title: SK1_U6_YPA_D

description:
This diploid strain lacks UME6 which codes for a transcription factor essential for meiosis.
It was grown in YPA to identify the mitotic regulon of Ume6 in the presence of a non-fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: W303_U6_YPA_D

status: Public on Jun 17 2002

type: RNA

city: Montpellier

first: Michel

last: Bellis

country: France

institute: CNRS

description:
This diploid strain lacks UME6 which codes for a transcription factor essential for meiosis.
It was grown in YPA to identify the mitotic regulon of Ume6 in the presence of a non fermentable carbon source.
Keywords = Yeast, ume6, meiosis

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast polyA+ RNA


title: W303_WT_YPD_C

description:
A diploid W303 wild type strain was grown in rich medium containing glucose (YPD) to identify the genes expressed in the presence of a fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: W303_WT_YPA_C

description:
A diploid W303 wild type strain was grown in rich medium containing acetate (YPA; generally used to culture cells prior sporulation) to identify the genes expressed in the presence of a nonfermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: W303_U6_YPD_C

description:
This diploid strain lacks UME6 which codes for a transcription factor essential for meiosis.
It was grown in YPD to identify the mitotic regulon of Ume6 in the presence of a fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: W303_U6_YPD_B


title: SK1_WT_YPA_C

description:
A diploid SK1 wild type strain was grown in rich medium containing acetate (YPA; generally used to culture cells prior sporulation) to identify the genes expressed in the presence of a nonfermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: W303_U6_YPA_C


title: SK1_WT_YPA_B


title: W303_WT_YPA_B


title: SK1_U6_YPD_C


title: W303_U6_YPA_B


title: W303_U6_YPD_A


title: W303_WT_YPA_A

description:
A diploid W303 wild type strain was grown in rich medium containing acetate (YPA; generally used to culture cells prior sporulation) to identify the genes expressed in the presence of a non fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: SK1_U6_YPA_B


title: SK1_U6_YPA_C


title: SK1_WT_YPD_B

description:
A diploid SK1 wild type strain was grown in rich medium containing glucose (YPD) to identify the genes expressed in the presence of a fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: SK1_WT_YPD_C

description:
A diploid SK1 wild type strain was grown in rich medium containing glucose (YPD) to identify the genes expressed in the presence of a fermentable carbon source
Keywords = Yeast, ume6, meiosis


title: SK1_WT_YPD_A


title: SK1_U6_YPD_B


title: SK1_WT_YPA_A

description:
A diploid SK1 wild type strain was grown in rich medium containing acetate (YPA; generally used to culture cells prior sporulation) to identify the genes expressed in the presence of a non fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: PGA-Csx_het_4a-m4

status: Public on Jul 11 2002

city: Cambridge

first: Martina

last: Schinke

state: MA

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

country: USA

institute: Harvard University

description:
Mouse model of congenital heart disease in Csx/Nkx2.5 mutant embryos.
Heterozygous embyronic day 9.5 mouse.
Keywords = congenital heart disease, Csx, Nkx2.5

organism: Mus musculus

source_name: Middle third of E9.5 mouse


title: W303_WT_YPD_B


title: SK1_U6_YPD_A


title: PGA-FVB_4w_11293-m5

status: Public on Jun 21 2002

description:
FVB benchmark dataset: 4 week old mouse
Keywords = cardiac development

source_name: Heart ventricle


title: Control #1

status: Public on Jun 26 2002

city: Denver

first: Russell

middle: P

last: Bowler

state: CO

address: 1400 Jackson Street, K736a

department: Medicine

institute: National Jewish Medical and Research Center

description:
A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke.

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of saline (control); first replicate; pooled mRNA from 6 brains.

source_name: Brain


title: W303_U6_YPA_A


title: SK1_U6_YPA_A

status: Public on May 17 2002

description:
This diploid strain lacks UME6 which codes for a transcription factor essential for meiosis.  It was grown in YPA to identify the mitotic regulon of Ume6 in the presence of a non-fermentable carbon source.
Keywords = yeast, expression profiling, GeneChip, microarrays


title: Lulu_S294-1H1

status: Public on May 29 2002

city: Memphis

first: Lu

last: Lu

state: TN

address: 855 Monroe Avenue

department: Center of Genomics and Bioinformatics

institute: University of Tennessee Health Science Center

description: Authors: Lu Lu

source_name: Murine Hippocampus


title: Lulu_S276-1H1

description: Authors: Lu Lu


title: SK1_WT_YPD_D


title: CF-1 wild-type 2month

status: Public on Jun 07 2002

city: Cleveland

first: John

middle: H

last: Nilson

state: OH

address: 2109 Adelbert Road

department: Pharmacology

institute: Case Western Reserve University, School of Medicine

description: Wild type ovary sample from 2 month old CF-1 mice for use in gene expression profiling experiment with LH hypersecreting mice (LHCTP)

source_name: mouse ovary CF-1 wild type


title: Lulu_S477-1H1

description: Authors: Lu Lu


title: Lulu_S265-1H1

description: Authors: Lu Lu


title: CF-1 transgenic hCG Tx 5mo ovary

description: Trangenic and hCG treated ovary (luteoma) from 5 month old CF-1 mouse for use in gene expression profiling experiment on LH hypersecreting mice (LHCTP)

source_name: hCG treated transgenic (LHCTP) ovary from 5 month old CF-1 mouse


title: Gamma-ray treated Arabidopsis thaliana

status: Public on May 03 2002

type: SAGE

anchor: NlaIII

city: Ardmore

first: Zeji

last: Du

state: OK

address: 2510 Sam Noble Parkway

department: Plant Biology Division

institute: Samuel Roberts Noble Foundation

description: 10-day-old Arabidopsis thaliana (Col) was treated with 218Gy of Gamma ray. After 24 hr, total RNA was isolated using TRIzol reagent. mRNA was isolated using oligo-dT beads.

organism: Arabidopsis thaliana

source_name: Arabidopsis (Col)


title: CF/B6 wild type 2mo ovary B

description: Wild type ovary sample from 2 month old CF-1xC57BL/6 F1 hybrid mouse for use in gene expression profiling experiment on LH hypersecreting mice (LHCTP)

source_name: Wild type ovary from CF-1/C57BL/6 F1 hybrid 2 month old mouse


title: UV-B treated Arabidopsis thaliana

description: 10-day-old Arabidopsis thaliana (Col) was treated with 8000 J M-2 UV-B. After 24 hr, total RNA was isolated using TRIzol reagent. mRNA was isolated using oligo-dT beads.


title: CF-1 wild type 2mo ovary chip B

description: Wild type ovary sample from 2 month old CF-1 mouse for use in gene expression profiling experiment on LH hypersecreting mice (LHCTP)

source_name: wild type ovary from 2 month old CF-1 mouse


title: PGA-swim_1w_s1023

status: Public on Aug 01 2002

description:
Mice sacrificed after swimming twice a day for 1 week.
Keywords = exercise induced hypertrophy

source_name: heart ventricle


title: W303_WT_YPD_A

description:
A diploid W303 wild type strain was grown in rich medium containing glucose (YPD) to identify the genes expressed in the presence of a fermentable carbon source.
Keywords = Yeast, ume6, meiosis


title: Clontech plyA human liver

status: Public on May 14 2002

city: La Jolla

first: Richard

last: Rouse

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
human liver plyA RNA purchased from Clontech was labeled with the Amersham Cyscribe indirect (aminoallyl) kit. The hybridization was done with an automated slide processor. 20pmols of both cy3 and cy5 labeled material were used for the hybridization
Keywords = liver plyA, clontech, automated slide processor

organism: Homo sapiens

source_name: cy3 labeled Clontech plyA human liver

source_name: cy5 labeled Clontech plyA human liver


title: prp4_5

status: Public on Apr 18 2002

city: Santa Cruz

first: Manuel

last: Ares

institute: UC Santa Cruz

description:
Temperature sensitive Prp4-1a strain and isogenic wt (SS330) are shifted from permissive (26deg) to restrictive (37deg) temperature and allowed to grow to 2 hrs.
Lot batch = Slide3-10

source_name: SS330(wt) - 2hrs @ 37 deg C

source_name: prp4-1a - 2hrs @ 37 deg C


title: prp4-TempShift-60mins_3

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-1051

source_name: SRY4-1a (prp4-1) @ 37 deg for 60 mins

source_name: SS330 (wt) @ 37 deg for 60 mins


title: Clontech plyA spleen

description:
This experiment compares the cy3 and cy5 labeling of plyA derived spleen RNA purchased from Clontech. The samples were labeled with the Amersham cyscribe indirect (aminoallyl) labeling kit. The hybridization was performed using an automated slide processor. 20pmols of both cy3 and cy5 labeled material were used.
Keywords = human, spleen plyA, automated slide processor

source_name: cy3 labeled Clontech plyA spleen

source_name: cy5 labeled Clontech plyA spleen


title: Clontech spleen plyA RNA

description:
This experiment compares the cy3 and cy5 labeling of plyA derived spleen RNA purchased from Clontech. The samples were labeled with the Amersham cyscribe indirect (aminoallyl) labeling kit. The hybridization was performed using an automated slide processor. 20pmols of both cy3 and cy5 labeled material were used.
Keywords = human, spleen, automated slide processor

source_name: cy3 labeled clontech spleen plyA RNA

source_name: cy5 labeled clontech spleen plyA RNA


title: prp4_3

description:
Temperature sensitive Prp4-1a strain and isogenic wt (SS330) are shifted from permissive (26deg) to restrictive (37deg) temperature and allowed to grow to 2 hrs.
Lot batch = Slide3-37

source_name: prp4-1a - 2 hrs @ 37 deg C

source_name: SS330(wt) - 2 hrs @ 37 deg C


title: prp4-TempShift-120mins_5

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-37

source_name: SS330 (wt) @ 37 deg for 120 mins

source_name: SRY4-1a (prp4-1) @ 37 deg for 120 mins


title: Clontech universal RNA 2

description:
This experiment compares the cy3 and cy5 labeling of plyA derived spleen RNA purchased from Clontech. The samples were labeled with the Amersham cyscribe indirect (aminoallyl) labeling kit. The hybridization was performed using an automated slide processor. 20pmols of both cy3 and cy5 labeled material were used.
Keywords = human, Clontech universal RNA, automated slide processor

source_name: cy3 labeled Clontech universal RNA

source_name: cy5 labeled Clontech universal RNA


title: prp4-TempShift-120mins_3

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-1052


title: prp4-TempShift-30mins_3

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-1050

source_name: SRY4-1a (prp4-1) @ 37 deg for 30 mins

source_name: SS330 (wt) @ 37 deg for 30 mins


title: prp4-TempShift-60mins_5

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-36


title: SK1_U6_YPD_D

description:
This diploid strain lacks UME6 which codes for a transcription factor essential for meiosis.
It was grown in YPD to identify the mitotic regulon of Ume6 in the presence of a fermentable carbon source.
Keywords = Yeast, ume6, meiosis

source_name: yeast polyA+ RNA


title: Clontech universal RNA

description:
This experiment compares the cy3 and cy5 labeling of universal RNA purchased from Clontech. The samples were labeled with the Amersham cyscribe indirect (aminoallyl) labeling kit. The hybridization was performed using an automated slide processor. 20pmols of both cy3 and cy5 labeled material were used.
Keywords = Clontech universal RNA, automated slide processor


title: prp4-TempShift-0mins_3

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-1046


title: R2-0

status: Public on Feb 26 2002

city: Bethesda

first: Pavel

last: Khil

state: MD

address: 5 Memorial Dr.

institute: NIDDK

description: To study the changes in gene expression after DNA damage in E. coli we used whole-genome gene arrays, containing all the annotated ORFs of E. coli. Bacterial cultures were grown to early- to mid-log phase and mitomycin C (MMC) was added to the growth media. Samples at several time points after induction of DNA damage were taken and total RNAs were purified from them. Radiolabeled probes were generated by reverse transcription of purified RNAs with a mixture of all the gene-specific oligonucleotides used as primers. Following purification, the probes were hybridized to gene arrays. In each experiment we compared the levels of expression of genes after the induction of DNA damage with their expression level before damage.

organism: Escherichia coli

source_name: 0' growth in the presense of 0.3 ug/ml MMC (reference)


title: R1-50

source_name: 10' exposure to 3.0 ug/ml MMC followed by 50' growth


title: M3-0


title: prp4-TempShift-5mins_3

status: Public on Apr 16 2002

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-1048

source_name: SRY4-1a (prp4-1) @ 37 deg for 5 mins

source_name: SS330 (wt) @ 37 deg for 5mins


title: R1-0

source_name: 0' growth in the presense of 3 ug/ml MMC (reference)


title: prp4-TempShift-5mins_5

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-33


title: M3-80

source_name: 80' growth in the presense of 0.3 ug/ml MMC


title: M1a-25

source_name: 25' growth in the presense of 0.3 ug/ml MMC


title: prp4-TempShift-15mins_5

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-34

source_name: SS330 (wt) @ 37 deg for 15mins

source_name: SRY4-1a (prp4-1) @ 37 deg for 15 mins


title: prp4-TempShift-15mins_3

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-1049


title: prp4-TempShift-0mins_5

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-32


title: M2-0


title: C2-80

status: Public on Feb 25 2002

source_name: 80' normal growth


title: C2-0

description: To study the changes in gene expression after DNA damage in E. coli we used whole-genome gene arrays, containing all the annotated ORFs of E. coli.  Bacterial cultures were grown to early- to mid-log phase and mitomycin C (MMC) was added to the growth media.  Samples at several time points after induction of DNA damage were taken and total RNAs were purified from them.  Radiolabeled probes were generated by reverse transcription of purified RNAs with a mixture of all the gene-specific oligonucleotides used as primers. Following purification, the probes were hybridized to gene arrays.   In each experiment we compared the levels of expression of genes after the induction of DNA damage with their expression level before damage.

source_name: 0' normal growth (reference)


title: M1a-0

source_name: 0' growth in presense of 0.3 ug/ml MMC


title: M1b-10

source_name: 10' growth in the presense of 0.3 ug/ml MMC (reference)


title: M2-40

source_name: 40' growth in the presense of 0.3 ug/ml MMC


title: prp4-TempShift-30mins_5

description:
Prp4-1 and wt strains were grown at 26deg to A600 of 1.0, then an equal volume of 48deg media was added to bring the temperature to 37deg.  Both strains were allowed to grow at 37deg and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.
Lot batch = Slide4-35

source_name: SRY4-1a (prp4-1) @ 37 deg for 30 mins


title: alpha factor release sample026

status: Public on Feb 12 2002

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
ScanAlyze version 2.03 scanning software was used.
Keywords = Cell-cycle
Keywords = Alpha factor block-release
Lot batch = y744n52

source_name: asynchrnous control (prep3)


title: C1-40

source_name: 40' normal growth


title: CLB2 induction 40minutes (possible against CLB5 0min)

description:
This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators
ScanAlyze version unknown scanning software was used.
Keywords = Cell-cycle
Keywords = Cell-cycle factors
Lot batch = y80n8a

source_name: CLB2 40 min


title: R2-70

source_name: 10' exposure to 0.3 ug/ml MMC followed by 70' growth


title: CGH_Albertson_T47D

type: genomic

city: San Francisco

first: Donna

middle: G

last: Albertson

department: Comprehensive Cancer Center

institute: University of California San Francisco

description: Breast ductal carcinoma cell line derived from a pleural effusion in a 54 year old female.

molecule: genomic DNA

source_name: Cell line T47D

source_name: normal male reference genomic DNA


title: alpha factor release sample024

description:
ScanAlyze version 2.03 scanning software was used.
Keywords = Cell-cycle
Keywords = Alpha factor block-release
Lot batch = y744n73

source_name: asynchronous

source_name: control


title: C1-0


title: DBY7286 37degree heat - 20 min

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y11-84

source_name: time = 0 min (at 30 degrees)

source_name: time = 20 min (at 37 degrees)


title: CF-1 transgenic 5mo ovary B (granulosa cell tumor)

description: Transgenic (LHCTP), granulosa cell tumor sample from ovary from 2 month old CF-1 mouse for use in gene expression profiling experiment on LH hypersecreting mice (LHCTP)

source_name: Transgenic (LHCTP) ovary from 5 month old CF-1 mouse (granulosa cell tumor)


title: FY3 pRZ-MSN4 - Msn4 overexpression

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y14-130

source_name: FY3 pRZ416 in galactose

source_name: FY3 pRZ-MSN4 in galactose


title: CGH_Albertson_SW837

description:
ATCC cell line CCL-235.
Adenocarcinoma of the rectum, grade IV, in a 53 year old.
The cells are negative for expression of CSAp (CSAp-) and colon antigen 3, negative. There is a C -> T mutation in codon 248 of the p53 gene resulting in an Arg -> Trp substitution.  The cells are positive for keratin by immunoperoxidase staining.

source_name: Cell line SW837


title: CGH_Albertson_HCT116

description:
ATCC cell line CCL-247.
Colorectal carcinoma in a male.
The cells are positive for keratin by immunoperoxidase staining. HCT 116 cells are positive for transforming growth factor beta 1 (TGF beta 1) and beta 2 (TGF beta 2) expression. This line has a mutation in codon 13 of the ras protooncogene, and can be used as a positive control for PCR assays of mutation in this codon.

source_name: Cell line HCT116


title: CGH_Albertson_MDA-MB-231

description:
ATCC cell line HTB-26.
Breast adenocarcinoma derived from pleural effusion in a 51 year old female.
The cell line is aneuploid female, with chromosome counts in the near-triploid range. Normal chromosomes N8 and N15 were absent. Eleven stable rearranged marker chromosomes are noted as well as unassignable chromosomes in addition to the majority of autosomes that are trisomic. Many of the marker chromosomes are identical to those shown in the karyotype reported by K.L. Satya-Prakash, et al.

source_name: Cell line MDA-MB-231


title: CGH_Albertson_MPE600

description: A breast carcinoma cell line.

source_name: Cell line MPE600


title: CGH_Albertson_HT29

description:
ATCC cell line HTB-38.
Colorectal adenocarcinoma in a 44 year old female.
Ultrastructural features include microvilli, microfilaments, large vacuolated mitochondria with dark granules, smooth and rough ER with free ribosomes, lipid droplets, few primary and many secondary lysosomes. No virus particles.
HT-29 cells express urokinase receptors, but do not have detectable plasminogen activator activity.  There is a G -> A mutation in codon 273 of the p53 gene resulting in an Arg -> His substitution.  The p53 antigen is overproduced. The cells are negative for CD4, but there is cell surface expression of galactose ceramide (a possible alternative receptor for HIV).  The line is positive for expression of c-myc, K-ras, H-ras, N-ras. Myb, sis and fos oncogenes.  N-myc oncogene expression was not detected.
The stemline chromosome number is hypertriploid with the 2S component occurring at 2.4%.  Seventeen marker chromosomes are found in most metaphases, generally in single copy per chromosome. The marker designations are: M1p-(=t(3p-;?) with a deleted short arm), t(7q;?), t(10q;?), i(13q), 19q+a; M6, ?t(8q;9q-), ?Xp, M9, 6q+, t(13;?)a, t(13;?)b, 19q+b, M14, M15, 15p+, and Xq-. Chromosome 13 is nullisomic and chromosomes 8 and 14 are generally monosomic. No Y chromosome was detected by QM band analysis.

source_name: Cell line HT29


title: CGH_Albertson_MDA-MB-453

description:
ATCC cell line HTB-131.
Breast adenocarcinoma derived from pleural effusion in a 48 year old female.
DA-MB-453 was derived in 1976 by R. Cailleau  et al. from an effusion of a 48 year old female patient with metastatic carcinoma of the breast, involving the nodes, brain and both pleural and pericardial cavities.
The cells overexpress FGF receptors.

source_name: Cell line MDA-MB-453


title: CGH_Albertson_S1514-010328

description: A breast carcinoma cell line.

source_name: Cell line S1514


title: CGH_Albertson_S0034-010405

description: A breast carcinoma cell line.

source_name: Cell line S0034


title: DBYmsn2-4- 37degree heat - 20 min

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y12-85


title: DBY msn2msn4 0.32 mM H2O2 - 20 min

description:
DBY msn2msn4 0.32 mM H2O2 - 20 min
ScanAlyze version 2.44 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y16-52

source_name: DBY msn2msn4 time = 0 min

source_name: DBY msn2msn4 0.32 mM H2O2 - 20 min


title: Heat Shock 000 minutes

description:
ScanAlyze version 2.24 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y12n109

source_name: Reference Pool

source_name: Heat Shock 000 minutes


title: Heat Shock 000 minutes (series 2)

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y13n021


title: DBYyap1 + 37degree heat (repeat)

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y15-119

source_name: 30 degrees

source_name: 37 degrees - 20 minutes


title: FY3 pRZ-MSN2 - Msn2 overexpression

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y14-129

source_name: FY3 pRZ-MSN2 in galactose


title: DBYmsn2msn4 (good strain) + 0.32 mM H2O2

description:
This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators
ScanAlyze version unknown scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y15-128

source_name: time = 0 min

source_name: time = 20 min


title: parent vs evolved 1

description:
ScanAlyze version 2.44 scanning software was used.
Keywords = Chemostat
Keywords = Evolution
Lot batch = p1ae1a36


title: SWI4 deletion unsynchronized cells in YPD (regrid)

description:
SWI4 deletion unsynchronized cells in YPD
ScanAlyze Pro scanning software was used.
Keywords = Transcription
Keywords = Cell-cycle factors
Lot batch = f49swi4b

source_name: swi4 deletion (YK73)

source_name: WT (YK74)


title: parent vs evolved 2

description:
ScanAlyze version 2.44 scanning software was used.
Keywords = Chemostat
Keywords = Evolution
Lot batch = p1be2b21


title: evolved1 vs evolved 1

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = Chemostat
Keywords = Evolution
Lot batch = e1ae1b37


title: DBYyap1 0.32 mM H2O2 - 20 min

description:
DBYyap1 0.32 mM H2O2 - 20 min
ScanAlyze version 2.44 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y16-51

source_name: DBY yap1 time = 0 min

source_name: DBYyap1 0.32 mM H2O2 - 20 min


title: parent vs evolved 3

description:
ScanAlyze version 2.33 scanning software was used.
Keywords = Chemostat
Keywords = Evolution
Lot batch = p1de3a.1.38


title: constant 0.32 mM H2O2 (40 min) rescan

description:
ScanAlyze version unknown scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y80-813

source_name: time = 40 min


title: DBY msn2msn4 37C - 20 min

description:
DBY msn2msn4 37C - 20 min
ScanAlyze version 2.44 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y16-53

source_name: DBY msn2msn4 30C

source_name: DBY msn2msn4 37C - 20 min


title: swi1 rich medium experiment 1

description:
swi1, YPD (a) FY2 vs. YPS1
ScanAlyze version unknown scanning software was used.
Keywords = Transcription
Keywords = swi_snf
Lot batch = swi1a

source_name: swi1 deletion (YPS1)

source_name: Wild-type (FY2)


title: Small Pre-BII cells 9b

status: Public on Dec 17 2001

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

country: Germany

institute: Institute for medical microbiology

description: B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 9

source_name: Small Pre-BII cells


title: heat shock 37 to 37, 30 minutes

description:
ScanAlyze version 2.44 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y13n001


title: MBP1 3xMYC IP with anti-MYC, unsynchronized cells (#A37)

description:
ScanAlyze Pro scanning software was used.
Keywords = Chromatin IP
Keywords = Cell-cycle factors
Lot batch = i101mbp1

source_name: MBP1 3xMYC


title: snf2 rich medium experiment 1

description:
snf2, YPD (a) FY2 vs. FY31
ScanAlyze version unknown scanning software was used.
Keywords = Transcription
Keywords = swi_snf
Lot batch = swi2a

source_name: snf2 deletion (FY31)


title: yap59

description:
This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators
ScanAlyze version unknown scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = yap59

source_name: wt

source_name: YAP1 overexpression


title: 1M sorbitol vs. YPD - basal

description:
Hypo-osmotic shock
ScanAlyze version 2.44 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y16-108

source_name: cells in YPD

source_name: cells adapted to 1M sorbitol


title: SWI4 (with or without 3xHA) IP with anti-HA, unsynchronized cells

description:
First Swi4 IP experiment
ScanAlyze Pro scanning software was used.
Keywords = Chromatin IP
Keywords = Cell-cycle factors
Lot batch = i39swi4

source_name: SWI4 3xHA


title: Small Pre-BII cells 9


title: Small Pre-BII cells 1

description: B220+CD25+sIg- Small Pre BII cells sorted out of mouse bone marrow, sort no. 1


title: CGH_Albertson_COLO320

description:
ATCC cell line CCL-220.
Colorectal carcinoma (Dukes' type C) in a 55 year old female.
The line is negative for CEA, CSAp and colon antigen 3.  The cells are weakly positive for keratins and vimentin.

source_name: Cell line COLO320

source_name: normal male reference genomic DNA


title: Mature B cells 8b

description: B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 8

source_name: Mature B cells


title: MBP1 3xMYC IP with anti-MYC, unsynchronized cells (#A35)

description:
ScanAlyze Pro scanning software was used.
Keywords = Chromatin IP
Keywords = Cell-cycle factors
Lot batch = i97mbp1


title: Mature B cells 3b

description: B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 3


title: DBYyap1- 37degree heat - 20 min (redo)

description:
ScanAlyze version 2.05 scanning software was used.
Keywords = starvation
Keywords = YPD-stationary-phase
Lot batch = y11-85

source_name: time = 0 min (at 30 degrees)

source_name: time = 20 min (at 37 degrees)


title: SAGE_SciencePark_MCF7_control_3h

status: Public on Nov 28 2001

city: Smithville

first: C

middle: Marcelo

last: Aldaz

state: TX

department: Science Park Research Division, Carcinogenesis

institute: M.D. Anderson Cancer Center

description:
MCF7 cells were grown in conditions devoid of estrogen for 48h - (IMEM media supplemented w/ 10% Charcoal Stripped Serum) at time 0h cells were treated with 10-8 M estradiol (E2) or vehicle - This SAGE library represents the 3h time-point of vehicle treatment
Sex: Female
Organ: Breast
Cell_type: epithelial
Cell_line: MCF7
Lab host: Top10 bacteria
Vector: pZero
Vector type: plasmid
R. Site 1: NlaIII
R. Site 2: BsmF1 as tagging enzyme
Sequences generated to date: 235

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = carcinoma
Keywords = cell line
Keywords = EST

source_name: Breast Carcinoma - Pleaural effusion


title: Arabidopsis thaliana seedlings

status: Public on Dec 04 2001

description: 10-day-old Arabidopsis thaliana (Col) seedlings were germinated in petri plates on solid MSO medium.  Seedlings were grown under 16 hour days.  Total RNA was isolated using TRIzol reagent.  mRNA was isolated using oligo-dT beads.

source_name: Arabidopsis (Col)


title: Mature B cells 9

description: B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 9


title: Pre-BI cells 2b

description: B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 2

source_name: Pre-BI cells


title: SAGE_SciencePark_MCF7_estradiol_3h

description:
MCF7 cells were grown in conditions devoid of estrogen for 48h - (IMEM media supplemented w/ Charcoal Stripped Serum) at time 0h cells were treated with 10-8 M estradiol (E2) - This SAGE library represents the 3h time-point of E2 treatment
Sex: Female
Organ: Breast
Cell_type: epithelial
Cell_line: MCF7
Lab host: Top10 bacteria
Vector: pZero
Vector type: plasmid
R. Site 1: NlaIII
R. Site 2: BsmF1 as tagging enzyme
Sequences generated to date: 1838

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = carcinoma
Keywords = cell line
Keywords = estrogen
Keywords = EST


title: Immature B cells 2b

description: B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 2

source_name: Immature B cells


title: SAGE_SciencePark_MCF7_Control_0h

description:
Estrogen receptor positive MCF7 cells were grown in conditions devoid of estrogen for 48h (i.e. IMEM media supplemented with 10% Charcoal Stripped Serum). This SAGE library represents the 0h time point (i.e. baseline, untreated cells) of an estrogen exposure time course experiment.
Sex: Female
Organ: Breast
Cell_type: epithelial
Cell_line: MCF7
Lab host: Top10 bacteria
Vector: pZero
Vector type: plasmid
R. Site 1: NlaIII
R. Site 2: BsmF1 as tagging enzyme
Sequences generated to date: 3055

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = carcinoma
Keywords = cell line
Keywords = EST


title: Mature B cells 1

description: B220hi sIgM+ Mature B cells sorted out of mouse bone marrow, sort no. 1


title: Immature B cells 11b

description: B220Low sIgM+ immature B cells sorted out of mouse bone marrow, sort no. 11


title: NOD_T2

status: Public on Nov 21 2001

first: Iain

last: Eaves

address: Hills Road

department: Medical genetics

country: United Kingdom

institute: Cambridge Institute for Medical Research

description: RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

source_name: Thymus


title: SAGE_SKBR3

description:
ATCC cell line SK-BR-3. Human breast adenocarcinoma, malignant pleural effusion, estrogen receptor negative. 43 yo female treated with radiation, steroids, cytoxan, 5-fluorouracil.
Sex: Female
Organ: Breast
Cell_type: Epithelium
Cell_line: SK-BR-3
Library treatment: non-normalized
Tissue description: ATCC cell line SK-BR-3.  Human breast adenocarcinoma from a malignant pleural effusion.  Estrogen receptor negative.  Patient treated with ratiation, steroids cytoxan and 5-fluorouracil.
Tissue supplier: C. Marcelo Aldaz
Sample type: Cell line
Producer: Aldaz Laboratory
Clones generated to date: 0
Sequences generated to date: 122

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = adenocarcinoma
Keywords = SAGE
Keywords = cell line
Keywords = CGAP
Keywords = non-normalized
Keywords = SAGE library method
Keywords = cell line

source_name: Adenocarcinoma, malignant effusion


title: Pre-BI cells 1

status: Public on Dec 12 2001

description: B220+c-kit+ Pre BI cells sorted out of mouse bone marrow, sort no. 1

source_name: Pre BI cells


title: SAGE_SciencePark_MCF7_estradiol_10h

description:
MCF7 cells were grown in conditions devoid of estrogen for 48h - (IMEM media supplemented w/ 10% Charcoal Stripped Serum) at time 0h cells were treated with 10-8 M estradiol (E2) - This SAGE library represents the 10h time-point of E2 treatment
Sex: Female
Organ: Breast
Cell_type: epithelial
Cell_line: MCF7
Lab host: Top10 bacteria
Vector: pZero
Vector type: plasmid
R. Site 1: NlaIII
R. Site 2: BsmF1 as tagging enzyme
Sequences generated to date: 2324

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = carcinoma
Keywords = cell line
Keywords = estrogen
Keywords = EST


title: SAGE_HMEC-B41

description:
Cell culture HMEC-B41 of normal human mammary epithelial cells derived from normal mammoplasty specimen from 51 yo female
Sex: Female
Organ: Breast
Cell_type: Epithelium
Cell_line: HMEC-B41
Library treatment: non-normalized
Tissue description: cell culture HMEC-B41 of normal human mammary epithelial cells derived from normal mammoplasty specimen
Tissue supplier: C. Marcelo Aldaz
Sample type: Cell line
Producer: Aldaz Laboratory
Clones generated to date: 0
Sequences generated to date: 144

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = epithelium
Keywords = normal
Keywords = SAGE
Keywords = cell line
Keywords = CGAP
Keywords = non-normalized
Keywords = SAGE library method
Keywords = cell line

source_name: Normal epithelial cells


title: Idd3_T2

description: RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Idd3+5_T2

description: RNA was extracted from a pool of two thymi taken from four week old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 B10 Idd5 R8 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Large Pre-BII cells 1

description: B220+CD25+sIg- Large Pre BII cells sorted out of mouse bone marrow, sort no. 1

source_name: Large Pre-BII cells


title: SAGE_MDA453

description:
Cell line MDA-MB-453: Human breast carcinoma, malignant effusion. Estrogen receptor negative. From a 48 yo female on radiation and chemotherapy.
Sex: Female
Organ: Breast
Cell_type: Malignant effusion
Cell_line: MDA-MB-453
Library treatment: non-normalized
Tissue description: Cell line MDA-MB-453 of human breast carcinoma, malignant effusion, estrogen receptor negative, from patient treated with radiation and chemotherapy.
Tissue supplier: C. Marcelo Aldaz
Sample type: Cell line
Producer: Aldaz Laboratory
Clones generated to date: 0
Sequences generated to date: 543

This library represents a Cancer Genome Anatomy Project library, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Keywords = mammary gland
Keywords = adenocarcinoma
Keywords = SAGE
Keywords = cell line
Keywords = CGAP
Keywords = non-normalized
Keywords = SAGE library method
Keywords = cell line

source_name: Carcinoma


title: Idd3+5_T1

description: RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 B10 Idd5 R8 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Idd9_T2

description: RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B10 Idd9 R28 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: B10.H2g7 Idd3_T1

description: RNA was extracted from a pool of three thymi taken from four week old C57BL/10 derived B10.NOD H2g7 Idd3 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: B10.H2g7 Idd3_T2


title: B10.H2g7_T1

description: RNA was extracted from a pool of three thymi taken from four week old C57BL/10 derived B10.NOD H2g7 mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: B10.H2g7_T2


title: Idd9_T1


title: Idd3_T1


title: Idd5_T1

description: RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B10 Idd5 R444 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: NOD_S2

description: RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

source_name: Spleen


title: NOD_T1


title: Idd3+5_S2

description: RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 B10 Idd5 R8 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Idd5_S2

description: RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B10 Idd5 R444 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: B10.H2g7_S2

description: RNA was extracted from a pool of three spleens taken from three month old C57BL/10 derived B10.NOD H2g7 mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Idd9_S2

description: RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B10 Idd9 R28 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: B10.H2g7 Idd3_S2

description: RNA was extracted from a pool of two spleens taken from three month old C57BL/10 derived B10.NOD H2g7 Idd3 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Idd3_S2

description: RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: NOD_S1

description: RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix).  Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000).  Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution.  These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set.  The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977).  These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: Idd3_S1


title: Idd3+5_S1


title: Idd5_S1


title: Idd9_S1


title: M1b-25

description: To study the changes in gene expression after DNA damage in E. coli we used whole-genome gene arrays, containing all the annotated ORFs of E. coli. Bacterial cultures were grown to early- to mid-log phase and mitomycin C (MMC) was added to the growth media. Samples at several time points after induction of DNA damage were taken and total RNAs were purified from them. Radiolabeled probes were generated by reverse transcription of purified RNAs with a mixture of all the gene-specific oligonucleotides used as primers. Following purification, the probes were hybridized to gene arrays. In each experiment we compared the levels of expression of genes after the induction of DNA damage with their expression level before damage.

source_name: 25' growth in the presense of 0.3 ug/ml MMC


title: 7B-IME

status: Public on Nov 10 2001

city: Stanford University

first: Yangrae

last: Cho

address: 385 Serra Mall

department: Biological Sciences

institute: Stanford University

description: One of duplicate hybridizations.

organism: Zea mays

source_name: 4 day old shoot

source_name: Immature ear (2.5 cm)


title: B10.H2g7_S1


title: 6T-HUSKS

description: One of duplicate hybridizations.

source_name: Husks


title: 8T-8DR

description: One of duplicate hybridizations.

source_name: 8 day old root


title: B10.H2g7 Idd3_S1

description: RNA was extracted from a pool of three spleens taken from three month old C57BL/10 derived B10.NOD H2g7 Idd3 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.


title: 7T-SILKS

description: One of duplicate hybridizations.

source_name: Silks before emergence


title: 6B-EMB

description: One of duplicate hybridizations.

source_name: Embryo 2 weeks after pollination


title: 8B-2WR

description: One of duplicate hybridizations.

source_name: 2 week old root


title: 4B-2WLS

description: One of duplicate hybridizations.

source_name: 2 week old leaf sheath


title: 22T-IME

status: Public on Nov 09 2001

description: One of duplicate hybridizations.


title: 3B-2WLS

description: One of duplicate hybridizations.


title: 3T-8DLS

description: One of duplicate hybridizations.

source_name: 8 day old leaf sheath


title: 4T-8DLS

description: One of duplicate hybridizations.


title: 5B-2WR

description: One of duplicate hybridizations.


title: 26T-2WLB

description: One of duplicate hybridizations.

source_name: 2 week old leaf blades


title: 21b-SILKS

description: One of duplicate hybridizations.


title: 222B-HUSKS

description: One of duplicate hybridizations.


title: 27T-4DR

description: One of duplicate hybridizations.

source_name: 4 day old root


title: 21t-4DR

description: One of duplicate hybridizations.


title: 5T-8DR

description: One of duplicate hybridizations.


title: GPBMC_CD34-2

status: Public on Oct 11 2001

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:
Comparison of gene expression in CD34+ cells from bone marrow and G-CSF mobilized peripheral blood by high density oligonucleotide array analysis.
CD34 cells were isolated from granulocyte colony stimulating factor mobilized peripheral blood CD34 cells (GPBMC) by a combination of magnetic bead enrichment and flow cytometry. Total RNA from was isolated with Qiagen RNEasy columns, pooled with further samples and converted to biotin-labeled cRNA by standard Affymetrix protocols.
For analysis the sample was scaled to an arbitrary value of 1000 by overall hybridization intensity to allow comparison of multiple samples.
Chip hybridization parameters are:
Background Avg: 652.56, Stdev: 13.33, Max: 674.1, Min: 635.3
Corner+ Avg:776, Count:32
Corner- Avg:44820, Count:32
BF= SDT=164.3(4.00Q) SRT=1.50 ABS={{3.0,4.0},{0.33,0.43},{0.90,1.30}} RawQ=23.77 QMult=2.80 RL=10.0 HZ=4 VZ=4 BG=2 CT=164.3 PCT=80 DD={{3.0,4.0},{0.33,0.43},{0.20,0.30},{0.90,1.30}} AvgNCT=200 FCMin=1.00 FCMax=1.00 STP=3.0 TGT=1000 NF=1.000000 SF=1.728414 SFGene=All

source_name: normal G-CSF mobilized peripheral blood CD34+ cells (>95% purity)


title: 20t-8DLB

description: One of duplicate hybridizations.

source_name: 8 day old leaf blade


title: 222T-EMBRYO

description: One of duplicate hybridizations.

source_name: 2 week old embryo


title: 2WLB

description: One of duplicate hybridization.

source_name: 2 week old leaf blade


title: BM_CD34-1b

description:
Comparison of gene expression in CD34+ cells from bone marrow and G-CSF mobilized peripheral blood by high density oligonucleotide array analysis.
This sample represents a separate biotinylated cRNA preparation from the cells described in sample BM_CD34-1a (GSM575), hybridized to a different chip.
Sample hybridization parameters:
Background Avg: 469.14, Stdev: 13.94, Max: 490.4, Min: 449.5
Corner+ Avg:1378, Count:32
Corner- Avg:45744, Count:32
BF= SDT=94.5(4.00Q) SRT=1.50 ABS={{3.0,4.0},{0.33,0.43},{0.90,1.30}} RawQ=17.08 QMult=2.80 RL=10.0 HZ=4 VZ=4 BG=2 CT=94.5 PCT=80 DD={{3.0,4.0},{0.33,0.43},{0.20,0.30},{0.90,1.30}} AvgNCT=200 FCMin=1.00 FCMax=1.00 STP=3.0 TGT=1000 NF=1.000000 SF=1.383271 SFGene=All

source_name: bone marrow flow-sorted CD34+ cells (>95% purity)


title: BM_CD34-1a

description:
Comparison of Gene Expression in CD34+ Cells from Bone Marrow and G-CSF Mobilized Peripheral Blood by High Density Oligonucleotide Array Analysis.
CD34 cells were isolated from cadaveric bone marrow by a combination of magnetic bead enrichment and flow cytometry. Total RNA was isolated with Qiagen RNEasy columns and converted to biotin-labeled cRNA by standard Affymetrix protocols.
For analysis the sample was scaled to an arbitrary value of 1000 by overall hybridization intensity to allow comparison of multiple samples. Chip hybridization parameters are:
Background Avg: 814.15, Stdev: 44.34, Max: 914.9, Min: 751.4
Corner+ Avg:1137, Count:32
Corner- Avg:43332, Count:32
BF= SDT=79.5(4.00Q) SRT=1.50 ABS={{3.0,4.0},{0.33,0.43},{0.90,1.30}} RawQ=27.98 QMult=2.80 RL=10.0 HZ=4 VZ=4 BG=2 CT=79.5 PCT=80 DD={{3.0,4.0},{0.33,0.43},{0.20,0.30},{0.90,1.30}} AvgNCT=200 FCMin=1.00 FCMax=1.00 STP=3.0 TGT=1000 NF=1.000000 SF=0.710555 SFGene=All


title: BM_CD34-2

description:
Comparison of gene Eexpression in CD34+ cells from bone marrow and G-CSF mobilized peripheral blood by high density oligonucleotide array analysis.
CD34 cells were isolated from cadaveric bone marrow by a combination of magnetic bead enrichment and flow cytometry. Total RNA from was isolated with Qiagen RNEasy columns, pooled with further samples and converted to biotin-labeled cRNA by standard Affymetrix protocols.
For analysis the sample was scaled to an arbitrary value of 1000 by overall hybridization intensity to allow comparison of multiple samples.
Chip hybridization parameters are:
Background Avg: 600.59, Stdev: 10.38, Max: 622.9, Min: 586.3
Corner+ Avg:753, Count:32
Corner- Avg:43627, Count:32
BF= SDT=139.2(4.00Q) SRT=1.50 ABS={{3.0,4.0},{0.33,0.43},{0.90,1.30}} RawQ=21.81 QMult=2.80 RL=10.0 HZ=4 VZ=4 BG=2 CT=139.2 PCT=80 DD={{3.0,4.0},{0.33,0.43},{0.20,0.30},{0.90,1.30}} AvgNCT=200 FCMin=1.00 FCMax=1.00 STP=3.0 TGT=1000 NF=1.000000 SF=1.595190 SFGene=All


title: 27B-8DLB

description: One of duplicate hybridizations.


title: trpEA2trpR2 vs. trpEA2, W3110 min +Trp 50ug/ml

status: Public on Jul 30 2001

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.24
Scanning parameters:
Lot batch = cy_dc2

source_name: trpEA2,W3110 min +Trp 50ug/ml, 30 ug total

source_name: trpEA2trpR2, W3110 min +Trp 50ug/ml, 30 ug total


title: GPBMC_CD34-1

description:
Comparison of gene expression in CD34+ cells from bone marrow and G-CSF mobilized peripheral blood by high density oligonucleotide array analysis.
CD34 cells were isolated from granulocyte colony stimulating factor mobilized peripheral blood CD34 cells (GPBMC) by a combination of magnetic bead enrichment and flow cytometry. Total RNA from was isolated with Qiagen RNEasy columns, pooled with further samples and converted to biotin-labeled cRNA by standard Affymetrix protocols.
For analysis the sample was scaled to an arbitrary value of 1000 by overall hybridization intensity to allow comparison of multiple samples.
Chip hybridization parameters are:
Background Avg: 699.85, Stdev: 29.11, Max: 749.0, Min: 651.9
Corner+ Avg:1805, Count:32
Corner- Avg:45324, Count:32
BF= SDT=127.3(4.00Q) SRT=1.50 ABS={{3.0,4.0},{0.33,0.43},{0.90,1.30}} RawQ=26.25 QMult=2.80 RL=10.0 HZ=4 VZ=4 BG=2 CT=127.3 PCT=80 DD={{3.0,4.0},{0.33,0.43},{0.20,0.30},{0.90,1.30}} AvgNCT=200 FCMin=1.00 FCMax=1.00 STP=3.0 TGT=1000 NF=1.000000 SF=1.212046 SFGene=All


title: Idd5_T2

description: RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B10 Idd5 R444 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

source_name: Thymus


title: 26B-AYLB

description: One of duplicate hybridizations.

source_name: 4 day old shoot

source_name: Adult young leaves


title: 22B-AYLB

description: One of duplicate hybridizations.


title: wt +trp vs. -trp, min+.2%glucose, W3110

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.21
Scanning parameters:
Lot batch = cy_ba

source_name: W3110 wt-trp, 30 ug total RNA

source_name: W3110 wt+trp, 30 ug total RNA


title: trpR2+50ug/ml Trp vs. wt+50ug/ml Trp

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.21
Scanning parameters:
Lot batch = cy_db

source_name: wt+50ug/ml Trp, 30 ug total RNA

source_name: trpR2+50ug/ml Trp, 30 ug total RNA


title: tnaA2trpR2 vs. tnaA2, W3110 min +Trp 50ug/ml

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.24
Scanning parameters:
Lot batch = cy_ba2

source_name: tnaA2,W3110 min +Trp 50ug/ml, 30 ug total

source_name: tnaA2trpR2, W3110 min +Trp 50ug/ml, 30 ug total


title: cy_b4

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
60' +50 ug/ml Trp vs. ref 0', minimal +.2%glu, W3100
Scanning Software: ScanAlyze
Software version: 2.44
Scanning parameters:
Lot batch = cy_b4

source_name: reference 0', min +.2% glu, 25 ug RNA

source_name: 60' + 50 ug/ml Trp in min +.2% glu, 25 ug RNA


title: 60' vs 0' in minimal medium +0.2% glu

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators
Scanning Software: unknown
Software version: unknown
Scanning parameters:
Lot batch = cya4

source_name: 60' in minimal medium +0.2% glu, 25 ug total RNA


title: trpR2 vs. wt, min+.2%glucose, W3110

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.21
Scanning parameters:
Lot batch = cy_ca

source_name: W3110 wt, min+.2%glucose, 30 ug RNA

source_name: W3110 trpR2,min+.2%glucose, 30 ug RNA


title: trpR2 +trp vs. -trp, min+.2%glucose, W3110

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.21
Scanning parameters:
Lot batch = cy_dc

source_name: W3110 trpR2 -trp, 30 ug total RNA

source_name: W3110 trpR2+trp, 30 ug total RNA


title: tnaA2trpA46PR9 vs. tnaA2, W3110 min

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.24
Scanning parameters:
Lot batch = cy_fe2

source_name: tnaA2,W3110 min,30 ug total

source_name: tnaA2trpA46PR9, W3110 min , 30 ug total


title: dnaC2 synchrony 30' after shift, print 7 array

description:
Category: DNA metabolism
Subcategory: Replication
Scanning Software: ScanAlyze
Software version: 2.44
Scanning parameters:
Lot batch = dnac30_2

source_name: dnaC2 90' at 42 deg, 2 ug gen DNA, pdN6 RT

source_name: dnaC2 30' at 30 deg, 2 ug gen DNA, pdN6 RT


title: 314 vs. Tigr/Astra ref trial 3

status: Public on Jul 25 2001

description:
Category: Genomic DNA
Subcategory: Strain Comparison
2ug T2 genomic DNA vs. 0.7 ug Astra genomic DNA +0.7 ug Tigr genomic DNA
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = hp4069

organism: Helicobacter pylori

source_name: 2ug 314 genomic DNA


title: Astra genomic DNA vs TIGR/Astra reference, trial 1

description:
Category: Genomic DNA
Subcategory: Strain Comparison
Astra genomic DNA vs TIGR/Astra reference, trail 1
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = hp4067

source_name: 2 ug Astra genomic DNA

source_name: 0.7 ug TIGR genomic DNA, 0.7 ug Astra genomic DNA


title: tnaA2,W3110 minimal +Trp 50ug/ml vs. dnaC genomic DNA

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.24
Scanning parameters:
Lot batch = a2_gmc

source_name: dnaC genomic DNA, Sau3A, 2 ug

source_name: tnaA2,W3110 minimal +Trp 50ug/ml, 25 ug total RNA


description:
Category: Genomic DNA
Subcategory: Strain Comparison
Astra genomic DNA vs TIGR/Astra reference, trial 2
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = hp4068


title: trpR2tnaA2,W3110 minimal +Trp 50ug/ml vs. dnaC genomic DNA

description:
Category: Amino Acid metabolism
Subcategory: Tryptophan
Scanning Software: ScanAlyze
Software version: 2.24
Scanning parameters:
Lot batch = b2_gmc

source_name: trpR2tnaA2,W3110 min +Trp 50ug/ml, 25 ug total RNA


title: fem3 #5 (red, channel 2) vs. fem1 #5 (green, channel 1)

status: Public on Jul 24 2001

description:
Category: germline
Subcategory: sperm/oocyte
Experimental details: fem-1(hc17) is a temperature sensitive loss-of-function mutation which, at 25 degrees Celsius, produces only oocytes and no sperm. Female soma and germline. fem-3(q23) is a temperature sensitive gain-of-function mutation which, at 25 degrees C, continually produces spermatids. Soma is female, germline is male. Both are fertile at 15 degrees. Growth conditions: Synchronized populations of worms were grown at 15C on15cm enriched peptone agar plates seed with E.Coli. Worms were purified by pouring over a Nytex filter. Total RNA was isolated using the glass bead extraction protocol. Poly(A)+ RNA was isolated using the Invitrogen FastTrack 2.0 kit.
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = rosetta_11433 (expt 1)

organism: Caenorhabditis elegans

source_name: fem1 #5 (green)

source_name: fem3 #5 (red)


title: Renal cell carcinoma: rccc-47, normal 2 (part 2 of 2)

status: Public on Jul 19 2001

city: Heidelberg

first: Wolfgang

last: Huber

address: Im Neuenheimer Feld 280

department: Molecular Genome Analysis

institute: German Cancer Research Center

description:
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626240 reuse=5 date=25-Oct-2000

source_name: normal kidney tissue (as reference)


title: circadian rhythm time at 36,24

status: Public on Jul 20 2001

description:
Category: Development
Subcategory: Rhythm
Scanning Software: ScanAlyze
Software version: 2.44
Scanning parameters:
Keywords = circadian rhythm
Lot batch = R42

source_name: time at 36 hours

source_name: time at 24 hours


title: Circadian 48,60

description:
Category: Development
Subcategory: Rhythm
plants grown 12 hours light/12 hours dark then put in continuous light. Harvested 24 hours and 36 hours after put into cont light. (ZT=48,60)
Scanning Software: ScanAlyze
Software version: 2.44
Scanning parameters:
Keywords = circadian rhythm
Lot batch = R20

source_name: time at 48 hours

source_name: time at 60 hours


title: Renal cell carcinoma: rccc-47, tumor 1 (part 1 of 2)

description:
clinical.stage=IV
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=8
died=TRUE
tumorsize.cm=5
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625211 reuse=4 date=22-Aug-2000

source_name: renal clear cell carcinoma (primary tumor)


title: fem-3(q23) (red, channel 2) vs. fem-1(hc17) (green, channel 1)

description:
Category: germline
Subcategory: sperm/oocyte
Experimental details: fem-1(hc17) is a temperature sensitive loss-of-function mutation which, at 25 degrees Celsius, produces only oocytes and no sperm. Female soma and germline. fem-3(q23) is a temperature sensitive gain-of-function mutation which, at 25 degrees C, continually produces spermatids. Soma is female, germline is male. Both are fertile at 15 degrees. Growth conditions: Synchronized populations of worms were grown at 15C on15cm enriched peptone agar plates seed with E.Coli. Worms were purified by pouring over a Nytex filter. Total RNA was isolated using the glass bead extraction protocol. Poly(A)+ RNA was isolated using the Invitrogen FastTrack 2.0 kit.
Scanning Software: GenePix
Software version: 2.0.1.15
Scanning parameters:
Lot batch = rosetta_10934 (expt 1)

source_name: fem-1(hc17) (green)


title: fem3 #4 (red, channel 2) vs. fem1 #4 (green, channel 1)

description:
Category: germline
Subcategory: sperm/oocyte
Experimental details: fem-1(hc17) is a temperature sensitive loss-of-function mutation which, at 25 degrees Celsius, produces only oocytes and no sperm. Female soma and germline. fem-3(q23) is a temperature sensitive gain-of-function mutation which, at 25 degrees C, continually produces spermatids. Soma is female, germline is male. Both are fertile at 15 degrees. Growth conditions: Synchronized populations of worms were grown at 15C on15cm enriched peptone agar plates seed with E.Coli. Worms were purified by pouring over a Nytex filter. Total RNA was isolated using the glass bead extraction protocol. Poly(A)+ RNA was isolated using the Invitrogen FastTrack 2.0 kit.
Scanning Software: GenePix
Software version: Pro
Scanning parameters:
Lot batch = rosetta_11432 (expt 1)

source_name: fem1 #4 (green)

source_name: fem3 #4 (red)


title: fem-3(q23) (red, channel 2) vs. fem-1(hc17) (green, channel 1)- repeat #1

description:
Category: germline
Subcategory: sperm/oocyte
Experimental details: fem-1(hc17) is a temperature sensitive loss-of-function mutation which, at 25 degrees Celsius, produces only oocytes and no sperm. Female soma and germline. fem-3(q23) is a temperature sensitive gain-of-function mutation which, at 25 degrees C, continually produces spermatids. Soma is female, germline is male. Both are fertile at 15 degrees. Growth conditions: Synchronized populations of worms were grown at 15C on15cm enriched peptone agar plates seed with E.Coli. Worms were purified by pouring over a Nytex filter. Total RNA was isolated using the glass bead extraction protocol. Poly(A)+ RNA was isolated using the Invitrogen FastTrack 2.0 kit.
Scanning Software: GenePix
Software version: 2.0.1.15
Scanning parameters:
Lot batch = rosetta_11431 (expt 1)


title: fem3 #1 (red, channel 2)  fem1 #1 (green, channel 1)

description:
Category: germline
Subcategory: sperm/oocyte
IMPORTANT: This experimental data has been reconstructed from files which contain a list of values proportional to the raw red and green background and intensity measurements for each gene. Since these values are not true signal and background values, the only valid data for this experiment are the RAT2N values (the normalized red-to-green ratio values).
Experimental details: fem-1(hc17) is a temperature sensitive loss-of-function mutation which, at 25 degrees Celsius, produces only oocytes and no sperm. Female soma and germline. fem-3(q23) is a temperature sensitive gain-of-function mutation which, at 25 degrees C, continually produces spermatids. Soma is female, germline is male. Both are fertile at 15 degrees.
Growth conditions: Synchronized populations of worms were grown at 15C on15cm enriched peptone agar plates seed with E.Coli. Worms were purified by pouring over a Nytex filter. Total RNA was isolated using the glass bead extraction protocol. Poly(A)+ RNA was isolated using the Invitrogen FastTrack 2.0 kit.
Scanning Software: ScanAlyze
Software version: 2.44
Scanning parameters:
Lot batch = rosetta_10932_RATIO (expt 1)

source_name: fem1 #1 (green)

source_name: fem3 #1 (red)


title: Renal cell carcinoma: rccc-46, normal 1 (part 2 of 2)

description:
sex=m
age=71
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626237 reuse=4 date=22-Aug-2000


title: Renal cell carcinoma: rccc-47, tumor 1 (part 2 of 2)

description:
clinical.stage=IV
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=8
died=TRUE
tumorsize.cm=5
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626240 reuse=4 date=22-Aug-2000


title: Renal cell carcinoma: rccc-45, tumor 2 (part 1 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=1
died=FALSE
tumorsize.cm=11
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625216 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-47, normal 1 (part 1 of 2)

description:
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625208 reuse=4 date=22-Aug-2000


title: circadian rhythm time at 24,36 dark

description:
Category: Development
Subcategory: Rhythm
Scanning Software: ScanAlyze
Software version: 2.44
Scanning parameters:
Keywords = circadian rhythm
Lot batch = R17

source_name: time at 24D hours

source_name: time at 36D hours


title: Renal cell carcinoma: rccc-46, tumor 1 (part 2 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=12
comment=hybround 4 was OK. In hybround 5, label incorporation was only 1% -> useless. In hybround 6, label incorporation for tumor was OK, for normal again 1% (probably degraded). poly-A RNA was used.
sex=m
age=71
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626238 reuse=4 date=22-Aug-2000


title: Renal cell carcinoma: rccc-46, tumor 1 (part 1 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=12
comment=hybround 4 was OK. In hybround 5, label incorporation was only 1% -> useless. In hybround 6, label incorporation for tumor was OK, for normal again 1% (probably degraded). poly-A RNA was used.
sex=m
age=71
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625207 reuse=4 date=22-Aug-2000


title: Renal cell carcinoma: rccc-47, tumor 2 (part 1 of 2)

description:
clinical.stage=IV
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=8
died=TRUE
tumorsize.cm=5
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625208 reuse=5 date=25-Oct-2000


title: Renal cell carcinoma: rccc-47, normal 2 (part 1 of 2)

description:
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625211 reuse=5 date=25-Oct-2000


title: Renal cell carcinoma: rccc-45, normal 2 (part 1 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625218 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-47, tumor 2 (part 2 of 2)

description:
clinical.stage=IV
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=8
died=TRUE
tumorsize.cm=5
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626239 reuse=5 date=25-Oct-2000


title: Renal cell carcinoma: rccc-47, normal 1 (part 2 of 2)

description:
sex=f
age=55
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626239 reuse=4 date=22-Aug-2000


title: Renal cell carcinoma: rccc-45, tumor 1 (part 1 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=1
died=FALSE
tumorsize.cm=11
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625218 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-45, tumor 2 (part 2 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=1
died=FALSE
tumorsize.cm=11
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626245 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-45, normal 2 (part 2 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626246 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-45, normal 1 (part 1 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625216 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-45, normal 1 (part 2 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626245 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-44, tumor 2 (part 1 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=3
died=FALSE
tumorsize.cm=8
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625209 reuse=7 date=10-Oct-2000


title: Renal cell carcinoma: rccc-44, normal 2 (part 2 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626202 reuse=5 date=10-Oct-2000


title: Renal cell carcinoma: rccc-44, normal 2 (part 1 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625210 reuse=7 date=10-Oct-2000


title: Renal cell carcinoma: rccc-43, tumor 1 (part 1 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=8.8
comment=tumor was diagnosed with papillary and chromophile parts
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625227 reuse=4 date=16-Aug-2000


title: Renal cell carcinoma: rccc-43, tumor 1 (part 2 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=8.8
comment=tumor was diagnosed with papillary and chromophile parts
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626244 reuse=4 date=16-Aug-2000


title: Renal cell carcinoma: rccc-43, normal 1 (part 1 of 2)

description:
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3624258 reuse=4 date=16-Aug-2000


title: Renal cell carcinoma: rccc-44, normal 1 (part 1 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625209 reuse=6 date=07-Aug-2000


title: Renal cell carcinoma: rccc-42, tumor 2 (part 2 of 2)

description:
clinical.stage=III
grade.of.malignancy=1
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=6
sex=f
age=68
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626247 reuse=5 date=18-Oct-2000


title: Renal cell carcinoma: rccc-43, normal 1 (part 2 of 2)

description:
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626243 reuse=4 date=16-Aug-2000


title: Renal cell carcinoma: rccc-44, tumor 2 (part 2 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=3
died=FALSE
tumorsize.cm=8
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626201 reuse=5 date=10-Oct-2000


title: Renal cell carcinoma: rccc-44, tumor 1 (part 2 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=3
died=FALSE
tumorsize.cm=8
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626202 reuse=4 date=07-Aug-2000


title: Renal cell carcinoma: rccc-43, tumor 2 (part 2 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=8.8
comment=tumor was diagnosed with papillary and chromophile parts
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626243 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-42, tumor 1 (part 1 of 2)

description:
clinical.stage=III
grade.of.malignancy=1
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=6
sex=f
age=68
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625220 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-43, normal 2 (part 2 of 2)

description:
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626244 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-44, normal 1 (part 2 of 2)

description:
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626201 reuse=4 date=07-Aug-2000


title: Renal cell carcinoma: rccc-42, normal 2 (part 1 of 2)

description:
sex=f
age=68
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625220 reuse=5 date=18-Oct-2000


title: Renal cell carcinoma: rccc-43, normal 2 (part 1 of 2)

description:
sex=m
age=62
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625227 reuse=5 date=23-Oct-2000


title: Renal cell carcinoma: rccc-42, normal 2 (part 2 of 2)

description:
sex=f
age=68
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626248 reuse=5 date=18-Oct-2000


title: Renal cell carcinoma: rccc-42, tumor 1 (part 2 of 2)

description:
clinical.stage=III
grade.of.malignancy=1
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=NA
died=NA
tumorsize.cm=6
sex=f
age=68
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626248 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-42, normal 1 (part 1 of 2)

description:
sex=f
age=68
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625219 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-41, normal 2 (part 1 of 2)

description:
sex=m
age=72
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_aug99 filter=3624223 reuse=7 date=18-Oct-2000


title: Renal cell carcinoma: rccc-41, tumor 2 (part 2 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=18
died=FALSE
tumorsize.cm=5
sex=m
age=72
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_aug99 filter=3624227 reuse=7 date=18-Oct-2000


title: Renal cell carcinoma: rccc-44, tumor 1 (part 1 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=3
died=FALSE
tumorsize.cm=8
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3625210 reuse=6 date=07-Aug-2000


title: Renal cell carcinoma: rccc-45, tumor 1 (part 2 of 2)

description:
clinical.stage=II
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=1
died=FALSE
tumorsize.cm=11
sex=f
age=70
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_nov99 filter=3626246 reuse=4 date=14-Aug-2000


title: Renal cell carcinoma: rccc-41, tumor 2 (part 1 of 2)

description:
clinical.stage=III
grade.of.malignancy=2
type=clearcell
tumor.site=kidney
multiplefoci=FALSE
survival.months=18
died=FALSE
tumorsize.cm=5
sex=m
age=72
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_aug99 filter=3624222 reuse=7 date=18-Oct-2000


title: Renal cell carcinoma: rccc-41, normal 2 (part 2 of 2)

description:
sex=m
age=72
RNA=total
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage3_aug99 filter=3624228 reuse=7 date=18-Oct-2000