title: Subject 25

source_name: Lymphocytes isolated from blood after the intervention

source_name: Lymphocytes isolated from blood before the intervention


title: mouse mammary tumor [240T1]

status: Public on Feb 01 2014

type: RNA

city: Berkeley

first: Jian-Hua

last: Mao

state: CA

address: One Cyclotron Road

country: USA

institute: Lawrence Berkeley National Laboratory

description: Gene expression data from mammary tumor.

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

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

data_processing: The data were analyzed with by Robust Multi-array Analysis (RMA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse mammary tumor

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

growth_protocol: spontaneous mammary tumors from genetically diverse MMTV-ErbB2 mice

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

tag: tissue

value: mammary tumor

tag: genotype

tag: genetic background

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: MCF7 Control, technical rep 3

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

hyb_protocol: Biotin-cRNA was mixed with Illumina hybridization buffer and placed onto Illumina Human HT-12 v4 BeadChips (Part No. BD-103-0204, Illumina, San Diego, CA, USA). Hybridization was performed at 58 ºC for 17h with rocking in an Illumina Hybridization Oven (Cat# SE-901-1001, Illumina, San Diego, CA, USA). The arrays were washed, blocked, and then stained with streptavidin-Cy3 (Cat# PA43001, Amersham/GE Healthcare, Piscataway, NJ, USA) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.

scan_protocol: BeadChips were scanned with the Illumina iScan System (ID #N054, Illumina, San Diego, CA, USA).

data_processing: The data was collected and analyzed using the GenomeStudio software v2011.1 (Illumina, San Diego, CA, USA).

organism: Homo sapiens

source_name: MCF7 cell line, control

label_protocol: Briefly, 200 ng total RNA was converted to amplified biotin-cRNA using the Ambion TotalPrep RNA Amplification Kit (Cat# AMIL1791, Ambion, Austin, TX, USA).

growth_protocol: The MCF7 cell line was obtained from the American Type Culture Collection and grown in appropriate medium at 37 oC in a humidified 5% CO2 incubator.

extract_protocol: For RNA isolation, the mirVana Isolation kit № AM1560 (Ambion, USA) was used without enrichment. All procedures were done according to the manufacturer's protocol. All required RNA sample preparations, the subsequent hybridization and performing microarray analysis were done at the University of Iowa DNA Facility according to the manufacturer's recommended protocols.

treatment_protocol: In order to constantly knockdown TFAP2C expression in the MCF7 cell line, commercially available MISSION shRNA Lentiviral Particles based on pLKO.1-puro vector containing shRNA targeting TFAP2C (Cat# TRCN0000019745) and Non-Mammalian shRNA Control (Cat# SHC002) were used (Sigma-Aldrich, St. Louis, MO, USA).

tag: cell line

tag: shRNA

value: control


title: Subject 20

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions on 4x44K human whole genome microarrays.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 was excited at a wavelengths of 532 nm. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 522 (Cy3), based on automatic establishment of ideal scan settings. Images were subsequently saved (resolution 5 micron, 16 bit tiff image).

data_processing: Bad and empty spots were flagged using the GenePix Pro software (version 6.0, Molecular Devices, Sunnyvale, CA). Quality control was performed in the statistical software environment R (version 2.10.1, The R Foundation for Statistical Computing, Vienna, Austria). Quantile normalization and subsequent data processing including background subtraction and Log2 transformation of spot intensities was performed in ArrayTrack (version 3.4, NCTR, Jefferson, AR).

label_protocol: Cyanine 3 (Cy3)- and Cyanine 5 (Cy5)-labeled cRNA probes were generated using the Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, the Netherlands) according to the manufacturer's protocol.

extract_protocol: Lymphocytes isolated from the blood drawn from each participant before and after the intervention were lysed with TRIzol® reagent (Invitrogen) and stored at -80C until RNA extraction. Total RNA extracted using Trizol following manufacturer's instructions. The RNeasy® Mini Kit was used to purify total RNA from salts and residual DNA (Qiagen).

treatment_protocol: Healthy volunteer consumed 1 litre of blueberry/apple juice per day for four weeks. Before and after the intervention lymphocytes were isolated from blood drawn from which RNA was isolated for transcriptomic analyses. Each subject acted as its own control.

tag: gender

value: male

tag: age (yrs)


title: mouse mammary tumor [236T1]


title: MCF7 Control, technical rep 1


title: Subject 19


title: mouse mammary tumor [038T1]


title: Subject 24

value: female


title: MCF7 Control, technical rep 2


title: Subject 22


title: TAX1BP1_16w_WT_mitral valves_1

city: Oita

first: Satoko

last: Nakano

address: 1-1 Idaigaoka Yufu

country: Japan

institute: Oita University

description: Laser capture microdissection from mitral valves of 16w WT mouse1

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Version 10.7.3.1, Agilent Technologies) with the manufacturer's recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed R statistical package ((Version 1.15.1). The strategy adopted in Agi4x44Preproces is to produce, for each set of replicated probes, a unique probe value obtained by computing the median of the intensities of the probes belonging to the replicated probe set. This has been implemented in the summarize.probe function. This function uses an RGList as an input and it produces another RGList where each set of replicated non-control probes have been collapsed into a single value.

source_name: 16w,WT,mitral valves,1

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit (Agilent Technologies).

extract_protocol: Mitral valves from 8 and 16 weeks age of male TAX1BP1-KO mice and their wild-type litter mates were collected by Arcturus XT laser capture microdissection system according to a manufacture's directions. Total RNA was purified from the mitral valves by using the RNeasy mini kit (Qiagen)

value: mitral valves

tag: age

tag: background strain


title: mouse mammary tumor [232T1]


title: TAX1BP1_8w_WT_mitral valves_3

description: Laser capture microdissection from mitral valves of 8w WT mouse 3

source_name: 8w,WT,mitral valves,3


title: MCF7 Control, rep 1


title: TAX1BP1_8w_WT_mitral valves_1

description: Laser capture microdissection from mitral valves of 8w WT mouse 1

source_name: 8w,WT,mitral valves,1


title: Wild type yeast  10 µg/ml fludioxonil 15 min rep3

city: Braunschweig

first: Anna

last: Buschart

address: Inhoffenstr. 7

department: BiSA

country: Germany

institute: Helmholtz-Centre for Infection Research

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix GeneChip Yeast Genome 2.0 Array for 16 hours at 45°C. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the mini_euk2v3_FS450 protocol (Affymetrix).

scan_protocol: Image Analysis was performed on GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix).

data_processing: Raw intensities were RMA (robust multi-array) using the affy  of Bioconductor/R.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae, 10 µg/ml fludioxonil, 15 min

label_protocol: 500 ng of total RNA were used for biotin labeling according the 3´ IVT Express Kit (Affymetrix).

growth_protocol: Wild type S. cerevisiae and transformants were maintained in SD or SD-ura, respectively (0.67% yeast nitrogen base without amino acids, 2% glucose, nucleosides and amino acids according to Rose, M. D., Winston, F., and Hieter, P. (1990) Methods in Yeast Genetics: A Laboratory Course Manual, Revised Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, without uracil) at 30°C.

extract_protocol: Cells were disrupted using glass beads (425-600 µm, Sigma) in presence of lysis buffer (Qiagen RLT). RNA was isolated using RNeasy columns (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h and functional analysis of recombinant strain was carried out in SG-ura.

tag: strain

tag: expression vector

tag: treatment

value: 10 µg/ml fludioxonil

tag: duration of treatment

value: 15 min


title: TAX1BP1_16w_KO_mitral valves_2

description: Laser capture microdissection from mitral valves of 16w KO mouse2

source_name: 16w,KO,mitral valves,2


title: mouse mammary tumor [223T1]


title: Wild type yeast  untreated 15 min rep3

source_name: S. cerevisiae, untreated, 15 min


title: mouse mammary tumor [217T3]


title: Wild type yeast  10 µg/ml fludioxonil 15 min rep1


title: MCF7 Control, rep 2


title: TAX1BP1_8w_KO_mitral valves_3

description: Laser capture microdissection from mitral valves of 8w KO mouse 3

source_name: 8w,KO,mitral valves,3


title: mouse mammary tumor [229T1]


title: mouse mammary tumor [218T2]


title: TAX1BP1_16w_KO_mitral valves_3

description: Laser capture microdissection from mitral valves of 16w KO mouse3

source_name: 16w,KO,mitral valves,3


title: Wild type yeast  10 µg/ml fludioxonil 15 min rep2


title: MCF7 Control, rep 3


title: TAX1BP1_8w_WT_mitral valves_2

description: Laser capture microdissection from mitral valves of 8w WT mouse 2

source_name: 8w,WT,mitral valves,2


title: mouse mammary tumor [215T1]


title: TAX1BP1_16w_KO_mitral valves_1

description: Laser capture microdissection from mitral valves of 16w KO mouse1

source_name: 16w,KO,mitral valves,1


title: Wild type yeast  untreated 15 min rep2


title: mouse mammary tumor [208T1]


title: Wild type yeast  untreated 15 min rep1


title: mouse mammary tumor [207T1]


title: Transformant yeast 1 M sorbitol 60 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, sorbitol, 60 min

growth_protocol: S. cerevisiae transformants were maintained in SD-ura (0.67% yeast nitrogen base without amino acids, 2% glucose, nucleosides and amino acids according to Rose, M. D., Winston, F., and Hieter, P. (1990) Methods in Yeast Genetics: A Laboratory Course Manual, Revised Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, without uracil) at 30°C.

treatment_protocol:
Cultures were treated with 1 M sorbitol.
Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h and functional analysis of recombinant strain was carried out in SG-ura.

value: 1 M sorbitol

value: 60 min


title: mouse mammary tumor [207T2]


title: TAX1BP1_8w_KO_mitral valves_2

description: Laser capture microdissection from mitral valves of 8w KO mouse 2

source_name: 8w,KO,mitral valves,2


title: Transformant yeast 1 M sorbitol 15 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, sorbitol, 15 min


title: mouse under regular diet, biological replicate 2

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

institute: University of Regensburg

description: Gene expression data from liver of a mouse under regular diet

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST 16-array plate consists of 16 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (Rev. 2).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: The intensities of the CEL files were normalized with the VSN algorithm (Huber, 2002) and summarized to gene expression levels based on entrez gene identifiers using the chip description file from brainarray (Dai, 2005)

source_name: liver of a 26-week old mouse fed with regular diet

label_protocol: The Ambion WT Expression Kit Protocol (Rev. C) was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (Rev. 2).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Mini Kit, Qiagen, Hilden, Germany)

value: regular diet

value: liver

value: 26 weeks


title: cells 4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: NK-cell leukemia cell lines

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: SNK-1, SNK-6 and SNT-8 cells were cultured in RPMI 1640 supplemented with 10% human serum, with 50 units/mL penicillin, 50 μg/mL streptomycin, and 700 units/mL recombinant human IL-2. KHYG-1 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), with 50 units/mL penicillin, 50 μg/mL streptomycin, 100 units/mL, and recombinant human IL-2. Peripheral NK-cells were isolated from peripheral blood mononuclear cells by immunomagnetic negative selection using a Dynabeads untouched human NK cells kit (Invitrogen, Carlsbad, CA).

extract_protocol: RNA samples were extracted from cells using mirVana RNA isolation kit  (Ambion, Austin, TX).

value: NK-cell leukemia cell line KHYG-1

tag: cell line ebv-status

value: negative for EBV


title: mouse mammary tumor [035T2]

source_name: mouse mammary tumor


title: Transformant yeast 10 µg/ml fludioxonil 60 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, fludioxonil, 60 min

treatment_protocol:
Cultures were treated with 10 µg/ml fludioxonil.
Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h and functional analysis of recombinant strain was carried out in SG-ura.


title: Transformant yeast 10 µg/ml fludioxonil 30 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, fludioxonil, 30 min

value: 30 min


title: TAX1BP1_8w_KO_mitral valves_1

description: Laser capture microdissection from mitral valves of 8w KO mouse 1

source_name: 8w,KO,mitral valves,1


title: Transformant yeast 10 µg/ml fludioxonil 15 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, fludioxonil, 15 min


title: mouse mammary tumor [204T3]


title: Transformant yeast untreated 60 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, untreated, 60 min

treatment_protocol:
Cultures were untreated.
Induction of transgene expression was achieved by incubation of transformants in SG-ura at 30°C for 16h and functional analysis of recombinant strain was carried out in SG-ura.


title: mouse mammary tumor [200T2]


title: cells 3

source_name: Nasal NK/T-cell lymphoma cell line

value: Nasal NK/T-cell lymphoma cell line SNT-8

value: positive for EBV


title: cells 1

value: Nasal NK/T-cell lymphoma cell line SNK-6


title: cells 2

value: Nasal NK/T-cell lymphoma cell line SNK-1


title: Transformant yeast untreated 30 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, untreated, 30 min


title: cells 5

description: Normal NK cells

source_name: Normal peripheral NK cells

tag: cell type

value: normal peripheral NK cells


title: Transformant yeast untreated 15 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, untreated, 15 min


title: mouse mammary tumor [206T1]

value: mammary tumor

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: KS002 untreat vs Targocil rep3 dyeswap norm

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

description: biological replicate 3, dyeswap

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95oC and hybridized 16-18 hours at 42oC to DNA microarray slides which had been prehybridized for at least 30 min at 42oC in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42oC, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.) Raw data files were produced from the scanned images using the GenePix Pro 4.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 4.0 software package such that the ratio of medians of all features was equal to 1

label: Alexa Fluor 647

organism: Bacillus subtilis

source_name: treated

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 microgram of total RNA. Total cDNA was labeled overnight with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen)

extract_protocol: RNA was extracted  using the Quiagen RNeasy Mini Kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNAse free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

treatment_protocol: Strain KS002 was grown in LB to an OD600 of 0.4 with agitation at 37 oC,  then the culture was split in two tubes and 20 µM targocil was added to one sample (treated sample) and DMSO alone to the other (untreated sample). Cells were incubated for another 30 min at 37 oC with agitationbefore harvesting.

value: Targocil treated

label: Alexa Fluor 555

source_name: untreated

value: untreated


title: KS002 untreat vs Targocil rep3 norm

description: biological replicate 3

source_name: Targocil treated


title: KS002 untreat vs Targocil rep2 dyeswap norm

description: biological replicate 2, dyeswap


title: mouse mammary tumor [200T1]


title: mouse mammary tumor [201T1]


title: mouse mammary tumor [195T1]


title: KS002 untreat vs Targocil rep2 norm

description: biological replicate 2


title: mouse mammary tumor [193T2]


title: KS002 untreat vs Targocil rep1 dyeswap norm

description: biological replicate 1, dyeswap


title: KS002 untreat vs Targocil rep1 norm

description: biological replicate 1


title: mouse mammary tumor [191T2]


title: Pool3 s

city: Barcelona

first: Andrea

last: Feliciano

address: Passeig Vall d´Hebron 119-129

country: Spain

institute: Vall d´Hebron Research Institute

hyb_protocol: Labeled RNA was dried and resuspended with Hybridization  Buffer and Blocking Agent, incubated 10’ at 100ºC and transfered to an ice water bath for 5’. Samples were hybridized in a volume of 45ul to the Human miRNA V2 Oligo Microarray (Agilent) for 20 hours at 55°C and 20rpm. Microarrays were then washed at room temperature for 5min in Gene Expression Wash Buffer 1 and 5min at 37ºC in Gene Expression Wash Buffer 2 (Agilent Technologies; Palo Alto, CA).

scan_protocol: Arrays were scanned on an Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for miRNA microarrays with 100% PMT and 5μm resolution.

data_processing: Data was extracted using Agilent Feature Extraction Software (Agilent Technologies; Palo Alto, CA). Extracted Log2-transformed intensities were quantile normalized to make all data comparable.

source_name: Pool normal tissue

label_protocol: 500ng of total RNA from each sample was dephosphorylated with Calf Intestinal Alkaline Phosphatase (CIP) at 37ºC for 30’ following a denaturalization and then a ligation for 2h at 16ºC using Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies; Palo Alto, CA). In this step a molecule of Cyanine3-pCp is incorporated to the 3’ end of RNA molecules.

extract_protocol: The frozen normal and tumor tissues were collected for RNA extraction. Total RNA was isolated with the MirVana kit (Ambion, Austin, TX)

tag: disease state

value: normal


title: Pool2 s


title: 09 3173

source_name: tumor tissue

value: breast cancer tumor


title: mouse mammary tumor [197T1]


title: Pool1S


title: 09 714


title: mouse mammary tumor [190T1]


title: 32_10mo_actKI

type: other

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
Extracted molecule: polysomal RNA
Amplification protocol
Target Amplified manufacturer/kit: NuGen WT-Ovation RNA Amplification kit
Target Amplified protocol: NuGEN
Rounds of amplification: 1

hyb_protocol: Amount labeled target hybridization to array: 2.5 µg

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software AGCC version 1.1 for the Genechip operating software.

data_processing: MATLAB R2011b (7.13.0.564) software and the Bioinformatics Toolbox.

molecule: other

source_name: PODOTrap Actn4tm1.1Plk kidney podocytes, P300

label_protocol: Encore Biotin Module

extract_protocol: Humphreys protocol: TRAP, modified (Based on published protocol: M Heiman, Cell 2008, 135 (4):738-48.

value: kidney podocytes (visceral epithelium of mature renal corpuscle, synonym:podocyte layer)

tag: Sex

value: unknown

value: kidney podocytes, P300

tag: thelier stage

tag: developmental stage

tag: specimen mutation

value: Tg:Col1a1-eGFPL10a and Actn4tm1.1Plk (MGI:3767564)

tag: mutation notes

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208728

tag: url

tag: experimental design

value: Col1a1-eGFPL10a mice were crossed against Actn4+/tm1.1Plk (KI) mice.  Wild-type or KI mice were subject to TRAP at the following time points:2, 5 and 44 weeks.


title: mouse mammary tumor [035T1]

tag: tissue

tag: genotype

tag: genetic background


title: 33_10mo_actKI

tag: strain

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208729


title: mouse mammary tumor [187T1]


title: 34_10mo_actKI

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208730


title: mouse mammary tumor [187T3]


title: mouse mammary tumor [185T1]


title: mouse mammary tumor [187T2]


title: 31_10mo_actKI

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208727


title: 26_5wks_actKI

source_name: PODOTrap Actn4tm1.1Plk kidney podocytes, P35

value: kidney podocytes, P35

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208726


title: 25_5wks_actKI

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208725


title: 09 13526


title: mouse mammary tumor [170T1]

source_name: mouse mammary tumor

value: mammary tumor

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: 09 13226


title: 09 1795


title: 09 5437


title: 09 2301


title: Transformant yeast 1 M sorbitol 30 min rep3

source_name: S. cerevisiae expressing C. albicans Nik1p, sorbitol, 30 min

tag: expression vector

value: 1 M sorbitol

value: 30 min


title: 09 5508

value: breast cancer tumor


title: 23_5wks_actKI

value: kidney podocytes (visceral epithelium of mature renal corpuscle, synonym:podocyte layer)

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208723


title: mouse mammary tumor [178T2]


title: mouse mammary tumor [168T1]


title: 19_2wks_actKI

source_name: PODOTrap Actn4tm1.1Plk kidney podocytes, P14

value: unknown

value: kidney podocytes, P14

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208719


title: 09 9873


title: 21_2wks_actKI

value: Tg:Col1a1-eGFPL10a and Actn4tm1.1Plk (MGI:3767564)

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208721

value: Col1a1-eGFPL10a mice were crossed against Actn4+/tm1.1Plk (KI) mice.  Wild-type or KI mice were subject to TRAP at the following time points:2, 5 and 44 weeks.


title: 24_5wks_actKI

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208724


title: 09 5308


title: 20_2wks_actKI

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208720


title: 08 29950


title: 09 13344


title: mouse mammary tumor [163T4]


title: 22_2wks_actKI

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element. Actn4tm1.1Plk - PMID:15208722


title: mouse mammary tumor [166T1]


title: mouse mammary tumor [033T1]


title: 09 9374


title: 17_10mo_ctrl

source_name: PODOTrap WT kidney podocytes, P300

value: kidney podocytes, P300

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element.


title: mouse mammary tumor [163T3]

value: mammary tumor

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: 16_10mo_ctrl


title: mouse mammary tumor [165T1]


title: mouse mammary tumor [160T1]


title: Male IL1-beta 2

city: North Grafton

first: Arlin

last: Rogers

state: MA

address: 200 Westoboro Road

department: Biomedical Sciences

institute: Tufts Cummings School of Vet Med

description: Biological replicate 2 of 2. IL1-beta male

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

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software pattern 014868 was used for background subtraction and LOWESS normalization.

source_name: Liver: Male IL1-beta

label_protocol: 10 µg of total RNA primed with 2 µl of 100 µM DNA primers at 65°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

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

treatment_protocol: Male and female 8-week-old C3H/HeN mice were inoculated intraperitoneally with 25 ug/kg recombinant murine IL1-beta or vehicle every other day for 2 weeks; livers harvested 1 hr after final injection.

value: Male

value: Liver

source_name: Universal Mouse Reference RNA (Agilent)

tag: source type

value: 11 mouse cell lines


title: Male IL1-beta 1

description: Biological replicate 1 of 2. IL1-beta male


title: mouse mammary tumor [145T6]


title: Female IL1-beta 2

description: Biological replicate 2 of 2. IL1-beta female

source_name: Liver: Female IL1-beta

value: Female


title: mouse mammary tumor [163T1]


title: 08 28798

value: breast cancer tumor


title: 09 5218


title: 09 7803


title: 8_5wks_ctrl

source_name: PODOTrap WT kidney podocytes, P35

value: kidney podocytes (visceral epithelium of mature renal corpuscle, synonym:podocyte layer)

value: unknown

value: kidney podocytes, P35


title: mouse mammary tumor [145T5]


title: mouse mammary tumor [142T2]


title: 09 1365


title: Male control 2

description: Biological replicate 2 of 2. Control male

source_name: Liver: Male control


title: 10_5wks_ctrl


title: 18_10mo_ctrl


title: 9_5wks_ctrl


title: 09 3889


title: mouse mammary tumor [145T1]

description: Gene expression data from mammary tumor.


title: Female IL1-beta 1

description: Biological replicate 1 of 2. IL1-beta female


title: Male control 1

description: Biological replicate 1 of 2. Control male


title: 08 28185


title: mouse mammary tumor [026T3]


title: 7_5wks_ctrl


title: 6_5wks_ctrl


title: mouse mammary tumor [141T1]


title: Female control 1

description: Biological replicate 1 of 2. Control female

source_name: Liver: Female control


title: mouse mammary tumor [139T2]


title: 3_2wks_ctrl

source_name: PODOTrap WT kidney podocytes, P14

value: kidney podocytes, P14


title: 2_2wks_ctrl

value: Col1a1-eGFPL10a mice were crossed against Actn4+/tm1.1Plk (KI) mice.  Wild-type or KI mice were subject to TRAP at the following time points:2, 5 and 44 weeks.


title: 5_2wks_ctrl


title: 09 7557


title: mouse mammary tumor [142T1]


title: 09 989


title: AT9

city: Boston

first: Alan

last: Branco

address: 665 Huntington Ave.

department: Environmental Health

institute: Harvard School of Public Health

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 400B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal. M-values obtained with the Limma package in R. (Branco et. al, Natural variation of the Y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in Drosophila simulans. Heredity)

organism: Drosophila simulans

source_name: Total RNA from D simulans genotypes with variable Y chromosomes.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

value: Yct

value: female (XXY)

tag: age

value: 2 days old, unmated


title: 08 28080


title: AT8

description: Biological replicate


title: mouse mammary tumor [139T1]


title: 09 13660


title: 09 6469


title: Female control 2

description: Biological replicate 2 of 2. Control female


title: 1_2wks_ctrl


title: mouse mammary tumor [135T1]


title: AT7

description: Biological replicate


title: Socs2 null mutant at Time 36 hours, Biological Replicate 1

first: Michael Todd

last: Valerius

address: 4 Blackfan Circle, Harvard Institute of Medicine, HIM-550

department: Renal Division

institute: Brigham and Women's Hospital

description: Socs2-null adult liver 36 hours after hepatectomy

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: CEL files generated from scanning the Affymetrix arrays where imported into dChip (Build Nov 10, 2012) for processing and analysis. Probeset annotation generated from Affymetrix file HT_MG-430_PM.na33.annot.csv downloaded on November 2, 2012. Arrays were normalized using probes of 'Quantiles' and 'Running median' smoothing with the baseline array set as Socs2-CNTRL-24. Expression/signal values were obtained using 'Model-based expression' modeling method and '5th percentile of region (PM-only)' as background subtraction (dChip methodologies described in the software and in Li, C., and Wong, W.H. (2001)).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 micrograms total RNA pooled from three animals (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total mRNA was purified from 30mg of liver tissue preserved in RNALater using the RNeasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Mice subjected to 2/3 hepatectomy, except Time zero. Liver tissue stored in RNAlator (Qiagen) until extraction.

tag: genotype/variation

value: Soc2 null mutant

value: liver, adult

tag: treatment

value: 2/3 hepatectomy

tag: time after hepatectomy

value: adult


title: AT5

description: Biological replicate

tag: Sex

value: Ysec


title: 09 5826

tag: disease state


title: Socs2 null mutant at Time 36 hours, Biological Replicate 2

source_name: Socs2-null adult liver 36 hours after hepatectomy


title: 09 869


title: mouse mammary tumor [132T1]

value: mammary tumor

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: AT39

description: Biological replicate


title: mouse mammary tumor [137T1]


title: AT40

description: Biological replicate


title: 15_10mo_ctrl

tag: cell type

value: kidney podocytes, P300

tag: thelier stage

tag: developmental stage

value: Construct generated in Ben Humphreys lab. A fusion transgene encoding eGFP and the ribosomal protein L10a was inserted downstream of the collagen1α1 promoter/enhancer element.


title: mouse mammary tumor [128T1]


title: Control at Time 36 hours, Biological Replicate 2

description: Wildtype adult liver 36 hours after hepatectomy

value: wildtype


title: Control at Time 36 hours, Biological Replicate 1

source_name: Wildtype adult liver 36 hours after hepatectomy


title: 08 27993T

source_name: tumor tissue

value: breast cancer tumor


title: 09 3265


title: Socs2 null mutant at Time 24 hours, Biological Replicate 2

description: Socs2-null adult liver 24 hours after hepatectomy


title: mouse mammary tumor [126T1]


title: 08 15674T


title: mouse mammary tumor [126T2]


title: mouse mammary tumor [178T1]


title: AT37

description: Biological replicate


title: 08 5600T


title: Socs2 null mutant at Time 24 hours, Biological Replicate 1

source_name: Socs2-null adult liver 24 hours after hepatectomy


title: AT38

description: Biological replicate


title: 08 27086T


title: mouse mammary tumor [123T2]


title: AT35

description: Biological replicate


title: Control at Time 24 hours, Biological Replicate 2

description: Wildtype adult liver 24 hours after hepatectomy


title: Control at Time 24 hours, Biological Replicate 1

source_name: Wildtype adult liver 24 hours after hepatectomy


title: AT36

description: Biological replicate


title: mouse mammary tumor [122T1]

source_name: mouse mammary tumor


title: AT34

description: Biological replicate


title: AT33

description: Biological replicate


title: 08 13959T


title: 08 4209T


title: Socs2 null mutant at Time 0, Biological Replicate 1

description: Socs2-null adult liver

source_name: Socs2-null adult liver


title: 08 29041


title: mouse mammary tumor [117T5]


title: Control at Time 0, Biological Replicate 2

description: Wildtype adult liver

source_name: Wildtype adult liver


title: mouse mammary tumor [117T3]


title: AT20

description: Biological replicate


title: mouse mammary tumor [026T2]


title: Socs2 null mutant at Time 0, Biological Replicate 2

description: Socs2-null adult liver


title: 08 25583T


title: AT3

description: Biological replicate


title: AT17

description: Biological replicate


title: mouse mammary tumor [117T2]


title: AT18

description: Biological replicate


title: 08 3050T


title: AT16

description: Biological replicate


title: AT2

description: Biological replicate


title: 08 24500T


title: 08 24450T


title: 08 12496T


title: 08 12643T


title: mouse mammary tumor [113T3]


title: 08 08906T


title: 08 2418T


title: Control at Time 0, Biological Replicate 1

description: Wildtype adult liver


title: mouse mammary tumor [113T1]


title: mouse mammary tumor [113T2]


title: 08 16764T


title: AT12

description: Biological replicate


title: AT14

description: Biological replicate


title: 08 07581T


title: A340

description: Biological replicate


title: AT15

description: Biological replicate


title: mouse mammary tumor [109T1]


title: 08 00861T


title: mouse mammary tumor [112T1]


title: AT1

description: Biological replicate


title: A339

description: Biological replicate


title: mouse mammary tumor [107T1]


title: mouse mammary tumor [106T3]


title: mouse mammary tumor [117T4]


title: AT10

description: Biological replicate


title: 08 07191T


title: mouse mammary tumor [026T1]


title: 08 28079T


title: 08 16127T


title: 08 00445T


title: mouse mammary tumor [108T2]


title: mouse mammary tumor [106T1]


title: mouse mammary tumor [085T1]


title: A338

description: Biological replicate

value: male (XY)


title: A336

description: Biological replicate


title: mouse mammary tumor [095T2]


title: LoVo 5FU 200mcM_2

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: 750ng of the biotin labeled cRNA probes were mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files were analyzed with Illumina’s GenomeStudio gene expression module (v1.8.0)

source_name: Human colon cancer cell line

label_protocol: Initially, 500ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate biotin labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

tag: cell line

value: 5-FU 200 microM for 24 hours

value: colon cancer cell line


title: mouse mammary tumor [086T1]


title: 08 00147T


title: LoVo 5FU 200mcM_1


title: A337

description: Biological replicate


title: A334

description: Biological replicate

value: Yct


title: LoVo Y15 10mcM_2

value: 10 microM Y15 for 24 hours


title: mouse mammary tumor [084T1]


title: mouse mammary tumor [079T1]


title: A335

description: Biological replicate

value: 2 days old, unmated


title: LoVo Y15 10mcM_1


title: LoVo untreated_2

value: control


title: SW620 5FU 200mcM_2


title: mouse mammary tumor [078T2]


title: mouse mammary tumor [017T1]


title: LoVo untreated_1


title: A331

description: Biological replicate


title: mouse mammary tumor [078T1]


title: mouse mammary tumor [P24T2]

value: FVB/N


title: SW620 5FU 200mcM_1


title: A330

description: Biological replicate


title: A332

description: Biological replicate


title: Control vs. PTH-stimulated

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global-normalized, background-subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Control MSCs

label_protocol: cDNA and Amino Allyl aRNA were synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye coupling and fragmentation were performed according to the protocol supplied by TORAY Industries, Inc.

growth_protocol: Human MSCs were isolated from a bone marrow sample obtained from a healthy adult volunteer. MSCs were cultured in advanced minimal essential medium (MEM; Invitrogen) supplemented with 5% FCS (Invitrogen), 100 mM ascorbic acid (Wako Chemicals), 2 mM L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin (all from Gibco).

extract_protocol: Total RNA was extracted with the QIAamp RNA Blood Mini Kit (Qiagen).

tag: disease status

value: healthy

value: mesenchymal stem cells (MSCs)

source_name: PTH-stimulated MSCs

treatment_protocol: MSCs were treated with 0.1 nM recombinant human PTH (N-terminal fragment, amino acids 1-34) for 48 hours.

value: parathyroid hormone (PTH)


title: A328

description: Biological replicate

value: Ysec


title: A329

description: Biological replicate


title: A298

description: Biological replicate

value: female (XXY)


title: mouse mammary tumor [P23T1]

tag: tissue

value: mammary tumor


title: SW620 Y15 10mcM_1


title: mouse mammary tumor [P22T3]

tag: genotype


title: A327

description: Biological replicate


title: A333

description: Biological replicate


title: A26

description: Biological replicate


title: SW620 Y15 10mcM_2


title: mouse mammary tumor [065T1]

tag: genetic background

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: mouse mammary tumor [P21T1]


title: SW620 untreated_2


title: mouse mammary tumor [P20T6]


title: A24

description: Biological replicate


title: A23

description: Biological replicate


title: TaFLS overexpression line 2 (OE2), biological rep3

city: Jinan

first: Mengcheng

last: Wang

address: 27 Shandanan Road

department: School of Life Science

country: China

institute: Shandong University

description: The content of flavonols in leaves and guard cells was increased

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis was grown in soils under the regime of a 16 h photoperiod at 22°C and 60% relative humidity for six weeks

treatment_protocol: Leaves of Arabidopsis seeldings were sampled and immediately stored in liquid nitrogen for RNA extraction

value: TaFLS overexpression line 2 (OE2)

value: Rosette leaves

value: Six-week old seedlings


title: SW620 untreated_1


title: fls1-3, biological rep2

source_name: fls1-3, biological rep2


title: mouse mammary tumor [P19T1]


title: TB10839_ LB_ LE_BR2

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

institute: Medical School Hannover

description: cells harvested at late exponential phase, 37°C LB

hyb_protocol: Hybridization, washing, staining of labeled cDNA was done by the Affymetrix Core Facility at the Helmholtz Centre for Infection Research (HZI), Braunschweig.

scan_protocol: Scanning and primary data evaluation of labeled cDNA was done by the Affymetrix Core Facility at the Helmholtz Centre for Infection Research (HZI), Braunschweig.

data_processing: Data analysis was performed using the Affymetrix Microarray Suite software 5.0 with Affymetrix default parameters. The average microarray hybridization signal intensity was scaled to 150. Experiments were carried out in duplicate; thus, a total of two GeneChips per strain and growth condition were scanned at 570 nm with 3 µm resolution by the Affymetrix scanner. Two GeneChips for the mutant and wild type were compared by the four-comparison survival method (Chen et al., 2000). The data were imported into a Microsoft Access database capable of searching for genes, which were found in all four pairings defined by the Affymetrix Microarray Suite Software as having significant changes in their signal intensities.

organism: Pseudomonas aeruginosa TBCF10839

label_protocol: To reduce variations in the abundance of specific mRNAs due to slight differences in growth conditions and RNA preparation, we pooled equal amounts of RNA from three cultures to get a final amount of 10 µg. The subsequent steps of cDNA generation and biotin-ddUTP terminal labeling were performed as described in the manufacturer's instructions for the P. aeruginosa GeneChip. The cDNA was purified with the QIAquick column (QIAGEN) and quantified by A260. cDNA was fragmented in One Phor-All buffer with 0.5 U of DNase I  per µg of cDNA for 10 min at 37°C and subsequent inactivation for 10 min at 98°C. To check if the majority of cDNA fragments were in a 50- to 200-bp range, 5 µl was loaded on a 2% (wt/vol) agarose gel stained with SYBR Green. The fragmentation product was end labeled with the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix, Santa Clara, CA.).

growth_protocol: Bacterial cells of TBCF10839 and TBCF10839nrtR::Tn5 grown in LB broth to late exponential phase at 37 oC were harvested by centrifugation at 3800 x g for 2 min at 4 oC.

extract_protocol: Total RNA from approximately 3 x 1010 cells was extracted according to the protocol provided by QIAGEN (RNeasy Mini Kit). DNA was digested by the addition of 40 units of DNaseI (Roche) and 20 units of SUPERaseIn (Ambion, Cambridgeshire, UK) in DNaseI buffer (50 mM Na-acetate, 10 mM MgCl2, 2 mM CaCl2, pH 6.5) for 30 min at 37 oC in a total volume of 200 µl. The yield of total cellular RNA was quantified by measuring the light absorption at 260 nm.

tag: strain

value: CF isolate


title: fls1-3, biological rep3

source_name: fls1-3, biological rep3


title: TB10839_ LB_ LE_BR1


title: mouse mammary tumor [P21T4]

data_processing: The data were analyzed with by Robust Multi-array Analysis (RMA).


title: A20

description: Biological replicate

value: male (XY)


title: A25

description: Biological replicate

value: Yct


title: fls1-3, biological rep1

source_name: fls1-3, biological rep1


title: TBCF10839nrtR::Tn5_ LB_LE_BR2


title: A19

description: Biological replicate


title: TBCF10839nrtR::Tn5_LB_LE_ BR1


title: A18

description: Biological replicate


title: TaFLS overexpression line 2 (OE2), biological rep1


title: mouse mammary tumor [P16T1]


title: mouse mammary tumor [P17T1]


title: mouse mammary tumor [P15T2]


title: mouse mammary tumor [P16T2]


title: mouse mammary tumor [P15T1]


title: A16

description: Biological replicate


title: TaFLS overexpression line 2 (OE2), biological rep2


title: TaFLS overexpression line 1 (OE1), biological rep3

description: The content of flavonols in leaves and guard cells was decreased

value: TaFLS overexpression line 1 (OE1)


title: A17

description: Biological replicate

value: 2 days old, unmated


title: TaFLS overexpression line 1 (OE1), biological rep1


title: mouse mammary tumor [P13T3]


title: Control 2

type: genomic

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

hyb_protocol: was carried out by Life & Brain GmbH, Bonn

label: Biotin

molecule: genomic DNA

source_name: whole blood

extract_protocol: DNA isolation was carried out according to the manufacture's protocol (Machery Nagel, Nucleo Spin Blood XL); for the bead chip array 500 ng of genomic DNA was treated with bisulfite (Dammann et al, 2011)

tag: gender

value: Female

tag: suicide background

value: No

tag: diagnosis

value: Normal (Control)


title: A14

description: Biological replicate

tag: age


title: Control 1

scan_protocol: was carried out by Life & Brain GmbH, Bonn


title: TaFLS overexpression line 1 (OE1), biological rep2

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

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

tag: genotype/variation


title: Col-0, biological rep2

description: Wild-type

source_name: Col-0, biological rep2


title: Col-0, biological rep3

description: Wild-type

source_name: Col-0, biological rep3


title: mouse mammary tumor [P12T2]

first: Jian-Hua

last: Mao

address: One Cyclotron Road

institute: Lawrence Berkeley National Laboratory

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

value: FVB/N


title: mouse mammary tumor [064T2]


title: A107

description: Biological replicate

source_name: Total RNA from D simulans genotypes with variable Y chromosomes.


title: mouse mammary tumor [P11T2]


title: BPD patient 8

data_processing: was carried out by Life & Brain GmbH, Bonn

value: Yes

value: Borderline Personality Disorder (BPD)


title: mouse mammary tumor [P10T3]


title: A108

description: Biological replicate

value: Ysec


title: in vitro 3

city: Taipei

first: Shih

middle: Yun

last: Lin

state: Taiwan

address: 128 Sec. 2, Academia Rd

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expresion file of polysomal mRNAs from"in vitro" cultured pollen tubes sample

hyb_protocol: The labeled aRNA was fragmented to 35-200 nt and Bud (4.9 μg), in vivo (12 μg) and in vitro (18 μg) samples were hybridized to GeneChip Arabidopsis ATH1 genome arrays (Affymetrix, Santa Clara, CA) for 16.5 hr at 45°C.

scan_protocol: The array signal was scanned by use of the Affymetrix GeneChip® Scanner 3000 scanner (Agilent Technologies).

data_processing: The per-array data normalization was used Microarray Suite version 5.0 (MAS 5.0).

source_name: The third biological replicate of polysomal mRNAs from"in vitro" cultured pollen tubes sample

label_protocol: The aRNAs from three different samples were labeled with biotin by in vitro transcription in amplification kit and their integrity was examined by use of an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: LAT52-HF-RPL18 transgenic Arabidopsis plants were grown in growth chamber under 18-h light/6-h dark at 22°C

extract_protocol: Polysomal RNA of the “Bud”, “in vivo”-grown pollen tubes and “in vitro”-cultured pollen tubes samples were further purified with an RNA purification kit (RNeasy Mini Kit, QIAGEN, Hilden, Germany), and then were treated with RNA amplification kit (MessageAmpTMPremier RNA amplification kit, Austin, TX, USA) to increase the RNA amount by single linear amplification and generate the antisense RNA (aRNA).

treatment_protocol: To isolate the polysomal RNAs from “Bud” stage, “in vivo”-grown pollen tubes, and “in vitro”-cultured pollen tube in LAT52-HF-RPL18 Arabidopsis, the ribosome-mRNA complexes of these three samples were separated through sucrose density gradients and the polysome region of the gradient pooled for mRNA extraction. Prior to polysome extraction, we used 1250 μl of polysome extraction buffer (PEB) (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, pH 8.3, 36 mM MgCl2, 5 mM dithiothreitol (DTT), 50 mg mL-1 cycloheximide, 50 mg mL-1 chloramphenicol, 0.5 mg mL-1, heparin, 1% (v/v) Triton X-100, 1% (v/v) Tween 20, 1% (w/v) Brij-35, 2% (v/v) polyoxyethylene, and 1% (w/v) deoxycholic acid) (Mustroph et al., 2009) to treat each sample. The crude extract of each sample in PEB was centrifuged at 12,000 rpm for 20 min at 4°C, the supernatant passed through a shredder column (Qiagen, Hilden, Germany) to remove residues and a spectrophotometer (DU® 648B, Beckman, IN, USA) used to detect the OD260 units of the flow through. The purified crude extract (500 μl, 30-40 OD260 units) was loaded on a 4.2 mL sucrose (20%-60%) density gradient and ultracentrifuged at 39,000 rpm for 3.5 hr at 4°C in a SW 41Ti rotor (Beckman, IN, USA). After centrifugation, the absorbance profile of the gradient was detected using a UV monitor (Monitor UVIS-920, GE Healthcare, NJ, USA) at Absorbance 260 nm. Fractions containing polysomes were collected for immunoprecipitation of the FLAG-tagged ribosome complexes by use of FLAG antibody-associated agarose beads (ANTI-FLAG® M2-Agarose from mouse, Sigma-Aldrich).

value: LAT52-HF-RPL18 transgenic

value: in vitro cultured pollen tube

value: pollen tube


title: A10

description: Biological replicate


title: Col-0, biological rep1

description: Wild-type

source_name: Col-0, biological rep1

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

value: Rosette leaves


title: BPD patient 2

label_protocol: was carried out by Life & Brain GmbH, Bonn


title: A106

description: Biological replicate


title: A110

description: Biological replicate


title: mouse mammary tumor [P10T1]

city: Berkeley

value: mammary tumor


title: A09

description: Biological replicate


title: in vitro 2

source_name: The second biological replicate of polysomal mRNAs from"in vitro" cultured pollen tubes sample


title: mouse mammary tumor [P09T1]


title: mouse mammary tumor [P08T1]


title: in vivo 3

description: Gene expression file of polysomal mRNAs from" in vivo" grown pollen tubes sample

source_name: The third biological replicate of polysomal mRNAs from" in vivo" grown pollen tubes sample

value: stage 14 floral buds


title: Control 11


title: in vitro 1

source_name: The first biological replicate of polysomal mRNAs from"in vitro" cultured pollen tubes sample


title: BPD patient 7


title: in vivo 2

source_name: The second biological replicate of polysomal mRNAs from" in vivo" grown pollen tubes sample


title: mouse mammary tumor [P07T1]

source_name: mouse mammary tumor


title: in vivo 1

source_name: The first biological replicate of polysomal mRNAs from" in vivo" grown pollen tubes sample


title: A07

description: Biological replicate

value: male (XY)


title: A06

description: Biological replicate

value: Yct


title: mouse mammary tumor [P05T8]


title: A05

description: Biological replicate


title: Bud 3

description: Gene expression profile of  polysomal mRNAs from 'bud" sample

source_name: The third biological replicate of polysomal mRNAs from 'bud" sample

value: stage 11-12 floral buds

value: pollen grains and tubes


title: BPD patient 23

value: Female


title: BPD patient 1

value: No


title: BPD patient 4


title: BPD patient 3


title: Control 10

value: Normal (Control)


title: BPD patient 22


title: A03

description: Biological replicate

value: 2 days old, unmated


title: mouse mammary tumor [P04T1]

value: FVB/N


title: BPD patient 21

value: Yes

value: Borderline Personality Disorder (BPD)


title: mouse mammary tumor [063T1]


title: mouse mammary tumor [P03T2]


title: Bud 2

source_name: The second biological replicate of polysomal mRNAs from 'bud" sample

value: LAT52-HF-RPL18 transgenic


title: BPD patient 25


title: mouse mammary tumor [P02T3]


title: mouse mammary tumor [F30T1]

value: F1:C57BL/6 x FVB/N


title: mouse mammary tumor [F29T3]


title: Control 9


title: BPD patient 24


title: Pre-ovulatory female scent stimulation, Dp brain tissue, replicate 6

city: Lisboa

first: José Miguel

last: Simões

address: Rua Jardim do Tabaco 34

department: Eco-Ethology Research Unit

country: Portugal

institute: ISPA - Instituto Universitário

description: Samples from blank stimulations (control) collected from eight different individuals (for both areas) were pooled and aliquoted to be used as reference in a reference based array design

hyb_protocol: A reference and experimental sample were competitively hybridized at 65oC overnight to a 19K A. burtoni cDNA microarray (GEO platform GPL6416) constructed from brain-specific and mixed tissue libraries representing a total of 17,712 cichlid-specific features

scan_protocol: Microarrays were scanned with an Axon 4000B scanner (Axon Instruments) using Genepix 4.0 software (Axon Instruments).

data_processing: Microarray data were processed using the LIMMA software package (v3.12.0; [62] in R (v2.15.0; the R Foundation for Statistical Computing, 2012).  Background-subtracted mean intensities were calculated using the minimum method and further normalized using within-array loess normalization. After this normalization step, Bayesian analysis was used to calculate gene expression levels using the ratios of intensities measured. Finally, to compare between expression profiles for the different olfactory stimulations, unsupervised hierarchical clustering analysis were done using the hclust function in R/Bioconductor.

organism: Oreochromis mossambicus

source_name: Dp Brain, PRE stimuli

label_protocol: mRNA (500 ng) from each experimental sample or reference were reverse transcribed using SuperScript II (Invitrogen) and labeled. Following this reverse transcription, RNA was hydrolyzed and purified before being dye-coupled with Cy3 or Cy5 post-labeling Reactive Dye Pack (Amersham).

growth_protocol: Mixed-sex groups which were kept in tanks with gravel substrate, which promotes nest digging by males and the establishment of territories and social hierarchies, at a temperature of 26 ± 2◦C and a 12L:12D photoperiod. Fish were fed twice daily with commercial cichlid sticks.

treatment_protocol: Dominant males were chemically stimulated with social relevant stimuli while electro-olfactograms measured their electrical activity at the level of the olfactory rosette. After stimulation the fish were killed, their brains dissected and brain samples were microdissected for analysis.

tag: brain tissue

value: Dp

tag: olfactory stimuli

value: pre-ovulatory female scent

source_name: Dp Brain, blank stimuli


title: BPD patient 19


title: Post-ovulatory female scent stimulation, Dp brain tissue, replicate 5

source_name: Dp Brain, POST stimuli

value: post-ovulatory female scent


title: BPD patient 20

source_name: whole blood

value: Male


title: Pre-ovulatory female scent stimulation, Dp brain tissue, replicate 5


title: BPD patient 26


title: 546691A11 - col_BR2 vs mips-cpsf30-complemented_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: How a mutation in the CPSF30 is able to suppress the cell death phenotype observed in the mips1-1 Arabidopsis mutant?

hyb_protocol: mips-cpsf30-complemented_BR2 Cy5 / col_BR2 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media=  hygrometry=60  Temperature=20°C  Light=200 mm/s/cm

treatment_protocol: no treatment

value: rosette

tag: ecotype

value: Columbia

value: (boyes et al. plant cell 2001):boyes:3.50

value: col


title: 546691A09 - col_BR2 vs mips-cpsf30_BR2

hyb_protocol: mips-cpsf30_BR2 Cy5 / col_BR2 Cy3 : 30pmol.

value: mips-cpsf30 mutant


title: 546691A08 - cpsf30_BR2 vs col_BR2

hyb_protocol: col_BR2 Cy5 / cpsf30_BR2 Cy3 : 30pmol.

value: cpsf30 mutant


title: 546691A12 - mips-cpsf30-complemented_BR2 vs col_BR2

hyb_protocol: col_BR2 Cy5 / mips-cpsf30-complemented_BR2 Cy3 : 30pmol.


title: Pre-ovulatory female scent stimulation, Dp brain tissue, replicate 4


title: Bud 1

source_name: The first biological replicate of polysomal mRNAs from 'bud" sample

value: stage 11-12 floral buds

value: pollen grains and tubes


title: 546691A10 - mips-cpsf30_BR2 vs col_BR2

hyb_protocol: col_BR2 Cy5 / mips-cpsf30_BR2 Cy3 : 30pmol.


title: 546691A07 - col_BR2 vs cpsf30_BR2

hyb_protocol: cpsf30_BR2 Cy5 / col_BR2 Cy3 : 30pmol.


title: Pre-ovulatory female scent stimulation, Dp brain tissue, replicate 3


title: Post-ovulatory female scent stimulation, Dp brain tissue, replicate 4


title: 546691A06 - mips-cpsf30-complemented_BR1 vs col_BR1

hyb_protocol: col_BR1 Cy5 / mips-cpsf30-complemented_BR1 Cy3 : 30pmol.


title: Post-ovulatory female scent stimulation, Dp brain tissue, replicate 3


title: BPD patient 10


title: BPD patient 18

value: Female


title: mouse mammary tumor [F29T1]

description: Gene expression data from mammary tumor.

value: mammary tumor


title: BPD patient 16

value: Yes

value: Borderline Personality Disorder (BPD)


title: BPD patient 15


title: 546691A03 - col_BR1 vs mips-cpsf30_BR1

hyb_protocol: mips-cpsf30_BR1 Cy5 / col_BR1 Cy3 : 30pmol.


title: mouse mammary tumor [F29T2]

value: F1:C57BL/6 x FVB/N


title: mouse mammary tumor [F27T1]


title: 546691A04 - mips-cpsf30_BR1 vs col_BR1

hyb_protocol: col_BR1 Cy5 / mips-cpsf30_BR1 Cy3 : 30pmol.


title: Subordinate male urine stimulation, Dp brain tissue, replicate 4

source_name: Dp Brain, SUB stimuli

value: Dp

value: subordinate male urine


title: mouse mammary tumor [P01T1]

value: FVB/N


title: BPD patient 9


title: Post-ovulatory female scent stimulation, Dp brain tissue, replicate 2

value: post-ovulatory female scent


title: 546691A02 - cpsf30_BR1 vs col_BR1

hyb_protocol: col_BR1 Cy5 / cpsf30_BR1 Cy3 : 30pmol.

value: rosette


title: 546691A05 - col_BR1 vs mips-cpsf30-complemented_BR1

hyb_protocol: mips-cpsf30-complemented_BR1 Cy5 / col_BR1 Cy3 : 30pmol.

value: Columbia


title: Pre-ovulatory female scent stimulation, Dp brain tissue, replicate 2

value: pre-ovulatory female scent


title: Dominant male urine stimulation, Dp brain tissue, replicate 5

source_name: Dp Brain, DOM stimuli

value: Dominant male urine


title: mouse mammary tumor [F23T1]


title: BPD patient 13


title: Control 8

value: No

value: Normal (Control)


title: Pre-ovulatory female scent stimulation, Dp brain tissue, replicate 1


title: Cy5-notochord & Cy3-nerve-cord

city: Toba

first: Lixy

last: Yamada

state: Mie

address: 429-63 Sugashima

department: Graduate School of Science,

institute: Nagoya University

hyb_protocol: A set of 1µg fluorescent-labeled cRNA targets from each sample was assembled into a hybridization reaction on the Ciona intestinalis Oligoarray ver.1, using In Situ Hybridization Kit Plus (Agilent Tech.).  Hybridized microarrays were washed according to the manufacture’s protocol.

scan_protocol: Scanned on an Agilent G2565BA Microarray Scanner System.

data_processing: Intensity of probes per array was extracted from scanned microarray images using Feature Extraction software (Agilent Tech. ver.A.7.5.1), which performs background subtraction and dye normalization using the Linear & LOWESS method.  All algorithms and parameters used in this analysis were the default condition of the software.  The Local Background Subtraction Method was used for background subtractions and the Locally Weighted Linear Regression Method (Linear & LOWESS method) for normalization.

organism: Ciona intestinalis

source_name: nerve-chord

label_protocol: Aliquots of total RNA were labeled with either Cy-3 CTP or Cy-5 CTP (Perkin-Elmer/NEN Life Sci.) by two-round linear amplification using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Tech.) as specified by the manufacture. The quality and size distribution of targets were determined by RNA 6000 Nano Lab-on-chip Assay (Agilent Tech.), and quantification was determined using a NanoDrop microscale spectrophotometer (NanoDrop Technologies).

growth_protocol: Adults of Ciona intestinalis were cultivated at the Maizuru Fisheries Research Station of Kyoto University, the Marine Field of Field Science Center.

treatment_protocol: Collection of Ciona intestinalis adults, preparation of eggs and sperm, dechorionation of fertilized eggs, and culture of naked embryos were carried out as described previously. Immediately after the embryo became the 64-cell stage, a block of A7.3+A7.4+A7.7+A7.8 was isolated from the embryo with a fine glass needle under a stereomicroscope.  A7.3+A7.7 look darker due to having abundant yolk granules in the cytoplasm while A7.4+A7.8 have more transparency. Then, a row of A7.3+A7.7 was separated from that of A7.4+A7.8 with a fine glass needle under a stereomicroscope.  The former was smaller in size than the latter.

tag: cell type

value: A7.4 and A7.8 blastomeres

source_name: notochord

value: A7.3 and A7.7 blastomeres


title: Control 7

value: Female


title: Cy3-notochord & Cy5-nerve-cord


title: 557282A04 - cyp715A1_bio3 vs Col0_bio3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: The microarray analysis is part of a project aimed at characterizing the function of the cytochrome P450 CYP715A1 in Arabidopsis thaliana.

hyb_protocol: Col0_bio3 Cy5 / cyp715A1_bio3 Cy3 : 30pmol. (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.

growth_protocol: flower bud - Media: soil, hygrometry:65%, temperature: 21°c jour et 18°C nuit, light: 12h/12h - 80 µmol.m-2.s-1.

value: flower buds

value: columbia

value: boyes:6.30 (Boyes et al. Plant Cell 2001)

value: cyp715A1 mutant


title: Post-challenged AM of SBP-AG

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

description: Alveolar macrophages were purified from BAL fluids by Percoll gradient method and adhesion purification.

data_processing: Quantitative RT-PCR was performed by Roche Light Cylcer LC-480 following the manufacturor's instruction. The data was analyzed by using the ddCT method by using the manufacture provided software (www.SABiosciences.com/pcrarraydataanalysis.php).

source_name: alveolar macrophages

label_protocol: Total 100ng of RNA was reverse-transcribedand by the RT² First Stand Kit (Qiagen).

extract_protocol: Total RNA was extracted from the cells by QIAzol kit (Qiagen).

value: alveolar macrophages

tag: subject

value: Mild asthmatics

tag: status

value: Post-allergen challenge


title: BPD patient 12

hyb_protocol: was carried out by Life & Brain GmbH, Bonn

value: Yes

value: Borderline Personality Disorder (BPD)


title: Pre-challenged AM of SBP-AG

value: Pre-allergen challenge


title: Zebra finch, Entopallium, testosterone, (LD), biological rep6

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

description: Entopallium was dissected from cryosections

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing:
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: E26R1204 Genomatix GmbH (http://www.genomatix.de)
ZF processed data files (ZF_HVc_to_ento.txt, ZF_Testo_HVCvsENTO.txt) on Series record, are the significance results obtained by ChipInspector.
The differential expression was analyzed using the group-wise exhaustive analysis i.e., HVc samples group compare to Ento samples group with False Discovery Rate set to zero and 10-significant probe minimum coverage. These result files consist in the table of transcripts and the fold changes for every data combination, also chromosome location (in TGU), Gene ID, Gene Symbol.
The statistic algorithm in ChipInspector is a T-test with a permuted artificial background. It is based on and enhances the original SAM algorithm by Tusher et al. (2001): Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98(9), pp 5116-5121. Exhaustive matching of the experiments introduces a second level of data volume enhancing. This means it is using the complete set of available data points by matching the values from every condition experiment to the values from every control experiment. This gives the results greater confidence and therefore increases the number of values that are recognized as significant (higher number of significant genes with lower FDR) (http://www.genomatix.de).

organism: Taeniopygia guttata

source_name: Entopallium

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult zebra finches housed in long light cycles in aviaries

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80 C till RNA preparation.

treatment_protocol: Testosterone

value: adult

value: Entopallium

tag: light cycle

value: long day

tag: treatment

value: testosterone


title: Dominant male urine stimulation, Dp brain tissue, replicate 3

value: Dp

value: Dominant male urine


title: 546691A01 - col_BR1 vs cpsf30_BR1

hyb_protocol: cpsf30_BR1 Cy5 / col_BR1 Cy3 : 30pmol.

value: cpsf30 mutant

tag: tissue

value: rosette

value: Columbia

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:3.50

value: col


title: Control 6

value: Female

value: No

value: Normal (Control)


title: BPD patient 11

value: Yes


title: Control 5


title: RU-treated_peri-ovulatory follicle RU-PeF3

city: Osaka

first: Kenjiro

last: Tsubota

address: 1-6, Kashima 2-chome

institute: Astellas Pharma

description: RU486-treated at 10:00, collected at 22:00 on the proestrus day

hyb_protocol: Hybridization and following washing by fluidics were performed with hybridization, wash and stain kit(Affymetrix Inc.), in accordance with the manufacturer's instruction.

scan_protocol: Gene chip  was scanned using GeneChip scanner GCS3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Scaling was not conducted. Signal intensity that was less than 1.0 was set as 1.0. 1st normalization was performed for the median of all probe sets(31099 probe sets) per chip and 2nd normalization was performed for the 1st normalized value per gene by Gene Spring 7.3(Agilent technology.). Statistical anlalysis(volcano plot analysis(welch t-test and 2 fold change)) and hierarchical analysis were performed by Gene Spring 7.3(Agilent technology.).

organism: Rattus norvegicus

source_name: ovarian follicle retrieved by LMD

label_protocol: In vitro transcription with IVT labeling kit(Affymetrix Inc.) generated multiple copies of biotin-labelled aRNA from the double-stranded cDNA templates.

growth_protocol: After 1-week of acclimatization, estrous phases of each animal was determined by vaginal smears for five consecutive days. During the study, animals were handled in accordance with Guidelines for Animal Experimentation issued by Astellas Pharma Inc., which is based on the guidelines for animal experimentation issued by the Japanese Association for Laboratory Animal Science.<br>The animals were sacrificed by exsanguination under anesthesia with ether at 10:00 a.m. on the proestrus day, 10:00 p.m. on the proestrus day, and 10:00 a.m. on the estrus day.

extract_protocol: The ovaries were removed and embedded in OCT (Tissue-Tek, Sakura Finetek, Torrance, CA), frozen in dry-ice-cold isopentan, and stored at -70°C until use. Frozen sections (8-micro-meter thick) were mounted on the membrane slides (MMI, Glatteburg, Zurich, Switzerland), and stained with HistogeneTM LCM frozen section staining kit (Arcturus Engineering, Mountain View, CA). Then, 15 follicles in each phase were retrieved by LMD system (CellCut Plus™, MMI). The collected follicle sections were lysed by the buffer RLT in the collection tube supplied in RNeasy Micro Kit (Qiagen, Hilden, Germany)

treatment_protocol: Animals were singly administered orally 4mg/kg of indomethacin (IM) at 16:00 or 100 mg/kg of RU486 (RU)  at 10:00 on the proestrus day, and sacrificed by exsanguination under anesthesia at 22:00 on the proestrus day (PeF: peri-ovulatory follicle), and 10:00 on the estrus day (PoF: post-ovulatory follicle).

value: peri-ovulatory follicle

value: Crl:CD(SD) rats

value: Ovarian follicle


title: RU-treated_peri-ovulatory follicle RU-PeF2

value: RU486-treated at 10:00, collected at 22:00 on the proestrus day


title: Subordinate male urine stimulation, Dp brain tissue, replicate 3

hyb_protocol: A reference and experimental sample were competitively hybridized at 65oC overnight to a 19K A. burtoni cDNA microarray (GEO platform GPL6416) constructed from brain-specific and mixed tissue libraries representing a total of 17,712 cichlid-specific features

value: subordinate male urine


title: 557282A03 - Col0_bio3 vs cyp715A1_bio3

hyb_protocol: cyp715A1_bio3 Cy5 / Col0_bio3 Cy3 : 30pmol. (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.

value: flower buds

tag: genotype

value: cyp715A1 mutant

value: columbia

value: boyes:6.30 (Boyes et al. Plant Cell 2001)


title: 550543A07 - Col0_bio1 vs cyp715A1_bio1

hyb_protocol: cyp715A1_bio1 Cy5 / Col0_bio1 Cy3 : 30pmol. (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: 557282A02 - cyp715A1_bio2 vs Col0_bio2

hyb_protocol: Col0_bio2 Cy5 / cyp715A1_bio2 Cy3 : 30pmol. (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: Control 4


title: 557282A01 - Col0_bio2 vs cyp715A1_bio2

hyb_protocol: cyp715A1_bio2 Cy5 / Col0_bio2 Cy3 : 30pmol. (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: RU-treated_peri-ovulatory follicle RU-PeF1

tag: strain


title: Post-ovulatory female scent stimulation, Dp brain tissue, replicate 1

value: Dp

value: post-ovulatory female scent


title: Zebra finch, Entopallium, testosterone, (LD), biological rep5

value: adult

value: Entopallium

value: long day

value: testosterone


title: Subordinate male urine stimulation, Dp brain tissue, replicate 1


title: BPD patient 6

tag: gender

value: Female

value: Borderline Personality Disorder (BPD)


title: Subordinate male urine stimulation, Dp brain tissue, replicate 2


title: 550543A08 - cyp715A1_bio1 vs Col0_bio1

hyb_protocol: Col0_bio1 Cy5 / cyp715A1_bio1 Cy3 : 30pmol. (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: Dominant male urine stimulation, Dp brain tissue, replicate 2

value: Dominant male urine


title: Dominant male urine stimulation, Dp brain tissue, replicate 1


title: Zebra finch, Entopallium, testosterone, (LD), biological rep3


title: Subordinate male urine stimulation, OB brain tissue, replicate 6

source_name: OB Brain, SUB stimuli

value: OB

source_name: OB Brain, blank stimuli


title: Pre-ovulatory female scent stimulation, OB brain tissue, replicate 6

source_name: OB Brain, PRE stimuli

value: pre-ovulatory female scent


title: Zebra finch, Entopallium, testosterone, (LD), biological rep2


title: Zebra finch, HVc, testosterone, (LD), biological rep6

description: HVC was dissected from cryosections

source_name: HVC

value: HVC


title: Zebra finch, HVc, testosterone, (LD), biological rep4

description: HVC was dissected from cryosections


title: BPD patient 5

tag: suicide background

value: Yes


title: Zebra finch, Entopallium, testosterone, (LD), biological rep1


title: IM-treated_peri-ovulatory follicle IM-PeF2

description: indomethacin-treated at 16:00, collected at 22:00 on the proestrus day

value: peri-ovulatory follicle

value: Crl:CD(SD) rats

value: Ovarian follicle


title: Control_post-ovulatory follicle C-PoF1

description: non-treated, collected at 10:00 on the estrus day

value: post-ovulatory follicle


title: IM-treated_peri-ovulatory follicle IM-PeF1

value: indomethacin-treated at 16:00, collected at 22:00 on the proestrus day


title: Control 3

value: No

tag: diagnosis

value: Normal (Control)


title: Pre-ovulatory female scent stimulation, OB brain tissue, replicate 4


title: Control_post-ovulatory follicle C-PoF2

value: non-treated, collected at 10:00 on the estrus day


title: L6_3

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

hyb_protocol: 1.65 ug of Cy3-labeled (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 4 - 180 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan settings for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039425_D_F_20120307) to obtain mean Green intensities and median Green background intesities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizion was done.

organism: Folsomia candida

source_name: total RNA from 30 animals

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer's guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil: 20 adult animals were incubated per container; containing a plaster of Paris base mixed with charcoal, to lay eggs for 2 days. The incubation conditions were 20°C, 75% RH and 12:12 hour dark:light cycle

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 days old, were exposed for two days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: sample type

value: field polluted soil


title: Zebra finch, HVc, testosterone, (LD), biological rep5

description: HVC was dissected from cryosections

tag: age

value: adult

value: long day

value: testosterone


title: Dominant male urine stimulation, OB brain tissue, replicate 5

source_name: OB Brain, DOM stimuli

tag: brain tissue

value: Dominant male urine


title: Control_peri-ovulatory follicle C-PeF2

description: non-treated, collected at 22:00 on the proestrus day


title: L4_3


title: IM-treated_peri-ovulatory follicle IM-PeF3


title: BPD patient 17

value: Female

value: Borderline Personality Disorder (BPD)


title: Dominant male urine stimulation, OB brain tissue, replicate 4

value: OB

tag: olfactory stimuli


title: Pre-ovulatory female scent stimulation, OB brain tissue, replicate 5

value: pre-ovulatory female scent


title: Post-ovulatory female scent stimulation, OB brain tissue, replicate 5

source_name: OB Brain, POST stimuli

value: post-ovulatory female scent


title: Zebra finch, HVc, testosterone, (LD), biological rep3

description: HVC was dissected from cryosections

value: HVC


title: Zebra finch, Entopallium, (LD), biological rep5

value: Entopallium

value: No treatment


title: Control_post-ovulatory follicle C-PoF3

value: post-ovulatory follicle

value: Crl:CD(SD) rats

value: Ovarian follicle


title: Post-ovulatory female scent stimulation, OB brain tissue, replicate 6


title: Control_peri-ovulatory follicle C-PeF3

value: peri-ovulatory follicle

value: non-treated, collected at 22:00 on the proestrus day


title: L5_3

value: field polluted soil


title: Zebra finch, HVc, testosterone, (LD), biological rep1

description: HVC was dissected from cryosections

value: adult

value: long day


title: Zebra finch, HVc, testosterone, (LD), biological rep2

description: HVC was dissected from cryosections

value: testosterone


title: L1_3


title: Zebra finch, Entopallium, (LD), biological rep6


title: Pre-ovulatory female scent stimulation, OB brain tissue, replicate 3


title: Pre-ovulatory female scent stimulation, OB brain tissue, replicate 1


title: LUFA_3

value: LUFA2.2 soil


title: Pre-ovulatory female scent stimulation, OB brain tissue, replicate 2


title: Zebra finch, Entopallium, (LD), biological rep4


title: L6_2


title: BN_Mammary_12week_E2_S27_rep2

city: Madison

first: James

last: Shull

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 42°C on Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Log2 values were generated by GCRMA with quantile normalization (R package gcrma version 2.18.1). Microarrays in this series were normalized in conjunction with other microarrays as part of a larger dataset.

source_name: Rat mammary 12 week treatment with 17beta-estradiol

label_protocol: Biotinylated cRNA were prepared from 2.5 ug total RNA using One-cycle Target Labeling Kits (Affymetrix, Santa Clara, CA).

growth_protocol: Original BN rat strain provided by Harlan Sprague Dawley, Inc.

extract_protocol: Absolutely RNA Miniprep Kits (Stratagene, La Jolla, CA) were used to isolate RNA from mammary tissues that were dissected from individual ACI rats that had been treated with 17beta-estradiol for 12 weeks, a time point that precedes development of palpable mammary cancer.

treatment_protocol: The rats were treated continuously with 17beta-estradiol delivered from subcutaneous implants, starting at 9 weeks of age. The rats were euthanized following 12 weeks of 17beta-estradiol treatment and the mammary glands were harvested, frozen in liquid nitrogen and stored at -80° C.

value: Brown Norway

value: 9 wks (at the time of treatment start)

tag: treated with

value: 17beta-estradiol for 12 wks

value: Mammary gland


title: Control_peri-ovulatory follicle C-PeF1


title: Zebra finch, Entopallium, (LD), biological rep3


title: BN_Mammary_12week_E2_S28_rep3


title: L5_2


title: BN_Mammary_12week_E2_S26_rep1


title: BN_Mammary_12week_E2_H5727_rep5


title: Zebra finch, Entopallium, (LD), biological rep2


title: Dominant male urine stimulation, Dp brain tissue, replicate 4

value: Dp

value: Dominant male urine

source_name: Dp Brain, blank stimuli


title: asthma patient-6

city: Changsha

first: Yang

last: Xiang

state: Hunan

address: 110 Xiangya Road

department: Physiology

institute: Central South University

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L22a were spread on each chip.
Biotin-16-dUTP

hyb_protocol: a. Warm the GEAhyb Hybridization Solution(3 ml for each array) to 60 °C to allow complete dissolution of the buffer components.  b. Heat the sheared salmon sperm DNA at 100 °C for 5 min and immediately chill on ice. Add the heat-denatured salmon sperm DNA to the pre-warmed GEAhyb Hybridization Solution to a final concentration of 100 µg/ml. Keep the GEAprehyb solution at 60 °C until needed.  c. Pre-wet the array membrane by adding roughly 5 ml of deionized water to the hybridization tube.  d. Discard the deionized water from the hybridization tube. Add 2 ml of the GEAprehyb solution, and vortex the tube gently for a few seconds.  e. Pre-hybridize in the hybridization oven at 60 °C for 1.5 hours with continuous agitation at 6 rpm.  f. Discard the GEAprehyb from the hybridization tube. Add the entire volume of denatured cDNA probe to 0.75 ml of pre-warmed GEAprehyb. Mix well and hybridize overnight (12 hours) at 60 °C with continuous agitation at 6 rpm.  g. Discard the GEAhyb solution from the hybridization tube. Wash the membrane twice with 5 ml Wash Solution 1 at 60 °C with 30 to 40 rpm agitation for 15 minutes each. Vortex the tube gently with each wash.  h. Discar Wash Solution 1. Wash the membrane twice with 5 ml Wash Solution 2 at 60 °C with 30 to 40 rpm agitation for 15 minutes each. Vortex the tube gently with each wash.

scan_protocol: After discarding the last wash, immediately add 1.5 ml GEAblocking Solution Q. Incubate for 40 min with continuous agitation.   Binding of alkaline phosphatase-conjugated streptavidin (AP)  Prepare Binding Buffer: Dilute 5X Buffer F five-fold to prepare excess 1X Buffer F. Dilute AP 1:7,500 into 1X Buffer F.  Discard the GEAblocking Solution Q from the tube. Add 2 ml Binding Buffer, and incubate for 10 min with continuous but gentle agitation.  Washing: Wash the membrane four times with 4 ml 1X Buffer F for 5 min with gentle agitation. Vortex the tube gently after each addition of fresh 1X Buffer F. Rinse or wash twice with 3 ml Buffer G.  Detection: Add 1.0 ml CDP-Star chemiluminescent substrate to the hybridization tube. Incubate at room temperature for 2 min.  Blot the membrane on a piece of filter paper to remove excess CDP-Star Solution. Place the membrane between two plastic sheets and smooth out any bubbles. Expose it on the X-ray film.  After exposing the membrane to X-ray film, use a desktop scanner to convert the image into a grayscale TIFF file. Be sure to save this file. Convert the image of spots into numerical data using the free ScanAlyze software. Save the raw data as a Microsoft Excel file.

data_processing: Use GEArray Analyzer software for background subtraction and data normalization. Each GEArrayTM Q Series membranes are spotted with negative controls (pUC18 DNA and blanks) and housekeeping genes, including β-actin, GAPDH, cyclophilin A and ribosomal protein L13a. All raw signal intensities should be corrected for background by subtracting the minimum value to avoid the appearance of negative numbers. All signal intensities should also be normalized to that of a housekeeping gene. These corrected, normalized signals can then be used to estimate the relative abundance of particular transcripts.

source_name: peripheral blood leucocytes

label_protocol: 5.0 µg  of total RNA was reverse-transcribed using MMLV Reverse Transcriptase (Promega) in the presence of 2μl Biotin-16-dUTP (1mM)

extract_protocol: RNA was extracted from leucocytes in peripheral blood of 4 normal adults and 6 asthma patients by using TRIzol Reagent.

tag: cell type

value: peripheral blood leucocytes

value: 42 years

tag: Sex

value: Male

value: asthma


title: asthma patient-5

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L21a were spread on each chip.
Biotin-16-dUTP

value: 40 years


title: BN_Mammary_12week_E2_H5726_rep4


title: Post-ovulatory female scent stimulation, OB brain tissue, replicate 4

value: OB

value: post-ovulatory female scent


title: Zebra finch, Entopallium, (LD), biological rep1

value: adult

value: Entopallium

value: No treatment


title: L2_3

value: field polluted soil


title: L3_2


title: Dominant male urine stimulation, OB brain tissue, replicate 3


title: asthma patient-4

description:
This microarray profiles the expression of 96 genes key to the functions of cell adhesion. A negative control (PUC18DNA and blank), and the housekeeping genes including β-actin, GAPDH, Cyclophilin A and ribose body protein L20a were spread on each chip.
Biotin-16-dUTP

value: 65 years


title: Zebra finch, HVc, (LD), biological rep6

description: HVC was dissected from cryosections

value: HVC

value: long day