title: REH_MLLN

status: Public on Dec 19 2008

type: genomic

first: Garrett

last: Frampton

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

description: ChIP-chip targeting MLL-N in REH leukemia cell line

hyb_protocol: Labeled DNA (5-6 µg) was mixed and hybridized to arrays in Agilent hybridization chambers for 36-42 hours at 40oC.

scan_protocol: Arrays were then washed and scanned using an Agilent DNA microarray scanner BA.  PMT settings were set manually to normalize bulk signal in the Cy3 and Cy5 channel.

data_processing: We used GenePix Pro software (Molecular Devices, Sunnyvale, CA) to obtain background-subtracted intensity values for each fluorophore for every feature on the arrays respectively.  Among the Agilent controls is a set of negative control spots that contain 60-mer sequences that do not cross-hybridize to human genomic DNA.  We calculated the median intensity of these negative control spots in each channel and then subtracted this number from the intensities of all other features.  To correct for different amounts of each sample of DNA hybridized to the chip, the negative control-subtracted median intensity value of control oligonucleotides from the Cy3-enriched DNA channel was then divided by the median of the control oligonucleotides from the Cy5-enriched DNA channel. This yielded a normalization factor that was applied to each intensity in the Cy5 DNA channel.

molecule: genomic DNA

source_name: MLL-N in REH leukemia cell line

label_protocol: Purified DNA was blunted and ligated to linker and amplified using a two-stage PCR protocol.  Amplified DNA was labeled and purified using Bioprime random primer labeling kits (Invitrogen), RNA Polymerase II, MLL-N, AF4, ENL,  H3K79me2, and H3K4me3 immunoenriched DNA was labeled with Cy5 fluorophore, whole cell extract and H3 (control ChIP for histone modifications) immunoenriched DNA was labeled with Cy3 fluorophore.

growth_protocol: Human SEM cells with the t(4;11) translocation and REH control cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. All cell lines were maintained in RPMI medium 1640 supplemented with 10% FBS.

extract_protocol: The antibodies for ChIP were specific for MLL-N terminus (Bethyl BL1289), MLL-C terminus (Nakamura et al. 2002), AF4-C terminus (wis50 Rabbit polyclonal raised against amino acids 767-931), H3K79me2 (Abcam, ab3594). H3K4me3 (Abcam, ab8580) (Santos-Rosa et al. 2002), H3 (Abcam, ab1791), ENL (wis11 provided by Eli Canaani), hypophosphorylated RNA polymerase II (8WG16) (Thompson et al. 1989) and High-affinity HA (Roche clone 3F10). Protocols describing all materials and methods have been previously described and can be downloaded from http://web.wi.mit.edu/young/hES_PRC and are described in detail (Lee et al. 2006). Human REH or SEM cells were grown to a final count of 5x107 – 1x108 cells for each chromatin immunoprecipitation (ChIP). Cells were chemically crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 15 minutes at room temperature. Cells were rinsed twice with 1xPBS, harvested by centrifugation and flash frozen in liquid nitrogen. Cells were stored at –80oC prior to use. Cells were resuspended, lysed and sonicated to solubilize and shear crosslinked DNA. Sonication conditions vary depending on cells, culture conditions, crosslinking and equipment. We used a Misonix Sonicator 3000 and sonicated at a power of 27W for 10 x 30 second pulses (90 second pause between pulses). Samples were kept on ice at all times. The resulting whole cell extract was incubated overnight at 4oC with 100 µl of Dynal Protein G magnetic beads that had been preincubated with approximately 10 µg of the appropriate antibody. The immunoprecipitation was allowed to proceed overnight.  Beads were washed 5 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65oC with occasional vortexing and crosslinking was reversed by overnight incubation at 65oC.  Whole cell extract DNA (reserved from the sonication step) was also treated for crosslink reversal. Immunoprecipitated DNA and whole cell extract DNA were then purified by treatment with RNAse A, proteinase K and multiple phenol:chloroform:isoamyl alcohol extractions. HA-ChIPs were performed as described above with the following modifications to the sonication/IP buffer (50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton-X, 0.1% DOC). Four washes were performed first with IP buffer, second with IP buffer containing 500 mM NaCl, third with RIPA buffer and fourth with TE.

tag: MLL-N ChIP

source_name: WCE in REH leukemia cell line

tag: WCE ChIP


title: SEM_MLLN

city: Cambridge

middle: M

country: USA

description: ChIP-chip targeting MLL-N in SEM leukemia cell line

organism: Homo sapiens

source_name: MLL-N in SEM leukemia cell line

source_name: WCE in SEM leukemia cell line


title: Cytoplasmic Control Rep 1

status: Public on Dec 20 2008

type: RNA

city: Columbus

first: Kathleen

last: Boris-Lawrie

state: OH

address: 1925 Coffey Rd

department: Department of Veterinary Biosciences

institute: The Ohio State University

description: Cytoplasmic RNA profile under normal levels of RHA

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the Rhesus Macaque Genome Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

label: biotin

molecule: total RNA

organism: Chlorocebus aethiops

source_name: Cytoplasmic fraction from lysates treated with control siRNAs

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Seven 100 mm plates seeded with 1 x 106 cells were transfected with siRNAs targeting RHA or scrambled control siRNA. Incubation for 4 hours at 37°C in medium without serum was followed by a 24 hour incubation in 10% FBS medium. Cells were split and 24 hours later transfected again with siRNAs as above and incubated at 37°C for 24 hours.

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

treatment_protocol: For RHA downregulation , COS cells were transfected with siRNAs (Dharmacon) targeted to the coding region (nucleotides 2701-2721 and 2784-2803) of human RHA (NCBI accession code NM_001357), or scrambled RHA siRNAs to a final concentration of 0.5 nM.

tag: kidney derived from CV-1 transformed with an origin-defective mutant of SV-41

tag: Total cytoplasmic RNA


title: DLD-1 cells in response to hypoxic shock (1% O2)

city: Minatoku

first: Yutaka

last: Suzuki

email: ysuzuki@k.u-tokyo.ac.jp, ysuzuki@hgc.jp

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: University of Tokyo

hyb_protocol: The labeled cRNAs were mixed and hybridized to the Agilent Whole Human Genome Array G4112F using Gene Expression Hybridization kit according to the manufacture's protocol. After hybridization, slides were washed and dried according to the the Agilent wash protocol

scan_protocol: Scanned on an Agilent G2565A/03N scanner. Images were quantified using Agilent Feature Extraction 9.5.3.1

data_processing: Agilent Feature Extraction Software, Protocol: GE2-v5_95_Feb07

label_protocol: cRNA synthesis was performed using a Low RNA Input Linear Amplification Kit (Agilent) according to the manufacture's protocol.

extract_protocol: For validation experiments using microarray, RNAs were isolated from the DLD-1 cells cultured in similar hypoxia (1 % O2) and normoxia (21 % O2) conditions. The RNAs were further processed according to the manufacturer's instructions Using the Agilent Human Gene Expression Array G4112F platform.

tag: ATCC number

source_name: DLD-1 cells cultured in similar normoxia (21 % O2)


title: Isogenic WT Salt Shock 30min rep1 (Crick strand; polyA RNA)

status: Public on Dec 18 2008

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

hyb_protocol: Hybridization was handled by the PAN facility at Stanford University according to Affymetrix protocols.

scan_protocol: Scanning was handled by the PAN facility at Stanford University according to Affymetrix protocols.

data_processing: Output files were generated post hybridization and scanning by Affymetrix software and the resulting files can be viewed using the Affymetrix Genome Browser software.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae reference RNA

label_protocol: Total RNA samples were prepared following the protocol exactly as described in David et al. PNAS 103(14):5320-5 (2006).  PolyA RNA samples were prepared as follows.  500ug of total RNA were polyA purified using Qiagen Oligotex suspension to produce approximately 10ug of polyA RNA as determined by OD260/280.  2ug of the polyA purified RNA were then used in the generation of cDNA as per Affymetrix First Strand and Second Strand Synthesis protocols utilizing a T7-Oligo(dT) as the primer for the First Strand, followed by in vitro transcription to generate biotin labeled cRNA, as outlined by Affymetrix protocols.  The cRNA was fragmented as described by Affymetrix, and then sent for hybridization and scanning by the PAN facility at Stanford University.

growth_protocol: Our unpublished studies suggested that among two dozen or so different conditions that we assayed, exposure to high salt (0.8M NaCl) results in the expression of the greatest fraction of known and novel transcripts, and thus was chosen as the experimental condition to use to find previously unannotated and low abundance transcripts.  Cells were grown at 30 degrees C in YPD to approximately 1x10^7 cells/ml as determined by a Beckman Coulter Z2 Particle Count and Size Analyzer.  1.6M NaCl (in YPD) was added in an equal volume of YPD prewarmed to 30 degrees C (final concentration 0.8M).  Cells were harvested after 30 minutes by filtration, frozen in liquid nitrogen, and kept at minus 80 degrees C until RNA extraction and purification.

extract_protocol: RNA was extracted from the cells using a slightly modified version of the traditional hot phenol protocol (Schmitt et al. 1990) followed by ethanol precipitation and washing.  Briefly, 5ml of lysis buffer (10mM EDTA ph 8.0, 0.5% SDS, 10mM Tris-HCl pH 7.5) and 5ml of acid phenol were added to frozen cells and incubated at 60 degrees C for 1 hour with occasional vortexing, then placed on ice.  The aqueous phase was extracted after centrifugation and additional phenol extraction steps were performed as needed, followed by a chloroform extraction.  Total RNA was precipitated from the final aqueous solution with 10% volume 3M sodium acetate pH 5.2 and ethanol, and resuspended in nuclease-free water.

tag: Strain Background is FY23 x FY86 (Winston et al. 1995), carrying the auxotrophic markers

value: his3-delta200, leu2-delta1, trp1-delta63, ura3-52.


title: SEM_H3K79me2

description: ChIP-chip targeting H3K79me2 in SEM leukemia cell line

source_name: H3K79me2 in SEM leukemia cell line

tag: H3K79me2 ChIP

source_name: H3 in SEM leukemia cell line

tag: H3 ChIP


title: Isogenic WT Salt Shock 30min rep1 (Crick strand; Total RNA)


title: REH_RNAP2

description: ChIP-chip targeting RNAP2 in REH leukemia cell line

source_name: RNAP2 in REH leukemia cell line

tag: RNAP2 ChIP


title: REH_ENL

description: ChIP-chip targeting ENL in REH leukemia cell line

source_name: ENL in REH leukemia cell line

tag: ENL ChIP


title: REH_AF4C

description: ChIP-chip targeting AF4-C in REH leukemia cell line

source_name: AF4-C in REH leukemia cell line

tag: AF4-C ChIP


title: REH_H3K79me2

description: ChIP-chip targeting H3K79me2 in REH leukemia cell line

source_name: H3K79me2 in REH leukemia cell line

source_name: H3 in REH leukemia cell line


title: SEM_H3K4me3

description: ChIP-chip targeting H3K4me3 in SEM leukemia cell line

source_name: H3K4me3 in SEM leukemia cell line

tag: H3K4me3 ChIP


title: SEM_ENL

description: ChIP-chip targeting ENL in SEM leukemia cell line

source_name: ENL in SEM leukemia cell line


title: REH_H3K4me3

description: ChIP-chip targeting H3K4me3 in REH leukemia cell line

source_name: H3K4me3 in REH leukemia cell line


title: SEM_RNAP2

description: ChIP-chip targeting RNAP2 in SEM leukemia cell line

source_name: RNAP2 in SEM leukemia cell line


title: SEM_AF4C

description: ChIP-chip targeting AF4-C in SEM leukemia cell line

source_name: AF4-C in SEM leukemia cell line


title: Polysomal mRNA level transformed WT RPL12B strain vs Mutated RPL12B-R66K strain Replicate2

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

country: Taiwan

description: Biological replicate 2 of 2

hyb_protocol: Hybridization was carried out for 20 h at 55°C using the MAUI Hybridization System (BioMicro Systems, Salt Lake City, UT). After hybridization was complete, arrays were disassembled in GE Wash Buffer 1 (Agilent technologies), washed in Gene Expression Wash Buffer 1 at room temperature for 1 min, followed washed in Gene Expression Wash Buffer 2 (Agilent technologies) at 37°C for 1 min.

scan_protocol: Scanned on a GenePix 4000B microarray scanner. Images were quantified using GenePix Pro 6.0 software .

data_processing: Processed gpr file by GeneSpring 7.0 software: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal.

label: Alexa Fluor 647

source_name: Polysomal mRNA from WT RPL12B strain

label_protocol: Reference URL : http://tools.invitrogen.com/content/sfs/manuals/superscript_plus_indirectcdnalabeling_man.pdf 25 ug of RNA were converted in either Alexa Fluor 555- or Alexa Flour 647- labeled cDNA probe using the Superscript indirect cDNA labeling kit (Invirogen).

growth_protocol: Cells were cultured in synthetic dextrose minimal medium (SD) with appropriate nutritional requirements at 30 oC until A600 = 0.5-0.6.

extract_protocol:
For total mRNA extraction, acid phenol/chloroform method was used.
For polysomal mRNA extraction, First, cell extracts were layered on top of a 10-40% sucrose gradient prepared in 20 mM Tris-HCl, pH 7.4, 500 mM NH4OAc, 100 mM MgCl2, and 5 mM beta-mercaptomethanol
Second, Centrifugation was carried out in a Beckman SW41 Ti rotor at 39,000 rpm, 4 oC for 4 h to separate ribosome monomer and polymer dependent on  their rate of sedimentation in a centrifuge.
Third, collected the polysome fractions, polysomal mRNAs were associated with polysomes. Fractions from sucrose gradient were precipitated by adding 3 volumes of cold ethanol and incubated at -20°C overnight to precipitated polyribosomes and associated mRNAs.
Fourth, The precipitates were collected by centrifugation and the pellet was air dried. It was then suspended in Buffer IV (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.2% SDS, and 0.8 mg/ml Proteinase K) and incubated for 20 min at 37 oC to digest ribosomal proteins.
Fifth, The RNAs in the sample were then extracted with acid phenol-chloroform as above.

treatment_protocol: For polysomal mRNA isolation, cycloheximide (50 ug/ml final concentration) was added to the rest of the cultures and the cells were cooled immediately on ice then collected by centrifugation.

label: Alexa Fluor 555

source_name: Polysomal mRNA from RPL12B-R66K mutant strain


title: Total mRNA level transformed WT RPL12B strain vs Mutated RPL12B-R66K strain Replicate2

description: Biological replicate 2 of 2

source_name: Total mRNA from WT RPL12B strain

source_name: Total mRNA from RPL12B-R66K mutant strain


title: Polysomal level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate3

description: Biological replicate 3 of 3

source_name: Polysomal mRNA from RPL12A/B double deletion strain 6EA1


title: Total mRNA level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate4

description: Biological replicate 4 of 4

source_name: Total mRNA from RPL12A/B double deletion strain 6EA1


title: Polysomal level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate3

description: Biological replicate 3 of 3


title: Total mRNA level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate4

description: Biological replicate 4 of 4


title: Total mRNA level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate3

description: Biological replicate 3 of 4


title: Polysomal level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate2

description: Biological replicate 2 of 3


title: Polysomal mRNA level transformed WT RPL12B strain vs Mutated RPL12B-R66K strain Replicate1

description: Biological replicate 1 of 2


title: Isogenic WT Salt Shock 30min rep1 (Watson strand; Total RNA)

source_name: S.cerevisiae reference RNA


title: Total mRNA level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate1

description: Biological replicate 1 of 4


title: XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Watson strand; polyA RNA)

source_name: S.cerevisiae experimental RNA

value: his3-delta200, leu2-delta1, trp1-delta63, ura3-52.  The XRLP mutant contains deletions in the genes XRN1, RRP6, LSM1, and PAT1.


title: XRLP (xrn1 rrp6 lsm1 pat1) Mutant Salt Shock 30min rep1 (Watson strand; Total RNA)


title: Total mRNA level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate2

description: Biological replicate 2 of 4


title: Polysomal level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate1

description: Biological replicate 1 of 3


title: Total mRNA level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate1

description: Biological replicate 1 of 4


title: Total mRNA level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate3

description: Biological replicate 3 of 4


title: Polysomal level transformed Mutated RPL12B-R66K strain vs RPL12A/B deletion strain Replicate2

description: Biological replicate 2 of 3


title: long_oligo_array_hyb3

type: other

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: Hybridization of nucleosome-reconstituted pool #3 (DT+ES pools combined)

hyb_protocol: Equal amounts of labeled input (Cy3 labeled) and reconstituted (Cy5 labeled) products along with 5µM of blocking primer were hybridized to tracking arrays in SSPE buffer containing 42% formamide and 0.01% SDS at 42°C for 20 hours.  Arrays were washed first with 6X SSPE and 0.005% sarcosine, followed by 0.6X SSPE.

scan_protocol: Arrays were scanned using Agilent Technologies microarray scanner G2565.

data_processing: Arrays were quantified and normalized (spatial detrending and Loess) using  Agilent Feature Extraction 9.5 Software.  Normalized data from both input (Cy3) and reconstituted (Cy5) channels are reported as log2(reconstituted/input) ratios.

molecule: other

organism: synthetic construct

source_name: Input

label_protocol: 1ng of each of the input and nucleosome-reconstituted pools were labeled via PCR using Cy3 and Cy5 labelled primers.

extract_protocol: 170-mer oligonucleotides containing a 150 base variable sequence and a 20 bp common sequence (5’- TCTCCCTATAGTGAGTCGTA-3’) were synthesized by Agilent.  10ng (0.2pmol) of the single stranded oligo pools was double stranded via primer extension.  Briefly, 2pmol of the reverse complement of the common sequence (5’-CTAATACGACTCACTATAGGG-3’) was first annealed to the oligos.  Sequences were double stranded using 1mM dNTP, 3U T4 DNA polymerase (NEB), 5U Klenow fragment (NEB), 1X NEB2 buffer, 1X BSA, and incubated at 30°C for 30 minutes.  The reaction product was phenol:chloroform extracted, precipitated with ammonium acetate and ethanol, washed with 70% ethanol, dried, and resuspended in dH¬2O.  10pmol of an M13 primer duplex (5’-CAGGAAACAGCTATGAGC-3’/5’-P-GCTCATAGCTGTTTCCTG-3’) was then ligated to the double stranded oligos using 400U T4 DNA ligase (NEB) overnight at 16°C. Ligation products were end-labeled with T4 polynucleotide kinase and [γ-32P] ATP and the expected 188bp product was isolated from a 4% polyacrylamide gel.  To remove potential concatamers, ligation products were PCR amplified using extended primers containing the SwaI restriction site:  Forward primer, 5’-GCATGATCGACTGCGAATTTGATTTAAATCTAATACGACTCACTATAGGG -3’; Reverse primer,  5’-ATGACACATTATGACCAAAGATCGATTTAAATCAGGAAACAGCTATGAGC-3’.   PCR products were digested with SwaI (NEB).   The resultant 197bp product was gel purified from a 2.8% agarose gel and assembled into nucleosomes  via salt gradient dialysis,  using 6 µg histone octamer + 12 µg DNA in a 200 µl volume.  The resulting nucleosomes were separated away from the remaining naked DNA by native polyacrylamide gel electrophoresis (5% (w/v) polyacrylamide) in 1/3x TBE buffer (TBE is 90 mM Tris, 90 mM boric acid, 2 mM EDTA, pH 8.3).  The nucleosome-containing band was excised from the gel, and its DNA extracted by crushing and soaking into 0.3 M NaOAc, 0.5 M NH4OAc, 0.1 mM EDTA, 0.1% (w/v) SDS, followed by ethanol precipitation.

tag: Starting oligonucleotide pool (before nucleosome reconstitution)

source_name: Nucleosomal

label_protocol: Refer to Channel 1 Label Protocol

extract_protocol: Refer to Channel 1 Extract Protocol

tag: Nucleosome-reconstituted pool


title: Total mRNA level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate2

description: Biological replicate 2 of 4


title: Whole-blood-RNA-Acute-day4-1396924011_A

city: Ho Chi Minh

first: Long

last: Hoang

address: 190 Ben Ham Tu

country: Viet Nam

institute: OUCRU

description: RNA sample was first reverse transcribed to cDNA. the cDNA was then used to synthesis the antisense RNA using IVT protocol (Ambion, Inc., Austin, TX). The antisense RNA was then purified before 850ng of the product was used for hybridization

hyb_protocol: Illumina hybridization standard procedure, in brief, Biotinylated amplified cRNA was generated by in vitro transcription (IVT) technology using Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer’s instructions. After purification, 850ng of cRNA was hybridized to an Illumina HumanRef-8 V1BeadChip (containing probes to 23,961 RefSeq gene sequences) at 55 °C for 18 hours following the manufacturer’s instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Chip was scanned using Illumina BeadArray Reader, scan factor 5

data_processing:
Intensity was acquired using Beadstudio software
Intensity was background normalised (Subtract the background value)

source_name: Whole blood RNA collected on day 4 of illness

label_protocol: After hybridization, the chip was washed, blocked and stained with streptavidine-Cy3 for 10 min.

extract_protocol: Whole-blood (2.5ml) was collected directly into PAXgene RNA tubes (Qiagen, Sussex, UK) at the bedside. RNA extraction was performed using Paxgene RNA kits (Qiagen). Purified RNA was stored at –80oC and quantified prior to use using a spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

tag: Whole blood RNA of DSS patient collected on day 4 of illness


title: Polysomal level transformed WT RPL12B strain vs RPL12A/B deletion strain Replicate1

description: Biological replicate 1 of 3


title: Whole-blood-RNA-Acute-day4-1387956034_D


title: Total mRNA level transformed WT RPL12B strain vs Mutated RPL12B-R66K strain Replicate1

description: Biological replicate 1 of 2


title: Whole-blood-RNA-Acute-day4-1396924023_D


title: long_oligo_array_hyb1

description: Hybridization of nucleosome-reconstituted pool #1 (DT pool)


title: long_oligo_array_hyb2

description: Hybridization of nucleosome-reconstituted pool #2 (ES pool)


title: Whole-blood-RNA-convalescent-Day30-1387956034_E

source_name: Whole blood RNA collected on day 30 of illness

tag: Whole blood RNA of DSS patient collected on day 30 of illness


title: Whole-blood-RNA-Acute-day4-1387956034_G


title: Isogenic WT Salt Shock 30min rep1 (Watson strand; polyA RNA)


title: Whole-blood-RNA-convalescent-day30-1387956034_H

tag: Whole blood RNA of uncomplicated dengue patient collected on day 30 of illness


title: Whole-blood-RNA-convalescent-Day30-1387956034_A


title: Whole-blood-RNA-convalescent-day30-1396924011_B

data_processing:
Intensity was acquired using Beadstudio software
Intensity was background normalised (Subtract the background value


title: Whole-blood-RNA-Acute-day4-1396924011_C

tag: Whole blood RNA of uncomplicated dengue patient collected on day 4 of illness


title: Whole-blood-RNA-Acute-day4-1396924011_H


title: Whole-blood-RNA-Acute-day4-1396924023_C


title: Whole-blood-RNA-Acute-day4-1396924052_F


title: Whole-blood-RNA-convalescent-day30-1396924023_F


title: Whole-blood-RNA-Acute-day4-1396924011_E


title: Whole-blood-RNA-convalescent-day30-1396924023_B


title: Colo741-Kras-G12V rep2

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

country: Italy

institute: IRCCS AOU San Martino – IST, Genova

description: Gene expression data from Pool of five cell clones from transfection of adenocarcinoma cell line Colo741 with pcDNA3.1-KRas2(Wt)

hyb_protocol: Fragmented cRNA, run on the Bioanalyzer to verify the correct electropherogram, was hybridized in a hybridization oven (16 hours, 45°C) to a Human Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were subsequently scanned using a confocal laser GeneChip Scanner 3000 7G and GeneChip Command Console (Affymetrix).

data_processing: Affymetrix raw data files (CEL files) are used as input files in expression console environment (Affymetrix, Inc., Santa Clara, CA). Briefly, Cel files were processed using Robust Multi-Array Analysis procedure (Irizarry et al., 2003). The RMA method was used, first, to convert the intensities from the multiple probes in a probeset into a single expression value with greater precision and reduced background noise, relying on the perfect match probes only (ignoring the mismatch probes) and, after, to normalize by sketch quantile normalization. Also quality assessement were performed in expression console environment.

label: Biotin

label_protocol: Briefly, accordingly to the recommendations of the manufacturer, 100 ng total RNA was used in the first-round synthesis of double-stranded cDNA. The RNA was reverse transcribed using a WT cDNA synthesis and amplification kit (Affymetrix). The resulting biotin-labeled cRNA was purified using an IVT clean-up kit (Affymetrix) and quantified using a UV spectrophotometer (A260/280; Beckman, Palo Alto, CA). An aliquot (15 µg) of cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 minutes.

growth_protocol: The human colorectal carcinoma cell line Colo741 was cultured in a growth medium [RPMI1640 (Euroclone, Milano, Italy)] supplemented with 10% fetal calf serum (GIBCO, Italy), 1% glutamine, 1% penicillin-streptomycin]. Cultures were incubated at 37°C in a 5% CO2 atmosphere.

extract_protocol:
TRizol (Invitrogen), DNase treatment and RNeasy Mini Kit (Qiagen).
RNA concentration and purity were determined from measuring absorbance at 260 and 280 nm; 2 μg total RNA was run on a 1% denaturing gel and 100 ng were loaded on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) to verify RNA integrity.

treatment_protocol: Transfection of the KRas2 constructs into Colo741 cells was performed with Fugene (Roche) according to the manufacturer's instructions. 48 h after transfection, the cells, stably expressing the various constructs, were selected in medium containing 200 µg/ml G418 for three weeks and then cloned using limiting dilution. The selected clones were screened by PCR using a KRas2 cds-specific forward primer and a BHG-specific reverse one. Possible contamination by genomic DNA was controlled by an "RT minus" control, consisted of a mock cDNA synthesis reaction performed using a harvested cell where the reverse transcriptase enzyme was omitted from the reaction.

tag: Pool of five cell clones from transfection of adenocarcinoma cell line Colo741 with pcDNA3.1-KRas2-G12V


title: Colo741-Kras-G12D rep2

tag: Pool of five cell clones from transfection of adenocarcinoma cell line Colo741 with pcDNA3.1-KRas2-G12D


title: Whole-blood-RNA-Acute-day30-1396924052_H


title: Whole-blood-RNA-Acute-day4-1396924057_H


title: Whole-blood-RNA-Acute-day4-1396924052_E


title: Whole-blood-RNA-convalescent-day30-1396924023_H


title: Whole-blood-RNA-convalescent-day30-1396924023_E


title: Whole-blood-RNA-Acute-day4-1396924023_A


title: Whole-blood-RNA-Acute-day4-1396924052_C


title: Whole-blood-RNA-Acute-day4-1396924055_F


title: Whole-blood-RNA-Acute-day4-1396924055_D


title: Whole-blood-RNA-Acute-day4-1396924052_D


title: Whole-blood-RNA-Acute-day4-1396924057_F


title: Whole-blood-RNA-Acute-day4-1396924057_D


title: Whole-blood-RNA-convalescent-day30-1396924057_E


title: Colo741-Kras-G12V rep1


title: Whole-blood-RNA-Convalescent-day30-1396924055_H


title: Colo741-Kras-WT rep2

tag: Pool of five cell clones from transfection of adenocarcinoma cell line Colo741 with pcDNA3.1-KRas2(Wt)


title: Whole-blood-RNA-convalescent-day30-1396924057_C

label_protocol:
Illumina labeling standard procedure
After hybridization, the chip was washed, blocked and stained with streptavidine-Cy3 for 10 min.


title: Colo741-Kras-G12D rep1


title: SK-N-AS_CRL2137_120203_1636

city: Trondheim

first: Tom

middle: Even

last: Wheeler

address: Olav Kyrresgt. 3

department: Department of cancer research and molecular medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

description: The universal human reference is used as "control" to enable comparision between a group of neuroendocrine cell lines and a group of non-neuroendocrine cell lines.

tag: SK-N-AS is a neuroblastoma cell line (ATCC nr; CRL2137) derived in 1981 from a bone marrow metastasis from a child with poorly differentiated embryonal

tag: neuroblastoma.

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to

tag: be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal

tag: reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were

tag: pooled to make the Universal Human Reference RNA. This Universal Reference RNA is suitable for microarray experiments.


title: relB-/-_10h_rep1

city: Jena

first: Daniela

last: Albrecht

address: Wildenbruchstr. 15

country: Germany

institute: BioControl Jena GmbH

description: no additional information

hyb_protocol: Standard Codelink protocol (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: using GenePix 4000B Array Scanner and GenePix Pro 4.0 software according to the settings suggested by GE Healthcare (supplier of CodeLink microarrays at experiment time, http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

data_processing: Raw data were analysed using Codelink Expression Analysis v.4.1 software to extract MDFCs (minimal detectable fold changes). Subsequent analysis was done using R and Bioconductor. Only probes with probe type „DISCOVERY“ and no MSR (Manufactory Slide Report) flag were used, leaving 19580 genes. Intensity values <0.01 were set to 0.01. Raw intensities were scaled to array median. After log2-transformation, quantile normalization was applied across all arrays.

organism: Mus musculus

source_name: mouse tissue, relB-/-, 10h

extract_protocol: total cellular RNA was isolated using RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions, possible contamination by genomic DNA was removed by DNAseI treatment using the RNAse-Free DNAse Set (Qiagen), quality was checked by spectrophotometry and agarose gel electrophoresis, 2µg RNA per sample was used for cDNA preparation when A260:A280 ratio was 1.8-2.1 and RNA was intact

tag: mouse embryonic fibroblasts (MEF)


title: relB-/-_10h_rep2

description: no additional information

label_protocol: Standard Codelink protocol (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)


title: Colo741-Kras-WT rep1


title: relB-/-_10h_rep3

description: no additional information


title: A-427_HTB-53_120203_1627

tag: A-427 cell line (ATCC nr

value: HTB-53) was derived from lung and is an epidermoid

tag: carcinoma.


title: BON1_120203_1644

tag: BON1 is a human cell line derived from a lymph node metastasis derived from a (peri-) pancreatic carsinoid tumor, and was first established in 1986. It originates from a 28 year old male.


title: A-172_CRL-1620_1940_082403

tag: The A172 cell line (ATCC nr

value: CRL-1620) is derived from human brain glioblastoma.


title: SK-N-FI_CRL-2142_1834_082403

tag: SK-N-FI is a neuroblastoma cell line (ATCC nr; CRL2142) derived in 1979 from a bone marrow metastasis from an 11 year old Caucasian male with poorly differentiated embryonal neuroblastoma.


title: TT_CRL-1803_1822_082403

tag: The TT cell line (ATCC nr; CRL1803) was established from a specimen obtained by

tag: needle biopsy from a 77 year old female with thyroid medullary carcinoma.


title: relB-/-_0h_rep1

description: no additional information

source_name: mouse tissue, relB-/-, 0h


title: NCI-H727_CRL-5815_1958_082403

tag: NCI-H727 (ATCC nr

value: CRL-5815) is the best differentiated of the available bronchial carcinoid lines.


title: relB-/-_0h_rep3

description: no additional information


title: A-427_HTB-53_2142_082103


title: relB-/-_0h_rep2

description: no additional information


title: SW480_CLL-228_1857_082403

tag: SW480 (ATCC nr

value: CLL-228) was isolated from the tissue of a 51-year-old Caucasian

tag: male and was established from a primary adenocarcinoma of the colon.


title: UMC-11_CRL-5975_1916_082403

tag: The UMC-11 cell line was derived from a human lung carcinoid (ATCC nr; CRL-


title: NCI-H727_CRL-5815_2230_082103


title: SW480_CLL-228_1845_082403


title: WiDr_CLL-218_1928_082403

tag: Widr is a colon adenocarcinoma line (ATCC; CLL-218) established from a 78 year old female.


title: UMC-11_CRL5975_2059_082103

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to

tag: Stratagene also supplies a QPCR Human Reference Total RNA, suitable for QRT-PCR, which has undergone further DNase treatment.


title: relA-/-_10h_rep2

description: no additional information

source_name: mouse tissue, relA-/-, 10h


title: TT_CRL1803_2118_082103

tag: be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal

tag: reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were


title: A-172_CRL-1620_2154_082103

tag: pooled to make the Universal Human Reference RNA. This Universal Reference RNA is suitable for microarray experiments.


title: WiDr_CLL-218_2206_082103


title: relA-/-_0h_rep3

description: no additional information

source_name: mouse tissue, relA-/-, 0h

tag: mouse embryonic fibroblasts (MEF)


title: wt_10h_rep2

description: no additional information

source_name: mouse tissue, wt, 10h


title: relA-/-_0h_rep2

description: no additional information


title: wt_10h_rep3

description: no additional information


title: wt_10h_rep1

description: no additional information


title: UsiA12_rep2

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description: mutant p53 as a regulator of transcription

hyb_protocol: Array hybridization was performed for 16 hrs at 55 °C. Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

scan_protocol: Image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Quantile normalization was done using the limma package within the R environment.

label: DIG-UTP

source_name: U251 glioblastoma cell line

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 µg of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).

extract_protocol: Total RNA was isolated applying the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quality and integrity of the total RNA was evaluated with the 2100 Bioanalyzer (Agilent Technologies).

tag: UsiA12 clone derived from the U251 cells stably transfected with the pSuper-p53 and pCI-neo vectors


title: SK-N-FI_CRL2142_2047_082103

tag: SK-N-FI is a neuroblastoma cell line (ATCC nr; CRL2142) derived in 1979 from a

tag: bone marrow metastasis from an 11 year old Caucasian male with poorly differentiated

tag: embryonal neuroblastoma.

tag: Stratagene also supplies a QPCR Human Reference Total RNA, suitable for QRT-PCR, which has undergone further DNase treatment. (http://www.stratagene.com/manuals/740000.pdf)


title: wt_0h_rep3

description: no additional information

source_name: mouse tissue, wt, 0h


title: SK-N-AS_CRL-2137_2218_082103

tag: SK-N-AS is a neuroblastoma cell line (ATCC nr; CRL2137) derived in 1981 from a

tag: bone marrow metastasis from a child with poorly differentiated embryonal

tag: neuroblastoma.


title: relA-/-_10h_rep3

description: no additional information


title: UsiA12_rep1


title: relA-/-_0h_rep1

description: no additional information


title: Primary rat spinal cord astrocytes NonTG-B

city: Montevideo

first: Marcelo

middle: R.

last: Vargas

address: Av. Italia 3318

department: Neurobiología Celular y Molecular

country: Uruguay

institute: Instituto Clemente Estable

description:
Labeling was done with the Affymetrix kits according to their one-cycle target labeling assay. Kits used were the one-cycle cDNA synthesis kit(900431), sample cleanup modules(900371), eukaryotic Poly-A RNA control kit (900433), IVT labeling kit(900449), Eukayotic hybridization control kit(900454)
5 ug of total RNA were used for the amplification.
Hybridization, washing and scanning was done according to the Affymetrix protocol in GeneChip Expression Analysis Technical Manual 701021 Rev. 5.

organism: Rattus norvegicus

source_name: Spinal cord astrocytes NonTG

extract_protocol: Total RNA extracted with RNeasy Mini (Qiagen)

tag: Primary spinal cord astrocytes from non-transgenic 1 day old rat littermates obtained from the breeding of a hSOD1G93A positive male with a negative female.

tag: Astrocytes were prepared as described in Cassina P, et al.J Neurosci Res. 2002;67(1):21-9.

tag: Transgenic hSOD1G93A rats were provided by D. S. Howland (Howland et al. 2002; PNAS, 99(3)


title: BON1_2130_082103

tag: BON is a human cell line derived from a lymph node metastasis derived from a (peri-) pancreatic carsinoid tumor, and was first established in 1986. It originates from a 28 year old male.

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were


title: wt_0h_rep2

description: no additional information


title: Primary rat spinal cord astrocytes NonTG-C

hyb_protocol: Hybridization, washing and scanning was done according to the Affymetrix protocol in GeneChip Expression Analysis Technical Manual 701021 Rev. 5

label_protocol: Labeling was done with the Affymetrix kits according to their one-cycle target labeling assay. Kits used were the one-cycle cDNA synthesis kit(900431), sample cleanup modules(900371), eukaryotic Poly-A RNA control kit (900433), IVT labeling kit(900449), Eukayotic hybridization control kit(900454)


title: Primary rat spinal cord astrocytes hSOD1G93A-C

scan_protocol: Hybridization, washing and scanning was done according to the Affymetrix protocol in GeneChip Expression Analysis Technical Manual 701021 Rev. 5

source_name: Spinal cord astrocytes from transgenic hSOD1G93A

tag: Primary spinal cord astrocytes from hSOD1G93A-transgenic 1 day old rat littermates obtained from the breeding of a hSOD1G93A positive male with a negative female.


title: Primary rat spinal cord astrocytes hSOD1G93A-A


title: L-1236

status: Public on Dec 17 2008

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: see Affymetrix standard protocols

scan_protocol: see Affymetrix standard protocols

data_processing: RMA

source_name: Lymphoma Cell line

label_protocol: see Affymetrix standard protocols

extract_protocol: guanidium isothiocyanate and centrifugation over a caesium chloride

treatment_protocol: pre-treatment

tag: Type:Cell line


title: Primary rat spinal cord astrocytes NonTG-A

hyb_protocol: Hybridization, washing and scanning was done according to the Affymetrix protocol in GeneChip Expression Analysis Technical Manual 701021 Rev. 5.


title: relA-/-_10h_rep1

description: no additional information


title: KM-H2


title: wt_0h_rep1

description: no additional information


title: U251_rep2

tag: Human glioblastoma cell line


title: L-428


title: U251_rep1

tag: human glioblastoma cell line


title: 352525

source_name: Adenite


title: 348644


title: 03K05283

source_name: Hodgkin's Lymphoma

tag: Type:Hodgkin's Lymphoma

tag: Histology:Nodular sclerosis


title: 348672

source_name: T-Cell/Histiocyte-Rich Large B-Cell Lymphomas


title: T123


title: 994136


title: 349726


title: 993413

tag: Histology:Mixed cellularity


title: 99K00442


title: T555


title: 333869


title: 994985


title: 10219


title: 347692


title: 1882


title: 347451


title: 354306


title: Primary rat spinal cord astrocytes hSOD1G93A-B


title: 03K05058


title: 347619


title: T786


title: 10690


title: 347622


title: T98


title: H102.5207


title: 347691


title: 03X00811


title: 03X01016


title: F4901


title: 347456


title: T567


title: T296


title: T447


title: 9673


title: H199.10869


title: 04B01240


title: H102.7765


title: F9461


title: 8586


title: F9669


title: N.11028


title: C0219418


title: N3871


title: G.4562


title: j13232


title: CO.315693


title: B9403904


title: 02B07606


title: H102.7668


title: 1826.bis


title: F7826


title: T693


title: N.15


title: 347455


title: 347618


title: 3075


title: T475


title: F2870


title: B04.652


title: 12142


title: 04B01622


title: B98.988


title: 11238


title: 9936

tag: Histology:Lymphocyte depleted


title: F14379


title: 10596


title: 1826


title: Negative Control 3

city: Naples

first: Vincenzo

middle: Alessandro

last: Gennarino

state: Italy

address: Via Pietro Castellino,111

department: TIGEM

institute: Telethon

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

source_name: Human cell line

label_protocol: standard Affymetrix procedure

extract_protocol: Total RNA was obtained using the miRNeasy kit (Quiagen) according to the manufacturer’s instructions.

tag: HeLa Cells


title: H100.6772


title: CO409469


title: Negative Control 2


title: Negative Control 1


title: 347624


title: mir-98 overexpression 2


title: E.coli_15min_CORM_AE_2

city: Oeiras

first: Lígia

middle: Santos

last: Nobre

address: Av. da Republica (EAN)

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica

description: not applicable

hyb_protocol: 1 µg of end-labeled, fragmented cDNA was used in a 80-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0006; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G controlled by Affymetrix GeneChip Operating Software version 1.4. All arrays were scaled to a target value of 500.

data_processing: Scanned arrays were analyzed with Affymetrix GCOS 1.4 software to obtain Detection calls and Expression values based on MAS 5.0 algorithms. All arrays were scaled to a target value of 500.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E.coli_15min_CORM-2 treated_aerobic

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip E. coli Genome 2.0 Arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 1.5 ug of cDNA was fragmented with DNase and end-labeled (GeneChip® WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

extract_protocol: The hot-phenol method was used to extract total RNA from two independent cultures of cells grown aerobically and treated with 250 μM CORM-2 during 15 min.

tag: Escherichia coli MG1655


title: mir-98 overexpression 3


title: E.coli_15min_ANA_1

description: not applicable

extract_protocol: The hot-phenol method was used to extract total RNA from two independent cultures of cells grown anaerobically


title: E.coli_15min_CORM_ANA_1

description: not applicable

source_name: E.coli_15min_CORM-2 treated_anaerobic

extract_protocol: The hot-phenol method was used to extract total RNA from two independent cultures of cells grown anaerobically and treated with 250 μM CORM-2 during 15 min.


title: mir-26b overexpression 2


title: mir-26b overexpression 3


title: E. coli_15min_ANA_2

description: not applicable

source_name: E. coli_15min_anaerobic


title: SAM_FEM_WK6_Cy5_23

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

description:
SAM_FEM_WK6_Cy5_23
Replicate H

hyb_protocol: Reactions were purified using QIAQuick PCR purification columns (Qiagen), and labeled RNA was hybridized to clones arrayed on a 2x2-cm field under a plastic HybriSlip (Grace BioLabs) in a humidified cassette (TeleChem) for 15 h at 65 degrees C.

scan_protocol: After the arrays were washed, fluorescence intensities were measured using a ScanArray 4000 (GSI Lumonics) laser scanner and converted to digital values using ScanAlyze software.

data_processing: The log2-transformed scores for all spot measures were normalized using a mixed model analysis implemented in the PROC MIXED procedure within the SAS system.

organism: Drosophila melanogaster

source_name: Samarkand, female, 6-week adult flies

label_protocol: Three milligrams of poly(A) mRNA was used as a template for each of six replicate cDNA synthesis reactions using Superscript II (GibcoBRL) in the presence of fluorescently labeled Cy3- or Cy5-dCTP (Amersham).

growth_protocol: Flies of the standard laboratory strains Oregon R and Samarkand were maintained on cornmeal and yeast food at 25 degrees C with a 12-h light/dark cycle.

extract_protocol: At the time of collection (1 or 6 wk), flies were sexed under CO2 anesthesia and immediately placed in liquid nitrogen. Total RNA was prepared from tubes of up to 400 whole flies using Trizol reagent (GibcoBRL). 10-12 of these preparations were pooled before isolating the poly(A) fraction for each genotype, sex and age combination using oligo(dT)-linked Oligotex resin (Qiagen).

treatment_protocol: Flies were collected within 12 h of eclosion, and placed in vials at a density of 60 to 70 flies/ vial.  Flies were transferred to fresh vials every 3-4 days.


title: ORE_FEM_WK6_Cy3_24

description:
ORE_FEM_WK6_Cy3_24
Replicate F

source_name: Oregon R, female, 6-week adult flies


title: E.coli_15min_CORM_AE_1

description: not applicable


title: E.coli_15min_AE_2

description: not applicable

extract_protocol: The hot-phenol method was used to extract total RNA from two independent cultures of cells grown aerobically


title: SAM_FEM_WK1_Cy3_23

description:
SAM_FEM_WK1_Cy3_23
Replicate H

source_name: Samarkand, female, 1-week adult flies


title: ORE_FEM_WK1_Cy5_24

description:
ORE_FEM_WK1_Cy5_24
Replicate F

source_name: Oregon R, female, 1-week adult flies


title: SAM_FEM_WK6_Cy5_22

description:
SAM_FEM_WK6_Cy5_22
Replicate G


title: E.coli_15min_AE_1

description: not applicable


title: mir-26b overexpression 1


title: SAM_FEM_WK1_Cy3_22

description:
SAM_FEM_WK1_Cy3_22
Replicate G


title: mir-98 overexpression 1


title: ORE_FEM_WK1_Cy5_21

description:
ORE_FEM_WK1_Cy5_21
Replicate E


title: E.coli_15min_CORM_ANA_2

description: not applicable


title: ORE_FEM_WK6_Cy3_21

description:
ORE_FEM_WK6_Cy3_21
Replicate E


title: SAM_MAL_WK1_Cy5_17

description:
SAM_MAL_WK1_Cy5_17
Replicate E

source_name: Samarkand, male, 1-week adult flies


title: ORE_MAL_WK6_Cy3_19

description:
ORE_MAL_WK6_Cy3_19
Replicate E

source_name: Oregon R, male, 6-week adult flies


title: ORE_MAL_WK6_Cy3_20

description:
ORE_MAL_WK6_Cy3_20
Replicate F


title: ORE_MAL_WK1_Cy5_19

description:
ORE_MAL_WK1_Cy5_19
Replicate E

source_name: Oregon R, male, 1-week adult flies


title: ORE_MAL_WK1_Cy5_20

description:
ORE_MAL_WK1_Cy5_20
Replicate F


title: SAM_MAL_WK6_Cy3_18

description:
SAM_MAL_WK6_Cy3_18
Replicate F

source_name: Samarkand, male, 6-week adult flies


title: SAM_MAL_WK6_Cy3_17

description:
SAM_MAL_WK6_Cy3_17
Replicate E


title: SAM_MAL_WK6_Cy5_14

description:
SAM_MAL_WK6_Cy5_14
Replicate D


title: SAM_FEM_WK1_Cy5_16

description:
SAM_FEM_WK1_Cy5_16
Replicate F


title: SAM_FEM_WK6_Cy3_16

description:
SAM_FEM_WK6_Cy3_16
Replicate F


title: SAM_FEM_WK1_Cy5_15

description:
SAM_FEM_WK1_Cy5_15
Replicate E


title: SAM_MAL_WK1_Cy5_18

description:
SAM_MAL_WK1_Cy5_18
Replicate F


title: SAM_FEM_WK6_Cy3_15

description:
SAM_FEM_WK6_Cy3_15
Replicate E


title: Eya3 muscle_rep7

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: male, age

value: 13 weeks

source_name: Wt RNA pool muscle

tag: RNA pool; male, age


title: Eya3 muscle_rep3


title: Eya3 muscle_rep1


title: Eya3 muscle_rep5


title: Eya3 muscle_rep6


title: Eya3 muscle_rep4


title: Eya3 muscle_rep8


title: Eya3 muscle_rep2


title: CD11c+CD103+ versus CD11c+CD103- dendritic cells_replicate1_M1993

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

description: Log ratio values were calculated by dividing rProcessedSignal values by gProcessedSignal values, thus positive log ratio values indicate enhanced mRNA expression levels within the CD11c+CD103- dendritic cell population.

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.0.1” (see http://www.agilent.com for details).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings, namely 100% and 5%, to increase the dynamic range of the measurements.

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.1.3.1” by using the recommended default extraction protocol file: GE2-v5_91_0806.xml.

source_name: gProcessedSignal values originated from CD11c+CD103+ dendritic cells

label_protocol: cRNA-synthesis was performed with the “Low RNA Input Linear Amplification Kit PLUS, Two-Color” (#5188-5340, Agilent Technologies) as directed by the manufacturer.

extract_protocol: Total RNA is extracted with the RNeasy mini kit from QIAGEN as directed by the manufacturer.

tag: Bone marrow cells from CX3CR1+/gfp C57BL/6 mice were sorted as follows

value: lineage negative (CD3, CD19, NK1.1, Ter119, Ly6G and CD11c) CX3CR1+c-kit+. Sorted cells were further cultured in vitro under the continuous presence of GM-CSF. lin-CX3CR1+c-kit+ bone marrow cells gave rise to CD103+ DC in vitro.

source_name: rProcessedSignal values originated from CD11c+CD103- dendritic cells

value: lineage negative (CD3, CD19, NK1.1, Ter119, Ly6G and CD11c) CX3CR1+c-kit+. Sorted cells were further cultured in vitro under the continuous presence of GM-CSF. lin-CX3CR1+c-kit+ bone marrow cells gave rise to CD103- DC in vitro.


title: 04B00364

source_name: Hodgkin's Lymphoma


title: CD11c+CD103+ versus CD11c+CD103- dendritic cells_replicate2_M2067

description: Log ratio values were calculated by dividing rProcessedSignal values by gProcessedSignal values, thus positive log ratio values indicate enhanced mRNA expression levels within the CD11c+CD103+ dendritic cell population.

source_name: gProcessedSignal values originated from CD11c+CD103- dendritic cells

source_name: rProcessedSignal values originated from CD11c+CD103+ dendritic cells


title: ORE_FEM_WK6_Cy5_12

description:
ORE_FEM_WK6_Cy5_12
Replicate D


title: SAM_MAL_WK1_Cy3_13

description:
SAM_MAL_WK1_Cy3_13
Replicate C


title: SAM_MAL_WK6_Cy5_13

description:
SAM_MAL_WK6_Cy5_13
Replicate C


title: Eya3 heart_rep7

source_name: Wt RNA pool heart


title: Eya3 heart_rep5


title: Eya3 heart_rep8


title: ORE_FEM_WK1_Cy3_12

description:
ORE_FEM_WK1_Cy3_12
Replicate D


title: SAM_MAL_WK1_Cy3_14

description:
SAM_MAL_WK1_Cy3_14
Replicate D


title: Eya3 heart_rep1


title: Eya3 heart_rep6


title: ORE_FEM_WK6_Cy5_11

description:
ORE_FEM_WK6_Cy5_11
Replicate C


title: Eya3 brain_rep8

source_name: Wt RNA pool brain


title: ORE_FEM_WK1_Cy3_11

description:
ORE_FEM_WK1_Cy3_11
Replicate C


title: Eya3 brain_rep5


title: Eya3 heart_rep4


title: Eya3 brain_rep6


title: ORE_MAL_WK6_Cy5_10

description:
ORE_MAL_WK6_Cy5_10
Replicate D


title: Eya3 brain_rep4


title: light lesion replicate 4

city: Ann Arbor

first: Peter

middle: F.

last: Hitchcock

state: MI

address: 1000 Wall Street

department: Ophthy and Vis Sci

institute: University of Michigan

description: Gene Expression for light lesioned experimental retina

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized on GeneChip Zebrafish Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with BRB Array Tools 3.6 using default analysis settings and global scaling for RMA normalization

organism: Danio rerio

source_name: Whole Retina

label_protocol: Affymetrix GeneChip Expression IVT Labeling Kit

extract_protocol: RNA was extracted using the Ambion RNaqueous kit per manufacturers instructions

tag: Adult zebrafish; Albino strain


title: Eya3 heart_rep3


title: Eya3 brain_rep3


title: Eya3 brain_rep2


title: ORE_MAL_WK1_Cy3_10

description:
ORE_MAL_WK1_Cy3_10
Replicate D


title: ORE_MAL_WK6_Cy5_09

description:
ORE_MAL_WK6_Cy5_09
Replicate C


title: light lesion replicate 3


title: ORE_MAL_WK1_Cy3_09

description:
ORE_MAL_WK1_Cy3_09
Replicate C


title: SAM_FEM_WK1_Cy3_08

description:
SAM_FEM_WK1_Cy3_08
Replicate B


title: SAM_FEM_WK6_Cy5_08

description:
SAM_FEM_WK6_Cy5_08
Replicate B

source_name: Samarkand, female, 6-week adult flies


title: light lesion replicate 2


title: SAM_FEM_WK6_Cy5_07

description:
SAM_FEM_WK6_Cy5_07
Replicate A


title: Eya3 heart_rep2


title: control replicate 4

description: Gene Expression for unlesioned control retina


title: Eya3 brain_rep7


title: light lesion replicate 1


title: control replicate 3


title: Eya3 brain_rep1


title: AD_51P back

city: Stockholm

first: Annika

last: Saaf

department: Department of Molecular Medicine & Surgery

country: Sweden

institute: Karolinska Institute, Karolinska University Hospital, Solna

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34008.gif
Disease State: lesional
Organism Part: back

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Human Reference

label_protocol: not provided

extract_protocol: not provided

tag: Stratagene Human Reference Amplified 9/30/2002

source_name: Skin, Disease State: lesional, Organism Part: back

tag: 51P back aRNA 9/25/02


title: SAM_FEM_WK1_Cy3_07

description:
SAM_FEM_WK1_Cy3_07
Replicate A

source_name: Samarkand, female, 1-week adult flies


title: SAM_MAL_WK6_Cy5_06

description:
SAM_MAL_WK6_Cy5_06
Replicate B


title: WT MOT1+ vs. TBP-F207L

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Poly (A)+ mRNA was harvested from WT MOT1, mot1-14, and the bypass strains TBP-Y185C and TBP-F207L to determine the effect of the mutant TBP alleles on transcription.  The reference sample for each of the three mutants (mot1-14, TBP-Y185C, and TBP-F207L) was from WT MOT1 cells.

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters and loaded into the Rosetta Resolver® system (Rosetta Biosoftware, Kirkland, WA).

source_name: AY138 + pAV20 (post-FOA)

label_protocol: Gene expression analysis was conducted using Agilent-011447 Yeast Oligo arrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Cells were grown in rich media (YPD) at 30?C to an OD 600 ~1.0.

extract_protocol: Total RNA was isolated using hot acid-phenol extraction as previously described (Schmitt, et al. 1990).  In brief, washed, pelleted cells were resuspended in 4 ml RNA Lysis Buffer (10 mM Tris-Cl pH 7.5, 10 mM EDTA, 0.5% SDS).  4 ml acid phenol (water-saturated, pH 4.3) was added, vortexed, and incubated at 1 hour at 65?C with occassional vortexing. Samples were spun, the aqueous later was removed, and the material was again phenol extracted (with no incubation) and chloroform extracted.  RNA was precipitated with ethanol and sodium acetate overnight, and pellets were washed 3 times with 70% ethanol before resuspending in the appropriate volume of sterile water.  Poly (A)+ mRNA was purified from 1 mg total RNA using the Qiagen Oligotex Midi Kit.

tag: MAT a, ura3-52, lys2-801, ade2-101, leu2-D1, his3-D200, trp1-D63, mot1D::kanMX, pAV2O (MOT1+, LEU2)

source_name: AY138 + pTBP-F207L (post-FOA)

label_protocol: Gene expression analysis was conducted using Agilent-011447 Yeast Oligo arrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.


title: control replicate 2


title: TBP-F207L vs. WT MOT1+


title: control replicate 1


title: AD_12M back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35286.gif
Disease State: lesional
Organism Part: back


title: TBP-Y185C vs. WT MOT1+

source_name: AY138 + pTBP-Y185C (post-FOA)


title: SAM_MAL_WK1_Cy3_06

description:
SAM_MAL_WK1_Cy3_06
Replicate B

source_name: Samarkand, male, 1-week adult flies


title: N_3M aRNA-9 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62394.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2040, 7480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.74; Parameter Scan Time = 11:50:24; Parameter PMT Volts = 590; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 211153; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.35; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.74; Parameter Scan Time = 11:50:24; Parameter PMT Volts = 750; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 430156; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.52; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

source_name: Skin, Disease State: Normal, Organism Part: back


title: SAM_MAL_WK6_Cy5_05

description:
SAM_MAL_WK6_Cy5_05
Replicate A

source_name: Samarkand, male, 6-week adult flies


title: SAM_MAL_WK1_Cy3_05

description:
SAM_MAL_WK1_Cy3_05
Replicate A


title: N_4M aRNA-12 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62395.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 7280; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 11:35:49; Parameter PMT Volts = 560; Parameter Scan Date = 2005-01-05; Parameter Pixel Size = 10; Parameter Laser on time = 211390; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 11:35:49; Parameter PMT Volts = 700; Parameter Scan Date = 2005-01-05; Parameter Pixel Size = 10; Parameter Laser on time = 430393; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: AD_23L back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34006.gif
Disease State: lesional
Organism Part: back

tag: 23L back aRNA 9/25/02


title: WT MOT1+ vs. TBP-Y185C


title: N_1M aRNA-3 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62393.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 7640; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 12:56:07; Parameter PMT Volts = 570; Parameter Scan Date = 2004-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 210457; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 12:56:07; Parameter PMT Volts = 700; Parameter Scan Date = 2004-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 429459; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: mot1-14 vs. WT MOT1+

source_name: AY138 + pMOT244 (post-FOA)


title: ORE_MAL_WK6_Cy5_04

description:
ORE_MAL_WK6_Cy5_04
Replicate B

source_name: Oregon R, male, 6-week adult flies


title: N_2P aRNA-5

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/61804.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 7320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 10:45:04; Parameter PMT Volts = 610; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 211087; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 10:45:04; Parameter PMT Volts = 730; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 430090; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: AD_10L arm

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35284.gif
Disease State: lesional
Organism Part: arm

source_name: Skin, Disease State: lesional, Organism Part: arm


title: N_3F aRNA-7

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/61805.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 7600; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.37; Parameter Scan Time = 11:19:05; Parameter PMT Volts = 590; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 211121; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.37; Parameter Scan Time = 11:19:05; Parameter PMT Volts = 740; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 430124; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: AD_12L leg

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35288.gif
Disease State: lesional
Organism Part: leg

source_name: Skin, Disease State: lesional, Organism Part: leg


title: AD_10P back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35283.gif
Disease State: lesional
Organism Part: back


title: AD_10M back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35285.gif
Disease State: lesional
Organism Part: back


title: AD_1M back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35361.gif
Disease State: lesional
Organism Part: back

tag: 1M back


title: WT MOT1+ vs. mot1-14


title: ORE_MAL_WK1_Cy3_04

description:
ORE_MAL_WK1_Cy3_04
Replicate B

source_name: Oregon R, male, 1-week adult flies


title: ORE_MAL_WK6_Cy5_03

description:
ORE_MAL_WK6_Cy5_03
Replicate A


title: ORE_MAL_WK1_Cy3_03

description:
ORE_MAL_WK1_Cy3_03
Replicate A


title: cerebellum_KO_3

city: Miami

first: Vance

middle: P

last: Lemmon

state: FL

address: 1095 NW 14th Terrace

department: Miami Project to Cure Paralysis

institute: University of Miami

description: Samples were processed at the Case Western Reserve University Cancer Center Gene Expression Array Core Facility

hyb_protocol: Followed standard Affymetrix protocols

scan_protocol: Followed standard Affymetrix protocols

data_processing: CEL files were imported into RMA Express version 1.0 for background correction, quantile normalization and log transformation.

source_name: Postnatal day 11 Cerebellum, knockout for L1CAM, replicate 3

label_protocol: Followed standard Affymetrix protocols

extract_protocol: Qiagen’s RNeasy Mini kit (# 74104)

tag: Strain

tag: Sex

value: male

tag: Genotype

value: L1CAM knockout (-/Y)


title: cerebellum_wildtype_3

source_name: Postnatal day 11 Cerebellum, wildtype; replicate 3

value: Wildtype


title: AD_1L leg

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35360.gif
Disease State: lesional
Organism Part: leg

tag: 1L leg


title: ORE_FEM_WK6_Cy5_02

description:
ORE_FEM_WK6_Cy5_02
Replicate B

source_name: Oregon R, female, 6-week adult flies


title: cerebellum_KO_2

source_name: Postnatal day 11 Cerebellum, knockout for L1CAM, replicate 2


title: AD_52L back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34167.gif
Disease State: lesional
Organism Part: back

source_name: Stratagene Human Reference

source_name: Skin, Disease State: lesional, Organism Part: back

tag: 52L back aRNA 9/25/02


title: AD_1P back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35352.gif
Disease State: lesional
Organism Part: back


title: AD_52M back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34168.gif
Disease State: lesional
Organism Part: back

tag: 52M back aRNA 9/25/02


title: AD_23P back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34005.gif
Disease State: lesional
Organism Part: back

tag: 23P back aRNA 9/25/02


title: AD_58L back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34677.gif
Disease State: lesional
Organism Part: back

tag: 58L back aRNA 9/25/02


title: ORE_FEM_WK1_Cy3_02

description:
ORE_FEM_WK1_Cy3_02
Replicate B

source_name: Oregon R, female, 1-week adult flies


title: ORE_FEM_WK6_Cy5_01

description:
ORE_FEM_WK6_Cy5_01
Replicate A


title: ORE_FEM_WK1_Cy3_01

description:
ORE_FEM_WK1_Cy3_01
Replicate A


title: cerebellum_wildtype_1

source_name: Postnatal day 11 Cerebellum, wildtype

extract_protocol: Qiagen’s RNeasy Mini kit (# 74104).


title: sdh3_delta_rep1

status: Public on Dec 16 2008

city: Kongens Lyngby

first: Kiran

middle: Raosaheb

last: Patil

address: Bulding 223, Søltofts Plads

country: Denmark

institute: Technical University of Denmark

description: Replicate 1 of 2.

hyb_protocol: cRNA was synthesized as described in the Affymetrix GeneChip Expression Analysis Manual, after which 15 micro-gram were hybridized to Yeast Genome S98 oligonucleotide arrays (Affymetrix).

scan_protocol: Microarrays were scanned in Agilent Gene Scanner (Affimetrix).

data_processing: Raw data processing was performed with the Microarray Suite software, version 5, with a global scaling factor for target intensity equal to 500. Average difference values, representing the absolute hybridization intensities were then calculated for each probe set.

source_name: Saccharomyces cerevisiae sdh3 deletion mutant

label_protocol: As described in the Affymetrix GeneChip Expression Analysis Manual.

growth_protocol: Batch growth conditions with minimal medium

extract_protocol: Duplicate samples for microarray analysis were collected during the aerobic batch experiments with the sdh3Δ strain when the glucose concentration had reached 20±2 g/liter. Culture aliquots of 20 ml were transferred to falcon tubes already filled with 25ml of crushed ice and immediately centrifuged at 4000 rpm for 5 minutes. The pellets were rapidly frozen in liquid nitrogen and stored at -80ºC until further use. Total RNA was extracted by using the Fast Pro Red Kit (Obiogene, USA) according to the manufacture’s instructions with minor modifications.

tag: sdh3 deletion mutant in CEN.PK113-7D background


title: cerebellum_KO_1

source_name: Postnatal day 11 Cerebellum, knockout for L1CAM


title: N_4P aRNA-11 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62225.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 7400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 11:17:00; Parameter PMT Volts = 570; Parameter Scan Date = 2005-01-05; Parameter Pixel Size = 10; Parameter Laser on time = 211371; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 11:17:00; Parameter PMT Volts = 710; Parameter Scan Date = 2005-01-05; Parameter Pixel Size = 10; Parameter Laser on time = 430374; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

source_name: Skin, Disease State: Normal, Organism Part: back


title: cerebellum_wildtype_2

source_name: Postnatal day 11 Cerebellum, wildtype; replicate 2


title: AD_51M back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34165.gif
Disease State: lesional
Organism Part: back

tag: 51M back aRNA 9/25/02


title: N_4F aRNA-10 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62224.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 7240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 11:01:11; Parameter PMT Volts = 560; Parameter Scan Date = 2005-01-05; Parameter Pixel Size = 10; Parameter Laser on time = 211355; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 11:01:11; Parameter PMT Volts = 720; Parameter Scan Date = 2005-01-05; Parameter Pixel Size = 10; Parameter Laser on time = 430358; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: Normal chow treated replicate 4 - SCAT

status: Public on Dec 15 2008

city: Lausanne

first: Carine

last: Poussin

address: Quartier UNIL-Sorge

country: Switzerland

institute: University of Lausanne

description: Biological replicate 4 of 4 for NCT group (SCAT)

hyb_protocol: Cy5-labeled RNA from adipose tissue and Cy3-labeled mouse universal reference of total RNA were hybridized on the M17K spotted array according published protocols (de Fourmestraux, J Biol Chem, 2004)

scan_protocol: Scanned on a Scanarray 4000 scanner. Tiff image analysis was done using the software ImaGene 4 (from BioDiscovery) in order to extract spot intensity signal for Cy3 and Cy5 channels.

data_processing: Print Tip Lowess normalized data obtained from log2 of processed Red signal/processed Green signal. The sma (Statistical Microarray Analysis) package from the statistical R software was used.

source_name: subcutaneous adipose tissue of normal chow fed-mouse treated with rimonabant

label_protocol: Indirect labeling of amplified RNA with Cy3 or Cy5 fluorascent dye according to published protocols (de Fourmestraux, J Biol Chem, 2004)

growth_protocol: Six-week-old C57BL/6J male mice (Janvier, France) were fed a normal chow (NC; 12% fat, 28% protein, and 60% carbohydrate) or a high fat diet (HFD; 72% fat, 28% protein, and <1% carbohydrate) for 7 months. Their body weight and tolerance to intraperitoneal

extract_protocol: RNA from each sample was extracted as described in the protocol of peqGOLD TriFast (from peqLab). RNA quality was checked before and after amplification with a bioanalyzer 2100 (Agilent). RNA was amplified with MessageAmpTM kit (Ambion) according the manu

treatment_protocol: Each mouse was further treated with vehicle (0.1% Tween 80 (Fluka) in H2O) or rimonabant (10 mg.kg-1.day-1) administrated daily by gavage for 1 month. Vehicle or rimonabant treatments were randomly assigned in each group of NC and HFD mice. The body weigh

tag: C57Bl/6J mouse

source_name: Mouse universal reference total RNA (DB Biosciences, ref: 636657)

tag: Commercial RNA


title: N_2F aRNA-4

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/61803.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 7240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 10:25:01; Parameter PMT Volts = 590; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 211067; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 10:25:01; Parameter PMT Volts = 730; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 430070; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf

tag: Stratagene Human Reference Amplified 9/30/2002


title: AD_52P back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34166.gif
Disease State: lesional
Organism Part: back

tag: 52P back aRNA 9/25/02


title: High treated replicate 5 - SCAT

description: Biological replicate 5 of 5 for HT group (SCAT)

source_name: subcutaneous adipose tissue, under high fat diet with high body weight treated with rimonabant


title: Normal chow treated replicate 1 -SCAT

description: Biological replicate 1 of 4 for NCT group (SCAT)


title: Normal chow treated replicate 2 - SCAT

description: Biological replicate 2 of 4 for NCT group (SCAT)


title: High treated replicate 4 - SCAT

description: Biological replicate 4 of 5 for HT group (SCAT)


title: High treated replicate 3 - SCAT

description: Biological replicate 3 of 5 for HT group (SCAT)


title: Medium treated replicate 4 - SCAT

description: Biological replicate 4 of 5 for MT group (SCAT)

source_name: subcutaneous adipose tissue, under high fat diet with medium body weight treated with rimonabant


title: Medium treated replicate 2 - SCAT

description: Biological replicate 2 of 5 for MT group (SCAT)


title: AD_51L back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34164.gif
Disease State: lesional
Organism Part: back

tag: 51L back aRNA 9/25/02


title: Medium treated replicate 3 - SCAT

description: Biological replicate 3 of 5 for MT group (SCAT)


title: High treated replicate 2 - SCAT

description: Biological replicate 2 of 5 for HT group (SCAT)


title: Medium treated replicate 5 - SCAT

description: Biological replicate 5 of 5 for MT group (SCAT)


title: Normal chow treated replicate 3 - SCAT

description: Biological replicate 3 of 4 for NCT group (SCAT)


title: Medium treated replicate 1 - SCAT

description: Biological replicate 1 of 5 for MT group (SCAT)


title: Low treated replicate 4 - SCAT

description: Biological replicate 4 of 5 for LT group (SCAT)

source_name: subcutaneous adipose tissue, under high fat diet with low body weight treated with rimonabant


title: Low treated replicate 3 - SCAT

description: Biological replicate 3 of 5 for LT group (SCAT)


title: High treated replicate 1 - SCAT

description: Biological replicate 1 of 5 for HT group (SCAT)


title: Low treated replicate 5 - SCAT

description: Biological replicate 5 of 5 for LT group (SCAT)


title: Low treated replicate 2 - SCAT

description: Biological replicate 2 of 5 for LT group (SCAT)


title: N_2M aRNA-2 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62222.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2040, 7400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 11:05:11; Parameter PMT Volts = 590; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 211108; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.16; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 11:05:11; Parameter PMT Volts = 740; Parameter Scan Date = 2005-01-04; Parameter Pixel Size = 10; Parameter Laser on time = 430110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: Low treated replicate 1 - SCAT

description: Biological replicate 1 of 5 for LT group (SCAT)


title: N_1P aRNA-2 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62221.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 7440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 12:36:11; Parameter PMT Volts = 620; Parameter Scan Date = 2004-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 210436; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.12; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 12:36:11; Parameter PMT Volts = 760; Parameter Scan Date = 2004-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 429439; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: N_1F aRNA-1 SHDD

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62220.gif
Disease State: Normal
Organism Part: back

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 7170; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Annika,,Saaf Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 12:11:21; Parameter PMT Volts = 580; Parameter Scan Date = 2004-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 210410; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 12:11:21; Parameter PMT Volts = 760; Parameter Scan Date = 2004-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 429413; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Annika,,Saaf


title: AD_58M back

description:
Simple annotation: Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34679.gif
Disease State: lesional
Organism Part: back

tag: 58M back aRNA 9/25/02


title: Normal chow control replicate 2 - SCAT

description: Biological replicate 2 of 5 for NCC group (SCAT)

source_name: subcutaneous adipose tissue of normal chow fed-mouse treated with the vehicle


title: Normal chow control replicate 3 - SCAT

description: Biological replicate 3 of 5 for NCC group (SCAT)


title: Normal chow control replicate 4 - SCAT

description: Biological replicate 4 of 5 for NCC group (SCAT)


title: High control replicate 4 - SCAT

description: Biological replicate 4 of 4 for HC group (SCAT)

source_name: subcutaneous adipose tissue, under high fat diet with high body weight treated with the vehicle


title: Normal chow control replicate 5 - SCAT

description: Biological replicate 5 of 5 for NCC group (SCAT)


title: Normal chow control replicate 1 - SCAT

description: Biological replicate 1 of 5 for NCC group (SCAT)


title: Medium control replicate 1 - SCAT

description: Biological replicate 1 of 4 for MC group (SCAT)

source_name: subcutaneous adipose tissue, under high fat diet with medium body weight treated with the vehicle


title: High control replicate 2 - SCAT

description: Biological replicate 2 of 4 for HC group (SCAT)


title: Medium control replicate 4 - SCAT

description: Biological replicate 4 of 4 for MC group (SCAT)


title: Medium control replicate 2 - SCAT

description: Biological replicate 2 of 4 for MC group (SCAT)


title: Low control replicate 4 - SCAT

description: Biological replicate 4 of 4 for LC group (SCAT)

source_name: subcutaneous adipose tissue, under high fat diet with low body weight treated with the vehicle


title: High control replicate 3 - SCAT

description: Biological replicate 3 of 4 for HC group (SCAT)


title: Low control replicate 3 - SCAT

description: Biological replicate 3 of 4 for LC group (SCAT)


title: High control replicate 1 - SCAT

description: Biological replicate 1 of 4 for HC group (SCAT)


title: Normal chow treated replicate 5 - VAT

description: Biological replicate 5 of 5 for NCT group (VAT)

source_name: visceral adipose tissue of normal chow fed-mouse treated with rimonabant


title: Low control replicate 1 - SCAT

description: Biological replicate 1 of 4 for LC group (SCAT)


title: Normal chow treated replicate 3 - VAT

description: Biological replicate 3 of 5 for NCT group (VAT)


title: High treated replicate 4 - VAT

description: Biological replicate 4 of 5 for HT group (VAT)

source_name: visceral adipose tissue, under high fat diet with high body weight treated with rimonabant


title: High treated replicate 2 - VAT

description: Biological replicate 2 of 5 for HT group (VAT)


title: Low control replicate 2 - SCAT

description: Biological replicate 2 of 4 for LC group (SCAT)


title: Normal chow treated replicate 1 - VAT

description: Biological replicate 1 of 5 for NCT group (VAT)


title: High treated replicate 3 - VAT

description: Biological replicate 3 of 5 for HT group (VAT)


title: High treated replicate 5 - VAT

description: Biological replicate 5 of 5 for HT group (VAT)