title: 4TO7 rigid TGFb set2


title: 4TO7 compliant TGFb set1

status: Public on Oct 31 2012

type: RNA

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Road, Rm 2404

country: USA

institute: Case Western Reserve University

hyb_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

data_processing:
The Thermo Scientific Dharmacon Synthetic microRNA Reference Probe Set is an equimolar mixture of 5'-Thermo Scientific DyLight 547-labeled, single-stranded synthetic miRNAs targeting all mature human, mouse, and rat miRNA sequences in the Sanger miRBase sequence database.  This  internal reference provides reproducible data normalization and controls for variations due to up-stream processes (array manufacture, washing and    hybridization processes, pipeting variation, etc.).
Data processing was performed with total 36 samples, yet data for 24 samples are presented. Relative intensity data for 36 samples was subjected to statistical quality filtering, keeping miRNA probes with P-value <=0.05 in at least 18 of the 36 experiments.  This resulted in 338 miRNA probes passing statistical quality fliters.  The remaining data was inter-array scaled and transformed to log2 prior to performing one-way ANOVA analyses for each cell line.
Post hoc analysis was undertaken to identify miRs whose expression was significantly (P<0.01) upregulated following administration of TGF-beta.

molecule: total RNA

organism: Mus musculus

growth_protocol: 67NR, 4TO7, and 4T1 cells were propagated for 6 days in 3D organotypic cultures

extract_protocol: Total RNA was prepared using the Qiagen Rneasy Plus Mini Kit and following the supplementary protocol for purification of miRNA (Qiagen).

treatment_protocol: Cells were treated with TGF-beta or a TGF-beta-type-I-receptor inhibitor

tag: cell line

tag: cell type

value: systemically invasive breast carcioma cells

tag: treated with

value: TGFb

tag: microenvironment

value: compliant

tag: molecule subtype

value: microRNA


title: 4TO7 rigid basal set1

scan_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

value: rigid


title: Non-Retinoblastoma serum -Replicate2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit(Agilent) according to the manufacturer's instructions

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.0 (Agilent) using default parameters

organism: Homo sapiens

source_name: Whole blood serum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using miRNA Complete Labeling and Hyb Kit(Agilent) according to the manufacturer's instructions

extract_protocol: RNA was prepared using the mirVana RNA Isolation kit(Ambion) following the manufacturer's recommendations

treatment_protocol: Freshly isolated whole blood serum from normal healthy individual and Retinoblastoma patients were obtained then perserved at -80 ºC

value: Non-Retinoblastoma


title: ESC FBS LINE ES02 PASSAGE 49

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
ESC FBS LINE ES02 PASSAGE 49
Raw data file: SAMPLE 28.txt

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ESC FBS LINE ES02 PASSAGE 49 (SAMPLE 28)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells.  Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.  Embryoid bodies were cultured in fibroblast medium (FBS; EB_mesend) or in hESC medium without bFGF (EB_ecto) in 60mm Corning Low Attachment dishes for a total of 8 days. Media were changed by sedimentation every 2 days. An important point to note is that the same lot number of FBS was used for all studies.

extract_protocol: RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

tag: class

value: ESC

tag: condition

value: FBS

tag: line

tag: passage

tag: gender

value: FEMALE

tag: processing control

value: SAMPLE 126


title: ESC KSR LINE ES01 PASSAGE 71

description:
ESC KSR LINE ES01 PASSAGE 71
Raw data file: SAMPLE 23.txt

source_name: ESC KSR LINE ES01 PASSAGE 71 (SAMPLE 23)

value: KSR

value: SAMPLE 125


title: ESC UNDIFF LINE ES02 PASSAGE 45

description:
ESC UNDIFF LINE ES02 PASSAGE 45
Raw data file: SAMPLE 27.txt

source_name: ESC UNDIFF LINE ES02 PASSAGE 45 (SAMPLE 27)

value: UNDIFF


title: ESC FBS LINE ES02 PASSAGE 45

description:
ESC FBS LINE ES02 PASSAGE 45
Raw data file: SAMPLE 25.txt

source_name: ESC FBS LINE ES02 PASSAGE 45 (SAMPLE 25)


title: 67NR rigid TGFb set2

label_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

value: nonmetastatic breast carcioma cells


title: 67NR rigid basal set1


title: 4T1 rigid TGFb set1

value: highly metastatic breast carcioma cells


title: 4T1 compliant TGFb set1


title: 4T1 rigid basal set2


title: 67NR compliant TGFb set2


title: ESC FBS LINE ES01 PASSAGE 71

description:
ESC FBS LINE ES01 PASSAGE 71
Raw data file: SAMPLE 22.txt

source_name: ESC FBS LINE ES01 PASSAGE 71 (SAMPLE 22)


title: ESC UNDIFF LINE ES01 PASSAGE 71

description:
ESC UNDIFF LINE ES01 PASSAGE 71
Raw data file: SAMPLE 24.txt

source_name: ESC UNDIFF LINE ES01 PASSAGE 71 (SAMPLE 24)


title: ESC UNDIFF LINE ES01 PASSAGE 67

description:
ESC UNDIFF LINE ES01 PASSAGE 67
Raw data file: SAMPLE 21.txt

source_name: ESC UNDIFF LINE ES01 PASSAGE 67 (SAMPLE 21)


title: Non-Retinoblastoma serum -Replicate1


title: Colony1

city: Poughkeepsie

first: Jodi

last: Schwarz

address: 124 Raymond Ave

institute: Vassar College

description: Biological replicate 1 of 5

hyb_protocol: Overnight hyb at 65 deg, wash and scan

scan_protocol: Scanned on an Axon scanner. Images were quantified using GenePix and TM4

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Orbicella franksi

source_name: Coral colony nubbin, ambient SW control

label_protocol: linear amplification of RNA; 1 µg of total RNA RT; labelled with Cy3 or Cy5

growth_protocol: Maintained in ambient conditions

extract_protocol: Total RNA extracted using RNEasy with glass beads and Dnase

tag: tissue

value: Whole tissue from colony; multiple polyps

tag: sample type

value: colony 1

tag: treatment

value: ambient seawater

source_name: Coral colony nubbin, SW supplemented with 50ppb copper

value: 50 ppb copper


title: Colony5

description: Biological replicate 5 of 5

value: colony 5


title: Colony3

description: Biological replicate 3 of 5

value: colony 3


title: 4T1 compliant TGFb set2

value: TGFb

value: compliant

value: microRNA


title: Colony2

description: Biological replicate 2 of 5

value: colony 2


title: Colony4

description: Biological replicate 4 of 5

value: colony 4


title: HUVEC_TNF&TGF_7

city: Westmead

first: Catherine

last: Emmanuel

state: NSW

address: Westmead Centre for Oral Health, Westmead Hospital

department: Oral Pathology

country: Australia

institute: University of Sydney

description: Biological replicate 3 of 4

hyb_protocol: Labelled cDNA were concentrated to 13.5 μl before addition of 25 μl of 2X hybridisation buffer composed of formamide (50%), NaCl (750 mM), sodium citrate (75 mM), SDS (0.2%), Poly A, salmon sperm and human Cot1 DNA in milli Q H2O. Mixtures were boiled for 1 min, cooled to room temperature and applied to a clean coverslip. Microarrays were inverted onto the coverslips, air bubbles were gently removed and placed inside a microarray hybridisation chamber in a 42ºC water bath overnight.

scan_protocol: Scanned on a Gene Pix 4000B scanner and data collected using GenePixPro v6.0 software

data_processing: Spots for which the intensity of fluorescence on both channels was not greater than twice the background fluorescence were excluded from further analysis. Remaining data was normalised using the Print-Tip Loess method.

source_name: HUVEC, TNF-α and TGF-β1, 8hr

label_protocol: 35 µg of total RNA were primed with 5 µl of 0.5 µg/µl polydT-15 primer at 70°C for 5 min, then reversed transcribed at 50°C for 3 h in the presence of SuperScript III RTase (Invitrogen), and 1 mM each dATP, dCTP, dGTP, with 600 µM aminoallyl-dUTP and 400 µM dTTP. cDNA was purified, spectrophotometrically quantitated and concentrated. A minimum of 750 ng was labelled with Cy3 or Cy5.

growth_protocol: HUVEC were grown in medium 199 (M199) supplemented with 20% fetal bovine calf serum, endothelial cell growth supplement (50 µg/ml) and heparin (30 U/ml) and including penicillin (100 U/ml), streptomycin (100 µg/ml) and amphotericin B (2.5 µg/ml).

extract_protocol: Total RNA extracted using RNAqueous kit (Ambion) following manufacturer's instructions and analysed using Agilent BioAnalyser. Only RNA with RIN of 10 was reverse transcribed.

treatment_protocol: HUVEC were seeded into 75 cm2 flasks and allowed to adhere overnight in complete culture medium. The next day, medium was removed, cells washed with M199 and stimulated with 4% bovine serum albumin in M199 containing either no cytokine or TNF-α (588 pM) or TGF-β1 (40pM) singly or combined as described.

value: primary HUVEC

value: endothelial cell

value: TNF-α and TGF-β1, 8hr

source_name: HUVEC, TGF-β1, 8hr

value: TGF-β1, 8hr


title: 67NR rigid basal set2

value: nonmetastatic breast carcioma cells

value: rigid


title: ESC FBS LINE ES01 PASSAGE 67

description:
ESC FBS LINE ES01 PASSAGE 67
Raw data file: SAMPLE 19.txt

source_name: ESC FBS LINE ES01 PASSAGE 67 (SAMPLE 19)

value: ESC

value: FBS

value: FEMALE

value: SAMPLE 125


title: HUVEC_TNF&TGF_8

description: Biological replicate 4 of 4


title: Leaf_Control_45days_rep1

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

description: Gene expression after 45 days in control leaf

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Helianthus annuus

source_name: Control leaf, 45d, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Field experiments were carried out at INTA Balcarce Experimental Station (37°45’S,  8°18’W) during the 2004/2005 crop season. Sunﬂower hybrid VDH 481 (Advanta Seeds) was sown at a 7.2  plants/m2 density and seeds emerged 11 days later. Diseases, weeds, and insects were adequately controlled. Soil fertility assured maximum yields under adequate water conditions. Rainfall was complemented with irrigation when necessary to avoid water deﬁcit, except for the case of water deﬁcit treatment.

extract_protocol: Samples were immediately frozen in liquid nitrogen and conserved at -80°C until their processing. High quality total RNA was isolated from 100 mg of frozen using the Trizol® method (Invitrogen, Argentina). The genomic DNA was eliminated after treatment with Dnase I for 20 min at RT using DNAse I® (Invitrogen, Argentina).  RNA concentration was measured using a Nanodrop ND-100 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware USA). Purity and integrity of total RNA was determined by 260/280 nm ratio and the integrity was checked by electrophoresis in 1% agarose gel and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

treatment_protocol: Water Deficit: a mild water deficit was achieved by covering the soil with a 200 mm plastic mesh to avoid rainfall penetration into the soil. The mesh was installed 10 days before flowering, and reduced about 40% the volumetric humidity of the soil. Controlled irrigation allowed keeping the deficit level from treatment application up to the sample harvest day.  Flower excision: the flower of several plants was cut with a fine scalpel 4 days before flowering, in order to suppress the reproductive sink.  Control: Untreated plants were kept as controls.

value: Leaf

tag: age

tag: stress

value: Control


title: ESC KSR LINE ES01 PASSAGE 67

description:
ESC KSR LINE ES01 PASSAGE 67
Raw data file: SAMPLE 20.txt

source_name: ESC KSR LINE ES01 PASSAGE 67 (SAMPLE 20)

value: KSR


title: HUVEC_TNF&TGF_4

description: Biological replicate 4 of 4

source_name: HUVEC, TNF-α, 8hr

value: TNF-α, 8hr


title: HUVEC_TNF&TGF_6

description: Biological replicate 2 of 4


title: 4TO7 compliant TGFb set2

value: systemically invasive breast carcioma cells

value: TGFb

value: compliant

value: microRNA


title: 4T1 compliant basal set1

value: highly metastatic breast carcioma cells


title: 4TO7 compliant basal set2


title: 4T1 rigid TGFb set2


title: HUVEC_TNF&TGF_3

description: Biological replicate 3 of 4

value: primary HUVEC

value: endothelial cell

value: TNF-α and TGF-β1, 8hr


title: HUVEC_TNF&TGF_5

description: Biological replicate 1 of 4

value: TGF-β1, 8hr


title: HUVEC_TNF&TGF_2

description: Biological replicate 2 of 4


title: ESC UNDIFF LINE BG02 PASSAGE 54

description:
ESC UNDIFF LINE BG02 PASSAGE 54
Raw data file: SAMPLE 12.txt

source_name: ESC UNDIFF LINE BG02 PASSAGE 54 (SAMPLE 12)

value: ESC

value: UNDIFF

value: MALE

value: SAMPLE 122


title: 67NR compliant basal set1

value: nonmetastatic breast carcioma cells


title: 4TO7 rigid TGFb set1

value: rigid


title: ESC KSR LINE BG02 PASSAGE 54

description:
ESC KSR LINE BG02 PASSAGE 54
Raw data file: SAMPLE 11.txt

source_name: ESC KSR LINE BG02 PASSAGE 54 (SAMPLE 11)

value: KSR


title: 67NR compliant TGFb set1


title: HUVEC_TNF&TGF_1

description: Biological replicate 1 of 4

value: TNF-α, 8hr


title: HUVEC_TNF_4

description: Biological replicate 4 of 4

source_name: HUVEC, No Cytokine, 8hr

value: No Cytokine, 8hr


title: ESC KSR LINE BG01 PASSAGE 67

description:
ESC KSR LINE BG01 PASSAGE 67
Raw data file: SAMPLE 5.txt

source_name: ESC KSR LINE BG01 PASSAGE 67 (SAMPLE 5)

value: SAMPLE 121


title: ESC KSR LINE BG02 PASSAGE 50

description:
ESC KSR LINE BG02 PASSAGE 50
Raw data file: SAMPLE 8.txt

source_name: ESC KSR LINE BG02 PASSAGE 50 (SAMPLE 8)


title: ESC UNDIFF LINE BG02 PASSAGE 50

description:
ESC UNDIFF LINE BG02 PASSAGE 50
Raw data file: SAMPLE 9.txt

source_name: ESC UNDIFF LINE BG02 PASSAGE 50 (SAMPLE 9)


title: HUVEC_TGF_1

description: Biological replicate 1 of 4


title: HUVEC_TGF_2

description: Biological replicate 2 of 4


title: HUVEC_TGF_4

description: Biological replicate 4 of 4


title: HUVEC_TGF_3

description: Biological replicate 3 of 4


title: Leaf_Control_50days_rep2

description: Gene expression after 50 days in control leaf

source_name: Control leaf, 50d, rep2

value: Leaf

value: Control


title: ESC FBS LINE BG02 PASSAGE 54

description:
ESC FBS LINE BG02 PASSAGE 54
Raw data file: SAMPLE 10.txt

source_name: ESC FBS LINE BG02 PASSAGE 54 (SAMPLE 10)

value: FBS


title: ESC FBS LINE BG02 PASSAGE 50

description:
ESC FBS LINE BG02 PASSAGE 50
Raw data file: SAMPLE 7.txt

source_name: ESC FBS LINE BG02 PASSAGE 50 (SAMPLE 7)


title: ESC UNDIFF LINE BG01 PASSAGE 67

description:
ESC UNDIFF LINE BG01 PASSAGE 67
Raw data file: SAMPLE 6.txt

source_name: ESC UNDIFF LINE BG01 PASSAGE 67 (SAMPLE 6)


title: ESC UNDIFF LINE BG01 PASSAGE 63

description:
ESC UNDIFF LINE BG01 PASSAGE 63
Raw data file: SAMPLE 3.txt

source_name: ESC UNDIFF LINE BG01 PASSAGE 63 (SAMPLE 3)


title: ESC FBS LINE BG01 PASSAGE 67

description:
ESC FBS LINE BG01 PASSAGE 67
Raw data file: SAMPLE 4.txt

source_name: ESC FBS LINE BG01 PASSAGE 67 (SAMPLE 4)


title: GFP-SAS siAURKA-1

city: Toon

first: Hiroshi

last: Tanaka

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University

description: Tongue

hyb_protocol: 7.5 µg fragmented and labeled aRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strips. Array Strips were washed and stained in the GeneAtlasTM Fluidics Station.

scan_protocol: Array Strips were scanned in the GeneAtlasTM imaging station.

data_processing: The robust multichip average (RMA) method was used for background correction and normalization using GeneSpring GX 12.1 software.

label: Biotin

source_name: GFP-SAS, siAURKA-1

label_protocol: 10 ng of total RNA was labeled using a GeneAtlasTM 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: GFP-SAS cells were incubated in a humidified atmosphere of 95% air and 5% CO2 at 37℃.

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

treatment_protocol: GFP-SAS cells were treated with siNT, siAURKA-1 or -2 (10 nM), DMSO, or MLN8237 (100nM) for 24 h.

value: GFP-SAS

value: squamous cell carcinoma cell line


title: 11885-5

type: genomic

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810198_S01_CGH-v4_95_Feb07_1_3.txt.

hyb_protocol: Hybridization on the arrays was performed according to the manufacturers protocols (Agilent Olgonucleotide Array-Based CGH for Genomic DNA Analysis, version 5.0, June 2007).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: The obtained log2-ratios (sample vs. reference sample) were Loess normalized on R statistical platform (package limma, version 2.12.10). Based on the original annotation provided by Agilent, the annotation provided in the GPL11288 platform and the NCBI/37 (mm9) mouse assembly information an updated platform annotation was created: GPL14006. Probes lacking a clearly defined genomic allocation were regarded as low identity probes and skipped in our further analysis.

molecule: genomic DNA

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 2

label_protocol: Extracted genomic DNA was labeled with Cy3 and Cy5 according to the manufacturers protocols (Agilent Olgonucleotide Array-Based CGH for Genomic DNA Analysis, version 5.0, June 2007).

extract_protocol: Genomic DNA from tumor samples and liver was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer’s instruction (Gentra)

tag: tumor

value: WAP-NP8 Mouse Mammary Carcinoma

tag: strain

value: Balb/c

tag: tumor grade

value: Grade 2

source_name: [reference] WAP-NP8 Mouse liver

tag: reference

value: WAP-NP8 Mouse liver reference


title: GFP-SAS siAURKA-2

description: Tongue

source_name: GFP-SAS, siAURKA-2

tag: cell line

tag: cell type


title: HUVEC_TNF_3

description: Biological replicate 3 of 4

source_name: HUVEC, TNF-α, 8hr

value: primary HUVEC

value: endothelial cell


title: HUVEC_TNF_2

description: Biological replicate 2 of 4


title: GFP-SAS siNon target

description: Tongue

source_name: GFP-SAS, siNT

value: siNT


title: ESC FBS LINE BG01 PASSAGE 63

description:
ESC FBS LINE BG01 PASSAGE 63
Raw data file: SAMPLE 1.txt

source_name: ESC FBS LINE BG01 PASSAGE 63 (SAMPLE 1)

tag: class

value: ESC

value: MALE


title: ESC KSR LINE BG01 PASSAGE 63

description:
ESC KSR LINE BG01 PASSAGE 63
Raw data file: SAMPLE 2.txt

source_name: ESC KSR LINE BG01 PASSAGE 63 (SAMPLE 2)

tag: condition

value: KSR


title: HUVEC_TNF_1

description: Biological replicate 1 of 4

value: TNF-α, 8hr

source_name: HUVEC, No Cytokine, 8hr

value: No Cytokine, 8hr


title: GFP-SAS MLN8237

description: Tongue

source_name: GFP-SAS, MLN8237


title: Aragones 2008 ripe grapes, EL36, biological replicate 3

status: Public on Oct 30 2012

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

description: Gene expression data from skin and pulp of ripe grapes

hyb_protocol: Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M NaCl, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC .

scan_protocol: Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization. Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method

label: biotin

organism: Vitis vinifera

source_name: ripe grapes

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA which was then fragmented at 94ºC for 35 min into 35-200 bases in length

growth_protocol: Grapevine plants were growing at Plansel´s vines located in Montemor-o-Novo (Southern Portugal).

extract_protocol: Total RNA was isolated essentially as described by Rerie et al. (1991, Mol Gen Genet) using phenol/ chloroform with modifications

treatment_protocol: Grapes corresponding to the developmental stages of EL 35 and 36 (E-L refers to the modified Eichhorn and Lorenz developmental scale) were immediately frozen in liquid nitrogen and transported to the lab in dry ice. Grapes were grinded in liquid nitrogen and seeds removed with a pincet

value: grape pulp and skin

tag: cultivar

value: Aragonês

tag: developmental stage

value: ripe grapes


title: Aragones 2008 ripe grapes, EL36, biological replicate 2


title: Aragones 2008 ripe grapes, EL36, biological replicate 1


title: Touriga Nacional 2008 veraison grapes, EL35, biological replicate 2

description: Gene expression data from skin and pulp of veraison grapes

source_name: veraison grapes

value: Touriga Nacional

value: veraison grapes


title: 4T1 compliant basal set2

value: highly metastatic breast carcioma cells

tag: treated with

tag: microenvironment

value: compliant

tag: molecule subtype

value: microRNA


title: Aragones 2008 veraison grapes, EL35, biological replicate 3

tag: tissue


title: Aragones 2008 veraison grapes, EL35, biological replicate 1


title: Touriga Nacional 2008 ripe grapes, EL36, biological replicate 1


title: GFP-SAS DMSO

description: Tongue

source_name: GFP-SAS, DMSO

value: GFP-SAS

value: squamous cell carcinoma cell line

tag: treatment

value: DMSO


title: Touriga Nacional 2008 ripe grapes, EL36, biological replicate 3


title: Touriga Nacional 2008 ripe grapes, EL36, biological replicate 2


title: Trincadeira 2008 ripe grapes, EL36, biological replicate 3

value: Trincadeira


title: Trincadeira 2008 ripe grapes, EL36, biological replicate 2


title: Touriga Nacional 2008 veraison grapes, EL35, biological replicate 1


title: Aragones 2008 veraison grapes, EL35, biological replicate 2


title: Trincadeira 2008 veraison grapes, EL35, biological replicate 3


title: Trincadeira 2008 ripe grapes, EL36, biological replicate 1


title: Touriga Nacional 2008 veraison grapes, EL35, biological replicate 3


title: Trincadeira 2008 veraison grapes, EL35, biological replicate 2


title: Trincadeira 2008 veraison grapes, EL35, biological replicate 1


title: ESC KSR LINE ES02 PASSAGE 45

description:
ESC KSR LINE ES02 PASSAGE 45
Raw data file: SAMPLE 26.txt

source_name: ESC KSR LINE ES02 PASSAGE 45 (SAMPLE 26)

value: ESC

tag: line

tag: passage

tag: gender

value: FEMALE

tag: processing control

value: SAMPLE 126


title: Lesioned side_L-DOPA+zonisamide_1

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal L-DOPA and zonisamide injection, lesioned side

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505C with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20100603) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: striatum, lesioned side, L-DOPA + zonisamide, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was > 7.7.

value: striatum

tag: strain

value: Wistar

value: male

tag: experimental group

value: the lesioned side of L-DOPA and ZNS-treated 6-OHDA-injected rats


title: Lesioned side_L-DOPA+zonisamide_2

source_name: striatum, lesioned side, L-DOPA + zonisamide, replicate2


title: Lesioned side_L-DOPA+zonisamide_3

source_name: striatum, lesioned side, L-DOPA + zonisamide, replicate3


title: Lesioned side_saline_1

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal normal saline injection, lesioned side

source_name: striatum, lesioned side, saline, replicate1

value: the lesioned side of saline-treated 6-OHDA-injected rats


title: Lesioned side_L-DOPA_3

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal L-DOPA injection, lesioned side

source_name: striatum, lesioned side, L-DOPA, replicate3

value: the lesioned side of L-DOPA-treated 6-OHDA-injected rats


title: Non-lesioned side_saline_1

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal normal saline injection, non-lesioned side

source_name: striatum, non-lesioned side, saline, replicate1

value: the non-lesioned side of saline-treated 6-OHDA-injected rats


title: Non-lesioned side_saline_2

source_name: striatum, non-lesioned side, saline, replicate2


title: Lesioned side_L-DOPA_1

source_name: striatum, lesioned side, L-DOPA, replicate1


title: Lesioned side_saline_2

source_name: striatum, lesioned side, saline, replicate2


title: Lesioned side_saline_3

source_name: striatum, lesioned side, saline, replicate3


title: Non-lesioned side_saline_3

source_name: striatum, non-lesioned side, saline, replicate3


title: Lesioned side_L-DOPA_2

source_name: striatum, lesioned side, L-DOPA, replicate2


title: 72hpf-zfish-Becl-3

city: Halifax

first: Sergey

last: Prykhozhij

state: Nova Scotia

address: 5850/5980 University Avenue

department: Pediatrics

country: Canada

institute: IWK Health Centre

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Zebrafish Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the AgilentG3_GX_1Color setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, 20 bit, Dye channel is set to Cy3 and the PMT is set to 100%).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The signals were background corrected with the normexp method (Limma package) and an offset of 1 was added to the intensities before normalization and log transformation, in order to ensure that all intensity values are positive. After background correction, the data were normalized between arrays using the quantile method.

organism: Danio rerio

source_name: 72 hpf zebrafish embryos

label_protocol: To produce Cy3-labeled cRNA, 3 µg of each RNA sample were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: AB wild-type zebrafish were maintained in the zebrafish facility of Max-Planck Institute for Molecular Genetics according to standard protocols at 28.5C. Embryos were collected and grown in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM, CaCl, 0.33 mM MgSO4) at 28.5C and staged by percentages of epiboly and somite numbers.

extract_protocol: RNA was extracted from all samples using RNeasy Mini Kit (QIAGEN, 74106) and genomic DNA was then removed using TurboDNA-free kit (Invitrogen, AM1907).

treatment_protocol: Embryos at 24 and 72 hpf stages were treated with either 0.1 % DMSO or 25 µM Beclomethasone for 3 hours in triplicate experiments and then frozen for RNA extraction.

value: AB wild-type

value: 72 hpf whole zebrafish embryos

value: 25 µM Beclomethasone for 3hrs


title: 24hpf-zfish-dmso-2

source_name: 24 hpf zebrafish embryos

value: 24 hpf whole zebrafish embryos

value: 0.1 % DMSO for 3hrs


title: 24hpf-zfish-Becl-1


title: 72hpf-zfish-Becl-1


title: 72hpf-zfish-dmso-1


title: 24hpf-zfish-Becl-2


title: 72hpf-zfish-dmso-2


title: 72hpf-zfish-Becl-2


title: MEHP 500mg_kg rep4

city: Dundee

first: Mark

middle: Peter

last: Chamberlain

state: Tayside

address: 2 James Lindsay Place

department: MCT

country: United Kingdom

institute: CXR Biosciences

hyb_protocol: Agilent 4x44K Whole Rat Genolme Oligo Microarray slides (G4131F) were hybridised, washed and then scanned.

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner according to CXR Method Sheet 'Microarray Hybridisation Scanning (1x44k, 4x44k and 8x15k)'

data_processing:
Genes that are significantly expressed above background on individual arrays are identified using Agilent Feature Extraction software. This process involves deletion control and background subtraction and calculation of a p value reflecting the probability that there is no difference in intensity for a given feature to that of background using a two sided T test. The P value calculation is based on an error calculated using an Agilent error model (Inc, A. t. (2007). Agilent Feature Extraction Software v9.5 User Guide. Agilent Publication number g4460-90005, 1-250.).
The 'significantly_altered_genes.txt' file content (available on Series records): In order to identify significantly altered genes, relative to the reference control  RNA sample, in the treated samples Rosetta Resolver software is used to calculate a p value based on an error weighted mean of the data for the treated samples. Rosetta software builds ratio experiments from one colour microarrays using data from the test array sets and the reference (control) array set. The reference control array data is used as the denominator (D) in thisratio such that up-regulation or down-regulation of genes in the test set (T) is expressed relative to the reference set (T/D).  The Rosetta error model [PMID 16522673] calculates both the propagated (technical) and scattered (biological) error and combines these two errors to make a more reliable error estimation. The p value allows an estimation of the confidence that a given feature/gene is not significantly different (the null hypothesis) relative to the reference. A p value of less than 0.01 is considered sufficient to reject the null hypothesis.

source_name: fetal testes_MEHP 500mg/kg

label_protocol: Total RNA 700ng was labelled prior to microarray hybridisation using the Agilent Quick Amp Labelling Kit One Colour (Agilent# 5190-0442), according to the CXR Method Sheet entitled 'Transcroptional profiling using standard Agilent one-colour protocol'.

extract_protocol: Pools of foetal testes from a minimum of three pups per litter (6 foetal testes) were disrupted using a qiashredder column and purified using Rneasy mini columns according to the CXR method entitled 'Method for Isolation of RNA from Foetal Testes for use in Microarray Analysis' (Plummer et al. 2007)

treatment_protocol: Pregnant dams were treated daily with vehicle (corn oil), TOTM, DEHP, EHO, MEHP at a dose of 500mg/kg by oral gavage on gestation days 12 to 19 inclusive.

tag: strain background

value: Han Wistar rats

value: fetal testes

tag: treated daily with

value: MEHP at a dose of 500mg/kg

tag: treated on

value: gestation days 12 to 19


title: 24hpf-zfish-dmso-3


title: TOTM 500mg_kg rep3

source_name: fetal testes_TOTM 500mg/kg

value: TOTM at a dose of 500mg/kg


title: TOTM 500mg_kg rep4


title: TOTM 500mg_kg rep1


title: TOTM 500mg_kg rep2


title: MEHP 500mg_kg rep3


title: 72hpf-zfish-dmso-3


title: EHO 500mg_kg rep2

source_name: fetal testes_EHO 500mg/kg

value: EHO at a dose of 500mg/kg


title: EHO 500mg_kg rep3


title: EHO 500mg_kg rep4


title: Control rep3

source_name: fetal testes_control

value: vehicle (corn oil)


title: DEHP 500mg_kg rep2

source_name: fetal testes_DEHP 500mg/kg

value: male

value: DEHP at a dose of 500mg/kg


title: 24hpf-zfish-Becl-3


title: MEHP 500mg_kg rep2


title: Control rep2


title: EHO 500mg_kg rep1


title: DEHP 500mg_kg rep1


title: DEHP 500mg_kg rep4


title: MEHP 500mg_kg rep1


title: Control rep1


title: Control rep4


title: 24hpf-zfish-dmso-1


title: DEHP 500mg_kg rep3


title: Wild type osmoresponsive gene expression_2

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

description:
Biological replicate 2 of 3
BY_2_BY_0.4M_NaCl_15min_2
Wild-type strain was grown at 30ºC and stressed or not with 0.4M NaCl.

hyb_protocol: The labeled cRNA was hybridized to the Agilent Yeast 4x44k 60-mer oligo microarray according to the manufacturer's protocol. The arrays were washed and dried.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT and 5 um resolution. Images were quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular spot finding option

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization, followed by scaling across chips. Differential expression analysis was performed using SAM (Significance Analysis of Microarrays, Tusher et al. 2001).

organism: Saccharomyces cerevisiae

source_name: wild type control

label_protocol: RNA (500 ng) was labeled using Agilent's Low Input RNA Labeling Kit, which involves reverse transcribing the mRNA in the presence of T7-oligo-dT primer to produce cDNA and then in vitro transcribing with T7 RNA polymerase in the presence of Cy3-CTP and Cy5-CTP to produce labeled cRNA

growth_protocol: grown to mid-log phase in YPD rich medium

extract_protocol: RNA was extracted with hot phenol (Körher K and Domdey H. Methods in Enzymology 194:398-405. 1991). Hybridizations were performed between stressed and control conditions by triplicate. Results were analyzed comparing thermo-responsive gene expression respect to the control in each individual strain.

treatment_protocol: not stressed with 0.4M NaCl

value: control

tag: time

value: 15 minutes

tag: cell type

value: wild type (BY4741)

source_name: wild type NaCl

treatment_protocol: osmotic shock 15 minutes 0.4M

value: 0.4M NaCl osmotic shock


title: Wild type osmoresponsive gene expression_1

description:
Biological replicate 1 of 3
BY_1_BY_0.4M_NaCl_15min_1
Wild-type strain was grown at 30ºC and stressed or not with 0.4M NaCl.


title: Wild type osmoresponsive gene expression_3

description:
Biological replicate 3 of 3
BY_3_BY_0.4M_NaCl_15min_3
Wild-type strain was grown at 30ºC and stressed or not with 0.4M NaCl.


title: STE.75-4

city: Aarhus

first: Henrik

last: Hornshøj

address: Brendstrupgårdsvej 100

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Statistical analysis was carried out in the R computing environment version 2.6 using the package Linear Models for Microarray Analysis (Limma, version 2.9.17) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-647 to Alexa-555 were normalized within-slide using the global-loess method with default parameters as implemented in Limma.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press ""button"" on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press ""button"" and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox)

scan_protocol: Scanner: GenePix Autoloader 4200AL, 5 µm resolution, 75 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.22, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

data_processing: Muscle tissue samples from heart (HEA), Vastus intermedius (VIN), Infraspinatus (ISP), Supraspinatus (SSP), Biceps femoris (BFE), Longissimus dorsi (LDO), Semimembranosus (SME), Semitendinosus (STE) and Triceps brachii (TBR). A reference sample was constructed by combining all samples. The exact same tissue samples were used for expression profiling with cDNA microarrays and 70-mer long oligonucleotide microarrays.

organism: Sus scrofa

source_name: STE.75-4, Semitendinosus

label_protocol: 20 µg total RNA was labelled with Alexa-647 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (red) from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen)

tag: Breed

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semitendinosus

source_name: reference: pool of all extractions

label_protocol: 20 µg total RNA was labelled with Alexa-555 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (green) from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions.

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: VIN.2971-5

source_name: VIN.2971-5, Vastus intermedius

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Vastus intermedius


title: BFE.2824-1

source_name: BFE.2824-1, Biceps femoris

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Biceps femoris

label_protocol: 20 µg total RNA was labelled with Alexa-555 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (green) from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions."


title: ISP.2630-5

source_name: ISP.2630-5, Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Infraspinatus


title: BFE.2836-7

source_name: BFE.2836-7, Biceps femoris


title: LDO.2836-7

source_name: LDO.2836-7, Longissimus dorsi

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Longissimus dorsi


title: SME.2836-7

source_name: SME.2836-7, Semimembranosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semimembranosus


title: SME.2824-1

source_name: SME.2824-1, Semimembranosus


title: LDO.75-4

source_name: LDO.75-4, Longissimus dorsi


title: VIN.2630-5

source_name: VIN.2630-5, Vastus intermedius


title: HEA.2824-1

source_name: HEA.2824-1, Heart

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Heart


title: SSP.75-4

source_name: SSP.75-4, Supraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Supraspinatus


title: LDO.2824-1

source_name: LDO.2824-1, Longissimus dorsi


title: HEA.2971-5

source_name: HEA.2971-5, Heart


title: VIN.2824-1

source_name: VIN.2824-1, Vastus intermedius


title: BFE.75-4

source_name: BFE.75-4, Biceps femoris


title: SME.2630-5

source_name: SME.2630-5, Semimembranosus


title: SSP.2824-1

source_name: SSP.2824-1, Supraspinatus

source_name: reference: pool of all extractions


title: SSP.2971-5

source_name: SSP.2971-5, Supraspinatus


title: VIN.2836-7

source_name: VIN.2836-7, Vastus intermedius


title: TBR.2630-5

source_name: TBR.2630-5, Triceps brachii

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Triceps brachii


title: HEA.75-4

source_name: HEA.75-4, Heart


title: TBR.75-4

source_name: TBR.75-4, Triceps brachii


title: ISP.2824-1

source_name: ISP.2824-1, Infraspinatus


title: SSP.2630-5

source_name: SSP.2630-5, Supraspinatus


title: ISP.75-4

source_name: ISP.75-4, Infraspinatus


title: LDO.2630-5

source_name: LDO.2630-5, Longissimus dorsi


title: VIN.75-4

source_name: VIN.75-4, Vastus intermedius


title: LDO.2971-5

source_name: LDO.2971-5, Longissimus dorsi


title: STE.2630-5

source_name: STE.2630-5, Semitendinosus


title: ISP.2971-5

source_name: ISP.2971-5, Infraspinatus


title: L47PT

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

hyb_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.1.5

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA) equipped with extended dynamic range (XDR) software according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual.

data_processing: Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol. All arrays were normalized together using a Lowess multi-array algorithm. Signals that were not detected according to GeneView flags, or were lower than 5, were considered below detection rate and were thresholded to 5. miR signal intensities from technical replicates were averaged.

source_name: Peritumor breast tissue

extract_protocol: Breast tumor tissue (50-100 mg) was manually homogenized in 1 ml of TRI Reagent lysis reagent (Ambion) according to manufacturer's instructions.

treatment_protocol: Following excision, tissue samples were immediately frozen in liquid nitrose and stored at -80° until RNA extraction.

value: Peritumor breast tissue

tag: subtype (of tumor or matched tumor)

value: Luminal

tag: estrogen receptor status

tag: progesteron receptor status

tag: her2 status

tag: hystotype

tag: grading

tag: tumor size

tag: nodal status


title: L48PT

label_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.1.5

tag: tissue


title: L50PT


title: L45PT


title: L46PT


title: L49PT


title: L44PT


title: L41PT


title: L40PT


title: L43PT


title: L39PT


title: L42PT


title: L38PT


title: L37PT


title: L35PT


title: L36PT


title: L33PT


title: L32PT


title: STE.2836-7

source_name: STE.2836-7, Semitendinosus


title: L30PT


title: L31PT


title: STE.2971-5

source_name: STE.2971-5, Semitendinosus


title: L28PT


title: L29PT


title: L24PT


title: L27PT


title: L23PT


title: TBR.2971-5

source_name: TBR.2971-5, Triceps brachii

source_name: reference: pool of all extractions


title: TBR.2836-7

source_name: TBR.2836-7, Triceps brachii


title: BFE.2630-5

source_name: BFE.2630-5, Biceps femoris


title: SME.75-4

source_name: SME.75-4, Semimembranosus


title: SME.2971-5

source_name: SME.2971-5, Semimembranosus


title: TBR.2824-1

source_name: TBR.2824-1, Triceps brachii


title: L22PT


title: HEA.2836-7

source_name: HEA.2836-7, Heart


title: L34PT


title: L18PT


title: L17PT


title: L16PT


title: L15PT


title: keratinocytes_anti-miR-Ctrl_rep1

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description:
Anti-miR-Ctrla
Gene expression data from keratinocytes transfected with control RNA with scrambled sequence.

hyb_protocol: The samples were hybridized to a Human Gene 1.1 ST Array Plate according to the standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.1 (Summarization: Plier, Background Correction: PM-GCBG, Normalization: Global Median).

source_name: keratinocytes transfected with anti-miR-Ctrl

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer's (Affymetrix) instructions.

growth_protocol: Human adult epidermal keratinocytes were purchased from Cascade Biologics and cultured in EpiLife® serum-free keratinocyte growth medium including Human Keratinocyte Growth Supplement at a final Ca2+ concentration of 0.06mM (Cascade Biologics) at 37°C in 5% CO2.

extract_protocol: 48 hours after transfection, the total RNA was extracted with the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The third passage keratinocytes at 30-50% confluence were transfected with 10 nM miR-31 hairpin inhibitor or microRNA hairpin inhibitor negative control #1 (ThermoFisher Scientific) using Lipofectamine 2000 (Invitrogen).

value: skin

value: keratinocytes

tag: hairpin rna

value: anti-miR-Ctrl


title: keratinocytes_anti-miR-Ctrl_rep3

description:
Anti-miR-Ctrlc
Gene expression data from keratinocytes transfected with control RNA with scrambled sequence.


title: keratinocytes_anti-miR-31_rep3

description:
Anti-miR-31c
Gene expression data from keratinocytes with inhibited miR-31 expression.

source_name: keratinocytes transfected with anti-miR-31


title: L13PT


title: L14PT


title: keratinocytes_anti-miR-31_rep2

description:
Anti-miR-31b
Gene expression data from keratinocytes with inhibited miR-31 expression.


title: L11PT


title: L12PT


title: keratinocytes_anti-miR-31_rep1

description:
Anti-miR-31a
Gene expression data from keratinocytes with inhibited miR-31 expression.


title: L10PT


title: L6PT


title: L3PT


title: L9PT


title: L8PT


title: L7PT


title: TN8PT

value: Basal-like


title: L5PT


title: L1PT


title: TN7PT


title: TN5PT


title: TN6PT


title: TN3PT


title: TN2PT


title: TN1PT


title: H3PT


title: L2PT


title: L4PT


title: keratinocytes_anti-miR-Ctrl_rep2

description:
Anti-miR-Ctrlb
Gene expression data from keratinocytes transfected with control RNA with scrambled sequence.


title: H5PT


title: Dry crust_time 7.6h_rep3

city: Berkeley

first: Lara

last: Rajeev

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

description:
Sample name: 79.6hr-C
Biological soil crust,7.6 hr after removal of water; third of 3 biological replicates

hyb_protocol: Four μg of the labeled cDNA was hybridized at 42C overnight to a custom 12X135k Roche-Nimblegen microarray.

scan_protocol: The arrays were scanned on a GenePix 4200A scanner according to Nimblegen's protocol

data_processing: The images were gridded and pair files generated using the Nimblescan software version 2.4 (Roche-Nimblegen). All time points were normalized together by RMA (Robust Multi-chip Average) analysis using Nimblescan v2.4

organism: Microcoleus vaginatus

source_name: Desert biological soil crust, water removed,7.6 hr

label_protocol: The extracted RNA was DNAse treated using Turbo DNA-free DNAse (Life Technologies, Carlsbad, USA), and the DNA-free RNA (50 ng) was amplified using the Sigma Whole Transcriptome Amplification 2 kit (Sigma). The resulting cDNA was cleaned up using Qiaquick PCR clean up kit (Qiagen), and was labeled with Cy3 9-mers using One color DNA labeling kit (Roche-Nimblegen) following the manufacturer’s protocol.

extract_protocol: Soil crust samples (0.5 g) were added to a 2 ml Lysing Matrix E tube (MP biomedical, OH), and extracted with 0.5 ml phenol-chloroform:isoamyl alcohol (25:24:1). 0.5 ml of CTAB buffer (5% CTAB, 0.25M phosphate buffer pH 8.0, 0.3M NaCl) and 50 μL of 0.1M aluminum ammonium sulfate were then added, and the samples were beat at 5.5 m/s for 30 s in a FastPrep-24 instrument (MP Biomedicals, OH, USA). Samples were then centrifuged at 16K g for 5 min at 4C, and the aqueous phase was transferred to MaxTRact High Density 2 ml tubes (Qiagen, MD, US). A second round of CTAB addition and beating was performed. The combined mixture was extracted with equal volumes of chloroform at 16k g for 5 min at 4C, and the nucleic acids were precipitated overnight from the aqueous phase with 2 volumes of 30% (w/v) polyethylene glycol 6000 and 1.6 M NaCl. After centrifugation at 16k g for 10 min at 4C, the nucleic acid mixture was resuspended in 30 ul of DEPC treated water. Fully automated separation of DNA and RNA was achieved using the AllPrep DNA/RNA Mini kit (Qiagen, MD, USA) and the QIAcube (Qiagen, Switzerland) following manufacturer's protocols.

treatment_protocol: Biological soil crust samples were hydrated by addition of water, and kept saturated for 72 hrs over 3 day/night periods in a temperature and humidity controlled environment to mimic natural desert conditions, after which the water was removed and drying was induced

tag: strains

value: PCC 9802 and FGP-2

tag: time since wetting

tag: soil crust status

value: water removed


title: Dry crust_time 75h_rep1

description:
Sample name: 147.6hr-A
Biological soil crust, 75 hr after removal of water; first of 3 biological replicates

source_name: Desert biological soil crust, water removed, 75 hr


title: H2PT


title: Dry crust_time 75h_rep2

description:
Sample name: 147.6hr-B
Biological soil crust, 75 hr after removal of water; second of 3 biological replicates


title: Dry crust_time 7.6h_rep1

description:
Sample name: 79.6hr-A
Biological soil crust,7.6 hr after removal of water; first of 3 biological replicates


title: Dry crust_time 3.9h_rep1

description:
Sample name: 75.9hr-B
Biological soil crust, 3.9 hr after removal of water; first of 2 biological replicates

source_name: Desert biological soil crust, water removed, 3.9 hr


title: H4PT


title: Dry crust_time 3.9h_rep2

description:
Sample name: 75.9hr-C
Biological soil crust, 3.9 hr after removal of water; second of 2 biological replicates


title: Dry crust_time 1.9h_rep3

description:
Sample name: 73.9hr-C
Biological soil crust, 1.9 hr after removal of water;third of 3 biological replicates

source_name: Desert biological soil crust, water removed,1.9 hr


title: L19PT

source_name: Peritumor breast tissue


title: Dry crust_time 75h_rep3

description:
Sample name: 147.6hr-C
Biological soil crust, 75 hr after removal of water; third of 3 biological replicates


title: H6PT


title: L52T

source_name: Breast primary tumor (Luminal)

value: Breast primary tumor

value: pos

value: neg

value: ILC


title: H1PT


title: Dry crust_time 0.8h_rep2

description:
Sample name: 72.8hr-B
Biological soil crust, 0.8 hr after removal of water; second of 3 biological replicates

source_name: Desert biological soil crust, water removed, 0.8 hr


title: Dry crust_time 7.6h_rep2

description:
Sample name: 79.6hr-B
Biological soil crust,7.6 hr after removal of water; second of 3 biological replicates


title: Dry crust_time 1.9h_rep2

description:
Sample name: 73.9hr-B
Biological soil crust, 1.9 hr after removal of water; second of 3 biological replicates


title: Dry crust_time 1.9h_rep1

description:
Sample name: 73.9hr-A
Biological soil crust, 1.9 hr after removal of water; first of 3 biological replicates


title: Wet crust_time 49.5hr_rep2

description:
Sample name: 49.5hr-B
Biological soil crust, 49.5 hr after addition of water; second of 3 biological replicates

source_name: Desert biological soil crust, wet, 49.5 hr

value: wet


title: Dry crust_time 0.8h_rep1

description:
Sample name: 72.8hr-A
Biological soil crust, 0.8 hr after removal of water; first of 3 biological replicates


title: L50T

value: IDC

value: N+


title: Wet crust_time 42hr_rep3

description:
Sample name: 42hr-C
Biological soil crust, 42 hr after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 42 hr

value: 42 hy


title: Wet crust_time 49.5hr_rep1

description:
Sample name: 49.5hr-A
Biological soil crust, 49.5 hr after addition of water; first of 3 biological replicates


title: Wet crust_time 49.5hr_rep3

description:
Sample name: 49.5hr-C
Biological soil crust, 49.5 hr after addition of water; third of 3 biological replicates


title: Dry crust_time 0.8h_rep3

description:
Sample name: 72.8hr-C
Biological soil crust, 0.8 hr after removal of water; third of 3 biological replicates


title: Wet crust_time 42hr_rep1

description:
Sample name: 42hr-A
Biological soil crust, 42 hr after addition of water; first of 3 biological replicates

value: 42 hr


title: Wet crust_time 42hr_rep2

description:
Sample name: 42hr-B
Biological soil crust, 42 hr after addition of water; second of 3 biological replicates


title: Wet crust_time 35.5hr_rep3

description:
Sample name: 35.5hr-C
Biological soil crust, 35.5 hr after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 35.5 hr


title: Wet crust_time 35.5hr_rep2

description:
Sample name: 35.5hr-B
Biological soil crust, 35.5 hr after addition of water; second of 3 biological replicates


title: L49T

value: unknown


title: L48T

value: Luminal


title: L51T


title: L46T


title: L45T


title: L44T


title: L43T


title: Wet crust_time 31.5hr_rep3

description:
Sample name: 31.5hr-C
Biological soil crust, 31.5 hr after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 31.5 hr


title: Wet crust_time 25.5hr_rep3

description:
Sample name: 25.5hr-C
Biological soil crust, 25.5 hr after addition of water; second of 2 biological replicates

source_name: Desert biological soil crust, wet, 25.5 hr


title: Wet crust_time 31.5hr_rep2

description:
Sample name: 31.5hr-B
Biological soil crust, 31.5 hr after addition of water; second of 3 biological replicates


title: Wet crust_time 31.5hr_rep1

description:
Sample name: 31.5hr-A
Biological soil crust, 31.5 hr after addition of water; first of 3 biological replicates


title: Wet crust_time 35.5hr_rep1

description:
Sample name: 35.5hr-A
Biological soil crust, 35.5 hr after addition of water; first of 3 biological replicates


title: L42T


title: Wet crust_time 22hr_rep3

description:
Sample name: 22hr-C
Biological soil crust, 22 hr after addition of water;third of 3 biological replicates

source_name: Desert biological soil crust, wet, 22 hr

value: 22 hr


title: Wet crust_time 22hr_rep1

description:
Sample name: 22hr-A
Biological soil crust, 22 hr after addition of water; first of 3 biological replicates


title: Wet crust_time 22hr_rep2

description:
Sample name: 22hr-B
Biological soil crust, 22 hr after addition of water; second of 3 biological replicates


title: Wet crust_time 18hr_rep3

description:
Sample name: 18hr-C
Biological soil crust, 18 hr after addition of water;third of 3 biological replicates

source_name: Desert biological soil crust, wet, 18 hr

value: 18 hr


title: L41T


title: Wet crust_time 25.5hr_rep2

description:
Sample name: 25.5hr-B
Biological soil crust, 25.5 hr after addition of water; first of 2 biological replicates


title: Wet crust_time 18hr_rep1

description:
Sample name: 18hr-A
Biological soil crust, 18 hr after addition of water; first of 3 biological replicates


title: Wet crust_time 11.5hr_rep3

description:
Sample name: 11.5hr-C
Biological soil crust, 11.5 hr after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 11.5 hr


title: Wet crust_time 11.5hr_rep1

description:
Sample name: 11.5hr-A
Biological soil crust, 11.5 hr after addition of water; first of 3 biological replicates


title: Wet crust_time 9hr_rep3

description:
Sample name: 9hr-C
Biological soil crust, 9 hr after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 9 hr

value: 9 hr


title: Wet crust_time 11.5hr_rep2

description:
Sample name: 11.5hr-B
Biological soil crust, 11.5 hr after addition of water; second of 3 biological replicates


title: Wet crust_time 18hr_rep2

description:
Sample name: 18hr-B
Biological soil crust, 18 hr after addition of water; second of 3 biological replicates


title: Wet crust_time 1hr_rep3

description:
Sample name: 1hr-C
Biological soil crust, 1 hr after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 1 hr

value: 1 hr


title: L38T


title: Wet crust_time 9hr_rep1

description:
Sample name: 9hr-A
Biological soil crust, 9 hr after addition of water; first of 3 biological replicates

value: PCC 9802 and FGP-2


title: Wet crust_time 1hr_rep2

description:
Sample name: 1hr-B
Biological soil crust, 1 hr after addition of water; second of 3 biological replicates


title: L37T


title: Wet crust_time 15 min_rep3

description:
Sample name: 15min-C
Biological soil crust, 15 min after addition of water; third of 3 biological replicates

source_name: Desert biological soil crust, wet, 15 min

value: 15 min


title: L39T

value: Breast primary tumor


title: Wet crust_time 15 min_rep2

description:
Sample name: 15min-B
Biological soil crust, 15 min after addition of water; second of 3 biological replicates


title: L40T

value: pos


title: L35T

value: neg


title: L36T


title: L32T


title: L34T


title: L33T


title: AgeControl_rep2

city: Worcester

first: Rachel

middle: Patton

last: McCord

state: MA

address: 364 Plantation St. LRB 570M

department: Program in Gene Function and Expression

institute: University of Massachusetts Medical School

description:
KC_11-2 patient8470
Healthy age-matched control.

hyb_protocol: The hybridization cocktail containing the fragmented and biotin-labeled cDNAs were hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Affymetrix Expression Console software and the CEL files generated.

data_processing: CEL files were processed with RMAExpress using Background Adjustment, Quantile Normalization, and Median Polish.

source_name: normal skin biopsy

label_protocol: For RNA labeling, 1 microgram of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip® WT Sense Target Labeling. The total RNA was first subjected to a ribosomal RNA reduction using the Invitrogen RiboMinus Transcriptome Isolation Kit. The remaining RNA was then reverse transcribed in the presence of dT7N6 primers to generate cDNA. An in vitro transcription was then performed and the resulting cRNA was purified. A first strand cDNA was generated from the cRNA in the presence of dUTPs. After RNA hydrolysis, the single-stranded cDNA was fragmented and end labeled with biotin.

growth_protocol: Cells were grown under 5% CO2 in MEM supplied by 15% FBS.

extract_protocol: RNA was isolated from 1 million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Total RNAs were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity were ensured using the Bioanalyzer (Agilent, Inc.) and NanoDrop (Thermo Scientific, Inc.), respectively.

tag: disease status

value: normal

value: skin biopsy

value: fibroblasts

tag: gender

value: female

tag: cell line

tag: passage


title: Wet crust_time 15 min_rep1

description:
Sample name: 15min-A
Biological soil crust, 15 min after addition of water; first of 3 biological replicates

value: wet


title: AgeControl_rep1

description:
KC_11-1 patient8470
Healthy age-matched control.

tag: cell type


title: Wet crust_time 9hr_rep2

description:
Sample name: 9hr-B
Biological soil crust, 9 hr after addition of water; second of 3 biological replicates


title: Dry crust_time 0_rep3

description:
Sample name: T0-C
Dry biological soil crust, prior to start of the experiment. This is third of 3 biological replicates

source_name: Desert biological soil crust, dry

value: 0 hr

value: dry


title: Wet crust_time 1hr_rep1

description:
Sample name: 1hr-A
Biological soil crust, 1 hr after addition of water; first of 3 biological replicates


title: L31T

tag: subtype (of tumor or matched tumor)

value: Luminal

tag: estrogen receptor status

value: IDC


title: Wet crust_time 0_rep1

description:
Sample name: 3min-A
Biological soil crust, immediately after addition of water, first of 3 biological replicates

source_name: Desert biological soil crust, wet, 3 min

value: 3 min


title: Wet crust_time 0_rep2

description:
Sample name: 3min-B
Biological soil crust, immediately after addition of water, second of 3 biological replicates


title: Wet crust_time 0_rep3

description:
Sample name: 3min-C
Biological soil crust, immediately after addition of water, third of 3 biological replicates


title: siRNAc

city: Frankfurt

first: Malte

last: Bachmann

address: Theodor Stern Kai 7

department: General Pharmacology

institute: University Hospital Frankfurt

description: Gene expression data from siRNAc transfected IL-18 simulated KG1 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneArray Scanner (Agilent).

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

source_name: siRNAc transfected IL-18 stimulated KG1-cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA..

growth_protocol: Cells were cultivated in RPMI 1640 supplemented with 100U/ml penicillin, 100µg/ml streptomycin and 10% heat-inactivated FCS. All incubations were performed at 37°C and 5% CO2.

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

treatment_protocol: KG1 cells were transfected by electroporation either with 1.98µg siRNA-Tbet or with 1.98µg siRNAc. After 5h of rest, transfected cells were stimulated with IL-18 (10ng/ml) for 12h.

value: KG1 cells

tag: transfection

value: siRNAc

tag: treatment

value: stimulated with IL-18


title: Dry crust_time 0_rep1

description:
Sample name: T0-A
Dry biological soil crust, prior to start of the experiment. This is first of 3 biological replicates

value: PCC 9802 and FGP-2


title: siRNA-Tbet

description: Gene expression data from siRNA-Tbet transfected IL-18 simulated KG1 cells

source_name: siRNA-Tbet transfected IL-18 stimulated KG1-cells

value: siRNA-Tbet


title: LDO.2824-1

description: Statistical analysis was carried out in the R computing environment version 2.6 using the package Linear Models for Microarray Analysis (Limma, version 2.9.17) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-647 to Alexa-555 were normalized within-slide using the global-loess method with default parameters as implemented in Limma.

scan_protocol: Scanner: GenePix Autoloader 4200AL, 5 µm resolution, 90 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.22, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

source_name: LDO.2824-1, Longissimus dorsi

tag: Breed

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Longissimus dorsi

source_name: reference: pool of all extractions

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: Dry crust_time 0_rep2

description:
Sample name: T0-B
Dry biological soil crust, prior to start of the experiment. This is second of 3 biological replicates


title: L29T

source_name: Breast primary tumor (Luminal)

value: Breast primary tumor

value: pos

tag: progesteron receptor status

value: neg

tag: her2 status

tag: hystotype

tag: grading

tag: tumor size


title: L28T

tag: tissue

tag: nodal status


title: LDO.2836-7

source_name: LDO.2836-7, Longissimus dorsi


title: L27T

value: N+


title: SME.2836-7

source_name: SME.2836-7, Semimembranosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semimembranosus


title: L22T

value: unknown


title: L23T


title: L21T


title: L20T


title: TBR.2971-5

source_name: TBR.2971-5, Triceps brachii

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Triceps brachii


title: SME.75-4

source_name: SME.75-4, Semimembranosus


title: STE.2836-7

source_name: STE.2836-7, Semitendinosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semitendinosus


title: HEA.2630-5

source_name: HEA.2630-5, Heart

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Heart


title: L24T

value: Luminal

value: IDC


title: L19T


title: HEA.75-4

source_name: HEA.75-4, Heart


title: VIN.2630-5

source_name: VIN.2630-5, Vastus intermedius

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Vastus intermedius


title: FT43_PASSAGE 21

city: MADRID

first: Juan

middle: C

last: Estrada

state: MADRID

address: MELCHOR FERNANDEZ ALMAGRO 3

department: REGENERATIVE CARDIOLOGY

institute: CNIC

description: passage 21

hyb_protocol: Cy3 labelled aRNA (1.65µg) was hybridized to a Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies) for 17 hours at 65ºC in 1X GEx Hybridization Buffer HI-RPM in a hybridization oven (G2545A, Agilent Technologies) set to 10rpm. Arrays were washed according to the manufacturer's instructions and dried by centrifugation.

scan_protocol: The samples were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) with the default settings for 4x44k format one-color arrays. Scanned images were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: Feature Extraction data files from were imported into GeneSpring® GX software version 9.0. (AgilentTechnologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe. Probes were also flagged (Present, Marginal, Absent) using GeneSpring® default settings. Probes with signal values above the lower percentile (20th), and flagged as Present or Marginal in 100% of replicates in at least one out of the two conditions under study, were selected for further analysis (23716 probes).

source_name: Adipose tissue-derived human mesenchymal stem cells, passage 21

label_protocol: The One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA) was used to amplify and label RNA. Briefly, 400ng of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. cDNA was then converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

growth_protocol: Adipose tissue-derived human mesenchymal stem cells were isolated as described from four female healthy donors. All cells were cultured in expansion medium (Dulbecco’s modified Eagle’s medium (DMEM), with 4.5 g/l D-glucose supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, 50 μg/ml penicillin/streptomycin; all culture reagents from Invitrogen, Carlsbad, CA)

extract_protocol: Total RNA was isolated by using the TRI Reagent protocol® (Applied biosystems), according with manufacturer's instructions

treatment_protocol: Long-term culture in standard conditions (Dulbecco’s modified Eagle’s medium (DMEM), with 4.5 g/l D-glucose supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, 50 μg/ml penicillin/streptomycin; all culture reagents from Invitrogen, Carlsbad, CA)

tag: tissue origin

value: Adipose

value: human mesenchymal stem cells


title: VIN.2971-5

source_name: VIN.2971-5, Vastus intermedius


title: BFE.2836-7

source_name: BFE.2836-7, Biceps femoris

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Biceps femoris


title: FT40_PASSAGE 2

description: passage 2

source_name: Adipose tissue-derived human mesenchymal stem cells, passage 2


title: FT40_PASSAGE 21

description: passage 21


title: FT43_PASSAGE 2

description: passage 2


title: L17T


title: L18T


title: SSP.2630-5

source_name: SSP.2630-5, Supraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Supraspinatus


title: FT34_PASSAGE21

description: passage 21


title: ISP.75-4

source_name: ISP.75-4, Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: FT34_PASSAGE 2

description: passage 2


title: TBR.2630-5

source_name: TBR.2630-5, Triceps brachii


title: L15T

value: Breast primary tumor

value: pos


title: L16T

value: neg

value: N+


title: FT36_PASSAGE 21

description: passage 21


title: L13T


title: L14T

value: ILC


title: hiPSCs, 24h after DMSO treatment

city: Kyoto, Sakyo-ku

first: Itsunari

last: Minami

address: Yoshida Ushinomiya-cho

institute: iCeMS

description: Gene expression data from hiPSCs at day3 after cardiac differentiation onset, 24h after control DMSO treatment

hyb_protocol: Synthesis of cDNA, in vitro transcription and biotin labeling cRNA, and hybridization to the Human Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.

data_processing: Data normalization and further analysis were performed with GeneSpring GX (Agilent Technologies). The genes ,whose GCRMA normalized values of 0h sample were less than 300, were excluded from further analysis. Ratios of gene expression relative to control samples (KY02111/DMSO) were calculated in each time point . The down-regulated and up-regulated genes in response to KY02111 were identified by more than 25 % changes of KY/DMSO ratios at both 12 hr and 24hr after KY02111 treatment (down-regulated genes = KY12h/DMSO12h < 0.75 and KY24h/DMSO24h < 0.75, up-regulated genes = KY12h/DMSO12h > 1.25 and KY24h/DMSO24h > 1.25) [ratio_data.txt available as a Series Supplementary file].

source_name: hiPSCs_24h_0.1% DMSO treatment

growth_protocol: hiPSCs (IMR90-1) were maintained on mitomycin C-treated mouse embryonic fibroblasts (MEF) in Primate ES Cell Culture Medium (ReproCell Inc., Japan) with 5ng/ml bFGF. Then, hiPSC colonies were harvested by digestion, and hiPSCs were cultured in 6 well plate (3-10×105 cells/cm3) in cardiac differentiation medium, which is IMDM (Sigma) containing 20% FBS (Gibco), 1% MEM non-essential amino acid solution (Sigma), 1% Penicillin-Streptomycin (Gibco), 2 mM L-glutamine (Sigma), 0.001 % 2-Mercaptoethanol (Gibco) and 0.005N NaOH, with 10ng/ml BMP4 (R&D).

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The medium was changed to cardiac differentiation medium with 10μM KY02111 or 0.1% DMSO at day3 after cardiac differentiation onset.

value: hiPSCs (IMR90-1)


title: FT36_PASSAGE 2

description: passage 2


title: STE.2971-5

source_name: STE.2971-5, Semitendinosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semitendinosus

source_name: reference: pool of all extractions


title: hiPSCs, 12h after KY02111 treatment

description: Gene expression data from hiPSCs at day3 after cardiac differentiation onset, 12h after KY02111 treatment

source_name: hiPSCs_12h_10μM KY02111 treatment

label_protocol: Synthesis of cDNA, in vitro transcription and biotin labeling cRNA, and hybridization to the Human Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols.


title: SSP.2824-1

source_name: SSP.2824-1, Supraspinatus


title: hiPSCs, 24h after KY02111 treatment

description: Gene expression data from hiPSCs at day3 after cardiac differentiation onset, 24h after KY02111 treatment

source_name: hiPSCs_24h_10μM KY02111 treatment


title: hiPSCs, 0h after KY02111 treatment

description: Gene expression data from hiPSCs at day3 after cardiac differentiation onset, 0h after KY02111 treatment

source_name: hiPSCs_0h_10μM KY02111 treatment


title: BFE.2824-1

source_name: BFE.2824-1, Biceps femoris


title: L12T

source_name: Breast primary tumor (Luminal)


title: hiPSCs, 12h after DMSO treatment

description: Gene expression data from hiPSCs at day3 after cardiac differentiation onset, 12h after control DMSO treatment

source_name: hiPSCs_12h_0.1% DMSO treatment


title: STE.2824-1

source_name: STE.2824-1, Semitendinosus


title: HEA.2824-1

source_name: HEA.2824-1, Heart

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Heart


title: L11T

value: Luminal


title: L10T

value: IDC


title: TBR.2824-1

source_name: TBR.2824-1, Triceps brachii

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Triceps brachii


title: PNST-2

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Canine Genome 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.4, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

organism: Canis lupus familiaris

source_name: Peripheral nerve sheath tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (3`-IVT Express labeling protocol) from 100ng total RNA.

extract_protocol: Cryopreserved tumor specimens were macrodissected to ensure high tumor cellularity and only sections that contained 90 % tumor cells were included in the study. Tissue sections were transferred into 300 µL of lysis buffer (NucleoSpin RNA; Macherey&Nagel) and homogenized (Bertin Technology). mRNA was extracted and purified using a commercial system (NucleoSpin RNA; Macherey&Nagel). RNA quality was controlled using the BioAnalyzer (Agilent Technologies, USA) and only high quality RNA (RIN>9) was used for microarray analyses.

tag: sample type

value: frozen tissue

tag: disease state

value: peripheral nerve sheath tumor


title: SME.2971-5

source_name: SME.2971-5, Semimembranosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semimembranosus


title: PNST-1


title: FiSa-3

source_name: Fibrosarcoma

value: fibrosarcomas


title: FiSa-2


title: L6T


title: L7T


title: PNST-3


title: SSP.2836-7

source_name: SSP.2836-7, Supraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Supraspinatus


title: Day2_Dark_6hr_Rep2

city: St Louis

first: Thanura

last: Elvitigala

state: MO

address: 1 Brookings Drive, Campus Box 1137

institute: Washington University

description: Samples collected after 6hr in the dark regime on day 2, replicate 2.

hyb_protocol: Microarray hybridization procedures have been performed as described in Stockel et al. (2008) Proc Natl Acad Sci U S A 105:6156-6161 (PMID 18427117).

scan_protocol: Agilent Technologies Scanner G2505C US83800207, Protocol GE2_105_Dec08 with MetricSet GE2_ZCMT_Dec08.

data_processing: Background-subtracted signal normalized using the robust version of LOWESS with a span of 25%. Lowess normalization was done using Matlab (R2009a).

organism: Crocosphaera subtropica ATCC 51142

label_protocol: RNA preparation has been performed as described in Stockel et al. (2008) Proc Natl Acad Sci U S A 105:6156-6161 (PMID 18427117).

growth_protocol: Cyanothece 51142 cultures were grown diazotrophically in 1L Roux culture bottles (Bellco Glass, Inc.) and ASP2 medium including 300 mM NaCl. The cultures were kept under alternating 12h light/dark cycles with 100 µmol photons/m2/s of white light at 30°C and air bubbling. Initially, cultures were inoculated with 1/10V of cells grown under nitrogen-sufficient conditions and continuous illumination of 50 µmol photons/m2/s of white light. After 7 days, 1/2.5V of the nitrogen-deficient pre-culture was used to inoculate fresh ASP2 media without added nitrate and further cultivated under the same conditions. After 3 days, the cultures were aerated with ambient and 8% CO2-enriched air at a flow rate of 100 mL/min.

treatment_protocol: For microarray analysis of cells grown in 8% CO2-enriched air versus ambient conditions, the cultures were adapted to 8% CO2-enriched air for 48h and samples were collected 30min, 2h, 6h, 13h, 18h, 30h and 42h after the transition to ambient CO2 conditions to determine short- and long-term responses of gene expression under ambient and CO2-rich conditions.

tag: strain

tag: co2 level

value: low

tag: time point

value: 42 hr

value: high


title: Day2_Dark_6hr_Rep3

description: Samples collected after 6hr in the dark regime on day 2, replicate 3.

extract_protocol: RNA preparation has been performed as described in Stockel et al. (2008) Proc Natl Acad Sci U S A 105:6156-6161 (PMID 18427117).


title: BFE.75-4

source_name: BFE.75-4, Biceps femoris

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Biceps femoris

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: L4T

value: Breast primary tumor

tag: subtype (of tumor or matched tumor)

tag: estrogen receptor status

value: pos

value: neg


title: L9T

value: N+


title: L3T

value: Luminal


title: LDO.75-4

source_name: LDO.75-4, Longissimus dorsi

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Longissimus dorsi


title: SSP.2971-5

source_name: SSP.2971-5, Supraspinatus

source_name: reference: pool of all extractions


title: Day2_Light_6hr_Rep3

description: Samples collected after 6hr in the light regime on day 2, replicate 3.

value: 30 hr


title: FiSa-1

value: frozen tissue


title: LDO.2971-5

source_name: LDO.2971-5, Longissimus dorsi


title: Day2_Dark_6hr_Rep1

description: Samples collected after 6hr in the dark regime on day 2, replicate 1.


title: P7 - 2MED

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

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

institute: Mount SinaiSchool of Medicine

description: whole skin tisue

hyb_protocol: RNA was hybridized to HG U133A 2.0 chips to measure relative gene expression according to manufacturer's protocol

scan_protocol: Hewlett-Packard GeneArray Scanner

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

source_name: whole skin tisue

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen Valencia, CA) according to manufacturer’s protocol with on-column Dnase digestion

tag: patient

tag: group


title: P9 - 2MED

description: whole skin tisue


title: STE.2630-5

source_name: STE.2630-5, Semitendinosus

tag: Breed

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semitendinosus


title: P3 - 2MED

description: whole skin tisue


title: P7 - NON IRRAD

description: whole skin tisue

value: NON IRRAD


title: P6 - 2MED

description: whole skin tisue


title: L2T

tag: progesteron receptor status

tag: her2 status

value: IDC


title: Day2_Light_6hr_Rep2

description: Samples collected after 6hr in the light regime on day 2, replicate 2.


title: L30T

tag: hystotype

tag: grading


title: Day2_Light_6hr_Rep1

description: Samples collected after 6hr in the light regime on day 2, replicate 1.


title: L1T

tag: tissue

tag: tumor size


title: TN8T

source_name: Breast primary tumor (Basal-like)

value: Basal-like

tag: nodal status


title: P1 - 2MED

description: whole skin tisue


title: HEA.2836-7

source_name: HEA.2836-7, Heart

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Heart


title: Day1_Dark_6hr_Rep3

description: Samples collected after 6hr in the dark regime on day 1, replicate 3.

value: 18 hr

value: low


title: Day1_Dark_6hr_Rep2

description: Samples collected after 6hr in the dark regime on day 1, replicate 2.

value: high


title: TN7T


title: TN6T


title: P5 - 2MED

description: whole skin tisue


title: P10 - NON IRRAD

description: whole skin tisue


title: ISP.2630-5

source_name: ISP.2630-5, Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: BFE.2630-5

source_name: BFE.2630-5, Biceps femoris

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Biceps femoris


title: TN5T

value: Breast primary tumor

value: neg

value: ILC


title: TN4T


title: HEA.2971-5

source_name: HEA.2971-5, Heart


title: Day1_Dark_6hr_Rep1

description: Samples collected after 6hr in the dark regime on day 1, replicate 1.


title: VIN.2836-7

source_name: VIN.2836-7, Vastus intermedius

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Vastus intermedius


title: TBR.2836-7

source_name: TBR.2836-7, Triceps brachii

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Triceps brachii


title: P6 - NON IRRAD

description: whole skin tisue


title: TN2T

value: N+


title: Day1_Dark_1hr_Rep3

description: Samples collected after 1hr in the dark regime on day 1, replicate 3.

value: 13 hr


title: P8 - NON IRRAD

description: whole skin tisue

value: NON IRRAD


title: Day1_Dark_1hr_Rep1

description: Samples collected after 1hr in the dark regime on day 1, replicate 1.


title: Day1_Dark_1hr_Rep2

description: Samples collected after 1hr in the dark regime on day 1, replicate 2.


title: Day1_Light_6hr_Rep2

description: Samples collected after 6hr in the light regime on day 1, replicate 2.

value: 6 hr


title: P8 - 2MED

description: whole skin tisue


title: TN3T

value: Basal-like

value: IDC


title: SME.2630-5

description: Statistical analysis was carried out in the R computing environment version 2.6 using the package Linear Models for Microarray Analysis (Limma, version 2.9.17) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-647 to Alexa-555 were normalized within-slide using the global-loess method with default parameters as implemented in Limma.

source_name: SME.2630-5, Semimembranosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semimembranosus


title: Day1_Light_6hr_Rep3

description: Samples collected after 6hr in the light regime on day 1, replicate 3.

value: low


title: P2 - NON IRRAD

description: whole skin tisue


title: P1 - NON IRRAD

description: whole skin tisue


title: TN1T


title: P3 - NON IRRAD

description: whole skin tisue


title: Day1_Light_6hr_Rep1

description: Samples collected after 6hr in the light regime on day 1, replicate 1.

value: high


title: P2 - 2MED

description: whole skin tisue


title: LDO.2630-5

source_name: LDO.2630-5, Longissimus dorsi

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Longissimus dorsi


title: ISP.2971-5

source_name: ISP.2971-5, Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Infraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of all RNA extractions


title: Day1_Light_2hr_Rep3

description: Samples collected after 2hr in the light regime on day 1, replicate 3.

value: 2 hr


title: ISP.2824-1

source_name: ISP.2824-1, Infraspinatus


title: H5T

source_name: Breast primary tumor (HER2+)

value: Breast primary tumor

value: neg

value: pos


title: H4T

value: ILC


title: Day1_Light_2hr_Rep2

description: Samples collected after 2hr in the light regime on day 1, replicate 2.


title: H3T

value: N+


title: SSP.75-4

source_name: SSP.75-4, Supraspinatus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Supraspinatus


title: H2T


title: H6T


title: Day1_Light_30min_Rep3

description: Samples collected after 30min in the light regime on day 1, replicate 3.

value: 30 min


title: H1T


title: STE.75-4

source_name: STE.75-4, Semitendinosus

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Semitendinosus

source_name: reference: pool of all extractions


title: P5 - NON IRRAD

description: whole skin tisue

source_name: whole skin tisue

value: NON IRRAD


title: Day1_Light_2hr_Rep1

description: Samples collected after 2hr in the light regime on day 1, replicate 1.


title: Day1_Light_30min_Rep1

description: Samples collected after 30min in the light regime on day 1, replicate 1.


title: Day1_Light_30min_Rep2

description: Samples collected after 30min in the light regime on day 1, replicate 2.


title: P9 - NON IRRAD

description: whole skin tisue


title: TBR.75-4

source_name: TBR.75-4, Triceps brachii

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Triceps brachii


title: P4 - NON IRRAD

description: whole skin tisue


title: P10 - 2MED

description: whole skin tisue


title: VIN.75-4

source_name: VIN.75-4, Vastus intermedius

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:Vastus intermedius


title: NH22 IL-6 KO SALINE

status: Public on Oct 29 2012

city: Linköping

first: Namik

last: Hamzic

address: Linköpings Universitet

department: Institution for clinical and experimental medicin

institute: University of Health

description: Gene expression data from mouse hypothalamus

hyb_protocol: Following fragmentation, 2 µg of cRNA were hybridized for 16-18hr at 45 °C on GeneChip Mouse 1.0 ST Array. GeneChips were washed and stained in the Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring software using RMA as normalization method.

source_name: Mouse hypothalamus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 200 ng total RNA.

growth_protocol: 9-12 weeks old C57bl6 male mice deficient in interleukin-6 and their corresponding wild-type littermates originating from the same parental animals were used. All animals were housed one per cage in a pathogen-free facility at ambient temperature of 20-21 °C with food and water available ad libitum, and on a 12-h light, 12-h dark cycle.

extract_protocol: The mice were perfused with 0.9% saline solution transcardially before samples of hypothalamus were collected. Total RNA from the hypothalamus was extracted using RNeasy Lipid Tissue Kit (Qiagen) according to the manufacturer’s instructions, including deoxyribonuclease treatment with ribonuclease-free deoxyribonuclease set (Qiagen).

treatment_protocol:
SALINE
Mice were stimulated with a single intraperitoneal injection of lipopolysaccharide from Escherichia coli in a dose of 120 µg/kg body weight. Control animals were given vehicle (saline) only. The mice were sacrificied three hours after the injection of LPS or saline using coldioxide.

tag: treatment

value: saline

value: Hypothalamus

tag: genotype/variation

value: IL-6 KO


title: MFP tumor from TSPAN12 KD cells 2

city: Clayton

first: Konstantin

last: Knoblich

state: VIC

address: 15 Innovation Walk

department: Biochemistry and Molecular Biology

institute: Monash University

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.

scan_protocol: The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Data are processed using GenePattern. The ExpressionFileCreator module is used to normalize (RMA normalization algorithm) and create processed file (gct)

source_name: tumor

label_protocol: RNA is converted to cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements.The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Tumors were grown in mammary fat pads of Nu/Nu nude mice for 34 days

extract_protocol: Tumors were extracted with a scalpel and frozen. Piece of the the tumor was used to extract and purify total RNA using Rneasy kit (Qiagen)

value: TSPAN12 Knockdown


title: MFP tumor from TSPAN12 KD cells 1


title: NH18 IL-6 KO LPS

treatment_protocol:
LPS
Mice were stimulated with a single intraperitoneal injection of lipopolysaccharide from Escherichia coli in a dose of 120 µg/kg body weight. Control animals were given vehicle (saline) only. The mice were sacrificied three hours after the injection of LPS or saline using coldioxide.

tag: strain


title: NH20 IL-6 KO LPS

value: lipopolysaccharide from Escherichia coli in a dose of 120 µg/kg body weight


title: NH19 WT SALINE

value: WT