title: Large_male_head_repl3

source_name: Large male head epidermis

value: Onthophagus taurus

source_name: Large male abdominal epidermis

value: dissected dorsal abdominal epidermis


title: IHA_145_2

status: Public on Sep 15 2010

type: genomic

city: Baltimore

first: Peter

last: Murakami

state: MD

address: 855 N Wolfe St, Rangos 580

department: Center for Epigenetics

country: USA

institute: Johns Hopkins University

description:
IHA_145_2 input
IHA_145_2 methyl-depleted

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

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol.

data_processing:
Arrays were processed using Nimblescan 2.4 software. The data processing methods are described in Ayree, Z. Wu, C. Ladd-Acosta, B. Herb, A. Feinberg, S. Yegnasubramanian, R. Irizarry. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics, (2010).
Briefly, processing involved background correction using a modified RMA convolution model, a modified control-probe loess procedure for within-array normalization, between-array normalization using quantile normalization, and estimation of percentages.

molecule: genomic DNA

organism: Homo sapiens

source_name: Input fraction from IHA_145_2

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol.

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 1~5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with the endonuclease McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: cell type

value: lymphocyte

tag: bmi

tag: Sex

value: female

tag: timepoint

source_name: Methyl-depleted fraction from IHA_145_2


title: IHA_148_1

description:
IHA_148_1 input
IHA_148_1 methyl-depleted

source_name: Input fraction from IHA_148_1

source_name: Methyl-depleted fraction from IHA_148_1


title: Large_male_head_repl2

type: RNA

city: Bloomington

first: Emilie

last: Snell-Rood

state: IN

address: 915 E 3rd St MY150

department: Biology

institute: Indiana University

description: This project sought to identify shared and divergent patterns of gene expression between two male morphs (horned/fighter and hornless/sneaker) of horned beetles in the genus Onthophagus.  We were interested in whether morph-biased expression was as divergent as sex-biased expression, so we also surveyed patterns of gene expression in females.  We investigated gene expression in three epidermal tissues (head horn, thoracic horn and legs) with respect to dorsal abdomindal epidermis, which does not express outgrowths.  We also surveyed gene expression in the central brain, relative to neural ganglia.

hyb_protocol: Labeled aRNAs from test and reference samples (adjusted to a total of 60pmol dye for each) were mixed with KREAblock (ULS aRNA Fluorescent Labeling kit, Kreatech, Amsterdam, Netherlands) and 2x enhanced cDNA hybridization buffer (Genisphere), and then heated at 80°C for 10 min. Microarrays were pre-treated for one hour at 55°C in pre-hybridization buffer consisting of 5xSSC, 0.1%SDS, and 1% I-block (Applied Biosystems, CA). Both mixed sample and the microarrays were kept at 55°C until hybridization. Hybridization was performed in a dark humidified chamber at 55°C overnight. Microarrays were rinsed in buffer A (2xSSC/0.2%SDS) at 55°C and then incubated in buffer A at 65°C for 10min. Arrays were then transferred to 2xSSC (room temperature) for 10 min, followed by incubation in 0.2x SSC for 10min (room temperature). Arrays were then dried by centrifugation at 500rcf for 4 min.

scan_protocol: Microarrays were scanned using a GenePix scanner 4200 (Molecular Devices).

data_processing: Data were filtered and extracted using GenePix v.5.0 and imported into Bioconductor. Normalization for M-values was performed using spatial and intensity dependent Lowess smoothing in OLIN and differential expression was assessed using Limma.

molecule: total RNA

organism: Onthophagus taurus

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002 (PMID 12186645)) as follows. One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen). Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion). Amplified RNA (aRNA) was labeled with Cy5 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

growth_protocol: All animals were reared under controlled laboratory conditions.

extract_protocol: Total RNA was extracted from dissected tissue using Qiagen RNeasy kit according to the manufacturers protocol.

treatment_protocol: Wild type (unmanipulated) animals were used.

tag: species

tag: sex

value: male

tag: morph

value: large, horned

tag: developmental stage

value: pupae within 24hrs after pupation

tag: tissue

tag: sample type

value: tissue pooled from 4 individuals

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002 (PMID 12186645)) as follows. One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen). Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion). Amplified RNA (aRNA) was labeled with Cy3 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

value: dissected dorsal head epidermis (head horn)


title: Arabinose grown cells vs soluble Wheat arabinoxylan grown cells

city: Urbana

first: Carl

middle: James

last: Yeoman

state: IL

address: 1207 W Gregory ave

department: Institute for Genomic Biology

institute: University of Illinois

description: Biological replicate

hyb_protocol: 450ng in 10ul of each labelled cDNA (one labelled with Cy3, one with Cy5) was combined with 5ul of 10x Blocking agent (Agilent Technologies, Inc., Santa Clara, CA, USA), and this was combined with 25ul GEx Hybridization buffer HI-RPM (Agilent). The final solution was mixed with a pipettor, then 45ul was added to the array. The array was sealed within the hybridization chamber (Agilent Technologies, Inc.) and then incubated in an Hybridization oven (Agilent Technologies, Inc.) at 65 deg C for 16 hours. The hybridized arrays were subsequently transferred to a container of Wash solution 1 (Agilent Technologies, Inc.) and the coverslip was removed. The array was then washed firstly in a second volume of Wash solution 1 (Agilent Technologies, Inc.) and then in wash solution 2 (Agilent) prewarmed to 37 deg C, as per the manufacturers instructions. The slides were then dipped into a container of acetonitrile and finally rinsed in Stabilization and drying solution Agilent Technologies, Inc.) for 30 seconds. The slides were then removed and scanned immediately.

scan_protocol: Microarray slides were scanned at 5 uM using a GenePix professional 4200 scanner and GenePix 6.0 software (Molecular devices, Sunnyvale, CA). Scans were optimized using automated photo-multiplier tube (PMT) adjustment to give 0.02 % saturation.

data_processing: All resulting data was combined and analyzed using single channel analysis in bioconductor. Within array normalization was achieved using a background correction of half (anything below 0.5 is reset to 0.5).

organism: Xylanibacter ruminicola

source_name: Arabinose grown cells

label_protocol: cDNAs were labelled using Cy3 and Cy5 dyes (GE healthcare, Piscataway, NJ, USA) as per the manufacturers instructions, All conditions had a minimum of three biological replicates including a dye-swap. Each gene was represented on the array by 5 identical 70mer probes for technical replication.

growth_protocol: P. ruminicola 23 (ATCC19189) was cultured anaerobically at 39 deg C in basal media containing 1.3 % (NH4)2SO4, 0.1% Hemin, 0.09% of each KH2PO4, NaCl and Methionine, 0.002% of each CaCl2 and MgCl2, 0.001% FeSO4, 0.0001% CoCl, 2.8x10^-2 M acetate, 9x10^-3 M propionate, 4.5x10^-3 n-butyrate, and 9x10^-4 of each isobutyrate, n-valerate, isovalerate and DL-2-methylbutyrate. The medium was supplemented with 30 mM (or an equivalent weight based upon the major constituent sugar for di-, tri-, oligo- and poly-saccharides) of the tested carbohydrate source. Cells were grown to mid-exponential growth phase as determined by OD at 600nm and then harvested by centrifugation.

extract_protocol: Harvested cells were ground under liquid nitrogen using an oven sterilized pestle and mortar. Cell homogenates were incubated in 1ml of Trizol (Invitrogen, Carlsbad, CA, USA) for 5 minutes at room temperature and then transferred to a sterile eppendorf tube. The homogenate was mixed with 200 ul of chloroform and the mixture was centrifuged at 12,000 x g for 15 mins at 4 deg C. The upper-acqueous layer was collected and RNA precipitated using 0.5 ml of isopropanol. Total RNA was pelleted by centrifgation at 12,000 x g for 20 mins at 4 deg C and then washed in 70 % ethanol (made up in DEPC-treated sterile ddH2O), before being resuspended in sterile DEPC-treated ddH2O. The resuspended DNA was then purified using an RNeasy kit (Qiagen, Hilden, Germany) as per the manufacturers instructions. Purified RNAs were analyzed for quality using a Bioanalyzer RNA 6000 nano-assay. All samples used gave an RNA index number (RIN) of 9 or greater. Total RNA was transcribed to cDNA using the Fairplay III system (Stratagene, La Jolla, CA)

treatment_protocol: The treatments were the different carbohydrate sources provided in the media for P. ruminicola to grow on. These were supplemented into the media prior to innoculation.

tag: growth conditions

value: Arabinose grown

tag: strain

source_name: Soluble wheat arabinoxylan

value: Soluble wheat arabinoxylan


title: IHA_151_1

description:
IHA_151_1 input
IHA_151_1 methyl-depleted

source_name: Input fraction from IHA_151_1

source_name: Methyl-depleted fraction from IHA_151_1


title: Large_male_brain_repl2

source_name: Large male brain

value: dissected central brain and optic lobes

source_name: Large male ganglia

value: dissected subesophageal and thoracic ganglia


title: IHA_144_1

description:
IHA_144_1 input
IHA_144_1 methyl-depleted

source_name: Input fraction from IHA_144_1

source_name: Methyl-depleted fraction from IHA_144_1


title: Insoluble Wheat arabinoxylan grown cells vs Arabinose grown cells

description: Biological replicate

source_name: Insoluble wheat arabinoxylan grown cells

value: Insoluble wheat arabinoxylan grown


title: IHA_135_2

description:
IHA_135_2 input
IHA_135_2 methyl-depleted

source_name: Input fraction from IHA_135_2

source_name: Methyl-depleted fraction from IHA_135_2


title: Large_male_legs_repl2

source_name: Large male legs

value: dissected legs


title: Arabinose grown cells vs Raffinose grown cells

description: Biological replicate

source_name: Raffinose grown cells

value: Raffinose grown


title: Large_male_thorax_repl1

source_name: Large male abdominal epidermis

source_name: Large male thoracic epidermis

value: dissected dorsal prothoracic epidermis


title: IHA_134_1

description:
IHA_134_1 input
IHA_134_1 methyl-depleted

source_name: Input fraction from IHA_134_1

source_name: Methyl-depleted fraction from IHA_134_1


title: IHA_143_1

description:
IHA_143_1 input
IHA_143_1 methyl-depleted

source_name: Input fraction from IHA_143_1

source_name: Methyl-depleted fraction from IHA_143_1


title: Large_male_brain_repl1

value: Onthophagus taurus


title: Large_male_legs_repl1

value: dissected dorsal abdominal epidermis


title: 13912825 - Suc-SUL rep 2 vs Sdm8#25 rep 2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Find endogenous targets of SDE3, SDE5 and IR71.

hyb_protocol: Sdm8#25 repet2 Cy5 / Suc-SUL repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Sdm8#25 rep 2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Solid Media: 1x MS medium (Duchefa), 1% sucrose and 0.8% agar. Plants were grown in Petri dishes (12 x 12 cm). Liquid Media: 1x MS medium (Duchefa), 1% sucrose. Plants were grown in 24 wholes plates.

treatment_protocol: no treatment

tag: ecotype

tag: genotype

value: mutant (sdm8#25)

tag: age

value: 14 day

tag: dev_stage (boyes et al. plant cell 2001)

source_name: Suc-SUL rep 2

value: mutant (suc-sul)


title: 13912827 - Sdm8#25 rep 2 vs Suc-SUL rep 2

hyb_protocol: Suc-SUL repet2 Cy5 / Sdm8#25 repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Large_male_head_repl1

source_name: Large male head epidermis

value: male

value: large, horned


title: 13968001 - IR71 rep 1 vs Col rep 1

hyb_protocol: Col repet1 Cy5 / IR71 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col rep 1

extract_protocol: Col repet1:10ug. (Qiagen_RNeasy.pdf)

source_name: IR71 rep 1

extract_protocol: IR71 repet1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (ir71 ko n°3)


title: 13968000 - Col rep 1 vs IR71 rep 1

hyb_protocol: IR71 repet1 Cy5 / Col repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IHA_142_1

description:
IHA_142_1 input
IHA_142_1 methyl-depleted

source_name: Input fraction from IHA_142_1

value: lymphocyte

value: female

source_name: Methyl-depleted fraction from IHA_142_1


title: Female_legs_replicate4

source_name: Female legs

tag: size

value: range

value: pupae within 24hrs after pupation

value: tissue pooled from 4 individuals

source_name: Female abdominal epidermis


title: IHA_129_1

description:
IHA_129_1 input
IHA_129_1 methyl-depleted

source_name: Input fraction from IHA_129_1

tag: cell type

source_name: Methyl-depleted fraction from IHA_129_1


title: 13967998 - Col rep 3 vs sde5 rep 3

hyb_protocol: sde5 repet3 Cy5 / Col repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: sde5 rep 3

extract_protocol: sde5 repet3:10ug. (Qiagen_RNeasy.pdf)

value: mutant (sde5)

source_name: Col rep 3

extract_protocol: Col repet3:10ug. (Qiagen_RNeasy.pdf)


title: 13967999 - sde5 rep 3 vs Col rep 3

hyb_protocol: Col repet3 Cy5 / sde5 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IHA_131_1

description:
IHA_131_1 input
IHA_131_1 methyl-depleted

source_name: Input fraction from IHA_131_1

tag: bmi

source_name: Methyl-depleted fraction from IHA_131_1


title: 13967997 - sde3 rep 3 vs Col rep 3

hyb_protocol: Col repet3 Cy5 / sde3 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: sde3 rep 3

extract_protocol: sde3 repet3:10ug. (Qiagen_RNeasy.pdf)

value: mutant (sde3)


title: IHA_127_1

description:
IHA_127_1 input
IHA_127_1 methyl-depleted

source_name: Input fraction from IHA_127_1

tag: Sex

source_name: Methyl-depleted fraction from IHA_127_1


title: Female_brain_replicate4

source_name: Female ganglia

value: dissected subesophageal and thoracic ganglia

source_name: Female brain

value: dissected central brain and optic lobes


title: IHA_145_1

description:
IHA_145_1 input
IHA_145_1 methyl-depleted

source_name: Input fraction from IHA_145_1

tag: timepoint

source_name: Methyl-depleted fraction from IHA_145_1


title: 13967996 - Col rep 3 vs sde3 rep 3

hyb_protocol: sde3 repet3 Cy5 / Col repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Female_thorax_replicate3

source_name: Female prothoracic epidermis

tag: species

value: Onthophagus taurus

value: dissected dorsal prothoracic epidermis


title: 13912831 - sde5 rep 2 vs Col rep 2

hyb_protocol: Col repet2 Cy5 / sde5 repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col rep 2

extract_protocol: Col repet2:10ug. (Qiagen_RNeasy.pdf)

source_name: sde5 rep 2

extract_protocol: sde5 repet2:10ug. (Qiagen_RNeasy.pdf)


title: IHA_114_2

description:
IHA_114_2 input
IHA_114_2 methyl-depleted

source_name: Input fraction from IHA_114_2

source_name: Methyl-depleted fraction from IHA_114_2


title: Female_thorax_replicate4

source_name: Female abdominal epidermis

tag: sex

value: dissected dorsal abdominal epidermis


title: Female_legs_replicate3

source_name: Female legs

value: dissected legs


title: IHA_122_2

description:
IHA_122_2 input
IHA_122_2 methyl-depleted

source_name: Input fraction from IHA_122_2

source_name: Methyl-depleted fraction from IHA_122_2


title: Female_head_replicate3

source_name: Female head epidermis

value: dissected dorsal head epidermis


title: 13912830 - Col rep 2 vs sde5 rep 2

hyb_protocol: sde5 repet2 Cy5 / Col repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: 14 day


title: IHA_144_2

description:
IHA_144_2 input
IHA_144_2 methyl-depleted

source_name: Input fraction from IHA_144_2

source_name: Methyl-depleted fraction from IHA_144_2


title: Female_brain_replicate3


title: 13912829 - sde3 rep 2 vs Col rep 2

hyb_protocol: Col repet2 Cy5 / sde3 repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: sde3 rep 2

extract_protocol: sde3 repet2:10ug. (Qiagen_RNeasy.pdf)


title: IHA_122_1

description:
IHA_122_1 input
IHA_122_1 methyl-depleted

source_name: Input fraction from IHA_122_1

source_name: Methyl-depleted fraction from IHA_122_1


title: IHA_114_1

description:
IHA_114_1 input
IHA_114_1 methyl-depleted

source_name: Input fraction from IHA_114_1

source_name: Methyl-depleted fraction from IHA_114_1


title: IHA_109_2

description:
IHA_109_2 input
IHA_109_2 methyl-depleted

source_name: Input fraction from IHA_109_2

source_name: Methyl-depleted fraction from IHA_109_2


title: IHA_113_2

description:
IHA_113_2 input
IHA_113_2 methyl-depleted

source_name: Input fraction from IHA_113_2

source_name: Methyl-depleted fraction from IHA_113_2


title: Female_head_replicate4

description: This project sought to identify shared and divergent patterns of gene expression between two male morphs (horned/fighter and hornless/sneaker) of horned beetles in the genus Onthophagus.  We were interested in whether morph-biased expression was as divergent as sex-biased expression, so we also surveyed patterns of gene expression in females.  We investigated gene expression in three epidermal tissues (head horn, thoracic horn and legs) with respect to dorsal abdomindal epidermis, which does not express outgrowths.  We also surveyed gene expression in the central brain, relative to neural ganglia.


title: Female_legs_replicate2


title: 13912824 - IR71 rep 2 vs Col rep 2

hyb_protocol: Col repet2 Cy5 / IR71 repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col rep 2

source_name: IR71 rep 2

extract_protocol: IR71 repet2:10ug. (Qiagen_RNeasy.pdf)


title: 13912828 - Col rep 2 vs sde3 rep 2

hyb_protocol: sde3 repet2 Cy5 / Col repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IHA_87_1

description:
IHA_87_1 input
IHA_87_1 methyl-depleted

source_name: Input fraction from IHA_87_1

source_name: Methyl-depleted fraction from IHA_87_1


title: IHA_82_2

description:
IHA_82_2 input
IHA_82_2 methyl-depleted

source_name: Input fraction from IHA_82_2

source_name: Methyl-depleted fraction from IHA_82_2


title: IHA_129_2

description:
IHA_129_2 input
IHA_129_2 methyl-depleted

source_name: Input fraction from IHA_129_2

source_name: Methyl-depleted fraction from IHA_129_2


title: Female_thorax_replicate1

source_name: Female prothoracic epidermis

source_name: Female abdominal epidermis


title: IHA_85_1

description:
IHA_85_1 input
IHA_85_1 methyl-depleted

source_name: Input fraction from IHA_85_1

source_name: Methyl-depleted fraction from IHA_85_1


title: Female_brain_replicate2

source_name: Female brain

source_name: Female ganglia


title: IHA_85_2

description:
IHA_85_2 input
IHA_85_2 methyl-depleted

source_name: Input fraction from IHA_85_2

source_name: Methyl-depleted fraction from IHA_85_2


title: 13912516 - Suc-SUL rep 1 vs Sdm8#25 rep 1

hyb_protocol: Sdm8#25 repet1 Cy5 / Suc-SUL repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Sdm8#25 rep 1

value: mutant (sdm8#25)

source_name: Suc-SUL rep 1

value: mutant (suc-sul)


title: Female_legs_replicate1

source_name: Female legs


title: IHA_81_1

description:
IHA_81_1 input
IHA_81_1 methyl-depleted

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

source_name: Input fraction from IHA_81_1

value: lymphocyte

source_name: Methyl-depleted fraction from IHA_81_1


title: Female_head_replicate1

hyb_protocol: Labeled aRNAs from test and reference samples (adjusted to a total of 60pmol dye for each) were mixed with KREAblock (ULS aRNA Fluorescent Labeling kit, Kreatech, Amsterdam, Netherlands) and 2x enhanced cDNA hybridization buffer (Genisphere), and then heated at 80°C for 10 min. Microarrays were pre-treated for one hour at 55°C in pre-hybridization buffer consisting of 5xSSC, 0.1%SDS, and 1% I-block (Applied Biosystems, CA). Both mixed sample and the microarrays were kept at 55°C until hybridization. Hybridization was performed in a dark humidified chamber at 55°C overnight. Microarrays were rinsed in buffer A (2xSSC/0.2%SDS) at 55°C and then incubated in buffer A at 65°C for 10min. Arrays were then transferred to 2xSSC (room temperature) for 10 min, followed by incubation in 0.2x SSC for 10min (room temperature). Arrays were then dried by centrifugation at 500rcf for 4 min.

value: female

source_name: Female head epidermis


title: 13912517 - Sdm8#25 rep 1 vs Suc-SUL rep 1

hyb_protocol: Suc-SUL repet1 Cy5 / Sdm8#25 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IHA_79_2

description:
IHA_79_2 input
IHA_79_2 methyl-depleted

source_name: Input fraction from IHA_79_2

source_name: Methyl-depleted fraction from IHA_79_2


title: Female_brain_replicate1

value: range


title: Female_head_replicate2

value: pupae within 24hrs after pupation


title: 13912518 - Col rep 2 vs IR71 rep 2

hyb_protocol: IR71 repet2 Cy5 / Col repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: IR71 rep 2

source_name: Col rep 2


title: Female_thorax_replicate2

source_name: Female abdominal epidermis

value: tissue pooled from 4 individuals

source_name: Female prothoracic epidermis


title: IHA_77_2

description:
IHA_77_2 input
IHA_77_2 methyl-depleted

source_name: Input fraction from IHA_77_2

source_name: Methyl-depleted fraction from IHA_77_2


title: IHA_78_1

description:
IHA_78_1 input
IHA_78_1 methyl-depleted

source_name: Input fraction from IHA_78_1

source_name: Methyl-depleted fraction from IHA_78_1


title: IHA_78_2

description:
IHA_78_2 input
IHA_78_2 methyl-depleted

source_name: Input fraction from IHA_78_2

source_name: Methyl-depleted fraction from IHA_78_2


title: IHA_74_1

description:
IHA_74_1 input
IHA_74_1 methyl-depleted

source_name: Input fraction from IHA_74_1

source_name: Methyl-depleted fraction from IHA_74_1


title: Dex_ETOH_rep2

city: Berkeley

first: Jen-Chywan

last: Wang

state: CA

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were pre-processed using lumi package in R with bgAdjust.affy for background correction, quantile normalization, slide effect removed using linear model, and offset 80 added.

label: biotin

organism: Mus musculus

source_name: Differentiated 3T3-L1 cells treated with Dex

label_protocol: Biotin-labeled cRNA samples were prepared with 750 ng of total RNA template. Following synthesis and purification, the biotin-labeled samples were evaluated by both 260/280 absorbance spectrophotometry and capillary electrophoresis.

extract_protocol: Total cellular RNA was isolated utilizing the NucleoSpin RNA II kit (Macherey-Nagel), per the manufacturers’ directions. RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system per the manufacturers’ instruction.

tag: cell line

value: Mouse 3T3-L1

tag: treatment

value: dexamethasone


title: glucose-lactose1

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

hyb_protocol: Two individual ,  differentially labeled ,  cDNAs were incubated at  , 95° C for 3' cooled down  , to 68° C and mixed ,  (final-volume 20 µl). To ,  these mixed cDNAs 180 µl  , of pre-heated (68° C) ,  Slidehyb#1 hybridization ,  buffer (Ambion Austin ,  USA) was added and the ,  resulting solution was ,  applied on a pre-heated ,  slide (68° C). Slides were ,  then hybridized at 44° C for  , 16 hours. Subsequently ,  slides were washed at ,  42°C once in 1 x ,  SSC/0.2% SDS and twice  , in 1 x SSC and dried by ,  centrifugation (1 x SSC is ,  0.15 M NaCl and 0.15 M ,  Sodium Citrate).

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

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. Normalization across samples was performed by total signal correction

organism: Lactiplantibacillus plantarum

source_name: Lactose 1

label_protocol: Annealing Mix  x µl RNA preparation  (=5µg) y µl  nuclease-free water 1 µl  Random Nonamers 11  µl TOTAL 1. mix  Annealing Mix in a 200  µl PCR tube gently by  pipetting up and down  2. incubate for 5’ 70°C  3. cool at room  temperature for 10’  (annealing) 4. spin down  the mixture to the  bottom of the tube 5.  place on ice Reverse  transcription Reverse  Transcription Mix 4 µl 5x  buffer 2 µl 0.1 M DTT 1  µl dNTP-mix 1 µl  AA-dUTP 1 µl TMIII  (keep only briefly  outside 20°C) 20 µl  TOTAL 1. Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.  Incubate for 3 hrs at  42°C (in PCR-machine)  3. Cool on ice for  immediate purification or  place at 20°C for  storage Degradation of  mRNA 1. Add 2 µl 2.5 M  NaOH 2. Mix (vortex)  and spin down 3.  Incubate for 15 min. at  37°C 4. Add 10 µl 2 M  HEPES free acid 5. Mix  (vortex) and spin down  6. Ready for purification  or store at 20°C  Labelling and  purification of cDNA  with cyanine dyes  Followed Ge Healthcare  kit Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA code  RPN5661 Labelling of  amino allyl-modified  cDNA with CyDye 1.  Add the amino allyl  modified cDNA (in 0.1 M  sodium bicarbonate)  directly into one aliquot  of CyDye NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.  Incubate at room  temperature, in the dark  for 60 to 90 minutes 3.  Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4. Mix  by stirring and incubate  at room temperature, in  the dark, for 15 minutes  5. Proceed directly to  purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed  Ge Healthcare kit  Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA

growth_protocol: Cultures were grown in batch fermentation on a chemically defined medium contiang the specific sugar untill an optical density of 1.0 before harvesting

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

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

value: wild type WCFS1

tag: carbon source

value: Lactose

source_name: Glucose 1

value: Glucose


title: Dex_ETOH_rep1

description: replicate 1


title: Dex_ETOH_rep3

description: replicate 3


title: IHA_77_1

description:
IHA_77_1 input
IHA_77_1 methyl-depleted

source_name: Input fraction from IHA_77_1

source_name: Methyl-depleted fraction from IHA_77_1


title: SMAD2 binding targets in murine R1 ES cells (1/2)

city: Beijing

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565BA scanner and probe features were extracted using Feature Extraction Software (version 10.0)

data_processing: Log ratios were calculated by limma (Bioconductor package) and underwent Lowess normalization.

source_name: murine R1 ES cells, immuno-enriched DNA

label_protocol: DNA was labeled with CGH labeling kits (Invitrogen)

growth_protocol: Murine R1 ES cells were cultured under typical feeder free ES cell conditions (DMEM supplemented with Knockout serum replacement (Invitrogen Gibco), leukemia inhibitory factor (LIF), non-essential amino acids, GlutaMax-I (Invitrogen Gibco), β-mercaptoethanol and penicillin/streptomycin.

extract_protocol: R1 ES cells (5x107 – 1x108 cells) were chemically cross-linked by addition of one tenth volume of freshly-prepared 11% formaldehyde solution to cell media for 15 min at room temperature.  Cells were rinsed twice with 1xPBS, harvested using a silicon scraper, frozen in liquid nitrogen and stored at -80°C prior to use.  Cells were resuspended, lysed (1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, proteinase inhibitors), and sonicated to obtain DNA fragments of about 300-500bp length on average. Samples were then centrifuged at 14,000 rpm for 10 min. The supernatant was diluted (20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors) and pre-absorbed by 50 ul protein A beads (Zymed) and then incubated with 10 ug antibodies (anti-Smad1/5) overnight at 4°C. The immunocomplex was collected with 100 ul protein A beads by 3 hour co-incubation and then washed sequentially with TSE I (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors), TSE II (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, proteinase inhibitors), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 mM LiCl, 0.1% NP-40, 1% deoxycholate sodium) and TE (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0). The bound immunocomplex was eluted with 400 ul fresh elution buffer (25 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) by heating at 65°C with occasional vortex for 15 min and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract (WCE) DNA (Input fraction reserved from the sonication step) was also treated for crosslinking reversal. Immunoprecipitated DNA and WCE DNA were then purified by treatment with RNaseA, proteinase K and multiple phenol:chloroform:isoamyl alcohol extraction.

treatment_protocol: Undifferentiated ES cells under normal culture conditions

tag: sample type

value: Elute from a Smad2 chromatin immunoprecipitation

value: R1 ES cell

source_name: murine R1 ES cells, WCE DNA

value: Input for Smad2 chromatin immunoprecipitation


title: glucose-fructose2

source_name: Fructose 2

value: Fructose

source_name: Glucose 2


title: 3T3-L1_ETOH_rep3

description: replicate 3

source_name: Differentiated 3T3-L1 cells treated with ethanol

value: control


title: glucose-fructose1

source_name: Fructose 1


title: 3T3-L1_ETOH_rep2

description: replicate 2


title: IHA_73_1

description:
IHA_73_1 input
IHA_73_1 methyl-depleted

source_name: Input fraction from IHA_73_1

source_name: Methyl-depleted fraction from IHA_73_1


title: 3T3-L1_ETOH_rep1

description: replicate 1


title: glucose-mannose2

source_name: Mannose 2

value: Mannose


title: glucose-lactose2

source_name: Lactose 2


title: IHA_70_2

description:
IHA_70_2 input
IHA_70_2 methyl-depleted

source_name: Input fraction from IHA_70_2

source_name: Methyl-depleted fraction from IHA_70_2


title: glucose-mannose1

source_name: Mannose 1


title: IHA_71_1

description:
IHA_71_1 input
IHA_71_1 methyl-depleted

source_name: Input fraction from IHA_71_1

source_name: Methyl-depleted fraction from IHA_71_1


title: glucose-sucrose1

source_name: Glucose 1

source_name: Sucrose 1

value: Sucrose


title: IHA_69_1

description:
IHA_69_1 input
IHA_69_1 methyl-depleted

source_name: Input fraction from IHA_69_1

value: lymphocyte

value: male

source_name: Methyl-depleted fraction from IHA_69_1


title: IHA_58_2

description:
IHA_58_2 input
IHA_58_2 methyl-depleted

source_name: Input fraction from IHA_58_2

value: female

source_name: Methyl-depleted fraction from IHA_58_2


title: glucose-sucrose2

source_name: Sucrose 2

source_name: Glucose 2


title: IHA_69_2

description:
IHA_69_2 input
IHA_69_2 methyl-depleted

source_name: Input fraction from IHA_69_2

source_name: Methyl-depleted fraction from IHA_69_2


title: IHA_51_1

description:
IHA_51_1 input
IHA_51_1 methyl-depleted

source_name: Input fraction from IHA_51_1

source_name: Methyl-depleted fraction from IHA_51_1


title: IHA_37_2

description:
IHA_37_2 input
IHA_37_2 methyl-depleted

source_name: Input fraction from IHA_37_2

source_name: Methyl-depleted fraction from IHA_37_2


title: IHA_51_2

description:
IHA_51_2 input
IHA_51_2 methyl-depleted

source_name: Input fraction from IHA_51_2

source_name: Methyl-depleted fraction from IHA_51_2


title: IHA_37_1

description:
IHA_37_1 input
IHA_37_1 methyl-depleted

source_name: Input fraction from IHA_37_1

source_name: Methyl-depleted fraction from IHA_37_1


title: IHA_49_2

description:
IHA_49_2 input
IHA_49_2 methyl-depleted

source_name: Input fraction from IHA_49_2

source_name: Methyl-depleted fraction from IHA_49_2


title: IHA_49_1

description:
IHA_49_1 input
IHA_49_1 methyl-depleted

source_name: Input fraction from IHA_49_1

source_name: Methyl-depleted fraction from IHA_49_1


title: IHA_42_2

description:
IHA_42_2 input
IHA_42_2 methyl-depleted

source_name: Input fraction from IHA_42_2

source_name: Methyl-depleted fraction from IHA_42_2


title: IHA_42_1

description:
IHA_42_1 input
IHA_42_1 methyl-depleted

source_name: Input fraction from IHA_42_1

source_name: Methyl-depleted fraction from IHA_42_1


title: Cells exposed to 0.05mM octanoic acid versus cells exposed to 0.05mM decanoic acid

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

description:
I130Ea13.gpr; cells exposed to 0.05mM octanoic acid_Cy3, Cells exposed to 0.05mM decanoic acid_Cy5
I130Ea14b.gpr; Cells exposed to 0.05mM decanoic acid_Cy3, cells exposed to 0.05mM octanoic acid_Cy5

hyb_protocol: Hybridation and washing were performed as indicated in the ChipShot kit

scan_protocol: the arrays were read with a Genepix 4000B scanner (Axon Instrument Inc.) and analyzed with Genepix Pro 4.0 (Axon Instrument Inc.). Artifactual or saturated spots were excluded from the analysis.

data_processing: Raw data were further analyzed using the LIMMA GUI R package. Data were first normalized for each slide according to a print tip group lowess and then normalized between slides according to the quantile procedure and then a linear analysis was performed to detect the differentially expressed genes revealed by this experimental design. Only genes with for which a qvalue higher than 0.05 after Benjamini and Hochberg’s (1995) FDR adjustment for multiple tests has been applied were retained for further analysis .

organism: Saccharomyces cerevisiae

source_name: cells exposed to 0.05mM octanoic acid

label_protocol: Fluorescent cDNAs were prepared using a ChipShot™ labelling and clean-Up system (Promega) by direct labelling using CyDye-coupled dNTPs according to the manufacturer instructions.

growth_protocol: S. cerevisiae U13 strain was pre-cultivated overnight in 10 ml agitated YPD media. Then, cells were diluted in 300 ml fresh YPD (1l Erlenmeyer) to obtain an OD660 of 0.05 and grown aerobically at 28°C until an OD660 of 1–1.1 was reached.

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies). Cells sample corresponding to 50 DO units were pelleted by centrifugation (5000 × g for 5 min) in two microcentrifuge tubes, resuspended in 400 μl Trizol and broken by vortexing for 4 min with 300 μl glass beads. The two extracts were pooled and the total volume was adjusted to 4 ml with Trizol reagent. After incubation for 5 min at room temperature, 0.8 ml chloroform was added to separate the aqueous and the organic phase with a brief agitation. After incubation for 3 min at room temperature the solution was centrifuged at 10 000 × g for 15 min and the aqueous phase was recovered. The RNA was precipitated by addition of an equal volume of cold (−20 ◦C) isopropyl alcohol and centrifugation at 10 000 × g for 10 min. The precipitate has been further dissolved in 150μl of RNAse free water and 100μg of RNA were further cleaned up with a RNeasy kit cartridge (Qiagen).

treatment_protocol: Cultures were split in three and 10g/l octanoïc or decanoïc acid (Sigma) dissolved in ethanol was added at a final concentration of 0.05 mM to one third of the culture. The same volume of ethanol was added to the control culture which did not receive any fatty acid.

value: YPD aerobic culture grown at 28°C, 1OD

tag: agent

value: 20 minute exposure to octanoic acid

source_name: Cells exposed to 0.05mM decanoic acid

value: 20 minute exposure exposure to decanoic acid


title: Non treated cells versus cells exposed to 0.05mM octanoic acid

description:
I130Ea09.gpr; cells exposed to 0.05mM octanoic acid_Cy3, Non treated cells_Cy5
I130Ea12.gpr; Non treated cells_Cy3, cells exposed to 0.05mM octanoic acid_Cy5

source_name: Non treated cells

tag: strain

value: 20 minute exposure exposure to octanoic acid


title: IHA_28_2

description:
IHA_28_2 input
IHA_28_2 methyl-depleted

source_name: Input fraction from IHA_28_2

source_name: Methyl-depleted fraction from IHA_28_2


title: IHA_24_1

description:
IHA_24_1 input
IHA_24_1 methyl-depleted

source_name: Input fraction from IHA_24_1

source_name: Methyl-depleted fraction from IHA_24_1


title: Non treated cells versus cells exposed to 0.05mM decanoic acid

description:
I130Ea08.gpr; Non treated cells_Cy3, 0.05mM decanoic acid_Cy5
I130Ea11c.gpr; Cells exposed to 0.05mM decanoic acid_Cy3, Non treated cells_Cy5

source_name: 0.05mM decanoic acid


title: IHA_22_1

description:
IHA_22_1 input
IHA_22_1 methyl-depleted

source_name: Input fraction from IHA_22_1

source_name: Methyl-depleted fraction from IHA_22_1


title: IHA_36_1

description:
IHA_36_1 input
IHA_36_1 methyl-depleted

source_name: Input fraction from IHA_36_1

source_name: Methyl-depleted fraction from IHA_36_1


title: IHA_33_1

description:
IHA_33_1 input
IHA_33_1 methyl-depleted

source_name: Input fraction from IHA_33_1

source_name: Methyl-depleted fraction from IHA_33_1


title: IHA_18_2

description:
IHA_18_2 input
IHA_18_2 methyl-depleted

source_name: Input fraction from IHA_18_2

source_name: Methyl-depleted fraction from IHA_18_2


title: Adult cerebellum_rep2

status: Public on Sep 14 2010

city: Frederiksberg C

first: Agnieszka

last: Podolska

address: Grønnegårdsvej 3 2nd floor

department: Department of Basic Animal and Veterinary Sciences

country: Denmark

institute: Faculty of Life Sciences, University of Copenhagen,

description: Adult_cerebellum_small RNA fraction

hyb_protocol: The miRCURY™ LNA microRNA Microarray version 11.0 was used for the array studies. Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland) for 16 hours followed by stringent washes.

scan_protocol: Slides were dried and scanned. The analysis was performed using the relevant GenePix® Array Lists (GAL files) (www.exiqon.com). The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA) to generate Tagged Image File Format (TIFF) images. The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.

data_processing:
The text files, generated by Imagene v.8.0, were imported into Rosetta Resolver and normalized as previously described:
Book: MicroRNA Profiling in Cancer: A Bioinformatics perspective. 2009. Editor Yuriy Gusev. Chapter: Søkilde R, Kaczkowski B, Barken K B, Mouritzen P, Møller S, Litman T. "MicroRNA Expression Analysis by LNA Enhanced Microarrays".
Data was filtered by using probes showing a standard deviation (SD) above 0.1. The final, filtered data set consisted of intensity values for 1088 probes. All clustering and statistical analysis was performed in TMeV. PCA plot of samples was performed using all 1088 probes, by using a median centering of the data set. For the two-way hierarchical clustering, the 181 probes on the array annotated as pig microRNAs was used (see the 'GSE24106_pig_annotation.txt' supplementary file). In case of lack of annotation in pig, human probes were used. The 1- Pearson correlation coefficient was used as a distance metric. Each probe is mean-centered and compared to the mean expression.

organism: Sus scrofa

source_name: Adult cerebellum, small RNA fraction

label_protocol: A total of 200 ng of small RNA fraction was used for each sample. MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturers’ recommendations. Spike-ins (used as control probes) were added in equal amounts to each reaction and labeled.

extract_protocol: The small RNA fractions were isolated from the individual tissues using the miRVana™ microRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA).

tag: breed

value: crossbreed between Landrace, Yorkshire and Duroc

tag: tissue

value: cerebellum

tag: developmental stage

value: adult


title: Adult cerebellum_rep1

description: Adult_cerebellum_small RNA fraction


title: Adult cortex_rep3

description: Adult_cortex_small RNA fraction

source_name: Adult cortex, small RNA fraction

value: cortex


title: IHA_21_2

description:
IHA_21_2 input
IHA_21_2 methyl-depleted

source_name: Input fraction from IHA_21_2

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 1~5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with the endonuclease McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

source_name: Methyl-depleted fraction from IHA_21_2


title: IHA_21_1

description:
IHA_21_1 input
IHA_21_1 methyl-depleted

source_name: Input fraction from IHA_21_1

source_name: Methyl-depleted fraction from IHA_21_1


title: IHA_18_1

description:
IHA_18_1 input
IHA_18_1 methyl-depleted

source_name: Input fraction from IHA_18_1

source_name: Methyl-depleted fraction from IHA_18_1


title: F100 cerebellum_rep2

description: F100_cerebellum_small RNA fraction

source_name: F100 cerebellum, small RNA fraction

value: gestation day 100


title: F100 cortex_rep3

description: F100_cortex_small RNA fraction

source_name: F100 cortex, small RNA fraction


title: IHA_22_2

description:
IHA_22_2 input
IHA_22_2 methyl-depleted

source_name: Input fraction from IHA_22_2

source_name: Methyl-depleted fraction from IHA_22_2


title: Adult cerebellum_rep3

description: Adult_cerebellum_small RNA fraction


title: F100 cerebellum_rep3

description: F100_cerebellum_small RNA fraction


title: Adult cortex_rep1

description: Adult_cortex_small RNA fraction


title: IHA_27_1

description:
IHA_27_1 input
IHA_27_1 methyl-depleted

source_name: Input fraction from IHA_27_1

source_name: Methyl-depleted fraction from IHA_27_1


title: IHA_13_2

description:
IHA_13_2 input
IHA_13_2 methyl-depleted

source_name: Input fraction from IHA_13_2

source_name: Methyl-depleted fraction from IHA_13_2


title: F100 cerebellum_rep1

description: F100_cerebellum_small RNA fraction


title: F100 cortex_rep2

description: F100_cortex_small RNA fraction


title: IHA_12_2

description:
IHA_12_2 input
IHA_12_2 methyl-depleted

source_name: Input fraction from IHA_12_2

source_name: Methyl-depleted fraction from IHA_12_2


title: IHA_19_1

description:
IHA_19_1 input
IHA_19_1 methyl-depleted

source_name: Input fraction from IHA_19_1

source_name: Methyl-depleted fraction from IHA_19_1


title: IHA_10_2

description:
IHA_10_2 input
IHA_10_2 methyl-depleted

source_name: Input fraction from IHA_10_2

source_name: Methyl-depleted fraction from IHA_10_2


title: rel mutant early exponential

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

description: R. etli CFN42 rel mutant was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.3, representing early exponential phase.

hyb_protocol: The Cy3-labeled cDNA was hybridized to the custom R. etli tiling expression array at 42°C for 16 hour using the NimbleGen Hybridization System and kit.

scan_protocol: GenePix 4000B.

data_processing: Data preprocessing was done by performing a nonlinear intensity dependent rescaling on non-background corrected data. To this end, a loess fit normalization with a span of 25% was performed for each array compared against an artificial reference array, consisting of the median intensity values of each probe across all arrays. To ensure that the artificial reference itself was not altered by this rescaling, the artificial reference expression levels were chosen for the average log intensity in the loess fit (instead of the mean expression levels of the respective array and the artificial reference). A robust median-polish procedure was used to combine measurements from multiple probes into a single value. Results are linked as supplementary GFF files in standard format with columns: seqname (chromosome name); source (article); feature (RNA); start; end; score (normalized expression value); strand (left empty); frame (empty for RNA); attribute (ID).

organism: Rhizobium etli CFN 42

source_name: rel mutant R. etli CFN42 at OD600 = 0.3

label_protocol: cDNA, median≥400bp, was synthesized using random decamers (Ambion) and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s protocol. All cDNA samples were labeled with Cy3 by Nimblegen using the NimbleGen One- Color DNA Labeling Kit (05223555001).

extract_protocol: Total RNA was extracted using the TRIzol Plus RNA Purification kit (Invitrogen). Cells were resuspended in 1 ml of TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 seconds with 0.25 ml of 0.1 mm glass beads before following the manufacturer’s instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by two treatments of 2 μl TURBO DNase (Ambion) and afterwards checked by PCR (45 cycles). To increase RNA yields and account for experimental variation, RNA from 6 different cultures was pooled. RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate, washed twice in ethanol and dissolved in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Biorad, Hercules, CA, before and after precipitation ). The sample had an RNA Quality Indicator value of 10. The ncRNA peak could be detected in each sample. RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio was ≥ 2.

tag: genetic background

value: CFN 42

tag: genotype

value: rel mutant


title: F50 cerebellum_rep3

description: F50_cerebellum_small RNA fraction

source_name: F50 cerebellum, small RNA fraction

value: gestation day 50


title: Adult cortex_rep2

description: Adult_cortex_small RNA fraction

source_name: Adult cortex, small RNA fraction


title: IHA_10_1

description:
IHA_10_1 input
IHA_10_1 methyl-depleted

source_name: Input fraction from IHA_10_1

tag: cell type

source_name: Methyl-depleted fraction from IHA_10_1


title: rel mutant late exponential

description: R. etli CFN42 rel mutant was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.7, representing late exponential phase.

source_name: rel mutant R. etli CFN42 at OD600 = 0.7

extract_protocol: Total RNA was extracted using the TRIzol Plus RNA Purification kit (Invitrogen). Cells were resuspended in 1 ml of TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 seconds with 0.25 ml of 0.1 mm glass beads before following the manufacturer’s instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by two treatments of 2 μl TURBO DNase (Ambion) and afterwards checked by PCR (45 cycles). To increase RNA yields and account for experimental variation, RNA from 6 different cultures was pooled. RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate, washed twice in ethanol and dissolved in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Biorad, Hercules, CA, before and after precipitation ). The sample had an RNA Quality Indicator value of 10. RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio was ≥ 2.


title: rel mutant early stationary

description: R. etli CFN42 rel mutant was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at 6 hours after reaching the maximum OD, representing early stationary phase.

source_name: rel mutant R. etli CFN42 at 6 hours after reaching the maximum OD


title: IHA_12_1

description:
IHA_12_1 input
IHA_12_1 methyl-depleted

source_name: Input fraction from IHA_12_1

tag: bmi

source_name: Methyl-depleted fraction from IHA_12_1


title: F50 cortex_rep1

description: F50_cortex_small RNA fraction

source_name: F50 cortex, small RNA fraction


title: F50 cortex_rep2

description: F50_cortex_small RNA fraction


title: F50 cerebellum_rep1

description: F50_cerebellum_small RNA fraction


title: IHA_13_1

description:
IHA_13_1 input
IHA_13_1 methyl-depleted

source_name: Input fraction from IHA_13_1

tag: Sex

source_name: Methyl-depleted fraction from IHA_13_1


title: IHA_36_2

description:
IHA_36_2 input
IHA_36_2 methyl-depleted

source_name: Input fraction from IHA_36_2

tag: timepoint

source_name: Methyl-depleted fraction from IHA_36_2


title: IHA_19_2

description:
IHA_19_2 input
IHA_19_2 methyl-depleted

source_name: Input fraction from IHA_19_2

source_name: Methyl-depleted fraction from IHA_19_2


title: Heart_high salt_enalapril+paricalcitol_rep3

city: Abbott Park

first: Paul

last: Kroeger

address: 200 Abbott Park Road

department: R4DI, AP52-1N

institute: Abbott Laboratories

hyb_protocol: Standard Affymetrix hybridization protocols were used.

scan_protocol: Scanned with the Affymetrix GSC3000.

data_processing: Data were processed and analyzed using the Rosetta Resolver System with the Affymetrix Intensity Experiment Builder pipeline. The pipeline uses inter-chip scaling for normalization. Intensity values with associated p-values were derived using the pipeline.

organism: Rattus norvegicus

source_name: left ventricle, high salt for 5 weeks + 4 weeks with enalapril and paricalcitol

label_protocol: Biotinylated cRNA probes were prepared according to standard Affymetrix protocols using 5 ug of total RNA per sample.

extract_protocol: Total RNA from left ventricles was isolated using Qiagen RNeasy procedures (Qiagen, Valencia, CA). Quality of recovered RNA was assessed with the Agilent 2100 Bioanalyzer. RIN scores were above 9 for all samples.

value: Dahl salt sensitive (Harlan SS/Hsd)

tag: gender

tag: age

value: 15 weeks

value: heart, left ventricle

tag: diet

value: high salt (6% NaCl)

value: enalapril and paricalcitol

tag: treatment time

value: 4 weeks


title: IHA_9_2

description:
IHA_9_2 input
IHA_9_2 methyl-depleted

source_name: Input fraction from IHA_9_2

value: lymphocyte

value: male

source_name: Methyl-depleted fraction from IHA_9_2


title: Heart_high salt_enalapril+vehicle_rep3

source_name: left ventricle, high salt for 5 weeks + 4 weeks with enalapril and vehicle

tag: treatment

value: enalapril and vehicle


title: Heart_high salt_enalapril+paricalcitol_rep4


title: Heart_high salt_enalapril+vehicle_rep2


title: Heart_high salt_paricalcitol_rep4

source_name: left ventricle, high salt for 5 weeks + 4 weeks with paricalcitol

value: paricalcitol


title: Heart_high salt_enalapril+paricalcitol_rep2


title: IHA_9_1

description:
IHA_9_1 input
IHA_9_1 methyl-depleted

source_name: Input fraction from IHA_9_1

source_name: Methyl-depleted fraction from IHA_9_1


title: Heart_high salt_enalapril+paricalcitol_rep1


title: Heart_high salt_paricalcitol_rep2


title: Heart_high salt_enalapril+vehicle_rep1


title: Heart_high salt_control_rep3

source_name: left ventricle, high salt for 5 weeks

value: 11 weeks

value: untreated


title: Heart_high salt_control_rep2


title: IHA_6_1

description:
IHA_6_1 input
IHA_6_1 methyl-depleted

source_name: Input fraction from IHA_6_1

source_name: Methyl-depleted fraction from IHA_6_1


title: Heart_high salt+vehicle_rep3

source_name: left ventricle, high salt for 5 weeks + 4 weeks with vehicle

value: vehicle


title: Heart_high salt_paricalcitol_rep1


title: Heart_high salt_paricalcitol_rep3


title: Heart_high salt+vehicle_rep2


title: Heart_high salt+vehicle_rep4


title: Heart_high salt+vehicle_rep1


title: Heart_high salt_control_rep4


title: Heart_high salt_control_rep1


title: IHA_4_2

description:
IHA_4_2 input
IHA_4_2 methyl-depleted

source_name: Input fraction from IHA_4_2

source_name: Methyl-depleted fraction from IHA_4_2


title: F50 cerebellum_rep2

description: F50_cerebellum_small RNA fraction

source_name: F50 cerebellum, small RNA fraction

value: crossbreed between Landrace, Yorkshire and Duroc

value: cerebellum


title: Sqadipose_t5_Adlib_a6

first: Kelly

middle: Scott

last: Swanson

address: 1207 W. Gregory Dr.

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 24 weeks

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine 2.0  Genome Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages.

organism: Canis lupus familiaris

source_name: Subcutaneous adipose tissue at 24 weeks

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Dogs were fed ad libitum (n=5) or to maintain baseline body weight (control; n=4).

extract_protocol: Total RNA was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were randomized to either ad libitum (n=5) or body weight maintenance (n=4) feeding.  All dogs were fed Purina® Pro Plan® Performance Formula.  All subcutaneous adipose samples were collected after an overnight fasting period.

value: subcutaneous adipose

tag: animal id

tag: time point

value: 24 weeks

value: Ad libitum

tag: batch

value: Beagle


title: Sqadipose_t5_Adlib_a7

tag: breed


title: Sqadipose_t5_Adlib_a8

tag: tissue


title: F100 cortex_rep1

description: F100_cortex_small RNA fraction

source_name: F100 cortex, small RNA fraction

value: cortex

tag: developmental stage

value: gestation day 100


title: Sqadipose_t5_Adlib_a5


title: F50 cortex_rep3

description: F50_cortex_small RNA fraction

source_name: F50 cortex, small RNA fraction

value: gestation day 50


title: Sqadipose_t5_Con_a9

description: Control dog gene expression data from subcutaneous adipose tissure at 24 weeks

value: Control


title: Sqadipose_t4_Adlib_a2

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 12 weeks

source_name: Subcutaneous adipose tissue at 12 weeks

value: 12 weeks


title: Sqadipose_t5_Con_a1


title: Sqadipose_t5_Con_a4


title: Sqadipose_t5_Con_a3


title: IHA_4_1

description:
IHA_4_1 input
IHA_4_1 methyl-depleted

source_name: Input fraction from IHA_4_1

value: lymphocyte

value: male

source_name: Methyl-depleted fraction from IHA_4_1


title: Sqadipose_t4_Adlib_a6


title: Sqadipose_t4_Adlib_a8


title: Sqadipose_t4_Adlib_a5


title: Sqadipose_t5_Adlib_a2


title: Sqadipose_t4_Con_a1

description: Control dog gene expression data from subcutaneous adipose tissure at 12 weeks


title: Sqadipose_t4_Adlib_a7


title: Sqadipose_t4_Con_a4


title: Sqadipose_t4_Con_a3


title: Sqadipose_t3_Adlib_a5

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 8 weeks

source_name: Subcutaneous adipose tissue at 8 weeks

value: 8 weeks


title: Sqadipose_t3_Adlib_a6


title: Sqadipose_t3_Adlib_a7


title: Sqadipose_t3_Adlib_a2


title: Sqadipose_t4_Con_a9


title: Sqadipose_t3_Con_a9

description: Control dog gene expression data from subcutaneous adipose tissure at 8 weeks


title: Sqadipose_t3_Con_a1


title: Sqadipose_t3_Adlib_a8


title: Sqadipose_t3_Con_a4


title: Sqadipose_t2_Adlib_a6

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at 4 weeks

source_name: Subcutaneous adipose tissue at 4 weeks

value: 4 weeks


title: Sqadipose_t2_Adlib_a2


title: Sqadipose_t3_Con_a3


title: Sqadipose_t2_Adlib_a5


title: Sqadipose_t2_Con_a9

description: Control dog gene expression data from subcutaneous adipose tissure at 4 weeks


title: IHA_1_1

description:
IHA_1_1 input
IHA_1_1 methyl-depleted

source_name: Input fraction from IHA_1_1

source_name: Methyl-depleted fraction from IHA_1_1


title: Sqadipose_t2_Con_a4


title: Sqadipose_t2_Adlib_a7


title: Sqadipose_t2_Con_a3


title: Sqadipose_t1_Adlib_a8

description: Ad libitum fed dog gene expression data from subcutaneous adipose tissure at baseline

source_name: Subcutaneous adipose tissue at baseline

value: 0 weeks


title: Sqadipose_t2_Adlib_a8


title: Sqadipose_t1_Adlib_a7


title: breast tumor_219

city: Oslo

first: Simen

last: Myhre

address: Montebello

department: Dept of Genetics

country: Norway

institute: Oslo University Hospital

description:
HB004J6
219

hyb_protocol: 10ug labeled and fragmneted cRNA was hybridized onto single channel Applied Biosystems Human Genome Survey micro arrays v2.0 for 16 hours at 55ºC according to the manufacturer’s protocol.

scan_protocol: After hybridization, slides were manually washed and prepared according to manufacturers’ recommendation before image capturing using the AB1700 reader. Identification and quantification of gene expression signals, signal-to-noise ratios and flagging of failed spots were conducted using the Applied Biosystems Expression System software. Raw data files were exported for further analysis.

data_processing: First, flagged intensities and probes with signal to noise ratio below 3 were removed from the raw data. Next, the number of probes was further reduced to 17910, by removing those that had missing values in more that 80% of the samples. The quantile normalization procedure was applied using ABarray library in R and the missing values were imputed using the k-nearest neighbors algorithm of the smida library in R. After re-scaling the expression on each array so that they sum to 1 a log2 transformation was applied.

label: digoxigenin

source_name: Mastectomy bulk primary tumor

label_protocol: For each sample, Digoxigenin-UTP labeled cRNA was generated from 500 ng total RNA according to the NanoAmp RT-IVT Labeling Kit Protocol.

extract_protocol: Approximately 40 mg of tissue was used for total RNA extraction using the Qiagen Midi kit Extraction column procedure (Qiagen) after homogenisation using the Mixer Mill (MM301, Retsch). RNA quality was assessed using the NanoDrop instrument (concentration and purity), and the Agilent Bioanalyser instrument (degradation). Samples showing a degradation factor > 20 % were excluded from further analyses: the remaining 218 RNA samples of good quality were stored at -80C

treatment_protocol: Primary breast tumors were collected after mastectomy. Fresh frozen and kept in storage at minus 80 degrees celcius.

tag: assayname

tag: disease state

value: Mastectomy bulk primary tumor

tag: tumor epi %

tag: tumor-stroma %

tag: adipocyte cells%

tag: dm = 1 nodm = -1


title: breast tumor_217

description:
HB004JI
217


title: breast tumor_218

description:
HB004JA
218


title: Sqadipose_t2_Con_a1


title: Sqadipose_t1_Con_a9

description: Control dog gene expression data from subcutaneous adipose tissure at baseline


title: breast tumor_213

description:
HB004LO
213


title: Sqadipose_t1_Adlib_a6


title: breast tumor_211

description:
HB005HM
211


title: Sqadipose_t1_Con_a3


title: breast tumor_214

description:
HB004JO
214


title: breast tumor_216

description:
HB004JJ
216


title: Sqadipose_t1_Adlib_a5


title: Sqadipose_t1_Con_a1


title: breast tumor_210

description:
HB005HN
210


title: Sqadipose_t1_Adlib_a2


title: breast tumor_209

description:
HB005HP
209


title: breast tumor_207

description:
HB005HS
207


title: breast tumor_208

description:
HB005HR
208


title: breast tumor_205

description:
HB005S2
205


title: breast tumor_204

description:
HB005S4
204


title: breast tumor_206

description:
HB005S1
206


title: breast tumor_203

description:
HB005S5
203


title: breast tumor_201

description:
HB005S7
201


title: breast tumor_199

description:
HB005SA
199


title: breast tumor_190

description:
HB0060Y
190


title: breast tumor_195

description:
HB005WT
195


title: breast tumor_197

description:
HB005WL
197


title: breast tumor_198

description:
HB005SB
198


title: breast tumor_196

description:
HB005WS
196


title: breast tumor_191

description:
HB0060X
191


title: breast tumor_193

description:
HB0060V
193


title: breast tumor_192

description:
HB0060W
192


title: breast tumor_188

description:
HB00610
188


title: breast tumor_183

description:
HB00618
183


title: breast tumor_181

description:
HB0061A
181


title: breast tumor_202

description:
HB005S6
202


title: breast tumor_179

description:
HB0061C
179


title: breast tumor_194

description:
HB0060U
194


title: breast tumor_182

description:
HB00619
182


title: breast tumor_180

description:
HB0061B
180


title: breast tumor_184

description:
HB00614
184


title: breast tumor_176

description:
HB0061G
176


title: breast tumor_175

description:
HB0061H
175


title: breast tumor_187

description:
HB00611
187


title: breast tumor_177

description:
HB0061E
177


title: breast tumor_173

description:
HB0061J
173


title: breast tumor_174

description:
HB0061I
174


title: breast tumor_178

description:
HB0061D
178


title: breast tumor_171

description:
HB0061L
171


title: breast tumor_172

description:
HB0061K
172


title: breast tumor_169

description:
HB0061O
169


title: breast tumor_166

description:
HB0061R
166


title: breast tumor_167

description:
HB0061Q
167


title: breast tumor_168

description:
HB0061P
168


title: breast tumor_163b

description:
HB0061U
163b


title: breast tumor_165

description:
HB0061S
165


title: breast tumor_164

description:
HB0061T
164


title: breast tumor_160

description:
HB0061X
160


title: breast tumor_157

description:
HB00620
157


title: breast tumor_162

description:
HB0061V
162


title: breast tumor_186

description:
HB00612
186


title: breast tumor_158

description:
HB0061Z
158


title: breast tumor_156

description:
HB00621
156


title: breast tumor_155

description:
HB00622
155


title: breast tumor_163a

description:
HB00613
163a


title: breast tumor_153

description:
HB00624
153


title: breast tumor_159

description:
HB0061Y
159


title: breast tumor_170

description:
HB0061M
170


title: breast tumor_152

description:
HB00625
152


title: breast tumor_145

description:
HB0064N
145


title: breast tumor_148

description:
HB0064J
148


title: breast tumor_150

description:
HB0064H
150


title: breast tumor_140

description:
HB0064S
140


title: breast tumor_142

description:
HB0064Q
142


title: breast tumor_154

description:
HB00623
154


title: breast tumor_138

description:
HB0066W
138


title: breast tumor_143

description:
HB0064P
143


title: breast tumor_133

description:
HB00673
133


title: breast tumor_144

description:
HB0064O
144


title: breast tumor_137

description:
HB0066X
137


title: breast tumor_135

description:
HB00671
135


title: breast tumor_139

description:
HB0066V
139


title: breast tumor_134

description:
HB00672
134


title: breast tumor_131

description:
HB00677
131


title: breast tumor_130

description:
HB00678
130


title: breast tumor_127

description:
HB0067C
127


title: breast tumor_132

description:
HB00676
132


title: breast tumor_151

description:
HB0064G
151


title: breast tumor_136a

description:
HB0066Y
136a


title: breast tumor_124

description:
HB0067H
124


title: breast tumor_129

description:
HB00679
129


title: breast tumor_128

description:
HB0067B
128


title: breast tumor_123

description:
HB0067I
123


title: breast tumor_125

description:
HB0067G
125


title: breast tumor_136b

description:
HB004LV
136b


title: breast tumor_119

description:
HB006JC
119


title: breast tumor_120

description:
HB006JB
120


title: breast tumor_122

description:
HB0067J
122


title: breast tumor_121

description:
HB0067K
121


title: breast tumor_126

description:
HB0067D
126


title: breast tumor_104b

description:
HB006JS
104b


title: Sqadipose_t1_Con_a4


title: breast tumor_112

description:
HB006JK
112


title: breast tumor_105

description:
HB006JR
105


title: breast tumor_113

description:
HB006JJ
113


title: breast tumor_116

description:
HB006JF
116


title: breast tumor_117

description:
HB006JE
117


title: breast tumor_108

description:
HB006JO
108


title: breast tumor_111

description:
HB006JL
111


title: breast tumor_114

description:
HB006JI
114


title: breast tumor_104a

description:
HB0060Z
104a


title: breast tumor_115

description:
HB006JH
115


title: breast tumor_109

description:
HB006JN
109


title: breast tumor_106

description:
HB006JQ
106


title: breast tumor_118

description:
HB006JD
118


title: breast tumor_100

description:
HB006JW
100


title: breast tumor_200

description:
HB005S8
200


title: breast tumor_101

description:
HB006JV
101


title: breast tumor_102

description:
HB006JU
102


title: breast tumor_110

description:
HB006JM
110


title: breast tumor_107

description:
HB006JP
107


title: breast tumor_98

description:
HB006SM
98


title: breast tumor_99

description:
HB006JX
99


title: breast tumor_93

description:
HB006WU
93


title: breast tumor_95

description:
HB006SZ
95


title: breast tumor_94

description:
HB006T1
94


title: breast tumor_96

description:
HB006SV
96


title: breast tumor_92

description:
HB006WV
92


title: breast tumor_97

description:
HB006SP
97


title: breast tumor_88

description:
HB006WZ
88


title: breast tumor_89

description:
HB006WY
89


title: breast tumor_90

description:
HB006WX
90


title: breast tumor_82

description:
HB006X5
82


title: breast tumor_79a

description:
HB006X9
79a


title: breast tumor_78

description:
HB006XA
78


title: breast tumor_85

description:
HB006X2
85


title: breast tumor_79b

description:
HB006JT
79b


title: breast tumor_83

description:
HB006X4
83


title: breast tumor_74

description:
HB006XE
74


title: breast tumor_84

description:
HB006X3
84


title: breast tumor_73

description:
HB006XF
73


title: breast tumor_76b

description:
HB006XC
76b


title: breast tumor_75

description:
HB006XD
75


title: breast tumor_68

description:
HB008N1
68


title: breast tumor_76a

description:
HB0064M
76a


title: breast tumor_62

description:
HB008N7
62


title: breast tumor_65

description:
HB008N4
65


title: breast tumor_67

description:
HB008N2
67


title: breast tumor_61

description:
HB008N8
61


title: breast tumor_60

description:
HB008NA
60


title: breast tumor_87

description:
HB006X0
87


title: breast tumor_80

description:
HB006X7
80


title: breast tumor_77

description:
HB006XB
77


title: breast tumor_58

description:
HB008NC
58


title: breast tumor_69

description:
HB008I5
69


title: breast tumor_57b

description:
HB0061W
57b


title: breast tumor_71

description:
HB008HW
71


title: breast tumor_56

description:
HB008NE
56


title: breast tumor_57a

description:
HB008ND
57a


title: breast tumor_55

description:
HB008NF
55


title: breast tumor_50b

description:
HB008NO
50b


title: breast tumor_50a

description:
HB006X1
50a


title: breast tumor_51

description:
HB008NJ
51


title: breast tumor_53

description:
HB008NH
53


title: breast tumor_52

description:
HB008NI
52


title: breast tumor_47

description:
HB008NT
47


title: breast tumor_48

description:
HB008NQ
48


title: breast tumor_49

description:
HB008NP
49


title: breast tumor_43b

description:
HB008NZ
43b


title: breast tumor_39a

description:
HB0064I
39a


title: breast tumor_42

description:
HB008O2
42


title: breast tumor_37c

description:
HB008OB
37c


title: breast tumor_59

description:
HB008NB
59


title: breast tumor_39b

description:
HB008O8
39b


title: breast tumor_46

description:
HB008NW
46


title: breast tumor_40

description:
HB008O6
40


title: breast tumor_38

description:
HB008O9
38


title: breast tumor_41

description:
HB008O3
41


title: breast tumor_43a

description:
HB008NG
43a


title: breast tumor_45

description:
HB008NX
45


title: breast tumor_35

description:
HB009BM
35


title: breast tumor_37b

description:
HB006X6
37b


title: breast tumor_36

description:
HB008OD
36


title: breast tumor_33a

description:
HB004JN
33a


title: breast tumor_37a

description:
HB008N6
37a


title: breast tumor_33b

description:
HB009BP
33b


title: breast tumor_31

description:
HB009GD
31


title: breast tumor_28

description:
HB009GG
28


title: breast tumor_29

description:
HB009GF
29


title: breast tumor_32

description:
HB009BQ
32


title: breast tumor_27

description:
HB009GH
27


title: breast tumor_30

description:
HB009GE
30


title: breast tumor_26

description:
HB009GI
26


title: breast tumor_20b

description:
HB009GO
20b


title: breast tumor_22b

description:
HB009GM
22b


title: breast tumor_21

description:
HB009GN
21


title: breast tumor_23

description:
HB009GL
23


title: breast tumor_22a

description:
HB008N3
22a


title: breast tumor_24

description:
HB009GK
24


title: breast tumor_16

description:
HB009GS
16


title: breast tumor_19

description:
HB009GP
19


title: breast tumor_25

description:
HB009GJ
25


title: breast tumor_12

description:
HB009GX
12


title: breast tumor_18

description:
HB009GQ
18


title: breast tumor_11

description:
HB009GY
11


title: breast tumor_9

description:
HB009H1
9


title: breast tumor_17

description:
HB009GR
17


title: breast tumor_8

description:
HB009H2
8


title: breast tumor_20a

description:
HB0064K
20a


title: breast tumor_10a

description:
HB009H0
10a


title: breast tumor_15

description:
HB009GT
15


title: breast tumor_5

description:
HB009H5
5


title: breast tumor_6

description:
HB009H4
6


title: breast tumor_14

description:
HB009GV
14


title: breast tumor_3

description:
HB009H7
3


title: breast tumor_2

description:
HB009H8
2


title: breast tumor_4

description:
HB009H6
4


title: Human Colonic Epithelial Cell line 1CT7C

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

description: Hybridized to SNP_5.4

hyb_protocol: Samples were hybridized with Affymetrix Genome-Wide Human SNP 5.0 according to manufacterer's protocol.

scan_protocol: The arrays were washed and stained on an Affymetrix Fluidics Station 450 using GCOS and GTYPE.

data_processing:
CEL files and TXT files were generated by Affymetrix GTYPE. Male Reference samples used were from the HapMap project this dataset can be found at http://www.affymetrix.com/support/technical/sample_data/genomewide_snp5_data.affx.
dChip software was used to process and normalize (Cheng Li and Wing Hung Wong (2001a) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl. Acad. Sci. Vol. 98, 31-36) and also for SNP analysis (Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH*, Li C*. (2004) dChipSNP: Significance Curve and Clustering of SNP-Array-Based Loss-of-Heterozygosity Data. Bioinformatics. 20: 1233-1240) for copy number variation.  The GSE24092_log2ratio_data.txt.gz contains the inferred log2ratios.

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Cells were maintained on Primaria culture plates under 2% oxygen and 5% carbon dioxide and cultured under standard growth conditions (4:1 high-glucose DMEM:medium 199 with 2% cosmic calf serum, 20ng/mL EGF, 1mg/mL hydrocortisone, 10mg/mL insulin, 2mg/mL transferrin, and 5nM sodium selenite).

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue Kit.

treatment_protocol: Untreated

tag: cell type

value: Human colonic epithelial cells

value: colon

tag: cell line

tag: gender

value: Male


title: breast tumor_13

description:
HB009GW
13


title: breast tumor_1

description:
HB009HA
1


title: Control 2 vs. Menopausal 3

city: Tucson

first: Heddwen

middle: L

last: Brooks

state: AZ

address: PO Box 245218 1656 E Mabel

institute: University of Arizona

description: Control mouse kidney cortex 2 vs. Menopausal mouse kidney cortex 3

hyb_protocol: cDNA was  hybridized to slides in the presence of Cot-1 cDNA (Invitrogen, cat.#  18440-016) for 16-24 hours at 42°C in a hybridization buffer containing 8X SSC,  60% Formamide, and 0.2% SDS.  After completion, a  short wash was run after which the slide was removed and dipped in 0.05X SSC to remove any  residual nonhybridized cDNA.

scan_protocol: Fluorescent array images were collected for both Alexa Fluor 546 and Alexa Fluor 647 with an arrayWoRxe biochip reader and software.  Description

data_processing: After local background subtraction, data was linlog (base 2) transformed and LOWESS normalized.

label: Alexa Fluor 546

source_name: Control

label_protocol: Total RNA was amplified using the Message Amp aRNA kit from  Ambion (cat.# 1750), following the kit's protocols for First and Second-strand cDNA synthesis (Parts B and C), cDNA purification (Part E), and In Vitro  Transcription to Synthesize aRNA (Part F).   Amplified aRNA was converted to single-stranded cDNA with incorporation  of amino allyl dUTP using the Ambion EndoFree RT kit (cat.# 1740).  The cDNA was labeled with Alexa fluor via the  free amine modification.

extract_protocol: total RNA was extracted from kidney cortex using Qiagen Rneasy mini columns according the the manufacturer's protocol

label: Alexa Fluor 647

source_name: Menopausal

value: VCD

value: Menopausal


title: Human Colonic Epithelial Cell line 1CT

description: Hybridized to SNP_5.1

source_name: Human Colonic Epithelial Cell line 1CT


title: Menopausal 3 vs. Control 1

description: Menopausal mouse kidney cortex 3 vs. Control mouse kidney cortex 1


title: Control 3 vs. Menopausal 1

description: Control mouse kidney cortex 3 vs. Menopausal mouse kidney cortex 1