 37895902

value: M


title: GSU

value: GSU

value: RIKEN


title: 37973802

value: Affected

value: F

value: Positive

value: Pooled from 6 healthy individuals


title: 37937102


title: GCIY

value: GCIY

value: poorly

value: male


title: Multiple myeloma patient 32

city: Leuven

first: Isabel

middle: Juliana Frans

last: Hofman

address: Herestraat 49

department: Oncology

country: Belgium

institute: KU Leuven

hyb_protocol: DNA was hybridized to the Affymetrix CytoScan HD array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics stations.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000.

data_processing: The intensity data in the original CEL files was analysed using Affymetrix Chromosome Analysis Suite (ChAS). The CYCHP files contain the output information of this analysis. The CYCHP files contain copy number, LOH, mosaicism and genotype call information.

label: Biotin

source_name: Bone marrow sample of patient at diagnosis

label_protocol: DNA was restriction digested, PCR amplified, fragmented and labeled according to the manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from bone marrow samples at diagnosis using the Maxwell system of Promega. DNA quality and quantity were assessed using a NanoDrop Spectrophotometer.

tag: disease state

value: multiple myeloma

value: bone marrow

tag: translocations

tag: hyperdiploidy

value: NO

tag: additional aberrations

value: None identified


title: SNU1

value: ATCC

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: 38108702

source_name: Germline DNA from Blood

tag: affection status (melanoma)

value: Unaffected

value: Negative


title: Multiple myeloma patient 31

tag: tissue

value: non IGH-t(8q24/MYC); t(11;14)/IGH-CCND1


title: SNU520

value: KCLB

tag: gender


title: Multiple myeloma patient 37

value: non IGH-t(8q24/MYC)

value: YES


title: Multiple myeloma patient 35


title: 38358502

value: Unknown

value: F

tag: cdkn2a mutation status

value: Positive


title: Multiple myeloma patient 33


title: Multiple myeloma patient 36


title: Multiple myeloma patient 30


title: Multiple myeloma patient 28


title: 37895002

value: Affected

tag: age

value: M

tag: sample type

value: Pooled from 6 healthy individuals


title: 37928602

tag: cdk4 mutation status


title: Multiple myeloma patient 27

value: multiple myeloma

value: bone marrow


title: GSS

tag: cell line

value: GSS

value: poorly

value: RIKEN

value: male


title: Multiple myeloma patient 26

value: NO


title: Multiple myeloma patient 24

value: None identified


title: SH-10-TC

tag: differentiation

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: 37973702


title: 37993802


title: Multiple myeloma patient 23


title: Multiple myeloma patient 22

value: unknown t(14q32/IGH)


title: Multiple myeloma patient 21

value: non IGH-t(8q24/MYC)


title: Multiple myeloma patient 38


title: 37928002

value: Unknown


title: 37996802


title: HGC27

tag: provider


title: Multiple myeloma patient 34

value: YES


title: SNU620

value: KCLB


title: OKAJIMA

value: OKAJIMA

value: IBL


title: SNU16

value: ATCC


title: 37973502

value: Positive

value: Pooled from 6 healthy individuals


title: HSC64

value: Kazuyoshi, Yanagihara


title: F22_3

city: Toulouse

first: Anne

last: Abot

address: 135 route de Narbone

department: LISBP

country: France

institute: INSA/INRA/CNRS

description: gene expression of fosmidic GH

hyb_protocol: For each sample, 1650 ng of labeled and amplified cRNA was used for hybridization. The hybridization master mix was prepared according to manufacturer’s protocol (Agilent Technologies, Massy, France) and 100 µl were dispensed onto a gasket slide, according to the Agilent Microarray Hybridization Chamber User Guide. Afterwards, the active side of the microarray slide was placed on top of the gasket to form a properly aligned “sandwich slide pair”. The microarray slides were inserted into the hybridization chamber (Agilent Technology) than placed at 65°C for 17 hours with rotation at 10 rpm. After hybridization, the microarray was washed over a 1-min period first using Gene Expression Wash Buffer 1 and then Gene Expression Wash Buffer 2 (Agilent Technologies, Massy, France) pre-warmed at 37°C.

scan_protocol: After washing, the arrays were immediately scanned using an MS200 scanner (NimbleGen Roche Diagnostics, Meylan, France) with NimbleGen MS200 software v1.2 at 2 micron resolution.

data_processing: The median signal of each spot in the hybridized arrays was determined and quantified using Feature Extraction software v11.5.1.1. The data from all the microarrays were normalized together using the “limma” package function “normalizeQuantiles” and the “quantile” method (Bolstad et al., 2003; Smyth et al., 2005). Normalization and statistical analyses of the data were performed using the Bioconductor packages (http://www.bioconductor.org) and R software v3.1.3. The normalized fluorescence intensities of three experimental replicates per sample were analyzed and the mean values, standard deviations and correlation coefficients (%CV) were calculated. To determine whether probes were specific and target genes present, limma one way ANOVA tests were carried out using the False Discovery Ratio method and an adjusted p value < 0.05. Limma t test using limma package, was conducted to know in which gene is differentially expressed.

organism: Bacteria

label_protocol: The One-Color Low Input Quick Amp WT Labeling Kit™ (Agilent Technologies, Massy, France) was used to amplify and label 100ng of RNA following the manufacturer's instructions. The efficiency of the labeling was checked using a NanoDrop spectrophotometer operating at 260 nm to quantify cRNA and at 550 or 660 nm to measure cyanine 3 (Cy3) and cyanine 5 (Cy5) dye incorporation respectively. Labeling efficiency was calculated as indicated by the manufacturer’s protocol (ratio cyanine quantity / amount of RNA) and was above 6.

growth_protocol: Different GH cloned in plasmid or fosmid (pDest vector) were expressed by recombinant E. coli strains as previously described , (Cecchini et al., 2013; Bastien et al., 2013; Arnal et al., 2015,  Vincentelli et al., 2011). (Tasse et al., 2010; Song et al., 2012;Ladevèze et al., 2013;). Briefly, cultures were stopped at OD600nm between 0.4 and 0.6, and cells were harvested by centrifugation for 10 minutes at 5000 rpm and 4°C. The supernatant was then discarded and the bacterial pellet immediately frozen at -80°C before RNA extraction.  Microbial consortia analyzes were performed on an anaerobic rumen-derived consortium RWS, which efficiently degrades lignocellulose, as reported by Lazuka et al. (Lazuka et al., 2015).

extract_protocol: Total RNA was extracted from bacterial pellets after lysis with 1mg/ml lysozyme (Sigma-Aldrich, Isle d'Abeau Chesnes, France) during 5 min at 25°C, using the RNeasy Mini Kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions. RNA concentration, purity and integrity was evaluated by measuring the absorbance ratio at 260/280 nm and 260/230 nm using a Nanodrop spectrophotometer (Labtech, Palaiseau, France). The Ratio Integrity Number (RIN) was evaluated using 2100 Bioanalyzer® (Agilent Technologies, Massy, France) and only samples with a RIN upper than 8 were hybridized on the microarray.  Total RNA of rumen derived consortium was extracted in two steps from nitrogen frozen samples using the PowerMicrobiome RNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA) (Lazuka et al., 2015). RNA purification was performed using AllPrep DNA/RNA minikit (Qiagen), following the manufacturer’s instructions.

treatment_protocol: no treatment was performed

tag: group

value: fosmidic GH


title: Multiple myeloma patient 17

value: multiple myeloma

value: bone marrow


title: SNU5

value: poorly

value: male


title: Multiple myeloma patient 18

value: NO

value: None identified


title: Multiple myeloma patient 19


title: KE39

value: RIKEN

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: F20_3

description: gene expression of fosmidic GH


title: F22_2

description: gene expression of fosmidic GH


title: 37895402

value: Affected

value: M


title: Multiple myeloma patient 20


title: Multiple myeloma patient 29

value: t(4;14)/IGH-FGFR3; non IGH-t(8q24/MYC)


title: F22_1

description: gene expression of fosmidic GH


title: 37927902


title: 37982202

value: Unaffected

value: F

value: Negative


title: NUGC3

value: JCRB


title: 37947502

value: Positive

value: Pooled from 6 healthy individuals


title: F20_2

description: gene expression of fosmidic GH

value: fosmidic GH


title: 37895202


title: TMK1

value: Atsushi, Ochiai


title: 37878502


title: 37928502


title: SNU719

value: moderately

value: KCLB


title: MKN45

value: poorly

value: male


title: SNU216


title: F20_1

description: gene expression of fosmidic GH


title: F18_2

description: gene expression of fosmidic GH


title: NUGC2


title: Multiple myeloma patient 14

value: multiple myeloma

value: bone marrow

value: None identified

value: YES


title: F18_3

description: gene expression of fosmidic GH


title: F18_1

description: gene expression of fosmidic GH


title: Multiple myeloma patient 15

value: non IGH-t(8q24/MYC)

value: NO

value: gain 1q21


title: Multiple myeloma patient 12


title: HSC57

value: well

value: Kazuyoshi, Yanagihara

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: Multiple myeloma patient 10 remission material

value: multiple myeloma (remission)


title: F16_3

description: gene expression of fosmidic GH

value: fosmidic GH


title: 37868902

value: Unaffected

value: M

value: Negative

value: Pooled from 6 healthy individuals


title: F16_2

description: gene expression of fosmidic GH


title: NCI-N87

value: ATCC

value: male


title: H-111-TC

value: RIKEN


title: 37947002

value: Affected

value: Positive


title: 37982402


title: Hs746T


title: F16_1

description: gene expression of fosmidic GH


title: SH101-P4


title: Multiple myeloma patient 11

value: multiple myeloma

value: bone marrow

value: None identified

value: YES


title: Multiple myeloma patient 16

value: NO


title: chicken spleen infected by Salmonella Enteritidis8

city: Shandong Taian

first: gui

middle: xian

last: wu

address: Taishanqu daizongdajie

institute: Shandong agriculture university

description: Chicken infected by Salmonella Enteritidis.

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Feature Extraction software.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program

organism: Gallus gallus

source_name: chicken Spleen

label_protocol: Total RNA (150 ng) was amplified and Cy5-labelled with Agilent's two Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling Kit). After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen) and quantified with the Nanodrop1000

extract_protocol: Total RNA was extracted with Trizon Reagent (Qiagen, Valencia, CA) following the manufacture instructions with minor modifications. RNA was quantified using Nanodrop1000 (ThermoScientific), and RNA integrity and quality was assessed using electrophoresis.

tag: treatment

value: Salmonella Enteritidis8

source_name: chicken spleen

label_protocol: Total RNA (150 ng) was amplified and Cy3-labelled with Agilent's two Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling Kit). After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen) and quantified with the Nanodrop1000


title: chicken spleen infected by Salmonella Enteritidis6

value: Salmonella Enteritidis6


title: 37947302

value: F


title: 37878302


title: 37996002


title: 37991402


title: Multiple myeloma patient 13


title: 37973902


title: 37896102

value: Unaffected


title: F14_3

description: gene expression of fosmidic GH

value: fosmidic GH


title: chicken spleen infected by Salmonella Enteritidis7

value: Salmonella Enteritidis7


title: chicken spleen infected by Salmonella Enteritidis3

value: Salmonella Enteritidis3


title: F14_2

description: gene expression of fosmidic GH


title: F10_3

description: gene expression of fosmidic GH


title: 37897102

value: M

value: Pooled from 6 healthy individuals


title: chicken spleen infected by Salmonella Enteritidis2

value: Salmonella Enteritidis2


title: Multiple myeloma patient 10


title: Multiple myeloma patient 05


title: MKN7

value: well

value: JCRB

value: male

value: mixture of genomic DNA from human peripheral blood mononuclear cells of 8 healthy donors


title: 37868502

value: Affected

value: Negative


title: 37973602

value: Positive


title: Multiple myeloma patient 07

value: multiple myeloma

value: bone marrow

value: None identified

value: YES


title: 37927702

value: F


title: 37974202

value: Unaffected


title: Multiple myeloma patient 09

value: NO


title: 37924202


title: F12_1

description: gene expression of fosmidic GH

value: fosmidic GH


title: F14_1

description: gene expression of fosmidic GH


title: F12_2

description: gene expression of fosmidic GH


title: F10_2

description: gene expression of fosmidic GH


title: 37926902

value: M

value: Pooled from 6 healthy individuals


title: 37924002


title: 37946902


title: Multiple myeloma patient 08


title: 37992402


title: 37993902


title: F10_1

description: gene expression of fosmidic GH


title: 37868602


title: chicken spleen infected by Salmonella Enteritidis5

value: Salmonella Enteritidis5


title: Multiple myeloma patient 02


title: 37996102


title: L+SAHA, 24h NaCl_1

city: Phayathai

first: Onsaya

last: Patanun

state: Bangkok

address: Rama6 rd. Phayathai

department: Biotechnology

country: Thailand

institute: Mahidol university

hyb_protocol: 600 ng of cRNAs from total RNA samples were hybridized at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Manihot esculenta

source_name: L+SAHA, 24h NaCl_1

label_protocol: 100 ng of total RNA were used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: 1-week old stem cut cassava TMS6044 were grown on liquid MS medium (no agar).

extract_protocol: Total RNA was extracted using Plant RNA Isolation Reagent (Invitrogen) following modified spin-column RNA precipitation using RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: The plantlets showing root elongation were treated with 100 µM SAHA for 24 h, followed by treatment with 200 mM NaCl for 2 and 24 h.

tag: authority

value: Manihot esculenta Crantz

tag: cultivar

value: Leaf

tag: salt condition

value: Salt treatment

tag: saha condition

value: with SAHA


title: L+SAHA, 24h NaCl_3

source_name: L+SAHA, 24h NaCl_3


title: Multiple myeloma patient 03

tag: disease state

tag: translocations

tag: hyperdiploidy

tag: additional aberrations


title: L+SAHA, 24h NaCl_2

source_name: L+SAHA, 24h NaCl_2

tag: tissue


title: L-SAHA, 24h NaCl_1

source_name: L-SAHA, 24h NaCl_1

value: without SAHA


title: L-SAHA, 24h NaCl_2

source_name: L-SAHA, 24h NaCl_2


title: L-SAHA, 24h NaCl_3

source_name: L-SAHA, 24h NaCl_3


title: L+SAHA, 2h NaCl_2

source_name: L+SAHA, 2h NaCl_2


title: F6_3

description: gene expression of fosmidic GH


title: L-SAHA, 2h NaCl_3

source_name: L-SAHA, 2h NaCl_3


title: chicken spleen infected by Salmonella Enteritidis4

value: Salmonella Enteritidis4


title: L+SAHA, 2h NaCl_1

source_name: L+SAHA, 2h NaCl_1


title: L+SAHA, 2h NaCl_3

source_name: L+SAHA, 2h NaCl_3


title: 37927802

tag: affection status (melanoma)

value: Affected

tag: age

tag: gender

tag: cdkn2a mutation status

value: Negative


title: F4_3

description: gene expression of fosmidic GH


title: Multiple myeloma patient 01

value: multiple myeloma

value: bone marrow


title: chicken spleen infected by Salmonella Enteritidis1

value: Salmonella Enteritidis1


title: 37895802

tag: sample type


title: F4_2

description: gene expression of fosmidic GH


title: 37974102

value: F


title: F8_2

description: gene expression of fosmidic GH


title: F8_1

description: gene expression of fosmidic GH


title: L-SAHA, 2h NaCl_2

source_name: L-SAHA, 2h NaCl_2


title: F2_3

description: gene expression of fosmidic GH


title: 38824102

value: Positive


title: 37926802


title: F4_1

description: gene expression of fosmidic GH

value: fosmidic GH


title: L-SAHA, 2h NaCl_1

source_name: L-SAHA, 2h NaCl_1


title: F6_1

description: gene expression of fosmidic GH


title: F8_3

description: gene expression of fosmidic GH


title: 37868402

value: M


title: L+SAHA_3

value: unstress condition


title: L+SAHA_2


title: F6_2

description: gene expression of fosmidic GH


title: 37926702

value: Unaffected

value: Pooled from 6 healthy individuals


title: L+SAHA_1

value: Manihot esculenta Crantz

value: Leaf


title: 37868802


title: 37895302


title: F2_1

description: gene expression of fosmidic GH


title: L-SAHA_3


title: F2_2

description: gene expression of fosmidic GH


title: 37815802


title: L-SAHA_2


title: F25_3

description: gene expression of fosmidic GH


title: 38358602

growth_protocol: Postive

value: Postive


title: 37979002


title: 37928702


title: F25_2

description: gene expression of fosmidic GH


title: R+SAHA, 24h NaCl_2

source_name: R+SAHA, 24h NaCl_2

value: Root

value: Salt treatment

value: with SAHA


title: F23_2

description: gene expression of fosmidic GH


title: 37979102

value: Affected


title: R-SAHA, 24h NaCl_3

source_name: R-SAHA, 24h NaCl_3

value: without SAHA


title: F23_3

description: gene expression of fosmidic GH


title: 38108802

source_name: Germline DNA from Blood


title: R+SAHA, 24h NaCl_3

source_name: R+SAHA, 24h NaCl_3


title: R+SAHA, 24h NaCl_1

source_name: R+SAHA, 24h NaCl_1


title: L-SAHA_1


title: F25_1

description: gene expression of fosmidic GH


title: F21_1

description: gene expression of fosmidic GH


title: R-SAHA, 24h NaCl_1

source_name: R-SAHA, 24h NaCl_1


title: 37926502


title: F23_1

description: gene expression of fosmidic GH


title: R-SAHA, 24h NaCl_2

source_name: R-SAHA, 24h NaCl_2


title: F21_2

description: gene expression of fosmidic GH


title: R+SAHA, 2h NaCl_3

source_name: R+SAHA, 2h NaCl_3


title: R+SAHA, 2h NaCl_2

source_name: R+SAHA, 2h NaCl_2


title: 37992302

value: Negative


title: 38824202


title: F21_3

description: gene expression of fosmidic GH


title: 37996202


title: R-SAHA, 2h NaCl_3

source_name: R-SAHA, 2h NaCl_3


title: R+SAHA, 2h NaCl_1

source_name: R+SAHA, 2h NaCl_1


title: F19_2

description: gene expression of fosmidic GH


title: F19_1

description: gene expression of fosmidic GH


title: F17_1

description: gene expression of fosmidic GH


title: R+SAHA_3


title: F17_3

description: gene expression of fosmidic GH


title: 37982302

value: Unknown

tag: cdk4 mutation status


title: R-SAHA, 2h NaCl_2

source_name: R-SAHA, 2h NaCl_2


title: R-SAHA, 2h NaCl_1

source_name: R-SAHA, 2h NaCl_1


title: 37896002


title: 37991502


title: 37878402


title: F15_3

description: gene expression of fosmidic GH

tag: group


title: F17_2

description: gene expression of fosmidic GH


title: F15_2

description: gene expression of fosmidic GH


title: 37878102


title: R+SAHA_1


title: F15_1

description: gene expression of fosmidic GH


title: R+SAHA_2


title: 37927602


title: 37973402


title: 37937602

value: F


title: 37897202

value: Positive


title: F19_3

description: gene expression of fosmidic GH

value: fosmidic GH


title: F11_3

description: gene expression of fosmidic GH


title: R-SAHA_3


title: R-SAHA_2


title: 37937302


title: F11_1

description: gene expression of fosmidic GH


title: 37996702


title: 37992202


title: 37928802

value: M


title: 37895702


title: R-SAHA_1

value: unstress condition


title: F9_3

description: gene expression of fosmidic GH


title: 37895102


title: F9_1

description: gene expression of fosmidic GH


title: 37878202


title: Ht

city: Toyonaka-shi

first: Masato

last: Wakabayashi

state: Osaka

address: 3-1-1, Futaba-cho

institute: Shionogi & Co., Ltd.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes, hybridized to Agilent Whole Rat Genome Oligo Microarrays (SurePrint G3 Rat GE 8x60K v2 Microarray) at 65°C for 17 hour in rotating at 10 rpm using Gene Expression Hybidization Kit (Agilent) following the manufacturers instructions. After hybridization, microarrays were washed using Gene Expression Wash Buffers Pack (Agilent) following manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the SureScan microarray scanner (G2600D) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Ht_dorsal skin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: Total RNAs of skin samples were extracted using TRIzol reagent (Thermo Fisher Scientific, Rockford, IL, USA), purified using RNeasy Mini kit (Qiagen, Hilden, Germany)  following the manufacturer's instructions. Extracted RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Drosal skins were prepared from WT and Ht rats at 25 weeks of age, frozen immediately, and stored at −80 °C.

tag: strain background

value: Wistar Bonn/Kobori (WBN/Kob)

tag: genotype/variation

value: Ht; Olmsted syndrome (OS) rat model

value: male

value: dorsal skin


title: 37895602

value: Pooled from 6 healthy individuals


title: 37928102

value: Unaffected


title: 37972702


title: F11_2

description: gene expression of fosmidic GH


title: F7_3

description: gene expression of fosmidic GH


title: 37929002


title: WT

source_name: WT_dorsal skin

value: wild type


title: F7_2

description: gene expression of fosmidic GH


title: F7_1

description: gene expression of fosmidic GH


title: Parathyroid Tumor 25

city: Baltimore

first: Nariman

last: Balenga

address: 655 W. Baltimore St, Room 10-010B

department: Surgery

institute: University of Maryland School of Medicine

description: Biological sample 25 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

hyb_protocol: The antisense aRNA for the sample and human reference RNA sample was then fluorescently labled with Cy3 and Cy5. The sample and reference were pooled and mixed with 1X hybridization buffer (50% formamide, 5x SSC, and 0.1% SDA), COT-1 DNA and poly-dA and heated to 95C for 2min.  The mixture was pipetted onto a microarray slide, a coverslip was placed and hybridized overnight at 42C.

scan_protocol: The array was washed at increasing stringencies and scanned on a GenePix 4000B scanner (Axon Instruments).

data_processing: Expression levels of the microarray were generated from the Axon GenePix 4000B scanner software and exported as *.gpr files. GeneSpring GX11.0 software was used for data analysis. Lowess normalization was performed along with a dye flip so that the ratio represented as sample/human reference.

source_name: human reference

label_protocol: Ambion Message Amp I kit (2003) was utilized to generate aRNA. Strategene Human Reference sample was labeled with either Cy5 or Cy 3 where indicated within the file naming convention.

growth_protocol: Parathyroid tissues were used directly for RNA isolation. Strategene Human Reference sample was purchased as RNA. In vitro cell growth was not performed.

extract_protocol: RNeasy kit (QIAGEN) was used to extract total RNA from parathyroid samples, following manufacturer's instructions. Human reference was purchased as RNA.

treatment_protocol: Parathyroid tissues were used directly for RNA isolation. Strategene Human Reference sample was purchased as RNA. In vivo or in vitro treatment was not performed.

tag: histopathology

value: pooled RNA from 10 human cell lines

source_name: PHPT 25

value: Adenoma


title: F5_3

description: gene expression of fosmidic GH


title: F5_1

description: gene expression of fosmidic GH


title: F3_1

description: gene expression of fosmidic GH


title: F1_3

description: gene expression of fosmidic GH


title: Parathyroid Tumor 23

description: Biological sample 23 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 23


title: F3_3

description: gene expression of fosmidic GH


title: F5_2

description: gene expression of fosmidic GH


title: F1_1

description: gene expression of fosmidic GH


title: Parathyroid Tumor 24

description: Biological sample 24 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 24


title: F1_2

description: gene expression of fosmidic GH


title: Parathyroid Tumor 21

description: Biological sample 21 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 21


title: Parathyroid Tumor 22

description: Biological sample 22 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 22


title: 256449110006_b3 - 16_D20_F2 vs 15_D20_V2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description:
maize (vitreous endosperm from dent maize) - harvest date: 21-08-14
maize (floury endosperm from dent maize) - harvest date: 21-08-14

hyb_protocol: 15_D20_V2 Cy5 / 16_D20_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Zea mays subsp. mays

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: seed - outdoor

extract_protocol: 15_D20_V2:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: time

value: 20 days after pollination

tag: harvest date

value: vitreous endosperm

tag: inbred line

value: dent maize

extract_protocol: 16_D20_F2:100mg. (Qiagen_RNeasy.pdf)

value: floury endosperm


title: E35_1

description: gene expression of plasmidic GH

value: plasmidic GH


title: 256449110006_b4 - 15_D20_V2 vs 16_D20_F2

description:
maize (floury endosperm from dent maize) - harvest date: 21-08-14
maize (vitreous endosperm from dent maize) - harvest date: 21-08-14

hyb_protocol: 16_D20_F2 Cy5 / 15_D20_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: F9_2

description: gene expression of fosmidic GH

value: fosmidic GH


title: E39_1

description: gene expression of plasmidic GH


title: F3_2

description: gene expression of fosmidic GH


title: E34_1

description: gene expression of plasmidic GH


title: E26_1

description: gene expression of plasmidic GH


title: E33_1

description: gene expression of plasmidic GH


title: E19_1

description: gene expression of plasmidic GH


title: Parathyroid Tumor 18

description: Biological sample 18 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 18


title: 256449110006_b2 - 7_D20_V1 vs 8_D20_F1

hyb_protocol: 8_D20_F1 Cy5 / 7_D20_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 8_D20_F1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 7_D20_V1:100mg. (Qiagen_RNeasy.pdf)


title: Parathyroid Tumor 19

description: Biological sample 19 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 19


title: E24_2

description: gene expression of plasmidic GH


title: Parathyroid Tumor 20

description: Biological sample 20 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 20


title: Parathyroid Tumor 16

description: Biological sample 16 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 16


title: Parathyroid Tumor 15

description: Biological sample 15 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 15


title: E32_1

description: gene expression of plasmidic GH


title: 256449110005_b4 - 13_D15_V2 vs 14_D15_F2

description:
maize (floury endosperm from dent maize) - harvest date: 14-08-14
maize (vitreous endosperm from dent maize) - harvest date: 14-08-14

hyb_protocol: 14_D15_F2 Cy5 / 13_D15_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 14_D15_F2:100mg. (Qiagen_RNeasy.pdf)

value: 15 days after pollination

extract_protocol: 13_D15_V2:100mg. (Qiagen_RNeasy.pdf)


title: E18_1

description: gene expression of plasmidic GH


title: E27_1

description: gene expression of plasmidic GH


title: 256449110006_b1 - 8_D20_F1 vs 7_D20_V1

hyb_protocol: 7_D20_V1 Cy5 / 8_D20_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Parathyroid Tumor 17

description: Biological sample 17 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 17


title: Parathyroid Tumor 14

description: Biological sample 14 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 14


title: 256449110005_b2 - 5_D15_V1 vs 6_D15_F1

hyb_protocol: 6_D15_F1 Cy5 / 5_D15_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 6_D15_F1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 5_D15_V1:100mg. (Qiagen_RNeasy.pdf)


title: 256449110005_b3 - 14_D15_F2 vs 13_D15_V2

description:
maize (vitreous endosperm from dent maize) - harvest date: 14-08-14
maize (floury endosperm from dent maize) - harvest date: 14-08-14

hyb_protocol: 13_D15_V2 Cy5 / 14_D15_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Parathyroid Tumor 13

description: Biological sample 13 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 13


title: E17_1

description: gene expression of plasmidic GH


title: E16_1

description: gene expression of plasmidic GH


title: 256449110005_b1 - 6_D15_F1 vs 5_D15_V1

hyb_protocol: 5_D15_V1 Cy5 / 6_D15_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E30_1

description: gene expression of plasmidic GH


title: E37_1

description: gene expression of plasmidic GH


title: Parathyroid Tumor 12

description: Biological sample 12 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 12


title: Parathyroid Tumor 11

description: Biological sample 11 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 11


title: Parathyroid Tumor 8

description: Biological sample 8 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 8


title: Parathyroid Tumor 9

description: Biological sample 9 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: human reference

source_name: PHPT 9


title: 256449110004_b2 - 3_C20_V1 vs 4_C20_F1

description:
maize (floury endosperm from flint maize) - harvest date: 21-08-14
maize (vitreous endosperm from flint maize) - harvest date: 21-08-14

hyb_protocol: 4_C20_F1 Cy5 / 3_C20_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 4_C20_F1:100mg. (Qiagen_RNeasy.pdf)

value: flint maize

extract_protocol: 3_C20_V1:100mg. (Qiagen_RNeasy.pdf)


title: 256449110004_b3 - 12_C20_F2 vs 11_C20_V2

description:
maize (vitreous endosperm from flint maize) - harvest date: 21-08-14
maize (floury endosperm from flint maize) - harvest date: 21-08-14

hyb_protocol: 11_C20_V2 Cy5 / 12_C20_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 11_C20_V2:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 12_C20_F2:100mg. (Qiagen_RNeasy.pdf)


title: E28_1

description: gene expression of plasmidic GH

extract_protocol: Total RNA was extracted from bacterial pellets after lysis with 1mg/ml lysozyme (Sigma-Aldrich, Isle d'Abeau Chesnes, France) during 5 min at 25°C, using the RNeasy Mini Kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions. RNA concentration, purity and integrity was evaluated by measuring the absorbance ratio at 260/280 nm and 260/230 nm using a Nanodrop spectrophotometer (Labtech, Palaiseau, France). The Ratio Integrity Number (RIN) was evaluated using 2100 Bioanalyzer® (Agilent Technologies, Massy, France) and only samples with a RIN upper than 8 were hybridized on the microarray.  Total RNA of rumen derived consortium was extracted in two steps from nitrogen frozen samples using the PowerMicrobiome RNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA) (Lazuka et al., 2015). RNA purification was performed using AllPrep DNA/RNA minikit (Qiagen), following the manufacturer’s instructions.


title: Parathyroid Tumor 10

description: Biological sample 10 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 10


title: 256449110004_b1 - 4_C20_F1 vs 3_C20_V1

hyb_protocol: 3_C20_V1 Cy5 / 4_C20_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Parathyroid Tumor 7

description: Biological sample 7 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 7


title: Parathyroid Tumor 6

description: Biological sample 6 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 6


title: E38_1

description: gene expression of plasmidic GH


title: 256449110003_b1 - 2_C15_F1 vs 1_C15_V1

description:
maize (vitreous endosperm from flint maize) - harvest date: 14-08-14
maize (floury endosperm from flint maize) - harvest date: 14-08-14

hyb_protocol: 1_C15_V1 Cy5 / 2_C15_F1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1_C15_V1:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 2_C15_F1:100mg. (Qiagen_RNeasy.pdf)


title: Parathyroid Tumor 5

description: Biological sample 5 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 5


title: E25_2

description: gene expression of plasmidic GH

hyb_protocol: For each sample, 1650 ng of labeled and amplified cRNA was used for hybridization. The hybridization master mix was prepared according to manufacturer’s protocol (Agilent Technologies, Massy, France) and 100 µl were dispensed onto a gasket slide, according to the Agilent Microarray Hybridization Chamber User Guide. Afterwards, the active side of the microarray slide was placed on top of the gasket to form a properly aligned “sandwich slide pair”. The microarray slides were inserted into the hybridization chamber (Agilent Technology) than placed at 65°C for 17 hours with rotation at 10 rpm. After hybridization, the microarray was washed over a 1-min period first using Gene Expression Wash Buffer 1 and then Gene Expression Wash Buffer 2 (Agilent Technologies, Massy, France) pre-warmed at 37°C.


title: 256449110003_b2 - 1_C15_V1 vs 2_C15_F1

description:
maize (floury endosperm from flint maize) - harvest date: 14-08-14
maize (vitreous endosperm from flint maize) - harvest date: 14-08-14

hyb_protocol: 2_C15_F1 Cy5 / 1_C15_V1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256449110003_b3 - 10_C15_F2 vs 9_C15_V2

hyb_protocol: 9_C15_V2 Cy5 / 10_C15_F2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 9_C15_V2:100mg. (Qiagen_RNeasy.pdf)

extract_protocol: 10_C15_F2:100mg. (Qiagen_RNeasy.pdf)


title: E23_1

description: gene expression of plasmidic GH


title: Parathyroid Tumor 4

description: Biological sample 4 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

extract_protocol: RNeasy kit (QIAGEN) was used to extract total RNA from parathyroid samples, following manufacturer's instructions. Human reference was purchased as RNA.

source_name: PHPT 4


title: Parathyroid Tumor 3

description: Biological sample 3 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 3


title: Parathyroid Tumor 2

description: Biological sample 2 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 2


title: E14_1

description: gene expression of plasmidic GH


title: Parathyroid Normal 5

description: Biological sample 5 of 6, normal parathyroid tissue, untreated; Human reference RNA.

source_name: N 5

value: Normal


title: E21_1

description: gene expression of plasmidic GH


title: 256449110003_b4 - 9_C15_V2 vs 10_C15_F2

hyb_protocol: 10_C15_F2 Cy5 / 9_C15_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Parathyroid Normal 6

description: Biological sample 6 of 6, normal parathyroid tissue, untreated; Human reference RNA.

hyb_protocol: The antisense aRNA for the sample and human reference RNA sample was then fluorescently labled with Cy3 and Cy5. The sample and reference were pooled and mixed with 1X hybridization buffer (50% formamide, 5x SSC, and 0.1% SDA), COT-1 DNA and poly-dA and heated to 95C for 2min.  The mixture was pipetted onto a microarray slide, a coverslip was placed and hybridized overnight at 42C.

source_name: N 6


title: Parathyroid Normal 4

description: Biological sample 4 of 6, normal parathyroid tissue, untreated; Human reference RNA.

source_name: N 4


title: Parathyroid Tumor 1

description: Biological sample 1 of 25, Adenomatous parathyroid tissue, untreated; Human reference RNA.

source_name: PHPT 1


title: Parathyroid Normal 3

description: Biological sample 3 of 6, normal parathyroid tissue, untreated; Human reference RNA.

source_name: N 3


title: E22_1

description: gene expression of plasmidic GH


title: Parathyroid Normal 1

description: Biological sample 1 of 6, normal parathyroid tissue, untreated; Human reference RNA.

source_name: N 1


title: E12_1

description: gene expression of plasmidic GH


title: E13_1

description: gene expression of plasmidic GH


title: E29_1

description: gene expression of plasmidic GH


title: E15_1

description: gene expression of plasmidic GH


title: E20_1

description: gene expression of plasmidic GH


title: Parathyroid Normal 2

description: Biological sample 2 of 6, normal parathyroid tissue, untreated; Human reference RNA.

source_name: N 2


title: Normal 1 [THJ-45N]

status: Public on Nov 30 2016

city: Jacksonville

first: John

middle: A

last: Copland

state: FL

address: 4500 San Pablo Road

department: Biochemistry & Molecular Biology

institute: Mayo Clinic College of Medicine

hyb_protocol: The IVT productswere column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C FOR 16 h

scan_protocol: Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA). All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: Raw data was processed by MAS.5 (Affymetrix) and analyzed using GeneSpring GX10

source_name: Normal Thyroid

label_protocol: The RNA products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA

extract_protocol: RNA was extracted from cell lines (Anaplastic Thyroid Cancer cell line, Normal Thyroid cell line) using TRIzol (Invitrogen) and chloroform (Sigma). RNA extracts were purified on Spin Chroma column (BD biosciences K1332-2). The 18S/28S bands were verified on a 1% agarose gel. RNA samples were shipped to Advanced Genomic Technology Center Gene Expression Core at the Mayo Clinic in Rochester, MN for further analysis. RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Reverse transcription to second strand cDNA was generated from 100 ng of good quality total RNA.

tag: cell type

value: normal thyroid


title: Fote_2

status: Public on Nov 08 2016

city: Berlin

first: Christian

last: Regenbrecht

address: Chariteplatz 1

department: Tumor stem cells

country: Germany

institute: Charité University Medicine Berlin, Germany

description: MeWoFote, Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization.
Gene expression of parental (n=1) and chemo-resistant derivatives (Eto, Fote n=3; Vind, Cis n=2) were measured on two Illumina BeadChips (HumanHT-12V4). After summarization via BeadStudio, data on each chip was quantile normalised (R package preprocessCore) and filtered (detection p<0.01 for at least one sample). After combination of chips by quantile normalization and batch correction (R package sva), significance thresholds for differential regulation were set to mean FC>=2 and adjusted P-value <0.05 (R package limma).
Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05, the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.

source_name: Melanoma cells, resistant to Fotemustine

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

growth_protocol: Cells were grown in Lebovitz medium (L15) in presence of 10% serum supplemented with penicillin and streptomycin.

extract_protocol: RNA isolation from frozen cell pellets was performed with the RNeasy Mini Kit (Qiagen,Germany), following the manufacturer's protocol. Reverse transcription of 500 ng - 2.5 μg RNA was performed with SuperScript VILO cDNA synthesis kit (Invitrogen, Germany) and diluted to a final volume of 50 μl, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. RIN-values were in a range of 9.6 - 10.0.

treatment_protocol: Cells were expanded under in vitro conditions.

tag: cell line

value: MeWo

value: Melanoma cell line

tag: resistance

value: Fotemustine


title: CRC Patient 145

status: Public on Nov 28 2016

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: RMA-sketch normalization on the core probeset using Affymetrix Power Tools (APT) followed by batch correction using the ComBat algorithm.

label: biotin

source_name: primary colon adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated proximal colon cancer specimens were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using the AllPrep DNA/RNA Micro Kit (Qiagen).

tag: patient id

tag: analysis batch

tag: other geo code

tag: age at diagnosis

value: male

tag: tumor stage

value: Tumor stage I

tag: primary site

value: left

tag: microsatellite status

value: MSS

tag: braf v600e status

value: wt

tag: kras codon 12, 13, 61 status


title: Cis_1

description: MeWoCis, Replicate 1

source_name: Melanoma cells, resistant to Cisplatin

value: Cisplatin


title: CRC Patient 147

tag: gender

value: Tumor stage II

value: right

value: mut


title: T3 [THJ-21T]

source_name: Anaplastic Thyroid Carcinoma

value: Anaplastic Thyroid Carcinoma (ATC)

tag: cell subtype

value: Spindle


title: CRC Patient 109

value: Tumor stage IV


title: Cis_2

description: MeWoCis, Replicate 2


title: Normal 2 [THJ-101N]


title: Vind_2

description: MeWoVind, Replicate 2

source_name: Melanoma cells, resistant to Vindesine

value: Vindesine


title: T2 [THJ-16T]


title: Fote_3

description: MeWoFote, Replicate 3


title: CRC Patient 121


title: T1 [THJ-11T]

value: Squamoid


title: Fote_1

description: MeWoFote, Replicate 1

value: MeWo


title: Vind_1

description: MeWoVind, Replicate 1

value: Melanoma cell line


title: Normal 3 [THJ-122N]

value: normal thyroid


title: T4 [THJ-29T]

value: Spindle/giant


title: Eto_3

description: MeWoEto, Replicate 3

source_name: Melanoma cells, resistant to Etoposide

value: Etoposide


title: Eto_1

description: MeWoEto, Replicate 1


title: Eto_2

description: MeWoEto, Replicate 2


title: 256449110004_b4 - 11_C20_V2 vs 12_C20_F2

description:
maize (floury endosperm from flint maize) - harvest date: 21-08-14
maize (vitreous endosperm from flint maize) - harvest date: 21-08-14

hyb_protocol: 12_C20_F2 Cy5 / 11_C20_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: time

value: 20 days after pollination

tag: tissue

value: floury endosperm

value: flint maize

value: vitreous endosperm


title: Par_1

description: MeWoPar

source_name: Melanoma cells, parental, sensitive


title: A549_culture in conditioned media from M2c macrophage_2 weeks_rep3

status: Public on Aug 25 2016

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The expression data were analyzed by the SAS JMP Genomics software (Version 4.0; SAS Institute Inc., Cary, NC). Affymetrix CEL files were transformed by GC-RMA algorithm, imported at the probe level and log2 transformed, and each probe set was summarized using the median of the corresponding probes. Each array was normalized by Quantile Normalization.

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: The human lung cancer cell line, A549, was grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

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

treatment_protocol: THP-1 cells were induced to differentiate into a macrophage-like phenotype by applying 3.2 × 10^-7 M phorbol myristate acetate (PMA; Sigma Chemical Co, St Louis, MO) and incubating for 24 hours. After washing three times, macrophages were incubated for an additional 24 hours to eliminate the effects of PMA and then incubated in serum-free media for 24 hours. The culture supernatants were collected as macrophage conditioned medium (CM). THP-1 cells (2 × 10^6) were cultured in macrophage CM for 3 days and then allowed to recover by incubating for an additional 3 days in normal media. The attached cells, corresponding to M0 macrophages, were polarized into M1, M2a, or M2c macrophages by adding 1 μg/ml lipopolysaccharide (LPS; Sigma) plus 20 ng/ml interferon (IFN-γ, 20 ng/ml interleukin (IL)-4, or 20 ng/ml IL-10 (BioLegend, San Diego, CA), respectively. Polarized macrophages were extensively washed to eliminate cytokines and LPS, and incubated in normal media for 24 hours as conditioned media. A549 cells were co-cultured with macrophages for 2 days.

tag: cell line source

value: 58-year-old caucasian male

tag: tissue source

value: lung adenocacinoma

value: adenocarcinomic human alveolar basal epithelial cells

tag: cultured with

value: M2c conditioned media (CM)


title: A549_culture in conditioned media from M2a macrophage_2 weeks_rep2

tag: cell line

tag: cell type

value: M2a conditioned media (CM)


title: A549_culture in conditioned media from M2a macrophage_2 weeks_rep3


title: A549_culture in conditioned media from M2c macrophage_2 weeks_rep2


title: A549_culture in conditioned media from M2a macrophage_2 weeks_rep1


title: A549_culture in conditioned media from M1 macrophage_2 weeks_rep2

value: M1 conditioned media (CM)


title: A549_culture in conditioned media from M2c macrophage_2 weeks_rep1


title: A549_culture in conditioned media from M0 macrophage_2 weeks_rep1

value: M0 conditioned media (CM)


title: A549_culture in conditioned media from M1 macrophage_2 weeks_rep1


title: Whole hESC-Neuron 3

status: Public on Jul 29 2016

city: Chapel Hill

middle: Marion

last: Taylor

state: North Carolina

address: 152 MacNider, CB 7575

department: Biomedical Engineering

institute: UNC-Chapel Hill

description:
RMA expression value derived from Expression Console software
N3_HuGene_2

hyb_protocol: cDNA was hybridized to Human Gene 2.0 ST Arrays (Affymetrix) and scanned with an Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader at the UNC School of Medicine Functional Genomics Core.

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

data_processing:
Analysis of individual microarray data was performed using the algorithms included in the Affymetrix Expression Console software with the default normalization method applied. Affymetrix Transcriptome Analysis Console v2.0 software algorithms were used to determine differential expression and statistical analysis.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: Whole hESC-Neuron

label_protocol: The Ovation One-Direct System (NuGEN) was used for cDNA synthesis and linear amplification followed by fragmentation and labeling using the Encore Biotin Module (NuGEN). Work was performed at the UNC School of Medicine Functional Genomics Core.

growth_protocol: Stem cell differentiation into neural progenitor cells (neuroepithelial cells) was performed according to previously published modifications of the original protocol [Zeng et al, PLoS One 5, e11853 (2010), Niedringhaus et al Sci. Rep. 5, 8353 (2015)]. Days in vitro (DIV) numbering began when H9 human embryonic stem cells were plated in Embroid body media to induce neuronal differentiation. On DIV24 neural progenitor cells were manually lifted and dissociated manually or with Accutase (Life Technologies).  Approximately 5x10e3 cells were seeded into one compartment of two-compartment axon isolating microfluidic chambers with N2B27 media supplemented with 100 ng/ml human recombinant brain derived neurotrophic factor (BDNF). Half of the media (100 µl) from each compartment was changed daily and cells were matured for at least 35 days (DIV59).

extract_protocol:
Whole neuron RNA was collected from hESC-neurons grown in microfluidic chambers not used for axonal RNA collection, this compartment contained soma, dendrites and axons which did not pass through the microgrooves. The majority of the media from the soma containing compartment was removed and the same procedure was followed, omitting constant aspiration.
On DIV59, isolation of RNA from microfluidic cultures using the RNAqueous-Micro Kit (Ambion) was performed as previously described15, 23. To collect whole hESC-neuron total RNA the majority of the media from the cell body compartment was removed and lysis buffer was added to one well, the reagent that flowed to the other well through the cell body compartment was collected as the whole hESC-neuron total RNA sample. Subsequent RNA purification was performed according to manufacturer’s instructions and RNA was eluted in a final volume of 10 µl. Samples were stored at -80°C until further processing.

value: hESC neuron

tag: compartment

value: whole neuron

tag: process date


title: A549 only_normal cuture_rep2

source_name: A549 control

value: control media


title: A549_culture in conditioned media from M0 macrophage_2 weeks_rep2


title: MFG KO animal id 11

status: Public on Jul 21 2016

city: Columbus

first: Sashwati

last: Roy

state: OH

institute: Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/ml), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences). Heat 65oC for 5 mins, 99oC for 5 mins, 45oC for 5 mins, centrifuge top speed for 5 mins. Hybridize 16hours at 45o at 60rpm. Fluidics script EukGE-WS2v4_450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using Command console

data_processing: GENESPRING 12.6; GCRMA

organism: Mus musculus

source_name: d5 wound-edge tissue of MFG KO mice

label_protocol: Samples were enzymatically fragmented and biotinylated using the Bioarray Highyield RNA Transcript Labeling Kit (Enzo)

extract_protocol: Extraction of total RNA was performed using miRVana isolation kit according to the manufacturer's instructions.

tag: genotype/variation

value: MFG-E8 KO

tag: strain

value: d5 wound edge tissues


title: A549_culture in conditioned media from M0 macrophage_2 weeks_rep3


title: A549 only_normal cuture_rep3


title: Whole hESC-Neuron 2

description:
RMA expression value derived from Expression Console software
N2_HuGene_2


title: MFG KO animal id 10


title: MFG KO animal id 12


title: Axon hESC-Neuron 2

description:
RMA expression value derived from Expression Console software
A2_HuGene_2

source_name: Axon hESC-Neuron

extract_protocol: On DIV59, isolation of RNA from microfluidic cultures using the RNAqueous-Micro Kit (Ambion) was performed as previously described15, 23. To collect pure axonal RNA continuous aspiration was applied to the somatodendritic compartment to prevent non-axonal material from entering the sample. Most of the axonal media was removed and lysis buffer was added to one well, the reagent that flowed to the other axonal well through the axonal compartment was collected as the total axonal RNA sample. Subsequent RNA purification was performed according to manufacturer’s instructions and RNA was eluted in a final volume of 10 µl. Samples were stored at -80°C until further processing.

value: axon


title: Whole hESC-Neuron 1

description:
RMA expression value derived from Expression Console software
N1_HuGene_2


title: 10081003:Tofacitinib,LS,Week 4

status: Public on Jun 30 2016

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: GeneChip Affymetrix protocol

tag: patient

tag: disease

value: Psoriasis

tag: treatment

value: Tofacitinib

value: lesional

value: Week 4

value: R


title: 10081003:Tofacitinib,LS,Week 2

value: Week 2


title: 10081003:Tofacitinib,LS,Day 0

value: Day 0


title: MFG WT animal id 4

source_name: d5 wound-edge tissue of MFG WT mice

value: MFG-E8 WT


title: 10081003:Tofacitinib,LS,Day 3

value: Day 3


title: A549_culture in conditioned media from M1 macrophage_2 weeks_rep3

value: 58-year-old caucasian male

value: lung adenocacinoma

value: adenocarcinomic human alveolar basal epithelial cells

value: M1 conditioned media (CM)


title: 10081003:Tofacitinib,NL,Day 0

value: non-lesional


title: A549 only_normal cuture_rep1

value: control media


title: MFG WT animal id 3

value: d5 wound edge tissues


title: MFG KO animal id 8

value: MFG-E8 KO


title: MFG WT animal id 2


title: 10081003:Tofacitinib,LS,Week 1

value: Psoriasis

value: Week 1


title: 10081003:Tofacitinib,LS,Day 1

value: Tofacitinib

value: lesional

value: Day 1


title: Axon hESC-Neuron 3

description:
RMA expression value derived from Expression Console software
A3_HuGene_2

value: hESC neuron

value: axon


title: Axon hESC-Neuron 1

description:
RMA expression value derived from Expression Console software
A1_HuGene_2


title: 10081003:Tofacitinib,LS,Week 12

value: Week 12

value: R


title: 10081002:Tofacitinib,LS,Week 12


title: 10081002:Tofacitinib,LS,Day 1


title: 10081002:Tofacitinib,LS,Week 4

value: Week 4


title: 10081002:Tofacitinib,NL,Day 0

value: Day 0


title: 10081002:Tofacitinib,LS,Week 2

value: Week 2


title: 10081001:Placebo,LS,Week 1

value: Placebo

value: NR


title: 10081002:Tofacitinib,LS,Day 3

value: Day 3


title: 10081001:Placebo,NL,Day 0

value: non-lesional


title: 10081002:Tofacitinib,LS,Day 0


title: 10081002:Tofacitinib,LS,Week 1


title: 10031002:Tofacitinib,LS,Week 4


title: 10031002:Tofacitinib,LS,Day 1


title: 10081001:Placebo,LS,Day 3


title: 10031001:Tofacitinib,LS,Day 1


title: 10081001:Placebo,LS,Week 4


title: 10081001:Placebo,LS,Week 12


title: 10031002:Tofacitinib,LS,Week 1


title: 10081001:Placebo,LS,Day 0


title: 10081001:Placebo,LS,Week 2


title: 10031002:Tofacitinib,LS,Day 3


title: 10031002:Tofacitinib,LS,Week 2


title: 10031002:Tofacitinib,LS,Week 12


title: 10031001:Tofacitinib,LS,Week 4


title: 10081001:Placebo,LS,Day 1


title: 10031001:Tofacitinib,LS,Week 2


title: 10031002:Tofacitinib,NL,Day 0


title: 10031002:Tofacitinib,LS,Day 0


title: 10031001:Tofacitinib,LS,Week 12


title: 10031001:Tofacitinib,LS,Day 3


title: 10031001:Tofacitinib,LS,Week 1


title: 10021004:Tofacitinib,LS,Week 12


title: 10021004:Tofacitinib,LS,Week 4


title: 10021004:Tofacitinib,LS,Week 1


title: 10031001:Tofacitinib,NL,Day 0


title: 10021002:Tofacitinib,LS,Week 4


title: 10021002:Tofacitinib,NL,Day 0


title: 10021004:Tofacitinib,NL,Day 0


title: 10031001:Tofacitinib,LS,Day 0


title: 10021002:Tofacitinib,LS,Day 1


title: 10021004:Tofacitinib,LS,Day 1


title: 10021004:Tofacitinib,LS,Day 3


title: 10021004:Tofacitinib,LS,Day 0


title: 10021004:Tofacitinib,LS,Week 2


title: 10021002:Tofacitinib,LS,Week 12


title: 10021001:Tofacitinib,NL,Day 0


title: 10021001:Tofacitinib,LS,Day 3


title: 10011005:Tofacitinib,LS,Week 1


title: 10011005:Tofacitinib,LS,Day 1


title: 10021001:Tofacitinib,LS,Day 0


title: 10021001:Tofacitinib,LS,Week 2


title: 10011005:Tofacitinib,LS,Week 2


title: 10011005:Tofacitinib,LS,Week 4


title: 10011005:Tofacitinib,LS,Week 12


title: 10021002:Tofacitinib,LS,Day 3


title: 10021002:Tofacitinib,LS,Week 2


title: 10011005:Tofacitinib,LS,Day 3


title: 10011005:Tofacitinib,LS,Day 0


title: 10021001:Tofacitinib,LS,Day 1


title: 10021002:Tofacitinib,LS,Day 0


title: 10021001:Tofacitinib,LS,Week 4


title: 10021001:Tofacitinib,LS,Week 1


title: healthy contralateral kidney 4

status: Public on Feb 16 2016

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

description:
replicate 4
CLK 4

data_processing: Data are normalized to snoRNA135 levels. Normalized_data.txt file reports normalized signal.  Non-normalized data.txt file reports raw Ct values. Fold change file reports fold change of all detectable snoRNA135 normalized average values of UUO divided by CLK. Each array is normalized (centered) using the median of the array.

label: FAM

source_name: Renal FoxD1-derivative cells, 10 days after UUO

label_protocol: For miRNA cDNA synthesis, total RNA was reverse transcribed using the miRNA reverse transcription kit (Applied Biosystems, Foster City, CA, USA) in combination with the stem-loop Megaplex Human primer pools A V2.1 (Applied Biosystems) according to manufacturer’s instructions. For each cDNA sample, 384 microRNAs including 6 controls (RNU44, RNU48, 4*U6), were profiled using TaqMan® Array MicroRNA Human Card A V2.0 (Applied Biosystems) according to manufacturer’s instructions. All arrays were run on a 7900HT Fast Real-Time PCR System (Applied Biosystems) and default thermal-cycling conditions

extract_protocol: Total RNA was extracted with standard Trizol-chloroform protocol.

treatment_protocol: Mice underwent unilateral urethral obstruction, kidney cell suspensions were FACS sorted

value: kidney

tag: Sex

value: male

tag: age

value: 8 weeks

tag: diagnosis

value: healthy


title: 10011005:Tofacitinib,NL,Day 0

value: Psoriasis

value: Tofacitinib

tag: time


title: 10011004:Placebo,LS,Week 2

tag: tissue

value: lesional


title: 10011004:Placebo,LS,Week 4


title: 10011004:Placebo,LS,Day 3


title: 10011003:Tofacitinib,LS,Week 12


title: healthy contralateral kidney 2

description:
replicate 2
CLK 2


title: healthy contralateral kidney 3

description:
replicate 3
CLK 3


title: 10011004:Placebo,LS,Day 0


title: 10011003:Tofacitinib,LS,Week 2


title: 10011004:Placebo,LS,Day 1

value: Day 1


title: 10011003:Tofacitinib,LS,Week 1

value: Week 1


title: 10011003:Tofacitinib,LS,Week 4

value: R


title: 10011004:Placebo,LS,Week 1


title: 10011001:Placebo,LS,Day 1


title: 10011001:Placebo,LS,Week 1


title: 10011001:Placebo,LS,Week 12

value: Week 12


title: CRC Patient 24

status: Public on Mar 02 2016

label_protocol: Approximately 3 ug of total RNA was processed to produce biotinylated sense DNA.

value: primary colon adenocarcinoma

tag: apc status

value: mut

tag: tumor stage

value: Tumor stage II

tag: rfs time in days

tag: rfs event

tag: analysis batch


title: 10011001:Placebo,LS,Week 4

value: Placebo

value: Week 4

value: NR


title: 10011003:Tofacitinib,LS,Day 0

value: Day 0


title: 10011003:Tofacitinib,NL,Day 0

value: non-lesional


title: fibrotic kidney 4

description:
replicate 3
UUO 4

value: kidney

value: male

value: 8 weeks

value: fibrotic


title: 10011003:Tofacitinib,LS,Day 3

value: Psoriasis

value: Tofacitinib

value: lesional

value: Day 3


title: 10011001:Placebo,NL,Day 0


title: 10011004:Placebo,NL,Day 0

value: R


title: 10011001:Placebo,LS,Week 2

value: Week 2


title: healthy contralateral kidney 1

description:
replicate 1
CLK 1

value: healthy


title: 10011003:Tofacitinib,LS,Day 1

value: Day 1


title: 10011001:Placebo,LS,Day 0

value: Placebo


title: fibrotic kidney 1

description:
replicate 1
UUO 1


title: 10021002:Tofacitinib,LS,Week 1

value: Week 1


title: 10011001:Placebo,LS,Day 3

value: NR


title: 10011004:Placebo,LS,Week 12

value: Week 12


title: fibrotic kidney 3

description:
replicate 2
UUO 3


title: shep2

status: Public on Mar 16 2013

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol

tag: cell type

value: Neuroblastoma cell

tag: cell line


title: normal tissue at age 62 (SA_BC98N)

status: Public on Aug 01 2014

city: Riyadh

first: Dilek

last: Colak

address: MBC03, PO Box 3354

department: Biostatistics, Epidemiology and Scientific Computing

country: Saudi Arabia

institute: KFSHRC

description:
SA_BC98N.CEL
Gene expression data from normal tissue at age 62 years

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed in the Affymetrix automated fluidic station and scanned with Affymetrix G7 3000 scanner.

scan_protocol: GeneChips were scanned using  Affymetrix G7 3000 scanner.

data_processing: The open source  R/Bioconductor  packages, (Fred Hutchinson Cancer Research Center, Seattle, WA, USA)were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. The CEL files or CEL/CHP files were utilized for further analysis using dChip, MEV,  and PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

source_name: normal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

growth_protocol: Tumors and adjacent disease free tissues obtained at time of surgical resection, according to institutional review board approved protocols.

tag: sample id

tag: tumor/normal

value: N

tag: grade

tag: er

tag: pr

tag: type

value: NORMAL

tag: age (years)


title: shsy5y