title: YPS2066.T194

description:
raw data files: 13615323.gpr, 13615237.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T284

status: Public on Oct 19 2010

type: RNA

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description:
raw data files: 13609232.gpr, 13615246.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf

hyb_protocol: Hybridized slides were incubated for 24–65 hours at 42◦C. Samples were hybridized to 2 dye-swapped microarrays. Unsynchronized MA line transcriptomes were produced with the same design. Corning UltraGAPS glass slides, spotted with the Operon AROS for Saccharomyces cerevisiae, V1.1, were used for all hybridizations. Each microarray targets 6388 protein-coding genes using 2 replicate spots per oligo, yielding 4 technical expression measurements per gene, strain, and timepoint. Slides were prepared for scanning by serial incubation in wash buffers and dried using both a vacuum and high-purity, filtered N2 gas.

scan_protocol: Slides were scanned at 10 μM resolution, 100% power, using an Agilent GenePix 4000B scanning confocal laser microscope. Gain was adjusted manually to optimize signal–noise ratios and to balance channel intensity distributions.

data_processing:
GenePix v6.0 (Agilent) was used for feature identification and subsequent spot quantification per channel. Bad spots were flagged manually for removal from further analysis; otherwise all spots were treated equally in GenePix. Briefly, data were log transformed and normalized for within and between slide normalization, including lowess transformation. Missing data were imputed using a combination of cubic spline interpolation and K-nearest neighbors. Details for data normalization are described in Supplemental materials and methods in the associated manuscript.
Normalized log2 fluorescence intensity of a gene at a particular timepoint of the cell cycle for a particular strain, relative to fluorescence intensity of that gene in a YPD media batch culture of the laboratory strain YPS183 in log phase; values are the average of within-slide (different spots) and between-slide (dye-swap) technical replicate measurements. The complete matrix of normalized data, including imputed expression data for 7 additional Samples (YPS2060.T111, YPS2060.T152, YPS2060.T194, YPS2067.T87, YPS2067.T111, YPS3137.T63, YPS3137.T227) since the overall experiment involves comparison of time series across yeast strains is provided as a supplementary file on the Series record.

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: Invitrogen AlexaFluor 555 and 647 fluorophores were used to label each cDNA sample.

growth_protocol: Strains were inoculated from frozen stock and cultured overnight in SD (synthetic dextrose) minimal medium at 30◦C (225 rpm). The next day cultures were diluted into fresh SD.

extract_protocol: Total RNA was extracted from each frozen cell culture sample using Qiagen’s RNeasy Kit, following manufacturer’s instructions. cDNA was prepared from 15 μg of each RNA sample using SuperScript III reverse transcriptase (Invitrogen) and compared directly to unsynchronized S. cerevisiae cDNA (YPS183 cultured at 30◦C in YPD until reaching OD600 1.1) on 2-channel spotted-oligo glass microarrays in a common reference design.

treatment_protocol: Upon reaching a culture density of OD600 ≈ 0.25, α-factor mating pheromone was added to a final concentration of 4 μM. Cultures were then incubated ≈75 min. until arrested and synchronized in late G1. The state of synchronization was determined by the appearance of < 10% shmoos and < 10% budding cells, visualized by light microscopy (100×, oil). Cultures were released from arrest by removing α-factor: 2× wash with 4◦C S medium (SD without dextrose) and resuspension of cell pellets with fresh 18◦C SD medium. Approximately 25 ml aliquots of each culture were distributed into 18 flasks and incubated at 18◦C (225 rpm). Incubation of cultures at 18◦C in SD medium more than doubles the CDC-period, allowing a more accurate comparison of measurements across strains by reducing temporal sampling variation.

tag: strain

tag: time (min after alpha-factor release)

tag: growth conditions

value: unsynchronized, log phase, YPD


title: YPS2066.T176

description:
raw data files: 13615324.gpr, 13615238.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T345

description:
raw data files: MDUser_13607916.gpr, MDUser_13615277.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T227

description:
raw data files: 13609230.gpr, 13609238.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T0

description:
raw data files: 13614997.gpr, 13615322.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T63

description:
raw data files: 13615319.gpr
raw data file dye swap pattern: X,1
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T218

description:
raw data files: 13609227.gpr, 13609234.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T325

description:
raw data files: MDUser_13615083.gpr, MDUser_13607929.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T48

description:
raw data files: 13615337.gpr, 13615320.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T24

description:
raw data files: 13609160.gpr
raw data file dye swap pattern: 0,X
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T301

description:
raw data files: MDUser_13607915.gpr, 13659913.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2066.T152

description:
raw data files: 13615325.gpr, 13615235.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T251

description:
raw data files: MDUser_13615086.gpr, MDUser_13615082.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T284

description:
raw data files: MDUser_13615084.gpr, MDUser_13607932.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T227

description:
raw data files: MDUser_13607917.gpr
raw data file dye swap pattern: 0,X
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T87

description:
raw data files: MDUser_13615089.gpr, MDUser_13607926.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T63

description:
raw data files: MDUser_13607920.gpr, MDUser_13615279.gpr, 13659912.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T325

description:
raw data files: 13608664.gpr, 13609166.gpr, 13607648.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T176

description:
raw data files: MDUser_13615088.gpr, MDUser_13607924.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T260

description:
raw data files: MDUser_13607918.gpr
raw data file dye swap pattern: 0,X
raw data file platform pattern: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T135

description:
raw data files: MDUser_13615087.gpr, MDUser_13607923.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T301

description:
raw data files: 13608663.gpr, 13607650.gpr, 13607651.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T48

description:
raw data files: MDUser_13615092.gpr, MDUser_13607925.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T227

description:
raw data files: 13607956.gpr, 13608263.gpr, 13607654.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T0

description:
raw data files: MDUser_13615091.gpr, MDUser_13607930.gpr, 13659914.gpr, MDUser_13607922.gpr, MDUser_13607928
raw data file dye swap pattern: 0,1,1,0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T218

description:
raw data files: 13607955.gpr, 13608266.gpr, 13607655.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T218

description:
raw data files: MDUser_13615085.gpr, MDUser_13607921.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T260

description:
raw data files: 13608665.gpr, 13609194.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T251

description:
raw data files: 13608668.gpr, 13614998.gpr, 13607652.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2060.T24

description:
raw data files: MDUser_13607919.gpr, MDUser_13615284.gpr, 13659915.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T87

description:
raw data files: 13613822.gpr, 13608149.gpr, 13607658.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T0

description:
raw data files: 13613477.gpr, 13608159.gpr, 13607663.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T135

description:
raw data files: 13607972.gpr, 13608146.gpr, 13607660.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T63

description:
raw data files: 13613474.gpr, 13608152.gpr, 13607661.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T345

description:
raw data files: 13608661.gpr, 13609165.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T48

description:
raw data files: 13613473.gpr, 13608151.gpr, 13607662.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T24

description:
raw data files: 13613476.gpr, 13608154.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T194

description:
raw data files: 13607966.gpr, 13608265.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T111

description:
raw data files: 13607971.gpr, 13608150.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T284

description:
raw data files: 13608666.gpr, 13609168.gpr, 13607653.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T345

description:
raw data files: 13608167.gpr, 13613785.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T152

description:
raw data files: 13607969.gpr, 13608144.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS2055.T176

description:
raw data files: 13607970.gpr, 13608264.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T260

description:
raw data files: 13608172.gpr, 13613790.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T227

description:
raw data files: 13607744.gpr, 13608171.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T251

description:
raw data files: FGC_13296537.gpr, MDUser_13467612.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T135

description:
raw data files: 13607722.gpr, MDUser_13467625.gpr, 13608175.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2006, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T111

description:
raw data files: 13609084.gpr, 13608178.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T218

description:
raw data files: 13607720.gpr, 13608174.gpr, 13659908.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T176

description:
raw data files: FGC_13296338.gpr, FGC_13291191.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2005
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T284

description:
raw data files: 13608168.gpr, 13613786.gpr, 13659905.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T152

description:
raw data files: 13607721.gpr, 13608176.gpr, 13659907.gpr
raw data file dye swap pattern: 0,1,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T325

description:
raw data files: FGC_13290704.gpr, 13613784.gpr, 13608166.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T301

description:
raw data files: 13608169.gpr, 13613787.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T194

description:
raw data files: 13607719.gpr, 13608173.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T87

description:
raw data files: 13609086.gpr, 13608180.gpr, 13659909.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: Snf5-deficient CD 8+ T-cells Lymphoma; biological replicate 4

city: Boston

first: Boris

middle: G.

last: Wilson

state: MA

address: 44 Binney Street

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from Snf5-deficient lymphomas

hyb_protocol: The cRNA is hybridized to a microarray chip. The bound cRNA is stained with fluorescent streptavidin.

scan_protocol: The microarray chip is then scanned using a laser, and the positions and intensities of the fluorescent emissions are captured. These measurements provide the basis of subsequent biostatistical analysis.

data_processing: Data was analyzed using the Gene Pattern software. RMA normalization.

label: biotin

organism: Mus musculus

source_name: Purified CD8+ T-cells from Snf5-deficient lymphomas

label_protocol: RNA of interest is converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA.

extract_protocol: Total RNA was isolated from MEF and Lymphoma samples using RNA Trizol per the manufacturer’s protocol and Qiagen RNAeasy purification. RNA was hybridized to Affymetrix Mouse 430A 2.0 arrays, and CEL files were preprocessed using Robust Multichip Average (RMA).

tag: age

value: 10-15 week old mice

tag: genotype

tag: cell type

value: CD8+ T-cells


title: Snf5-deficient CD 8+ T-cells Lymphoma; biological replicate 5


title: YPS183.T0

description:
raw data files: 13609090.gpr, 13608181.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T63

description:
raw data files: 13609085.gpr, 13608179.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T48

description:
raw data files: FGC_13296332.gpr, MDUser_13467623.gpr
raw data file dye swap pattern: 0,1
raw data file platform pattern: J.Kim Yeast 2005, J.Kim Yeast 2006
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: YPS183.T24

description:
raw data files: 13609088.gpr, 13608182.gpr, 13659911.gpr
raw data file dye swap pattern: 0,1,0
raw data file platform pattern: J.Kim Yeast 2007, J.Kim Yeast 2007, J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf


title: Snf5-deficient CD 8+ T-cells Lymphoma; biological replicate 3


title: Wild Type CD8+ T-cells; biological replicate 5

description: Gene expression data from CD8+ T-cells

source_name: Purified CD8+ T-cells from WT mice

value: Wild Type


title: Snf5-deficient CD 8+ T-cells Lymphoma; biological replicate 1


title: 19-8

description:
Platform printing: J.Kim Yeast 2007
PROTOCOLS web link: http://kim.bio.upenn.edu/software/yeast-cdc/KimLab_yeast_microarray_protocol.pdf

data_processing:
GenePix v6.0 (Agilent) was used for feature identification and subsequent spot quantification per channel. Bad spots were flagged manually for removal from further analysis; otherwise all spots were treated equally in GenePix. Briefly, data were log transformed and normalized for within and between slide normalization, including lowess transformation. Missing data were imputed using a combination of cubic spline interpolation and K-nearest neighbors. Details for data normalization are described in Supplemental materials and methods in the associated manuscript.
Normalized log2 fluorescence intensity of a gene at a particular timepoint of the cell cycle for a particular strain, relative to fluorescence intensity of that gene in a YPD media batch culture of the laboratory strain YPS183 in log phase; values are the average of within-slide (different spots) and between-slide (dye-swap) technical replicate measurements

growth_protocol: Strains were inoculated from frozen stock and cultured overnight in YPD medium at 30◦C (225 rpm).

treatment_protocol: Upon reaching a culture density of OD600 ≈ 1.0, each culture was placed on dry ice, mixed with 20 ml of −20◦C 100% EtOH in a 50 ml Falcon tube, inverted, and placed immediately into a −80◦C freezer.

tag: growth condition

value: MA line 19-8


title: 19-50

value: MA line 19-50


title: Snf5-deficient CD 8+ T-cells Lymphoma; biological replicate 2


title: 19-6

value: MA line 19-6


title: Wild Type CD8+ T-cells; biological replicate 6

description: Gene expression data from CD8+ T-cells


title: 19-7

value: MA line 19-7


title: Wild Type CD8+ T-cells; biological replicate 4

description: Gene expression data from CD8+ T-cells


title: 19-49

value: MA line 19-49


title: 19-40

value: MA line 19-40


title: Wild Type CD8+ T-cells; biological replicate 3

description: Gene expression data from CD8+ T-cells


title: 19-42

value: MA line 19-42


title: 19-44

value: MA line 19-44


title: 19-45

value: MA line 19-45


title: Wild Type CD8+ T-cells; biological replicate 2

description: Gene expression data from CD8+ T-cells


title: Wild Type CD8+ T-cells; biological replicate 1

description: Gene expression data from CD8+ T-cells


title: 19-27

value: MA line 19-27


title: Snf5 Ezh2-deficient MEFs; biological replicate 1

description: Gene expression data from Snf5 Ezh2-deficient MEFs

source_name: Mouse embryonic fibroblasts

value: Snf5 Ezh2-deficient

value: embryonic fibroblasts


title: 19-25

value: MA line 19-25


title: Wild Type MEFs; biological replicate 3; control for Snf5 Ezh2-deficient MEFs

description: Gene expression data from WT MEFs


title: 19-20

value: unsynchronized, log phase, YPD

value: MA line 19-20


title: 19-28

value: MA line 19-28


title: 19-4

value: MA line 19-4


title: 19-2

value: MA line 19-2


title: 19-22

value: MA line 19-22


title: Snf5 Ezh2-deficient MEFs; biological replicate 2


title: Ezh2-deficient MEFs; biological replicate 2

description: Gene expression data from Ezh2-deficient MEFs


title: 19-21

value: MA line 19-21


title: 19-24

value: MA line 19-24


title: Wild Type MEFs; biological replicate 1; control for Snf5 Ezh2-deficient MEFs

description: Gene expression data from WT MEFs

value: Wild Type


title: Wild Type MEFs; biological replicate 2; control for Snf5 Ezh2-deficient MEFs

description: Gene expression data from WT MEFs


title: 19-19

value: MA line 19-19


title: 19-16

value: MA line 19-16


title: Ezh2-deficient MEFs; biological replicate 3


title: Ezh2-deficient MEFs; biological replicate 1


title: Wild Type MEFs; biological replicate 2; control for Ezh2-deficient MEFs

description: Gene expression data from WT MEFs


title: 19-10

value: MA line 19-10


title: 19-1

value: MA line 19-1


title: 19-15

value: MA line 19-15


title: Wild Type MEFs; biological replicate 3; control for Ezh2-deficient MEFs

description: Gene expression data from WT MEFs


title: Cdkn2a knockout retroviral insertional mutagenesis 9

city: New York

first: Adolfo

middle: A

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Gene expression data from Cdkn2a knock out- Retroviral insertional mutagenesis T-cell lymphoblastic tumor

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

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.

source_name: T-cell lymphoblastic tumor

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

growth_protocol: Cells extracted from T-cell lymphoblastic tumor

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

tag: cells

value: T-cell lymphoblasts

value: TLX1 negative lymphoma


title: Cdkn2a knockout retroviral insertional mutagenesis 6


title: Snf5 Ezh2-deficient MEFs; biological replicate 3

value: Snf5 Ezh2-deficient

value: embryonic fibroblasts


title: Wild Type MEFs; biological replicate 1; control for Ezh2-deficient MEFs

description: Gene expression data from WT MEFs


title: Cdkn2a knockout retroviral insertional mutagenesis 7


title: Cdkn2a knockout retroviral insertional mutagenesis 8


title: Cdkn2a knockout retroviral insertional mutagenesis 5


title: Cdkn2a knockout retroviral insertional mutagenesis 2


title: beta-catenin transgenic 1

description: Gene expression data from beta -catenin T-cell lymphoblastic tumor


title: Ikaros Plastic 3

description: Gene expression data from Ikaros Plastic T-cell lymphoblastic tumor


title: Cdkn2a knockout retroviral insertional mutagenesis 4


title: Ikaros Plastic 1


title: colorectal cancer cell line VACO5

city: John Radcliffe hospital

first: Jenny

last: Wilding

state: Headington, Oxford

address: Weatherall institute of molecular medicine

department: oncology

country: United Kingdom

institute: University of Oxford

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data were normalised and analysed using Partek Genomic Suite software.  Log2 RMA (with GC correction) quantile normalisation with Median Polish.

organism: Homo sapiens

source_name: colorectal cancer cell line, replication error positive

label_protocol: 20 micrograms RNA sent to Molecular biology core facility of the Paterson Institute for Cancer Research.

growth_protocol: DMEM 10% FCS

extract_protocol: samples were extracted using Qiagen Rneasy kit.

tag: cell line

value: colorectal cancer cell line VACO5

tag: genotype/variation

value: Replication error positive (RER+/MSI+)


title: Cdkn2a knockout retroviral insertional mutagenesis 3


title: beta-catenin transgenic 2


title: Cdkn2a knockout retroviral insertional mutagenesis 1


title: Pokemon transgenic 2

description: Gene expression data from Pokemon transgenic T-cell lymphoblastic tumor


title: colorectal cancer cell line SW1222

source_name: colorectal cancer cell line, replication error negative

value: colorectal cancer cell line SW1222

value: Replication error negative (RER-/MSI-)


title: beta-catenin transgenic 3


title: colorectal cancer cell line SW1417

value: colorectal cancer cell line SW1417


title: colorectal cancer cell line RKO

value: colorectal cancer cell line RKO


title: Ikaros Plastic 2


title: colorectal cancer cell line WIDR

value: colorectal cancer cell line WIDR


title: Nup98HoxD13  transgenic 3

description: Gene expression data from Nup98HoxD13 transgenic T-cell lymphoblastic tumor


title: colorectal cancer cell line SKCO1

value: colorectal cancer cell line SKCO1


title: LiPS-57-3

city: Dalian

first: Lan

last: Kang

address: 9 West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

description: biological repeat 3

hyb_protocol: Hybridization, Wash and Stain Kit(Affymetrix, Inc.)

scan_protocol: GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.)

data_processing: GCOS 1.4 software provided by Affymetrix

source_name: inducible pluripotent stem cell derived from mouse embryonic fibroblast using 3 factors

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

growth_protocol: cultured in embryonic stem cell culture medium

extract_protocol: following manufacturer’s recommendation using Trizol reagent (Invitrogen)  WT cDNA Synthesis and Amplification Kit(Affymetrix, Inc.)

value: inducible pluripotent stem cell

tag: protocol

value: with tetraploid embryo complementation competence


title: colorectal cancer cell line PCJW

value: colorectal cancer cell line PCJW


title: colorectal cancer cell line SNUC2B

value: colorectal cancer cell line SNUC2B


title: colorectal cancer cell line SW48

value: colorectal cancer cell line SW48


title: colorectal cancer cell line RCM1

value: colorectal cancer cell line RCM1


title: colorectal cancer cell line Lovo

value: colorectal cancer cell line Lovo


title: LiPS-57-1

description: biological repeat 1


title: LiPS-50-3

description: biological repeat 3

value: without tetraploid embryo complementation competence


title: colorectal cancer cell line LS513

value: colorectal cancer cell line LS513


title: Pokemon transgenic 1

value: T-cell lymphoblasts

value: TLX1 negative lymphoma


title: LiPS-50-2

description: biological repeat 2


title: Nup98HoxD13  transgenic 2


title: Nup98HoxD13  transgenic 1


title: colorectal cancer cell line LS180

value: colorectal cancer cell line LS180

value: Replication error positive (RER+/MSI+)


title: colorectal cancer cell line LS411

value: colorectal cancer cell line LS411


title: LiPS-50-1

description: biological repeat 1


title: rag E2A knockout 2

description: Gene expression data from rag E2A knock out T-cell lymphoblastic tumor


title: colorectal cancer cell line LS174T

value: colorectal cancer cell line LS174T


title: LiPS-47-2

description: biological repeat 2


title: rag E2A knockout 1


title: colorectal cancer cell line HRA19

value: colorectal cancer cell line HRA19

value: Replication error negative (RER-/MSI-)


title: LiPS-57-2

description: biological repeat 2

value: inducible pluripotent stem cell


title: colorectal cancer cell line HT29

value: colorectal cancer cell line HT29


title: LiPS-47-3

description: biological repeat 3


title: colorectal cancer cell line Gp2d

value: colorectal cancer cell line Gp2d


title: LiPS-47-1

description: biological repeat 1


title: colorectal cancer cell line Lim1863

value: colorectal cancer cell line Lim1863


title: colorectal cancer cell line HCT116

value: colorectal cancer cell line HCT116


title: colorectal cancer cell line HCT15

value: colorectal cancer cell line HCT15


title: colorectal cancer cell line Colo741

value: colorectal cancer cell line Colo741


title: colorectal cancer cell line HCA7

value: colorectal cancer cell line HCA7


title: E2A knockout 2

description: Gene expression data from E2A knock out T-cell lymphoblastic tumor


title: colorectal cancer cell line NCIH716

value: colorectal cancer cell line NCIH716


title: colorectal cancer cell line CC20

value: colorectal cancer cell line CC20


title: colorectal cancer cell line DLD1

value: colorectal cancer cell line DLD1


title: olig1-LMO1 double transgenic 2

description: Gene expression data from olig1-LMO1 double transgenic T-cell lymphoblastic tumor

value: T-cell lymphoblasts

value: TLX1 negative lymphoma


title: E2A knockout 1


title: colorectal cancer cell line CCK81

value: colorectal cancer cell line CCK81

value: Replication error positive (RER+/MSI+)


title: colorectal cancer cell line C84

value: colorectal cancer cell line C84


title: LiPS-45-1

description: biological repeat 1

value: with tetraploid embryo complementation competence


title: olig1-LMO1 double transgenic 3


title: LiPS-45-3

description: biological repeat 3

value: inducible pluripotent stem cell


title: colorectal cancer cell line C99

value: colorectal cancer cell line C99

value: Replication error negative (RER-/MSI-)


title: LiPS-45-2

description: biological repeat 2


title: olig1-LMO1 double transgenic 1


title: RTX12 T12

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description: twenty patients with ra (17 women and 3 men, average age +/- sem: 52,6+/-3,8 years) were included in the study. All patients met the American College of Rheumatology classification criteria for the diagnosis of RA. All patients had active disease at the time of tissue sampling and were resistant to TNF blockade. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All of them had a swollen knee at inclusion. Rituximab therapy was administrated at a dose of 1,000 mg IV at baseline (T0) and at week 2, together with 125 mg IV Methylprednisolone. Clinical parameters at baseline (T0) and 12 weeks after the initiation of therapy (T12) was evaluated using DAS(28)-CRP scores and clinical responses were assessed using EULAR response criteria. Synovial biopsies were obtained by needle-arthroscopy of an affected knee from all patients at T0 and T12. For each procedure, 4 to 8 synovial samples were kept overnight at 4°C in a RNA stabilizing solution (RNALater, Ambion, Applied Biosystems, TX, USA) and then stored at –80°C for later RNA extraction. The same amount of tissue was snap-frozen in liquid nitrogen and kept at –80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formaldehyde and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation. The study was approved by the ethics committee of the Université catholique de Louvain and informed consent was obtained from all patients.

hyb_protocol: GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides, grouped in 54,675 probe sets informative for about 47,000 transcripts originated from not less than 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°C in monoplicates with 10 µg cRNA.

scan_protocol: The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.

data_processing: For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 40 and 50% on each slide. After scaling of all probe sets to a value of 100, the range of the reported amplification scales was between 0,8 and 6,7. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GADPDH 3’/5’ ratio < 2.3 in all the slides) were indicative of the good quality of the amplification and hybridization procedures.

label: Biotin

source_name: Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Poor-responder).

label_protocol: Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E.Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35 -minute incubation at 95°C.

extract_protocol: Samples stored at –80°C after overnight incubation in RNALater were used for the microarray hybridizations. Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. At least 1 µg total RNA could be extracted from 12 paired samples at T0 and T12 for further processing. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent technologies Inc).

tag: treatment

value: 12 weeks of RTX therapy

tag: gender

value: F

tag: age (y)

tag: sample type

value: synovial knee biopsy

tag: disease state

value: rheumatoid arthritis

tag: response

value: EULAR Poor-responder

tag: tissue

value: synovium


title: Tal1-LMO2 double transgenic 3

description: Gene expression data from Tal1-LMO2 double transgenic T-cell lymphoblastic tumor


title: RTX11 T0

value: baseline


title: Tal1-LMO2 double transgenic 2


title: RTX11 T12


title: Tal1-LMO2 double transgenic 1


title: RTX9 T12

source_name: Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Moderate-responder).

value: EULAR Moderate-responder


title: LMO1 transgenic 3

description: Gene expression data from LMO1 T-cell lymphoblastic tumor

value: T-cell lymphoblasts


title: RTX12 T0


title: colorectal cancer cell line C80

value: colorectal cancer cell line C80


title: Hippocampus_DKO_1wk

city: Nashville

first: Lindsay

last: Wieczorek

state: TN

address: 1115 Light Hall

department: Pediatrics

institute: Vanderbilt University

hyb_protocol: Following fragmentation, cDNA was hybridized for 17 hr at 45C on Mouse 1.0ST Gene Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G Plus Targeted Genotyping System.

data_processing: Expression Console (Affymetrix ver. 1.1) was used for normalizatin (RMA) and primary data analysis

source_name: Hippocampus, DKO, 1wk

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA.

extract_protocol: Qiagen miRNAeasy Mini Kit (Cat #74104) was used to obtain total RNA

treatment_protocol: baseline (no treatment); conditioned fear mice: one 0.7mA x 2sec shock

tag: strain

value: AC1 and AC8 knock-out (DKO)

tag: sex

value: male

value: hippocampus


title: RTX10 T12

value: M


title: Hippocampus_WT_1wk

source_name: Hippocampus, WT, 1wk

value: wild type

tag: age


title: RTX9 T0


title: Amygdala_WT_1wk

source_name: Amygdala, WT, 1wk

value: amydgdala


title: RTX10 T0


title: Amygdala_DKO_1wk

source_name: Amygdala, DKO, 1wk


title: Hippocampus_DKO_48hr

source_name: Hippocampus, DKO, 48hr


title: LMO1 transgenic 1

tag: genotype

value: TLX1 negative lymphoma


title: RTX8 T12

value: 12 weeks of RTX therapy


title: Tal1 transgenic 2

description: Gene expression data from Tal1 T-cell lymphoblastic tumor


title: RTX8 T0

value: F


title: Amygdala_DKO_48hr

source_name: Amygdala, DKO, 48hr


title: RTX7 T12

value: synovial knee biopsy


title: RTX6 T0

value: rheumatoid arthritis


title: Tal1 transgenic 1


title: LMO1 transgenic 2


title: RTX7 T0


title: RTX6 T12


title: Hippocampus_DKO_1hr

source_name: Hippocampus, DKO, 1hr


title: Amygdala_WT_48hr

source_name: Amygdala, WT, 48hr


title: WT_MEFs_Ezh2

type: genomic

hyb_protocol: ~ 2ug of labeled DNA were hybridized for 16 hr at 45C on tiling arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The MAT algorithm (Johnson et al., 2006) was used to identify promoters enriched in ChIP experiments with a p-value threshold being set at 1× 10-4 in MEFs and 1× 10-6 in cerebellum.
Note: Controls 183WTMEFInput_MmP.CEL and 183WTMEFInput_MmPa.CEL are identical, 1Snf5MEFInput_MmP.CEL are 1Snf5MEFInput_MmPa.CEL identical

molecule: genomic DNA

source_name: Ezh2 ChIP DNA from WT MEFs

label_protocol: Eluate and Input DNA was digested to 50-100bp fragments using DNAseI and labeled with biotin using TdT.

growth_protocol: MEFs were harvested at embryonic day 13.5 and cultured in Dulbecco’s modified eagle media (DMEM) supplemented with 10% fetal bovine serum (FBS) and non-essential amino acids.

extract_protocol: For the cross-linking procedure, ~1X107 cells are crosslinked using formaldehyde (1%)(Sigma,#F8775) for 15 minutes in PBS at room  temperature. MEFs were scraped off the plate after crosslinking into PBS + 2×protease inhibitors (Complete, Mini,  EDTA-free Roche; cat. #11836170001) and frozen directly as a cell pellet at -80C. Cerebellar were crosslinked as a suspension. Cells were then lysed  using 400 µl of lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris (pH 8.0)) + protease inhibitors for 10  minutes on ice and sonicated 3× for 8 to 10 second pulses on power setting 3 using the sonic dismembrator  (Fisher; Model 100). Supernatants were collected after centrifugation for 10 minutes at 18,000 r.c.f. Sonicated  extracts were combined with a mixture of protein A (Invitrogen; 100.01D) + protein G (Invitrogen; 100.03D)  dynal beads coupled to antibodies and incubated over night at 4°C.  Beads were then washed 1× with buffer1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl(pH 8.0),  500mM NaCl), 1× with buffer 2 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl(pH 8.0), 150 mM  NaCl), 1× with LiCl wash buffer (20mM Tris-HCl (pH 8.0), 2mM EDTA, 0.7% NaDOC, 1% NP-40, 0.5M  LiCl), and 2× TE (10 mM Tris (pH 8.0), 1mM EDTA). DNA was then eluted 2× for 30 minutes at room  temperature in 100µl of 1% SDS + 0.1M NaHCO3. Eluated DNA was RNAse treated, proteinase K treated, and  crosslinks were reversed overnight at 65C in 0.2M NaCl. This mixture was then subjected to phenol chloroform  extraction and ethanol precipitation.

value: WT

tag: cell type

value: MEFs

tag: antibody

tag: antibody manufacturer

value: Millipore

tag: antibody catalog #

tag: antibody lot #

source_name: Input DNA from WT MEFs


title: RTX4 T0

data_processing: For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 40 and 50% on each slide. After scaling of all probe sets to a value of 100, the range of the reported amplification scales was between 0,8 and 6,7. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GADPDH 3’/5’ ratio < 2.3 in all the slides) were indicated of the good quality of the amplification and hybridization procedures.

value: baseline

value: EULAR Moderate-responder

value: synovium


title: RTX3 T0

source_name: Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Good-responder).

value: EULAR Good-responder


title: RTX3 T12


title: RTX5 T0

source_name: Human synovial biopsies from the knee of a patient with severe rheumatoid arthritis


title: Amygdala_DKO_1hr

source_name: Amygdala, DKO, 1hr

tag: genotype/variation

value: AC1 and AC8 knock-out (DKO)

value: male


title: Snf5-deficient_MEFs_Ezh2

source_name: Ezh2 ChIP DNA from Snf5-deficient MEFs

source_name: Input DNA from Snf5-deficient MEFs


title: RTX4 T12

tag: treatment

value: M


title: Hippocampus_WT_1hr

source_name: Hippocampus, WT, 1hr

value: wild type

value: hippocampus


title: RTX5 T12

source_name: Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Moderate-responder).

tag: gender


title: Hippocampus_WT_48hr

source_name: Hippocampus, WT, 48hr


title: RTX2 T0

tag: age (y)


title: Snf5-deficient_MEFs_H3K27me3

source_name: H3K27me3 ChIP DNA from Snf5-deficient MEFs

value: Upstate


title: Amygdala_WT_1hr

source_name: Amygdala, WT, 1hr

value: amydgdala


title: RTX2 T12

value: 12 weeks of RTX therapy

value: F

tag: sample type


title: Cerebellum_H3K27me3

source_name: H3K27me3 ChIP DNA from Cerebellum

value: 7-14 days old mice

value: Cerebellum

source_name: Input DNA from Cerebellum


title: WT_MEFs_H3K27me3

source_name: H3K27me3 ChIP DNA from WT MEFs

value: WT

value: MEFs


title: Pten knockout 6

description: Gene expression data from Pten knock T-cell lymphoblastic tumor

source_name: T-cell lymphoblastic tumor

tag: cells

value: T-cell lymphoblasts

value: TLX1 negative lymphoma


title: RTX1 T0

value: baseline

value: synovial knee biopsy

tag: disease state

value: rheumatoid arthritis

tag: response

value: synovium


title: Hippocampus_DKO_0hr

source_name: Hippocampus, DKO, 0hr

tag: strain

value: AC1 and AC8 knock-out (DKO)

value: male

tag: tissue


title: ThPOK transgenic 2

description: Gene expression data fromThPOK transgenic T-cell lymphoblastic tumor


title: RTX1 T12

value: EULAR Good-responder


title: ThPOK transgenic 3


title: Pten knockout 5


title: ThPOK transgenic 1


title: Amygdala_DKO 0hr

source_name: Amygdala, DKO 0hr

tag: sex

tag: age


title: Pten knockout 4

tag: genotype


title: Hippocampus_WT_0hr

source_name: Hippocampus, WT, 0hr

value: wild type

value: hippocampus


title: Hippocampus_DKO_Baseline

source_name: Hippocampus, DKO, Baseline


title: Amygdala_WT_0hr

source_name: Amygdala, WT, 0hr

value: amydgdala


title: Amygdala_DKO_Baseline

source_name: Amygdala, DKO, Baseline


title: Pten knockout 2


title: Pten knockout 1


title: Pten knockout 3


title: Liver tissue, high-CLA diet, biological replicate 7

city: Dublin

first: Helen

middle: M

last: Roche

state: Belfield

address: UCD Conway Institute of Biomolecular and Biomedical Research

country: Ireland

institute: University College Dublin

description: Gene expression data from liver tissue of ob/ob mice fed a high-CLA diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were processed using the affy and gcrma libraries in the R statistical software, using gcrma background correction and normalization.

source_name: Liver tissue from mice fed a diet with high-CLA beef

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

growth_protocol: 4 week old male, ob/ob (C57BL/6J) mice were exposed to 12 hrs light/ 12 hrs dark cycles, and maintained at a constant temperature of 22 degrees Celcius.

extract_protocol: RNA was later extracted using a Qiagen Rneasy extraction kit, according to the manufacturer extraction protocol.

treatment_protocol: Test diet blends were prepared by mixing low- or high-CLA beef at a 36% inclusion rate to equal portions of wheat feed and maize (corn) feed.  Final feeds were prepared by mixing 100ml warm water with 100g test diet blend. Dietary food intake was measured daily and the animals received freshly prepared food each day.

value: liver tissue

value: ob/ob

value: high-CLA diet


title: Liver tissue, high-CLA diet, biological replicate 4


title: Liver tissue, control diet, biological replicate 3

description: Gene expression data from liver tissue of ob/ob mice fed a low-CLA control diet

source_name: Liver tissue from mice fed a diet with low-CLA beef

value: control diet


title: Liver tissue, high-CLA diet, biological replicate 5


title: Liver tissue, high-CLA diet, biological replicate 3


title: Amygdala_WT_Baseline

data_processing: Expression Console (Affymetrix, ver. 1.1) was used for normalizatin (RMA) and primary data analysis

source_name: Amygdala, WT, Baseline


title: Liver tissue, high-CLA diet, biological replicate 2


title: Liver tissue, control diet, biological replicate 5


title: Liver tissue, high-CLA diet, biological replicate 1


title: Liver tissue, high-CLA diet, biological replicate 6


title: p53 knockout 2

description: Gene expression data from p53 knock outT-cell lymphoblastic tumor


title: Liver tissue, control diet, biological replicate 7


title: Muscle tissue, high-CLA diet, biological replicate 6

description: Gene expression data from skeletal muscle tissue of ob/ob mice fed a high-CLA diet

source_name: Skeletal muscle tissue from mice fed a diet with high-CLA beef

value: skeletal muscle tissue


title: TLX1 transgenic 5

description: Gene expression data from Tlx1 transgenic T-cell lymphoblastic tumor

value: T-cell lymphoblasts

value: TLX1 positive lymphoma


title: TLX1 transgenic 6


title: p53 knockout 3

value: TLX1 negative lymphoma


title: p53 knockout 1


title: Liver tissue, control diet, biological replicate 2


title: Liver tissue, control diet, biological replicate 4


title: Liver tissue, control diet, biological replicate 6


title: Hippocampus_WT_Baseline

source_name: Hippocampus, WT, Baseline


title: Liver tissue, control diet, biological replicate 1


title: TLX1 transgenic 4


title: Muscle tissue, high-CLA diet, biological replicate 4


title: Muscle tissue, high-CLA diet, biological replicate 5


title: Muscle tissue, control diet, biological replicate 6

description: Gene expression data from skeletal muscle tissue of ob/ob mice fed a low-CLA control diet

source_name: Skeletal muscle tissue from mice fed a diet with low-CLA beef


title: Muscle tissue, high-CLA diet, biological replicate 2


title: Muscle tissue, control diet, biological replicate 5


title: Muscle tissue, high-CLA diet, biological replicate 1


title: Muscle tissue, high-CLA diet, biological replicate 3


title: TLX1 transgenic 1


title: Muscle tissue, control diet, biological replicate 3


title: TLX1 transgenic 2


title: Muscle tissue, control diet, biological replicate 4


title: 1 ug/ml endotoxin stimulation at 2 hours-biological rep 2

city: Ames

first: Susan

middle: J

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

description: SAMPLE 16 (2-1-2)(time-dose-rep)

hyb_protocol: The reagents for hybridization, wash and stain were also purchased from Affymetrix (Part No: 900720). The hybridization was conducted at 45oC for 16 hours in a GeneChip® hybridization oven 640 with constant rotation at 60 rpm. The arrays were washed and stained in the GeneChip® fludics station 450

scan_protocol: scanned with GeneChip® scanner 3000 7G. Affymetrix® GeneChip® Operation Software (GCOS) was used to control the fludics stations and scanner and to generate generic data (.DAT) files, probe cell intensity data (.CEL) files, and the Probe-level summarization (.CHP) files..

data_processing: Data were normalized and expression measures computed using the Robust Multiarray Average (RMA) method (Irizarry et al., 2003), Bioconductor package 'affy.' A linear model with fixed effects for replications, endotoxin doses, times, and interactions between doses and times were fit to the expression data for each gene using the R package limma (Smyth, 2004, 2005). As part of each linear model analysis, P-values were obtained for the test for dose-by-time interaction, the test for changes over time within endotoxin dose groups, and the test for a dose effect at each time point.  The P-values for each test were converted to q-values for false discovery rate estimation using the method of Nettleton et al. (2006).

organism: Gallus gallus

source_name: chicken macrophages

label_protocol: Samples were labeled with the GeneChip® 3' IVT Express Kit (Affymetrix, part number 901229)

growth_protocol: HD11 cells were cultured in RPMI 1640 medium (Sigma) supplemented with 10% heat-inactivated newborn calf serum, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 100 U/ml penicillin, 100 μg/ml streptomycin, 10 mM HEPES and 5 × 10−5 M 2-mercaptoethanol (pH 7.3) at 41 °C and 5% CO2.

extract_protocol: Total RNA was isolated using RNAquous© (Ambion, Austin, TX) according to manufacturer's instructions

treatment_protocol: cell were treated with 1 ug/ ml of endotoxin from Salmonella typhimurium-798 for 1, 2, 4 and 8 hours

tag: cell line

value: macrophage cell line HD-11

tag: agent

value: endotoxin

tag: time

value: 2 hours


title: 1 ug/ml endotoxin stimulation at 8 hours-biological rep 3

description: SAMPLE 18 (8-1-3)(time-dose-rep)

value: 8 hours


title: 1 ug/ml endotoxin stimulation at 1 hours-biological rep 3

description: SAMPLE 19 (1-1-3)(time-dose-rep)

value: 1 hour


title: Injury-4hrs (251506410306_1_2)

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: spinal cord, 5mm distal to lesion site, pooled from 5 animals

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Agilent feature extraction (version 9.5.3.1 3) followed by importing into GeneSpring GX 7

organism: Danio rerio

source_name: Spinal cord, 5mm caudal from lesion site

label_protocol: NuGEN WT-Ovation kit

growth_protocol: Before surgery fish were kept in groups of 10 under conditions of 14 hrs light/10 hrs dark, after surgery, kept individually

extract_protocol: Spinal cord segments, dissected 5mm caudal from injury site, were pooled from 5 animals and prepared using Qiagen RNeasy Micro Kit.

treatment_protocol: Spinal cord transection performed on anesthetized (0.033% aminobenzoic acid ethymethylester, MS222) between two vertebraa at a level halfway between dorsal fin and operculum, about 4 mm caudal to brainstem/spinal cord transitional zone.  Wounds were sealed with Histacryl.  Control treatment (sham injury) was performed by making the incision without spinal cord lesion.

value: spinal cord

value: injury

value: 6 months


title: Muscle tissue, control diet, biological replicate 1

value: male


title: 1 ug/ml endotoxin stimulation at 2 hours-biological rep 3

description: SAMPLE 20 (2-1-3)(time-dose-rep)


title: BAT from per2-/- mice, biological rep1

city: Irvine

first: benedetto

last: grimaldi

state: CA

address: 2226B Gillespie NRF

department: pharmacology

institute: university of california, irvine

description: Gene expression data from BAT of 20-week-old per2-/- mouse.

hyb_protocol: Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45°C with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix array.  The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and the cell intensities (*.DAT and *.CEL files) were obtained using Affymetrix’s GeneChip Operating Software, Ver. 1.4 (GCOS).

data_processing:
The PLIER (Probe Logarithmic Intensity ERror) algorithm developed by Affymetrix was used.
Data were analyzed with Cyber-T software (http://cybert.microarray.ics.uci.edu/).

source_name: BAT from 20-week-old per2-/- mouse

label_protocol: The fragmented single-stranded DNA was end-labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Per2-/- and per2+/+ mice (Bae et al., 2001) were grown under 12 hr light/12 hr dark (LD) cycles.

extract_protocol: Total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNA was quantified (Nanodrop 1000) with a portion of the recovered total RNA adjusted to a final concentration of 250ng/ul.

treatment_protocol: All mice were fed a chow diet (ProLab RMH2500 5P14) ad libitum.

value: 20 weeks

value: fresh brown adipose tissue


title: BAT from per2+/+ mice, biological rep3

description: Gene expression data from BAT of 20-week-old per2+/+ mouse.

source_name: BAT from 20-week-old per2+/+ mouse


title: BAT from per2-/- mice, biological rep2


title: 0 ug/ml endotoxin stimulation 4 hours-biological rep 2

description: SAMPLE 15 (4-0-2)(time-dose-rep)

value: untreated

value: 4 hours


title: TLX1 transgenic 3

source_name: T-cell lymphoblastic tumor


title: Injury-4hrs (251506410306_1_3)


title: BAT from per2-/- mice, biological rep3


title: Injury-4hrs (251506410306_1_1)


title: Muscle tissue, control diet, biological replicate 2

value: skeletal muscle tissue

value: ob/ob

value: control diet


title: 1 ug/ml endotoxin stimulation at 4 hours-biological rep 3

description: SAMPLE 17 (4-1-3)(time-dose-rep)


title: Injury-12hrs (251506410305_1_4)


title: Adipose tissue, high-CLA beef diet, biological replicate 5

description: Gene expression data from subcutaneous adipose tissue of ob/ob mice fed a high-CLA diet

source_name: Subcutaneous adipose tissue from mice fed a diet with high-CLA beef

value: subcutaneous adipose tissue

value: high-CLA beef diet diet


title: Control-4hrs (251506410306_1_4)

value: sham injury (control)


title: 0 ug/ml endotoxin stimulation 8 hours-biological rep 2

description: SAMPLE 13 (8-0-2)(time-dose-rep)

value: macrophage cell line HD-11


title: 0 ug/ml endotoxin stimulation 2 hours-biological rep 2

description: SAMPLE 14 (2-0-2)(time-dose-rep)

value: 2 hours


title: 1 ug/ml endotoxin stimulation at 4 hours-biological rep 2

description: SAMPLE 10 (4-1-2)(time-dose-rep)

value: endotoxin


title: BAT from per2+/+ mice, biological rep2


title: Control-4hrs (251506410305_1_2)

value: spinal cord


title: Adipose tissue, high-CLA beef diet, biological replicate 6


title: WAT from per2-/- mice, biological rep2

description: Gene expression data from WAT of 20-week-old per2-/- mouse.

source_name: WAT from 20-week-old per2-/- mouse

value: fresh white adipose tissue


title: Injury-12hrs (251506410305_1_3)

value: injury

value: 6 months


title: Adipose tissue, high-CLA beef diet, biological replicate 2

value: male


title: BAT from per2+/+ mice, biological rep1

value: 20 weeks

value: fresh brown adipose tissue


title: Adipose tissue, high-CLA beef diet, biological replicate 3


title: WAT from per2-/- mice, biological rep3


title: 1 ug/ml endotoxin stimulation at 1 hours-biological rep 2

description: SAMPLE 12 (1-1-2)(time-dose-rep)

value: 1 hour


title: 0 ug/ml endotoxin stimulation at 1 hour-biological rep 2

description: SAMPLE 11 (1-0-2)(time-dose-rep)

value: untreated


title: WAT from per2-/- mice, biological rep1


title: WAT from per2+/+ mice, biological rep3

description: Gene expression data from WAT of 20-week-old per2+/+ mouse.

source_name: WAT from 20-week-old per2+/+ mouse


title: 1 ug/ml endotoxin stimulation at 2 hours-biological rep 1

description: SAMPLE 8 (2-1-1)(time-dose-rep)


title: Control-12hrs (251506410304_1_3)


title: WAT from per2+/+ mice, biological rep2


title: Adipose tissue, high-CLA beef diet, biological replicate 1

value: ob/ob


title: Adipose tissue, high-CLA beef diet, biological replicate 4


title: Control-4hrs (251506410305_1_1)


title: 1 ug/ml endotoxin stimulation at 8 hours-biological rep 2

description: SAMPLE 9 (8-1-2)(time-dose-rep)

value: 8 hours


title: Adipose tissue, control diet, biological replicate 7

description: Gene expression data from subcutaneous adipose tissue of ob/ob mice fed a low-CLA control diet

source_name: Subcutaneous adipose tissue from mice fed a diet with low-CLA beef

value: subcutaneous adipose tissue

value: control diet


title: Adipose tissue, control diet, biological replicate 5


title: Injury-264hrs (251506410303_1_2)


title: Control-264hrs (251506410303_1_4)

value: sham injury (control)


title: Adipose tissue, control diet, biological replicate 6


title: Adipose tissue, control diet, biological replicate 4


title: 0 ug/ml endotoxin stimulation at 4 hours- biological rep 1

description: SAMPLE 7 (4-0-1)(time-dose-rep)

value: macrophage cell line HD-11

value: 4 hours


title: 1 ug/ml endotoxin stimulation at 4 hours-biological rep 1

description: SAMPLE 6 (4-1-1)(time-dose-rep)

value: endotoxin


title: Control-12hrs (251506410304_1_2)

value: spinal cord


title: 0 ug/ml endotoxin stimulation at 2 hr-biological rep 1

description: SAMPLE 3 (2-0-1)(time-dose-rep)

value: 2 hours


title: Control-264hrs (251506410303_1_3)


title: 1 ug/ml endotoxin stimulation at 8 hours-biological rep 1

description: SAMPLE 5 (8-1-1)(time-dose-rep)


title: Injury-264hrs (251506410302_1_2)


title: Adipose tissue, control diet, biological replicate 3


title: Injury-12hrs (251506410304_1_1)

value: injury


title: Injury-264hrs (251506410303_1_1)

value: 6 months


title: bone at 14d

city: Matsdo

first: Jian

last: Zhao

address: 2-870-1 Sakaecho-nishi

country: Japan

institute: Nihon University School of Dentistry at Matsudo

description: Gene expression data from beagle dog mandible

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Canine_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Ò Scanner 3000

data_processing:
The data were analyzed using GeneChip Operating Software (Affymetrix, Santa Clara, CA), and imported into GeneSpring GX software (Agilent Technologies, Inc Santa Clara, CA) for selection of induced and repressed genes in each expriment. Each measurement was divided by the 50.0th percentile of all measurements in that sample.
Signal calculated by GeneSpring GX software.

organism: Canis lupus familiaris

source_name: beagle dog mandible

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: After premolars extraction, there are 3 months healing in beagle dog mandibles.

extract_protocol: Total RNA was isolated from bone biopsies with the Rneasy Fibrous Tissue Mini Kit according to the manufacturer's protocol.

treatment_protocol: And then drill the holes (4.5 mm diameter, 8 mm length) in beagle dog mandibles, implant with and without beta-TCP. At 4-, 7-, 14-day, cylindrical specimens (4.5 mm diameter, 8 mm length) were collected from beagle dog mandibles.

value: mandible

tag: treatment time

value: 14 days

value: 9 year old


title: Adipose tissue, control diet, biological replicate 2

value: male


title: Injury-264hrs (251506410302_1_1)


title: bone implanted b-TCP at 14d

description: Gene expression data from beagle dog mandible implanted with beta-TCP

value: beta-TCP


title: 0 ug/ml endotoxin stimulation at 8 hours-biological rep 1

description: SAMPLE 2 (8-0-1)(time-dose-rep)

value: untreated


title: 1 ug/ml endotoxin stimulation at 1 hours-biological rep 1

description: SAMPLE 1 (1-1-1) (time-dose-rep)

value: 1 hour


title: bone implanted b-TCP at 7d

value: 7 days


title: 0 ug/ml endotoxin stimulation at 1 hour-biological rep 1

description: SAMPLE 4 (1-0-1)(time-dose-rep)


title: bone at 4d

value: 4 days


title: Adipose tissue, control diet, biological replicate 1

value: subcutaneous adipose tissue

value: ob/ob

value: control diet


title: WAT from per2+/+ mice, biological rep1

value: 20 weeks

value: fresh white adipose tissue


title: HMCL-KMS12

status: Public on Oct 18 2010

city: Sutton

first: Brian

last: Walker

address: 15 Cotswold Road

department: Haemato-Oncology Research Unit

institute: The Institute of Cancer Research

description: bisulfite modified genomic DNA

data_processing: files were analyzed in GenomeStudio (Illumina) as per manufacturers (Illumina) instructions using the methylation module v1.5.5, and are described as beta values

label: DNP/biotin

source_name: Cell line

growth_protocol: cell lines were grown in RPMI media with 10% FCS

extract_protocol: DNA was extracted using the AllPrep protocol (Qiagen)

treatment_protocol: all cells were derived from patients prior to treatment with chemotherapy

value: bone marrow

tag: cell type

value: MGUS plasma cell


title: HMCL-U266

description: bisulfite modified genomic DNA

hyb_protocol: as per manufacturers (Illumina) instructions


title: HMCL-RPMI8266

description: bisulfite modified genomic DNA

scan_protocol: as per manufacturers (Illumina) instructions


title: HMCL-MM1s

description: bisulfite modified genomic DNA

label_protocol: as per manufacturers (Illumina) instructions

value: Multiple myeloma plasma cell


title: HMCL-KMS11

description: bisulfite modified genomic DNA


title: Plasma cell-1

description: bisulfite modified genomic DNA

source_name: CD138+ bone marrow cells

value: peripheral blood

value: Plasma cell leukaemia cell


title: Plasma cell leukaemia-6

description: bisulfite modified genomic DNA

source_name: CD138+ peripheral blood


title: HMCL-LP1

description: bisulfite modified genomic DNA


title: Plasma cell-3

description: bisulfite modified genomic DNA


title: bone at 7d

value: mandible

tag: treatment

value: 9 year old


title: Plasma cell leukaemia-4

description: bisulfite modified genomic DNA


title: bone implanted b-TCP at 4d

value: beta-TCP


title: HMCL-KMS26

description: bisulfite modified genomic DNA


title: Plasma cell-2

description: bisulfite modified genomic DNA


title: Plasma cell leukaemia-5

description: bisulfite modified genomic DNA


title: Myeloma-159

description: bisulfite modified genomic DNA

tag: myeloma translocation

value: Not known


title: Myeloma-161

description: bisulfite modified genomic DNA


title: Plasma cell leukaemia-2

description: bisulfite modified genomic DNA


title: Plasma cell leukaemia-1

description: bisulfite modified genomic DNA


title: Myeloma-158

description: bisulfite modified genomic DNA


title: Plasma cell leukaemia-3

description: bisulfite modified genomic DNA


title: HMCL-MM1r

description: bisulfite modified genomic DNA


title: Myeloma-157

description: bisulfite modified genomic DNA


title: Plasma cell leukaemia-7

description: bisulfite modified genomic DNA


title: Myeloma-156

description: bisulfite modified genomic DNA


title: Myeloma-153

description: bisulfite modified genomic DNA


title: Myeloma-154

description: bisulfite modified genomic DNA


title: Myeloma-160

description: bisulfite modified genomic DNA


title: HMCL-H929

description: bisulfite modified genomic DNA


title: Myeloma-155

description: bisulfite modified genomic DNA


title: Myeloma-152

description: bisulfite modified genomic DNA


title: Myeloma-149

description: bisulfite modified genomic DNA


title: Myeloma-145

description: bisulfite modified genomic DNA


title: Myeloma-142

description: bisulfite modified genomic DNA


title: Myeloma-147

description: bisulfite modified genomic DNA


title: Control-12hrs (251506410304_1_4)

value: spinal cord

value: sham injury (control)

value: 6 months


title: Myeloma-150

description: bisulfite modified genomic DNA


title: Myeloma-144

description: bisulfite modified genomic DNA


title: Myeloma-151

description: bisulfite modified genomic DNA


title: Myeloma-137

description: bisulfite modified genomic DNA


title: Myeloma-146

description: bisulfite modified genomic DNA


title: Myeloma-140

description: bisulfite modified genomic DNA


title: Myeloma-143

description: bisulfite modified genomic DNA


title: Myeloma-139

description: bisulfite modified genomic DNA


title: Myeloma-148

description: bisulfite modified genomic DNA


title: Myeloma-132

description: bisulfite modified genomic DNA


title: Myeloma-138

description: bisulfite modified genomic DNA


title: Myeloma-134

description: bisulfite modified genomic DNA


title: Myeloma-136

description: bisulfite modified genomic DNA


title: Myeloma-131

description: bisulfite modified genomic DNA


title: Myeloma-133

description: bisulfite modified genomic DNA


title: Myeloma-129

description: bisulfite modified genomic DNA


title: Myeloma-99

description: bisulfite modified genomic DNA

value: No split


title: Myeloma-135

description: bisulfite modified genomic DNA


title: Myeloma-130

description: bisulfite modified genomic DNA


title: Myeloma-98

description: bisulfite modified genomic DNA


title: Myeloma-93

description: bisulfite modified genomic DNA

value: Normal plasma cell


title: Myeloma-89

description: bisulfite modified genomic DNA


title: Myeloma-88

description: bisulfite modified genomic DNA


title: Myeloma-94

description: bisulfite modified genomic DNA


title: Myeloma-97

description: bisulfite modified genomic DNA


title: Myeloma-96

description: bisulfite modified genomic DNA


title: Myeloma-92

description: bisulfite modified genomic DNA


title: Myeloma-84

description: bisulfite modified genomic DNA


title: Myeloma-85

description: bisulfite modified genomic DNA


title: Myeloma-9

description: bisulfite modified genomic DNA


title: Myeloma-91

description: bisulfite modified genomic DNA


title: Myeloma-87

description: bisulfite modified genomic DNA


title: Myeloma-83

description: bisulfite modified genomic DNA


title: Myeloma-82

description: bisulfite modified genomic DNA


title: Myeloma-80

description: bisulfite modified genomic DNA


title: Myeloma-95

description: bisulfite modified genomic DNA


title: Myeloma-79

description: bisulfite modified genomic DNA


title: Myeloma-90

description: bisulfite modified genomic DNA


title: Myeloma-86

description: bisulfite modified genomic DNA


title: Myeloma-76

description: bisulfite modified genomic DNA


title: Myeloma-73

description: bisulfite modified genomic DNA


title: Myeloma-81

description: bisulfite modified genomic DNA


title: Myeloma-74

description: bisulfite modified genomic DNA


title: Myeloma-75

description: bisulfite modified genomic DNA


title: Myeloma-77

description: bisulfite modified genomic DNA


title: Myeloma-8

description: bisulfite modified genomic DNA


title: Myeloma-78

description: bisulfite modified genomic DNA


title: Myeloma-141

description: bisulfite modified genomic DNA


title: 100 µM phloretin-1-2

city: Heidelberg

first: Martin

last: Wurst

address: INF 282

country: Germany

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

hyb_protocol: Slides were pre-hybridized in 5xSSC, 0.1 % SDS and 1% BSA at 42 °C for 45 min. Meanwhile, the Cy3- and Cy5- labelled cDNAs were mixed and vacuum dried to about 10 µl. The cDNAs were then added to 40 µl of hybridisation buffer (5xSSC, 0.1 % SDS, 40 % Formamide, 0.6 mg/ml salmon sperm DNA), denatured at 95 °C for 5 min, placed on ice for 2 min and applied ot the pre-hybridised slides. A lifterslip (Implen) was mounted and the slides were incubated at 42 °C overnight in the Slidebooster SB800 hybridisation station (Advalytix). Slides were washed for 10 min each at 50 °C in low stringency buffer (2 x SSC, 0.5 % SDS), at room temperature in medium stringency buffer (0.2xSSC, 0.5 %SDS) and in high stringency buffer (0.1xSSC), then airdried.

scan_protocol: Slides were scanned with SanArray 5000 (Packard BioScience, Dreieich, Germany) and analysis of resulting images was performed using GenePix Pro 6 software

data_processing: Data analysis was performed using the ExpressConverter and MIDAS software which are freely available at http://www.tm4.org. Files obtained from the scan were transformed into .mev – files and background substracted using the ExpressConverter. Using MIDAS the signal intensities were normalized by locally weighted linear regression (LOWESS), duplicate spots on each slide were merged and dye-swap reversed. Intensities of Cy3 and Cy5 were used to calculate log2 ratios. Log2 transformed data were exported to SAM. Only RNAs with a p-value of 0.5 or lower were considered as significantly regulated.

organism: Trypanosoma brucei

source_name: BS WT

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions, labelling reaction for 2 hours. Samples purified using QIAGEN oligo nucleotide removal kit before hybridization.

extract_protocol: Exponentially growing bloodstream-form trypanosomes (density 6x105 cells/ml) were treated with 100 µM phloretin for 24 h. RNA was isolated using peqgold Trifast.

tag: growth stage

value: Lister 427 Bloodstream form

source_name: BS WT treated with 100 µM phloretin for 24h


title: Ref1.1 (LC)

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

description: Reference RNA was developed from FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON)

hyb_protocol: Hybridizations were carried out overnight on µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) using 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C overnight. Each detection probe on the microfluidic chip consisted of a chemically-modified nucleotide coding segment complementary to target microRNA or other RNA (control sequences), and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Images were acquired using a GenePix 4000B (Molecular Device) laser scanner by LC Sciences. Intensity data were collected using Array-Pro image analysis software (Media Cybernetics) with a scan resolution of 10 microns and PTM between 480 and 540V.

data_processing: Analysis was conducted on background subtracted signal intensities. Background was determined using a regression-based background mapping method. Spots yielding true signal (i.e., present) had signal intensities higher than 3×(background standard deviation) and standard deviation/signal intensity < 0.5. CV is calculated by (standard deviation)/(signal intensity). Probes repeated multiple times on an array were called present if the signals from at least 50% of the probes were above detection level.

source_name: Total RNA with small fraction

label_protocol: LC Sciences arrays were performed in one colour by the company at the LC Sciences Headquarters (Houston, TX) using two replicates of each reference pool. Briefly, 1 ug of total reference RNA was extracted with Trizol reagent (Invitrogen) and size fractionated using a YM-100 Microcon filter (Millipore). Small RNAs less than 300 nucleotides in length were extended with a poly(A) tail using poly(A) polymerase. Poly(A) tails were ligated with an oligonucleotide tag for subsequent dye staining.

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.

tag: sample

value: Reference 1

tag: sample type

value: pool of equal amounts of total RNA from mouse testicle, ovary and 10-12 day embryo.

tag: microarray barcode


title: Ref1.2 (LC)


title: Ref2.1 (LC)

value: Reference 2

value: pool of equal parts RNA from heart, lung and liver


title: Ref2.2 (LC)


title: 100 µM phloretin-1-1


title: 100 µM phloretin-3


title: 100 µM phloretin-2-2


title: Myeloma-72

description: bisulfite modified genomic DNA

value: bone marrow

value: Multiple myeloma plasma cell


title: 100 µM phloretin-2-1


title: Myeloma-7

description: bisulfite modified genomic DNA


title: Myeloma-69

description: bisulfite modified genomic DNA


title: Myeloma-67

description: bisulfite modified genomic DNA


title: Myeloma-71

description: bisulfite modified genomic DNA


title: Myeloma-65

description: bisulfite modified genomic DNA


title: Myeloma-68

description: bisulfite modified genomic DNA


title: Myeloma-70

description: bisulfite modified genomic DNA


title: Myeloma-66

description: bisulfite modified genomic DNA


title: Myeloma-62

description: bisulfite modified genomic DNA


title: AF_251332613771

hyb_protocol: Agilent Mouse G4121B Microarrays (containing approximately 22,000 probes) were hybridized with 5 µg Cy5-labelled liver RNA and 5 µg Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated overnight at 60 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned using a ScanArray Express (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, CA, USA).

data_processing: The median signal intensity of each microarray sample were lowess normalized. Technical replicates were not averaged.  Data for each probe was flagged (flag=1) if the median signal intensity for that probe was less than the mean of the negative controls ((-)3xSLv1) plus three standard deviations.

source_name: IFN-β + APAP 4 h

label_protocol: Individual 2.5 µg aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON Canada) and purified using Rneasy Mini Kits (QIAgen Inc., Mississauga, ON, Canada). RNA quantity was measured using a  Spectrophotometer (ND-1000 Nanodrop technologies) and RNA quality was measured using an Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip (Agilent Technologies, Canada Inc., Mississauga, ON, Canada.)

treatment_protocol: Mice  were divided into four groups of 10 and given one of following treatments: 1) vehicle control  (25mM Hepes, pH 6.0, 500 mM NaCl, 6% glycerol, 0.5% Ethanol, 0.05% MSA; 2) Acetaminophen (Sigma-Aldrich Canada ) (300mg/kg) dissolved in vehicle; 3) Interferon β (3.75 x 107 U/kg) dissolved in vehicle; 4) Acetaminophen (Sigma-Aldrich Canada ) (300mg/kg) + Interferon β (PBL Biomedical Laboratories USA NJ )(3.75 x 107 U/kg) dissolved in vehicle.

value: Liver

value: Male

value: 6-8 weeks

value: IFN-β + APAP

value: 4 h

tag: hybridization group

value: Hybridization Block 6

source_name: universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)

extract_protocol: purchased from Stratagene

tag: reference

value: Total RNA derived from 11 mouse cell lines


title: Myeloma-63

description: bisulfite modified genomic DNA

tag: tissue


title: Myeloma-61

description: bisulfite modified genomic DNA


title: Myeloma-64

description: bisulfite modified genomic DNA


title: AF_251332613528

source_name: IFN-β 4 h

tag: sex

tag: strain

value: IFN-β alone


title: AF_251332613529

source_name: APAP 4 h

tag: age

value: APAP alone


title: AF_251332613365

source_name: Veh 1.5 h

value: Vehicle Control


title: AF_251332613770

source_name: IFN-β + APAP 1.5 h


title: Myeloma-6

description: bisulfite modified genomic DNA


title: Myeloma-59

description: bisulfite modified genomic DNA


title: AF_251332613778

value: Hybridization Block 2


title: Myeloma-58

description: bisulfite modified genomic DNA


title: Myeloma-57

description: bisulfite modified genomic DNA


title: AF_251332613525

source_name: Veh 4 h


title: Myeloma-60

description: bisulfite modified genomic DNA


title: AF_251332613527

source_name: IFN-β 1.5 h


title: Myeloma-55

description: bisulfite modified genomic DNA


title: AF_251332613777


title: Myeloma-54

description: bisulfite modified genomic DNA


title: Myeloma-56

description: bisulfite modified genomic DNA


title: AF_251332613779


title: AF_251332613697


title: AF_251332613776

value: Hybridization Block 1


title: Myeloma-52

description: bisulfite modified genomic DNA


title: Myeloma-5

description: bisulfite modified genomic DNA


title: Myeloma-51

description: bisulfite modified genomic DNA


title: AF_251332613342

value: Hybridization Block 4


title: Myeloma-50

description: bisulfite modified genomic DNA


title: AF_251332613362

source_name: APAP 1.5 h

value: Hybridization Block 5


title: AF_251332613344


title: AF_251332613363


title: Myeloma-48

description: bisulfite modified genomic DNA


title: Myeloma-53

description: bisulfite modified genomic DNA


title: Myeloma-49

description: bisulfite modified genomic DNA


title: AF_251332613361


title: AF_251332613360


title: AF_251332613343


title: AF_251332613340


title: Myeloma-44

description: bisulfite modified genomic DNA


title: Myeloma-45

description: bisulfite modified genomic DNA


title: AF_251332613312

value: Hybridization Block 3


title: Myeloma-43

description: bisulfite modified genomic DNA

value: bone marrow


title: Myeloma-46

description: bisulfite modified genomic DNA

value: Multiple myeloma plasma cell


title: AF_251332613314

value: Liver


title: Myeloma-47

description: bisulfite modified genomic DNA


title: AF_251332613307

value: Male


title: Total RNA with small fraction Reference 2 251911910767_200906171315_S01_miRNA-v1_10_Apr08_2_3

description: Reference RNA was developed from FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON). Two references were made from the various stocks. Reference # 1 was a pool of equal amounts of total RNA from mouse testicle, ovary and 10-12 day embryo. Reference #2 was a pool of equal parts total RNA from mouse liver, heart and lung.

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.

data_processing: Cyclic Lowess

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).

value: Reference 2

tag: source

value: pool of equal parts RNA from heart, lung and liver

tag: internal id

value: Microarray Barcode 251911910767


title: AF_251332613341

value: 6-8 weeks

value: IFN-β + APAP

tag: time

value: 4 h


title: Total RNA with small fraction Reference 1 251911910767_200906171315_S01_miRNA-v1_10_Apr08_2_2

value: Reference 1

value: pool of equal amounts of total RNA from mouse testicle, ovary and 10-12 day embryo.


title: AF_251332613311

value: Total RNA derived from 11 mouse cell lines


title: AF_251332613313

value: Vehicle Control


title: Total RNA with small fraction Reference 1 251911910767_200906171315_S01_miRNA-v1_10_Apr08_2_4


title: Myeloma-42

description: bisulfite modified genomic DNA


title: Myeloma-41

description: bisulfite modified genomic DNA


title: AF_251332613306

value: Hybridization Block 1


title: Total RNA with small fraction Reference 2 251911910767_200906171315_S01_miRNA-v1_10_Apr08_1_2


title: AF_251332613310

value: APAP alone


title: Total RNA with small fraction Reference 1 251911910767_200906171315_S01_miRNA-v1_10_Apr08_1_3


title: Total RNA with small fraction Reference 2 251911910767_200906171315_S01_miRNA-v1_10_Apr08_1_4


title: Total RNA with small fraction Reference 2 251911910767_200906171315_S01_miRNA-v1_10_Apr08_2_1


title: Myeloma-39

description: bisulfite modified genomic DNA


title: Myeloma-38

description: bisulfite modified genomic DNA


title: AF_251332613304

value: Hybridization Block 3


title: Myeloma-4

description: bisulfite modified genomic DNA

value: bone marrow


title: Fresh_D_10_Slide 1_24h

data_processing:
Data were extracted from scanned images using Agilent Feature Extraction software version 9.5.3.1. Median signal intensities for the 4th and 24hr time points were quantile normalized separately.  Technical replicates for Probe level and miRNA level were averaged using the median.  Data was flagged if the raw signal intensity was less than the mean plus three standard deviations of the negative controls or if the median of the technical replicates was flagged to be in the background.

Sample Data table header definitions:
Raw is the median signal intensity.
Norm (i.e., VALUE) is the quantile normalized signal intensity of the log2 of the median signal intensity.
Flag indicates whether the raw signal intensity for the spot is within the background (mean plus three standard deviations of the negative controls).
Norm.Collapsed.Probe is the median of the probe technical replicates.
Flag.Probe indicates whether the median of the probe technical replicates was within the background.
Norm.Collapsed.miRNA is the median of the miRNA technical replicates.
Flag.miRNA indicates whether the median of the miRNA technical replicates was within the background.

source_name: Total RNA, mouse liver, BaP exposure

value: Median liver lobe

tag: gender

tag: exposure

value: 150 mg/kg Benzo(a)pyrene (CAS number 50-32-8)

tag: rna storage

value: <7 days at -80C

tag: time post exposure


title: AF_251332613303

value: Liver

value: Male

tag: treatment

value: IFN-β alone


title: AF_251332613300

value: 6-8 weeks


title: Myeloma-35

description: bisulfite modified genomic DNA

tag: cell type

value: Multiple myeloma plasma cell

tag: myeloma translocation


title: Fresh_D_9_Slide 1_24h


title: Myeloma-40

description: bisulfite modified genomic DNA


title: AF_251332613302


title: Myeloma-36

description: bisulfite modified genomic DNA


title: AF_251332613294

value: IFN-β + APAP

value: 4 h

value: Hybridization Block 5


title: Fresh_D_11_Slide 1_24h


title: Fresh_D_12_Slide 1_24h


title: Myeloma-37

description: bisulfite modified genomic DNA


title: AF_251332613293

value: Total RNA derived from 11 mouse cell lines


title: Myeloma-34

description: bisulfite modified genomic DNA


title: Fresh_C_12_Slide 1_24h

source_name: Total RNA, mouse liver

value: 0 mg/kg BaP


title: AF_251332613292


title: Frozen_D_6_Slide 12

value: 6-8 weeks at -80C


title: Myeloma-32

description: bisulfite modified genomic DNA


title: Frozen_C_7_Slide 12


title: Reference_2_Slide 11

description: Pool

source_name: Total RNA, mouse liver, pooled 6 control + 6 BaP treated

value: Pooled mouse reference RNA (equal proportions all samples)


title: Fresh_C_19_Slide 1_24h


title: Myeloma-33

description: bisulfite modified genomic DNA

source_name: CD138+ bone marrow cells


title: Fresh_C_11_Slide 1_24h


title: AF_251332613291


title: Frozen_D_5_Slide 12


title: Frozen_D_3_Slide 11


title: Frozen_C_5_Slide 12


title: Reference_1_Slide 11

description: Pool


title: Myeloma-31

description: bisulfite modified genomic DNA


title: Frozen_D_7_Slide 11


title: AF_251332613290

value: Hybridization Block 4


title: Myeloma-30

description: bisulfite modified genomic DNA

value: bone marrow


title: Frozen_C_6_Slide 11

value: Median liver lobe


title: Myeloma-3

description: bisulfite modified genomic DNA


title: Frozen_C_1_Slide 10


title: Reference_1_Slide 10

description: Pool


title: Myeloma-29

description: bisulfite modified genomic DNA


title: Reference_2_Slide 10

description: Pool


city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: benign epithelium from age- and BMI-matched control prostate needle biopsy #11.

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction (FE) software was used to grid, extract, and normalize data. Spots of poor quality or average intensity levels <300 were removed from further analysis.   The Agilent FE file "LogRatio" column data were converted from log10 scale to log2 scale.

source_name: HGS [reference]

label_protocol: WTA amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set. This RNA was amplified using the TransPlex WTA Kit following procedures used for the study.

value: male

tag: reference pool

value: LNCaP, DU145, PC3, and CWR22 cell lines

source_name: 11_BABE [test]

extract_protocol: Total RNA from laser-capture microdissected experimental samples was isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA.) This RNA was converted to a cDNA library and amplified and amino-allyl labeled using the TransPlex WTA Kit (Sigma-Aldrich Corp, St. Louis, MO) and its purity was confirmed by spectrophotometric analysis.

tag: specimen name

tag: ethnicity

value: Caucasian

value: benign epithelium

tag: disease state

value: control


description: benign epithelium from prostate needle biopsy with high grade(Gleason 8-10) prostate cancer #8.

source_name: 8_CABE [test]

tag: tissue

value: prostate cancer

tag: tumor grade

value: Gleason 8-10


description: benign epithelium from prostate needle biopsy with high grade(Gleason 8-10) prostate cancer #9.

source_name: 9_CABE [test]

value: non-Caucasian


title: Frozen_C_2_Slide 10

value: Male

tag: age

tag: strain

value: 4 h


title: Myeloma-27

description: bisulfite modified genomic DNA

value: Multiple myeloma plasma cell


title: Fresh_C_5_Slide 12

value: 0 mg/kg BaP

value: <7 days at -80C


title: Frozen_C_3_Slide 10

value: 6-8 weeks at -80C


title: Frozen_D_1_Slide 10

value: 150 mg/kg Benzo(a)pyrene (CAS number 50-32-8)


description: benign epithelium from prostate needle biopsy with high grade(Gleason 8-10) prostate cancer #7.

source_name: 7_CABE [test]


title: Frozen_D_2_Slide 10


title: Reference_1_Slide 9

description: Pool

tag: reference

value: Pooled mouse reference RNA (equal proportions all samples)


title: Reference_1_Slide 12

description: Pool

value: Median liver lobe


title: Myeloma-24

description: bisulfite modified genomic DNA

value: bone marrow


title: Myeloma-26

description: bisulfite modified genomic DNA


description: benign epithelium from age- and BMI-matched control prostate needle biopsy #4.

value: male

value: LNCaP, DU145, PC3, and CWR22 cell lines

source_name: 4_BABE [test]


description: benign epithelium from prostate needle biopsy with high grade(Gleason 8-10) prostate cancer #6.

source_name: 6_CABE [test]

value: Caucasian

value: benign epithelium


title: Fresh_D_3_Slide 8


title: Reference_1_Slide 8

description: Pool


title: Reference_2_Slide 8

description: Pool


description: benign epithelium from age- and BMI-matched control prostate needle biopsy #3.

source_name: 3_BABE [test]

value: control


title: Myeloma-28

description: bisulfite modified genomic DNA


description: benign epithelium from age- and BMI-matched control prostate needle biopsy #2.

source_name: 2_BABE [test]


title: Myeloma-25

description: bisulfite modified genomic DNA


title: AF_251332613305

value: Liver

tag: sex

value: 6-8 weeks

value: APAP alone

tag: time

tag: hybridization group

value: Hybridization Block 1

source_name: universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)

value: Total RNA derived from 11 mouse cell lines


title: Fresh_C_7_Slide 8

tag: gender

value: Male

tag: exposure

value: 0 mg/kg BaP

tag: rna storage

value: 4 h


title: Fresh_D_1_Slide 9

value: 150 mg/kg Benzo(a)pyrene (CAS number 50-32-8)

value: <7 days at -80C

tag: time post exposure


title: Fresh_C_1_Slide 8

value: Median liver lobe


title: Myeloma-22

description: bisulfite modified genomic DNA

value: bone marrow

tag: cell type

value: Multiple myeloma plasma cell

tag: myeloma translocation


title: Myeloma-23

description: bisulfite modified genomic DNA


title: Reference_Slide 7

description: Pool

value: Pooled mouse reference RNA (equal proportions all samples)

value: 6-8 weeks at -80C


title: Myeloma-2

description: bisulfite modified genomic DNA


title: Reference_1_Slide 6

description: Pool


title: Fresh_D_7_Slide 6


title: Fresh_D_2_Slide 7


title: Myeloma-20

description: bisulfite modified genomic DNA


title: Reference_2_Slide 5

description: Pool


title: Myeloma-21

description: bisulfite modified genomic DNA


title: Fresh_C_3_Slide 7


title: Norm.1.col.Ref2.2 (Exiqon)

description: Hy3: CHIP # 4 flipUS22502706_13974278_S01_Exiqon1.txt

hyb_protocol: Hybridisations were performed in SureHyb chambers (Agilent) for 16 hours at 56ºC. Slides were washed according to manufacturer’s instructions

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 9.5.3.1, using an FE protocol available on-demand from Exiqon.

data_processing: Data were extracted from scanned images using Agilent Feature Extraction software version 9.5.3.1. Median signal intensities were lowess normalized for the 2 colour analysis and cyclic lowess normalized for the one colour analysis.  Technical replicates for each miRNA level were averaged using the median.  Data was flagged if the raw signal intensity was less than the mean plus three standard deviations of the negative controls or if the median of the technical replicates was flagged to be in the background.

source_name: Total RNA with small fraction

label_protocol: One microgram of each mouse Reference RNA sample was labelled with a Hy5 fluorophore (Exiqon, Woburn, MA, USA) and co-hybridised with 1 g of the other Reference RNA standard in Hy3. Labelling reactions were performed using Exiqon’s miRCURY LNA miRNA power labelling kit, according to the manufacturer’s protocol.

tag: sample

value: Reference 2

value: pool of equal parts RNA from heart, lung and liver

tag: sample type

value: Reference RNA was developed from FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON)


title: Fresh_D_6_Slide 5


title: Fresh_C_6_Slide 5


title: Fresh_C_2_Slide 7