title: RTEC11 cells cultured at nonpermissive temperature for 3 days-2

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: A rat conditionally immortalized tracheal epithelial cell line, RTEC11, derived from transgenic rats harboring a temperature-sensitive simian virus 40 large T-antigen was used. RTEC11 cells were cultured at nonpermissive (39°C) temperature for 3 days.

hyb_protocol: Hybridization Protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: phycoerythrin

source_name: Rat tracheal epithelial cell line RTEC11

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K.K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.


title: B cell line RPMI8226control (6h)

status: Public on Jul 17 2007

type: RNA

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description: B cell line RPMI8226control (6h)

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16 h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: total RNA

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates, according to the manufacturer’s protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy (QIAGEN), according to manufacture’s instructions.

tag: Lymphocyte


title: NK cell line

description: NK cell line


title: U937 control

description: U937 control

tag: Myelomonocytic leukemia


title: Normal bronchial epithelial cell, primary

tag: Normal epithelial cell,primary


title: RTEC11 cells cultured at nonpermissive temperature for 3 days-1

organism: Rattus norvegicus

tag: Rat tracheal epithelial cell line RTEC11


title: RTEC11 cells cultured at permissive temperature for 3 days-1

description: A rat conditionally immortalized tracheal epithelial cell line, RTEC11, derived from transgenic rats harboring a temperature-sensitive simian virus 40 large T-antigen was used. RTEC11 cells were cultured at permissive (33°C) temperature for 3 days.


title: Intraabdominal stromo vascular fraction, rep2

city: Boston

first: Stephane

last: Gesta

state: MA

address: One Joslin Place

country: USA

institute: Joslin Diabetes Center

description: Stromo vascular fraction from intraabdominal adipose tissue

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome U74Av2  . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 G7

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

label: Biotin

organism: Mus musculus

label_protocol: Double-stranded cDNA synthesis was reverse-transcribed from 15 µg of isolated mRNA by using the SuperScript Choice system (Invitrogen) with an oligo(dT) primer containing a T7 RNA polymerase promoter site. Double-stranded cDNA was purified with Phase Lock Gel (Eppendorf). Biotin-labeled cRNA was transcribed by using a BioArray RNA transcript labeling kit (Enzo).

growth_protocol: To obtain purified cell fractions, ten 6- to 7-week-old C57BL/6 males were killed, and epididymal and flank subcutaneous adipose tissue was removed under sterile conditions. Tissues from each depot were pooled, minced, and digested with 1 mg/ml collagenase for 45 min at 37°C in DMEM/Ham’s F-12 1:1 (DMEM/F12) containing 1% BSA and antibiotics (100 units/ml penicillin, 0.1 mg/ml streptomycin, 2.5 mg/ml fungizone, and 50 mg/ml gentamicin). Digested tissues were filtered through sterile 150-µm nylon mesh and centrifuged at 250 × g for 5 min. The floating fraction consisting of pure isolated adipocytes was then removed and washed two more times before proceeding to RNA extraction. The pellet, representing the SVF containing preadipocytes and other cell types, was resuspended in erythrocyte lysis buffer consisting of 154 mM NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA for 10 min. The cell suspension was centrifuged at 500 × g for 5 min and then resuspended in a culture medium consisting of DMEM/F12, 10% FCS, and antibiotics. This cell suspension was filtered through a 25-µm sterile nylon mesh before being plated on a 10-cm plate at 60,000 cells per cm². Sixteen hours after plating, cells were extensively washed with PBS and then subjected to RNA extraction

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

tag: Strain

tag: Gender

value: male

tag: Age

value: 42 to 49 days

tag: Tissue

value: epididymal adipose tissue


title: Intraabdominal stromo vascular fraction, rep1

source_name: Stromo vascular fraction from intraabdominal adipose tissue


title: B cell line Raji-1

description: B cell line Raji-1


title: Subcutaneous stromo vascular fraction, rep3

description: Stromo vascular fraction from subcutaneous adipose tissue

value: subcutaeous flank adipose tissue


title: Intraabdominal isolated adipocytes, rep2

description: Isolated adipocytes from intraabdominal adipose issue


title: RTEC11 cells cultured at permissive temperature for 3 days-2


title: Subcutaneous stromo vascular fraction, rep2

source_name: Stromo vascular fraction from subcutaneous adipose tissue


title: Intraabdominal isolated adipocytes, rep1

source_name: Isolated adipocytes from intraabdominal adipose issue


title: Subcutaeous isolated adipocytes, rep2

description: Isolated adipocytes from subcutaeous adipose tissue


title: Subcutaeous isolated adipocytes, rep3

source_name: Isolated adipocytes from subcutaeous adipose tissue


title: Subcutaneous stromo vascular fraction, rep1


title: Subcutaeous isolated adipocytes, rep1


title: Intraabdominal isolated adipocytes, rep3


title: 110spc4 aerobic PSY 3

status: Public on Jul 14 2007

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: Gene expression data from B. japonicum wild-type strain grown aerobically

hyb_protocol: Modification of Affymetrix protocol used for P. aeruginosa (2-2.5 mg of free-living cultures and 6-7.5 mg of nodules cDNA were hybridised)

scan_protocol: standard Affymetrix procedures

data_processing: GeneChip Operating Software (GCOS) version 1.1 (Affymetrix), global scaling to a target intensity of 500

organism: Bradyrhizobium japonicum

label_protocol: 2.8 mg (free-living cultures) and 7.8 mg (nodules)  cDNA were labeled with biotin

growth_protocol: cells were grown until OD600 0.4-0.5 in PSY medium or as soybean bacteroids

extract_protocol: cells were prepared as described by Pessi et al.(2007) accepted manuscript

treatment_protocol: no treatment was applied

tag: Genotype

tag: Growth condition

value: aerobic

tag: Medium

value: PSY


title: 110spc4 aerobic PSY 15

source_name: B. japonicum wild-type strain grown aerobically


title: 110spc4 aerobic PSY 13


title: 110spc4 aerobic PSY 7


title: 110spc4 aerobic PSY 6


title: 110spc4 aerobic PSY 9


title: 110spc4 aerobic PSY 2


title: soybean root control 3

description: Gene expression data from Glycine max roots

organism: Glycine max

source_name: Soybean root RNA extract w/o bacteria

value: soybean

tag: Time

value: 21 Days


title: 110spc4 aerobic PSY 11


title: 110spc4 aerobic PSY 12


title: soybean root control 2


title: 110spc4 micro PSY 22

description: Gene expression data from B. japonicum wild-type strain grown microaerobically

value: micro


title: 110spc4 aerobic PSY 5


title: 110spc4 micro PSY 19

source_name: B. japonicum wild-type strain grown microaerobically


title: 110spc4 aerobic PSY 4


title: 110spc4 micro PSY 18


title: 110spc4 micro PSY 20


title: 110spc4 micro PSY 21


title: 110spc4 aerobic PSY 14


title: 110spc4 micro PSY 23


title: 110spc4 aerobic PSY 10


title: 110spc4 aerobic PSY 8


title: 110spc4 micro PSY 16


title: 110spc4 micro PSY 15


title: 110spc4 aerobic PSY 1


title: 110spc4 micro PSY 17


title: 110spc4 micro PSY 14


title: soybean root control 1


title: 110spc4 micro PSY 13


title: 110spc4 micro PSY 10


title: 110spc4 micro PSY 9


title: 110spc4 micro PSY 11


title: 110spc4 micro PSY 12


title: 110spc4 micro PSY 7


title: 110spc4 micro PSY 6


title: 110spc4 micro PSY 8


title: 110spc4 micro PSY 4


title: 110spc4 micro PSY 1


title: 110spc4 micro PSY 2


title: 110spc4 micro PSY 3


title: 110spc4 micro PSY 5


title: 110spc4 nodules soybean 21 Days 3

description: Gene expression data from B. japonicum wild-type strain in nodules soybean 21 days post infection

value: nodules


title: Col-0_mock_9h_set3

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

description: Col-0 infiltrated with water, harvested 9h after infiltration in set3 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. Col-0_mock_3h_set1, Col-0_hrcC_3h_set1, pad4-1_hrcC_3h_set1, sid2-2_hrcC_3h_set1, Col-0_mock_9h_set1, Col-0_hrcC_9h_set1, pad4-1_hrcC_9h_set1, sid2-2_hrcC_9h_set1, Col-0_mock_3h_set2, Col-0_hrcC_3h_set2, pad4-1_hrcC_3h_set2, sid2-2_hrcC_3h_set2, Col-0_mock_9h_set2, Col-0_hrcC_9h_set2, pad4-1_hrcC_9h_set2, sid2-2_hrcC_9h_set2, Col-0_mock_3h_set3, Col-0_hrcC_3h_set3, pad4-1_hrcC_3h_set3, sid2-2_hrcC_3h_set3, Col-0_mock_9h_set3, Col-0_hrcC_9h_set3, pad4-1_hrcC_9h_set3, sid2-2_hrcC_9h_set3, were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0, leaves, Pseudomonas syringae pv. tomato DC3000 mock-infiltrated, 9h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 9h later.

value: leaves

value: 4 week-old

tag: Treatment

value: water

tag: Time point


title: Col-0_mock_3h_set3

description: Col-0 infiltrated with water, harvested 3h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, Pseudomonas syringae pv. tomato DC3000 mock-infiltrated, 3h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 3h later.


title: 110spc4 nodules soybean 13 Days 3

description: Gene expression data from B. japonicum wild-type strain in nodules soybean 13 days post infection

value: 13 Days


title: sid2-2_hrcC_3h_set3

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 3h later.


title: sid2-2_hrcC_9h_set3

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 9h later.


title: 110spc4 nodules soybean 21 Days 4

source_name: B. japonicum wild-type strain in nodules soybean 21 days post infection


title: pad4-1_hrcC_9h_set3

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: 110spc4 nodules soybean 21 Days 1


title: 110spc4 nodules soybean 21 Days 2


title: 110spc4 nodules soybean 13 Days 2

source_name: B. japonicum wild-type strain in nodules soybean 13 days post infection


title: 110spc4 nodules soybean 10 Days 2

description: Gene expression data from B. japonicum wild-type strain in nodules soybean 10 days post infection

value: 10 Days


title: 110spc4 nodules soybean 13 Days 1


title: 110spc4 nodules soybean 13 Days 4


title: 110spc4 nodules soybean 31 Days 3

description: Gene expression data from B. japonicum wild-type strain in nodules soybean 31 days post infection

value: 31 Days


title: pad4-1_hrcC_3h_set3

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: 110spc4 nodules soybean 10 Days 1

source_name: B. japonicum wild-type strain in nodules soybean 10 days post infection


title: U937+antibody

source_name: total RNA


title: Col-0_mock_9h_set2

description: Col-0 infiltrated with water, harvested 9h after infiltration in set2 experiment.


title: Col-0_mock_3h_set2

description: Col-0 infiltrated with water, harvested 3h after infiltration in set2 experiment.


title: pad4-1_hrcC_9h_set2

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set2 experiment.


title: 110spc4 nodules soybean 31 Days 2

source_name: B. japonicum wild-type strain in nodules soybean 31 days post infection


title: N50-97 aerobic PSY 5

description: Gene expression data from B. japonicum rpoN12 mutant strain grown aerobically


title: 110spc4 nodules soybean 31 Days 1


title: pad4-1_hrcC_3h_set2

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set2 experiment.


title: Col-0_hrcC_9h_set2

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h


title: N50-97 aerobic PSY 1

source_name: B. japonicum rpoN12 mutant strain grown aerobically


title: Col-0_mock_9h_set1

description: Col-0 infiltrated with water, harvested 9h after infiltration in set1 experiment.


title: Col-0_mock_3h_set1

description: Col-0 infiltrated with water, harvested 3h after infiltration in set1 experiment.


title: N50-97 aerobic PSY 3


title: N50-97 aerobic PSY 6


title: sid2-2_hrcC_9h_set1

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set1 experiment.


title: N50-97 micro PSY 5

description: Gene expression data from B. japonicum rpoN12 mutant strain grown microaerobically


title: sid2-2_hrcC_9h_set2

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set2 experiment.


title: Col-0_hrcC_9h_set3

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set3 experiment.


title: N50-97 micro PSY 3

source_name: B. japonicum rpoN12 mutant strain grown microaerobically


title: sid2-2_hrcC_3h_set2

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set2 experiment.


title: N50-97 aerobic PSY 2


title: pad4-1_hrcC_9h_set1

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set1 experiment.


title: Col-0_hrcC_3h_set2

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h


title: pad4-1_hrcC_3h_set1

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set1 experiment.


title: sid2-2_hrcC_3h_set1

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set1 experiment.


title: N50-97 aerobic PSY 4


title: Col-0_hrcC_3h_set1

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set1 experiment.


title: N50-97 nodules soybean 21 Days 5

description: Gene expression data from B. japonicum rpoN12 mutant in nodules soybean 21 days post infection


title: N50-97 micro PSY 4


title: N50-97 nodules soybean 21 Days 2

source_name: B. japonicum rpoN12 mutant in nodules soybean 21 days post infection


title: N50-97 micro PSY 1


title: N50-97 nodules soybean 21 Days 3


title: Col-0_hrcC_9h_set1

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in set1 experiment.


title: N50-97 micro PSY 2


title: Liver CORT 23B

status: Public on Jul 13 2007

city: Logan

first: Abby

middle: D

last: Benninghoff

state: UT

address: 4815 Old Main Hill

department: Animal, Dairy and Veterinary Sciences

institute: Utah State University

description: Ch1 = REF pool, Cy5; Ch2 = CORT liver, sample 23B, Cy3

hyb_protocol: For detection of gene expression on the OSUrbt array, the Genisphere 3DNA Array 350 kit (Hatfield, PA) was used in a dye-swap, reference sample design following the supplier’s protocol. During reverse transcription (SuperScript II, Invitrogen) of total RNA (7 μg) using the supplied Genisphere oligo d(T) primers, each biological sample was tagged separately with a capture sequence for one of two fluorescent dendromer reagents, Cy3 or Cy5. Each reverse transcription reaction also included spiked in mRNA corresponding to the SpotReport Alien Oligo controls. Corresponding reference RNA was reverse transcribed with the capture sequence for the opposite reagent (Cy3 or Cy5). To account for any differences in dye labeling efficiency, technical replicates were performed for two of the three biological replicates in which the capture sequence tags were swapped between the sample and reference. Following reverse transcription, equal amounts of capture sequence-tagged sample and reference cDNA were combined, concentrated using the Millipore Microcon YM-30 (Billerica, MA) and treated with RNase cocktail (Ambion, Austin, TX) to degrade any remaining RNA. Hybridization of cDNA and capture reagents to the OSUrbt arrays was performed as described previously (Tilton et al., 2005) with a few modifications. Sterile 20x SSC was prepared with 3 M sodium chloride and 0.3 M sodium citrate at a pH of 7.0; appropriate dilutions were made with sterile water for hybridization wash buffers. Sodium dodecyl sulfate (SDS) was also added to some hybridization wash buffers at a 0.1% (w/v) final concentration. Prior to hybridization, arrays were pre-washed with gentle mixing on a rocking platform twice in 0.1% SDS for 5 min at room temperature (RT), twice in 2x SSC, 0.1% SDS for 10 min at 47°C, once in 0.1x SSC at RT for 5 min and once in ultra-pure water for 5 min. Slides were dried by centrifugation. cDNA was hybridized to the arrays in formamide-based hybridization buffer (25% formamide, 4x SCC, 0.5% SDS and 2x Denhardt’s solution, Genisphere, Inc.) for 16 hrs at 47°C in a Hybex Microarray Incubation System (SciGene Corporation, Sunnyvale, CA). Post hybridization, the arrays were rinsed in 2x SCC, 0.1% SDS for 10 min at 47°C in the Hybex water bath. Then, arrays were washed with gentle mixing twice in 2x SSC, 0.1% SDS for 5 min at 47°C, twice in 1x SSC for 5 min at RT and twice in 0.1x SCC for 5 min at RT. Slides were dried by centrifugation and pre-warmed to 49°C. Next, the 3DNA Cy3/Cy5 capture reagent mixture was hybridized to the arrays for 3 hrs at 49°C in the dark. After this second hybridization, the arrays were rinsed, washed and dried again as previously described in SCC buffers containing 100 μM DTT in the dark. All arrays were treated with DyeSaver2 Anti-fade Coating (Genisphere, Inc.) to preserve fluorescence of the capture reagent.

scan_protocol: Within 24 hrs of hybridization, array images at a resolution of 5 μm were obtained using the ScanArray 4000 (PerkinElmer) with 90% laser power at 543 nm and 633 nm excitation wavelengths for Cy3 and Cy5, respectively. Photomultiplier tube (PMT) settings were adjusted using the intensities of the SpotReport Alien Oligo controls to balance global intensities for the Cy3 and Cy5 fluors and to normalize across slides. Array image files were processed and spot intensities were quantified using QuantArray software (PerkinElmer); raw median signal and background values were obtained and uploaded to BioArray Software Environment (BASE) (Saal et al., 2002) for database management and data normalization.

data_processing:
VALUE = ratio of Sample Instensity/Reference Intensity using background-corrected, Lowess normalized data.
Complete analysis: Background-corrected, LOWESS normalized, log2 values were exported to Excel (Microsoft Corp,. Redmond, WA) and TM4 MultiExperiment Viewer (TMeV) (Saeed et al., 2003). Average fold change values were calculated by determining the geometric mean for array technical replicates (duplicate spots for each element per array), treatment technical replicates (dye-swaps) and finally for the biological replicates (N = 3) so that triplicate fold change expression values were available for every array element. Statistical analyses of gene expression were performed in TMeV using the normalized, geometric mean expression values for each biological replicate to compare experimental treatments to the control; a statistically significant change in gene expression was inferred when P < 0.05 (Welch’s t-test, between subjects and assuming unequal variances). Multiple criteria were used to reduce the original raw data sets to subsets of genes considered as significantly regulated by any one of the experimental treatments. These criteria included filters for statistical significance (P-value < 0.05 by Welch’s t-test with unequal variance), spot consistency (>1.5-fold change in 9 out of the 10 biological and technical replicate features) and mean fold change (>2-fold).

organism: Oncorhynchus mykiss

source_name: Reference

label_protocol: Labeled using Genisphere Array 350 kit adapted from manufacturer protocol.

growth_protocol: Mt. Shasta strain rainbow trout were hatched and reared at the Sinnhuber Aquatic Research Laboratory (SARL) at Oregon State University in Corvallis, Oregon. Fish were maintained in flow-through 375-l tanks with activated carbon water filtration, water temperature at 12 °C and a 12:12 hr light:dark cycle. Each experimental group consisted of three tanks containing 15 juvenile trout approximately 15 months old. Fish were fed a maintenance ration (2.8% of body weight) of Oregon Test Diet (OTD), a semi-purified casein-based diet with menhaden oil as the lipid, for two weeks prior to experimental treatments.

extract_protocol: Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Eight experimental treatments were selected to examine hepatic gene expression in response to estrogens, a selective estrogen receptor modulator (SERM) and non-estrogens. Treatments and concentrations (calculated with respect to diet wet weight) are as follows: control (CON), 5 ppm estradiol (E2), 50 ppm tamoxifen (TAM), 5 ppm E2 + 50 ppm TAM (E2+TAM), 2 ppm diethylstilbestrol (DES), 500 ppm dehydroepiandrosterone (DHEA), 5 ppm dihydrotestosterone (DHT) and 5 ppm cortisol (CORT). Test chemicals were added directly to the oil portion of the OTD. Experimental treatments were administered for 14 days, and feeding occurred five days per week. On day 15, trout were euthanized with an overdose (250 ppm) of tricane methanesulfonate. Four males were sampled from every experimental tank. Immediately after sacrifice, an approximate 200 mg portion of each liver was quick frozen in TRIzol reagent and stored at -80°C. Equal amounts of RNA from each individual liver sample were sub-pooled according to tank (four males pooled per tank) resulting in three biological replicates for each treatment. A reference RNA pool was made by combining equal amounts of RNA from all individual male CON liver samples (12 liver samples total).

value: Mt. Shasta

value: 13 months (juvenile)

value: Liver

value: Male

source_name: CORT-exposed liver

treatment_protocol: Eight experimental treatments were selected to examine hepatic gene expression in response to estrogens, a selective estrogen receptor modulator (SERM) and non-estrogens. Treatments and concentrations (calculated with respect to diet wet weight) are as follows: control (CON), 5 ppm estradiol (E2), 50 ppm tamoxifen (TAM), 5 ppm E2 + 50 ppm TAM (E2+TAM), 2 ppm diethylstilbestrol (DES), 500 ppm dehydroepiandrosterone (DHEA), 5 ppm dihydrotestosterone (DHT) and 5 ppm cortisol (CORT). Test chemicals were added directly to the oil portion of the OTD. Experimental treatments were administered for 14 days, and feeding occurred five days per week. On day 15, trout were euthanized with an overdose (250 ppm) of tricane methanesulfonate. Four males were sampled from every experimental tank. Immediately after sacrifice, an approximate 200 mg portion of each liver was quick frozen in TRIzol reagent and stored at -80°C. Equal amounts of RNA from each individual liver sample were sub-pooled according to tank (four males pooled per tank) resulting in three biological replicates for each treatment. A reference RNA pool (REF) was made by combining equal amounts of RNA from all individual male CON liver samples (12 liver samples total).


title: Liver CORT 24

description: Ch1 = CORT liver, sample 24, Cy5; Ch2 = REF pool, Cy3


title: N50-97 nodules soybean 21 Days 4


title: Liver DHT 20A

description: Ch1 = DHT liver, sample 20A, Cy5; Ch2 = REF pool, Cy3

source_name: DHT-exposed liver


title: Liver CORT 23A

description: Ch1 = CORT liver, sample 23A, Cy5; Ch2 = REF pool, Cy3


title: Liver DHT 19A

description: Ch1 = DHT liver, sample 19A, Cy5; Ch2 = REF pool, Cy3


title: Liver DHEA 18

description: Ch1 = DHEA liver, sample 18, Cy5; Ch2 = REF pool, Cy3

source_name: DHEA-exposed liver


title: Liver DHT 21

description: Ch1 = DHT liver, sample 21, Cy5; Ch2 = REF pool, Cy3


title: Liver DHEA 17A

description: Ch1 = DHEA liver, sample 17A, Cy5; Ch2 = REF pool, Cy3


title: Liver DHT 20B

description: Ch1 = REF pool, Cy5; Ch2 = DHT liver, sample 20B, Cy3


title: Liver DHEA 17B

description: Ch1 = REF pool, Cy5; Ch2 = DHEA liver, sample 17B, Cy3


title: Liver CORT 22B

description: Ch1 = REF pool, Cy5; Ch2 = CORT liver, sample 22B, Cy3


title: Liver E2+TAM 15

description: Ch1 = E2+TAM liver, sample 15, Cy5; Ch2 = REF pool, Cy3

source_name: E2+TAM exposed liver


title: Liver E2+TAM 14B

description: Ch1 = REF pool, Cy5; Ch2 = E2+TAM liver, sample 14B, Cy3


title: Liver DHT 19B

description: Ch1 = REF pool, Cy5; Ch2 = DHT liver, sample 19B, Cy3


title: Liver CORT 22A

description: Ch1 = CORT liver, sample 22A, Cy5; Ch2 = REF pool, Cy3


title: N50-97 nodules soybean 21 Days 1

description: Gene expression data from B. japonicum rpoN12 mutant in nodules soybean 21 days post infection


title: Liver TAM 11B

description: Ch1 = REF pool, Cy5; Ch2 = TAM liver, sample 11B, Cy3

source_name: TAM-exposed liver


title: Liver DHEA 16B

description: Ch1 = REF pool, Cy5; Ch2 = DHEA liver, sample 16B, Cy3


title: Liver E2+TAM 13B

description: Ch1 = REF pool, Cy5; Ch2 = E2+TAM liver, sample 13B, Cy3


title: Liver DHEA 16A

description: Ch1 = DHEA liver, sample 16A, Cy5; Ch2 = REF pool, Cy3


title: Liver TAM 12

description: Ch1 = TAM liver, sample 12, Cy5; Ch2 = REF pool, Cy3


title: Liver E2+TAM 13A

description: Ch1 = E2+TAM liver, sample 13A, Cy5; Ch2 = REF pool, Cy3


title: Liver E2+TAM 14A

description: Ch1 = E2+TAM liver, sample 14A, Cy5; Ch2 = REF pool, Cy3


title: Liver TAM 10B

description: Ch1 = REF pool, Cy5; Ch2 = TAM liver, sample 10B, Cy3


title: Liver TAM 11A

description: Ch1 = TAM liver, sample 11A, Cy5; Ch2 = REF pool, Cy3


title: Liver DES 8A

description: Ch1 = DES liver, sample 8A, Cy5; Ch2 = REF pool, Cy3

source_name: DES-exposed liver


title: Liver DES 9

description: Ch1 = DES liver, sample 9, Cy5; Ch2 = REF pool, Cy3


title: Liver DES 8B

description: Ch1 = REF pool, Cy5; Ch2 = DES liver, sample 8B, Cy3


title: Liver DES 7B

description: Ch1 = REF pool, Cy5; Ch2 = DES liver, sample 7B, Cy3


title: Liver E2 5A

description: Ch1 = E2 liver, sample 5A, Cy5; Ch2 = REF pool, Cy3

source_name: Estradiol-exposed liver


title: Liver E2 6

description: Ch1 = E2 liver, sample 6, Cy5; Ch2 = REF pool, Cy3


title: Liver E2 5B

description: Ch1 = REF pool, Cy5; Ch2 = E2 liver, sample 5B, Cy3


title: Liver DES 7A

description: Ch1 = DES liver, sample 7A, Cy5; Ch2 = REF pool, Cy3


title: Liver CON 2B

description: Ch1 = REF pool, Cy5; Ch2 = CON liver, sample 2B, Cy3

source_name: Control liver


title: Liver CON 3

description: Ch1 = CON liver, sample 3, Cy5; Ch2 = REF pool, Cy3


title: Liver E2 4B

description: Ch1 = REF pool, Cy5; Ch2 = E2 liver, sample 4B, Cy3


title: Liver CON 1A

description: Ch1 = CON liver, sample 1A, Cy5; Ch2 = REF pool, Cy3


title: Liver TAM 10A

description: Ch1 = TAM liver, sample 10A, Cy5; Ch2 = REF pool, Cy3


title: Liver E2 4A

description: Ch1 = E2 liver, sample 4A, Cy5; Ch2 = REF pool, Cy3


title: Liver CON 2A

description: Ch1 = CON liver, sample 2A, Cy5; Ch2 = REF pool, Cy3


title: Liver CON 1B

description: Ch1 = REF pool, Cy5; Ch2 = CON liver, sample 1B, Cy3


title: Col-0_hrcC_3h_set3

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in set3 experiment.


title: N50-97 micro PSY 6

description: Gene expression data from B. japonicum rpoN12 mutant strain grown microaerobically


title: Pax5-/- vs WT pro-B cells, biological replicate 2

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohr-Gasse 7

country: Austria

institute: Research Institute of Molecular Pathology

hyb_protocol: For hybridisation protocol, see Schebesta et al., Immunity 2002

scan_protocol: Images were quantified using GenePix Pro 4.1.1.4

data_processing: Print tip LOESS normalized, background subtracted. VALUE data obtained from log2 of processed Red signal/processed Green signal. Pre-processing using marray package from BioConductor

source_name: wild-type pro-B cells directly sorted from bone marrow

label_protocol: RNA amolified as described in Bouchard et al., Development 2005; for labeling protocol, see Schebesta et al., Immunity 2002: 5mg of total RNA were used

growth_protocol: no growth

extract_protocol: Total RNA extracted using Trizol following manufacturer's protocol

treatment_protocol: B200+ c-Kit+ pro-B cells

tag: WT +/+ #2 pro-B-cells

value: 2 weeks

value: Bone marrow

source_name: Pax5-/- pro-B cells


title: Pax5-/- vs WT pro-B cells, biological replicate 1

tag: WT +/+ #1 pro-B-cells


title: 24 hr muscle, biological rep 2

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description: Gene expression data from embryonic muscle cells after 24 hr in culture

hyb_protocol: Following fragmentation, 10-15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Caenorhabditis elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized using Robust Multiarray analysis (RMA) in GeneTraffic (Stratagene). RMA normalized data were subjected to Significance Analysis of Microarray (SAM, Stanford) analysis. Enriched genes were obtained by finding genes with a 1.7x enriched at a False Discovery Rate (FDR) of less than or equal to 1.8% (0hr) or less than or equal to 1.2% (24hr)..

organism: Caenorhabditis elegans

source_name: myo-3::GFP positive cells after 24 hr in culture

label_protocol: A 2-round IVT protocol (modified from the Affymetrix small-sample protocol) was used to convert 100 ng total RNA into biotinylated cRNA.

growth_protocol: Gravid adults expressing myo-3::GFP were subjected to bleach/NaOH treatment to release embryos. Embryos were harvested and then treated with chitinase to degrade the eggshell. Cells were dissociated and either sorted immediately (0hr dataset) or plated on poly-L-lysine coated dishes for 24 hrs to allow differentiation and then removed from the culture dish and sorted (24 hr dataset). Cells were sorted using the FACStar Plus (Becton Dickinson, San Jose, CA) that had been flushed with egg buffer. ~90% enrichment of GFP+ cells was obtained. For Reference dataset, wildtype (N2) animals were subjected to the same dissociation/cell culture treatment. FACS isolated all non-propidium iodide stained (i.e. living) cells.

extract_protocol: RNA was isolated from sorted cells using the micro-RNA isolation kit (Stratagene) using the recommended volumes for 1 million cells.

tag: cultured embryonic cells from myo-3::GFP transgenic animals


title: 24 hr Reference, biological rep 3

description: Gene expression data from all wildtype embryonic nematode cells after 24 hr in culture

source_name: All living Caenorhabditis elegans sorted cells after 24 hr in culture

tag: cultured embryonic cells from wildtype (N2 isolate) nematodes


title: 24 hr muscle, biological rep 1


title: 24 hr Reference, biological rep 4


title: Pax5-/- Rag2-/- vs Pax5+/+ Rag2-/- pro-B cells 20MM121

source_name: in vitro cultured Pax5+/+ Rag2-/- pro-B cells

label_protocol: For labeling protocol, see Schebesta et al., Immunity 2002: 5mg of total RNA were used

growth_protocol: Pro-B cells were cultured on irradiated ST2 cells in IL-7-containing Iscove's modified Dulbecco's medium supplemented with 50 microM beta-mercaptoethanol, 1 mM glutamine, 1mM penicillin, 1mM streptomycin, 2% heat-inactivated fetal calf serum and 0.03% (w/v) primatone.

treatment_protocol: sorted B220+ c-Kit+ pro-B cells followed by in vitro culture

tag: RAG2 -/- Pax5 +/+ #2 pro-B-cell line

tag: cultured for 3-4 weeks

tag: RAG2 -/- Pax5 -/- pro-B-cell line

source_name: Pax5-/- Rag2-/- pro-B cells


title: Pax5-/- Rag2-/- vs Pax5+/+ Rag2-/- pro-B cells 20MM102

tag: RAG2 -/- Pax5 +/+ #1 pro-B-cell line

tag: Strain

tag: RAG2 -/- Pax5 -/- C2 pro-B-cell line


title: Scc1 distribution in eco1-1 cells (ChIP fraction) after DSB

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: ChIP fraction of Scc1 in eco1-1 cells after DSB induction

hyb_protocol: Hybridization, blocking and washing were carried out as previously described (http://chromosomedynamics.bio.titech.ac.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3'-biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 42C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: S. cerevisiae arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: The primary analysis of tiling chip data was performed following exactly the statistical algorithm used for Affymetrix GeneChip Operating Software (GCOS). The detailed information for the algorithm used can be downloaded from the Affymetrix web site at http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Chromatin-immunoprecipitated DNA by Scc1

label_protocol: DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) or Biotin-11-ddATP for 1 hour at 37C as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.

extract_protocol: Extract preparation was processed following the Shirahige lab protocol (http://everythingchromosomevi.gsc.riken.go.jp ). 5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka). Whole cell extract was sonicated to obtain 400-600 bp genomic DNA fragments. Anti-Flag monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Dynal, protein A Dynabeads) were used for chromatin immunoprecipitation. The immunprecipates were eluted and incubated over night at 65C to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp.

tag: eco1-1, MCD1-3FLAG, GAL:HO cells containing a HO recognition site at ChrV


title: Scc1 distribution in G2/M (ChIP) in Wild

description: Scc1 distribution in Wild type cells (with DSB).

tag: Strain with GAL:HO and FLAG-labelled Mcd1 after DSB induction


title: 24 hr Reference, biological rep 2


title: Scc1 distribution in eco1-1 cells (SUP fraction)

description: SUP fraction for the normalization of Scc1 distribution in eco1-1 cells

tag: eco1-1, Scc1-3FLAG, GAL:HO cells containing a HO recognition site at ChrV were used


title: Distribution of Scc1 in smc6 mutant (SUP)

description: SUP fraction used for normalization of Scc1 distribution in smc6-56 (with DSB).

source_name: SUP fraction after ChIP (equal to Whole cell extract DNA)

tag: smc6-56 cells with GAL:HO and FLAG-labelled Mcd1


title: Scc1 distribution in G2/M (SUP) in Wild

description: Sup fraction for the normalization of Scc1 distribution in Wild type cells (with DSB).

tag: Cells with GAL:HO and FLAG-labelled Scc1


title: 24 hr Reference, biological rep 1


title: rH2AX after 0h of DSB induction in G2

description: rH2AX ChIP before DSB. This data was used for normalization of rH2AX ChIP data after 2h of DSB induction.

source_name: Chromatin-immunoprecipitated DNA by rH2AX

tag: Wild type cell arrested in G2 phase was used. Before DSB induction.


title: 24 hr muscle, biological rep 3


title: rH2AX after 2h of DSB induction in G2

description: rH2AX ChIP 2h after inducion of DSB.

tag: Wild type cells after 2h induction of DSB in G2.


title: Scc1 distribution in eco1-1 cells (ChIP fraction) before DSB

description: ChIP fraction of Scc1 in eco1-1 cells before DSB induction

tag: eco1-1, MCD1-3FLAG, GAL:HO cells containing a HO recognition site at ChrV were used. Before Induction of DSB.


title: Uncleavable Scc1 distribution in G2 phase (SUP fraction)

description: Uncleavable Scc1 distribution in G2.

tag: Starin expressing FLAG tagged uncleavable Scc1 was used.


title: Pax5-/- vs WT pro-B cells 20MM103

source_name: in vitro cultured WT pro-B cells

tag: WT +/+ #2 pro-B-cell line

tag: Tissue

tag: MF -/- #2 pro-B-cell line


title: Uncleavable Scc1 distribution in G2 phase (ChIP fraction)

description: Uncleavable Scc1 distribution in G2.

tag: Cells expressing uncleavable Scc1 were arrested in G2 phase.


title: Hippocampus_Rasgrf1KO_rep2

city: Salamanca

first: Javier

last: De Las Rivas

address: Campus Miguel de Unamuno

department: CSIC and University of Salamanca

country: Spain

institute: Cancer Research Center (CiC-IBMCC)

description: Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of Rasgrf1 knockout mice brains

hyb_protocol: Gene Chip microarray hybridization protocol (Affymetrix Expression Analysis Technical Manual).

scan_protocol: Gene Chip microarray scan protocol (Affymetrix Expression Analysis Technical Manual).

data_processing: GCOS

label: Standard Gene Chip microarray hybridization protocol

source_name: Hippocampus from mouse Rasgrf1 knockout

label_protocol: Gene Chip microarray label protocol (Affymetrix Expression Analysis Technical Manual, http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: The RNAs extracted from microdissected tissue sections were pre-amplified prior to microarray hybridization using the Gene Chip Expression 3′-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA, USA; #900432), the Gene Chip Sample Cleanup Module (Affymetrix #900371) and the MEGAscript T7 High Yield Transcription Kit (Ambion, Austin, TX, USA; #1334), according to Affymetrix instruction manual #701025 rev. 5.


title: Pax5-/- vs WT pro-B cells 20MM104

tag: WT +/+ #5 pro-B-cell line

tag: cultured for 3-4 weeks

tag: MF -/- #3 pro-B-cell line


title: Pax5-/- vs WT pro-B cells 18MM85

tag: Strain


title: Hippocampus_Rasgrf1KO_rep1

tag: Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of Rasgrf1 knockout mice brains


title: 0 hr muscle, biological rep 2

description: Gene expression data from freshly dissociated embryonic muscle cells

source_name: myo-3::GFP positive sorted cells from freshly dissociated embryos

tag: embryonic cells from myo-3::GFP transgenic animals


title: Pax5-/- Rag2-/- vs Pax5+/+ Rag2-/- pro-B cells 18MM83

source_name: n vitro cultured Pax5+/+ Rag2-/- pro-B cells

tag: RAG2 -/- Pax5 +/+ #1 pro-B-cell line

tag: RAG2 -/- Pax5 -/- C2 pro-B-cell line


title: Scc1 distribution in G2 phase (ChIP fraction)

description: Scc1 distribution in G2.

tag: Strain expressing FLAG tagged Scc1 was arrested in G2 phase.


title: Pax5-/- Rag2-/- vs Pax5+/+ Rag2-/- pro-B cells 18MM92

tag: RAG2 -/- Pax5 +/+ #2 pro-B-cell line

tag: RAG2 -/- Pax5 -/- pro-B-cell line


title: Scc1 distribution in G2 phase

description: Sup fraction for the normalization of Scc1 distribution in G2 phase.

scan_protocol: S. cerevisiae arrays were scanned using the Genechip Scanner3000 7G following the library array description. All the cel files data and processed data files can be downloaded from GEO database or from our Web sites.

source_name: Sup fraction after ChIP (equal to Whole cell extract DNA)

tag: Strain that express Scc1 tagged by FLAG was used.


title: Scc1 distribution in G2/M (ChIP) in smc6-56

description: Scc1 distribution in smc6-56 (with DSB).

tag: smc6-56 cells with GAL:HO and FLAG-labelled Scc1


title: WCE fraction with DSB (for Scc2 distribution)

description: WCE fraction for the normalization of Scc2 distribution in G2 phase with DSB.

source_name: Whole cell extract

tag: Strain with DSB on Chr 3. Cells were arrested at G2/M phase.


title: 0 hr muscle, biological rep 3


title: 0 hr muscle, biological rep 1


tag: WT +/+ #2 pro-B-cells

tag: 2 weeks

tag: Tissue


tag: WT +/+ #1 pro-B-cells


title: Hippocampus_Rasgrf1KO_rep3


title: 0 hr Reference, biological rep 3

description: Gene expression data from all freshly dissociated wildtype embryonic nematode cells

source_name: All living Caenorhabditis elegans sorted cells from freshly dissociated embryos

tag: embryonic cells from wildtype (N2 isolate) nematodes


title: Hippocampus_WildType_rep1

description: Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of wild type mice brains

source_name: Hippocampus from mouse


title: Hippocampus_WildType_rep3

tag: Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of wild type mice brains


title: WCE fraction w/o DSB (for Scc2 distribution)

description: Sup fraction for the normalization of Scc2 distribution.

source_name: Sup fraction (equal to Whole cell extract DNA)

tag: Strain with DSB site on Chr3. Before Induction of HO.


title: Scc2 distribution in G2 phase w/o DSB

description: ChIP fraction of Scc2.

source_name: Chromatin-immunoprecipitated DNA by Scc2 antibody

tag: Strain with DSB site at Chr3 (before induction of HO).


title: 0 hr Reference, biological rep 1


title: Scc2 distribution in G2 phase with DSB

description: ChIP fraction for the Scc2 distribution in G2 phase with DSB.

tag: Strain with DSB site at chr 3. Cells were arrested at G2-phase. After induction of DSB by HO.


title: 0 hr Reference, biological rep 2


title: Hippocampus_WildType_rep2


title: WT vs WT_PEROX

status: Public on Jul 12 2007

city: Wageningen

first: L.

middle: Mariela

last: Serrano

address: Nieuwe Kanaal 9A

country: Netherlands

institute: TI Food and Nutrition

description: WT vs WT_PEROX

hyb_protocol: Hybridization version 4.1" Agilent hybridization  protocol v 4.

scan_protocol: Scanning protocol Using the Scan Array  Express microarray  scanner. 1.Turn on the scanner and  the computer (in this order) 2.Login: scanner 3.Double click the  'ScanArray Express' icon 4.Switch on lasers 1 and 3  at least 15 minutes prior to  scanning arrays 5.Click the 'File' button This is to prevent you from  accidentally turning off the  laser after the 15 minutes  warming-up phase 6.Insert the slide with the  array-side up and the label  towards the outside. On  Agilent slides the array side  is the side with the label  that has the word "Agilent"  on it 7.Press 'Scan | Prescan' 8.Put resolution at 50  m,  select both labels used,  and set PMT values for  both channels at for  instance 40% (Agilent  arrays) 9.Press 'Start' 10.Press 'Palette,' 'Green'  as soon as projection of  the image has started (first  dye), select the red colour  as soon as scanning of the  second layer (second dye)  has started 11.Adjust PMT values to  balance signals obtained  for both channels. If  necessary do a few  low-resolution scans to  obtain a optimal balance 12.Click the 'Scan' button  again 13.Select frame for high  resolution scan, adjust  resolution (to 10  m) and  scan the array for both  dyes 14.Press 'File | Save' to  save the files, 'Save all'  saves both dye layers "Create a new folder for  each array "'Save all' saves the  signals from both layers in  individual files 15.Switch off the lasers  and the scanner after use

data_processing: Data Processing" 1.- Background correction  (Mean values) 2.-Filtering Flagged spots 3.-Normalization Lowes

organism: Lactiplantibacillus plantarum WCFS1

source_name: WT

label_protocol: Labeling Protocol 1.1  Annealing Annealing Mix 	x µl	 RNA preparation (=25  µg) 	y µl	 nuclease-free water 	1 µl	 Random Nonamers 	11 µl	 TOTAL  1.	mix Annealing  Mix in a 200 µl PCR  tube gently by pipetting  up and down 2.	incubate for  5’ 70°C 3.	cool at room  temperature for 10’  (annealing) 4.	spin down the  mixture to the bottom of  the tube 5.	place on ice  Reverse transcription  Reverse Transcription  Mix 	4 µl	5x  buffer 	2 µl	0.1  M DTT 	1 µl	 dNTP-mix 	1 µl	 AA-dUTP 	1 µl  	 TMIII (keep only briefly  outside  20°C) 	20 µl	 TOTAL  1.	Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.	Incubate for 3  hrs at 42°C (in  PCR-machine) 3.	Cool on ice  for immediate  purification or place at   20°C for storage  Degradation of mRNA 1.	Add 2 µl 2,5  M NaOH 2.	Mix (vortex)  and spin down 3.	Incubate for  15 min. at 37°C 4.	Add 10 µl 2 M  HEPES free acid 5.	Mix (vortex)  and spin down 6.	Ready for  purification or store at   20°C    Labelling of cDNA with  cyanine dyes  Purification of amino  allyl-modified cDNA Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA" code  RPN5661  Labelling of amino  allyl-modified cDNA with  CyDye 1.	Add the  amino allyl modified  cDNA (in 0.1 M sodium  bicarbonate) directly into  one aliquot of CyDye  NHS Ester. Resuspend  the ester completely by  pipetting several times  and transfer the solution  to an amber 1.5 ml tube 2.	Incubate at  room temperature, in the  dark for 60 to 90  minutes 3.	Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4.	Mix by stirring  and incubate at room  temperature, in the dark,  for 15 minutes 5.	Proceed  directly to purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed Ge Healthcare  kit "Ame

extract_protocol: Extraction RNA version  1.2 Collecting cells Quenching Buffer 66.7 mM	HEPES (pH  6.5) 60%Methanol Extraction Mixture -500 µll  phenol/Chloroform -30 µl10% SDS -30 µl3 M NaAc (pH 5.2) -500 mg glass-beads  (75-150 µm) -400 µlTE buffer  Prepare in a screw-cap  tube  1.For each sample  prepare a tube with  Extraction Mixture 2.Harvest cells and  quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of cell culture 3.Mix and store the  sample at -40°C 4.Centrifuge cells at  -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet with  a pre-cooled spatula to  a screw-crap tube with  Extraction Mixture 6.Mix the cell pellet  thoroughly with  Extraction Mixture by  shaking by hand 7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in the  Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary) 9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer 500 µl of  the supernatant to a  new tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with the  "High Pure RNA  Isolation Kit" from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA in at  least 2 aliquots, one of  20 µl (for concentration  and quality analysis and  labelling) and one  back-up of 30 µl at   80°C.

source_name: WTperox

tag: L. plantarum containing an empty plasmid (pNZ7021) + 3.5 mM hydrogen peroxide stress


title: WT_PEROX vs TRXB1_PEROX II

description: WT_PEROX vs TRXB1_PEROX II

tag: L. plantarum carrying plasmid pMS040 (overexpression of trxB1 after constituitive pPEPN promotor) + 3.5 mM hydrogen peroxide stress


title: Pax5-/- vs WT pro-B cells 18MM100

tag: WT +/+ #5 pro-B-cell line

tag: cultured for 3-4 weeks

tag: Strain

tag: MF -/- #3 pro-B-cell line

source_name: Pax5-/- pro-B cells


title: WT VS WT_PEROX BIO

description: WT VS WT_PEROX BIO

tag: L. plantarum containing an empty plasmid (pNZ7021)


title: WT vs WT_PEROX II

description: WT vs WT_PEROX II


title: WT_PEROX vs TRXB1_PEROX

description: WT_PEROX vs TRXB1_PEROX


title: WT vs TRXB1

description: wt vs TRXB1

tag: L. plantarum carrying plasmid pMS040 (overexpression of trxB1 after constituitive pPEPN promotor)


title: HMEC 184 day 7 sample 2

city: Belmont

first: Katherine

middle: J

last: Martin

address: 61 Carleton Rd

institute: Bioarray Consulting

description: We analyzed gene expression in 184 (finite life span) and HMT3522 S1 (immortal non-malignant) HMECs on successive days (3, 5, and 7) post-seeding in a laminin-rich extracellular matrix assay. Both HMECs underwent growth arrest in G0/G1 and differentiated into polarized acini between days 5 and 7.

hyb_protocol: Affymetrix Generic Hybridization

scan_protocol: Affymetrix Scanning

data_processing: Experiments with Affymetrix-present P-call rates of >30% were included in the analysis. Signal values from each of the 22,283 probe sets were calculated by means of robust multi-array analysis (RMA) using Bioconductor. (http://www.bioconductor.org) in the R computing environment. The signal values were inverse log2 transformed and then imported into GeneSpring software (SiliconGenetics); and each array was normalized to its median signal intensity.

source_name: HMEC 184

label_protocol: Affymetrix in vitro transcription

growth_protocol: Cells cultured in a H14 medium (DMEM/F12 containing 250 ng/ml insulin, 10 µg/ml transferrin, 2.6 ng/ml sodium selenite, 10-10 M estradiol, 1.4 x 10-6 M hydrocortisone, 10 ng/ml EGF and 5 µg /ml prolactin) were grown for 7 days in a 3D laminin-rich extracellular matrix (Matrigel BD Biosciences).

extract_protocol: Total cellular RNA was extracted and purified using the QIAGEN RNAeasy kit by following the kit protocol. It was stored at -70C until use.

tag: BioSourceType

tag: DevelopmentalStage

value: adult

tag: OrganismPart

value: mammary gland

tag: TargetedCellType

value: human mammary epithelial

tag: Sex

value: female

tag: Organism

value: Homo sapiens

tag: CellLine

value: HMEC 184


title: HMEC 184 day 3 sample 1

growth_protocol: Cells cultured in a H14 medium (DMEM/F12 containing 250 ng/ml insulin, 10 µg/ml transferrin, 2.6 ng/ml sodium selenite, 10-10 M estradiol, 1.4 x 10-6 M hydrocortisone, 10 ng/ml EGF and 5 µg /ml prolactin) were grown for 3 days in a 3D laminin-rich extracellular matrix (Matrigel BD Biosciences).


title: WT_PEROX vs TRXB1_PEROX BIO

description: WT_PEROX vs TRXB1_PEROX BIO


title: HMEC 184 day 7 sample 1


title: WT VS TRXB1 BIO

description: wt vs trxB1_BIO


title: HMEC 184 day 5 sample 2

growth_protocol: Cells cultured in a H14 medium (DMEM/F12 containing 250 ng/ml insulin, 10 µg/ml transferrin, 2.6 ng/ml sodium selenite, 10-10 M estradiol, 1.4 x 10-6 M hydrocortisone, 10 ng/ml EGF and 5 µg /ml prolactin) were grown for 5 days in a 3D laminin-rich extracellular matrix (Matrigel BD Biosciences).


title: WT vs TRXB1 II

description: WT vs TRXB1 II


title: HMEC S1 day 5 sample 1

source_name: HMEC S1

value: HMT3522S1 (HMEC S1)


title: HMEC 184 day 3 sample 2

tag: ioSourceType


title: HMEC S1 day 7 sample 1


title: HMEC 184 day 5 sample 1


title: HMEC S1 day 5 sample 2


title: HMEC S1 day 7 sample 2


title: Muscle_inadequate protein_female_rep6

status: Public on Jul 11 2007

city: West Lafayette

first: Wayne

last: Campbell

state: IN

address: 700 West State Street

department: Foods and Nutrition

institute: Purdue University

description: Gene expression data from older female during 1 week of inadequate protein intake

hyb_protocol: Affymetrix protocol

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

data_processing: The data were summarized with Microarray Suite version 5.0 (MAS 5.0)

source_name: vastus lateralis muscle, inadequate protein

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from a minimum of 5 ug total RNA

extract_protocol: Total RNA was isolated from the frozen muscle sample using Tri-Reagent following the manufacturer’s instructions.  Isolated total RNA was further purified using RNeasy Mini Kits following manufacturer’s protocol

treatment_protocol: controlled diets that contained 1.2 g protein•kg-1•d-1 (adequate protein) for one wk followed by 0.5 g protein•kg-1•d-1 (inadequate protein) for a second wk.  Fasting state vastus lateralis muscle biopsies were taken on day 7 and day 14 of both dietary trials

value: Female

tag: Protein intake

value: 0.5 g/kg/day


title: Rep4, SparcTm1Cam129SvEv bone vs control, sl21-40

city: Cardiff

first: Fiona

middle: Catherine

last: Mansergh

state: Wales

address: Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

description: Arrays were repeated 5 times with fluor switching, in order to counteract any issues of dye bias that may have arisen from direct labelling. Repetition sets used biological samples derived from at least four control and four experimental animals per set, in order to control for biological variation between individual animals. Scanned images were stored and filtered, then analysed using the GeneTac Analyser spot finding software (Genomic Solutions, Cambridgeshire, UK). Analysis  and other methods were carried out similarly to another published experiment, please see Mansergh et al. 2004 PMID: 15303089 for more details.

hyb_protocol: Array slides were incubated in prehybe for 1 hour at 42oC (50% formamide, 5XSSC, 0.1% SDS, 1% BSA). Targets were dried down via vacuum centrifugation then resuspended in 50l hybe solution (49.9% de-ionised formamide, 49.9% 20xSSC, 0.2% SDS) with added 1l Cot1 DNA and 1l poly A oligo as blocking agents, heated to 95oC for 5 minutes and then added to the face of one slide. The printed face of the second slide of the pair was then placed face to face with the first, using the same probe. Slide pairs were then placed on a  level plastic cover above some 1xSSC moistened tissue in a slide box. The slide box was sealed with Nescofilm (Karlan Research Products Corporation, Santa Rosa, CA, USA), placed floating in a waterbath and  hybridized for 24-48 hours at 42oC.  Following hybridization, slides were washed once in Wash solution 1 (1X SSC, 2% SDS, filtered autoclaved ddH2O) for 20 minutes, then twice in Wash solution 2 (0.1X SSC, 0.2% SDS, filtered autoclaved distilled deionised H2O (ddH2O) for 20 minutes each. Slides were dipped in nuclease free filtered water, then spray dried, finally, the backs of the slides were cleaned with filtered autoclaved ddH2O, then wiped with 100% EtOH, then wiped dry and scanned.

scan_protocol: Scans were carried out at 12.5 micrometers, using the averaging setting (GeneTac LSIV scanner, (Genomic Solutions, Cambridgeshire, UK)). It is possible to carry out quick draft scans using this scanner, gain and black settings, which affect image intensity and background were varied slightly in order to optimize the signal/noise ratio for each channel and each slide before proper scans were initiated.

data_processing: Output files from GeneTac analyser were saved in MS Excel spreadsheet format. MS Excel was used for all further data manipulation. We normalised each channel via total array methods, via calculation of the mean intensity value. Normalised intensities were then analysed using two different methods. Firstly, we transferred normalised intensity values for each of 5 experimental repetitions into a separate Excel file, ensuring a standard order of samples. These data were then formatted for Significance Analysis of Microarrays (SAM; http://www-stat.stanford.edu/~tibs/SAM ). SAM analysis was carried out and genes that showed a fold change of 2 or above and that appeared in a SAM analysis as statistically significant above a delta value of 0.5 (which denotes an error rate of 5%) were selected for further appraisal. SAM, however, has some disadvantages; all replicates have to be in the same order to use SAM, precluding some methods of data filtration. In addition, each cDNA probe (represented by a single accession number) is spotted on the HGMP NIA array slides twice. Using SAM, it is impossible to assess both duplicate spots together. Hence, we supplemented SAM analysis with a second analysis method as follows: Following normalisation, we used approximately 700 blank spots per slide to calculate a mean background value + 2 standard deviations of that background value, for each channel. Genes that fell below this cutoff in BOTH control and experimental channels were removed. Genes that failed to show a fold change of 2 were also removed. Remaining data (above background + 2SD values, fold change of > 2) were retained, combined with similar data from other replicates and sorted via accession number. Genes that appeared above background + 2SD values with a fold change of > 2, in at least 8 out of 10 replicates (this analysis combined values from duplicate spots, giving 10 replicates per EST), were retained for further analysis. Finally, accession numbers obtained from this method and from SAM were compared. Genes appearing as differentially regulated using BOTH methods were deemed significant by us. In other words, significant ESTs are changed in expression by at least two fold, are above background + 2SD in at least one channel and have a delta value of 0.5 using SAM.  These ESTs were subjected to bioinformatic analysis and were ALL assessed via RT PCR in order to confirm array results

source_name: SparcTm1Cam129Sv/Ev null bone, 9 months, male, cortical femur

label_protocol: Different pooled RNA samples were used for labelling array repetitions. 10ug of total RNA was labelled with either Cy3 or Cy5 dyes using the CyScribe labelling system (GE Healthcare, Chalfont St.Giles, Bucks, UK), according to the manufacturer’s protocol. 1ul of labelled cDNA was combined with 2ul 50% glycerol, run on a ‘John gel’ (a microscope slide sized, 1.5% agarose gel) and scanned using a GeneTac LS IV scanner (Genomic Solutions, Huntingdon, Cambs. UK) in order to assess successful incorporation of label. Control and experimental samples were then combined and prepared for hybridization.

growth_protocol: Mice were maintained and killed under Home Office licence in accordance with British law (comparable with U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals). Transgenic and control animals were maintained on RM3 diet (1.15% calcium, 0.82% phosphorus, 4088.65I.U./kg Vitamin D, Special Diet Services, Witham, Essex CM8 3AD, UK), ad libitum.

extract_protocol: Femoral midshaft samples were transferred from RNAlater into TRIzol (Invitrogen, Paisley, UK) and immediately homogenized using a Yellowline DI18 basic electronic homogenizer (Yellowline, IKA, Staufen, Germany) prior to RNA extraction via the manufacturer’s protocol. RNA samples were quantitated using formaldehyde gel electrophoresis and spectrophotometry (Camspec, Sawston, Cambs., UK).

treatment_protocol: Animals were sacrificed via cervical dislocation. Whole femurs and tibias were dissected free of surrounding tissue. Whole femurs were dissected free of surrounding tissue. Bone marrow was flushed via needle and syringe, using 0.5ml PBS per femur.A 0.4 cm section of the femoral midshaft was obtained in order to minimize contamination by muscle and cartilage adhering to femoral epiphyses and standardise anatomical localization. Material from 2-6 femoral cortices was pooled in RNAlater (Ambion, Huntingdon, Cambs, UK). Where tissue from more than one animal was used, material from litter mates was pooled.

tag: Sparc Tm1Cam knockout mouse, on a 129SvEv background, 9months old, male. Cortical femur, midsection, marrow flushed away before RNA extraction from bone.

tag: 129SvEv Sparctm1cam null mice

value: 129SvEv refers to mice of inbred strain 129 and substrain SvEv. Sparctm1cam refers to “Sparc, targeted mutation 1, University of Cambridge”. This targeted mutation is in exon 6 of the Sparc gene. Described in Gilmour et al, 1998 PMID:9524110

source_name: 129Sv/Ev mouse, 9 months, male, cortical femur

tag: 129SvEv background wild type , 9months old, male. Cortical femur, midsection, marrow flushed away before RNA extraction from bone.

tag: Wild type inbred line from which the ES cells used to create the Sparc null mice were derived.


title: HMEC S1 day 3 sample 1

source_name: HMEC  S1


title: Rep2, SparcTm1Cam129SvEv bone vs control, sl21-40

value: 129SvEv refers to mice of inbred strain 129 and substrain SvEv. Sparctm1cam refers to “Sparc, targeted mutation 1, University of Cambridge”. This targeted mutation is in exon 6 of the Sparc gene. Described in Gilmour et al, 1998 PMID:9524110.


title: HMEC S1 day 3 sample 2

treatment_protocol: Cells cultured in a H14 medium (DMEM/F12 containing 250 ng/ml insulin, 10 µg/ml transferrin, 2.6 ng/ml sodium selenite, 10-10 M estradiol, 1.4 x 10-6 M hydrocortisone, 10 ng/ml EGF and 5 µg /ml prolactin) were grown for 3 days in a 3D laminin-rich extracellular matrix (Matrigel BD Biosciences).


title: Rep1, SparcTm1Cam129SvEv bone vs control, sl21-40


title: Rep4, SparcTm1Cam129SvEv bone vs control, 4month, sl21-40

description: Arrays were repeated 5 times with fluor switching, in order to counteract any issues of dye bias that may have arisen from direct labelling. Repetition sets used biological samples derived from at least four control and four experimental animals per set, in order to control for biological variation between individual animals. Scanned images were stored and filtered, then analysed using the GeneTac Analyser spot finding software (Genomic Solutions, Cambridgeshire, UK). Analysis  and other methods were carried out similarly to another published experiment, please see Mansergh et al. 2004 PMID: 15303089 for more details

data_processing: Output files from GeneTac analyser were saved in MS Excel spreadsheet format. MS Excel was used for all further data manipulation. We normalised each channel via total array methods, via calculation of the mean intensity value. Normalised intensities were then analysed using two different methods. Firstly, we transferred normalised intensity values for each of 5 experimental repetitions into a separate Excel file, ensuring a standard order of samples. These data were then formatted for Significance Analysis of Microarrays (SAM; http://www-stat.stanford.edu/~tibs/SAM ). SAM analysis was carried out and genes that showed a fold change of 2 or above and that appeared in a SAM analysis as statistically significant above a delta value of 0.5 (which denotes an error rate of 5%) were selected for further appraisal. SAM, however, has some disadvantages; all replicates have to be in the same order to use SAM, precluding some methods of data filtration. In addition, each cDNA probe (represented by a single accession number) is spotted on the HGMP NIA array slides twice. Using SAM, it is impossible to assess both duplicate spots together. Hence, we supplemented SAM analysis with a second analysis method as follows: Following normalisation, we used approximately 700 blank spots per slide to calculate a mean background value + 2 standard deviations of that background value, for each channel. Genes that fell below this cutoff in BOTH control and experimental channels were removed. Genes that failed to show a fold change of 2 were also removed. Remaining data (above background + 2SD values, fold change of > 2) were retained, combined with similar data from other replicates and sorted via accession number. Genes that appeared above background + 2SD values with a fold change of > 2, in at least 8 out of 10 replicates (this analysis combined values from duplicate spots, giving 10 replicates per EST), were retained for further analysis. Finally, accession numbers obtained from this method and from SAM were compared. Genes appearing as differentially regulated using BOTH methods were deemed significant by us. In other words, significant ESTs are changed in expression by at least two fold, are above background + 2SD in at least one channel and have a delta value of 0.5 using SAM.  These ESTs were subjected to bioinformatic analysis and were ALL assessed via RT PCR in order to confirm array results.

source_name: SparcTm1Cam129Sv/Ev null bone, 4 months, male, cortical femur

tag: Sparc Tm1Cam knockout mouse, on a 129SvEv background, 4 months old, male. Cortical femur, midsection, marrow flushed away before RNA extraction from bone.

source_name: 129Sv/Ev mouse, 4 months, male, cortical femur

tag: 129SvEv background wild type , 4 months old, male. Cortical femur, midsection, marrow flushed away before RNA extraction from bone.


title: Muscle_adequate protein_female_rep6

description: Gene expression data from older female during 1 week of adequate protein intake

source_name: vastus lateralis muscle, adequate protein

value: 1.2 g/kg/day


title: Rep5, SparcTm1Cam129SvEv bone vs control, sl21-40

label: Cy 5


title: Rep3, SparcTm1Cam129SvEv bone vs control, 4month, sl21-40


title: Rep5, SparcTm1Cam129SvEv bone vs control, 4month, sl21-40


title: Rep2, SparcTm1Cam129SvEv bone vs control, 4month, sl21-40


title: Muscle_adequate protein_female_rep5


title: Muscle_inadequate protein_female_rep4


title: Rep1, SparcTm1Cam129SvEv bone vs control, 4month, sl21-40


title: Muscle_adequate protein_female_rep4


title: Rep3, SparcTm1Cam129SvEv bone vs control, sl21-40


title: Muscle_adequate protein_female_rep3


title: Muscle_inadequate protein_female_rep2


title: Muscle_inadequate protein_female_rep3


title: Rep4, SparcTm1Cam129SvEv bone vs control, 4month, sl1-20


title: Muscle_adequate protein_female_rep2


title: pbx2-MO;pbx4-MO, 18s, rep3

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

description: Gene expression data from zebrafish 18 somite stage embryos

hyb_protocol: cRNA was hybridized onto Affymetrix zebrafish genome arrays

scan_protocol: GeneChips were scanned with GENECHIP software

data_processing: The data were normalized by RMA using the Affy package of Bioconductor

organism: Danio rerio

source_name: zebrafish 18 somite stage embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

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

treatment_protocol: Embryos were injected at the 1-2 cell stage with pbx2 and pbx4 morpholinos

tag: AB background, 18 somite embryos


title: Rep5, SparcTm1Cam129SvEv bone vs control, 4month, sl1-20


title: Muscle_inadequate protein_female_rep5


title: Rep1, SparcTm1Cam129SvEv bone vs control, 4month, sl1-20

description: : Arrays were repeated 5 times with fluor switching, in order to counteract any issues of dye bias that may have arisen from direct labelling. Repetition sets used biological samples derived from at least four control and four experimental animals per set, in order to control for biological variation between individual animals. Scanned images were stored and filtered, then analysed using the GeneTac Analyser spot finding software (Genomic Solutions, Cambridgeshire, UK). Analysis  and other methods were carried out similarly to another published experiment, please see Mansergh et al. 2004 PMID: 15303089 for more details.


title: Rep5, SparcTm1Cam129SvEv bone vs control, sl1-20


title: Rep2, SparcTm1Cam129SvEv bone vs control, 4month, sl1-20


title: Muscle_inadequate protein_female_rep1


title: Muscle_inadequate protein_male_rep5

description: Gene expression data from older male during 1 week of inadequate protein intake


title: Rep3, SparcTm1Cam129SvEv bone vs control, 4month, sl1-20


title: Rep4 SparcTm1Cam129SvEv bone vs control, sl1-20

growth_protocol: : Mice were maintained and killed under Home Office licence in accordance with British law (comparable with U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals). Transgenic and control animals were maintained on RM3 diet (1.15% calcium, 0.82% phosphorus, 4088.65I.U./kg Vitamin D, Special Diet Services, Witham, Essex CM8 3AD, UK), ad libitum.


title: pbx2-MO;pbx4-MO, 18s, rep2


title: Control MO, 18s, rep3

treatment_protocol: Embryos were injected at the 1-2 cell stage with control (pbx2 mutant) morpholinos


title: Muscle_adequate protein_female_rep1


title: pbx2-MO;pbx4-MO, 18s, rep1


title: Muscle_adequate protein_male_rep4

description: Gene expression data from older male during 1 week of adequate protein intake


title: Muscle_adequate protein_male_rep5


title: Muscle_inadequate protein_male_rep4


title: Muscle_inadequate protein_male_rep3


title: Control MO, 18s, rep1


title: Rep2, SparcTm1Cam129SvEv bone vs control, sl1-20


title: Control MO, 18s, rep2


title: pbx2-MO;pbx4-MO, 10s, rep3

description: Gene expression data from zebrafish 10 somite stage embryos

source_name: zebrafish 10 somite stage embryos

tag: AB background, 10 somite embryos


title: Rep 1 SparcTm1Cam129SvEv bone vs control, sl1-20

source_name: 129Sv/Ev null bone, 9 months, male, cortical femur


title: pbx2-MO;pbx4-MO, 10s, rep2


title: Rep3, SparcTm1Cam129SvEv bone vs control, sl1-20


title: Muscle_adequate protein_male_rep1


title: Muscle_adequate protein_male_rep2


title: Muscle_inadequate protein_male_rep1


title: Control MO, 10s, rep2


title: Muscle_inadequate protein_male_rep2


title: Control MO, 10s, rep1


title: Muscle_adequate protein_male_rep3


title: Control MO, 10s, rep3


title: Contralateral 5

status: Public on Jul 10 2007

city: London

first: Tom

last: Appleton

state: ON

address: Rm 0061 DSB The University of Western Ontario

department: Physiology & Pharmacology

country: Canada

institute: The University of Western Ontario

description: Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit.

hyb_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

scan_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Scanner 3000 with Workstation.

data_processing: Raw data gene expression files from Affymetrix GeneChips were imported into GeneSpring, version 7.2, software (Silicon Genetics, Redwood City, CA). GC-robust multichip analysis preprocessing was performed. Raw data transformation set values <0.01 at 0.01, per-chip normalization was set at the 50th percentile, and per-gene normalization was set to the median and to values in control/sham samples. Data sets from sham-operated samples were assigned to the normal treatment group, and thus defined baseline expression for each probe. The remaining data sets (samples from contralateral and ipsilateral joints) were assigned to diseased treatment groups, averaged, and used in subsequent analysis. All data were interpreted using the log-ratio setting. From the starting list of 31,099 probes, 17,597 probes were determined to have a reliable signal, using the GeneSpring 7.2 SG1a-1 signal intensity quality control script. The script was adjusted to require signal intensity above a threshold of 50 in 2 of the 3 conditions. The data were then passed through a parametric Welch one-way analysis of variance (ANOVA) script, with P values less than 0.05 considered significant, which reduced the list to 3,877 probes. Post hoc Bonferroni multiple comparison testing was performed to identify statistically significant changes in expression between sham-operated samples and contralateral samples, and between sham-operated samples and ipsilateral samples, with P values less than 0.05 considered significant.

label: Affymetrix Hyb/Wash/Stain Kit

source_name: Contralateral knee articular cartilage, 4 weeks following OA surgery

extract_protocol: Tissue dissection and immediate immersion/homogenization in TRIzol. Aqueous phase transferred to QIAgen RNeasy Mini column for RNA prep.

treatment_protocol: OA Surgery: ACL transection and partial medial meniscectomy; Exercise protocol: 30 minutes walking on rotating cylinder 3x per week

tag: Strain

value: Sprague-Dawley, Gender:male, Weight:350 g


title: OA 5

source_name: Knee articular cartilage, 4 weeks following OA surgery

label_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.


title: Sham 2

source_name: Knee articular cartilage, 4 weeks following sham surgery


title: Contralateral 3


title: Contralateral 4


title: Sham 3


title: pbx2-MO;pbx4-MO, 10s, rep1


title: Sham 4


title: Sham 5


title: Contralateral 2


title: T02-145(1) DNR RNA - mAdbID:42413

status: Public on Jul 07 2007

city: bethesda

first: binwu

last: tang

state: MD

address: 9000 rockville pike

department: nci

institute: nih

description: mAdb experiment ID: 42413

hyb_protocol: FairPlay Microarray Labeling Kit  Other: Use the FairPlay Microarray Labelling Kit instruction from Stratagen, CA.

scan_protocol: GenePix 4000B

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

label_protocol: Sample Labeling Protocol - generic

extract_protocol: Extraction method: Trizol  Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

value: athymic nude mouse; Tissure:Tumor; Cell type:human breast cancer cell line Xenografted into nude mice; Disease state:breast cancer

label: cy 3

source_name: Universal Human Reference RNA

tag: Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: OA 2


title: Sham 1


title: OA 3


title: T02-145(2) DNR RNA - mAdbID:42726

description: mAdb experiment ID: 42726


title: T02-148(1)-2 DNR RNA - mAdbID:42957

description: mAdb experiment ID: 42957


title: T02-147(2)-2 DNR RNA - mAdbID:42662

description: mAdb experiment ID: 42662


title: T02-144(1)-2 DNR RNA - mAdbID:42724

description: mAdb experiment ID: 42724


title: T02-148(1) DNR RNA - mAdbID:42414

description: mAdb experiment ID: 42414


title: T02-147(1) DNR RNA - mAdbID:42725

description: mAdb experiment ID: 42725


title: OA 4


title: T02-136(2)-3 Control RNA - mAdbID:42946

description: mAdb experiment ID: 42946

source_name: T02-136(2)-3 Control RNA


title: T02-136(1)-3 Control RNA - mAdbID:42934

description: mAdb experiment ID: 42934

source_name: T02-136(1)-3 Control RNA


title: T02-148(1)-3 DNR RNA - mAdbID:42941

description: mAdb experiment ID: 42941


title: stb3-null 3 days in YPD + 2%glucose for 10 minutes B

status: Public on Jul 06 2007

city: Madison

first: Warren

last: Heideman

state: WI

address: 777 Highland Ave

department: Pharmacy

institute: University of Wisconsin

description: Saccharomyces cerevisiae cells grown for 3 days in rich media and, when noted, supplied with 2% glucose and collected after 10 minutes of glucose addition

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

label: biotinylated dUTP, stained with streptavidin linked phycoerythrin

source_name: stb3-null 10minutes+glucose B

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: Strains used are BY4742 as wild type and a stb3-null in the BY4742 background


title: T02-135(2) Control RNA - mAdbID:42659

description: mAdb experiment ID: 42659

source_name: T02-135(2) Control RNA


title: stb3-null 3 days in YPD A

source_name: stb3-null post-log A

growth_protocol: Saccharomyces cerevisiae cells grown for 3 days in rich media and, when noted, supplied with 2% glucose and collected after 10 minutes of glucose addition


title: BY4742 3 days in YPD + 2% glucose for 10 minutes B

source_name: BY4742 10minutes +glucose B


title: T02-135(1) Control RNA - mAdbID:42722

description: mAdb experiment ID: 42722

source_name: T02-135(1) Control RNA


title: BY4742 3 days in YPD A

source_name: BY4742 post-log A


title: BY4742 3 days in YPD B

source_name: BY4742 post-logB


title: T02-134(1) Control RNA - mAdbID:42721

description: mAdb experiment ID: 42721

source_name: T02-134(1) Control RNA


title: T02-136(1)-2 Control RNA - mAdbID:42660

description: mAdb experiment ID: 42660

source_name: T02-136(1)-2 Control RNA


title: T02-136(2)-2 Control RNA - mAdbID:42661

description: mAdb experiment ID: 42661

source_name: T02-136(2)-2 Control RNA


title: BY4742 3 days in YPD + 2% glucose for 10 minutes A

source_name: BY4742 10 minutes+glucose A


title: stb3-null 3 days in YPD + 2% glucose for 10 minutes A

source_name: stb3-null 10minutes+glucose A


title: Tcf3 Targets in Mouse Embryonic Stem Cells,E14

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis Street

department: Stem Cell and Developmental Biology

country: Singapore

institute: GIS

description: All cell cultures were maintained at 37 °C with 5% CO2. The culture of mouse ESCs, E14 (ATCC: CRL-1821) either on feeders or in feeder-free conditions was described previously{Zhang, 2006 #49}. HEK 293T/17 (ATCC: CRL-11268) cells were maintained in DMEM supplemented with 10% heat-inactivated FBS and penicillin/streptomycin..ChIP assays with feeder-free E14 mouse ESCs were carried out as described previously{Zhang, 2006 #49}. Briefly, cells were cross-linked with 1% formaldehyde for 10 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine. Chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using antibodies. The antibodies used for immunoprecipitation were Tcf3 (M-20), HA (Y-11), Tle2 (H-321), Tle3 (M-201), CtBP (H-440), GST (Z-5, all from Santa Cruz). For all ChIP experiments, quantitative PCR analyses were performed in real-time using the ABI PRISM 7900 Sequence Detection System and SYBR Green Master Mix as described previously {Zhang, 2006 #49}. Relative occupancy values were calculated by determining the apparent immunoprecipitation efficiency (ratios of the amount of immunoprecipitated DNA to that of the input sample) and normalized to the level observed.

hyb_protocol: ChIP combined with DNA microarray was carried out according to Agilent Mammalian ChIP-on-chip protocol (version 3) {Boyer, 2005 #28}. Briefly, immunoprecipitated (IP) DNA was blunted with T4 polymerase and ligated to linkers with T4 DNA ligase. For reference, 200 ng of input DNA was used. Ligated DNA was amplified with two rounds of PCR cycles. Two ug of each amplified sample were labeled with Cy5 for IP DNA, and Cy3 for input DNA using CGH labeling kit (Invitrogen). Four ug of each labeled sample was blocked with mouse Cot-1 DNA (Invitogen) and blocking agent (Agilent), and hybridized to DNA microarrays (G4490A, Agilent) for 40 h at 65oC. The microarrays were washed and stabilized with acetonitrile (Sigma), followed by stabilization and drying solution (Agilent).

scan_protocol: The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (G2567AA, version 9.1).

data_processing: Agilent Feature Extraction Software (G2567). The data was then analysed with ChIP Analytics 1.3 (G4477AA), according to the Whitehead Neighbourhood Model, P(Xbar)<0.001, with intra-array median normalization {Boyer, 2005 #28}. Bound targets which was determined by the algorithm was validated by qPCR on a selected number of genes. The false positive rate was determined.

source_name: Input DNA using CGH labeling kit (Invitrogen) (Cye3)

label_protocol: Cy3 labelled with standard protocol

extract_protocol: Invitrogen CGH input DNA

tag: Input DNA

source_name: Amplified IP DNA (Cy5)

label_protocol: Cy5 labelled with standard protocol

extract_protocol: Agilent mammalian ChIP-on-chip protocol, version 3.

tag: E14 ESC


title: stb3-null 3 days in YPD B

source_name: stb3-null post-log B


title: T02-137(1) Control RNA - mAdbID:42723

description: mAdb experiment ID: 42723

source_name: T02-137(1) Control RNA

source_name: Universal Human Reference RNA


title: WAT_PPARb-knockout_control_pool

status: Public on Jul 04 2007

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: PPARb/d knockout animals fed a control diet (chow)

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCRMA version 2.20, empirical Bayes

source_name: Epididymal white adipose tissue (WAT)

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions

value: PPARb/d knock-out on a mixed background (Sv129/C57BL/6)

tag: Gender

value: male

tag: Age

value: 12 weeks

tag: Tissue

value: WAT


title: T02-134(2) Control RNA - mAdbID:42933

description: mAdb experiment ID: 42933

source_name: T02-134(2) Control RNA


title: WAT_wildtype_control_pool

description: Wild-type animals fed a control diet (chow)

scan_protocol: According to standard Affymetrix protocols.

value: 12-16 weeks

value: white adipose tissue


title: CET at 150 µg/kg BW for 24 h + PBS for 8h_2

city: Bangalore

first: priyanka

last: samji

state: Karnataka

address: Malleswaram

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

description: Description Probe level measurements produced by Affymetrix microarray suite 5.0. Analysis performed at level of raw signals (See Affymetrix Microarray suite 5.0 reference on web site for description).

scan_protocol: Scan protocol Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001) using scanner 3000 series

data_processing: Data processing MAS5.0, data was normalized with standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

organism: Macaca radiata

source_name: CL from female bonnet monkey (CET at 150 µg/kg BW for 24 h + PBS for 8h)

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma Aldrich Co., St.Louis, MO) followed by clean up step using RNeasy mini purification kit (# 74104, Qiagen).

treatment_protocol: Female monkeys receiving CET treatment on day 7 of luteal phase were administered 20 IU/kg BW of rhLH or PBS (0.5 ml) i.v. at 24 h post CET treatment and blood samples were collected before and after rhLH/PBS treatments. To study changes in gene expression associated with LH replacement following inhibition of endogenous LH secretion by CET, CL was collected at 8 h (n=2) following LH replacement from female monkeys treated previously with CET for 24 h. Monkeys receiving CET on day 7 of luteal phase and 1X PBS at 24 h following CET treatment served as control (n=2) for the present study. Corpora lutea following different treatments were cut into small quarters and snap frozen in liquid nitrogen.


title: Tcf3 Targets in Mouse Embryonic Stem Cells,E14 2_2


title: CET at 150 µg/kg BW for 24 h + rhLH for 8h_3

hyb_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

source_name: CL from female bonnet monkey (CET at 150 µg/kg BW for 24 h + rhLH for 8h)


title: CET at 150 µg/kg BW for 24 h + rhLH for 8h_4

label_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev.3, 2001)

tag: CL from female bonnet monkey (CET at 150 µg/kg BW for 24 h + rhLH for 8h)


title: CET at 150 µg/kg BW for 24 h + PBS for 8h_1

tag: CL from female bonnet monkey (CET at 150 µg/kg BW for 24 h + PBS for 8h)


title: HSF6 (EB) vs HSF1 (EB)

city: Los Angeles

last: Sun

state: CA

address: 635, Charles E. Young Dr. South

department: Molecular and Medical Pharmacology

institute: UCLA

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: Data processing using Agilent Feature Extration 9.5 and default parameters

source_name: HSF6 hESC-derived NPCs

label_protocol: Agilent cRNA labeling protocol

extract_protocol: Trizol

tag: Undifferentiated hNPCs are derived using embryonic body (EB) formation method

source_name: HSF1 hESC-derived NPCs


title: HSF6 (EB) vs HSF1 (monolayer)

source_name: HSF-1 hESC-derived NPCs

tag: Undifferentiated hNPCs are derived using monolayer conversion method (100ng/ml noggin added)


title: T98G 4 hr PDGF+CHX vs T98G 4 hr PDGF Cy3-Cy5 rep 1

status: Public on Jul 03 2007

city: Boston

first: Geoffrey

middle: M

last: Cooper

address: 5 Cummington St

department: Biology

institute: Boston University

description: For each treated sample, three independent replicate microarray experiments were performed.

hyb_protocol: For each slide, 4 micrograms of both treated and untreated cyanine-labeled aRNA samples were combined with a hybridization buffer (2.3X SSC, 18 mM HEPES, 0.2 mg/ml BSA, 0.6 mg/ml poly(A), 0.2% SDS), heat denatured for 3 minutes at 95 degrees C, and applied to microarrays under a LifterSlip coverslip (Erie Scientific).  The slides were placed in a hybridization chamber (Dietech) and incubated in a 63 degree C water bath for 16 hr.  Following hybridization, the slides were successively washed in 0.6X SSC with 0.025% SDS, 0.05X SSC, and water, then dried by centrifugation at 1000 rpm for 3 min.

scan_protocol: The microarrays were scanned with an Axon 4000B scanner and adaptive spot segmentation performed with GenePix Pro software (version 5.0) (Axon Instruments).

data_processing: Triplicate dye-swap, background-subtracted median intensity values were used as input to the LIMMA analysis package (Smyth, 2005) in Bioconductor (Gentleman et al., 2004), and average LOESS-corrected log2 ratios were used to estimate differential gene expression.  For the PDGF-treated samples, genes with positive log2 ratios greater than or equal to 1 (2-fold) relative to untreated samples and FDR-corrected (Benjamini et al., 1995) moderated t-test p-values less than 0.01 were considered differentially expressed.  Additional microarray dye-swap experiments were performed to identify genes with PDGF-stimulated inductions that were independent of new protein synthesis.  RNA was extracted from cells treated with the translation inhibitor, cycloheximide (CHX), for 30 min followed by 2 or 4 hr PDGF treatments.  For each of three replicates, two microarray experiments were performed with different reference samples.  The first compared CHX and PDGF-treated samples to untreated samples, while the other compared CHX and PDGF-treated samples to PDGF-treated samples.  Based on this data and a linear model of the experimental design, the LIMMA program was used to calculate PDGF inductions in the presence of cycloheximide at 2 and 4 hrs as log2 ratios relative to untreated cells.  The effect of cycloheximide prior to PDGF stimulation was calculated as the percent inhibition of inductions by PDGF alone at 2 or 4 hrs.

molecule: polyA RNA

label_protocol: Starting with 100 ng of poly(A)+ RNA, one round of RNA amplification was performed with the MessageAmp aRNA Amplification Kit (Ambion) using a 4:1 amino-allyl UTP:UTP ratio for aRNA incorporation.  For each sample, 8 micrograms of aRNA was coupled to N-hydroxysuccinimidyl esters of cyanine-3 or cyanine-5 (Amersham).  Following clean-up, treated and untreated aRNA samples with opposing cyanine labels were combined, concentrated, and treated with a fragmentation reagent (Ambion) according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent (Invitrogen) followed by poly(A)+ RNA isolation with an Oligotex mRNA Midi Kit (Qiagen) according to each manufacturer's protocol.

treatment_protocol: T98G human glioblastoma cells were grown in Minimal Essential Medium (Invitrogen) supplemented with fetal calf serum (10%).  Cells were rendered quiescent by incubation in serum-free medium for 72 h, and either left unstimulated, or stimulated for 0.5, 2, or 4 hr with human PDGF-BB (50 ng/ml) (Sigma).  When called for, cycloheximide (10 micrograms/ml) was added 30 min prior to PDGF addition.

tag: T98G human glioblastoma cells

source_name: 72 hr serum-deprived T98G cells with 4 hr PDGF treatment and cycloheximide added 0.5 hr prior to PDGF


title: T98G 4 hr PDGF vs Untreated Cy3-Cy5 rep 2

source_name: 72 hr serum-deprived T98G cells (untreated)

source_name: 72 hr serum-deprived T98G cells with 4 hr PDGF treatment


title: T98G 4 hr PDGF+CHX vs T98G 4 hr PDGF Cy5-Cy3 rep 1


title: T98G 2 hr PDGF+CHX vs T98G 2 hr PDGF Cy5-Cy3 rep 2

source_name: 72 hr serum-deprived T98G cells with 2 hr PDGF treatment and cycloheximide added 0.5 hr prior to PDGF


title: T98G 4 hr PDGF+CHX vs T98G 4 hr PDGF Cy3-Cy5 rep 2


title: T98G 4 hr PDGF+CHX vs Untreated Cy5-Cy3 rep 2


title: T98G 4 hr PDGF+CHX vs Untreated Cy5-Cy3 rep 1


title: T98G 4 hr PDGF vs Untreated Cy5-Cy3 rep 2


title: T98G 2 hr PDGF+CHX vs T98G 2 hr PDGF Cy3-Cy5 rep 2

source_name: 72 hr serum-deprived T98G cells with 2 hr PDGF treatment


title: T98G 2 hr PDGF+CHX vs Untreated Cy5-Cy3 rep 2


title: T98G 4 hr PDGF+CHX vs Untreated Cy3-Cy5 rep 1


title: T98G 2 hr PDGF+CHX vs Untreated Cy3-Cy5 rep 1


title: T98G 4 hr PDGF vs Untreated Cy5-Cy3 rep 3


title: T98G 2 hr PDGF+CHX vs T98G 2 hr PDGF Cy3-Cy5 rep 1


title: T98G 4 hr PDGF vs Untreated Cy3-Cy5 rep 3


title: T98G 2 hr PDGF+CHX vs Untreated Cy3-Cy5 rep 2


title: T98G 2 hr PDGF vs Untreated Cy3-Cy5 rep 3


title: T98G 4 hr PDGF+CHX vs Untreated Cy5-Cy3 rep 3


title: T98G 2 hr PDGF+CHX vs Untreated Cy5-Cy3 rep 1


title: T98G 2 hr PDGF vs Untreated Cy3-Cy5 rep 2


title: T98G 4 hr PDGF vs Untreated Cy3-Cy5 rep 1


title: T98G 4 hr PDGF+CHX vs T98G 4 hr PDGF Cy3-Cy5 rep 3


title: T98G 4 hr PDGF vs Untreated Cy5-Cy3 rep 1


title: T98G 2 hr PDGF+CHX vs T98G 2 hr PDGF Cy5-Cy3 rep 1


title: T98G 4 hr PDGF+CHX vs T98G 4 hr PDGF Cy5-Cy3 rep 2


title: T98G 4 hr PDGF+CHX vs T98G 4 hr PDGF Cy5-Cy3 rep 3


title: T98G 4 hr PDGF+CHX vs Untreated Cy3-Cy5 rep 2


title: T98G 2 hr PDGF vs Untreated Cy5-Cy3 rep 2


title: T98G 2 hr PDGF+CHX vs T98G 2 hr PDGF Cy3-Cy5 rep 3


title: T98G 0.5 hr PDGF vs Untreated Cy5-Cy3 rep 2

source_name: 72 hr serum-deprived T98G cells with 0.5 hr PDGF treatment