title: slr1738 null mutant cadmium (CdSO4 50 (M 180 min), replicate 1

source_name: (Slr1738 mutant treated 180 min with CdSO4 50 (M

tag: wild type strain treated 180 min with CdSO4 50 (M


title: Synechocystis cells grown in an iron depleted medium (1-0.5 (M) 96h , replicate 2

status: Public on Dec 07 2005

type: RNA

city: Gif sur yvette CEDEX

first: Franck

last: Chauvat

department: DSV/DBJC

country: France

institute: CEA Saclay

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

data_processing: After background correction and removal of flagged values, expression ratios were normalised using LOWESS method (Genespring software) to obtain values given in the data table.

molecule: total RNA

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis cells grown in an standard medium (iron 17 (M) 96h

label_protocol: The cDNA from treated and untreated cells RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 4 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 30 µl of buffer containing 21% formamide, 0.2% DSD, 1x denhardt's, 7x SSPE, and 10 µg each of mouse Cot1 DNA, yeast tRNA and polydeoxyadenylic acid (to limit non-specific hybridization) for hybridization to the microarray.

growth_protocol: For iron depletion, cells were grown in iron depleted medium (Fe concentration ______or_________during 2 rounds of 48h growth. 300 ml of mid-log phase liquid culture (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation, rapidly harvested and disrupted.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 µg) was annealed with 2 µg of random hexanucleotide primers and 0.5 ng of Human TFR mRNA (Takara) used as external control. Then, the reverse-transcription into cDNA was done with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.1 mM dTTP, 0.4 mM amino-allyl dUTP. After hydrolysis of RNA with 3 U of RNAse H (Amersham Pharmacia), cDNA was purified with a Microcon-30 concentrator.


title: pleC_deletion-rep1

status: Public on Dec 08 2005

city: Princeton

first: Alison

last: Hottes

state: NJ

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

country: USA

institute: Princeton University

description: Sample compares mRNA expression between LS3032 (CB15 wild-type) and the same strain with a deletion of the pleC histidine kinase.

scan_protocol: Images were collected for both Cy3 (CH2) and Cy5 (CH1) with a GenePix 4000B scanner.  Image intensity data were extracted using GenePix Pro 4.0 software.

data_processing: Data was filtered and normalized as described in PMID 14973021.

organism: Caulobacter vibrioides

label_protocol: RNA was directly labeled for microarray hybridization by reverse transcription. 20 µg RNA and 3 µg random hexamer primers (Invitrogen) in a total volume of 15 µl was heated to 65ºC for 10 minutes and cooled on ice.  Next, the sample was brought to a final volume of 30 µl with the following final concentrations: 10 mM DTT, 1 x Superscript RT buffer, 0.5 mM each of ATP, GTP, TTP, 0.2 mM CTP, 400U Superscript II reverse transcriptase (Invitrogen) and 0.1mM of Cy5-dCTP (Amersham). The reaction was incubated at room temperature for 10 minutes and then at 42ºC for 2 hours. After reverse transcription, the RNA was degraded by addition of 1.5µl of 1N NaOH and incubation at 65ºC for 10 minutes; the reaction was neutralized immediately by adding 1.5 µl 1N HCl. The cDNA from the two samples to be compared were combined and purified using Qiagen's PCR purification Kit.  Samples were eluted in EB buffer and were concentrated to less than 5 µl using Microcon-30 columns (Millipore). Sample volume was then brought up to 5 µl using EB.  A hybridization mixture containing the labeled cDNAs, 20 µg yeast tRNA, 5x SSC, 0.1% SDS and 30% formamide in a final volume of 15µl was incubated for 1 minute at 100ºC.  After allowing the sample to cool to 42ºC for 1 minute, 12 µl of the mixture was placed on a 22x22mm coverslip and the microarray slide was placed on the coverslip.  Then, 12 µl of drops of 3X SSC were placed at the edges of the slide.  The slide was quickly put into a sealed hybridization chamber, which was placed in a 44ºC water bath overnight. Prior to use, slides were blocked by shaking sequentially in 0.2% SDS (2 minutes, 2 times), distilled water (2 minutes, 2 times), aldehyde blocking solution (0.75 g sodium borohydride, 225 ml 1X PBS, 75 ml 95% ethanol, 15 minutes), 0.2% SDS (2 minutes, 2 times), and water (2 minutes, 2 times) and then dried by spinning at 1000 rpm for 2 minutes in a Sorvall Legend RT tabletop centrifuge.  Arrays were washed for 10 minutes at 37ºC in 2X SSC, 0.2% SDS, followed by a 10 minute wash in 2x SCC and a 10 minute wash in 0.2x SSC, both at room temperature. Slides were then dried by spinning at 1000 rpm in a Sorvall Legend RT tabletop centrifuge for 2 minutes at room temperature.

extract_protocol: For RNA extraction, ~7.5 ml of cell culture was pelleted by centrifugation for 1 minute in a microfuge at 14,500 g. (Each 7.5 ml sample was split among five 2 ml tubes.) After removing the supernatant, 150 µl of Trizol (Invitrogen) was added to each pellet.  The five parts of each sample were combined into a single tube and incubated for 10 minutes at 65ºC to lyse the cells.  Next, 200 µl of chloroform was added, and samples were mixed vigorously and incubated at room temperature for 5 minutes. Phases were then separated by centrifugation (15 minutes, 4ºC, 14,500 g) and the aqueous phase, containing the RNA, was transferred to a new tube.  RNA was precipitated with 0.5 ml of isopropanol at -80ºC for at least one hour, pelleted (30 minutes, 4ºC, 14,500 g), washed with -20°C 70% ethanol, and resuspended in 50 µl Nuclease free water (Ambion). To digest DNA in the sample, we added 2 µl DNase I (Ambion, 2 U/ul) and 5 µl 10X DNase I buffer and incubated at 37°C for two hours.  RNA was isolated using an acid phenol extraction.  Specifically, 150 µl DEPC-treated water and 200 µl acid phenol chloroform (5:1, pH 4.5, Ambion) were added and the mixture was vortexed vigorously.  Then, samples were spun at 14,500 g at 4°C for 10 minutes to separate the phases.  The aqueous (upper) phase was transfered to a new tube.   RNA was precipitated by adding 20 µl 3 M sodium acetate (pH 5.2) and 500 µl -20°C ethanol and freezing overnight at -80°C.  RNA was then pelleted by centrifugation (10 minutes, 4°C,  14,500 g).  Pellets were washed in 1 ml 70% ethanol, spun for 5 minutes at 4°C at 14,500 g.  Supernatant was poured out, samples were spun for 30 seconds at 14,500 g at room temperature, and the residual ethanol was removed with a pipet.  Samples were air dried for ~10 minutes and then were suspended in 20 µl Nuclease-free water (Ambion). To aid in dissolving the RNA, samples were kept at room temperature for 30 minutes or for 4 hours at 4°C.  RNA was stored at -80°C.  RNA quality was visualized on agarose gels and concentration was measured using a spectrophotometer.

tag: Asynchronous exponential phase culture of CB15 (LS3032) grown in PYE at 30°C to OD600 = 0.2526.

source_name: LS3767 (CB15 del pleC)

label_protocol: RNA was directly labeled for microarray hybridization by reverse transcription. 20 µg RNA and 3 µg random hexamer primers (Invitrogen) in a total volume of 15 µl were heated to 65ºC for 10 minutes and cooled on ice.  Next, the sample was brought to a final volume of 30 µl with the following final concentrations: 10 mM DTT, 1 x Superscript RT buffer, 0.5 mM each of ATP, GTP, TTP, 0.2 mM CTP, 400 U Superscript II reverse transcriptase (Invitrogen) and 0.1 mM of Cy3-dCTP (Amersham). The reaction was incubated at room temperature for 10 minutes and then at 42ºC for 2 hours. After reverse transcription, the RNA was degraded by addition of 1.5 µl of 1 N NaOH and incubation at 65ºC for 10 minutes; the reaction was neutralized immediately by adding 1.5 µl 1 N HCl. The cDNA from the two samples to be compared were combined and purified using Qiagen's PCR purification Kit.  Samples were eluted in EB buffer and were concentrated to less than 5 µl using Microcon-30 columns (Millipore). Sample volume was then brought up to 5 µl using EB.  A hybridization mixture containing the labeled cDNAs, 20 µg yeast tRNA, 5x SSC, 0.1% SDS and 30% formamide in a final volume of 15 µl was incubated for 1 minute at 100ºC.  After allowing the sample to cool to 42ºC for 1 minute, 12 µl of the mixture was placed on a 22x22mm coverslip and the microarray slide was placed on the coverslip.  Then, 12 µl of drops of 3X SSC were placed at the edges of the slide.  The slide was quickly put into a sealed hybridization chamber, which was placed in a 44ºC water bath overnight. Prior to use, slides were blocked by shaking sequentially in 0.2% SDS (2 minutes, 2 times), distilled water (2 minutes, 2 times), aldehyde blocking solution (0.75 g sodium borohydride, 225 ml 1X PBS, 75 ml 95% ethanol, 15 minutes), 0.2% SDS (2 minutes, 2 times), and water (2 minutes, 2 times) and then dried by spinning at 1000 rpm for 2 minutes in a Sorvall Legend RT tabletop centrifuge.  Arrays were washed for 10 minutes at 37ºC in 2X SSC, 0.2% SDS, followed by a 10 minute wash in 2x SCC and a 10 minute wash in 0.2x SSC, both at room temperature. Slides were then dried by spinning at 1000 rpm in a Sorvall Legend RT tabletop centrifuge for 2 minutes at room temperature.

extract_protocol: For RNA extraction, ~7.5 ml of cell culture was pelleted by centrifugation for 1 minute in a microfuge at 14,500 g. (Each 7.5 ml sample was split among five 2 ml tubes.) After removing the supernatant, 150 µl of Trizol (Invitrogen) was added to each pellet.  The five parts of each sample were combined into a single tube and incubated for 10 minutes at 65ºC to lyse the cells.  Next, 200 µl of chloroform was added, and samples were mixed vigorously and incubated at room temperature for 5 minutes. Phases were then separated by centrifugation (15 minutes, 4ºC, 14,500 g) and the aqueous phase, containing the RNA, was transferred to a new tube.  RNA was precipitated with 0.5 ml of isopropanol at -80ºC for at least one hour, pelleted (30 minutes, 4ºC, 14,500 g), washed with -20°C 70% ethanol, and resuspended in 50 µl Nuclease free water (Ambion). To digest DNA in the sample, we added 2ul DNase I (Ambion, 2U/ul) and 5 µl 10X DNase I buffer and incubated at 37°C for two hours.  RNA was isolated using an acid phenol extraction.  Specifically, 150 µl DEPC-treated water and 200 µl acid phenol chloroform (5:1, pH 4.5, Ambion) were added and the mixture was vortexed vigorously.  Then, samples were spun at 14,500 g at 4°C for 10 minutes to separate the phases.  The aqueous (upper) phase was transfered to a new tube.   RNA was precipitated by adding 20ul 3M sodium acetate (pH 5.2) and 500 µl -20°C ethanol and freezing overnight at -80°C.  RNA was then pelleted by centrifugation (10 minutes, 4°C,  14,500 g).   Pellets were washed in 1 ml 70% ethanol, spun for 5 minutes at 4°C at 14,500 g.  Supernatant was poured out, samples were spun for 30 seconds at 14,500 g at room temperature, and the residual ethanol was removed with a pipet.  Samples were air dried for ~10 minutes and then were suspended in 20 µl Nuclease-free water (Ambion). To aid in dissolving the RNA, samples were kept at room temperature for 30 minutes or for 4 hours at 4°C.  RNA was stored at -80°C.  RNA quality was visualized on agarose gels and concentration was measured using a spectrophotometer.

tag: Asynchronous exponential phase culture of LS3767 (CB15 del pleC) grown in PYE at 30°C to OD600 = 0.269.


title: Synechocystis cells grown in an iron depleted medium (2-0.5 (M) 96h , replicate 1

tag: Synechocystis cells grown in an standard medium (iron 17 (M) 96h


title: Synechocystis cells treated 360 min with iron 17 mM (ferric ammonium citrate,), replicate 2

description: Synechocystis cells treated 360 min with iron 17 mM (ferric ammonium citrate)

source_name: Synechocystis cells treated 360 min with iron 17 (M (ferric ammonium citrate)

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 360 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: Synechocystis cells grown in an iron depleted medium (1-0.5 (M) 96h , replicate 1


title: Synechocystis cells grown in an iron depleted medium (2-0.5 (M) 96h , replicate 2


title: Synechocystis cells treated 240 min with iron 17 mM (ferric ammonium citrate,), replicate 2

description: Synechocystis cells treated 240 min with iron 17 mM (ferric ammonium citrate)

source_name: Synechocystis cells treated 240 min with iron 17 (M (ferric ammonium citrate)

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 240 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: Synechocystis cells treated 360 min with iron 17 mM (ferric ammonium citrate,), replicate 1

source_name: Synechocystis cells treated 360 min with iron 17 mM (ferric ammonium citrate)

tag: Synechocystis cells treated 360 min with iron 17 (M (ferric ammonium citrate)


title: pleC_deletion-rep3

source_name: LS3768 (CB15 del pleC)

tag: Asynchronous exponential phase culture of LS3768 (CB15 del pleC) grown in PYE at 30°C to OD600 = 0.3443.

tag: Asynchronous exponential phase culture of CB15 (LS3032) grown in PYE at 30°C to OD600 = 0.3221.


title: Synechocystis cells treated 240 min with iron 17 mM (ferric ammonium citrate,), replicate 1

source_name: Synechocystis cells treated 240 min with iron 17 mM (ferric ammonium citrate)

tag: Synechocystis cells treated 240 min with iron 17 (M (ferric ammonium citrate)


title: Tcf1 knock-out pancreatic islets_replicate 1 (MG-U74A)

city: New York

first: Markus

last: Stoffel

state: NY

address: 1230 York Avenue

department: Metabolic Diseases

institute: Rockefeller University

description: Pancreatic islets total RNA

data_processing: MAS 4.0

label: Affymetrix standard protocol

organism: Mus musculus

source_name: Tcf1 knock-out pancreatic islets

tag: Isolated pancreatic islets by collagenase digestion and ficoll gradient centrifugation


title: Synechocystis cells treated 15 min with 3mM H2O2, replicate 2

description: Synechocystis cells treated 15 min with 3 mM H2O2

source_name: Synechocystis cells treated 15 min with 0 mM H2O2

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 15 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: Synechocystis cells treated 30 min with zinc 776 (M (ZnSO4), replicate 1

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 30 min. Following growth, all cell samples were rapidly harvested and disrupted.

tag: Synechocystis cells treated 30 min with zinc 776 (M (ferric ammonium citrate)

source_name: Synechocystis cells treated 30 min with zinc 776 nM (ZnSO4)


title: Synechocystis cells treated 30 min with zinc 776 (M (ZnSO4), replicate 2

tag: Synechocystis cells treated 30 min with zinc 776 nM (ferric ammonium citrate)


title: Synechocystis cells treated 15 min with 3mM H2O2, replicate 1

source_name: Synechocystis cells treated 15 min with 3 mM H2O2

tag: Synechocystis cells treated 15 min with 0 mM H2O2


title: Synechocystis cells treated 30 min with 3mM H2O2, replicate 2

description: Synechocystis cells treated 30 min with 3 mM H2O2

source_name: Synechocystis cells treated 0 min with 3 mM H2O2


title: Synechocystis cells treated 30 min with 3mM H2O2, replicate 1

source_name: Synechocystis cells treated 30 min with 3 mM H2O2

source_name: Synechocystis cells treated 30 min with 0 mM H2O2


title: Synechocystis cells treated 300 min with 3mM H2O2, replicate 2

description: Synechocystis cells treated 300 min with 3 mM H2O2

source_name: Synechocystis cells treated 300 min with 0 mM H2O2

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 300 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: Synechocystis cells treated 300 min with 3mM H2O2, replicate 1

source_name: Synechocystis cells treated 300 min with 3 mM H2O2

tag: Synechocystis cells treated 300 min with 0 mM H2O2


title: 18ET_405_18_U_i_h

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: Array hybridization was performed simultaneously for the two cDNA probes of the corresponding twins (pregnant twin and control twin), each with the set of three arrays (LAFUGA Cattle subtr lib 18ET v1.0). Hybridization signals for array B were too weak and were not used for further data analysis.

hyb_protocol: Hybridization was done as follows: Pre-hybridization was done for up to six arrays together in one 15 cm glass hybridization bottle: 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 2 x 10 min 10 ml 0.1 x PBS / 1 % SDS at 85 °C; 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C. Hybridization probes were denatured for 15 min at 96 °C immediately before adding to the hybridization solution. Hybridization was done in plastic vials (30 ml, Sarstedt AG, Nuembrecht, Germany) in 3 ml 1 x PBS, pH 7.5 / 10 % SDS for 45 hrs at 65 °C. After hybridization, arrays were put together in one 15 cm glass hybridization bottle and washed as follows: 3 x 5 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 3 x 10 min 10 ml 1 x PBS / 10 % SDS at 65 °C; 3 x 10 min 10 ml 0.1 x PBS / 1 % SDS at 65 °C and finally 2 x 5 min 10 ml 1 x PBS / 1 % SDS / 2 mmol/l EDTA at room temperature. Filters were dried by baking at 80 °C for 20 min and exposed to an imaging plate BAS-SR (Fuji Photo Film Co., Ltd.).

scan_protocol: Imaging plates were scanned with a phosphor imager (Storm 860 or Typhoon 9400, Amersham Biosciences) at 50 µm resolution.

data_processing: AIDA Image Analyzer software (Version 4.00, Raytest, Straubenhardt, Germany); background subtraction: weighted image regions function; raw data were exported to Microsoft Excel; Normalization: (integral-background) over median of (integral-backgrounds) of reference cDNAs, definition of reference cDNAs: integral-background >30.000, ratio of integral-background between twin pairs >0.5 and <2.0, normalized values were then multiplied by 12 for array A, and 30 for array C (values of detectable signals >=1.0). Normalization was done separately for each array.

organism: Bos taurus

source_name: Uterus, endometrium, ipsilateral, caudal uterine horn, Day 18 of pregnancy

label_protocol: Double-stranded cDNA was synthesized starting from 50 µg total RNA using Superscript III (Invitrogen) for first strand synthesis and cDNA primer 1 (AACTGCGGCCGCGTACAGC(T20)VN). Synthesis of the second strand was performed with RNase H, E. coli DNA ligase, and E. coli DNA polymerase I (Invitrogen) according to the instructions of the manufacturer. 33P-labeled cDNA probes were generated from ds cDNA corresponding to appr. 10 µg of total RNA. cDNA was heat-denatured for 10 min at 96 °C and then chilled on ice. High Prime reaction mixture (Roche Molecular Biochemicals, Mannheim, Germany), dNTP mixture (dCTP final concentration 10 pmol/µl, dATP, dGTP, and dTTP final concentration each 100 pmol/µl) and 90 µCi [33P]-dCTP were added to a final volume of 20 µl. Reactions were incubated for 4 hrs at 37 °C, 20 min at 65 °C and subsequently purified with ProbeQuant G50 Micro Columns (Amersham Biosciences, Freiburg, Germany) to remove unincorporated nucleotides and to estimate labeling efficiency.

extract_protocol: Total RNA from endometrial tissue samples was isolated using Trizol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer's recommendations. The quantity and quality of total RNA was determined by spectrometry and agarose gel electrophoresis.

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat, two in vitro produced bovine blastocysts (day 7 after in vitro fertilization) in 200 µl culture medium were transferred into the ipsilateral uterine horn. In vitro production of embryos was performed as described previously (Stojkovic M. 1999) with minor modifications. The animal was slaughtered on Day 18 of pregnancy. Serum progesterone level just before slaughter was 2.5 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Pregnancy was confirmed by the presence of an apparently normal conceptus in the uterine lumen. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing. For gene expression analyses only those tissues samples of pregnant animals, which had been in contact with an embryo were used.

tag: Simmental heifer (Deutsches Fleckvieh), monozygotic twin generated by embryo splitting, non-lactating, Age

value: 66 month, Lactations:2, Animal ID:405


title: 18ST_406_18_U_i_h

source_name: Uterus, endometrium, ipsilateral, caudal uterine horn, Day 18 of estrous cycle

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat this animal received a sham-transfer of 200 µl transfer medium without embryos into the ipsilateral uterine horn and served as control. The animal was slaughtered on Day 18 of the estrous cycle. Serum progesterone level just before slaughter was 1.9 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing.

value: 66 month, Lactations:1, Animal ID:406


title: Synechocystis cells treated 420 min with 3mM H2O2, replicate 2

description: Synechocystis cells treated 420 min with 3 mM H2O2

source_name: Synechocystis cells treated 420 min with 0 mM H2O2

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 420 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: Synechocystis cells treated 240 min with zinc 776 (M (ZnSO4), replicate 2

source_name: Synechocystis cells treated 240 min with zinc 776 nM (ZnSO4)

tag: Synechocystis cells treated 240 min with zinc 776 nM (ferric ammonium citrate)


title: 18ST_412_18_U_i_h

description: Array hybridization was performed simultaneously for the two cDNA probes of the corresponding twins (pregnant twin and control twin), each with the set of three arrays (LAFUGA Cattle subtr lib 18ET v1.0).

data_processing: AIDA Image Analyzer software (Version 4.00, Raytest, Straubenhardt, Germany); background subtraction: weighted image regions function; raw data were exported to Microsoft Excel; Normalization: (integral-background) over median of (integral-backgrounds) of reference cDNAs, definition of reference cDNAs: integral-background >30.000, ratio of integral-background between twin pairs >0.5 and <2.0, normalized values were then multiplied by 12 for array A, 16 for array B and 30 for array C (values of detectable signals >=1.0). Normalization was done separately for the three arrays.

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat this animal received a sham-transfer of 200 µl transfer medium without embryos into the ipsilateral uterine horn and served as control. The animal was slaughtered on Day 18 of the estrous cycle. Serum progesterone level just before slaughter was 4.3 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing.

value: 68 month, Lactations:1, Animal ID:412


title: Synechocystis cells treated 180 min with 3mM H2O2, replicate 2

description: Synechocystis cells treated 180 min with 3 mM H2O2

source_name: Synechocystis cells treated 180 min with 0 mM H2O2

growth_protocol: 300 ml of mid-log phase liquid culture grown in standard conditions (2.5x107 cells ml-1) were rapidly concentrated 40-fold by centrifugation and spotted as 20 µl dots on BG11 plates with or without H2O2, 3 mM. Then the plates were incubated ˆ 30¡C under standard light for 180 min. Following growth, all cell samples were rapidly harvested and disrupted.


title: Synechocystis cells treated 420 min with 3mM H2O2, replicate 1

source_name: Synechocystis cells treated 420 min with 3 mM H2O2

tag: Synechocystis cells treated 420 min with 0 mM H2O2


title: Synechocystis cells treated 240 min with zinc 776 (M (ZnSO4), replicate 1

tag: Synechocystis cells treated 240 min with zinc 776 (M (ferric ammonium citrate)

tag: Synechocystis cells treated 240 min with zinc 776 nM (ZnSO4)


title: Synechocystis cells treated 180 min with 3mM H2O2, replicate 1

source_name: Synechocystis cells treated 180 min with 3 mM H2O2

tag: Synechocystis cells treated 180 min with 0 mM H2O2


title: 18ET_429_18_U_i_h

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat, two in vitro produced bovine blastocysts (day 7 after in vitro fertilization) in 200 µl culture medium were transferred into the ipsilateral uterine horn. In vitro production of embryos was performed as described previously (Stojkovic M. 1999) with minor modifications. The animal was slaughtered on Day 18 of pregnancy. Serum progesterone level just before slaughter was 7.6 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Pregnancy was confirmed by the presence of an apparently normal conceptus in the uterine lumen. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing. For gene expression analyses only those tissues samples of pregnant animals, which had been in contact with an embryo were used.

value: 61 month, Lactations:1, Animal ID:429


title: 18ST_430_18_U_i_h

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat this animal received a sham-transfer of 200 µl transfer medium without embryos into the ipsilateral uterine horn and served as control. The animal was slaughtered on Day 18 of the estrous cycle. Serum progesterone level just before slaughter was 4.5 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing.

value: 61 month, Lactations:1, Animal ID:430


title: 18ET_407_18_U_i_h

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat, two in vitro produced bovine blastocysts (day 7 after in vitro fertilization) in 200 µl culture medium were transferred into the ipsilateral uterine horn. In vitro production of embryos was performed as described previously (Stojkovic M. 1999) with minor modifications. The animal was slaughtered on Day 18 of pregnancy. Serum progesterone level just before slaughter was 3.2 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Pregnancy was confirmed by the presence of an apparently normal conceptus in the uterine lumen. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing. For gene expression analyses only those tissues samples of pregnant animals, which had been in contact with an embryo were used.

value: 69 month, Lactations:3, Animal ID:407


title: 18ST_416_18_U_i_h

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat, two in vitro produced bovine blastocysts (day 7 after in vitro fertilization) in 200 µl culture medium were transferred into the ipsilateral uterine horn. In vitro production of embryos was performed as described previously (Stojkovic M. 1999) with minor modifications. The animal was slaughtered on Day 18 of pregnancy. Serum progesterone level just before slaughter was 2.6 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Pregnancy was confirmed by the presence of an apparently normal conceptus in the uterine lumen. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing. For gene expression analyses only those tissues samples of pregnant animals, which had been in contact with an embryo were used.

value: 62 month, Lactations:1, Animal ID:416


title: 18ET_417_18_U_i_h

value: 62 month, Lactations:1, Animal ID:417


title: 18ST_408_18_U_i_h

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat this animal received a sham-transfer of 200 µl transfer medium without embryos into the ipsilateral uterine horn and served as control. The animal was slaughtered on Day 18 of the estrous cycle. Serum progesterone level just before slaughter was 2.2 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing.

value: 69 month, Lactations:3, Animal ID:408


title: 18ET_413_18_U_i_h

treatment_protocol: Estrous cycle was synchronized by a single intramuscular injection of 500 µg Cloprostenol (Estrumate®; Essex Tierarznei, München, Germany) at diestrus. Animals were observed for sexual behavior (i.e. toleration, sweating, vaginal mucus) to determine standing heat, which occurred around 60 h after Estrumate® injection. Seven days after standing heat, two in vitro produced bovine blastocysts (day 7 after in vitro fertilization) in 200 µl culture medium were transferred into the ipsilateral uterine horn. In vitro production of embryos was performed as described previously (Stojkovic M. 1999) with minor modifications. The animal was slaughtered on Day 18 of pregnancy. Serum progesterone level just before slaughter was 5.7 ng/ml. The uterine horns were opened longitudinally with a scissors and intercaruncular endometrial tissue samples from defined uterine regions (for further details see Bauersachs S. et al. 2005) were dissected using a scalpel. Pregnancy was confirmed by the presence of an apparently normal conceptus in the uterine lumen. Tissue samples of the endometrium were transferred into tubes containing 4 ml of RNAlater™ (Ambion, Huntigton, UK) within 20 minutes after slaughter, stored overnight at 4°C and then at -20°C until further processing. For gene expression analyses only those tissues samples of pregnant animals, which had been in contact with an embryo were used.

value: 68 month, Lactations:2, Animal ID:413


title: HTC avian macrophage cells stimulated with Eimeria maxima - 48hr vs 18hr

status: Public on Dec 06 2005

city: Newark

first: Calvin

last: Keeler

state: DE

department: Animal and Food Sciences

institute: University of Delaware

description: This sample set is part of an experiment examining gene expression during stimulation of HTC avian macrophage cells with 3 species of Eimeria across a 48 hour timecourse (0, 4, 18, & 48hr).

data_processing: Images acquired using Applied Precision ArrayWoRx scanner and related software; intensity values calculated using SoftWorx Tracker software.

molecule: polyA RNA

organism: Gallus gallus

source_name: HTC avian macropahge cell line - Stimulated with E. maxima for 48 hours

tag: mRNA sample directly labeled with Alexa555 dye

source_name: HTC avian macropahge cell line - Stimulated with E. maxima for 18 hours

tag: mRNA sample directly labeled with Alexa647 dye


title: Slide 1427

city: Dunedin

first: Orla

middle: Mary

last: Keane

state: Otago

address: 710 Cumberland St

department: Animal Genomics

country: New Zealand

institute: AgResearch

description: Comparing gene expression in duodenum tissue of parasite resistant and susceptible sheep

data_processing: Normalized using a spatial mixed model analysis which includes splines

organism: Ovis aries

source_name: Duodenum, resistant animal 85R

tag: Resistant to gastrointestinal nematodes

source_name: Duodenum, susceptible animal 91S

tag: Susceptible to gastrointestinal nematodes


title: Slide 1425

source_name: Duodenum, resistant animal 77R


title: C82T

city: San Diego

first: Jack

last: Yu

state: CA

address: 3210 Merryfield Row

institute: Veridex, LLC

description: Colon Duke's B tumor

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Homo sapiens

source_name: colon

label_protocol: Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA from breast primary tumor samples according to Qiagen RNeasy Mini Kit protocol.

tag: Colon Duke's B tumor, snap frozen


title: HTC avian macrophage cells stimulated with Eimeria tenella - 48hr vs Control

source_name: HTC avian macropahge cell line - Stimulated with E. tenella for 48 hours

source_name: HTC avian macropahge cell line - Unstimulated


title: HTC avian macrophage cells stimulated with Eimeria acervulina - 48hr vs Control

source_name: HTC avian macropahge cell line - Stimulated with E. acervulina for 48 hours


title: HTC avian macrophage cells stimulated with Eimeria maxima - 4hr vs Control

source_name: HTC avian macropahge cell line - Stimulated with E. maxima for 4 hours


title: C8T

description: Colon Duke's B tumor


title: C8R

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, RNAlater preserved


title: Slide 1422

source_name: Duodenum, resistant animal 79R

source_name: Duodenum, susceptible animal 90S


title: Slide 1426


title: Slide 1423


title: Slide 1424

source_name: Duodenum, resistant animal 76R


title: HTC avian macrophage cells stimulated with Eimeria acervulina - Control vs 4hr

source_name: HTC avian macropahge cell line - Stimulated with E. acervulina for 4 hours


title: HTC avian macrophage cells stimulated with Eimeria maxima - 18hr vs 4hr


title: C9T

description: Colon Duke's B tumor


title: HTC avian macrophage cells stimulated with Eimeria tenella Control vs 4hr

source_name: HTC avian macropahge cell line - Stimulated with E. tenella for 4 hours


title: HTC avian macrophage cells stimulated with Eimeria tenella - 18hr vs 48hr

source_name: HTC avian macropahge cell line - Stimulated with E. tenella for 18 hours


title: C82R

description: Colon Duke's B tumor


title: HTC avian macrophage cells stimulated with Eimeria acervulina - 18hr vs 48hr

source_name: HTC avian macropahge cell line - Stimulated with E. acervulina for 18 hours


title: HTC avian macrophage cells stimulated with Eimeria maxima - Control vs 48hr

source_name: HTC avian macropahge cell line - Stimulated with E. maxima for 48 hours


title: HTC avian macrophage cells stimulated with Eimeria acervulina - 4hr vs 18hr


title: HTC avian macrophage cells stimulated with Eimeria Tenella - 4hr vs 18hr


title: C9R

description: Colon Duke's B tumor


title: C80T

description: Colon Duke's B tumor

data_processing: Affymetrix Microarray Suite version 5.3


title: C80R

description: Colon Duke's B tumor


title: Slide 1420


title: Slide 1421


title: Slide 1419

source_name: Duodenum, susceptible animal 88S


title: C7R

description: Colon Duke's B tumor


title: C7T

description: Colon Duke's B tumor


title: Slide 1415

source_name: Duodenum, susceptible animal 81S

source_name: Duodenum, Resistant animal 85R


title: Slide 1416


title: Slide 1418

source_name: Duodenum, resistant animal 85R


title: C79T

description: Colon Duke's B tumor

source_name: colon


title: Slide 1417

source_name: Duodenum, resistant animal 77R


title: C76R

description: Colon Duke's B tumor


title: C79R

description: Colon Duke's B tumor


title: C76T

description: Colon Duke's B tumor


title: Slide 1412


title: C74T

description: Colon Duke's B tumor


title: Slide 1413

source_name: Duodenum, Resistant animal 77R

source_name: Duodenum susceptible animal 81S


title: C77T

description: Colon Duke's B tumor


title: C77R

description: Colon Duke's B tumor


title: C75R

description: Colon Duke's B tumor


title: C74R

description: Colon Duke's B tumor


title: C73T

description: Colon Duke's B tumor


title: C72T

description: Colon Duke's B tumor


title: S26_M

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage.  Total RNA was isolated from nine replications of B73, Mo17, and F1 maize seedling genotypes (6 individual seedlings pooled for each genotype in each replication) using Trizol reagent (Invitrogen, Carlbad, CA) with slight modifications to manufacturer’s protocol.  Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer’s protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridize to the GP2613 platform.

hyb_protocol: Fluorescent targets were hybridized as described in the “cDNA microarray protocol” file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (27 total) was scanned a minimum of six times in ascending amounts of laser power and PMT gain settings. Slides 1-15 were scanned using the ScanArray5000 (Packard, Meriden, CA).  Slides 16-27 were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA).  Two scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.

data_processing: The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide.  Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications.  Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides.  Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

organism: Zea mays

source_name: Seedling stage above ground tissue

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.   Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dy molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.

extract_protocol: total RNA extraction with Trizol (Invitrogen, Carlsbad, CA) with minor modifications to manufacturer’s instructions, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer’s instructions

tag: Genotype:	Mo17

tag: Tissue

value: above ground seedling

tag: Dev stage

value: 14 days old

tag: Sample name:	P12 Mo17 Cy3

tag: Genotype:	B73

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P12 B73 Cy5


title: C75T

description: Colon Duke's B tumor


title: S24_M

tag: Sample name:	P11 B73 Cy3

tag: Sample name:	P11 Mo17 Cy5


title: S25_M

tag: Genotype:	F1

tag: Sample name:	P12 F1 Cy3

tag: Sample name:	P12 Mo17 Cy5


title: S23_M

tag: Sample name:	P11 F1 Cy3

tag: Sample name:	P11 B73 Cy5


title: Slide 1414

tag: Susceptible to gastrointestinal nematodes

source_name: Duodenum, resistant animal 79R

tag: Resistant to gastrointestinal nematodes


title: C6T

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, snap frozen


title: C72R

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, RNAlater preserved


title: C73R

description: Colon Duke's B tumor


title: C5R

description: Colon Duke's B tumor


title: C18T

description: Colon Duke's B tumor


title: S22_M

tag: Genotype:	Mo17

tag: Tissue

tag: Dev stage

tag: Sample name:	P11 Mo17 Cy3

tag: Sample name:	P11 F1 Cy5


title: S27_M

tag: Genotype:	B73

tag: Sample name:	P12 B73 Cy3

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	P12 F1 Cy5


title: C20R

description: Colon Duke's B tumor


title: C5T

description: Colon Duke's B tumor


title: S20_M

tag: Sample name:	P8 B73 Cy3

tag: Sample name:	P8 Mo17 Cy5


title: S18_M

tag: Sample name:	P7 Mo17 Cy3

tag: Sample name:	P7 B73 Cy5


title: C20T

description: Colon Duke's B tumor


title: S21_M

tag: Sample name:	P8 Mo17 Cy3

tag: Genotype:	F1

tag: Sample name:	P8 F1 Cy5


title: C6R

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, RNAlater preserved


title: C18R

description: Colon Duke's B tumor


title: S19_M

tag: Tissue

tag: Sample name:	P7 F1 Cy3


title: S15_M

tag: Dev stage

tag: Sample name:	P6 B73 Cy3

tag: Sample name:	P6 F1 Cy5


title: C17T

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, snap frozen


title: C16R

description: Colon Duke's B tumor


title: S16_M

tag: Genotype:	B73

tag: Sample name:	P7 B73 Cy3

tag: Tissue:		above ground seedling

tag: Sample name:	P7 F1 Cy5


title: S14_M

tag: Genotype:	Mo17

tag: Sample name:	P6 Mo17 Cy3

tag: Dev stage:	 14 days old

tag: Sample name:	P6 B73 Cy5


title: S13_M

tag: Genotype:	F1

tag: Sample name:	P6 F1 Cy3

tag: Sample name:	P6 Mo17 Cy5


title: C16T

description: Colon Duke's B tumor


title: C15R

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, RNAlater preserved


title: S12_M

tag: Tissue

tag: Sample name:	P5 B73 Cy3

tag: Sample name:	P5 Mo17 Cy5


title: S17_M

tag: Dev stage

tag: Sample name:	P7 F1 Cy3

tag: Sample name

value: P7 Mo17 Cy5


title: C14T

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, snap frozen


title: C15T

description: Colon Duke's B tumor


title: C14R

description: Colon Duke's B tumor


title: C17R

description: Colon Duke's B tumor


title: S10_M

tag: Sample name:	P5 Mo17 Cy3

tag: Tissue:		above ground seedling

tag: Sample name:	P5 F1 Cy5


title: B91T

description: Breast primary tumor

source_name: breast

tag: Tumor, snap frozen


title: S8_M

tag: Genotype:	B73

tag: Sample name:	P10 B73 Cy3

tag: Genotype:	Mo17

tag: Dev stage:	 14 days old

tag: Sample name:	P10 Mo17 Cy5


title: S11_M

tag: Genotype:	F1

tag: Sample name:	P5 F1 Cy3

tag: Sample name:	P5 B73 Cy5


title: S3_M

tag: Tissue

tag: Sample name:	P2 Mo17 Cy3

tag: Sample name:	P2 F1 Cy5


title: S7_M

tag: Dev stage

tag: Sample name:	P10 F1 Cy3

tag: Sample name:	P10 B73 Cy5


title: B92T

description: Breast primary tumor


title: S1_M

tag: Sample name

value: P2 F1 Cy3

tag: Tissue:		above ground seedling

tag: Sample name:	P2 B73 Cy5


title: C13R

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, RNAlater preserved


title: S6_M

tag: Sample name:	P3 F1 Cy3

tag: Sample name:	P3 Mo17 Cy5


title: S9_M

tag: Genotype:	Mo17

tag: Sample name:	P10 Mo17 Cy3

tag: Dev stage:	 14 days old

tag: Sample name:	P10 F1 Cy5


title: S4_M

tag: Sample name:	P3 Mo17 Cy3

tag: Genotype:	B73

tag: Sample name:	P3 B73 Cy5


title: B92R

description: Breast primary tumor

tag: Tumor, RNAlater preserved


title: S5_M

tag: Tissue

tag: Dev stage

tag: Sample name:	P3 B73 Cy3

tag: Genotype:	F1

tag: Sample name:	P3 F1 Cy5


title: B91R

description: Breast primary tumor


title: C13T

description: Colon Duke's B tumor

tag: Colon Duke's B tumor, snap frozen


title: S2_M

tag: Sample name:	P2 B73 Cy3

tag: Tissue:		above ground seedling

tag: Sample name:	P2 Mo17 Cy5


title: pxylX_dnaA_cell_cycle_#1_195min_rep1

description: Sample taken 195 min into the first repetition of the PxylX::dnaA cell cycle

label_protocol: RNA was directly labeled for microarray hybridization by reverse transcription. 20 µg RNA and 3 µg random hexamer primers (Invitrogen) in a total volume of 15 µl were heated to 65ºC for 10 minutes and cooled on ice.  Next, the sample was brought to a final volume of 30 µl with the following final concentrations: 10 mM DTT, 1 x Superscript RT buffer, 0.5 mM each of ATP, GTP, TTP, 0.2 mM CTP,  300 U Superscript II reverse transcriptase (Invitrogen) and 0.1 mM of Cy5-dCTP (Amersham). The reaction was incubated at room temperature for 10 minutes and then at 42ºC for 1 hour and 50 minutes. After reverse transcription, the RNA was degraded by addition of 1.5 µl of 1 N NaOH and incubation at 65ºC for 10 minutes; the reaction was neutralized immediately by adding 1.5 µl 1 N HCl. The cDNA from the two samples to be compared were combined and purified using Qiagen's PCR purification kit. Samples were eluted in EB buffer and were concentrated to less than 5 µl using Microcon-30 columns (Millipore). Sample volume was then brought up to 5 µl using EB.  A hybridization mixture containing the labeled cDNAs, 20 µg yeast tRNA, 5X SSC, 0.1% SDS and 30% formamide in a final volume of 15 µl was incubated for 1 minute at 100ºC.  After allowing the sample to cool to 42ºC for 1 minute, 12 µl of the mixture was placed on a 22x22 mm coverslip and the microarray slide was placed on the coverslip.   The slide was quickly put into a sealed hybridization chamber, which was placed in a  44 ºC water bath overnight. Prior to use, slides were blocked by shaking sequentially in 0.2% SDS (2 minutes, 2 times), distilled water (2 minutes, 2 times), aldehyde blocking solution (0.75 g sodium borohydride, 225 ml 1X PBS, 75 ml 95% ethanol, 15 minutes), 0.2% SDS (2 minutes, 2 times), and water (2 minutes, 2 times) and then dried by spinning at 1000 rpm for 2 minutes in a Sorvall Legend RT tabletop centrifuge.  Following hybridization, arrays were washed for 10 minutes at 37ºC in 2X SSC, 0.2% SDS, followed by a 10 minute wash in 2X SCC and a 10 minute wash in 0.2X SSC, both at room temperature. Slides were then dried by spinning at 1000 rpm in a Sorvall Legend RT tabletop centrifuge for 2 minutes at room temperature.

extract_protocol: For RNA extraction, ~6 ml of cell culture was pelleted by spinning for 1 minute in a microfuge at 14,500 g. (Each 6 ml sample was split among three 2 ml tubes.)  After removing the supernatant, the pellets were frozen in liquid nitrogen.  Later, 350 µl of Trizol (Invitrogen) was added to each pellet.  The three parts were combined to make a single sample with a volume of ~1 ml and were incubated for 10 minutes at 65ºC to lyse the cells.  Next, 200 µl of chloroform was added and samples were mixed vigorously and incubated at room temperature for 5 minutes. Phases were then separated by centrifugation (15 minutes, 4ºC, 14,500 g) and the aqueous phase, containing the RNA, was transferred to a new tube.  RNA was precipitated with 0.5 ml of isopropanol at -80ºC or -20°C overnight, pelleted (30 minutes, 4ºC, 14,500 g), washed with -20°C 70% ethanol, and resuspended in  50 µl Nuclease free water (Ambion). To digest DNA in the sample, we added 2 µl DNase I (Ambion, 2 U/µl) and 5 µl 10X DNase I buffer and incubated at 37°C for two hours.  RNA was isolated using an acid phenol extraction.  Specifically, 150 µl DEPC-treated water and 200 µl acid phenol chloroform (5:1, pH 4.5, Ambion) were added and the mixture was vortexed vigorously.  Then, samples were spun at 14,500 g at 4°C for 10 minutes to separate the phases.  The aqueous (upper) phase was transfered to a new tube.   RNA was precipitated by adding 20 µl 3 M sodium acetate (pH 5.2) and 500 µl -20°C ethanol and freezing overnight at -80C.  RNA was then pelleted by centrifuging at 4°C at 14,500 g for 10 minutes.   Pellets were washed in 1 ml 70% ethanol, spun for 5 minutes at 4°C at 14,500 g.  Supernatant was poured out, samples were spun for 30 seconds at 14,500 g at room temperature, the residual ethanol was removed with a pipet.  Samples were air dried for ~10 minutes and then were suspended in  20 µl Nuclease-free water (Ambion). To aid in dissolving the RNA, samples were put at 55°C for 10 minutes or kept at room temperature for 30 minutes.  RNA was stored at -80°C or -20°C.  RNA quality was visualized on agarose gels and concentration was measured using a spectrophotometer.  In order to obtain enough RNA to allow the same reference samples to be used for many arrays, multiple samples were taken, processed independently, and pooled.

tag: Asynchronous log phase culture of CB15N cells grown in M2GX at 30°C to OD660 = 0.3727.

source_name: LS3350 (GM2471)  del dnaA, PxylX::dnaA

label_protocol: RNA was directly labeled for microarray hybridization by reverse transcription. 20 µg RNA and 3 µg random hexamer primers (Invitrogen) in a total volume of 15 µl were heated to 65ºC for 10 minutes and cooled on ice.  Next, the sample was brought to a final volume of 30 µl with the following final concentrations: 10 mM DTT, 1 x Superscript RT buffer, 0.5 mM each of ATP, GTP, TTP, 0.2 mM CTP,  300 U Superscript II reverse transcriptase (Invitrogen) and 0.1 mM of Cy3-dCTP (Amersham). The reaction was incubated at room temperature for 10 minutes and then at 42ºC for 1 hour and 50 minutes. After reverse transcription, the RNA was degraded by addition of 1.5 µl of 1 N NaOH and incubation at 65ºC for 10 minutes; the reaction was neutralized immediately by adding 1.5 µl 1 N HCl. The cDNA from the two samples to be compared were combined and purified using Qiagen's PCR purification kit. Samples were eluted in EB buffer and were concentrated to less than 5 µl using Microcon-30 columns (Millipore). Sample volume was then brought up to 5 µl using EB.  A hybridization mixture containing the labeled cDNAs, 20 µg yeast tRNA, 5X SSC, 0.1% SDS and 30% formamide in a final volume of 15 µl was incubated for 1 minute at 100ºC.  After allowing the sample to cool to 42ºC for 1 minute, 12 µl of the mixture was placed on a 22x22 mm coverslip and the microarray slide was placed on the coverslip.   The slide was quickly put into a sealed hybridization chamber, which was placed in a  44 ºC water bath overnight. Prior to use, slides were blocked by shaking sequentially in 0.2% SDS (2 minutes, 2 times), distilled water (2 minutes, 2 times), aldehyde blocking solution (0.75 g sodium borohydride, 225 ml 1X PBS, 75 ml 95% ethanol, 15 minutes), 0.2% SDS (2 minutes, 2 times), and water (2 minutes, 2 times) and then dried by spinning at 1000 rpm for 2 minutes in a Sorvall Legend RT tabletop centrifuge.  Following hybridization, arrays were washed for 10 minutes at 37ºC in 2X SSC, 0.2% SDS, followed by a 10 minute wash in 2X SCC and a 10 minute wash in 0.2X SSC, both at room temperature. Slides were then dried by spinning at 1000 rpm in a Sorvall Legend RT tabletop centrifuge for 2 minutes at room temperature.

extract_protocol: For RNA extraction, ~6 ml of cell culture was pelleted by spinning for 1 minute in a microfuge at 14,500 g. (Each 6 ml sample was split among three 2 ml tubes.)  After removing the supernatant, the pellets were frozen in liquid nitrogen.  Later, 350 µl of Trizol (Invitrogen) was added to each pellet.  The three parts were combined to make a single sample with a volume of ~1 ml and were incubated for 10 minutes at 65ºC to lyse the cells.  Next, 200 µl of chloroform was added and samples were mixed vigorously and incubated at room temperature for 5 minutes. Phases were then separated by centrifugation (15 minutes, 4ºC, 14,500 g) and the aqueous phase, containing the RNA, was transferred to a new tube.  RNA was precipitated with 0.5 ml of isopropanol at -80ºC or -20°C overnight, pelleted (30 minutes, 4ºC, 14,500 g), washed with -20°C 70% ethanol, and resuspended in  20 µl Nuclease-free water (Ambion). To aid in dissolving the RNA, samples were put at 55°C for 10 minutes or kept at room temperature for 30 minutes.  RNA was stored at -80°C or -20°C.  RNA quality was visualized on agarose gels and concentration was measured using a spectrophotometer.  Since the same reference samples were used for many arrays, multiple samples were taken, processed independently, and pooled.

tag: Swarmer-stage cells were isolated from a 30°C log phase M2GX (0.2% glucose, 0.3% xylose) culture and released into M2G at 30°C.  After 74 minutes, dnaA expression was induced by adding xylose to 0.3%.  Samples were taken every 15 minutes.  This sample was taken at 195 min. At 0 minutes, the OD660 was 0.42; at 210 minutes, the OD660 was 1.1


title: B87T

description: Breast primary tumor

tag: Tumor, snap frozen


title: B88T

description: Breast primary tumor


title: B85T

description: Breast primary tumor


title: B8R

description: Breast primary tumor


title: B86T

description: Breast primary tumor


title: B86R

description: Breast primary tumor


title: B88R

description: Breast primary tumor


title: B7R

description: Breast primary tumor


title: B6T

description: Breast primary tumor


title: B87R

description: Breast primary tumor


title: B85R

description: Breast primary tumor


title: B32R

description: Breast primary tumor


title: B7T

description: Breast primary tumor


title: B5T

description: Breast primary tumor


title: B5R

description: Breast primary tumor


title: B8T

description: Breast primary tumor


title: B30T

description: Breast primary tumor


title: B31R

description: Breast primary tumor


title: B6R

description: Breast primary tumor


title: B31T

description: Breast primary tumor


title: B28T

description: Breast primary tumor


title: B30R

description: Breast primary tumor


title: B28R

description: Breast primary tumor


title: B27T

description: Breast primary tumor


title: B26R

description: Breast primary tumor


title: B26T

description: Breast primary tumor


title: B29R

description: Breast primary tumor


title: B29T

description: Breast primary tumor


title: B25T

description: Breast primary tumor


title: B32T

description: Breast primary tumor


title: B25R

description: Breast primary tumor


title: B27R

description: Breast primary tumor


title: B23T

description: Breast primary tumor


title: B23R

description: Breast primary tumor


title: B22T

description: Breast primary tumor


title: B21T

description: Breast primary tumor


title: B19R

description: Breast primary tumor


title: B16R

description: Breast primary tumor


title: B18R

description: Breast primary tumor


title: B14T

description: Breast primary tumor


title: B20T

description: Breast primary tumor


title: B22R

description: Breast primary tumor


title: B17T

description: Breast primary tumor


title: B18T

description: Breast primary tumor


title: B14R

description: Breast primary tumor


title: B17R

description: Breast primary tumor


title: B19T

description: Breast primary tumor


title: B15R

description: Breast primary tumor


title: B20R

description: Breast primary tumor


title: B12R

description: Breast primary tumor

data_processing: Affymetrix Microarray Suite version 5.1


title: B16T

description: Breast primary tumor


title: B21R

description: Breast primary tumor


title: B13R

description: Breast primary tumor


title: B12T

description: Breast primary tumor


title: B15T

description: Breast primary tumor


title: B13T

description: Breast primary tumor


title: B10R

description: Breast primary tumor


title: B10T

description: Breast primary tumor


title: SW-837

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-07/30371.gif; format: GIF

source_name: Cy3 (channel 1): Universal mRNA reference

source_name: Cy5 (channel 2): colon cancer cell line


title: NCI-H747

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33060.gif; format: GIF


title: SW948

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48598.gif; format: GIF


title: CACO-2

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33061.gif; format: GIF


title: LOVO

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-07/30370.gif; format: GIF


title: HCT116+Ch3

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2005-03/60327.gif; format: GIF


title: SW-480

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33053.gif; format: GIF


title: COLO320

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48603.gif; format: GIF


title: SK-CO-1

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33059.gif; format: GIF


title: HT-29

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-07/30367.gif; format: GIF


title: HCT15

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33058.gif; format: GIF


title: HCT116+Ch2

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2005-03/60329.gif; format: GIF


title: SW48

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-07/30297.gif; format: GIF


title: RKO

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-07/30369.gif; format: GIF


title: COLO741

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48602.gif; format: GIF


title: SW1417

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48597.gif; format: GIF


title: GP2D

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48599.gif; format: GIF


title: HCT116

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33052.gif; format: GIF


title: COLO205

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48604.gif; format: GIF


title: SW-1116

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33057.gif; format: GIF


title: DLD-1

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33055.gif; format: GIF


title: LIM1215

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48606.gif; format: GIF


title: SW620

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33056.gif; format: GIF


title: SW-403

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33051.gif; format: GIF


title: HCA7

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48608.gif; format: GIF


title: HCT 116

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2005-03/60328.gif; format: GIF


title: GP5D

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48607.gif; format: GIF


title: SNUC2B

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48609.gif; format: GIF


title: LIM2412

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48605.gif; format: GIF


title: 4OHE2_sample 40

status: Public on Dec 02 2005

city: Leicester

first: Jerry

middle: A

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

country: United Kingdom

institute: University of Leicester

description: Total RNA from uterus from 3 month old CD1 mouse dosed on days 1-5 after birth with 4-hydroxyestradiol

label: Cy3 control

source_name: uterus

tag: Strain

tag: Gender

value: female

tag: Age

value: 3 months

value: uterus

label: Cy5 treated


title: LS-180

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33048.gif; format: GIF


title: LS411

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48600.gif; format: GIF


title: LS-174T

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33050.gif; format: GIF


title: 4OHE2_sample 41

label: Cy5 control

label: Cy3 treated


title: 4OHE2_sample 39


title: T84

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-01/48601.gif; format: GIF


title: NCI-H508

description:
Simple annotation: Colon, cell line
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/33062.gif; format: GIF


title: 4OHE2_sample 37


title: Tamoxifen_human_sample 47

description: Total RNA from uterus from human female treated with tamoxifen

value: adult


title: Tamoxifen_human_sample 52


title: ERKO_tamoxifen_sample_05

description: Total RNA from uterus from 3 month old ERKO alpha mouse dosed on days 1-5 after birth with tamoxifen

value: ERKOalpha


title: 4OHE2_sample 38


title: Tamoxifen_human_sample 54


title: Tamoxifen_human_sample 53


title: 4OHE2_sample 42


title: Tamoxifen_human_sample 46


title: Tamoxifen_human_sample 43


title: ERKO_tamoxifen_sample_02


title: ERKO_tamoxifen_sample_08


title: ERKO_tamoxifen_sample_09


title: ERKO_tamoxifen_sample_06


title: Tamoxifen_human_sample 45


title: Tamoxifen_sample 26

description: Total RNA from uterus from 3 month old CD1 mouse dosed on days 1-5 after birth with tamoxifen


title: ERKO_tamoxifen_sample_04


title: ERKO_tamoxifen_sample_07


title: Tamoxifen_sample 25


title: ERKO_tamoxifen_sample_03


title: Tamoxifen_sample 24


title: Tamoxifen_sample 19


title: Tamoxifen_sample 23


title: E2_sample 41

description: Total RNA from uterus from 3 month old CD1 mouse dosed on days 1-5 after birth with estradiol


title: E2_sample 42


title: Tamoxifen_sample 20


title: Tamoxifen_sample 22


title: E2_sample 43


title: Tamoxifen_sample 21


title: E2_sample 40


title: E2_sample 39


title: E2_sample 44


title: TWT Temperature 43 vs Ref_rep3

city: Marseille

first: nicolas

last: crapoulet

address: 27 BD J. Moulin

institute: Unité des Rickettsies (CNRS-UMR 6020)

description: The data filtering and normalization were then processed with Microsoft Excel software. Spots with background-corrected signal intensity (median) in both channels lower than two-fold the background intensity (median) were excluded from further analysis.

hyb_protocol: Hybridization and washing. Microarrays washed in 0.1% SDS (1 min.) and rinsed with H2O (1 min.) were boiled 3 min in H2O in order to denaturate spotted double-strand DNA. Following prehybridization at 42°C for 45 min. in 5 X SSC, 0.1% SDS and 0.1% BSA solution, microarrays were rinsed in H2O (1 min.) and dried with compressed nitrogen. Hybridization was then carried out using twice 10 µg cDNA labeled with Cy3- or Cy5-dCTP pooled and evaporated (SpeedVac™ concentrator) and resuspended in 6 µl of nuclease free H2O. The mixture was heated at 95°C at least 2 min. and then cooled on ice for 30 sec. before addition of 7.5 µl of microarray hybridization buffer (supplied in the CyScribe kit) and 15 µl of 100% (v/v) formamide and applied to the microarray slide by covering a 24 X 60 mm glass coverslip. Following 18 h hybridization at 42°C, microarrays were washed in 2 X SSC with 0.2% SDS for 10 min., then in 2 X SSC and then in 0.2 X SSC. Finally, microarrays were dried with compressed nitrogen and scanned at a resolution of 10 µm by using a ScanArray® Express (Perkin Elmer, Boston, MA, USA).

scan_protocol: The signal intensity and local background measurements were obtained for each spot by using ScanArray® Express Microarray Analysis System version 2.1.8 software (Perkin Elmer).

data_processing: total intensity normalization methods

organism: Tropheryma whipplei

source_name: Reference

label_protocol: RNA labeling. Fluorescently labeled cDNA was prepared using the CyScribe™ First-Strand cDNA Labeling Kit (Amersham Biosciences). Briefly, 10 µg of total RNA, supplemented with control RNAs (Universal ScoreCard™ kit, Amersham Biosciences), was annealed with random nonamer primers. Total RNA was directly reverse-transcribed and labeled by incorporation of Cy3-dCTP or Cy5-dCTP (Amersham Biosciences) using CyScript reverse transcriptase. Remaining RNA was then degraded with an alkaline hydrolysis treatment and, after neutralization, labeled first-strand cDNA was purified with the CyScribe™ GFX™ Purification Kit (Amersham Biosciences). Before hybridization, the level of Cy3- and Cy5-incorporation was quantified by absorbance measurement at 550 and 650 nm, respectively. Hybridizations were performed with incorporation levels ranging from 80 to 200 pmol of fluorochromes per µg of cDNA.

growth_protocol: Strain, medium and growth conditions. All experiments were performed on mid-log cultures of T. whipplei (strain Twist) {La Scola, 2001 71 /id} grown in DMEM/F12 medium (Invitrogen Life Technologies, Carlsbad, USA) supplemented with 10% foetal calf serum, 1% L-glutamine and 1% human non-essential amino acids (Invitrogen). Bacterial growth was monitored by flow cytometry counting using the Microcyte® portable flow cytometer (Optoflow AS; Oslo, Norway) and by quantitative PCR as previously described {Renesto, 2003 23 /id;Fenollar, 2002 290 /id}.

extract_protocol: RNA purification. In the shock experiments, bacterial suspension were cooled at 4°C or 28°C for 6 hours or alternatively heated in a 43°C water bath for 15 min. before sonication of bacteria in 1 ml of Trizol® Reagent (Invitrogen Life Technologies) for RNA extraction {Crapoulet, 2005 305 /id}. Purified RNA samples resuspended in DEPC-treated water were treated with RNase-Free DNase Set (QIAGEN) and cleaned-up on to RNeasy column (QIAGEN) to remove eventual DNA contamination. Amount and quality of each RNA sample was checked by automated capillary gel electrophoresis using the Bioanalyzer 2100 with RNA Nano LabChips™ (Agilent, Palo Alto, CA, USA). 400 ml of T. whipplei axenic culture were required to obtain 10 µg of purified RNA.

tag: Strain Twist

tag: Axenic culture

tag: Day 28

tag: Temperature 37°C

source_name: 43°C (test)

tag: Exponential growth (Day 13)

tag: Temperature 43°C

tag: 15 min.


title: TWT Temperature 43 vs Ref_rep1


title: TWT Temperature 43 vs Ref_rep2


title: 4OHE2_sample 44

tag: Tissue


title: E2_sample 38


title: E2_sample 37


title: TWT Temperature 28 vs Ref_rep2

source_name: 28°C (test)

tag: Temperature 28°C

tag: 6 hours


title: TWT Temperature 4 vs Ref_rep2

source_name: 4°C (test)

tag: Temperature 4°C


title: NIA-NEUROARRAY_DH3

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

description: SON 3d dehydrated

data_processing: ImageQuant software

label: CTP Radiolabel

organism: Rattus norvegicus

source_name: Supraoptic nucleus_3d dehydrated

value: Sprague Dawley

value: Male

value: 10-12 weeks

value: Supraoptic nucleus


title: TWT Temperature 4 vs Ref_rep1


title: TWT Temperature 37 vs Ref_rep2

source_name: 37°C (test)


title: TWT Temperature 37 vs Ref_rep3


title: TWT Temperature 28 vs Ref_rep3


title: NIA-NEUROARRAY_DH1

description: SON 3d dehydrated


title: 4OHE2_sample 43


title: Tamoxifen_human_sample 74


title: TWT Temperature 37 vs Ref_rep1


title: Tamoxifen_human_sample 73


title: Tamoxifen_human_sample 72


title: Tamoxifen_human_sample 69


title: NIA-NEUROARRAY_CT3

description: SON control

source_name: Supraoptic nucleus_control


title: NIA-NEUROARRAY_DH2

description: SON 3d dehydrated

source_name: Supraoptic nucleus_3d dehydration


title: Tamoxifen_human_sample 71


title: TWT Temperature 28 vs Ref_rep1


title: TWT Temperature 4 vs Ref_rep3


title: Tamoxifen_human_sample 70


title: Tamoxifen_human_sample 66


title: NIA-NEUROARRAY_CT2

description: SON control


title: Tamoxifen_human_sample 67


title: Tamoxifen_human_sample 64


title: Tamoxifen_human_sample 63


title: NIA-NEUROARRAY_CT1

description: SON control


title: Tamoxifen_human_sample 65


title: HEK293_HNF1b_#2_uninduced

status: Public on Dec 01 2005

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Hepatocyte nuclear factor 1beta (HNF1beta, TCF2) is a tissue-specific transcription factor whose mutation in humans leads to renal cysts, genital malformations, pancreas atrophy and maturity onset diabetes of the young (MODY5). Furthermore, HNF1beta overexpression has been observed in clear cell cancer of the ovary. To identify potential HNF1beta target genes whose activity may be deregulated in human patients we established a human embryonic kidney cell line (HEK293) expressing HNF1beta conditionally. Using Flp recombinase we introduced wildtype or mutated HNF1beta at a defined chromosomal position allowing a most reproducible induction of the HNF1beta derivatives upon tetracycline addition. By oligonucleotide microarrays we identified 25 HNF1beta regulated genes. By an identical approach we identified that the closely related transcription factor HNF1alpha (TCF1) affects only nine genes in HEK293 cells and thus is a less efficient factor in these kidney cells. The HNF1beta target genes dipeptidyl peptidase 4 (DPP4), angiotensin converting enzyme 2 (ACE2) and osteopontin (SPP1) are most likely direct target genes, as they contain functional HNF1 binding sites in their promoter region. Since nine of the potential HNF1beta target genes are deregulated in clear cell carcinoma of the ovary, we propose that HNF1beta overexpression in the ovarian cancer participates in the altered expression pattern.

hyb_protocol: Hybridization, washing and staining of HG-U133A arrays (EukGE-WS2v4 protocol) was performed exactly as described in the Affymetrix Expression Technical Manual (rev. 3). Biotinylated hybridization controls (BioB, BioC, BioDN, CreX) from Affymetrix were included in the hybridization cocktail as recommended by Affymetrix.

scan_protocol: Arrays were scanned with an Affymetrix GeneArray 2500 scanner after the second staining step. GeneChip CEL files are deposited in the GEO raw data depository.

data_processing: Data extraction and normalization: Signals and detection calls were determined by single array analysis using the statistical algorithm implemented in the Affymetrix Microarray Suite 5.0 software. Global scaling to a target intensity of 1000 units was chosen as a normalization procedure.

label: Biotin

source_name: HEK293 cell line #2 with uninduced HNF1beta

label_protocol: Biotinylated cRNA targets were prepared starting with 13.5 microgram of total RNA exactly as described in the Affymetrix Expression Technical Manual (rev. 3). Polyadenylated B. subtilis DapX, LysX, PheX, ThrX, and TrpnX transcripts were added in staggered concentrations as polyA+ spike-in controls prior to cDNA synthesis.

growth_protocol: HEK293 cell line carrying the tetracycline inducible transgenes were generated and grown essentially as described in the Flp-In T-REx Core Kit Manual from Invitrogen.

extract_protocol: Total RNA was extracted using  TRIzol (Invitrogen). RNA quality was checked by agarose gel electrophoresis and found to show no signs of degradation. All cRNAs hybridized displayed 3’/5’-ratos for beta Actin below 2.0.

treatment_protocol: vehicle only

tag: Flp-InTMT-RExTM-293 (Invitrogen) cell line derived from the human embryonic kidney cell line HEK293 carrying tetracycline inducible transgene


title: Tamoxifen_human_sample 68


title: Tamoxifen_human_sample 44


title: HEK293_HNF1b_#2_induced

source_name: HEK293 cell line #2 with induced HNF1beta

treatment_protocol: 24 hrs tetracycline (1000 ng/ml) to induce expression of the transcription factor.


title: Tamoxifen_human_sample 62


title: Tamoxifen_human_sample 61


title: HEK293_HNF1b_#1_uninduced

source_name: HEK293 cell line #1 with uninduced HNF1beta


title: HEK293_HNF1b_#1_induced

source_name: HEK293 cell line #1 with induced HNF1beta


title: HEK293_HNF1a_#4_uninduced

source_name: HEK293 cell line #4 with uninduced HNF1alpha

treatment_protocol: vehile only


title: HEK293_HNF1a_#4_induced

source_name: HEK293 cell line #4 with induced HNF1alpha

treatment_protocol: 24 hrs tetracycline (1000 ng/ml) to induce expression of the transcription factors


title: HEK293_A263insGG_#5_uninduced

source_name: HEK293 cell line #5 with uninduced HNF1beta mutant A263insGG


title: HEK293_A263insGG_#5_induced

source_name: HEK293 cell line #5 with induced HNF1beta mutant A263insGG

treatment_protocol: 24 hrs tetracycline (1000 ng/ml) to induce expression of the transcription factors.


title: HEK293_HNF1a_#1_induced

source_name: HEK293 cell line #1 with induced HNF1alpha


title: HEK293_A263insGG_#6_induced


title: cysteine treated, 12 h, replicate 2

city: Crawley

first: Rachel

last: Clifton

state: Western Australia

address: 4th Floor CMS Building M310, University of Western Australia

department: Biochemistry, UWA

country: Australia

institute: Plant Energy Biology, ARC Centre of Excellence

description: Wild type Arabidopsis suspension cell culture, pale green in colour

organism: Arabidopsis thaliana

source_name: suspension cell culture, cysteine 12 h

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 120 ul of 1 M chloramphenicol to obtain a final concentration of 1 mM in the flask, samples were collected 12 h after treatment.

tag: Arabidopsis suspension cell culture, cv Lansberg erecta, 4 days post sub-culturing, sample collected 3  h post-treatment with treatment starting 2 h into the light cycle of a 16 h light 8 h dark light cycle


title: chloramphenicol treated, 12 h, replicate 1

source_name: suspension cell culture, chloramphenicol 12 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 100 ul of 0.24 M chloramphenicol to obtain a final concentration of 200 uM in the flask, samples were collected 12 h after treatment.


title: norflurazon treated, 12 h, replicate 1

source_name: suspension cell culture, norflurazon 12 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 100 ul of 120 mM rotenone to obtain a final concentration of 100 uM in the flask, samples were collected 12 h after treatment.


title: cysteine treated, 12 h, replicate 1


title: rotenone treated, 12 h, replicate 2

source_name: suspension cell culture, rotenone 12 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 480 ul of 10 mM rotenone to obtain a final concentration of 40 uM in the flask, samples were collected 12 h after treatment.


title: chloramphenicol treated, 12 h, replicate 2


title: Sox4 KO pancreas sample 1

city: San Francisco

first: Michael

middle: Scott

last: German

address: 513 Parnassus, HSW 1090

department: Diabetes Center

institute: University of California San Francisco

description:
The purpose of this experiment was to assess global changes in gene expression pattern in the pancreas from Sox4-/- embryos vs. pancreas from Sox4 wild-type embryos at embryonic day 12.5. [Sox4 gene knock-out (Schilham, M. W. et al. (1996) Defects in cardiac outflow tract formation and pro-B-lymphocyte expansion in mice lacking Sox-4. Nature 380, 711-4.)]
Sample preparation: embryonic pancreases from homozygous mutants and their wild-type littermates were isolated and then pooled in 2 groups for total RNA isolation. The RNA from both groups was then amplified using a linear amplification method and used to prepare the hybridization samples through indirect labeling. All protocols used are described below.
Protocol for RNA extraction: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase (Qiagen) according to the manufacturer’s protocol. http://www1.qiagen.com/literature/handbooks/PDF/RNAStabilizationAndPurification/FromAnimalAndPlantTissuesBacteriaYeastAndFungi/RNY_Mini/1016272HBRNY_062001WW.pdf
Protocol for RNA amplification: 2ug of total RNA were amplified with the MessageAmp aRNA Kit (Ambion). http://www.ambion.com/techlib/detail_results.html

Protocol for cDNA synthesis and labeling:  5 µg of amplified RNA was primed by 5 ug of a dT(16) oligomer and the mixture was heated to 70°C for 10 min, and then transferred to ice. A premixed solution, consisting of 200 U Superscript II (Gibco), buffer, 100mM DTT 0.5mM dNTP, was added to the RNA. The reaction was then incubated at 42°C for 2 hours. Nucleotides were used at these final concentrations: 0.5 mM for dATP, dCTP, and dGTP and 0.1 mM for dTTP and 0.4mM for aminoallyl-dUTP (Sigma ref: A0410). NaOH and EDTA were then added and RNA was hydrolyzed by incubation at 65°C for 15min. After neutralization using Hepes, the aminoallyl cDNA was purified using a Bio-spin6 column (BioRad, ref: 732-6002) and concentrated using Centricon-30 microconcentrators (Amicon, ref 42410). NaHCO3 pH9 was added to a final concentration of 0.05M and each cDNA was combined with an aliquot of Cy3 or Cy5 monofunctional dye ester (Amersham, ref: PA25001/2) and incubated for an hour of coupling in the dark. Dye-coupled cDNA was purified using Qiaquick column (Qiagen ref: UB300) and concentrated with a Centricon-30 microconcentrator.
Sample labeling: sample from Sox4-/- embryos was always labeled with Cy3, while sample from Sox4+/+ embryos was labeled with Cy5.
Hybridization protocol: Purified, labeled cDNA was resuspended in 11 µl of 3xSSC containing 0.75mg/ml polydA (Amersham ref: 27-4110-01), 25mM Hepes and 0.23 % SDS. Before hybridization, the solution was boiled for 2 min and then allowed to cool to room temperature. The solution was applied to the microarray under a cover slip, and the slide was placed in a custom hybridization chamber which was subsequently incubated for 12 to 16  hours in a water bath at 63°C. Before scanning, slides were washed in 0.6xSSC, 0.02% SDS for 1 min, and then 0.05xSSC for 1 min. Slides were dried before scanning by centrifugation at 500 rpm in a Beckman CS-6R centrifuge.
See detailed protocol on http://mmc.ucsf.edu/PDF%20files/Protocol%20MMC%20June04.pdf
However for these studies
-the amount of amplifiedRNA used was 5ug,
-the amount of oligodT to prime the reverse transcription reaction was 5ug,

Protocol for scanning and acquiring data
After hybridization and washing, the microarrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City California, USA) to detect Cy5 and Cy3 fluorescence. Data were acquired and analyzed using Genepix Pro-4 software (Axon instruments). The composite pixel intensity threshold for inclusion into a feature was set to 200 and the background subtraction based on feature local background median.

source_name: RNA from Sox4 WT littermates e12.5 pancreas

source_name: RNA from Sox4 KO littermates e12.5 pancreas


title: HEK293_A263insGG_#6_uninduced

source_name: HEK293 cell line #6 with uninduced HNF1beta mutant A263insGG


title: untreated 12 h replicate 2

source_name: suspension cell culture, untreated, 12 h


title: 100 uM salicylic acid treated, 3 h, replicate 2

source_name: suspension cell culture, 100 uM salicylic acid 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 120 ul of 100 mM salicylic acid to obtain a final concentration of 100 uM in the flask, samples were collected 3 h after treatment.


title: untreated 12 h replicate 1


title: 10 uM salicylic acid treated, 3 h, replicate 2

source_name: suspension cell culture, 10 uM salicylic acid 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 12 ul of 100 mM salicylic acid to obtain a final concentration of 10 uM in the flask, samples were collected 3 h after treatment.


title: 10 uM salicylic acid treated, 3 h, replicate 1


title: 100 uM salicylic acid treated, 3 h, replicate 1


title: rotenone treated, 3 h, replicate 2

source_name: suspension cell culture, rotenone 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 480 ul of 10 mM rotenone to obtain a final concentration of 40 uM in the flask, samples were collected 3 h after treatment.


title: Sox4 KO pancreas sample 6

description: The purpose of this experiment was to assess global changes in gene expression pattern in the pancreas from Sox4-/- embryos vs. pancreas from Sox4 wild-type embryos at embryonic day 12.5. [Sox4 gene knock-out (Schilham, M. W. et al. (1996) Defects in cardiac outflow tract formation and pro-B-lymphocyte expansion in mice lacking Sox-4. Nature 380, 711-4.)]

source_name: RNA from Sox4 WT littermates e12.5 pancrea

source_name: RNA from Sox4 KO littermates e12.5 pancrea


title: Sox4 KO pancreas sample 5


title: Sox4 KO pancreas sample 4


title: treated with N2 to replace air,  3 h, replicate 1

source_name: suspension cell culture, N2 air replacement, 3 h


title: norflurazon treated, 12 h, replicate 2


title: rotenone treated, 3 h, replicate 1


title: Sox4 KO pancreas sample 2


title: untreated 3 h replicate 4

source_name: suspension cell culture, untreated, 3 h


title: flagellen treated, 3 h, replicate 1

source_name: suspension cell culture, chloramphenicol 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of flagellen to obtain a final concentration of 1 uM in the flask, samples were collected 3 h after treatment.


title: cold treated, 3 h, replicate 1

treatment_protocol: 250 mL flasks of suspension cells were cold (10°C) treated, samples were collected 3 h after treatment.


title: flagellen treated, 3 h, replicate 2


title: treated with N2 gas to replace air,  3 h, replicate 2


title: Sox4 KO pancreas sample 3


title: rotenone treated, 12 h, replicate 1


title: cold treated, 3 h, replicate 2


title: untreated 3 h replicate 2


title: chitin treated, 3 h, replicate 2

source_name: suspension cell culture, chitin, 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of chitin to obtain a final concentration of 50 mg/L in the flask, samples were collected 3 h after treatment.


title: untreated 3 h replicate 3


title: 1.25 uM oligomycin treated, 3 h, replicate 2

source_name: suspension cell culture, 1.25 uM oligomycin, 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 150 uL of 1 mM oligomycin dissolved in ethanol to obtain a final concentration in the flask of 1.25 uM, samples were collected 3 h after treatment.


title: chloramphenicol treated, 3 h, replicate 2

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 100 ul of 0.24 M chloramphenicol to obtain a final concentration of 200 uM in the flask, samples were collected 3 h after treatment.


title: 1.25 uM oligomycin treated, 3 h, replicate 1


title: 0.125 uM oligomycin treated, 3 h, replicate 2

source_name: suspension cell culture, 0.125 uM oligomycin, 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 15 uL of 1 mM oligomycin dissolved in ethanol to obtain a final concentration in the flask of 0.125 uM, samples were collected 3 h after treatment.


title: chitin treated, 3 h, replicate 1


title: hydrogen peroxide treated, 3 h, replicate 2

source_name: suspension cell culture, 10 mM hydrogen peroxide, 3 h

treatment_protocol: 250 mL flasks of suspension cells were treated by the addition of 130 uL 8.82 M hydrogen peroxide to a final concentration of 10 mM samples were collected 3 h after treatment.


title: untreated 3 h replicate 1


title: chloramphenicol treated, 3 h, replicate 1


title: Mouse Brain - pons (MoPo.Feml)

status: Public on Oct 28 2005

type: MPSS

city: Hayward

first: Daixing

last: Zhou

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

description:
Strain: C57BL6
Mouse Brain - pons total RNA (MoPo.Feml) received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoPo.Feml.sig21
Cell type Mouse Brain - pons
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library 	DpnII restriction - (signature cloning using MmeI)
Sequence length	20 bp
MPSS:
runs
MoPo.Feml_sig21.5611F.a-20	10/24/2005	669173	15872	QC Passed
MoPo.Feml_sig21.5570F.f-20	9/28/2005	417791	11525	QC Passed
MoPo.Feml_sig21.5570W.c-20	9/13/2005	311048	12054	QC Passed
MoPo.Feml_sig21.5570W.b-20	8/26/2005	622967	11838	QC Passed
Run group:
Total Beads successfully sequenced - 2020979
Processed Signatures - 18810

source_name: Mouse Brain - pons total RNA


title: hydrogen peroxide treated, 3 h, replicate 1


title: Mouse Brain - pons (MoPo.Male)

description:
Strain: C57BL6
Mouse Brain - pons total RNA (MoPo.Male) received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoPo.Male.sig21
Cell type Mouse Brain - pons
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library 	DpnII restriction - (signature cloning using MmeI)
Sequence length	20 bp
MPSS:
runs
MoPo.Male_sig21.5582W.b-20	10/10/2005	706082	15936	QC Passed
MoPo.Male_sig21.5582F.b-20	10/7/2005	391648	11867	QC Passed
MoPo.Male_sig21.5582F.a-20	9/30/2005	538696	13345	QC Passed
MoPo.Male_sig21.5582W.a-20	9/30/2005	526920	18266	QC Passed
MoPo.Male_sig21.5569F.d-20	9/15/2005	429492	13175	QC Passed
Run group:
Total Beads successfully sequenced - 2592838
Processed Signatures - 21628


title: mannitol treated, 3 h, replicate 1

source_name: suspension cell culture, 3% (w/v) mannitol, 3 h


title: 0.125 uM oligomycin treated, 3 h, replicate 1


title: Mouse Brain - medulla (MoMe.Male)

description:
Strain: C57BL6
Mouse Brain - medulla total RNA (MoMe.Male) received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoMe.Male.sig21
Cell type Mouse Brain - medulla
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library 	DpnII restriction - (signature cloning using MmeI)
Sequence length	20 bp
MPSS:
runs
MoMe.Male_sig21.5566F.e-20	10/24/2005	669666	20197	QC Passed
MoMe.Male_sig21.5578W.d-20	9/23/2005	684889	20913	QC Passed
MoMe.Male_sig21.5566F.c-20	9/21/2005	549729	14565	QC Passed
MoMe.Male_sig21.5578W.b-20	9/12/2005	383858	13928	QC Passed
Run group:
Total Beads successfully sequenced - 2288142
Processed Signatures - 26581

source_name: Mouse Brain - medulla total RNA


title: X9B52 (HG-U133B)

status: Public on Oct 21 2005

city: Singapore

first: Lance

middle: David

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

country: Singapore

institute: Genome Institute of Singapore

description: Series of 251 tumours

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Breast Tumor

label_protocol: Approximately 10ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: Breast Tumor tissue


title: X90A63 (HG-U133B)

description: Series of 251 tumours


title: X94A16 (HG-U133B)

description: Series of 251 tumours


title: X85A03 (HG-U133B)

description: Series of 251 tumours


title: X87A79 (HG-U133B)

description: Series of 251 tumours


title: X84A44 (HG-U133B)

description: Series of 251 tumours


title: X79A35 (HG-U133B)

description: Series of 251 tumours


title: Mouse Brain - medulla (MoMe.Feml)

description:
Strain: C57BL6
Mouse Brain - medulla total RNA (MoMe.Feml) received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
Cells/tissue:
Library MoMe.Feml.sig21
Cell type Mouse Brain - medulla
Source NHGRI
RNA isolation LYNX mRNA QC passed
cDNA library:
Library 	DpnII restriction - (signature cloning using MmeI)
Sequence length	20 bp
MPSS:
runs
MoMe.Feml_sig21.5581F.b-20	10/7/2005	590400	16383	QC Passed
MoMe.Feml_sig21.5581W.a-20	9/30/2005	541564	16245	QC Passed
MoMe.Feml_sig21.5581F.a-20	9/30/2005	458500	13073	QC Passed
MoMe.Feml_sig21.5565W.d-20	9/13/2005	397702	12089	QC Passed
Run group:
Total Beads successfully sequenced - 1988166
Processed Signatures - 21773


title: X72A92 (HG-U133B)

description: Series of 251 tumours


title: X70A79 (HG-U133B)

description: Series of 251 tumours


title: X6B85 (HG-U133B)

description: Series of 251 tumours


title: X76A44 (HG-U133B)

description: Series of 251 tumours


title: X75A01 (HG-U133B)

description: Series of 251 tumours


title: X69A93 (HG-U133B)

description: Series of 251 tumours


title: X86A40 (HG-U133B)

description: Series of 251 tumours


title: X77A50 (HG-U133B)

description: Series of 251 tumours


title: X7B96 (HG-U133B)

description: Series of 251 tumours


title: X8B87 (HG-U133B)

description: Series of 251 tumours


title: X73A01 (HG-U133B)

description: Series of 251 tumours


title: X74A63 (HG-U133B)

description: Series of 251 tumours


title: X82A83 (HG-U133B)

description: Series of 251 tumours


title: X99A50 (HG-U133A)

description: Series of 251 tumours


title: X96A21 (HG-U133A)

description: Series of 251 tumours


title: X9B52 (HG-U133A)

description: Series of 251 tumours


title: HEK293_HNF1a_#1_uninduced

source_name: HEK293 cell line #1 with uninduced HNF1alpha

treatment_protocol: vehicle only


title: X67A43 (HG-U133B)

description: Series of 251 tumours


title: X88A67 (HG-U133A)

description: Series of 251 tumours


title: X66A84 (HG-U133B)

description: Series of 251 tumours