title: BC5329


title: BC5328

status: Public on Oct 11 2011

type: RNA

city: Köln

first: Karsten

middle: Ernst

last: Weber

address: Nattermannallee 1

country: Germany

institute: Sividon Diagnostics GmbH

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

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 set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary breast cancer sample, fresh-frozen

label_protocol: from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit (Roche Applied Science, Mannheim, Germany), according to the manufacturer’s instructions

growth_protocol: primary tumor tissue, fresh-frozen after surgery

extract_protocol: RNeasy kit, Qiagen. according to the manufacturer's instructions

tag: center/subcohort

value: Mainz

tag: metastasis (1

value: yes, 0:no/censored):0

tag: metastasis free interval (months)

tag: tumor size

tag: positive lymph nodes

tag: adjuvant patient treatment

value: Tamoxifen


title: BC5320


title: BC5316

value: unknown


title: BC5317

value: yes, 0:no/censored):1


title: BC5313


title: BC5339


title: BC5340


title: BC5333


title: BC5338


title: BC5318


title: BC5336


title: BC5323


title: BC5334


title: BC5312


title: BC5311


title: BC5319


title: BC5314


title: BC5309


title: BC5306


title: BC5304


title: BC5305


title: BC5307


title: BC5302


title: BC5308


title: BC6203: Mainz_N0_untreated_frozen _180

status: Public on Jul 01 2008

city: Leverkusen

first: Mathias

last: Gehrmann

address: Kaiser-Wilhelm-Allee

department: BTS-PT-AS-AT

institute: Bayer Technology Services GmbH

description: Gene expression data from primary breast tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer’s instructions

extract_protocol: Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For all tumors, samples were snap frozen and stored at -80°C. Tumor cell content exceeded 40% in all samples

tag: storage

value: fresh frozen

tag: node

tag: grade

tag: clinic


title: BC6212: Mainz_N0_untreated_frozen _188


title: BC6230: Mainz_N0_untreated_frozen _198


title: BC6227_2: Mainz_N0_untreated_frozen _197


title: BC6216: Mainz_N0_untreated_frozen _190


title: BC6220: Mainz_N0_untreated_frozen _194


title: BC6201: Mainz_N0_untreated_frozen _179


title: BC6211: Mainz_N0_untreated_frozen _187


title: BC6200: Mainz_N0_untreated_frozen _178


title: BC6231: Mainz_N0_untreated_frozen _199


title: BC6214: Mainz_N0_untreated_frozen _189


title: BC6221: Mainz_N0_untreated_frozen _195


title: BC6208: Mainz_N0_untreated_frozen _185


title: BC6232: Mainz_N0_untreated_frozen _200


title: BC6210: Mainz_N0_untreated_frozen _186


title: BC6219: Mainz_N0_untreated_frozen _193


title: BC6218: Mainz_N0_untreated_frozen _192


title: BC6205: Mainz_N0_untreated_frozen _182


title: BC6207: Mainz_N0_untreated_frozen _184


title: BC6198: Mainz_N0_untreated_frozen _176


title: BC6199: Mainz_N0_untreated_frozen _177


title: BC6192: Mainz_N0_untreated_frozen _172


title: BC6196: Mainz_N0_untreated_frozen _174


title: BC6193: Mainz_N0_untreated_frozen _173


title: BC6217: Mainz_N0_untreated_frozen _191


title: BC6204: Mainz_N0_untreated_frozen _181


title: BC6191: Mainz_N0_untreated_frozen _171


title: BC6190: Mainz_N0_untreated_frozen _170


title: BC6184: Mainz_N0_untreated_frozen _164


title: BC6177: Mainz_N0_untreated_frozen _157


title: BC6183: Mainz_N0_untreated_frozen _163


title: BC6176: Mainz_N0_untreated_frozen _156


title: BC6171: Mainz_N0_untreated_frozen _153


title: BC6181: Mainz_N0_untreated_frozen _161


title: BC6167: Mainz_N0_untreated_frozen _151


title: BC6174: Mainz_N0_untreated_frozen _155


title: BC6188: Mainz_N0_untreated_frozen _168


title: BC6185: Mainz_N0_untreated_frozen _165


title: BC6189: Mainz_N0_untreated_frozen _169


title: BC6224: Mainz_N0_untreated_frozen _196


title: BC6187: Mainz_N0_untreated_frozen _167


title: BC6170: Mainz_N0_untreated_frozen _152


title: BC6182: Mainz_N0_untreated_frozen _162


title: BC6166: Mainz_N0_untreated_frozen _150


title: BC6180: Mainz_N0_untreated_frozen _160


title: BC6186: Mainz_N0_untreated_frozen _166


title: BC6179: Mainz_N0_untreated_frozen _159


title: BC6178: Mainz_N0_untreated_frozen _158


title: BC6164wdh: Mainz_N0_untreated_frozen _148


title: BC6173: Mainz_N0_untreated_frozen _154


title: BC6159: Mainz_N0_untreated_frozen _144


title: BC6165: Mainz_N0_untreated_frozen _149


title: BC6163: Mainz_N0_untreated_frozen _147


title: BC6162wdh: Mainz_N0_untreated_frozen _146


title: BC6161wdh: Mainz_N0_untreated_frozen _145


title: BC5325


title: BC6151wdh: Mainz_N0_untreated_frozen _137


title: BC6152: Mainz_N0_untreated_frozen _138


title: BC6154: Mainz_N0_untreated_frozen _139


title: BC6144: Mainz_N0_untreated_frozen _131


title: BC6156: Mainz_N0_untreated_frozen _141


title: BC6134: Mainz_N0_untreated_frozen _124


title: BC6138: Mainz_N0_untreated_frozen _126


title: BC6147: Mainz_N0_untreated_frozen _134


title: BC6140: Mainz_N0_untreated_frozen _128


title: BC6141: Mainz_N0_untreated_frozen _129


title: BC6139: Mainz_N0_untreated_frozen _127


title: BC6157: Mainz_N0_untreated_frozen _142


title: BC6145: Mainz_N0_untreated_frozen _132


title: BC6155: Mainz_N0_untreated_frozen _140


title: BC6142: Mainz_N0_untreated_frozen _130


title: BC6133: Mainz_N0_untreated_frozen _123


title: BC6136: Mainz_N0_untreated_frozen _125


title: BC6146wdh: Mainz_N0_untreated_frozen _133


title: BC6132: Mainz_N0_untreated_frozen _122


title: BC6131: Mainz_N0_untreated_frozen _121


title: BC6126wdh: Mainz_N0_untreated_frozen _117


title: BC6148: Mainz_N0_untreated_frozen _135


title: BC6127: Mainz_N0_untreated_frozen _118


title: BC6129: Mainz_N0_untreated_frozen _119


title: BC6130: Mainz_N0_untreated_frozen _120


title: BC6125: Mainz_N0_untreated_frozen _116


title: BC6110: Mainz_N0_untreated_frozen _104


title: BC6114: Mainz_N0_untreated_frozen _107


title: BC6111: Mainz_N0_untreated_frozen _105


title: BC6109: Mainz_N0_untreated_frozen _103


title: BC6104: Mainz_N0_untreated_frozen _098


title: BC6102: Mainz_N0_untreated_frozen _096


title: BC6108: Mainz_N0_untreated_frozen _102


title: BC6118: Mainz_N0_untreated_frozen _111


title: BC6106: Mainz_N0_untreated_frozen _100


title: BC6101wdh: Mainz_N0_untreated_frozen _095


title: BC6105: Mainz_N0_untreated_frozen _099


title: BC6120: Mainz_N0_untreated_frozen _113


title: BC6107: Mainz_N0_untreated_frozen _101


title: BC6117: Mainz_N0_untreated_frozen _110


title: BC6112: Mainz_N0_untreated_frozen _106


title: BC6119: Mainz_N0_untreated_frozen _112


title: BC6115: Mainz_N0_untreated_frozen _108


title: BC6122: Mainz_N0_untreated_frozen _115


title: BC6121: Mainz_N0_untreated_frozen _114


title: BC6100: Mainz_N0_untreated_frozen _094


title: BC6116wdh: Mainz_N0_untreated_frozen _109


title: BC6099: Mainz_N0_untreated_frozen _093


title: BC6096: Mainz_N0_untreated_frozen _090


title: BC6095: Mainz_N0_untreated_frozen _089


title: BC6103: Mainz_N0_untreated_frozen _097


title: BC6097: Mainz_N0_untreated_frozen _091


title: BC6098: Mainz_N0_untreated_frozen _092


title: BC6197: Mainz_N0_untreated_frozen _175


title: BC6094: Mainz_N0_untreated_frozen _088


title: BC6091: Mainz_N0_untreated_frozen _085


title: BC6089: Mainz_N0_untreated_frozen _084


title: BC6093: Mainz_N0_untreated_frozen _087


title: BC6087: Mainz_N0_untreated_frozen _082


title: BC6085: Mainz_N0_untreated_frozen _080


title: BC6092: Mainz_N0_untreated_frozen _086


title: BC6084: Mainz_N0_untreated_frozen _079


title: BC6088: Mainz_N0_untreated_frozen _083


title: BC6083: Mainz_N0_untreated_frozen _078


title: BC6080: Mainz_N0_untreated_frozen _075


title: BC6081: Mainz_N0_untreated_frozen _076


title: BC6082: Mainz_N0_untreated_frozen _077


title: BC6076: Mainz_N0_untreated_frozen _071


title: BC6079: Mainz_N0_untreated_frozen _074


title: BC6078: Mainz_N0_untreated_frozen _073


title: BC6074: Mainz_N0_untreated_frozen _069


title: BC6077: Mainz_N0_untreated_frozen _072


title: BC6071: Mainz_N0_untreated_frozen _066


title: BC6073: Mainz_N0_untreated_frozen _068


title: BC6086: Mainz_N0_untreated_frozen _081


title: BC6075: Mainz_N0_untreated_frozen _070


title: BC6070: Mainz_N0_untreated_frozen _065


title: BC6072: Mainz_N0_untreated_frozen _067


title: BC6069: Mainz_N0_untreated_frozen _064


title: BC6067: Mainz_N0_untreated_frozen _062


title: BC6066wdh: Mainz_N0_untreated_frozen _061


title: BC6068: Mainz_N0_untreated_frozen _063


title: BC6158: Mainz_N0_untreated_frozen _143


title: BC6063: Mainz_N0_untreated_frozen _058


title: BC6062wdh: Mainz_N0_untreated_frozen _057


title: BC6057: Mainz_N0_untreated_frozen _052


title: BC6064_2: Mainz_N0_untreated_frozen _059


title: BC6058: Mainz_N0_untreated_frozen _053


title: BC6060wdh: Mainz_N0_untreated_frozen _055


title: BC6061: Mainz_N0_untreated_frozen _056


title: BC6059: Mainz_N0_untreated_frozen _054


title: BC6056wdh: Mainz_N0_untreated_frozen _051


title: BC6065: Mainz_N0_untreated_frozen _060


title: BC6055: Mainz_N0_untreated_frozen _050


title: BC6052: Mainz_N0_untreated_frozen _047


title: BC6048: Mainz_N0_untreated_frozen _043


title: BC6050: Mainz_N0_untreated_frozen _045


title: BC6054: Mainz_N0_untreated_frozen _049


title: BC6053: Mainz_N0_untreated_frozen _048


title: BC6049: Mainz_N0_untreated_frozen _044


title: BC6045: Mainz_N0_untreated_frozen _040


title: BC6044: Mainz_N0_untreated_frozen _039


title: BC6046: Mainz_N0_untreated_frozen _041


title: BC6047: Mainz_N0_untreated_frozen _042


title: BC6051_2: Mainz_N0_untreated_frozen _046


title: BC6150: Mainz_N0_untreated_frozen _136


title: BC6040: Mainz_N0_untreated_frozen _035


title: BC6037: Mainz_N0_untreated_frozen _033


title: BC6041: Mainz_N0_untreated_frozen _036


title: BC6042: Mainz_N0_untreated_frozen _037


title: BC6039: Mainz_N0_untreated_frozen _034


title: BC6043: Mainz_N0_untreated_frozen _038


title: BC6033: Mainz_N0_untreated_frozen _030


title: BC6022: Mainz_N0_untreated_frozen _020


title: BC6032: Mainz_N0_untreated_frozen _029


title: BC6030: Mainz_N0_untreated_frozen _027


title: BC6031: Mainz_N0_untreated_frozen _028


title: BC6024: Mainz_N0_untreated_frozen _021


title: BC6025: Mainz_N0_untreated_frozen _022


title: BC6035: Mainz_N0_untreated_frozen _031


title: BC6026: Mainz_N0_untreated_frozen _023


title: BC6028_3: Mainz_N0_untreated_frozen _025


title: BC6029: Mainz_N0_untreated_frozen _026


title: BC6036: Mainz_N0_untreated_frozen _032


title: BC6020_3: Mainz_N0_untreated_frozen _018


title: BC6012: Mainz_N0_untreated_frozen _011


title: BC6019: Mainz_N0_untreated_frozen _017


title: BC6013: Mainz_N0_untreated_frozen _012


title: BC6009: Mainz_N0_untreated_frozen _009


title: BC6008: Mainz_N0_untreated_frozen _008


title: BC6014: Mainz_N0_untreated_frozen _013


title: BC6015: Mainz_N0_untreated_frozen _014


title: BC6017: Mainz_N0_untreated_frozen _016


title: BC6027: Mainz_N0_untreated_frozen _024


title: BC6007: Mainz_N0_untreated_frozen _007


title: BC6011: Mainz_N0_untreated_frozen _010


title: BC6004_r: Mainz_N0_untreated_frozen _004


title: BC6006: Mainz_N0_untreated_frozen _006


title: BC6021: Mainz_N0_untreated_frozen _019


title: Exp105Un on 74A

status: Public on Apr 21 2005

city: Farmington

first: Baikang

last: Pei

state: CT

country: USA

institute: University of Connecticut

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp105Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

organism: Mus musculus

source_name: Exp105Un, total_rna, calvaria, unsorted calvarial osteoblast


title: BC6003_r: Mainz_N0_untreated_frozen _003


title: BC6005wdh: Mainz_N0_untreated_frozen _005


title: Exp106Pos on 74A

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp106Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp106Pos, total_rna, calvaria, sorted calvarial osteoblast GFP positive


title: Exp105Pos on 74A

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp105Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp105Pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: Exp103pos on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp103pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp103pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: Exp99Pos on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp99Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp99Pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: Exp101pos on 74A

description:
7 day new born mice.
Cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp101pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp101pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: Exp103Un on 74A

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp103Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp103Un, total_rna, cell culture, unsorted calvarial osteoblast


title: Exp99Un on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp99Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp99Un, total_rna, cell culture, unsorted calvarial osteoblast


title: Exp100Un on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp100Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp100Un, total_rna, cell culture, unsorted calvarial osteoblast


title: Exp106Un on 74A

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid bGP.
10ug Exp106Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp106Un, total_rna, calvaria, unsorted calvarial osteoblast


title: BC6001_r: Mainz_N0_untreated_frozen _001


title: Exp101Un on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp101Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp101Un, total_rna, cell culture, unsorted calvarial osteoblast


title: Exp100Pos on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Adiition of Asc acid and bGP.
10ug EXp100Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: EXp100Pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: BC6016: Mainz_N0_untreated_frozen _015


title: BC6002_r: Mainz_N0_untreated_frozen _002