title: Gene expression profiling of Ankrd2(+)clS9 (A)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: We compared the transcription profiles of Ankrd2 overexpressing clone S9 by microarray competitive hybridization against C2C12 control cells.

hyb_protocol: Labeled RNAs were concentrated by ethanol precipitation and dissolved in 115μl of hybridization buffer (5XSSC, 0.1% SDS, 25% formamide). Labeled aRNA target from transfected clone and control myoblasts were mixed before precipitation. After denaturation at 90°C for 2 min, the labeled targets were added to the microarrays, previously incubated in prehybridization buffer (5X SSC, 0.1% SDS,100ng/ul ss-DNA, 5X Denhardt) for 2-3 hours at 48°C. Hybridization was carried on overnight at 48°C in an ArrayBooster microarray incubator (Advalytix), followed by a series of post-hybridization washings.

scan_protocol: Fluorescence detection was carried out on a GSI Lumonics LITE dual confocal laser scanner (Perkin-Elmer) with ScanArray Microarray Analysis Software, and raw scanner images were analyzed with QuantArray software (Perkin-Elmer).

data_processing: Normalization of the expression levels was performed with MIDAW tool (Romualdi et al., 2005).

source_name: C2C12 Ankrd2 overexpressing myoblasts clS9 (test)

label_protocol: Linear amplification of mRNA from 500ng of total RNA was carried on using the Amino Allyl Message-Amp-aRNA kit (Ambion) with one round of amplification according to the manufacturer’s recommendations. 7μg of aRNA from the sample was coupled to Cy3 dye (Amersham Pharmacia Biotech) to obtain labeled aRNA ready for microarray hybridization.

growth_protocol: DMEM + 2mM Glutamine + 10% Fetal Bovine Serum (FBS) + 500 ug/ml G418

extract_protocol: Total RNA was purified from Ankrd2 transfected myoblasts following the standard Trizol protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

treatment_protocol: Overexpression of Ankrd2 gene in C2C12 cells: clone Ankrd2(+)clS9

tag: The Ankrd2 transcript was cloned in pcDNA 3.0 mammalian expression vector. The construct was transfected into C2C12 cells. Cells were selected for ten days and about 48 G418-resistant clones were tested for Ankrd2 silencing.

source_name: C2C12 myoblasts (reference)

label_protocol: Linear amplification of mRNA from 500ng of total RNA was carried on using the Amino Allyl Message-Amp-aRNA kit (Ambion) with one round of amplification according to the manufacturer’s recommendations. 7μg of aRNA from the sample was coupled to Cy5 dye (Amersham Pharmacia Biotech) to obtain labeled aRNA ready for microarray hybridization.

growth_protocol: DMEM + 2mM Glutamine + 10% Fetal Bovine Serum (FBS).

extract_protocol: Total RNA was purified from C2C12 myoblasts following the standard Trizol protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

tag: - C2C12 cell line

tag: - Species

value: mouse, C3H; Tissue:muscle

tag: - Morphology

value: Myoblast

tag: - Properties

value: differentiation; muscle proteins express; myogenesis


title: Gene expression profiling of Ankrd2(+)clS9(B)

status: Public on Dec 09 2008

type: RNA

molecule: total RNA

organism: Mus musculus

tag: The Ankrd2 transcript was cloned in pcDNA 3.0 mammalian expression vector. The construct was transfected into C2C12 cells. Cells were selected for ten days and about 48 G418-resistant clones were tested for Ankrd2 overexpression.


title: Onne06 muscle_JS_replicate 2

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

country: Canada

institute: Fisheries and Oceans Canada

description: White muscle tissue from a single fish compared to a major reference pool of muscle from all collected samples (n=79).

hyb_protocol: The array hybridization was performed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). Two ul of poly dA was added to the targets, which were then denatured for 10min at 80oC, followed by the addition of 125 ul of pre-warmed SlideHybe3 buffer (Ambion, TX, USA) before loading into the hybridization chamber. Hybridizations were performed in batches of 12-24 samples and conducted over a two-week period to minimize technical variance. Slide processing steps within the Tecan HS were conducted as follows: two 30 s slide wash steps (0.1% SDS followed by water) at 23oC, 3 min slide denaturation at 85oC with agitation, 1 min wash (5x SSC, 0.01% SDS, 1% BSA) at 43oC with a 30 s soak time, 1 h prehybridization at 43oC with medium agitation, two 1 min washes (water followed by 8x SSC, 0.1% SDS, 4X Denhardt’s) at 43oC, sample injection at 43oC with agitation, hybridization for 16 h at 43oC with low frequency agitation, two 30 s wash steps, one at 43oC (2x SSC, 0.01% SDS) followed by one at 23oC (0.25x SSC), slide drying at 23oC for 2.5 min.

scan_protocol: All arrays were scanned using a Perkin Elmer ScanArray Express (Perkin Elmer, Boston, MA), adjusting the PMT gain for optimized visualization of each image.

data_processing: The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com) and processed to GeneSight (version 4.1, BioDiscovery, Inc. El Segundo, CA, www.biodiscovery.com).  Data was prepared in GeneSight according to the following steps: correct for background intensity using local background correction; omit multiple spots with flags (1,2,3,4,5,6,7); raise all values below a specified value to the minimum threshold (20.0); replace missing values by the experimental means for each gene; LOWESS normalization is done locally with smoothing parameter of 0.2 and linear degree of fitness; finally, calculate the log base 2 and the difference of the log2 of 2 channels. This pairMean log difference (VALUE) was used for all subsequent data analysis.

label: Alexa 555

organism: Oncorhynchus nerka

source_name: Muscle tissue from a wild fish non-destructively sampled at Johnson Straight

label_protocol: Five ug of aRNA were reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer’s instructions. Briefly, the cDNA was purified using Zymo-25 clean-up columns (Zymo Research, Orange, CA) and eluted using the 2X coupling buffer, supplied by Invitrogen. During dye labelling, samples were processed individually by first adding DMSO, then cDNA to the Alexa dye tube and incubating for 1h at room temperature. Then labeled sample were cleaned up by adding 50 ul of DNA binding buffer (Zymo) to each Alexa tube and then combining the sample and references for each slide into Zymo-25 clean-up columns. The unbound portion of the labelled cDNA was removed by centrifugation at 13,000 rpm/min. The labelled cDNA was washed three times with DNA wash buffer (Zymo) and eluted in 9 ul of 1X TE buffer.

extract_protocol: Total RNA was purified from white muscle tissue using Magmax™-96 for Microarrays Kits (Ambion Inc, Austin, TX, USA) with a Biomek NXP (Beckman Coulter, Mississauga, ON, Canada) automated liquid-handling instrument. Approximately 10 mg of frozen tissue was homogenized with stainless steel beads in TRI-reagent (Ambion Inc, Austin, TX, USA) on a MM301 mixer mill (Retsch Inc., Newtown, PA, USA). One hundred microlitre aliquots of homogenate were pipetted into 96-well plates and extractions were carried out according to the manufacturer's instructions using the No-Spin Procedure for frozen tissues, on the Biomek FXP. In the final step, RNA was eluted with RNAase-, DNAase-free water and RNA yield was determined by measuring the A260 of the eluate. Purity was assessed by measuring the A260/A280 ratio of the eluate. 500 ng to 5 ug of total RNA was amplified using a MessageAmpTMII-96 kit (Ambion, TX, USA), performed manually according to manufacturer’s instructions. Amplification steps were performed on a single 96-well plate for all samples at once.

tag: Number of individuals

tag: Mean weight

tag: Tissue

value: white muscle

label: Alexa 647

source_name: Pooled reference sample from all individuals collected

extract_protocol: Muscle tissue from each individual was extracted and amplified separately as described for the channel 1 sample. Equal quantities of aRNA from each sample were mixed for the pooled sample.


title: Onne06 muscle_JDFS_replicate 15

source_name: Muscle tissue from a wild fish non-destructively sampled at Juan De Fuca


title: Onne06 muscle_JDFS_replicate 12


title: Onne06 muscle_JDFS_replicate 16


title: Gene expression profiling of Ankrd2(-)clA9 (A)

description: We compared the transcription profiles of Ankrd2 silencing clone A9 by microarray competitive hybridization against C2C12 control cells.

source_name: C2C12 Ankrd2 silencing myoblasts clA9 (test)

label_protocol: Linear amplification ofmRNA from 500ng of total RNA was carried on using the Amino Allyl Message-Amp-aRNA kit (Ambion) with one round of amplification according to the manufacturer’s recommendations. 7μg of aRNA from the sample was coupled to Cy3 dye (Amersham Pharmacia Biotech) to obtain labeled aRNA ready for microarray hybridization.

treatment_protocol: C2C12 silencing of Ankrd2 gene: clone Ankrd2(-)clA9

tag: The Ankrd2 transcript was cloned in pcDNA 3.0 mammalian expression vector in antisense orientation. The construct was transfected into C2C12 cells. Cells were selected for ten days and about 48 G418-resistant clones were tested for Ankrd2 silencing.


title: Onne06 muscle_JDFS_replicate 7


title: Onne06 muscle_JDFS_replicate 9


title: Onne06 muscle_JDFS_replicate 4


title: Gene expression profiling of Ankrd2(+)clS12 (A)

description: We compared the transcription profiles of Ankrd2 overexpressing clone S12 by microarray competitive hybridization against C2C12 control cells.

source_name: C2C12 Ankrd2 overexpressing myoblasts clS12 (test)

treatment_protocol: Overexpression of Ankrd2 gene in C2C12 cells: clone Ankrd2(+)clS12


title: Gene expression profiling of Ankrd2(+)clS12 (B)


title: Onne06 muscle_JDFS_replicate 8


title: Onne06 muscle_JDFS_replicate 3


title: Gene expression profiling of Ankrd2(-)clA9 (B)


title: Onne06 muscle_JDFS_replicate 6


title: Gene expression profiling of Ankrd2(-)clA10 (B)

description: We compared the transcription profiles of Ankrd2 silencing clone A10 by microarray competitive hybridization against C2C12 control cells.

source_name: C2C12 Ankrd2 silencing myoblasts clA10 (test)

label_protocol: Linear amplification ofmRNA from 500ng of total RNA was carried on using the Amino Allyl Message-Amp-aRNA kit (Ambion) with one round of amplification according to the manufacturer’s recommendations. 7μg of aRNA from the sample was coupled to Cy5 dye (Amersham Pharmacia Biotech) to obtain labeled aRNA ready for microarray hybridization.

treatment_protocol: C2C12 silencing of Ankrd2 gene: clone Ankrd2(-)clA10

tag: The Ankrd2 transcript was cloned in pcDNA 3.0 mammalian expression vectors in antisense orientation. The construct was transfected into C2C12 cells. Cells were selected for ten days and about 48 G418-resistant clones were tested for Ankrd2 silencing.


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + dihydrotestosterone C57BL/6J animal 62

status: Public on Dec 08 2008

city: Los Angeles

first: Leslie

last: Ingram-drake

state: CA

department: Medicine/MIMG/Human Genetics

country: USA

institute: UCLA

description: Liver tissue from the hormone treated group consists of 40 female and male C57BL/6J mice fed a chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were gonadectomized at 8 weeks of life, implanted with hormone pellets at 12 weeks, and sacrificed at 14 weeks.  Male and female mice of the hormone treated groups received subcutaneous implants of either 0.5 mg estradiol (E2) pellet (plasma yield of 300 picogram/ml) or a 5 mg dihydrotestosterone (DHT) pellet (plasma yield of 1-2 nanogram/ml), designed to release over 21 days, (Innovative Research of America, 17B-estradiol: Cat. No. E-121 0.5mg/pellet, 5a-dihydrotestosterone: Cat. No. A-16).  Control mice were treated with the placebo pellet (Innovative Research of America, placebo: Cat. No. C-111).  At 14 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: pool of Liver C57BL/6J mice on chow diet(n=40)

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

source_name: Liver, Castrated + dihydrotestosterone C57BL/6J animal 62  Gender:Male

tag: Liver, Castrated + dihydrotestosterone animal 62


title: knockdown_1_1

city: Frederick

first: Andrei

middle: S

last: Zolotukhin

state: MD

address: P.O. Box B

institute: NCI-Frederick

description: Biological replicate 1 of 2.

hyb_protocol: CodeLink human whole genome bioarrays were hybridized with cRNA and stained with Cy5-streptavidin.

scan_protocol: Slides were washed and then scanned on an Axon GenePix 4000B scanner.

data_processing: Data were analyzed for quality with CodeLink software package, and data points were subject to median normalization, as recommended by the manufacturer.

label: biotin

organism: Homo sapiens

source_name: knockdown cells expressing shRNA targeted to the SFPQ gene, clone #1_1

label_protocol: mRNAs were reverse transcribed into cDNAs, amplified into biotinylated cRNAs, and fragmented to uniform size. At all steps, the RNA/DNA were quality controlled using Bioanalyzer (Agilent).

extract_protocol: Total RNA was extracted using the RiboPure RNA kit (Ambion), and quantified by UV spectrophotometry.

tag: HeLa cells stably transfected with IMG800 vector expressing shRNA #1 to SFPQ.


title: control_6_4

description: Biological replicate 2 of 2.

source_name: control cells expressing nontargeted shRNA, clone #6_4

tag: HeLa cells stably transfected with IMG800 vector expressing nontargeting shRNA.


title: Gene expression profiling of Ankrd2(-)clA10 (A)

extract_protocol: Total RNA was purified from C2C12 myoblasts following the standard Trizol protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001


title: Onne06 muscle_JDFS_replicate 1


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + dihydrotestosterone C57BL/6J animal 63

tag: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Castrated + dihydrotestosterone C57BL/6J animal 63  Gender:Male

tag: Liver, Castrated + dihydrotestosterone animal 63


title: control_6_2

description: Biological replicate 1 of 2.

source_name: control cells expressing nontargeted shRNA, clone #6_2


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + dihydrotestosterone C57BL/6J animal 61

source_name: Liver, Castrated + dihydrotestosterone C57BL/6J animal 61  Gender:Male

tag: Liver, Castrated + dihydrotestosterone animal 61


title: Onne06 muscle_JDFS_replicate 2


title: knockdown_3_1

description: Biological replicate 2 of 2.

source_name: knockdown cells expressing shRNA targeted to the SFPQ gene, clone #3_1

tag: HeLa cells stably transfected with IMG800 vector expressing shRNA #3 to SFPQ


title: Onne06 muscle_JDFS_replicate 5


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + dihydrotestosterone C57BL/6J animal 59

source_name: Liver, Castrated + dihydrotestosterone C57BL/6J animal 59  Gender:Male

tag: Liver, Castrated + dihydrotestosterone animal 59


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 54

source_name: Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 54  Gender:Female

tag: Liver, Ovarectomized  + dihydrotestosterone animal 54


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + dihydrotestosterone C57BL/6J animal 60

source_name: Liver, Castrated + dihydrotestosterone C57BL/6J animal 60  Gender:Male

tag: Liver, Castrated + dihydrotestosterone animal 60


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 52

source_name: Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 52  Gender:Female

tag: Liver, Ovarectomized  + dihydrotestosterone animal 52


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 51

source_name: Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 51  Gender:Female

tag: Liver, Ovarectomized  + dihydrotestosterone animal 51


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + estrogen C57BL/6J animal 41

source_name: Liver, Castrated + estrogen C57BL/6J animal 41  Gender:Male

tag: Liver, Castrated + estrogen  animal 41


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + estrogen C57BL/6J animal 45

source_name: Liver, Castrated + estrogen C57BL/6J animal 45  Gender:Male

tag: Liver, Castrated + estrogen animal 45


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + estrogen C57BL/6J animal 34

source_name: Liver, Ovarectomized + estrogen C57BL/6J animal 34  Gender:Female

tag: Liver, Ovarectomized + estrogen animal 34


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated  + placebo C57BL/6J animal 26

source_name: Liver, Castrated + placebo  C57BL/6J animal 26  Gender:Male

tag: Liver, Castrated + placebo  animal 26


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 50

source_name: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 50  Gender:Female

tag: Liver, Ovarectomized  + dihydrotestosterone animal 50


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + estrogen C57BL/6J animal 33

source_name: Liver, Ovarectomized + estrogen C57BL/6J animal 33  Gender:Female

tag: Liver, Ovarectomized + estrogen animal 33


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + estrogen C57BL/6J animal 36

source_name: Liver, Ovarectomized + estrogen  C57BL/6J animal 36  Gender:Female

tag: Liver, Ovarectomized + estrogen  animal 36


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + estrogen C57BL/6J animal 37

source_name: Liver, Ovarectomized + estrogen  C57BL/6J animal 37  Gender:Female

tag: Liver, Ovarectomized + estrogen  animal 37


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + estrogen C57BL/6J animal 44

tag: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Castrated + estrogen C57BL/6J animal 44  Gender:Male

tag: Liver, Castrated + estrogen animal 44


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated  + placebo C57BL/6J animal 28

source_name: Liver, Castrated + placebo  C57BL/6J animal 28  Gender:Male

tag: Liver, Castrated + placebo animal 28


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + estrogen C57BL/6J animal 35

source_name: Liver, Ovarectomized + estrogen  C57BL/6J animal 35  Gender:Female

tag: Liver, Ovarectomized + estrogen  animal 35


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 53

source_name: Liver, Ovarectomized + dihydrotestosterone C57BL/6J animal 53  Gender:Female

tag: Liver, Ovarectomized  + dihydrotestosterone animal 53


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + estrogen C57BL/6J animal 43

source_name: Liver, Castrated + estrogen C57BL/6J animal 43  Gender:Male

tag: Liver, Castrated + estrogen  animal 43


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated  + placebo C57BL/6J animal 27

source_name: Liver, Castrated + placebo  C57BL/6J animal 27  Gender:Male

tag: Liver, Castrated + placebo animal 27


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated  + placebo C57BL/6J animal 25

source_name: Liver, Castrated + placebo C57BL/6J animal 25  Gender:Male

tag: Liver, Castrated + placebo animal 25


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated + estrogen C57BL/6J animal 46

source_name: Liver, Castrated + estrogen C57BL/6J animal 46  Gender:Male

tag: Liver, Castrated + estrogen animal 46


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Castrated  + placebo C57BL/6J animal 24

source_name: Liver, Castrated + placebo d C57BL/6J animal 24  Gender:Male

tag: Liver, Castrated + placebo  animal 24


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized  + placebo C57BL/6J animal 20

source_name: Liver, Ovarectomized + placebo  C57BL/6J animal 20  Gender:Female

tag: Liver, Ovarectomized + placebo  animal 20


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized  + placebo C57BL/6J animal 19

source_name: Liver, Ovarectomized + placebo  C57BL/6J animal 19  Gender:Female

tag: Liver, Ovarectomized + placebo  animal 19


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized  + placebo C57BL/6J  animal 16

source_name: Liver, Ovarectomized + placebo  C57BL/6J animal 16  Gender:Female

tag: Liver, Ovarectomized + placebo animal 16


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized  + placebo C57BL/6J animal 18

source_name: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Ovarectomized + placebo  C57BL/6J animal 18  Gender:Female

tag: Liver, Ovarectomized + placebo  animal 18


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J  animal 11

source_name: Liver, Intact C57BL/6J animal 11  Gender:Male

tag: Liver,Intact animal 11


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J  animal 3

source_name: Liver, Intact C57BL/6J animal 3  Gender:Female

tag: Liver,Intact  animal 3


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 9

source_name: Liver, Intact C57BL/6J animal 9  Gender:Male

tag: Liver,Intact animal 9


title: Onne06 muscle_JS_replicate 12

source_name: Muscle tissue from a wild fish non-destructively sampled at Johnson Straight

tag: Number of individuals

tag: Mean weight

tag: Tissue

source_name: Pooled reference sample from all individuals collected


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-, animal 24

description: Liver tissue from the "Four Core Genotype" treated group consists of 20 female and male C57BL/6J mice fed a chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were gonadectomized at 8 weeks of life.  In mice of the "four core genotypes" (FCG), the Y chromosome is deleted for the testis-determining gene Sry, producing the Y- chromosome.  The Sry transgene is inserted onto an autosome, so that testis determination is independent of the complement of sex chromosomes.  XY-Sry gonadal males are bred with XX gonadal females, producing progeny with four different genotypes: two types of gonadal males (XX.Sry and XY-Sry) and two types of gonadal females (XX and XY-).  At 12 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

source_name: pool of Liver C57BL/6J mice on chow diet(n=17)

source_name: Liver, XY- C57BL/6J animal 24 Gender:Female

tag: Liver, XY- animal 24


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 2

tag: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Intact C57BL/6J animal 2  Gender:Female

tag: Liver,Intact  animal 2


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-, animal 30

tag: pool of Liver C57BL/6J mice on chow diet(n=17)

source_name: Liver, XY- C57BL/6J animal 30  Gender:Female

tag: Liver, XY- animal 30


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 4

source_name: Liver, Intact  C57BL/6J animal 4  Gender:Female

tag: Liver,Intact  animal 4


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 10

source_name: Liver, Intact  C57BL/6J animal 10  Gender:Male

tag: Liver,Intact animal 10


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX animal 2

source_name: Liver, XX  C57BL/6J animal 2  Gender:Female

tag: Liver, XX  animal 2


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-, animal 3

source_name: Liver, XY- C57BL/6J animal 3  Gender:Female

tag: Liver, XY- animal 3


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX  animal 35

source_name: Liver, XX  C57BL/6J animal 35  Gender:Female

tag: Liver, XX  animal 35


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-, animal 22

source_name: Liver, XY- C57BL/6J animal 22  Gender:Female

tag: Liver, XY- animal 22


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 8

source_name: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Intact C57BL/6J animal 8  Gender:Male

tag: Liver,Intact animal 8


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 1

source_name: Liver, Intact C57BL/6J animal 1  Gender:Female

tag: Liver,Intact  animal 1


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-, animal 12

source_name: Liver, XY- C57BL/6J animal 12  Gender:Female

tag: Liver, XY- animal 12


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J  animal 12

source_name: Liver, Intact  C57BL/6J animal 12  Gender:Male

tag: Liver,Intact  animal 12


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Intact C57BL/6J animal 5

source_name: Liver, Intact C57BL/6J animal 5  Gender:Female

tag: Liver,Intact  animal 5


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX animal 6

source_name: Liver, XX  C57BL/6J animal 6  Gender:Female

tag: Liver, XX  animal 6


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX  animal 29

source_name: pool of Liver C57BL/6J mice on chow diet(n=17)

source_name: Liver, XX  C57BL/6J animal 29  Gender:Female

tag: Liver, XX  animal 29


title: pool of liver from C57BL/6J mice on chow diet (n=40) vs. Liver, Ovarectomized  + placebo C57BL/6J animal 17

tag: pool of Liver C57BL/6J mice on chow diet(n=40)

source_name: Liver, Ovarectomized + placebo  C57BL/6J animal 17  Gender:Female

tag: Liver, Ovarectomized + placebo  animal 17


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX  animal 21

tag: pool of Liver C57BL/6J mice on chow diet(n=17)

source_name: Liver, XX  C57BL/6J animal 21  Gender:Female

tag: Liver, XX  animal 21


title: Bacillus subtilis A163 60ºC

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

country: Netherlands

institute: TNO

hyb_protocol: Microarray slides were incubated for 45 min at 42ºC with prehybridization solution (1% bovine serum albumin, 5x SCC and 0.1% SDS, filtered), washed three times with milliQ water, and dried by the use of a nitrogen flow. The Cy3-labeled cDNA from untreated cells sampled at 30ºC, was mixed with Cy5-labeled cDNA from heat-treated cells for each hybridization. After 2 min denaturation at 95 ºC, hybridizations of microarray slides were performed overnight at 42ºC in 40 μl of EasyHyb buffer (BioCat, Heidelberg, Germany) with both labeled cDNAs and 2.5 mg ml-1 yeast tRNA (final concentration). Microarray slides were washed at room temperature for 10 sec in 1x SSC/0.2% SDS at 37 ºC, 10 sec in 0.5x SSC at 37 ºC, and twice for 10 min in 0.2x SSC at room temperature. Slides were dried by the use of a nitrogen flow.

scan_protocol: ch1: laser power(%)/sensitivity(%): 90 / 65 ch2: laser power(%)/sensitivity(%): 100 / 60 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

data_processing: Data were processed by the use of Microsoft Office Excel 2003 SP2. The intensities of 8200 spots were calculated by extraction of the median background (B) from the median signal (S) and values for S-B < 1 were set to 1. The raw Cy5/Cy3 ratios (r) were calculated from the remaining background-corrected median signals. The total intensity normalization was carried out by the normalization factor N, defined as the average Cy5 (S-B) divided by the average Cy3 (S-B)). The normalization factor was determined from spot intensities with S/B > 2 for both Cy5 and Cy3 channels in order to avoid bias resulting from the degradation of the major of the transcripts at temperatures from 57-62°C. The normalised Cy5/Cy3 ratios (R=r/N) with S/B > 2 for either the Cy5 or Cy3 channel were calculated. Ratios from duplicate spots on the array and 2 independent experiments were averaged and 2log transformed.

organism: Bacillus subtilis

source_name: strain A163, exposed to 60ºC

label_protocol: Fluorescently labeled cDNA was prepared from 12.5 μg of total RNA by random hexamer pd(N)6-primer (Roche, Mannheim, Germany) polymerization using Superscript II reverse transcriptase (Life Technologies). Concentrations of nucleotides in labeling reaction mixture were 0.4 mM dATP, dGTP, dCTP and 0.2 mM dTTP. The final concentration of Cy3-dUTP or Cy5-dUTP (GE Healthcare) was 0.1 mM. Unincorporated Cy-dye-labeled dUTP, dNTP’s, primers and salts were removed by purification with AutoSeq G50 columns (GE Healthcare).

growth_protocol: An overnight culture of B. subtilis was diluted 20x in TSB to a volume of 600 ml and incubated at 30°C at 100 rpm till OD600 reached 0.5.

extract_protocol: Immediate quenching of metabolic activity in the samples was performed with cold methanol, according to described methods. Briefly, 40-ml culture samples were sprayed in 160-ml of a stirred solution of 60% methanol, 66.7 mM HEPES, pH 6.5 that was kept at -45ºC in an ethanol bath. Subsequently, cells were disrupted in a 2-ml screw-cap tube in the presence of 100-um zirconium beads and SDS/phenol for 60 seconds in the Minibeadbeater 8TM (Biospec Products). After chloroform extraction, nucleic acids were precipitated, vacuum-dried, dissolved in distilled water and incubated for 15 min in the presence of DNase I (Qiagen). Finally, RNA was purified by phenol/chloroform extraction and ethanol precipitation as verified by absorption properties in the 200-300 nm region by the use of the ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA).

treatment_protocol: Portions of 40-ml of the pre-culture of B. subtilis were exposed to seven different temperature regimes in 250-ml bottles in a reciprocal-shaking water bath at 65ºC. Duplicate samples were taken when the temperature in the bottles reached 40, 50, 57, 58, 59, 60, and 62ºC (at incubation times of approximately 100, 200, 300, 320, 380, 500 and 720 s, respectively).

tag: strain A163 (food prodcut isolate)

source_name: strain A163, exposed to 30ºC


title: Bacillus subtilis A163 50ºC

scan_protocol: ch1: laser power(%)/sensitivity(%): 80 / 65 ch2: laser power(%)/sensitivity(%): 100 / 60 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

source_name: strain A163, exposed to 50ºC


title: Bacillus subtilis MC85 50ºC

scan_protocol: ch1: laser power(%)/sensitivity(%): 90 / 65 ch2: laser power(%)/sensitivity(%): 100 / 70 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

source_name: strain MC85, exposed to 50ºC

tag: strain MC85 (food product isolate)

source_name: strain MC85, exposed to 30ºC


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-Sry, animal 14

source_name: Liver, XY-Sry C57BL/6J animal 14  Gender:Male

tag: Liver, XY-Sry animal 14


title: Bacillus subtilis 1A1 62ºC replicate 1

scan_protocol: ch1: laser power(%)/sensitivity(%): 85 / 70 ch2: laser power(%)/sensitivity(%): 90 / 70 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

source_name: strain 1A1, exposed to 62ºC

tag: strain 1A1 (lab strain)

source_name: strain 1A1, exposed to 30ºC


title: Bacillus subtilis 1A1 62ºC replicate 2

scan_protocol: ch1: laser power(%)/sensitivity(%): 90 / 70 ch2: laser power(%)/sensitivity(%): 100 / 70 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).


title: Bacillus subtilis MC85 60ºC

source_name: strain MC85, exposed to 60ºC


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-Sry, animal 5

source_name: Liver, XY-Sry C57BL/6J animal 5  Gender:Male

tag: Liver, XY-Sry animal 5


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX Sry, animal 31

source_name: Liver, XX Sry C57BL/6J animal 31  Gender:Male

tag: Liver, XX Sry animal 31


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX Sry, animal 38

source_name: Liver, XX Sry C57BL/6J animal 38  Gender:Male

tag: Liver, XX Sry animal 38


title: drought_seedling

city: Saint Louis

first: Xuefeng

last: Zhou

state: MO

address: One Brooking Dr.

department: Department of Computer Science and Engineering

institute: Washington University in St. Louis

description: Four-week old seedlings small RNAs

data_processing: Sequences of small RNAs were BLAST-matched to the Version 5.0 build of Oryza sativa genome

organism: Oryza sativa

source_name: Four-week old seedlings; drought

growth_protocol: Oryza sativa plants were grown under standard greenhouse conditions

extract_protocol: Total RNA was isolated from the frozen seedlings by using the Trizol (Invitrogen, USA)

tag: Four-week old seedlings


title: salt_seedling

description: Four-week old seedlings small RNAs

source_name: Four-week old seedlings; salt


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-Sry, animal 19

source_name: pool of Liver C57BL/6J mice on chow diet(n=17)

source_name: Liver, XY-Sry C57BL/6J animal 19  Gender:Male

tag: Liver, XY-Sry animal 19


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-Sry, animal 20

source_name: Liver, XY-Sry C57BL/6J animal 20  Gender:Male

tag: Liver, XY-Sry animal 20


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX Sry, animal 32

source_name: Liver, XX Sry C57BL/6J animal 32  Gender:Male

tag: Liver, XX Sry animal 32


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX Sry, animal 18

source_name: Liver, XX Sry C57BL/6J animal 18  Gender:Male

tag: Liver, XX Sry animal 18


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XX Sry, animal 9

source_name: Liver, XX Sry C57BL/6J animal 9  Gender:Male

tag: Liver, XX Sry animal 9


title: control_seedling

description: Four-week old seedlings small RNAs

source_name: Four-week old seedlings; control


title: Bacillus subtilis 1A1 60ºC replicate 1

source_name: strain 1A1, exposed to 60ºC


title: Bacillus subtilis 1A1 60ºC replicate 2


title: Bacillus subtilis 1A1 59ºC replicate 2

scan_protocol: ch1: laser power(%)/sensitivity(%): 90 / 75 ch2: laser power(%)/sensitivity(%): 100 / 70 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

source_name: strain 1A1, exposed to 59ºC


title: Bacillus subtilis 1A1 59ºC replicate 1


title: GM12878_sample20

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Stanford-Myers

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

source_name: GM12878, Stanford

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 STarrays

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol or RNEasy protocol

treatment_protocol: cells were supplied as frozen pellets, pellets in trizol, pellets in RNA later or pellets in RLT buffer

tag: cell pellet in RLT

tag: Coriell cell line repository identifier


title: pool of liver from C57BL/6J mice on chow diet (n=17) vs Liver, XY-Sry, animal 27

tag: pool of Liver C57BL/6J mice on chow diet(n=17)

source_name: Liver, XY-Sry C57BL/6J animal 27  Gender:Male

tag: Liver, XY-Sry animal 27


title: Bacillus subtilis 1A1 58ºC replicate 2

source_name: strain 1A1, exposed to 58ºC

source_name: strain 1A1, exposed to 30ºC


title: GM12878_sample17

description: Uwash-Stamatoyannopoulos

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

source_name: GM12878, Uwash

tag: cell pellet in RNA later


title: Bacillus subtilis 1A1 57ºC replicate 2

source_name: strain 1A1, exposed to 57ºC


title: GM12878_sample18

description: Uwash-Stamatoyannopoulos

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays


title: GM12878_sample19

description: Stanford-Myers


title: Bacillus subtilis 1A1 50ºC replicate 2

scan_protocol: ch1: laser power(%)/sensitivity(%): 85 / 70 ch2: laser power(%)/sensitivity(%): 100 / 65 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

source_name: strain 1A1, exposed to 50ºC


title: GM12878_sample15

description: Broad-Bernstein

source_name: GM12878, Broad

tag: cell pellet in Trizol


title: Bacillus subtilis 1A1 57ºC replicate 1

scan_protocol: ch1: laser power(%)/sensitivity(%): 90 / 65 ch2: laser power(%)/sensitivity(%): 100 / 65 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).


title: Bacillus subtilis 1A1 58ºC replicate 1


title: K562_sample21

description: Stanford-Myers

source_name: K562, Stanford

tag: K562 (ATCC)


title: GM12878_sample14

description: Yale-Snyder

source_name: GM12878, Yale


title: GM12878_sample13

description: Yale-Snyder


title: GM12878_sample16

description: Broad-Bernstein


title: GM12878_sample12

description: Yale-Snyder


title: GM12878_sample11

description: Affymetrix-Gingeras

source_name: GM12878, Affymetrix


title: Bacillus subtilis 1A1 50ºC replicate 1

scan_protocol: ch1: laser power(%)/sensitivity(%): 85 / 65 ch2: laser power(%)/sensitivity(%): 90 / 70 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).

tag: strain 1A1 (lab strain)


title: K562_sample18

description: Uwash-Stamatoyannopoulos

source_name: K562, Uwash


title: GM12878_sample10

description: Affymetrix-Gingeras


title: K562_sample20

description: Stanford-Myers


title: K562_sample19

description: Uwash-Stamatoyannopoulos


title: K562_sample15

description: Yale-Snyder

source_name: K562, Yale


title: Bacillus subtilis 1A1 40ºC replicate 2

source_name: strain 1A1, exposed to 40ºC


title: Bacillus subtilis 1A1 40ºC replicate 1

scan_protocol: ch1: laser power(%)/sensitivity(%): 80 / 70 ch2: laser power(%)/sensitivity(%): 95 / 75 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).


title: K562_sample14

description: Yale-Snyder


title: Bacillus subtilis 1A1 30ºC

scan_protocol: ch1: laser power(%)/sensitivity(%): 80 / 60 ch2: laser power(%)/sensitivity(%): 90 / 70 Slides were scanned with a ScanArray 5000 laser scanner (Perkin Elmer Life Sciences). The TIFF-images were quantified with the software package ImaGene version 5.6.1 (BioDiscovery, El Segundo, CA, USA).


title: K562_sample13

description: Affymetrix-Gingeras

source_name: K562, Affymetrix


title: K562_sample16

description: Broad-Bernstein

source_name: K562, Broad


title: iPS M2, technical rep3

status: Public on Dec 07 2008

city: Beijing

first: hongkui

last: deng

address: Yiheyuan Road 5#, Haidian District

department: College of Life Sciences

country: China

institute: Peking University

description: Gene expression data from Induced pluripotent stem cell line (iPS) M2

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

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

data_processing: Raw data were first normalized with dChip. To compare every two samples, the median of each probe in three replications of each sample was chosen as the signal value of this probe by the following selection criteria:  coefficient of variation (C.V) <0.5 i

organism: Macaca mulatta

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Fibroblasts were cultured in Dulbeccos modified eagle medium (DMEM, Hyclone) containing 10% fetal bovine serum (FBS, Invitrogen). Embryonic stem (ES) cells (R366.4) were maintained on mitomycin C-treated MEFs in DMEM (Invitrogen) with 15% FBS (Hyclone),

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

treatment_protocol: ES and ES cells with good morphology were manually removed from culture for total RNA purification.

tag: derived form Rhesus monkey(0237#) ear skin firoblasts


title: iPS M2, technical rep2

source_name: Induced pluripotent stem cell line (iPS) M2

tag: derived form Rhesus monkey(0236#) ear skin firoblasts


title: K562_sample17

description: Broad-Bernstein


title: ES 366.4, technical rep3

description: Gene expression data from Rhesus monkey embryonic stem cell line(366.4)

tag: Established by JAMES A. THOMSON, etal, (1995, PNAS)


title: K562_sample12

description: Affymetrix-Gingeras


title: ES 366.4, technical rep1

source_name: Rhesus monkey embryonic stem cell line(366.4)


title: iPS M2, technical rep1

tag: derived form Rhesus monkey(0235#) ear skin firoblasts


title: Fibroblast, technical rep3

description: Gene expression data from Rhesus monkey(0235#) ear skin firoblasts.

source_name: Adult somatic skin fibroblasts(0235#)

tag: 3 years old Rhesus monkey(0235#) ear skin firoblasts


title: ES 366.4, technical rep2


title: Fibroblast, technical rep2


title: Fibroblast, technical rep1


title: eve07h.61slide87

status: Public on Dec 31 2008

city: Chicago

first: Christopher

middle: David

last: Brown

state: IL

department: Human Genetics

institute: University of Chicago

description: no additional information

hyb_protocol: Samples were hybridized to a PCR spotted whole genome Drosophila microarray as previously described (Li and White 2003, PMID: 12852852).

scan_protocol: Slides were scanned on a GenePix 4000B at 560 (red) and 530 (green) PMT.

data_processing: The developmental time course gene expression data was obtained from wild-type, as well as FTZ and EVE mutant flies.  Probes not present in all the arrays, flagged, and BLANK probes were removed from the data before the normalization.  This resulted in 13,229 probes included per array.  All data analyses were conducted in Perl and R (R Development Core Team).  Background subtraction was performed with the normexp function (offset=50) in the LIMMA package using median foreground and background intensities.  Within-array normalization was performed with print-tip loess, between array normalization was performed by quantile normalization, as implemented in the LIMMA package (6).  Differentially expressed genes were identified using an empirical Bayes methodology (Smyth 2004), with a false discovery rate of 0.001 (Benjamini and Hochberg 1995), also implemented in the LIMMA package.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster embryos,eve mutant,7hours AEL

label_protocol: RNA samples were directly compared to a Drosophila common reference sample collected throughout embryogenesis from 0-22h as previously described (Arbeitman et al., 2002).

extract_protocol: Trizol

treatment_protocol: ftz and eve mutant flies were maintained over GFP balancers.  Desired stages were collected and genotyped for microarrays as previously described (Ghanim and White 2006, PMID: 17068956).

tag: experimental genotype

source_name: Reference

tag: Common reference RNA, collected from embryos throughout embryogenesis (0-22h)


title: ftz08h.52slide8

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,8hours AEL


title: Seedlings Constant White Light 20hr Rev

status: Public on Dec 06 2008

city: La Jolla

first: Samuel

middle: P

last: Hazen

address: 9500 Gilman Drive

department: Cell and Developmental Biology

institute: University of California San Diego

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G, GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor Affy package

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings after 20 h in constant white light

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

growth_protocol: Seeds sown on filter paper on media (1x MS, 3% sucrose, 0.8% agar); stratified at 4C for 4 d; grown for 7 d at 22C in 12-h light (cool white fluorescence tubes, ~100 µmol m-2 s-1)/12-h dark cycles before being released into free-running conditions of constant white light, 22C; sample collection initiated at subjective dawn of day 8

extract_protocol: Qiagen's RNeasy Plant Mini Kit was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: Samples were collected at 4-h intervals (by freezing in liquid nitrogen) while growing in constant light conditions

tag: Genotype

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:20 hrs


title: Seedlings Constant White Light 00hr Rev

source_name: Arabidopsis seedlings after 0 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:0 hrs


title: Fetal Heart-4

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

description: Fetal Heart-4

hyb_protocol: 825 ng of Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol. cRNA was hybridized to 4x44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer’s instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

source_name: Fetal Heart-4

label_protocol: Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent Technologies, Santa Clara, CA, USA), cDNA was reverse transcribed from each RNA sample, and cRNA was then transcribed and fluorescently labeled from each cDNA sample.

extract_protocol: Total RNA was isolated as described previously in Trizol (Invitrogen) followed by purification over a Qiagen RNeasy column (Qiagen).

tag: Fetal cardiomyocytes

source_name: Pooled Reference

tag: Pooled RNA from undifferentiated and differentiated hESCs


title: Seedlings Constant White Light 04hr Rev

source_name: Arabidopsis seedlings after 4 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:4 hrs


title: Seedlings Constant White Light 32hr Rev

source_name: Arabidopsis seedlings after 32 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:32 hrs


title: Seedlings Constant White Light 16hr Rev

source_name: Arabidopsis seedlings after 16 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:16 hrs


title: Seedlings Constant White Light 24hr Rev

source_name: Arabidopsis seedlings after 24 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:24 hrs


title: Seedlings Constant White Light 24hr Fwd


title: Seedlings Constant White Light 28hr Rev

source_name: Arabidopsis seedlings after 28 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:28 hrs


title: Seedlings Constant White Light 12hr Rev

source_name: Arabidopsis seedlings after 12 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:12 hrs


title: Seedlings Constant White Light 20hr Fwd


title: Seedlings Constant White Light 08hr Rev

source_name: Arabidopsis seedlings after 8 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:8 hrs


title: Seedlings Constant White Light 36hr Rev

source_name: Arabidopsis seedlings after 36 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:36 hrs


title: Seedlings Constant White Light 04hr Fwd


title: Seedlings Constant White Light 12hr Fwd


title: Seedlings Constant White Light 44hr Fwd

source_name: Arabidopsis seedlings after 44 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:44 hrs


title: Fetal Heart-1

description: Fetal Heart-1

source_name: Fetal Heart-1


title: Seedlings Constant White Light 08hr Fwd


title: Fetal Heart-2

description: Fetal Heart-2

source_name: Fetal Heart-2


title: Seedlings Constant White Light 40hr Rev

source_name: Arabidopsis seedlings after 40 h in constant white light

value: Wild-type; Ecotype:Col-0; Tissue:whole seedling; Time in entraining conditions:7 d; Time in constant white light:40 hrs


title: Fetal Heart-3

description: Fetal Heart-3

source_name: Fetal Heart-3


title: hESC-CM-1

tag: Cardiomyocytes that were differentiated then purified from hESCs


title: Seedlings Constant White Light 16hr Fwd


title: hESC-CM-2


title: Seedlings Constant White Light 44hr Rev


title: UACC62

status: Public on Dec 05 2008

type: protein

city: Cambridge

first: Jinyan

last: Du

state: MA

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Institute

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G12 of Output 050307-3.csv

hyb_protocol: antibody coupled beads were incubated with total protein lysates to capture targeted analytes; the beads were then labelled with biotinylated phospho-tyrosine antibodies and streptavidin, R-phycoerythrin conjugates

scan_protocol: The data were collected with a Luminex 100 instrument

data_processing: The background readings for each capture antibody were obtained using microspheres incubated with 1x cell lysis buffer (Cell Signaling Technology). Values were considered positive if they were 3-fold over the background and represented by log2-transformation of the folds over background. Negative values were threshold to -5.

molecule: protein

source_name: melanoma

label_protocol: According to manufacturer's protocol

growth_protocol: Cells from each cell line were grown on a 100mm dish to about 80% confluency.

extract_protocol: Media were removed and ice-cold 1x cell lysis buffer were added (2ml per 100mm dish); lysates were collected by scrapping and then incubated on ice for 30min; after centrifuging at 13000rpm on a desktop centrifuge for 10min; supernatant was collected; the

tag: melanoma


title: ZR-75-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F5 of Output 050307-3.csv

source_name: breast

tag: breast


title: UO31

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H11 of Output 050307-3.csv

source_name: osteosarcoma

tag: osteosarcoma


title: Seedlings Constant White Light 32hr Fwd


title: U2OS

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H1 of Output 050307-3.csv


title: U251

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E5 of Output 050307-3.csv

source_name: glioma

tag: glioma


title: Seedlings Constant White Light 36hr Fwd


title: U87

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G2 of Output 050307-3.csv


title: Control_lung

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: See the manuscript by Hiratsuka and co-workers.

hyb_protocol: According to standard Affymetrix's procedure.

label: biotin-labelled

source_name: normal lung

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets according to standard Affymetrix's procedure.

growth_protocol: See Materials and Methods in the text by Hiratsuka and co-workers.

extract_protocol: Total RNA were isolated from frozen tissues by TRIzol reagent.

tag: Normal lungs of C57BL/6 mice without injection of tumor cells.


title: U138MG

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B9 of Output 050307-3.csv


title: B16-bearing lung

scan_protocol: According to standard Affymetrix's procedure.

source_name: B16-bearing lung

treatment_protocol: See Materials and Methods in the text by Hiratsuka and co-workers.

tag: The lung of C57BL/6 mice injected with 1x107 B16 melanoma cells. See materials and methods in the text by Hiratsuka and co-workers.


title: Beating EB-1

description: Beating EB-1

source_name: Beating EB-1

tag: Beating embryoid bodies that were differentiated from hESCs

source_name: Pooled Reference


title: LLC-bearing lung

source_name: LLC-bearing lung

extract_protocol: Total RNA samples (lungs from B16-, LLC-bearing and normal mouse) were isolated from frozen tissues by TRIzol reagent.

tag: Lings of of C57BL/6 mice injected by Lewis lung carcinoma cells


title: hESC-CM-3

tag: Pooled RNA from undiffereniated and differentiated hESCs


title: U118

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B2 of Output 050307-3.csv


title: hESC-3

tag: Undifferentiated human embryonic stem cells


title: Beating EB-4

description: Beating EB-4

source_name: Beating EB-4


title: Beating EB-2

description: Beating EB-2

source_name: Beating EB-2


title: hESC-CM-4


title: Beating EB-3

description: Beating EB-3

source_name: Beating EB-3


title: hESC-4


title: Seedlings Constant White Light 40hr Fwd


title: TT

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B10 of Output 050307-3.csv

source_name: thyroid

tag: thyroid


title: THP-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G2 of Output 050307-2.csv

source_name: AML

tag: AML


title: TK-10

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D3 of Output 050307-2.csv

source_name: renal

tag: renal


title: TC71

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G10 of Output 050307-3.csv

source_name: EWS

tag: EWS


title: TF-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E2 of Output 050307-2.csv

source_name: erythroleukemia

tag: erythroleukemia


title: T47D

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B6 of Output 050307-3.csv


title: T98G

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E9 of Output 050307-3.csv


title: TC32

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H7 of Output 050307-3.csv


title: TC466

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F2 of Output 050307-3.csv


title: SW620

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G11 of Output 050307-3.csv

source_name: colon

tag: colon


title: SW480

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C1 of Output 050307-2.csv


title: SNU387

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F1 of Output 050307-2.csv

source_name: liver

tag: liver


title: SNU-5

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E11 of Output 050307-1.csv

source_name: gastric

tag: gastric


title: SNB75

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D11 of Output 050307-3.csv

source_name: glioma


title: SKMEL2

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H12 of Output 050307-3.csv

source_name: melanoma

tag: melanoma


title: SKMEL5

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H10 of Output 050307-3.csv


title: Seedlings Constant White Light 28hr Fwd

source_name: Arabidopsis seedlings after 28 h in constant white light

tag: Genotype


title: SNB-19

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A3 of Output 050307-3.csv

tag: glioma


title: SKBR3

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B8 of Output 050307-3.csv

source_name: breast

tag: breast


title: SN12C

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A11 of Output 050307-3.csv


title: SF539

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E1 of Output 050307-3.csv


title: SF295

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C9 of Output 050307-3.csv


title: Seedlings Constant White Light 00hr Fwd

source_name: Arabidopsis seedlings after 0 h in constant white light

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: OVCAR8

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A2 of Output 050307-3.csv

source_name: ovary

tag: ovary


title: PC-3

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H2 of Output 050307-3.csv

source_name: prostate

tag: prostate


title: SK-ES-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E3 of Output 050307-2.csv


title: SHSY5Y

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E2 of Output 050307-3.csv

source_name: neuroblastoma

tag: neuroblastoma


title: MDAMB453

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A4 of Output 050307-3.csv


title: MDAMB231

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F4 of Output 050307-3.csv


title: OVCAR4

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F10 of Output 050307-3.csv


title: OVCAR5

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D4 of Output 050307-3.csv


title: NCI-H1568

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C11 of Output 050307-2.csv

source_name: lung

tag: lung


title: OVCAR3

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F3 of Output 050307-2.csv


title: NCI-H1395

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A10 of Output 050307-2.csv


title: NCI-ADR-RES

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C8 of Output 050307-3.csv


title: MMIS

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H11 of Output 050307-2.csv

source_name: MM

tag: MM


title: LOXIMVI

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B4 of Output 050307-3.csv


title: M059K

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C3 of Output 050307-2.csv


title: MCF-7

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E6 of Output 050307-3.csv


title: MOLT4

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B3 of Output 050307-2.csv

source_name: ALL

tag: ALL


title: MeWo

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B12 of Output 050307-3.csv


title: LnCAP

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D5 of Output 050307-3.csv


title: Ramos

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H2 of Output 050307-2.csv

source_name: Burkitt's lymphoma

tag: Burkitt's lymphoma


title: RDES

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B1 of Output 050307-3.csv

source_name: EWS


title: SF268

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A12 of Output 050307-3.csv


title: RPMI-8226

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D7 of Output 050307-3.csv


title: LN827

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H4 of Output 050307-3.csv


title: LMS676

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G5 of Output 050307-3.csv

source_name: LMS

tag: LMS


title: LN18

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C11 of Output 050307-3.csv


title: LMS05

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C7 of Output 050307-3.csv


title: LN229

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A9 of Output 050307-3.csv


title: K562

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G6 of Output 050307-3.csv

source_name: CML

tag: CML


title: REH

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A3 of Output 050307-2.csv

source_name: AML

tag: AML


title: Jurkat

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A7 of Output 050307-3.csv


title: IGR-OVI

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F7 of Output 050307-3.csv


title: Hs683

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A6 of Output 050307-3.csv


title: Hs578T

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H6 of Output 050307-3.csv


title: KATO-III

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D11 of Output 050307-1.csv

source_name: stomach

tag: stomach


title: Kasumi

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G8 of Output 050307-3.csv


title: KM12

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C6 of Output 050307-3.csv

source_name: colon

tag: colon


title: Huh7

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D2 of Output 050307-2.csv

source_name: liver

tag: liver


title: HT-29

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B5 of Output 050307-3.csv


title: HeLa

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H11 of Output 050307-1.csv

source_name: Cervix

tag: Cervix


title: Hep3B2

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C1 of Output 050307-3.csv


title: HepG2

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B3 of Output 050307-3.csv


title: HOS

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E10 of Output 050307-1.csv

source_name: Osteosarcoma

tag: Osteosarcoma


title: HOP-92

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E3 of Output 050307-3.csv


title: LMS04

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G7 of Output 050307-3.csv


title: HOP-62

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C2 of Output 050307-3.csv


title: LMS03

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G1 of Output 050307-2.csv


title: HCT-116

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F6 of Output 050307-3.csv


title: HCT15

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B1 of Output 050307-2.csv


title: HCC-95

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D3 of Output 050307-3.csv


title: HCC-827

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D9 of Output 050307-2.csv


title: H82

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D8 of Output 050307-3.csv


title: HCC-4006

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F10 of Output 050307-2.csv


title: HCC515

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D10 of Output 050307-3.csv


title: H4

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A8 of Output 050307-3.csv

source_name: glioma

tag: glioma


title: H522

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B11 of Output 050307-3.csv


title: HCC1359

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E10 of Output 050307-3.csv


title: H526

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E7 of Output 050307-3.csv


title: H358

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E1 of Output 050307-2.csv


title: H322M

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D6 of Output 050307-3.csv


title: HCC38

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C11 of Output 050307-1.csv

source_name: breast

tag: breast


title: INA6

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A12 of Output 050307-2.csv


title: H187

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A2 of Output 050307-2.csv


title: HCC2935

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E7 of Output 050307-2.csv


title: H1975

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G12 of Output 050307-2.csv


title: H1944

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B12 of Output 050307-2.csv


title: H226

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F9 of Output 050307-3.csv


title: H23

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G8 of Output 050307-2.csv


title: H1650

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G4 of Output 050307-2.csv


title: H3K9me3 in the dim-5 mutant

type: genomic

city: Eugene

first: Zachary

middle: A

last: Lewis

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

description: ChIP-chip experiment

hyb_protocol: See Lee et al. (2006) Nature Protocols

scan_protocol: Arrays were scanned using the Genepix 4000 scanner. Data was aquired using Genepix pro software (Axon).

data_processing: The Value column was determined by creating a log2 value from the median normalized log2 value from the .gpr file

molecule: genomic DNA

organism: Neurospora crassa

source_name: dim-5 mutant (Selker lab strain N3436)

label_protocol: See Lee et al. (2006) Nature Protocols

growth_protocol: See Tamaru et al. (2003) Nature Genetics for procedure

tag: total input

tag: methylated DNA immunoprecipitated fraction


title: H69

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C3 of Output 050307-3.csv


title: GOS3

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E12 of Output 050307-3.csv


title: H1299

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C5 of Output 050307-3.csv


title: GIST882

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B2 of Output 050307-2.csv

source_name: GIST

tag: GIST


title: GAMG

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A10 of Output 050307-3.csv


title: DU145

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D9 of Output 050307-3.csv

source_name: prostate

tag: prostate


title: DSK-8

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G11 of Output 050307-1.csv


title: EKVX

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F1 of Output 050307-3.csv

source_name: lung

tag: lung


title: DK-MG

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F2 of Output 050307-2.csv


title: EWS502

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H3 of Output 050307-3.csv

tag: EWS


title: DLD-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F11 of Output 050307-1.csv


title: H460

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G3 of Output 050307-3.csv


title: DBTRG-05MG

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F12 of Output 050307-3.csv


title: H2009

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B8 of Output 050307-2.csv


title: COLO205

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G1 of Output 050307-3.csv


title: CAKI-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A5 of Output 050307-3.csv

source_name: renal

tag: renal


title: CaPan-2

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: B11 of Output 050307-1.csv

source_name: Pancreas

tag: Pancreas


title: BT549

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F11 of Output 050307-3.csv


title: BT20

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: G9 of Output 050307-3.csv


title: BE(2)C

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H1 of Output 050307-2.csv

source_name: neuroblastoma

tag: neuroblastoma


title: CCRF-CEM

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C12 of Output 050307-3.csv

source_name: ALL

tag: ALL


title: ACHN

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D1 of Output 050307-3.csv


title: AsPC-1

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: A11 of Output 050307-1.csv


title: A673

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D1 of Output 050307-2.csv

source_name: EWS


title: A549

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: E4 of Output 050307-3.csv


title: A498

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: F3 of Output 050307-3.csv


title: A431

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C2 of Output 050307-2.csv


title: distal colon AOM rat 3

city: Sydney

first: Caroline

middle: Audrey

last: Kerr

state: NSW

address: 11 Julius Ave North Ryde

department: Moelcular health Technologies

country: Australia

institute: CSIRO

description: Gene expression data from azoxymethane treated rat colonic epithelium.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Rattus norvegicus

source_name: Rat scraped colonic epithelium (distal)

label_protocol: Approximately 4.5 µg of total RNA was processed to produce biotinylated cRNA targets according to the standard Affymetrix protocol.

growth_protocol: Animals were housed in wire-bottomed caging in a temperature controlled room (22-24°C) with a 12 h light/dark cycle. They were randomly allocated into two groups (n=20) with approximately equal body weights. They were given free access to water and modified AIN-93G diet.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by QIAGEN RNAeasy column cleanup.

treatment_protocol: Rats were injected with azoxymethane (AOM; 15 mg/kg subcutaneously).  Six hours after injection the rats were anaesthetised with isoflurane and killed by exsanguination. The large bowel (excluding the rectum) was removed, opened longitudinally along the mesenteric border and digesta removed. The colon was rinsed clean with PBS and transferred to a chilled ceramic plate for dissection and the distal and proximal sections scraped off with a microscope slide and placed in RNAlater solution then stored at -80oC!Sample_growth_protocol = Animals were housed in wire-bottomed caging in a temperature controlled room (22-24°C) with a 12 h light/dark cycle.

tag: Dawley rats weighing approximately 176 +- 2.4g


title: distal colon AOM rat 10


title: distal colon AOM rat 5


title: proximal colon AOM rat 6

source_name: Rat scraped colonic epithelium (proximal)


title: proximal colon AOM rat 10


title: proximal colon AOM rat 8


title: A172

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H5 of Output 050307-3.csv


title: distal colon AOM rat 7


title: distal colon AOM rat 4


title: 8MGBA

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: H9 of Output 050307-3.csv


title: distal colon AOM rat 8


title: distal colon AOM rat 6


title: proximal colon AOM rat 7


title: distal colon AOM rat 2


title: 786-0

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D2 of Output 050307-3.csv


title: 501mel

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: D12 of Output 050307-3.csv

source_name: melanoma

tag: melanoma


title: distal colon AOM rat 1


title: proximal colon AOM rat 5


title: proximal colon AOM rat 3