title: S1P replicate 2

tag: glioblastoma cell line, replicate 2, Sphingosine 1-phosphate treatment


title: S1P replicate 1

status: Public on May 13 2006

type: RNA

city: Chicago

first: Chris

middle: D

last: McCabe

state: IL

address: 2430 N Halsted

department: Neurobiology

country: USA

institute: Children's Memorial Hospital

description: Sphingosine 1-phosphate treated glioblastoma cell line

data_processing: MAS 5.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: glioblastoma cell line

treatment_protocol: Sphingosine 1-phosphate treatment in vitro

tag: glioblastoma cell line, replicate 1, Sphingosine 1-phosphate treatment


title: EGF replicate 3

description: Epidermal growth factor treated glioblastoma cell line

treatment_protocol: Epidermal growth factor treatment in vitro

tag: glioblastoma cell line, replicate 3, epidermal growth factor treatment


title: The effects of chronic immune stimulation on muscle growth in rainbow trout-EE037-020

city: Hagerman

first: Ken

last: Overturf

state: ID

address: 3059-F National Fish Hatchery Road

department: ARS

institute: USDA

description: RNA from Muscle from rainbow trout (Oncorhynchus mykiss) white muscle of the mid lateral side was isolated from saline injected control animals and LPS injected fish and hybridized to the GRASP array

hyb_protocol: Hybridization was carried out using a Tecan HS400 hybridization machine.  GRASP (Genomic Research on Atlantic Salmon Project) version 1 16,008 sequence microarray slides (Rice et al., 2004) were prepared by washing for 30 seconds at 23°C with 0.2x SSC, 0.05% SDS, soaking in the same buffer for 2 minutes at 23°C, and washing for 1 minute at 45°C with 4x SSC, 0.05% SDS.  Probed were injected onto slides and hybridization was carried out for 18 hours at 45°C with low agitation frequency.  Slides were washed for 30 seconds and soaked for 1 minute at 43°C with 2x SSC, 0.1% SDS; this step was repeated two more times.  Slides were then washed for 30 seconds and soaked for 1 minute at 25°C with 2x SSC; this step was repeated two more times.  Slides were then washed for 30 seconds and soaked for 30 seconds at 25°C with 0.2x SSC, 0.05% SDS. Cy3 and Cy5 capture reagents (Genisphere, Hatfield, PA) were prepared according to Genisphere’s protocol, and mixed with 50 μl Ambion SlideHyb 3 buffer and 50 μl nuclease-free H2O.  The mixture was incubated at 80°C for 10 minutes, and then injected onto the slides.  Hybridization was carried out for 3 hours, 30 minutes at 45°C with low agitation frequency.  Slides were washed as described following first hybridization, and then dried for 2 minutes at 30°C.

scan_protocol: Scanning was performed using a Perkin Elmer ScanArray 5000 and images and data were processed using ScanArray Express software (Perkin Elmer, Wellesley, MA).  The adaptive circle method was used for quantitation, and mean background of spots was subtracted and LOWESS normalization was performed.

data_processing: Used Cy3 and Cy5 ratio of mean spot Data was filtered by eliminating sequences that did not have a minimum of 2-fold difference in expression on at least one of the dye-flip slides and that did not have a spot mean minus background pixel intensity of at least 1000.

organism: Oncorhynchus mykiss

source_name: white muscle from mid lateral of rainbow trout (Oncorhynchus mykiss)

label_protocol: Each cDNA probe set was concentrated using Microcon YM-30 cut-off columns, mixed with 100 μl SlideHyb 3 hybridization buffer and 1 μg human Cot-1 DNA, incubated at 95°C for 10 minutes, then held at 45°C (hybridization temperature) until ready to use.   Hybridization was carried out using a Tecan HS400 hybridization machine. Cy3 and Cy5 capture reagents (Genisphere, Hatfield, PA) were prepared according to Genisphere’s protocol, and mixed with 50 μl Ambion SlideHyb 3 buffer and 50 μl nuclease-free H2O.

growth_protocol: Fish were fed once daily using a pair-feeding regime: the LPS-injected groups were fed to satiation to a maximum of 5% body weight, the amount eaten by each LPS-injected tank was determined, then the saline-injected control groups were fed the average of the amount eaten by the LPS-injected tanks.

extract_protocol: total RNA was extracted using TRIZol and then purified with Promegas SV RNA Isolation Kit

treatment_protocol: Rainbow trout (Oncorhynchus mykiss) were injected with 10mg/kg bw of 0.1ml sterile PBS.

tag: mixed sex of CSI Housecreek strain of rainbow trout (Oncorhynchus mykiss) RNA isolated from white muscle tissue removed from mid lateral side

growth_protocol: Fish rearing was carried out at the University of Idaho’s Hagerman Fish Culture Experiment Station.  Experiments were conducted in 140L tanks with a constant temperature 15°C spring water flow of approximately 11.5L/min.  Photoperiod was maintained at 14h/day. All fish used were of the CSI-Oregon strain of rainbow trout.

extract_protocol: Tissue collected for RNA isolation was placed in RNAlater (Ambion, Austin, TX) and stored at 4°C for no longer than 3 weeks, according to the protocol recommended by Ambion.  RNA was isolated using the TRIzol (Invitrogen, Rockville, MD) method.  Tissue was first homogenized by placing a 5mm sterile, RNase-free, stainless steel bead into a round-bottom 2ml tube containing TRIzol and the tissue, then placing tubes in a Retsch (Haan, Germany) MM300 Laboratory Vibration Mill for four minutes at 20 Hz.  The protocol recommended by Invitrogen was followed for the rest of the RNA isolation.

treatment_protocol: Those groups receiving LPS treatments were injected intraperitoneally every 72 hours at a dose of 10mg/kg bw in a volume of 0.1ml sterile PBS.


title: The effects of chronic immune stimulation on muscle growth in rainbow trout-EE037-22

source_name: liver tissue from rainbow trout (Oncorhynchus mykiss)

treatment_protocol: Rainbow trout (Oncorhynchus mykiss) were IP injected with 10mg/kg bw of 0.1ml sterile PBS.

tag: CSI Housecreek strain rainbow trout, mixed sexes, liver tissue

treatment_protocol: Groups received LPS treatment they were injected intraperitoneally every 72 hours at a dose of 10mg/kg bw in a volume of 0.1ml sterile PBS.


title: EGF replicate 2

tag: glioblastoma cell line, replicate 2, epidermal growth factor treatment


title: The effects of chronic immune stimulation on muscle growth in rainbow trout-EE307-21

source_name: liver tissue from Oncorhynchus mykiss

tag: CSI Housecreek strain rainbow trout (Oncorhynchus mykiss) liver tissue


title: 2.5

status: Public on May 12 2006

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

country: Germany

institute: University Hospital Hamburg-Eppendorf

description: Testicular "sandwich" biopsy from a patient with Sertoli-cell-only syndrom, categorized by Johnsen scoring.

data_processing: Spot quantification with Codelink 4.0 software

label: Biotin-11-UTP labeled cRNA

source_name: Score 2 #4

tag: Patient with Sertoli-cell-only syndrom


title: PBMC treated_SEB_03H_1A_083100_Sum

status: Public on May 19 2006

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: RNA isolated from PBMC

data_processing: Local background correction and intrachip LOWESS normalization was accomplished by Genespring® 7.0 (Agilent Tech., CA).

source_name: PBMC treated with SEB

tag: treated with SEB


title: 2.3

source_name: Score 2 #2


title: The effects of chronic immune stimulation on muscle growth in rainbow trout-EE037-019

source_name: mid lateral white muscle from rainbow trout (Oncorhynchus mykiss)

tag: mixed sex of CSI strain HouseCreek rainbow trout

tag: tissue-  Cy3 muscle saline injected

source_name: white muscle from Oncorhynchus mykiss

tag: white muscle from mid lateral side of mixed sex of CSI strain Housecreek

tag: tissue-  Cy5 muscle


title: EFG replicate 1

tag: glioblastoma cell line, replicate 1, epidermal growth factor treatment


title: 2.6

source_name: Score 2 #5


title: Bthetaiotaomicron_NMRIcecum_PRchow_10d_3_#8431

status: Public on May 14 2006

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

description: Bacteroides thetaiotaomicron monoassociated in gnotobiotic NMRI mice on a standard polysaccharide-rich (PR)diet, harvested from the cecum after 10 days.

data_processing: MAS5; scaling = 500

organism: Bacteroides thetaiotaomicron

source_name: Bacteroides thetaiotaomicron, monoassociation, cecum NMRI mice, 10days


title: 2.4

source_name: Score 2 #3


title: 5.2

description: Testicular "sandwich" biopsy from a patient with spermatogenic arrest at spermatocyte stage, categorized by Johnsen scoring.

source_name: Score 5 #2

tag: Patient with aspermatogenesis


title: 8.5

description: Testicular "sandwich" biopsy from a patient with spermatogenic arrest at spermatid stage, categorized by Johnsen scoring.

source_name: Score 8 #5

tag: Patient with hypospermatogenesis


title: 5.5

source_name: Score 5 #5


title: 8.4

source_name: Score 8 #4


title: 5.3

source_name: Score 5 #3


title: 5.1

source_name: Score 5 #1


title: 8.6

source_name: Score 8 #6


title: 2.1

source_name: Score 2 #1


title: 8.2

source_name: Score 8 #2


title: 8.1

source_name: Score 8 #1


title: 5.4

source_name: Score 5 #4


title: 10.11

description: Testicular "sandwich" biopsy from a patient with full testicular spermatogenesis, categorized by Johnsen scoring.

source_name: Score 10 #11

tag: Patient with full testicular spermatogenesis


title: 8.3

source_name: Score 8 #3


title: 10.12

source_name: Score 10 #12


title: 10.10

source_name: Score 10 #10


title: 10.8

source_name: Score 10 #8


title: 10.9

source_name: Score 10 #9


title: 10.6

source_name: Score 10 #6


title: 10.3

source_name: Score 10 #3


title: Ndc10 in mitosis

status: Public on May 10 2006

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: This is the raw data file for Figure S7 panel B.

data_processing: The protocol provided by Affymetrix (GCOS ver1.4) was used.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Chromatin-immunoprecipitated DNA

tag: Strain SK1 was used. Ndc10 was tagged by 6XHA.


title: 10.2

source_name: Score 10 #2


title: SSC GDNF/GFRalpha1 2-hr replacement Rep1

status: Public on May 11 2006

city: University Park

first: Jon

last: Oatley

state: PA

address: 324 Henning

department: Dairy and Animal Science

institute: Pennsylvania State University

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 2-hr.
Replicate 1
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

data_processing: MAS 5.0, signal intensities scaled to a mean value of 150

label: PE

organism: Mus musculus

source_name: Cultured mouse spermatogonial stem cells

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 2-hr.
Replicate 1

tag: Spermatogonial stem cell enriched germ cell cultures established from 6 day old C57BL/6 male mice.


title: SSC GDNF/GFRalpha1 8-hr replacement Rep2

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 8-hr.
Replicate 2
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 8-hr.
Replicate 2


description: SUP fraction used for normalization of Pph22 (GSM108191).

source_name: Sup fraction (equal to Whole cell extract DNA)

tag: Strain SK1 was used.


title: 10.5

source_name: Score 10 #5


title: 10.7

source_name: Score 10 #7


title: SSC GDNF/GFRalpha1 18-hr withdrawal Rep1

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1.
Replicate 1
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1.
Replicate 1


title: 10.4

source_name: Score 10 #4


title: SSC GDNF/GFRalpha1 4-hr replacement Rep1

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 4-hr.
Replicate 1
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 4-hr.
Replicate 1


title: SSC GDNF/GFRalpha1 4-hr replacement Rep3

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 4-hr.
Replicate 3
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 4-hr.
Replicate 3


title: SSC GDNF/GFRalpha1 2-hr replacement Rep2

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 2-hr.
Replicate 2
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 2-hr.
Replicate 2


title: 10.1

source_name: Score 10 #1


title: SSC GDNF/GFRalpha1 8-hr replacement Rep1

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 8-hr.
Replicate 1
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 8-hr.
Replicate 1


description: SUP fraction used for normalization of Cse4, NDC10, and REC8 (w/o rts1) (GSM108184, GSM108189, GSM108192, GSM108196, GSM108261).


title: SSC GDNF/GFRalpha1 4-hr replacement Rep2

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 4-hr.
Replicate 2
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 4-hr.
Replicate 2


title: SSC GDNF/GFRalpha1 Rep2

description:
Spermatogonial stem cells cultured with GDNF, GFRalpha1, and bFGF.
Replicate 2
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice. Cultures were continually maintained in a serum-free, defined media with GDNF, GFRalpha1 and bFGF.

treatment_protocol:
Spermatogonial stem cells maintained in the presence of GDNF and GFRalpha1.
Replicate 2


title: SSC GDNF/GFRalpha1 18-hr withdrawal Rep2

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1.
Replicate 2
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1.
Replicate 2


title: SSC GDNF/GFRalpha1 2-hr replacement Rep3

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 2-hr.
Replicate 3
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 2-hr.
Replicate 3


description: SUP fraction used for normalization of RTS1, BUB1, and SCC1 (GSM108185, GSM108187, GSM108188, GSM108190, GSM108195).


title: SSC GDNF/GFRalpha1 18-hr withdrawal Rep3

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1.
Replicate 3
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1.
Replicate 3


description: SUP fraction used for the normalization of Rec8 and Sgo1 (GSM108186, GSM108193, GSM108194).

source_name: Sup fraction after ChIP (equal to Whole cell extract DNA)


title: SSC GDNF/GFRalpha1 Rep3

description:
Spermatogonial stem cells cultured with GDNF, GFRalpha1, and bFGF.
Replicate 3
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice. Cultures were continually maintained in a serum-free, defined media with GDNF, GFRalpha1 and bFGF.

treatment_protocol:
Spermatogonial stem cells maintained in the presence of GDNF and GFRalpha1.
Replicate 3


title: SSC GDNF/GFRalpha1 Rep1

description:
Spermatogonial stem cells cultured with GDNF, GFRalpha1, and bFGF.
Replicate 1
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice. Cultures were continually maintained in a serum-free, defined media with GDNF, GFRalpha1 and bFGF.

data_processing: MAS 5.0, signal intensities scaled to a mean singal of 150

treatment_protocol: Spermatogonial stem cells maintained in the presence of GDNF and GFRalpha1


title: RTS1 in Meiosis

description: This is the raw data file for Figure 5 panel a.

tag: Strain SK1 was used. RTS1 was tagged by 3XPK.


title: Rec8 distribution in meiosis w/o rts1.

description: This is the raw data file for Figure S3 panel f.

tag: Strain SK1 was used (rts1 was disrupted). Rec8 was tagged by 3XHA.


title: Sgo1 distribution in meiosis

tag: Strain SK1 was used. Sgo1 was tagged by 6XPK.


title: Cse4 in Meiosis

tag: Strain SK1 was used. Cse4 was tagged by 6XHA.


title: RTS1 in Mitosis

description: This is the raw data file for Figure S7 panel B.

tag: SK1 strain was used. RTS1 was tagged by 3XPK.


title: CSE4 distribution in Mitotic G2 phase

description: This is the raw data file for the Figure S7 panel B.

data_processing: Data was processed following the protocol provided by Affymetrix (GCOS ver 1.4).

label: Labelled with Biotin-11-ddATP

tag: Strain SK1 was used. Cse4 was tagged by 6XHA. Mitotic cells were treated with benomyl (30ug/ml) to arrest in G2.


title: Rec8 distribution in meiosis

description: This is the raw data file for Figure 5 panel a and FigureS3 panel f.

tag: Strain SK1 was used. Rec8 was tagged by 3XHA.


title: Sgo1 distribution in mitosis

tag: Strain SK1 was used. Sgo1 was tagged by PKX6.


title: BUB1 in meiosis

description: This is the raw data file for Figure S7 panel A.

tag: Strain SK1 was used. Bub1 was tagged by 6XPK.


title: Ndc10 in meiosis


title: Scc1 distribution in G2 phase

tag: Strain SK1 was used. Cells were treated with 30ug/ml benomyl to arrest in G2 phase. Scc1 was tagged by 3XHA.


title: Bub1 in mitosis


title: EScell_7 days after the neuronal induction (7 days)_rep2

status: Public on May 09 2006

city: Seoul

first: Young Ju

last: Suh

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

description: Neuronal differentiation of ES cells was performed by an 8-day induction progress (Bain et al., 1995). We used the suspension method for EB to study differentiation of ES cells. Cell suspensions were cultured to form floating aggregates, EBs for four days. Cells were supplemented with 1 x 10-6M ATRA for four days. After an 8-day induction period EBs, transferred to tissue culture dishes, had the media changed for the ES cells without LIF and ß-mercaptoethanol. After washing the samples over time with PBS, total RNA from each cell was prepared using the TRIZOL reagent (Invitrogen, CA., USA). Total RNA, quantity and quality, was assessed by spectrophotometry. Fluoroscence labeled probes for cDNA microarrays were hybridized using 100 µg of total RNA from each cell by oligo dT, SuperscriptII (Invitrogen) and Cy3-UTP or Cy5-UTP (Amersham). After hybridization, the slides were washed in SSC and SDS solutions.

data_processing: LOWESS normalization

source_name: Undifferentiated

tag: Embryonic stem cell

source_name: Differentiated


title: EScell_2 days for neuronal induction (2 after)_rep2


title: EScell_2 days after the neuronal induction (2 days)_rep2


title: 1F9 cell line E2A -/-, +bHLHERTX

city: La Jolla

first: Ruth

last: Schwartz

state: CA

address: Gilman Drive

institute: UCSD

description: The 1F9 cell line (E2A-/-) was transduced with a retrovirus carrying an E47/ER hybrid protein. One day after infection, cells were incubated with 4-OHT for 6 hours. mRNA was extracted, processed and hybridized to probes

data_processing: Samples were analyzed using CodeLink analysis software.  Expression levels from scanned images were determined using Corgon software.  Genes with p-values for presence of 0.1 or less were considered for further analysis.  Expression levels from all experimental conditions were normalized simultaneously using multi-loess technique.  We calculated the absolute and relative changes of the expression levels for every gene and sorted the genes based on their interest statistics. The interest statistic design was based on the software package Focus.

molecule: polyA RNA

source_name: E2A deficient lymphoma cell line

tag: Cell line derived from a thymoma developed in an E2A knockout mouse. The mouse was 3 months old.


title: Rat_Ventricle_Diabetic_42days_rep3

status: Public on May 08 2006

city: Cincinnati

first: Mohammed

middle: Abdul

last: Matlib

state: OH

department: Pharmacology and Cell Biophysics

institute: University of Cincinnati

description: Gene expression data from diabetic rat ventricles 42 days after injection

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized on Affymetrix GeneChip Rat genome RG-U34A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: Diabetic Rat ventricle after 42 days, diastolic and systolic dysfunction

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

growth_protocol: Rats were kept separate in steel cages with full access to standard feed and water.  Ventricles removed at 03/28/42 day time points, frozen and total RNA extracted by Trizol method

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

treatment_protocol: 150g male Wistar rats (Harlan) were injected with 65 mg/kg streptozotocin (STZ) (Diabetic) or citrate buffer (Control).  Ventricles were collected and frozen after 3/28/42 days, corresponding to diabetes response with no symptoms, diastolic symptoms, and full diastolic and systolic symptoms of diabetic cardiomyopathy.

tag: Genotype

value: male Wistar rat 150g at time of injection

tag: State

value: Diabetic

tag: Age

value: 42 days post injection

tag: Body Weight (g)

tag: Ventricle Weight (g)

tag: Blood Glucose (mg/dL)

tag: Ventricle Weight/Body Weight Ratio

tag: Body Weight vs Control average


title: Trophoblast 118 hours expression

city: Rochester

first: Jesus

last: Gonzalez Bosquet

state: MN

address: 200 First Street, SW

department: Gynecologic Oncology

institute: Mayo Clinic

description: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

label: Biotin-labeled cRNA

source_name: Trophoblast

tag: Extract from trophoblast cell cultures (after 118 hours)


title: 1F9 cell line E2A -/-, +ER47TX

description: The 1F9 cell line (E2A-/-) was transduced with a retrovirus carrying an E47/ER hybrid protein. One day after infection, cells were incubated with 4-OHT for 6 hours. mRNA was extracted, processed and hybridized to probes.

source_name: Thymoma derived cell line (E2A-/-) +E47

tag: Cell line derived from the thymoma of an E2A knockout mouse. The mouse was 3 months old.


title: Rat_Ventricle_Diabetic_42days_rep2


title: Rat_Ventricle_Control_42days_rep4

description: Gene expression data from control rat ventricles 42 days after injection

source_name: Control Rat ventricle after 42 days

value: Control


title: Rat_Ventricle_Diabetic_42days_rep4


title: Rat_Ventricle_Diabetic_42days_rep1


title: Pph22 in meiosis

tag: Strain SK1 was used. Pph22 was tagged by 6XPK.


title: Rat_Ventricle_Control_42days_rep3


title: Rat_Ventricle_Diabetic_28days_rep4

description: Gene expression data from diabetic rat ventricles 28 days after injection

source_name: Diabetic Rat ventricle after 28 days, diastolic dysfunction

value: 28 days post injection


title: EScell_started with a treatment with ATRA (Start)_rep2


title: Trophoblast 6 hours expression

tag: Extract from trophoblast cells cultures (after 6 hours)


title: Rat_Ventricle_Control_42days_rep2


title: Rat_Ventricle_Control_42days_rep1


title: Rat_Ventricle_Diabetic_28days_rep1


title: Rat_Ventricle_Diabetic_28days_rep2


title: Rat_Ventricle_Control_28days_rep4

description: Gene expression data from control rat ventricles 28 days after injection

source_name: Control Rat ventricle after 28 days


title: Rat_Ventricle_Control_28days_rep3


title: Rat_Ventricle_Diabetic_28days_rep3


title: Rat_Ventricle_Control_28days_rep2


title: Rat_Ventricle_Control_28days_rep1


title: srb4 ts mutant in s. pombe expression change-4

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description: Cell cultures were  grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium. then turn to 37 degree 90 minutes. collect the cells and extract the total RNA. Purify RNA with Qiagen RNA purification kit, label with Cy3 or cy5 respectively.

organism: Schizosaccharomyces pombe

tag: srb4 ts mutant in Schizosaccharomyces pombe RNA

source_name: wt cy5

tag: wt RNA


title: srb4 ts mutant in s. pombe expression change-3


title: srb4 ts mutant in s. pombe expression change


title: srb4 ts mutant ORF change-2

description: IgG beads were used for ChIP of chromatin extracts from Med7-TAP srb4 ts mutant and WT cells. Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium, then turn to 37 degree 90minutes. fixing cells with formaladehyde and ChIP. The resulting ChIP DNA was labeled with cy3 and Cy5 respectively. hybridized to the IGR+ORF

source_name: CHIP IP Med7-2 ORF in srb4 ts mutant

tag: IP sample Med7-2 ORF in Srb4 ts mutant

source_name: CHIP IP Med7-2 ORF in WT

tag: IP sample Med7-2 ORF in WT


title: srb4 ts mutant ORF change-1

source_name: CHIP IP Med7-1 ORF in srb4 ts mutant

tag: IP sample Med7-1 ORF in Srb4 ts mutant

source_name: CHIP IP Med7-1 ORF in WT

tag: IP sample Med7-1 ORF in WT


title: Rat_Ventricle_Diabetic_03days_rep3

description: Gene expression data from diabetic rat ventricles 3 days after injection

source_name: Diabetic Rat ventricle before cardiovascular changes

tag: Genotype

tag: State

value: 3 days post injection


title: Rat_Ventricle_Diabetic_03days_rep4

tag: Age

tag: Body Weight (g)


title: srb4 ts mutant IGR change-2

source_name: CHIP IP Med7-2 IGR in srb4 ts mutant

tag: IP sample Med7-1 IGR in Srb4 ts mutant

source_name: CHIP IP Med7-1 IGR in WT

tag: IP sample Med7-2 IGR in WT


title: srb4 ts mutant IGR change-1

description:
IgG beads were used for ChIP of chromatin extracts from Med7-TAP srb4 ts mutant and WT cells. Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium, then turn to 37 degree 90minutes. fixing cells with formaladehyde and ChIP. The resulting ChIP DNA was labeled with cy3 and Cy5 respectively. hybridized to the IGR+ORF
microarrays to produce genome wide mediator occupancy profile.

source_name: CHIP IP Med7-1 IGR in srb4 ts mutant

tag: IP sample Med7-1 IGR in WT


title: Rat_Ventricle_Diabetic_03days_rep2

tag: Ventricle Weight (g)

tag: Blood Glucose (mg/dL)

tag: Ventricle Weight/Body Weight Ratio

tag: Body Weight vs Control average


title: srb4 ts mutant in s. pombe expression change-2

tag: srb4 ts mutant in Schizosaccharomyces pombe RNA


title: Rat_Ventricle_Control_03days_rep4

description: Gene expression data from control rat ventricles 3 days after injection

source_name: Control Rat ventricle before cardiovascular changes


title: Rat_Ventricle_Diabetic_03days_rep1


title: EScell_0 day after the neuronal induction (0 day)_rep2

source_name: Undifferentiated

tag: Embryonic stem cell

source_name: Differentiated


title: Rat_Ventricle_Control_03days_rep2


title: Rat_Ventricle_Control_03days_rep3


title: Rat_Ventricle_Control_03days_rep1


title: chondrocyte_5azatreated_rep3

status: Public on May 06 2006

first: Tammy

last: Vallender

department: Human Genetics

institute: University of Chicago

description: treated with 5-aza-2'-deoxycytidine for 72 hours plus 24 hours in normal medium; biological replicate 3

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: MAS 5.0 data processing and normalization

label: biotin labeled with standard Affymetrix fluorescent stain cocktail

source_name: primary chondrocytes treated

label_protocol: standard Affymetrix IVT labeling and staining protocols

growth_protocol: Cultures were maintained in DMEM with L-glutamine and high glucose (Invitrogen) plus 10% heat-inactivated FBS (Invitrogen) and 100 U/mL penicillin streptomycin (Invitrogen) at 37 oC and 5% CO2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).

extract_protocol: RNeasy total RNA extraction protocol (Qiagen)

treatment_protocol: Freshly prepared 5A2dC (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 5 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 72-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.

tag: strain

value: B6; gender:mix; age:0-2d; tissue:rib cartilage; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:3


title: chondrocyte_5azatreated_rep2

description: treated with 5-aza-2'-deoxycytidine for 72 hours plus 24 hours in normal medium; biological replicate 2

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:2


title: osteoblast_control_rep1

description: untreated; biological replicate 1

source_name: primary osteoblasts untreated

growth_protocol: Cultures were maintained in α-MEM (Stem Cell Technologies; Vancouver, BC, Canada) with 10% FBS (Invitrogen) and 100 U/mL penicillin streptomycin (Invitrogen) at 37 oC and 5% CO2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).

treatment_protocol: untreated

value: B6; gender:mix; age:0-2d; tissue:calvariae; passage #:4; treatment:control; biological replicate:1


title: Chondrocyte_control_rep2

description: untreated; biological replicate 2

source_name: primary chondrocytes untreated

value: B6; gender:mix; age:0-2d; tissue:rib cartilage; passage #:4; treatment:control; biological replicate:2


title: osteoblast_control_rep2

description: untreated; biological replicate 2

value: B6; gender:mix; age:0-2d; tissue:calvariae; passage #:4; treatment:untreated; biological replicate:2


title: chondrocyte_5azatreated_rep1

description: treated with 5-aza-2'-deoxycytidine for 72 hours plus 24 hours in normal medium; biological replicate 1

value: B6; gender:mix; age:0-2d; tissue:rib cartilage; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:1


title: osteoblast_5azatreated_rep3

description: treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 3

source_name: primary osteoblasts treated

treatment_protocol: Freshly prepared 5A2dC (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 5 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 96-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.

value: B6; gender:mix; age:0-2d; tissue:calvariae; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:3


title: osteoblast_control_rep3

description: untreated; biological replicate 3

value: B6; gender:mix; age:0-2d; tissue:calvariae; passage #:4; treatment:untreated; biological replicate:3


title: osteoblast_5azatreated_rep2

description: treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 2

value: B6; gender:mix; age:0-2d; tissue:calvariae; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:2


title: chondrocyte_control_rep3

description: untreated; biological replicate 3

value: B6; gender:mix; age:0-2d; tissue:rib cartilage; passage #:4; treatment:control; biological replicate:3


title: osteoblast_5azatreated_rep1

description: treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 1

value: B6; gender:mix; age:0-2d; tissue:calvariae; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:1


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q29-14688-V1.0

status: Public on May 05 2006

city: Minneapolis

first: Bhupinder

last: Juneja

address: 1988 Fitch Avenue S

institute: University Of Minnesota

description: Freshly isolated islets from ~ 3 year old Landrace sows were isolated and cultured free-floating in Medium 199 (Mediatech, Inc., Herndon, VA) supplemented with 10% v/v heat-inactivated donor pig serum, 2 mmol/L GlutaMAX-1 (Gibco-BRL), 1% v/v ITS + Premix (Collaborative Biomedical Products), 5 mmol/L sodium pyruvate (Sigma), 16.7 mM zinc sulfate (Sigma), and 20 mg/mL ciprofloxacin for 48 hours at 37*C in 100% air. Islets were cultured an additional 48 hours with the indicated variable.

data_processing: The genes with front-channel signal higher than 200 from either cy3 or cy5 channels in atleast 24 out of 30 arrays were considered genes with significant signal.

organism: Sus scrofa

source_name: Adult Isolated Porcine Islets

tag: 16.7 mM glucose ,cytokine = 2ng/ml IL-1b, 1000 U/ml TNF-alpha; 1000 U/ml IFN-gamma

tag: 16.7 mM glucose


title: Prostate - PC3

city: Stanford

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27548.gif; format: GIF

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: control

tag: prostate cancer cell line

tag: PC3 control

source_name: 5-aza-dC treated

tag: PC3 1uM 5-aza-dC 4 days


title: chondrocyte_control_rep1

description: untreated; biological replicate 1

value: B6; gender:mix; age:0-2d; tissue:rib cartilage; passage #:4; treatment:untreated; biological replicate:1


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q31-14688-V1.0


title: Prostate - MDA-2A

description:
Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27550.gif; format: GIF

tag: MDA-2A control

tag: MDA-2A 1uM 5-aza-dC 5 days


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q26-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q24-14688-V1.0

tag: 5.6 mM glucose ,cytokine = 2ng/ml IL-1b, 1000 U/ml TNF-alpha; 1000 U/ml IFN-gamma

tag: 5.6 mM glucose


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q32-14688-V1.0


title: Prostate - DU145

description:
Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27547.gif; format: GIF

tag: DU145 control

tag: DU145 1uM 5-aza-dC 3 days


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q25-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q28-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q27-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q21-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q23-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q22-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q19-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q14-14688-V1.0

tag: 16.7 mM glucose , cytokine = 2ng/ml IL-1b, 1000 U/ml TNF-alpha; 1000 U/ml IFN-gamma

tag: 5.6 mM glucose , cytokine = 2ng/ml IL-1b, 1000 U/ml TNF-alpha; 1000 U/ml IFN-gamma


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q16-14688-V1.0


title: Prostate - LNCaP

description:
Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27543.gif; format: GIF

tag: LNCaP control

tag: LNCaP 1uM 5-aza-dC 5 days


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q15-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q13-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q20-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q12-14688-V1.0


title: regression_Myc off 6 days-sample3

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

description: RNA linearly amplified x2 prior to hybridization

data_processing: normalized by RMA

source_name: laser-captured pancreatic islets

treatment_protocol: daily tamoxifen injectionx21 days then sacrificed 6 days after last dose

tag: 2 month old, double transgenic (InsMycER+,RIP-BclXL+)


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q10-14688-V1.0


title: regression_Myc off 6 days-sample2


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO9-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q11-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO8-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO3-14688-V1.0


title: ‘Gala” scion on Supporter 4 rootstocks

first: Izabela

last: Makalowska

address: 502 Wartik Lab

description: First of two reps

data_processing: mean values calculated from signal intensities of six probes for each gene; RMA normalization

label: Biotin

organism: Malus domestica

source_name: actively growing shoot tip

tag: Greenhouse grown tree; first year bench graft


title: ‘Gala” scion on Supporter 4 rootstocks (rep 3)

description: Third of three reps


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q18-14688-V1.0


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO5-14688-V1.0

tag: 5.6mM glucose


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO7-14688-V1.0

tag: 16.7 mM glucose


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO6-14688-V1.0


title: ‘Gala” scion on Supporter 4 rootstocks (rep 2)

description: Second of three reps


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q02-14688-V1.0

tag: 16.7 mM Glucose


title: ‘Gala” scion on M9 rootstocks (rep 2)

description: Second of two reps


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-QO4-14688-V1.0


title: regression_Myc off 6 days-sample1


title: regression_Myc off 4 days-sample3

treatment_protocol: daily tamoxifen injectionx21 days then sacrificed 4 days after last dose


title: regression_Myc off 4 days-sample2


title: regression_Myc off 2 days-sample3

treatment_protocol: daily tamoxifen injectionx21 days then sacrificed 2 days after last dose


title: regression_Myc off 2 days-sample2


title: regression_Myc off 4 days-sample1


title: ‘Gala” scion on M9 rootstocks (rep 1)

description: First of two reps


title: ‘Gala” scion on M7 rootstocks (rep 3)

description: Third of three reps


title: 21day 4OHT-treated-sample1

treatment_protocol: sacrificed following 21 days of daily tamoxifen injection


title: 21day 4OHT-treated-sample3


title: ‘Gala” scion on M27 rootstocks (rep 3)

description: Third of three reps


title: 24h 4OHT-treated-sample3

treatment_protocol: sacrificed 24hrs post-4OHT injection


title: 21day 4OHT-treated-sample2


title: regression_Myc off 2 days-sample1


title: UMN/DiabetesInstitute/FahrenkrugLab-SS-Q17-14688-V1.0


title: ‘Gala” scion on M27 rootstocks (rep 2)

description: Second of three reps


title: ‘Gala” scion on M111 rootstocks (rep 1)

description: First of two reps


title: ‘Gala” scion on M7 rootstocks

description: First of three reps


title: ‘Gala” scion on M27 rootstocks (rep 1)

description: First of three reps


title: ‘Gala” scion on G30 rootstocks (rep 1)

description: First of three reps


title: 24h 4OHT-treated-sample1


title: ‘Gala” scion on G30 rootstocks (rep 2)

description: Second of three reps


title: ‘Gala” scion on G30 rootstocks (rep 3)

description: Third of three reps


title: 8h 4OHT-treated-sample1

treatment_protocol: sacrificed 8hrs post-4OHT injection


title: ‘Gala” scion on M111 rootstocks (rep 2)

description: Second of two reps


title: 8h 4OHT-treated-sample3


title: ‘Gala” scion on B9 rootstocks (rep 1)

description: First of two reps


title: ‘Gala” scion on B9 rootstocks (rep 2)

description: Second of two reps


title: 4h 4OHT-treated-sample3

treatment_protocol: sacrificed 4hrs post-4OHT injection


title: 4h 4OHT-treated-sample2


title: ‘Melrose’ scions on B9 rootstocks (rep 1)

description: First of three reps

tag: Field grown tree


title: ‘Melrose’ scions on B9 rootstocks (rep 3)

description: Third of three reps


title: ‘Melrose’ scions on B9 rootstocks (rep 2)

description: Second of three reps


title: 2h 4OHT-treated-sample3

treatment_protocol: sacrificed 2hrs post-4OHT injection


title: 24h 4OHT-treated-sample2


title: 4h 4OHT-treated-sample1


title: 2h 4OHT-treated-sample2

data_processing: normalized by RMA;


title: 2h 4OHT-treated-sample1


title: untreated-sample2

description: total RNA linearly amplified x2 prior to hybridization


title: untreated-sample3


title: ‘Gala’ scions on B9 rootstocks (rep 2)

description: Second of three reps


title: untreated-sample1

data_processing: Normalized by RMA


title: Tslc1 +/+ mice_rep2

city: Tokyo

first: Murakami

last: Yoshinori

address: 5-1-1 Tsukiji Chuo-ku

department: Tumor Suppression and Functional Genomics Project

institute: National Cancer Center Reseach Institute

data_processing: MAS5.0, scaled to 1000

source_name: Testis

tag: Strain

tag: Gender

value: Male

tag: Age

value: 16 weeks

tag: Tissue

value: testis


title: Tslc1-/- mice_rep1


title: Tslc1 +/+ mice_rep1

value: male


title: Tslc1 -/- mice_rep2


title: ‘Gala’ scions on B9 rootstocks (rep 1)

description: First of three reps


title: Ambrosia’ scions on B9 rootstocks (rep 2)

description: Second of three reps

extract_protocol: Gasic, K., A. Hernandez, and S.S. Korban. 2004. RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA library construction. Plant Mol. Biol. Reptr. 22: 437a-437g


title: ‘Ambrosia’ scions on B9 rootstocks (rep 3)

description: Third of three reps


title: ‘Ambrosia’ scions on B9 rootstocks (rep 1)

description: One of three reps

tag: Field grown trees


title: C57BL/6j mesenteric lymph nodes_infected_Y.enterocolitica_12 hour

status: Public on May 04 2006

city: St. Louis

first: Scott

middle: Allyn

last: Handley

address: 660 South Euclid Avenue

department: Molecular Microbiology

description: C57BL/6j mesenteric lymph nodes 12 hours post oral infection with Yersinia enterocolitica.

data_processing: normalized to 150 using MAS5.0

source_name: C57BL/6j mesenteric lymph nodes


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_Day 7_02

description: Uninfected Peyer's patch data used in study to quantify transcriptional changes occuring following infection with Yersinia enterocolitica.

data_processing: Scaled to 150 using MAS 5.0

source_name: C57BL/6j Peyer's patches

extract_protocol: Trizol

tag: Peyer's patches from 5 week old female C57BL/6j mice Day 7 post oral infection with ~5x10^8 cfu Yersinia enterocolitica. Replicate 2 of 2.


title: C57BL/6j mesenteric lymph nodes_infected_Y.enterocolitica_day 4

description: C57BL/6j mesenteric lymph nodes 4 days post oral infection with Yersinia enterocolitica.


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_Day 4_01

source_name: C57Bl/6j Peyer's patches

tag: Peyer's patches from 5 week old female C57BL/6j mice Day 4 post oral infection with ~5x10^8 cfu Yersinia enterocolitica. Replicate 1 of 2.


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_Day 2_02

tag: Peyer's patches from 5 week old female C57BL/6j mice 2 days post oral infection with ~5x10^8 cfu Yersinia enterocolitica. Replicate 2 of 2.


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_Day 7_01

tag: Peyer's patches from 5 week old female C57BL/6j mice Day 7 post oral infection with ~5x10^8 cfu Yersinia enterocolitica. Replicate 1 of 2.


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_12 hours_02

tag: Peyer's patches from 5 week old female C57BL/6j mice 12 hours post oral infection with ~5x10^8 cfu Yersinia enterocolitica. replicate 2.


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_Day 2_01

tag: Peyer's patches from 5 week old female C57BL/6j mice 2 days post oral infection with ~5x10^8 cfu Yersinia enterocolitica. Replicate 1 of 2.


title: C57BL/6j mesenteric lymph nodes_infected_Y.enterocolitica_2 days

description: C57BL/6j mesenteric lymph nodes 2 days post oral infection with Yersinia enterocolitica.


title: G-CSF 7

status: Public on May 03 2006

city: Duesseldorf

first: Michael

last: Rosskopf

address: Universitaetsstrasse 1

department: Bioinformatics

institute: University of Duesseldorf

description: Peg-G-CSF-mobilized CD34+ cells

data_processing: Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project (http://www.bioconductor.org/) data from cel files of each sample were normalized by variance stabilizing transformations  (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

label: Biotin/Streptavidin-PE

source_name: peripheral blood

tag: age:	51

tag: gender:	female

tag: disease:	MM LC k

tag: stage:	IIIB

tag: previous chemotherapy:	ID

tag: number of cycles:	3

tag: radiatio therapy:	no

tag: mobilization chemotherapy:	Cyc

tag: cytokine:	G-CSF


title: C57BL/6j Peyer's patches_Uninfected_01

tag: 5 week old C57BL/6j Peyer's patches isolated from the wall of the small intestine


title: G-CSF 4

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	68

tag: gender:	male

tag: disease:	MM IgG l

tag: stage:	IIIA

tag: number of cycles:	6


title: G-CSF 3

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	48

tag: disease:	MM IgG k


title: G-CSF 5

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	51

tag: number of cycles:	2


title: G-CSF 2

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	63

tag: gender:	female

tag: stage:	IA


title: ‘Gala” scion on M7 rootstocks (rep 2)

description: Second of three reps

tag: Greenhouse grown tree; first year bench graft


title: C57BL/6j Peyer's patches_Uninfected_02

source_name: C57BL/6j mice

tag: Peyer's patches from 5 week old female C57BL/6j mice


title: G-CSF 1

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	62

tag: previous chemotherapy:	ID

tag: number of cycles:	4

tag: radiatio therapy:	no

tag: mobilization chemotherapy:	Cyc


title: Peg-G-CSF 9

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	60

tag: gender:	male

tag: disease:	MM IgA k

tag: number of cycles:	3

tag: radiatio therapy:	yes

tag: cytokine:	Peg-G-CSF


title: G-CSF 6

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	55

tag: disease:	MM IgG k

tag: stage:	IIIA

tag: cytokine:	G-CSF


title: Peg-G-CSF 8

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	66

tag: gender:	female

tag: number of cycles:	2


title: Peg-G-CSF 7

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	62

tag: previous chemotherapy:	ID


title: Peg-G-CSF 6

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	43


title: Peg-G-CSF 1

description: Peg-G-CSF-mobilized CD34+ cells

tag: stage:	IIA

tag: number of cycles:	4

tag: radiatio therapy:	no

tag: mobilization chemotherapy:	Cyc


title: Peg-G-CSF 5

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	54

tag: disease:	MM IgA k

tag: number of cycles:	3


title: Peg-G-CSF 2

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	63

tag: gender:	male

tag: cytokine:	Peg-G-CSF


title: CTIP 20 #2

status: Public on May 02 2006

city: Irvine

first: Wen-Hwa

last: Lee

address: 140 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

description: Human mammary epithelial MCF10A cells grown in 3-D Matrigel for 15 h after depletion of CTIP by viral RNAi

label: Biotin labeled

source_name: MCF10A cells in 3-D culture

tag: Human mammary epithelial MCF10A cells


title: LUC 20 KD #1


title: LUC 20 KD #2


title: LUC KD #1

description: Human mammary epithelial MCF10A cells grown in 3-D Matrigel for 15 h after depletion of BRCA1 by viral RNAi


title: Mel

status: Public on Apr 01 2006

city: Pittsburgh

first: Dorothea

last: Becker

address: 5117 Centre Avenue

department: Department of Pathology

institute: University of Pittsburgh

description: RNA obtained from Cell Applications Inc.

source_name: short term cultures of epidermal melanocytes

tag: Gender

tag: Source tissue

value: foreskin


title: BRCA1 KD #1


title: LN1

description: Melanoma-infiltrated lymph node

source_name: lymph node metastasis

tag: Age

tag: Source

value: axilla


title: ‘Gala’ scions on B9 rootstocks (rep 3)

description: Second of three reps

tag: Field grown tree


title: Ker

source_name: short term cultures of epidermal keratinocytes


title: LUC KD #2


title: BRCA1 KD #2


title: CTIP 20 #1


title: LN2

description: Melanoma-infiltrated lymph node

value: female

value: left groin


title: LN3

description: Melanoma-infiltrated lymph node

value: neck


title: VGP1

description: VGP melanoma

source_name: VGP melanoma

value: back


title: C57BL/6j mesenteric lymph nodes_infected_Y.enterocolitica_day 7

description: C57BL/6j mesenteric lymph nodes 7 days post oral infection with Yersinia enterocolitica.


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_Day 4_02

tag: Peyer's patches from 5 week old female C57BL/6j mice Day 4 post oral infection with ~5x10^8 cfu Yersinia enterocolitica. Replicate 2 of 2.


title: VGP2

description: VGP melanoma

value: skin, left heel


title: MGP2

description: MGP melanoma

source_name: MGP melanoma

value: left arm


title: in situ 2

description: Melanoma in situ, with RGP and some invasive component

source_name: melanoma in situ

value: skin, neck


title: AN2

description: Compound nevus with moderate atypia

source_name: atypical nevi

value: skin, abdomen


title: MGP1

description: Melanoma in transit

value: left lower leg


title: in situ 1

description: Melanoma in situ, no invasive component

value: skin, left ear


title: BN2

description: Intradermal nevus

source_name: benign nevi

value: skin, right scapula


title: NS1

description: Non-melanoma control

source_name: normal skin

value: skin, hip


title: AN1

description: Compound nevus with mild to moderate atypia

value: skin, left flank


title: NS2

description: Non-melanoma control

value: skin, left thigh


title: 44261

status: Public on Jan 28 2006

city: Beltsville

first: Robert

middle: W

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: Single channel hybridization of biotin-labeled samples detected by Cy3-streptavidin staining

data_processing: is based on the SAS Mixed Model

organism: Bos taurus

source_name: Fat pad of an intact animal treated with estrogen

tag: both the raw and normalized values are log 2 based.


title: 47554

source_name: Fat pad of an intact animal treated with corn oil (control)


title: 47465

source_name: Fat pad of an OVX animal treated with estrogen


title: 44522


title: 44519


title: 44526


title: Peg-G-CSF 4

description: Peg-G-CSF-mobilized CD34+ cells

tag: age:	51

tag: gender:	female

tag: disease:	MM IgG k

tag: stage:	IIIA

tag: previous chemotherapy:	ID

tag: number of cycles:	4


title: C57BL/6j Peyer's patches_Infected_Y.enterocolitica_12 Hours

institute: Washington University

tag: Peyer's patches from 5 week old female C57BL/6j mice 12 hours post oral infection with ~5x10^8 cfu Yersinia enterocolitica.


title: 44257

source_name: Fat pad of an OVX animal treated with corn oil (control)


title: 41772


title: C57BL/6j mesenteric lymph nodes_uninfected

description: C57BL/6j mesenteric lymph nodes. Uninfected controls for comparison with Yersinia enterocolitica infected mesenteric lymph nodes.

data_processing: Normalized to 150 using MAS 5.0

source_name: C57BL/6j mesenteric lymph nodes


title: 43596


title: 41938


title: 43240

source_name: Parenchyma of an OVX animal treated with estrogen


title: 44222


title: 43228


title: 41768


title: 41761


title: 42473


title: 41916


title: Peg-G-CSF 3

description: Peg-G-CSF-mobilized CD34+ cells

source_name: peripheral blood

tag: age:	55

tag: disease:	MM IgG l

tag: stage:	IIA

tag: number of cycles:	3

tag: radiatio therapy:	yes

tag: mobilization chemotherapy:	Cyc


title: 42497

source_name: Parenchyma of an intact animal treated with estrogen


title: 42508


title: 41023


title: 42514

source_name: Parenchyma of an OVX animal treated with corn oil (control)


title: 41646

source_name: Parenchyma of an intact animal treated with corn oil (control)


title: JRS948 #9438

status: Public on Dec 19 2005

city: Atlanta

first: June

last: Scott

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University

description: Total RNA was isolated by CsCl2 method and labeled cDNA was generated using the Fairplay microarray labelling kit from Stratagene using random hexamers.  Labeled cDNA was purified using QiaQuick PCR purification columns from Qiagen and concentrated using Microcon YM30 columns from Amicon.  The amount of incorporated label was determined by measuring the absorbance at 550nm (Cy3) or 650nm (Cy5). 60 pmol each of Cy-dye (reference cDNA (Cy5) and test cDNA (Cy3)) were combined in 60 ml hybridization buffer 1 (Ambion), denatured and hybridized to the array at 42°C for at least 16 h, followed by subsequent washes.  Output data (F635 mean-B635, F532 mean-B532, flags) was filtered to set any spots that did not exceed 2SD above a background threshold to the threshold value to avoid spurious expression ratios. Remaining spots were averaged, filtered to remove genes not present in JRS4 (the strain examined) and normalized before statistical analysis.

data_processing: glabal normalization after removing genes not present in JRS4

organism: Streptococcus pyogenes

source_name: CsCl2 total RNA from M6 serotype GAS JRS948

tag: Strain

value: JRS948  RNA prep:D

source_name: Pooled CsCl2 total RNA from M6 serotype GAS JRS4 and isogenic covR mutant JRS948

tag: Strains

value: JRS4, JRS948   RNA preps:A, B, C, D for each strain


title: JRS948 #9437


title: JRS4 #9431

source_name: CsCl2 total RNA from M6 serotype GAS JRS4

tag: RNA prep

value: C

value: JRS4, JRS948

tag: RNA preps

value: A, B, C, D for each strain


title: JRS948 #9432


title: JRS948 #9433

value: JRS948  RNA prep:C


title: JRS4 #9429


title: 42519

tag: both the raw and normalized values are log 2 based.


title: 39034

tag: both the raw and normalized vaules are log 2 based


title: 39137


title: 39144


title: 39031


title: JRS4 #9435

value: JRS4  RNA prep:D


title: JRS948 #9428

value: B


title: JRS4 #9436


title: 44270


title: JRS948 #9427


title: 39030


title: JRS4 #9426


title: P. putida JLR11 native_rep3

status: Public on Nov 05 2005

city: Louvain-la-Neuve

first: Laurent

last: Eyers

address: Place Croix du Sud 2/19

department: Unit of bioengineering

country: Belgium

institute: Catholic University of Louvain

description: Dissociation curves were generated by increasing the temperature of the microarray (1°C/min) from 20°C to 68°C and recording signal intensities every 1°C or 2°C (Urakawa et al. 2003, Appl. Environ. Microbiol. 68:235-244).

hyb_protocol: 5 µg of fragmented and labeled RNA was hybridised and washed as previously described (El Fantroussi et al. 2003, Appl. Environ. Microbiol. 69:2377-2382), except that hybridisation time was 1 h. Each hybridisation experiment was done in triplicate.

scan_protocol: Fluorescence signal intensities were recorded for each probe on the microarray with a custom epifluorescence microscope and software (Guschin et al. 1997, Anal. Biochem. 250:203-211).

data_processing: The hybridisation signals were corrected by subtracting the local background signal and normalising the corrected hybridisation signal to the background (Fotin et al. 1998, Nucleic Acids Res. 26:1515-1521).

label: lissamine rhodamine

organism: Pseudomonas putida

source_name: Native RNA of Pseudomonas putida JLR11

label_protocol: RNA was simultaneously fragmented and end-labeled following Bavykin et al. (2001, Appl. Environ. Microbiol. 67:922-928) except that RNA was fragmented in solution rather than on-column. In brief, RNA (30 µg) was suspended in 20 µl of diethyl pyrocarbonate (DEPC)-treated water and incubated at 95°C for 4 min. The RNA solution was mixed with 122 µl of preheated (95ºC for 30 s), filtered (0.22 µm) fragmentation and labeling solution that contained 700 µl of 25 mM sodium phosphate buffer (pH 7.0), 30 µl of 150 mM 1,10-phenanthroline, 3 µl of 150 mM CuSO4, and 6 µl of 100 mg/ml lissamine rhodamine B ethylenediamine (Molecular Probes, Inc., Eugene, OR). Three microliters of 200 mM H2O2 and 5 µl of 600 mM NaCNBH3 were added, and the mixture was incubated at 95°C for 10 min. The reaction was stopped with 540 µl of cold 100% ethanol and 20 µl of stop solution (2.6 M sodium acetate and 68 mM EDTA, pH 8.0). Following precipitation at -80°C for 10 min, RNA was centrifuged and washed three times with 100% ethanol. The RNA pellet was suspended in 20 µl of DEPC-treated water.

extract_protocol: Native RNA from P. putida was isolated with the Qiagen RNeasy mini kit (Valencia, CA) following the manufacturer’s instructions.

tag: Pseudomonas putida sp. JLR 11 was provided by Dr. J.L. Ramos (CSIC, Estacion Experimental del Zaidin, Spain). The strain is described as able to denitrate TNT (Esteve-Nunez and Ramos 1998, Environ. Sci. Technol. 32:3802-3808).


title: JRS4 #9425


title: P. putida JLR11 native_rep2


title: P. putida JLR11 native_rep1


title: P. putida JLR11 transcribed_rep3

source_name: In vitro transcribed product of 16S rDNA amplified from Pseudomonas putida JLR11

extract_protocol: Total DNA from P. putida was extracted by lysozyme and sodium dodecylsulfate lysis followed by phenol extraction (Maniatis et al. 1982, Cold Spring Harbor Press). PCR was done with primers BACT 11 F (Kane et al. 1993, Appl. Environ. Microbiol. 59:682-686) containing the T7 promoter sequence and S-D-Bact-1512-a-A-16 (Fry et al. 1997, Appl. Environ. Microbiol. 63:1498-1504) in a thermal cycler (Thermo Hybaid US, Franklin, MA) in 100 µl reactions under the following conditions (reagents were from Invitrogen (Carlsbad, CA)): 1 X PCR buffer, 2 µl of deoxynucleoside triphosphate mixture (2.5 mM each), 2.5 µM of each primer, 5 U of Taq DNA polymerase, and 100 ng of template DNA. An initial denaturation step of 3 min at 94°C was followed by 30 cycles of 30 s at 94°C, 30 s at 55°C, and 1 min at 72°C. A final extension at 72°C for 7 min was also done. PCR products were purified with the Qiaquick PCR purification kit (Qiagen, Inc.) following the manufacturer's instructions. In vitro transcription was used to produce 16S rRNA according to the manufacturer's protocol (Invitrogen, Inc.). RNA samples were purified with the Qiagen RNeasy mini kit.

tag: Pseudomonas putida sp. JLR 11 was provided by Dr. J.L. Ramos (CSIC, Estacion Experimental del Zaidin, Spain). The strain is described as able to denitrate TNT (Esteve-Nunez and Ramos 1998, Environ. Sci. Technol. 32:3802-3808)


title: JRS948 #9424

value: A


title: JRS948 #9423


title: P. putida JLR11 transcribed_rep2


title: JRS4 #9422


title: P. putida JLR11 transcribed_rep1


title: TNT-contaminated soil_rep3

organism: unidentified

source_name: In vitro transcribed product of 16S rDNA amplified from an TNT-contaminated soil sample

label_protocol: RNA was simultaneously fragmented and end-labeled following Bavykin et al. (2001, Appl. Environ. Microbiol. 67:922-928) except that RNA was fragmented in solution rather than on-column. Fragmentation and labeling of RNA samples of uncontaminated and TNT-contaminated soils was done in parallel at the same time with the same freshly prepared reactants. In brief, RNA (30 µg) was suspended in 20 µl of diethyl pyrocarbonate (DEPC)-treated water and incubated at 95°C for 4 min. The RNA solution was mixed with 122 µl of preheated (95ÂºC for 30 s), filtered (0.22 µm) fragmentation and labeling solution that contained 700 µl of 25 mM sodium phosphate buffer (pH 7.0), 30 µl of 150 mM 1,10-phenanthroline, 3 µl of 150 mM CuSO4, and 6 µl of 100 mg/ml lissamine rhodamine B ethylenediamine (Molecular Probes, Inc., Eugene, OR). Three microliters of 200 mM H2O2 and 5 µl of 600 mM NaCNBH3 were added, and the mixture was incubated at 95°C for 10 min. The reaction was stopped with 540 µl of cold 100% ethanol and 20 µl of stop solution (2.6 M sodium acetate and 68 mM EDTA, pH 8.0). Following precipitation at -80°C for 10 min, RNA was centrifuged and washed three times with 100% ethanol. The RNA pellet was suspended in 20 µl of DEPC-treated water.

extract_protocol: DNA was extracted from soil samples with the UltraClean Soil DNA kit from Mo Bio (Carlsbad, CA) following the manufacturer's instructions. PCR was done with primers BACT 11 F (Kane et al. 1993, Appl. Environ. Microbiol. 59:682-686) containing the T7 promoter sequence and S-D-Bact-1512-a-A-16 (Fry et al. 1997, Appl. Environ. Microbiol. 63:1498-1504) in a thermal cycler (Thermo Hybaid US, Franklin, MA) in 100 µl reactions under the following conditions (reagents were from Invitrogen (Carlsbad, CA)): 1 X PCR buffer, 2 µl of deoxynucleoside triphosphate mixture (2.5 mM each), 2.5 µM of each primer, 5 U of Taq DNA polymerase, and 100 ng of template DNA. An initial denaturation step of 3 min at 94°C was followed by 30 cycles of 30 s at 94°C, 30 s at 55°C, and 1 min at 72°C. A final extension at 72°C for 7 min was also done. PCR products were purified with the Qiaquick PCR purification kit (Qiagen, Inc.) following the manufacturer's instructions. In vitro transcription was used to produce 16S rRNA according to the manufacturer's protocol (Invitrogen, Inc.). RNA samples were purified with the Qiagen RNeasy mini kit.

tag: Top 5-cm layer of soil, homogenised. Contains 23g TNT/g soil


title: JRS4 #9421


title: TNT-contaminated soil_rep1


title: TNT-contaminated soil_rep2


title: non-contaminated soil_rep2

source_name: In vitro transcribed product of 16S rDNA amplified from an uncontaminated soil sample

tag: Top 5-cm layer of soil, homogenised.

tag: Sampled a few meters from a 2,4,6-trinitrotoluene contaminated soil sample.


title: non-contaminated soil_rep1


title: non-contaminated soil_rep3


title: G-CSF mobilized PB monocytes_2

status: Public on Oct 25 2005

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: The gene expression profile of normal, uncultured peripheral blood monocytes was investigated.

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 Âµl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software.

data_processing: 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.

label: Cy 5

source_name: G-CSF mobilized peripheral blood monocytes_uncultured_2

label_protocol: The RNA (30 µg) was annealed with 5 Âµg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42Â°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. The cDNA was covalently coupled with Cy5 monoreactive fluor in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine.

growth_protocol: Cells were freshly isolated.

extract_protocol: All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.

tag: Donors were treated for 5 days prior to monocyte isolation with recombinant human G-CSF at a dose of 16 ug/kg.

tag: CD14+ cells were isolated from mobilized peripheral blood mononuclear cells by staining with anti CD14 antibody Tuek4 and magnetic bead (AutoMacs) selection.

label: Cy 3

source_name: Stratagene universal reference RNA

label_protocol: The RNA (30 Âµg) was annealed with 5 Âµg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42Â°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. The cDNA was covalently coupled with Cy3 monoreactive fluor in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine.

tag: A mixture of RNA from 10 human cell lines approximating the expression profile of the majority of human genes


title: G-CSF mobilized PB monocytes_3

source_name: G-CSF mobilized peripheral blood monocytes_uncultured_3


title: BN1

description: Intradermal nevus

source_name: benign nevi

tag: Gender

value: female

tag: Age

tag: Source

value: skin, left leg


title: G-CSF mobilized PB monocytes_1

source_name: G-CSF mobilized peripheral blood monocytes_uncultured_1


title: Normal Skeletal Muscle

status: Public on Apr 03 2005

city: Evanston

first: Xijin

last: Ge

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute

description:
Normal human tissue:Normal Skeletal
 Muscle
Keywords = Human, Normal Tissue, Normal Skeletal
 Muscle

source_name: Normal Skeletal Muscle , Commercial mRNA for normal human tissue


title: Normal PB monocytes_2

source_name: Normal peripheral blood monocytes_uncultured_2

tag: CD14+ cells were isolated from peripheral blood mononuclear cells from a normal donor by staining with anti CD14 antibody Tuek4 and magnetic bead (AutoMacs) selection.


title: Normal PB monocytes_3

source_name: Normal peripheral blood monocytes_uncultured_3


title: Nor:HIF2a rep 2

status: Public on Apr 01 2005

city: Bethesda

first: Victoria

last: Wang

institute: NCI

description:
mAdb experiment ID: 44964
Comparison of HIF2a transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.1p9-042203
cell_line: HEK293T

source_name: HIF2a transfectant

source_name: Normoxia 16hs


title: Nor:HIF1amut rep 2

description:
mAdb experiment ID: 51089
Comparison of HIF1amut transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.2p10-082503
cell_line: HEK293T

source_name: HIF1amut transfectant


title: Nor:HIF1a rep 3

description:
mAdb experiment ID: 43945
Comparison of HIF1a transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.1p9-042203
cell_line: HEK293T

source_name: HIF1a transfectant


title: Nor:HIF2a rep 3

description:
mAdb experiment ID: 43946
Comparison of HIF2a transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.1p9-042203
cell_line: HEK293T


title: Normal PB monocytes_1

source_name: Normal peripheral blood monocytes_uncultured_1


title: Nor:HIF2a rep 1

description:
mAdb experiment ID: 44963
Comparison of HIF2a transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.1p9-042203
cell_line: HEK293T


title: Nor:Hypo rep 1

description:
mAdb experiment ID: 47646
Comparison of hypoxia treated cells with untreated cells.
Array Print: Hs-OperonV2-vB1.2p10-082503
cell_line: HEK293T

source_name: Hypoxia 16hs


title: Nor:HIF1a rep 1

description:
mAdb experiment ID: 44961
Comparison of HIF1a transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.1p9-042203
cell_line: HEK293T


title: Nor:Hypo rep 2

description:
mAdb experiment ID: 47644
Comparison of hypoxia treated cells with untreated cells.
Array Print: Hs-OperonV2-vB1.2p10-082503
cell_line: HEK293T


title: Nor:HIF1amut rep 1

description:
mAdb experiment ID: 50554
Comparison of HIF1amut transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.2p10-082503
cell_line: HEK293T


title: Nor:HIF1a rep 2

description:
mAdb experiment ID: 44962
Comparison of HIF1a transfected cells with untreated cells
Array Print: Hs-OperonV2-vB1.1p9-042203
cell_line: HEK293T


title: cultured MGP melanoma cells

description: From the Wistar Institute

source_name: metastatic melanoma culture

value: male

tag: Source tissue

value: lymph node of the scalp/neck


title: 43227

source_name: Parenchyma of an intact animal treated with corn oil (control)


title: 39429


title: 60d vs 7 wk oligo1

status: Public on Sep 01 2006

city: East Lansing

first: Catherine

middle: W.

last: Ernst

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

description:
Skeletal muscle tissue samples were obtained from the hind limbs of pig fetuses at 60 days of gestation and postnatal pigs at 7 weeks of age.  For fetal samples, tissues from several pigs within each litter were pooled, whereas postnatal samples were obtained from individual animals.
Keywords = pig, skeletal muscle, microarray

data_processing: Log ratio of Loess normalized data

source_name: skeletal muscle 7 wk E

value: 7 weeks postnatal

source_name: skeletal muscle 60 d A

value: 60 days of gestation


title: A X202B44

status: Public on May 31 2006

city: Singapore

first: Lance

middle: David

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

country: Singapore

institute: Genome Institute of Singapore

description: Series of 249 tumours

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Breast Tumor

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

extract_protocol: Qiagen RNeasy Mini Kit

tag: INDEX (ID)

tag: Elston (NGS) histologic grade

tag: Genetic grade signature status prediction (by SWS classifier)

tag: Probability 1-like (by SWS classifier)

tag: Probability 3-like (by SWS classifier)

tag: DFS TIME (yrs)

tag: DFS EVENT (0=censored; 1=event defined as any type of recurrence (local, regional or distant) or death from breast cancer

tag: All patients (1=included in survival analysis)

tag: ER+, endocrine therapy only (1=included in survival analysis)

tag: No systemic therapy (1=included in survival analysis):

tag: ER status

value: ER+

tag: Lymph node status

value: LN-

tag: p53 seq mut status (p53+=mutant; p53-=wildtype)

tag: age at diagnosis

tag: tumor size (mm)


title: 809 - mAdbID:52105

first: Sandeep

last: Dave

address: 9000 Rockville Pike

institute: National Cancer Institute

description: mAdb experiment ID: 52105

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on LymphDX Custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Sample Extraction Protocol

tag: Gender

tag: Age

tag: Tissue

value: lymph node

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL ABC

value: Follow up status:dead

value: Follow up years:0.51

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:1.31

value: Number of nodal sites:0


title: Pt.7 IE-CTL NKG2C+

status: Public on May 15 2006

city: Chicago

first: Bana

last: Jabri

address: 5841 S Maryland Ave, S354

institute: University of Chicago

description: Gene expression data from IE-CTLs from adult celiac patient.

data_processing: Data analyses were preformed using DNA-Chip Analyzer 1.3 (dChip) with the *.CEL files obtained from GeneChip Operating System 1.3 (GCOS 1.3). A PM-only model was used to estimate gene expression level and the invariant set approach was used for normalization.

source_name: Intraepithelial Lymphocytes

tag: TCRab+ CD8+ NKG2C+ IE-CTL from active celiac disease patient.


title: SSC GDNF/GFRalpha1 8-hr replacement Rep3

status: Public on May 11 2006

city: University Park

first: Jon

last: Oatley

address: 324 Henning

department: Dairy and Animal Science

institute: Pennsylvania State University

description:
Established cultures of spermatogonial stem cells subjected to an 18-hr withdrawal of GDNF and GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 8-hr.
Replicate 3
Total RNA from spermatogonial stem cell enriched germ cell cultures that were established from 6 day old C57BL/6 male mice.

data_processing: MAS 5.0, signal intensities scaled to a mean value of 150

source_name: Cultured mouse spermatogonial stem cells

treatment_protocol:
Established spermatogonial stem cell cultures subjected to an 18-hr withdrawal of GDNF/GFRalpha1 followed by replacement of GDNF/GFRalpha1 for 8-hr.
Replicate 3

tag: Spermatogonial stem cell enriched germ cell cultures established from 6 day old C57BL/6 male mice.


title: 8h 4OHT-treated-sample2

first: Elizabeth

last: Lawlor

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

description: RNA linearly amplified x2 prior to hybridization

data_processing: normalized by RMA

source_name: laser-captured pancreatic islets

tag: 2 month old, double transgenic (InsMycER+,RIP-BclXL+)