title: ESC shRNA linc1335_1.1-130_R2 (batch1)

value: shRNA knockdown of linc1335


title: ESC shRNA linc1335_1.1-130_R1 (batch1)

status: Public on Aug 30 2011

type: RNA

city: Cambridge

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute

hyb_protocol: We mixed 600ng of cRNA with blocking agent and fragmentation buffer (Agilent, 5190 0404) and fragmented for 30 minutes in the dark at 60°C.  We added 2x Hybridization Buffer to each sample and loaded 40ul onto an 8-pack Hybridization gasket.  We placed the microarray slides on top, sealed in the Hybridization Chamber, and incubated for 18 hours at 65°C.  We washed the slides for 1 minute in room temperature GE Wash Buffer 1 and then for 1 minute in 37°C GE Wash Buffer 2 (Agilent 5188 5327, no triton addition).  We scanned the microarrays using an Agilent Scanner C (G2565CA) using the following settings: Dye Channel = Red&Green, Scan Region = ScanArea (61x21.6mm), Scan Resolution = 3 m. We prepared all of the samples simultaneously using homogenous master mixes to limit variability. Fragmentation and hybridization was staggered over time in batches of 3 to 4 slides (24 to 32 samples).

scan_protocol: Each array was processed and data extracted using the Agilent feature extraction software (G4462AA, Version 10.7.3).

data_processing: Gene expression values were determined using the gProcessedSignal intensity values. Probes were flagged if they were not detectable well above background or had an expression level lower than the lowest detectable spike-in control value. The values were floored across all samples by taking the maximum of the minimum non-flagged values across all experiments. Any value less than this maximum value were set to the maximum. To normalize expression values across arrays, we performed quantile normalization as previously described. Briefly, we ranked each array from lowest to highest expression. For each rank, we computed the average expression and each experiment with this value at the associated rank. For each probe, we computed the difference between the second smallest expression value and the second largest expression value. If this difference was less than 2, we filtered the probe. This metric was chosen to eliminate bias due to single sample outliers.

molecule: total RNA

organism: Mus musculus

source_name: mESC shRNA treated 4 days

label_protocol: Using Agilent’s One-Color Quick Amp Labelling kit (5190-0442), we amplified and labelled total RNA for hybridization to prototype mouse lincRNA arrays (G4140-90040) according to manufacturer’s instructions with a few variations. The cRNA samples were prepared by diluting 200ng of RNA in 8.3ul water and adding positive control one-color RNA spike-in mix (Agilent, 5188-5282) that was diluted serially 1:20, then 1:25 and finally 1:10. We annealed the T7 promoter primer from the kit by incubating at 65°C for 10 minutes.  We prepared the cDNA master mix and added to the annealed RNA and incubated at 40°C for 2 hours, followed by 65°C for 15 minutes.  We prepared the cRNA transcription master mix and added it to the cDNA and incubated at 40°C for 2 hours protected from light. We purified the labeled cRNA using Qiagen’s RNeasy 96-well columns (Qiagen, 74181) by adding 350ul of Qiagen RLT (without BME) to the cRNA followed by the addition of 250ul of 95% ethanol before applying to the plate column.  After a 4 minute spin at 6000RPM, we washed the columns 3 times with 800ul buffer RPE. We dried the columns by spinning for 10 minutes and eluted the cRNA with 50ul of water.  We measured the cRNA yield and dye incorporation using the Nanodrop 8000 Microarray measurement setting.

growth_protocol: V6.5 ES cells were plated at a density of 5000 cells/well in 100ul mES media onto pre-gelatinized 96-well dishes (VWR; BD356689).  Cells were infected with 5ul of a lentiviral shRNA stock and incubated at 37°C for 30 minutes.  Puromycin resistant DR4 MEFs (GlobalStem; GSC-6004G) were then added to the plates at a density of ~6000/well and incubated overnight at 37°C, 5% CO2.  After 24 hours, all media was removed from the cells and replaced with media containing 1ug/mL puromycin.  Media was then changed every other day with fresh media containing 1ug/mL puromycin.

extract_protocol: ES cells were infected and lysed at day 4 with 150ul of Qiagen’s RLT buffer and 3 replicates of each virus plate were pooled for RNA extraction using Qiagen’s RNeasy 96-well columns (74181).  RNA extraction was completed following Qiagen’s RNeasy 96-well protocol with the following modifications: 450ul of 70% ethanol was added to 450ul total lysate prior to the first spin.  An additional RPE wash was added to the protocol, for a total of 3 RPE washes.

tag: cell line

tag: knockdown


title: ESC shRNA linc1315_1.1-672_R1 (batch1)

treatment_protocol: Cells were infected with 5ul of a lentiviral shRNA stock and incubated at 37°C for 30 minutes.

value: shRNA knockdown of linc1315


title: ESC shRNA linc1315_1.1-672_R2 (batch1)


title: ESC shRNA linc1346_1.1-3679_R1 (batch1)

value: shRNA knockdown of linc1346


title: ESC shRNA linc1349_1.1-13_R3 (batch1)

value: shRNA knockdown of linc1349


title: ESC shRNA linc1328_1.1-510_R1 (batch1)

value: shRNA knockdown of linc1328


title: ESC shRNA linc1307_1.1-277_R1 (batch1)

value: shRNA knockdown of linc1307


title: ESC shRNA linc1304_1.1-903_R2 (batch1)

value: shRNA knockdown of linc1304


title: ESC shRNA linc1293_1.1-4738_R2 (batch1)

value: shRNA knockdown of linc1293


title: ESC shRNA linc1304_1.1-903_R1 (batch1)


title: ESC shRNA linc1283_4.1-56_R2 (batch1)

value: shRNA knockdown of linc1283


title: ESC shRNA linc1312_1.1-185_R2 (batch1)

value: shRNA knockdown of linc1312


title: ESC shRNA linc1283_2.1-199_R1 (batch1)


title: ESC shRNA linc1293_1.1-4738_R1 (batch1)


title: ESC shRNA linc1312_1.1-185_R1 (batch1)


title: ESC shRNA linc1290_1.1-177_R1 (batch1)

value: shRNA knockdown of linc1290


title: ESC shRNA linc1270_2.1-672_R1 (batch1)

value: shRNA knockdown of linc1270


title: ESC shRNA linc1267_1.1-135_R2 (batch1)

value: shRNA knockdown of linc1267


title: ESC shRNA linc1346_1.1-3679_R2 (batch1)


title: ESC shRNA linc1283_4.1-56_R1 (batch1)


title: ESC shRNA linc1262_1.1-229_R2 (batch1)

value: shRNA knockdown of linc1262


title: ESC shRNA linc1259_1.1-1491_R1 (batch1)

value: shRNA knockdown of linc1259


title: ESC shRNA linc1262_1.1-229_R1 (batch1)


title: ESC shRNA linc1253_2.1-1304_R2 (batch1)

value: shRNA knockdown of linc1253


title: ESC shRNA linc1283_2.1-199_R2 (batch1)


title: ESC shRNA linc1244_1.1-301_R2 (batch1)

value: shRNA knockdown of linc1244


title: ESC shRNA linc1267_1.1-135_R1 (batch1)


title: ESC shRNA linc1256_1.1-745_R2 (batch1)

value: shRNA knockdown of linc1256


title: ESC shRNA linc1259_1.1-1491_R2 (batch1)


title: ESC shRNA linc1244_1.1-301_R1 (batch1)


title: ESC shRNA linc1253_2.1-567_R2 (batch1)


title: ESC shRNA linc1242_1.1-730_R1 (batch1)

value: shRNA knockdown of linc1242


title: ESC shRNA linc1253_2.1-567_R1 (batch1)


title: ESC shRNA linc1242_1.1-730_R2 (batch1)


title: ESC shRNA linc1256_1.1-745_R1 (batch1)


title: ESC shRNA linc1253_2.1-1304_R1 (batch1)


title: ESC shRNA linc1239_1.1-1423_R1 (batch1)

value: shRNA knockdown of linc1239


title: ESC shRNA linc1261_1.1-363_R1 (batch1)

value: shRNA knockdown of linc1261


title: ESC shRNA linc1235_1.1-158_R2 (batch1)

value: shRNA knockdown of linc1235


title: ESC shRNA linc1270_2.1-672_R2 (batch1)


title: ESC shRNA linc1235_1.1-158_R1 (batch1)


title: ESC shRNA linc1230_1.1-370_R1 (batch1)

value: shRNA knockdown of linc1230


title: ESC shRNA lacZ_165_R1 (batch1)

value: shRNA knockdown of LacZ


title: ESC shRNA lacZ_656_R1 (batch1)


title: ESC shRNA linc1261_1.1-363_R2 (batch1)


title: ESC shRNA clonetechGfp_437_R3 (batch1)

value: shRNA knockdown of GFP


title: ESC shRNA clonetechGfp_477_R1 (batch1)


title: ESC shRNA clonetechGfp_437_R4 (batch1)


title: ESC shRNA lacZ_133_R1 (batch1)


title: patient 69 after treatment (paired analysis)

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: patient 69 after treatment

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer

scan_protocol: Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing:
Probe intensities were extracted from Affymetrix CEL files and normalized using RMA and summarized at the transcript cluster level using the R/Bioconductor (http://bioconductor.org) oligo package.  Array quality control was performed to remove arrays that significantly differed in performance.  Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package.  Significance testing was performed using a moderated t-test, and comparisons of pre- (V0) and post-treatment (V1) individuals were performed using a moderated paired t-test.  Gene set analysis was performed using the MSigDB (http://www.pnas.org/content/102/43/15545.abstract) and libraries generated from the Halloran labs Pathogenesis Based Transcript (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets.  The PBTs represent the major biologic events in cellular graft rejection and were derived from experimental mouse kidney transplants, cultured cells and human kidney biopsies.  Gene sets were converted to HUGO gene symbols and analysis was executed using the limma romer function.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

label: biotin

organism: Homo sapiens

source_name: post-treatment

label_protocol: Follow protocols of Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using QIAGEN PAXgene Blood RNA Kit (Catalog Number 762164, Qiagen, USA). Briefly, centrifuged the PAXgene Blood RNA tube, pellet was visibly dissolved by adding 350 μl buffer BR1 and vortexing.  The proteins was digested using 40 μl proteinase K  for 10 minutes at 55°C  with a shaker–incubator at 1000 rpm. Lysate was directly flowing through a PAXgene Shredder spin column.  After adding  350 μl ethanol (96–100%) into flowing through lysate,  the lysate-ethanol mix was transferred into a PAXgene RNA spin column, following a DNA digestion using DNAse I and several wash, total RNA was eluted and dissolved into RNAse free water (All Reagents and Columns are from Kit).

treatment_protocol: 2.5 ml of Patient’s whole blood was collected into one PAXgene RNA Tube (Catalog Number 762165, Qiagen, USA)  using standard venipuncture and storaged in -20c  for 24 hours, then transferred in -70c until use.

tag: tissue

value: blood

tag: treatment

value: post intravenous immune globulin (IVIG) and rituximab desensitization

tag: individual

value: patient 69 after treatment


title: ESC shRNA clonetechGfp_197_R1 (batch1)


title: SON_LAB_Cy3_HAB_Cy5_rep2

city: München

first: Ludwig

last: Czibere

address: Kraepelinstrasse 2

country: Germany

institute: Max Planck Institute of Psychiatry

description: technical replicate dye-swapped 2 of 5 from pooled samples

hyb_protocol: Ten array slides per brain region (MPI24K Arrays, MPI of Psychiatry, Munich, Germany) – serving as technical replicates - were prehybridized prior to the experiment in the prehybridization buffer for 1h at 42°C, then washed in water and isopropanol and dried by centrifugation (Megafuge 1.0R, Heraeus, Hanau, Germany) at 1500g for 3min in 50ml tubes (Sarstedt). Dye coupled aRNA samples were mixed with the contrary dye coupled sample from the other mouse line of the specific regions and loaded with a hybridization buffer to five arrays each under m-Series LifterSlips (Menzel). All arrays were hybridized at 50°C over 16-17h in separate hybridization chambers. Then arrays were washed in 2xSSC and 0.1% SDS for 5min at 42°C, 10min room temperature in 0.1xSSC and 0.1% SDS, four times in 0.1xSSC for 1min and finally for 20s in 0.01xSSC solutions. Slides were dried by centrifugation at 1,500rpm for 3min.

scan_protocol: The arrays were scanned on a PerkinElmer ScanArray 4000 (PerkinElmer Life and Analytical Sciences, Shelton, CT) laser scanner using automatic focusing and adapting laser power between 60 and 80 for Cy3 and 40 and 70 for Cy5. This ensured that for both dyes - in average - the same fluorescence intensities were reached and that not more than 1-2% of spots showed fluorescence intensities over the point of saturation.

data_processing: Quantification of all arrays was performed with QuantArray-software (GSI Lumonics, Billerica, MA) applying a fixed-circle quantification protocol and manual positioning of all grids over the hybridized spots. To provide a negative control for the hybridization and evaluation procedure, excess aRNA was used for an additional hybridization in both Cy3 and Cy5 combinations. For statistical evaluation, analytic methods were applied as previously described (Dudoit et al., 2002; Yang et al., 2002). In brief, first an MA-plot was generated to display raw fluorescence intensities of Cy5 (R) and Cy3 (G) with M = log2 R/G and A = log2sqrt(RG). Data were normalized to exclude systematic and technical errors. For two normalization steps, a function c was subtracted from the logarithmized fluorescence intensities (log2 R and log2 G). First a global normalization was performed, based on the assumption that R and G correlate. In a second normalization step, an intensity-dependent normalization was added, which was performed applying a LOESS smooth, as it is implied in the R software package (http://www.r-project.org). From the MA-plot, 40% of values were used to calculate the smooth. In several other normalization steps, differences were minimized that resulted from unequal distribution of probes from the array production or from unbalanced fluorescence intensities within one array slide. All data were merged in a matrix, p-values for multiple testing were calculated by permutation and are therefore called adjusted p-values.

source_name: supraoptic nucleus, HAB mice, basal

label_protocol: Extracted total RNA was amplified and dye coupled in two rounds with Ambion’s Amino Allyl MessageAmp aRNA kit (Ambion) according to the manufacturer’s protocol using T7 oligo(dT) primers for the first round to select specifically for mRNA for reverse transcription and random hexamer primers for the second round of reverse transcription. The procedure included the synthesis of a first then a second strand of cDNA and an in vitro transcription step overnight. cDNA synthesis was carried out in PCR tubes (Abgene, Hamburg, Germany) using a thermal cycler (GeneAmp PCR System 9700, PE Applied Biosystems, Foster City, CA). For in vitro transcription, the tubes provided by the kit’s manufacturer were used, after pipetting all reagents, tubes were sealed with parafilm (American National Can, Neenah, WI) and incubated at 37°C in a warm room constantly heated. In the second round of in vitro transcription, an amino allyl extension to every second uracyl base was incorporated to receive the amino allyl RNA (aRNA) for the following indirect dye coupling reaction. Before aRNA purification the filters were equilibrated with 100µl aRNA binding buffer and incubated for 5min. All samples were pooled to one sample per line and brain region. The dye swapped experimental design required coupling of one half of each pooled sample to cyanine 3 (Cy3, Amersham Biosciences, Buckinghamshire, UK) the other half to cyanine 5 (Cy5, Amersham Biosciences). Correct quantification of aRNA was ensured by photometric assessment of the optic density in a photometer (Ultrospec II, Pharmacia LKB Biochrom, Cambridge, United Kingdom) and additional analysis on agarose gel.

extract_protocol: Total RNA was extracted in presterilized 1.5ml Safelock tubes (Eppendorf, Hamburg, Germany) using a TRIzol (Invitrogen, Karlsruhe, Germany) chloroform standard protocol. After tissue homogenization in 300µl of TRIzol by pipetting, 1µl linear acrylamide (5mg/ml, Ambion, Austin, TX) and 60µl of chloroform (Carl Roth, Karlsruhe, Germany) were added and the samples vortexed. Centrifugation for 5min at 18°C and 13,000rpm followed, then RNA was precipitated with 180µl isopropanol (Carl Roth) overnight at -20°C, centrifuged at 4°C and 13,000rpm for 30min and washed twice in 500µl 70% ethanol (Carl Roth) with centrifugation steps at 4°C and 13,000rpm of 10min in between. Following the last centrifugation step, all remaining liquid was removed with a pipet, pellets were dried in an incubator for 15min at 45°C and resolved in 13µl of autoclaved bidistilled water.

treatment_protocol: Brains were collected, dissected in slices of 200µm and mounted to Superfrost microscope slides (Menzel, Braunschweig, Germany) in a cryostat (Microm MH50, Microm, Walldorf, Germany) from rostral to caudal. From these frozen slices the brain areas of interest were acquired by micropuncture as described before (Palkovits, 1973) utilizing punchers with a diameter of 0.5 or 1mm (Fine Science Tools, Heidelberg, Germany). The brain regions collected included the anterior part of the cingulate cortex (Cg), the nucleus accumbens core and shell (NAc), the PVN, the supraoptic nucleus (SON) and the basolateral/lateral (BLA/LA), central (CeA) and medial (MeA) amygdala. Punches of 1mm diameter were collected from Bregma +1.3mm to +0.9mm, twice sampling the tissue medially about 0.5mm from the dorsal tissue border to receive the Cg and bilaterally sampling the NAc core and unpreventably a minor part of its shell around the anterior commissure. Further tissue was collected medially 0.8mm above the ventral tissue limit (Ø=1mm) and bilaterally from the optic tract (Ø=0.5mm) to acquire tissue from the PVN and SON, from Bregma -0.56mm to -0.96mm. Amygdala tissue samples were collected bilaterally from two slides for each region acquiring punches of 1mm diameter. CeA was collected from Bregma -0.96mm to -1.36mm dorsomedially from the ventral end of the external capsule, MeA from -1.16mm to -1.56mm dorsolaterally from the optic tract and BLA/LA was collected from Bregma -1.36mm to -1.76mm from in between the bifurcation of the external capsule. Coordinates are according to the Mouse brain Atlas (Paxinos and Franklin, 2001).

tag: strain

value: CD-1 (ICR)

tag: gender

value: male

tag: age

value: 10 weeks

source_name: supraoptic nucleus, LAB mice, basal


title: patient 108 before treatment (paired analysis)

description: patient 108 before treatment

source_name: pre-treatment

value: pre intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 108 before treatment


title: ESC shRNA lacZ_208_R1 (batch1)


title: SON_LAB_Cy3_HAB_Cy5_rep3

description: technical replicate dye-swapped 3 of 5 from pooled samples


title: ESC shRNA lacZ_300_R1 (batch1)


title: ESC shRNA clonetechGfp_231_R1 (batch1)


title: ESC shRNA clonetechGfp_506_R1 (batch1)


title: ESC shRNA linc1230_1.1-370_R2 (batch1)


title: patient 61 after treatment (paired analysis)

description: patient 61 after treatment

value: patient 61 after treatment


title: ESC shRNA linc1331_2.1-399_R2 (batch1)

value: shRNA knockdown of linc1331


title: ESC shRNA clonetechGfp_437_R1 (batch1)


title: SON_LAB_Cy3_HAB_Cy5_rep4

description: technical replicate dye-swapped 4 of 5 from pooled samples


title: patient 108 after treatment (paired analysis)

description: patient 108 after treatment

value: patient 108 after treatment


title: patient 69 before treatment (paired analysis)

description: patient 69 before treatment

value: patient 69 before treatment


title: patient 62 before treatment (paired analysis)

description: patient 62 before treatment

value: patient 62 before treatment


title: patient 112 before treatment (paired analysis)

description: patient 112 before treatment

value: patient 112 before treatment


title: ESC shRNA clonetechGfp_437_R2 (batch1)


title: patient 62 after treatment (paired analysis)

description: patient 62 after treatment

value: patient 62 after treatment


title: SON_LAB_Cy3_HAB_Cy5_rep5

description: technical replicate dye-swapped 5 of 5 from pooled samples


title: patient 56 before treatment (paired analysis)

description: patient 56 before treatment

value: patient 56 before treatment


title: patient 56 after treatment (paired analysis)

description: patient 56 after treatment

value: patient 56 after treatment


title: patient 59 after treatment (paired analysis)

description: patient 59 after treatment

value: blood

value: patient 59 after treatment


title: patient 59 before treatment (paired analysis)

description: patient 59 before treatment

value: patient 59 before treatment


title: SON_HAB_Cy3_LAB_Cy5_rep1

description: technical replicate 1 of 5 from pooled samples

value: CD-1 (ICR)


title: patient 38 after treatment (paired analysis)

description: patient 38 after treatment

value: post intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 38 after treatment


title: patient 38 before treatment (paired analysis)

description: patient 38 before treatment

value: pre intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 38 before treatment


title: patient 40 before treatment (paired analysis)

description: patient 40 before treatment

value: patient 40 before treatment


title: Cg_LAB_Cy3_HAB_Cy5_rep2

source_name: cingulate cortex, HAB mice, basal

value: male

value: 10 weeks

source_name: cingulate cortex, LAB mice, basal


title: patient 61 before treatment (paired analysis)

description: patient 61 before treatment

value: patient 61 before treatment


title: SON_HAB_Cy3_LAB_Cy5_rep2

description: technical replicate 2 of 5 from pooled samples


title: SON_HAB_Cy3_LAB_Cy5_rep4

description: technical replicate 4 of 5 from pooled samples


title: SON_HAB_Cy3_LAB_Cy5_rep3

description: technical replicate 3 of 5 from pooled samples


title: Cg_LAB_Cy3_HAB_Cy5_rep4


title: SON_LAB_Cy3_HAB_Cy5_rep1

description: technical replicate dye-swapped 1 of 5 from pooled samples


title: Cg_LAB_Cy3_HAB_Cy5_rep3


title: Cg_HAB_Cy3_LAB_Cy5_rep4


title: Cg_LAB_Cy3_HAB_Cy5_rep1


title: Cg_HAB_Cy3_LAB_Cy5_rep3


title: Cg_LAB_Cy3_HAB_Cy5_rep5


title: patient 139 untreated control (non-paired analysis)

description: patient 139 untreated control

source_name: untreated

value: untreated

value: patient 139 untreated control


title: Cg_HAB_Cy3_LAB_Cy5_rep5

description: technical replicate 5 of 5 from pooled samples


title: paitent 32 untreated control (non-paired analysis)

description: paitent 32 untreated control

value: paitent 32 untreated control


title: patient 40 after treatment (paired analysis)

description: patient 40 after treatment

value: patient 40 after treatment


title: Cg_HAB_Cy3_LAB_Cy5_rep1


title: patient 55 untreated control (non-paired analysis)

description: patient 55 untreated control

value: patient 55 untreated control


title: paitent 134 untreated control (non-paired analysis)

description: paitent 134 untreated control

value: blood

value: paitent 134 untreated control


title: patient 26 untreated control (non-paired analysis)

description: patient 26 untreated control

value: patient 26 untreated control


title: patient 135 untreated control (non-paired analysis)

description: patient 135 untreated control

value: patient 135 untreated control


title: patient 91 untreated control (non-paired analysis)

description: patient 91 untreated control

value: patient 91 untreated control


title: patient 112 after treatment (non-paired analysis)

description: patient 112 after treatment

value: post intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 112 after treatment


title: paitent 18 untreated control (non-paired analysis)

description: paitent 18 untreated control

value: paitent 18 untreated control


title: MeA_LAB_Cy3_HAB_Cy5_rep1

source_name: medial amygdala, HAB mice, basal

value: CD-1 (ICR)

source_name: medial amygdala, LAB mice, basal


title: patient 108 after treatment (non-paired analysis)

description: patient 108 after treatment

value: patient 108 after treatment


title: MeA_HAB_Cy3_LAB_Cy5_rep5

value: male

value: 10 weeks


title: patient 31 untreated control (non-paired analysis)

description: patient 31 untreated control

value: untreated

value: patient 31 untreated control


title: MeA_LAB_Cy3_HAB_Cy5_rep2


title: MeA_LAB_Cy3_HAB_Cy5_rep5


title: MeA_LAB_Cy3_HAB_Cy5_rep4


title: patient 6 untreated control (non-paired analysis)

description: patient 6 untreated control

value: patient 6 untreated control


title: patient 108 before treatment (non-paired analysis)

description: patient 108 before treatment

value: pre intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 108 before treatment


title: Cg_HAB_Cy3_LAB_Cy5_rep2


title: patient 112 before treatment (non-paired analysis)

description: patient 112 before treatment

value: blood

value: patient 112 before treatment


title: MeA_LAB_Cy3_HAB_Cy5_rep3


title: patient 69 after treatment (non-paired analysis)

description: patient 69 after treatment

value: patient 69 after treatment


title: MeA_HAB_Cy3_LAB_Cy5_rep2


title: MeA_HAB_Cy3_LAB_Cy5_rep1


title: patient 62 before treatment (non-paired analysis)

description: patient 62 before treatment

value: patient 62 before treatment


title: ESC shRNA linc1307_1.1-277_R2 (batch1)

value: shRNA knockdown of linc1307


title: MeA_HAB_Cy3_LAB_Cy5_rep4


title: patient 61 after treatment (non-paired analysis)

description: patient 61 after treatment

value: post intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 61 after treatment


title: patient 56 before treatment (non-paired analysis)

description: patient 56 before treatment

value: patient 56 before treatment


title: MeA_HAB_Cy3_LAB_Cy5_rep3

value: CD-1 (ICR)


title: patient 62 after treatment (non-paired analysis)

description: patient 62 after treatment

value: patient 62 after treatment


title: patient 59 before treatment (non-paired analysis)

description: patient 59 before treatment

value: patient 59 before treatment


title: NAc_LAB_Cy3_HAB_Cy5_rep4

source_name: nucleus accumbens, HAB mice, basal

value: male

value: 10 weeks

source_name: nucleus accumbens, LAB mice, basal


title: NAc_HAB_Cy3_LAB_Cy5_rep3


title: patient 69 before treatment (non-paired analysis)

description: patient 69 before treatment

value: patient 69 before treatment


title: NAc_LAB_Cy3_HAB_Cy5_rep5


title: NAc_LAB_Cy3_HAB_Cy5_rep3


title: patient 40 after treatment (non-paired analysis)

description: patient 40 after treatment

value: patient 40 after treatment


title: NAc_LAB_Cy3_HAB_Cy5_rep1


title: NAc_LAB_Cy3_HAB_Cy5_rep2


title: CeA_LAB_Cy3_HAB_Cy5_rep1

source_name: central amygdala, HAB mice, basal

source_name: central amygdala, LAB mice, basal


title: CeA_LAB_Cy3_HAB_Cy5_rep5


title: NAc_HAB_Cy3_LAB_Cy5_rep4


title: CeA_LAB_Cy3_HAB_Cy5_rep4


title: CeA_HAB_Cy3_LAB_Cy5_rep1


title: CeA_HAB_Cy3_LAB_Cy5_rep5


title: NAc_HAB_Cy3_LAB_Cy5_rep1


title: NAc_HAB_Cy3_LAB_Cy5_rep2


title: SON_HAB_Cy3_LAB_Cy5_rep5


title: NAc_HAB_Cy3_LAB_Cy5_rep5


title: CeA_LAB_Cy3_HAB_Cy5_rep2


title: patient 59 after treatment (non-paired analysis)

description: patient 59 after treatment

value: patient 59 after treatment


title: patient 40 before treatment (non-paired analysis)

description: patient 40 before treatment

value: pre intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 40 before treatment


title: Quadriceps normal rep1

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Genespring GX software (version 7.3)

source_name: Mouse quadriceps

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer's instructions, starting with 400 ng total quadriceps RNA.  Successful cRNA generation was checked using the Bioanalyzer 2100.

extract_protocol: Total RNA was extracted from flash frozen quadriceps using TRIzol. Quality control was by Agilent Bioanalyzer 2100 using the RNA 6000 Nano kit.

tag: vendor

value: Harlan

value: 5-6 weeks

value: quadriceps

tag: Sex

value: female


title: Quadriceps Early cachexia rep2


title: Quadriceps normal rep4


title: Quadriceps normal rep2


title: Quadriceps severe cachexia rep4


title: CeA_LAB_Cy3_HAB_Cy5_rep3


title: BLA_LAB_Cy3_HAB_Cy5_rep2

source_name: basolateral amygdala, HAB mice, basal

source_name: basolateral amygdala, LAB mice, basal


title: BMM infected with HN878 24h rep-1

city: Newark

first: Mi-Sun

last: Koo

state: NJ

address: 225 Warren Street, W250Q

department: Public Health Research Institute

institute: University of Medicine and Dentistry of New Jersey

description:
Gene expression data of Mtb-infected cells
HN 24h-1

hyb_protocol: After fragmentation, labeled single stranded DNA was hybridized unto mouse ST 1.0 array.

scan_protocol: Genechip was scanned using Affymetrix Genechip Scanner 7G Plus

data_processing: We used the RMA (Robust Multiarray Analysis) method to normalize and to summarize the probe-level intensity measurement from mouse Affymetrix ST 1.0 chip using Partek software.

source_name: mouse bone marrow derived macrophages

label_protocol: 300 ng of total RNA was processed using GeneChip WT labeling protocol, version 4

growth_protocol: Differentiated BMM were infected with Mtb at the moi of 5 in triplicate for 3 hrs and cells were harvested at 6 and 24 hr after infection to isolate total RNA..

extract_protocol: Trizol method was used for RNA extraction.  DNaseI was treated to get rid of remaining DNA.

treatment_protocol: The cells isolated from mouse femurs were differentiated in DMEM with 10% FBS supplemented with 20% L929 for 7 days

tag: cell type

value: macrophage (differentiated for 7 days)


title: BMM infected with CDC1551 24h rep-3

description:
Gene expression data of Mtb-infected cells
CDC 24h-3


title: BMM infected with CDC1551 24h rep-2

description:
Gene expression data of Mtb-infected cells
CDC 24h-2


title: CeA_HAB_Cy3_LAB_Cy5_rep2


title: patient 61 before treatment (non-paired analysis)

description: patient 61 before treatment

value: blood

value: patient 61 before treatment


title: BMM infected with HN878 24h rep-2

description:
Gene expression data of Mtb-infected cells
HN 24h-2


title: patient 38 after treatment (non-paired analysis)

description: patient 38 after treatment

source_name: post-treatment

value: post intravenous immune globulin (IVIG) and rituximab desensitization

value: patient 38 after treatment


title: BLA_LAB_Cy3_HAB_Cy5_rep5

value: CD-1 (ICR)


title: BLA_LAB_Cy3_HAB_Cy5_rep4

value: male


title: Quadriceps severe cachexia rep3


title: BLA_LAB_Cy3_HAB_Cy5_rep1

value: 10 weeks


title: Quadriceps normal rep3


title: BLA_HAB_Cy3_LAB_Cy5_rep5


title: Quadriceps Early cachexia rep1


title: BLA_LAB_Cy3_HAB_Cy5_rep3


title: CeA_HAB_Cy3_LAB_Cy5_rep4


title: BLA_HAB_Cy3_LAB_Cy5_rep4


title: CeA_HAB_Cy3_LAB_Cy5_rep3


title: BLA_HAB_Cy3_LAB_Cy5_rep3


title: BLA_HAB_Cy3_LAB_Cy5_rep2


title: BMM infected with CDC1551 24h rep-1

description:
Gene expression data of Mtb-infected cells
CDC 24h-1


title: BMM infected with HN878 24h rep-3

description:
Gene expression data of Mtb-infected cells
HN 24h-3


title: BMM infected with HN878 6h rep-3

description:
Gene expression data of Mtb-infected cells
HN 6h-3


title: PVN_LAB_Cy3_HAB_Cy5_rep5

source_name: hypothalamic paraventricular nucleus, HAB mice, basal

source_name: hypothalamic paraventricular nucleus, LAB mice, basal


title: BMM without infection 24h rep-1

description:
Gene expression data of Mtb-infected cells
Uninf 24h-1


title: BMM without infection 24h rep-3

description:
Gene expression data of Mtb-infected cells
Uninf 24h-3


title: BMM infected with HN878 6h rep-2

description:
Gene expression data of Mtb-infected cells
HN 6h-2


title: BLA_HAB_Cy3_LAB_Cy5_rep1


title: PVN_LAB_Cy3_HAB_Cy5_rep4

description: technical replicate dye-swapped 4 of 5 from pooled samples


title: BMM infected with CDC1551 6h rep-1

description:
Gene expression data of Mtb-infected cells
CDC 6h-1


title: BMM infected with CDC1551 6h rep-3

description:
Gene expression data of Mtb-infected cells
CDC 6h-3


title: BMM without infection 6h rep-3

description:
Gene expression data of Mtb-infected cells
Uninf 6h-3


title: PVN_LAB_Cy3_HAB_Cy5_rep1


title: baeR mutant in LB +20mM Tungstate Replicate 4

type: mixed

city: Norwich

first: Corinne

last: Appia-Ayme

state: Norfolk

address: UEA

department: BIO

country: United Kingdom

institute: University of East Anglia

hyb_protocol: Hybridisations were carried out in a 50μl volume per array. The volume of CyDye label cDNA was reduced in a SpeedVac and be adjusted to 21.5μL then denatured at 94°C for 2 min, centrifuge 2 min and let it cool at RT for 1 min. the labelled cDNA with 37.5μL of hybridisation buffer (Morpholine-4-ethanesulfonic acid (MES) hydrate (pH 6.5) (Sigma, M2933) 50 mM, Sodium chloride 1 M, 99% Formamide (Sigma, F5786) 20 % (w/v), EDTA 20 mM, Triton X-100 (Sigma, T8532) 1 % (w/v)). 50μl of hybridisation mix was pipetted onto the GASKET slide and an OGT array slide was placed in contact with the hybridisation mix. In a tight chamber, the arrays were hybridise at 55°C for 60 hours in a light tight hybridisation oven at 4 to 8 rpm. The slide was removed from the hybridisation chamber and washed with buffer 1 (6XSSPE, 0.005% N-lauryl sarcosine) for 5min under agitation and for 5 min with the wash buffer 2 (0.06X SSPE, 0.18% polyethylene glycol 200) then dried in a centrifuge.

scan_protocol: Scanned on an GenePix 4000A scanner (Axon Instruments, Inc.). Images were quantified using Axon GenePrix Pro7

data_processing: Data were normalised using the Batch Anti-Banana Algorithm in R (BABAR) algorithm and software package which uses cyclic loess to normalise across the complete dataset (Alston et al., 2010).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: baeR mutant in LB +20mM Tungstate OD600 =1

label_protocol:
Total RNA  (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (StrataScript, Stratagene).
2 µg of chromosomal was labelled with Cy3 dCTP using the Gibco Bioprime DNA labelling System.

growth_protocol: The media was inoculated with 1/1000 of over night culture and grown to OD600=1 at 37 C upon 200rpm agitation.

extract_protocol: Total RNA extracted using Promega SV total RNA extration kit following manufacturer's instructions

treatment_protocol: The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.

tag: growth media

value: LB +20mM Tungstate

tag: genotype

value: baeR

molecule: other

source_name: Wild Type in LB

value: Wild type

value: LB


title: PVN_LAB_Cy3_HAB_Cy5_rep3

description: technical replicate dye-swapped 3 of 5 from pooled samples


title: baeR mutant in LB +20mM Tungstate Replicate 5


title: PVN_HAB_Cy3_LAB_Cy5_rep2

description: technical replicate 2 of 5 from pooled samples


title: BMM without infection 24h rep-2

description:
Gene expression data of Mtb-infected cells
Uninf 24h-2


title: PVN_HAB_Cy3_LAB_Cy5_rep4

description: technical replicate 4 of 5 from pooled samples


title: BMM infected with CDC1551 6h rep-2

description:
Gene expression data of Mtb-infected cells
CDC 6h-2


title: baeR mutant in LB +20mM Tungstate Replicate 1


title: PVN_HAB_Cy3_LAB_Cy5_rep5

description: technical replicate 5 of 5 from pooled samples


title: PVN_HAB_Cy3_LAB_Cy5_rep3

description: technical replicate 3 of 5 from pooled samples


title: BMM infected with HN878 6h rep-1

description:
Gene expression data of Mtb-infected cells
HN 6h-1


title: PVN_HAB_Cy3_LAB_Cy5_rep1

description: technical replicate 1 of 5 from pooled samples


title: PVN_LAB_Cy3_HAB_Cy5_rep2

description: technical replicate dye-swapped 2 of 5 from pooled samples


title: BMM without infection 6h rep-1

description:
Gene expression data of Mtb-infected cells
Uninf 6h-1


title: Wild Type in LB +20mM Tungstate Replicate 2

source_name: Wild Type in LB +20mM Tungstate OD600 =1


title: baeR mutant in LB +20mM Tungstate Replicate 3


title: BMM without infection 6h rep-2

description:
Gene expression data of Mtb-infected cells
Uninf 6h-2


title: baeR mutant in LB +20mM Tungstate Replicate 2


title: Wild Type in LB Replicate 2

source_name: Wild Type in LB OD600 =1


title: baeR mutant in LB Replicate 3

source_name: baeR mutant in LB OD600 =1


title: Wild Type in LB +20mM Tungstate Replicate 3


title: Wild Type in LB +20mM Tungstate Replicate 1


title: Wild Type in LB Replicate 3

source_name: Wild Type in LB  OD600 =1


title: Wild Type in LB Replicate 1


title: baeR mutant in LB Replicate 2


title: baeR mutant in LB Replicate 1


title: Lupulone treated Replicate 1

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

country: China

institute: Jilin university

description: Biological replicate 1 of 2. Control DMSO treated, harvested after several passages.

hyb_protocol: The samples were hybridized with Agilent whole genome oligo microarray,performed by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)in Agilent’s SureHyb Hybridization Chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis Lupulone

label_protocol: The samples were labeled using the Agilent Quick Amp labeling kit.

growth_protocol: Mycobacterium tuberculosis H37Rv was incubated in a rotary shaker. Subsequently, Lupulone stock solution, prepared in dimethyl sulfoxide (DMSO), and DMSO was added to the culture,respectively. Then, the the cells were further incubated for a certain time.

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

value: Mycobacterium tuberculosis H37Rv

value: lupulone

source_name: Mycobacterium tuberculosis DMSO

value: DMSO


title: Lupulone treated Replicate 2


title: Wt_1 with array type ATH1 from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: Geminivirus diseases are among the most important economic impact on crops, including beans, cassava, cotton, cucurbits, corn, peppers and tomatoes. Geminiviruses have a genome composed of one or two molecules of single-stranded DNA, depending on mono or bipartite. The BCTV genome consists of a single strand of DNA that contains six reading frames for proteins CP, V2, Rep, C2, Ren, and C4. To determine the mechanism by which C2 of BCTV induce genes, we performed transgenic Arabidopsis expressing BCTV C2. We are interesting to study the difference between the wild type and two mutants.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Arabidopsis thaliana

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: aerial - -Media: MS Temperatura: 24 ºC Light: 18 hours

treatment_protocol: no treatment

value: arabidopsis thaliana (columbia)

tag: genotype/variation

value: wildtype

tag: dev.stage (boyes et al. plant cell 2001)

value: boyes 2


title: Wt_3 with array type ATH1 from Affymetrix

tag: harvest date


title: l2.4_1 with array type ATH1 from Affymetrix

growth_protocol: aerial - Media: MS Temperatura: 24 ºC Light: 18 hours

value: L2.4 mutant


title: Metastatic S100A4+ stromal cells

city: Boston

first: Joyce

middle: Tse

last: O'Connell

address: 330 Brookline Avenue

department: Division of Matrix Biology, Department of Medicine

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

data_processing: Data was normalized by rank invariant normalization with BeadStudio.

source_name: S100A4+ stromal cells from metastatic lung

label_protocol: Biotinylated cRNA was prepared with the NuGEN WT-Ovation Pico Kit according to the technical notes for Illumina arrays.

extract_protocol: RNA was extracted with the Qiagen RNeasy plus micro kit.

value: BALB/c

tag: source tissue

value: metastatic lung

value: S100A4+ Stromal Cells


title: REC5-1

city: Gainesville

first: Laurence

middle: M

last: Morel

state: FL

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

description: Gene expression data from B6.Sle1c2 CD4+ T cells

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000, running GeneChip Command Console Software (AGCC v1.1)

data_processing: The microarray data analysis was based on the use of “internal standards”  (generalization of the “Error Model” (Rocke and Durbin 2001) as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009); see also early variants of software packages MDAT (Knowlton, Dozmorov et al. 2004) and  Bioconductor variant: http://www.bioconductor.org/packages/2.5/bioc/vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf.   Rocke, D. M. and B. Durbin (2001). A model for measurement error for gene expression arrays. J Comput Biol 8(6): 557-69.  Dozmorov, I. and M. Centola (2003). An associative analysis of gene expression array data. Bioinformatics 19(2): 204-11.  Dozmorov, I. and I. Lefkovits (2009). Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res 37(19): 6323-39.  Knowlton, N., I. M. Dozmorov, et al. (2004). Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics 20(18): 3687-90.

source_name: CD4+ T cells from B6.Sle1c2 mice

label_protocol: cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.).

growth_protocol: Female mice aged 6 months under SPF conditions.

extract_protocol: Total RNA was extracted using Rneasy kits (Qiagen).

treatment_protocol: CD4+ T cells were enriched from splenocytes using magnetic bead negative selection (Miltenyi).

value: female

value: 6 months

value: CD4+ T cells


title: REC5-5


title: B6-3

description: Gene expression data from B6 CD4+ T cells

source_name: CD4+ T cells from B6 mice


title: REC5-2


title: Wt_2 with array type ATH1 from Affymetrix


title: B6-5


title: REC5-4


title: Normal S100A4+ stromal cells

source_name: S100A4+ stromal cells from normal lung

value: normal lung


title: WT Zuo1 365-433 S427G

city: Madison

first: Elizabeth

last: Craig

state: Wisconsin

address: 433 Babcock Dr.

institute: University of Wisconsin

hyb_protocol: 12x137K NimbleGen S. cerevisiae array (05543835001)

scan_protocol: MS 200 Microarray Scanner

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Saccharomyces cerevisiae

label_protocol: one color Cy3 labeling kit

growth_protocol: DS10 strain of yeast were grown in LEU d.o. media to log phase.

extract_protocol: hot phenol extraction

treatment_protocol: Fresh transformants containing pRS415 GPD-TAP, pRS415 GPD Ssz1 S295F, pRS415 GPD Zuo1 aa 365-433 S427G

tag: overexpression


title: B6-2


title: REC5-3


title: Lung 1 Day Post-infection Viral Strain Mex/4487, total infectious dose of 7 x 10^6 TCID50 rep2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description:
gene expression,1 Day Post-infection Viral Strain Mex/4487, replicate 1
H1N1_Exp2_RML2_Rh_Mx4487_LLl_D1_M3_r1

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

organism: Macaca fascicularis

source_name: Lung 1 Day Post-infection Viral Strain Mex/4487, replicate 1 total infectious dose of 7 x 10^6 TCID50

growth_protocol: Cynomolgus macaques (Macaca fascicularis), 4-15 years old, weighing 3.0-8.7 kg, were evenly distributed in regards to age and weight over the different groups and infected with either A/Mexico/InDRE4487/2009,  A/Kawasaki/UTK-4/2009, or A/Mexico/4108/2009 under anesthesia through a combination of intratracheal (4 ml),intranasal (0.5 ml per nostril), conjunctival (0.5 ml per eyelid) and oral (1 ml) routes with a suspension containing 1x10^6 TCID50/ml (total infectious dose was 7x10^6 TCID50).

extract_protocol: Global gene expression was measured by microarray in samples taken from the lower lung lobes of animals that were euthanized and necropsied  on day 1 post infection with A/Mexico/InDRE4487/2009 (n=3),  A/Kawasaki/UTK-4/2009 (n=3), or A/Mexico/4108/2009 (n=2) .

treatment_protocol: Tissue samples were placed in RNAlater (Ambion) for subsequent RNA extraction (QIAGEN, RNAeasy kit).

tag: sample type

value: Left Lung,intratracheal (4 ml), intranasal (0.5 ml each nostril), intraocular (o.5 ml each eye), and oral (1 ml)

tag: infection

value: F

value: Left Lung


title: Lung  1 Day Post-infection Viral Strain K-UTK4, total infectious dose of 7 x 10^6 TCID50 rep1

description:
gene expression,1 Day Post-infection Viral Strain K-UTK4, replicate 1
H1N1_Exp2_RML2_Rh_KUTK-4_LLl_D1_K3_r1

source_name: Lung  1 Day Post-infection Viral Strain K-UTK4, replicate 1 total infectious dose of 7 x 10^6 TCID50

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

tag: tissue


title: B6-1


title: Lung  1 Day Post-infection Viral Strain K-UTK4, total infectious dose of 7 x 10^6 TCID50 rep3

description:
gene expression,1 Day Post-infection Viral Strain K-UTK4, replicate 1
H1N1_Exp2_RML2_Rh_KUTK-4_RLl_D1_K2_r1

value: Right Lung,intratracheal (4 ml), intranasal (0.5 ml each nostril), intraocular (o.5 ml each eye), and oral (1 ml)

value: Right Lung


title: l2.4_2 with array type ATH1 from Affymetrix


title: l2.5_2 with array type ATH1 from Affymetrix

value: L2.5 mutant


title: WT Ssz1 S295F

source_name: WT Ssz1 S295F

value: Ssz1 S295F


title: B6-4


title: Mock rep2

description:
gene expression,No Post-infection Mock
H1N1_Exp1_Battelle Lung CR

source_name: Mock

value: Mock, pooled

value: Mock

value: Lung


title: Lung  1 Day Post-infection Viral Strain K-UTK4, total infectious dose of 7 x 10^6 TCID50 rep2

description:
gene expression,1 Day Post-infection Viral Strain K-UTK4, replicate 2
H1N1_Exp2_RML2_Rh_KUTK-4_RLl_D1_K1_r2

source_name: Lung  1 Day Post-infection Viral Strain K-UTK4, replicate 2 total infectious dose of 7 x 10^6 TCID50

value: M


title: Lung 1 Day Post-infection Viral Strain Mex/4487, total infectious dose of 7 x 10^6 TCID50 rep1

description:
gene expression,1 Day Post-infection Viral Strain Mex/4487, replicate 1
H1N1_Exp2_RML2_Rh_Mx4487_LLl_D1_M1_r1


title: Lung  1 Day Post-infection Viral Strain Mex/4108 total infectious dose of 7 x 10^6 TCID50 rep2

description:
gene expression,1 Day Post-infection Viral Strain Mex/4108
H1N1_Exp1_Mx_D1_RL_L_144


title: l2.5_1 with array type ATH1 from Affymetrix

value: arabidopsis thaliana (columbia)


title: WT vector

source_name: WT vector

value: vector


title: l2.5_3 with array type ATH1 from Affymetrix


title: l2.4_3 with array type ATH1 from Affymetrix

value: L2.4 mutant


title: Mock rep1


title: LNCaP_Scrambled_72h

status: Public on Aug 29 2011

city: Helsinki

first: Maija

middle: K

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

description: LNCaP cells transfected (72 hrs) with AllStarsNegative (Qiagen) scrambled control siRNA.

hyb_protocol: Purified total RNA (500 ng) was amplified with the TotalPrep Kit (Ambion, Austin, TX) and the biotin-labelled cRNA was hybridized to Sentrix HumanRef-8 Expression BeadChips (Illumina, San Diego, CA).

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalisation with beadarray and lumi R/Bioconductor packages and transformed using the variance stabilizing transformation (VST) method.

source_name: LNCaP cells, scrambled, 72h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: LNCaP cells were grown in T-Medium (Invitrogen). The non-malignant RWPE-1 prostate cells were purchased from American Type Culture Collection (LGC Promochem AB, Borås, Sweden) and grown in the media recommended by the distributor.

extract_protocol: Total RNA was extracted using RNeasy (QIAGEN) according to the manufacturer’s protocol. Integrity of the RNA was monitored prior to hybridization using a Bioanalyzer 2100 (Agilent Technologies) according to manufacturer’s instructions.

treatment_protocol: Gene expression changes following FAM110B silencing in LNCaP cells (48 h: pooled FAM110B siRNA vs. Scrambled siRNA; 72 h: FAM110B siRNAs 1 - 4 and pooled siRNA vs. Scrambled siRNA) and ectopic FAM110B expression in both RWPE-1 and LNCaP cells (FAM110B-pEGFP vs. pEGFP, 48 h) were analyzed.The siRNAs were used either separately or as a pool containing an equal amount of 4 siRNAs (QIAGEN GmbH, Hilden, Germany). The individual siRNAs were SI00640507, SI00640514, SI00640521 and SI00640528.

tag: cell line

value: LNCaP

tag: atcc number

tag: tissue derivation

value: prostate

tag: morphology

value: epithelial

tag: disease state

value: carcinoma

tag: derived from metastatic site

value: left supraclavicular lymph node

tag: tumorigenic

value: yes

value: male

tag: ethnicity

value: Caucasian

tag: treatment

value: scrambled siRNA

tag: treatment duration

value: 72 hrs


title: LNCaP_C8siRNA3_72h

description: LNCaP cells transfected (72 hrs) with SI00640521 against FAM110B mRNA.

source_name: LNCaP cells, C8 siRNA3, 72h

tag: gender

value: FAM110B siRNA


title: LNCaP_C8siRNA4_72h

description: LNCaP cells transfected (72 hrs) with SI00640528 against FAM110B mRNA.

source_name: LNCaP cells, C8 siRNA4, 72h


title: Lung  1 Day Post-infection Viral Strain Mex/4108 total infectious dose of 7 x 10^6 TCID50 rep1

description:
gene expression,1 Day Post-infection Viral Strain Mex/4108
H1N1_Exp1_613F_b_Mx_LL_Day1

value: Left Lung, intratracheal (4 ml), intranasal (0.5 ml each nostril), intraocular (o.5 ml each eye), and oral (1 ml)

value: F

tag: age

value: Left Lung


title: LNCaP_C8pool_72h

description: LNCaP cells transfected (72 hrs) with pool of SI00640507, SI00640514, SI00640521 and SI00640528 against FAM110B mRNA.

source_name: LNCaP cells, C8 pool, 72h

value: pool of FAM110B siRNA


title: LNCaP_Control_72h

description: LNCaP cells transfected (72 hrs) with lipid only (siLentFect Lipid Reagent, Bio-Rad Laboratories, Hercules, CA).

source_name: LNCaP cells, control, 72h

value: no siRNA


title: prostate cancer_sample_15 [aCGH]

type: genomic

hyb_protocol: Hybridization was performed according to the protocol (oligonucleotide array-based CGH for genomic DNA analysis, protocol version 2.0, August 2005, Agilent Technologies).

scan_protocol: Arrays were scanned with a laser confocal scanner (Agilent Technologies).

data_processing: Feature Extraction software (version 8.1.1.1, Agilent Technologies) was used for image analysis using manufacturer’s recommended settings (44K_CGH_0605).

molecule: genomic DNA

source_name: prostate cancer_lymph node metastasis

label_protocol: 12 µg of genomic DNA was digested overnight with AluI and RsaI, followed by standard phenol-chloroform purification. 3 µg of digested tumor DNA and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Waltham, MA), respectively, in a random priming reaction using Bioprime Array CGH Genomic Labeling Module (Invitrogen).

extract_protocol: Genomic DNA was extracted from the samples after overnight proteinase K treatment using standard protocols.

value: Advanced prostate cancer

value: lymph node metastatic tumor

source_name: Male genomic DNA, Promega, Cat# G1471

tag: reference

value: Promega normal male genomic DNA


title: RWPE-1_noDNA_48h

description: RWPE-1 cells transfected (48 hrs) with lipid only (Fugene HD transfection reagent, F. Hoffmann-La Roche Ltd, Basel, Switzerland).

source_name: RWPE-1 cells, no DNA, 48h

value: prostate

value: epithelial

value: normal

value: no

value: no DNA

value: 48 hrs


title: prostate cancer sample 16 [gene expr]

hyb_protocol: 15 micrograms of fragmented cRNA from each sample was used for hybridizations. The arrays were stained with phycoerythrin-streptavidin and the signal intensity was amplified by treatment with a biotin-conjugated anti-streptavidin antibody, followed by a second staining using phycoerythrin-streptavidin.

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

data_processing: Basic GeneChip array analysis was performed for the obtained image file. Data preprocessing was done using the RMA algorithm implemented in the Bioconductor package “affy.

label_protocol: Biotinylated cRNA was prepared from 3 micrograms of mRNA per sample according to manufacturers (Affymetrix) instructions.

extract_protocol: Total RNA was extracted using either TRIzol (Invitrogen, Carlsbad, CA) or LiCl / urea isolation–based methods.


title: prostate cancer_sample_16 [aCGH]


title: LNCaP_C8siRNA2_72h

description: LNCaP cells transfected (72 hrs) with SI00640514 against FAM110B mRNA.

source_name: LNCaP cells, C8 siRNA2, 72h

value: LNCaP

value: carcinoma

value: left supraclavicular lymph node

value: yes

value: male

value: Caucasian


title: prostate cancer_sample_10 [aCGH]

source_name: prostate cancer_advanced

value: Androcur (3 months)

value: prostate cancer tumor


title: prostate cancer_sample_14 [aCGH]

value: Advanced prostate cancer


title: prostate cancer sample 17 [gene expr]

source_name: prostate cancer_lymph node metastasis, castration-resistant

value: Castration-resistant prostate cancer

value: Orchiectomy, Casodex

value: lymph node metastatic tumor


title: RWPE-1_C8pEGFP_48h

description: RWPE-1 cells transfected (48 hrs) with FAM110B cDNA (TC127806, OriGene Technologies Inc., Rockville, MD) cloned into the pEGFP-C1 vector (BD Biosciences Clontech, Mountain View, CA).

source_name: RWPE-1 cells, C8 pEGFP, 48h

value: prostate

value: epithelial

value: FAM110B over-expression


title: LNCaP_C8siRNA1_72h

description: LNCaP cells transfected (72 hrs) with SI00640507 against FAM110B mRNA.

source_name: LNCaP cells, C8 siRNA1, 72h

value: FAM110B siRNA

value: 72 hrs


title: prostate cancer_sample_17 [aCGH]

value: Promega normal male genomic DNA


title: RWPE-1_GFP_48h

description: RWPE-1 cells transfected (48 hrs) with the pEGFP-C1 vector (BD Biosciences Clontech, Mountain View, CA).

source_name: RWPE-1 cells, GFP, 48h

value: normal

value: no

value: vector

value: 48 hrs


title: prostate cancer sample 14 [gene expr]


title: LNCaP_noDNA_48h

description: LNCaP cells transfected (48 hrs) with lipid only (Fugene HD transfection reagent, F. Hoffmann-La Roche Ltd, Basel, Switzerland).

source_name: LNCaP cells, no DNA, 48h

value: LNCaP

value: carcinoma

value: left supraclavicular lymph node

value: yes

value: male

value: Caucasian

value: no DNA


title: prostate cancer_sample_12b [aCGH]

source_name: prostate cancer_liver metastasis

value: Advanced prostate cancer

value: liver metastatic tumor


title: LNCaP_C8pEGFP_48h

description: LNCaP cells transfected (48 hrs) with FAM110B cDNA (TC127806, OriGene Technologies Inc., Rockville, MD) cloned into the pEGFP-C1 vector (BD Biosciences Clontech, Mountain View, CA).

source_name: LNCaP cells, C8 pEGFP, 48h

value: prostate

value: epithelial

value: FAM110B over-expression


title: prostate cancer sample 13 [gene expr]

value: Castration-resistant prostate cancer

value: Zoladex + flutamide

value: lymph node metastatic tumor


title: LNCaP_Control_48h

description: LNCaP cells transfected (48 hrs) with lipid only (siLentFect Lipid Reagent, Bio-Rad Laboratories, Hercules, CA).

source_name: LNCaP cells, control, 48h

value: no siRNA


title: prostate cancer_sample_13 [aCGH]

value: Zoladex + Flutamide

value: Promega normal male genomic DNA


title: prostate cancer_sample_9 [aCGH]

value: Orchiectomy

value: prostate cancer tumor


title: prostate cancer_sample_7 [aCGH]

value: Casodex, Suprefact


title: prostate cancer_sample_12a [aCGH]

source_name: prostate cancer_lung metastasis

value: lung metastatic tumor


title: prostate cancer sample 15 [gene expr]


title: prostate cancer_sample_11 [aCGH]

value: Androcur (1 month)


title: LNCaP_GFP_48h

description: LNCaP cells transfected (48 hrs) with the pEGFP-C1 vector (BD Biosciences Clontech, Mountain View, CA).

source_name: LNCaP cells, GFP, 48h

value: LNCaP

value: carcinoma

value: left supraclavicular lymph node

value: yes

value: male

value: Caucasian

value: vector

value: 48 hrs


title: prostate cancer_sample_6 [aCGH]

value: Castration-resistant prostate cancer

value: Casodex, Avodart


title: prostate cancer sample 8 [gene expr]


title: LNCaP_Scrambled_48h

description: LNCaP cells transfected (48 hrs) with AllStarsNegative (Qiagen) scrambled control siRNA.

source_name: LNCaP cells, scrambled, 48h

value: prostate

value: epithelial

value: scrambled siRNA


title: prostate cancer_sample_4 [aCGH]

value: Orchiectomy

value: prostate cancer tumor

value: Promega normal male genomic DNA


title: prostate cancer sample 12a [gene expr]

value: Advanced prostate cancer

value: lung metastatic tumor


title: v-ras-Ha transformed keratinocytes with IL1ra, rep3

city: Frederick

first: Rosalba

last: Salcedo

state: MD

address: 1050 Boyles Street, Bldg. 567

institute: SAIC-NCI

hyb_protocol: cRNA was fragmented to uniform size and hybridized to Agilent Whole Genome 4x44K arrays.

scan_protocol: Slides were washed and scanned on an Agilent G2565 Microarray Scanner.

data_processing: The gProcessSignal of Agilent Feature Extraction data was normalized using a global median-based method and filtered by the Agilent feature extraction flag “gIswellAboveBG” to eliminate bad probes with signals consistently lower than background  across the samples. All of these procedures were done with customized R scripts (www.r-project.org).

source_name: v-ras-Ha transformed keratinocytes with IL1ra treatment

label_protocol: First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

extract_protocol: Total RNA was harvested from cultured v-rasHa-transduced keratinocytes in the presence of PBS or Anakinra. Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions.  RNA was purified using the RNAeasy Min-elute (Qiagen) RNA isolation kit. Total RNA samples were quantitated by UV spectrophotometry (OD260/280). Quality of the total RNA was assessed by using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Primary mouse keratinocytes and hair follicle buds were isolated from newborn epidermis from wild type mice.  Keratinocytes were adenovirus infected for 30 min with serum-free medium with a multiplicity of infection of 10 viral particles/cell and 4 ug/ml of Polybrene (Sigma) to enhance uptake.  Five hours post v-rasHa-transduction, interleukin-1-receptor antagonist, Anakinra (Amgen, Inc, Thousand Oaks, CA), was added to the keratinocytes cultures at a final concentration of 5 ug/ml . Cultures were kept for an extra 3 days but IL-1Ra was replaced after 2 days. Thereafter, RNA from IL1R antagonist- or PBS-treated cultures was prepared.

tag: genotype

value: wild type

tag: developmental stage

value: newborn

value: epidermis

tag: cell type

value: v-ras-Ha-transduced keratinocytes

value: Anakinra


title: prostate cancer_sample_5 [aCGH]

value: Orchiectomy + Lynoral

tag: tissue


title: prostate cancer sample 6 [gene expr]


title: prostate cancer sample 7 [gene expr]

value: Casodex, Suprefact


title: v-ras-Ha transformed keratinocytes with IL1ra, rep2


title: LNCaP_C8pool_48h

description: LNCaP cells transfected (48 hrs) with pool of SI00640507, SI00640514, SI00640521 and SI00640528 against FAM110B mRNA.

source_name: LNCaP cells, C8 pool, 48h

tag: cell line

value: LNCaP

value: carcinoma

value: left supraclavicular lymph node

value: yes

value: male

value: Caucasian

value: pool of FAM110B siRNA

value: 48 hrs


title: prostate cancer_sample_1 [aCGH]

value: Castration-resistant prostate cancer

value: Suprefact + Androcur, orchiectomy, Flutamide

value: prostate cancer tumor

source_name: Male genomic DNA, Promega, Cat# G1471

value: Promega normal male genomic DNA


title: prostate cancer sample 3 [gene expr]

value: Orchiectomy


title: prostate cancer sample 4 [gene expr]


title: prostate cancer_sample_3 [aCGH]


title: v-ras-Ha transformed keratinocytes with IL1ra, rep1

value: wild type

value: newborn

value: epidermis

value: v-ras-Ha-transduced keratinocytes


title: prostate cancer_sample_8 [aCGH]


title: prostate cancer sample 1 [gene expr]

value: Suprefact + Androcur, orchiectomy, flutamide


title: prostate cancer_sample_2 [aCGH]

value: Orchiectomy, Androcur


title: Mer2 clb5delta clb6delta double-mutant 4h meiosis, biological repeat 2

status: Public on Aug 28 2011

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

country: Austria

institute: University of Vienna, MFPL

hyb_protocol: Hybridization to Affymetrix S. cerevisiae Tiling  1.0R Arrays was carried out at 42C for 16 hours. The following washing and staining steps were done with an Affymetrix 450 station. All reagents used are described in the Affymetrix ChIP Assay Protocol.

scan_protocol: Each array was scanned by Genechip Scanner 3000 (Affymetrix, CA) at default settings

data_processing:
Primary data analysis was performed with GeneChip Operating Software (GCOS, Affymetrix). Resulting Cel files were analyzed by the Tiling Analysis Software (TAS, v 1.1.02, Affymetrix, two sample comparison analysis (IP versus WCE), without normalization and results in linear scale were exported as  RPT text file) in the format specified by Affymetrix.
Text files are in tab separated format provided by Affymetrix Tiling Analysis Software. The first column represents the chromosomal position, the second column "fold enrichment" over the control experiment (WCE, 4 hours, if not specified otherwise). The columns are separated by 25 headers specifying the identity of the chromosome; sequence #8-#23 contain chromosome1 to chromosome16, sequence #24 mitochondrial DNA, sequence #25 the yeast 2mikron plasmid.

source_name: Mer2-myc ChIP with anti-myc antibody in clb5delta clb6delta double-mutant

label_protocol: Two rounds of amplification, DNA fragmentation, and end-labeling, were performed according to the Affymetrix ChIP protocol.

growth_protocol: Meiotic cultures of diploid S. cerevisiae SK1 strain were set up as follows: A saturated YPD culture was used to inoculate 300 ml liquid SPS medium (.5% yeast extract, 1% Bacto peptone, 1% potassium acetate, .17% Yeast nitrgen base w/o aa, 0.05 M potassium biphtalate, pH 5.5) 1:400 and grown in a 3-liter baffled flask at 200 rpm at 30°C for 14 hrs. Cells were harvested, washed once, resuspended at an OD660 of  1.1 in sporulation medium (1% potassium acetate pH 7.0, supplemented with amino acids and  .001% PPG) and shaken at 200 rpm at 30°C for 4 hrs.

extract_protocol: Cells were fixed in 1% formaldehyde for 30min. 1X10^9 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka). Chromosomal DNA was shared into the average size of 500-1000bp by sonication. Chromatin IP was performed as described in Katou et al. (Methods Enzym., 409,389-410, 2006).

tag: genetic background

value: FKY4009:Mat a/alpha,  MER2-myc9::TRP/=, clb5D::KanMX/=, clb6D::TRP/=

tag: bait protein

tag: antibody

value: mouse, anti-myc 9E13

tag: meiotic timepoint

value: 4 hours

source_name: WCE 4h meiosis

extract_protocol: Cells were fixed in 1% formaldehyde for 30min. 1X10^9 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka). Chromosomal DNA was shared into the average size of 500-1000bp by sonication. Isolation of genomic DNA was performed as described in Katou et al. (Methods Enzym., 409,389-410, 2006).

value: rad50S mutation


title: Rec114 rec8delta mutant, 4h meiosis, biological repeat 2

source_name: Rec114-myc ChIP with anti-myc antibody in rec8delta mutant

value: FKY3683:Mat a/alpha,  REC114-myc13::KanMX6/=, rec8D::KanMX/=

value: mouse, anti-myc 9E12


title: Mer2 red1delta, 4h meiosis, biological repeat 2

source_name: Mer2-myc ChIP with anti-myc antibody in red1delta mutant

value: FKY3972:Mat a/alpha,  MER2-HA3int, red1D::LEU

value: mouse, anti-HA 16B15


title: Mer2 hop1delta, 4h meiosis

source_name: Mer2-myc ChIP with anti-myc antibody in hop1delta mutant

value: FKY4006:Mat a/alpha,  MER2-HA3int, hop1D::LEU2

value: mouse, anti-HA 16B14


title: v-ras-Ha transformed keratinocytes without IL1ra, rep1

source_name: v-ras-Ha transformed keratinocytes with PBS treatment

value: PBS


title: Mer2, 4h meiosis, biological repeat 2

source_name: Mer2-HA ChIP with anti-HA antibody

value: FKY3775:Mat a/alpha,  MER2-HA3int+B14

value: mouse, anti-HA 12CA5 (made in-house)

value: wild type


title: v-ras-Ha transformed keratinocytes without IL1ra, rep3

value: newborn

value: epidermis

value: v-ras-Ha-transduced keratinocytes


title: mer2-S30A , 3h meiosis

source_name: mer2-S30A-myc ChIP with anti-myc antibody

value: FKY4108:Mat a/alpha,  mer2S30A-myc9::TRP/=

value: 3 hours


title: Rec114 red1delta mutant, 4h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in red1delta mutant

value: FKY3466:Mat a/alpha,  REC114-myc13::KanMX6/=, red1D::LEU/=

value: 4 hours


title: Hop1 rec8delta mutant, 4h meiosis, biological repeat 1

source_name: Hop1 ChIP with anti -Hop1 antibody in rec8delta mutant

value: FKY3683:Mat a/alpha,  REC114-myc13::KanMX6/=, rec8D::KanMX/=

value: rabbit, anti-Hop1

value: rad50S mutation


title: Wilms' Tumor T16

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.

source_name: Total DNA from Wilms' Tumor T16

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments and fractionated on a 1% agarose gel. The extracted fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: disease state

value: Wilms' Tumor

tag: agedx

value: FEMALE

tag: central pathology (rcpat)

value: CCSK


title: Wilms' Tumor T21

source_name: Total DNA from Wilms' Tumor T21

value: FAVOR


title: Mer2 red1delta, 4h meiosis, biological repeat 1

value: FKY3858:Mat a/alpha,  MER2-myc9::TRP/=, red1D::LEU/=

value: mouse, anti-myc 9E12


title: HPF H3K9me2, array 2 of 4

city: Baltimore

first: Andrew

last: Feinberg

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

scan_protocol: Performed according to standard NimbleGen protocol with NimbleGen software

data_processing: Partial quantile normalization. See Wen et al. (2009) Nature Genetics 41:246--250 for details.

source_name: ChIP against H3K9me2

label_protocol: Labels with Cy3 and Cy5 were performed according to standard NimbleGen protocol

extract_protocol: Primary Human Pulmonary Fibroblasts (ScienCell) were cultured according to the ScienCell protocol. Native chromatin IP against H3K9me2 antibody (Abcam 1220) were performed as described (Wen et al. Nat Genet., 2009, 41:246-50).

value: Primary Pulmonary Fibroblasts

value: H3K9me2 (Abcam 1220)

source_name: input DNA control

value: none (input)


title: Rec114 hop1delta mutant, 4h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in hop1delta mutant

value: FKY3016:Mat a/alpha,  REC114-myc13::KanMX6/=, hop1D::LEU/=

value: wild type


title: Rec114 rec8delta mutant, 4h meiosis, biological repeat 1


title: Mer2 clb5delta clb6delta double-mutant 4h meiosis, biological repeat 1

value: FKY4009:Mat a/alpha,  MER2-myc9::TRP/=, clb5D::KanMX/=, clb6D::TRP/=


title: Mer2 mei4delta, 3h meiosis

source_name: Mer2-myc ChIP with anti-myc antibody in mei4delta mutant

value: FKY3265:Mat a/alpha,  MER2-myc9::TRP/=, mei4D::KanMX/=, REC8-HA3::URA3/=

value: 3 hours


title: Rec104, 4h meiosis, biological repeat 2

source_name: Rec102-myc ChIP with anti-myc antibody

value: FKY3837:Mat a/alpha,  REC102-myc18::TRP/=

value: 4 hours


title: HPF H3K9me2, array 1 of 4

hyb_protocol: Performed according to standard NimbleGen protocol


title: Hop1 rec8delta mutant, 4h meiosis, biological repeat 2

value: FKY3683:Mat a/alpha,  REC114-myc13::KanMX6/=, rec8D::KanMX/=

value: rabbit, anti-Hop1

value: rad50S mutation


title: Mer2 rec114delta, 4h meiosis, biological repeat 2

source_name: Mer2-HA ChIP with anti-HA antibody in rec114delta mutant

value: FKY4005:Mat a/alpha,  MER2-HA3int, rec114D::KanMX

value: mouse, anti-HA 16B13


title: Calu-3 cells, fMLP+PMN+CD47 Ab, 90 m + 4 h

city: Denver

first: Rachel

last: Zemans

state: CO

address: 1400 Jackson St

institute: National Jewish Health

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >7.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Signal intensities were normalized using combined rank consistency filtering with LOWESS intensity normalization in Agilent Feature Extraction software.

source_name: FMLP+PMN+CD47 90 min + 4 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in DMEM + 10% FBS. The cultures were grown at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using Qiagen RNeasy miniprep kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Calu-3 cells were plated on the undersurface of 1.12 cm2 semi-permeable transwell inserts with 0.4 um pores.  fMLP (1 uM) was placed in the bottom chamber and 6 million human neutrophils were placed in the top chamber.  In indicated wells, Calu-3 cells were pretreated with neutralizing anti-CD47 Ab.  Migration was allowed to proceed for 90 m after which cells were placed back into growth media for the indicated time.

tag: treatment

value: anti-CD47 antibodies, fMLP, and neutrophil transmigration


title: Calu-3 cells, fMLP, 90 m + 24 h

source_name: FMLP 90 min + 24h

value: fMLP


title: Calu-3 cells, fMLP+PMN+CD47 Ab, 0 h

source_name: FMLP+PMN+CD47 0h


title: Calu-3 cells, fMLP, 90 m + 72 h

source_name: FMLP 90min + 72h


title: Calu-3 cells, fMLP, 90 m + 48 h

source_name: FMLP 90min + 48h


title: Wilms' Tumor T10

source_name: Total DNA from Wilms' Tumor T10

value: Wilms' Tumor

value: FEMALE

value: FAVOR


title: HPF H3K9me2, array 3 of 4

value: Primary Pulmonary Fibroblasts

value: H3K9me2 (Abcam 1220)

value: none (input)


title: Calu-3 cells, fMLP+PMN+CD47 Ab, 90 m

source_name: FMLP+PMN+CD47 90 min


title: Calu-3 cells, fMLP+PMN+CD47 Ab, 90 m + 2 h

source_name: FMLP+PMN+CD47 90 min + 2 h


title: mer2-S30A , 4h meiosis

source_name: mer2-S30A-myc ChIP with anti-myc antibody

value: FKY4108:Mat a/alpha,  mer2S30A-myc9::TRP/=

value: mouse, anti-myc 9E12

value: wild type

source_name: WCE 4h meiosis


title: with 200 mg/L alachlor (IC20)_biological rep3

city: Lisboa

first: Cristina

middle: Anjinho

last: Viegas

address: Av Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Técnico

description: Gene expression data from cells incubated with the IC20 of alachlor

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0003; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org, Wong Lab, Harvard) applying a probeset mask file excluding all probes on the array representing Schizosaccharomyces pombe transcripts. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the 12 arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001). Replicate data for the same sample type were weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2 .

source_name: Cell population incubated with 200 mg/L alachlor (IC20)

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Yeast Genome 2.0 Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Exponential cell populations (OD640nm = 0.25 ± 0.05) of S. cerevisiae BY4741 were incubated in minimal growth medium (pH 6.5), at 30ºC, with orgital agitation (250 RPM) in each of the exposure conditions indicated above.

extract_protocol: Total RNA isolation was performed using the hot-phenol method (Koher & Domdey, 1991, Methods in Enzimology 194:398-405).

treatment_protocol: Cells were harvested by centrifugation (10000 rpm, 3 min, 0ºC) and immediately frozen in liquid nitrogen and stored at -80ºC until RNA extraction.

tag: strain

tag: cell population

value: Exponential cells (O.D.640nm = 0.25 ± 0.05)


title: Mer2 rec114delta, 4h meiosis, biological repeat 1

source_name: Mer2-myc ChIP with anti-myc antibody in rec114delta mutant

value: FKY3264:Mat a/alpha,  MER2-myc9::TRP/=, rec114D::KanMX/=, REC8-HA3::URA3/=

value: 4 hours


title: prostate cancer sample 2 [gene expr]

value: Castration-resistant prostate cancer

value: Orchiectomy, Androcur

value: prostate cancer tumor


title: v-ras-Ha transformed keratinocytes without IL1ra, rep2

source_name: v-ras-Ha transformed keratinocytes with PBS treatment

value: newborn

value: epidermis

value: v-ras-Ha-transduced keratinocytes

value: PBS


title: Calu-3 cells, fMLP 90 m + 4 h

source_name: FMLP 90m + 4h

value: fMLP


title: Calu-3 cells, fMLP+PMN+CD47 Ab, 90 m + 24 h

source_name: FMLP+PMN+CD47 90 min + 24 h

value: anti-CD47 antibodies, fMLP, and neutrophil transmigration


title: Calu-3 cells, fMLP, 90 m

source_name: FMLP 90min


title: Wilms' Tumor T1

source_name: Total DNA from Wilms' Tumor T1

value: Wilms' Tumor

tag: gender

value: FEMALE

value: FAVOR


title: Rec114, clb5delta clb6delta double-mutant 4h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in clb5delta clb6delta double-mutant

value: FKY4196:Mat a/alpha,  REC114-myc13::KanMX6/=, clb5D::KanMX/=, clb6D::TRP/=

value: mouse, anti-myc 9E12

value: rad50S mutation


title: Rec114, rec104delta mutant 3h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in rec104delta mutant

value: FKY2999:Mat a/alpha,  REC114-myc13::KanMX6/=, rec104D::KanMX/=, REC8-HA3::URA3/=

value: 3 hours

value: wild type


title: Rec114, spo11-Y135f mutant 4h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in spo11-Y135f mutant

value: FKY2993:Mat a/alpha,  REC114-myc13::KanMX6/=, spo11Y135F-HA::URA3/=

value: 4 hours


title: with 200 mg/L alachlor (IC20)_biological rep2

value: Exponential cells (O.D.640nm = 0.25 ± 0.05)


title: Rec104, 4h meiosis, biological repeat 1

source_name: Rec104-myc ChIP with anti-myc antibody

value: FKY4370:Mat a/alpha,  REC104-myc9::TRP/=


title: with 200 mg/L alachlor (IC20)_biological rep1


title: Wilms' Tumor T9

source_name: Total DNA from Wilms' Tumor T9

value: MALE


title: without alachlor (IC20 exp)_biological rep3

description: Gene expression data from cells incubated without alachlor

source_name: Cell population incubated without alachlor (IC20)


title: Rec114, 4h meiosis, biological repeat 2

source_name: Rec114-myc ChIP with anti-myc antibody

value: FK3307:Mat a/alpha,  REC114-myc13::KanMX7/=


title: Red1, 4h meiosis

source_name: V5-Red1 ChIP with anti-V5 antibody

value: FKY3870:Mat a/alpha,  V5-RED1::HygromycinB/=

value: mouse, anti-V5 (Serotec)

tag: antibody manufacturer

value: Serotec

tag: antibody catalog #


title: Hop1, 4h meiosis

source_name: Hop1 ChIP with anti -Hop1 antibody

tag: genotype

value: FKY3307:Mat a/alpha,  REC114-myc13::KanMX6/=

value: rabbit, anti-Hop1


title: without alachlor (IC20 exp)_biological rep2


title: without alachlor (IC20 exp)_biological rep1


title: Rec8, 4h meiosis

source_name: Rec8-HA ChIP with anti-HA antibody 12CA5 (made in-house)

value: FKY1091:MATa/alpha, REC8-HA3::URA3/=

value: mouse, anti-HA 12CA5 (made in-house)

source_name: WCE 4h meiosis


title: Calu-3 cells, fMLP+PMN, 90 m + 48 h

source_name: FMLP+PMN 90min + 48h

value: fMLP and neutrophil transmigration


title: Calu-3 cells, fMLP+PMN, 90 m + 24 h

source_name: FMLP+PMN 90 min + 24 h


title: Calu-3 cells, fMLP+PMN, 90 m + 4 h

source_name: FMLP+PMN 90m + 4h


title: Zip1, 4h meiosis

source_name: Zip1 ChIP with anti -Zip1 antibody

value: FKY1:Mat a/alpha, HO

value: rabbit, anti-Zip1

value: zip1 deletion

source_name: zip1 deletion


title: with 110 mg/L alachlor (LOEC)_biological rep3

description: Gene expression data from cells incubated with the LOEC of alachlor

source_name: Cell population incubated with 110 mg/L alachlor (LOEC)


title: Calu-3 cells, fMLP+PMN, 90 m + 2 h

source_name: FMLP+PMN 90m + 2h


title: with 110 mg/L alachlor (LOEC)_biological rep1


title: with 110 mg/L alachlor (LOEC)_biological rep2


title: without alachlor (LOEC exp)_biological rep3

source_name: Cell population incubated without alachlor (LOEC)


title: Calu-3 cells, Control, 90 m + 24 h

source_name: Control 90 m + 24h

value: untreated


title: Calu-3 cells, fMLP+PMN, 0h

source_name: FMLP+PMN 0h


title: Calu-3 cells, Control, 90 m + 4 h

source_name: Control 90 m + 4h


title: Rec114, 3h meiosis

value: FK3307:Mat a/alpha,  REC114-myc13::KanMX7

value: mouse, anti-myc 9E12

value: 3 hours

value: wild type

value: rad50S mutation


title: Rec114, mei4delta mutant 3h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in mei4delta mutant


title: Rec114, mer2delta mutant 3h meiosis

source_name: Rec114-myc ChIP with anti-myc antibody in mer2delta mutant


title: Rec114, 4h meiosis, biological repeat 1

source_name: Rec114-myc ChIP with anti-myc antibody

value: 4 hours


title: Mer2, 4h meiosis, biological repeat 1

source_name: Mer2-myc ChIP with anti-myc antibody

value: FK3222:Mat a/alpha,  MER2-myc9::TRP

value: mouse, anti-myc 9E11


title: without alachlor (LOEC exp)_biological rep1

value: Exponential cells (O.D.640nm = 0.25 ± 0.05)


title: HPF H3K9me2, array 4 of 4

source_name: ChIP against H3K9me2

tag: cell type

value: Primary Pulmonary Fibroblasts

value: H3K9me2 (Abcam 1220)

source_name: input DNA control

value: none (input)


title: Calu-3 cells, fMLP+PMN, 90 m

source_name: FMLP+PMN 90 min

value: fMLP and neutrophil transmigration


title: Calu-3 cells, Control, 0 h

source_name: Control 0h


title: without alachlor (LOEC exp)_biological rep2


title: Calu-3 cells, fMLP+PMN, 90 m + 72 h

source_name: FMLP+PMN 90min + 72h


title: Bcl11b KO vs. WT Tregs 4752wt2_Cy3_4748ko2_Cy5

city: albany

first: dorina

last: avram

address: 47 new scotland ave

department: center for immunology and microbial disease

institute: albany medical college

hyb_protocol: Samples were hybridized to Mouse Whole Genome, 4x44k (AMADID 014868) arraysincubated in SureHyb chambers for 17hrs at 10rpm in a 65C incubator

scan_protocol: Slides were scanned on an Agilent C scanner and the data extracted using Feature Extraction 10.5.1.

data_processing: default Agilent Feature Extraction 10.5.1

source_name: sorted wild type  Treg cells from 3 mice

label_protocol: Amplified cRNA was generated from total RNA using Agilent QuickAmp Labeling Kit, No Dye (Cat. No. 5190-0424).  aRNA was labeled with cyanine dyes using Kreatech ULS aRNA Fluorescent Labeling Kit (Cat. No. EA-006).Concentration, purity and dye-incorporation levels were determined using a Nanodrop ND-1000. Total RNA fidelity was measured using a Bioanalyzer 2100. Cy3 and Cy5 labeled components were normalized to 825ng each and were fragmented at 60C for 30 minutes prior to hybridization.

growth_protocol: sorted Treg cells

extract_protocol: standard Agilent protocol

value: T reg

source_name: sorted KO type  Treg cells


title: Bcl11b KO vs. WT Tregs WT2TReg_Cy3_KO2TReg_Cy5

source_name: sorted wild type Foxp3-Gfp+ Treg cells from 3 mice

source_name: sorted KO type Foxp3-Gfp+ Treg cells


title: Prone - HVt, biological rep 2

status: Public on Aug 27 2011

city: Aurora

last: Edwards

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures, using the Affy GCS3000

data_processing: Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.

organism: Rattus norvegicus

source_name: Rat Lung - dorsal caudal quadrant

label_protocol: Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.

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

treatment_protocol: Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.

value: Sprague-Dawley

tag: condition

value: High Vt

tag: body position

value: Prone

value: Male


title: Supine - SVt, biological rep 1

value: Supine


title: year: 2006 - developmental stage: UD:0000037 36E-L - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Ten clusters of Pinot Noir, clone  ENTAV 115,  were collected on 08/09/2006 (10 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

hyb_protocol: Affy-Eukaryotic Target Hybridization

scan_protocol: Affy-Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Vitis vinifera

source_name: fruit_year 2006_developmental stage: UD:0000037 36E-L

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: hot borate RNA extraction protocol

tag: germplasm name

value: clone entav 115

tag: organism part

tag: development stage

tag: growth media

value: field soil


title: Mei4, 4h meiosis

source_name: Mei4-HA ChIP with anti-HA antibody

tag: genetic background

value: FK2385:Mat a/alpha,  MEI4-HA3::HIS/=

tag: bait protein

tag: antibody

value: mouse, anti-HA 12CA5 (made in-house)

tag: meiotic timepoint

value: wild type

source_name: WCE 4h meiosis

value: rad50S mutation


title: year: 2006 - developmental stage: UD:0000035 34E-L - rep2

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/19/2006 (7 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2006_developmental stage: UD:0000035 34E-L


title: year: 2006 - developmental stage: UD:0000037 36E-L - rep2

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 08/09/2006 (10 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.


title: year: 2006 - developmental stage: UD:0000034 33E-L - rep2

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/05/2006 (5 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2006_developmental stage: UD:0000034 33E-L


title: year: 2006 - developmental stage: UD:0000035 34E-L - rep1


title: Prone - HVt, biological rep 3

tag: strain


title: Prone - HVt, biological rep 1


title: Control - NV, biological rep 2

value: Non-ventilated


title: year: 2006 - developmental stage: UD:0000035 34E-L - rep3


title: Supine - SVt, biological rep 2


title: Supine - SVt, biological rep 3


title: year: 2006 - developmental stage: UD:0000034 33E-L - rep3


title: year: 2005 - developmental stage: UD:0000037 36E-L - rep3

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 08/10/2005 (10 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2005_developmental stage: UD:0000037 36E-L


title: year: 2005 - developmental stage: UD:0000037 36E-L - rep2


title: Control - NV, biological rep 1


title: year: 2006 - developmental stage: UD:0000037 36E-L - rep1


title: tofu diet, biological rep4

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.708010717639708
upper limit: 2.79368901975911
saturation: 2.99247546773371
gamma: 49.0337181367777
sigma: 0.809487763947756
mu: 1.89413527542731

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C, according to the manual supplied by Affymetrix (P/N 702232 Rev. 2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with a GCS 3000 scanner (GCOS V1.2, Affymetrix).

data_processing: The data were analyzed by using SuperNORM (V 1.7, Skylight Biotech Inc.) accoring to a parametric method (Konishi, T., 2008, Stat Appl Genet Mol Biol 7: Article 25.). A row of the data table presents z-scores of the PM data of a gene, in accordance with the order of the Cell appears in the CDF file. The PM data are further summarized to find z-scores and pseudo data value of a gene. The signal intensity represents the pseudo data, of which center of intensity for each array was arbitrarily set to 256.  For details of the methodology, visit http://www.super-norm.com/eng/index.html.

source_name: rat liver, tofu diet fed for 14 days

label_protocol: Ten micrograms of total RNA was processed to prepare biotinylated cRNA using One-Cycle Target Labeling and Control Reagents (Afflymetrix).

growth_protocol: Male Sprague-Dawley rats were obtained from Charles River Japan (Kanagawa, Japan) at 4 week of age. Animals were housed individually in a room with a controlled temperature (20-22ºC), humidity (55-65%), and 12-h-light/-dark cycle. During their adaptation to the conditions, rats were fed a commercial non-purified diet (Type NMF; Oriental Yeast Co., Tokyo, Japan) for 5 days. Rats were allowed free access to diet and water.

extract_protocol: At the end of the experimental period, the animals were sacrificed by bleeding from the abdominal aorta under diethyl ether anesthesia, and the liver was quickly excised. Hepatic total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Each group was fed a diet containing 200 g/kg of protein in the form of casein, soy protein, or freeze-dried tofu. The experimental diets were as follows: 1) casein diet (C); 2) C containing isoflavone (CI); 3) soy protein diet (S); 4) S containing isoflavone (SI); 5) a diet containing 100 g/kg each of protein derived from casein and freeze-dried tofu (T10); and 6) a diet containing 200 g/kg of protein derived from freeze-dried tofu (T20) (Table 1). CI and SI were supplemented with a mixture of isoflavones to match the isoflavone level of T20.

tag: sex

value: male

tag: tissue

value: liver


title: year: 2006 - developmental stage: UD:0000034 33E-L - rep1


title: tofu diet, biological rep5

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.402185413063392
upper limit: 2.62548510224213
saturation: 2.99247546773371
gamma: 52.4558035154239
sigma: 0.796201600637588
mu: 1.89024841313523


title: tofu diet, biological rep3

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.646845656724445
upper limit: 2.53373751086924
saturation: 2.93131040681845
gamma: 47.2670837205132
sigma: 0.810422751433752
mu: 1.87379286797521


title: tofu diet, biological rep2

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.417476678292208
upper limit: 1.76917424942845
saturation: 3.08422305910661
gamma: 58.2603841225164
sigma: 0.810469037121926
mu: 1.87351486176534


title: tofu diet, biological rep1

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.55509806535155
upper limit: 1.75388298419963
saturation: 2.87014534590318
gamma: 55.664173645881
sigma: 0.816273522695693
mu: 1.84628906542116


title: year: 2005 - developmental stage: UD:0000035 34E-L - rep3

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/20/2005 (7 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for  Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2005_developmental stage: UD:0000035 34E-L


title: year: 2005 - developmental stage: UD:0000035 34E-L - rep1


title: year: 2005 - developmental stage: UD:0000035 34E-L - rep2


title: casein + tofu diet, biological rep2

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.616263126266813
upper limit: 2.57961130655568
saturation: 3.08422305910661
gamma: 56.1227360171011
sigma: 0.794262063471563
mu: 1.91796650863495

source_name: rat liver, casein + tofu diet fed for 14 days


title: year: 2005 - developmental stage: UD:0000034 33E-L - rep1

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 07/06/2005 (5 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2005_developmental stage: UD:0000034 33E-L


title: casein + tofu diet, biological rep5

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.616263126266813
upper limit: 2.77839775453029
saturation: 2.93131040681845
gamma: 49.1344525822738
sigma: 0.799019273817775
mu: 1.85570085069526


title: soy protein+isoflavone diet, biological rep5

description:
The following parameters for data distribution were found by using SuperNORM data service.
under limit: -0.753884513326155
upper limit: 2.44198991949634
saturation: 4.00169897283555
gamma: 47.5846588466925
sigma: 0.768467729190564
mu: 1.85557716788944

source_name: rat liver, soy protein+isoflavone diet fed for 14 days


title: year: 2005 - developmental stage: UD:0000034 33E-L - rep3


title: year: 2003 - developmental stage: UD:0000037 36E-L - rep2

description: Ten clusters of Pinot Noir, clone ENTAV 115,  were collected on 08/06/2003 (10 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.

source_name: fruit_year 2003_developmental stage: UD:0000037 36E-L