title: AI Rat no DL-273

city: Quebec

first: Jacques

last: Couet

address: 2725 chemin Sainte-Foy

country: Canada

institute: Centre de Recherche de l'Hopital Laval

hyb_protocol: The lyophilized biotin-labeled cRNA preparations were hybridized to BeadChip RatRef-12 microarrays (Illumina) according to Illumina’s protocol (11286340 rev. A), using 750 ng cRNA per array. After hybridization and washes, arrays were incubated in streptavidin-Cy3 solution

scan_protocol: Cy3 fluorescence signals were read on a BeadArray reader (Illumina).

data_processing: Raw fluorescence data were processed and normalized with the lumi package (FlexArray microarray analysis software, version 1.3.1), using RMA background adjustment, VST variance stabilization, and Robust Spline Normalization algorithms.

source_name: Cardiac left ventricle

label_protocol: Total RNA extracts were treated for double-stranded cDNA synthesis and labeling of cRNA with biotin according to the Eberwine method (Van Gelder et al 1990), using the Illumina TotalPrep RNA Amplification kit reagents and protocol (Ambion cat no IL1791).

extract_protocol: Total RNA was extracted from stored tissues using Trizol (Invitrogen), and further purified on column with RNeasy MinElute (Qiagen). RNA concentration and integrity were assessed by UV spectrophotometry (Nanodrop ND-1000, Thermo Scientific) and microfluidic electrophoresis (Bioanalyzer 2100, Agilent), respectively.

value: male

value: Wistar


title: AI Rat no DL-310

status: Public on Mar 31 2010

type: RNA

label: biotin

molecule: total RNA

organism: Rattus norvegicus

tag: gender

tag: strain


title: pachytene spermatocytes_fraction8_day15_1

city: Toyoake

first: Hiroshi

last: Kogo

state: Aichi

address: 1-98, Dengakugakubo, Kutsukake

department: ICMS

country: Japan

institute: Fujita Health University

description: Gene expression data from isolated pachytene spermatocytes of 15-day testes

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Set 430 or GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in a fluidics system.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with GeneChip Operating Software (GCOS, version 1) using Affymetrix default analysis settings.

organism: Mus musculus

source_name: Percoll-isolated mouse pachytene spermatocytes from fraction 8 of 15-day testis

label_protocol: Biotinylated cRNA were prepared using MessageAmp aRNA Kit (Ambion) according to  the manufacturer's instructions from 1 ug total RNA.

growth_protocol: The C57BL/6 mice were obtained from a commercial breeder.

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Testes were decapsulated and incubated with 1mg/ml hyaluronidase, 1mg/ml trypsin, and 1mg/ml collagenase for 10 min. After the tubular fragments were repeatedly pipetted and washed, second enzymatic incubation was performed for 10 min. After being washed, the isolated cells were collected by filtration through 70μm screen and layered on a discontinuous Percoll density gradient in a polypropylene tube. The gradient was centrifuged at 800 x g for 30 min at 25˚C. Cells found in the interface between the different density suspensions were collected as fraction 1-10.

tag: tissue

value: testis

tag: age

value: 15-day old


title: leptotene and zygotene spermatocytes_fraction5_day12_2

description: Gene expression data from isolated leptotene/zygotene spermatocytes of 12-day testes

source_name: Percoll-isolated mouse leptotene and zygotene spermatocytes from fraction 5 of 12-day testis

value: 12-day old


title: whole testis_2

description: Gene expression data from whole testis of 15-day old mice

source_name: whole testis of 15-day old mice


title: Sham Rat no DL-335


title: pachytene spermatocytes_fraction8_day15_2


title: whole testis_1


title: spermatogonia_fraction2_day8_1

description: Gene expression data from isolated spermatogonia of 8-day testes

source_name: Percoll-isolated mouse spermatogonia from fraction 2 of 8-day testis

value: 8-day old


title: AI Rat no DL-357


title: mixed somatic tissues_1

description: Gene expression data from mixed somatic tissues of 15-day old mice

source_name: mixture of 11 somatic tissues of 15-day old mice


title: leptotene and zygotene spermatocytes_fraction5_day12_1


title: Sham Rat no DL-333


title: mixed somatic tissues_2


title: spermatogonia_fraction2_day8_2


title: AI Rat no DL-285


title: Sham Rat no DL-332


title: Sham Rat no DL-331


title: Sham Rat no DL-327


title: AI Rat no DL-281


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 6 days rep 2

status: Public on Mar 30 2010

city: Turku

first: Ubaid Ullah

last: Sheikh

state: Turku

address: Tykistökatu

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: Cy3 labeled linearly amplified cRNA, 10X blocking agent, nuclease free water and 25X fragmentation buffer were mixed in recommended proportion and incubated at 60 C for 30 min.  2X GEx hybridization buffer was added and mixed well by gently pipeting to stop the fragmentation, centrifugated for 1 min at 13000 RPM and placed onto the array as soon as possible.  Agilent SureHyb chambers were used according to manufacturer's instructions.  Assembled slide chamber was rotated in a 65°C hybridization oven at 10 rpm for 17 hours.

scan_protocol: Slides were scanned using Agilent Microarray Scanner (G2565BA) followed by data extraction by Agilent Feature Extraction software version 9.5.3.

data_processing: The normalization was done using GeneSpring GX 10 using the recommended Percentile Shift Normalization. It is a global normalization, where the locations of all the spot intensities in an array are adjusted. This normalization takes each column in an experiment independently, and computes the percentile of the expression values for this array, across all spots (where n has a range from 0-100 and n=50 is the median). It subtracts this value from the expression value of each entity.

organism: Homo sapiens

source_name: Naïve human CD4+ T cells isolated from cord blood

label_protocol: Labeling was performed with Agilent's Quick Amp Labeling Kit. It generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 200 ng and 1 μg of total RNA or a minimum of 10 ng of poly A+ RNA for one-color processing. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP. There is routinely at least a 100-fold RNA amplification with use of this kit.

growth_protocol: Isolated naïve T cells were cutured in RPMI medium supplemented with penicillin (50 U/ml), Streptomycin (50mg/ml) and 10% FCS.

extract_protocol: Total RNA was extracted using RNeasy mini kit. Breifly, 200 μl of PBS was added to the cell suspension and was pelleted. 350μl of RLT buffer was added followed by sonication. The debris was removed by centrifugation. RNA extraction was performed as per the manufacturer’s instructions. The RNA was eluted in 30 μl of RNase-free water.

treatment_protocol: Cells were harvested and frozen in RNALater before RNA isolation.

tag: sex

value: Female

value: 18-30 Years

tag: treatment

value: stimulated with antiCD3 anti-CD28 andtibodies in Th2 polarizing condition(IL4 supplemented media) for 6 days


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 6 days IL4/R neutralizing antibodies added days 3-5 rep 1

value: Naïve human CD4+ T cells isolated from cord blood

value: stimulated with antiCD3 anti-CD28 andtibodies in Th2 polarizing condition(IL4 supplemented media) for 6 days, Neutralizing IL4 and IL4R antibodies added to culture media on Days 3, 4 and 5


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 6 days IL4/R neutralizing antibodies added days 3-5 rep 2


title: (B2) hVISA MM66 and VISA MM66-3

status: Public on Mar 25 2010

city: Las Cruces

first: John

middle: E

last: Gustafson

email: jgustafs@nmsu.edu, amuthai@gmail.com

state: NM

address: PO Box 30001 Dept. 3AF

department: Department of Biology and Molecular Biology Program

country: USA

institute: New Mexico State University

description: Genes analyzed using these programs were further sorted and grouped based on their function using our in-house software Staphylococcus aureus Gene Sorter (SAGS).

hyb_protocol: Purified labelled cDNA was hybridised with S. aureus genome microarray version 4 as previously described by Mongodin et al. (2003) and Riordon et al. (2007). Briefly, the slides were prehybridized in a buffer containing 5X SSC, 0.1% SDS and 0.1% BSA, and then washed and blown to dry. The two differentially labelled cDNA samples were dried and the resuspended in hybridization solution [40% deionized formamide, 5X SSC, 0.1% SDS, 0.6 µg/µl sheared Salmon sperm DNA (Ambion)]. The labelled cDNA samples were hybridized with the slides at 42 °C for 18-20 h. After hybridization, the slides were washed in low stringency buffer (2X SSC, 0.1% SDS) for 2 min, then in medium stringency (0.1x SSC, 0.1% SDS) buffer for 5 min and finally high stringency buffer (0.1x SSC) for 10 min.

scan_protocol: Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 4.0 software and scans were saved as TIFF image.

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html software.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus

label_protocol: cDNA was generated by using random hexamers (Invitrogen) as primers for reverse transcription. The primers were annealed (70°C for 10 min, followed by snap-freezing in ice for 1 min) to total RNA (2 μg) and were extended with SuperScript II reverse transcriptase (Invitrogen) with 0.1 M dithiothreitol 12.5 mM dNTP/ aa-UTP (Ambion, Austin, TX) mix at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then labeled with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacturer’s instruction.

extract_protocol: Total bacterial RNA was extracted from 3 ml of culture which was mixed with 6 ml of bacterial RNA protect solution (Qiagen, Valencia, CA) and the mixture was centrifuged at 3000 rpm for 20 min in swinging-bucket rotor centrifuge to collect the cells. Pellets were resuspended in 1 ml of Trizol (Invitrogen, Grand Island, NY) and the cells were broken using the FastPrep system (Qbiogene, Irvine, CA) at a speed of 6.0 for 40 seconds. From the broken cell lysate RNA was extracted as per the manufacturer’s instructions. Extracted RNA was purified using the RNeasy mini kit (Qiagen). DNase treated and purified mRNA was used for microarray analysis.

value: hVISA strain MM66

tag: genotype/variation

value: parent (clinical origin)

value: VISA strain MM66-3

value: mutant (laboratory-derived )


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 6 days rep 1


title: (B1) hVISA MM66 and VISA MM66-3


title: (A2) hVISA MM66 and VISA MM66-3


title: (A1) hVISA MM66 and VISA MM66-3

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded.  Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html software.


title: (B2) hVISA MM66 and VISA MM66-4

value: VISA strain MM66-4


title: (B1) hVISA MM66 and VISA MM66-4


title: (A2) hVISA MM66 and VISA MM66-4


title: (A1) hVISA MM66 and VISA MM66-4


title: untreated rep1

value: untreated


title: untreated rep2


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 5 days rep 2

value: stimulated with antiCD3 anti-CD28 andtibodies in Th2 polarizing condition(IL4 supplemented media) for 5 days


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 5 days IL4/R neutralizing antibodies added days 3-4 rep 2

value: stimulated with antiCD3 anti-CD28 andtibodies in Th2 polarizing condition(IL4 supplemented media) for 5 days, Neutralizing IL4 and IL4R antibodies added to culture media on Days 3 and 4


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 5 days IL4/R neutralizing antibodies added days 3-4 rep 1


title: antiCD3, antiCD28 stimulated in Th2 polarizing condition for 5 days rep 1


title: Pchartarum_repB

status: Public on Mar 01 2010

type: genomic

city: Pretoria

first: Eugenia

last: Barros

state: Gauteng

address: Meiring Naude Rd

department: Building 20

country: South Africa

institute: CSIR

description: Biological replicate

hyb_protocol: Microarray slides were pre-hybridized for 40 min at 42°C in a solution containing 3.5× SSC, 0.2% SDS, and 1% BSA (Roche Diagnostics). Slides were rinsed three times in deionized water and dried with N2 gas. The Cy5-labeled probe was then dissolved in hybridization solution containing 50% formamide (SIGMA), 25% 2× hybridization buffer (Amersham Pharmacia Biotech), and 25% deionized water. The mixture was denatured at 92°C for 5 min and stored at room temperature for hybridization. The denatured probe (approximately 35 μl) was pipetted directly onto the microarray surface and covered with a glass coverslip (24×60 mm, No.1, Marienfeld, Germany). Slides were placed in a custom-made hybridization chamber (N.B. Engineering Works, Pretoria, South Africa) and incubated for 16–18 h in a 53°C water bath. After hybridization, the slides were washed twice in 2x SSC and 0.2% SDS at 37°C for 6 minutes, once in 0.2x SSC and 0.2% SDS at room temperature for 5 minutes and twice in 0.075x SSC at room temperature for 5 min. The slides were rinsed in deionised water for 2 s and dried by centrifugation at 1000g for 5 minutes.

scan_protocol: Arrays were scanned with an Axon GenePix 4000A scanner and the images were analyzed with GenePix Pro 6.0 software (Axon Instruments).

data_processing: Raw data processing was performed with GenePix Pro 6.0. Individual net signal intensities were obtained by subtracting the local background from the raw spot intensity value. Irregular spots were manually flagged for removal. Further data analysis was performed in the Microsoft Excel software (Microsoft, Richmond, Washington). Anomalous spots not detected through manual inspection were flagged for removal, if the signal intensity of a spot varied more than 10% from the mean of the sixteen replicates on each slide. Signal intensities of the sixteen replicates were then averaged and intensity values were normalized across slides by global regression on the spot intensity data of the internal transcribed spacer oligonucleotides ITS1, ITS3 and ITS4, which were used as a reference for normalization of all spot intensity data (reference design). The net signal intensity of each spot was divided by the median signal intensity of the sixteen replicates and spots with an SNR ((Signal median – Background median) x Standard deviation Background-1) value below the median were removed from the analysis [32].  Each spot was then either assigned a 1 (present, SNR>/= 2.0) or a 0 (absent, SNR<2.0) according to the median SNR value.  The probes with the highest SNR value were considered to be the best target-probe match.  These SNR values were then converted to binary score with 1 indicating presence and 0 absence.

molecule: genomic DNA

organism: Pseudopithomyces chartarum

source_name: Pithomyces chartarum, fungal culture

label_protocol: Two micrograms of the total fungal DNA extracted was labelled with Cy5 by using a Cy™Dye Post-labelling Reactive Dye Pack (GE Healthcare, UK). Each labelling reaction contained DNA diluted in 5 μl 0.2 M Na2CO3 (pH9) and 2.5 μl Cy5 mono NHS ester 4000 pmol dye resuspended in 12 μl DMSO. The reactions were incubated at room temperature for 90 minutes in the dark. Free dye was removed with the QIAGEN PCR Purification Kit (QIAGEN, Valencia, CA).

extract_protocol: A total of forty food-borne fungi obtained from the Agricultural Research Council culture collection (ARC), Pretoria, South Africa, were grown on 1.5% malt extract agar at 25°C for 1-2 weeks. Total genomic fungal DNA was extracted following the DNA extraction protocol described by Raeder and Broda (1985) and column-purified using the QIAquick PCR Purification Kit (QIAGEN).

tag: fungus

value: Pithomyces chartarum

tag: fungal type

value: Food-borne fungal culture

value: 7 days


title: Pchartarum_rep2

description: Technical replicate


title: Pviridicatum_repB

description: Biological replicate

organism: Penicillium viridicatum

source_name: Penicillium viridicatum, fungal culture

value: Penicillium viridicatum


title: Pchartarum_rep1

description: Sample


title: Pviridicatum_rep2

description: Technical replicate


title: Pviridicatum_rep1

description: Sample


title: Prugulosum_rep1

description: Sample

organism: Talaromyces rugulosus

source_name: Penicillium rugulosum, fungal culture

value: Penicillium rugulosum


title: Prugulosum_rep2

description: Technical replicate


title: Prugulosum_repB

description: Biological replicate


title: Pitalicum_rep1

description: Sample

organism: Penicillium italicum

source_name: Penicillium italicum, fungal culture

value: Penicillium italicum


title: Pislandicum_rep1

description: Sample

organism: Talaromyces islandicus

source_name: Penicillium islandicum, fungal culture

value: Penicillium islandicum


title: Pitalicum_repB

description: Biological replicate


title: Pfuniculosum_rep2

description: Technical replicate

organism: Talaromyces funiculosus

source_name: Penicillium funiculosum, fungal culture

value: Penicillium funiculosum


title: Pfuniculosum_rep1

description: Sample


title: Pislandicum_repB

description: Biological replicate


title: Pislandicum_rep2

description: Technical replicate


title: Pitalicum_rep2

description: Technical replicate


title: Pexpansum_rep1

description: Sample

organism: Penicillium expansum

source_name: Penicillium expansum, fungal culture

value: Penicillium expansum


title: Pfellutanum_rep2

description: Technical replicate

organism: Penicillium fellutanum

source_name: Penicillium fellutanum, fungal culture

value: Penicillium fellutanum


title: Pfellutanum_repB

description: Biological replicate


title: Pexpansum_repB

description: Biological replicate


title: Pfellutanum_rep1

description: Sample


title: Pfuniculosum_repB

description: Biological replicate


title: Pcorylophilum_rep1

description: Sample

organism: Penicillium corylophilum

source_name: Penicillium corylophilum, fungal culture

value: Penicillium corylophilum


title: Fsubglutinans_repB

description: Biological replicate

organism: Fusarium subglutinans

source_name: Fusarium subglutinans, fungal culture

value: Fusarium subglutinans


title: Pcorylophilum_rep2

description: Technical replicate


title: Fsubglutinans_rep2

description: Technical replicate


title: Pexpansum_rep2

description: Technical replicate


title: Fsporotrichioides_repB

description: Biological replicate

organism: Fusarium sporotrichioides

source_name: Fusarium sporotrichioides, fungal culture

value: Fusarium sporotrichioides


title: Fsubglutinans_rep1

description: Sample


title: Fsolani_rep2

description: Technical replicate

organism: Fusarium solani

source_name: Fusarium solani, fungal culture

value: Fusarium solani


title: Fsemitectum_repB

description: Biological replicate

organism: Fusarium incarnatum

source_name: Fusarium semitectum, fungal culture

value: Fusarium semitectum


title: Fsemitectum_rep2

description: Technical replicate


title: Fsolani_rep1

description: Sample


title: Fsporotrichioides_rep1

description: Sample


title: Fsolani_repB

description: Biological replicate


title: Fsporotrichioides_rep2

description: Technical replicate


title: Pcorylophilum_repB

description: Biological replicate


title: Fsambucinum_repB

description: Biological replicate

organism: Fusarium sambucinum

source_name: Fusarium sambucinum, fungal culture

value: Fusarium sambucinum


title: Fsambucinum_rep2

description: Technical replicate


title: Frugulosum_rep2

description: Technical replicate

organism: Fusarium sp.

source_name: Fusarium rugulosum, fungal culture

value: Fusarium rugulosum


title: Fsambucinum_rep1

description: Sample


title: Frugulosum_rep1

description: Sample


title: Frugulosum_repB

description: Biological replicate


title: Foxysporum_repB

description: Biological replicate

organism: Fusarium oxysporum

source_name: Fusarium oxysporum, fungal culture

value: Fusarium oxysporum


title: Fsemitectum_rep1

description: Sample

value: Food-borne fungal culture


title: Fverticillioides_rep2

description: Technical replicate

organism: Fusarium verticillioides

source_name: Fusarium verticillioides, fungal culture

value: Fusarium verticillioides

value: 7 days


title: Foxysporum_rep2

description: Technical replicate


title: Fverticillioides_rep1

description: Sample


title: Foxysporum_rep1

description: Sample


title: Fverticillioides_repB

description: Biological replicate


title: Fgraminearum_repB

description: Biological replicate

organism: Fusarium graminearum

source_name: Fusarium graminearum, fungal culture

value: Fusarium graminearum


title: Fgraminearum_rep1

description: Sample


title: Fequiseti_rep1

description: Sample

organism: Fusarium equiseti

source_name: Fusarium equiseti, fungal culture

value: Fusarium equiseti


title: Fequiseti_rep2

description: Technical replicate


title: Fglobosum_rep1

description: Sample

organism: Fusarium globosum

source_name: Fusarium globosum, fungal culture

value: Fusarium globosum


title: Fglobosum_rep2

description: Technical replicate


title: Fequiseti_repB

description: Biological replicate


title: Fgraminearum_rep2

description: Technical replicate


title: Fdecemcellulare_rep2

description: Technical replicate

organism: Fusarium decemcellulare

source_name: Fusarium decemcellulare, fungal culture

value: Fusarium decemcellulare


title: Fglobosum_repB

description: Biological replicate


title: Fdecemcellulare_repB

description: Biological replicate


title: Fdecemcellulare_rep1

description: Sample


title: Fcrookwellense_repB

description: Biological replicate

organism: Fusarium cerealis

source_name: Fusarium crookwellense, fungal culture

value: Fusarium crookwellense


title: Fcompactum_repB

description: Biological replicate

source_name: Fusarium compactum, fungal culture

value: Fusarium compactum


title: Fcompactum_rep2

description: Technical replicate


title: Fcrookwellense_rep1

description: Sample


title: Favenaceum_repB

description: Biological replicate

organism: Fusarium avenaceum

source_name: Fusarium avenaceum, fungal culture

value: Fusarium avenaceum


title: Fcompactum_rep1

description: Sample


title: Fanthophilum_rep1

description: Sample

organism: Fusarium anthophilum

source_name: Fusarium anthophilum, fungal culture

value: Fusarium anthophilum


title: Favenaceum_rep1

description: Sample


title: Fanthophilum_rep2

description: Technical replicate


title: Favenaceum_rep2

description: Technical replicate


title: Fanthophilum_repB

description: Biological replicate


title: Fcrookwellense_rep2

description: Technical replicate


title: Echevalieri_repB

description: Biological replicate

organism: Aspergillus chevalieri

source_name: Eurotium chevalieri, fungal culture

value: Eurotium chevalieri


title: Facuminatum_rep1

description: Sample

organism: Fusarium acuminatum

source_name: Fusarium acuminatum, fungal culture

value: Fusarium acuminatum


title: Facuminatum_repB

description: Biological replicate


title: Facuminatum_rep2

description: Technical replicate


title: Echevalieri_rep2

description: Technical replicate


title: Eamstelodami_repB

description: Biological replicate

organism: Aspergillus amstelodami

source_name: Eurotium amstelodami, fungal culture

value: Eurotium amstelodami


title: Echevalieri_rep1

description: Sample


title: Eamstelodami_rep1

description: Sample


title: Smaydis_rep2

description: Technical replicate

organism: Stenocarpella maydis

source_name: Stenocarpella maydis, fungal culture

value: Stenocarpella maydis


title: Smaydis_repB

description: Biological replicate


title: Drechslera_rep2

description: Technical replicate

organism: Drechslera sp.

source_name: Drechslera spp, fungal culture

value: Drechslera


title: Drechslera_repB

description: Biological replicate


title: Drechslera_rep1

description: Sample


title: Smaydis_rep1

description: Sample


title: Clunata_repB

description: Biological replicate

organism: Curvularia lunata

source_name: Curvularia lunata, fungal culture

value: Curvularia lunata


title: Clunata_rep2

description: Technical replicate

value: Food-borne fungal culture


title: Eamstelodami_rep2

description: Technical replicate


title: Clunata_rep1

description: Sample


title: Bsorokiniana_rep1

description: Sample

organism: Bipolaris sorokiniana

source_name: Bipolaris sorokiniana, fungal culture

value: Bipolaris sorokiniana


title: Bsorokiniana_repB

description: Biological replicate

value: 7 days


title: Cpurpurea_rep1

description: Sample

organism: Claviceps purpurea

source_name: Claviceps purpurea, fungal culture

value: Claviceps purpurea


title: Bsorokiniana_rep2

description: Technical replicate


title: Cpurpurea_repB

description: Biological replicate


title: Cpurpurea_rep2

description: Technical replicate


title: Aniger_rep3

description: Biological replicate

organism: Aspergillus niger

source_name: Aspergillus niger, fungal culture

value: Aspergillus niger


title: Aversicolor_rep2

description: Technical replicate

organism: Aspergillus versicolor

source_name: Aspergillus versicolor, fungal culture

value: Aspergillus versicolor


title: Aversicolor_rep1

description: Sample


title: Aparasiticus_rep2

description: Technical replicate

organism: Aspergillus parasiticus

source_name: Aspergillus parasiticus, fungal culture

value: Aspergillus parasiticus


title: Aparasiticus_repB

description: Biological replicate


title: Aversicolor_repB

description: Biological replicate


title: Aparasiticus_rep1

description: Sample


title: Aniger_rep2

description: Technical replicate


title: Amulticolor_rep1

description: Sample

organism: Aspergillus multicolor

source_name: Aspergillus multicolor, fungal culture

value: Aspergillus multicolor


title: Aclavatus_repB

description: Biological replicate

organism: Aspergillus clavatus

source_name: Aspergillus clavatus, fungal culture

value: Aspergillus clavatus


title: Aniger_rep1

description: Sample


title: Amulticolor_repB

description: Biological replicate


title: Amulticolor_rep2

description: Technical replicate


title: Aclavatus_rep2

description: Technical replicate


title: Acarbonarius_repB

description: Biological replicate

organism: Aspergillus carbonarius

source_name: Aspergillus carbonarius, fungal culture

value: Aspergillus carbonarius


title: Acarbonarius_rep2

description: Technical replicate


title: Aclavatus_rep1

description: Sample


title: Aalternata_repB

description: Biological replicate

organism: Alternaria alternata

source_name: Alternaria alternata, fungal culture

value: Alternaria alternata


title: Aalternata_rep2

description: Technical replicate


title: Acarbonarius_rep1

description: Sample


title: Aalternata_rep1

description: Sample


title: Chondros_0

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from OA Cartilage or mesenchymal stem cells extracted after different timepoints (0d, 3d, 7d and 14d).

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.0, from SAS. Gene expression profiling was performed using arrays of human133_plus2 -type from Affymetrix. A Custom CDF Version 10 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

label: Biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Chondrocytes were isolated by collagenase (Collagenase Type I, Worthington; Cat.No.: CLS1) digestion overnight and expanded in DMEM (DMEM, Low Glucose, 1x, Invitrogen; Cat.No.: 21885-108) supplemented  with 10% FCS; 1% Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted after 0, 3, 6, 7 and 14 days using a two-step extraction protocol as described elsewhere [Hoemann et. al, 2002]. Briefly, 1 pellet was mixed with 350 µl of RLT-β-mercapto-ethanol solution (RNeasy kit, Qiagen, Germany) and incubated for 30 minutes at 4°C in a thermomixer (shaking vigorously). After centrifugation at 15,000 x g for 10 minutes at 4°C the procedure was repeated with the pellet and 250 µl of RLT-β-mercapto-ethanol solution and a centrifugation at 21,000 x g (10 minutes). Both supernatants were mixed and the RNeasy procedure was carried out as described by the manufacturer.

treatment_protocol: P0-cells were cultured in high-density pellet cultures. Briefly, 1,500,000 cells were placed into a conical polypropylene tube in chondrogenic medium. The cells were centrifuged at 500xg for 10 minutes. Cell pellets were cultured in DMEM with 1% ITS (Insulin-Transferrin-Selenium 100x, Invitrogen, Germany), 100 U/ml penicillin, 100 µg/ml streptomycin, 210 µmol  ascorbic acid, 10 nmol dexamethasone (Sigma Aldrich, Germany) and 10  ng/ml TGF-ß3 (Strathmann Biotec, Germany) at 37°C, 5% CO2 with medium changes every third day.

tag: cell type

value: pooled Total RNA of OA Cartilage from five patients (female, mean age 74 years, range 61-85) undergoing knee alloarthroplasty at timepoint 0d


title: Chondros_14

value: pooled Total RNA of OA Cartilage from five patients (female, mean age 74 years, range 61-85) undergoing knee alloarthroplasty at timepoint 14d


title: MSC_14

growth_protocol: MSCs were kindly provided by the stem cell lab after Ficoll gradient centrifugation from iliac crest-harvested bone marrow aspirates.

value: pooled Total RNA of MSC from five healthy donors (female, mean age 45 years, range 42-48) at timepoint 14d


title: MSC_3

value: pooled Total RNA of MSC from five healthy donors (female, mean age 45 years, range 42-48) at timepoint 3d


title: Chondros_7

value: pooled Total RNA of OA Cartilage from five patients (female, mean age 74 years, range 61-85) undergoing knee alloarthroplasty at timepoint 7d


title: MSC_7

value: pooled Total RNA of MSC from five healthy donors (female, mean age 45 years, range 42-48) at timepoint 7d


title: Chondros_3

value: pooled Total RNA of OA Cartilage from five patients (female, mean age 74 years, range 61-85) undergoing knee alloarthroplasty at timepoint 3d


title: Ovary-BRCA2-2

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

description: RNA from Ovary BRCA2 mutant

hyb_protocol: each sample a total of 2.2 ug of ssDNA, labeled and fragmented with the NuGEN kit, was hybridized to Affymetrix arrays

scan_protocol: arrays were scanned with the Affymetrix GeneChip Scanner 3000

data_processing: CEL fles were normalized using RMA and bioconductor

source_name: Ovary BRCA2 'one-hit' mutant cells from subject 2

label_protocol: RNA was biotinylated

extract_protocol: RNA was prepared from cultured cells by extraction in guanidinium isothiocyanate-based buffer containing -mercaptoethanol and acid phenol

value: Epithelial cell culture


title: Ovary-BRCA2-3

description: RNA from Ovary BRCA2 mutant

source_name: Ovary BRCA2 'one-hit' mutant cells from subject 3


title: MSC_0

value: pooled Total RNA of MSC from five healthy donors (female, mean age 45 years, range 42-48) at timepoint 0d


title: Ovary-BRCA2-4

description: RNA from Ovary BRCA2 mutant

source_name: Ovary BRCA2 'one-hit' mutant cells from subject 4


title: Ovary-WT-5

description: RNA from Ovary WT

source_name: Ovary wild type cells from subject 5


title: Ovary-BRCA2-6

description: RNA from Ovary BRCA2 mutant

source_name: Ovary BRCA2 'one-hit' mutant cells from subject 6


title: Ovary-BRCA1-6

description: RNA from Ovary BRCA1 mutant

source_name: Ovary BRCA1 'one-hit' mutant cells from subject 6


title: Ovary-BRCA1-4

description: RNA from Ovary BRCA1 mutant

source_name: Ovary BRCA1 'one-hit' mutant cells from subject 4


title: Ovary-BRCA2-5

description: RNA from Ovary BRCA2 mutant

source_name: Ovary BRCA2 'one-hit' mutant cells from subject 5


title: Ovary-WT-6

description: RNA from Ovary WT

source_name: Ovary wild type cells from subject 6


title: Ovary-WT-3

description: RNA from Ovary WT

source_name: Ovary wild type cells from subject 3


title: Ovary-WT-4

description: RNA from Ovary WT

source_name: Ovary wild type cells from subject 4


title: Ovary-BRCA2-1

description: RNA from Ovary BRCA2 mutant

source_name: Ovary BRCA2 'one-hit' mutant cells from subject 1


title: Ovary-WT-1

description: RNA from Ovary WT

source_name: Ovary wild type cells from subject 1


title: Ovary-BRCA1-5

description: RNA from Ovary BRCA1 mutant

source_name: Ovary BRCA1 'one-hit' mutant cells from subject 5


title: Breast-BRCA2-6

description: RNA from Breast BRCA2 mutant

source_name: Breast BRCA2 'one-hit' mutant cells from subject 6


title: Ovary-BRCA1-3

description: RNA from Ovary BRCA1 mutant

source_name: Ovary BRCA1 'one-hit' mutant cells from subject 3


title: Ovary-WT-2

description: RNA from Ovary WT

source_name: Ovary wild type cells from subject 2


title: Ovary-BRCA1-1

description: RNA from Ovary BRCA1 mutant

source_name: Ovary BRCA1 'one-hit' mutant cells from subject 1


title: Ovary-BRCA1-2

description: RNA from Ovary BRCA1 mutant

source_name: Ovary BRCA1 'one-hit' mutant cells from subject 2


title: Breast-BRCA2-5

description: RNA from Breast BRCA2 mutant

source_name: Breast BRCA2 'one-hit' mutant cells from subject 5


title: Breast-BRCA2-4

description: RNA from Breast BRCA2 mutant

source_name: Breast BRCA2 'one-hit' mutant cells from subject 4


title: Breast-BRCA2-3

description: RNA from Breast BRCA2 mutant

source_name: Breast BRCA2 'one-hit' mutant cells from subject 3


title: Breast-BRCA2-2

description: RNA from Breast BRCA2 mutant

source_name: Breast BRCA2 'one-hit' mutant cells from subject 2


title: Breast-WT-6

description: RNA from Breast WT

source_name: Breast wild type cells from subject 6


title: Breast-BRCA2-1

description: RNA from Breast BRCA2 mutant

source_name: Breast BRCA2 'one-hit' mutant cells from subject 1


title: Breast-WT-3

description: RNA from Breast WT

source_name: Breast wild type cells from subject 3


title: Breast-WT-5

description: RNA from Breast WT

source_name: Breast wild type cells from subject 5


title: Breast-BRCA1-3

description: RNA from Breast BRCA1 mutant

source_name: Breast BRCA1 'one-hit' mutant cells from subject 3


title: Breast-BRCA1-1

description: RNA from Breast BRCA1 mutant

source_name: Breast BRCA1 'one-hit' mutant cells from subject 1


title: Breast-WT-2

description: RNA from Breast WT

source_name: Breast wild type cells from subject 2


title: Breast-BRCA1-6

description: RNA from Breast BRCA1 mutant

source_name: Breast BRCA1 'one-hit' mutant cells from subject 6


title: Breast-BRCA1-2

description: RNA from Breast BRCA1 mutant

source_name: Breast BRCA1 'one-hit' mutant cells from subject 2


title: Breast-WT-1

description: RNA from Breast WT

source_name: Breast wild type cells from subject 1


title: Breast-WT-4

description: RNA from Breast WT

source_name: Breast wild type cells from subject 4


title: Breast-BRCA1-5

description: RNA from Breast BRCA1 mutant

source_name: Breast BRCA1 'one-hit' mutant cells from subject 5


title: Old cells (nonsenescent; PD 53) under 3% oxygen, biological rep3

city: Blacksburg

first: Bernd

middle: Robert

last: Stab II

state: VA

address: Life Sciences 1 Washington Str

department: Biochemistry

institute: Virginia Tech

description: Gene expression data of old nonsenescent cells grown under 3% oxygen growth conditions, age matched to the 20% senescent cells

hyb_protocol: Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.

data_processing: The data were analyzed with GeneSpring GX (Agilent Technologies).  The RMA aligorithm was used for background subtraction, normalization, and summarization of data.  An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations.  The data was permuted from all spots randomly 100 times to determine the FDR.  The FDR was corrected for multiple testing using the Benjamini-Hochberg approach.  The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment.  Spots showing changes of 2 fold or more across one or more conditions were considered significant.

source_name: Imr90 cells, old (nonsenescent; PD 53), 3% oxygen growth conditions

label_protocol: Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase.  Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.

growth_protocol: Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD)  27.  Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC.  Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days.  Separate incubators were used for both the 3% and 20% oxygen growth conditions.  Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator.  Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator.  The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml).  Population doublings were calculated by the following formula:  log (N/Ni) x 3.33 (N = number of cells, Ni = initial seeded number of cells).   Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis.  The old cells grown under the 20% oxygen condition were senescent.

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells.  No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.

treatment_protocol: Treatment was the 3% oxygen growth conditions.

tag: cell line

tag: oxygen growth conditions

tag: growth stage

value: Old


title: Breast-BRCA1-4

description: RNA from Breast BRCA1 mutant

source_name: Breast BRCA1 'one-hit' mutant cells from subject 4


title: Young cells (PD 30) under 3% oxygen, biological rep3

description: Gene expression data of young cells grown under 3% oxygen growth conditions, age-matched to the young 20% cells

source_name: Imr90 cells, young (PD 30), 3% oxygen growth conditions

value: Young


title: Old cells (nonsenescent; PD 53) under 3% oxygen, biological rep2


title: CHMP2B 299-99

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Gene expression data from human motor neurons
10 um cervical spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each individual 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430A GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: mutation

value: CHMP2B mutant individual

value: motor neuron


title: Young cells (PD 30) under 3% oxygen, biological rep2


title: Old cells (nonsenescent; PD 53) under 3% oxygen, biological rep1


title: Young cells (PD 30) under 3% oxygen, biological rep1


title: CHMP2B 96-06


title: Senescent cells (PD 48) under 20% oxygen, biological rep1

description: Gene expression data of senescent cells grown under 20% oxygen growth conditions

source_name: Imr90 cells, senescent (PD 48), 20% oxygen growth conditions


title: Senescent cells (PD 48) under 20% oxygen, biological rep2


title: CHMP2B 04-06


title: Young cells (PD 30) under 20% oxygen, biological rep3

description: Gene expression data of young cells grown under 20% oxygen growth conditions

source_name: Imr90 cells, young (PD 30), 20% oxygen growth conditions


title: Young cells (PD 30) under 20% oxygen, biological rep2


title: Young cells (PD 30) under 20% oxygen, biological rep1


title: Peripheral blood lymphocytes_3

city: Stockholm

first: Cecilia

last: Götherström

address: Karolinska University Hospital Huddinge

department: Department for Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description:
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.

hyb_protocol: Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.

scan_protocol: Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.

data_processing:
Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).

Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.

source_name: Maternal Peripheral blood lymphocytes

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

growth_protocol: Peripheral blood from three pregnant women (gestational weeks 12+0, 12+0 and 13+1) with continuing pregnancies were taken. Adult maternal peripheral blood lymphocytes were prepared by centrifuging peripheral blood layered on a Ficoll gradient at 500g for 20 minutes at room temperature. The interphase was collected, washed twice in phosphate buffer saline by centrifugation and then re-suspended in PBS. Mononuclear cells were counted and the cell pellets snap frozen in  80ºC.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.

tag: developmental stage

value: pregnant (maternal)

value: female

value: Peripheral blood lymphocytes


title: 124250_HB00FKH_1/25/08_11:35_AM

city: Tromsoe

first: Vanessa

last: Dumeaux

address: University of Tromsoe

country: Norway

institute: "The Norwegian Women and Cancer project"

description: NWbAB_ 302

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit Protocol.

scan_protocol: Applied Biosystems.

data_processing: A total of 304 arrays, including 18 technical replicates, were analyzed. Data analysis was performed using R (http://cran.r-project.org), an open-source-interpreted computer language for statistical computation and graphics, and tools from the Bioconductor project (http://www.bioconductor.org), adapted to our needs. Using R, we set the expression intensity to missing for genes with flagging value > 8191. We filter out samples which had less than 40% probes with a signal to noise ratio (S/N) ≥ 3. When a technical replicate was conducted, the array with the least of probes with S/N ≥ 3 was excluded. Probes which had S/N ≥ 3 in less than 50% of the samples were also filtered out. After samples and spot filtration, we proceed with log transformation, quantile normalization and imputation of missing values using k-nearest neighbourhood method (k=10). A total of 286 arrays and 16,185 probes are analyzed. All significant technical variables in the global Ancova analysis with a multivariate permuted p-value<0.0001 were included in the gene-wise linear model selection (i.e. array lot number, RNA extraction date as random variables, and time between blood collection and storage as fixed variable) and expression values were adjusted for their effects.

label: digoxigenin

source_name: whole blood

label_protocol: Applied Biosystems NanoAmp RT-IVT labeling kit.

growth_protocol: PAXgene™ blood RNA tubes were thawed at room temperature for 4 h.

extract_protocol: PAXgene™ Blood RNA Isolation Kit, according to the manufacturer’s manual.

tag: rnaextraction date

tag: rnacc

tag: amplification date

tag: crnacc

tag: arraylot

tag: smoking status

value: Yes

tag: hormone therapy use

value: No

tag: medication use

tag: fasting status

value: FALSE

tag: days between blood collection and storage

tag: menopausal status

value: post

tag: bmi group

tag: agegroup


title: 125761_HB00FJZ_1/25/08_11:57_AM

description: NWbAB_ 304


title: 124678_HB00FKD_1/17/08_1:44_PM

description: NWbAB_ 303


title: 124329_HB007BV_7/10/07_11:22_AM

description: NWbAB_ 295


title: 122907_HB007BS__7/11/07_10:28_AM

description: NWbAB_ 298


title: 123536_HB007CA_7/10/07_10:49_AM

description: NWbAB_ 293

value: TRUE


title: 124507_HB00FKK_1/17/08_1:28_PM

description:
NWbAB_ 301
Replicate: 3_r2


title: 125964_HB007BP_7/10/07_12:43_PM

description: NWbAB_ 297


title: 125620_HB007BO_7/10/07_12:01_PM

description: NWbAB_ 296


title: Peripheral blood lymphocytes_2

tag: gender

tag: cell type


title: Peripheral blood lymphocytes_1


title: 126106_HB007BW_7/6/07_11:20_AM

description: NWbAB_ 289


title: 126250_HB007CF_7/6/07_10:44_AM

description: NWbAB_ 290


title: 125694_HB007BX__7/11/07_10:12_AM

description: NWbAB_ 300


title: 123132_HB007C9_7/10/07_10:29_AM

description: NWbAB_ 292


title: Senescent cells (PD 48) under 20% oxygen, biological rep3

tag: cell line

tag: oxygen growth conditions

tag: growth stage


title: 126521_HB007C3_7/6/07_10:26_AM

description: NWbAB_ 291

tag: rnaextraction date

tag: rnacc


title: 123956_HB007C4_7/10/07_11:06_AM

description: NWbAB_ 294

tag: amplification date

tag: crnacc


title: 126675_HB007C2__7/5/07_9:06_AM

description: NWbAB_ 287

tag: arraylot

tag: smoking status


title: 126029_HB007CD_7/6/07_11:04_AM

description: NWbAB_ 288

tag: hormone therapy use

tag: medication use


title: 125693_HB007BQ__7/5/07_8:50_AM

description: NWbAB_ 286

tag: fasting status

tag: days between blood collection and storage


title: 124204_HB007C5__7/5/07_8:35_AM

description: NWbAB_ 285

tag: menopausal status

tag: bmi group


title: 123556_HB007CH_6/21/07_11:21_AM

description: NWbAB_ 282

tag: agegroup


title: 126712_HB007BZ_6/20/07_11:00_AM

description: NWbAB_ 280


title: 124544_HB007BM_6/20/07_10:29_AM

description: NWbAB_ 277


title: 124414_HB00FJI_1/16/08_12:24_PM

description: NWbAB_ 271


title: 122949_HB007C8_6/21/07_11:00_AM

description: NWbAB_ 281


title: 123344_HB007CI__7/5/07_8:19_AM

description: NWbAB_ 284


title: 125192_HB0085I_1/16/08_11:37_AM

description: NWbAB_ 273


title: 126132_HB007BT_6/20/07_11:17_AM

description: NWbAB_ 279


title: 125421_HB007BR_6/20/07_10:44_AM

description: NWbAB_ 278


title: 123591_HB0085G_1/16/08_12:40_PM

description:
NWbAB_ 269
Replicate: 8_r2


title: 125756_HB0085W_1/16/08_11:52_AM

description: NWbAB_ 274


title: 123617_HB00860_1/17/08_11:45_AM

description:
NWbAB_ 270
Replicate: 7_r2


title: 126158_HB007C7_6/21/07_11:41_AM

description: NWbAB_ 283


title: 123393_HB0085P_1/16/08_12:56_PM

description:
NWbAB_ 268
Replicate: 9_r2


title: 124981_HB007C1__7/11/07_10:44_AM

description: NWbAB_ 276


title: 124549_HB0085K_1/16/08_11:21_AM

description:
NWbAB_ 272
Replicate: 2_r2


title: 122722_HB0085Q_1/16/08_12:08_PM

description:
NWbAB_ 266
Replicate: 15_r2


title: 123054_HB0085R_1/17/08_11:29_AM

description:
NWbAB_ 267
Replicate: 12_r2


title: 123908_HB007BY__7/11/07_9:56_AM

description:
NWbAB_ 275
Replicate: 17_r2


title: 125594_HB0085S_12/6/07_1:07_PM

description: NWbAB_ 263


title: 125972_HB00862_12/6/07_12:50_PM

description: NWbAB_ 264


title: 123049_HB0085H_1/16/08_1:13_PM

description:
NWbAB_ 265
Replicate: 18_r2


title: tag of rice callus

type: SAGE

anchor: NlaIII

city: Shenzhen

first: Guangwu

last: Guo

state: Guangdong Province

address: Main Building,Beishan Industrial Zone, Yantian District

department: Bioinformatics center

country: China

institute: Beijing Genomics Institute at Shenzhen

description: We chose RNA from panicle at filling stage to construct mRNA tag library, 6μg total RNA was consumed. Firstly, mRNA (PolyA+ RNA) was enriched by the Dynalbeads™ Oligo(dT)25 (Invitrogen) according to the manufacturer’s instructions. At the last step, beads with mRNA were suspended in 1×first strand buffer. Instead of elute mRNA from magnetic beads; the process of reverse transcription was performed on the beads, and the oligodT linked to beads was used as primer. We introduced the following reagent ordinal for first strand cDNA synthesis: 0.1M DTT, and 10mM dNTPs (NEB), 40U of RNaseOUT™, 400U of Superscript II reverse transcriptase (Invitrogen), and added DEPC H2O to a final volume of 50 μl. This reaction mix was incubated at 42°C in a thermomixer spin at 1400rpm for 1 hours sustainedly, followed by inactivate the reaction at 70°C for 15 minutes (spin at 1400rpm for 15sec and stand for 2min). For second strand cDNA fabrication, 10mM dNTPs (NEB), 200U of E. coli DNA PolymeraseⅠ(Invitrogen) and 4U of E. coli RNase H (Invitrogen) were mix in the tube to a total volume of 150 μl; this reaction mix was incubated at 16℃ for 2.5 hours in a thermomixer (spin at 1400rpm for 15sec and stand for 2min). lastly, beads with cDNA was suspended in 1×NEBuffer 4 (NEB). The cDNA covalent linked to dynalbeads was digested using 10U of NlaⅢ (NEB) by incubating at 37℃ for 1 hours (spin at 1400rpm for 15sec and stand for 2min). Then, the cDNA was ligated to NlaⅢ adapter 1 by 5U of T4 DNA ligase (Invitrogen), and the reaction was processed at 20℃ for 2 hours in a thermomixer spin at 1400rpm sustainedly. Sequentially, 8U of MmeⅠ(NEB) was added to digest cDNA into 17bp｡ｫ19bp fragment, the procedure was done in a thermomixer spin at 1400rpm sustainedly at 37℃ for 1.5 hours. Then, the supernatant was transferred into a new tube, and CIAP (Invitrogen) was introduced to dephosphorylate for 1 hr at 37°C. After purification by Phenol/chloroform/isoamyl alcohol 25:24:1 (Invitrogen), the cDNA fragment was deposited by 100% ethanol combined with glycogen (Ambion) and acetate sodium (Novagen) and resolved in ultra pure water. The eluted cDNA was ligated to GEX adapter 2 utilized 5U of T4 DNA ligase (Invitrogen) by incubate at 20°C for 2 hours without any vibration. Subsequently, the cDNA fragment was amplified by 15 cycles PCR. The composition of liquid system and thermo cycling steps were the same as cDNA library procedure except the primer using GEX PCR primer 1 and GEX PCR primer 2 replace of primer1.1 and primer2.1. The products were purified by electrophoresis with 6% Novex™ TBE gel (Invitrogen) and ｡ｫ85nt DNA band on gel was separated and recovered. Then, we utilized 1×NEbuffer 2 (NEB) rotating at room temperature for 2 hours to facilitate elution and used Spin-X Cellulose Acetate filters (Fisher) to separate gel debris. Afterward, DNA was precipitated using 100% ethanol combined with glycogen (Ambion) and acetate sodium (Novagen). All oligonucleotides were provided by Illumina. Finally, the library products were sequenced using the 1G Illumina Genome Analyzer.

data_processing: 21 bp short tags consisting of CATG and 17bp tag sequence were extracted from total reads and then adaptor tag ,low quality tag(containing Ns) were removed

organism: Oryza sativa

source_name: callus of rice

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.

tag: tissue

value: callus

tag: subspecies

value: indica cv. 9311


title: 123651_HB0085F_12/6/07_12:34_PM

description: NWbAB_ 261


title: 123325_HB0085Y_12/6/07_12:00_PM

description: NWbAB_ 259


title: 125749_HB00BWR_4/17/07_10:06_AM

description: NWbAB_ 258


title: 124929_HB00BSP_4/17/07_11:00_AM

description: NWbAB_ 255


title: 123916_HB00BXA_4/16/07_3:03_PM

description: NWbAB_ 251


title: 123529_HB00FJH_12/6/07_1:23_PM

description: NWbAB_ 260


title: 124585_HB0085T_12/6/07_12:18_PM

description: NWbAB_ 262


title: 125710_HB00BX6_4/16/07_3:54_PM

description: NWbAB_ 253


title: 123755_HB00BWN_4/16/07_4:17_PM

description: NWbAB_ 250


title: 125576_HB007AJ_6/21/07_10:12_AM

description: NWbAB_ 245


title: 123148_HB00BWV_4/16/07_2:10_PM

description: NWbAB_ 246


title: 125575_HB00BS4_4/17/07_10:22_AM

description: NWbAB_ 257


title: 123122_HB007A7_6/21/07_10:28_AM

description: NWbAB_ 242


title: tag of rice booting panicle

source_name: booting pancile of rice

value: panicle

tag: stage

value: booting stage


title: 125406_HB00BSJ_4/17/07_10:42_AM

description: NWbAB_ 256


title: 124558_HB00BWY_4/16/07_3:20_PM

description: NWbAB_ 252


title: 123485_HB00BWZ_4/16/07_2:47_PM

description: NWbAB_ 248


title: 123186_HB00BWS_4/16/07_3:38_PM

description: NWbAB_ 247


title: 122899_HB0079X_6/21/07_10:44_AM

description: NWbAB_ 241


title: 123303_HB007A3_6/21/07_9:40_AM

description: NWbAB_ 243


title: 123454_HB007A2_6/21/07_9:56_AM

description: NWbAB_ 244


title: 125957_HB0079T_6/20/07_12:25_PM

description: NWbAB_ 240


title: 124048_HB0079M_6/20/07_11:49_AM

description: NWbAB_ 238


title: 125227_HB007A1_6/20/07_11:33_AM

description: NWbAB_ 239


title: 125955_HB007AD_6/19/07_10:16_AM

description: NWbAB_ 235


title: 126127_HB0079O_6/19/07_10:32_AM

description: NWbAB_ 236


title: 125060_HB0079V_6/19/07_11:20_AM

description: NWbAB_ 231


title: 125602_HB007A4_6/19/07_11:37_AM

description: NWbAB_ 232


title: 123738_HB007AG_6/20/07_12:07_PM

description: NWbAB_ 237


title: 126796_HB007AA_6/15/07_10:34_AM

description: NWbAB_ 228


title: 125254_HB00BV6_3/2/07_1:42_PM

description: NWbAB_ 221


title: 125924_HB0079N_6/19/07_10:00_AM

description: NWbAB_ 234


title: 123157_HB0079Q_6/15/07_10:50_AM

description: NWbAB_ 222


title: 124365_HB007AB_6/19/07_11:05_AM

description: NWbAB_ 230


title: 123570_HB00BVD_3/2/07_1:09_PM

description: NWbAB_ 219


title: 126447_HB0079R_6/15/07_10:01_AM

description: NWbAB_ 226


title: 125855_HB007AH_6/19/07_9:44_AM

description: NWbAB_ 233


title: 123491_HB007A9_6/15/07_11:38_AM

description: NWbAB_ 225


title: 123469_HB00BV5_3/2/07_12:53_PM

description: NWbAB_ 218


title: 124172_HB0079W_6/19/07_10:49_AM

description: NWbAB_ 229


title: 126699_HB0079U_6/15/07_10:17_AM

description: NWbAB_ 227


title: 123720_HB00BVE_3/2/07_1:25_PM

description: NWbAB_ 220


title: 123231_HB0079Z_6/15/07_11:06_AM

description: NWbAB_ 223


title: 123410_HB007AI_6/15/07_11:23_AM

description: NWbAB_ 224


title: 123385_HB00BV4_3/2/07_11:55_AM

description: NWbAB_ 217


title: 123156_HB00BVC_3/2/07_11:39_AM

description: NWbAB_ 216


title: 123130_HB0058K_3/2/07_11:23_AM

description: NWbAB_ 215


title: 122898_HB00G5C_1/25/08_12:43_PM

description:
NWbAB_ 211
Replicate: 14_r2


title: 122737_HB00G55_1/25/08_12:13_PM

description: NWbAB_ 212

value: peri


title: 123248_HB00G4T_1/25/08_12:58_PM

description: NWbAB_ 213


title: 125392_HB00G49_1/17/08_12:54_PM

description: NWbAB_ 210


title: 124068_HB00G4B_1/17/08_12:23_PM

description:
NWbAB_ 209
Replicate: 4_r2


title: 123847_HB00CK6_6/5/07_11:24_AM

description: NWbAB_ 204


title: 123417_HB00CKE_6/5/07_11:08_AM

description: NWbAB_ 203


title: 126297_HB00EF7_6/15/07_9:45_AM

description: NWbAB_ 206


title: 124429_HB00ATX_2/13/07_1:48_PM

description: NWbAB_ 193


title: 125992_HB00EF6_5/25/07_11:59_AM

description: NWbAB_ 201


title: 123317_HB00EEN_4/27/07_12:47_PM

description: NWbAB_ 196


title: 124037_HB00EEO_4/27/07_12:31_PM

description: NWbAB_ 199


title: 123686_HB00G4A_1/17/08_1:12_PM

description: NWbAB_ 207


title: 123101_HB00CKC_6/5/07_10:51_AM

description: NWbAB_ 202


title: 123621_HB00ATF_2/13/07_1:14_PM

description: NWbAB_ 191


title: 125765_HB00AJS_2/27/07_10:57_AM

description: NWbAB_ 189


title: 125511_HB00EEX_4/27/07_1:03_PM

description: NWbAB_ 200


title: 123620_HB00EFA_4/27/07_12:00_PM

description: NWbAB_ 197


title: 124300_HB00ATK_2/13/07_1:31_PM

description: NWbAB_ 192


title: 123931_HB00G48_1/17/08_12:38_PM

description: NWbAB_ 208


title: 125848_HB00CKJ_6/5/07_11:43_AM

description: NWbAB_ 205


title: 123085_HB00EEI_4/27/07_1:20_PM

description: NWbAB_ 194


title: 123110_HB00EEQ_4/27/07_11:44_AM

description: NWbAB_ 195


title: 125507_HB00AX9_2/27/07_1:00_PM

description: NWbAB_ 188


title: 123930_HB00EFB_4/27/07_12:16_PM

description: NWbAB_ 198


title: 124666_HB00AWT_2/27/07_12:43_PM

description: NWbAB_ 187


title: 123293_HB00AT5_2/13/07_12:58_PM

description: NWbAB_ 190


title: 124105_HB00AX0_2/22/07_12:24_PM

description: NWbAB_ 178


title: 123592_HB00AWZ_2/22/07_12:08_PM

description: NWbAB_ 177


title: 122938_HB00AX1_2/22/07_11:18_AM

description: NWbAB_ 174


title: 123636_HB00AM1_2/16/07_2:08_PM

description: NWbAB_ 171


title: 123137_HB00AMI_2/13/07_12:08_PM

description: NWbAB_ 165


title: 124827_HB00ALV_2/22/07_1:18_PM

description: NWbAB_ 181


title: 124455_HB00AXC_2/22/07_12:45_PM

description: NWbAB_ 179


title: 123308_HB00AOF_2/22/07_11:51_AM

description: NWbAB_ 176


title: 122996_HB00AX6_2/22/07_11:35_AM

description: NWbAB_ 175


title: 123691_HB00AMD_2/16/07_2:23_PM

description: NWbAB_ 172


title: 123003_HB00AME_2/13/07_11:51_AM

description: NWbAB_ 164


title: 125731_HB00AJU_2/16/07_12:54_PM

description: NWbAB_ 173


title: 123632_HB00AMA_2/16/07_1:48_PM

description: NWbAB_ 170


title: 123457_HB00AM4_2/16/07_1:12_PM

description: NWbAB_ 168


title: 124135_HB007GE_7/25/07_12:00_PM

description: NWbAB_ 162


title: 124505_HB007GD_7/25/07_11:23_AM

description: NWbAB_ 163


title: 123547_HB00AJX_2/27/07_11:13_AM

description: NWbAB_ 182


title: 123512_HB00AM8_2/16/07_1:29_PM

description: NWbAB_ 169


title: 123856_HB00AOG_2/27/07_12:11_PM

description: NWbAB_ 185


title: 123775_HB00AM0_2/27/07_11:50_AM

description: NWbAB_ 184


title: 124159_HB00AX4_2/27/07_12:27_PM

description: NWbAB_ 186


title: 123207_HB00AMF_2/13/07_12:25_PM

description: NWbAB_ 166


title: 124112_HB007FS_7/25/07_11:07_AM

description: NWbAB_ 161


title: 123252_HB00AM3_2/13/07_12:41_PM

description: NWbAB_ 167


title: 125467_HB007FP_7/4/07_12:25_PM

description: NWbAB_ 156


title: 123262_HB007FW_7/25/07_12:16_PM

description: NWbAB_ 158


title: 125640_HB007GC_7/4/07_12:47_PM

description: NWbAB_ 157


title: 123138_HB007G8_7/4/07_10:49_AM

description: NWbAB_ 154


title: 123995_HB007FV_7/4/07_12:08_PM

description: NWbAB_ 155


title: 123831_HB007GI_7/25/07_10:50_AM

description: NWbAB_ 160


title: 123209_HB007EU__7/11/07_11:17_AM

description: NWbAB_ 153


title: 123830_HB007G6_7/25/07_11:41_AM

description: NWbAB_ 159


title: 2817GM

city: Lleida

first: Romi

middle: N

last: Pena

address: 191 Av Alcalde Rovira Roure

department: Genètica i Millora Animal

country: Spain

institute: IRTA

description: Duroc commercial line

hyb_protocol: Hybridisation protocol as recommented by Affymetrix using the Porcine Genome Array from Affymetrix.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A, as recommended by Affymetrix

data_processing: Data pre-processing, normalisation and class comparison analysis were carried out with the BRB-ArrayTools software version 3.7.1, which is available online at http://linus.nci.nih.gov/BRB-ArrayTools.html, as follows: microarray data normalisation was performed using the gcRMA algorithm, which corrects the intensity of each probe by its GC content; genes showing minimal variation across the set of arrays were excluded from the analysis, that is, only genes whose expression differed above 1.5 fold from the median in at least 20% of the arrays were retained. From the total 23937 spots of the array, 4299 spots passed these filtering conditions. For each probe, expression fold-change was calculated as the ratio between median values in both groups.

organism: Sus scrofa

source_name: gluteus medius muscle from 190-days-old pigs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Duroc pigs were grown in standart commercial condictions, fed a commercial pellet diet and slaughtered at 190 days of age. Tissue samples were collected at slaughter, snap froxen in LN2 and stored at -80ºC until analysis

extract_protocol: total RNA was extracted from gluteus medius muscle using Ribopure kit (AMBION) following the manufacturer's protocol

treatment_protocol: After slaughter, controled animals (n=350) were ranked based in 13 carcass, plasma and muscle fat deposition and fat composition traits. The top amd bottom extreme of this distribution were selected to form the HIGH (n=34) and LOW (n=34) groups.

tag: group

value: gluteus medius muscle

tag: age

value: 190 days-old


title: 2809GM

description: Duroc commercial line


title: 2561GM

description: Duroc commercial line


title: 124719_HB007FE_7/20/07_11:00_AM

description: NWbAB_ 150

tag: rnaextraction date

tag: rnacc


title: 2551GM

description: Duroc commercial line


title: 8692GM

description: Duroc commercial line


title: 8700GM

description: Duroc commercial line


title: 8693GM

description: Duroc commercial line


title: 125522_HB007FC_7/20/07_12:06_PM

description: NWbAB_ 151

tag: amplification date

tag: crnacc


title: 2549GM

description: Duroc commercial line


title: 122909_HB007ET_7/20/07_10:07_AM

description: NWbAB_ 147

tag: arraylot

tag: smoking status


title: 124581_HB007F7_7/20/07_11:49_AM

description: NWbAB_ 149

tag: hormone therapy use

tag: medication use


title: 122871_HB007FD_7/20/07_11:33_AM

description: NWbAB_ 146

tag: fasting status

tag: days between blood collection and storage


title: 2189GM

description: Duroc commercial line


title: 123415_HB007FI_7/20/07_10:40_AM

description: NWbAB_ 148

tag: menopausal status

tag: bmi group


title: 123211_HB007F8_9/4/07_11:43_AM

description: NWbAB_ 152

tag: agegroup


title: 122834_HB007ER_7/20/07_11:17_AM

description: NWbAB_ 145


title: 2174GM

description: Duroc commercial line

tag: tissue


title: 122791_HB007EQ_7/20/07_10:24_AM

description: NWbAB_ 144


title: 2172GM

description: Duroc commercial line


title: 2168GM

description: Duroc commercial line


title: 123509_HB007EP_7/18/07_11:01_AM

description: NWbAB_ 139


title: 126286_HB007F6_7/18/07_11:33_AM

description: NWbAB_ 143


title: 2187GM

description: Duroc commercial line


title: 2157GM

description: Duroc commercial line


title: 124983_HB007ES_7/18/07_10:44_AM

description: NWbAB_ 141


title: 123027_HB007FF_7/12/07_10:42_AM

description: NWbAB_ 137


title: 123784_HB007F3_7/18/07_10:26_AM

description: NWbAB_ 140


title: 1919GM

description: Duroc commercial line


title: 123117_HB007EN_7/12/07_10:09_AM

description: NWbAB_ 138


title: 1918GM

description: Duroc commercial line


title: 2164GM

description: Duroc commercial line


title: 125783_HB007F1_7/18/07_11:17_AM

description: NWbAB_ 142


title: 1624GM

description: Duroc commercial line


title: 1910GM

description: Duroc commercial line


title: 123606_HB007FG__7/11/07_11:01_AM

description: NWbAB_ 136


title: 123246_HB007F2__7/11/07_11:33_AM

description: NWbAB_ 135


title: 123432_HB007F4_7/4/07_11:28_AM

description: NWbAB_ 133


title: 1604GM

description: Duroc commercial line


title: 1602GM

description: Duroc commercial line


title: 1586GM

description: Duroc commercial line


title: 123283_HB007EO_7/4/07_11:12_AM

description: NWbAB_ 132


title: 124665_HB007F0_7/4/07_11:46_AM

description: NWbAB_ 134


title: 1559GM

description: Duroc commercial line


title: 123260_HB007F9_7/18/07_11:50_AM

description: NWbAB_ 130


title: 1551GM

description: Duroc commercial line


title: 1550GM

description: Duroc commercial line


title: 1539GM

description: Duroc commercial line


title: 123053_HB007F5_7/4/07_10:29_AM

description: NWbAB_ 131


title: 1444GM

description: Duroc commercial line


title: 124039_HB00CSW_11/29/07_2:44_PM

description: NWbAB_ 126


title: 123097_HB00CSI_11/29/07_1:33_PM

description: NWbAB_ 123


title: 1456GM

description: Duroc commercial line


title: 1404GM

description: Duroc commercial line


title: 1467GM

description: Duroc commercial line


title: 1495GM

description: Duroc commercial line


title: 122651_HB007FA_7/18/07_12:38_PM

description: NWbAB_ 128


title: 123661_HB00CSK_11/29/07_3:05_PM

description: NWbAB_ 125


title: 125792_HB00CSS_11/29/07_1:51_PM

description: NWbAB_ 127


title: 122743_HB007EY_7/18/07_12:22_PM

description: NWbAB_ 129


title: 1403GM

description: Duroc commercial line


title: 123066_HB00CSP_11/29/07_2:08_PM

description: NWbAB_ 122


title: 1402GM

description: Duroc commercial line


title: 123350_HB00CT2_11/29/07_3:23_PM

description: NWbAB_ 124


title: 8695GM

description: Duroc commercial line


title: 123656_HB00CSN_11/28/07_1:16_PM

description: NWbAB_ 119


title: 8697GM

description: Duroc commercial line


title: 8688GM

description: Duroc commercial line


title: 8689GM

description: Duroc commercial line


title: 123036_HB00CST_11/28/07_1:50_PM

description: NWbAB_ 118


title: 123018_HB00CSB_11/28/07_1:34_PM

description: NWbAB_ 117


title: 124496_HB009QM_2/16/07_12:36_PM

description: NWbAB_ 115


title: 2820GM

description: Duroc commercial line


title: 123626_HB009Q7_2/16/07_12:20_PM

description: NWbAB_ 114


title: 2807GM

description: Duroc commercial line


title: 123413_HB009KK_1/18/07_1:28_PM

description: NWbAB_ 112


title: 2808GM

description: Duroc commercial line


title: 123435_HB009QN_1/18/07_1:44_PM

description: NWbAB_ 113


title: 2823GM

description: Duroc commercial line


title: 123384_HB009KL_1/18/07_1:11_PM

description: NWbAB_ 111


title: 2801GM

description: Duroc commercial line


title: 123336_HB009Q0_1/18/07_12:54_PM

description: NWbAB_ 110


title: 2805GM

description: Duroc commercial line


title: 123288_HB009QK_1/18/07_11:19_AM

description: NWbAB_ 108


title: 123820_HB00CI6_4/27/07_11:27_AM

description: NWbAB_ 107


title: 2724GM

description: Duroc commercial line


title: 2737GM

description: Duroc commercial line


title: 123952_HB00CI1_4/24/07_1:20_PM

description: NWbAB_ 106


title: 123304_HB009Q4_1/18/07_11:36_AM

description: NWbAB_ 109


title: 2709GM

description: Duroc commercial line


title: 123893_HB00CIC_4/24/07_12:11_PM

description: NWbAB_ 105


title: 2552GM

description: Duroc commercial line


title: 2705GM

description: Duroc commercial line


title: 2546GM

description: Duroc commercial line


title: 123689_HB00CIK_4/24/07_11:38_AM

description: NWbAB_ 104


title: 2704GM

description: Duroc commercial line


title: 123155_HB00CHZ_4/24/07_11:21_AM

description: NWbAB_ 101


title: 123005_HB00CIF_4/24/07_1:05_PM

description: NWbAB_ 100


title: 123553_HB00CIM_4/24/07_11:55_AM

description: NWbAB_ 103


title: 122963_HB00CIB_4/24/07_12:28_PM

description: NWbAB_ 99


title: 123428_HB00CIE_4/24/07_12:47_PM

description: NWbAB_ 102


title: 2545GM

description: Duroc commercial line


title: 1911GM

description: Duroc commercial line


title: 1619GM

description: Duroc commercial line


title: 2144GM

description: Duroc commercial line


title: 2151GM

description: Duroc commercial line


title: 124167_HB00CI2_4/20/07_1:00_PM

description: NWbAB_ 98


title: 123638_HB00CIG_4/20/07_11:47_AM

description: NWbAB_ 96


title: 1563GM

description: Duroc commercial line


title: 1605GM

description: Duroc commercial line


title: 123804_HB00CIR_4/20/07_12:25_PM

description: NWbAB_ 97


title: 123510_HB00CII_4/20/07_12:03_PM

description: NWbAB_ 95


title: 2176GM

description: Duroc commercial line


title: 123365_HB00CIT_4/20/07_1:32_PM

description: NWbAB_ 94


title: 123063_HB00CIL_4/20/07_12:43_PM

description: NWbAB_ 92


title: 1540GM

description: Duroc commercial line


title: 1538GM

description: Duroc commercial line


title: 123017_HB00CIH_4/20/07_1:16_PM

description: NWbAB_ 91


title: 1536GM

description: Duroc commercial line


title: 1496GM

description: Duroc commercial line


title: 123969_HB00CIN_4/17/07_11:59_AM

description: NWbAB_ 90


title: 1469GM

description: Duroc commercial line


title: 1533GM

description: Duroc commercial line


title: 1443GM

description: Duroc commercial line


title: 123958_HB00CI5_4/17/07_11:43_AM

description: NWbAB_ 89


title: 1429GM

description: Duroc commercial line


title: 1452GM

description: Duroc commercial line


title: 1468GM

description: Duroc commercial line


title: 123210_HB00CIS_4/20/07_11:29_AM

description: NWbAB_ 93


title: 124510_HB00CSO_12/4/07_12:08_PM

description: NWbAB_ 84


title: 125090_HB00CSC_12/4/07_12:59_PM

description: NWbAB_ 86


title: 123785_HB00CI7_4/17/07_12:21_PM

description: NWbAB_ 88


title: 124651_HB00CSY_12/4/07_12:41_PM

description: NWbAB_ 85


title: 124296_HB00CT0_12/4/07_11:36_AM

description: NWbAB_ 83


title: 126292_HB00CSL_12/4/07_1:33_PM

description: NWbAB_ 87


title: 122951_HB00CT5_12/4/07_12:25_PM

description: NWbAB_ 82


title: 123474_HB009OX_1/18/07_2:01_PM

description: NWbAB_ 79


title: Fgf3+/-;Fgf10+/- vs. Fgf3-/-;Fgf10-/-, replica 2

city: Salt Lake City

first: Suzanne

middle: L.

last: Mansour

state: UT

address: 15 North 2030 East

department: Human Genetics

institute: University of Utah

description: Biological replicate 2 of 3. Comparison of 10 pooled placodal ectoderms (one replica) from Fgf3+/-;Fgf10+/- and  10 from Fgf3-/-;Fgf10-/-.

hyb_protocol: Samples were hybridized using the standard Agilent two-color gene expression hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution using the extended dynamic range (XDR) protocol.

data_processing:
Images were processed with Agilent Feature Extraction software version 9.5.1.1.
Lowess-normalized log2 ratio of (cy5/cy3) was calculated. Non-uniform features and features not flagged as well above background were excluded.

organism: Mus musculus

source_name: placodal ectoderm, Fgf3+/-;Fgf10+/-

label_protocol: Samples were labeled using the Agilent Two-Color Low RNA Input Linear Amplification Kit

growth_protocol: 4-8 somite-staged embryos were harvested from the mothers (no treatments).  Placodes were microdissected and immediately dissociated and frozen at -70°C in Qiagen RLT buffer prior to RNA extraction.

extract_protocol: Ten placodes were pooled in three different pools (3 Fgf3+/-;Fgf10+/- and 3 Fgf3-/-;Fgf10-/- biologic replicas) and total RNA was extracted using a Qiagen MicroRNA Easy kit according to manufacturer's instructions.

treatment_protocol: No treatments.  Embryos were harvested from pregnant females; the otic placodes recovered and stored for RNA extraction.

value: ten pooled (4-8s) murine placodal ectoderms

tag: genotype/variation

source_name: placodal ectoderm, Fgf3-/-;Fgf10-/-

value: ten pooled 4-8s murine placodal ectoderms


title: 122878_HB00CSG_12/4/07_11:52_AM

description: NWbAB_ 81


title: 123483_HB009RQ_1/18/07_2:18_PM

description: NWbAB_ 80


title: 122918_HB009RV_1/16/07_3:45_PM

description: NWbAB_ 77


title: 122919_HB009MH_1/16/07_4:03_PM

description: NWbAB_ 78


title: Fgf3+/-;Fgf10+/- vs. Fgf3-/-;Fgf10-/-, replica 3

description: Biological replicate 3 of 3. Comparison of 10 pooled placodal ectoderms (one replica) from Fgf3+/-;Fgf10+/- and  10 from Fgf3-/-;Fgf10-/-.


title: Fgf3+/-;Fgf10+/- vs. Fgf3-/-;Fgf10-/-, replica 1

description: Biological replicate 1 of 3. Comparison of 10 pooled placodal ectoderms (one replica) from Fgf3+/-;Fgf10+/- and  10 from Fgf3-/-;Fgf10-/-.


title: 122887_HB009S0_1/16/07_3:12_PM

description: NWbAB_ 75


title: 122864_HB009M2_1/16/07_2:39_PM

description: NWbAB_ 73


title: 122851_HB009LW_1/16/07_2:06_PM

description: NWbAB_ 71


title: 122868_HB009M7_1/16/07_2:55_PM

description: NWbAB_ 74


title: 122894_HB009S1_1/16/07_3:28_PM

description: NWbAB_ 76


title: 122811_HB009RW_1/11/07_1:17_PM

description: NWbAB_ 69


title: Lung, 12h post HBSS treatment, biological replicate 3

city: Research Triangle Park

first: Cherie

middle: M.

last: Pucheu-Haston

state: NC

address: 109 T.W. Alexander Drive

department: NHEERL

institute: U.S. Environmental Protection Agency

description: Gene expression data after a single administration of agents of high or low allergenicity or vehicle control

hyb_protocol: Following fragmentation, cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip (mouse 430A_2.0) overnight at 45°C.  Bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) and amplified with biotinylated anti-streptavidin antibody and additional SAPE

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip scanner 3000 with Affymetrix Gene Chip Operating Software (GCOS)

data_processing: GeneChip quality was checked using Simpleaffy.  Scan data were uploaded to Rosetta Resolver for analysis.  Scan normalization and processing were performed using the Affymetrix Rosetta intensity profile builder.  Where appropriate, additional processing was performed using the Affymetrix Rosetta intensity experiment builder (group dependent) or the Affymetrix Rosetta ratio builder (no error weighting).

source_name: Mouse lung 12h after HBSS administration

label_protocol: Biotinylated cRNA were prepared from cDNA by first-cycle IVT amplification catalyzed by T7 polymerase using biotinylated CTP and UTP

extract_protocol: Total RNA was isolated from liquid nitrogen snap-frozen whole left lungs using a Qiagen Rneasy Mini kit, according to manufacturer's instructions

treatment_protocol: Mice were administered a single dose of MACA (20µg in 50µl HBSS), BSA (20µg in 50µl HBSS) or HBSS alone (50µl) by intratracheal aspiration (IA)

tag: agent

value: HBSS

value: Whole homogenized left lung

tag: strain

value: BALB/c

value: 8 weeks

tag: gender

value: Female


title: 122790_HB009M3_1/11/07_1:00_PM

description: NWbAB_ 68

tag: rnaextraction date

tag: rnacc

value: Yes

value: FALSE


title: Lung, 12h post HBSS treatment, biological replicate 4

tag: age


title: 122848_HB009RJ_1/11/07_1:33_PM

description: NWbAB_ 70

tag: amplification date

tag: crnacc

tag: arraylot

value: No

value: post


title: 122853_HB009M4_1/16/07_2:22_PM

description: NWbAB_ 72

tag: smoking status

tag: hormone therapy use

tag: medication use


title: CLL CD14+ FA1

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description: circulating endothelial cells (CEC), chronic lymphocytic leukemia (CLL),

hyb_protocol: 825 ng of Cy5-labelled cRNA were mixed with the same amount of Cy3-labeled reference cRNA and then cRNA mixtures were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent Technologies). Samples were hybridized for 17 h at 65°C on 4X44K Whole Human Genome Microarray (Agilent Technologies), comprising over 33’000 (60-mer) experimentally validated oligonucleotide probes and then scanned using a confocal laser scanner (Agilent Technologies).

scan_protocol: Fluorescence data were analyzed with Feature Extraction Software v.9.1 (Agilent Technologies).

data_processing: Result data from each scan (Log10 Cy5/Cy3) were imported into the gene expression analysis software Luminator (Rosetta Bio software, Seattle, WA, USA). Two-dimensional clustering analysis was performed using an agglomerative algorithm with an average link heuristics and a correlation with mean subtraction.The identification of genes differentially expressed between subgroups was performed using both Significant Analysis of Microarray (SAM) algorithm with false discovery ratio (FDR)<5% and enhanced Analysis of Variance (ANOVA) with p-value <0.001. To increase the statistical power, the enhanced ANOVA uses as input data both expression level and the estimated technology error associated with the expression level. As a result, the false-positive rate is reduced when the number of replicates is small and, then, sensitivitydetection is increased.

source_name: UHR

label_protocol: Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA)

extract_protocol: COMMERCIAL RNA (STRATAGENE)

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: CLL CD14+ FA1

extract_protocol: RNeasy Mini Kit (QIAGEN, Valencia, CA, USA)

tag: CD14+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: 122769_HB009M0_1/11/07_12:41_PM

description: NWbAB_ 67

tag: fasting status

tag: days between blood collection and storage

tag: menopausal status

tag: bmi group

tag: agegroup


title: Lung, 12h post BSA treatment, biological replicate 4

source_name: Mouse lung 12h after BSA administration

tag: agent

value: BSA (in HBSS)

tag: tissue

tag: strain

tag: gender


title: 122754_HB009M9_1/11/07_12:08_PM

description: NWbAB_ 65

tag: rnaextraction date

tag: rnacc

tag: amplification date


title: HB0090H_12/12/06_12:56_PM

description: NWbAB_ 62

tag: crnacc

tag: arraylot

tag: smoking status

value: TRUE


title: Lung, 12h post HBSS treatment, biological replicate 2

tag: age


title: CLL CD14+ GS1

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: CLL CD14+ GS1

tag: CD14+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: CLL CD14+ GAI

source_name: CLL CD14+ GAI


title: 122725_HB0094V_1/11/07_11:51_AM

description: NWbAB_ 64

tag: hormone therapy use

tag: medication use

tag: fasting status

tag: days between blood collection and storage


title: Lung, 12h post BSA treatment, biological replicate 3

tag: agent


title: Lung, 12h post HBSS treatment, biological replicate 1

tag: tissue


title: Lung, 12h post BSA treatment, biological replicate 1

tag: strain


title: Lung, 12h post BSA treatment, biological replicate 2

tag: gender


title: CLL CD14+ GI

source_name: CLL CD14+ GI


title: CLL CD14+ RM2

source_name: CLL CD14+ RM2


title: CLL CD14+ RM1

source_name: CLL CD14+ RM1


title: 122758_HB009PA_1/11/07_12:25_PM

description: NWbAB_ 66

tag: rnaextraction date

tag: menopausal status

tag: bmi group

tag: agegroup


title: HB005QI_10/6/06_1:15_PM

description: NWbAB_ 60

tag: rnacc

tag: amplification date

tag: crnacc

tag: arraylot


title: Lung, 12h post MACA treatment, biological replicate 3

source_name: Mouse lung 12h after MACA administration

value: MACA

tag: age


title: CLL CD14+ GS2

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: CLL CD14+ GS2

tag: CD14+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: Lung, 12h post MACA treatment, biological replicate 2


title: HB005QF_10/6/06_1:34_PM

description: NWbAB_ 59

source_name: whole blood

tag: smoking status

tag: hormone therapy use

tag: medication use

tag: fasting status


title: CLL CD14+ FOA

source_name: CLL CD14+ FOA


title: 123377_HB007Y2_8/3/07_11:19_AM

description: NWbAB_ 58

tag: days between blood collection and storage


title: Lung, 12h post MACA treatment, biological replicate 1

tag: agent

tag: tissue

tag: strain

tag: gender


title: 123200_HB007Y1_8/3/07_10:35_AM

description: NWbAB_ 56

tag: rnaextraction date

tag: menopausal status

tag: bmi group

tag: agegroup


title: 124527_HB0086Q_9/11/07_11:31_AM

description: NWbAB_ 53

tag: rnacc

tag: amplification date

tag: crnacc

tag: arraylot


title: 125746_HB00870_9/11/07_12:04_PM

description: NWbAB_ 55

tag: smoking status


title: 123230_HB007XT_8/3/07_10:58_AM

description: NWbAB_ 57

tag: hormone therapy use


title: Lung, 3h post HBSS treatment, biological replicate 2

source_name: Mouse lung 3h after HBSS administration

tag: age


title: Lung, 3h post BSA treatment, biological replicate 3

source_name: Mouse lung 3h after BSA administration


title: Lung, 3h post BSA treatment, biological replicate 2


title: Lung, 3h post HBSS treatment, biological replicate 1


title: 125167_HB0086W_9/11/07_11:47_AM

description: NWbAB_ 54

tag: medication use

tag: fasting status


title: CLL CD19+ GS1

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: CLL CD19+ GS1

tag: CD19+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: CLL CD14+ FM

source_name: CLL CD14+ FM

tag: CD14+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: CLL CD19+ RM2

source_name: CLL CD19+ RM2


title: CLL CD19+ GI

source_name: UHR

source_name: CLL CD19+ GI


title: CLL CD14+ MG

source_name: CLL CD14+ MG


title: 124153_HB00873_9/11/07_11:14_AM

description: NWbAB_ 52

tag: days between blood collection and storage


title: Lung, 3h post HBSS treatment, biological replicate 3

tag: agent

tag: tissue

tag: strain

tag: gender


title: Lung, 3h post BSA treatment, biological replicate 1


title: 123516_HB0086N_9/11/07_10:58_AM

description: NWbAB_ 51

tag: rnaextraction date

tag: rnacc

tag: menopausal status

tag: bmi group

tag: agegroup


title: Lung, 3h post MACA treatment, biological replicate 4

source_name: Mouse lung 3h after MACA administration


title: CLL CD19+ BRF

source_name: CLL CD19+ BRF


title: CLL CD19+ GAI

source_name: CLL CD19+ GAI


title: 123513_HB0086T_9/11/07_10:41_AM

description: NWbAB_ 50

tag: amplification date

tag: crnacc

tag: arraylot

tag: smoking status

tag: hormone therapy use


title: Lung, 3h post MACA treatment, biological replicate 3

tag: age


title: CLL CD19+ FOA

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: CLL CD19+ FOA

tag: CD19+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: 123190_HB0086J_9/11/07_10:08_AM

description: NWbAB_ 48

tag: medication use

tag: fasting status

tag: days between blood collection and storage


title: 123306_HB0086O_9/11/07_10:24_AM

description: NWbAB_ 49


title: CLL CD19+ GS2

source_name: CLL CD19+ GS2


title: Lung, 3h post MACA treatment, biological replicate 1

tag: agent

tag: tissue

tag: strain

tag: gender


title: CLL CD19+ MU

source_name: CLL CD19+ MU

tag: CD19+ CELLS FROM PERIPHERAL BLOOD OF A CLL PATIENT


title: 125886_HB0086Y_9/6/07_12:47_PM

description: NWbAB_ 47

tag: rnaextraction date

tag: rnacc

tag: menopausal status

tag: bmi group

tag: agegroup


title: Lung, 3h post MACA treatment, biological replicate 2


title: nCD19+ NF

source_name: nCD19+ NF

tag: CD19+ CELLS PURIFIED FROM PERIPHERAL BLOOD OF A HEALTHY CONTROL


title: CLL CD19+ BF

source_name: CLL CD19+ BF


title: CLL CD19+ FA1

source_name: CLL CD19+ FA1


title: CLL CD19+ MG

source_name: CLL CD19+ MG


title: 124517_HB0086Z_9/6/07_11:55_AM

description: NWbAB_ 45

source_name: whole blood

tag: amplification date

tag: crnacc

tag: arraylot

tag: smoking status

tag: hormone therapy use


title: 124113_HB0086D_9/6/07_11:02_AM

description: NWbAB_ 44

tag: medication use

tag: fasting status

tag: days between blood collection and storage


title: CLL CD19+ FM

tag: Universal Human Reference RNA (UHR) (Stratagene, Cedar Creek, TX), consisted of equal amount of total RNA from 10 human cancer cell lines, was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Agilent Technologies) in each experiment.

source_name: CLL CD19+ FM


title: 123160_HB0086F_9/6/07_11:34_AM

description: NWbAB_ 42


title: 125338_HB0086R_9/6/07_12:12_PM

description: NWbAB_ 46


title: 123982_HB0086C_9/6/07_10:45_AM

description: NWbAB_ 43

value: peri


title: CLLCEC MU

hyb_protocol: 825 ng of Cy5-labelled cRNA were mixed with the same amount of Cy3-labeled reference cRNA and then cRNA mixtures were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent Technologies). Samples were hybridized for 17 h at 65°C on 4x44K Whole Human Genome Microarray (Agilent Technologies), comprising over 33’000 (60-mer) experimentally validated oligonucleotide probes and then scanned using a confocal laser scanner (Agilent Technologies).

extract_protocol: COMMERCIAL RNA

source_name: CLLCEC MU

tag: CIRCULATING ENDOTHELIAL CELLS FROM CLL PATIENT


title: 123139_HB0086U_9/6/07_11:19_AM

description: NWbAB_ 41


title: 122944_HB00872_9/4/07_2:08_PM

description: NWbAB_ 40


title: CLLCEC GS1

source_name: CLLCEC GS1


title: CLLCEC GS2

source_name: UHR

source_name: CLLCEC GS2


title: 125479_HB0086X_9/6/07_12:29_PM

description: NWbAB_ 39


title: CLLCEC RM2

source_name: CLLCEC RM2


title: 123411_HB0086S_9/4/07_12:25_PM

description: NWbAB_ 36


title: 123501_HB00868_9/4/07_12:45_PM

description: NWbAB_ 37


title: CLLCEC RM1

source_name: CLLCEC RM1


title: CLLCEC GAI

source_name: CLLCEC GAI


title: CLLCEC GI

source_name: CLLCEC GI


title: 123166_HB0086V_9/4/07_12:09_PM

description: NWbAB_ 34


title: 122692_HB00871_9/4/07_1:49_PM

description: NWbAB_ 33


title: 123367_HB0086K_9/4/07_1:04_PM

description: NWbAB_ 35


title: 124622_HB007Z3_8/7/07_12:18_PM

description: NWbAB_ 32


title: CLLCEC FOA

source_name: CLLCEC FOA


title: 124130_HB007Z1_8/7/07_12:02_PM

description: NWbAB_ 31


title: CLLCEC MG

source_name: CLLCEC MG


title: CLLCEC FM

source_name: CLLCEC FM


title: CLLCEC FA1

source_name: CLLCEC FA1


title: CLLCEC BRF

source_name: CLLCEC BRF


title: 123900_HB007ZA_8/7/07_11:23_AM

description: NWbAB_ 30


title: nCEC MM

label_protocol: Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA).

source_name: nCEC MM

extract_protocol: RNeasy Mini Kit (QIAGEN, Valencia, CA, USA).

tag: CIRCULATING ENDOTHELIAL CELLS FROM HEALTHY CONTROL


title: 123277_HB007ZB_8/7/07_10:03_AM

description: NWbAB_ 29

tag: rnaextraction date


title: 123244_HB007ZH_8/7/07_12:35_PM

description: NWbAB_ 28

tag: rnacc


title: 123205_HB007ZF_8/7/07_11:07_AM

description: NWbAB_ 27

tag: menopausal status


title: 122779_HB007ZG_8/7/07_11:43_AM

description: NWbAB_ 26

tag: bmi group


title: Embryonic Drosophila cells, Kc167 cells, Nup98 DamID

city: Amsterdam

first: Maarten

last: Fornerod

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Replicates were averaged: 5378902 (CH1 = Cy5, CH2 = Cy3), 10391502 (CH1 = Cy3, CH2 = Cy5)

hyb_protocol: Arrays were hybridized in a TECAN hybridization station according to NKI Central Microarray Facility protocol (http://cmfdb.nki.nl/process/protocolView).

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel (Red or Green), a variable resolution (5 or 10 um per pixel) and a suitable scan area.

data_processing: Scanned images were processed using NimbleScan software (www.nimblegene.com) using automatic alignment and exported as pair files. Further data processing was done using the Ringo software package (J. Toedling, O. Sklyar, T. Krueger, J. J. Fischer, S. Sperling, and W. Huber. Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics, 8:221, 2007.). Data were normalized within arrays using "loess" normalization and between arrays using "Aquantile" and  log2 transformed. Replicates were averaged using mean values. Data was limited to probes mapped on major chromosomes 2L, 2R, 3L, 3R, X and 4 and duplicate and 100 bp spacing probes were removed. Probes corresponding to Nup98 were removed to avoid plasmid derived signals. Data were smoothed using running medians with windowHalfSize = 1000.

label: Cy3, Cy5

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Nup98

label_protocol: 0.5 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 labelled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. Full length Nup98 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: cell line

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Plasmid pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Embryonic Drosophila cells, Kc167 cells, NDC1 DamID

description: Replicates were averaged: 329740 (CH1 = Cy5, CH2 = Cy3), 329741 (CH1 = Cy3, CH2 = Cy5)

data_processing: Scanned images were processed using NimbleScan software (www.nimblegene.com) using automatic alignment and exported as pair files. Further data processing was done using the Ringo software package (J. Toedling, O. Sklyar, T. Krueger, J. J. Fischer, S. Sperling, and W. Huber. Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics, 8:221, 2007.). Data were normalized within arrays using "loess" normalization and between arrays using "Aquantile" and  log2 transformed. Replicates were averaged using mean values. Data was limited to probes mapped on major chromosomes 2L, 2R, 3L, 3R, X and 4 and duplicate and 100 bp spacing probes were removed. Probes corresponding to NDC1, Nup98 and white were removed to avoid plasmid derived signals. Data were smoothed using running medians with windowHalfSize = 1000.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing NDC1-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. NDC1 was cloned into pCMycDam (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

source_name: Embryonic Drosophila cells, Kc167 cells.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C.

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003). The total genomic DNA was randomly methylated by   partial methylation using recombinant Dam methylase (Biolabs) prior to the DamID enzymatic reactions.


title: 126540_HB007VU_12/5/07_1:11_PM

description: NWbAB_ 21

source_name: whole blood

tag: agegroup


title: 124768_HB007ZE_8/3/07_12:22_PM

description: NWbAB_ 25

tag: amplification date


title: 123543_HB007YT_8/3/07_11:35_AM

description: NWbAB_ 22

tag: crnacc


title: 124004_HB007Z9_8/3/07_11:51_AM

description: NWbAB_ 23

tag: arraylot


title: Embryonic Drosophila cells, Kc167 cells, NPC-tethered Nup98 DamID

description: Replicates were averaged: 5379202 (CH1 = Cy5, CH2 = Cy3), 10397902 (CH1 = Cy3, CH2 = Cy5)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing NDC1-Nup98(1-576)-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23C. NDC1-Nup98(1-576) was cloned into pCMycDam (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) into which as Gateway cassette (Invitrogen) had been inserted in frame. Plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: 124481_HB0086I_9/4/07_1:20_PM

description: NWbAB_ 38

tag: smoking status