title: Liver confinement timecourse LS24L vs HS24L

status: Public on Nov 24 2010

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

description: The fish used in the study were sexually immature, mixed sex, adult rainbow trout from two lines of fish selectively bred for either a high (HR) or low (LR) corticosteroid response to a standardized confinement stressor. The selection programme used to generate the HR and LR lines of trout has been described previously (Pottinger and Carrick, 1999 and 2001). In brief, single parent matings of individuals identified as either HR or LR by their corticosteroid response to a series of standardized confinement stressors were used to generate F1 lines of HR and LR progeny. An individual-within-family selection process was adopted to establish the F2 and subsequently the F3 generation, used in this study. The F3 generation hatched during spring 2003 and these fish were therefore in their second year (18 months old) at the time of this study. The mean weight and fork length of the two lines at the time of the study was LR: 181 g, 24.7 cm; HR: 185 g, 24.9 cm.

hyb_protocol: Cy3-labelled and Cy5-labelled cDNA were dried and resuspended in 22 microL of hybridisation mix (5X Denhardt, 3.5X SSC, 0.3% SDS (Bio-Rad), 0.5 microg/microL yeast tRNA (Invitrogen), 0.5 microg/microL polyA RNA (Invitrogen) and 50 % formamide). Slides were prehybridized with a solution containing 50mM ethanolamine, 100mM Tris base, 0.1% SDS, pH 9.0 at 50 ºC for 15 min followed by two washes in 18 MW water. Next slides were incubated in a solution containing 4X SSC and 0.1% SDS at 50 ºC for 15 min followed by one wash with 18 MW water and centrifugation (260g) for 3 minutes at room temperature. Slides were incubated in prehybridisation solution (3.5X SSC, 0.3% SDS, 1% BSA) at 42 ºC for 1h. Slides were washed 5 times with 18 MW water and dried by centrifugation (260g) for 3 min. Before hybridisation, Cy3- and Cy5-labelled targets were pooled and denatured at 100 ºC for 2 min. Targets were applied to the microarray slide and covered with a coverslip (Erie Scientific). Hybridisation of the slides was performed in a hybridisation chamber (Genetix) humidified with 3X SSC at an annealing temperature of 42 ºC overnight followed by immersion of slides in 2% SSC, 0.1% SDS for the removal of the coverslip. Slides were washed with 1X SSC for 2 min and followed by 2 washes with 0.2X SSC for 2 min each. Slides were dried by centrifugation (260g) for 3 min at room temperature and immediately scanned.

scan_protocol: ScanArray Express HT Microarray Scanner (Perkin Elmer) - GenePix software (GenePix Pro 6.0.1.25) was used for feature acquisition from the TIF images (Molecular Devices Corp).

data_processing: Intensity values used were signal median values and local background was automatically subtracted. Data from the time course experiment was analysed using separate channel analysis of two color data using Limma. The raw data from this loop experiment was normalised within slide using the 'printtiploess' method and the 'normexp' background correction method (Smyth and Speed, 2003). Log2 fold changes and standard errors were estimated by using linear models and empirical Bayes moderated F statistics for each gene. P values were adjusted for multiple testing by using the method of Benjamini and Hochberg (Smyth, 2004).

organism: Oncorhynchus mykiss

label_protocol: Five microg of total RNA was used to synthesize labelled cDNA using the ChipShotTM Direct Labeling and Clean-Up System (Promega) following the manufacturer¢s protocol. Labelled cDNA was quantified using a NanoDropTM ND 1000 spectrophotometer (Thermo Scientific).

growth_protocol: Prior to the study the fish were held in 1000-litre circular glassfibre tanks. Each tank received a single pass flow-through (20 litres min-1) of untreated Windermere lake water at ambient temperature (annual range approx 4oC - 17oC). Stocking densities were in the order of 20 g/litre. The fish were fed three times weekly with commercial pellets (Skretting Standard Expanded 40) at a ration size of approx 5% body weight.

extract_protocol: Total RNA was isolated using the RNeasy Midi Kit (Qiagen) following the manufacturer's recommended protocol after homogenising 0.2 - 0.3 mg of tissue in Qiazol reagent (Qiagen). Contaminating genomic DNA was degraded using an on-column DNase I treatment using RNase-free DNase Kit (Qiagen). The quality of RNA was checked using the Agilent Bioanalyser 2100. RNA integrity numbers (RIN) were 10 for most of the samples. Total RNA was quantified by UV spectrophotometry at 260 nm (Eppendorf Biophotometer).

treatment_protocol: A time-course study using HR and LR fish from the F3 generation was carried out during August and September 2004. During July, LR and HR fish (LR weight: 181.3 g; length: 24.7 cm; HR weight: 184.7 g; length: 24.9 cm) were distributed between twenty-two 1000 litre holding tanks (approx 110 fish/tank, 11 for each line). Each tank was supplied with a constant flow of untreated Windermere lake water (20 litres min-1) at ambient temperature (mean 16.7 oC). After a 2 week period of acclimation, LR fish from a single holding tank were transferred to twenty-two 50 litre confinement tanks, 5 fish per tank, each supplied with a constant flow of lake water. At intervals (0, 2, 4, 6, 8, 24, 48, 96, 168, 336, 504h) a total of 6 fish (3 fish from each of two tanks) were sampled, with undisturbed LR fish in pairs of holding tanks acting as controls. At each time-point livers were collected and immediately frozen in liquid nitrogen for subsequent analysis. The confinement and sampling procedure was repeated 1 week later for the HR fish. Fish were fasted for 2 days prior to the study and offered food on day 3 of the study and three times weekly thereafter. Plasma cortisol was measured by a validated radioimmunoassay procedure (Pottinger and Carrick, 2001).

tag: genetic line

value: Low response

tag: condition

value: stress

tag: time

value: High response


title: Liver confinement timecourse LC6L vs LC24L

type: RNA

molecule: total RNA

value: control


title: Liver confinement timecourse LC6L vs LS6L


title: Liver confinement timecourse LC24L vs LS24L_2


title: Liver confinement timecourse HS24L vs HS168L_2


title: Liver confinement timecourse HS6L vs HS24L


title: Liver confinement timecourse HS6L vs HC6L


title: Liver confinement timecourse LC168L vs LC6L


title: Liver confinement timecourse LC168L vs LS168L


title: Liver confinement timecourse LC24L vs LC168L


title: Liver confinement timecourse HS168L vs HC168L


title: LS45F

hyb_protocol: Cy3-labelled and Cy5-labelled cDNA were dried and resuspended in 22 microL of hybridisation mix (5X Denhardt, 3.5X SSC, 0.3% SDS (Bio-Rad), 0.5 microg/microL yeast tRNA (Invitrogen), 0.5 microg/microL polyA RNA (Invitrogen) and 50 % formamide). Slides were prehybridized with a solution containing 50mM ethanolamine, 100mM Tris base, 0.1% SDS, pH 9.0 at 50 °C for 15 min followed by two washes in 18 MW water. Next slides were incubated in a solution containing 4X SSC and 0.1% SDS at 50 °C for 15 min followed by one wash with 18 MW water and centrifugation (260g) for 3 minutes at room temperature. Slides were incubated in prehybridisation solution (3.5X SSC, 0.3% SDS, 1% BSA) at 42 °C for 1h. Slides were washed 5 times with 18 MW water and dried by centrifugation (260g) for 3 min. Before hybridisation, Cy3- and Cy5-labelled targets were pooled and denatured at 100 °C for 2 min. Targets were applied to the microarray slide and covered with a coverslip (Erie Scientific). Hybridisation of the slides was performed in a hybridisation chamber (Genetix) humidified with 3X SSC at an annealing temperature of 42 °C overnight followed by immersion of slides in 2% SSC, 0.1% SDS for the removal of the coverslip. Slides were washed with 1X SSC for 2 min and followed by 2 washes with 0.2X SSC for 2 min each. Slides were dried by centrifugation (260g) for 3 min at room temperature and immediately scanned.

data_processing: Data was processed in GeneSpring v7.3. Intensity values used were signal median values and local background was automatically subtracted. To account for dye swap, the signal channel and control channel measurements for appropriate samples were reversed. Values below 0.01 were set to 0.01. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Genespring automatically averages spots with the same ID so all triplicate were averaged. Finally the output from GeneSpring is log2 transformed.

tag: stress response

value: Low

tag: fish number

source_name: REFERENCE

tag: reference

value: Pooled samples


title: LS47F


title: Liver confinement timecourse LS168L vs HS168L


title: Liver confinement timecourse HC168L vs HC6L


title: Liver confinement timecourse LS168L vs LS6L


title: Liver confinement timecourse HC24L vs HC168L


title: Liver confinement timecourse HS168L vs HS6L


title: Liver confinement timecourse HC6L vs HC24L


title: LS48R


title: LS47R


title: LS44R


title: LS43F


title: Liver confinement timecourse HS24L vs HC24L


title: LS44F


title: LS45R


title: LS48F


title: HS47F

value: High


title: HS47R


title: LS43R


title: HS46R


title: LKKI_42_4_2

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

hyb_protocol: Labeled cDNA was hybridized to the arrays according to the protocol recommended by CombiMatrix except for using 2X formamide based hybridization buffer (Genisphere) containing Salmon testis DNA (1 μg / μl, Sigma) and shorter hybridization time (1h).

scan_protocol: After hybridization semiconductor microarray surfaces were covered by imaging solution and were scanned using a fluorescence LS200 scanner (TECAN).

data_processing: Combimatrix Microarray Images Software was used for gridding, excluding bad quality spots and export of signal intensities. Further data analysis was peformed in R software environment for statistical computing and graphics (http://www.r-project.org/). Bioconductor´s package affy was used for quality control, preprocessing and statistical significance testing. Backround was not substracted. The data was normalized using the Quantile normalization.

organism: Escherichia coli

source_name: cell culture

label_protocol: Purified RNA (approximately 30 µg) was used for the cDNA synthesis and direct labeling (Superscript II, Invitrogen). Luciferase control mRNA (1 ng/µg; Promega) and 3 µg of random primers were added to each RNA sample. This was followed by 10 minutes of incubation at 70°C and immediate chilling on ice. cDNA synthesis was carried out using SuperScript II reverse transcriptase (Invitrogen) according to manufacturer’s instructions. Synthesised cDNA was purified using MinElute PCR purification Kit (Qiagen). The concentration of cDNA, efficiency of dye (Cy5) integration and integrity of labeled cDNA were checked by NanoDrop and gel electrophoresis.

growth_protocol: Bacterial inoculum E. coli BL21 pET3a with inserted gene sequence coding for hG-CSF protein (production strain) or E. coli BL21 pET3a without inserted gene sequence coding for hG-CSF protein (control strain) was prepared in a shake flask culture and grown overnight at 25°C and at 160 rpm in the LBPG/amp100 medium

extract_protocol: Cultures were stabilized with RNA protect Bacteria Reagent (Qiagen), aliquoted, centrifuged and the bacterial pellet was stored at – 80°C for further. RNA isolation and DNase treatment was performed as described by Petek et al [BMC Mocrobiology, 2010], except for substituting lysostaphin with lysocyme (500 mg/ml) in the cell lysis step. RNA quality, quantity and integrity was checked by NanoDrop (NanoDrop Technologies, USA), gel electrophoresis and Bioanalyzer (Agilent Technologies).

treatment_protocol: After reaching suitable optical density at OD600nm ≈ 4 the inoculum was transferred to the GYSP medium and immediately induced with IPTG. The cultures were then incubated in shake flasks at 160 rpm and at three different temperatures (i.e. T = 25°C, 37°C and 42°C, respectively) until the appropriate culture´s optical density (OD), indicating the transition from the exponent to the stationary phase was reached (OD600nm ≈ 4 or 10 for the culture grown at 25 °C and OD600 nm ≈ 4 for the cultures grown at 37°C or 42°C). The cultivation experiment was repeated 3 times.

tag: strain

value: production

tag: growth temperature

tag: harvest od

tag: replicate


title: LKKI_42_4_3


title: HS45F


title: HS44F


title: HS43F


title: HS44R


title: LKKI_37_4_3


title: HS43R


title: HS46F


title: HS45R


title: LKKI_37_4_2


title: BL21_42_4_1


title: LKKI_42_4_1


title: BL21_42_4_2


title: BL21_25_4_2


title: LKKI_37_4_1


title: BL21_25_10_1


title: LKKI_25_4_3


title: BL21_37_4_3


title: BL21_37_4_1


title: BL21_25_4_1


title: LKKI_25_10_2


title: LKKI_25_10_1


title: BL21_42_4_3


title: BL21_37_4_2


title: BL21_25_10_2


title: BL21_25_4_3


title: BL21_25_10_3


title: LKKI_25_4_1


title: LKKI_25_4_2


title: HC_NucPos_clr-D232N_rep#2

type: genomic

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

country: USA

institute: University of California, San Francisco

description: No further descriptions

hyb_protocol: Hybridizations and washes were conducted in accordance to the Agilent Yeast ChIP-on-chip Analysis protocol. 1450 ng of material was used for each channel.

scan_protocol: Arrays were scanned at a resolution of 5 pixels/um on an Axon 4000B Scanner using GenePix Pro 5.0 software

data_processing: Data were corrected for background by subtracting the median background value.  Data were then normalized using a Loess algorithm.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Cells grown in YS

label_protocol: Amplified material containing aminoallyl-dUTP was coupled to the indicated Cy dye according to manufacturer (Amersham Biosciences) instructions.

extract_protocol: Cells were grown to ~0.75-0.80 OD600 in YS at 30°C and crosslinked for 20 min. at 30°C using 1% formaldehyde followed by a 0.125M glycine quench for 5 min. Seventy-five to eighty OD600 units of cells were resuspended with 0.5mg Zymolase 100-T in 0.5mL of CES buffer. The cells were spheroplasted at 30°C for 1 hr. on a rocker.  Spheroplasts were collected by centrifugation at 3000 x g for 3 min. at 4°C then washed with cold 1.2M sorbitol twice.  The spheroplasts were then resuspended in a total volume of 0.8mL using pNP-S buffer.  The source material for this channel was obtained from 0.2mL of resuspended spheroplasts that was added and mixed with 0.3mL of pNP-S buffer containing 0 units of MNase and then was incubated at  at 37°C for 15 minutes.  The reaction was then quenched by adding EDTA pH 8.0 to a final concentration of 50mM. The spheroplasts were lysed with 0.1% SDS and centrifuged at 20k x g for 5 minutes. The supernatant containing solublized chromatin was incubated at 65°C overnight with 0.4 mg/ml proteinase K to deproteinize DNA and reverse methylene crosslinks. DNA was recovered by two extractions with equal amounts of equilibrated phenol and chloroform followed by ethanol precipitation and resuspension in water supplemented with 10μg/mL RNase A.  After a 30 min. treatment at 37°C, the DNA was amplified and labeled with a Cy dye using an Invitrogen Bioprime protocol and a high concentration of Klenow exo- and random nonamer primers.

tag: sample type

value: input

extract_protocol: Cells were grown to ~0.75-0.80 OD600 in YS at 30°C and crosslinked for 20 min. at 30°C using 1% formaldehyde followed by a 0.125M glycine quench for 5 min. Seventy-five to eighty OD600 units of cells were resuspended with 0.5mg Zymolase 100-T in 0.5mL of CES buffer. The cells were spheroplasted at 30°C for 1 hr. on a rocker.  Spheroplasts were collected by centrifugation at 3000 x g for 3 min. at 4°C then washed with cold 1.2M sorbitol twice.  The spheroplasts were then resuspended in a total volume of 0.8mL using pNP-S buffer.  The source material for this channel was obtained from 0.2mL of resuspended spheroplasts that was added and mixed with 0.3mL of pNP-S buffer containing 150 units of MNase and then was incubated at  at 37°C for 15 minutes.  The reaction was then quenched by adding EDTA pH 8.0 to a final concentration of 50mM. The spheroplasts were lysed with 0.1% SDS and centrifuged at 20k x g for 5 minutes. The supernatant containing solublized chromatin was incubated at 65°C overnight with 0.4 mg/ml proteinase K to deproteinize DNA and reverse methylene crosslinks. DNA was recovered by two extractions with equal amounts of equilibrated phenol and chloroform followed by ethanol precipitation and resuspension in water supplemented with 10μg/mL RNase A.  After a 30 min. treatment at 37°C, the DNA was amplified and labeled with a Cy dye using an Invitrogen Bioprime protocol and a high concentration of Klenow exo- and random nonamer primers.

value: MNase treated genomic DNA


title: HC_NucPos_mit1-K587A_rep#1

description: No further descriptions

extract_protocol: Cells were grown to ~0.75-0.80 OD600 in YS at 30°C and crosslinked for 20 min. at 30°C using 1% formaldehyde followed by a 0.125M glycine quench for 5 min. Seventy-five to eighty OD600 units of cells were resuspended with 0.5mg Zymolase 100-T in 0.5mL of CES buffer. The cells were spheroplasted at 30°C for 1 hr. on a rocker.  Spheroplasts were collected by centrifugation at 3000 x g for 3 min. at 4°C then washed with cold 1.2M sorbitol twice.  The spheroplasts were then resuspended in a total volume of 0.8mL using pNP-S buffer.  The source material for this channel was obtained from 0.2mL of resuspended spheroplasts that was added and mixed with 0.3mL of pNP-S buffer containing 0 units of MNase and then was incubated at  at 37°C for 15 minutes.  The reaction was then quenched by adding EDTA pH 8.0 to a final concentration of 50mM. The spheroplasts were lysed with 0.1% SDS and centrifuged at 20k x g for 5 minutes. The supernatant containing solublized chromatin was incubated at 65°C overnight with 0.4 mg/ml proteinase K to deproteinize DNA and reverse methylene crosslinks. DNA was recovered by two extractions with equal amounts of equilibrated phenol and chloroform followed by ethanol precipitation and resuspension in water supplemented with 10μg/mL RNase A.  After a 30 min. treatment at 37°C, approximately 80μg DNA was then treated lightly with 1.5U of MNase for 15 minutes.  After a phenol::chloroform extraction and ethanol precipitation, the DNA was amplified and labeled with a Cy dye using an Invitrogen Bioprime protocol and a high concentration of Klenow exo- and random nonamer primers.


title: HC_NucPos_chp2_rep#2

description: No further descriptions

extract_protocol: Cells were grown to ~0.75-0.80 OD600 in YS at 30°C and crosslinked for 20 min. at 30°C using 1% formaldehyde followed by a 0.125M glycine quench for 5 min. Seventy-five to eighty OD600 units of cells were resuspended with 0.5mg Zymolase 100-T in 0.5mL of CES buffer. The cells were spheroplasted at 30°C for 1 hr. on a rocker.  Spheroplasts were collected by centrifugation at 3000 x g for 3 min. at 4°C then washed with cold 1.2M sorbitol twice.  The spheroplasts were then resuspended in a total volume of 0.8mL using pNP-S buffer.  The source material for this channel was obtained from 0.2mL of resuspended spheroplasts that was added and mixed with 0.3mL of pNP-S buffer containing 0 units of MNase and then was incubated at  at 37°C for 15 minutes.  The reaction was then quenched by adding EDTA pH 8.0 to a final concentration of 50mM. The spheroplasts were lysed with 0.1% SDS and centrifuged at 20k x g for 5 minutes. The supernatant containing solublized chromatin was incubated at 65°C overnight with 0.4 mg/ml proteinase K to deproteinize DNA and reverse methylene crosslinks. DNA was recovered by two extractions with equal amounts of equilibrated phenol and chloroform followed by ethanol precipitation and resuspension in water supplemented with 10μg/mL RNase A.  After a 30 min. treatment at 37°C, the approximately 80μg DNA was then treated lightly with 1.5U of MNase for 15 minutes.  After a phenol::chloroform extraction and ethanol precipitation, the DNA was amplified and labeled with a Cy dye using an Invitrogen Bioprime protocol and a high concentration of Klenow exo- and random nonamer primers.


title: HC_TransMap_WT_rep#1

type: mixed

description: No further descriptions

hyb_protocol: Hybridizations and washes were conducted in accordance to the Agilent Yeast ChIP-on-chip Analysis protocol. 800 ng of material was used for each channel.

data_processing: Watson and Crick probes were processed independently. Data were corrected for background by subtracting the median background value.  Data were then centered by the mean of the bottom 15-30% of euchromatin control probes.

label_protocol: cDNA material containing aminoallyl-dUTP was coupled to the indicated Cy dye according to manufacturer (Amersham Biosciences) instructions.

extract_protocol: Genomic DNA was prepared from 200mL of a saturated culture grown at 30°C in YS.  The cells were collected by centrifugation at 3000 x g for 5 min., resuspended in 25mL of CES buffer and spheroplasted with 25mg of Zymolyase-100T at 37°C for 90 minutes with shaking.  Spheroplasts were recovered by centrifugation at 3000 x g for 5 minutes and resuspended in 30mL of 5X TE. SDS was added to a final concentration of 1% to lyse spheroplasts, and then potassium acetate was added to a concentration of 1.5M, followed by a 30 min. incubation on ice to precipitate protein and SDS.  The supernatant was cleared by centrifugation (4500 x g, 20 min. at 4°C) and filtered through cheese cloth.  The resulting DNA was concentrated by precipitation using 1 volume of isopropanol. The DNA pellet was resuspended in 5X TE supplemented with 10μg/mL RNase A.  After 1 hr. at 37°C, proteinase K was added to 0.4mg/ml, followed by a further incubation at 55°C for 1 hour.  The protienase K treated material was extracted twice with equal amounts of  equilibrated phenol and chloroform then subjected to ethanol precipitation (0.1 volumes of 3M sodium acetate followed by 2 volumes of ethanol).  The DNA pellet was then resuspended in deionized H2O.  Genomic DNA was sonicated for 1 hr. in a water bath sonicator (Bioruptor) at full power in cycles of 30 sec. on and 60 sec. off.   DNA was then amplified into cRNA as described (Liu et al., 2003).  Briefly, sonicated DNA was treated with calf intestinal phosphatase (New England biolabs) to remove 3’ phosphates from DNA.  The DNA was then treated with terminal dideoxytransferase (New England Biolabs) to add 3’ poly(T) tails. Next, the DNA was subjected to Klenow exo- (New England Biolabs) second strand synthesis using a primer containing a T7 promoter and a poly(A) tail. Reference RNA was then generated using the T7 Megascript kit (Ambion).  Approximately 20μg of DNase-treated RNA was used cDNA synthesis by standard reverse transcription reactions in the presence of 6 ng/mL of Actinomycin D to prevent snap-back synthesis and 1:1 aminoallyl-dUTP:dTTP dNTP mix for subsequent labeling in 100 μL reaction volumes.  25 μg of random nonamers were used for priming the RT reactions. RNA was hydrolyzed in the presence of sodium hydroxide and heat. Hydrolyzed RNA was then removed and cDNA were cleaned using Qiaquick spin columns.

extract_protocol: Cells were grown to OD600 0.7-0.8 and harvested by centrifugation at 3000 x g for 5 minutes.  Total RNA was isolated from 70-80 OD600 cell units as described in Rougemaille et al. (2008).  50μg of total RNA was treated with 2 μL of Turbo DNase (Ambion) for 1 hr. at 37°C in 1x reaction buffer.  After 30 min., the DNase reaction was supplemented with an additional 1μL of Turbo DNase.  Next, 0.2 reaction volume of DNase inactivation beads (Ambion) were incubated with the reaction for 2 min. at room temperature to clear and inactivate the DNase.  The beads were removed by centrifugation at 10k x g for 1.5 min. Approximately 20μg of DNase-treated RNA was used cDNA synthesis by standard reverse transcription reactions in the presence of 6 ng/mL of Actinomycin D to prevent snap-back synthesis and 1:1 aminoallyl-dUTP:dTTP dNTP mix for subsequent labeling in 100 μL reaction volumes.  25 μg of random nonamers and 25 μg of oligo dT were used for priming the RT reactions. RNA was hydrolyzed in the presence of sodium hydroxide and heat. Hydrolyzed RNA was then removed and cDNA were cleaned using Qiaquick spin columns.


title: HC_TransMap_clr4_rep#1

description: No further descriptions

value: h-, clr4::KanMx, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_NucPos_swi6_rep#1

description: No further descriptions

value: h-, swi6::KanMx, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_NucPos_WT_rep#2

description: No further descriptions


title: HC_NucPos_swi6_rep#2

description: No further descriptions


title: HC_TransMap_clr4_rep#2

description: No further descriptions


title: HC_NucPos_Clr4_rep#1

description: No further descriptions

value: h-, clr4::kanMX, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_NucPos_rsc1_rep#2

description: No further descriptions

value: h-, rsc1::kanMx, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_NucPos_clr3-D232N_rsc1_rep#2

description: No further descriptions

value: h-, clr3::clr3-D232N-NatMx, rsc1::KanMx, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_TransMap_clr4_rrp6_rep#1

description: No further descriptions

value: h-, clr4::KanMx, rrp6::NatMx, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_NucPos_WT_rep#1

description: No further descriptions


title: HC_TransMap_WT_rep#2

description: No further descriptions


title: HC_NucPos_rsc1_rep#1

description: No further descriptions


title: HC_NucPos_clr4_rep#2

description: No further descriptions


title: HC_TransMap_clr4_rrp6_rep#2

description: No further descriptions


title: HC_NucPos_mit1-K587A_rep#2

description: No further descriptions

value: h-, mit1::mit1-K587A-HygBMx, smt0, ade6-M210, leu1-32, ura4-D18


title: HC_NucPos_chp2_rep#1

description: No further descriptions


title: HC_NucPos_clr3-D232N_rsc1_rep#1

description: No further descriptions


title: 8629T12 tumor untreated grade3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: Gene expression data from microdissected adenocarcinomas

hyb_protocol: Following fragmentation, 4 ug of cDNA was hybridized for 16 hr at 45C on Mouse 430A_2 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix 3000 7G scanner.

data_processing: R version 2.11.0 (x86_64-pc-linux-gnu), affyPLM_1.24.0, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.0, Biobase_2.8.0

label: biotin

organism: Mus musculus

source_name: 8629T12 tumor untreated grade3

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using Nugen Ovation RNA amplification system V2 according to the manufacturers instructions.

growth_protocol: Tumors were extrracted from 10 week old animals

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

treatment_protocol: For treated samples tamoxifen was administered IP in 2 injections. Tumors were collected 7 days after first injection.

tag: tissue

value: lung tumor

tag: gender

value: male


title: 8629T10 tumor untreated grade3

source_name: 8629T10 tumor untreated grade3


title: 8700T3 tumor untreated grade2

description: Gene expression data from microdissected adenomas

source_name: 8700T3 tumor untreated grade2


title: HC_NucPos_clr-D232N_rep#1

description: No further descriptions


title: 8565T4 tumor untreated grade2

source_name: 8565T4 tumor untreated grade2


title: 8700T1 tumor untreated grade2

source_name: 8700T1 tumor untreated grade2


title: 8565T3 tumor untreated grade2

source_name: 8565T3 tumor untreated grade2


title: 8565T1 tumor untreated, grade3

source_name: 8565T1 tumor untreated, grade3


title: 8688T9 tumor treated, grade2

description: Gene expression data from microdissected p53 restored adenomas

source_name: 8688T9 tumor treated, grade2

value: female


title: Postnatal_24

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

hyb_protocol: Hybridized according to Agilent Two-Color Microarray_based Gene Expression Analysis protocol

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction software (Version 9.5.1)

organism: Bos taurus

source_name: Wagyu sample from 30 months old

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Muscle samples of 1 to 2 g were removed using a scalpel and immediately snap-frozen using liquid nitrogen for RNA analyses. Total RNA was prepared from each sample biopsy using TRIzol reagent(Invitrogen) in accordance with the manufacturers protocol.

tag: sample

tag: treatment

value: Wagyu sample from 30 months old

value: longissimus dorsi skeletal muscle biopsy

source_name: Piedmontese sample from 30 months old

value: Piedmontese sample from 30 months old


title: 8639T4 tumor treated, grade2

source_name: 8639T4 tumor treated, grade2


title: Postnatal_23

source_name: Piedmontese sample from 25 months old

value: Piedmontese sample from 25 months old

source_name: Wagyu sample from 25 months old

value: Wagyu sample from 25 months old


title: Postnatal_22


title: Postnatal_21


title: 8688T8 tumor treated, grade2

source_name: 8688T8 tumor treated, grade2


title: Postnatal_18

source_name: Piedmontese sample from 7 months old

value: Piedmontese sample from 7 months old

source_name: Wagyu sample from 7 months old

value: Wagyu sample from 7 months old


title: Postnatal_19

source_name: Wagyu sample from 12 months old

value: Wagyu sample from 12 months old

source_name: Piedmontese sample from 12 months old

value: Piedmontese sample from 12 months old


title: 8688T6 tumor treated, grade3

description: Gene expression data from microdissected p53 restored adenocarcinomas

source_name: 8688T6 tumor treated, grade3


title: 8584T3 tumor untreated, grade3

source_name: 8584T3 tumor untreated, grade3


title: Postnatal_20

source_name: Wagyu sample from 20 months old

value: Wagyu sample from 20 months old

source_name: Piedmontese sample from 20 months old

value: Piedmontese sample from 20 months old


title: 8688T1 tumor treated, grade3

source_name: 8688T1 tumor treated, grade3


title: 8688T2 tumor treated, grade3

source_name: 8688T2 tumor treated, grade3


title: 8688T10 tumor treated, grade2

source_name: 8688T10 tumor treated, grade2


title: 8688T11 tumor treated, grade3

source_name: 8688T11 tumor treated, grade3


title: 8688T5 tumor treated, grade3

source_name: 8688T5 tumor treated, grade3


title: Postnatal_16

source_name: Wagyu sample from 30 months old

source_name: Piedmontese sample from 30 months old


title: KPR8 cells - EtOH treatment

description: Gene expression data from an adenocarcinoma derived cell line

source_name: KPR8 cells - control

growth_protocol: Cells were grown in DME with 10% FBS and antibiotic

treatment_protocol: 250 nM 4-OH tamoxifen dissolved in EtOH. 24 hours prior to RNA collection

tag: cell line


title: Postnatal_17

source_name: Piedmontese sample from 3 months old

value: Piedmontese sample from 3 months old

source_name: Wagyu sample from 3 months old

value: Wagyu sample from 3 months old


title: 8688T3 tumor treated, grade3

source_name: 8688T3 tumor treated, grade3


title: Postnatal_15

source_name: Piedmontese sample from 25 months old

source_name: Wagyu sample from 25 months old


title: Postnatal_12


title: Postnatal_13


title: Postnatal_14


title: KPR5 cells - Tamoxifin treatment

description: Gene expression data from an adenocarcinoma derived cell line following reactivation of p53 expression by tamoxifen treatment

source_name: KPR5 cells - reactivated p53


title: Postnatal_11

source_name: Piedmontese sample from 12 months old

source_name: Wagyu sample from 12 months old


title: KPR5 cells - EtOH treatment

source_name: KPR5 cells - control


title: Postnatal_8

source_name: Wagyu sample from 20 months old

source_name: Piedmontese sample from 20 months old


title: KPR8 cells - Tamoxifin treatment

source_name: KPR8 cells - reactivated p53


title: KPR4 cells - Tamoxifin treatment

source_name: KPR4 cells - reactivated p53


title: KPR4 cells - EtOH treatment

source_name: KPR4 cells - control


title: Postnatal_10

source_name: Wagyu sample from 7 months old

source_name: Piedmontese sample from 7 months old


title: Postnatal_9


title: Postnatal_7


title: Control at -0.5 kPa C2

city: Kgs Lyngby

first: Gamze

last: Gulez

address: Miljoevej 113

department: Environmental Engineering

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Labeled cDNA was hybridized to the array probes on the array as per manufacturer’s protocol (Micro-array base prokaryotic analysis, Fairplay III, Agilent, CA, USA).

scan_protocol: scanning was performed as per manufacturer's protocol (DNA microarray scanner, Agilent, CA, USA)

data_processing: Gene expression data  were analyzed in the statistical software R (www.r-project.org) using the limma package (Smyth, 2004) available in Bioconducter (www.bioconductor.org). Data were normalized using quantile method (Workman et al., 2002).

organism: Pseudomonas putida

source_name: surface colonies

label_protocol: cDNA synthesis and labeling (CY-3 dye) were performed as per manufacturers’ protocol (Micro-array base prokaryotic analysis, Fairplay III, Agilent, CA, USA).

extract_protocol: cells were flooded with stop solution (5% phenol in 100% ethanol ), and harvested with a cytological brush (Gynobrush, Heinz Herenz, Hamburg, Germany). Harvested cells were suspended in 2 ml Eppendorf tubes containing 200 ml of the stop solution. Immediately after, RNA extraction was performed using Agilent MiniRNA Kit (CA, USA) following the manufacturer‘s protocol.

tag: stress


title: Postnatal_3


title: PEG at -0.5 MPa PEG5_1


title: Pressure_2 at 0.4 MPa

source_name: liquid culture

value: gas pressure at 0.4 MPa


title: PEG at -0.5 MPa PEG5_2


title: 72 hr at -0.4 MPa P72_3

value: 72 hr


title: Control C_Pressure_1 at 0.1 MPa (atmospheric)

value: gas pressure at 0.1 MPa (atmospheric)


title: 72 hr at -0.4 MPa P72_2


title: Postnatal_2


title: PEG at -1.0 MPa PEG10_1


title: Control at -0.5 kPa C3


title: 72 hr at -0.4 MPa P72_4


title: Pressure_1 at 0.4 MPa


title: Control at -0.5 kPa C4


title: 72 hr at -0.4 MPa P72_1

value: 24 hr


title: Postnatal_4


title: Postnatal_5

source_name: Piedmontese sample from 3 months old

source_name: Wagyu sample from 3 months old


title: Postnatal_6


title: Control at -0.5 kPa C1


title: 4 hr at -0.4 MPa P4_4

value: 4 hr


title: 24 hr at -0.4 MPa P24_3


title: Diet_9

source_name: Belmont Red sample from weight loss diet at time 2

value: longissimus dorsi skeletal muscle biopsy

source_name: Belmont Red sample from weight growth diet at time 2


title: Diet_8

source_name: Belmont Red sample from weight growth diet at time 1

source_name: Belmont Red sample from weight loss diet at time 1


title: 24 hr at -0.4 MPa P24_2


title: 24 hr at -0.4 MPa P24_1


title: Diet_7

value: Belmont Red sample from weight loss diet at time 1

value: Belmont Red sample from weight growth diet at time 1


title: Diet_11

value: Belmont Red sample from weight growth diet at time 2

value: Belmont Red sample from weight loss diet at time 2


title: Diet_10


title: Diet_12


title: Postnatal_1


title: 4 hr at -0.4 MPa P4_1


title: Diet_6


title: 4 hr at -0.4 MPa P4_3


title: 4 hr at -0.4 MPa P4_2


title: EC_NucPos_Clr4_rep#1

description: No further descriptions

source_name: Cells grown in YS

value: h-, clr4::kanMX, smt0, ade6-M210, leu1-32, ura4-D18

value: input

value: MNase treated genomic DNA


title: Lentinula edodes-mature fruit body after spore formation (LongSAGE)

type: SAGE

anchor: NlaIII

city: Shatin

first: Hoi Shan

last: Kwan

state: Hong Kong SAR

department: Biology

country: China

institute: The Chinese University of Hong Kong

description: To facilitate comparison of LongSAGE and SAGE data in GEO, LongSAGE tags (15bp) were trimmed to become 10bp and uploaded in previous submission (GSM87320, GSM87321). The current submission are actual LongSAGE experimental data without any extrapolation from SAGE data.

data_processing: SAGE Analysis Software (version B) (Invitrogen)

organism: Lentinula edodes

source_name: Strain L54 of Lentinula edodes (Shiitake mushroom)

extract_protocol: I-SAGE Long Kit (version C) (Invitrogen)

tag: Stage

value: mature fruit body after sporulation

tag: medium

value: sawdust


title: EC_NucPos_WT_rep#2

description: No further descriptions


title: Lentinula edodes-mature fruit body before sporulation (LongSAGE)

value: mature fruit body before sporulation


title: ATCC33200T_004_2

city: Lausanne 26

first: Bernard

last: Berger

address: Vers-Chez-Les-Blanc

department: Nutrition & Health

country: Switzerland

institute: Nestlé Research Center

hyb_protocol: The hybridization conditions and the washing of the slide were performed as follows. To the 20 ul of DNA , 25 ul of control target Agilent, 60 ul of H2O and 105 ul of Agilent buffer were added. After 10 minutes of incubation at 80°C and 15 minutes at 65°C, the reaction was loaded on a pre-warmed slide in the hybridization chamber and incubated for 16 hours at 65°C, at four rpm in an Agilent oven. The cDNA hybridization was washed 10 min at 42°C in 6x SSC, 0.005% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100. The 3DNA hybridization was carried out as described in the Genisphere protocol except for the hybridization volume which was increased to 204 l and the washing modified as follows : 10 min at 65°C in 2x SSC, 0.0016% Triton x-100, 5 min at RT in 2x SSC, 0.0016% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100.

scan_protocol: The slides were scanned at 10 um with a Scanarray 4000 (Packard Biochip Technologies, Billerica, MA, USA)

data_processing:
Data were extracted with Imagene 5.6 (Biodiscovery, El Segundo, CA, USA). Data were treated with homemade scripts in Python language (www.python.org) and a local installation of the ArrayPipe web server (Hokamp, K., et al. 2004. Nucleic Acids Res. 32:W457-W459). Probes showing a signal smaller than twice the standard deviation of the local background were considered without signal. Probes showing no signal or saturated signals in both channels were discarded from the analysis.
The distribution of the log2-transformed signal ratios was analyzed for each hybridization reaction separately. The mean of a normal distribution fitting the main peak was calculated. The log2 signal ratio of each spot was then modified in order to shift the mean of the main peak of each hybridization reaction to 0.

organism: Lactobacillus johnsonii

label_protocol: Genomic DNA labelling as described in Berger et al. Journal of Bacteriology, February 2007, p. 1311-1321, Vol. 189, No. 4NA labelling and cDNA synthesis were carried out using the 3DNA Array 900 MPX Genisphere kit (Genisphere Inc., Hatfield, PA, USA) combined with the In situ Hybridization Kit Plus.

growth_protocol: in MRS cystein medium

extract_protocol: Genomic DNA extraction as described in Berger et al. Journal of Bacteriology, February 2007, p. 1311-1321, Vol. 189, No. 4

value: ATCC 33200T


title: NCC533_004_1


title: EC_NucPos_clr4_rep#2

description: No further descriptions


title: EC_NucPos_WT_rep#1

description: No further descriptions


title: Diet_4

source_name: Belmont Red sample from weight loss diet at time 0

source_name: Belmont Red sample from weight growth diet at time 0


title: ATCC33323T_005_2

organism: Lactobacillus gasseri

value: ATCC 33323T


title: Diet_5


title: Prenatal_10

source_name: Wagyu sample from 135 days gestation

value: Wagyu sample from 135 days gestation

source_name: Piedmontese sample from 135 days gestation


title: EGFP vs. EGFP-importin alpha2 full-length

city: Clayton

first: Yoichi

last: Miyamoto

state: VIC

address: Building 77 Level 1, Wellington Road

department: Biochemistry and Molecular Biology

institute: Monash University

hyb_protocol: 750 ng of the Cy3-labeled control EGFP sample and 750 ng of either the Cy5-labeled EGFP-importin alpha2 full-length or CAS-binding mutant sample were mixed and incubated with an Agilent 60-mer oligo microarray slide (Whole Human Genome, Agilent Tchnologies) for 17 h.

scan_protocol: Slides were scanned using the Agilent DNA microarray scanner and expression data were obtained by the Agilent Feature Extraction software.

data_processing: Feature Extraction Software A.7.5.1 default protocol. Grid:012391_d_20040930.xml. Background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: pEGFP, 48 hr

label_protocol: High-quality RNA samples (300 ng each) acquired from HeLa cells transfected with pEGFP were amplified and labelled with Cyanine3 CTP, and RNAs from HeLa cells transfected with either pEGFP-importin alpha2 full-length or CAS-binding mutant constructs were amplified and labelled with Cyanine5 CTP, respectively, to produce labelled cRNA using Agilent Low RNA Fluorescent Linear Amplification Kit following the manufacturer's protocol. The labelled cRNAs were purified by RNeasy mini spin columns (Qiagen).

growth_protocol: HeLa cells (6 x 10^5) were grown in DMEM with 10% FSC at 37oC under an atmosphere of 5% CO2 in 100 mm dish for 24 h.

extract_protocol: The number of collected cells was 4 x 10^5 from each transfection. Total RNA was extracted using Qiagen RNeasy micro kits (Qiagen). The RNA quality was evaluated on an Agilent 2100 Bioanalyzer (Agilent Tchnologies).

treatment_protocol: pEGFPC1, pEGFPC1-mouse importin alpha2 full-length and pEGFP-mouse importin alpha2 CAS-binding mutant constructs were transfected using Effectene Transfection Regent (Qiagen). After 24 h, the medium was changed to DMEM containing 10% FCS and 1 mg/ml G418 and the cells were cultured for 24 h.

value: HeLa

tag: transfection

value: pEGFP

source_name: pEGFP-importin alpha2 full-length, 48 hr

value: pEGFP-importin alpha2 full-length


title: Keratinocyte culture, ID 4, IL17

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description:
Keratinocyte culture, ID 4, IL17

Batch_99_H
4440791099_H

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Using the lumi package in R, data was normalized using quantile normalization in two steps: (1) within each batch and (2) across batches.

source_name: Keratinocyte culture, IL17

label_protocol: Total RNA was labeled using the MessageAmp Premier RNA Amplification kit (Ambion Inc., TX).

growth_protocol: Primary keratinocytes were cultured in Epilife medium (Cascade Biologics, Portland, OR, U.S.A.) with EDGS (Cascade Biologic) and Penicillin Streptomycin (100 IU mL-1 and 0.1 mg mL-1, respectively) (Gibco, Carlsbad, CA, U.S.A.) at 37°C.

extract_protocol: RNA was extracted from cultured macrophages using the RNeasy Mini KIT (Qiagen, Valencia, CA, U.S.A.) and on-column DNAse digestion (RNAse-free DNAse Set, Qiagen), and used for either RT-PCR or gene array.

treatment_protocol: Once the cells were 80% confluent, the medium was supplemented with or without the following cytokines: recombinant human (rh)-IL-17 (R&D System, Minneapolis, MN, U.S.A.) 200 ng mL-1 and TNFα (Sigma-Aldrich Corp, St. Louis, MO, USA) 1 ng mL-1 or 10 ng mL-1 for 24 h before harvesting for other analyses.

tag: ID

tag: cell type

value: cultured primary keratinocytes


title: Prenatal_12

source_name: Piedmontese sample from 280 days gestation (birth)

value: longissimus dorsi skeletal muscle biopsy

source_name: Wagyu sample from 280 days gestation (birth)


title: Keratinocyte culture, ID 5, IL17

description:
Keratinocyte culture, ID 5, IL17

Batch_99_I
4440791099_I


title: Diet_3

value: Belmont Red sample from weight growth diet at time 0

value: Belmont Red sample from weight loss diet at time 0


title: Prenatal_9

source_name: Piedmontese sample from 60 days gestation

source_name: Wagyu sample from 60 days gestation

value: Wagyu sample from 60 days gestation


title: BL263_005_1

organism: Lactobacillus iatae


title: Keratinocyte culture, ID 5, Control

description:
Keratinocyte culture, ID 5, Control

Batch_99_G
4440791099_G

source_name: Keratinocyte culture, control


title: Diet_1


title: Prenatal_7

source_name: Piedmontese sample from 195 days gestation

source_name: Wagyu sample from 195 days gestation

value: Wagyu sample from 195 days gestation


title: Prenatal_8

value: Wagyu sample from 280 days gestation (birth)

value: Piedmontese sample from 280 days gestation (birth)


title: Prenatal_11

value: Piedmontese sample from 195 days gestation


title: NCC533_003_2


title: Keratinocyte culture, ID 4, Control

description:
Keratinocyte culture, ID 4, Control

Batch_99_F
4440791099_F


title: Diet_2


title: EGFP vs. EGFP-importin alpha2 C-mutant

source_name: pEGFP-importin alpha2 CAS-binding mutant, 48 hr


title: Keratinocyte culture, ID 3, TNFα10

description:
Keratinocyte culture, ID 3, TNFa10

Batch_99_E
4440791099_E

source_name: Keratinocyte culture, 10ng/ml TNFα

value: 10 ng/ml TNFα


title: Prenatal_6

value: Piedmontese sample from 135 days gestation


title: ATCC33200T_003_1

value: ATCC 33200T


title: BL263_001_2


title: Keratinocyte culture, ID 3, TNFα

description:
Keratinocyte culture, ID 3, TNFa

Batch_99_D
4440791099_D

source_name: Keratinocyte culture, 1ng/ml TNFα

value: 1 ng/ml TNFα


title: Keratinocyte culture, ID 3, IL17 + 10 TNFα

description:
Keratinocyte culture, ID 3, IL17+10 TNFa

Batch_90_L
4440791090_L

source_name: Keratinocyte culture, IL17 + 10ng/ml TNFα

value: IL17 + 10 ng/ml TNFα


title: Keratinocyte culture, ID 3, IL17

description:
Keratinocyte culture, ID 3, IL17

Batch_90_J
4440791090_J


title: Prenatal_3


title: Keratinocyte culture, ID 3, IL17 + 1 TNFα

description:
Keratinocyte culture, ID 3, IL17+1 TNFa

Batch_90_K
4440791090_K

source_name: Keratinocyte culture, IL17 + 1ng/ml TNFα

value: IL17 + 1 ng/ml TNFα


title: Prenatal_5

value: Piedmontese sample from 60 days gestation


title: Prenatal_4


title: BL261_001_1


title: ∆pde2∆tpk3 +4mM cAMP rep1

city: Canterbury

first: Campbell

middle: William

last: Gourlay

state: Kent

address: Giles Lane

department: Biosciences

country: United Kingdom

institute: University of Kent

hyb_protocol: hybridisation protocol was carried out as per the standard protocl at the University of Manchester COGEME facility

scan_protocol: scan protocol was carried out as per the standard protocol at the University of Manchester COGEME facility

data_processing: Statistical analysis was carried out using LIMA and quality control carried out using dchip software

organism: Saccharomyces cerevisiae

source_name: yeast 4mM cAMP

label_protocol: Standard Yeast 2 Affymatrix labelling protocol utilised by the COGEME facility at the University of Manchester

growth_protocol: Yeast growth medum YPD (1% yeast extract, 2% Bacto-peptone, 2% glucose)

extract_protocol: Qiagen RNAeasy extraction kit as per manufacturers guidlines

treatment_protocol: 4mM cAMp treatment for 24h

tag: genetic background

tag: genotype

value: 4mM cAMP


title: ∆pde2 +4mM cAMP rep3


title: ∆pde2∆tpk3 +4mM cAMP rep2


title: Prenatal_1


title: Keratinocyte culture, ID 2, TNFα

description:
Keratinocyte culture, ID 2, TNFa

Batch_90_G
4440791090_G

value: cultured primary keratinocytes


title: ∆pde2 +4mM cAMP rep2


title: Wild type + 4mMcAMP rep3

value: Wild type


title: ∆pde2 +4mM cAMP rep1


title: Wild type + 4mMcAMP rep1


title: Wild type + 4mMcAMP rep2


title: Keratinocyte culture, ID 3, Control

description:
Keratinocyte culture, ID 3, Control

Batch_90_I
4440791090_I


title: Keratinocyte culture, ID 2, IL17 + 1 TNFα

description:
Keratinocyte culture, ID 2, IL17+1 TNFa

Batch_90_A
4440791090_A


title: Keratinocyte culture, ID 2, IL17 + 10 TNFα

description:
Keratinocyte culture, ID 2, IL17+10 TNFa

Batch_90_B
4440791090_B


title: Keratinocyte culture, ID 2, TNFα10

description:
Keratinocyte culture, ID 2, TNFa10

Batch_90_H
4440791090_H


title: Prenatal_2

source_name: Wagyu sample from 135 days gestation

value: Wagyu sample from 135 days gestation

value: longissimus dorsi skeletal muscle biopsy

source_name: Piedmontese sample from 135 days gestation


title: Keratinocyte culture, ID 2, IL17

description:
Keratinocyte culture, ID 2, IL17

Batch_87_L
4444581087_L


title: Keratinocyte culture, ID 2, Control

description:
Keratinocyte culture, ID 2, Control

Batch_87_K
4444581087_K


title: BCL6KO macrophages unstimulated, technical replicate 1

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: technical replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: primary bone marrow derived macrophages

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Bcl6-/- in c57Bl6/J bkg

tag: age

value: 10 week old

value: macrophages

value: c57Bl6/J bkg

value: male

value: unstimulated


title: BCL6KO macrophages unstimulated, technical replicate 2

description: technicall replicate 2


title: BCL6KO macrophages LPS stimulated, technical replicate 1

description: technical replicate 1

value: LPS


title: Keratinocyte culture, ID 1, TNFα10

description:
Keratinocyte culture, ID 1, TNFa10

Batch_87_J
4444581087_J

value: 10 ng/ml TNFα


title: wildtype macrophages LPS stimulated, technical replicate 1

description: technical replicate 1

value: wildtype c57Bl6/J bkg


title: wildtype macrophages LPS stimulated, technical replicate 2

description: technicall replicate 2


title: Keratinocyte culture, ID 1, IL17 + 10 TNFα

description:
Keratinocyte culture, ID 1, IL17+10 TNFa

Batch_87_D
4444581087_D

value: IL17 + 10 ng/ml TNFα


title: wildtype macrophages unstimulated, technical replicate 1

description: technical replicate 1


title: Keratinocyte culture, ID 1, TNFα

description:
Keratinocyte culture, ID 1, TNFa

Batch_87_I
4444581087_I

value: 1 ng/ml TNFα


title: wildtype macrophages unstimulated, technical replicate 2

description: technicall replicate 2


title: Keratinocyte culture, ID 1, IL17 + 1 TNFα

description:
Keratinocyte culture, ID 1, IL17+1 TNFa

Batch_87_C
4444581087_C

value: IL17 + 1 ng/ml TNFα


title: BCL6KO macrophages LPS stimulated, technical replicate 2

description: technicall replicate 2


title: Macrophages_DD second day_CT16

city: Berlin

first: Bert

last: Maier

address: Hessische Straße 3-4

department: Institute for Medical Immunology

country: Germany

institute: Charité Universitätsmedizin

hyb_protocol: following cDNA synthesis, using random hexamers coupled with a T7 promotor sequence, obtained cRNA is converted into single stranded DNA, which then is fragmented by a treatment with a combination of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. Fragmented DNA was labeled by deoxynucleotidyl transferase reaction with labeling reagent that is linked to biotin. Hybridization and washing steps were done using the Affimetrix Hybridization and Wash and Stain Kit (according to manufacturer's instructions).

scan_protocol: Gene chips were scanned using the scanner type M10 (Pixel size 0.7, Filter 570).

data_processing: Data were analyzed by using the RMA gene default signal.

source_name: peritoneal macrophages, second day after release in DD, CT16

label_protocol: RNA biotin labeling was carried out using the Affimetrix GeneChip Whole Transcript Sense Target Labeling Assay according to the manufacturer's instructions.

growth_protocol: mice were entrained for two weeks in a 12 hour LD cycle before transferring them into DD. At indicated circadian times macrophages were harvested by lavage of the peritoneal cavity in 4hour intervalls and enriched by magnetic cell sorting based on the expression of the CD11b antigen

extract_protocol: total RNA was extracted by using the RNeasy Mini Kit (Qiagen). Total RNA of three mice per sampling time was pooled in equal amounts (48 ng/ µL).

value: peritoneal macrophage

tag: time

value: second day CT16


title: Macrophages_DD second day_CT12

source_name: peritoneal macrophages, second day after release in DD, CT12

value: second day CT12


title: Keratinocyte culture, ID 1, IL17

description:
Keratinocyte culture, ID 1, IL17

Batch_87_B
4444581087_B

source_name: Keratinocyte culture, IL17

value: cultured primary keratinocytes


title: Keratinocyte culture, ID 1, Control

description:
Keratinocyte culture, ID 1, Control

Batch_87_A
4444581087_A


title: Macrophages_DD second day_CT20

source_name: peritoneal macrophages, second day after release in DD, CT20

value: second day CT20


title: Macrophages_DD second day_CT8

source_name: peritoneal macrophages, second day after release in DD, CT8

value: second day CT8


title: 214_1

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: treated with 5-NA

hyb_protocol: Affymetrix standard label  protocol

scan_protocol: Affymetrix standard label  protocol

data_processing: RMA by software Partek

source_name: treated with 5-NA

label_protocol: Affymetrix standard label  protocol

growth_protocol: 293T cells from ATCC were maintained according to standard procedures.

extract_protocol: RNA was extracted using the Quiagen RNeasy RNA isolation kit (Valencia, CA)

treatment_protocol: Cells were treated with EerI, CBU-028, or 5-NA each at 10uM in duplicates for 10h


title: Macrophages_DD second day_CT4

source_name: peritoneal macrophages, second day after release in DD, CT4

value: second day CT4


title: Macrophages_DD first day_CT20

source_name: peritoneal macrophages, first day after release in DD, CT20

value: first day CT20


title: 214_2

description: treated with 5-NA


title: 211_1

description: treated with CBU-028

source_name: treated with CBU-028


title: Eer1_2

description: treated with Eer1

source_name: treated with Eer1


title: WT group, rep1

city: Wuhan

first: Meilin

last: Jin

address: 1 Shizishan Street, Wuhan, Hubei, 430070, P.R. China

institute: Huazhong Agricultural University

description: spleen samples 3 days after WT inoculated,sample 1

hyb_protocol: 1.Mix the following components together(Hybridization solution).   Fragmented cRNA: 5 μg;  Control Oligonucleotide B2(3nM): 1.7 μL;  20× Eukaryotic Hybridization Controls(bioB, bioC, bioD, cre): 5 μL;   Herring Sperm DNA(10mg/mL): 1 μL;   Acetylated BSA(50mg/mL): 1 μL;   2× Hybridization Buffer: 50 μL;  DMSO: 10μL;  H2O: 31.3μL;  2. Equilibrate probe array to room temperature immediately before use.  3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.  4. Meanwhile, wet the array by filling it through one of the septa with appropriate volume of 1X Hybridization Buffer using a micropipettor and appropriate tips.  5. Incubate the probe array filled with 1X Hybridization Buffer at 45°C for 10 minutes with rotation.  6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.  7. Spin hybridization cocktail(s) at maximum speed in a microcentrifuge for 5 minutes to remove any insoluble material from the hybridization mixture.  8. Remove the buffer solution from the probe array cartridge and fill with appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube.  9. Place probe array into the Hybridization Oven, set to 45°C.  Avoid stress to the motor; load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.  10. Hybridize at 45℃ for 16 h with constant rotation at 60rpm.  11. After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of the following Non-Stringent Wash Buffer(Wash Buffer A:6X SSPE, 0.01% Tween-20).  Post Hyb Wash #1: 10 cycles of 2 mixes/cycle with Wash  Buffer A at 25°C.   12. Preparing the Staining Reagents.  12.1 SAPE Stain Solution(Mix well and divide into two aliquots of 600 μL each to be used for stains 1 and 3):  2X Stain Buffer 600.0 μL;  50 mg/mL BSA 48.0 μL;   1 mg/mL Streptavidin Phycoerythrin (SAPE) 12.0 μL;  DI H20 540.0 μL;  12.2 Antibody Solution:  2X Stain Buffer 300.0 μL;  50 mg/mL BSA 24.0 μL;  10 mg/mL Goat IgG Stock 6.0 μL;  0.5 mg/mL biotinylated antibody 3.6 μL;  DI H20 266.4 μL;  13. Post Hyb Wash #2: 4 cycles of 15 mixes/cycle with Wash Buffer B(100 mM MES, 0.1M [Na+], 0.01% Tween-20) at 50°C.  14. Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C.   15. Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C.   16. 2nd Stain: Stain the probe array for 10 minutes in antibody solution at 25°C.  17. 3rd Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C.  18. Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C.  Annotation: Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The probe arrays were scanned using the Affymetrix® GeneChip® Scanner 3000.  Apply the spots just before scanning:  1. On the back of the probe array cartridge, clean excess fluid from around septa.  2. Carefully apply one Tough-Spots to each of the two septa. Press to ensure that the spots remain flat. If the Tough-Spots do not apply smoothly, that is, if you observe bumps, bubbles, tears, or curled edges, do not attempt to smooth out the spot. Remove the spot and apply a new spot.  3. Insert the cartridge into the scanner and test the autofocus to ensure that the Tough-Spots do not interfere with the focus.  Scanning the Probe Array:  1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar.  ⇒ The Scanner dialog box appears with a drop-down list of experiments that have not been run.  2. Select the experiment name that corresponds to the probe array to be scanned.  A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.  3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.  4. Once the experiment has been selected, click the Start button.  ⇒ A dialog box prompts you to load an array into the scanner.  5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.  ■ Pixel value = 3 μm  ■ Wavelength = 570 nm  If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.  6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner.  7. Click OK in the Start Scanner dialog box.  ⇒ The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1). Natural logarithms were then taken on quantile normalization (GeneSpring 7.31). Identification of DE genes was conducted using SAS (Ver.8.1, T-test). The p value cutoff for DE genes was set at 0.05.

organism: Sus scrofa

label_protocol: GeneChip® IVT Labeling Kit (Affymetrix) protocol:1.Transfer the needed amount of template cDNA (12 μL) to RNase-free microfuge tubes and add Rnase-free Water(8 μL), 10× IVT Labeling Buffer (4 μL), IVT Labeling NTP Mix(12 μL), IVT Labeling Enzyme Mix(4 μL) in the order. 2. Carefully mix the reagents and collect the mixture at the bottom of the tube by brief (5 second) microcentrifugation.3. Incubate at 37°C for 16 hours. To prevent condensation that may result from water bath-style incubators,incubations are best performed in oven incubators for even temperature distribution, or in a thermal cycler.4.Store labeled cRNA at -20°C, or -70°C if not purifying immediately.

growth_protocol: One hour before inoculation, all pigs were given 2 ml of 1% acetic acid (pH 2.9) intranasally to enhance the sensitivity of the S. suis challenge. Two groups were inoculated intranasally with 1ml of 2×106CFU of WT strain or ΔHP0197 respectively, and the rest group inoculated with PBS was served as control

extract_protocol: Spleens from both the treatment group and the control group were snap frozen in liquid nitrogen after collection and stored at –80℃ until RNA extraction. TRIzol (Invitrogen) and RNeasy Mini Kit (QIAGEN) were used for RNA extractions and purifications respectively followed by manufacturer’s instructions. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity(close to 2.0).Integrity of total RNA samples were also checked by Agilent Bioanalyser 2100.

treatment_protocol: Spleen samples were aseptically collected and immediately frozen in liquid nitrogen for future RNA isolation

value: spleen


title: WT group, rep3

description: spleen samples 3 days after WT inoculated,sample 5


title: Macrophages_DD first day_CT16

source_name: peritoneal macrophages, first day after release in DD, CT16

value: male

value: first day CT16


title: Hibernoma case 15

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Genomic DNA extracted from hibernoma biopsies were analyzed for DNA copy number aberrations using Illumina Human Omni-Quad BeadChips (Illumina).

hyb_protocol: Hybridization was done according to the Infinium_HD_Super_Assay_Manual_EUC_EUC_11294817RevA (Human CNV370-Quad v3.0) and Infinium_HD_Assay_Gemini_Manual_EUC11311015RevA (Human1M-Duo v3.0) protocols.

scan_protocol: Scanning was done according to the Infinium_HD_Super_Assay_Manual_EUC_EUC_11294817RevA (Human CNV370-Quad v3.0) and Infinium_HD_Assay_Gemini_Manual_EUC11311015RevA (Human1M-Duo v3.0) protocols.

data_processing: Genomic DNA extracted from hibernoma biopsies was analyzed for DNA copy number aberrations using Illumina Human1M-Duo v3.0 BeadChips (Illumina).

label: unlabeled

source_name: Hibernoma

label_protocol: unlabeled

extract_protocol: DNA was extracted from fresh frozen tumour biopsies using the DNeasy Tissue Kit including the optional RNaseH treatment, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).

value: Female

value: Hibernoma

tag: disease state

value: soft tissue tumour


title: WT group, rep2

description: spleen samples 3 days after WT inoculated,sample 2


title: control group, rep3

description: spleen samples 3 days after mock-infected, sample 3


title: Macrophages_DD second day_CT0

source_name: peritoneal macrophages, second day after release in DD, CT0

value: second day CT0


title: control group, rep2

description: spleen samples 3 days after mock-infected, sample 2


title: control group, rep1

description: spleen samples 3 days after mock-infected, sample 1


title: 211_2

description: treated with CBU-028


title: Macrophages_DD first day_CT12

source_name: peritoneal macrophages, first day after release in DD, CT12

value: first day CT12


title: ΔHP0197 group, rep3

description: spleen samples 3 days after ΔHP0197 inoculated,sample 5


title: Macrophages_DD first day_CT8

source_name: peritoneal macrophages, first day after release in DD, CT8

value: first day CT8


title: Macrophages_DD first day_CT4

source_name: peritoneal macrophages, first day after release in DD, CT4

value: peritoneal macrophage

value: first day CT4


title: Normal blood DNA case 2

description: Genomic DNA extracted from normal blood were analyzed for DNA copy number aberrations using Illumina Human CNV370-Quad v3.0 BeadChips (Illumina). The results were compared to the DNA copy number aberrations found in the corresponding tumour samples, analyzed using the same platform.

hyb_protocol: Hybridization was done according to the Infinium HD Super Assay Manual EUC EUC 11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.

scan_protocol: Scanning was done according to the Infinium HD Super Assay Manual EUC EUC 11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.

source_name: Blood

extract_protocol: DNA was extracted from blood sample using the DNeasy Kit including the optional RNaseH treatment, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).

value: Male

value: Blood

value: normal


title: Normal blood DNA case 1


title: Control_2

description: control

source_name: control


title: Control_1

description: control


title: Hibernoma case 6 (CNV370-Quad)

description: Genomic DNA extracted from hibernoma biopsies were analyzed for DNA copy number aberrations using Illumina Human CNV370-Quad v3.0 BeadChips (Illumina).


title: Macrophages_DD first day_CT0

source_name: peritoneal macrophages, first day after release in DD, CT0

value: first day CT0


title: Hibernoma case 4 (CNV370-Quad)


title: Hibernoma case 2 (CNV370-Quad)


title: ΔHP0197 group, rep1

description: spleen samples 3 days after ΔHP0197 inoculated,sample 2


title: ΔHP0197 group, rep2

description: spleen samples 3 days after ΔHP0197 inoculated,sample 4


title: Eer1_1

description: treated with Eer1


title: HepG2 cells_GW7647_24h_rep1

status: Public on Nov 23 2010

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using RMA in Bioconductor.

source_name: HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 24h

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted from HepG2 cells with TRIzol reagent (Invitrogen) and subsequently purified using the SV Total RNA Isolation System (Promega). RNA quality was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies) using 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only when samples showed intact bands corresponding to the 18S and 28S rRNA subunits, displayed no chromosomal peaks or RNA degradation products and had a RNA integrity number (RIN) above 8.0. Five micrograms of RNA were used for one cycle cRNA synthesis (Affymetrix).

treatment_protocol: The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells were harvested for RNA isolation after 6 or 24 hours of incubation with GW7647.

value: hepatoma

value: PPARα agonist GW7647

tag: treatment duration

value: 24 hr


title: HepG2 cells_GW7647_24h_rep2


title: HepG2 cells_GW7647_24h_rep3


title: HepG2 cells_GW7647_6h_rep3

source_name: HepG2 cells treated with PPARα agonist GW7647 at 100 nM for 6h

value: 6 hr


title: Normal blood DNA case 6

tag: tissue


title: HepG2 cells_GW7647_6h_rep1


title: HepG2 cells_GW7647_6h_rep2


title: HepG2 cells_control_rep3

source_name: HepG2 cells treated with vehicle (DMSO)

value: DMSO vehicle


title: HepG2 cells_control_rep1


title: HepG2 cells_control_rep2


title: HAZLAZ_32

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description: Total RNA

hyb_protocol: As per Affymetrix's recommendations

scan_protocol: As per Affymetrix's recommendations

data_processing: RMA signal condensation performed. The RMA was done using justRMA() from bioconductor in R-2.9.2.

source_name: Primary biopsy

label_protocol: As per Affymetrix's recommendations

extract_protocol: Trizol

value: testicular biopsies with cryptorchidism


title: HAZLAZ_30

description: Total RNA


title: HAZLAZ_21

description: Total RNA


title: Hibernoma case 12

description: Genomic DNA extracted from hibernoma biopsies were analyzed for DNA copy number aberrations using Illumina Human1M-Duo v3.0 BeadChips (Illumina).

hyb_protocol: Hybridization was done according to the Infinium HD Super Assay Manual EUC EUC11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.

scan_protocol: Scanning was done according to the Infinium HD Super Assay Manual EUC EUC11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.

tag: gender

value: Hibernoma


title: Control_27

description: Total RNA

value: contralateral descended testes


title: Control_25

description: Total RNA


title: Control_24

description: Total RNA


title: HAZLAZ_29

description: Total RNA


title: Hibernoma case 1 (CNV370-Quad)

value: Female

value: soft tissue tumour


title: Hibernoma case 10


title: Normal blood DNA case 4


title: Hibernoma case 14


title: Control_26

description: Total RNA


title: HAZLAZ_09

description: Total RNA


title: HAZLAZ_04

description: Total RNA


title: HAZLAZ_08

description: Total RNA


title: HAZLAZ_07

description: Total RNA


title: HAZLAZ_11

description: Total RNA


title: HAZLAZ_03

description: Total RNA


title: anti-Sall1_ChIP

city: Heraklion

first: Androniki

last: Kretsovali

state: Crete

address: Plastira 100

department: Institute of Molecular Biology & Biotechnology

country: Greece

institute: Foundation of Research & Technology

description:
anti_Sall1 Chip Biol. Rep 1-2, promoter. anti-Sall1 ChIP DNA vs. INPUT DNA; anti_Fras Chip DNA.
Non-commercial antibodies.
Anti-Sall1 and anti-Nanog were prepared by us and anti-Fras was offered by Prof. G.Chalepakis.
Antibody details:
1. anti-Sall1 antiserum was prepared by rabbits immunization with a bacterially produced His-Sall1 (aa 1-702).
2. anti-Nanog antiserum was prepared by rabbits immunization with a bacterially produced full length His-Nanog protein.
3.anti-Fras antiserum was kindly provided by Prof. G.Chalepakis (Vrontou et al, Nature Genetics 34, 209 - 214,2003) and was produced following rabbit immunization with a bacterially overexpressed peptide corresponding to amino acids 1,212-1,525 of Fras1.

hyb_protocol: Approximately 7.5μg of DNA were hybridized using the GeneChip® Hybridization,Wash, and Stain Kit (P/N 900720). Arrays were hybridized for 16 hours at 45° at 60rpm.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
Data were analyzed using the MAT software.
Results file description: Bar files were generated using the MAT software. Each bar file is an average of the biological replicates, normalized to INPUT.

source_name: anti-Sall1 ChIP DNA from mouse embryonic stem cells

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the GeneChip® Hybridization,Wash, and Stain Kit (P/N 900720) to add biotinylated compound to the ends of the fragments

growth_protocol: Mouse embryonic stem cells were grown in GMEM (10% serum, 1000units LIF)

extract_protocol: DNA was extracted according to Affymetrix protocol

value: embryo (ICM)

tag: strain

value: male

tag: antibody

source_name: INPUT DNA from mouse embryonic stem cells; anti_Fras Chip DNA from mouse embryonic stem cells


title: HAZLAZ_05

description: Total RNA


title: HAZLAZ_12

description: Total RNA


title: HAZLAZ_18

description: Total RNA


title: HAZLAZ_02

description: Total RNA


title: Hibernoma case 9


title: anti-Fras_ChIP

description:
anti_Fras Chip Biol. Rep. 1, promoter. anti-Fras ChIP DNA vs. INPUT DNA
Non-commercial antibodies.
Anti-Sall1 and anti-Nanog were prepared by us and anti-Fras was offered by Prof. G.Chalepakis.
Antibody details:
1. anti-Sall1 antiserum was prepared by rabbits immunization with a bacterially produced His-Sall1 (aa 1-702).
2. anti-Nanog antiserum was prepared by rabbits immunization with a bacterially produced full length His-Nanog protein.
3.anti-Fras antiserum was kindly provided by Prof. G.Chalepakis (Vrontou et al, Nature Genetics 34, 209 - 214,2003) and was produced following rabbit immunization with a bacterially overexpressed peptide corresponding to amino acids 1,212-1,525 of Fras1.

source_name: anti-Fras ChIP DNA from mouse embryonic stem cells

tag: cell line

source_name: INPUT DNA from mouse embryonic stem cells


title: HAZLAZ_17

description: Total RNA


title: Hibernoma case 11


title: anti-Nanog_ChIP

description:
anti_Nanog Chip Biol. Rep 1-2, promoter. anti-Nanog ChIP DNA vs. INPUT DNA; anti_Fras Chip DNA.
Non-commercial antibodies.
Anti-Sall1 and anti-Nanog were prepared by us and anti-Fras was offered by Prof. G.Chalepakis.
Antibody details:
1. anti-Sall1 antiserum was prepared by rabbits immunization with a bacterially produced His-Sall1 (aa 1-702).
2. anti-Nanog antiserum was prepared by rabbits immunization with a bacterially produced full length His-Nanog protein.
3.anti-Fras antiserum was kindly provided by Prof. G.Chalepakis (Vrontou et al, Nature Genetics 34, 209 - 214,2003) and was produced following rabbit immunization with a bacterially overexpressed peptide corresponding to amino acids 1,212-1,525 of Fras1.

source_name: anti-Nanog ChIP DNA from mouse embryonic stem cells


title: HAZLAZ_10

description: Total RNA


title: Hibernoma case 13

source_name: Hibernoma


title: CD16 Stimulated

city: Tyler

first: Rohan

last: Dhiman

state: Texas

department: Centre for Pulmonary and Infectious Disease Control

institute: University of Texas Health Science Center at Tyler

data_processing: See http://www.phalanxbiotech.com/ for updated protocols and additional information

source_name: stimulated CD14loCD16+ monocytes from peripheral human blood

growth_protocol: CD14loCD16+ monocytes were isolated from human peripheral blood using magnetic beads for CD16. 1.5 million cells were cultured in 1 ml of complete RPMI medium with 10% human serum.

extract_protocol: After 48 hours stimulated or control CD14loCD16+ monocytes were harvested and RNA was isolated using Trizol (Invitrogen) acc. to manufacturer's protocol.

treatment_protocol: Stimulated with 10 microgram/ml of gamma-M. tuberculosis for 48 hours.

value: CD14loCD16+ monocytes isolated from peripheral human blood by CD16 microbeads


title: HAZLAZ_16

description: Total RNA


title: Hibernoma case 8


title: Hibernoma case 6

value: Male


title: CD14 Stimulated

hyb_protocol: See http://www.phalanxbiotech.com/ for updated protocols

source_name: stimulated CD14hiCD16- monocytes from peripheral human bloood

growth_protocol: CD14hiCD16- monocytes were isolated from human peripheral blood using magnetic beads for CD14. 1.5 million cells were cultured for in 1 ml of complete RPMI medium with 10% human serum.

extract_protocol: After 48 hours stimulated or control CD14hiCD16- monocytes were harvested and RNA was isolated using Trizol (Invitrogen) acc. to manufacturer's protocol.

value: CD14hiCD16- monocytes isolated from peripheral human blood by CD14 microbeads


title: Hibernoma case 5

scan_protocol: Scanning was according to the Infinium HD Super Assay Manual EUC EUC11294817 Rev A (Human CNV370-Quad v3.0) and Infinium HD Assay Gemini Manual EUC11311015 Rev A (Human1M-Duo v3.0) protocols.


title: CD14 Control

scan_protocol: See http://www.phalanxbiotech.com/ for updated protocols

source_name: unstimulated CD14hiCD16- monocytes from peripheral human bloood

treatment_protocol: untreated


title: HAZLAZ_06

description: Total RNA


title: Hibernoma case 4


title: Hibernoma case 7


title: TB pool vs NID whole blood 2

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

institute: MPIIB

description: TB pooled whole blood RNA vs NID whole blood RNA

hyb_protocol: Quantity and labelling efficiency were verified before hybridization of the samples to whole-genome oligonucleotide microarray (Agilent Technologies)

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Raw microarray data were processed using the function read.maimages of the Bioconductor R package limma30 and intensities of the spots not flagged out  were background corrected using the method norm-exp. Background-corrected values were lowess normalized to obtain as unbiased red/green ratios as possible. For global comparability, the data of all arrays were quantile normalized

source_name: TB

label_protocol: Total RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was isolated from 2,5 ml of peripheral whole blood collected in PAXgene tubes, using the PAXgene Blood RNA Kit (PreAnalystics, Europe BD, Belgium).

tag: group

value: tuberculosis patients

value: Whole blood

source_name: NID

value: healthy non-infected donors


title: TB pool vs NID whole blood 4


title: NID whole blood vs TB pool 1

description: NID whole blood RNA vs TB pooled whole blood RNA


title: NID whole blood vs LTBI pool 2

description: NID whole blood RNA vs LTBI pooled whole blood RNA

source_name: LTBI

value: healthy donors latently infected with M. tuberculosis


title: LTBI vs TB whole blood 15

description: LTBI vs TB whole blood RNA


title: LTBI pool vs NID whole blood 2

description: LTBI pooled whole blood RNA vs NID whole blood RNA


title: Hibernoma case 1


title: NID whole blood vs LTBI pool 1


title: NID whole blood vs TB pool 2


title: NID whole blood vs LTBI pool 4


title: TB pool vs NID whole blood 3


title: TB pool vs NID whole blood 1


title: LTBI vs TB whole blood 8

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 10

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 13

description: LTBI vs TB whole blood RNA


title: LTBI pool vs NID whole blood 3


title: LTBI pool vs NID whole blood 1


title: LTBI vs TB whole blood 18

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 14

description: LTBI vs TB whole blood RNA


title: NID whole blood vs LTBI pool 3


title: LTBI vs TB whole blood 12

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 16

description: LTBI vs TB whole blood RNA


title: Hibernoma case 3


title: LTBI vs TB whole blood 19

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 11

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 17

description: LTBI vs TB whole blood RNA


title: HAZLAZ_01

description: Total RNA


title: Hibernoma case 2


title: LTBI vs TB whole blood 9

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 5

description: LTBI vs TB whole blood RNA


title: TB vs LTBI whole blood 17

description: TB vs LTBI whole blood RNA


title: LTBI vs TB whole blood 3

description: LTBI vs TB whole blood RNA


title: LTBI vs TB whole blood 2

description: LTBI vs TB whole blood RNA


title: TB vs LTBI whole blood 11

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 13

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 15

description: TB vs LTBI whole blood RNA


title: LTBI vs TB whole blood 6

description: LTBI vs TB whole blood RNA


title: TB vs LTBI whole blood 12

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 19

description: TB vs LTBI whole blood RNA


title: DRG axon from an adult rat, biological replicate 4

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

hyb_protocol: The cRNAs were fragmented and hybridized onto Rat Genome 230 2.0 Arrays at 45 degree Celcius for 16 h.  Followed by wash and stain in Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned with Affymetrix GCS 3000 7G scanner

data_processing: Data analyzed using Agilent Genespring GX v7.3 with RMA

label: Biotin

organism: Rattus norvegicus

source_name: axons excised from DRG neurons from an adult animal

label_protocol: Biotinylated cRNAs were generated using Affymetrix GeneChip IVT Labeling Kit following manufacturer's instruction

growth_protocol: DRG explants were cultured in a compartmentalised chamber for 4 days and the axons (>1 cm in length) were isolated in the outer compartment of the chamber

extract_protocol: Axonal RNAs were extracted using Trizol (Invitrogen) according to manufacturer's instruction

value: DRG Neurons

tag: developmental stage

value: adult


title: TB vs LTBI whole blood 18

description: TB vs LTBI whole blood RNA


title: LTBI vs TB whole blood 7

description: LTBI vs TB whole blood RNA


title: TB vs LTBI whole blood 14

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 16

description: TB vs LTBI whole blood RNA


title: CD16 Control

source_name: unstimulated CD14loCD16+ monocytes from peripheral human blood

label_protocol: See http://www.phalanxbiotech.com/ for updated protocols


title: DRG axon from an adult rat, biological replicate 5


title: DRG axon from an adult rat, biological replicate 3


title: LTBI vs TB whole blood 1

description: LTBI vs TB whole blood RNA


title: TB vs LTBI whole blood 9

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 8

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 7

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 10

description: TB vs LTBI whole blood RNA


title: LTBI vs TB whole blood 4

description: LTBI vs TB whole blood RNA


title: xenopus_stage_32_growth_cones_3

description: localized mRNA from the growth cones of retinal ganglion cells from stage 32 embryo

hyb_protocol: 15ug of biotin-labelled RNA were hybridized onto Xenopus Laevis or Mouse 430 2.0 arrays for 16 h at 45C.  Followed by washing and staining using Affymetrix Fluidics Station FS450 according to manufacturing instructions

scan_protocol: The arrays were scanned by Affymetrix GeneChip Scanner 3000 7G using AGCC Software 2.0

data_processing: The arrays were normalized by robust multiarray average (RMA) using Affymetrix Expression Console software.

organism: Xenopus laevis

source_name: Growth cones of retinal ganglion cells from stage 32 embryo

label_protocol: aRNA were biotin-labelled using GeneChip IVT labeling kit (Affymetrix)

growth_protocol: Whole eye primordia from stage 24 and 32 Xenopus embryos were cultured on polyethylene terephthalate membrane slides for 17h and 20 h respectively.  Mouse retinal explants were obtained from E15 embryos and were cultured for 24 h

extract_protocol: Total RNA were extracted from laser capture microdissected samples using RNAqueous Microkit (Ambion)  and were amplified using the two-cycle TargetAmp kit (Epicentre)

value: retinal ganglion


title: xenopus_stage_32_growth_cones_4

value: growth cones of retinal ganglion cells from stage 32 embryo


title: mouse_growth_cones_4

description: localized mRNA from the axons of retinal ganglion cells

source_name: Axons of retinal ganglion cells

value: axons of retinal ganglion cells


title: mouse_growth_cones_5


title: mouse_growth_cones_3


title: xenopus_stage_32_growth_cones_1


title: mouse_growth_cones_1


title: DRG axon from an E16 rat embryo, biological replicate 5

source_name: axons excised from DRG neurons from an E16 embryo

value: E16 embryo


title: xenopus_axons_4


title: xenopus_stage_32_growth_cones_2


title: TB vs LTBI whole blood 2

description: TB vs LTBI whole blood RNA


title: TB vs LTBI whole blood 6

description: TB vs LTBI whole blood RNA


title: DRG axon from an E16 rat embryo, biological replicate 4


title: xenopus_stage_24_growth_cones_3

description: localized mRNA from the growth cones of retinal ganglion cells from stage 24 embryo

source_name: Growth cones of retinal ganglion cells from stage 24 embryo


title: DRG axon from an adult rat, biological replicate 2


title: TB vs LTBI whole blood 1

description: TB vs LTBI whole blood RNA


title: mouse_growth_cones_2


title: TB vs LTBI whole blood 5

description: TB vs LTBI whole blood RNA


title: xenopus_stage_24_growth_cones_4

value: growth cones of retinal ganglion cells from stage 24 embryo


title: DRG axon from an E16 rat embryo, biological replicate 2


title: DRG axon from an adult rat, biological replicate 1


title: TB vs LTBI whole blood 3

description: TB vs LTBI whole blood RNA


title: xenopus_stage_24_growth_cones_5


title: xenopus_axons_5


title: TB vs LTBI whole blood 4

description: TB vs LTBI whole blood RNA


title: xenopus_stage_24_growth_cones_2


title: DRG axon from an E16 rat embryo, biological replicate 1


title: xenopus_stage_24_growth_cones_1


title: DRG axon from an E16 rat embryo, biological replicate 3


title: xenopus_axons_3


title: HNSCC cell - GFP si vs p63 si - 48h - rep1

city: Boston

first: benjamin

middle: robert

last: ory

address: 55 fruit street

institute: Mas General Hospital Cancer Center

description:
supplementary_file_ch1:1_Exiqon_13889286_S01_Cropped.txt
supplementary_file_ch2:0_Exiqon_13889289_S01_Cropped.txt
After having passed sample quality control on the Bioanalyser2100, the samples were labelled using the miRCURY™ Hy3™/Hy5™ power labelling kit and hybridized on the miRCURY™ LNA Array (v.10.0) (Exiqon). Spike-in controls were added in various concentrations covering the full signal range, in both Hy3 and Hy5 labelling reactions giving the opportunity to evaluate the labelling reaction, hybridization and the performance of the array experiment in general.

hyb_protocol: Using Tecan hybridization stations the hybridization and washing steps are fully automated for excellent reproducibility

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.

data_processing:
The data obtained is normalized using methods applicable to the performed experiment. The project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA).
The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. The data only represent the microRNAs that passed the filtering criteria across samples; Fold Change > 1.50.
normalised Hy3/Hy5 ratios (log2 transformed) from all 2 hybridizations. The ratios are tranferred from the excel-sheets named Slide-x.xls, and shown is the median of replicated measurements of the same miRNA from each slide

source_name: head and neck squamous cell carcinoma cell line

label_protocol: miRCURY™ LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias.

growth_protocol: RPMI FBS 10%

extract_protocol: For each sample, 2μg of Trizol extracted total RNA were purified using the RNeasy Mini Cleanup Kit (Qiagen) following manufacturer's instructions

treatment_protocol: p63-directed or control lentiviral shRNA for 48h

value: human head and neck squamous cell carcinoma

tag: treatment

value: 48h lentiviral shRNA against GFP

value: 48h lentiviral shRNA against p63


title: xenopus_axons_2


title: xenopus_axons_1


title: infected vs uninfected late time point 1

status: Public on Nov 22 2010

city: Pretoria

first: Dave

middle: K

state: Gauteng

address: Room 6-26, Agricultural Sciences Building, University of Pretoria, Lunnon Rd

department: Plant Science, Forestry & Agricultural Biotech. Instit. (FABI)

country: South Africa

institute: University of Pretoria

hyb_protocol: Probes were prepared by combining selected Cy3 and Cy5 labelled samples, which were then dried in a vacuum desiccator, and resuspended in 45 µl hybridisation buffer [50% formamide, 25% hybridisation buffer (Amersham Biosciences), 25% deionised water].  Probes were denatured at 92ºC for 5 min.The glass slide was initially incubated in pretreatment solution (3.5X SSC; 0.2% SDS; 1% bovine serum albumin) without probe at 60ºC for 20 min.  Thereafter, the slide was placed in a HybUP hybridisation chamber (NB Engineering, Pretoria, South Africa) with the denatured probe solution at 42ºC for 16 h.  After hybridisation, slides were washed for 4 min at 42ºC with 1 X SSC/0.2% SDS, 0.1 X SSC/0.2% SDS (twice) followed by three washes in 0.1 X SSC for 1 min at room temperature.  Slides were rinsed with distilled water, and dried by centrifugation (2000Xg for 2 min).

scan_protocol: Washed slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA).  Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: Scanned images (tiff images) were imported into GenePix Pro 5.0 (Axon Instruments), and fluorescence intensity in both red (CyanineTM-5 dye) and green (CyanineTM-3 dye) channels for each spot was quantified.  Grids were predefined and manually adjusted to ensure optimal spot recognition, and spots with dust or locally high background were flagged as bad.  Fluorescence data from a total of 12 slides were imported into limmaGUI (linear models for microarray data Graphical User Interface) (Wettenhall and Smyth, 2004) in the R computing environment where data was normalised (within array global loess normalisation and between array quantile normalisation), and linear models were fitted in order to contrast post treatment expression values with the non-treated sample (time = 0 h). Differentially expressed genes for each treatment were defined as those with a fold-change (expression ratio) greater than or equal to two between a particular time point and t=0, and were significant at P ≤ 0.05 (moderated t test as implemented in limmaGUI with Bonferonni correction for multiple testing (Wettenhall and Smyth 2004).

organism: Arabidopsis thaliana

source_name: Uninfected leaf, wilt symptom 3-4

label_protocol: 500ng mRNA was used per labelling reaction using the Amersham indirect labeling kit according to manufacturer's protocol. The samples were purified using the Qiagen PCR purification kit.

growth_protocol: Arabidopsis Col-5 seeds were sterilised in 1.5% sodium hypochlorite and 70% ethanol and germinated on MS media for two weeks before planting into Jiffy pots. Plants were maintained in control conditions and grown for four weeks under 16hr light, 25-26 deg C, 50% relative humidity and 300-350lum/sqf. Plants were watered with Feedall fertiliser once a week.

extract_protocol: Total RNA was isolated from leaves using TriReagent (Sigma, Aldrich) according to the manufacturer's instructions.  mRNA was isolated using the OligoTex mRNA isolation Kit (Qiagen).

treatment_protocol: Infections were preformed according to Deslandes et al. 1998. Jiffy pots were cut in half to expose the roots and soaked in a 1E08 cfu/ml of R. solanacearum BCCF401. Control plants were treated with media only. Plants were maintained on vermiculite and disease symproms post inoculation were recorded.

tag: infection

tag: ecotype

source_name: Infected leaf, wilt symptom 3-4

value: Ralstonia solanacearum isolate BCCF401


title: infected vs uninfected early time point 1, dye swap

source_name: Uninfected leaf, wilt symptom 1-2

source_name: Infected leaf, wilt symptom 1-2


title: infected vs uninfected late time point 2


title: infected vs uninfected late time point 1, dye swap


title: infected vs uninfected early time point 2


title: infected vs uninfected early time point 2, dye swap


title: CD8 KLF13 WT 2

first: Dazhi

last: Lai

address: 10 Center Dr, 7B20A

department: NHLBI

institute: NIH

hyb_protocol: Four replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse Gene ST 1.0 GeneChip

scan_protocol: scanned on Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix GCOS software.

data_processing: Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that are up- or down-regulated more than 2 fold and with a p<0.001 were considered significant.  Significant genes were analyzed for enrichment for pathways using DAVID bioinformatics database (http://david.abcc.ncifcrf.gov/) and Ingenuity Pathway Analysis software.

source_name: CD8 KLF13 WT

label_protocol: 200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer's protocol.

extract_protocol: Total RNA was isolated with RNAeasy kit from Qiagen RNeasy. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

value: BALB/c

tag: cell type

value: CD8 T

tag: genotype/variation

value: wild type


title: CD8 KLF13 WT 1


title: EYE, replicate 1

city: Naples

first: Marianthi

last: Karali

address: Via Pietro Castellino, 111

country: Italy

institute: Telethon Institute for Genetics & Medicine (TIGEM)

description:
(9) (EYE 1)
Slide 9
present call rate per slide: 0.596314907872697
Hy3 raw: 1_Exiqon_13973499_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973499_S01_Cropped.txt

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing:
The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Project_Summary Report version 3.5 results presented in Sample data tables.
When calling of a particular miRNA failed on an array this is indicated by the acronym null. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 3 or more of the 4 replicated measures of this miRNA were flagged (i.e. the signal is below background) by the image analysis software. Further, all capture probes with Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide is indicated by the acronym null.

source_name: Total RNA from entire eyeballs from adult mice

label_protocol: One µg total RNA from sample and reference (Eye sample) was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: not applicable

extract_protocol: Total RNA extracted with the miRNeasy kit (Qiagen)

treatment_protocol: not applicable

value: Entire Eyeball


title: RPE , replicate 2

description:
(8) (RPE 2)
Slide 8
present call rate per slide: 0.634840871021776
Hy3 raw: 1_Exiqon_13973498_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973498_S01_Cropped.txt

source_name: Total RNA from RPE of adult mice (RPE 2)

value: Retinal Pigment Epithelium