title: MPI-082

description: Mature aggressive B-cell lymphoma

value: male

value: III

value: extranodal

value: alive

value: CRu

value: Test


title: MPI-091

status: Public on Jun 07 2006

type: RNA

city: Berlin

first: Michael

last: Hummel

address: Hindenburgdamm 30

department: Institute of Pathology

country: Germany

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

description: Mature aggressive B-cell lymphoma

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Frozen tissue

tag: Relapse

value: unk

tag: Age

tag: Sex

value: female

value: aggressive B-NHL.unclassifiable

value: present

value: absent

value: IG-MYC

tag: Lesions

tag: Radiotherapy

tag: RITUXIMAB

tag: Chemotherapy

value: mBL

value: unclassified

value: Training

value: no


title: MPI-079

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: I

value: CR

value: ALL-like


title: MPI-086

description: Mature aggressive B-cell lymphoma

value: male

value: MYC-negative

value: II

value: nodal + extranodal

value: alive

value: GCB


title: MPI-081

description: Mature aggressive B-cell lymphoma

value: present

value: IV

value: Test


title: MPI-234

description: Mature aggressive B-cell lymphoma

value: unk

value: female

value: DLBCL

value: absent

value: III

value: dead

value: CHOP-like

value: non-mBL


title: MPI-077

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: BL

value: IG-MYC

value: CR

value: ALL-like

value: mBL

value: Training

value: yes


title: MPI-078

description: Mature aggressive B-cell lymphoma

value: present

value: MYC-negative

value: II

value: nodal

value: alive

value: GCB

value: Test


title: MPI-085

description: Mature aggressive B-cell lymphoma

value: female

value: atypical BL

value: absent

value: IV


title: MPI-139

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: IG-MYC

value: III


title: MPI-071

description: Mature aggressive B-cell lymphoma

value: nodal + extranodal

value: dead

value: CR

value: ALL-like

value: mBL


title: MPI-090

description: Mature aggressive B-cell lymphoma

value: unk

value: DLBCL

value: present

value: Training


title: MPI-065

description: Mature aggressive B-cell lymphoma

value: female

value: MYC-negative

value: GCB


title: MPI-048

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: absent

value: II

value: alive

value: Test


title: MPI-033

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: BL

value: IG-MYC

value: yes


title: MPI-055

description: Mature aggressive B-cell lymphoma

value: I

value: nodal

value: CR

value: ALL-like

value: mBL


title: MPI-075

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: present

value: extranodal

value: CHOP-like

value: Training


title: MPI-044

description: Mature aggressive B-cell lymphoma

value: absent

value: III

value: nodal + extranodal

value: alive

value: CRu

value: GCB


title: MPI-054

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: atypical BL

value: IG-MYC

value: intermediate

value: Test


title: MPI-034

description: Mature aggressive B-cell lymphoma

value: unk

value: DLBCL

value: mBL

value: unclassified


title: MPI-080

description: Mature aggressive B-cell lymphoma

value: present

value: Training


title: MPI-028

description: Mature aggressive B-cell lymphoma

value: absent

value: non-IG-MYC

value: II

value: nodal

value: yes

value: CR

value: CHOP-like


title: MPI-027

description: Mature aggressive B-cell lymphoma

value: female

value: atypical BL

value: dead

value: GCB

value: no


title: MPI-032

description: Mature aggressive B-cell lymphoma

value: unk

value: IG-MYC

value: I

value: alive

value: ALL-like

value: Test


title: MPI-017

description: Mature aggressive B-cell lymphoma

value: male

value: BL

value: present

value: absent

value: IV

value: nodal + extranodal

value: mBL

value: Training


title: GV milrinone repl3

city: Basel

first: Mareike

last: Puschendorf

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: GV oocytes

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix and Expressionist

label: biotin

organism: Mus musculus

source_name: GV oocytes

label_protocol: 15 µg of biotinylated fragmented cRNA was hybridized to each chip

extract_protocol: RNA was extracted from oocytes using Absolutely RNA oprep Kit (Stratagene)

tag: GV oocytes from superovulated CF1 females, cultured in 2.5 ?M milrinone for 48h


title: GV milrinone repl2

description: GV oocytes


title: GV milrinone repl4

description: GV oocytes


title: GV milrinone repl1

description: GV oocytes


title: MPI-002

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: II

value: nodal


title: GV ctrl repl4

description: GV oocytes

tag: GV oocytes from superovulated CF1 females, untreated


title: GV ctrl repl2

description: GV oocytes


title: MPI-018

description: Mature aggressive B-cell lymphoma

value: no

value: DLBCL

value: dead

value: Progress

value: GCB


title: MPI-003

description: Mature aggressive B-cell lymphoma

value: female

value: IG-MYC

value: alive

value: Test


title: MPI-006

description: Mature aggressive B-cell lymphoma

value: present

value: absent

value: MYC-negative


title: GV ctrl repl1

description: GV oocytes


title: MPI-005

description: Mature aggressive B-cell lymphoma

value: male

value: mBL


title: MPI-016

description: Mature aggressive B-cell lymphoma

value: unk

value: atypical BL

value: Training


title: GV ctrl repl3

description: GV oocytes


title: LPS&PGE2- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 3)

status: Public on Jun 06 2006

city: Pasadena

first: Sangdun

last: Choi

state: CA

address: 1200 E. California Blvd

department: Biology

country: USA

institute: California Institute of Technology

description: Gene expression changes comparing LPS&PGE2- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells

scan_protocol: The arrays were scanned using Agilent Scanner G2505A (Agilent Technologies) with the scan resolution set to 10 micrometer and the laser intensity adjusted so that both the maximum red and green (Cy5 and Cy3) fluorescence intensity were around 20,000.

data_processing: The image files were extracted with background-subtraction (the Local background subtraction method) and dye-normalization (the Rank consistent filter and the LOWESS algorithm) using the Agilent G2566AA Extraction Software Version A.6.1.1.

label: Cyanine-3 (green)

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 10 micromolar prostaglandin E2 for 4h

label: Cyanine-5 (red)

source_name: RAW 264.7 cells cultured in media for 4h


title: LPS&PGE2- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 2)

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 10 micromolar prostaglandin E2 for 4h

tag: RAW 264.7 cells cultured in media for 4h


title: MPI-001

description: Mature aggressive B-cell lymphoma

value: no

value: II

value: nodal + extranodal

value: yes

value: ALL-like


title: LPS&PGE2- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 1)


title: UT 4h Raw 264.7 cells vs LPS&PGE2- 4h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 4h Raw 264.7 cells vs LPS&PGE2- 4h RAw 264.7 cells


title: UT 4h Raw 264.7 cells vs LPS&PGE2- 4h RAw 264.7 cells . (set 2)


title: LPS&ISO- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS&ISO- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 50 nM isoproterenol for 4h


title: 4.5.05 J1 TH1-TH2 7

city: Stanford

first: Justin

last: Odegaard

address: 269 Campus Dr

department: CCSR 3110

institute: Stanford University

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60989.gif; format: GIF

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

source_name: IFNg/LPS

tag: IFNg/LPS

source_name: E17.5 Ref RNA

tag: E17.5 Ref RNA


title: UT 4h Raw 264.7 cells vs LPS&PGE2- 4h RAw 264.7 cells . (set 1)


title: UT 4h Raw 264.7 cells vs LPS&ISO- 4h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 4h Raw 264.7 cells vs LPS&ISO- 4h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 50 nM isoproterenol for 4h


title: UT 4h Raw 264.7 cells vs LPS&ISO- 4h RAw 264.7 cells . (set 1)


title: 4.5.05 J1 TH1-TH2 6

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60988.gif; format: GIF


title: LPS&ISO- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 2)


title: LPS&ISO- 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 1)


title: UT 4h Raw 264.7 cells vs LPS&ISO- 4h RAw 264.7 cells . (set 2)


title: 4.5.05 J1 TH1-TH2 9

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60991.gif; format: GIF


title: 4.5.05 J1 TH1-TH2 5

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60987.gif; format: GIF


title: ISO 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing ISO 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 50 nM isoproterenol for 4h


title: 4.5.05 J1 TH1-TH2 4

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60986.gif; format: GIF


title: ISO 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 2)

tag: RAW 264.7 cells cultured in 50 nM isoproterenol for 4h


title: UT 4h Raw 264.7 cells vs PGE2 4h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing UT 4h Raw 264.7 cells vs PGE2 4h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 10 micromolar prostaglandin E2 for 4h


title: UT 4h Raw 264.7 cells vs PGE2 4h RAw 264.7 cells . (set 3)

tag: RAW 264.7 cells cultured in 10 micromolar prostaglandin E2 for 4h


title: UT 4h Raw 264.7 cells vs ISO 4h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 4h Raw 264.7 cells vs ISO 4h RAw 264.7 cells


title: PGE2 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing PGE2 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells


title: UT 4h Raw 264.7 cells vs PGE2 4h RAw 264.7 cells . (set 2)


title: PGE2 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 1)


title: PGE2 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 3)


title: UT 4h Raw 264.7 cells vs ISO 4h RAw 264.7 cells . (set 2)


title: UT 4h Raw 264.7 cells vs ISO 4h RAw 264.7 cells . (set 1)


title: ISO 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 1)


title: 4.5.05 J1 TH1-TH2 8

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60990.gif; format: GIF


title: 4.5.05 J1 TH1-TH2

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60982.gif; format: GIF

source_name: LG

tag: LG


title: 4.5.05 J1 TH1-TH2 2

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60984.gif; format: GIF


title: UT 4h Raw 264.7 cells vs LPS 4h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 4h Raw 264.7 cells vs LPS 4h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 4h


title: 4.5.05 J1 TH1-TH2 3

description:
Simple annotation: Stimulation, Interleukins
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60985.gif; format: GIF


title: LPS 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing LPS 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 4h


title: UT 2h Raw 264.7 cells vs LPS&PGE2- 2h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing UT 2h Raw 264.7 cells vs LPS&PGE2- 2h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in media for 2h

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 10 micromolar prostaglandin E2 for 2h


title: UT 2h Raw 264.7 cells vs LPS&PGE2- 2h RAw 264.7 cells . (set 3)

tag: RAW 264.7 cells cultured in media for 2h

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 10 micromolar prostaglandin E2 for 2h


title: UT 2h Raw 264.7 cells vs LPS&PGE2- 2h RAw 264.7 cells . (set 2)


title: UT 4h Raw 264.7 cells vs LPS 4h RAw 264.7 cells . (set 3)


title: LPS&PGE2- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS&PGE2- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells


title: LPS&ISO- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS&ISO- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 50 nM isoproterenol for 2h


title: LPS&PGE2- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 1)


title: LPS 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 3)


title: UT 4h Raw 264.7 cells vs LPS 4h RAw 264.7 cells . (set 1)


title: LPS 4h Raw 264.7 cells vs UT 4h RAw 264.7 cells . (set 2)


title: LPS&PGE2- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 2)


title: LPS&ISO- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 2)

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 50 nM isoproterenol for 2h


title: PGE2 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing PGE2 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 10 micromolar prostaglandin E2 for 2h


title: LPS&ISO- 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 1)


title: UT 2h Raw 264.7 cells vs PGE2 2h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 2h Raw 264.7 cells vs PGE2 2h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 10 micromolar prostaglandin E2 for 2h


title: ISO 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing ISO 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 50 nM isoproterenol for 2h


title: UT 2h Raw 264.7 cells vs LPS&ISO- 2h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 2h Raw 264.7 cells vs LPS&ISO- 2h RAw 264.7 cells


title: PGE2 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 3)


title: PGE2 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 2)


title: UT 2h Raw 264.7 cells vs LPS&ISO- 2h RAw 264.7 cells . (set 3)


title: UT 2h Raw 264.7 cells vs PGE2 2h RAw 264.7 cells . (set 1)


title: UT 2h Raw 264.7 cells vs ISO 2h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 2h Raw 264.7 cells vs ISO 2h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 50 nM isoproterenol for 2h


title: LPS 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing LPS 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 2h


title: UT 2h Raw 264.7 cells vs LPS 2h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 2h Raw 264.7 cells vs LPS 2h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 2h


title: UT 2h Raw 264.7 cells vs LPS&ISO- 2h RAw 264.7 cells . (set 1)


title: UT 2h Raw 264.7 cells vs PGE2 2h RAw 264.7 cells . (set 2)


title: UT 2h Raw 264.7 cells vs ISO 2h RAw 264.7 cells . (set 2)


title: UT 2h Raw 264.7 cells vs LPS 2h RAw 264.7 cells . (set 3)


title: UT 2h Raw 264.7 cells vs LPS 2h RAw 264.7 cells . (set 1)


title: ISO 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 1)


title: UT 1h Raw 264.7 cells vs LPS&PGE2- 1h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 1h Raw 264.7 cells vs LPS&PGE2- 1h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in media for 1h

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 10 micromolar prostaglandin E2 for 1h


title: LPS&PGE2- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing LPS&PGE2- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 10 micromolar prostaglandin E2 for 1h

tag: RAW 264.7 cells cultured in media for 1h


title: LPS 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 1)


title: LPS&ISO- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS&ISO- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 50 nM isoproterenol for 1h


title: LPS 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 3)


title: UT 1h Raw 264.7 cells vs LPS&PGE2- 1h RAw 264.7 cells . (set 1)


title: UT 2h Raw 264.7 cells vs ISO 2h RAw 264.7 cells . (set 1)


title: LPS&PGE2- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 3)


title: ISO 2h Raw 264.7 cells vs UT 2h RAw 264.7 cells . (set 3)


title: UT 1h Raw 264.7 cells vs LPS&ISO- 1h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 1h Raw 264.7 cells vs LPS&ISO- 1h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 50 nM isoproterenol for 1h


title: LPS&ISO- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 2)


title: UT 1h Raw 264.7 cells vs LPS&PGE2- 1h RAw 264.7 cells . (set 3)


title: LPS&PGE2- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 2)


title: LPS&ISO- 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 1)


title: UT 1h Raw 264.7 cells vs LPS&ISO- 1h RAw 264.7 cells . (set 1)


title: UT 1h Raw 264.7 cells vs LPS&ISO- 1h RAw 264.7 cells . (set 2)


title: PGE2 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing PGE2 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 10 micromolar prostaglandin E2 for 1h


title: UT 1h Raw 264.7 cells vs PGE2 1h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing UT 1h Raw 264.7 cells vs PGE2 1h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 10 micromolar prostaglandin E2 for 1h


title: UT 1h Raw 264.7 cells vs PGE2 1h RAw 264.7 cells . (set 2)


title: PGE2 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 1)


title: UT 1h Raw 264.7 cells vs ISO 1h RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 1h Raw 264.7 cells vs ISO 1h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 50 nM isoproterenol for 1h


title: ISO 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing ISO 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 50 nM isoproterenol for 1h


title: UT 1h Raw 264.7 cells vs ISO 1h RAw 264.7 cells . (set 3)


title: ISO 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 2)


title: UT 1h Raw 264.7 cells vs LPS 1h RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 1h Raw 264.7 cells vs LPS 1h RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 1h


title: LPS&IFG- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing LPS&IFG- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 5 nM interferon gamma for 004hr

source_name: RAW 264.7 cells cultured in media for 004hr


title: LPS 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 1)

description: Gene expression changes comparing LPS 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 1h


title: ISO 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 1)


title: UT 004hr Raw 264.7 cells vs LPS&IFG- 004hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 004hr Raw 264.7 cells vs LPS&IFG- 004hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in media for 004hr

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 5 nM interferon gamma for 004hr


title: LPS 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 2)


title: UT 1h Raw 264.7 cells vs ISO 1h RAw 264.7 cells . (set 1)


title: UT 004hr Raw 264.7 cells vs LPS&2MA- 004hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 004hr Raw 264.7 cells vs LPS&2MA- 004hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 004hr


title: LPS 1h Raw 264.7 cells vs UT 1h RAw 264.7 cells . (set 3)


title: UT 1h Raw 264.7 cells vs LPS 1h RAw 264.7 cells . (set 1)


title: LPS&2MA- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 1)

description: Gene expression changes comparing LPS&2MA- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 004hr


title: UT 1h Raw 264.7 cells vs LPS 1h RAw 264.7 cells . (set 2)


title: LPS&2MA- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 2)


title: UT 004hr Raw 264.7 cells vs LPS&2MA- 004hr RAw 264.7 cells . (set 1)


title: UT 004hr Raw 264.7 cells vs LPS&IFG- 004hr RAw 264.7 cells . (set 1)


title: UT 004hr Raw 264.7 cells vs LPS&2MA- 004hr RAw 264.7 cells . (set 3)


title: LPS&IFG- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 3)


title: UT 004hr Raw 264.7 cells vs LPS&IFG- 004hr RAw 264.7 cells . (set 2)


title: LPS&2MA- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 3)


title: LPS&IFG- 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 1)


title: 2MA 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing 2MA 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 500 micromolar 2-methyl-thio-ATP for 004hr


title: UT 004hr Raw 264.7 cells vs 2MA 004hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 004hr Raw 264.7 cells vs 2MA 004hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 500 micromolar 2-methyl-thio-ATP for 004hr


title: UT 004hr Raw 264.7 cells vs 2MA 004hr RAw 264.7 cells . (set 1)


title: 2MA 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 1)


title: UT 004hr Raw 264.7 cells vs IFG 004hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 004hr Raw 264.7 cells vs IFG 004hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 5 nM interferon gamma for 004hr


title: UT 004hr Raw 264.7 cells vs 2MA 004hr RAw 264.7 cells . (set 2)


title: IFG 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing IFG 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 5 nM interferon gamma for 004hr


title: 2MA 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 2)


title: LPS&IFG- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS&IFG- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 5 nM interferon gamma for 002hr

source_name: RAW 264.7 cells cultured in media for 002hr


title: UT 004hr Raw 264.7 cells vs LPS 004hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 004hr Raw 264.7 cells vs LPS 004hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 004hr


title: LPS 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 004hr


title: LPS&2MA- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 1)

description: Gene expression changes comparing LPS&2MA- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 002hr

tag: RAW 264.7 cells cultured in media for 002hr


title: UT 004hr Raw 264.7 cells vs LPS 004hr RAw 264.7 cells . (set 1)


title: UT 002hr Raw 264.7 cells vs LPS&2MA- 002hr RAw 264.7 cells . (set 1)

description: Gene expression changes comparing UT 002hr Raw 264.7 cells vs LPS&2MA- 002hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 002hr


title: IFG 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 3)


title: LPS&2MA- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 3)


title: UT 002hr Raw 264.7 cells vs LPS&IFG- 002hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing UT 002hr Raw 264.7 cells vs LPS&IFG- 002hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 5 nM interferon gamma for 002hr


title: LPS&2MA- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 2)


title: UT 004hr Raw 264.7 cells vs IFG 004hr RAw 264.7 cells . (set 2)


title: UT 002hr Raw 264.7 cells vs 2MA 002hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 002hr Raw 264.7 cells vs 2MA 002hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 500 micromolar 2-methyl-thio-ATP for 002hr


title: UT 004hr Raw 264.7 cells vs LPS 004hr RAw 264.7 cells . (set 2)


title: 2MA 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing 2MA 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 500 micromolar 2-methyl-thio-ATP for 002hr


title: LPS 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 1)


title: UT 002hr Raw 264.7 cells vs LPS&2MA- 002hr RAw 264.7 cells . (set 3)


title: UT 002hr Raw 264.7 cells vs LPS&2MA- 002hr RAw 264.7 cells . (set 2)


title: UT 002hr Raw 264.7 cells vs LPS&IFG- 002hr RAw 264.7 cells . (set 1)


title: LPS 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 2)


title: IFG 004hr Raw 264.7 cells vs UT 004hr RAw 264.7 cells . (set 1)


title: LPS&IFG- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 2)


title: UT 002hr Raw 264.7 cells vs LPS&IFG- 002hr RAw 264.7 cells . (set 3)


title: UT 004hr Raw 264.7 cells vs IFG 004hr RAw 264.7 cells . (set 1)


title: LPS&IFG- 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 1)


title: 2MA 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 2)


title: UT 002hr Raw 264.7 cells vs 2MA 002hr RAw 264.7 cells . (set 2)


title: UT 002hr Raw 264.7 cells vs 2MA 002hr RAw 264.7 cells . (set 1)


title: UT 002hr Raw 264.7 cells vs IFG 002hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 002hr Raw 264.7 cells vs IFG 002hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 5 nM interferon gamma for 002hr


title: 2MA 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 1)


title: LPS 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing LPS 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 002hr


title: UT 002hr Raw 264.7 cells vs IFG 002hr RAw 264.7 cells . (set 1)

tag: RAW 264.7 cells cultured in 5 nM interferon gamma for 002hr


title: UT 002hr Raw 264.7 cells vs IFG 002hr RAw 264.7 cells . (set 2)


title: IFG 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing IFG 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells


title: IFG 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 1)


title: UT 002hr Raw 264.7 cells vs LPS 002hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 002hr Raw 264.7 cells vs LPS 002hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 002hr


title: UT 001hr Raw 264.7 cells vs LPS&2MA- 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 001hr Raw 264.7 cells vs LPS&2MA- 001hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in media for 001hr

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 001hr


title: IFG 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 2)


title: LPS&2MA- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS&2MA- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 500 micromolar 2-methyl-thio-ATP for 001hr

tag: RAW 264.7 cells cultured in media for 001hr


title: LPS&IFG- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing LPS&IFG- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 5 nM interferon gamma for 001hr


title: UT 001hr Raw 264.7 cells vs LPS&IFG- 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 001hr Raw 264.7 cells vs LPS&IFG- 001hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 5 nM interferon gamma for 001hr


title: LPS&IFG- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 3)


title: LPS&2MA- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 2)


title: UT 001hr Raw 264.7 cells vs LPS&2MA- 001hr RAw 264.7 cells . (set 2)


title: LPS&2MA- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 1)


title: 2MA 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing 2MA 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 500 micromolar 2-methyl-thio-ATP for 001hr


title: 2MA 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 1)

tag: RAW 264.7 cells cultured in 500 micromolar 2-methyl-thio-ATP for 001hr


title: UT 002hr Raw 264.7 cells vs LPS 002hr RAw 264.7 cells . (set 2)


title: UT 001hr Raw 264.7 cells vs LPS&IFG- 001hr RAw 264.7 cells . (set 1)


title: UT 002hr Raw 264.7 cells vs LPS 002hr RAw 264.7 cells . (set 1)


title: LPS 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 1)


title: UT 001hr Raw 264.7 cells vs 2MA 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 001hr Raw 264.7 cells vs 2MA 001hr RAw 264.7 cells


title: LPS&IFG- 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 1)


title: UT 001hr Raw 264.7 cells vs LPS&IFG- 001hr RAw 264.7 cells . (set 2)


title: UT 001hr Raw 264.7 cells vs 2MA 001hr RAw 264.7 cells . (set 2)


title: 2MA 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 2)


title: LPS 002hr Raw 264.7 cells vs UT 002hr RAw 264.7 cells . (set 3)


title: UT 001hr Raw 264.7 cells vs LPS&2MA- 001hr RAw 264.7 cells . (set 1)


title: UT 001hr Raw 264.7 cells vs 2MA 001hr RAw 264.7 cells . (set 1)


title: UT 001hr Raw 264.7 cells vs IFG 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 001hr Raw 264.7 cells vs IFG 001hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 5 nM interferon gamma for 001hr


title: LPS 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing LPS 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells

source_name: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 001hr


title: UT 001hr Raw 264.7 cells vs LPS 001hr RAw 264.7 cells . (set 3)

description: Gene expression changes comparing UT 001hr Raw 264.7 cells vs LPS 001hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 100 ng/ml lipopolysaccharides and 100 pM lipid binding protein for 001hr


title: Oligo - L428 vs HUR #82 - mAdbID:46562

city: Gaithersburg

first: David

last: Petersen

state: MD

address: 8717 Grovemont Circle

institute: NCI

description: mAdb experiment ID: 46562

hyb_protocol: Oligo Hybridization Protocol Other: The microarrays were prehybridized in 40 ul of 5X SSC, 0.1% SDS and 1% BSA at 42C for 30 min. The prehybridization solution was removed and arrays were hybridized for 16 h at 42C in 5X SSC buffer containing Cy3/Cy5 labeled targets, 25% formamide, 0.1% SDS, 1 ug Cot-1 DNA and 1 ug polyA RNA. The arrays were washed at room temperature in 2x SSC, 0.1% SDS for 2 min, 1X SSC for 2 min, and 0.2X SSC for 2 min. The slides were dried by spinning at 650 r.p.m. for 3 min.

data_processing: Data were background corrected by subtracting the median background pixel intensity from the mean foreground intensity, because the median background subtraction makes the tiny dust particles less significant and the mean foreground is preferable to the median foreground for spots that lack signal in the center, called doughnuts. Signals < 100 were floored at 100. Spots flagged for poor quality were eliminated from the analysis and genes with missing data were eliminated.

label_protocol:
Cy5 Labeling Protocol
Label amount: 20 ug
Label method: indirect amino-allyl method
Other: The cDNA was synthesized and labeled by the indirect amino-allyl method using reagents and protocols supplied with the Strategene FairPlay(TM) Microarray Labeling Kit. For cDNA synthesis, Stratascript reagents (Stratagene) were used, and Cy5 fluorophore amino-allyl reagents were obtained from Amersham (Piscataway, NJ). For each synthesis, 20 ug of total RNA were used. Labeled cDNA targets were purified using the Minelute purification kits (Qiagen, Valencia, CA).

growth_protocol:
Cell line Growth Protocol
Other: MCF10A (benign mammary epithelial), LNCAP (prostate carcinoma), Jurkat (T-cell lymphoma), SUDHL6 (germinal center B-cell like diffuse large B-cell lymphoma), OCI-Ly6 (activated B-cell like diffuse rare B-cell lymphoma) and L428 (Hodgkin's lymphoma) were grown under standard conditions (Chen et al., 1996)

extract_protocol:
RNA Extraction Protocol
Other: RNA was isolated from the cells using TriReagent following the manufacturer's protocol (Molecular Research Center, Inc., Cincinnati, OH). The integrity of the RNA was confirmed by analysis with the Agilent 2100 Bioanalyzer (Palo Alto, CA) using the RNA6000LabChipkit.

tag: Cell line

tag: Disease state

value: Hodgkinüs lymphoma

source_name: Universal Human Reference RNA - cy3

label_protocol:
Cy3 Labeling Protocol
Label amount: 20 ug
Label method: indirect amino-allyl method
Other: The cDNA was synthesized and labeled by the indirect amino-allyl method using reagents and protocols supplied with the Strategene FairPlay(TM) Microarray Labeling Kit. For cDNA synthesis, Stratascript reagents (Stratagene) were used, and Cy3 fluorophore amino-allyl reagents were obtained from Amersham (Piscataway, NJ). For each synthesis, 20 ug of total RNA were used. Labeled cDNA targets were purified using the Minelute purification kits (Qiagen, Valencia, CA).

tag: Cell type

value: mixture of liver, testis, mammary gland, cervix, brain, skin, liposarcoma, macrophage, T-lymphoblast and B-lymphocyte


title: Oligo - L428 vs HUR #84 - mAdbID:46627

description: mAdb experiment ID: 46627


title: IFG 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 2)

description: Gene expression changes comparing IFG 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells

tag: RAW 264.7 cells cultured in 5 nM interferon gamma for 001hr


title: SCC-6 cells transfected with p63 siRNA

city: Nashville

first: Jennifer

last: Pietenpol

state: TN

address: 23rd Ave South at Pierce

department: Biochemistry

institute: Vanderbilt University Medical Center

description: Gene expression data on Affy HG133 Plus 2.0 from SCC-6 cells transfected with p63 siRNA

hyb_protocol: biotinylated cRNA (15µg) was fragmented and hybridized to the Affymetrix GeneChip U133 Plus 2.0.  Hybridized cRNAs were washed and detected via streptavidin coupled to phycoerythrin using the Affymetrix 450 Fluidics Station and recommended protocols.

scan_protocol: Results were visualized by laser scanner (Affymetrix GeneChip Scanner 3000).

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

molecule: polyA RNA

source_name: SCC-6 cells transfected with vector expressing p63 siRNA

label_protocol: 300 ng of mRNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

growth_protocol: Cells were grown in DMEM+10% FBS at 37C and harvested for mRNA after selection with Hygromycin

extract_protocol: mRNA isolation was performed as described in Flatt, P. M., Tang, L. J., Scatena, C. D., Szak, S. T., and Pietenpol, J. A. (2000) Mol Cell Biol 20, 4210-4223

treatment_protocol: Cells were transfected using Fugene 6 (Roche, Indianapolis, IN).  Cells were selected with hygromycin B 48 h after transfection and harvested for mRNA isolation.

tag: head and neck squamous cell carcinoma


description: Gene expression data on Affy HG133 Plus 2.0 from SCC-6 cells transfected with control vector


title: HaCaT cells transfected with p63 siRNA

description: Gene expression data on Affy HG133 Plus 2.0 from HaCaT cells transfected with p63 siRNA

source_name: HaCaT cells transfected with vector expressing p63 siRNA

tag: immortalized keratinocyte cells


title: UT 001hr Raw 264.7 cells vs IFG 001hr RAw 264.7 cells . (set 1)


description: Gene expression data on Affy HG133 Plus 2.0 from HaCaT cells transfected with control vector


title: UT 001hr Raw 264.7 cells vs LPS 001hr RAw 264.7 cells . (set 2)


title: Oligo - L428 vs HUR #83 - rev.fluor. - mAdbID:46563

description: mAdb experiment ID: 46563

source_name: L428 - cy3 (rev.fluor.)

source_name: Universal Human Reference RNA, cy5-r.fl.


description: Gene expression data on Affy HG133 Plus 2.0 from SCC-012 cells transfected with p63 siRNA

source_name: SCC-012 cells transfected with vector expressing p63 siRNA

growth_protocol: Cells were grown in RPMI+10% FBS at 37C and harvested for mRNA after selection with Hygromycin


title: Oligo - Jurkat vs HUR #72 - rev.fluor. - mAdbID:45834

description: mAdb experiment ID: 45834

source_name: Jurkat - cy3 (rev.fluor.)

value: Jurkat

value: T-cell lymphoma


title: LPS 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 2)


title: Oligo - L428 vs HUR #76 - ref.fluor. - mAdbID:45866

description: mAdb experiment ID: 45866


title: Oligo - OCILY vs HUR #77 - mAdbID:45926

description: mAdb experiment ID: 45926

source_name: OCI-Ly6 - cy5

value: activated B-cell like diffuse rare B-cell lymphoma


title: LPS 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 1)


title: IFG 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 1)


title: UT 001hr Raw 264.7 cells vs LPS 001hr RAw 264.7 cells . (set 1)


description: Gene expression data on Affy HG133 Plus 2.0 from SCC-012 cells transfected with control vector


title: IFG 001hr Raw 264.7 cells vs UT 001hr RAw 264.7 cells . (set 3)


title: UT 001hr Raw 264.7 cells vs IFG 001hr RAw 264.7 cells . (set 2)


title: Oligo - Jurkat vs HUR #73 - mAdbID:45835

description: mAdb experiment ID: 45835

source_name: Jurkat - cy5


title: Oligo - L428 vs HUR #75 - rev.fluor. - mAdbID:45864

description: mAdb experiment ID: 45864


title: Oligo - OCILY vs HUR #68 - rev.fluor. - mAdbID:45768

description: mAdb experiment ID: 45768

source_name: OCI-Ly6 - cy3 (rev.fluor.)


title: Oligo - LNCAP vs HUR #55 - rev. fluor. - mAdbID:45704

description: mAdb experiment ID: 45704

source_name: LNCAP - cy3 (rev.fluor.)

value: LNCAP

value: prostate carcinoma


title: Oligo - SUDHL vs HUR #64 - mAdbID:45710

description: mAdb experiment ID: 45710

source_name: SUDHL6 - cy3 (rev.fluor.)

value: germinal center B-cell like diffuse large B-cell lymphoma


title: Oligo - MCF10A vs HUR #52 - rev.fluor. - mAdbID:45701

description: mAdb experiment ID: 45701

source_name: MCF10A - cy3 (rev.fluor.)

value: benign mammary epithelial


title: Oligo - Jurkat vs HUR #71 - rev.fluor. - mAdbID:45678

description: mAdb experiment ID: 45678


title: Oligo - OCILY vs HUR #66 - mAdbID:45673

description: mAdb experiment ID: 45673


title: patient.ID VS64

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

description: patient.ID VS64

hyb_protocol: ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; after removal of bad quality spots and filtering for expression intensity, generalized log ratios from 17047 cDNA clones were given in the data table

source_name: synovial membrane

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 500ng Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dTTP, 0.4 mM dATP, 0.24 mM dCTP, 0.125mM Cy-3 dCTP. After hydrolysis of RNA in 0.2 M NaOH; Cy3- and Cy5-labeled probes were purified with Microcon YM-30 column.

extract_protocol: total RNA was extracted using Qiagen RNeasy Midi Kit reagents; 100 ng total RNA was amplified two-times based on T7 RNA Polymerase (cDNA Synthesis System,Roche and MEGAScript T7, Ambion)

tag: VNS

source_name: Universal human reference RNA (Stratagene), two rounds amplified

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 500ng Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dTTP, 0.4 mM dATP, 0.24 mM dCTP, 0.125mM Cy-5 dCTP . After hydrolysis of RNA in 0.2 M NaOH; Cy3- and Cy5-labeled probes were purified with Microcon YM-30 column.

extract_protocol: 2 µg total RNA was amplified two-times based on T7 RNA Polymerase (cDNA Synthesis System,Roche and MEGAScript T7, Ambion)

tag: common reference sample


title: Oligo - MCF10A vs HUR #51 - mAdbID:45700

description: mAdb experiment ID: 45700

source_name: MCF10A - cy5


title: Oligo - MCF10A vs HUR #49 - rev.fluor. - mAdbID:45655

description: mAdb experiment ID: 45655


title: Oligo - SUDHL vs HUR #61 - mAdbID:45669

description: mAdb experiment ID: 45669

source_name: SUDHL6 - cy5


title: Oligo - MCF10A vs HUR #48 - mAdbID:45654

description: mAdb experiment ID: 45654

source_name: Universal Human Reference RNA - cy3


title: patient.ID VS59

description: patient.ID VS59


title: Oligo - LNCAP vs HUR #53 - mAdbID:45658

description: mAdb experiment ID: 45658

source_name: LNCAP - cy5


title: patient.ID VS58

description: patient.ID VS58


title: Oligo - L428 vs HUR #74 - mAdbID:45863

description: mAdb experiment ID: 45863


title: Oligo - SUDHL vs HUR #63 - mAdbID:45709

description: mAdb experiment ID: 45709


title: Oligo - OCILY vs HUR #67 - rev.fluor. - mAdbID:45674

description: mAdb experiment ID: 45674


title: patient.ID VS62

description: patient.ID VS62


title: patient.ID VS63

description: patient.ID VS63


title: Oligo - L428 vs HUR #57 - mAdbID:45665

description: mAdb experiment ID: 45665


title: Oligo - Jurkat vs HUR #70 - mAdbID:45677

description: mAdb experiment ID: 45677


title: Oligo - LNCAP vs HUR #54 - rev.fluor. - mAdbID:45660

description: mAdb experiment ID: 45660


title: patient.ID VS61

description: patient.ID VS61


title: Oligo - SUDHL vs HUR #62 - rev.fluor. - mAdbID:45670

description: mAdb experiment ID: 45670


title: Oligo - L428 vs HUR #58 - rev.fluor. - mAdbID:45666

description: mAdb experiment ID: 45666


title: patient.ID VS57

description: patient.ID VS57


title: HaCaT RG cells transfected with p63 siRNA 2

description: Gene expression data on Affy HG133B from HaCaT RG cells transfected with p63 siRNA

hyb_protocol: biotinylated cRNA (15µg) was fragmented and hybridized to the Affymetrix GeneChip U133B.  Hybridized cRNAs were washed and detected via streptavidin coupled to phycoerythrin using the Affymetrix 450 Fluidics Station and recommended protocols.

source_name: HaCaT RG cells, a rapidly growing variant of HaCaT, transfected with vector expressing p63 siRNA


title: patient.ID VS54

description: patient.ID VS54


title: patient.ID RA16

description: patient.ID RA16

tag: RA


title: SCC-1 cells transfected with control vector 2

description: Gene expression data on Affy HG133B from SCC-1 cells transfected with control vector

source_name: SCC-1 head and neck squamous cell carcinoma cells transfected with control vector


title: patient.ID RA18

description: patient.ID RA18


title: patient.ID RA17

description: patient.ID RA17


title: SCC-1 cells transfected with p63 siRNA 2

description: Gene expression data on Affy HG133B from SCC-1 cells transfected with p63 siRNA

source_name: SCC-1 head and neck squamous cell carcinoma cells transfected with vector expressing p63 siRNA


title: Oligo - OCILY vs HUR #69 - mAdbID:45769

description: mAdb experiment ID: 45769


title: patient.ID RA12

description: patient.ID RA12


title: patient.ID RA14

description: patient.ID RA14


title: Oligo - LNCAP vs HUR #56 - mAdbID:45705

description: mAdb experiment ID: 45705


title: patient.ID RA11

description: patient.ID RA11


title: HaCaT RG cells transfected with control vector 2

description: Gene expression data on Affy HG133B from HaCaT RG cells transfected with control vector

source_name: HaCaT RG cells, a rapidly growing variant of HaCaT, transfected with control vector


title: patient.ID RA15

description: patient.ID RA15


title: patient.ID VS55

description: patient.ID VS55


title: Oregon R and 2B3 RIL 9 male D. melanogaster, biological rep4

city: Gainesville

first: Lauren

middle: M.

last: McIntyre

state: FL

department: Dept. of Molecular Genetics and Microbiology

institute: University of Florida

description: Oregon R and 2B3 RIL male D. melanogaster

data_processing: Imagene v6.0 was used to process image and all results from Imagene listed

organism: Drosophila melanogaster

tag: 20 pooled adult male individuals


title: patient.ID RA13

description: patient.ID RA13


title: Oregon R and 2B3 RIL 9 male D. melanogaster, biological rep2

source_name: Oregon R and 2B3 RIL male D. melanogaster


title: patient.ID RA10

description: patient.ID RA10


title: patient.ID VS56

description: patient.ID VS56


title: patient.ID RA09

description: patient.ID RA09


title: patient.ID RA08

description: patient.ID RA08


title: Oregon R and 2B3 RIL 9 female D. melanogaster, biological rep4

description: Oregon R and 2B3 RIL female D. melanogaster

tag: 20 pooled adult female individuals


title: Oregon R and 2B3 RIL 9 female D. melanogaster, biological rep2

source_name: Oregon R and 2B3 RIL female D. melanogaster


title: Oregon R and 2B3 RIL 9 male D. melanogaster, biological rep1


title: Oregon R and 2B3 RIL 9 female D. melanogaster, biological rep1


title: Oregon R and 2B3 RIL 78 male D. melanogaster, biological rep4


title: patient.ID VS60

description: patient.ID VS60


title: Oregon R and 2B3 RIL 78 male D. melanogaster, biological rep3


title: patient.ID RA07

description: patient.ID RA07


title: patient.ID RA05

description: patient.ID RA05


title: patient.ID OA34

description: patient.ID OA34

tag: OA


title: patient.ID RA04

description: patient.ID RA04


title: patient.ID RA01

description: patient.ID RA01


title: patient.ID RA03

description: patient.ID RA03


title: patient.ID OA35

description: patient.ID OA35


title: patient.ID OA36

description: patient.ID OA36


title: Oregon R and 2B3 RIL 78 female D. melanogaster, biological rep4


title: patient.ID RA02

description: patient.ID RA02


title: Oregon R and 2B3 RIL 78 male D. melanogaster, biological rep1


title: Oregon R and 2B3 RIL 70 male D. melanogaster, biological rep2


title: patient.ID OA33

description: patient.ID OA33


title: patient.ID OA32

description: patient.ID OA32


title: Oregon R and 2B3 RIL 70 male D. melanogaster, biological rep1


title: Oligo - L428 vs HUR #59 - rev. fluor. - mAdbID:45706

description: mAdb experiment ID: 45706

source_name: L428 - cy3 (rev.fluor.)

source_name: Universal Human Reference RNA, cy5-r.fl.


title: patient.ID RA06

description: patient.ID RA06


title: patient.ID OA37

description: patient.ID OA37


title: patient.ID OA31

description: patient.ID OA31


title: Oregon R and 2B3 RIL 70 male D. melanogaster, biological rep4


title: Oregon R and 2B3 RIL 78 female D. melanogaster, biological rep1


title: Oregon R and 2B3 RIL 78 female D. melanogaster, biological rep2


title: Oregon R and 2B3 RIL 70 female D. melanogaster, biological rep2


title: patient.ID OA29

description: patient.ID OA29


title: Oregon R and 2B3 RIL 78 female D. melanogaster, biological rep3


title: patient.ID OA27

description: patient.ID OA27


title: Oregon R and 2B3 RIL 70 female D. melanogaster, biological rep4


title: patient.ID OA28

description: patient.ID OA28


title: patient.ID OA30

description: patient.ID OA30


title: Oregon R and 2B3 RIL 70 female D. melanogaster, biological rep1


title: patient.ID OA22

description: patient.ID OA22


title: patient.ID OA21

description: patient.ID OA21


title: patient.ID OA26

description: patient.ID OA26


title: patient.ID OA25

description: patient.ID OA25


title: patient.ID OA23

description: patient.ID OA23


title: Oregon R and 2B3 RIL 38 male D. melanogaster, biological rep2


title: patient.ID OA24

description: patient.ID OA24


title: Oregon R and 2B3 RIL 15 female D. melanogaster, biological rep2


title: patient.ID OA20

description: patient.ID OA20


title: Oregon R and 2B3 RIL 38 male D. melanogaster, biological rep4


title: Oregon R and 2B3 RIL 38 female D. melanogaster, biological rep2


title: Oregon R and 2B3 RIL 15 female D. melanogaster, biological rep4


title: Oregon R and 2B3 RIL 38 female D. melanogaster, biological rep1


title: Oregon R and 2B3 RIL 12 male D. melanogaster, biological rep4


title: Oregon R and 2B3 RIL 12 male D. melanogaster, biological rep2


title: Oregon R and 2B3 RIL 38 male D. melanogaster, biological rep1


title: cDNA - L428 vs HUR #74 - mAdbID:46628

description: mAdb experiment ID: 46628

hyb_protocol: cDNA Hybridization Protocol Other: The microarrays were prehybridized in 40 ul of 5X SSC, 0.1% SDS and 1% BSA at 42C for 30 min. The prehybridization solution was removed and arrays were hybridized for 16 h at 42C in 5X SSC buffer containing Cy3/Cy5 labeled targets, 25% formamide, 0.1% SDS, 1 ug Cot-1 DNA and 1 ug polyA RNA. The arrays were washed at room temperature in 2x SSC, 0.1% SDS for 2 min, 1X SSC for 2 min, 0.2X SSC for 2 min and 0.05X SSC for 1 min. The slides were dried by spinning at 650 r.p.m. for 3 min.


title: cDNA - L428 vs HUR #75 - rev.fluor. - mAdbID:46625

description: mAdb experiment ID: 46625


title: cDNA - OCILY vs HUR #66 - mAdbID:45868

description: mAdb experiment ID: 45868

source_name: OCI-Ly6 - cy5


title: cDNA - L428 vs HUR #67 - rev.fluor. - mAdbID:45927

description: mAdb experiment ID: 45927


title: cDNA - Jurkat vs HUR #65 - rev.fluor. - mAdbID:45833

description: mAdb experiment ID: 45833

source_name: Jurkat - cy3 (rev.fluor.)


title: patient.ID OA19

description: patient.ID OA19


title: cDNA - L428 vs HUR #76 - rev.fluor. - mAdbID:46626

description: mAdb experiment ID: 46626


title: Oregon R and 2B3 RIL 38 female D. melanogaster, biological rep4


title: cDNA - Jurkat vs HUR #64 - mAdbID:45831

description: mAdb experiment ID: 45831

source_name: Jurkat - cy5


title: Oregon R and 2B3 RIL 15 male D. melanogaster, biological rep2


title: Oregon R and 2B3 RIL 12 female D. melanogaster, biological rep2


title: Oregon R and 2B3 RIL 12 female D. melanogaster, biological rep4


title: Oregon R and 2B3 RIL 78 male D. melanogaster, biological rep2


title: cDNA - OCILY vs HUR #61 - rev.fluor. - mAdbID:45772

description: mAdb experiment ID: 45772

source_name: OCI-Ly6 - cy3 (rev.fluor.)


title: cDNA - OCILY vs HUR #60 - mAdbID:45771

description: mAdb experiment ID: 45771


title: Oregon male D. melanogaster, biological rep2

description: Oregon male D. melanogaster

source_name: Oregon male D. melanogaster


title: Oregon R and 2B3 RIL 15 male D. melanogaster, biological rep4


title: cDNA - MCF10a vs HUR #31 - mAdbID:45764

description: mAdb experiment ID: 45764

source_name: MCF10A - cy5


title: cDNA - L428 vs HUR #57 - mAdbID:45770

description: mAdb experiment ID: 45770


title: cDNA - MCF10a vs HUR #32 - rev.fluor. - mAdbID:45765

description: mAdb experiment ID: 45765

source_name: MCF10A - cy3 (rev.fluor.)


title: cDNA - SUDHL vs HUR #55 - rev.fluor. - mAdbID:45707

description: mAdb experiment ID: 45707

source_name: SUDHL6 - cy3 (rev.fluor.)


title: cDNA - SUDHL vs HUR #56 - mAdbID:45708

description: mAdb experiment ID: 45708

source_name: SUDHL6 - cy5

source_name: Universal Human Reference RNA - cy3


title: Oregon female D. melanogaster, biological rep2

description: Oregon female D. melanogaster

source_name: Oregon female D. melanogaster


title: cDNA - LNCAP vs HUR #47 - rev.fluor. - mAdbID:45703

description: mAdb experiment ID: 45703

source_name: LNCAP - cy3 (rev.fluor.)


title: Oregon female D. melanogaster, biological rep3

description: Oregon female D. melanogaster


title: Oregon male D. melanogaster, biological rep1

description: Oregon male D. melanogaster


title: Oregon female D. melanogaster, biological rep4

description: Oregon female D. melanogaster


title: cDNA - LNCAP vs HUR #46 - mAdbID:45702

description: mAdb experiment ID: 45702

source_name: LNCAP - cy5


title: Oregon female D. melanogaster, biological rep1

description: Oregon female D. melanogaster


title: cDNA - Jurkat vs HUR #63 - rev.fluor. - mAdbID:45676

description: mAdb experiment ID: 45676


title: cDNA - SUDHL vs HUR #54 - rev.fluor. - mAdbID:45668

description: mAdb experiment ID: 45668


title: 2B3 male D. melanogaster, biological rep3

description: 2B3 male D. melanogaster

source_name: 2B3 male D. melanogaster


title: cDNA - OCILY vs HUR #59 - rev.fluor. - mAdbID:45672

description: mAdb experiment ID: 45672


title: cDNA - SUDHL vs HUR #53 - mAdbID:45667

description: mAdb experiment ID: 45667


title: cDNA - OCILY vs HUR #58 - mAdbID:45671

description: mAdb experiment ID: 45671


title: 2B3 female D. melanogaster, biological rep1

description: 2B3 female D. melanogaster

source_name: 2B3 female D. melanogaster


title: 2B3 male D. melanogaster, biological rep1

description: 2B3 male D. melanogaster


title: 2B3 female D. melanogaster, biological rep3

description: 2B3 female D. melanogaster


title: 2B3 female D. melanogaster, biological rep4

description: 2B3 female D. melanogaster


title: 2B3 male D. melanogaster, biological rep2

description: 2B3 male D. melanogaster


title: 2B3 female D. melanogaster, biological rep2

description: 2B3 female D. melanogaster


title: cDNA - LNCAP vs HUR #34 - rev.fluor. - mAdbID:45657

description: mAdb experiment ID: 45657


title: 2B3 male D. melanogaster, biological rep4

description: 2B3 male D. melanogaster


title: Oregon male D. melanogaster, biological rep3

description: Oregon male D. melanogaster


title: cDNA - L428 vs HUR #48 - mAdbID:45662

description: mAdb experiment ID: 45662


title: cDNA - LNCAP vs HUR #33 - mAdbID:45656

description: mAdb experiment ID: 45656


title: cDNA - L428 vs HUR #49 - rev.fluor. - mAdbID:45663

description: mAdb experiment ID: 45663

source_name: L428 - cy3 (rev.fluor.)


title: cDNA - MCF10A vs HUR #35 - mAdbID:45634

description: mAdb experiment ID: 45634


title: SCC-1 cells transfected with p63 siRNA 1

description: Gene expression data on Affy HG133A from SCC-1 cells transfected with p63 siRNA

hyb_protocol: biotinylated cRNA (15µg) was fragmented and hybridized to the Affymetrix GeneChip U133A.  Hybridized cRNAs were washed and detected via streptavidin coupled to phycoerythrin using the Affymetrix 450 Fluidics Station and recommended protocols.

source_name: SCC-1 head and neck squamous cell carcinoma cells transfected with vector expressing p63 siRNA


title: cDNA - MCF10A vs HUR #30 - rev.fluor. - mAdbID:45632

description: mAdb experiment ID: 45632

source_name: Universal Human Reference RNA, cy5-r.fl.


title: SCC-1 cells transfected with control vector 1

description: Gene expression data on Affy HG133A from SCC-1 cells transfected with control vector

source_name: SCC-1 head and neck squamous cell carcinoma cells transfected with control vector


title: cDNA - Jurkat vs HUR #62 - mAdbID:45675

description: mAdb experiment ID: 45675

source_name: Jurkat - cy5


title: Oregon male D. melanogaster, biological rep4

description: Oregon male D. melanogaster


title: HaCaT RG cells transfected with p63 siRNA 1

description: Gene expression data on Affy HG133A from HaCaT RG cells transfected with p63 siRNA

source_name: HaCaT RG cells, a rapidly growing variant of HaCaT, transfected with vector expressing p63 siRNA


title: HaCaT RG cells transfected with control vector 1

description: Gene expression data on Affy HG133A from HaCaT RG cells transfected with control vector

source_name: HaCaT RG cells, a rapidly growing variant of HaCaT, transfected with control vector


title: PCN, biological rep4b

status: Public on Jun 03 2006

city: Denver

first: Linda

middle: C

last: Quattrochi

state: CO

department: Medicine

institute: University of Colorado at Denver and Health Sciences

description: Gene expression data from adult rat liver; PCN (100 mg/kg); 8 h treatment

hyb_protocol: Following fragmentation, cRNA were hybridized at 45c for 16 h using a Affymetrix GeneChip Hybridization Oven 640

scan_protocol: Affymetrix GeneChip Scanner 3000

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

organism: Rattus norvegicus

source_name: Rattus, adult liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: RNeasy kit, DNase I treatment on column, following manufacturer's instructions

treatment_protocol: After an overnight fast, animal received a single intraperitoneal dose of PCN (100 mg/kg) and sacrificed 8 h later

tag: Sprague-Dawley, 150-200 g


title: PCN, biological rep5B


title: PCN, biological rep2b


title: PCN, biological rep3b


title: PCN, biological rep1b


title: corn oil control, biological rep4b

description: Gene expression data from adult rat liver; corn oil-control; 8 h treatment

treatment_protocol: After an overnight fast, animal received a single intraperitoneal dose of corn oil and sacrificed 8 h later.


title: corn oil control, biological rep5b

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

treatment_protocol: After an overnight fast, animal received a single intraperitoneal dose of corn oil and sacrificed 8 h later


title: PCN, biological rep5a


title: corn oil control, biological rep1b


title: Mouse F9 cells, EZH2 NG Min promoter, Replicate 2

type: genomic

city: Davis

first: Sharon

last: Squazzo

address: 4617 GBSF, 451 E. Health Sci. Dr.

department: Pharmacology

institute: UC Davis Genome Center

description: F9 cells

data_processing: log base 2 ratios

molecule: genomic DNA

source_name: F9 cells

tag: EZH2 antibody

tag: control total input


title: PCN, biological rep4a


title: PCN, biological rep3a


title: PCN, biological rep2a


title: PCN, biological rep1a


title: Mouse F9 cells, EZH2 NG Min promoter, Replicate 1

description: F9 cells


title: corn oil control, biological rep5a

treatment_protocol: After an overnight fast, animal received a single intraperitoneal dose of corn oil and sacrificed 8 h late.r


title: corn oil control, biological rep4a


title: Mouse F9 cells, H3me3K27 NG Min promoter, Replicate 2

description: F9 cells

tag: H3me3K27 antibody


title: Mouse mES cells, H3me3K27 NG Min promoter

description: mES cells

source_name: mES cells


title: corn oil control, biological rep2a


title: corn oil control, biological rep1a

extract_protocol: RNeasy kit, DNase I treatment on column, following manufacturer's instructions.


title: Human Ntera2 cells, RNAPII Replicate 2

description: Human Ntera2 cells

source_name: Ntera2 cells

tag: RNAPII antibody


title: Mouse F9 cells, EED1 NG Min promoter

description: F9 cells

tag: EED1 antibody


title: corn oil control, biological rep3a


title: 40oC 15min vs 29oC - 3000030749R

status: Public on Jun 01 2006

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)]

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked? in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization

organism: Xylella fastidiosa

label_protocol: 20ug of total RNA was reverse transcribed and labeled using CyScribe Post-labelling kit (GE Healthcare). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

growth_protocol: Xylella fastidiosa strain 9a5c isolated form CVC symptomatic Citrus (L.) Osbeck trees were grown in Periwinkle wilt (PW) broth media at 29oC with 100 rpm rotatory agitation in the dark. A culture started from a single colony was weekly passaged through serial transfers at a 1/10 dilution in PW medium.

extract_protocol: Total RNA was isolated with phenol-chloroform (Ausubel , 1995) and residual DNA was removed by treatment with 10U of RQ1 RNAse-free DNAse I (Promega) and 40U RNAse inhibitor RNAsin (Promega). The integrity of the RNA was checked by agarose gel electrophoresis and the lack of residual DNA was checked by PCR.

source_name: 40oC 15min (cy5)

treatment_protocol: Heat shock at 40oC was applied to 7 days old cultures, using a water bath incubator with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 15 minutes and immediately harvested for RNA extraction.

tag: 40oC 15min (cy5)


title: Mouse F9 cells, Suz12 NG Min promoter, Replicate 2

description: F9 cells

tag: Suz12 antibody


title: 40oC 15min vs 29oC - 3000030749L


title: Human Ntera2 cells, Oct4 Replicate 2

description: Human Ntera2 cells

tag: Oct4 antibody


title: 40oC 15min vs 29oC - 3000030746R

source_name: 40oC 15min (cy3)

tag: 40oC 15min (cy3)


title: Mouse F9 cells, H3meK9 NG Min promoter

description: F9 cells

tag: H3meK9 antibody


title: 40oC 15min vs 29oC - 3000030746L


title: Mouse mES cells, Suz12 NG Min promoter

description: mES cells


title: Human Ntera2 cells, RNAPII Replicate 1

description: Human Ntera2 cells


title: 40oC 15min vs 29oC - 3000030724L


title: Human Ntera2 cells, Oct4 Replicate 1

description: Human Ntera2 cells


title: 40oC 15min vs 29oC - 3000030724R


title: Mouse F9 cells, H3me3K27 NG Min promoter, Replicate 1

description: F9 cells


title: 40oC 15min vs 29oC - 3000030715R


title: Mouse F9 H3meK27

description: Mouse F9 cells


title: Human MCF7 Suz12 cells

description: Human MCF7

source_name: MCF7 cells


title: Mouse mES cells, H3me3K9 NG Min promoter

description: mES cells

tag: H3me3K9 antibody


title: Mouse mES cells, RNAPII NG Min promoter

description: mES cells


title: 40oC 15min vs 29oC - 3000030715L


title: 40oC 15min vs 29oC - 2000097956R


title: 40oC 07min vs 29oC - 3000030720R

source_name: 40oC 07min (cy3)

treatment_protocol: Heat shock at 40oC was applied to 7 days old cultures, using a water bath incubator with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 07 minutes and immediately harvested for RNA extraction.

tag: 40oC 07min (cy3)


title: 40oC 07min vs 29oC - 3000030720L


title: 40oC 15min vs 29oC - 2000097956L


title: 40oC 07min vs 29oC - 3000030714R


title: Mouse F9 Suz12, replicate 1

description: Mouse F9 cells


title: 40oC 45min vs 29oC - 3000030717R

source_name: 40oC 45min (cy3)

treatment_protocol: Heat shock at 40oC was applied to 7 days old cultures, using a water bath incubator with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 45 minutes and immediately harvested for RNA extraction.

tag: 40oC 45min (cy3)


title: 40oC 45min vs 29oC - 3000030721R

source_name: 40oC 45min (cy5)

tag: 40oC 45min (cy5)


title: 40oC 45min vs 29oC - 3000030722L


title: Mouse F9 cells, RNAPII NG Min promoter

description: F9 cells


title: 40oC 45min vs 29oC - 2000097958L


title: 40oC 45min vs 29oC - 2000097958R


title: Mouse F9 Suz12, replicate 2

description: Mouse F9 cells


title: 40oC 45min vs 29oC - 3000030721L


title: 40oC 07min vs 29oC - 3000030714L


title: Mouse mES cells, EED1 NG Min promoter

description: mES cells


title: Human SW480 Suz12 cells

description: Human SW480

source_name: SW480 cells


title: 40oC 07min vs 29oC - 3000030723R

source_name: 40oC 07min (cy5)

tag: 40oC 07min (cy5)


title: 40oC 07min vs 29oC - 3000030748R


title: Mouse F9 cells, Suz12 NG Min promoter, Replicate 1

description: F9 cells


title: 40oC 07min vs 29oC - 3000030719R


title: Human Ntera Suz12 cells

description: Human Ntera cells

source_name: Ntera cells


title: 40oC 07min vs 29oC - 2000097955L


title: 40oC 07min vs 29oC - 3000030748L


title: 40oC 07min vs 29oC - 2000097955R


title: 40oC 45min vs 29oC - 3000030722R


title: 40oC 25min vs 29oC - 3000030716R

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and  in 0.1xSSC for 1 min. The slides were shrinked? in water for 10s and dried with nitrogen gas.

source_name: 40oC 25min (cy3)

label_protocol: 20ug of total RNA was reverse transcribed and labeled using CyScribe Post-labelling kit (GE Healthcare). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4  washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

extract_protocol: Total RNA was isolated with phenol-chloroform (Ausubel , ??) and residual DNA was removed  by treatment with 10U of RQ1 RNAse-free DNAse I (Promega) and 40U RNAse inhibitor RNAsin (Promega). The integrity of the RNA was checked by agarose gel electrophoresis and the lack of residual DNA was checked by PCR.

treatment_protocol: Heat shock at 40oC was applied to 7 days old cultures, using a water bath incubator with rotatory agitation of 150 rpm. 50ml aliquots of cell cultures were taken at time point 25 minutes and immediately harvested for RNA extraction.

tag: 40oC 25min (cy3)


title: 40oC 25min vs 29oC - 2000097954R


title: Mouse F9 EZH2

description: Mouse F9 cells


title: 40oC 25min vs 29oC - 2000097957L

source_name: 45oC 25min (cy5)

tag: 45oC 25min (cy5)


title: 40oC 07min vs 29oC - 3000030719L


title: 40oC 25min vs 29oC - 3000030750R


title: 40oC 25min vs 29oC - 2000097954L


title: 40oC 15min vs 29oC - 2000097984L

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.


title: Self-self 29oC vs 29oC - 2000097946R


title: 40oC 25min vs 29oC - 2000097957R


title: 40oC 07min vs 29oC - 3000030723L


title: 40oC 25min vs 29oC - 3000030725R


title: Self-self 29oC vs 29oC - 2000097943R


title: Self-self 29oC vs 29oC - 2000097947L


title: 40oC 15min vs 29oC - 2000097983R

extract_protocol: Total RNA was isolated with phenol-chloroform (Ausubel , ??) and residual DNA was removed by treatment with 10U of RQ1 RNAse-free DNAse I (Promega) and 40U RNAse inhibitor RNAsin (Promega). The integrity of the RNA was checked by agarose gel electrophoresis and the lack of residual DNA was checked by PCR.


title: 40oC 25min vs 29oC - 3000030725L


title: 40oC 25min vs 29oC - 3000030750L


title: 40oC 15min vs 29oC - 2000097984R


title: 40oC 25min vs 29oC - 3000030716L


title: Yeast cell cycle-time point 110 min 2001-04-11_0110.rfm

city: Seattle

first: Tata

last: Pramila

state: WA

address: 1100, Fairview Avenue N

department: Basic Sciences

institute: FHCRC

description: Yeast cell cycle

data_processing: normalized log ratio using Rosetta Resolver

organism: Saccharomyces cerevisiae

source_name: Yeast cell cycle-time point 110 min

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

tag: Yeast cell cycle-time point 110 min

source_name: Yeast asynchronous culture

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

tag: Yeast asynchronous culture


title: 40oC 15min vs 29oC - 2000097983L


title: 40oC 07min vs 29oC - 2000097849R


title: Yeast cell cycle-time point 120 min 2001-04-11_0120.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 120 min

tag: Yeast cell cycle-time point 120 min


title: Yeast cell cycle-time point 70 min 2001-04-11_0070.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 70 min

tag: Yeast cell cycle-time point 70 min


title: Self-self 29oC vs 29oC - 2000097947R


title: 40oC 07min vs 29oC - 2000097848L


title: Yeast cell cycle-time point 80 min 2001-04-11_0080.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 80 min

tag: Yeast cell cycle-time point 80 min


title: Yeast cell cycle-time point 90 min 2001-04-11_0090.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 90 min

tag: Yeast cell cycle-time point 90 min


title: Self-self 29oC vs 29oC - 2000097946L


title: 40oC 07min vs 29oC - 2000097848R


title: Yeast cell cycle-time point 50 min 2001-04-11_0050.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 50 min

tag: Yeast cell cycle-time point 50 min


title: Yeast cell cycle-time point 20 min 2001-05-03_0020.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 20 min

tag: Yeast cell cycle-time point 20 min


title: Yeast cell cycle-time point 60 min 2001-04-11_0060.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 60 min

tag: Yeast cell cycle-time point 60 min


title: Yeast cell cycle-time point 30 min 2001-05-03_0030.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 30 min

tag: Yeast cell cycle-time point 30 min


title: Yeast cell cycle-time point 40 min 2001-04-11_0040.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 40 min

tag: Yeast cell cycle-time point 40 min


title: Yeast cell cycle-time point 0 min 2001-05-03_0000.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 0 min

tag: Yeast cell cycle-time point 0 min


title: Yeast cell cycle-time point 10 min 2001-05-03_0010.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 10 min

tag: Yeast cell cycle-time point 10 min


title: 40oC 07min vs 29oC - 2000097849L

source_name: 40oC 07min (cy5)


title: AURATUS goldfish genome project: slide15-EE2 experiment

status: Public on May 31 2006

first: Christopher

middle: Joseph

last: Martyniuk

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description: Additional information for microarray can be found at auratus.ca and in Martyniuk et al. (pending publishing)"Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol"

data_processing: The array quality filter test (AQF) (Sauer et al., 2005); The intensity-dependent Lowess normalization with span 0.4 was chosen for normalization

organism: Carassius auratus

source_name: Carassius auratus; hypothalamus; control (EtOH) EtOH for ethinylestradiol experiment

tag: Male adult goldfish

tag: Hypothalamus

tag: 2-3 years of age

tag: sexually mature (May)

tag: 2 week exposure to 30 ng/L EE2

tag: slide 15

source_name: Carassius auratus; hypothalamus;  30ng/L EE2 for ethinylestradiol experiment


title: AURATUS goldfish genome project: slide 18-EE2 experiment

description:
Additional information in Martyniuk et al.
Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol (pending publishing)

data_processing: The array quality filter test (AQF) (Sauer et al., 2005) ;intensity-dependent Lowess normalization with span 0.4 was chosen for normalization

source_name: Carassius auratus; hypothalamus; 300 ng/L EE2 for ethinylestradiol experiment

tag: Hypothalmus

tag: sexually mature (March)

tag: slide 18


title: Control, biological rep2 CHC Con-3

status: Public on Apr 30 2006

city: Cambridge

first: gabriel

last: kreiman

state: MA

address: 77 Massachusetts Avenue MIT 46-5155

department: BCS

institute: MIT

description: Gene expression data from mouse primary visual cortex

hyb_protocol: Affymetrix hybridization protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: Mouse primary visual cortex (V1)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 to 45 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals came from different litters and the tissue was derived from primary visual cortex (V1) of at least two different animals. In both groups of animals, monocular and binocular portions were included for analysis. Mice were anesthetized with Nembutal before tissue extraction.

extract_protocol: Followed the “Eukaryotic Target Preparation”  Affymetrix manual.

treatment_protocol: We followed the Eukaryotic Target Preparation” protocol as described in the Affymetrix manual.

tag: 129/SvEv male and female mice P27 primary visual cortex

tag: monocular deprivation was started at P11-12 before eye opening


title: AURATUS goldfish genome project: slide 32-EE2 experiment

description:
Additional information in Martyniuk et al.
Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol

data_processing: intensity-dependent Lowess normalization with span 0.4 was chosen for normalization

tag: hypothalamus

tag: adult male goldfish

tag: control

tag: 300 ng/L EE2


title: AURATUS goldfish genome project: slide 13-EE2 experiment

tag: slide 13


title: Control, biological rep2 CHC Con-1


title: Control, biological rep2 CHC Con-2


title: AURATUS goldfish genome project: slide 3-EE2 experiment

description: Further details in "Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol" - Martyniuk et al., 2006 (Manuscript to be submitted)

data_processing: Array quality filter test used; Intensity-dependent Lowess normalization with span 0.4 was chosen for normalization

source_name: Carassius auratus; hypothalamus; 30ng/L EE2 EtOH for ethinylestradiol experiment

tag: Sexually mature (March 2004)

tag: Adults approx. 2-3 years of age

source_name: Carassius auratus; hypothalamus; control (EtOH) for ethinylestradiol experiment


title: Dark rearing, biological rep2 CHC DR-3


title: Monocular deprivation right cortex, biological rep1 CHC MD-4


title: AURATUS goldfish genome project: slide 49-EE2 experiment

description:
Additional information in Martyniuk et al.
Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol (publication pending)

source_name: Carassius auratus; hypothalamus; 300 ng/L EE2 EtOH for ethinylestradiol experiment

tag: 300 ng/L group


title: Dark rearing, biological rep2 CHC DR-2

tag: animals reared in darkness until P27


title: Monocular deprivation left cortex, biological rep2 CHC MD-6


title: Monocular deprivation right cortex, biological rep1 CHC MD-1


title: Monocular deprivation right cortex, biological rep1 CHC MD-3


title: Monocular deprivation left cortex, biological rep2 CHC MD-5


title: Monocular deprivation right cortex, biological rep1 CHC MD-2


title: Dark rearing, biological rep2 CHC DR-1


title: MCL cell line REC (replicate 2)

status: Public on Apr 10 2006

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via Vela 6

department: Experimental Oncology

institute: Institute of Southern Switzerland

description: human B cell lymphoma

hyb_protocol: standard Affymetrix procedures using Fluidics Station 400

scan_protocol: standard Affymetrix procedures using GeneChip Scanner 3000

data_processing: Affymetrix GeneChip GCOS 1.1, GTYPE (with CNAT 3.0)

source_name: MCL cell line REC

label_protocol: standard Affymetrix protocol starting from 250 ng of DNA.

extract_protocol: genomic DNA was extracted using the Puregen DNA Isolation kit (Gentra Systems, Minneapolis, MN, USA), dissolved in reduced EDTA TE buffer.

tag: human mantle cell lymphoma sample


title: MCL cell line REC (replicate 1)

description: human B cell lymphoma


title: MCL cell line JEKO

description: human B cell lymphoma

source_name: MCL cell line JEKO


title: MCL cell line GRANTA-519

description: human B cell lymphoma

source_name: MCL human cell line GRANTA-519


title: MCL cell line NCEB

description: human B cell lymphoma

source_name: MCL cell line NCEB


title: MCL patient 1861

description: human B cell lymphoma

source_name: MCL patient 1861

extract_protocol: genomic DNA was extracted using the Qiagen DNA Mini kit (Qiagen, Hilden, Germany) dissolved in reduced EDTA TE buffer.

tag: human mantle cell lymphoma clinical sample


title: AURATUS goldfish genome project: slide 41-EE2 experiment

description: Additional information for microarray can be found at auratus.ca and in Martyniuk et al. (pending publishing). Gene expression profiling in the brain of male goldfish (Carassius auratus) exposed to 17α-ethinylestradiol

tag: Male adult goldfish

tag: 2-3 years of age

tag: slide 41


title: MCL patient 05-140

description: human B cell lymphoma

source_name: MCL patient 05-140


title: MCL patient 05-119

description: human B cell lymphoma

source_name: MCL patient 05-119


title: T911

status: Public on Feb 09 2006

city: Boston

first: Andrea

last: Richardson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: Tumor T911 and normal breast tissue B911 from the same case

data_processing: genotype call using software-see manufacturer's web site http://www.affymetrix.com/products/arrays/specific/10k.affx

source_name: Human Breast tissue

tag: Breast Carcinoma


title: MCL patient 05-115

description: human B cell lymphoma

source_name: MCL patient 05-115


title: MCL patient 05-111

description: human B cell lymphoma

source_name: MCL patient 05-111


title: MCL patient 05-118

description: human B cell lymphoma

source_name: MCL patient 05-118


title: T92

description: Tumor T92 and normal breast tissue B92 from the same case

label: see manufacturer's web site http://www.affymetrix.com/products/arrays/specific/10k.affx


title: MCL patient 05-113

description: human B cell lymphoma

source_name: MCL patient 05-113


title: MCL patient 2578

description: human B cell lymphoma

source_name: MCL patient 2578


title: MCL patient 05-114

description: human B cell lymphoma

source_name: MCL patient 05-114


title: T81

description: Tumor T81 and normal breast tissue B81 from the same case


title: MCL patient 05-116

description: human B cell lymphoma

source_name: MCL patient 05-116


title: MCL patient 05-110

description: human B cell lymphoma

source_name: MCL patient 05-110


title: T44

description: Tumor T44 and normal breast tissue B44 from the same case


title: T73

description: Tumor T73 and normal breast tissue Bb73 from the same case


title: T84

description: Tumor T84 and normal Blood buffy coat B84 from the same case


title: T50

description: Tumor T50 and normal breast tissue B50 from the same case


title: T41

description: Tumor T41 and normal breast tissue B41 from the same case


title: T636

description: Breast Carcinoma

tag: Breast Cancinoma


title: MCL patient 05-112

description: human B cell lymphoma

source_name: MCL patient 05-112


title: T38

description: Tumor T38 and normal breast tissue B38 from the same case


title: T4

description: Tumor T4 and normal Blood buffy coat B4 from the same case


title: T56

description: Tumor T56 and normal breast tissue B56 from the same case


title: T21

description: Tumor T21 and normal breast tissue B21 from the same case


title: T37

description: Tumor T37 and normal breast tissue B37 from the same case


title: T183

description: Tumor T183 and normal breast tissue B183 from the same case


title: T175

description: Tumor T175 and normal breast tissue B175 from the same case


title: T178

description: breast carcinoma


title: T162

description: breast carcinoma

tag: breast carcinoma


title: T161

description: Tumor T161 and normal breast tissue B161 from the same case


title: T147

description: Breast Carcinoma


title: T152

description: Breast Carcinoma


title: T140

description: Tumor T140 and normal Blood buffy coat B140 from the same case


title: T149

description: Tumor T149 and normal breast tissue B149 from the same case


title: T151

description: Tumor T151 and normal breast tissue B151 from the same case


title: T134

description: Tumor T134 and normal Blood buffy coat B134 from the same case

tag: Normal breast tissue


title: T137

description: Tumor T137 and normal breast tissue B137 from the same case


title: T144

description: Tumor T144 and normal breast tissue B144 from the same case


title: T123

description: Tumor T123 and normal breast tissue B123 from the same case


title: T30

description: Tumor T30 and normal Blood buffy coat B30 from the same case


title: T143

description: Tumor T143 and normal Blood buffy coat B143 from the same case


title: T146

description: Tumor T146 and normal breast tissue B146 from the same case


title: T119

description: Tumor T119 and normal breast tissue B119 from the same case


title: T118

description: Tumor T118 and normal Blood buffy coat B118 from the same case


title: T145

description: Tumor T145 and normal Blood buffy coat B145 from the same case


title: T130

description: Tumor T130 and normal Blood buffy coat B130 from the same case


title: T141

description: Tumor T141 and normal breast tissue B141 from the same case


title: B84

description: Tumor T84 and normal Blood buffy coat B84 from the same case

source_name: Normal, Blood buffy coat

tag: Normal, Blood buffy coat


title: T116

description: Tumor T116 and normal Blood buffy coat B116 from the same case


title: T133

description: Tumor T133 and normal breast tissue B133 from the same case


title: T117

description: Tumor T117 and normal Blood buffy coat B117 from the same case


title: T129

description: Tumor T129 and normal breast tissue B129 from the same case


title: B81

description: Tumor T81 and normal breast tissue B81 from the same case


title: Yeast cell cycle-time point 100 min 2001-04-11_0100.rfm

description: Yeast cell cycle

source_name: Yeast cell cycle-time point 100 min

tag: Yeast cell cycle-time point 100 min

source_name: Yeast asynchronous culture

tag: Yeast asynchronous culture


title: T115

description: Tumor T115 and normal breast tissue B115 from the same case


title: B56

description: Tumor T56 and normal breast tissue B56 from the same case


title: T74

description: Breast carcinoma

tag: Breast carcinoma


title: B73

description: Tumor T73 and normal breast tissue B73 from the same case


title: B37

description: Tumor T37 and Normal Blood buffy coat B37 from the same case


title: B41

description: Tumor T41 and normal breast tissue B41 from the same case


title: B149

description: Tumor T149 and normal breast tissue B149 from the same case


title: B44

description: Tumor T44 and normal breast tissue B44 from the same case


title: B4

description: Tumor T4 and normal Blood buffy coat B4 from the same case


title: B50

description: Tumor T50 and normal breast tissue B50 from the same case


title: B183

description: Tumor T183 and normal breast tissue B183 from the same case


title: B92

description: Tumor T92 and normal breast tissue B92 from the same case


title: B161

description: Tumor T161 and normal breast tissue B161 from the same case


title: B21

description: Tumor T21 and Normal Blood buffy coatB21 from the same case


title: B146

description: Tumor T146 and normal breast tissue B146 from the same case


title: B911

description: Tumor T911 and normal breast tissue B911 from the same case


title: B151

description: Tumor T151 and normal breast tissue B151 from the same case


title: B38

description: Tumor T38 and Normal Blood buffy coat B38 from the same case


title: B134

description: Tumor T134 and normal Blood buffy coat B134 from the same case


title: B143

description: Tumor T143 and normal Blood buffy coat B143 from the same case


title: B141

description: Tumor T141 and normal breast tissue B141 from the same case


title: B137

description: Tumor T117 and normal breast tissue B117 from the same case


title: B175

description: Tumor T175 and normal breast tissue B175 from the same case


title: B140

description: Tumor T140 and normal Blood buffy coat B140 from the same case


title: B144

description: Tumor T144 and normal breast tissue B144 from the same case


title: B30

description: Tumor T30 and normal Blood buffy coat B30 from the same case


title: B119

description: Tumor T119 and normal breast tissue B119 from the same case


title: B133

description: Tumor T133 and normal breast tissue B133 from the same case


title: B118

description: Tumor T118 and normal Blood buffy coat B118 from the same case


title: B117

description: Tumor T117 and normal Blood buffy coat B117 from the same case


title: B129

description: Tumor T129 and normal breast tissue B129 from the same case


title: B115

description: Tumor T115 and normal breast tissue B115 from the same case


title: B130

description: Tumor T130 and normal Blood buffy coat B130 from the same case


title: Madin-Darby bovine kidney epithelial cells BEKC 46404 control C1

status: Public on Jan 05 2006

city: Beltsville

first: Robert

middle: W

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: After hybridization and washing, the biotin labels were detected with Cy3-streptavidin

data_processing: RMA normalized, not log transformed

organism: Bos taurus

source_name: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), untreated (control, C1) for 24h


title: B123

description: Tumor T123 and normal breast tissue B123 from the same case


title: Patient#14 Blood DNA

status: Public on Jul 21 2005

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Blood DNA for patient #14

data_processing: SNP Call

tag: #14 Blood


title: Madin-Darby bovine kidney epithelial cells BEKC 44371 sodium butyrate treated BT1

source_name: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase),treated with 10mM sodium butyrate for 24h


title: Patient#12 BCC DNA

description: BCC DNA for patient #12

tag: #12 BCC


title: B116

description: Tumor T116 and Normal Blood buffy coat B116 from the same case


title: Madin-Darby bovine kidney epithelial cells BEKC 46395 sodium butyrate treated BT2

source_name: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), treated with 10mM sodium butyrate (BT2) for 24h


title: B145

description: Tumor T145 and normal Blood buffy coat B145 from the same case


title: Patient#13 Blood DNA

description: Blood DNA for patient #13

tag: #13 Blood


title: Patient#11 Blood DNA

description: Blood DNA for patient #11

tag: #11 Blood


title: Patient#14 BCC DNA

description: BCC DNA for patient #14

tag: #14 BCC


title: Patient#13 BCC DNA

description: BCC DNA for patient #13

tag: #13 BCC


title: BT474 (ATCC nr. HTB-20) Breast tumor cell line  BT474_b42_s56

status: Public on Dec 19 2005

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via the VUMC MACF website Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004)  Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).

label_protocol:
DNA labeling protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

growth_protocol: according to ATCC conditions

extract_protocol:
DNA isolation protocol available via the VUMC MACF website
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192

tag: BT474 (ATCC nr. HTB-20) breast tumor cell line

tag: Gender

value: female

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: Pooled DNA from the blood of 10 normal male individuals


title: SKBR7: epithelial Breast tumor cell line  SKBR7_b39_s31

growth_protocol: DMEM + 10% FCS + penn/strep, 37°C, 5% CO2.

value: epithelial breast tumor cell line

tag: pleural effusion derived


title: Patient#11 BCC DNA

description: BCC DNA for patient #11

tag: #11 BCC


title: Madin-Darby bovine kidney epithelial cells BEKC 43979 control C2

source_name: The Madin-Darby bovine kidney epithelial cells, when at approximately 50% confluence (during the exponential phase), untreated (control) for 24h

tag: The Madin-Darby bovine kidney epithelial cells cultured in Eagle’s minimal essential medium supplemented with 5% fetal bovine serum, when at approximately 50% confluence (during the exponential phase), untreated (control) for 24h


title: Patient#12 Blood DNA

description: Blood DNA for patient #12

tag: #12 Blood


title: Patient#10 BCC DNA

description: BCC DNA for patient #10

tag: #10 BCC


title: Patient#10 Blood DNA

description: Blood DNA for patient #10

tag: #10 Blood


title: Patient#8 BCC DNA

description: BCC DNA for patient #8

tag: #8 BCC


title: Patient#8 Blood DNA

description: Blood DNA for patient #8

tag: #8 Blood


title: Patient#9 Blood DNA

description: Blood DNA for patient #9

tag: #9 Blood


title: Patient #5 BCC DNA

description: BCC DNA for patient #5

tag: #5 BCC


title: Patient #5 Blood DNA

description: Blood DNA for patient #5

tag: #5 Blood


title: Patient#7 BCC DNA

description: BCC DNA for patient #7

tag: #7 BCC


title: Patient#7 Blood DNA

description: Blood DNA for patient #7

tag: #7 Blood


title: Patient#9 BCC DNA

description: BCC DNA for patient #9

tag: #9 BCC


title: Patient#6 BCC DNA

description: BCC DNA for patient #6

tag: #6 BCC


title: Patient#6 Blood DNA

description: Blood DNA for patient #6

tag: #6 Blood


title: Patient #4 BCC DNA

description: BCC DNA for patient #4

tag: #4 BCC


title: Patient #4 Blood DNA

description: Blood DNA for patient #4

tag: #4 Blood


title: Patient #3 Blood DNA

description: Blood DNA for patient #3

tag: #3 Blood


title: Patient#1 BCC DNA

description: BCC DNA for patient #1

tag: #1 BCC


title: Patient #2 BCC DNA

description: BCC DNA for patient #2

tag: #2 BCC


title: Patient #3 BCC DNA

description: BCC DNA for patient #3

tag: #3 BCC