title: Csac_H2-Csac_N2

first: Robert

last: Kelly

state: MI

address: Campus Box 7905

institute: North Carolina State University

description: log2 ratio of (H2/N2)

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a GenePix 4000B scanner (Molecular Devices) using 532 nm and 635 nm lasers simultaneously. An automatic photomultiplier (PMT) gain adjustment was used to balance the 532 nm and 635 nm channels prior to scanning the whole slide. A pixel size of 10 microns was selected for the image resolution. Separate images were saved for the 532 and 635 nm scans, and analyzed together using  GenePix Pro (v6.0) software.

data_processing: Signals for each channel were obtained using GenePix Pro (v6.0) using circular features and were background substrated using the median local intensity around the spot. Once all the slides were quantitated, data from the dye-flip was analyzed with JMP Genomics 5.0 (SAS, NC), normalized using Lowess then ANOVA to estimate the global fixed effects of dye & treatment and the random effects array and block followed by using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

label: Cy3, Cy5

organism: Caldicellulosiruptor saccharolyticus

source_name: Cell Pellet

label_protocol: Producing cDNA: In a sterile PCR tube add 20 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70 degree C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix. Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III Invitrogen. dNTP mix: 3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) Ambion, 6.8uL nuclease free water. Incubate at 46 degree C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65 degree C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 1,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate at room temp. for 1 min. Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0. Mix up and down with pipette for good mixing. Dissolve and mix thoroughlythe Cy™ dye to be used with 20uL of DMSO. Tpically Cye dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O

growth_protocol: C. saccharolyticus DSM 8903 (also ATCC 43494) was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen. C. saccharolyticus was grown in sterilized modified DSMZ 640 medium containing NH4Cl (0.9 g/L), KH2PO4 (0.75 g/L), K2HPO4 (1.5 g/L), yeast extract (1 g/L), modified trace element solution SL-10 (1 ml/L; van Niel et al. 2002, where MnCl2•4H2O and Na2SeO35H2O were replaced by MnSO4•H2O and SeO2). Resazurin (0.5 mg/L) was added as an redox indicator. Separately sterilized solution of glucose (4 g/L), MgCl2 (0.4 g/L) and cysteine-HCL (0.5 g/L) were added to the medium prior to inoculation with a batch pre-culture (5% v/v). The continuous cultures were glucose-limited unless stated otherwise. Cultivations were performed under anaerobic conditions in a 2-L jacketed bioreactor (Applikon) with a working volume of 1 L and an internal reactor pressure equal to the atmospheric pressure. Fermentations were run at 70°C with a dilution rate of 0.1 h-1. The pH was controlled at 7.0 by automatic addition of 2 N NaOH.

extract_protocol: At each sample point culture broth from the bioreactor was rapidly cooled to 4°C and cells were harvested by centrifugation (4800xg, 20 min at 4 oC). Cell pellets were stored at -80°C. Total RNA was isolated using a modified Trizol (Invitrogen) protocol in combination with an RNAeasy kit (Qiagen). RNA quality was determined with an Experion bioanalyzer (Bio-Rad). The biological replicates were pooled prior to cDNA construction.

treatment_protocol: Samples used for transcriptome analysis were taken under low H2 partial pressure (low PH2) and high PH2 conditions. The low PH2 condition was achieved by sparging the broth with N2 using a stirring speed of 300 rpm, to minimize H2 build-up in the broth. The high PH2 condition was established by flushing the headspace with H2 gas at a lower stirring speed of 50 rpm, to saturate the system with H2. A low stirring speed was maintained to secure mixing and headspace flushing prevented CO2 build-up in the system.

tag: head space

value: High H2 partial pressure (H2)

label: Cy5, Cy3

value: Low H2 partial pressure (N2)


title: YG001-T1

status: Public on Aug 28 2013

type: RNA

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization (see protocols.txt on the series record for full protocol)

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS using R2.12.1 with Loess function in marray v1.20.0, as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., >2^15) in either channel were not considered for the estimation of the LOESS curve.

molecule: total RNA

organism: Mus musculus

label_protocol: robot amplification and labeling v1.0 (see protocols.txt on the series record for full protocol)

extract_protocol: RNA extraction cellLine (Trizol followed by RNeasy, see protocols.txt on the series record for full protocol)

tag: cell type

value: 3T3-L1 undifferentiated

tag: genotype/variation

value: 3T3-L1 mature adipocytes


city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: 1-Adult mouse cardiac mesenchymal progenitor from Atrial, Postmortem.txt

hyb_protocol: Hybridization and washing steps were using Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using DNA MicroArray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 9.5.3 and further analyzed using GeneSpring GX software version 11.0.2. Data were normalized to the 75 th percentile (median).

label_protocol: 250 ng of total RNA was labelled with Cy3 using the Low RNA Fluorecent Linear Amplification Kit PLUS, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: CMPs were cultured on Collagen I coated dish in DMEM/F12 supplemented with 10% FBS, 40 ng/ml bFGF.

extract_protocol: Total RNA was extracted from each samples using the RNeasy Plus Mini Kit (QIAGEN).

tag: strain background

tag: tissue source

value: mouse cardiac mesenchymal progenitor (mCMP)


title: Fetal mHeat-Tg_E16.5_B6_aMHC-GFP

description: 7-Fetal mHeat-Tg_E16.5_B6_aMHC-GFP.txt

source_name: fetal mouse heart

tag: age

value: embryonic day 16.5

tag: tissue

value: Cardiac tissue


title: Monerey Bay Water column B4A

status: Public on Aug 27 2013

type: mixed

city: Boston

first: Jennifer

middle: L

last: Bowen

state: MA

address: 100 Morrissey Blvd

department: Biology

country: USA

institute: University of Massachusetts Boston

description: 1000 ng random priming amplified DNA from Monterey Bay Barrel experiment (acidified D6)

hyb_protocol: hybridization at 65 oC using Contech hybridization solution

scan_protocol: Arrays were scanned on an Agilent High-Resolution C Scanner Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).

molecule: other

organism: synthetic construct

source_name: 20-mer DNA oligo

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa.  The amplified product was post labeled by conjugation of Cy3 to the dUaa

extract_protocol: Bioifilms in the Vineyard Sound experiment were extracting using the MoBio Power Soil DNA extraction kit. Water Column DNA was extracted from filters using the Puregene DNA extraction kit

tag: sample type

value: 20-mer DNA oligo

molecule: genomic DNA

organism: environmental samples

source_name: cells filtered from 1L of seawater from D6 (acidified)

tag: location

value: Monterey Bay Seawater

tag: treatment

value: acidified


title: Monerey Bay Water column B2

description: 1000 ng random priming amplified DNA from Monterey Bay Barrel experiment (ambient D6)

source_name: cells filtered from 1L of seawater from D6 (ambient)

value: ambient


title: Monerey Bay Water column B4


title: Monerey Bay Water column B3

description: 1000 ng random priming amplified DNA from Monterey Bay Barrel experiment (acidified D1)

source_name: cells filtered from 1L of seawater from D1 (acidified)


title: Monerey Bay Water column B1A

description: 1000 ng random priming amplified DNA from Monterey Bay Barrel experiment (ambient D1)

source_name: cells filtered from 1L of seawater from D1 (ambient)


title: Monerey Bay Water column B2A


title: Monerey Bay Water column B3A


title: Monerey Bay Water column B1


title: Vineyard SoundBiofilms W7A

description: 1000 ng random priming amplified DNA from Vineyard Sound acidification experiment (-CO2, +nutrients)

source_name: ~0.5 g biofilm

value: aquarium tank walls

value: ambient plus nutrients


title: Vineyard SoundBiofilms W3A

description: 1000 ng random priming amplified DNA from Vineyard Sound acidification experiment (+CO2, +nutrients)

value: acidified plus nutrients


title: Vineyard SoundBiofilms W6A

description: 1000 ng random priming amplified DNA from Vineyard Sound acidification experiment (-CO2)


description: 2-Adult mouse cardiac mesenchymal progenitor from Ventricle, Postmortem.txt


title: Vineyard SoundBiofilms W2A

description: 1000 ng random priming amplified DNA from Vineyard Sound acidification experiment (+CO2)


title: Vineyard SoundBiofilms W2


title: Vineyard SoundBiofilms W7


title: Vineyard SoundBiofilms W6


title: Vineyard SoundBiofilms W3


title: DH_OE19_FU5

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

description: miRNA

hyb_protocol: Affymetrix Hybridisation oven for 16 hours at 48 deg.C and 60 rpm, Arrays washed using FluidicsScript 450-0003.

scan_protocol: Affymetrix 3000 7G

data_processing: Cel files were analyzed with Partek genomics suite (version 6.5) using RMA background correction, quantile normalization and mean probe summarisation.

label: biotin

organism: Homo sapiens

label_protocol: Genisphere FlashTag Biotin Labelling Kit

growth_protocol: Resistant sublines of KYSE410 (esophageal squamous cell carcinoms) and OE19 (esophageal adenocarcinoma) cell lines were generated using a pulsatile treatment approach which included repetitive treatment of cells with constant concentrations of cisplatin or 5-FU. Briefly, KYSE 410 cells were subjected to a 4-day exposure of 2 μM cisplatin or 5 μM 5-FU, and OE 19 cells were exposed to 5 μM cisplatin or 10 μM 5-FU for 3 days. The medium was not changed during this period, thereby providing a constant exposure to the chemotherapy agent. After removal of the chemotherapy agent, cells were allowed to recover, and then split when reaching approximately 70–80% confluency, followed by the next cycle of chemotherapy. All derived cell lines were shown to have significant resistance to the corresponding chemotherapy agent.

extract_protocol: Cells from the chemotherapy resistant variants and their original cell line were seeded into 6 replicate flasks each. Prior to harvest, resistant cell lines were allowed to grow for at least 24-48 hours in chemotherapy-free medium in order to avoid an acute toxicity response to the respective chemotherapeutic agent. Then, cells were harvested at a confluency of about 80% in TRIzol® (Invitrogen) and total RNA was extracted from the cells according to the manufacturer’s protocol. RNA concentration was measured using UV spectrophotometry (NanoDrop® ND-8000 Spectrophotometer, Thermo Fisher Scientific), and quality determined by visualization of distinct 28S and 18S rRNA species via electrophoresis through a 1% agarose gel. 500ng of total RNA was used for microarray studies.

tag: cell line


title: CRC vs NOR colorectal normal mucosa, patient 108

city: Brest

first: Laurent

last: Corcos

address: 22, Avenue Camille Desmoulins

department: Faculty of Medicine

country: France

institute: INSERM U1078-ECLA

description: colorectal normal mucosa biopsy

hyb_protocol: Labeling with cyanine3-CTP, fragmentation of cRNA, hybridization, and washing were performed according to the manufacturer’s instructions (Agilent).

scan_protocol: Agilent Microarray Scanner: DNA microarray scanner with Surescan High-resolution Technology G2565C

data_processing: Software: GeneSpring GX 11.0.2, Normalization algorithm: Shift to percentile = 75,  Filtered on flags: present at least 75.0% of the values in any 1 out of 2 condition,  Filtered on expression: lower cut-off = 100 in the raw data

source_name: colorectal normal mucosa biopsy sample, patient 108

label_protocol: Double-stranded cDNA was synthesized from 500 ng of total RNA using the Quick Amp Labeling kit, One-color, as instructed by the manufacturer (Agilent).

extract_protocol: Total RNA were extracted with the AllPrep DNA/RNA Mini kit (Qiagen, Courtabœuf, France) from homogenized tissue samples (20 mg), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent, Massy, France) and the 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ≥ 7.0 were used for microarray analyses.

value: normal mucosa

tag: gender

value: male

tag: localisation

value: left colon


title: CRC vs NOR colorectal normal mucosa, patient 120

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 120

value: female

value: right colon


title: CRC vs NOR colorectal normal mucosa, patient 132

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 132

value: cecum


title: CRC vs NOR colorectal normal mucosa, patient 118

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 118

value: right angle


title: CRC vs NOR colorectal normal mucosa, patient 117

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 117


title: CRC vs NOR colorectal normal mucosa, patient 89

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 89

value: rectum / anal canal


title: CRC vs NOR colorectal adenocarcinoma, patient 132

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 132

value: adenocarcinoma


title: CRC vs NOR colorectal adenocarcinoma, patient 108

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 108


title: CRC vs NOR colorectal normal mucosa, patient 115

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 115

value: sigmoid colon


title: embryo_24hpf_mispair_rep2

city: Waterloo

first: Matt

last: Vijayan

state: Ontario

address: 200 University Avenue W

country: Canada

institute: University of Waterloo

description:
24MP2
Gene expression in 24hpf embryos after microinjection of 4.4ng of glucocorticoid receptor mispair control oligonucleotide

hyb_protocol: 1.65 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and  Agilent blocking agent following the manufacturers instructions. Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Oligo Microarrays V2 (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Gene expression was quantified with Agilent Feature Extraction 10.5.1.1.  Green processed signal from the Feature Extraction output was entered into Agilent GeneSpring 7.3.1 for analyis.  Data was normalized by flooring values below 0.05 to 0.05 and normalizing per chip to a set of positive control genes that were selected on the criteria that raw data was above 50 for all samples.

organism: Danio rerio

source_name: whole homogenized embryos_24 hpf_control treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA following the Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol v6 and purified using the Rneasy mini kit (Qiagen) and quantified with a Nanodrop spectrophotometer (Thermo Scientific)

extract_protocol: RNA was extracted from pools of embryos with the RNeasy Mini Kit (Qiagen) with on-column DNAse (Qiagen) treatment to remove genomic DNA contamination. Preliminary RNA quantification was performed via a Nanodrop spectrophotometer (260 nm; Thermo Scientific) and confirmed along with quality assessment by a Agilent 2100 bioanalyzer.

treatment_protocol: Zebrafish embryos were microinjected at the single-cell stage with either: active morpholino designed against the start site of translation for the glucocorticoid receptor transcript (sequence: 5’-CTCCAGTCCTCCTTGATCCATTTTG-3’, 4.4ng in 1nl injection volume) or a mispair control with five changed basepairs (5’-CTCCAGTCCTCCTTGATCCATTTTG-3’, 4.4ng in 1nl injection volume). Pools of 25 embryos were flash frozen at 24 and 36 hpf for RNA extraction. This experiment was repeated three times for three independent replicates.

value: embryo

tag: injected with

value: mispair control oligonucleotide

tag: hours post fertilization (hpf)


title: CRC vs NOR colorectal adenocarcinoma, patient 123

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 123


title: CRC vs NOR colorectal adenocarcinoma, patient 118

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 118


title: CRC vs NOR colorectal adenocarcinoma, patient 86

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 86


title: CRC vs NOR colorectal adenocarcinoma, patient 115

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 115


title: CRC vs NOR colorectal normal mucosa, patient 86

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 86


title: CRC vs NOR colorectal adenocarcinoma, patient 89

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 89


title: CRC vs CRA colorectal adenocarcinoma, patient 132

description: colorectal adenocarcinoma biopsy

extract_protocol: Total RNA were extracted with the AllPrep DNA/RNA Mini kit (Qiagen, Courtabœuf, France) from homogenized tissue samples (20 mg), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent, Massy, France) and the 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ? 7.0 were used for microarray analyses.


title: CRC vs NOR colorectal adenocarcinoma, patient 120

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 120


title: CRC vs CRA colorectal adenocarcinoma, patient 123

description: colorectal adenocarcinoma biopsy


title: CRC vs NOR colorectal adenocarcinoma, patient 117

description: colorectal adenocarcinoma biopsy

source_name: colorectal adenocarcinoma biopsy sample, patient 117


title: CRC vs NOR colorectal normal mucosa, patient 123

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 123


title: CRC vs CRA colorectal adenocarcinoma, patient 89

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenocarcinoma, patient 117

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenocarcinoma, patient 118

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenocarcinoma, patient 120

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenocarcinoma, patient 86

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenocarcinoma, patient 115

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenocarcinoma, patient 108

description: colorectal adenocarcinoma biopsy


title: CRC vs CRA colorectal adenoma, patient 93

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 93

value: adenoma

value: rectum


title: CRC vs CRA colorectal adenoma, patient 84, sample 2

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 84, sample 2


title: ΔIP_rpoBmutant_N967I

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

institute: juntendo university

description:
N315: Pre-MRSA strain carrying a functional mecI encoding mecA gene repressor.
N315P: Penicillinase plasmid-free strain derived from N315.
∆IP: mecI null mutant derived from N315P.
H5 (∆IPH5): rpoB mutant derived from DIP by selection with 8 mg/liter imipenem.

hyb_protocol: Labeled samples were hybridized onto the microarray at 50°C for 16-20 hr. After hybridization, the arrays were washed in the following buffers, and dry by spin slide. 2X SSC/0.05% SDS, for 15 min 0.2X SSC/0.05% SDS, for 15 min 0.5X SSC, for 3 min 0.2X SSC, for 3 min

scan_protocol: Nimblegen

data_processing:
Software: NimbleScan
Algorithm: Robust Multi-Array Analysis (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Biostatistics. 2003 Apr;4(2):249-64 (PMID 12925520)).
Normalize: global normalization

organism: Staphylococcus aureus

label_protocol: SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).

extract_protocol:
See reference:
Neoh HM, et al.: Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob Agents Chemother. 2008 Jan;52(1):45-53.

tag: background strain

value: ΔIP

tag: genotype

value: rpoB mutation (selection with 8 mg/liter imipenem)

source_name: ΔIP

tag: strain

value: wild-type


title: CRC vs CRA colorectal adenoma, patient 84, sample 1

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 84, sample 1


title: Low25 [time course]

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: female

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used May, 2010.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) at 100% PMT (Agilent Microarray Scanner with SureScan Technology).  Agilent Feature Extraction Software (v10.7)  calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Loess Normalization with filtered intensities applied Low115 (at 3.3) to remove effect of a hybridization bubble

organism: Pimephales promelas

source_name: liver; FHMsexually regressed

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Trizol protocol for total RNA

tag: dose

value: 29 ng/L

tag: agent

value: phenanthrene

tag: time point

value: 48 hr


title: Cntl62 [time course]

description: female

value: 0 ng/L

value: 72 hr

value: female


title: Low115 [time course]

description: female

value: 24 hr


title: Low69 [time course]

description: female


title: Cntl5 [time course]

description: female


title: Cntl55 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 78

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 78


title: CRC vs CRA colorectal adenoma, patient 44

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 44

value: male


title: CRC vs CRA colorectal adenoma, patient 35

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 35


title: Cntl95 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 53

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 53


title: Cntl4 [time course]

description: female


title: Low26 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 103

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 103

value: left colon


title: Low24 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 37

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 37

value: right colon


title: Low74 [time course]

description: female


title: Cntl7 [time course]

description: female


title: Low23 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 18

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 18


title: CRC vs CRA colorectal adenoma, patient 82

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 82

value: sigmoid colon


title: CRC vs CRA colorectal adenoma, patient 17

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 17

value: rectosigmoid junction


title: Low22 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 94

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 94

value: adenoma

value: cecum


title: Vineyard SoundBiofilms W6

source_name: Universal Internal Standard + 70-mer

source_name: ~0.5 g biofilm

value: Monterey Bay Seawater

value: ambient


title: Vineyard SoundBiofilms W7

value: ambient plus nutrients


title: CRC vs CRA colorectal adenoma, patient 79

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 79


title: CRC vs CRA colorectal adenoma, patient 15

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 15


title: Low107 [time course]

description: female

value: 29 ng/L


title: CRC vs CRA colorectal adenoma, patient 72

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 72

value: bauhin's valve


title: CRC vs CRA colorectal adenoma, patient 74

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 74


title: Vineyard SoundBiofilms W3

value: acidified plus nutrients


title: Monerey Bay Water column B4

source_name: cells filtered from 1L of seawater from D6 (acidified)

value: aquarium tank walls

value: acidified


title: Vineyard SoundBiofilms W2


title: Low116 [time course]

description: female

source_name: liver; FHMsexually regressed

value: phenanthrene

value: female


title: Monerey Bay Water column B3

source_name: cells filtered from 1L of seawater from D1 (acidified)


title: Monerey Bay Water column B2

source_name: cells filtered from 1L of seawater from D6 (ambient)


title: Monerey Bay Water column B1

source_name: cells filtered from 1L of seawater from D1 (ambient)


title: Low70 [time course]

description: female

value: 72 hr


title: CRC vs CRA colorectal adenoma, patient 70

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 70

value: male


title: Cntl92 [time course]

description: female

value: 0 ng/L

value: 24 hr


title: CRC vs CRA colorectal adenoma, patient 54

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 54

value: sigmoid colon


title: Cntl54 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 91

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 91

value: adenoma

value: rectosigmoid junction


title: Cntl6 [time course]

description: female

value: 48 hr


title: CRC vs CRA colorectal adenoma, patient 60

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 60

value: rectum


title: Low114 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 58

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 58

value: transversal colon


title: Cntl3 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 132

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 132

value: cecum


title: Low75 [time course]

description: female

value: 29 ng/L


title: Cntl103 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 95

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 95


title: CRC vs CRA colorectal adenoma, patient 86

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 86

value: right colon


title: CRC vs CRA colorectal adenoma, patient 83

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 83


title: Low111 [time course]

description: female


title: Cntl59 [time course]

description: female


title: CRC vs CRA colorectal adenoma, patient 80

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 80


title: N315_rpoBmutant_N967I

description:
Three replicates
test1 : _2013-02-15_5320001.pair , _2013-02-15_6350001.pair
test2 : _2013-02-15_5320002.pair , _2013-02-15_6350002.pair
test3 : _2013-02-15_5320003.pair , _2013-02-15_6350003.pair

scan_protocol: Nimblegen MS200

value: rpoB mutation (N976I)

value: wild-type


title: Negative control-shRNA exprssing HL60, PMA 3day, rep1

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

description: Expression profiles of HL60cells expressing control shRNA (PMA 3d)

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Array as a standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: CHP and CEL files were obtained using an Affymetrix GCOS software packaging.

source_name: Total RNA from HL60-derivatives expressing negative control shRNA, PMA for 3d

label_protocol: Biotinylated cRNA were prepared using GeneChip 3'IVT Express kits according to the standard Affymetrix protocol from 100 ng of total RNA.

growth_protocol: RPMI1640 supplemented with 10%FCS, 37C, 5%CO2 Passage: three times/week

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

treatment_protocol: HL60 derivatives expressing shRNAs were cultured in the presence of PMA (30nM) for 0, 1, 2 and 3 days.

tag: transduction

value: negative control shRNA

value: phorbol 12-myristate 13-acetate

tag: duration

value: 3 days

tag: pretreatment(dose)


title: Low25 loess normalized

description: female

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used April 2012

data_processing: Normalized signal intensity provided here is Loess Normalization with filtered intensities in Med36 (set at 0.9) to remove effect of hybridization bubble

source_name: Liver; FHM 48hr exposure

value: phenanthrene

value: female


title: CRC vs CRA colorectal adenoma, patient 71

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 71

tag: tissue

value: male


title: Negative control-shRNA exprssing HL60, PMA 3day, rep2


title: Negative control-shRNA exprssing HL60, PMA 2day, rep3

description: Expression profiles of HL60cells expressing control shRNA (PMA 2d)

source_name: Total RNA from HL60-derivatives expressing negative control shRNA, PMA for 2d

value: 2 days


title: Med36 loess normalized

description: female


title: Negative control-shRNA exprssing HL60 rep2

description: Expression profiles of HL60cells expressing control shRNA

source_name: Total RNA from HL60-derivatives expressing negative control shRNA

value: 0 day


title: CRC vs CRA colorectal adenoma, patient 69

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 69

value: adenoma

value: rectosigmoid junction


title: Negative control-shRNA exprssing HL60 rep3


title: Negative control-shRNA exprssing HL60, PMA 1day, rep1

description: Expression profiles of HL60cells expressing control shRNA (PMA 1d)

source_name: Total RNA from HL60-derivatives expressing negative control shRNA, PMA for 1d

value: 1 day


title: Negative control-shRNA exprssing HL60, PMA 2day, rep2


title: Negative control-shRNA exprssing HL60, PMA 2day, rep1


title: Negative control-shRNA exprssing HL60, PMA 1day, rep2


title: Negative control-shRNA exprssing HL60, PMA 1day, rep3


title: Negative control-shRNA exprssing HL60, PMA 3day, rep3


title: CRC vs CRA colorectal adenoma, patient 73

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 73

value: left colon


title: Cntl5 loess normalized

description: female

value: 0 ng/L


title: CRC vs CRA colorectal adenoma, patient 42

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 42

value: sigmoid colon


title: HFD, 12weeks, replicate 8

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

description:
HFD_12wk 8
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturer's procedure using the Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequentially following Agilent's recommendations and finally covered with Ozone-barrier slides.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.5.5.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106 (PMID 14570982)) based on the Cy3-reference pool, and log2 transformed.

source_name: epididymal white adipose tissue, HFD, 12 weeks

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis. The cDNA was split into two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent Low RNA Input Fluorescent Linear Amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010 (PMID 20472610)).

extract_protocol: Total RNA was isolated from epididymal white adipose tissue using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer's instructions. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with the Experion automated electrophoresis system (BioRad).

treatment_protocol: Animals were fed a purified high-fat diet (HDF) or low-fat diet (LFD); diets are published elsewhere (Hoevenaars et al., Genes Nutrition 2012 (PMID 22228221)). All  groups received the diet ad-libitum during 5 days or 12 weeks intervention. Animals were fasted for 2 hr prior to anaesthetization and sacrification.

value: wildtype

tag: developmental stage

value: adult

value: epididymal white adipose

value: high-fat diet

tag: treatment duration

value: 12 weeks

source_name: Reference pool of all samples

tag: sample type

value: reference


title: USP2-shRNA exprssing HL60, PMA 3day, rep1

description: Expression profiles of HL60cells expressing shRNA for USP2  (PMA 3d)

source_name: Total RNA from HL60-derivatives expressing USP2shRNA, PMA for 3d

value: USP2 shRNA

tag: treatment

value: phorbol 12-myristate 13-acetate

value: 3 days


title: HFD, 12weeks, replicate 10

description:
HFD_12wk 10
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: gender

value: male


title: Negative control-shRNA exprssing HL60 rep1

value: negative control shRNA

value: 0 day


title: USP2-shRNA exprssing HL60, PMA 3day, rep3


title: Cntl96 [time course]

description: female

source_name: liver; FHMsexually regressed

value: 24 hr

value: female


title: HFD, 12weeks, replicate 9

description:
HFD_12wk 9
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: High44 loess normalized

description: female

value: phenanthrene


title: CRC vs CRA colorectal adenoma, patient 34

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 34

value: adenoma

tag: localisation


title: Low23 loess normalized

description: female

value: 29 ng/L


title: Med27 loess normalized

description: female


title: USP2-shRNA exprssing HL60, PMA 2day, rep2

description: Expression profiles of HL60cells expressing shRNA for USP2  (PMA 2d)

source_name: Total RNA from HL60-derivatives expressing USP2shRNA, PMA for 2d

value: 2 days


title: USP2-shRNA exprssing HL60, PMA 2day, rep3


title: CRC vs CRA colorectal adenoma, patient 24

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 24

value: right colon


title: CRC vs CRA colorectal adenoma, patient 129

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 129

value: left colon


title: USP2-shRNA exprssing HL60, PMA 1day, rep2

description: Expression profiles of HL60cells expressing shRNA for USP2  (PMA 1d)

source_name: Total RNA from HL60-derivatives expressing USP2shRNA, PMA for 1d

value: 1 day


title: HFD, 12weeks, replicate 7

description:
HFD_12wk 7
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype

value: adult

value: epididymal white adipose

value: high-fat diet

value: 12 weeks


title: HFD, 12weeks, replicate 6

description:
HFD_12wk 6
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: male

value: reference


title: HFD, 12weeks, replicate 5

description:
HFD_12wk 5
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Cntl4 loess normalized

description: female

source_name: Liver; FHM 48hr exposure

value: 0 ng/L


title: USP2-shRNA exprssing HL60, PMA 1day, rep1

value: USP2 shRNA

value: phorbol 12-myristate 13-acetate


title: USP2-shRNA exprssing HL60, PMA 3day, rep2

value: 3 days


title: CRC vs CRA colorectal adenoma, patient 14

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 14

value: adenoma

value: rectum


title: USP2-shRNA exprssing HL60, PMA 1day, rep3


title: High42 loess normalized

description: female

value: phenanthrene

value: female


title: CRC vs CRA colorectal adenoma, patient 106

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 106

value: left colon


title: Cntl63 [time course]

description: female

value: 72 hr


title: Low26 loess normalized

description: female

value: 29 ng/L


title: USP2-shRNA exprssing HL60, PMA 2day, rep1

value: 2 days


title: Med35 loess normalized

description: female


title: HFD, 12weeks, replicate 4

description:
HFD_12wk 4
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype

value: adult

value: epididymal white adipose


title: HFD, 12weeks, replicate 2

description:
HFD_12wk 2
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: male

value: high-fat diet

value: 12 weeks


title: mTAG_sperm_89C

type: genomic

city: Toronto

first: Viviane

last: Labrie

address: 250 College st.

institute: Centre for Addiction and Mental Health

description:
label: mTAG
mTAG
Samples were enriched with mTAG-click (25% labelling efficiency). The resulting files were obtained after quantile normalization, subtraction of total input and kernel based smoothing of each sample. The probe coordinates map to hg19.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

source_name: Sperm

label_protocol: standard Affymetrix protocol

extract_protocol: not specified

tag: cell type

value: Sperm

tag: sample source

value: Petronis Lab Sperm Collection

tag: sample id

tag: method

value: mTAG-click

tag: outlier

value: NO


title: mTAG_sperm_89B


title: mTAG_sperm_89A


title: CRA vs NOR colorectal normal mucosa, patient 89

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 89

value: normal mucosa

value: rectum / anal canal


title: USP2-shRNA exprssing HL60 rep2

description: Expression profiles of HL60cells expressing shRNA for USP2

source_name: Total RNA from HL60-derivatives expressing USP2shRNA

value: USP2 shRNA

value: phorbol 12-myristate 13-acetate

value: 0 day


title: CRC vs CRA colorectal adenoma, patient 12

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 12

value: adenoma

value: cecum


title: USP2-shRNA exprssing HL60 rep3


title: HFD, 12weeks, replicate 3

description:
HFD_12wk 3
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: strain

tag: genotype

value: wildtype

value: reference


title: CRA vs NOR colorectal normal mucosa, patient 86

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 86

value: female

value: right colon


title: High41 loess normalized

description: female

tag: dose

tag: agent

value: phenanthrene


title: Cntl7 loess normalized

description: female

value: 0 ng/L


title: Med38 loess normalized

description: female


title: USP2-shRNA exprssing HL60 rep1

tag: transduction

tag: duration

tag: pretreatment(dose)


title: HFD, 5days, replicate 10

description:
HFD_5d 10
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: epididymal white adipose tissue, HFD, 5 days

value: male

tag: developmental stage

value: adult

tag: tissue

value: epididymal white adipose

value: high-fat diet

tag: treatment duration

value: 5 days


title: mTAG_sperm_111B

value: Sperm

value: Petronis Lab Sperm Collection

value: mTAG-click

value: NO


title: HFD, 5days, replicate 9

description:
HFD_5d 9
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: gender

tag: treatment

source_name: Reference pool of all samples

tag: sample type


title: CRA vs NOR colorectal normal mucosa, patient 123

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 123

value: normal mucosa

tag: localisation


title: mTAG_sperm_111A

tag: cell type

tag: sample source

tag: sample id


title: mTAG_sperm_117C

tag: method

tag: outlier


title: Low24 loess normalized

description: female

tag: dose

value: 29 ng/L


title: mTAG_sperm_111C


title: HFD, 12weeks, replicate 1

description:
HFD_12wk 1
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: epididymal white adipose tissue, HFD, 12 weeks

tag: strain

tag: genotype

value: wildtype

value: 12 weeks


title: CRA vs NOR colorectal normal mucosa, patient 132

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 132

value: female

value: cecum


title: CRA vs NOR colorectal normal mucosa, patient 120

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 120

value: right colon


title: HFD, 5days, replicate 7

description:
HFD_5d 7
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: reference


title: CRA vs NOR colorectal normal mucosa, patient 118

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 118

value: male

value: right angle


title: HFD, 5days, replicate 8

description:
HFD_5d 8
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: adult

value: epididymal white adipose


title: mTAG_sperm_117B


title: CRA vs NOR colorectal normal mucosa, patient 117

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 117


title: CRA vs NOR colorectal normal mucosa, patient 115

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 115

value: sigmoid colon


title: mTAG_sperm_95C

value: Sperm


title: Med32 loess normalized

description: female

source_name: Liver; FHM 48hr exposure

tag: agent

value: phenanthrene


title: HFD, 5days, replicate 6

description:
HFD_5d 6
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: high-fat diet

value: 5 days


title: Low22 loess normalized

description: female


title: HFD, 5days, replicate 5

description:
HFD_5d 5
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: High46 loess normalized

description: female


title: mTAG_sperm_95B

value: Petronis Lab Sperm Collection

value: mTAG-click

value: NO


title: mTAG_sperm_117A


title: HFD, 5days, replicate 3

description:
HFD_5d 3
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype


title: High45 loess normalized

description: female

value: female


title: mTAG_sperm_95A


title: mTAG_sperm_37C


title: HFD, 5days, replicate 4

description:
HFD_5d 4
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Cntl3 loess normalized

description: female

value: 0 ng/L


title: CRA vs NOR colorectal normal mucosa, patient 108

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample, patient 108

value: normal mucosa

value: left colon


title: mTAG_sperm_37B


title: mTAG_sperm_37A


title: LFD, 12weeks, replicate 10

description:
LFD_12wk 10
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: epididymal white adipose tissue, LFD, 12 weeks

value: male

value: low-fat diet

value: 12 weeks

value: reference


title: HFD, 5days, replicate 2

description:
HFD_5d 2
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: adult

value: epididymal white adipose


title: CRA vs NOR colorectal adenoma, patient 95

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 95

value: adenoma

value: rectum


title: mTAG_brain_1071C

source_name: Brain

value: Brain

value: Harvard Brain Tissue Resource Centre


title: HFD, 5days, replicate 1

description:
HFD_5d 1
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: high-fat diet

value: 5 days


title: CRA vs NOR colorectal adenoma, patient 83

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 83

value: right colon


title: CRA vs NOR colorectal adenoma, patient 86

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 86

value: female


title: mTAG_brain_1071B

value: mTAG-click

value: NO


title: LFD, 12weeks, replicate 9

description:
LFD_12wk 9
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype


title: Cntl6 loess normalized

description: female

value: 0 ng/L


title: LFD, 12weeks, replicate 8

description:
LFD_12wk 8
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: male

value: low-fat diet


title: CRA vs NOR colorectal adenoma, patient 80

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 80

value: rectosigmoid junction


title: LFD, 12weeks, replicate 7

description:
LFD_12wk 7
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: adult

value: 12 weeks

value: reference


title: mTAG_brain_1071A

description:
label: mTAG
mTAG
Samples were enriched with mTAG-click (25% labelling efficiency). The resulting files were obtained after quantile normalization, subtraction of total input and kernel based smoothing of each sample. The probe coordinates map to hg19.


title: CRA vs NOR colorectal adenoma, patient 91

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 91

value: adenoma


title: CRA vs NOR colorectal adenoma, patient 69

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 69


title: LFD, 12weeks, replicate 5

description:
LFD_12wk 5
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: epididymal white adipose

source_name: Reference pool of all samples


title: mTAG_brain_1030C

value: Brain

value: Harvard Brain Tissue Resource Centre


title: CRA vs NOR colorectal adenoma, patient 73

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 73

value: left colon


title: LFD, 12weeks, replicate 6

description:
LFD_12wk 6
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: mTAG_brain_1030B


title: CRA vs NOR colorectal adenoma, patient 71

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 71

value: rectum


title: whole lung RNA, adiponectin deficient mouse, ozone exposed, male replicate 1

first: Stephanie

middle: A

last: Shore

address: 665 Huntigton Av Bld1 room 307

department: Environmental Health

institute: Harvard School of Public Health

description: gene expression data from lung of an adiponectin deficient male mouse exposed to ozone for 72 h

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to Affymetrix 430A 2.0 mouse expression array chips

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 450, and scanned in the Affymetrix 3000 7G scanner

data_processing: Expression values were computed from .cel files using Robust Microarray Analysis (RMA).  Log (base 2) expression values were imported into dCHIP for statistical analysis.

source_name: exposure: ozone (0.3 ppm) for 72 hours

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: male and female mice (average age 14 weeks) that were either wildtype (C57BL/6) or genetically deficient in adiponectin

extract_protocol: The left lung was homogenized and total RNA purified using an RNeasy Column kit (Qiagen, Valencia, CA) according to the manufacturer's specifications.

treatment_protocol: Mice were exposed for 72 h to either room air or ozone (0.3 ppm).  Immediately after exposure, mice were euthanized with an overdose of sodium pentobarbital and the lungs were excised and placed in RNAlater.  24 h later, the lung tissue was removed from RNAlater, placed in a clean tube and  frozen at -80oC until extracted.

tag: background strain

value: lung

tag: exposure

value: ozone (0.3 ppm) for 72 hours

value: adiponectin deficient


title: LFD, 12weeks, replicate 4

description:
LFD_12wk 4
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype

tag: developmental stage

tag: tissue


title: LFD, 12weeks, replicate 3

description:
LFD_12wk 3
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: gender

tag: treatment duration


title: mTAG_brain_1030A

value: mTAG-click

value: NO


title: whole lung RNA, wildtype mouse, ozone exposed, female replicate 1

description: gene expression data from lung of a female wildtype mouse exposed to room air for 72 h

value: female

value: wild type


title: LFD, 12weeks, replicate 2

description:
LFD_12wk 2
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: male

value: adult

tag: treatment

value: low-fat diet

tag: sample type


title: CRA vs NOR colorectal adenoma, patient 34

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 34

value: adenoma

tag: localisation

value: sigmoid colon


title: whole lung RNA, wildtype mouse, ozone exposed, male replicate 2

description: gene expression data from lung of a male wildtype mouse exposed to ozone for 72 h


title: whole lung RNA, adiponectin deficient mouse, ozone exposed, male replicate 2


title: whole lung RNA, adiponectin deficient mouse, ozone exposed, female replicate 2

description: gene expression data from lung of an adiponectin deficient female mouse exposed to ozone for 72 h


title: whole lung RNA, adiponectin deficient mouse, air exposed, female replicate 2

description: gene expression data from lung of an adiponectin deficient female mouse exposed to room air for 72 h

source_name: exposure: room air for 72 hours

value: room air for 72 hours


title: mTAG_brain_1018C

value: Brain

tag: sample source

value: Harvard Brain Tissue Resource Centre


title: whole lung RNA, wildtype mouse, ozone exposed, female replicate 2

description: gene expression data from lung of a female wildtype mouse exposed to ozone for 72 h


title: LFD, 12weeks, replicate 1

description:
LFD_12wk 1
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: epididymal white adipose

value: 12 weeks

value: reference


title: mTAG_brain_1018B

tag: sample id


title: CRA vs NOR colorectal adenoma, patient 42

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 42


title: CRA vs NOR colorectal adenoma, patient 24

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 24

value: right colon


title: whole lung RNA, wildtype mouse, ozone exposed, male replicate 1

value: lung

value: ozone (0.3 ppm) for 72 hours


title: whole lung RNA, adiponectin deficient mouse, ozone exposed, female replicate 1

value: adiponectin deficient


title: LFD, 5days, replicate 10

description:
LFD_5d 10
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: epididymal white adipose tissue, LFD, 5 days

value: wildtype

value: 5 days


title: MeDIP_sperm_89C

description:
label: MeDIP
MeDIP
The resulting files were obtained after quantile normalization, subtraction of total input and kernel based smoothing of each sample. The probe coordinates map to hg19.

source_name: Sperm

tag: cell type

value: Sperm

value: Petronis Lab Sperm Collection

tag: method

value: MeDIP

value: NO


title: MeDIP_sperm_89B

tag: outlier


title: CRA vs NOR colorectal adenoma, patient 12

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 12

value: adenoma

value: male

value: cecum


title: mTAG-P01-Brain_mTAGLMWGA_A8

description:
label: mTAG-non labelled
mTAG

source_name: Brain

value: fetal lung

value: Harvard Brain Tissue Resource Centre

value: mTAG


title: CRA vs NOR colorectal adenoma, patient 129

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 129

value: female

value: left colon


title: CRA vs NOR colorectal adenoma, patient 106

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 106


title: whole lung RNA, adiponectin deficient mouse, air exposed, female replicate 1

value: lung

value: room air for 72 hours


title: CRA vs NOR colorectal adenoma, patient 14

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 14

value: rectum


title: MeDIP_sperm_89A


title: whole lung RNA, adiponectin deficient mouse, air exposed, male replicate 2

description: gene expression data from lung of an adiponectin deficient male mouse exposed to room air for 72 h

value: adiponectin deficient


title: LFD, 5days, replicate 8

description:
LFD_5d 8
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: strain

value: wildtype

value: adult

value: epididymal white adipose

value: low-fat diet

value: 5 days

value: reference


title: mTAG-P01-Brain_mTAGLMWGA_A4

description:
label: mTAG-non labelled
mTAG

value: NO


title: whole lung RNA, adiponectin deficient mouse, air exposed, male replicate 1

value: male

tag: genotype


title: CRA vs NOR colorectal adenoma, patient 93

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 93

value: adenoma


title: mTAG_brain_1018A

description:
label: mTAG
mTAG
Samples were enriched with mTAG-click (25% labelling efficiency). The resulting files were obtained after quantile normalization, subtraction of total input and kernel based smoothing of each sample. The probe coordinates map to hg19.

value: Brain

value: Harvard Brain Tissue Resource Centre

value: mTAG-click


title: whole lung RNA, wildtype mouse, air exposed, female replicate 2

value: female

value: wild type


title: LFD, 5days, replicate 6

description:
LFD_5d 6
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: LFD, 5days, replicate 9

description:
LFD_5d 9
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: LFD, 5days, replicate 5

description:
LFD_5d 5
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: CRA vs NOR colorectal adenoma, patient 82

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 82

value: sigmoid colon


title: whole lung RNA, wildtype mouse, air exposed, male replicate 1

description: gene expression data from lung of a male wildtype mouse exposed to room air for 72 h

value: lung

value: room air for 72 hours


title: CRA vs NOR colorectal adenoma, patient 84, sample 2

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 84, sample 2


title: whole lung RNA, wildtype mouse, air exposed, male replicate 2


title: mTAG-P01-Brain_mTAGLMWGA_A12

description:
label: mTAG-non labelled
mTAG

value: fetal lung

value: mTAG


title: CRA vs NOR colorectal adenoma, patient 84, sample 1

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 84, sample 1

value: left colon


title: MeDIP_sperm_111B

value: Sperm

value: Petronis Lab Sperm Collection

value: MeDIP


title: MeDIP_sperm_111C

value: NO


title: mTAG-P01-Brain_mTAGLMWGA_A7array2

description:
label: mTAG
mTAG


title: whole lung RNA, wildtype mouse, air exposed, female replicate 1


title: LFD, 5days, replicate 4

description:
LFD_5d 4
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype

value: male

value: adult

value: epididymal white adipose

value: low-fat diet

value: 5 days

source_name: Reference pool of all samples

value: reference


title: CRA vs NOR colorectal adenoma, patient 78

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 78

value: adenoma

value: female

value: rectum


title: LFD, 5days, replicate 7

description:
LFD_5d 7
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: LFD, 5days, replicate 2

description:
LFD_5d 2
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: mTAG-P01-Brain_mTAGLMWGA_A6array2

description:
label: mTAG
mTAG

value: fetal lung

value: Harvard Brain Tissue Resource Centre


title: MeDIP_sperm_117B


title: CRA vs NOR colorectal adenoma, patient 37

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 37

value: right colon


title: MeDIP_sperm_117C

value: Sperm


title: mTAG-P01-Brain_mTAGLMWGA_A5

description:
label: mTAG
mTAG

value: mTAG


title: CRA vs NOR colorectal adenoma, patient 44

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 44

value: sigmoid colon


title: MeDIP_sperm_95C

value: Petronis Lab Sperm Collection

value: MeDIP

value: NO


title: mTAG-P01-Brain_mTAGLMWGA_A1

description:
label: mTAG
mTAG


title: mTAG-P01-Brain_mTAGLMWGA_A3

description:
label: mTAG
mTAG


title: mTAG-P01-Brain_mTAGLMWGA_A9array2

description:
label: mTAG
mTAG


title: LFD, 5days, replicate 1

description:
LFD_5d 1
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: wildtype

value: male

value: adult


title: CRA vs NOR colorectal adenoma, patient 35

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 35


title: MeDIP_sperm_95A


title: mTAG-P01-Brain_mTAGLMWGA_A11

description:
label: mTAG
mTAG


title: CRA vs NOR colorectal adenoma, patient 53

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 53


title: MeDIP_sperm_111A


title: 6h_USP2KD_treated_2

description: 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells, 6h, biological rep 2

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4852A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid:028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized signal intensity calculated using GeneSpring 12.1GX. Setting is : Advanced Flag Import (Feature is not positive and significant, Not Detected; Feature in not Uniform, Compromised; Feature is not above background, Not Detected; Feature is Saturated, Compromised; Feature is a population outlier, Compromised), Normalization Option (Threshold raw signals to 1.0; Normaliation algorithm, Percentile Shift; Percentile target, 75), Preprocess Baseline Options (Do not perform baseline transformation)

source_name: differentated 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells for 6 hrs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp WT Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: 3T3-L1 cells were grown in DMEM  with 10% FCS. For differentiation into adipocyte-like cells, we cultured the cells in the adipogenic medium (Takara) for 1 week.

extract_protocol: Total cellular RNA was prepared with TRIzol reagent according to a manual.

treatment_protocol: After differentiation, 3T3-L1 cells were treated with 2-fold diluted supernatant with supernatants of USP2 knockdown or mock transfected HL-60 cells for 3 or 6 hrs.  Supernatants were prepared from 5 day culture of USP2 knockdown or control cells in Opti medium (Invitrogen) with 30nM PMA

tag: cell line

value: adipocytes


title: MeDIP_sperm_37C

source_name: Sperm


title: mTAG-P01-Brain_mTAGLMWGA_A10

description:
label: mTAG
mTAG


title: LFD, 5days, replicate 3

description:
LFD_5d 3
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: epididymal white adipose tissue, LFD, 5 days

value: epididymal white adipose

value: low-fat diet

value: 5 days

value: reference


title: MeDIP_sperm_117A


title: CRA vs NOR colorectal adenoma, patient 15

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 15

value: adenoma

value: female


title: mTAG-P01-Brain_Input_1099_mTAG

description:
label: input
total input (unenriched)

source_name: Brain

value: fetal lung

value: Harvard Brain Tissue Resource Centre


title: MeDIP_sperm_37B

value: Sperm


title: MeDIP_sperm_37A


title: CRA vs NOR colorectal adenoma, patient 103

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 103

value: left colon


title: CRA vs NOR colorectal adenoma, patient 94

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 94

value: cecum


title: CRA vs NOR colorectal adenoma, patient 18

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 18

value: rectum


title: mTAG-P01-Brain_Input_1064_mTAG

description:
label: input
total input (unenriched)

value: mTAG

value: NO


title: CRA vs NOR colorectal adenoma, patient 17

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 17

value: male

value: rectosigmoid junction


title: 6h_USP2KD_treated_1

description: 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells, 6h, biological rep 1

value: adipocytes


title: MeDIP_brain_1071C

description:
label: MeDIP
Brain
The resulting files were obtained after quantile normalization, subtraction of total input and kernel based smoothing of each sample. The probe coordinates map to hg19.

value: Brain

value: MeDIP


title: 3h_USP2KD_treated_2

description: 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells, 3h, biological rep 2

source_name: differentated 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells for 3 hrs


title: mTAG-click-chip_c1128

value: mTAG-click


title: MeDIP_brain_1030A


title: 6h_control_treated_2

description: 3T3-L1 cells stimulated with supernatant of control vector-transfected HL-60 cells, 6h, biological rep 2

source_name: differentated 3T3-L1 cells stimulated with supernatant of mock-transfected HL-60 cells for 6 hrs


title: 6h_control_treated_1

description: 3T3-L1 cells stimulated with supernatant of control vector-transfected HL-60 cells, 6h, biological rep 1


title: 3h_USP2KD_treated_1

description: 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells, 3h, biological rep 1


title: CRA vs NOR colorectal adenoma, patient 79

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 79

value: right colon


title: mTAG-click-chip_c1024

description:
label: mTAG
mTAG
Samples were enriched with mTAG-click (25% labelling efficiency). The resulting files were obtained after quantile normalization, subtraction of total input and kernel based smoothing of each sample. The probe coordinates map to hg19.


title: CRA vs NOR colorectal adenoma, patient 74

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 74

value: adenoma


title: mTAG-click-chip_c1005


title: mTAG-click-chip_BRAIN_P3_H7

description:
label: input
total input (unenriched)


title: MeDIP_brain_1018C


title: MeDIP_brain_1018B


title: CRA vs NOR colorectal adenoma, patient 72

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 72

value: bauhin's valve


title: 3h_control_treated_1

description: 3T3-L1 cells stimulated with supernatant of control vector-transfected HL-60 cells, 3h, biological rep 1

source_name: differentated 3T3-L1 cells stimulated with supernatant of mock-transfected HL-60 cells for 3 hrs


title: 3h_contro_treated_2

description: 3T3-L1 cells stimulated with supernatant of control vector-transfected HL-60 cells, 3h, biological rep 2


title: CRA vs NOR colorectal adenoma, patient 70

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 70


title: mTAG-click-chip_BRAIN_P3_H6

description:
label: input
total input (unenriched)


title: CRA vs NOR colorectal adenoma, patient 60

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 60

value: female


title: mTAG-click-chip_BRAIN_P3_H5

description:
label: input
total input (unenriched)

value: Harvard Brain Tissue Resource Centre


title: CRA vs NOR colorectal adenoma, patient 58

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 58

value: transversal colon


title: MRE-chip_s1024

description:
label: MRE
MRE
The resulting files were obtained after quantile normalization and subtraction of total input. The probe coordinates map to hg19.

value: MRE


title: CRA vs NOR colorectal adenoma, patient 54

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 54

value: sigmoid colon


title: mTAGdehmC_D4_NoSssl_NoGlu

description:
label: Not Sssl exposed and not glysylated
Not Sssl exposed and not glysylated

source_name: pool of 6 brain samples

value: pool of 6 brain samples

value: Not Sssl exposed and not glysylated


title: mTAGdehmC_D3_NoSssl_Glu

description:
label: Not M.SssI exposed and glycosylated
Not M.SssI exposed and glycosylated

value: Not M.SssI exposed and glycosylated

value: NO


title: MRE-chip_s1005


title: mTAGdehmC_D1_Sssl_Glu

description:
label: M.SssI exposed and glycosylated
M.SssI exposed and glycosylated

value: M.SssI exposed and glycosylated


title: mTAGdehmC_D2_Sssl_NoGlu

description:
label: M.SssI exposed and not glycosylated
M.SssI exposed and not glycosylated

value: M.SssI exposed and not glycosylated


title: mTAGdehmC_C3_NoSssl_Glu

value: Brain


title: mTAGdehmC_C2_Sssl_NoGlu


title: CRA vs NOR colorectal adenoma, patient 132

description: colorectal adenoma biopsy

source_name: colorectal adenoma biopsy sample, patient 132

value: cecum


title: mTAGdehmC_C1_Sssl_Glu


title: Progesterone receptor null mice treated with E+EP24h, biological rep 3

city: Houston

first: Ashlee

middle: Renae

last: Lain

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
PRKO_E+EP24h3
Gene expression data from progesterone receptor null mouse mammary glands after hormone treatment.

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and normalized using the Robust Multichip Analysis tool in Bioconductor.

source_name: Mammary glands of 10-week-old progesterone receptor null mice treated with E+EP24h

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

growth_protocol: 10-week-old ovariectomized mice.

extract_protocol: RNA extraction using the Qiagen RNeasy Lipid Tissue Midi Kit according to the manufacturer's instructions.

treatment_protocol: Treated subcutaneously with 17β-Estradiol (100ng) for 24 hours and then 17β-Estradiol (100ng) plus Progesterone (2.5ug) for 8 or 24 hours.

tag: strain/background

value: BALB/c

value: progesterone receptor null

value: mammary gland

tag: age

value: 10 weeks

value: 17β-estradiol for 24 hours and then 17β-estradiol plus progesterone for 24 hrs


title: Progesterone receptor null mice treated with E+EP24h, biological rep 2

description:
PRKO_E+EP24h2
Gene expression data from progesterone receptor null mouse mammary glands after hormone treatment.

value: female


title: Wildtype mice treated with E+EP24h, biological rep 3

description:
WT_E+EP24h3
Gene expression data from wildtype mouse mammary glands after hormone treatment.

source_name: Mammary glands of 10-week-old wildtype mice treated with E+EP24h

value: wildtype


title: Progesterone receptor null mice treated with E+EP24h, biological rep 1

description:
PRKO_E+EP24h1
Gene expression data from progesterone receptor null mouse mammary glands after hormone treatment.


title: mTAGdehmC_B4_NoSssl_NoGlu

value: Harvard Brain Tissue Resource Centre


title: cow 25 ODM/TDM

city: JOUY-EN-JOSAS

last: GALIO

address: Domaine de Vilvert

institute: INRA

description: mammary tissue sampled by biopsy after 8 day of unilateral once daily milking compared to twice daily

hyb_protocol: Samples were combined according to their fluorescence intensity (in picomoles), denatured 2 min at 95°C, and cohybridized on the 13,257 oligoarray at 42°C for 16 to 18 h using the Pronto! Universal Microarray Kits (Corning, Bagneaux-sur-Loing, France) according to the manufacturer’s recommendations.

scan_protocol: After stringent washes to remove unbound cDNA, slides were scanned using an Agilent scanner (Agilent technologies) and features were analyzed with Agilent quantification software (Agilent technologies).

data_processing: Data were normalized by a global loess regression followed by a subtraction of the median by block and analyzed using a mixture model that identifies clusters of genes with equal variance using the “anapuce” R package (http://www.r-project.org/). Statistical significant raw P values were adjusted for multiple comparisons using the Benjamini-Hochberg (BH) procedure that controls the false discovery rate (FDR).

organism: Bos taurus

source_name: Mammary gland

label_protocol: 20 µg of each RNA sample was converted into aminoallyl-labeled cDNA with oligo-dT primers, amino-allyl-dUTP (Sigma, Saint-Quentin-Fallavier, France), and superscript II Reverse Transcriptase (Invitrogen). The resulting cDNA was purified on a Microcon PCR column according to the manufacturer’s protocol (Millipore, St-Quentin-en-Yvelines, France) and added to an aliquot of fluorescent dye (Cy3 or Cy5; GE HealthCare, Velizy, France). Unused reactive sites were blocked by 4 M hydroxylamine, and fluorescent probes were purified on QiaQuick columns according to the manufacturer’s recommendations (Qiagen). Every probe was quantified using a Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

growth_protocol: Five Holstein cows housed at the Méjusseaume experimental dairy farm of INRA, UMR1348 IEPL (Le Rheu, France) were used in this study. They were at different stages of lactation (45 day in milk (DIM), n = 2; 120 DIM, n = 1 and 320 DIM, n = 2) and with different lactation rank (rank 1, n = 1; rank 2, n = 2 and rank 4, n = 2). One cow of rank 1 was  in early gestation (45 days), the others were empty. We selected these cows because of their well-balanced milk yield between the udder halves. The cows were milked twice daily from the onset of lactation.

extract_protocol: RNA was extracted from mammary biopsies with a Trizol extraction followed by a purification using the column from the RNeasy Minikit (Qiagen, Courtaboeuf, France) according to the manufacturer’s recommendations including the DNase digestion. The RNA pellet was suspended in RNase-free water and the quantity of total RNA was determined with an Agilent 2100 bioanalyzer (Agilent Technologies, Massy, France). RNA quality was assessed using the RNA integrity number generated by version B.02 of Agilent 2100 Expert Software (Agilent Technologies).

treatment_protocol: 5 cows were milked unilaterally, once daily on one udder half and twice daily on the other one for 7 days, the mammary tissue of each udder half was sampled using biopsie on the 8th days of treatment. Each mammary biopsy RNA sample from the udder half of one cow was compared to the one of the contralateral udder half in 5 dye-swaps.

value: Mammary gland

tag: milking frequency

value: Once daily milking (ODM)

value: Twice daily milking (TDM)


title: cow 11 TDM/ODM

description: mammary tissue sampled by biopsy after 8 day of unilateral twice daily milking compared to once daily

tag: tissue


title: Wildtype mice treated with E+EP24h, biological rep 2

description:
WT_E+EP24h2
Gene expression data from wildtype mouse mammary glands after hormone treatment.

tag: gender


title: Wildtype mice treated with E+EP24h, biological rep 1

description:
WT_E+EP24h1
Gene expression data from wildtype mouse mammary glands after hormone treatment.


title: cow 11 ODM/TDM


title: Progesterone receptor null mice treated with E+EP8h, biological rep 1

description:
PRKO_E+EP8h1
Gene expression data from progesterone receptor null mouse mammary glands after hormone treatment.

source_name: Mammary glands of 10-week-old progesterone receptor null mice treated with E+EP8h

value: 17β-estradiol for 24 hours and then 17β-estradiol plus progesterone for 8 hrs


title: mTAGdehmC_C4_NoSssl_NoGlu

value: pool of 6 brain samples

value: Not Sssl exposed and not glysylated

value: NO


title: cow 01 TDM/ODM


title: mTAGdehmC_B2_Sssl_NoGlu

value: Brain

value: M.SssI exposed and not glycosylated


title: mTAGdehmC_B3_NoSssl_Glu

value: Not M.SssI exposed and glycosylated


title: mTAGdehmC_B1_Sssl_Glu

value: M.SssI exposed and glycosylated


title: Progesterone receptor null mice treated with E+EP8h, biological rep 3

description:
PRKO_E+EP8h3
Gene expression data from progesterone receptor null mouse mammary glands after hormone treatment.

value: BALB/c

value: progesterone receptor null

value: mammary gland


title: cow 3049 TDM/ODM


title: cow 01 ODM/TDM


title: mTAGdehmC_A4_NoSssl_NoGlu


title: mTAGdehmC_A3_NoSssl_Glu


title: cow 25 TDM/ODM


title: Progesterone receptor null mice treated with E+EP8h, biological rep 2

description:
PRKO_E+EP8h2
Gene expression data from progesterone receptor null mouse mammary glands after hormone treatment.

value: female

value: 10 weeks


title: mTAGdehmC_A2_Sssl_NoGlu

value: Harvard Brain Tissue Resource Centre


title: Wildtype mice treated with E+EP8h, biological rep 3

description:
WT_E+EP8h3
Gene expression data from wildtype mouse mammary glands after hormone treatment.

source_name: Mammary glands of 10-week-old wildtype mice treated with E+EP8h

value: wildtype


title: cow 3049 ODM/TDM

value: Mammary gland

value: Once daily milking (ODM)


title: mTAG-MeDIP-arrayD_Repli1_MeDIP_mTAG

description:
label: MeDIP
MeDIP
Probe coordinates map to the human reference genome NCBI36 (hg18).

source_name: fetal lung fibroblast (IMR90 cell line)

value: fetal lung

value: IMR90 cells

value: R. Lister (cell line originally from ATCC)

value: MeDIP


title: Wildtype mice treated with E+EP8h, biological rep 2

description:
WT_E+EP8h2
Gene expression data from wildtype mouse mammary glands after hormone treatment.

value: 17β-estradiol for 24 hours and then 17β-estradiol plus progesterone for 8 hrs


title: mTAG-MeDIP-arrayD_mTAG_80%_1_B1

description:
label: mTAG
mTAG
Probe coordinates map to the human reference genome NCBI36 (hg18).

value: mTAG-80% labelling efficiency

value: NO


title: mTAGdehmC_A1_Sssl_Glu

description:
label: M.SssI exposed and glycosylated
M.SssI exposed and glycosylated

value: Brain

value: pool of 6 brain samples

value: M.SssI exposed and glycosylated


title: mTAG-MeDIP-arrayD_Sonicated_MeDIP_mTAG

description:
label: input
total input (unenriched)


title: mTAG-MeDIP-arrayD_Repli2_MeDIP_mTAG


title: mTAG-MeDIP-arrayD_mTAG_80%_1_A1


title: mTAG-MeDIP-arrayD_mTAG_60%_1_A2

value: mTAG-60% labelling efficiency


title: mTAG-MeDIP-arrayD_mTAG_25%_1_A3

value: mTAG-25% labelling efficiency


title: mTAG-MeDIP-arrayD_mTAG_10%_3_C4

value: mTAG-10% labelling efficiency


title: mTAG-MeDIP-arrayD_mTAG_10%_2_B4


title: Wildtype mice treated with E+EP8h, biological rep 1

description:
WT_E+EP8h1
Gene expression data from wildtype mouse mammary glands after hormone treatment.

value: BALB/c

value: female

value: mammary gland

value: 10 weeks


title: Compound 6 treated 48h rep4

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

hyb_protocol: For hybridization, 825ng of Cy3-labeled and its respective Cy5-labeled cRNA were added to a microarray slide for 17 hours at 65 C at 10 rpm using the Hybridization Oven kit procedure provided by Agilent Technologies. After hybridization, the slides were then washed per Agilent’s SSPE wash protocol as detailed in Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) v6.5 May 2010 (Agilent Technologies, Palo Alto, CA).

scan_protocol: The microarray slides were scanned at 3 µm, 20bit resolution with a G2505C DNA microarray scanner (Agilent Technologies, Palo Alto, CA). Data were then extracted from images by the Feature Extraction software version 10.7.3.1, protocol GE2_107_Sep09 (Agilent Technologies, Palo Alto, CA).

data_processing: Cy3/Cy5 ratios were log2-transformed and lowess-normalized

source_name: MDA-MB-231 treated with G9a inhibitor compound 6 for 48h

label_protocol: The samples were labelled with Cy3-labeled CTP fluorescent dyes and the control, untreated total RNA were  labelled with Cy5-labeled CTP fluorescent dyes following the Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) v6.5 May 2010 (Agilent Technologies, Palo Alto, CA). The dye-incorporation ratio and the cRNA quantity were determined using the Nanodrop spectrophotometer.

growth_protocol: MDA-MB-231 cells were cultured in DMEM-Medium supplemented with 10% FCS (#02.00.830, First Link (UK), 2mM L-Glutamine (#25030-024, Invitrogen), 100U/ml Penicillin and 100μg/ml Streptavidin (#15070-063, Invitrogen) until they were ~60% confluent and then treated for either 48h or 72h with a compound.

extract_protocol: Total RNA was extracted using QIAshredder spin columns combined with RNeasy spin-columns. Briefly, medium was removed, cells were lysed and homogenised with 600 of RTL Buffer and then put on a Qiashredder spin column.  To the RNA containing flow-through 600of 70% ethanol was added, mixed well and transferred onto RNeasy spin-columns. The columns were treated according to the manufactures protocol and RNA was eluted using 50µRNase free water and immediately stored at -80 °C.

treatment_protocol: Cell cultures were treated for either 48h or 72h with an EZH2/G9a inhibitor compound. Compounds were diluted in DMSO at Stocks of 10mM.

source_name: Untreated MDA-MB-231 cultured for 48h


title: cow 7849 TDM/ODM

value: Mammary gland

value: Once daily milking (ODM)

value: Twice daily milking (TDM)


title: mTAG-MeDIP-arrayD_mTAG_10%_1_A4

value: fetal lung

value: IMR90 cells

value: R. Lister (cell line originally from ATCC)


title: cow 7849 ODM/TDM


title: mTAG-MeDIP-arrayD_mTAG_0%_1_A5

description:
label: mTAG-non labelled
mTAG

value: mTAG-0% labelling efficiency (not labelled)

value: NO


title: Compound 6 treated 48h rep3


title: Compound 6 treated 24h rep1

source_name: MDA-MB-231 treated with G9a inhibitor compound 6 for 24h

source_name: Untreated MDA-MB-231 cultured for 24h


title: Compound 6 treated 24h rep4


title: Compound 6 treated 48h rep2


title: Compound 3 treated 48h rep4

source_name: MDA-MB-231 treated with EZH2 inhibitor compound 3 for 48h


title: Compound 6 treated 24h rep2


title: Compound 3 treated 48h rep3


title: Compound 6 treated 24h rep3


title: Compound 3 treated 24h rep3

source_name: MDA-MB-231 treated with EZH2 inhibitor compound 3 for 24h


title: Compound 3 treated 24h rep4


title: Compound 3 treated 48h rep1


title: Compound 6 treated 48h rep1


title: Injected C.albicans in zebrafish_18hpi_rep1

status: Public on Aug 26 2013

city: Hsin-chu

first: Yan-Yu

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: NTHU

description: Gene expression after 18hr in injected C. albicans in infected zebrafish

hyb_protocol: The fragmented labeled cRNA was then hybridized to oligo microarray at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA),  image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Candida albicans

source_name: Injected C.albicans in zebrafish_18hpi

label_protocol: 0.625μg of Cy3 cRNA for C. albicans array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's recommendations. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).

treatment_protocol: Each fish was intraperitoneally injected with 1×108 C. albicans cells suspended in 10μL sterile 1× phosphate-buffered saline (PBS)

tag: post-infection time points


title: Injected C.albicans in zebrafish_16hpi_rep2

description: Gene expression after 16hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_16hpi


title: Injected C.albicans in zebrafish_18hpi_rep2


title: Injected C.albicans in zebrafish_12hpi_rep3

description: Gene expression after 12hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_12hpi


title: Injected C.albicans in zebrafish_12hpi_rep2


title: Injected C.albicans in zebrafish_18hpi_rep3


title: Injected C.albicans in zebrafish_8hpi_rep2

description: Gene expression after 8hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_8hpi


title: Injected C.albicans in zebrafish_12hpi_rep1


title: Compound 3 treated 24h rep2


title: Injected C.albicans in zebrafish_16hpi_rep3


title: Injected C.albicans in zebrafish_6hpi_rep2

description: Gene expression after 6hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_6hpi


title: Compound 3 treated 48h rep2


title: Compound 3 treated 24h rep1


title: Injected C.albicans in zebrafish_4hpi_rep2

description: Gene expression after 4hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_4hpi


title: Injected C.albicans in zebrafish_4hpi_rep3


title: Injected C.albicans in zebrafish_6hpi_rep3


title: Injected C.albicans in zebrafish_6hpi_rep1


title: Injected C.albicans in zebrafish_8hpi_rep1


title: Injected C.albicans in zebrafish_16hpi_rep1


title: Injected C.albicans in zebrafish_4hpi_rep1


title: Injected C.albicans in zebrafish_2hpi_rep3

description: Gene expression after 2hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_2hpi


title: Injected C.albicans in zebrafish_8hpi_rep3


title: Injected C.albicans in zebrafish_2hpi_rep2


title: Injected C.albicans in zebrafish_2hpi_rep1


title: Injected C.albicans in zebrafish_1hpi_rep2

description: Gene expression after 1hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_1hpi


title: Injected C.albicans in zebrafish_1hpi_rep3


title: Injected C.albicans in zebrafish_0.5hpi_rep3

description: Gene expression after 0.5hr in injected C. albicans in infected zebrafish

source_name: Injected C.albicans in zebrafish_0.5hpi


title: Injected C.albicans in zebrafish_0.5hpi_rep2

treatment_protocol: Each fish was intraperitoneally injected with 1×10^8 C. albicans cells suspended in 10μL sterile 1× phosphate-buffered saline (PBS)


title: Injected C.albicans in zebrafish_1hpi_rep1


title: Injected C.albicans in zebrafish_0.5hpi_rep1


title: LSEC hepatectomized-3

city: Heidelberg

first: Junhao

last: Hu

address: Im Neuenheimer Feld 280

department: Division of Vascular Oncology and Metastasis

country: Germany

institute: German Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LSEC

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

growth_protocol: no in vitro culture. LSEC were directly lysed in TRIZOL after isolation.

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

treatment_protocol: No treatment. LSEC were directly lysed in TRIZOL after isolation.

value: liver sinusoidal endothelial cells

tag: treatment

value: hepatectomized

value: 8 weeks


title: LSEC sham operated-4

value: sham