title: DH6-HHCY dogs

city: Valhalla

first: Caroline

last: Ojaimi

state: NY

institute: New York Medical College

description: DH6- chronic HHCY dog. Dog was fed methionine in drinking water for two weeks.

label: Affymetrix labeling

organism: Canis lupus familiaris

source_name: Cardiac tissues

tag: Male dogs weighing 23-27 kg; Tissue

value: cardiac cells


title: 1 C DMSO/Vehicle/6h/NG

status: Public on Dec 31 2006

type: RNA

city: Chapel Hill

first: Monte

middle: S

last: Willis

state: NC

address: 103 Mason Farm Road

department: Pathology & Laboratory Medicine

country: USA

institute: UNC

description: Gene expression analysis was conducted using Agilent G4130A Rat 22K microarray slides.  Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.  2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol.  Slides were  washed as indicated in the Agilent protocol.  Arrays were then scanned with an Axon GenePix 4000b.  Data was obtained using the GenePix Pro 6 software package.

data_processing: loess normalization, log2 transformation

molecule: total RNA

organism: Rattus norvegicus

source_name: RNA prepared from 1 day old whole rat pups

extract_protocol: GITC/Phenol/CHcl3 extraction CsCl2 banding

treatment_protocol: Untreated rat pups for reference RNA

tag: 1 day old whole rat pups

source_name: Rat aortic smooth muscle (tmt: DMSO/Vehicle/6h/NG )

growth_protocol: The rat aortic smooth muscle cells were maintained at 37oC (5% CO2) in Dulbecco Minimal Essential Medium supplemented with 10% FBS, 2 mM L-glutamine, 100U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.

treatment_protocol: Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with drug/vehicle, insulin/vehicle in NG/HG for 6/24 hours and were extracted for RNA.

tag: Cell line

value: Rat aortic smooth muscle cells (RASMC)


title: 2 A DMSO/Vehicle/24h/NG

hyb_protocol: 2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol.

scan_protocol: Slides were  washed as indicated in the Agilent protocol.  Arrays were then scanned with an Axon GenePix 4000b.  Data was obtained using the GenePix Pro 6 software package.

label_protocol: Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.

source_name: Rat aortic smooth muscle (tmt: DMSO/Vehicle/24h/NG )


title: 7 D DMSO/Insulin/6h/HG

source_name: Rat aortic smooth muscle (tmt: DMSO/Insulin/6h/HG)


title: 7 C DMSO/Insulin/6h/HG


title: 1 A DMSO/Vehicle/6h/NG


title: DH7-HHCY dogs

description: DH7- chronic HHCY dog. Dog was fed methionine in drinking water for two weeks.

source_name: cardiac tissues


title: DC1-Control dog

description: DC1- control dog for hyperhomocysteinemia study

source_name: Cardiac Tissue


title: DH8-HHCY dogs

description: DH8- chronic HHCY dog. Dog was fed methionine in drinking water for two weeks.


title: DC3-Control dog

description: DC3- control dog for hyperhomocysteinemia study


title: DC2-Control dog

description: DC2- control dog for hyperhomocysteinemia study


title: DH5-HHCY dogs

description: DH5- chronic HHCY dog. Dog was fed methionine in drinking water for two weeks.


title: 8 D DMSO/Insulin/24h/HG

source_name: Rat aortic smooth muscle (tmt: DMSO/Insulin/24h/HG)


title: 7 B DMSO/Insulin/6h/HG


title: 8 B DMSO/Insulin/24h/HG


title: DC4-Control dog

description: DC4- control dog for hyperhomocysteinemia study


title: 8 A DMSO/Insulin/24h/HG


title: 7 A DMSO/Insulin/6h/HG


title: 6 D DMSO/Insulin/24h/NG

source_name: Rat aortic smooth muscle (tmt: DMSO/Insulin/24h/NG)


title: 5 C DMSO/Insulin/6h/NG

source_name: Rat aortic smooth muscle (tmt: DMSO/Insulin/6h/NG)


title: 6 B DMSO/Insulin/24h/NG


title: 5 D DMSO/Insulin/6h/NG


title: 6 C DMSO/Insulin/24h/NG


title: 6 A DMSO/Insulin/24h/NG


title: 5 B DMSO/Insulin/6h/NG


title: 5 A DMSO/Insulin/6h/NG


title: Muscle_freeze_6h_rep446

city: Morgantown

first: Petia

middle: P

last: Simeonova

state: WV

address: 1095 Willowdale Rd.

institute: NIOSH, CDC

description: Mouse sacrificed at 6-hours post-injury and injured tibialis anterior muscle excised

hyb_protocol: As per Affmetrix Expression Analysis Technical Manual

label: Phycoerythrin

organism: Mus musculus

source_name: Muscle, freeze injury, 6 hours post-injury, sample 446

extract_protocol: Homogenize in TRIzol followed by purification with Qiagen RNeasy Mini kit

treatment_protocol: Injured using 6-mm diameter steel probe cooled to temperature of dry ice; applied for 10 seconds

tag: Strain

tag: Gender

value: female

tag: Age

value: 2-3 months

tag: Tissue

value: Tibialis anterior muscle


title: Muscle_freeze_6h_rep418

scan_protocol: As per Affmetrix Expression Analysis Technical Manual

source_name: Muscle, freeze injury, 6 hours post-injury, sample 418


title: Muscle_freeze_7d_rep454

description: Mouse sacrificed at 7-days post-injury and injured tibialis anterior muscle excised

source_name: Muscle, freeze injury, 7 days post-injury, sample 454

label_protocol: As per Affmetrix Expression Analysis Technical Manual


title: Muscle_freeze_3d_rep436

description: Mouse sacrificed at 3-days post-injury and injured tibialis anterior muscle excised

source_name: Muscle, freeze injury, 3 days post-injury, sample 436


title: Muscle_freeze_1d_rep460

description: Mouse sacrificed at 1-day post-injury and injured tibialis anterior muscle excised

source_name: Muscle, freeze injury, 1 day post-injury, sample 460


title: Muscle_freeze_3d_rep468

source_name: Muscle, freeze injury, 3 days post-injury, sample 468


title: Muscle_freeze_7d_rep440

source_name: Muscle, freeze injury, 7 days post-injury, sample 440


title: Muscle_freeze_3d_rep450

source_name: Muscle, freeze injury, 3 days post-injury, sample 450


title: Muscle_freeze_6h_rep432

source_name: Muscle, freeze injury, 6 hours post-injury, sample 432


title: Muscle_contraction_6h_rep445

source_name: Muscle, contraction injury, 6 hours post-injury, sample 445

treatment_protocol: Injured by 150 in vivo eccentric contractions


title: Muscle_control_rep3

description: Mouse sacrificed and tibialis anterior muscle excised

source_name: Muscle, control, sample 3


title: Muscle_contraction_7d_rep453

source_name: Muscle, contraction injury, 7 days post-injury, sample 453


title: Muscle_control_rep1

source_name: Muscle, control, sample 1


title: Muscle_contraction_7d_rep425

source_name: Muscle, contraction injury, 7 days post-injury, sample 425


title: Muscle_contraction_6h_rep417

source_name: Muscle, contraction injury, 6 hours post-injury, sample 417


title: Muscle_freeze_1d_rep422

source_name: Muscle, freeze injury, 1 day post-injury, sample 422


title: Muscle_freeze_1d_rep464

source_name: Muscle, freeze injury, 1 day post-injury, sample 464


title: Muscle_contraction_7d_rep439

source_name: Muscle, contraction injury, 7 days post-injury, sample 439


title: Muscle_contraction_6h_rep431

source_name: Muscle, contraction injury, 6 hours post-injury, sample 431


title: Muscle_control_rep2

source_name: Muscle, control, sample 2


title: Muscle_contraction_3d_rep449

source_name: Muscle, contraction injury, 3 days post-injury, sample 449


title: Muscle_contraction_3d_rep435

source_name: Muscle, contraction injury, 3 days post-injury, sample 435


title: Muscle_contraction_1d_rep463

source_name: Muscle, contraction injury, 1 day post-injury, sample 463


title: NOD Dbl single positive rep 3

status: Public on Dec 30 2006

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: NOD negative selection CD4+ thymocytes

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

source_name: mouse thymocyte

label_protocol: Affymetrix GeneChip Eukaryotic Small Sample Target Labelling Assay Version II protocol was used on total RNA from 100000-1000000 cells

extract_protocol: Total RNA was extracted from sorted thymus using trizol and further purified using RNeasy spin columns.

tag: NOD diabetic, 6-8 week old, double transgenic TCR:insHEL, CD4+ thymocytes


title: 36 C Rapa 1/Vehicle/24h/HG

source_name: RNA prepared from 1 day old whole rat pups

source_name: Rat aortic smooth muscle (tmt: Rapa 1/Vehicle/24h/HG)


title: NOD Dbl single positive rep 2

description: NOD negative selection CD4+ thymocytes


title: Muscle_contraction_1d_rep421

source_name: Muscle, contraction injury, 1 day post-injury, sample 421


title: NOD Dbl single positive rep 1

description: NOD negative selection CD4+ thymocytes


title: B10 TCR single positive rep 3

description: B10 positive selection CD4+ thymocytes

tag: B10, 6-8 week old, CD4+ thymocytes


title: B10 TCR single positive rep 2

description: B10 positive selection CD4+ thymocytes


title: B10 Dbl double positive rep 3

description: B10 pre-selection double transgenic TCR:insHEL thymocytes

tag: B10, 6-8 week old, double transgenic TCR:insHELfemale mouse, double positive  thymocytes


title: B10 Dbl single positive rep 1

description: B10 negative selection CD4+ thymocytes

tag: B10, 6-8 week old, double transgenic TCR:insHEL, CD4+ thymocytes


title: B10 TCR single positive rep 1

description: B10 positive selection CD4+ thymocytes


title: NOD Dbl double positive rep 2

description: NOD pre-selection double transgenic TCR:insHEL thymocytes

tag: NOD diabetic, 6-8 week old, double transgenic TCR:insHELfemale mouse, double positive  thymocytes


title: B10 Dbl single positive rep 3

description: B10 negative selection CD4+ thymocytes


title: NOD TCR single positive rep 2

description: NOD positive selection CD4+ thymocytes

tag: NOD diabetic, 6-8 week old, CD4+ thymocytes


title: Muscle_contraction_3d_rep467

source_name: Muscle, contraction injury, 3 days post-injury, sample 467


title: NOD TCR single positive rep 1

description: NOD positive selection CD4+ thymocytes


title: NOD TCR double positive rep 3

description: NOD pre-selection transgenic TCR thymocytes

tag: NOD diabetic, 6-8 week old female mouse, double positive thymocytes


title: B10 Dbl double positive rep 2


title: NOD Dbl double positive rep 3


title: NOD TCR double positive rep 1


title: NOD Dbl double positive rep 1


title: NOD TCR double positive rep 2


title: B10 TCR double positive rep 3

description: B10 pre-selection transgenic TCR thymocytes

tag: B10, 6-8 week old female mouse, double positive thymocytes


title: NOD TCR single positive rep 3

description: NOD positive selection CD4+ thymocytes


title: B10 Dbl single positive rep 2

description: B10 negative selection CD4+ thymocytes


title: B10 TCR double positive rep 1


title: B10 TCR double positive rep 2


title: D39 over-expression of RR06 rep 4

status: Public on Dec 23 2006

city: Adelaide

first: Alistair

last: Standish

address: North Terrace

department: School of Molecular and Biomedical Sciences

institute: University of Adelaide

description: Effect of over-expression of response regulator RR06 on gene expression in D39 S. pneumoniae

hyb_protocol: As described in Genisphere Array 900 MPX Kit

scan_protocol: Axon GenePix 4000B scanner

data_processing: SPOT software

label: Alexa 555

organism: Streptococcus pneumoniae

label_protocol: Genisphere Array 900 MPX Kit

extract_protocol: Acid/Phenol

tag: S. pneumoniae D39 transformed with prr06

label: Alexa 647

tag: S. pneumoniae D39 transformed with pLS1RGFP


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v2) array 4

status: Public on Oct 31 2006

type: genomic

city: Cambridge

first: Ashraf

last: Ibrahim

address: Hills Road

department: Pathology

country: United Kingdom

institute: Univeristy of Cambridge

description: This experiment was designed to assess the levels of methylation of the CpG islands within the colorectal cell line HCT116.

hyb_protocol: Labelled DNA was purified using a Qiaquick PCR purification column and then vacuum dried. Both dye-coupled DNAs were then resuspended together in 85 ul of DIG Easy Hyb solution (Roche Diagnostics) together with 5 ul of salmon sperm DNA (10 ug/ul) and denatured at 95 C for 5 min. The hybridization mixture was allowed to cool briefly and 5 ul of yeast tRNA (10 ug/ul) was added and the mixture was held at 65 C for 2 min and allowed to cool to room temperature. Hybridization to the microarray was carried out under a cover-slip in a humidified chamber at 37 C for 8 h. The cover slip was floated off in 1 x SSC and each slide was washed three times in 1x SSC, 0.1% SDS at 50 C for 15 min followed by removal of SDS at room temperature in 1 x SSC and 0.1x SSC for 5 min each.

scan_protocol: The slides were dried by centrifugation at 500 r/min for 5 min and scanned immediately using the GenePix 4000A scanner (Axon). The settings for PMT gain were adjusted during the initial rapid scan to achieve a balance between the two channels and these settings were used for the high resolution scan. GenePix version 4.1 was used to perform image analysis and feature segmentation.

data_processing: The Arabidopsis thaliana probes were used for normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116 colorectal cancer cell line

label_protocol: 300 ng of PCR product together with 0.5 ng of control Arabidopsis thaliana cDNA (synthesized from pARAB obtained from the Microarray Centre, University Health Network, Toronto, Canada) were indirectly labeled using aminoallyl-dUTP and the the BioPrime Labeling Kit (Invitrogen).

growth_protocol: HCT116 colon cancer cells were cultured in McCoy's 5A modified medium supplemented with 10% foetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of unmethylated sequences, the sample was restricted by McrBC restriction enzyme. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments.

treatment_protocol: Untreated.

tag: Amplicon of unmethylated MseI fragments (CpG islands) with spikes.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of methylated sequences, the sample was restricted by an optimised combination of methylation-sensitive restriction enzyme. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments.

tag: Amplicon of methylated MseI fragmnets (CpG islands) with spikes.


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v2) array 3

tag: Amplicon of methylated MseI fragments (CpG islands) with spikes.


title: Retinoblastoma 5450

status: Public on Dec 20 2006

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: see Gratias et al., submitted

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen et al., 2005). Background intensities were not subtracted. Signal intensities were normalized by subgrid LOWESS and chromosomal regions sharing the same DNA copy number were segmented by circular binary segmentation. Segments exceeding a log2 ratio of +/- 0.2 were considered as an aberration.

source_name: genomic DNA isolated from sporadic unilateral retinoblastoma (unfixed material)

label_protocol: DNA was labelled by random priming. Detailed protocols are available at our website

extract_protocol: The tumour sample is homogenized in a glass homogenisator or using a Pasteur pipette in 250 µl of 75 mM NaCl/24 mM EDTA/10mM Tris HCl pH 8 and transferred in a 1.5 ml tube. After addition of 250 µl of 75 mM NaCl/24 mM EDTA, 25 µl 10% SDS and 10 µl Proteinase K (10 mg/ml) the mix is vortexed and incubated for 4 hours at 37°C in a water bath or on a rotating thermomixer (850 rpm). Phenol (300 µl) is added, mixed, and the sample is spun down 3-5 min at 13,000 rpm. The aqueous (upper) phase is collected with a pipette and transferred in a new tube. After adding 300 µl of chloroform/isoamylalcohol (96% CHCl3/ 4% IAA) the solution is well shaken and centrifuged 3-5 min at 13,000 rpm. The last two steps have to be repeated 2 times. Next, the upper phase is transferred to a new tube, and 50 µl NaOAc and 900 µl 100% ethanol are added. The DNA precipitates from the solution after inverting the tube. The DNA is removed, washed in 70% ethanol, 15 min dried in the air, and dissolved in TE buffer (on a rolling device for about 2 days).

tag: Age at dx

value: c751C>T, LOH

tag: Treatment

value: primary enucleation

source_name: genomic reference DNA

tag: genomic reference DNA isolated from placental tissue of a healthy donor


title: B10 Dbl double positive rep 1


title: D39 over-expression of RR06 rep 3


title: D39 over-expression of RR06 rep 2


title: Retinoblastoma 5715

description: see Gratias et al., submitted

source_name: Sporadic unilateral retinoblastoma

tag: Gender

value: 1002 days

tag: RB1 genotype

value: c1816insT, LOH


title: D39 over-expression of RR06 rep 1


title: Bthetaiotaomicron_NMRIcecum_P30_#9306

status: Public on Sep 01 2006

city: St. Louis

first: Magnus

middle: K

last: Bjursell

state: MO

address: 4444 Forest Park Ave

department: Molecular Biology and Pharmacology

institute: Washington University School of Medicine

description: Bacteroides thetaiotaomicron, monoassociation from birth, cecum, harvested at P30

data_processing: MAS5; scaling = 500; probemask = only Bt probesets, no intergenic probesets

organism: Bacteroides thetaiotaomicron


title: MMASS: an optimised array-based method for assessing CpG island (Nouzova et al method) array_1

hyb_protocol: Labelled DNA was purified using a Qiaquick PCR purification column and then vacuum dried. Both dye-coupled DNAs were then resuspended together in 85 ul of DIG Easy Hyb solution (Roche Diagnostics) together with 5 ul of salmon sperm DNA (10 ug/ul) and denatured at 95 C for 5 min. The hybridization mixture was allowed to cool briefly and 5 ul of yeast tRNA (10 ug/ul) was added and the mixture was held at 65 C for 2 min and allowed to cool to room temperature. Hybridization to the microarray was carried out under a cover-slip in a humidified chamber at 37 C for 8 h. The cover slip was floated off in 1 x SSC and each slide was washed three times in 1x SSC, 0.1% SDS at 50 C for 15 min followed by removal of SDS at room temperature in 1 x SSC and 0.1x SSC for 5 min each

data_processing: Global loess normalisation was used.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. Then a linker PCR was carried out using the adaptor ligated to all the MseI fragments.

tag: MMASS

value: an optimised array-based method for assessing CpG island comparison to the Nouzova et al method.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of unmethylated sequences McrBC restriction enzyme was use to digest methylated sequences followed by a linker PCR of the unmethylated fragments.

tag: Amplicon of unmethylated CpG islands prepared using McrBC restriction enzyme.


title: MMASS: an optimised array-based method for assessing CpG island (Nouzova et al method) array_4

tag: Amplicon of unmethylated CpG islands prepared using McrBC restriction enzyme (spiked).

extract_protocol: Genomic DNA was digested using MseI then ligated to linker followed by a linker PCR of the all MseI fragments.

tag: Genomic DNA was digested using MseI then ligated to linker followed by a linker PCR of the all MseI fragments (spiked).


title: Bthetaiotaomicron_NMRIcecum_P30_#9304

source_name: Bacteroides thetaiotaomicron, monoassociation from birth, cecum, harvested at P30


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v1) array 4

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of unmethylated sequences, the sample was restricted by McrBC restriction enzyme. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments

tag: Amplicon of unmethylated MseI fragmnets (CpG islands) with spikes.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of methylated sequences, the sample was restricted by a combination of BstUI, HhaI and HpaII. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments.


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v1) array 1

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of methylated sequences, the sample was restricted by a combination of BstUI, HhaI and HpaII. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments

tag: Amplicon of methylated MseI fragments (CpG islands).

tag: Amplicon of unmethylated MseI fragmnets (CpG islands).


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v2) array 1

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of methylated sequences, the sample was restricted by an optimised combination of methylation-sensitive restriction enzyme. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments

tag: Amplicon of methylated MseI fragmnets (CpG islands).

tag: Amplicon of unmethylated MseI fragments (CpG islands).


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v2) array 2


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_3

data_processing: Normalisation was performed using a subset of high-intensity methylated clones that demonstrated consistent log-ratios between replicate arrays.

value: an optimised array-based method for assessing CpG island with spikes.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of unmethylated sequences, subtraction hybrididzation was used to remove an amplicon of methylated sequences prepared as described under channel 1.

tag: Amplicon of unmethylated CpG islands prepared using (MMASS_sub) method with spikes.


title: Bthetaiotaomicron_NMRIcecum_P30_#9303

tag: monoassociation from birth, cecum, harvested at P30


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_1)

hyb_protocol: Labelled DNA was purified using a Qiaquick PCR purification column and then vacuum dried. Both dye-coupled DNAs were then resuspended together in 85 ul of DIG Easy Hyb solution (Roche Diagnostics) together with 5 ul of salmon sperm DNA (10 ug/ul) and denatured at 95 C for 5 min. The hybridization mixture was allowed to cool briefly and 5 ul of yeast tRNA (10 ug/ul) was added and the mixture was held at 65 C for 2 min and allowed to cool to room temperature. Hybridization to the microarray was carried out under a cover-slip in a humidified chamber at 37 C for 8 h. The cover slip was floated off in 1 x SSC and each slide was washed three times in 1x SSC, 0.1% SDS at 50 C for 15 min followed by removal of SDS at room temperature in 1 x SSC and 0.1 x SSC for 5 min each.

label_protocol: 300 ng of PCR product together with 0.5 ng of control Arabidopsis thaliana cDNA (synthesized from pARAB obtained from the Microarray Centre, University Health Network, Toronto, Canada) were indirectly labeled using aminoallyl-dUTP  and the the BioPrime Labeling Kit (Invitrogen).

tag: Amplicon of methylated CpG islands prepared using (MMASS_sub) method.

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of unmethylated sequences, subtraction hybrididzation was used to remove an amplicon   of methylated sequences prepared as described under channel 1.

tag: Amplicon of unmethylated CpG islands prepared using (MMASS_sub) method.


title: MMASS: an optimised array-based method for assessing CpG island (Nouzova et al method) array_3

extract_protocol: Genomic DNA was digested using MseI then ligated to linker followed by a linker PCR of the unmethylated fragments.

value: an optimised array-based method for assessing CpG island comparison to the Nouzova et al method. This is an amplicon of all MseI fragments. This sample was spikes.


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v1) array 2


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_4

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of unmethylated sequences, subtraction hybrididzation was used to remove an amplicon of methylated sequences prepared as described under channel 2.

tag: Amplicon of unmethylated CpG islands prepared using (MMASS_sub) method

extract_protocol: enomic DNA was digested using MseI then ligated to linker. For representation of methylated sequences, the sample was restricted by a combination of BstUI, HhaI and HpaII. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments.


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_v1) array 3

tag: Amplicon of methylated MseI fragments (CpG islands) with spikes.


title: Bthetaiotaomicron_NMRIcecum_P30_#8956


title: MMASS: an optimised array-based method for assessing CpG island (Nouzova et al method) array_2

tag: Amplicon of all MseI fragments (methylated and unmethylated).


title: MMASS: an optimised array-based method for assessing CpG island (MMASS_sub) array_2

label_protocol: 300 ng of PCR product together with 0.5 ng of control Arabidopsis thaliana cDNA (synthesized from pARAB obtained from the Microarray Centre, University Health Network, Toronto, Canada) were indirectly labeled using aminoallyl-dUTP and the the BioPrime Labeling Kit (Invitrogen)

treatment_protocol: Untreated

growth_protocol: HCT116 colon cancer cells were cultured in McCoy's 5A modified medium supplemented with 10% foetal bovine serum and 1% penicillin/streptomycin


title: Bthetaiotaomicron_NMRIcecum_P30_#9305


title: Bthetaiotaomicron_NMRIcecum_P17_#8953

description: Bacteroides thetaiotaomicron, monoassociation from birth, cecum, harvested at P17


title: Bthetaiotaomicron_NMRIcecum_P30_#8955


title: Bthetaiotaomicron_TRPLAC_Tryptone_#7158

description: Bacteroides thetaiotaomicron in tryptone media after lactose addition

tag: tryptone media after lactose addition


title: Bthetaiotaomicron_TRPLAC_Tryptone_#7153

description: Bacteroides thetaiotaomicron in tryptone media before lactose addition

tag: tryptone media before lactose addition


title: 8 C DMSO/Insulin/24h/HG

description: Gene expression analysis was conducted using Agilent G4130A Rat 22K microarray slides.  Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.  2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol.  Slides were  washed as indicated in the Agilent protocol.  Arrays were then scanned with an Axon GenePix 4000b.  Data was obtained using the GenePix Pro 6 software package.

extract_protocol: GITC/Phenol/CHcl3 extraction CsCl2 banding

tag: 1 day old whole rat pups

source_name: Rat aortic smooth muscle (tmt: DMSO/Insulin/24h/HG)

extract_protocol: The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.

tag: Cell line


title: Bthetaiotaomicron_TRPLAC_Tryptone_#7152

source_name: Bacteroides thetaiotaomicron in tryptone media before lactose addition


title: Bthetaiotaomicron_NMRIcecum_P17_#9225

source_name: Bacteroides thetaiotaomicron, monoassociation from birth, cecum, harvested at P17


title: Bthetaiotaomicron_TRPLAC_Tryptone_#7159

source_name: Bacteroides thetaiotaomicron in tryptone media after lactose addition


title: Bthetaiotaomicron_TRPLAC_Tryptone_#6845


title: Bthetaiotaomicron_NMRIcecum_P17_#9224

tag: monoassociation from birth, cecum, harvested at P17


title: Bthetaiotaomicron_TRPGLC_Tryptone_#7160

description: Bacteroides thetaiotaomicron in tryptone media before glucose addition

tag: tryptone media before glucose addition


title: Bthetaiotaomicron_TRPGLC_Tryptone_#7166

description: Bacteroides thetaiotaomicron in tryptone media after glucose addition

tag: tryptone media after glucose addition


title: Bthetaiotaomicron_TRPLAC_Tryptone_#6669


title: Bthetaiotaomicron_NMRIcecum_P17_#9521


title: Bthetaiotaomicron_NMRIcecum_P17_#8954


title: Bthetaiotaomicron_TRPLAC_Tryptone_#6846


title: Bthetaiotaomicron_TRPGLC_Tryptone_#7161

source_name: Bacteroides thetaiotaomicron in tryptone media before glucose addition


title: Bthetaiotaomicron_TRPGLC_Tryptone_#7167

source_name: Bacteroides thetaiotaomicron in tryptone media after glucose addition


title: Bthetaiotaomicron_TRPGAL_Tryptone_#7598

description: Bacteroides thetaiotaomicron in tryptone media before galactose addition


title: Bthetaiotaomicron_NMRIcecum_P17_#9226


title: Bthetaiotaomicron_TRPGAL_Tryptone_#7603

description: Bacteroides thetaiotaomicron in tryptone media after galactose addition

tag: tryptone media after galactose addition


title: Bthetaiotaomicron_TRPGAL_Tryptone_#7597

source_name: Bacteroides thetaiotaomicron in tryptone media before galactose addition


title: Bthetaiotaomicron_TRPLAC_Tryptone_#6671


title: Bthetaiotaomicron_TRPGAL_Tryptone_#7604

source_name: Bacteroides thetaiotaomicron in tryptone media after galactose addition


title: 514_Leukocyte_affy

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

description: LOH and Copy number analysis of colorectal tumors

hyb_protocol: Affymetrix GeneChip Human Mapping 10K Array Xba131 Standard Protocol

data_processing: GDAS, dChip v 1.3

label: Biotin

source_name: Leukocyte DNA from patient 514 on affymetrix SNP platform

extract_protocol: Miller, S. A., Dykes, D. D., & Polesky, H. F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215 (1988)

tag: leukocyte DNA of female patient with rectal adenoma


title: 108_Leukocyte_affy

hyb_protocol: Affymetrix GeneChip Human Mapping 10K Array Xba142 Standard Protocol

source_name: Leukocyte DNA from patient 108 on affymetrix SNP platform

tag: leukocyte DNA of male patient with rectal carcinoma


title: 44_Carcinoma_BAC

description: Copy number analysis of colorectal tumors

data_processing: limma

source_name: Tumor DNA from patient 44 on BAC platform

extract_protocol: From fresh frozen tissue, twenty 30-microm-thick sections were cut from each tumor. DNA was isolated with the Genomic Wizard kit, according to the manufacturers protocol (Promega, Madison, WI)

tag: Tumor DNA of male patient with colorectal carcinoma

source_name: female reference DNA

tag: Gender mismatched pooled reference DNA


title: 514_adenoma_BAC

source_name: Tumor DNA from patient 514 on BACarray platform

tag: Tumor DNA from female patient with colorectal adenoma

source_name: male reference DNA


title: 514_adenoma_affy

source_name: Tumor DNA from patient 514 on affymetrix SNP platform

tag: adenoma DNA of female patient with rectal adenoma


title: 44_Carcinoma_affy

source_name: Tumor DNA from patient 44 on affymetrix SNP platform

extract_protocol: From fresh frozen tissue, twenty 30-μm-thick sections were cut from each tumor. DNA was isolated with the Genomic Wizard kit, according to the manufacturers’ protocol (Promega, Madison, WI)

tag: tumor DNA of male patient with rectal carcinoma


title: 108_Carcinoma_BAC

source_name: Tumor DNA from patient 108 on BACarray platform

tag: Tumor DNA from male patient with colorectal carcinoma


title: 106_Carcinoma_BAC

source_name: Tumor DNA from patient 106 on BACarray platform

tag: Tumor DNA from female patient on BAC array


title: 108_Carcinoma_affy

source_name: Tumor DNA from patient 108 on affymetrix SNP platform


title: Yeast yox1yhp1 mutant cell cycle-time point 70 min 2001-04-12_2665-70

status: Public on Aug 31 2006

city: Seattle

first: Tata

last: Pramila

state: WA

address: 1100, Fairview Avenue N

department: Basic Sciences

institute: FHCRC

description: Yeast yox1yhp1 mutant cell cycle

data_processing: log10 ratio of medians[(F635-B635)/(F532-BF532)], normalized

organism: Saccharomyces cerevisiae

treatment_protocol: Cells were arrested with alpha factor,and released into YEPD to get a synchronized population. Cells were sampled every 10 min after relase.

source_name: Yeast (wild type) asynchronous culture

treatment_protocol: Cells were grown overnight to an OD of 0.6 in YEPD

tag: Yeast (wild type) asynchronous culture


title: Yeast yox1yhp1 mutant cell cycle-time point 120 min 2001-04-12_2665-120

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 110 min 2001-04-12_2665-110

description: Yeast yox1yhp1 mutant cell cycle


title: 106_Leukocyte_affy

source_name: Leukocyte DNA from patient 106 on affymetrix SNP platform

tag: leukocyte DNA of female patient with rectal carcinoma


title: Yeast yox1yhp1 mutant cell cycle-time point 90 min 2001-04-12_2665-90

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 60 min 2001-04-12_2665-60

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 100 min 2001-04-12_2665-100

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 20 min 2001-04-12_2665-20

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 0 min 2001-04-12_2665-0

description: Yeast yox1yhp1 mutant cell cycle


title: 44_Leukocyte_affy

source_name: Leukocyte DNA from patient 44 on affymetrix SNP platform

tag: leukocyte DNA of male patient with rectal adenoma


title: Yeast yox1yhp1 mutant cell cycle-time point 80 min 2001-04-12_2665-80

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 50 min 2001-04-12_2665-50

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 30 min 2001-04-12_2665-30

description: Yeast yox1yhp1 mutant cell cycle


title: Yeast yox1yhp1 mutant cell cycle-time point 40 min 2001-04-12_2665-40

description: Yeast yox1yhp1 mutant cell cycle


title: 106_Carcinoma_affy

source_name: Tumor DNA from patient 106 on affymetrix SNP platform

tag: tumor DNA of female patient with rectal carcinoma


title: Yeast yox1yhp1 mutant cell cycle-time point 10 min 2001-04-12_2665-10

description: Yeast yox1yhp1 mutant cell cycle


title: Per2Cry1 adrenal 54hrs DD C

status: Public on Aug 08 2006

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

institute: University of Lübeck

description: Per2/Cry1 animals are circadian clock-deficient. This set was used to identify clock regulated genes in the adrenal that are not necessarily rhythmic.

data_processing: expression values for the whole series were normalized (PM/MM model) using DChip 1.3 software

source_name: Per2Cry1 mutant mouse whole adrenal 54hrs after lights off

extract_protocol: RNeasy Micro Kit (QIAGEN)

treatment_protocol: animals were LD entrained for two weeks and subsequently released into DD; whole adrenals were dissected at the specified time points after

tag: strain

value: Per2Brdm1/Cry1-/- (C57BL6x129Sv) gender:male age:3 months tissue:whole adrenal gland


title: Head_AggrI_Gen21_rep1

status: Public on Aug 18 2006

city: San Diego

first: Herman

middle: Albert

last: Dierick

state: CA

address: 10640 John J. Hopkins Drive

institute: The Neurosciences Institute

description: Males were frozen in groups of ~120 between 2:00 and 2:30 PM at 5 days of age, and were randomly collected from culture bottles and stored in groups of ~40

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

organism: Drosophila melanogaster

label_protocol: Standard Affymetrix

extract_protocol: Trizol extraction

treatment_protocol: Male flies were selected for aggressive behavior for 21 generations

tag: Line

value: Canton-S selected

tag: Gender

value: male

tag: Age

value: 5 days

tag: Tissue

value: head


title: Head_AggrII_Gen21_rep2

value: Male


title: Head_NeutrII_Gen21_rep1

treatment_protocol: Male flies were randomly selected from population cage with 120 males after 15-30 aggressive males were removed over the course of 21 generations


title: Head_NeutrI_Gen21_rep1

value: Canton-S


title: Head_NeutrII_Gen21_rep2


title: Head_AggrI_Gen21_rep2


title: Head_AggrI_Gen21_rep3


title: Per2Cry1 adrenal 54hrs DD


title: Head_NeutrI_Gen21_rep3


title: Head_NeutrI_Gen21_rep2


title: Head_AggrII_Gen21_rep3


title: patient 14 D28/D0

status: Public on Aug 01 2006

city: Paris

first: Didier

last: Payen de la Garanderie

address: 2 rue Ambroise Pare

department: DAR-ICU

country: France

institute: Hopital Lariboisiere

description:
patient = male
age = 36y
Organ failure = 3
SAPSII = 41
SOFA = 14
alive at D7
alive at D28
inclusion delay = 1
bacterial = poly
site of infection = soft tissus

data_processing: Genesight and AIDA softwares; background substraction; spikes correction; ratio Cy5/Cy3; log10 ratio for transformation; Lowess normalization; ANOVA across all samples

source_name: sample D0 in Cy3

tag: Peripheral blood mononuclear cells

source_name: sample D28 in Cy5


title: Per2Cry1 adrenal 46hrs DD B

source_name: Per2Cry1 mutant mouse whole adrenal 46hrs after lights off


title: Patient 7 D28/D0

description:
patient = male
age = 69y
Organ failure = 3
SAPSII = 43
SOFA = 10
alive at D7
alive at D28
inclusion delay = 3
bacterial = G+
site of infection = hip joint


title: Per2Cry1 adrenal 46hrs DD C


title: Patient 4 D28/D0

description:
patient = female
age = 61y
Organ failure = 3
SAPSII = 55
SOFA = 10
alive at D7
alive at D28
inclusion delay = 3
bacterial = not determined
site of infection = lung


title: Head_NeutrII_Gen21_rep3


title: Per2Cry1 adrenal 54hrs DD B


title: Human Ntera2 cells, Oct4 ENCODE Sample G

city: Columbus

first: Victor

middle: X

last: Jin

state: OH

address: 333 West 10th Ave

department: Biomedical Informatics

institute: OSU Medical Center

description: Human Ntera2 cells

data_processing: log base 2 ratios

source_name: Ntera2 cells

tag: Oct4 antibody

tag: control total input


title: Patient 16 D28/D0

description:
patient = female
age = 52y
Organ failure = 3
SAPSII = 33
SOFA = 7
alive at D7
alive at D28
inclusion delay = 1
bacterial = G-
site of infection = abdomen


title: Patient 12 D7/D0

description:
patient = male
age = 76y
Organ failure = 4
SAPSII = 64
SOFA = 14
alive at D7
alive at D28
inclusion delay = 1
bacterial = poly
site of infection = abdomen+blood

source_name: sample D7 in Cy5


title: Patient 16 D7/D0


title: Patient 12 D28/D0


title: patient 3 D28/D0

description:
patient = male
age = 50y
Organ failure = 4
SAPSII = 32
SOFA = 7
alive at D7
alive at D28
inclusion delay = 1
bacterial = not determined
site of infection = soft tissus

source_name: sample D0 in cy3


title: Patient 17 D7/D0

description:
patient = male
age = 71y
Organ failure = 3
SAPSII = 55
SOFA = 15
alive at D7
alive at D28
inclusion delay = 1
bacterial = G-
site of infection = abdomen


title: Per2Cry1 adrenal 46hrs DD

treatment_protocol: animals were LD entrained for two weeks and subsequently released into DD; whole adrenals were dissected at the specified time points after "lights off"

value: Per2Brdm1/Cry1-/- (C57BL6x129Sv)

tag: gender

tag: age

value: 3 months

tag: tissue

value: whole adrenal gland


title: Patient 5 D7/D0

description:
Patient = male
age = 47y
Organ failure = 3
SAPSII = 38
SOFA = 8
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = poly
Site of infection = abdomen+blood


title: Patient 6 D7/D0

description:
Patient = female
age = 64y
Organ failure = 2
SAPSII = 42
SOFA = 6
alive at D7
alive at D28
Inclusion delay = 3
Bacterial = not determined
Site of infection = cervical


title: Head_AggrII_Gen21_rep1


title: Patient 7 D7/D0


title: Human Ntera2 cells, Oct4 ENCODE Sample H

description: Human Ntera2 cells


title: patient 13 D7/D0

description:
Patient = male
Age = 62y
organ failure = 3
SAPSII = 60
SOFA = 14
alive at D7
alive at D28
inclusion delay = 2
bacterial = G+
site of infection = abdomen


title: Patient 11 D7/D0

description:
patient = male
age = 50y
Organ failure = 3
SAPSII = 32
SOFA = 8
alive at D7
alive at D28
inclusion delay = 1
bacterial = not determined
site of infection = urinary tract


title: patient 15 D28/D0

description:
patient = male
age = 44y
Organ failure = 3
SAPSII = 56
SOFA = 10
alive at D7
alive at D28
inclusion delay = 1
bacterial = poly
site of infection = abdomen+pelvis


title: Patient 11 D1/D0

description:
Patient = male
Age = 50y
Organ Failure = 3
SAPSII = 32
SOFA = 8
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = not determined
Site of infection = urinary tract

source_name: sample D1 in Cy5


title: Patient 7 D1/D0

description:
Patient = male
Age = 69y
Organ Failure = 3
SAPSII = 43
SOFA = 10
alive at D7
alive at D28
Inclusion delay = 3
Bacterial = G+
Site of infection = hip joint


title: Patient 12 D1/D0

description:
Patient = male
Age = 76y
Organ Failure = 4
SAPSII = 64
SOFA = 14
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = poly
Site of infection = abdomen+blood


title: Human Ntera2 cells, Oct4 ENCODE Sample D

description: Human Ntera2 cells


title: patient 14 D7/D0

source_name: sample D7 in cy5


title: Patient 8 D1/D0

description:
Patient = male
Age = 65y
Organ Failure = 2
SAPSII = 42
SOFA = 6
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = poly
Site of infection = abdomen


title: Patient 3 D1/D0

description:
Patient = male
age = 50y
Organ failure = 4
SAPSII = 32
SOFA = 7
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = not determined
Site of infection = soft tissus


title: Patient 6 D1/D0

description:
Patient = female
age = 64y
Organ failure = 2
SAPSII = 42
SOFA = 6
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = not determined
Site of infection = cervical


title: Patient 4 D7/D0

description:
Patient = female
age = 61y
Organ failure = 3
SAPSII = 55
SOFA = 10
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = not determined
Site of infection = lung


title: Patient 2 D1/D0

description:
Patient = male
age = 87y
organ failure =4
SAPSII = 62
SOFA = 15
dead at D7
dead at D28
Inclusion delay = 2
Bacterial = G-
Site of infection =Abdo+blood


title: Human Ntera2 cells, Oct4 ENCODE Sample E1

description: Human Ntera2 cells


title: Patient 1 D1/D0

description:
Patient = male
age = 60y
organ failure =4
SAPSII = 81
SOFA = 12
dead at D7
dead at D28
Inclusion delay = 1
Bacterial = G+
Site of infection =catheter


title: Patient 5 D1/D0


title: Patient 9 D1/D0

description:
Patient = male
age = 93y
Organ failure = 4
SAPSII = 70
SOFA = 9
dead at D7
dead at D28
Inclusion delay = 1
Bacterial = poly
Site of infection = abdomen


title: patient 13 D28/D0

description:
patient = male
age = 62y
Organ failure = 3
SAPSII = 60
SOFA = 14
alive at D7
alive at D28
inclusion delay = 2
bacterial = G+
site of infection = abdomen


title: patient 13 D1/D0

description:
Patient = male
age = 62y
Organ failure = 3
SAPSII = 60
SOFA = 14
alive at D7
alive at D28
Inclusion delay = 2
Bacterial = G+
Site of infection = abdomen


title: patient 15 D1/D0

description:
Patient = Male
Age = 44y
Organ failure = 3
SAPSII =56
SOFA=10
alive at D7
alive at D28
Inclusion delay =1
Bacterial = Poly
Site of infection =Abdo+pelvis
Sepsis in a postoperative context


title: patient 14 D1/D0

description:
Patient = Male
Age = 36y
Organ failure = 3
SAPSII =41
SOFA=14
alive at D7
alive at D28
Inclusion delay =1
Bacterial = Poly
Site of infection =soft tissues


title: Patient 10 D1/D0

description:
Patient = male
Age = 36y
Organ Failure = 2
SAPSII = 49
SOFA = 8
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = poly
Site of infection = lung


title: Human Ntera2 cells, Oct4 ENCODE Sample N

description: Human Ntera2 cells


title: SPC-HA

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: SPC-HA

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ex vivo

extract_protocol: RNeasy

treatment_protocol: Dispase/Dnase digestion of the lung tissue to release AEC II followed by untouched fluorescence activaed cell sorting

tag: genetic modification

value: Isolated from transgenic mice expressing influenza hemagglutinin under the transcriptional control of the surfactant protein C promotor

value: alveolar epithelial cell type II


title: HepG2_5-aza_TSA_rep4

city: Indianapolis

first: Howard

last: Edenberg

state: IN

institute: Indiana University School of Medicine

description: Gene expression data 5-aza-dC plus Trichostatin A  treated HepG2 cells.

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.

source_name: HepG2 cells; (HB-8065; ATCC, Manassas, VA)

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Cell Culture, 100 mm dishes, minimum essential medium (Sigma) plus 10% fetal bovine serum (Life Technologies, Rockville, MD) and 2 mM glutamine in a 5% CO2 atmosphere.

extract_protocol: RNeasy® Mini Kit, according to the manufacturer's instructions.

treatment_protocol: HepG2 cells treated with 2.5 microMolar  5-aza-dC for 4 days, with medium replaced daily; Trichostatin A  at 500 nM was added for the last 24 h

tag: HepG2 cells treated with 5-aza-dC plus Trichostatin A


title: HepG2_5-aza_rep4

description: Gene expression data 5-aza-dC treated HepG2 cells.

treatment_protocol: HepG2 cells treated with 2.5 microMolar 5-aza-dC for 4 days, with medium replaced daily

tag: HepG2 cells treated with 5-aza-dC


title: HepG2_5-aza_TSA_rep2


title: HepG2_5-aza_rep2


title: SPC-HA x TCR-HA

description: SPC-HA x TCR-HA

value: Isolated from double transgenic mice expressing influenza hemagglutinin (HA) under the transcriptional control of the surfactant protein C promotor and an MHC class II restricted alpha beta TCR specific for the HA peptide 110-120.


title: HepG2_5-aza_TSA_rep3


title: HepG2_control_rep4

description: Gene expression data untreated HepG2 cells (control).

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

tag: untreated control


title: HepG2_5-aza_rep1


title: HepG2_TSA_rep3

description: Gene expression data Trichostatin A  treated HepG2 cells.

treatment_protocol: HepG2 cells treated with 500 nanoMolar Trichostatin A  for 24 h

tag: HepG2 cells treated with Trichostatin A


title: Human Ntera2 cells, Oct4 ENCODE Sample K

description: Human Ntera2 cells


title: HepG2_control_rep1


title: HepG2_5-aza_rep3


title: SPC-HA_2


title: HepG2_control_rep3


title: HepG2_control_rep2


title: 5dpi rep A Control (Cy5) vs. Saprotroph (Cy3) (12670162)

status: Public on Jul 31 2006

city: Raleigh

first: Chris

last: Smith

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

hyb_protocol: Hybridization and stringency washes were done according to the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).

data_processing: Raw intensity generated with QuantArray and statistically analysed using 2-interconnected mixed linear model approach.

organism: Pinus sylvestris

source_name: Pinus sylvestris root tissues rep A Control (Cy5)

label_protocol: The cDNA generated from the roots was labelled using a Klenow method following the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were mock-inoculated with sterile distilled water and harvested at 5dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Pinus sylvestris unchallenged (control)

source_name: rep A Saprotroph (Cy3)

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Trichoderma aureoviride and harvested at 5dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Pinus sylvestris challenged for 5 days with

value: Saprotroph (Trichoderma aureoviride)


title: 5dpi rep C Pathogen (Cy5) vs. Saprotroph (Cy3) (12669957)

source_name: Pinus sylvestris root tissues rep C Pathogen (Cy5)

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Heterobasidion annosum and harvested at 5dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Pinus sylvestris roots challenged for 5 days with

value: Pathogen (Heterobasidion annosum)

source_name: rep C Saprotroph (Cy3)


title: 5dpi rep C Mycorrhiza (Cy5) vs. Pathogen (Cy3) (12669958)

source_name: Pinus sylvestris root tissues rep C Mycorrhiza (Cy5)

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Laccaria bicolor and harvested at 5dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

value: Mycorrhiza (Laccaria bicolor)

source_name: rep C Pathogen (Cy3)


title: 5dpi rep B Saprotroph (Cy5) vs. Control (Cy3) (12669940)

source_name: Pinus sylvestris root tissues rep B Saprotroph (Cy5)

source_name: rep B Control (Cy3)


title: Control

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Strasse 1

institute: Fraunhofer Institut

description:
Further, the average difference values for each target were calculated. These are calculated as the average of the signal intensities for the perfect match probe (PM) minus the mismatch probe (MM). These designs both used 10 probe pairs per target. Values that differ from the mean by more than 2.5 standard deviations are dropped from the calculation. Then these data were normalized (each set of expression values is divided by the standard deviation of that array only)
and rescaled to account for between chip variations. The standard deviation of the whole set of arrays was used to
give a scaling factor.

data_processing: Data in the VALUE column of our table were generated by calculating the mean signal for the collection of pixels that makes up the feature at a given position.

source_name: Hepatocytes

tag: Human hepatocytes isolated from surgical material


title: Aroclor1254 treatment, 20µM, 72h

description: Further, the average difference values for each target were calculated. These are calculated as the average of the signal intensities for the perfect match probe (PM) minus the mismatch probe (MM). These designs both used 10 probe pairs per target. Values that differ from the mean by more than 2.5 standard deviations are dropped from the calculation. Then these data were normalized (each set of expression values is divided by the standard deviation of that array only) and rescaled to account for between chip variations. The standard deviation of the whole set of arrays was used to give a scaling factor.


title: patient 3 D7/D0

description:
Patient = male
age = 50y
Organ failure = 4
SAPSII = 32
SOFA = 7
alive at D7
alive at D28
Inclusion delay = 1
Bacterial = not determined
Site of infection = soft tissus

source_name: sample D0 in Cy3


title: 5dpi rep B Mycorrhiza (Cy5) vs. Pathogen (Cy3) (12669939)

source_name: Pinus sylvestris root tissues rep B Mycorrhiza (Cy5)

source_name: rep B Pathogen (Cy3)


title: SPC-HA x TCR-HA_2

description: SPC-HA x TCR-HA_2


title: 5dpi rep A Mycorrhiza (Cy5) vs. Control (Cy3) (12669927)

source_name: Pinus sylvestris root tissues rep A Mycorrhiza (Cy5)

source_name: rep A Control (Cy3)


title: 5dpi rep C Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12669716)

source_name: Pinus sylvestris root tissues rep C Saprotroph (Cy5)

source_name: rep C Mycorrhiza (Cy3)


title: HepG2_5-aza_TSA_rep1

source_name: HepG2 cells; (HB-8065; ATCC, Manassas, VA)


title: 5dpi rep A Mycorrhiza (Cy5) vs. Pathogen (Cy3) (12669855)

source_name: rep A Pathogen (Cy3)


title: 5dpi rep B Pathogen (Cy5) vs. Control (Cy3) (12669717)

source_name: Pinus sylvestris root tissues rep B Pathogen (Cy5)


title: HepG2_TSA_rep1


title: 5dpi rep A Pathogen (Cy5) vs. Saprotroph (Cy3) (12669715)

source_name: Pinus sylvestris root tissues rep A Pathogen (Cy5)

source_name: rep A Saprotroph (Cy3)


title: 5dpi rep B Saprotroph (Cy5) vs. Pathogen (Cy3) (12669714)


title: HepG2_TSA_rep4


title: patient 15 D7/D0

description:
patient = male
age = 44y
Organ failure = 3
SAPSII = 56
SOFA = 10
alive at D7
alive at D28
inclusion delay = 1
bacterial = poly
site of infection = abdomen+pelvis

source_name: sample D7 in Cy5


title: 5dpi rep B Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12669851)

source_name: rep B Mycorrhiza (Cy3)


title: 5dpi rep C Control (Cy5) vs. Saprotroph (Cy3) (12669694)

source_name: Pinus sylvestris root tissues rep C Control (Cy5)

source_name: rep C Saprotroph (Cy3)


title: 5dpi rep C Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12669670)

source_name: Pinus sylvestris root tissues rep C Pathogen (Cy5)


title: 5dpi rep B Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12669926)

source_name: Pinus sylvestris root tissues rep B Saprotroph (Cy5)


title: 5dpi rep B Control (Cy5) vs. Saprotroph (Cy3) (12669669)

source_name: Pinus sylvestris root tissues rep B Control (Cy5)

source_name: rep B Saprotroph (Cy3)


title: 5dpi rep B Control (Cy5) vs. Mycorrhiza (Cy3) (12669925)


title: 5dpi rep A Saprotroph (Cy5) vs. Control (Cy3) (12669695)

source_name: Pinus sylvestris root tissues rep A Saprotroph (Cy5)


title: 5dpi rep A Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12669668)

source_name: Pinus sylvestris root tissues rep A Mycorrhiza (Cy5)


title: 5dpi rep A Control (Cy5) vs. Mycorrhiza (Cy3) (12665084)

source_name: Pinus sylvestris root tissues rep A Control (Cy5)

source_name: rep A Mycorrhiza (Cy3)


title: 5dpi rep A Pathogen (Cy5) vs. Control (Cy3) (12669943)

source_name: rep A Control (Cy3)


title: 5dpi rep B Pathogen (Cy5) vs. Saprotroph (Cy3) (12670159)


title: 5dpi rep C Saprotroph (Cy5) vs. Pathogen (Cy3) (12665082)

source_name: Pinus sylvestris root tissues rep C Saprotroph (Cy5)

source_name: rep C Pathogen (Cy3)


title: 5dpi rep C Control (Cy5) vs. Mycorrhiza (Cy3) (12665055)

source_name: rep C Mycorrhiza (Cy3)


title: 5dpi rep C Mycorrhiza (Cy5) vs. Control (Cy3) (12669697)

source_name: Pinus sylvestris root tissues rep C Mycorrhiza (Cy5)

source_name: rep C Control (Cy3)


title: 5dpi rep B Mycorrhiza (Cy5) vs. Control (Cy3) (12669667)

source_name: Pinus sylvestris root tissues rep B Mycorrhiza (Cy5)

source_name: rep B Control (Cy3)


title: 5dpi rep C Control (Cy5) vs. Pathogen (Cy3) (12665080)

source_name: Pinus sylvestris root tissues rep C Control (Cy5)


title: 5dpi rep A Control (Cy5) vs. Pathogen (Cy3) (12670160)

source_name: rep A Pathogen (Cy3)


title: 5dpi rep B Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12665054)


title: 5dpi rep A Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12669672)


title: HepG2_TSA_rep2

source_name: HepG2 cells; (HB-8065; ATCC, Manassas, VA)


title: 15dpi rep A Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12784934)

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Trichoderma aureoviride and harvested at 15dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Pinus sylvestris roots challenged for 15 days with

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Laccaria bicolor and harvested at 15dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Pinus sylvestris challenged for 15 days with


title: 15dpi rep B Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12784936)

source_name: Pinus sylvestris root tissues rep B Pathogen (Cy5)

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were inoculated with homogenized mycelium of Heterobasidion annosum and harvested at 15dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

source_name: rep B Mycorrhiza (Cy3)


title: 15dpi rep A Control (Cy5) vs. Saprotroph (Cy3) (12784935)

treatment_protocol: Pinus sylvestris seedlings (14 days post-germination) were mock-inoculated with sterile distilled water and harvested at 15dpi. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

source_name: rep A Saprotroph (Cy3)


title: 5dpi rep C Saprotroph (Cy5) vs. Control (Cy3) (12665052)


title: 15dpi rep A Pathogen (Cy5) vs. Saprotroph (Cy3) (12784919)

source_name: Pinus sylvestris root tissues rep A Pathogen (Cy5)


title: 5dpi rep A Saprotroph (Cy5) vs. Pathogen (Cy3) (12665081)

source_name: Pinus sylvestris root tissues rep A Saprotroph (Cy5)


title: 5dpi rep C Pathogen (Cy5) vs. Control (Cy3) (12665083)

source_name: Pinus sylvestris root tissues rep C Pathogen (Cy5)


title: 15dpi rep A Pathogen (Cy5) vs. Control (Cy3) (12784921)

source_name: rep A Control (Cy3)


title: 15dpi rep C Control (Cy5) vs. Pathogen (Cy3) (12784957)


title: 15dpi rep C Saprotroph (Cy5) vs. Control (Cy3) (12784903)

source_name: Pinus sylvestris root tissues rep C Saprotroph (Cy5)


title: 5dpi rep B Control (Cy5) vs. Pathogen (Cy3) (12669696)

source_name: Pinus sylvestris root tissues rep B Control (Cy5)

source_name: rep B Pathogen (Cy3)


title: 15dpi rep C Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12784954)

source_name: Pinus sylvestris root tissues rep C Mycorrhiza (Cy5)

source_name: rep C Saprotroph (Cy3)


title: 15dpi rep B Saprotroph (Cy5) vs. Pathogen (Cy3) (12784868)

source_name: Pinus sylvestris root tissues rep B Saprotroph (Cy5)


title: 5dpi rep C Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12669852)


title: 15dpi rep C Pathogen (Cy5) vs. Control (Cy3) (12780957)

source_name: rep C Control (Cy3)


title: 15dpi rep B Mycorrhiza (Cy5) vs. Pathogen (Cy3) (12784937)

source_name: Pinus sylvestris root tissues rep B Mycorrhiza (Cy5)


title: 15dpi rep A Control (Cy5) vs. Pathogen (Cy3) (12784923)

source_name: Pinus sylvestris root tissues rep A Control (Cy5)

source_name: rep A Pathogen (Cy3)


title: 15dpi rep A Saprotroph (Cy5) vs. Pathogen (Cy3) (12784920)


title: 15dpi rep B Saprotroph (Cy5) vs. Control (Cy3) (12784864)

source_name: rep B Control (Cy3)


title: 15dpi rep C Mycorrhiza (Cy5) vs. Pathogen (Cy3) (12780956)

source_name: rep C Pathogen (Cy3)


title: 15dpi rep A Mycorrhiza (Cy5) vs. Pathogen (Cy3) (12784918)

source_name: Pinus sylvestris root tissues rep A Mycorrhiza (Cy5)


title: 15dpi rep A Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12770660)

source_name: rep A Saprotroph (Cy3)


title: 15dpi rep C Mycorrhiza (Cy5) vs. Control (Cy3) (12784867)


title: 15dpi rep C Control (Cy5) vs. Mycorrhiza (Cy3) (12784866)

source_name: Pinus sylvestris root tissues rep C Control (Cy5)

source_name: rep C Mycorrhiza (Cy3)


title: 15dpi rep B Control (Cy5) vs. Saprotroph (Cy3) (12770657)

source_name: rep B Saprotroph (Cy3)


title: 15dpi rep A Control (Cy5) vs. Mycorrhiza (Cy3) (12770659)

source_name: rep A Mycorrhiza (Cy3)


title: 15dpi rep C Saprotroph (Cy5) vs. Pathogen (Cy3) (12780951)

source_name: Pinus sylvestris root tissues rep C Saprotroph (Cy5)


title: 15dpi rep C Pathogen (Cy5) vs. Saprotroph (Cy3) (12780950)

source_name: Pinus sylvestris root tissues rep C Pathogen (Cy5)


title: 15dpi rep A Saprotroph (Cy5) vs. Control (Cy3) (12780949)

source_name: Pinus sylvestris root tissues rep A Saprotroph (Cy5)

source_name: rep A Control (Cy3)


title: 15dpi rep B Control (Cy5) vs. Mycorrhiza (Cy3) (12384124)

source_name: Pinus sylvestris root tissues rep B Control (Cy5)

source_name: rep B Mycorrhiza (Cy3)


title: 15dpi rep C Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12770661)


title: 15dpi rep C Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12784865)


title: Lung_high_13weeks_20h

status: Public on Jul 28 2006

city: Cologne

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

institute: Miltenyi Biotec GmbH

description: 2 µg of linear amplified RNA from cigarette smoke exposed and unexposed (control) rat tissue were labeled by reverse transcription with Cy5 and Cy3 fluorescence, respectively. Cy5 and Cy3 labeled cDNA were combined and subdivided into two parts to perform co-hybridizations with the arrays PIQOR 348 and PIQOR 350

scan_protocol: Image capture and signal quantification were done with the ScanArray Lite (Perkin Elmer, Boston, MA) and ImaGene software version 5.0 (BioDiscovery, Los Angeles, MA)

data_processing: PubmedID

source_name: L7, lung tissue

tag: control

source_name: L9, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 13 weeks exposure, 20 hours recovery time after exposure


title: 15dpi rep A Mycorrhiza (Cy5) vs. Control (Cy3) (12770658)


title: 15dpi rep B Pathogen (Cy5) vs. Control (Cy3) (12784955)

source_name: Pinus sylvestris root tissues rep B Pathogen (Cy5)


title: 15dpi rep B Control (Cy5) vs. Pathogen (Cy3) (12780954)

source_name: rep B Pathogen (Cy3)


title: 15dpi rep C Control (Cy5) vs. Saprotroph (Cy3) (12784938)

source_name: rep C Saprotroph (Cy3)


title: 15dpi rep B Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12384128)

source_name: Pinus sylvestris root tissues rep B Mycorrhiza (Cy5)


title: 15dpi rep B Mycorrhiza (Cy5) vs. Control (Cy3) (12770544)

source_name: rep B Control (Cy3)


title: Lung_high_13weeks_2h

source_name: L1, lung tissue

source_name: L3, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 13 weeks exposure, 2 hours recovery time after exposure


title: 15dpi rep A Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12780946)

source_name: Pinus sylvestris root tissues rep A Pathogen (Cy5)


title: 5dpi rep A Pathogen (Cy5) vs. Mycorrhiza (Cy3) (12665053)

source_name: rep A Mycorrhiza (Cy3)


title: NbCD3-1

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

country: Japan

institute: Shinshu University

description: Nicotiana benthamiana leaves were infiltrated with Agrobacterium tumefaciens carrying plasmids harboring genes for NbCD3, respectively, in the glucocorticoid-inducible gene expression cassette GVG.  Two days after agroinfiltration, the leaves were treated with dexamethasone (DEX) to induce expression of the transgenes.   Four hours after DEX treatment, leaves were harvested, and RNA was isolated for SuperSAGE Array analysis.

data_processing: RMA algorithum

organism: Nicotiana benthamiana

source_name: NbCD3 verexpressing leaf

tag: For SuperSAGE and oligonucleotide array analysis in Nicotiana benthamiana, Agrobacterium tumefaciens cells carrying plasmids as described below were infiltrated into leaves.   Two days after infiltration, leaves were treated with dexamethasone (DEX), and harvested for RNA extraction 4 hrs after treatment.


title: 15dpi rep B Pathogen (Cy5) vs. Saprotroph (Cy3) (12784956)

source_name: rep B Saprotroph (Cy3)


title: ACC 3 cell line Sox4-RNAi replicate 3

city: Charlottesville

first: Christopher

middle: A.

last: Moskaluk

state: VA

address: P.O. Box 800214, OMS Rm. 3890,  Jefferson Park Ave

institute: Christopher Moskaluk

description: shRNA sequences present in pENTR plasmid vector transfected by electroporation (0.35 kV, with 550 _F capacitance). RNA harvested 48 hours after electroportation.

hyb_protocol: Affymetrix: Expression Analysis Technical Manual

data_processing: dCHIP 2006 (Li and Wong)

source_name: ACC3 cell line, Sox4 RNAi knockdown with lacZ as control

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA)

tag: Biological Material

value: Cell line, grown invitro; Tissue derivation:Adenoid cystic carinoma of the parotid gland


title: NbCD1-1

description: Nicotiana benthamiana leaves were infiltrated with Agrobacterium tumefaciens carrying plasmids harboring genes for NbCD1 (control), respectively, in the glucocorticoid-inducible gene expression cassette GVG.  Two days after agroinfiltration, the leaves were treated with dexamethasone (DEX) to induce expression of the transgenes.   Four hours after DEX treatment, leaves were harvested, and RNA was isolated for SuperSAGE Array analysis.

source_name: NbCD1 overexpressing leaf

tag: For SuperSAGE and oligonucleotide array analysis in Nicotiana benthamiana, Agrobacterium tumefaciens cells carrying plasmids as described below were infiltrated into leaves.   Two days after infiltration, leaves were treated with dexamethasone (DEX), and harvested for RNA extraction 4 hrs after treatment .


title: Lung_high_7weeks_2h

source_name: 7-L1, lung tissue

source_name: 7-L3, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 7 weeks exposure, 2 hours recovery time after exposure


title: Lung_low_2weeks_20h

source_name: 2-L7, lung tissue

source_name: 2-L8, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 2 weeks exposure, 20 hours recovery time after exposure


title: ACC 3 cell line Sox4-RNAi replicate 1

scan_protocol: Affymetrix: Expression Analysis Technical Manual


title: 15dpi rep B Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12384127)

source_name: Pinus sylvestris root tissues rep B Saprotroph (Cy5)

source_name: rep B Mycorrhiza (Cy3)


title: Lung_high_13weeks_6h

source_name: L4, lung tissue

source_name: L6, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 13 weeks exposure, 6 hours recovery time after exposure


title: Lung_high_7weeks_20h

source_name: 7-L7, lung tissue

source_name: 7-L9, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 7 weeks exposure, 20 hours recovery time after exposure


title: ACC 3 cell line lacZ-RNAi replicate 3

label_protocol: Affymetrix: Expression Analysis Technical Manual


title: Lung_low_2weeks_6h

source_name: 2-L4, lung tissue

source_name: 2-L5, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 2 weeks exposure, 6 hours recovery time after exposure


title: Nb GFP1

description: Nicotiana benthamiana leaves were infiltrated with Agrobacterium tumefaciens carrying plasmids harboring genes for GFP (control), respectively, in the glucocorticoid-inducible gene expression cassette GVG.  Two days after agroinfiltration, the leaves were treated with dexamethasone (DEX) to induce expression of the transgenes.   Four hours after DEX treatment, leaves were harvested, and RNA was isolated for SuperSAGE Array analysis.

source_name: GFP overex pressing leaf

tag: For SuperSAGE and oligonucleotide array analysis in Nicotiana benthamiana, Agrobacterium tumefaciens cells carrying GFP plasmids as described below were infiltrated into leaves.   Two days after infiltration, leaves were treated with dexamethasone (DEX), and harvested for RNA extraction 4 hrs after treatment


title: ACC 3 cell line lacZ-RNAi replicate 2


title: Lung_low_13weeks_2h

source_name: L1, lung tissue

source_name: L2, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 13 weeks exposure, 2 hours recovery time after exposure


title: Lung_high_7weeks_6h

source_name: 7-L4, lung tissue

source_name: 7-L6, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 7 weeks exposure, 6 hours recovery time after exposure


title: Lung_low_7weeks_6h

source_name: 7-L5, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 7 weeks exposure, 6 hours recovery time after exposure


title: Lung_low_13weeks_20h

description: 2 µg of linear amplified RNA from cigarette smoke exposed and unexposed (control) rat tissue were labelled by reverse transcription with Cy5 and Cy3 fluorescence, respectively. Cy5 and Cy3 labelled cDNA were combined and subdivided into two parts to perform co-hybridizations with the arrays PIQOR 348 and PIQOR 350

source_name: L7, lung tissue

source_name: L8, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 13 weeks exposure, 20 hours recovery time after exposure


title: Lung_low_13weeks_6h

source_name: L5, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 13 weeks exposure, 6 hours recovery time after exposure


title: Lung_low_2weeks_2h

data_processing: Pubmed ID

source_name: 2-L1, lung tissue

tag: control

source_name: 2-L2, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 2 weeks exposure, 2 hours recovery time after exposure


title: placenta, patUpDp7 proxT65H, U74C

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

description: Tissue-specific comparison of gene expression levels in T65H translocation mice, either with or without uniparental duplications of Chrs 7 & 11. Identification of highly differentially expressed transcripts. See T65H series record.

hyb_protocol: 0.15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol.

scan_protocol: The Affymetrix Scanner 3000 system was used. Standard protocol.

data_processing: MAS5/GCOS: TGT=500, otherwise default values.

source_name: 13.5dpc placenta, patUpDp7 proxT65H (=matUpDp11)

label_protocol: Caesium chloride isolated total RNA was quantified on an Agilent Bioanalyser and 5 to 7µg were used to prepare biotin-labeled cRNA target, as prescribed in the Affymetrix expression manual (Affymetrix, 2004). The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.

extract_protocol: Total RNA was isolated from tissues in guanidine isothiocyanate by centrifugation through caesium chloride.

treatment_protocol: Tissues were snap frozen in liquid nitrogen, permanently stored at -80C, and put on dry ice during transport.

tag: Strain

value: T65H translocation mouse (Beechey et al., Mammalian Genome 8(4):236-240, 1997) having a paternally-derived uniparental duplication of Chr 7 proximal of the T65H breakpoint (7F4) and, consequently, a maternally-derived uniparental duplication of Chr 11 proximal of the T65H breakpoint (11B1.1)

tag: Age

tag: Tissue

value: placenta


title: Lung_low_7weeks_20h

source_name: 7-L8, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 7 weeks exposure, 20 hours recovery time after exposure


title: Lung_high_2weeks_6h

source_name: 2-L6, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 2 weeks exposure, 6 hours recovery time after exposure


title: placenta, matUpDp7 proxT65H, U74C

source_name: 13.5dpc placenta, matUpDp7 proxT65H (=patUpDp11)

value: T65H translocation mouse (Beechey et al., Mammalian Genome 8(4):236-240, 1997) having a maternally-derived uniparental duplication of Chr 7 proximal of the T65H breakpoint (7F4) and, consequently, a paternally-derived uniparental duplication of Chr 11 proximal of the T65H breakpoint (11B1.1)


title: ACC 3 cell line Sox4-RNAi replicate 2

source_name: ACC3 cell line, Sox4 RNAi knockdown with lacZ as control

tag: Biological Material


title: Lung_high_2weeks_20h

source_name: 2-L7, lung tissue

source_name: 2-L9, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 2 weeks exposure, 20 hours recovery time after exposure


title: Lung_high_2weeks_2h

source_name: 2-L3, lung tissue

tag: rats exposed to high concentration of cigarette smoke, 2 weeks exposure, 2 hours recovery time after exposure


title: colorectal tumor c986

city: Helsinki

first: Antti

last: Kokko

address: POBOX 63 (Haartmaninkatu 8)

department: Dept of Medical Genetics

country: Finland

institute: University of Helsinki

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Distal Location , Tumor Grade 2

data_processing: Affymetrix Microarray Suite version 5.0

source_name: cololrectal tumor

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: colon tumor samples.Total RNA extracted from the fresh frozen tumors using Trizol reagent (GibcoBRL) an purified using RNeasy kit (Qiagen).

tag: tumor tissue


title: ACC 3 cell line lacZ-RNAi replicate 1


title: colorectal tumor c988

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, female, Proximal Location , Tumor Grade 2


title: stationary 21C replicate 5

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: rat bubo compared to 21C exp; 21C sta; 37C exp; 37C sta

hyb_protocol: P. aeruginosa

scan_protocol: RML-chipa510998 custom

data_processing: Affymetrix GCOS v 1.1

organism: Yersinia pestis

source_name: stationary 21C

label_protocol: Approximately 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: stationary 21C


title: Lung_low_7weeks_2h

source_name: 7-L1, lung tissue

source_name: 7-L2, lung tissue

tag: rats exposed to low concentration of cigarette smoke, 7 weeks exposure, 2 hours recovery time after exposure


title: stationary 21C replicate 3


title: colorectal tumor c931


title: stationary 21C replicate 6


title: colorectal tumor c981


title: colorectal tumor c978

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Distal Location , Tumor Grade 3


title: colorectal tumor c917


title: colorectal tumor c939

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Distal Location , Tumor Grade 1


title: stationary 21C replicate 2


title: placenta, matUpDp7 distT65H, U74C

source_name: 13.5dpc placenta, matUpDp7 distT65H (=patUpDp11)

value: T65H translocation mouse (Beechey et al., Mammalian Genome 8(4):236-240, 1997) having a maternally-derived uniparental duplication of Chr 7 distal of the T65H breakpoint (7F4) and, consequently, a paternally-derived uniparental duplication of Chr 11 distal of the T65H breakpoint (11B1.1)


title: placenta, normal, U74C

source_name: 13.5dpc placenta, normal

value: T65H translocation mouse (Beechey et al., Mammalian Genome 8(4):236-240, 1997) without uniparental duplications (normal)


title: stationary 21C replicate 4


title: liver, patUpDp7 proxT65H, U74C

source_name: newborn liver, patUpDp7 proxT65H (=matUpDp11)

value: newborn

value: liver


title: liver, normal, U74C

source_name: newborn liver, normal


title: embryo, normal, U74C

source_name: 13.5dpc embryo, normal

value: embryo


title: liver, matUpDp7 proxT65H, U74C

source_name: newborn liver, matUpDp7 proxT65H (=patUpDp11)


title: exponential 37C replicate 6

source_name: exponential 37C

tag: exponential 37C


title: stationary 21C replicate 1


title: exponential 37C replicate 4


title: exponential 37C replicate 1


title: colorectal tumor c707

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, female, Distal Location , Tumor Grade 2


title: exponential 37C replicate 3


title: colorectal tumor c664

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, cancer in the family, male, Proximal Location , Tumor Grade 2


title: exponential 21C replicate 5

source_name: exponential 21C

tag: exponential 21C


title: colorectal tumor c711


title: E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions - 60 min exposure to air

city: Sheffield

first: Jonathan

last: Partridge

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: The University of Sheffield

description: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 400 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (30 mM) as the carbon source with the dilution rate being 0.2 h-1.  Anaerobic cultures were maintained by sparging the chemostat with oxygen-free nitrogen (95 %) and carbon dioxide (5 %) (0.2 l min-1).  The switch to aerobic conditions was achieved by sparging the culture with air (2.0 l min-1) in place of the above gas mix. After a period of 60 min exposure to air cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Data from control samples were used in indirect comparisons with 5 min, 10 min, 15 min and 60 min exposures. Dye swaps and biological repeats were carried out giving two biological repeats and two technical repeats (see supplementary files).

data_processing: Control (anaerobic) and 60 min oxygen exposure samples from two biological replicates and two dye swap experiments were compared, LOG2 LOWESS normalized data is shown.

label: Cy3/5 dye swap

organism: Escherichia coli

source_name: Steady-state continuous cultured control samples in absence of oxygen

source_name: Steady-state continuous cultured experimental samples after 60 min exposure to oxygen


title: exponential 21C replicate 4


title: embryo, matUpDp7 distT65H, U74C

source_name: 13.5dpc embryo, matUpDp7 distT65H (=patUpDp11)


title: colorectal tumor c668

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSI, no cancer in the family, female, Proximal Location , Tumor Grade 3


title: exponential 37C replicate 5


title: colorectal tumor c810

description: conventional colorectal tumor, non-mucinous, Dukes Stage b, MSS, no cancer in the family, female, Distal Location , Tumor Grade 2


title: E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions - 15 min exposure to air

description: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 400 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (30 mM) as the carbon source with the dilution rate being 0.2 h-1.  Anaerobic cultures were maintained by sparging the chemostat with oxygen-free nitrogen (95 %) and carbon dioxide (5 %) (0.2 l min-1).  The switch to aerobic conditions was achieved by sparging the culture with air (2.0 l min-1) in place of the above gas mix. After a period of 15 min exposure to air cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Data from control samples were used in indirect comparisons with 5 min, 10 min, 15 min and 60 min exposures. Dye swaps and biological repeats were carried out giving two biological repeats and two technical repeats (see supplementary files).

data_processing: Control (anaerobic) and 15 min oxygen exposure samples from two biological replicates and two dye swap experiments were compared, LOG2 LOWESS normalized data is shown.

source_name: Steady-state continuous cultured experimental samples after 15 min exposure to oxygen


title: carcass, patUpDp7 proxT65H, U74C

source_name: newborn carcass, patUpDp7 proxT65H (=matUpDp11)

value: carcass


title: exponential 21C replicate 1


title: exponential 37C replicate 2


title: exponential 21C replicate 6


title: exponential 21C replicate 3


title: E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions - 10 min exposure to air

description: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 400 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (30 mM) as the carbon source with the dilution rate being 0.2 h-1.  Anaerobic cultures were maintained by sparging the chemostat with oxygen-free nitrogen (95 %) and carbon dioxide (5 %) (0.2 l min-1).  The switch to aerobic conditions was achieved by sparging the culture with air (2.0 l min-1) in place of the above gas mix. After a period of 5 min exposure to air cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Data from control samples were used in indirect comparisons with 5 min, 10 min, 15 min and 60 min exposures. Dye swaps and biological repeats were carried out giving two biological repeats and two technical repeats (see supplementary files).

data_processing: Control (anaerobic) and 10 min oxygen exposure samples from two biological replicates and two dye swap experiments were compared, LOG2 LOWESS normalized data is shown.

source_name: Steady-state continuous cultured experimental samples after 10 min exposure to oxygen


title: exponential 21C replicate 2


title: stationary 37C replicate 4

source_name: stationary 37C

tag: stationary 37C


title: stationary 37C replicate 3


title: stationary 37C replicate 5


title: colorectal tumor c613

source_name: cololrectal tumor


title: carcass, matUpDp7 proxT65H, U74C

source_name: newborn carcass, matUpDp7 proxT65H (=patUpDp11)


title: stationary 37C replicate 6


title: bubo from rat replicate 6

source_name: bubo from rat

tag: bubo from rat


title: colorectal tumor c616

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Proximal Location , Tumor Grade 2


title: placenta, patUpDp7 proxT65H, U74B

source_name: 13.5dpc placenta, patUpDp7 proxT65H (=matUpDp11)


title: colorectal tumor c463


title: bubo from rat replicate 3


title: stationary 37C replicate 2


title: colorectal tumor c416


title: control vehicle only day 3

city: Bracknell

first: Michael

last: Csukai

state: Berkshire

address: Jealott's Hill

institute: Syngenta

description: Gene expression data following +/- chemical treatment.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Yeast Genome S98 Array YG-S98. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 as previously described (Zhu et al., 2001).

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip® Scanner.

data_processing: Data were analyzed using the RMA algorithm using Expressionist Pro (GeneData Inc., Switzerland).

source_name: Saccharomyces cerevisiae S288c following 5 hours exposure to 15 uM tomatidine (dissolved in the carrier solvet DMF)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix (Expression Analysis Technical Manual, 2001, Affymetrix & Zhu et al., 2001). ).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA) was performed according to the manufacturer's instructions.

treatment_protocol: An overnight culture of strain S288C was diluted to an OD600nm of 0.1.  After 1 hour of growth at 30?C, the compounds (or solvent alone) were added and the cultures were incubated for an additional 5 hours. Growth inhibition was monitored by measuring the OD600nm

tag: strain

tag: Cells were pelleted and frozen in liquid nitrogen.  Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120.


title: E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions - 5 min exposure to air

data_processing: Control (anaerobic) and 5 min oxygen exposure samples from two biological replicates and two dye swap experiments were compared, LOG2 LOWESS normalized data is shown.

source_name: Steady-state continuous cultured experimental samples after 5 min exposure to oxygen


title: placenta, normal, U74B

source_name: 13.5dpc placenta, normal

tag: Strain


title: colorectal tumor c438

description: conventional colorectal tumor, mucinous, Dukes Stage c, MSS, no cancer in the family, male, Distal Location , Tumor Grade 2


title: stationary 37C replicate 1


title: colorectal tumor c466

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, female, Distal Location , Tumor Grade 1


title: bubo from rat replicate 2


title: colorectal tumor c482


title: control vehicle only day 2


title: Tomatidine 0.625 ppm day 3


title: placenta, matUpDp7 proxT65H, U74B

description: Tissue-specific comparison of gene expression levels in T65H translocation mice, either with or without uniparental duplications of Chrs 7 & 11. Identification of highly differentially expressed transcripts. See T65H series record.

source_name: 13.5dpc placenta, matUpDp7 proxT65H (=patUpDp11)

tag: Age


title: bubo from rat replicate 5


title: colorectal tumor c367


title: Fenpropimorph 0.313 ppm day 3


title: bubo from rat replicate 1


title: colorectal tumor c337


title: Tomatine 13.9 ppm day 3


title: colorectal tumor c330


title: placenta, matUpDp7 distT65H, U74B

source_name: 13.5dpc placenta, matUpDp7 distT65H (=patUpDp11)

tag: Tissue


title: liver, patUpDp7 proxT65H, U74B

source_name: newborn liver, patUpDp7 proxT65H (=matUpDp11)


title: bubo from rat replicate 4


title: Tomatidine 0.625 ppm day 2


title: Fenpropimorph 0.313 ppm day 2


title: Tomatine 13.9 ppm day 1


title: heart, patUpDp7 proxT65H, U74B

source_name: newborn heart, patUpDp7 proxT65H (=matUpDp11)

value: heart


title: Tomatine 13.9 ppm day 2


title: liver, normal, U74B

source_name: newborn liver, normal


title: heart, matUpDp7 proxT65H, U74B

source_name: newborn heart, matUpDp7 proxT65H (=patUpDp11)


title: liver, matUpDp7 proxT65H, U74B

source_name: newborn liver, matUpDp7 proxT65H (=patUpDp11)


title: colorectal tumor c356


title: Fenpropimorph 0.313 ppm day 1


title: Tomatidine 0.625 ppm day 1


title: embryo, patUpDp7 proxT65H, 430A

source_name: 13.5dpc embryo, patUpDp7 proxT65H (=matUpDp11)


title: control vehicle only day 1


title: brain, patUpDp7 proxT65H, 430A

source_name: newborn brain, patUpDp7 proxT65H (=matUpDp11)

value: brain


title: embryo, normal, U74B

source_name: 13.5dpc embryo, normal


title: placenta, patUpDp7 proxT65H, U74A


title: colorectal tumor c23

source_name: cololrectal tumor


title: carcass, patUpDp7 proxT65H, U74B

source_name: newborn carcass, patUpDp7 proxT65H (=matUpDp11)


title: colorectal tumor c280

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Proximal Location ,


title: colorectal tumor c217

description: conventional colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Distal Location , Tumor Grade 2


title: placenta, matUpDp7 proxT65H, U74A


title: brain, matUpDp7 proxT65H, 430A

source_name: newborn brain, matUpDp7 proxT65H (=patUpDp11)


title: embryo, matUpDp7 proxT65H, 430A

source_name: 13.5dpc embryo, matUpDp7 proxT65H (=patUpDp11)


title: colorectal tumor E-356-B

description: serrated colorectal tumor, mucinous, Dukes Stage c, MSS, , female, Distal Location , Tumor Grade 2


title: embryo, matUpDp7 distT65H, U74B

source_name: 13.5dpc embryo, matUpDp7 distT65H (=patUpDp11)


title: colorectal tumor c176


title: colorectal tumor c117


title: colorectal tumor E-51-B

description: serrated colorectal tumor, non-mucinous, Dukes Stage d, MSS, , female, Distal Location , Tumor Grade 2


title: colorectal tumor c181


title: carcass, matUpDp7 proxT65H, U74B

source_name: newborn carcass, matUpDp7 proxT65H (=patUpDp11)


title: placenta, matUpDp7 distT65H, U74A


title: heart, patUpDp7 proxT65H, U74A


title: colorectal tumor c476

description: serrated colorectal tumor, mucinous, Dukes Stage c, MSS, cancer in the family, male, Proximal Location , Tumor Grade 3


title: colorectal tumor c537

description: serrated colorectal tumor, non-mucinous, Dukes Stage c, MSS, no cancer in the family, male, Proximal Location , Tumor Grade 2


title: colorectal tumor P2000

description: serrated colorectal tumor, non-mucinous, Dukes Stage b, MSS, no cancer in the family, male, Distal Location , Tumor Grade 2


title: placenta, normal, U74A

source_name: 13.5dpc placenta, normal


title: brain, patUpDp7 proxT65H, 430B


title: colorectal tumor c634

description: serrated colorectal tumor, non-mucinous, Dukes Stage c, MSS, cancer in the family, female, Proximal Location , Tumor Grade 1


title: liver, matUpDp7 proxT65H, U74A


title: liver, patUpDp7 proxT65H, U74A


title: retroperitoneal adipose tissue, Day 17, Control

city: Lincoln

last: LaRosa

state: NE

address: 19th & Vine

department: Center of Biotechnology

institute: University of Nebraska, Lincoln

description: Gene expression data from retroperitoneal adipose tissue of C57BK/6J mice fed control diet.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 420 2.0 arrays using the Hybridization Oven 640, the hybridized array washed with the Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with robust multi-array analysis RMA.  The RMA signal values wre log2 transformed.

source_name: mouse retroperitoneal fat pad

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Two retroperitoneal fat pads excised from each of 10 mice, pooled, frozen in liquid N2 and later extracted in Trizol solution.

value: 9 wk old mice


title: liver, normal, U74A


title: AdERb +TOT replicate3

city: Santa Monica

first: Edmund

middle: C

last: Chang

state: California

address: 2225 Colorado Ave

institute: Kite Pharma

description: AdERb(moi10)-infected, TOT-treated

hyb_protocol: standard Affymetrix procedures

data_processing: R/Bioconductor GCRMA

source_name: MCF-7 breast cancer cells

label_protocol: Approximately 8 micrograms of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: MCF-7 cells expressing endogenous ERalpha were plated in 100mm dish in 5% CD-stripped calf serum.  Cells were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 5 or 50.  Cells were infected with adenovirus for a period of 48hr before treatment with ligand (vehicle control (veh), 10nM 17beta-estradiol (E2), or 10nM trans-hydroxytamoxifen (TOT)) for a additional period of 24hr before harvest.  Total RNA was extracted using 1mL of TRIzol (Invitrogen) per 100mm dish.

tag: AdERb(moi10)-infected, TOT-treated for 24hr


title: embryo, matUpDp7 proxT65H, 430B


title: retroperitoneal adipose tissue, Day 17, CLA treat

description: Gene expression data from retroperitoneal adipose tissue of C57BK/6J mice fed 0.5% trans-10 cis-12 conjugated linoleic acid.


title: AdERb +E2 replicate3

description: AdERb(moi10)-infected, E2-treated

tag: AdERb(moi10)-infected, E2-treated for 24hr


title: heart, matUpDp7 proxT65H, U74A


title: AdERb +TOT replicate1

description: AdERb(moi10)-infected, TOT-treated


title: embryo, normal, U74A


title: embryo, matUpDp7 distT65H, U74A


title: retroperitoneal adipose tissue, Day 17, CLA treat, Rep_2


title: embryo, patUpDp7 proxT65H, 430B


title: AdERb +TOT replicate2

description: AdERb(moi10)-infected, TOT-treated


title: AdERb +E2 replicate1

description: AdERb(moi10)-infected, E2-treated


title: brain, matUpDp7 proxT65H, 430B


title: retroperitoneal adipose tissue, Day 10, Control Rep 2


title: retroperitoneal adipose tissue, Day 10, CLA treat, Rep_2


title: AdERb +E2 replicate2

description: AdERb(moi10)-infected, E2-treated


title: retroperitoneal adipose tissue, Day 10, Control


title: carcass, patUpDp7 proxT65H, U74A


title: retroperitoneal adipose tissue, Day 7, CLA treat, Rep_2


title: carcass, matUpDp7 proxT65H, U74A


title: retroperitoneal adipose tissue, Day 7, Control Rep 2


title: AdERb +veh replicate2

description: AdERb(moi10)-infected, veh-treated

tag: AdERb(moi10)-infected, veh-treated for 24hr


title: retroperitoneal adipose tissue, Day 7, Control


title: retroperitoneal adipose tissue, Day 3, Control Rep 2


title: retroperitoneal adipose tissue, Day 17, Control Rep 2


title: AdERb +veh replicate3

description: AdERb(moi10)-infected, veh-treated


title: retroperitoneal adipose tissue, Day 2, Control Rep 2


title: colorectal tumor c809

description: serrated colorectal tumor, mucinous, Dukes Stage d, MSS, no cancer in the family, male, Proximal Location , Tumor Grade 2


title: retroperitoneal adipose tissue, Day 4, Control Rep 2


title: retroperitoneal adipose tissue, Day 2, CLA treat, Rep_2


title: Ad+TOT replicate2

description: Ad(moi10)-infected, TOT-treated

tag: Ad(moi10)-infected, TOT-treated for 24hr


title: Ad+TOT replicate1

description: Ad(moi10)-infected, TOT-treated


title: retroperitoneal adipose tissue, Day 2, Control


title: retroperitoneal adipose tissue, Day 4, Control


title: retroperitoneal adipose tissue, Day 4, CLA treat, Rep_2


title: retroperitoneal adipose tissue, Day 10, CLA treat


title: Ad+TOT replicate3

description: Ad(moi10)-infected, TOT-treated


title: AdERb +veh replicate1

description: AdERb(moi10)-infected, veh-treated


title: Ad+E2 replicate2 b

description: Ad(moi10)-infected, E2-treated

tag: Ad(moi10)-infected, E2-treated for 24hr


title: Ad+veh replicate1 b

description: Ad(moi10)-infected, vehicle-treated

tag: Ad(moi10)-infected, vehicle-treated for 24hr


title: Growth arrested control polysome fraction

status: Public on Jul 27 2006

city: Salt Lake City

first: Douglas

middle: I.

last: Schmid

state: UT

department: HMBG

institute: University of Utah

description: These samples were collected as part of a polysome profiling experiment in which monosome and polysome associated mRNA was collected via centrifugation and fractionation using an Isco fractionator.  This sample is the growth arrested polysome fraction used to calculate a translation index as follows:  (Serum polysome/Serum monosome)/(growth arrested polysome/growth arrested monosome).

data_processing: The value column was generated by dividing the SIGNAL_RAW values by the median signal intensity of the entire membrane.  This was done in order to compare multiple array values.

label: alpha-33P dCTP

source_name: Primary HUVEC, growth arrested overnight before subjecting to polysome profiling

tag: Primary HUVEC cultured on gelatin coated flasks derived from 7 different umbilical cords, isolated as described by Jaffe, et al.  Cells were grown to confluence before growth arresting overnight.  The experimental cells were stimulated by adding medium containing 20% pooled human serum for 6 hours.


title: retroperitoneal adipose tissue, Day 7, CLA treat


title: retroperitoneal adipose tissue, Day 3, Control


title: retroperitoneal adipose tissue, Day 3, CLA treat


title: Ad+E2 replicate3

description: Ad(moi10)-infected, E2-treated