title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg .25days exp4519 rep3 81425

description:
HybID: 81425
treated sample for experiment (RepID) 4519
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM222680: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_.25days_exp4519_rep2_19916
Replicate experimental sample: GSM222679: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_.25days_exp4519_rep1_81300
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

value: male


title: EAC tumor biopsy from 40356

status: Public on Jun 01 2008

type: genomic

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: The EAC biopsies used in this study were collected as part of the Australian Cancer Study.

hyb_protocol: The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.

scan_protocol: After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). EAC samples log_R_ratio values were generated using the squamous sample 192R as a reference. All genomic positions were based upon hg17 from the UCSC Genome Browser.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Esopageal Adenocarcinoma Tumor Biopsy

label_protocol: The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.

extract_protocol: As per QIAGEN tissue lyser protocol using ALLPREP Kit

treatment_protocol: Fresh tissue was placed directly into RNAlater solution, stored at 4°C overnight, then -20°C. Long-term storage was then at -80°C after access RNAlater was removed.

tag: Biopsy taken by endoscopy prior to treatment. Subject details

tag: Gender

tag: Age

value: 78 years

tag: Tissue

value: EAC tumor

tag: Tumor stage

value: III


title: erythroid; pair 3

status: Public on Jan 03 2008

type: RNA

city: Richmond

first: Latasha

middle: C

last: Redmond

state: VA

address: 401 College Street

department: Human Genetics

country: USA

institute: Virginia Commonwealth University

description: Gene expression data from pair 3 E9.5 yolk sac erythroid precursors

hyb_protocol: Fifteen μg of labeled erythroid or epithelial cRNA was fragmented and 10 μg was hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays for 18 hours (Affymetrix Inc.).  The 8 microarrays were washed and stained with streptavidin–phycoerythrin as described  (Redmond et al., Blood Cells Molecules and  Diseases 2006, 37:27).

scan_protocol: Image analysis was performed on the E9.5 yolk sac data set using the GeneChip Operating System version 1.4 (GCOS1.1, Affymetrix Inc.).  The image of the scanned array was stored as a DAT file using the Affymetrix software.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background and noise were analyzed and similar, thus making all comparisons valid.  The raw intensities for each probe set were stored in electronic formats by the GCOS software.  Scaling factors used to normalize the chips to a target value (TGT), and in this study, the TGT was set at 100. Probe set expression summaries were calculated with the Microarray Suite version 5.0 (MAS5) algorithm. MAS5 expression summaries were obtained using the mas5 function in the affy package in R/Bioconductor. Significance score (S-score) method was used to compare 4 sets of paired GeneChips to determine significant changes in gene expression between erythroid and epithelial cells. A paired set consisted of an erythroid and epithelial GeneChip, for which the two different cell types were isolated from the same yolk sacs.  It uses an error-based model to determine the variances for probe pair signals and follows a normal standard distribution. S-score values were obtained using the SScore function in the sscore package in Bioconductor.  Probe sets with absolute values of the S-score greater or equal to 2.00 were considered to correspond to significant differences between the two types of samples.  P-values were calculated from S-score values and were combined using Fisher’s procedure for combining p-values.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Pair 3-Mus musculus E9.5 yolk sac erythroid precursors

label_protocol: Ten to 39 ng of erythroid or epithelial RNA was used to generate double stranded cDNA with the T7-oligo (dT) primer according to the Affymetrix GeneChip Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA).  Labeled cRNA yield and purity was determined as described (Redmond et al., 2006).

growth_protocol: Timed-pregnant FVB/N mice were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo and cryoprotected in PBS with 20% sucrose.

extract_protocol: Total RNA was isolated from 4 different pairs of erythroid and epithelial cells using reagents from the (ToTALLY RNA isolation kit; Ambion Inc., Austin, TX, USA) and quality assessment by capillary electrophoresis were performed as previously described (Redmond et al., Blood Cells Molecules and  Diseases 2006, 37:27).

treatment_protocol: E9.5 yolk sacs tissues were rinsed once in 1:1 20% sucrose PBS:Optimal Cutting Temperature freezing media (OCT, Tissue-Tek), then OCT alone and frozen.  Eight micron E9.5 sections were stained with the LCM frozen section staining kit (Molecular Devices, Mountain View, CA, USA) and used for laser capture dissection experiments. Using the PixCell II Laser Capture Microdissection System (Arcturus Bioscience), approximately 1 E9.5 yolk sac erythroid cell was collected for every 2 to 3 laser pulses, and 1 epithelial cell was collected per pulse on LCM HS Capsure caps. Epithelial cells were collected from the same microscope slides immediately following procurement of the erythroid cells, and were used as the non-erythroid control.  Approximately 12 to 50 microscope slides, using 2 to 4 yolk sacs from 2 different litters were used per biological replicate.

tag: FVB/N embryonic day 9.5


title: epithelial; pair 3

description: Gene expression data from pair 3 E9.5 yolk sac epithelial cells

source_name: Pair 3-Mus musculus E9.5 yolk sac epithelial cells


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 1days exp4548 rep3 19918

status: Public on Mar 28 2008

city: Mountain View

first: Jeremy

last: Gollub

state: CA

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 19918
treated sample for experiment (RepID) 4548
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM222683: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp4548_rep2_19917
Replicate experimental sample: GSM222682: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_1days_exp4548_rep1_81507
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: LIVER, LIPOPOLYSACCHARIDE E. COLI O55:B5, 1.25mg/kg, 1 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

tag: Sprague-Dawley

tag: age

value: 6 to 8 weeks

tag: sex

tag: tissue

value: LIVER

tag: treatment compound

value: LIPOPOLYSACCHARIDE E. COLI O55:B5

tag: dose

tag: solvent

value: SALINE

tag: administration route

value: INTRAVENOUS

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 1 days

tag: experiment date


title: EAC tumor biopsy from 40359

tag: Biopsy taken by endoscopy prior to treatment. Subject details :-

value: 55 years

value: EAC

value: I


title: EAC tumor biopsy from 40323

tag: Biopsy taken by endoscopy prior to treatment. Subject details

tag: Gender

value: 60 years

value: IVA


title: EAC tumor biopsy from 40362

tag: Age

value: 65 years

tag: Tissue


title: EAC tumor biopsy from 53145

value: male

value: 52 years

tag: Tumor stage

value: IV


title: erythroid; pair 2

description: Gene expression data from pair 2 E9.5 yolk sac erythroid precursors

source_name: Pair 2-Mus musculus E9.5 yolk sac erythroid precursors

tag: FVB/N embryonic day 9.5


title: EAC tumor biopsy from 40361

value: 75 years

value: EAC tumor

value: III


title: NP+B220+_d2_rep2

status: Public on Jan 01 2008

city: Birmingham

first: Kai-Michael

last: Toellner

address: Medical School

department: Immunity and Infection

country: United Kingdom

institute: University of Birmingham

description: FACS sorted splenic B cells 2 days after immunization with NP-Ficoll

data_processing: Data was processed using SDS 2.1 software (Applied Biosystems, Foster City, CA), and the Ct value (threshold cycle, the fractional cycle number at which the fluorescence passes the threshold for a given gene within a sample) was determined using auto-baseline and a threshold of 0.25. B2m was chosen as the reference gene and each sample CT was subtracted from B2m CT to give the log2 difference (delta CT). The normalized value was calculated as 2exp(delta Ct). For delta CT calculations, a CT value of 40 was used for any replicate that had CT > 40.

source_name: B cell

label_protocol: Each TaqMan assay was run from total RNA on TaqMan low density arrays. Assays were run with Qiagen Quantitect Probe RT-PCR kit on Applied Biosystems 7900 Fast Real-Time PCR System using universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

extract_protocol: RNeasy Mini columns (Qiagen, Hilden, Germany)

treatment_protocol: 2 days after intraperitoneal immunization with NP-Ficoll

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220high lymphocytes.


title: EAC tumor biopsy from 40364

value: 71 years


title: erythroid; pair 4

description: Gene expression data from pair 4 E9.5 yolk sac erythroid precursors

source_name: Pair 4-Mus musculus E9.5 yolk sac erythroid precursors


title: NP+B220+_d2_rep3


title: NP+B220+_d2_rep1


title: EAC tumor biopsy from 53048

description: The 28 EAC biopsies used in this study were collected as part of the Australian Cancer Study.

value: 70 years

value: II


title: EAC tumor biopsy from 40360

value: 78 years

value: IIA


title: NP+B220+_d0_rep3

description: FACS sorted splenic B cells

treatment_protocol: non-immunized

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220pos lymphocytes.


title: B220+_d0_rep4

description: FACS sorted splenic B cells

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted B220pos lymphocytes.


title: EAC tumor biopsy from 40325

value: 62 years


title: NP+B220iCD138+_d3_rep1

description: FACS sorted splenic plasmablasts 3 days after immunization with NP-Ficoll

source_name: plasmablast

treatment_protocol: 3 days after intraperitoneal immunization with NP-Ficoll

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220-intermediate, CD138pos lymphocytes.


title: NP+B220+_d0_rep1

description: FACS sorted splenic B cells


title: NP+B220+_d0_rep2

description: FACS sorted splenic B cells


title: EAC tumor biopsy from 40341

value: 79 years


title: EAC tumor biopsy from 40353

value: 63 years


title: EAC tumor biopsy from 40320

value: IIB


title: EAC tumor biopsy from 40340

value: 66 years%


title: EAC tumor biopsy from 40358

value: 56 years

value: IVA


title: EAC tumor biopsy from 40334

value: male

value: 68 years


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 5days exp4541 rep2 19922

status: Public on Jun 23 2007

description:
HybID: 19922
treated sample for experiment (RepID) 4541
replicate 2 of 2
Experimental sample
Replicate experimental sample: GSM204555: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_5days_exp4541_rep1_80576
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, LIPOPOLYSACCHARIDE E. COLI O55:B5, 1.25mg/kg, 5 days

tag: age

value: 6 to 8 weeks

tag: sex

tag: tissue

value: LIVER

tag: treatment compound

value: LIPOPOLYSACCHARIDE E. COLI O55:B5

tag: dose

value: SALINE

value: INTRAVENOUS

value: DAILY

value: 5 days


title: EAC tumor biopsy from 54043

value: 73 years

value: EAC

value: II


title: LIVER LIPOPOLYSACCHARIDE E. COLI O55:B5 1.25mg/kg 5days exp4541 rep1 80576

description:
HybID: 80576
treated sample for experiment (RepID) 4541
replicate 1 of 2
Experimental sample
Replicate experimental sample: GSM204556: LIVER_LIPOPOLYSACCHARIDE_E._COLI_O55:B5_1.25mg/kg_5days_exp4541_rep2_19922
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

tag: solvent

tag: administration route

tag: frequency of dosing

tag: treatment duration

tag: experiment date


title: erythroid; pair 1

description: Gene expression data from pair 1 E9.5 yolk sac erythroid precursors

source_name: Pair 1-Mus musculus E9.5 yolk sac erythroid precursors


title: EAC tumor biopsy from 40338

tag: Biopsy taken by endoscopy prior to treatment. Subject details :-

tag: Gender

tag: Age

value: 72 years

tag: Tissue

value: IVB


title: Transplant Series 25 Right, Transplant # 5

status: Public on Apr 20 2007

city: Boston

first: Penelope

middle: Lyn

last: Miron

state: MA

department: Cancer Biology

institute: Dana Farber Cancer Institute

description:
Sample_ID: 25.24
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on rat RAE-230A microrray gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: dChip

source_name: rat mammary tumor; transplant Series 25R , Transplant # 5

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

extract_protocol: Total RNA was extracted from frozen tissue using RNeasy Mini Kit according to manufacturers instructions

tag: female wistar-furth rats


title: EAC tumor biopsy from 42199

tag: Biopsy taken by endoscopy prior to treatment. Subject details

value: female

value: 74 years

value: EAC tumor

tag: Tumor stage

value: IIA


title: Transplant Series 25 Right, PrimaryTumor

description:
Sample_ID: 25R
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25R , PrimaryTumor


title: EAC tumor biopsy from 54014

value: male

value: 80 years

value: x


title: Transplant Series 25 Left, Transplant # 5

description:
Sample_ID: 25.14
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25L , Transplant # 5


title: Transplant Series 25 Right, Transplant # 4

description:
Sample_ID: 25.23
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25R , Transplant # 4


title: Transplant Series 25 Left, Transplant # 4

description:
Sample_ID: 25.13
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25L , Transplant # 4


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer ChIP-on-chip capable array S4

status: Public on Jun 07 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: No additional information.

hyb_protocol: Arrays were hybridized following a slightly modified version of the Agilent 60-mer oligo microarray processing protocol v2.0 for 22K arrays protocol. Briefly, oppositely labeled microarray probe pairs (0.75 microg of each) were mixed together, and brought to a final volume of 200 microL using ddH20. The samples were incubated at 98 degrees C for 3 min, spun, and 50 microL of pre-aliquoted 10x control targets and 250 microL of Agilent 2x hybridization buffer was added. 490 microL of the mixture were loaded on the microarray and hybridized for 17 h in a 65 degrees C on a hybridization oven rotating at 4 rpm. Arrays were washed following a slightly modified version of the Two-Color Microarray-Based Gene Expression Analysis Protocol for 22K Agilent oligo microarrays Version 4.0.2 April 2006. Briefly, the slide rack was washed washed twice on 100% acetonitrile for 5 minutes (each wash) and rinsed with copious amounts of ddH2O.  After disassembling the hybridization chamber, the array-gasket sandwiches were submerged into Gene Expression Wash Buffer 1 and opened. The microarray slide was then submerged into fresh Gene Expression Wash Buffer 1 and the liquid was stirred for 1 minute. In the next step, the slides were submerged into Gene Expression Wash Buffer 2 at 37 degrees C stirred for 1 minute and then submerged into and also stirred for 1 minute. Finally, slides were submerged into the Stabilization and Drying Solution and stirred for 30 seconds.

scan_protocol: Scanned using a G2565BA Agilent Microarray Scanner (Agilent, Wilmington, DE, USA) at 10 micrometers resolution.

data_processing: Agilent Feature Extraction software (v.8.5) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

organism: Clostridium acetobutylicum

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain growing in exponential phase.

label_protocol: An indirect labeling approach was followed where cDNA was first made in the presence of nucleotides and aminoallyl dUTP, purified, and then the aminoallyl dUTP groups were coupled to a monoreactive dye (Cy3 or Cy5). Total RNA (25 microg) was mixed with 15 microg random hexamers (Roche, Indianapolis, IN, USA) and the volume brought up to 18.5 microL with RNase-free water. Samples were incubated at 70 degrees C for 10 min and then snap-frozen in a dry ice/ethanol bath for 30 sec. Deoxynucleotide triphosphates (Invitrogen; 0.6 mM dATP, 0.4 mM dCTP, 0.4 mM dGTP, and 0.36 mM dTTP), 0.24 mM aminoallyl dUTP (Sigma), 400 units SuperScript II reverse transcriptase (Invitrogen), First Strand Buffer (Invitrogen), and 6 microM dithiothreitol were added to a final volume of 30 microL. The samples were incubated for 3 h to overnight at 42 degrees C, and the reaction was stopped by addition of 0.5 M EDTA (pH 8.0). The remaining RNA was degraded by addition of NaOH (final concentration 11 mM), incubation at 65oC for 15 min, and neutralization with HCl (final concentration 11 mM). The cDNA was purified by bringing up the volume to 450 microL with sterile water and concentrating three times on a Millipore YM-30 column. The samples were dried in a rotary SpeedVac, redissolved in 4.5 microL of a 0.1 M sodium carbonate buffer (pH 9.0), and combined with 54 nmol NHS-ester Cy3 or Cy5 monofunctional dye (Amersham Biosciences) dissolved in an equal volume of DMSO. The mixture was incubated in the dark for 1 h. To purify the labeled cDNA, 35 microL of a 100 mM sodium acetate solution (pH 5.2) was added before purifying on a Qiagen Qiaquick PCR purification column (Valencia, CA, USA). cDNA quantity, quality, and dye incorporation was measured (A260, A280, A550 [Cy3 probe], and A649 [Cy5 probe]) on a spectrophotometer. Only samples with a dye incorporation of at least 10 dye molecules per 1,000 nucleotides were hybridized on microarrays. Samples were stored at -20 degrees C for up to 3 weeks until microarray hybridization.

growth_protocol: C. acetobutylicum ATCC 824 (American Type Culture Collection, Manassas, VA) was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose.

extract_protocol: Cell pellets were collected by centrifuging 3 to 10 mL of cultures at 5,000xg for 10 min, 4 degrees C. Cells were then lysed by resuspending in 200 microL SET buffer (25% sucrose, 50 mM EDTA [pH 8.0], 50 mM Tris [pH 8.0]) with 20 mg/mL lysozyme (Sigma) and incubation at 37 degrees C for 4 min. One milliliter of ice cold TRIzol (Invitrogen, Carlsbad, CA, USA) was added and the sample was vortexed. Samples were immediately stored at -85 degrees C and used within one month to minimize RNA degradation. To isolate and purify the RNA, samples were thawed at room temperature; 500 microL of sample was diluted with an equal amount of ice cold TRIzol and then purified following manufacturer's instructions. The RNA was resuspended in 20-30 microL RNase-free water and quantitated in a spectrophotometer by measuring absorbance at 260 and 280 nm. Samples were only used if the A260/A280 ratio was greater than 1.8. RNA integrity was also verified by running 0.5 microL of sample on a 1.0% agarose gel. Purified RNA were stored at -85 degree C and used within one week of purification.

treatment_protocol: Samples taken at OD (600 nm) = {1.09, 1.8, 2.6, 2.0} were mixed together.

tag: Clostridium acetobutylicum ATCC 824

source_name: Mixture of mRNAs from C. acetobutylicum M5 strain growing in exponential phase.

label_protocol: Same as channel 1

growth_protocol: Same as channel 1

extract_protocol: Same as channel 1

treatment_protocol: Samples taken at OD (600 nm) = {0.868, 1.36, 2.40, 3.20,  4.20} were mixed together.


title: Transplant Series 25 Right, Transplant # 3

description:
Sample_ID: 25.22
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25R , Transplant # 3


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer ChIP-on-chip capable array S2

description: No additional information.


title: Transplant Series 25 Left, PrimaryTumor

description:
Sample_ID: 25L
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25L , PrimaryTumor


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer Transcriptional array S4

description: No additional information.


title: EAC tumor biopsy from 40345

description: The EAC biopsies used in this study were collected as part of the Australian Cancer Study.

source_name: Esopageal Adenocarcinoma Tumor Biopsy

value: 61 years

value: III


title: Transplant Series 25 Right, Transplant # 1

description:
Sample_ID: 25.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25R , Transplant # 1


title: Transplant Series 25 Right, Transplant # 2

description:
Sample_ID: 25.21
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25R , Transplant # 2


title: Transplant Series 25 Left, Transplant # 2

description:
Sample_ID: 25.11
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25L , Transplant # 2


title: Transplant Series 25 Left, Transplant # 3

description:
Sample_ID: 25.12
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25L , Transplant # 3


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer ChIP-on-chip capable array S3

description: No additional information.

growth_protocol: C. acetobutylicum was stored at -85 degrees C in clostridial growth media (CGM) (94) containing 15% glycerol. Solid cultures were carried out on agar-solidified 2xYTG (YTG is 8 g/liter tryptone, 5 g/liter yeast extract, 2 g/liter NaCl, 2.5 g/liter glucose, and 7.5 g/l agar, pH 5.8) plates. Liquid cultures were inoculated with single colonies from plates at least 4 days old and heat shocked at 70 to 80°C for 10 min. Cultures were grown in an anaerobic chamber (Forma Scientific, Marietta, OH) in Clostridial Growth Medium (CGM, Wiesenborn, D. P., et al. 1988. Appl. Environ. Microbiol. 54:2717-2722) supplemented with 80 g/liter glucose.

tag: Clostridium acetobutylicum M5


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer Transcriptional array S1

description: No additional information.


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer Transcriptional array S2

description: No additional information.


title: Transplant Series 42 , Transplant # 2

description:
Sample_ID: 42.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 42 , Transplant # 2


title: Transplant Series 25 Left, Transplant # 1

description:
Sample_ID: 25.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 25L , Transplant # 1


title: Transplant Series 42 , Transplant # 3

description:
Sample_ID: 42.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 42 , Transplant # 3


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer ChIP-on-chip capable array S1

description: No additional information.


title: Transplant Series 42 , Transplant # 5

description:
Sample_ID: 42.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 42 , Transplant # 5


title: Transplant Series 42 , Transplant # 4

description:
Sample_ID: 42.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 42 , Transplant # 4


title: Transplant Series 42 , PrimaryTumor

description:
Sample_ID: 42
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 42 , PrimaryTumor


title: Transplant Series 42 , Transplant # 1

description:
Sample_ID: 42.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 42 , Transplant # 1


title: Transplant Series 34 , Transplant # 5

description:
Sample_ID: 34.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 34 , Transplant # 5


title: Transplant Series 36 , Transplant # 5

description:
Sample_ID: 36.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 36 , Transplant # 5


title: Transplant Series 34 , Transplant # 1

description:
Sample_ID: 34.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 34 , Transplant # 1


title: Transplant Series 34 , Transplant # 4

description:
Sample_ID: 34.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 34 , Transplant # 4


title: Transplant Series 36 , Transplant # 2

description:
Sample_ID: 36.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 36 , Transplant # 2


title: Transplant Series 34 , Transplant # 3

description:
Sample_ID: 34.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 34 , Transplant # 3


title: Transplant Series 36 , PrimaryTumor

description:
Sample_ID: 36
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 36 , PrimaryTumor


title: Transplant Series 36 , Transplant # 1

description:
Sample_ID: 36.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 36 , Transplant # 1


title: Transplant Series 36 , Transplant # 3

description:
Sample_ID: 36.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 36 , Transplant # 3


title: Transplant Series 33 , Transplant # 1

description:
Sample_ID: 33.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 33 , Transplant # 1


title: Transplant Series 33 , Transplant # 4

description:
Sample_ID: 33.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 33 , Transplant # 4


title: Transplant Series 33 , Transplant # 2

description:
Sample_ID: 33.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 33 , Transplant # 2


title: Transplant Series 33 , Transplant # 3

description:
Sample_ID: 33.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 33 , Transplant # 3


title: Transplant Series 33 , Transplant # 5

description:
Sample_ID: 33.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 33 , Transplant # 5


title: Transplant Series 33 , PrimaryTumor

description:
Sample_ID: 33
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 33 , PrimaryTumor


title: Transplant Series 32 , Transplant # 3

description:
Sample_ID: 32.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 32 , Transplant # 3


title: Transplant Series 32 , PrimaryTumor

description:
Sample_ID: 32
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 32 , PrimaryTumor


title: Transplant Series 19 , Transplant # 5

description:
Sample_ID: 19.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 19 , Transplant # 5


title: Transplant Series 34 , Transplant # 2

description:
Sample_ID: 34.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 34 , Transplant # 2


title: Transplant Series 36 , Transplant # 4

description:
Sample_ID: 36.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 36 , Transplant # 4


title: Transplant Series 32 , Transplant # 1

description:
Sample_ID: 32.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 32 , Transplant # 1


title: Transplant Series 32 , Transplant # 5

description:
Sample_ID: 32.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 32 , Transplant # 5


title: Transplant Series 19 , Transplant # 1

description:
Sample_ID: 19.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 19 , Transplant # 1


title: Transplant Series 19 , Transplant # 4

description:
Sample_ID: 19.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 19 , Transplant # 4


title: Transplant Series 19 , PrimaryTumor

description:
Sample_ID: 19
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 19 , PrimaryTumor


title: Transplant Series 19 , Transplant # 3

description:
Sample_ID: 19.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 19 , Transplant # 3


title: Transplant Series 34 , PrimaryTumor

description:
Sample_ID: 34
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 34 , PrimaryTumor


title: Transplant Series 17 , Transplant # 5

description:
Sample_ID: 17.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 17 , Transplant # 5


title: Transplant Series 32 , Transplant # 2

description:
Sample_ID: 32.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 32 , Transplant # 2


title: Transplant Series 32 , Transplant # 4

description:
Sample_ID: 32.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 32 , Transplant # 4


title: Transplant Series 17 , Transplant # 4

description:
Sample_ID: 17.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 17 , Transplant # 4


title: Transplant Series 17 , Transplant # 2

description:
Sample_ID: 17.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 17 , Transplant # 2


title: Transplant Series 13 , PrimaryTumor

description:
Sample_ID: 13
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 13 , PrimaryTumor


title: Transplant Series 10 , Transplant # 4

description:
Sample_ID: 10.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 10 , Transplant # 4


title: Transplant Series 17 , PrimaryTumor

description:
Sample_ID: 17
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 17 , PrimaryTumor


title: Transplant Series 13 , Transplant # 2

description:
Sample_ID: 13.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 13 , Transplant # 2


title: Transplant Series 10 , Transplant # 3

description:
Sample_ID: 10.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 10 , Transplant # 3


title: Transplant Series 13 , Transplant # 4

description:
Sample_ID: 13.4
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 13 , Transplant # 4


title: Transplant Series 10 , Transplant # 1

description:
Sample_ID: 10.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 10 , Transplant # 1


title: Transplant Series 10 , Transplant # 2

description:
Sample_ID: 10.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 10 , Transplant # 2


title: Transplant Series 13 , Transplant # 1

description:
Sample_ID: 13.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 13 , Transplant # 1


title: Transplant Series 19 , Transplant # 2

description:
Sample_ID: 19.2
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 19 , Transplant # 2


title: Transplant Series 13 , Transplant # 5

description:
Sample_ID: 13.5
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 13 , Transplant # 5


title: Transplant Series 17 , Transplant # 3

description:
Sample_ID: 17.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 17 , Transplant # 3


title: Transplant Series 10 , PrimaryTumor

description:
Sample_ID: 10
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 10 , PrimaryTumor


title: 0 hr Ctl B-chip 3-13-03

status: Public on Oct 29 2003

city: Baltimore

first: Jerry

middle: M.

last: Wright

state: MD

address: 725 N. Wolfe St

department: Physiology

institute: Johns Hopkins Medical Institutions

description: IB3-1 (deltaF508/W1282X) bronchial epithelial cells were cultured in T75 flasks with gentamicin-free LHC-8 medium.  A T75 flask of confluent IB3-1 cells was rinsed twice with ice cold Hank’s buffer then scraped into 3ml of ice cold TRIzol (Gibco BRL) then rinsed with 3 ml ice cold TRIzol and the mRNA was isolated according to the TRIzol protocol.    Cells were fed with 10 ml of media every 2 to 3 days. Array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches.  Chip scanning and expression analysis was performed using Microarray Analysis Suite 5.0 software and scaled to an average probe set intensity of 150.

source_name: IB3-1 bronchial epithelial cell line


title: 0 HR Ctl B-chip 1-21-03


title: 0 hr Ctl B-chip 6-11-03


title: 0 hr Ctl A-chip 6-13-02


title: 0 hr Ctl ORCC A-chip


title: 0 hr Ctl ORCC B-chip


title: 0 hr Ctl A-chip 3-13-03


title: 0 hr Ctl A-chip 6-11-02


title: 0 hr Ctl A-chip 1-21-03


title: f2#84 versus pool Mouse muscle tissue

status: Public on Jul 07 2006

type: other

city: Los Angeles

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

institute: UCLA

description: Muscle tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

data_processing: Arrays were quantified on the basis of spot intensity relative to background (Qhyb program, Rosetta), adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to an error model to determine significance (type I error).  Gene expression is reported as the ratio of the mean log10 intensity (mlratio) relative to the pool derived from 150 mice randomly selected from the F2 population. Normalized values are the reported as the ratio of the mlratio relative to the pool.

molecule: other

tag: strain

value: C57BL/6J and C3H/HeJ on ApoE null Age:24 weeks Gender:male

source_name: pool

tag: Strain:C57BL/6J and C3H/HeJ on ApoE null Age:24 weeks (150 randomly selected F2)


title: Transplant Series 17 , Transplant # 1

description:
Sample_ID: 17.1
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 17 , Transplant # 1


title: Clostridium acetobutylicum 60-mer Selection Test Agilent 60-mer Transcriptional array S3

description: No additional information.

source_name: Mixture of mRNAs from C. acetobutylicum M5 strain growing in exponential phase.

source_name: Mixture of mRNAs from C. acetobutylicum ATCC824 strain growing in exponential phase.


title: 0 hr Ctl b-chip 7-12-02


title: Transplant Series 13 , Transplant # 3

description:
Sample_ID: 13.3
Gene expression data from serially transplanted rat mammary tumors with varying invasive phenotypes.

source_name: rat mammary tumor; transplant Series 13 , Transplant # 3