title: control mouse, PFC, sacrificed at 72 hours, biological replicate 6, repeat group 1


title: whole blood_18

status: Public on Apr 15 2016

type: RNA

city: Gaithersburg

first: Mustimbo

last: Roberts

state: MD

address: One MedImmune Way

country: USA

institute: MedImmune

description: HGU133 Plus array data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed ArrayAssist Lite

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

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

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

treatment_protocol: unstimulated whole blood and whole blood stimulated with anti-CD3 and anti-CD28 using the TruCulture ex-vivo method

tag: tissue

value: whole blood

tag: diagnosis

value: COPD


title: whole blood_11

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 72 hours, biological replicate 34, repeat group 1

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

hyb_protocol: Following fragmentation, cRNA samples were hybridized for 16 hr to GeneChip Mouse Genome 430 2.0 arrays by procedures outlined by Affymetrix.

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarrays were separated by RNA hybridization batch for initial normalization. Each batch was background corrected with the Robust Multi-array Average (RMA) technique and normalized by quantile normalization. The second step involved subjecting all microarrays together to another round of quantile normalization. Finally, ComBat with hybridization group as the batch effect was used to remove any remaining batch effects reflected in the data. The only exception to this procedure was the prefrontal cortex where repeat group was used as only the batch effect correction factor. Network analysis with WGCNA and bioinformatics analysis were used to identify modules of co-expressed genes representing specific biological pathways. Modules were overlapped with genes differentially expressed between CIE and Ctrl mice at each time-point to identify modules regulated at specific times after CIE.

organism: Mus musculus

source_name: medial PFC brain dissection, air inhalation chamber, tissue harvested 72 hours after final inhalation chamber session

label_protocol: Botinylated cRNA samples were prepared according to Affymetrix protocols.

extract_protocol: Tissue from individual mice was homogenized using a Tekmar homogenizer, and total RNA was isolated with reagents and procedures provided by the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Adult male C57BL/6J mice were divided into two groups of 24. One group (CIE) received ethanol vapor exposure for 16 hours/day for 4 days while the other group was similarly handled but received only air exposure. For CIE mice, ethanol was volatized by passing air through an air stone submerged in 95% ethanol. Chamber ethanol concentrations were monitored daily and air flow was adjusted to maintain ethanol concentrations within a range (10-13 mg/l air). Before each chronic ethanol exposure cycle, intoxication was initiated in the CIE group by administration of ethanol (1.6 g/kg), and blood ethanol concentration was stabilized by injection of the alcohol dehydrogenase inhibitor pyrazole (1 mmol/kg).  Both ethanol and pyrazole were administered intraperitoneally (i.p.) in a volume of 0.02 ml/g body weight.  Ctrl mice were handled similarly, but administered saline and pyrazole (i.p.) prior to being placed in control chambers that delivered only air. Following 4 days in the inhalation chamber, mice underwent 7 days of complete abstinence from ethanol. At the end of the abstinence period, mice were returned to the inhalation chamber to begin the next cycle of CIE. This pattern of 4 days CIE (or control air) exposure followed by 7 days abstinence was repeated for four complete cycles.

tag: strain

value: brain, medial prefrontal cortex

tag: sacrifice time

value: 72 hours post final vapor chamber session

tag: Sex

value: male


title: control mouse, PFC, sacrificed at 72 hours, biological replicate 44, repeat group 1


title: whole blood_14

description: HGU133 Plus array data


title: Cold-Serum-Exo#2

city: Bonn

first: Yong

last: Chen

address: Sigmund-Freud-Strasse 25

country: Germany

institute: University of Bonn

description: exosomes in serum from cold exposed mice

data_processing: Data was processed by using DataAssist Software v3.01. Processed data was normalized by Global Normalization

label: FAM

source_name: serum exosome (Serum-Exo)

label_protocol: PCR assays were performed usingTaqMan® Low Density Array Rodent MicroRNA panel kit ( Thermo Fisher Scientific) according to manufacturer's instruction. Reverse transcription was performed from 100ng total RNA using TaqMan® MicroRNA Reverse Transcription Kit ( Thermo Fisher Scientific). Quantitative real-time PCR were performed with 40 cycles at 95˚C for 15 seconds and 60˚C for 60 seconds.

growth_protocol: BA-exosomes were from mature brown adipocytes in vitro. BAT-SVF cells were dissected from newborn C57BL/6 mice, then differentiated to mature brown adipocytes in proadipogenic medium

extract_protocol: exosome isolation from medium in vitro and serum in vivo by using Total Exosome Isolation Kits from life technologies. Total RNA was extracted from the exosomes by using Total Exosome RNA and Protein Isolation Kit from life technologies. All kits were used according to the User Guide supported by the manufacturer

treatment_protocol: mature brown adipocytes were treated with cAMP for 48 hours in vitro; C57BL/6 mice were either injected (I.P.) daily with CL316.243, or exposed to cold (4˚C) for 7 days

value: serum


title: Cold-Serum-Exo#1


title: Serum-Exo#2

description: exosomes in serum from wt mice


title: Serum-Exo#1

description: exosomes in serum from wt mice


title: Helicobacter pylori_wild type versus tlpD mutant_experiment 1

city: Hannover

first: Christine

last: Josenhans

address: Carl-Neuberg-Strasse 1

department: Institute for Medical Microbiology

institute: Hannover Medical School

hyb_protocol: according to manufacturer's recommendations

scan_protocol: scanned with Affymetrix 428 scanner

data_processing:
data processing performed with IMAGENE and MAVI (MWG Biotech)
Blank values were not positive for one of several quality parameters implemented in the analysis software, such as low signal intensity or bad spots etc.

organism: Helicobacter pylori N6

source_name: Helicobacter pylori N6 wild type

label_protocol: random hexamer primers (Invitrogen) were mixed with 15 to 25 µg of total RNA, after preincubation at 65°C for 10 min, and 10 min at room temperature, reverse transcription (direct labelling) was carried out at 42°C for 2 h using the Superscript III system (Invitrogen), fluorescence dyes Cy3 and Cy5 (0.5 mM, Amersham Pharmacia) were incorporated into cDNA

growth_protocol: bacteria were grown in liquid culture under standard incubation conditions (brain heart infusion broth supplemented with 2.5 g per l yeast extract and 10% horse serum, 37°C, microaerobic, agitation)

extract_protocol: bacteria were pelleted by centrifugation, total RNA was extracted with the RNeasy spin column kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: no further treatment

tag: genotype/variation

value: wild type

tag: growth conditions

value: liquid culture

source_name: Helicobacter pylori N6 tlpD mutant bacteria

value: tlpD mutant


title: Helicobacter pylori_wild type versus tlpD mutant_experiment 3


title: Helicobacter pylori_wild type versus tlpD mutant_experiment 2


title: Helicobacter pylori_wild type versus tlpD mutant_experiment 4


title: cAMP-BA-Exo

description: exosomes from cAMP treated mature adipocytes in vitro

source_name: mesenchymal stem cells derived exosome (MSCs-Exo)

value: brown adipose tissue (BAT)


title: control mouse, PFC, sacrificed at 8 hours, biological replicate 66, repeat group 1

source_name: medial PFC brain dissection, air inhalation chamber, tissue harvested 8 hours after final inhalation chamber session

value: 8 hours post final vapor chamber session


title: control mouse, PFC, sacrificed at 0 hours, biological replicate 48, repeat group 1

source_name: medial PFC brain dissection, air inhalation chamber, tissue harvested 0 hours after final inhalation chamber session

value: 0 hour post final vapor chamber session


title: whole blood_10

description: HGU133 Plus array data

value: Smoker


title: TAP-Tagged Ppr1 vs. wild type Replicate 2

type: genomic

city: Montreal

first: Walters

middle: Aji

last: Tebung

state: Quebec

address: 7141 Rue Sherbrooke Ouest

department: Chemistry and Biochemistry

country: Canada

institute: Concordia University

hyb_protocol: The microarray slides were pre-hybridized for 1 hour at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIG easy Hyb solution (Roche) containing 0.5 ug/ul of Bakers tRNA and 0.5 ug/ul of salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: The scanning was done using GenePix4000B microarray scanner Images were quantified using GenePix Pro 7

data_processing: Normalized Red signal/normalized Green signal. GenePix Pro 7 software was used for image normalization and final normalization and inspection of the data was done using MultiExperiment Viewer.

molecule: genomic DNA

organism: Candida albicans

source_name: DNA from Ppr1-TAP ChIP

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen).

growth_protocol: YPD medium at 30°C

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow.

treatment_protocol: Overnight cultures in YPD were diluted to OD600nm =0.1 and grown to OD600nm=0.6 in 40 ml YPD at 30°C. Cultures were harvested by centrifugation at 3,000 × g for 5 minutes.

tag: cell type

value: Yeast cells

source_name: DNA from SN148 ChIP


title: control mouse, PFC, sacrificed at 0 hours, biological replicate 20, repeat group 1


title: whole blood_7

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 0 hours, biological replicate 56, repeat group 1


title: control mouse, PFC, sacrificed at 0 hours, biological replicate 12, repeat group 1


title: control mouse, PFC, sacrificed at 0 hours, biological replicate 78, repeat group 1


title: whole blood_4

description: HGU133 Plus array data


title: whole blood_6

description: HGU133 Plus array data


title: BA-Exo

description: exosomes from mature adipocytes in vitro


title: whole blood_8

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 0 hours, biological replicate 2, repeat group 1


title: whole blood_9

description: HGU133 Plus array data


title: whole blood_5

description: HGU133 Plus array data


title: whole blood_2

description: HGU133 Plus array data


title: control mouse, PFC, sacrificed at 72 hours, biological replicate 52, repeat group 1


title: TAP-Tagged Ppr1 vs. wild type Replicate 1


title: whole blood_3

description: HGU133 Plus array data


title: mouse uterus, experimental group (SF-1 transgenic) 2

status: Public on Apr 14 2016

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: According to Affymetix protocol.

scan_protocol: According to Affymetix protocol.

data_processing: Processed the CEL files using dChip (PM-MM model, Quantile normalization).

source_name: mouse uterus

label_protocol: According to Affymetix protocol.

growth_protocol: To generate a mouse with uterine specific expression of SF1, the Pgrcre/+ mouse was crossed with the mouse line SF1LsL/+. This breeding strategy allowed us to conditionally express SF1 in the Pgrcre/+ SF1LsL/+ and utilize the littermates carrying the Pgrcre/+ or the SF1LsL/+ alleles as wild-type controls.

extract_protocol: Uterine horns were dissected from anesthetized mice two weeks after each respective surgery and cervix was discarded. Tissue was homogenized in 1 mL of TriZOL 6 times for 10 seconds and rested intermittently for 10 seconds on ice. Homogenates were centrifuged 10 minutes at max speed in 4C to pellet cellular debris. Supernatant was transferred to a new 1.5 mL centrifuge tube and 200 uL of chloroform was mixed by shaking the tubes. Samples were rested for 3 minutes at room temperature and subsequently centrifuged at max speed for 18 minutes at 4C. Approximately 600 uL of aqueous layer was transferred to a new tube and mixed with equal parts of 70% ethanol. This mix was filtered in columns from the RNAeasy Mini kit (QIAGEN). Columns were washed once with 700 uL of RWT buffer and three times with 500 uL of RPE buffer. RNA was eluted with RNAse free water. RNA from two mice was pooled for each control and experimental group for microarray gene expression analysis. Independent samples were utilized for RNA isolation in experiments validating the microarray results.

treatment_protocol: Expression analysis was conducted on triplicate samples containing RNA isolated from two mouse uteri for each genotype control (SF1LsL/+) and SF1 expressing (Pgrcre/+ SF1LsL/+)    using the GeneChip Mouse Genome 430 2.0 Array (Affymetrix).

value: experimental group (SF-1 transgenic) (Pgrcre/+ SF1LsL/+)


title: whole blood_21

description: HGU133 Plus array data


title: AML patient with a three way translocation

city: Dallas

first: Jiadi

last: Wen

state: TEXAS

address: 2330 Inwood Rd

institute: UT Southwester Medical Center

description: sex matched control

hyb_protocol: hybridization using the Oligo aCGH/ChIP Hybridization Kit and Agilent oven

scan_protocol: Agilent Technologies DNA Microarray Scanner (G1505C) and Agilent Scan Control software were used for scanning Agilent CGH+SNP arrays

data_processing: Agilent Feature Extraction to create the raw data set; Agilent Cytogenomics Edition 2.5.7.0 to generate the interval reports and Rank Consistency Linear Normalization method was used for data normalization.

source_name: Bone marrow

label_protocol: labeling of genomic DNA using the SureTag Complete DNA Labeling Kit

growth_protocol: Whole BM was cultured for 24hrs in RPMI1640 supplemented with 10% fetal bovine serum, 1% L-glutamine and 1% Pen-strep. These short term cultures were harvested following standard protocols.

extract_protocol: Prepare samples for purification of total DNA using the 5 Prime ArchivePure DNA Blood Kit

tag: disease

value: AML

source_name: control/reference human genomic DNA

tag: reference

value: sex matched control


title: whole blood_1

description: HGU133 Plus array data

value: whole blood


title: mouse uterus, Control 3

description: mouse uterus, Control

value: wild-type control (SF1LsL/+)


title: mouse uterus, Control 1

description: mouse uterus, Control


title: mouse uterus, Control 2

description: mouse uterus, Control


title: mouse uterus, experimental group (SF-1 transgenic) 1


title: E11.5 Six2-GFP-positive cultured 19days-1

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

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

source_name: E11.5 embryo

label_protocol: Total RNA was amplified using Ovation Pico WTA System V2 (NuGEN Technologies, Inc.Cat #3302-60) according to the manufacturer's instructions. Amplified cDNA were labeled with Cyanine 3 (Cy3) using SureTag DNA Labeling Kit (Agilent Technologies, Cat.5190-4240) according to the manufacturer's instructions.

growth_protocol: Isolated Six2-positive nephron progenitors from Six2-GFP transgenic mice embryonic stage at E11.5 by FACS were cultured for 8 or 19 days in conditioned media.

extract_protocol: Each embryonic progenitor cells were sorted by a FACS Aria II (Becton Dickinson). Total RNA was extracted using Rneasy Plus Micro Kit purchased from QIAGEN following manufacture's protocol.

tag: background strain

value: embryo

tag: developmental stage

value: Six2-GFP transgenic mice


title: mouse uterus, experimental group (SF-1 transgenic) 3


title: E3

data_processing: Processed the CEL files using Bioconductor (RMA method).

growth_protocol: All animal studies were conducted in accordance with the standard procedures approved by the Baylor College of Medicine Institutional Animal Care and Use Committee.

extract_protocol: According to Affymetix protocol.

treatment_protocol: pGIPZ lentivirus shRNAs for CPT1 and CPT2 were purchased from the C-BASS core at Baylor College of Medicine. In ETX treatment study, the mice were treated with vehicle or ETX (50 mg/kg body weight, IP) every alternative day. Tumors were monitored by manual observation and luciferase bioluminescence imaging (IVIS Lumina XR). For tail vein injection metastatic study, 1.5E05  MDA231 cells 48 hours pretreated with vehicle or ETX injected into the tail veins of 4-5 weeks old NOD SCID Gamma mice. ETX treatment continued in mice for one more week (50 mg/kg body weight, IP).

tag: cell line


title: E11.5 Six2-GFP-positive cultured 8days-2


title: E11.5 Six2-GFP-positive cultured 19days-2


title: P0 Six2-GFP-negative-2

source_name: P0 neonate


title: E11.5 Six2-GFP-positive cultured 8days-1


title: P0 Six2-GFP-positive-1


title: F1


title: F3


title: D3

description: MDA231-Scramble +ETX

source_name: MDA231-Scramble +ETX


title: P0 Six2-GFP-negative-1


title: E11.5 Six2-GFP-positive-2


title: C2


title: F2


title: E11.5 Six2-GFP-positive-1


title: E2


title: D2

description: MDA231-Scramble +ETX


title: C3


title: E1


title: D1

description: MDA231-Scramble +ETX


title: control mouse, PFC, sacrificed at 72 hours, biological replicate 24, repeat group 1

value: brain, medial prefrontal cortex

value: 72 hours post final vapor chamber session

value: male


title: B1

growth_protocol: For generating cybrids, mitochondrial donor cells (A1N4 and SUM159) were enucleated by overnight actinomycin-D treatment and fused with the SUM159 ρ0 cells using 45% polyethylene glycol (MW 1450; Sigma cat P-5402) for 60 seconds. One day following fusion, cells were cultured in selection medium with bromodeoxyuridine (BrdU) but without uridine. Unfused control SUM159 ρ0 cells could not survive without uridine and mitochondria donor cells were killed by BrdU. Cybrids containing mitochondria derived from A1N4 and SUM159 cells with SUM159 ρ0 cells as nuclear background are named as A1/SUM159 and 159/SUM159 cybrids, respectively.

extract_protocol: Briefly, RNA from cybrid groups were extracted in triplicate and 5 µg of total RNA was used for first- and second-strand cDNA synthesis, according to Affymetrix protocol.


title: whole blood_15

description: HGU133 Plus array data

value: COPD


title: C1


title: P0 Six2-GFP-positive-2


title: Skin_fibroblasts_IL-1alpha/TGF-beta_1

city: Örebro

first: Anita

last: Koskela von Sydow

address: Södra Grev Rosengatan 32

country: Sweden

institute: Örebro University

hyb_protocol: A total of 600 ng of cyanine 3–labeled, linearly amplified cRNA was used for the hybridization. The cRNA was hybridized to the Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray in a G2545A hybridization oven (Agilent Technologies).

scan_protocol: The slides were scanned with the Agilent Microarray Scanner G2565AA (Agilent Technologies). Agilent Feature extraction software (version 10.7.3.1, Agilent Technologies) was used to compute expression values and to monitor hybridization quality. Only hybridizations meeting the quality standard as established in the feature extraction software were used for subsequent data analysis.

data_processing: The raw expression data were background corrected and quantile normalized as previously described (Smyth GK, Speed T. Normalization of cDNA microarray data. Methods. 2003;31(4):265–73.), using the packages marray and arrayQualityMetrics within the Bioconductor Software Collection for R.

source_name: Addition of IL-1alpha/TGF-beta

label_protocol: Synthesis and labeling of cRNA were performed with the Low Input Quick Amp Labeling one-color kit (Agilent Technologies). The cRNA was purified using RNeasy Mini kits, and concentration was measured with a spectrophotometer. Only samples with cRNA yield ≥0.825 μg and specific activity ≥6.0 pmol Cy3/μg cRNA were used.

growth_protocol: Skin fibroblasts were isolated from dermis explants. Fibroblast were seeded in Dulbecco’s Modified Eagle Medium (Invitrogen AB Lidingö, Sweden) supplemented with 10% fetal bovine serum (Invitrogen AB). The fibroblasts were incubated (37°C and 5% CO2) and cultured until confluence. Cultures were trypsinized, resuspended in cryomedium 50% Dulbecco’s Modified Eagle Medium, 10% dimethyl sulfoxide (Merck Schuchardt OHG Hohenbrunn Germany) and 40% fetal bovine serum, and frozen in liquid nitrogen.

extract_protocol: Fibroblasts were harvested for RNA isolation between passages 5 and 8. Total RNA was extracted using the RNeasy Plus purification kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The concentration and purity of extracted RNA were measured using a Nano-Drop ND-1000 spectrophotometer (Nano-Drop Technology Inc., Wilmington, DE, USA) (OD260/280=1.9–2.1; OD260/230=1.7–2.0). Further analysis of RNA quality was performed according to the manufacturer’s guidelines with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Only samples with a RIN (RNA integrity number) value above 8.0 were used.

treatment_protocol: Cells were seeded 250.000 cells per well in a 6-well plates a  ≥24 hours incubation followed to allow the fibroblasts to attach to the bottom, then the medium was removed and each well washed twice with phosphate buffered saline (PBS) to eliminate all serum residues. Serum free medium was added and the cells were serum starved for another 24 hours. Cells were incubated with 0.5 ng/ml TGF-β , wells that were incubated with IL-1α were pre incubated with 0.2 ng/ml IL-1α 3h before TGF-β were added, both from Sigma-Aldrich (St. Louis, MO, USA). Cells were harvested after 16 hours.

value: Skin

value: fibroblast

tag: gender

value: female

tag: additative


title: B3


title: Skin_fibroblasts_IL-1alpha/TGF-beta_2


title: Skin_fibroblasts_TGF-beta_3

source_name: Addition of TGF-beta

value: TGF-beta


title: Skin_fibroblasts_TGF-beta_2


title: Skin_fibroblasts_TGF-beta_1


title: Skin_fibroblasts_control_3

source_name: Control


title: Skin_fibroblasts_control_2


title: Skin_fibroblasts_IL-1alpha/TGF-beta_3


title: Dye flip of 12hrs/Control,  biological rep 2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: II. Prehybridization  1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS  2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides.  3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC.  4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down.  5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down.  6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization  III. Hybridization  1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS  2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe.  IV. Post Hyb washes (next day)  1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.  2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.  3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4200AL scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix Pro and the resulting text files were exported to Microsoft Excel.

data_processing: The chips were normalized by the print-tip Lowess method (Dudoit, 2000). The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip. The ratio of the average median intensity of Cy5 over the average median intensity of Cy3 was determined for each spot.  The data was then processed for statistical significance using Partek Genomics Suite ver 6.5. A false discovery rate (FDR) of 5% was set as cut-off to select for significantly differentially expressed genes from the normalized and processed expression data

organism: Mycobacterium tuberculosis H37Rv

source_name: M.tb in Log phase

label_protocol: I. Synthesis and Labeling of cDNA  1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix: 5.0µl 5X First-Strand buffer 2.5µl 100 mM DTT 2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock) 1.5ul Cy3 or Cy5 Then add 1.2ul Superscript, vortex to mix and spin to collect contents  4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine. **Can freeze or leave at 4oC overnight if necessary  5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl).  6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.  7. Bring sample to 5µl with TE.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: M.tb H37 Rv culture was grown upto log phase.

extract_protocol: Trizol method was used for RNA isolation as per manufactures protocol.

treatment_protocol: To the test sample added 5 mM DTT (reduced) for 3hrs.

tag: treatment

value: DTT 5mM 12hrs

value: control


title: C57/CBA thymus from 10 day old mouse, biological rep 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube Estate

country: United Kingdom

institute: The University of Glasgow

description: Gene expression data from whole thymus of 10 day old C57/CBA mouse

hyb_protocol: 5500 ng fragmented cDNA were hybridised for 18 hr at 45 degrees celcius at 60rpm on GeneChip Mouse Gene 1.0 ST Arrays, then GeneChips were washed and stained in the GeneChip Fluidics Station 450 using protocol FS450_0007 (GeneChip Expression Wash, Stain and Scan manual (P/N 702731)).

scan_protocol: GeneChips were scanned with the Affymetrix Scanner 7G using default settings.

data_processing: The data were analyzed  with the RMA algorithm of the Affymetrix Expression Console 1.4.

source_name: Whole thymus from 10 day old mouse

label_protocol: Biotinylated cDNA were prepared from 250ng total RNA as per the manufacturer's protocol (Ambion WT Expression kit (Applied Biosystems) and GeneChip WT terminal Labelling and hybridisation protocol)

extract_protocol: Total RNA was isolated by RNeasy kit (Qiagen) according to the manufacturer's instructions. Quality was assessed using an Agilent 2100 Bioanalyser and NanoDrop 2000 (Thermo Scientific)

value: thymus

tag: genotype

tag: age

value: 10 days old


title: DTT_12hrs/Control, biological rep 1

description: DTT_12hrs/Control, biological rep 1


title: DTT_12hrs/Control, biological rep 3

description: DTT_12hrs/Control, biological rep 3


title: Runx2/Myc thymus from 10 day old mouse, biological rep 3

description: Gene expression data from whole thymus of 10 day old Runx2/Myc transgenic mouse

tag: tissue


title: Runx2/Myc thymus from 10 day old mouse, biological rep 2


title: DTT_3hrs/Control, biological rep 3

description: DTT_3hrs/Control, biological rep 3

value: DTT 5mM 3hrs


title: A3


title: C57/CBA thymus from 10 day old mouse, biological rep 2


title: A2


title: C57/CBA thymus from 10 day old mouse, biological rep 1


title: Dye flip of 3hrs/Control, biological rep 2


title: A1


title: DTT_3hrs/Control, biological rep 1

description: DTT_3hrs/Control, biological rep 1


title: Skin_fibroblasts_control_1


title: HCS_6 (SCC control) [lncRNA]

status: Public on Apr 13 2016

city: Bochum

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

description: We identified 1516 significantly up- and 2586 down-regulated lncRNAs (FC ≥2 and p<0.05) in cSCC compared to skin (control)

hyb_protocol: For hybridization 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarrays which were incubated in an Agilent hybridization oven (Agilent Technology, Santa Clara, USA) for 17 hours at 65°C.

scan_protocol: Finally, arrays were washed, fixed and scanned with Agilent DNA Microarray Scanner G2505C (Agilent Technologies, Santa Clara, USA).

data_processing: Quantile normalization which was applied to raw data and further data processing was performed with GeneSpring GX v12.0 software package (Agilent Technologies, Santa Clara, USA). Only lncRNAs and mRNAs that at least in 3 out of 6 samples have flags in Marginal or Present (“All Targets Value”) were chosen for further data analysis. Hierarchical clustering was performed with R software (version 2.15, http://www.r-project.org/) in order to arrange samples into groups based on their expression levels.

source_name: skin

label_protocol: The samples were amplified with a mixture of oligo (dT) and random priming method (Arraystar Flash RNA Labeling Kit, Arraystar) and transcribed in fluorescent cRNA which was purified by RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers protocol. Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) was measured with NanoDrop ND-1000. Next, to 1 μg of each labeled cRNA, 5 μl 10 × Blocking Agent (Agilent Technology, Santa Clara, USA) and 1 μl of 25 × Fragmentation Buffer was added (Agilent Technology, Santa Clara, USA). The mixture was heated at 60 °C for 30 min and 25 μl 2 × GE Hybridization buffer (Agilent Technology, Santa Clara, USA) was added to dilute the labeled cRNA.

growth_protocol: A total of three patients with cSCC were biopsied. A total of three control (non-lesional skin) were biopsied.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies, Carlsbad, USA) following the manufacturers protocol.  RNA quantity and quality was determined with NanoDrop ND-1000 and RNA integrity with standard denaturing agarose gel electrophoresis. To purify mRNA from total RNA, rRNA was removed with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, USA).

treatment_protocol: Punch biopsies (4 mm) were obtained under local anaesthesia and immediately put in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C until RNA extraction.

value: Male

value: non-lesional skin (control)


title: HCS_8 (SCC control) [lncRNA]


title: SCC_29T [lncRNA]

source_name: squamous cell carcinoma

value: cutaneous squamous cell carcinoma


title: 414C2-MSC-SS2 (24h Dox)

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

description: Gene expression data from human mesenchymal stromal cells derived from PSCs through neural crest cell lineage

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA algorithm.

source_name: human induced mesenchymal stromal cells expressing SS18-SSX2

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: hPSCs were cultured in Primate ES Cell medium supplemented with 4ng/ml of bFGF on SNL feeder cells. hPSC-NCCs were maintained in CDM supplemented with 10 µM of SB431542, 20 ng/ml of EGF, and 20 ng/ml of bFGF on a fibronectin-coated dish. hPSC-MSCs were induced and maintained in αMEM supplemented with 10% FBS.

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: hPSC-NCCs and hPSC-MSCs were treated with 0.3 µg/ml of doxycycline for 24 hours.

value: human induced mesenchymal stromal cells


title: KhES1-MSC-Stuffer (24h Dox)

source_name: human induced mesenchymal stromal cells


title: KhES1-MSC-SS2 (24h Dox)


title: SCC_18T [lncRNA]


title: HCS_11 (SCC control) [lncRNA]

value: Female


title: KhES1-NCC-SS2 (24h Dox)

description: Gene expression data from human neural crest cells derived from PSCs

source_name: human induced neural crest cells expressing SS18-SSX2

value: human induced neural crest cells


title: Runx2/Myc thymus from 10 day old mouse, biological rep 1


title: 414C2-MSC-Stuffer (12h Dox)

source_name: MSC-Stuffer derived from 414C2-Stuffer

treatment_protocol: hPSC-NCCs and hPSC-MSCs were treated with 0.3 µg/ml of doxycycline for 12 hours.


title: KhES1-MSC-Stuffer (12h Dox)

source_name: MSC-Stuffer derived from KhES1-Stuffer


title: Fuji

description: Gene expression data from human synovial sarcoma cell line

source_name: Fuji

value: human synovial sarcoma cell line


title: 414C2-MSC-Stuffer (24h Dox)


title: 414C2-NCC-Stuffer (12h Dox)

source_name: NCC-Stuffer derived from 414C2-Stuffer


title: 414C2-NCC-Stuffer (24h Dox)

source_name: human induced neural crest cells


title: KhES1-NCC-Stuffer (24h Dox)


title: 414C2-NCC-SS2 (12h Dox)

source_name: NCC-SS2 derived from 414C2-SS2

value: human induced neural crest cells expressing SS18-SSX2


title: SCC_13T [lncRNA]


title: 1273/99


title: KhES1-MSC-SS2 (12h Dox)

source_name: MSC-SS2 derived from KhES1-SS2

value: human induced mesenchymal stromal cells expressing SS18-SSX2


title: 414C2-NCC-SS2 (24h Dox)


title: KhES1-NCC-SS2 (12h Dox)

source_name: NCC-SS2 derived from KhES1-SS2


title: 414C2-MSC-SS2 (12h Dox)

source_name: MSC-SS2 derived from 414C2-SS2


title: KhES1-NCC-Stuffer (12h Dox)

source_name: NCC-Stuffer derived from KhES1-Stuffer


title: Identification of miR-145-5p target genes in PC3

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: prostate cancer

tag: transfection

value: no transfection

source_name: miR-145-5p transfected cell line


title: Identification of miR-145-3p target genes in PC3

source_name: miR-145-3p transfected cell line


title: Identification of miR-375 target genes in TE9

value: esophageal cancer

source_name: miR-375 transfected cell line


title: Differentially expressed genes by knocking down of LAMP1-3 in PC3

source_name: si-LAMP1-3 transfected cell line


title: Identification of miR-375 target genes in Panc-1

value: pancreatic cancer


title: Differentially expressed genes by knocking down of LAMP1-2 in PC3

source_name: si-LAMP1-2 transfected cell line


title: Differentially expressed genes by knocking down of UHRF1-3 in 786-O

value: renal cell carcinoma

source_name: si-UHRF1-3 transfected cell line


title: SYO-1


title: Identification of miR-375 target genes in TE8


title: Identification of miR-29a target genes in PC3

source_name: miR-29a transfected cell line


title: Identification of miR-375 target genes in sw1990


title: Identification of miR-26a target genes in PC3

source_name: miR-26a transfected cell line


title: Differentially expressed genes by knocking down of MMP11-2 in BOY

value: BOY

value: bladder cancer

source_name: si-MMP11-2 transfected cell line


title: Differentially expressed genes by knocking down of LOXL2-3 in BOY

source_name: si-LOXL2-3 transfected cell line


title: Differentially expressed genes by knocking down of UHRF1-3 in BOY


title: Differentially expressed genes by knocking down of MMP11-2 in T24


title: Differentially expressed genes by knocking down of UHRF1-1 in T24

source_name: si-UHRF1-1 transfected cell line


title: Differentially expressed genes by knocking down of PLOD2-3 in 786-O

source_name: si-PLOD2-3 transfected cell line


title: Identification of miR-218 target genes in BOY in vivo

source_name: miR-218 transfected cell line in vivo


title: Differentially expressed genes by knocking down of UHRF1-1 in BOY


title: Differentially expressed genes by knocking down of PLOD2-3 in A-498


title: Differentially expressed genes by knocking down of LOXL2-1 in BOY

source_name: si-LOXL2-1 transfected cell line


title: Identification of miR-320a target genes in PC3

source_name: miR-320a transfected cell line


title: Differentially expressed genes by knocking down of FOXM1-2 in C4-2

source_name: si-FOXM1-2 transfected cell line


title: Differentially expressed genes by knocking down of PLOD2-1 in BOY

source_name: mock

source_name: si-PLOD2-1 transfected cell line


title: Identification of miR-218 target genes in EBC-1

value: lung squamous cell carcinoma

source_name: miR-218 transfected cell line


title: Identification of miR-29a target genes in A549


title: Identification of miR-145-5p target genes in EBC-1

source_name: miR-145-5p transfected cell line


title: Differentially expressed genes by knocking down of UHRF1-2 in 786-O

source_name: si-UHRF1-2 transfected cell line


title: Identification of miR-145-3p target genes in EBC-1

source_name: miR-145-3p transfected cell line


title: Differentially expressed genes by knocking down of PLOD2-2 in BOY

source_name: si-PLOD2-2 transfected cell line


title: Differentially expressed genes by knocking down of FOXM1-3 in C4-2

source_name: si-FOXM1-3 transfected cell line


title: Identification of miR-29a target genes in MRC-5

value: lung fibroblast

source_name: miR-29a transfected cell line


title: B2


title: hypoxic cardiomyocytes without FGF21, biological rep3

city: Wuhan

first: Xiang

last: Cheng

state: Hubei

address: No.1277 Jiefang Avenue

country: China

institute: Institute of Cardiology, Union Hospital, Tongji Medical College of Huazhong University of Science and Technology

description:
Gene expression data from hypoxic cardiomyocytes in the absence of FGF21
X-12h-3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G Plus.

data_processing: The data were analyzed with R 3.2.2 using Bioconductor’s ‘affy’ package and RMA as normalization method.

source_name: neonatal cardiomyocytes exposed to hypoxia for 12 h in the absence of FGF21

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Hearts from 1-day-old C56BL/6 mice were obtained, washed with chilled DMEM medium and cut into 1 mm3 pieces. The first digestion was discarded, in which the heart pieces were digested with trypsin/EDTA at 4C for 30 minutes with rotation. After another 5-6 rounds of digestion with Liberase TH at 37C for 10 min, the cell suspension was collected, filtered through a 70 µm cell strainer and seeded onto fibronectin-coated 12-well tissue culture plates in DMEM supplemented with 20% fetal bovine serum and antibiotics at 37°C in a 95% O2 and 5% CO2 incubator. After 1 hour of incubation, the cardiomyocytes-enriched suspension was collected, centrifuged, resuspended and seeded onto another fibronectin-coated 12-well tissue culture plate.

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

treatment_protocol: Cardiomyocytes were exposed to hypoxia (in 2% oxygen, 5% CO2 and 93% N2) for 12 h in the absence or presence of FGF21 (1 μg/ml).

tag: strain

value: heart

value: cultured neonatal cardiomyocytes

tag: stress

value: hypoxia

tag: agent

value: control


title: hypoxic cardiomyocytes with FGF21, biological rep2

description:
Gene expression data from hypoxic cardiomyocytes in the presence of FGF21
X-12h+2

source_name: neonatal cardiomyocytes exposed to hypoxia for 12 h in the presence of FGF21


title: hypoxic cardiomyocytes with FGF21, biological rep1

description:
Gene expression data from hypoxic cardiomyocytes in the presence of FGF21
X-12h+1


title: Legionella Infection + TNFAIP2 siRNA transfection rep3

city: Berlin

first: Brian

last: Caffrey

address: Ihnestrasse 63-73

institute: Max Planck Institute for molecular Genetics

description: SAMPLE 11

hyb_protocol: Hybridization was performed with the human HT12 v4 expression BeadChip Kit according to the manufacturer´s recommendation

scan_protocol: Illumina iScan system. Scanned images were visually inspected and quality control was performed with Illumina´s Genome Studio Gene Expression software.

data_processing: variance stabilizing transformation (vst) and quantile normalisation were performed using the Lumi Bioconductor package in R

label_protocol: standard Illumina protocol

growth_protocol: Adherent cells were culured in Ham´s F12 Medium with 10 % FCS and 1 % L-Glutamin. Cells were grown to confluency and split every 3 days.

extract_protocol: Total RNA was extracted by Phenol-Chloroform precipitation.

treatment_protocol: cells were transfected with ctrl or TNFAIP2 siRNA at a final concentration of 5 nM for 24 h. Afterwards, cells were infected with Legionella for 4 h at a MOI of 50.

value: adenocarcinomic human alveolar basal epithelial cell


title: hypoxic cardiomyocytes without FGF21, biological rep2

description:
Gene expression data from hypoxic cardiomyocytes in the absence of FGF21
X-12h-2


title: hypoxic cardiomyocytes without FGF21, biological rep1

description:
Gene expression data from hypoxic cardiomyocytes in the absence of FGF21
X-12h-1


title: Legionella Infection MOI 50 4h rep3

description: SAMPLE 10


title: hypoxic cardiomyocytes with FGF21, biological rep3

description:
Gene expression data from hypoxic cardiomyocytes in the presence of FGF21
X-12h+3


title: Legionella Infection + TNFAIP2 siRNA transfection rep1

description: SAMPLE 3


title: mice treated with cisplatin

city: Beijing

first: Chong

last: Li

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Gene expression data from tumors with drug treatment

hyb_protocol: The Cy3TM-labeled samples were hybridizedaccording to the manufacturer's protocol (Arraystar Inc).

scan_protocol: The slides were scanned usingthe Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed.

source_name: prostate cancer_cisplatin

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer's guideline.

value: LNCaP

tag: xenograft host

value: male NOD/SCID mice


title: Legionella Infection + TNFAIP2 siRNA transfection rep2

description: SAMPLE 7

tag: cell type


title: untreated rep3

description: SAMPLE 8


title: Legionella Infection MOI 50 4h rep2

description: SAMPLE 6


title: untreated rep1

description: SAMPLE 4


title: ctrl siRNA transfection (5 nM) rep2

description: SAMPLE 5


title: Legionella Infection MOI 50 4h rep1

description: SAMPLE 2


title: ctrl siRNA transfection (5 nM) rep1

description: SAMPLE 1


title: 5-aza-dC exposed differentiated adipocytes Day 10, 3 + 4 (pooled)

city: Wageningen

first: Myrthe

last: van den Dungen

address: Tuinlaan 5

country: Netherlands

institute: Wageningen University

description: Bone-marrow derived hMSCs from 43 years old black male

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: R-based open software (R 3.1.2)

label: Cy5 and Cy3

source_name: Independent experiment 3 + 4 (pooled)

label_protocol: Standard Illumina Protocol

growth_protocol: hMSCs were obtained and cultured according to the standard protocols (Lonza, Walkersville, USA).

extract_protocol: DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Venlo, the Netherlands).

treatment_protocol: Cells were either exposed to the vehicle control (DMSO) or continuously to 5-aza-dC.

tag: group

value: Differentiated + 5-aza-dC

tag: time point

value: Day 10

value: Bone-marrow derived hMSCs

value: 43 years

tag: race

value: black

tag: Sex

value: male


title: mice treated with vehicle PBS

description: Gene expression data from tumors with PBS treatment

source_name: prostate cancer_vehicle

value: prostate cancer

tag: cell line


title: TSU SCC

status: Public on Apr 12 2016

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young

institute: UCLA

description: Were deriveed and characterized previously by various labs, grown in DMEM + 10%FBS

hyb_protocol: Labeled cRNA was mixed with hybridization mix according to Affymetrix protocol and hybridized in Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed on Affymetrix 7G scanner with target intensity 500

data_processing: CEL files were normalized by RMA.  Probesets with a raw value of less than 50 in all cell types were eliminated.

source_name: derived from human SCC tumor tissue

label_protocol: Labeling was performed with Ambion MESSAGEAMP PREMIER kit (cat#: 4383452).

growth_protocol: For tissue derived cell types, primary cells were derived and cultured in appropriate culture medium for up to 3 weeks.  For pluripotent derived cell types, hESCs and hiPSCs were cultured under standard conditions with feeders and driven to differentiate under conditions as described previously.  For both tissue and pluripotent stem cell (PSC) derived cells, the indicated cell types were purified from mixed cultures either by expression of reporter construct (such as AFP-GFP for hepatocytes) and FACS, or by manual dissection based on morphology (such as rosettes for NPCs)(Patterson et al., 2011).  All purified cell types were judged to be pure if > 90% positive by immunostaining for at least 3 appropriate marker genes.  Many of these cell types were also assayed for appropriate function(Patterson et al., 2011).

extract_protocol: RNA was extracted according to manufacturers protocol with Total RNA kit from Stratagene

treatment_protocol: there were no experimental manipulations.  Cells were purified and profile in their native state

value: SCC

tag: protocol

value: collagenase/trypsin isolated and culture


title: Day 3 Hips1 p61

description: pluripotent stem cell derived definitive endoderm hESCs and hiPSCs were starved for serum replacer and administered Activin A. Four days later, these cultures showed a dramatic morphological change, and the cells induced expression of definitive endoderm markers such as SOX17 and FOXA2. Immunostaining and gene expression analysis demonstrated that these cells were at least 95% pure(Chan et al., 2012). These endodermal cultures were assayed for their ability to be further differentiated into endodermal cell types, such as hepatocytes ((Patterson et al., 2011) and below).

source_name: derived from PSC differentiated toward endoderm

value: PSC-endoderm

value: trypsinized culture


title: TH 212 SCC


title: H9 undiff

description: pluripotent stem cells hESCs and hiPSCs were generated as described previously (Chin et al., 2009; Lowry et al., 2008) and cultured in standard growth conditions on immortalized feeders in DMEM containing Knockout Serum Replacer. The following lines were profiled, and some were used to make differentiated progeny described below: H1, HSF1, H9, XFiPSC2(Karumbayaram et al., 2011), hiPSC1, hiPSC2, hiPSC18(Lowry et al., 2008), hiPSC19, and hiPSC21(Chin et al., 2009; Chin et al., 2010). Each line analyzed was extensively characterized by: immunostaining for pluripotency factors (OCT4 and NANOG) and cell surface markers such as Tra1-81; Embroid body (EB) formation and Teratoma analysis was conducted to demonstrate pluripotency; and Karyotyping analysis was conducted by Cell Line Genetics to ensure a stable karyotype. Immunostaining and gene expression analysis demonstrated that these cells were at least 95% pure(Chin et al., 2009; Lowry et al., 2008).

source_name: cultivated in standard hESC conditions with feeders

value: PSC-undiff

value: isolated by collagenase treated of culture


title: pMIPhiPSC3


title: hips2 p54


title: TH 686 SCC


title: ctrl siRNA transfection (5 nM) rep3

description: SAMPLE 9


title: hips1 p61


title: H1 undiff


title: HOC 313 SCC


title: Day 3 HSF1 P70


title: HSF1


title: HSF1 p51b [reanalysis]


title: Hips2 undiff


title: pMIPhiPSC2


title: Differentiated adipcytes Day 10, 4

source_name: Independent experiment 4

value: Differentiated


title: H1 p60 [reanalysis]


title: Differentiated adipcytes Day 10, 2

source_name: Independent experiment 2


title: Differentiated adipcytes Day 10, 1

source_name: Independent experiment 1


title: H9 p44 [reanalysis]


title: Undifferentiated hMSC 3

source_name: Independent experiment 3

value: Undifferentiated

value: Day 0


title: 5-aza-dC exposed differentiated adipocytes Day 10, 1 + 2 (pooled)

source_name: Independent experiment 1 + 2 (pooled)


title: Undifferentiated hMSC 1


title: DOLAp8(FADdediff)(myoep)

description: tissue-mesothelial, kidney epithelial, and myoepithelial cells were isolated, grown and prepared as described previously(Rheinwald et al., 1987).

source_name: derived from human mammary gland

value: tissue myoepithelial

value: mechanically isolated


title: hiPSC E [reanalysis]


title: Undifferentiated hMSC 4


title: Undifferentiated hMSC 2


title: DOLAp7(GIBdiff)(myoep)


title: KiN(Kid)

source_name: derived from human kidney

value: tissue Kidney epithelium


title: WL1_HK1

description: tissue-fibroblasts, keratinotyes and hepatocytes were isolated from discarded anonymized human dermis or liver obtained from Lonza (FBs and Heps) or Invitrogen (Keratinocytes). Fibroblasts were grown in fibroblast media (DMEM + FBS) for two weeks prior to lysis for RNA extraction. Keratinocytes were grown in KSFM (Invitrogen). Hepatocytes were grown in Bullet Kit (Lonza). Hepatocytes were shown to be functional by albumin secretion and PAS assays, and purity was assayed by staining for Albumin(Patterson et al., 2011). Fibroblasts were assayed for their ability to secrete appropriate collagens (Patterson et al., 2011), and keratinocytes were assayed for their function in a calcium switch assay as described(Blanpain et al., 2006).

source_name: derived from human skin

value: Tissue-Keratinocytes

value: separated from dermis by trypsin


title: BRSOp8(FADdediff)(myoep)


title: Hep Lonza ReadyHeps

source_name: derived from human liver

value: Tissue Hepatocytes


title: BRSOp9(GIBdiff)(myoep)


title: HM3(mesoth)

value: tissue mesothelial


title: NHDF3975 - Ad fem [reanalysis]

source_name: Derived from human skin

value: Tissue-Fibroblasts

value: enzymatically and mechanically isolated and briefly expanded


title: HK2


title: LP9(mesoth)


title: HK3


title: Hep Lonza 7F3475


title: Lonza


title: NHDF17430 - Ad fem [reanalysis]


title: G5E(HK)


title: NHDF3284 - Ad fem [reanalysis]


title: N(HK)p4


title: NHDF17914 - Ad fem [reanalysis]


title: NHDF3535 p5b - Ad fem [reanalysis]


title: HKi20(Kid)


title: NHDF1


title: IMR90 - EMB fem [reanalysis]


title: HUtSMC (8030602.2P)

description: tissue-endothelial cells, and smooth muscle cells were isolated and prepared from appropriate human tissue by Promocell. Each were judged by the manufacturer to be at least 95% pure by immunostaining for various markers.

source_name: derived from human vasculature

value: derived from human vasculature

value: mechanically isolated and expanded briefly


title: BJ NHDF


title: HUtSMC (8011507.2P)


title: HUVEC (9120901P)

value: tissue endothelial


title: HAoSMC (9052004.8p)


title: HUAEC (8071403.1P)


title: HCAEC(9100101.7P)


title: HDLEC (8010907.1P)


title: HAoSMC (0121402.2p)


title: HUAEC (8071701.1P)


title: HCAEC(8112001.12P)


title: HDLEC (0070602P)


title: HSF1 3WK DCX+NEURONS

description: pluripotent stem cell derived neurons PSC-NPCs were subjected to growth factor withdrawal and allowed to differentiate towards neurons and glia. The cultures were transfected with DCX-GFP, which shows high specificity to neurons in culture. Neurons were then isolated by FACS for GFP positive cells, and collected into RNA lysis buffer.

source_name: differentiated from PSCs

value: PSC-neurons

value: purified by facs for DCX-GFP reporter


title: HSF1 NPC p1 (1) [reanalysis]

description: pluripotent stem cell derived neural progenitor cells hESCs and hiPSCs were driven towards the neural lineage by addition of Neural induction medium (DMEM + B27, N2, EGF, FGF, Retinoic Acid, and Shh). Two weeks later, neural rosettes formed, and were manually dissected from the culture and plated onto Laminin/Ornithine coated plates. This purification scheme produced cultures that were at least 92% pure as judged by immunostaining for a variety of NPC markers (SOX2, PAX6, SOX1, MUSASHI etc)(Patterson et al., 2011). The differentiation capacity of these NPCs was demonstrated upon growth factor withdrawal, where two weeks later, neurons and glia were generated(Patterson et al., 2011).

value: PSC-derived NPCs

value: mechanically purified


title: H9 3WK DCX+NEURONS


title: HSF1 EB-NPC p1


title: HUVEC (9112602P)


title: HAoEC (7071706.1P)


title: Hep HSF1 d13-14

description: pluripotent stem cell derived hepatocytes hESC and hiPSC derived definitive endoderm was further differentiated towards hepatocytes by the addition of various growth factors (HGF, KGF etc). Additionally, the cultures were transfected with AFP-GFP construct to highlight the hepatocyte lineage. Hepatocytes were then isolated by FACS and lysed for gene expression analysis(Patterson et al., 2011). These hepatocytes were judged to be functional by both PAS assay and their ability to secrete albumin(Patterson et al., 2011).

value: PSC-derived hepatocytes

value: purified by FACS for AFP-GFP reporter


title: H9 EB-NPC p1


title: HSF1 NPC p1 (2)


title: hiPSC-E NPC p1 [reanalysis]


title: hiPSC2 NPC p2


title: H9  NPC p1 [reanalysis]


title: hiPSC2 3WK DCX+NEURONS


title: Hep H9 D12


title: Hips2 NPC p1


title: Hips1 neural p1


title: Hep hiPSC2 d12 AFPGFPT


title: FB HSF1 p7

description: pluripotent stem cell derived fibroblasts hESCs and hiPSCs were treated with collagenase to produce floating embryoid bodies in non-adherent plates. Two days later, the EBs were allowed to reattach to culture dishes in Fibroblast medium (DMEM + 10% FBS). Colonies with fibroblast morphology were manually isolated and plated into new dishes with FB medium. Cells were passaged four more times to generate pure cultures morphologically. Cell purity was assessed by immunostaining and judged to be 99% pure(Patterson et al., 2011).

value: PSC-derived Fibroblasts

value: purified mechanically


title: FB hiPSC1 p5


title: FB hiPSC18 p5


title: HAoEC (1102501.3P)


title: FB hiPSC-E p4


title: Fetal 16w Br2

description: tissue-NPCs Fetal brain and spinal cord specimens were obtained as discarded, anonymized tissues (IRB exempt). These specimens were physically and chemically dissociated to single cells and placed into NPC induction medium (see above) on Laminin/Ornithine coated plates. These cells were judged to be 100% pure NPCs by immunostaining(Patterson et al., 2011).

source_name: fetal tissue

value: mid gestation NPC

value: physically and mechanically isolated


title: Fetal 19w Br


title: FB H9 p5


title: Hep hiPSC18 d12 AFPGFPT


title: hiPSC18 NPC p1


title: Fetal 16w Brain p1


title: Fetal 16w SC p1


title: Fetal 6.5w SC

value: early gestation NPC


title: Fetal 15.5 SC p1


title: Fetal 8wk Cevical


title: Fetal 7.5w SC


title: Fetal 8wk Br


title: Fetal 8wk Thoracic


title: hFc-FNDC4 treated replicate 1

city: Solna

first: Estelle

last: Proux-Wéra

department: Department of Biochemistry and Biophysics

institute: Science for Life laboratory

description:
Bone marrow-derived macrophages from male C57Bl6N mice treated after differentiation with 100nM recombinant protein in 1% FCS DMEM
F4-1

hyb_protocol: 3ug of ss DNA target was  hybridized to  a Mouse Gene 1.1 ST Array Plate and washed and stained in the Gene Titan instrument.

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

data_processing:
Normalized probeset data generated with plier (Analysis Software = Expression Console, Method = plier (med-norm, target=0, doavg=false, calctarget=true, lowprecision=false,pm-gcbg))
Linear data transformation

label: Biotin

source_name: Bone marrow-derived macrophages treated for 24h with 100nM hFc-FNDC4 protein

label_protocol: 150ng of total RNA was used to generate amplified sense strand DNA targets with Ambion WT Expression Kit followed by fragmentation and biotinylation  with Affymetrix WT Expression Kit

growth_protocol: Bone marrow-derived macrophages were grown in growth media (DMEM, 10% FCS, 1% PenStrep and 20% L929 media)

extract_protocol: Trizol followed by RNAeasy cleanup

treatment_protocol: Before treatment with recombinant proteins, macrophages were starved for 24h in 1% FCS-DMEM and subsequently treated with 100nM hFc-FNDC4 or hFc control protein for 24h (also in 1% FCS-DMEM)

tag: gender

value: male

value: BMDM

value: hFc-FNDC4 protein


title: hFc treated replicate 3

description:
Bone marrow-derived macrophages from male C57Bl6N mice treated after differentiation with 100nM recombinant protein in 1% FCS DMEM
hFc-3

source_name: Bone marrow-derived macrophages treated for 24h with 100nM hFc control protein

tag: treatment

value: hFc control protein


title: hFc treated replicate 2

description:
Bone marrow-derived macrophages from male C57Bl6N mice treated after differentiation with 100nM recombinant protein in 1% FCS DMEM
hFc-2


title: hFc-FNDC4 treated replicate 2

description:
Bone marrow-derived macrophages from male C57Bl6N mice treated after differentiation with 100nM recombinant protein in 1% FCS DMEM
F4-2


title: hFc treated replicate 1

description:
Bone marrow-derived macrophages from male C57Bl6N mice treated after differentiation with 100nM recombinant protein in 1% FCS DMEM
hFc-1


title: Fetal 8wk Lumbar


title: hFc-FNDC4 treated replicate 3

description:
Bone marrow-derived macrophages from male C57Bl6N mice treated after differentiation with 100nM recombinant protein in 1% FCS DMEM
F4-3


title: colorectal cancer sample AUS2_276

city: Oslo

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

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

hyb_protocol: Samples were hybridized onto GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to the manufacturer's protocol.

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

data_processing: Exon-level expression signals were obtained from raw data by the RMA procedure implemented in the Affymetrix Expression Console software.

source_name: Colorectal cancer patient

label_protocol: Single-stranded cDNA was generated from amplified cRNA using the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from colorectal cancer biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol.

value: colorectal cancer biopsy


title: colorectal cancer sample AUS2_274


title: colorectal cancer sample AUS2_275


title: colorectal cancer sample AUS2_271


title: colorectal cancer sample AUS2_261


title: colorectal cancer sample AUS2_256


title: colorectal cancer sample AUS2_260


title: colorectal cancer sample AUS2_281


title: colorectal cancer sample AUS2_269


title: colorectal cancer sample AUS2_254


title: colorectal cancer sample AUS2_236


title: colorectal cancer sample AUS2_244


title: colorectal cancer sample AUS2_253


title: colorectal cancer sample AUS2_223


title: colorectal cancer sample AUS2_229


title: colorectal cancer sample AUS2_228


title: colorectal cancer sample AUS2_238


title: colorectal cancer sample AUS2_239


title: colorectal cancer sample AUS2_243


title: colorectal cancer sample AUS2_219


title: colorectal cancer sample AUS2_227


title: colorectal cancer sample AUS2_215


title: colorectal cancer sample AUS2_221


title: colorectal cancer sample AUS2_249


title: colorectal cancer sample AUS2_248


title: colorectal cancer sample AUS2_247


title: colorectal cancer sample AUS2_250


title: colorectal cancer sample AUS2_255


title: colorectal cancer sample AUS2_193


title: colorectal cancer sample AUS2_213


title: colorectal cancer sample AUS2_194


title: colorectal cancer sample AUS2_196


title: colorectal cancer sample AUS2_192


title: colorectal cancer sample AUS2_258


title: colorectal cancer sample AUS2_214


title: colorectal cancer sample AUS2_198


title: colorectal cancer sample AUS2_264


title: colorectal cancer sample AUS2_191


title: Liver_interleukin-18 knockout_6w-biological rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: whole liver derived from 6 week-old IL-18KO strain

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for data processing.

source_name: whole liver derived from 6w IL-18KO strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from whole livers stored in RNA later (Ambion), derived from wild type and interleukin-18 knockout mice using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

value: BALB/c

tag: organ

value: Liver

tag: genotype

value: interleukin-18 knockout

value: 6 week-old


title: Liver_wild type_12w-biological rep3

description: whole liver derived from 12 week-old wild type strain

source_name: whole liver derived from 12w wild type strain

value: wild type

tag: age

value: 12 week-old


title: colorectal cancer sample AUS2_176

tag: tissue


title: Liver_interleukin-18 knockout_12w-biological rep3

description: whole liver derived from 12 week-old IL-18KO strain

source_name: whole liver derived from 12w IL-18KO strain

tag: strain


title: Liver_interleukin-18 knockout_6w-biological rep3


title: Liver_interleukin-18 knockout_12w-biological rep1


title: Liver_wild type_12w-biological rep2


title: Liver_interleukin-18 knockout_12w-biological rep2


title: Liver_interleukin-18 knockout_6w-biological rep1


title: colorectal cancer sample AUS2_179


title: colorectal cancer sample AUS2_172


title: colorectal cancer sample AUS2_174


title: colorectal cancer sample AUS2_181


city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
microarray hybridization date: 11/30/2009
CCL-153 cells, 4-hour control, replicate C4

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: Sample CEL files from 07/28/2009 and 11/30/2009 microarray hybridization date batches were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output separately.

source_name: human fetal lung fibroblasts CCL-153

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Cells were seeded at a density of 20,000 cells per square millimeter in collagen I-coated BioFlex 6-well plates (FlexCell int.,Hillsborough, NC) in 10% FBS-supplemented F12K medium and incubated at 37 degrees Celsius and 5% carbon dioxide for 24 hours.

extract_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

treatment_protocol: Media was then replaced with FBS-free F12K medium for 24 hours after which cells were left unstretched (control) or stretched 30% (strain rate~0.5%/second) and kept stretched for 4 hours or 24 hours, and then harvested for RNA extraction.


title: colorectal cancer sample AUS2_188


description:
microarray hybridization date: 11/30/2009
A549 cells, 4-hour control, replicate C5

source_name: human adenocarcinoma alveolar basal epithelial cell A549


title: colorectal cancer sample AUS2_154


title: colorectal cancer sample AUS2_139


description:
microarray hybridization date: 11/30/2009
A549 cells, 4-hour 30% stretch, replicate B6


title: colorectal cancer sample AUS2_138


title: colorectal cancer sample AUS2_151


description:
microarray hybridization date: 11/30/2009
CCL-153 cells, 4-hour 30% stretch, replicate C3


title: colorectal cancer sample AUS2_211


title: Liver_wild type_6w-biological rep2

description: whole liver derived from 6 week-old wild type strain

source_name: whole liver derived from 6w wild type strain


title: colorectal cancer sample AUS2_136


title: colorectal cancer sample AUS2_143


description:
microarray hybridization date: 11/30/2009
CCL-153 cells, 4-hour control, replicate B4


description:
microarray hybridization date: 11/30/2009
16HBE14o- cells, 4-hour control, replicate C2

source_name: human bronchial epithelial cells 16HBE14o-


description:
microarray hybridization date: 11/30/2009
A549 cells, 4-hour control, replicate C1


title: Liver_wild type_6w-biological rep1


description:
microarray hybridization date: 11/30/2009
16HBE14o- cells, 4-hour control, replicate B3


description:
microarray hybridization date: 11/30/2009
CCL-153 cells, 4-hour 30% stretch, replicate B5


description:
microarray hybridization date: 11/30/2009
16HBE14o- cells, 4-hour 30% stretch, replicate B2


description:
microarray hybridization date: 11/30/2009
A549 cells, 4-hour 30% stretch, replicate B1


title: sh2-shRNA treated primary kidney proximal tubular epithelial cells at day 25  replicate3

city: GRONINGEN

first: Jun

state: Netherlands

address: Esdoornlaan

department: Genetics

institute: University Medical Center Groningen

description:
mRNA expression analysis SETD2-shRNA (sh2) transduced PTECs at day 25
Sample 18
Cy3 signals in raw data files represent unrelated samples

hyb_protocol: Each Cy-5 sample was mixed with the same amount of a cy3-labeled sample, which was non-relevant for this study, and hybridized at 65°C overnight on Agilent-050524 SurePrint G3 Custom Human 8x60K Microarrays.

scan_protocol: On the following day, slides were washed and signals were scanned with GenePix 4000B (Agilent).

data_processing: Signal intensities from scanned images were processed and converted into Linear and Lowess normalized data using Agilent Feature Extraction software version 10.7.3.1. Data was analyzed by GeneSpring GX 12.5 software (Agilent Technologies). The data was subject to quantile normalization without base line transformation.

source_name: PTECs_N3_SH2_day 25

label_protocol: First strand cDNA was synthesized from 50-100ng RNA, followed by cRNA amplification and labeling with Cy5 according to manufacturer's protocol (Agilent). Purification of Cy5 labeled cRNA was carried out with Qiagen RNeasy Mini kit.

growth_protocol: Primary proximal tubular epithelial cells (PTECs) were cultured in DMEM/F-12 GLUTMAX-1 (Sigma-Aldrich, St. Louis, MO, USA ) containing 10% FBS, 1% P/S (100 U/ml penicillin and 100 µg/ml streptomycin), 5μg/ml ITS (Sigma-Aldrich) and 5ng/ml EGF respectively.

extract_protocol: Total RNA was isolated by using Gene JET RNA purification kit (Fermentas, Waltham, MA, USA) with the instruction offered by the manufacture.

treatment_protocol: Primary PTECs were transduced with SETD2 shRNA (sh1 and sh2), and non-targeting shRNA (NT); PTECs without virus treatment were included as a control. Both control and NT-PTECs (high MOI) were harvested at day 6 were named as PTECs_CON and PTECs_NT; PTECs harvested at day 16 were  named as PTECs_S_CON and PTECs_S_NT;  PTECs transduced with SETD2 shRNA (sh1 and sh2, low MOI) that were prevented from senescence were harvest at day 25 after transduction and named as  PTECs_SH1/SH2.

value: kidney

value: proximal tubular epithelial cells


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 24-hour control, replicate c

source_name: human fetal lung fibroblasts CCL-151


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 24-hour 30% stretch, replicate c


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 4-hour 30% stretch, replicate c


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 4-hour control, replicate c


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 24-hour 30% stretch, replicate b


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 24-hour control, replicate b


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 24-hour 30% stretch, replicate a


title: sh2-shRNA treated primary kidney proximal tubular epithelial cells at day 25  replicate1

description:
mRNA expression analysis SETD2-shRNA (sh2) transduced PTECs at day 25
Sample 16
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N1_SH2_day 25


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 4-hour control, replicate b


title: sh2-shRNA treated primary kidney proximal tubular epithelial cells at day 25  replicate2

description:
mRNA expression analysis SETD2-shRNA (sh2) transduced PTECs at day 25
Sample 17
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N2_SH2_day 25


title: sh1-shRNA treated primary kidney proximal tubular epithelial cells at day 25 replicate1

description:
mRNA expression analysis SETD2-shRNA (sh1) transduced PTECs at day 25
Sample 13
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N1_SH1_day 25


title: NT-shRNA treated primary kidney proximal tubular epithelial cells at day 16  replicate3

description:
mRNA expression analysis of NT-shRNA transduced PTECs at day 16 days
Sample 12
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_S_N3_NT_day 16


title: sh1-shRNA treated primary kidney proximal tubular epithelial cells at day 25 replicate2

description:
mRNA expression analysis SETD2-shRNA (sh1) transduced PTECs at day 25
Sample 14
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N2_SH1_day 25


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 24-hour control, replicate a


title: sh1-shRNA treated primary kidney proximal tubular epithelial cells at day 25 replicate3

description:
mRNA expression analysis SETD2-shRNA (sh1) transduced PTECs at day 25
Sample 15
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N3_SH1_day 25


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 4-hour 30% stretch, replicate a


description:
microarray hybridization date: 07/28/2009
CCL-151 cells, 4-hour control, replicate a


title: Hybrid weakness, root of a parental cultivar, Nipponbare, biological rep1

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

description: Gene expression of normal roots of a parental cultivar, 'Nipponbare'.

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 400 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2565BA.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.3.1 (Agilent). We slightly modified manufacturer's default extraction protocol called 'GE1-v5_95_Feb07' as follows: 'Background Subtraction Method' was set to 'Average of Negative Control Features', and 'Use Surrogates' was set to 'False'. Then 'gBGSubSignal' columns were extracted from the text data files produced by FeatureExtraction, and introduced into GeneSpring 7.3.1 (Agilent). Positive and negative control features (such as spike-in or dark corner) were removed before data introduction into GeneSpring. Introduced signal intensities were scaled to median per chip, and the lowest value of scaled signal intensity was set to 0.01. Normalized signal intensities of some probes locating multiple positions on a array were average values of all corresponding probes.

organism: Oryza sativa Japonica Group

source_name: Root, two-week old seedling of Nipponbare

label_protocol: Cy3-labeled cRNA were prepared from 100 ng of total RNA using Quick-Amp Labeling Kit (Agilent) according to manufacturer's protocol.

growth_protocol: Plants were aseptically germinated and cultivated on MS medium at 25˚C under continuous light (20 Em–2 s–1). After two weeks cultivation, seedlings were used for measurement.

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

treatment_protocol: Collected biological samples were frozen in liquid nitrogen and kept at -80˚C until RNA extraction.

tag: subspecies

value: japonica

tag: cultivars

value: Nipponbare


title: Hybrid weakness, root of a parental cultivar, Nipponbare, biological rep3


title: Hybrid weakness, root of a parental cultivar, Nipponbare, biological rep2


title: Hybrid weakness, root of a parental cultivar, Jamaica, biological rep2

description: Gene expression of normal roots of a parental cultivar, 'Jamaica'.

source_name: Root, two-week old seedling of Jamaica

value: Jamaica


title: Hybrid weakness, root of a parental cultivar, Jamaica, biological rep1


title: Liver_wild type_12w-biological rep1

description: whole liver derived from 12 week-old wild type strain


title: NT-shRNA treated primary kidney proximal tubular epithelial cells at day 16  replicate2

description:
mRNA expression analysis of NT-shRNA transduced PTECs at day 16 days
Sample 11
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_S_N2_NT_day 16


title: Hybrid weakness, root of the F1 hybrid between Nipponbare and Jamaica, biological rep4

description: Gene expression of abnormal roots in hybrid weakness.

source_name: Root, two-week old seedling of F1 hybrid between Nipponbare and Jamaica

value: F1 hybrid between Nipponbare X Jamaica


title: non-treated primary kidney proximal tubular epithelial cells at day 16 replicate3

description:
mRNA expression analysis of wildtype PTECs at day 16
Sample 9
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_S_N3_CON_day 16


title: NT-shRNA treated primary kidney proximal tubular epithelial cells at day 6  replicate3

description:
mRNA expression analysis of NT-shRNA transduced PTECs at day 6 days
Sample 6
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N3_NT_day 6


title: NT-shRNA treated primary kidney proximal tubular epithelial cells at day 6  replicate2

description:
mRNA expression analysis of NT-shRNA transduced PTECs at day 6 days
Sample 5
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N2_NT_day 6


title: non-treated primary kidney proximal tubular epithelial cells at day 16 replicate2

description:
mRNA expression analysis of wildtype PTECs at day 16
Sample 8
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_S_N2_CON_day 16


title: Hybrid weakness, root of a parental cultivar, Jamaica, biological rep3


title: non-treated primary kidney proximal tubular epithelial cells at day 16 replicate1

description:
mRNA expression analysis of wildtype PTECs at day 16
Sample 7
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_S_N1_CON_day 16


title: non-treated primary kidney proximal tubular epithelial cells at day 6 replicate2

description:
mRNA expression analysis of wildtype PTECs at day 6
Sample 2
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N2_CON_day 6


title: NT-shRNA treated primary kidney proximal tubular epithelial cells at day 16  replicate1

description:
mRNA expression analysis of NT-shRNA transduced PTECs at day 16 days
Sample 10
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_S_N1_NT_day 16


title: non-treated primary kidney proximal tubular epithelial cells at day 6 replicate1

description:
mRNA expression analysis of wildtype PTECs at day 6
Sample 1
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N1_CON_day 6


title: Hybrid weakness, root of the F1 hybrid between Nipponbare and Jamaica, biological rep2


title: non-treated primary kidney proximal tubular epithelial cells at day 6 replicate3

description:
mRNA expression analysis of wildtype PTECs at day 6
Sample 3
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N3_CON_day 6


title: Liver_wild type_6w-biological rep3

description: whole liver derived from 6 week-old wild type strain

source_name: whole liver derived from 6w wild type strain


title: NT-shRNA treated primary kidney proximal tubular epithelial cells at day 6  replicate1

description:
mRNA expression analysis of NT-shRNA transduced PTECs at day 6 days
Sample 4
Cy3 signals in raw data files represent unrelated samples

source_name: PTECs_N1_NT_day 6


title: Hybrid weakness, root of the F1 hybrid between Nipponbare and Jamaica, biological rep1


title: Hybrid weakness, root of the F1 hybrid between Nipponbare and Jamaica, biological rep3


title: Transgenic NA1363 Strain Replicate 5

city: CHATENAY-MALABRY

first: Claudine

last: DELOMENIE

address: 5, rue Jean-Baptiste Clément

department: Transcriptomique

country: France

institute: University Paris Sud 11

description: Biological replicate (culture batch) 2 of 2. Individual culture 1 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After washing, slides were scanned using the Agilent Microarray Scanner (G2565CA) at 5-µm resolution.

scan_protocol: After washing, slides were scanned using the Microarray Scanner (G2565CA) from Agilent at 5-µm resolution and at high and low photomultiplier voltages. Images were quantified using Agilent Feature Extraction 10.7.3.1. software with default protocols and settings.

data_processing: Data were computed using Genespring GX software version 12.6 (Agilent Technologies). Fluorescence signals were background-subtracted and a filtering procedure excluded data points considered unreliable as they corresponded to probe sets associated with low signal intensities or bad quality features. A within-array loess normalization was performed, followed by an inter-array scaling normalization.

organism: Aspergillus nidulans

source_name: transgenic NA1363 strain (LacZ)

label_protocol: 200 ng of total RNA were labelled using the Low Input Quick Amp Labelling Kit, Two-Color (Agilent Technologies), using Cy5-CTP for the reference RNA pool  made of a mix of all samples, and Cy3-CTP for individual samples.

growth_protocol: Mycelia were grown at 30°C for 15 h in 400 mL minimal medium with shaking at 150 rpm, in the presence of fructose (0.1%) as the carbon source and urea (5 mM) as the nitrogen source. Media composition, supplements and basic growth conditions were as described by Cove DJ (Biochim Biophys Acta. 1966 Jan 11;113(1):51-6. PMID: 5940632 1966). For each strain, 4 cultures were carried out in each one of two independent experiments.

extract_protocol: Total RNA was isolated as previously described (Total RNA was isolated with guanidine as  described (Robellet X et al. 2010 Curr Genet. 2010 56(4):341-8. doi: 10.1007/s00294-010-0303-5. Epub 2010 May 22). An additional purification step was performed using Trizol following manufacturer's instructions

value: NA1363 (pabaA1) harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in chromosome VIII. This construct, carried out in a derivative of the pBR322 vector, contained the E. coli lacZ sequence (encoding ß-galactosidase) fused to the A. nidulans trpC terminator and placed under the control of the strong and constitutive promoter of the A. nidulans gpdA gene, and the riboB gene as selection marker.

value: mycelium

source_name: pooled WT and TG strains

value: mix of 4 strains  CV125 (pabaA1) and 3 transgenic (pabaA1) strains harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in different chromosomes (NA1363, in chromosome VIII; NA1360, in chromosome V; NA1359, in chromosome II).


title: Transgenic NA1363 Strain Replicate 8

description: Biological replicate (culture batch) 2 of 2. Individual culture 4 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.


title: Transgenic NA1363 Strain Replicate 6

description: Biological replicate (culture batch) 2 of 2. Individual culture 2 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 23

city: Penrith

first: Christine

middle: L

last: Chiu

state: New South Wales

address: Locked Bag 1797

department: School of Medicine

country: Australia

institute: Western Sydney University

description: normal placenta

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then pre-processed in the R package wateRmelon using the dasen function. processed data: dasen normalized beta

source_name: placental biopsy collected <30mins of delivery

extract_protocol: Genomic DNA extracted from placental biopsies using Qiagen DNA mini kit as per manufacturer's protocols

value: Male

tag: disease

value: normal/healthy

tag: gestation (wk)

value: placenta


title: Transgenic NA1363 Strain Replicate 3

description: Biological replicate (culture batch) 2 of 2. Individual culture 3 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.


title: Transgenic NA1363 Strain Replicate 7

description: Biological replicate (culture batch) 2 of 2. Individual culture 3 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 19

description: normal placenta


title: Transgenic NA1363 Strain Replicate 4

description: Biological replicate (culture batch) 2 of 2. Individual culture 4 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 24

description: normal placenta

value: Female


title: genomic DNA from placental biopsy 20

description: normal placenta


title: genomic DNA from placental biopsy 21

description: normal placenta


title: Transgenic NA1363 Strain Replicate 1

description: Biological replicate (culture batch) 2 of 2. Individual culture 1 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 17

description: normal placenta


title: KMS11 hypoxia

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

description: SAMPLE 7

hyb_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intensity with 75%tile normalization.

source_name: KMS11 hypoxia

growth_protocol: normoxia: 21%O2, hypoxia: 1%O2.

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: RPMI1640 plus 10% FCS.

tag: oxygen status

value: hypoxia

tag: cell type

value: myeloma


title: MM.1S hypoxia

description: SAMPLE 8

source_name: MM.1S hypoxia

label_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).


title: KMS12BM hypoxia

description: SAMPLE 6

source_name: KMS12BM hypoxia


title: Control CV125 Strain Replicate 6

description: Biological replicate (culture batch) 1 of 2. Individual culture 2 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.

source_name: control CV125 strain (WT)

value: CV125 (pabaA1)


title: genomic DNA from placental biopsy 22

description: normal placenta


title: genomic DNA from placental biopsy 14

description: normal placenta


title: Control CV125 Strain Replicate 7

description: Biological replicate (culture batch) 1 of 2. Individual culture 3 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 18

description: normal placenta


title: genomic DNA from placental biopsy 9

description: normal placenta


title: Control CV125 Strain Replicate 8

description: Biological replicate (culture batch) 1 of 2. Individual culture 4 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 13

description: normal placenta


title: genomic DNA from placental biopsy 16

description: normal placenta


title: genomic DNA from placental biopsy 5

description: preeclampsia placenta

value: preeclampsia


title: genomic DNA from placental biopsy 12

description: normal placenta


title: genomic DNA from placental biopsy 15

description: normal placenta


title: genomic DNA from placental biopsy 6

description: preeclampsia placenta


title: genomic DNA from placental biopsy 1

description: preeclampsia placenta

source_name: placental biopsy collected <30mins of delivery from foetal side. Rinsed in PBS.


title: genomic DNA from placental biopsy 10

description: normal placenta


title: genomic DNA from placental biopsy 7

description: preeclampsia placenta


title: Control CV125 Strain Replicate 5

description: Biological replicate (culture batch) 1 of 2. Individual culture 1 of 4. Transgenic NA1363 strain, untreated, cultured in an individual vial and harvested.


title: MM.1S normoxia

description: SAMPLE 4

source_name: MM.1S normoxia

value: normoxia


title: genomic DNA from placental biopsy 3

description: preeclampsia placenta


title: genomic DNA from placental biopsy 4

description: preeclampsia placenta


title: KMS11 normoxia

description: SAMPLE 3

source_name: KMS11 normoxia


title: genomic DNA from placental biopsy 2

description: preeclampsia placenta


title: Homo_control

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

institute: Third Affiliated Hospital of Soochow University

description: control serum

data_processing: The Ct (cycle threshold) was automatically given by SDS 2.3 software (Applied Biosystems) and is defined as the fractional cycle number at which the fluorescence passes the fixed threshold. U6 embedded in the TaqMan Human MicroRNA Arrays was used as an internal control. The relative expression levels of miRNAs were calculated using the comparative ΔΔCt method.

source_name: pooled serum samples from 20 healthy controls

label_protocol: For cDNA synthesis, 30 ng of total RNA was subjected to reverse transcription using a TaqMan® microRNA Reverse Transcription Kit (#4366596; Applied Biosystems) and Megaplex RT primers (Human Pool A + B; Applied Biosystems) following the manufacturer’s protocol, allowing simultaneous reverse transcription of 739 mature human miRNAs to generate a miRNA cDNA library corresponding to each serum sample. Reverse transcription was performed with the following cycling conditions: 40 cycles at 16°C for 2 min, 42°C for 1 min and 50°C for 1 s followed by a final step of 80°C for 5 min to inactivate reverse transcriptase. Thereafter, to generate enough miRNA cDNA template for the following real-time PCR, the cDNA libraries were pre-amplified using Megaplex PreAmp primer and PreAmp Master Mix (Applied Biosystems) following the manufacturer’s instructions. The PreAmp primer pool used here consisted of forward primers specific for each of the 739 human miRNAs and a universal reverse primer. The pre-amplification cycling conditions were as follows: 95°C for 10 min, 55°C for 2 min, 72°C for 2 min followed by 12 cycles at 95°C for 30 s and 60°C for 4 min; the samples were then held at 99.9°C for 10 min. After the preamplification step, the products were diluted with RNase-free water, combined with TaqMan gene expression Master Mix and then loaded into TaqMan TaqMan Low Density Array (TLDA) (Applied Biosystems), which are two 384-well formatted plates and real-time PCR-based microfluidic cards with embedded TaqMan primers and probes in each well for the 739 different mature human miRNAs. Real-time PCR was performed on an ABI PRISM 7900HT sequence detection system (Applied Biosystems) with the following cycling conditions: 50°C for 2 min, 94.5°C for 10 min followed by 40 cycles at 95°C for 30 s and 59.7°C for 1 min.

extract_protocol: Total RNA was isolated from each pool of serum samples using the mirVana miRNA Isolation Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The pre-operative blood samples were obtained from meningioma patients prior to surgery and/or chemotherapy. The control blood samples were obtained from healthy people. All extracted serum samples were stored in phased liquid nitrogen.

tag: subject status

value: healthy control

value: serum


title: Homo_meningioma

description: pre-operative meningioma serum

source_name: pooled serum samples from 20 pre-operative meningioma patients

value: pre-operative meningioma patients