title: last stage follicle, biological rep2

status: Public on Mar 15 2008

type: RNA

city: Beijing

first: ning

last: Li

address: Yuanmingyuan West Road 2

country: China

institute: China Agricultural University

description: Gene expression data from porcine primordial follicles before growth initiation .

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: porcine ovarian follicle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual,P/N900223 or 90365, Affymetrix).

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

tag: the last stage,large antral follicle

tag: isolated from ovaries of prepubertal gilts


title: Laminitis, right foot, L4

status: Public on Mar 22 2008

city: Philadelphia

first: Murat

middle: T

last: Budak

state: PA

country: USA

institute: University of Pennsylvania

description: Total RNA isolated from each sample was processed and hybridized to the bovine GeneChip array according to the protocols described in the GeneChip Expression Analysis Technical Manual of 2005 (Affymetrix, Santa Clara, CA). Briefly, total RNA was used to generate double-stranded cDNA by using a T7-linked oligo(dT) primer. Linear amplification-biotin labeling and fragmentation were performed with the one-cycle target labeling kit (Affymetrix, P/N 900493) to have target cRNAs per manufacturer’s recommendation. cRNA yields and purity were assessed by Nanodrop spectroscopy. Samples were hybridized to bovine GeneChips (Affymetrix) per the manufacturer’s instructions. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Agilent model G2500A GeneArray scanner at the Penn microarray core facility.

hyb_protocol: See manufacturer`s web side.

scan_protocol: See manufacturer`s web side.

data_processing:
Data was normalized according to per chip median in GC-RMA algorithm. "*.CEL" file was used for that normalization. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches. The 3'/5' ratios for housekeeping genes were confirmed to be within acceptable limits (up to 3, normal range is up to 5), scale factors were 1.2-1.5 (normal range is up to 5) and all spike controls were as expected. In addition, data quality was assessed by review of the average background (background average = 74-84, usually less than 100) and percent present calls (%Present=%19-21) for each array. GeneChip expression data were exported to GeneSpring 7.2 where per chip normalization to the 50th percentile expression level and per gene normalization to the median expression intensity in all samples was performed. Values below 0.01 were set to 0.01. Replicates based cross gene error model was activated in GeneSpring normalizations. Statistical evaluation of replicate experiments: The data for Affymetrix control probe probe sets were removed prior to analysis. Differentially expressed genes were identified by significance analysis of microarrays (SAM), which is a nonparametric, permutation-based method. Normalized raw data was used as an input for SAM. Lists of differentially expressed genes were described by false discovery rate (FDR) (Benjamini and Hochberg, 1995).
Transcript conversion to similar human proteins: There is  a very limited database to analyze the gene expression information for bovines, we decided, then,  to convert the bovine transcript information to highly similar human protein equivalents to see the biological connection within the significant gene list. Statistically significant bovine transcripts were converted to similar human proteins  using the NCBI data base. Transcript sequences were used to find similar human proteins at the level of 80% identity cutoff threshold for blast for match by using the human protein Refseq IDs. The human transcripts which recognize the same protein conversion on human U133 plus ver2 GeneChip has been done to analyze in public databases too. This conversion has been done by using the NetAffx™ Analysis Center of Affymetrix.
Data mining and functional clustering: Human RefSeq IDs and human affy U133v.2 transcript IDs were used for gene ontology (GO) based biological functional grouping, and functional clustering with enriched terms on DAVID 2.1software.

label: Biotin labelling.

organism: Equus caballus

source_name: Equine lamellar hoof tissue, diseased

label_protocol: See manufacturer`s web side.

extract_protocol: Total RNA was extracted from lamellar tissues using the TRI Reagent (Ambion, Austin, TX) and purified using the RNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Briefly, frozen lamellar tissue was pulverized in liquid nitrogen using a mortar and pestle and transferred into TRI Reagent. The solution was homogenized by five aspirations through a 19-gauge needle followed by five aspirations through a 21-gauge needle. RNA was purified by phenol/bromochloropropane (BCP) extraction. After centrifugation, transition to the RNeasy micro kit protocol for cells was done after mixing the aqueous phase with the same amount of 70% ethanol. At the end of this protocol, RNA was eluted with 40 µl of DEPC-treated water.

tag: Laminitis generated Equine lamellar tissue


title: Normal, right foot, N2

source_name: Equine lamellar hoof tissue, normal

tag: Equine lamellar hoof tissue, normal


title: Normal, right foot, N4

data_processing: Data was normalized according to per chip median in GC-RMA algorithm. "*.CEL" file was used for that normalization. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches. The 3'/5' ratios for housekeeping genes were confirmed to be within acceptable limits (up to 3, normal range is up to 5), scale factors were 1.2-1.5 (normal range is up to 5) and all spike controls were as expected. In addition, data quality was assessed by review of the average background (background average = 74-84, usually less than 100) and percent present calls (%Present=%19-21) for each array. GeneChip expression data were exported to GeneSpring 7.2 where per chip normalization to the 50th percentile expression level and per gene normalization to the median expression intensity in all samples was performed. Values below 0.01 were set to 0.01. Replicates based cross gene error model was activated in GeneSpring normalizations. Statistical evaluation of replicate experiments: The data for Affymetrix control probe sets were removed prior to analysis. Differentially expressed genes were identified by significance analysis of microarrays (SAM), which is a nonparametric, permutation-based method. Normalized raw data was used as an input for SAM. Lists of differentially expressed genes were described by false discovery rate (FDR) (Benjamini and Hochberg, 1995). Transcript conversion to similar human proteins: There is a very limited database to analyze the gene expression information for bovines, we decided, then, to convert the bovine transcript information to highly similar human protein equivalents to see the biological connection within the significant gene list. Statistically significant bovine transcripts were converted to similar human proteins using the NCBI data base. Transcript sequences were used to find similar human proteins at the level of 80% identity cutoff threshold for blast for match by using the human protein Refseq IDs. The human transcripts which recognize the same protein conversion on human U133 plus ver2 GeneChip has been done to analyze in public databases too. This conversion has been done by using the NetAffx™ Analysis Center of Affymetrix.


title: middle stage follicle, biological rep2

tag: the middle stage,secondary follicle


title: #349 vs #443

city: Akita

first: Atsushi

last: Komatsuda

address: Hondo 1-1-1

country: Japan

institute: Akita University School of Medicine

description: Filgen Array Human25K

hyb_protocol: We prehybridized microarrays for 1h at 42 ºC in a solution containing 5×saline-sodium citrate (SSC) (1×SSC: 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), and 0.1 mg/ml bovine serum albumin. We washed microarrays at room temperature in distilled water 3 times for 2 min and in 2-propanol for 1 min. We performed hybridization for 16-20 h at 42 ºC in solution containing 5×SSC/0.1% SDS and 10% formamide, and pre-heat-denatured samples (4 mg of each fluorescence-labeled antisense RNA, 10 mg of Human Cot I DNA (Invitrogen), 10 mg of poly dA (GE Healthcare Bio-Science Corp.), and 10 mg of yeast tRNA (Invitrogen)). We then washed microarrays in 2×SSC/0.1% SDS at 42 ºC for 4 min, 0.1×SSC/0.1% SDS at room temperature for 4 min, 0.1×SSC at room temperature for 2 min, 0.1×SSC at room temperature for 1 min, and 0.1×SSC at room temperature for 1 min.

scan_protocol: We obtained fluorescence image of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (http://www.axon.com).

data_processing: We used Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays. We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas. We normalized biases in net intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) using a software [Yang et al. 2002]. Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.). These data were total signal value (Cy3 and Cy5) of 1,000 or more and ratio value of 1.5 or more.

organism: Homo sapiens

source_name: #349 (relapse)

label_protocol: Fluorescence-labeled antisense RNA was then synthesized by direct incorporation of Cy3-UTP or Cy5-UTP (GE Healthcare Bio-Science Corp., Piscataway, NJ, USA) using 2 mg of total RNA and an RNA Transcript SureLABEL Core Kit (TaKaRa BIO Inc., Tokyo, Japan).

extract_protocol: Total RNA was prepared from PBMC from three patients with MCNS during nephrosis and remission phases, using a TRIzol reagent (Gibco-BRL, Gaithersburg, MD, USA).

tag: Strain

value: Human

tag: Gender

value: female

tag: Age

tag: Tissue

value: peripheral blood mononuclear cells

tag: Tumor stage

value: MCNS in relapse

source_name: #443 (remission)

value: MCNS in remission


title: #251 vs #329

description: Filgen Array Human25K

source_name: #251 (relapse)

tag: Stage

source_name: #329 (remission)


title: Normal, right foot, N3

source_name: Equine Lamellar hoof tissue, Normal

tag: Equine Lamellar hoof tissue, Normal


title: Laminitis, right foot,L1

description: Total RNA isolated from each sample was processed and hybridized to the bovine GeneChip array according to the protocols described in the GeneChip Expression Analysis Technical Manual of 2005 (Affymetrix, Santa Clara, CA). Briefly, total RNA was used to generate double-stranded cDNA by using a T7-linked oligo(dT) primer. Linear amplification-biotin labeling and fragmentation were performed with the one-cycle target labeling kit (Affymetrix, P/N 900493) to have target cRNAs per manufacturer’s recommendation. cRNA yields and purity were assessed by Nanodrop spectroscopy.  Samples were hybridized to bovine  GeneChips (Affymetrix) per the manufacturer’s instructions. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Agilent model G2500A GeneArray scanner at the Penn microarray core facility.

data_processing:
Data was normalized according to per chip median in GC-RMA algorithm. "*.CEL" file was used for that normalization.
After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches. The 3'/5' ratios for housekeeping genes were confirmed to be within acceptable limits (up to 3, normal range is up to 5), scale factors were 1.2-1.5 (normal range is up to 5) and all spike controls were as expected. In addition, data quality was assessed by review of the average background (background average = 74-84, usually less than 100) and percent present calls (%Present=%19-21) for each array.  GeneChip expression data were exported to GeneSpring 7.2  where per chip normalization to the 50th percentile expression level and per gene normalization to the median expression intensity in all samples was performed. Values below 0.01 were set to 0.01. Replicates based cross gene error model was activated in GeneSpring normalizations.
Statistical evaluation of replicate experiments: The data for Affymetrix control probe sets were removed prior to analysis. Differentially expressed genes were identified by significance analysis of microarrays (SAM), which is a nonparametric, permutation-based method (SAM ref). Normalized raw data was used as an input for SAM. Lists of differentially expressed genes were described by false discovery rate (FDR) (Benjamini and Hochberg, 1995).
Transcript conversion to similar human proteins: There is  a very limited database to analyze the gene expression information for bovines, we decided, then,  to convert the bovine transcript information to highly similar human protein equivalents to see the biological connection within the significant gene list. Statistically significant bovine transcripts were converted to similar human proteins  using the NCBI data base. Transcript sequences were used to find similar human proteins at the level of 80% identity cutoff threshold for blast for match by using the human protein Refseq IDs. The human transcripts which recognize the same protein conversion on human U133 plus ver2 GeneChip has been done to analyze in public databases too. This conversion has been done by using the NetAffx™ Analysis Center of Affymetrix.

label: Biotin labelling

tag: Laminitis generated right lameller hoof tissue


title: middle stage follicle, biological rep1


title: last stage follicle, biological rep1


title: Obese Control-3

status: Public on Mar 04 2008

city: washington DC

first: swasti

last: Tiwari

state: DC

address: 4000 reservoir road, NW

institute: Georgetown University

description: model for diabetes

hyb_protocol: Protocol	EukGE-WS2v4_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module 1

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scanner ID	50103010 Number of Scans	1 Scanner Type	M10

data_processing: MAS 5.0

organism: Rattus norvegicus

source_name: kidney tissues from obese rats on control diet

label_protocol: Enzo RNA Transcript Labeling

extract_protocol: Trizol Reagent (Invitrogen)

tag: Zucker rats


title: primordial follicle, biological rep1

tag: the early stage,primordial follicle


title: Laminitis, right foot, L3


title: primordial follicle, biological rep2


title: Obese Control-1

description: model for diabetes

hyb_protocol: Protocol	EukGE-WS2v4_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module 3

source_name: Kidney tissue from obese rats on control diet


title: Obese rosiglitazone-3

description: model for diabetes

hyb_protocol: Protocol	EukGE-WS2v4_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module 2

source_name: Kidney tissue from obese rats on diet with rosiglitazone


title: lean control-3

description: model for diabetes

source_name: kidney tissues from lean rats on control diet


title: lean rosiglitazone 2

description: model for diabetes

source_name: kidney tissues from lean rats on diet with rosiglitazone


title: Obese Control-2

description: model for diabetes


title: #257 vs #259

description: Filgen Array Human25K

source_name: #257 (relapse)

source_name: #259 (remission)


title: lean rosiglitazone-3

description: model for diabetes

hyb_protocol: Protocol	EukGE-WS2v4_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module 4


title: Jurkat RPS3 siRNA 6h TCR - mAdbID:81329

status: Public on Mar 01 2008

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 81329

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 780;; 710 ScanPower: 100;; 100 LaserPower: 3.08084;; 2.97281 Temperature: 30.9046

data_processing:
mAdb Standard Data Processing Protocol
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Control siRNA - 6 hour

label_protocol:
Cy3 Labeling Protocol
Other: Isolated RNA (50 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cy3-conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature. Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

extract_protocol:
Trizol Reagent Extraction Protocol
Extraction method: Trizol Reagent
Other: Total RNA was prepared using the Trizol reagent (Gibco BRL) according to manufacturer's instructions.

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 6 hour
In-vivo treatment: Jurkat cells were transfected with nonspecific siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 6 hr.

tag: Cell line

value: Jurkat Cell Line

source_name: RPS3 siRNA - 6 hour

label_protocol:
Cy5 Labeling Protocol
Other: Isolated RNA (50 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cy5-conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature. Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 6 hour
In-vivo treatment: Jurkat cells were transfected with RPS3 siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 6 hr.


title: Jurkat RPS3 siRNA 1h TCR - mAdbID:81328

description: mAdb experiment ID: 81328

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 680 ScanPower: 100;; 100 LaserPower: 3.03;; 3.34 Temperature: 30.78

source_name: Control siRNA - 1 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 1 hour
In-vivo treatment: Jurkat cells were transfected with nonspecific siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 1 hr.

source_name: RPS3 siRNA - 1 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 1 hour
In-vivo treatment: Jurkat cells were transfected with RPS3 siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 1 hr.


title: Obese rosiglitazone-1

description: model for diabetes

source_name: kidney tissues from obese rats on diet with rosiglitazone


title: OCI-Ly10 c-myc siRNA SMARTpool vs. no siRNA 6h - mAdbID:46757

description: mAdb experiment ID: 46757

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 630;; 680 ScanPower: 100;; 100 LaserPower: 1.1;; 1.84 Temperature: 32.87

source_name: Control Solution T - 6 hour

treatment_protocol:
Treatment time: 6 hour
In-vivo treatment: OCI-Ly10 cells were transfected with no siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 6 hours before harvest.

value: OCI-Ly10 Cell Line

source_name: c-myc siRNA SMARTpool - 6 hour

treatment_protocol:
Treatment time: 6 hour
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM c-myc siRNA SMARTpool (Dharmacon) using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 6 hours before harvest.


title: OCI-Ly10 c-myc siRNA SMARTpool vs. no siRNA 24h - mAdbID:46760

description: mAdb experiment ID: 46760

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [47890] PMTVolts: 630;; 680 ScanPower: 100;; 100 LaserPower: 1.17;; 1.88 Temperature: 33.13

source_name: Control Solution T - 24 hour

treatment_protocol:
Treatment time: 24 hour
In-vivo treatment: OCI-Ly10 cells were transfected with no siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 24 hours before harvest.

source_name: c-myc siRNA SMARTpool - 24 hour

treatment_protocol:
Treatment time: 24 hour
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM c-myc siRNA SMARTpool (Dharmacon) using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 24 hours before harvest.


title: Obese rosiglitazone-2

description: model for diabetes


title: lean control-2

description: model for diabetes

hyb_protocol: Protocol	EukGE-WS2v4_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	4


title: HP 26695, salt, growth, 1.5% (HP 26695_salt_1.5_4)

city: Nashville

first: John

last: Loh

state: TN

address: A2320 MCN VUMC

department: Infectious Diseases

institute: Vanderbilt University

hyb_protocol: The labeled cDNA was then hybridized to nylon Panorama H. pylori DNA arrays (Sigma-Genosys) using the manufacturer’s protocols.  Briefly, gene arrays were prehybridized in hybridization (5 X SSPE, 2% SDS, 5X denhardts, 100 ug/ml denatured salmon sperm DNA) solution for 1 h, 65oC prior to the addition of labeled cDNA.  Following hybridization (overnight) at 65oC, the membranes were washed with wash solution (0.5 X SSPE, 0.2% SDS) 3x for 20 min at 65oC.

scan_protocol: Scanning of the hybridized arrays was performed with a phosphoimager (Fuji Inc), and the hybridization signals were quantified with ImageQuant (Fuji Inc.) and Array Vision (Imaging Research Inc.) software.  Array vision software is designed by Imaging Research to analyze all the spots on the H. pylori array.

data_processing: For each array feature, a normalized signal intensity was calculated as a ratio of the signal intensity for the individual array feature divided by the total signal intensity of the entire array.

organism: Helicobacter pylori

source_name: HP 26695, salt, growth, 1.5%

label_protocol: Total RNA (1 μg) was used to generate 33P-labeled cDNA using H. pylori-specific cDNA labeling primers (Sigma-Genosys).  The reverse transcriptase reaction was performed for 2 h at 42o C, in the presence of 10 mM DTT, 0.33 mM dGTP, dCPT and dTTP, 5 μM dATP, 20 μCi [33P-dATP] (Perkin Elmer), 1 U RNAsin ribonuclease inhibitor (Promega) and 50 U of reverse transcriptase (Superscript II; Gibco BRL).  Unincorporated 33P-dATP was removed by passage of the sample through NucAway Spin Columns (Ambion).

growth_protocol: H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.5%)  The bacterial cells (OD600 = 0.4 to 0.5) were then centrifuged and resuspended in BB-FBS-1.5% media (OD600=0.1)   The bacteria were grown for 10 h, harvested by centrifugation, and frozen at -80oC

extract_protocol: RNA isolation was performed using the acid guanidinium-phenol-chloroform method (Trizol; Gibco BRL).  Contaminating DNA was removed from the samples by treatment with RQ1 (RNA qualified) RNAse-free DNAse (Promega), and RNA was purified using the RNA Easy kit (Qiagen).

tag: Helicobacter pylori, strain 26695


title: HP 26695, salt, growth, 1.5% (HP 26695_salt_1.5_2)


title: HP 26695, salt, growth, 1.5% (HP 26695_salt_1.5_3)


title: Jurkat p65 siRNA 6h TCR - mAdbID:81327

description: mAdb experiment ID: 81327

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 750;; 680 ScanPower: 100;; 100 LaserPower: 2.93;; 3.31 Temperature: 30.54

source_name: p65 siRNA - 6 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 6 hour
In-vivo treatment: Jurkat cells were transfected with p65 siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 6 hr.


title: Lean Rosiglitazone 1

description: model for diabetes

source_name: Kidney tissues from lean rats on diet with rosiglitazone


title: lean control-1

description: model for diabetes

hyb_protocol: Protocol	EukGE-WS2v4_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	3


title: OCI-Ly10 c-myc siRNA SMARTpool vs. siRNA 24h - mAdbID:44647

description: mAdb experiment ID: 44647

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 690;; 650 ScanPower: 100;; 100 LaserPower: 1.81;; 2.15 Temperature: 43.06

source_name: Control Renilla Luc siRNA - 24 hour

treatment_protocol:
Treatment time: 24 hour
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM nonspecific Renilla Luc siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 24 hours before harvest.


title: HP 26695, salt, growth, 0.25% (HP 26695_salt_0.25_1)

growth_protocol: H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.5%)  The bacterial cells (OD600 = 0.4 to 0.5) were then centrifuged and resuspended in fresh BB-FBS-0.25% media (OD600=0.1)   The bacteria were grown for 10 h, harvested by centrifugation, and frozen at -80oC


title: HP 26695, salt, growth, 1.5% (HP 26695_salt_1.5_1)


title: WT - repeat 1 - mAdbID:52495

city: Seoul

first: Seung-yong

last: Seong

address: 28 Yongon-dong, Jongno-gu

department: Microbiology and Immunology

country: South Korea

institute: Wide River Institute of Immunology, Seoul National University College of Medicine

description: mAdb experiment ID: 52495

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 3.34;; 3.57 Temperature: 29.99

organism: Mus musculus

source_name: WT Stimulated

label_protocol:
Ambion Cy5 RNA Labeling Kit
Other: Labeled RNA using RNA labeling kit (Ambion, Inc., Austin, TX) following manufacturer's instructions.

extract_protocol:
Qiagen RNeasy Kit
Other: Samples were extracted using Qiagen RNeasy Kit according to manufacturer's protocol.

treatment_protocol: In-vivo treatment: Peritoneal cells were stimulated with 2 x 10e6 necrotic fibroblast cells/ml for 18 hours in 96 well plates.

tag: Cell type

value: peritoneal macrophages

tag: genotype/variation

source_name: WT Control

label_protocol:
Ambion Cy3 RNA Labeling Kit
Other: Labeled RNA using RNA labeling kit (Ambion, Inc., Austin, TX) following manufacturer's instructions.

treatment_protocol: In-vivo treatment: Peritoneal cells were treated with medium for 18 hours in 96 well plates. Before extraction, medium-treated peritoneal cells in the control group were also mixed with 2 x 10e6 necrotic fibroblast cells/ml which had been incubated in the CO2 incubator for 18 hrs in separate wells to normalize the total amount of RNA.


title: OCI-Ly10 c-myc siRNA SMARTpool vs. siRNA 8h - mAdbID:44645

description: mAdb experiment ID: 44645

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 690;; 650 ScanPower: 100;; 100 LaserPower: 1.8;; 2.14 Temperature: 42.99

source_name: Control Renilla Luc siRNA - 8 hour

treatment_protocol:
Treatment time: 8 hour
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM nonspecific Renilla Luc siRNA using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 8 hours before harvest.

source_name: c-myc siRNA SMARTpool - 8 hour

treatment_protocol:
Treatment time: 8 hour
In-vivo treatment: OCI-Ly10 cells were transfected with 4uM c-myc siRNA SMARTpool (Dharmacon) using the Amaxa electroporator. In brief, 8X10^6 cells were used for each time point. Cells were pelleted and resuspended in Solution T (Amaxa) and RNAi. After transferring cells to the cuvettes, they were electroporated using the program A-23. Cells were then transferred to pre-warm medium and incubated for 8 hours before harvest.


title: HP 26695, salt, growth, 0.25% (HP 26695_salt_0.25_4)

growth_protocol: H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.5%)  The bacterial cells (OD600 = 0.4 to 0.5) were then centrifuged and resuspended in fresh BB-FBS-0.25% (OD600=0.1)   The bacteria were grown for 10 h, harvested by centrifugation, and frozen at -80oC


title: Jurkat p65 siRNA 3h TCR - mAdbID:81326

description: mAdb experiment ID: 81326

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 770;; 690 ScanPower: 100;; 100 LaserPower: 2.89;; 2.74 Temperature: 30.36

source_name: Control siRNA - 3 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 3 hour
In-vivo treatment: Jurkat cells were transfected with nonspecific siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 3 hr.

source_name: p65 siRNA - 3 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 3 hour
In-vivo treatment: Jurkat cells were transfected with p65 siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 3 hr.


title: CD14-KO - repeat 2 - mAdbID:52496

description: mAdb experiment ID: 52496

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 3.34;; 3.57 Temperature: 30.2

source_name: CD14-KO Stimulated

tag: genotype/variation gene knock out

source_name: CD14-KO Control


title: WT - repeat 2 - mAdbID:52346

description: mAdb experiment ID: 52346

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.4;; 3.31 Temperature: 29.87


title: Jurkat RPS3 siRNA 3h TCR - mAdbID:81133

description: mAdb experiment ID: 81133

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 830;; 770 ScanPower: 100;; 100 LaserPower: 1.72;; 2.39 Temperature: 36.59

source_name: RPS3 siRNA - 3 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 3 hour
In-vivo treatment: Jurkat cells were transfected with RPS3 siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 3 hr.


title: Jurkat p65 siRNA 1h TCR - mAdbID:81132

description: mAdb experiment ID: 81132

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 820;; 770 ScanPower: 100;; 100 LaserPower: 1.76;; 2.36 Temperature: 36.18

source_name: Control siRNA - 1 hour

source_name: p65 siRNA - 1 hour

treatment_protocol:
Treatment dose: 1 ug
Treatment time: 1 hour
In-vivo treatment: Jurkat cells were transfected with p65 siRNA, then stimulated with 1 ug of anti-CD3/CD28 for 1 hr.


title: CD14-KO - repeat 1 - mAdbID:52420

description: mAdb experiment ID: 52420

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.37;; 3.32 Temperature: 29.96


status: Public on Feb 26 2008

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_hypothetical protein SERP0311 (apsX) with 10ug/ml human beta defensin 3 biological rep 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus epidermidis

source_name: apsX treated rep 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For microarray experiments, overnight cultures were diluted 1:100 into 50 ml of TSB and incubated at 37C with shaking at 180rpm until grown to an OD600 of 2.5-3.0 (mid-logarithmic growth phase). Cultures were then split in two equal volumes and cells were washed twice in 10 mM sodium phosphate buffer (pH 6.5) with 100 mM NaCl and resuspended in the same buffer.

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: To one sample, hBD3 was added to a final concentration of 10ug /ml. Samples were incubated at 37°C for 3 h.


description: Gene expression data from_hypothetical protein SERP0311 (apsX) with 10ug/ml human beta defensin 3 biological rep 1

source_name: apsX treated rep 1


description: Gene expression data from_hypothetical protein SERP0311 (apsX) without human beta defensin 3 biological rep 1

source_name: apsX untreated rep 1


title: HP 26695, salt, growth, 0.25% (HP 26695_salt_0.25_2)


title: HP 26695, salt, growth, 0.25% (HP 26695_salt_0.25_3)

growth_protocol: H. pylori strain 26695 (SC#7) was grown for 15 h in BB-FBS medium containing 0.5% sodium chloride (i.e. BB-FBS-0.25%)  The bacterial cells (OD600 = 0.4 to 0.5) were then centrifuged and resuspended in fresh BB-FBS-0.25% media (OD600=0.1)   The bacteria were grown for 10 h, harvested by centrifugation, and frozen at -80oC


description: Gene expression data from_hypothetical protein SERP0311 (apsX) without human beta defensin 3 biological rep 2

source_name: apsX untreated rep 2


description: Gene expression data from_hypothetical protein SERP0311 (apsX) without human beta defensin 3 biological rep 3

source_name: apsX untreated rep 3


description: Gene expression data from_wt with 10ug/ml human beta defensin 3 biological rep 2 exp 2

source_name: wt treated rep 2 exp 2


description: Gene expression data from_wt with 10ug/ml human beta defensin 3 biological rep 1 exp 2

source_name: wt treated rep 1 exp 2


description: Gene expression data from_wt with 10ug/ml human beta defensin 3 biological rep 3 exp 2

source_name: wt treated rep 3 exp 2


description: Gene expression data from_wt without human beta defensin 3 biological rep 3 exp 2

source_name: wild type untreated rep 3 exp 2


description: Gene expression data from_hypothetical protein SERP0311 (apsX) with 10ug/ml human beta defensin 3 biological rep 2

source_name: apsX treated rep 2


description: Gene expression data from_wt without human beta defensin 3 biological rep 1 exp 2

source_name: wild type untreated rep 1 exp 2


title: Bronchoalveolar lavage sample Viro3P10-192

city: San Francisco

first: Joe

last: DeRisi

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: amplified RNA from a BAL sample from a patient at Stanford with critical respiratory illness

hyb_protocol: 65 degree incubation overnight in standard microarray hybridization chamber

scan_protocol: microarray scanned with GenePix scanner

data_processing: Median feature intensity minus median background intensity

organism: Viruses

source_name: amplified RNA from a BAL sample from a patients at Stanford with critical respiratory illness

label_protocol: labeling of aminoallyl dNTP with Cy3/Cy5; Cy3 for amplified sample RNA, Cy5 for Probe70 (internal reference)

extract_protocol: RNA extraction using Zymo(TM) kit from bronchoalveolar lavage fluid

tag: HMPV


description: Gene expression data from_response regulator mutant (apsR) with 10ug/ml human beta defensin 3 biological rep 3

source_name: apsR treated rep 3


description: Gene expression data from_response regulator mutant (apsR) without human beta defensin 3 biological rep 3

source_name: apsR untreated rep 3


description: Gene expression data from_wt without human beta defensin 3 biological rep 2 exp 2

source_name: wild type untreated rep 2 exp 2


description: Gene expression data from_histidine kinase (apsS) with 10ug/ml human beta defensin 3 biological rep 3

source_name: apsS treated rep 3


description: Gene expression data from_response regulator mutant (apsR) with 10ug/ml human beta defensin 3 biological rep 2

source_name: apsR treated rep 2


description: Gene expression data from_response regulator mutant (apsR) without human beta defensin 3 biological rep 2

source_name: apsR untreated rep 2


description: Gene expression data from_response regulator mutant (apsR) with 10ug/ml human beta defensin 3 biological rep 1

source_name: apsR treated rep 1


description: Gene expression data from_histidine kinase (apsS) with 10ug/ml human beta defensin 3 biological rep 1

source_name: apsS treated rep 1


description: Gene expression data from_histidine kinase (apsS) without human beta defensin 3 biological rep 3

source_name: apsS untreated rep 3


description: Gene expression data from_histidine kinase (apsS) without human beta defensin 3 biological rep 2

source_name: apsS untreated rep 2


description: Gene expression data from_histidine kinase (apsS) without human beta defensin 3 biological rep 1

source_name: apsS untreated rep 1


description: Gene expression data from_wt with 10ug/ml human beta defensin 3 biological rep 2

source_name: wt treated rep 2


description: Gene expression data from_response regulator mutant (apsR) without human beta defensin 3 biological rep 1

source_name: apsR untreated rep 1


description: Gene expression data from_wt with 10ug/ml human beta defensin 3 biological rep 3

source_name: wt treated rep 3


description: Gene expression data from_wt without human beta defensin 3 biological rep 3

source_name: wild type untreated rep 3


description: Gene expression data from_wt with 10ug/ml human beta defensin 3 biological rep 1

source_name: wt treated rep 1


description: Gene expression data from_histidine kinase (apsS) with 10ug/ml human beta defensin 3 biological rep 2

source_name: apsS treated rep 2


title: Adult cardiomyocytes stimulated with the cytokine domain (aa 25-100) of fractalkine, array 5

status: Public on Feb 01 2008

city: Oslo

first: Cathrine

last: Husberg

address: Kirkeveien 166

country: Norway

institute: Institute for experimental medical research

description: Gene expression was examined in adult cardiomyocytes after stimulation with fractalkine. Cardiomyocytes exposed to BSA were used as controls.

hyb_protocol: Agilent oligo microarray kit hybridization protocol

scan_protocol: The arrays were controlled for spatial and intensity dependent effects by visual inspections of the array images and of ratio/intensity (RI) plots. To retain saturated spots (with more than half of the pixels in saturation) we performed additional lower scans of the arrays and modified the saturated intensities according to the algorithm described in Lyng, Badiee et al (2004). As measures of the spot intensities we used the median of the foreground pixel intensities, and log-transformed them to obtain approximate normality. No further normalisation was done because this is taken care of in our model-based analysis described below

data_processing: Our model is based on a log-linear mixed effect model according to Kerr et al (2000).  The base2 logarithm of each of the measured fluorescent intensity was modelled as a sum of dye, gene and array effects plus effects of the interaction terms array*gene (i.e. spot effects), dye*gene and time*variety*gene (the time-dependent effect of the specific variety – here myocardial infarction or  control - on each gene). The latter is the parameter of main concern, and we note that the difference here for a given gene between myocardial infarction and control is the log2 ratio (normalised for experimental noise) in gene expression between the two types. Parameter estimates were obtained using the MicroArray ANOVA (MAANOVA) package by Wu et al (2002), for the statistical language R. We sat the threshold of significance of 30% change and p<0.05.

source_name: Adult cardiomyocytes, treated with the cytokine domain (aa 25-100) of fractalkine, 24 hours

label_protocol: Agilent Low RNA input fluorescent linear amplification kit

extract_protocol: SV total RNA isolation system, Promega

tag: Cardiomyocytes isolated from adult rat hearts, kept in culture for 26 hours, treated with the cytokine domain (aa 25-100) of fractalkine for 24 hours

source_name: Adult cardiomyocytes, controls treated with BSA , 24 h

tag: Cardiomyocytes isolated from adult rat hearts, kept in culture for 26 hours, treated with BSA for 24 hours


description: Gene expression data from_wt without human beta defensin 3 biological rep 2

source_name: wild type untreated rep 2


description: Gene expression data from_wt without human beta defensin 3 biological rep 1

source_name: wild type untreated rep 1


title: CHX-SGIV infected GS cell at 8 h p.i.

status: Public on Jan 28 2008

city: Guangzhou

first: yong

last: teng

address: 135 West Xingang Road

institute: Sun yet-san university

description: In a comparison analysis, we used Significance Analysis of Microarrays (SAM) software to identify the groups of different expression genes between the drug-treated samples and untreated samples. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Significance is based on an estimated of FDR≤5% and a 2 fold-change cutoff.

hyb_protocol: The labeled DNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel), resuspended in Elution buffer and check O.D. Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 12 μl hybridization solution (3×SSC, 0.2% SDS, 50% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95°C for 3 min prior loading on a microarray. The hybridization was performed in water bath under 42°C overnight under SmartSlideTM cover slide (CapitalBio) which mainly consists of a molded coverslip enabling a controllable liquid layer between the microarray and coverslip. Through decreasing the diffusion distance of target DNA to the probe in the chip, this device increased the hybridization sensitivity in comparison with conventional coverslips and comparable with microfluidic systems. The array was hybridized at 42°C overnight and  washed with two consecutive washing solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2×SSC for 5 min at room temperature).

scan_protocol: Following this step, the microarrays were dried at 500 rpm for 5 min and scanned with a confocal LuxScanTM scanner (CapitalBio). and obtained images were analyzed with SpotDataTM software (CapitalBio).

data_processing: After visual inspection for the presence of image artifacts, such as scratches, dirt, contamination, high region, or overall background on the array, the scanned images were saved as TIF files and further analyzed to generate raw data using SpotDataTM software (CapitalBio). After filtering the low-intensity spots and background-noise value, a global scaling procedure was performed to normalize among the different arrays and the different channels of same arrays using housekeeping gene of piscine 18S RNA which was also spotted in triplicate.

organism:
Iridovirus
Epinephelus coioides

source_name: mock infected cells at 8 h p.i.

label_protocol: An aliquot of 20 μg total RNA was reverse transcripted with SuperScript II (Invitrogen, USA) and cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany). Because of the relatively low efficiency of fluorescence dye incorporation of reverse transcriptase, Klenow enzyme labeling strategy was adopted after reverse transcription (RT), which facilitated the hybridization kinetics. In brief, the cDNA from the RT reaction and 4 μg of random primer were heated to 95°C for 3 min, snap cooled on ice. Next, 10 × buffer, dNTP and Cy3-dCTP (GE Healthcare, USA) were added at final concentration of 120 μM each dATP, dGTP, dTTP, and 1 μl 60 μM dCTP and 40 μM Cy-dye respectively. Klenow enzyme (Takara, Japan) was added and reaction was performed at 37°C for 60 min.

extract_protocol: Total RNA was extracted from the collected cells at indicated time points with TRIzol (Invitrogen, USA) and subjected to DNase I (Takara, Japan) treatment according to the manufacturer’s protocols.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides (46) were cultured in Leibovitz’s L-15 medium, mock infected cells at 8 h p.i.

source_name: CHX-SGIV infected cells at 8 h p.i.

label_protocol: An aliquot of 20 μg total RNA was reverse transcripted with SuperScript II (Invitrogen, USA) and cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany). Because of the relatively low efficiency of fluorescence dye incorporation of reverse transcriptase, Klenow enzyme labeling strategy was adopted after reverse transcription (RT), which facilitated the hybridization kinetics. In brief, the cDNA from the RT reaction and 4 μg of random primer were heated to 95°C for 3 min, snap cooled on ice. Next, 10 × buffer, dNTP and Cy5-dCTP (GE Healthcare, USA) were added at final concentration of 120 μM each dATP, dGTP, dTTP, and 1 μl 60 μM dCTP and 40 μM Cy-dye respectively. Klenow enzyme (Takara, Japan) was added and reaction was performed at 37°C for 60 min.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides (46) were cultured in Leibovitz’s L-15 medium, GS monolayers were treated for 1 h prior to, during and throughout the viral infection with CHX, at 8 h p.i.


title: Adult cardiomyocytes stimulated with the cytokine domain (aa 25-100) of fractalkine, array 1

source_name: Adult cardiomyocytes, controls treated with BSA, 24 h


title: Adult cardiomyocytes stimulated with the cytokine domain (aa 25-100) of fractalkine, array 4


title: Adult cardiomyocytes stimulated with the cytokine domain (aa 25-100) of fractalkine, array 2


title: Adult cardiomyocytes stimulated with full-length fractalkine, array 3

source_name: Adult cardiomyocytes, treated with full-length fractalkine, 24 hours

tag: Cardiomyocytes isolated from adult rat hearts, kept in culture for 26 hours, treated with full-length fractalkine for 24 hours


title: Adult cardiomyocytes stimulated with the cytokine domain (aa 25-100) of fractalkine, array 3


title: Adult cardiomyocytes stimulated with full-length fractalkine, array 1

source_name: Adult cardiomyocytes, controls treated with BSA

tag: Cardiomyocytes  isolated from adult rat hearts, kept in culture for 26 hours, treated with full-length BSA for 24 hours

tag: Cardiomyocytes  isolated from adult rat hearts, kept in culture for 26 hours, treated with full-length fractalkine for 24 hours


title: Adult cardiomyocytes stimulated with full-length fractalkine, array 5


title: Adult cardiomyocytes stimulated with full-length fractalkine, array 4


title: Adult cardiomyocytes stimulated with full-length fractalkine, array 2


title: PAA-SGIV infected GS cells at 36 h p.i.

source_name: mock infected cells at 36 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides (46) were cultured in Leibovitz’s L-15 medium, mock infected at 36 h p.i.

source_name: PAA-SGIV infected cells at 36 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides (46) were cultured in Leibovitz’s L-15 medium, GS monolayers were treated for 1 h prior to, during and throughout the viral infection with PAA, at 36 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (9 d p.i.)

description: In a temporal expression analysis, the expression intensity of the viral genes was considered as the average fluorescent intensity of the replicated spots from viral-infect samples minus that from no viral-infect samples. MATLAB 7.0 software was used to draw the temporal trend of each ORF with the import data of log2-transformed expression intensity

organism: Epinephelus tauvina

source_name: mock infected grouper spleen, 9 d p.i.

label_protocol: An aliquot of 20 μg total RNA was reverse transcripted with SuperScript II (Invitrogen, USA) and cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany). Because of the relatively low efficiency of fluorescence dye incorporation of reverse transcriptase, Klenow enzyme labeling strategy was adopted after reverse transcription (RT), which facilitated the hybridization kinetics. In brief, the cDNA from the RT reaction and 4 μg of random primer were heated to 95°C for 3 min, snap cooled on ice. Next, 10 × buffer, dNTP and Cy5-dCTP (GE Healthcare, USA) were added at final concentration of 120 μM each dATP, dGTP, dTTP, and 1 μl 60 μM dCTP and 40 μM Cy-dye respectively. Klenow enzyme (Takara, Japan) was added and reaction was performed at 37°C for 60 min

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 9 d p.i.

organism:
Iridovirus
Epinephelus tauvina

source_name: SGIV infected grouper spleen, 9 d p.i.

label_protocol: An aliquot of 20 μg total RNA was reverse transcripted with SuperScript II (Invitrogen, USA) and cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany). Because of the relatively low efficiency of fluorescence dye incorporation of reverse transcriptase, Klenow enzyme labeling strategy was adopted after reverse transcription (RT), which facilitated the hybridization kinetics. In brief, the cDNA from the RT reaction and 4 μg of random primer were heated to 95°C for 3 min, snap cooled on ice. Next, 10 × buffer, dNTP and Cy3-dCTP (GE Healthcare, USA) were added at final concentration of 120 μM each dATP, dGTP, dTTP, and 1 μl 60 μM dCTP and 40 μM Cy-dye respectively. Klenow enzyme (Takara, Japan) was added and reaction was performed at 37°C for 60 min

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 9 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (11 d p.i.)

source_name: mock infected grouper spleen, 11 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 11 d p.i.

source_name: SGIV infected grouper spleen, 11 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 11 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (15 d p.i.)

source_name: mock infected grouper spleen, 15 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 15 d p.i.

source_name: SGIV infected grouper spleen, 15 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 15 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (5 d p.i.)

source_name: mock infected grouper spleen, 5 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 5d p.i.

source_name: SGIV infected grouper spleen, 5 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 5 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (7 d p.i.)

source_name: mock infected grouper spleen, 7 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 7 d p.i.

source_name: SGIV infected grouper spleen, 7 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 7 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (72 h p.i.)

hyb_protocol: The labeled DNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel), resuspended in Elution buffer and check O.D. Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 12 µl hybridization solution (3×SSC, 0.2% SDS, 50% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95°C for 3 min prior loading on a microarray. The hybridization was performed in water bath under 42°C overnight under SmartSlideTM cover slide (CapitalBio) which mainly consists of a molded coverslip enabling a controllable liquid layer between the microarray and coverslip. Through decreasing the diffusion distance of target DNA to the probe in the chip, this device increased the hybridization sensitivity in comparison with conventional coverslips and comparable with microfluidic systems. The array was hybridized at 42°C overnight and  washed with two consecutive washing solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2×SSC for 5 min at room temperature).

organism: Epinephelus coioides

source_name: mock infected GS cells, 72 h p.i.

label_protocol: An aliquot of 20 µg total RNA was reverse transcripted with SuperScript II (Invitrogen, USA) and cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany). Because of the relatively low efficiency of fluorescence dye incorporation of reverse transcriptase, Klenow enzyme labeling strategy was adopted after reverse transcription (RT), which facilitated the hybridization kinetics. In brief, the cDNA from the RT reaction and 4 µg of random primer were heated to 95°C for 3 min, snap cooled on ice. Next, 10 × buffer, dNTP and Cy3-dCTP (GE Healthcare, USA) were added at final concentration of 120 µM each dATP, dGTP, dTTP, and 1 µl 60 µM dCTP and 40 µM Cy-dye respectively. Klenow enzyme (Takara, Japan) was added and reaction was performed at 37°C for 60 min.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 72 h p.i.

source_name: SGIV infected GS cells, 72 h p.i.

label_protocol: An aliquot of 20 µg total RNA was reverse transcripted with SuperScript II (Invitrogen, USA) and cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany). Because of the relatively low efficiency of fluorescence dye incorporation of reverse transcriptase, Klenow enzyme labeling strategy was adopted after reverse transcription (RT), which facilitated the hybridization kinetics. In brief, the cDNA from the RT reaction and 4 µg of random primer were heated to 95°C for 3 min, snap cooled on ice. Next, 10 × buffer, dNTP and Cy5-dCTP (GE Healthcare, USA) were added at final concentration of 120 µM each dATP, dGTP, dTTP, and 1 µl 60 µM dCTP and 40 µM Cy-dye respectively. Klenow enzyme (Takara, Japan) was added and reaction was performed at 37°C for 60 min.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 72 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (4 d p.i.)

source_name: mock infected grouper spleen, 4 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 1 d p.i.

source_name: SGIV infected grouper spleen, 4 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 1 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (3 d p.i.)

source_name: mock infected grouper spleen, 3 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC,  3 d p.i.

source_name: SGIV infected grouper spleen, 3 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 3 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (1 d p.i.)

source_name: mock infected grouper spleen, 1 d p.i.

extract_protocol: Total RNA was extracted from the collected spleen samples at indicated time points with TRIzol (Invitrogen, USA) and subjected to DNase I (Takara, Japan) treatment according to the manufacturer’s protocols.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 µl DMEM and held in tanks supplied with running seawater at 25oC. 1 d p.i.

source_name: SGIV infected grouper spleen, 1 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 µl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC. 1 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (96 h p.i.)

source_name: mock infected GS cells, 96 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 96 h p.i.

source_name: SGIV  infected GS cells, 96 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 96 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vivo (2 d p.i.)

source_name: mock infected grouper spleen, 2 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl DMEM and held in tanks supplied with running seawater at 25oC, 2 d p.i.

source_name: SGIV infected grouper spleen, 2 d p.i.

tag: Grouper Epinephelus tauvina juveniles with approximately 40-50 g, were experimentally infected with 150 μl of the SGIV inoculum (5.0×105.5 TCID50/ml) and held in tanks supplied with running seawater at 25oC, 2 d p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (36 h p.i.)

source_name: mock infected GS cells, 36 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 36 h p.i.

source_name: SGIV infected GS cells, 36 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 36 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (48 h p.i.)

source_name: mock infected GS cells, 48 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 48 h p.i.

source_name: SGIV infected GS cells, 48 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 48 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (12 h p.i.)

source_name: mock infected GS cells, 12 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 12 h

source_name: SGIV infected GS cells, 12 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 12 h


title: Whole-genome transcriptional profiles of SGIV in vitro (24 h p.i)

source_name: mock infected GS cells, 24 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 24 h p.i.

source_name: SGIV infected GS cells, 24 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium,SGIV infected 24 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (4 h p.i.)

source_name: mock infected GS cells, 4 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 4 h

source_name: SGIV infected GS cells, 4 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 4 h


title: Whole-genome transcriptional profiles of SGIV in vitro (10 h p.i.)

source_name: mock infected GS cells, 10 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 10 h

source_name: SGIV infected GS cells, 10 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 10 h


title: Whole-genome transcriptional profiles of SGIV in vitro (8 h p.i.)

source_name: mock infected GS cells, 8 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 8 h

source_name: SGIV infected GS cells, 8 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIVinfected 8 h


title: Whole-genome transcriptional profiles of SGIV in vitro (16 h p.i.)

source_name: mock infected GS cells, 16 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 16 h

source_name: SGIV infected GS cells, 16 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 16 h


title: Whole-genome transcriptional profiles of SGIV in vitro (6 h p.i.)

source_name: mock infected GS cells, 6 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 6 h

source_name: SGIV infected GS cells, 6 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 6 h


title: Whole-genome transcriptional profiles of SGIV in vitro  (1 h p.i.)

source_name: mock infected GS cells, 1 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 1 h p.i.

source_name: SGIV infected GS cells, 1 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium,  SGIV (strain A3/12/98 PPD), isolated originally from diseased brown-spotted grouper, Epinephelus tauvina, in Singapore, infected GS 1 h p.i.


title: Whole-genome transcriptional profiles of SGIV in vitro (2 h p.i.)

source_name: mock infected GS cells, 2 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, mock infected 2 h

source_name: SGIV infected GS cells, 2 h p.i.

tag: The spleen of orange-spotted grouper cells (GS) from Epinephelus coioides, cultured in Leibovitz’s L-15 medium, SGIV infected 2 h


title: JT_Sm3_11

status: Public on Jan 01 2008

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: sham operated male control mouse

hyb_protocol: Fifteen micrograms of each cRNA sample was hybridized for 16 hours at 45°C to rat expression Affymetrix RAE 430A GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

scan_protocol: Affymetrix GeneChip System confocal scanner 2500

data_processing: Affymetrix GeneChip Operating Software (GCOS)

label: biotin labeled

source_name: sham operated male

label_protocol: The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality evaluated by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (TIBMOL Biol, Berlin, Germany) one to three micrograms of total RNA were used for double-stranded cDNA synthesis (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (Affymetrix, Santa Clara, CA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mM Tris-acetate (pH 8.2), 100 mM potassium acetate, and 50 mM magnesium acetate) at 94°C for 35 minutes.

growth_protocol: 12-14 week old male and female C57BL/6J mice were housed under climate-controlled conditions with a 12h light/dark cycle and were provided with standard food and water ad libitum.

extract_protocol: Total RNA was isolated 14 days after surgery of the left ventricle using TRIzol Reagent (Invitrogen).

treatment_protocol: Mice were sham operated. Animals received buprenorphine (0.05mg/kg body weight) bid for the first 2 days following thoracotomy. All procedures were in accordance with animal welfare guidelines and were approved by the respective governmental agencies.

tag: strain

tag: age

value: 12-14 weeks

tag: sex

value: male


title: JT_Sm4_12

description: sham operated male control mouse


title: JT_Sm2_10

description: sham operated male control mouse


title: JT_Sw2_14

description: sham operated female control mouse

source_name: sham operated female


title: JT_Sm1_09

description: sham operated male control mouse


title: JT_Sw1_13

description: sham operated female control mouse


title: JT_Sw4_16

description: sham operated female control mouse


title: JT_Gw5_08

description: female mouse with cardiac hypertrophy induced by transverse aortic constriction

source_name: hypertrophy in females

treatment_protocol: Transverse aortic constriction (TAC) was preformed to induce cardiac hypertrophy. For the TAC the animals were anesthetized via the intra-peritoneal injection of ketamine (50mg/kg body weight) in combination with isoflurane (2-3%). Animals received buprenorphine (0.05mg/kg body weight) bid for the first 2 days following thoracotomy. All procedures were in accordance with animal welfare guidelines and were approved by the respective governmental agencies.


title: JT_Gw3_07


title: JT_Gm5_04

description: male mouse with cardiac hypertrophy induced by transverse aortic constriction

source_name: hypertrophy in males


title: Control -DOX at 50% survival, biological rep 4

city: Los Angeles

first: Diana

last: Abdueva

address: 443 S San Pedro St, STE 403

institute: USC

description: Gene expression data from Control -DOX at 50% survival

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr to GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner

data_processing: Gene expression measures were computed using the Robust Multichip Average (RMA) {Irizarry, 2003} in the Affy package for the R statistical programming language

organism: Drosophila melanogaster

source_name: Adult male progeny resulting from the cross between Oregon R control strain and the rtTA(3)E2 transactivator line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 mg total RNA

growth_protocol: cultured at 25oC in urine specimen bottles

extract_protocol: 35 mg RNA was isolated from groups of 30 adult male Drosophila using the RNAqueous kit (Ambion)

treatment_protocol: Adult control flies treatedwithout doxycycline

tag: Line

value: control line

tag: DOX Condition

value: Minus

tag: Age

value: 50% survival of DOX- flies (~day 73)


title: JT_Gw2_06


title: Control -DOX at 50% survival, biological rep 2


title: JT_Gw1_05


title: Control -DOX at 50% survival, biological rep 3


title: JT_Gm2_02


title: Control -DOX at 50% survival, biological rep 1


title: MnSOD transgenic line +DOX 50% survival, biological rep 4

description: Gene expression data from MnSOD transgenic line +DOX 50% survival

source_name: Adult male progeny resulting from the cross between MnSOD transgenic line (MnSOD(2)22) and the rtTA(3)E2 transactivator line

treatment_protocol: Adult transgenic flies treated with doxycycline

value: MnSOD transgenic line

value: Plus

value: 50% survival for DOX+ (~day 83)


title: JT_Gm1_01


title: MnSOD transgenic line +DOX at -DOX 50% survival, biological rep 4

description: Gene expression data from MnSOD transgenic line +DOX at -DOX 50% survival


title: JT_Gm4_03


title: MnSOD transgenic line +DOX at -DOX 50% survival, biological rep 2


title: MnSOD transgenic line +DOX 50% survival, biological rep 3


title: JT_Sw3_15

description: sham operated female control mouse


title: MnSOD transgenic line +DOX 50% survival, biological rep 2


title: MnSOD transgenic line -DOX at 50% survival, biological rep 2

description: Gene expression data from MnSOD transgenic line -DOX at 50% survival

treatment_protocol: Adult transgenic flies treated without doxycycline


title: MnSOD transgenic line -DOX at 50% survival, biological rep 1


title: MnSOD transgenic line +DOX 50% survival, biological rep 1


title: MnSOD transgenic line +DOX at -DOX 50% survival, biological rep 3


title: MnSOD transgenic line +DOX at -DOX 50% survival, biological rep 1


title: MnSOD transgenic line -DOX at 50% survival, biological rep 4


title: MnSOD transgenic line -DOX at 50% survival, biological rep 3


title: C mock 3 dpi rep 2 with array type rice from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Whereas plant disease resistance is well documented at the transcriptomic level, very few analyses have been conducted, especially in cereals, on plant disease susceptibility. In addition, in rice, susceptibility is often not well defined at the phenotypical level and some interactions termed as compatible can be in fact a mixture of compatible and incompatible interactions. We designed a specific experiment in which the interaction between rice and its fungal pathogen Magnaporthe grisea was truly compatible (complete absence of background resisatnce) in order to identify genes that would be differentially regulated in such condition. These genes may potentially represent targets for effectors of the pathogen.

hyb_protocol: labelled extract quantity: 15ug

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

data_processing: Normalized data by GCRMA

label: Biotin

organism: Oryza sativa

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

growth_protocol: leaf - Growth on soil- 60% humidity- 28degreeC day/25degreeC dark- 12h day

treatment_protocol: Name:infection_rice_mock - environmental treatment - pathogen infection,magnaporthe grisea :. Plants were inoculated with gelatine 0.5% (Berruyer et al, TAG 2005)

tag: Oriza sativa  - dev.stage (Boyes et al. Plant Cell 2001):last emerged leaf (3d leaf)


title: G mock 4 dpi rep 2 with array type rice from Affymetrix


title: H FR13 4 dpi rep 2 with array type rice from Affymetrix

treatment_protocol: Name:infection_rice_pathogen - environmental treatment - pathogen infection,gelatine 0.5% :. Plants were inoculated with Magnaporthe grisea spore suspension as described in Berruyer et al, TAG 2005. Spores were resuspended in gelatine 0.5% at a concentration of 200000 spores/mL. The virulent isolate FR13 was used.


title: A mock 3 dpi rep 1 with array type rice from Affymetrix


title: Bone marrow sample 73 large Pre- BII cells

status: Public on Dec 31 2007

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

institute: Institute for medical microbiology

description: Gene expression data from human B cell precursors in bone marrow

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Value: dchip PM/MM MBEI. Call and Detection p value by MAS5

source_name: Human large Pre-BII cells

label_protocol: Biotinylated cRNA were prepared according to a tw cycle mRNA amplification procedue (Hoffmann et al  Genome Res., Jan 2002; 12: 98 - 111 ; doi:10.1101/gr.201501)

treatment_protocol: Sorted as kappalambda- VpreB- large

tag: Human large Pre-BII cells


title: Bone marrow sample 73 VpreB+ large Pre- BII cells

source_name: Human VpreB+ large Pre-BII cells

treatment_protocol: Sorted as VpreB+ CD34-

tag: Human large VpreB+ Pre-BII cells


title: D FR13 3 dpi rep 2 with array type rice from Affymetrix


title: Bone marrow sample 67 large Pre- BII cells


title: F FR13 4 dpi rep 1 with array type rice from Affymetrix


title: Bone marrow sample 65 large Pre- BII cells


title: Bone marrow sample 65 VpreB+ large Pre- BII cells


title: Bone marrow sample 67 Pre BI cells

source_name: Human Pre-BI cells

treatment_protocol: Sorted as VpreB+ CD34+

tag: Human Pre-BI cells


title: Bone marrow sample 73 small Pre- BII cells

source_name: Human small Pre-BII cells

treatment_protocol: Sorted as kappalambda- VpreB- small

tag: Human small Pre-BII cells


title: E mock 4 dpi rep 1 with array type rice from Affymetrix

hyb_protocol: labelled extract quantity: 12ug


title: Bone marrow sample 58 Pre BI cells


title: Bone marrow sample 65 small Pre- BII cells


title: Bone marrow sample 67 VpreB+ large Pre- BII cells


title: Bone marrow sample 65 Pre BI cells


title: Bone marrow sample 73 Pre BI cells


title: Bone marrow sample 58 VpreB+ large Pre- BII cells


title: Bone marrow sample 58 large Pre- BII cells


title: Bone marrow sample 57 small Pre- BII cells


title: Bone marrow sample 58 small Pre- BII cells


title: B FR13 3 dpi rep 1 with array type rice from Affymetrix


title: Bone marrow sample 51 Pre BI cells


title: Bone marrow sample 51 small Pre- BII cells


title: Bone marrow sample 57 large Pre- BII cells


title: Bone marrow sample 57 VpreB+ large Pre- BII cells


title: 3H BASAL - 2

status: Public on Dec 30 2007

city: NICE

first: GEORGIOS

last: FITSIALOS

address: avenue de Valombrose

institute: INSERM

description:
3H blesse/3H non_blesse
Date:2003/11/19

hyb_protocol: 48 degree_C during 12 hours

scan_protocol: Scanned on a ScanArray5000 (Perkin Elmer) Image intensity data were extracted with Quantarray software.

data_processing: No normalization performed : VALUE column is the LOG2(CH1/CH2).

source_name: 3H blesse (injured)

label_protocol: Corning, kit Cyscribe, Amersham.

extract_protocol: CHOMCZINSKI protocol.

tag: 3H blesse

source_name: 3H non_blesse (uninjured)

tag: 3H non_blesse


title: 3H U0126 - 1

description:
3HU0 non_blesse/3HU0 blesse
Date:2003/11/19

source_name: 3HU0 non_blesse (uninjured)

tag: 3HU0 non_blesse

source_name: 3HU0 blesse (injured)

tag: 3HU0 blesse


title: 15H U0126 - 1

description:
15HU0 non_blesse/15HU0 blesse
Date:2003/11/19

source_name: 15HU0 non_blesse (uninjured)

tag: 15HU0 non_blesse

source_name: 15HU0 blesse (injured)

tag: 15HU0 blesse


title: 15H U0126 - 2

description:
15HU0 blesse/15HU0 non_blesse
Date:2003/11/19


title: 24H BASAL - 1

description:
24H non_blesse/24H blesse
Date:2003/10/30

source_name: 24H non_blesse (uninjured)

tag: 24H non_blesse

source_name: 24H blesse (injured)

tag: 24H blesse


title: 15H SB203 - 2

description:
15HSB blesse/15HSB non_blesse
Date:2003/11/27

source_name: 15HSB blesse (injured)

tag: 15HSB blesse

source_name: 15HSB non_blesse (uninjured)

tag: 15HSB non_blesse


title: 6H SB203 - 2

description:
6HSB blesse/6HSB non_blesse
Date:2003/11/27

source_name: 6HSB blesse (injured)

tag: 6HSB blesse

source_name: 6HSB non_blesse (uninjured)

tag: 6HSB non_blesse


title: 3H BASAL - 1

description:
3H non_blesse/3H blesse
Date:2003/11/19


title: 15H SB203 - 1

description:
15HSB non_blesse/15HSB blesse
Date:2003/11/27


title: 15H BASAL - 1

description:
15H non_blesse/15H blesse
Date:2003/11/19

source_name: 15H non_blesse (uninjured)

tag: 15H non_blesse

source_name: 15H blesse (injured)

tag: 15H blesse


title: 6H SB203 - 1

description:
6HSB non_blesse/6HSB blesse
Date:2003/11/27


title: 15H BASAL - 2

description:
15H blesse/15H non_blesse
Date:2003/11/19


title: 3H U0126 - 2

description:
3HU0 blesse/3HU0 non_blesse
Date:2003/11/19


title: 1H U0126 - 1

description:
1HU0 non_blesse/1HU0 blesse
Date:2003/10/30

source_name: 1HU0 non_blesse (uninjured)

tag: 1HU0 non_blesse

source_name: 1HU0 blesse (injured)

tag: 1HU0 blesse


title: 6H BASAL - 1

description:
6H non_blesse/6H blesse
Date:2003/10/22

source_name: 6H non_blesse (uninjured)

tag: 6H non_blesse

source_name: 6H blesse (injured)

tag: 6H blesse


title: 6H BASAL - 2

description:
6H blesse/6H non_blesse
Date:2003/10/22


title: 24H BASAL - 2

description:
24H blesse/24H non_blesse
Date:2003/10/30


title: 3H LY294 - 2

description:
3HLY blesse/3HLY non_blesse
Date:2003/10/14

source_name: 3HLY blesse (injured)

tag: 3HLY blesse

source_name: 3HLY non_blesse (uninjured)

tag: 3HLY non_blesse


title: 1H U0126 - 2

description:
1HU0 blesse/1HU0 non_blesse
Date:2003/10/30


title: 24H LY294 - 2

description:
24HLY blesse/24HLY non_blesse
Date:2003/10/30

source_name: 24HLY blesse (injured)

tag: 24HLY blesse

source_name: 24HLY non_blesse (uninjured)

tag: 24HLY non_blesse


title: 1H LY294 - 1

description:
1HLY non_blesse/1HLY blesse
Date:2003/10/14

source_name: 1HLY non_blesse (uninjured)

tag: 1HLY non_blesse

source_name: 1HLY blesse (injured)

tag: 1HLY blesse


title: 24H LY294 - 1

description:
24HLY non_blesse/24HLY blesse
Date:2003/10/30


title: 15H LY294 - 1

description:
15HLY non_blesse/15HLY blesse
Date:2003/10/22

source_name: 15HLY non_blesse (uninjured)

tag: 15HLY non_blesse

source_name: 15HLY blesse (injured)

tag: 15HLY blesse


title: 1H LY294 - 2

description:
1HLY blesse/1HLY non_blesse
Date:2003/10/14


title: 6H LY294 - 2

description:
6HLY blesse/6HLY non_blesse
Date:2003/10/22

source_name: 6HLY blesse (injured)

tag: 6HLY blesse

source_name: 6HLY non_blesse (uninjured)

tag: 6HLY non_blesse


title: Adult Replicate1 cy3

status: Public on Dec 20 2007

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

description: Raw intensity values were extracted from images with ArrayVision. An individual spot background was extracted for each spot using the following software settings: Background: Mean; Enable background subtraction; corners between spots; mode: individual.

hyb_protocol: In situ Hybridization Kit Plus (Agilent Technologies)

scan_protocol: GenePix 4000B microarray scanner (Axon Instruments)

data_processing: Spot signals below individual spot background are marked 'null' in the VALUE column. Low intensity data points below the average plus 3 standard deviations of the negative control signal were filtered out and are also marked 'null' in the VALUE column. Controls were excluded and are marked 'null' in the VALUE column. Data intensity from each array was corrected using LOWESS, followed by another normalization using 20% trimmed mean.

organism: Schistosoma mansoni

source_name: Total RNA from 42 days old adult worms, labeled with Cyanine-3 (green).

label_protocol: Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: Adult parasites were obtained from portal vein perfusion of hamsters 7-8 weeks after infection. Worms were conserved in RNAlater (Ambion) according to the manufacturer instructions.

extract_protocol: TRIZOL (Invitrogen) extraction.

tag: Pool of 42 days old adult worms.


title: 15H LY294 - 2

description:
15HLY blesse/15HLY non_blesse
Date:2003/10/22


title: 6H LY294 - 1

description:
6HLY non_blesse/6HLY blesse
Date:2003/10/22


title: 6H U0126 - 1

description:
6HU0 non_blesse/6HU0 blesse
Date:2003/10/22

source_name: 6HU0 non_blesse (uninjured)

tag: 6HU0 non_blesse

source_name: 6HU0 blesse (injured)

tag: 6HU0 blesse


title: 1H BASAL - 1

description:
1H non_blesse/1H blesse
Date:2003/10/14

source_name: 1H non_blesse (uninjured)

tag: 1H non_blesse

source_name: 1H blesse (injured)

tag: 1H blesse


title: Adult Replicate1 cy5

source_name: Total RNA from 42 days old adult worms, labeled with Cyanine-5 (red).


title: Adult Replicate2 cy3


title: 1H BASAL - 2

description:
1H blesse/1H non_blesse
Date:2003/10/14


title: Adult Replicate2 cy5


title: 3H LY294 - 1

description:
3HLY non_blesse/3HLY blesse
Date:2003/10/14


title: FDCPmix_ES cell line_23h_rep4

status: Public on Oct 01 2007

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: Treated FDCP mix, 23h

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Tamoxifen treated FDCPmix cell line, 23h

source_name: Treated FDCP mix, 0h

tag: Tamoxifen treated FDCPmix cell line, 0h


title: FDCPmix_ES cell line_23h_rep1


title: FDCPmix_ES cell line_12h_rep1

source_name: Treated FDCP mix, 12h

tag: Tamoxifen treated FDCPmix cell line, 12h


title: 3H SB203 - 2

description:
3HSB blesse/3HSB non_blesse
Date:2004/01/13

source_name: 3HSB blesse (injured)

tag: 3HSB blesse

source_name: 3HSB non_blesse (uninjured)

tag: 3HSB non_blesse


title: FDCPmix_ES cell line_7h_rep4

source_name: Treated FDCP mix, 7h

tag: Tamoxifen treated FDCPmix cell line, 7h


title: 6H U0126 - 2

description:
6HU0 blesse/6HU0 non_blesse
Date:2003/10/22


title: 3H SB203 - 1

description:
3HSB non_blesse/3HSB blesse
Date:2004/01/13


title: 1H SB203 - 1

description:
1HSB non_blesse/1HSB blesse
Date:2004/01/07

source_name: 1HSB non_blesse (uninjured)

tag: 1HSB non_blesse

source_name: 1HSB blesse (injured)

tag: 1HSB blesse


title: FDCPmix_ES cell line_7h_rep3


title: FDCPmix_ES cell line_23h_rep3


title: FDCPmix_ES cell line_12h_rep4


title: FDCPmix_ES cell line_12h_rep2


title: FDCPmix_ES cell line_3h_rep2

source_name: Treated FDCP mix, 3h

tag: Tamoxifen treated FDCPmix cell line, 3h


title: FDCPmix_ES cell line_3h_rep4


title: FDCPmix_ES cell line_7h_rep1


title: FDCPmix_ES cell line_rep3

source_name: Treated FDCP mix

tag: Tamoxifen treated FDCPmix cell line

source_name: Non-treated FDCPmix cell line

tag: untreated FDCPmix cell line


title: FDCPmix_ES cell line_12h_rep3


title: FDCPmix_ES cell line_7h_rep2


title: FDCPmix_ES cell line_rep4


title: FDCPmix_ES cell line_3h_rep1


title: FDCPmix_ES cell line_rep2


title: Acid1_fibroblast_10h_rep2

source_name: Treated fibroblasts

tag: NIH3T3 mouse fibroblasts, overexpression of Acid1, 10 hours after treatment with Tamoxifen

source_name: Non-treated fibroblasts

tag: NIH3T3 mouse fibroblasts, overexpression of Acid1, untreated


title: FDCPmix_ES cell line_3h_rep3


title: Acid1_fibroblast_10h_rep3


title: FDCPmix_ES cell line_rep1


title: Acid1_fibroblast_3h_rep3

tag: NIH3T3 mouse fibroblasts, overexpression of Acid1, 3 hours after treatment with Tamoxifen


title: 1H SB203 - 2

description:
1HSB blesse/1HSB non_blesse
Date:2004/01/07


title: Kidney Cortex, 20 week old male rat, diabetic (Kidney_20WOM_DM_Rep2)

status: Public on Sep 30 2007

city: Omaha

first: Pascale

middle: Hammond

last: Lane

state: NE

address: 982169 Nebraska Medical Center

department: Pediatrics

institute: University of Nebraska

description: All labeling, hybridization, and scanning were performed in the microarray core facility of the University of Nebraska Medical Center

hyb_protocol: Per Affymetrix instructions

scan_protocol: GeneChip Scanner 3,000 6G per Affymetrix instructions

data_processing: Images were analyzed using GCOS imaging software.  Quality metric parameters including noise level, background, and the efficiency of reverse transcription were ascertained for all hybridizations.  Data sets passing the stringent quality recommendations were normalized using the GCOS software, and the raw intensity values exported for further analysis

label_protocol: cRNA probes were biotinylated in a core facility

extract_protocol: Aurum Total RNA Mini Kit (BioRAd Laboratories, Hercules, CA)

treatment_protocol: Injected with streptozocin, 65 mg/kg iv, at 14 weeks of age; insulin palmitate pellet placed 3 days later; ad lib food and water; blood glucose 350-450 mg/dl for 6 weeks

tag: Sprague Dawley rat, male, diabetic from 14-20 weeks of age; kidney cortex


title: Acid1_fibroblast_3h_rep2


title: Kidney Cortex, 20 week old male rat, diabetic (Kidney_20WOM_DM_Rep3)


title: Acid1_fibroblast_10h_rep1


title: Acid1_fibroblast_3h_rep4


title: Kidney Cortex, 20 week old male rat, diabetic (Kidney_20WOM_DM_Rep1)


title: Kidney Cortex, 10 week old male rat, diabetic (Kidney_10WOM_DM_Rep3)

treatment_protocol: Injected with streptozocin, 65 mg/kg iv, at 4 weeks of age; insulin palmitate pellet placed 3 days later; ad lib food and water; blood glucose 350-450 mg/dl for 6 weeks

tag: Sprague Dawley rat, male, diabetic from 4-10 weeks of age; kidney cortex


title: Kidney Cortex, 10 week old male rat, nondiabetic (Kidney_10WOM_ND_Rep2)

treatment_protocol: Injected with vehicle at 4 weeks of age; palmitate vehicle pellet placed 3 days later; ad lib food and water

tag: Sprague Dawley rat, male, nondiabetic; studied from  4-10 weeks of age; kidney cortex


title: Kidney Cortex, 10 week old male rat, diabetic (Kidney_10WOM_DM_Rep2)


title: Kidney Cortex, 10 week old male rat, nondiabetic (Kidney_10WOM_ND_Rep3)

tag: Sprague Dawley rat, male, nondiabetic; studied from 4-10 weeks of age; kidney cortex


title: Kidney Cortex, 10 week old male rat, nondiabetic (Kidney_10WOM_ND_Rep1)


title: Kidney Cortex, 20 week old male rat, nondiabetic (Kidney_20WOM_ND_Rep1)

treatment_protocol: Injected with vehicle at 14 weeks of age; palmitate vehicle pellet placed 3 days later; ad lib food and water

tag: Sprague Dawley rat, male, nondiabetic; studied from 14-20 weeks of age; kidney cortex


title: 2002-01-10_2399-110

city: Seattle

first: Tata

last: Pramila

state: WA

address: 1100, Fairview Avenue N

department: Basic Sciences

institute: FHCRC

description: Yeast yox1 mutant cell cycle

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

organism: Saccharomyces cerevisiae

source_name: Yeast yox1mutant cell cycle-time point 110 min

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.

tag: Yeast yox1 mutant cell cycle-time point 110 min

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: Acid1_fibroblast_3h_rep1


title: Kidney Cortex, 20 week old male rat, nondiabetic (Kidney_20WOM_ND_Rep2)


title: 2002-01-10_2399-80

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 80 min

tag: Yeast yox1 mutant cell cycle-time point 80 min


title: 2002-01-10_2399-85

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 85 min

tag: Yeast yox1 mutant cell cycle-time point 85 min


title: 2002-01-10_2399-75

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 0 min

tag: Yeast yox1 mutant cell cycle-time point 0 min


title: 2002-01-10_2399-60

description: Yeast yox1 mutant cell cycle

source_name: Yeast yox1mutant cell cycle-time point 60 min

tag: Yeast yox1 mutant cell cycle-time point 60 min


title: Kidney Cortex, 20 week old male rat, nondiabetic (Kidney_20WOM_ND_Rep3)