title: Acute leukemia cell line ME-1-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line K-562-250knsp

status: Public on Sep 02 2009

type: genomic

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

description: Acute leukemia cell line

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line in culture

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Qiagen DNA blood mini

tag: Cell line in culture


title: Acute leukemia cell line Kasumi-2-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line HL-60-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line CMK-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line Jurkat-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line AT1-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line CCRF-CEM-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line BV173-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line 697-250knsp

description: Acute leukemia cell line


title: Acute leukemia cell line Kasumi-1-250knsp

description: Acute leukemia cell line


title: Acute myeloid leukemia in remission Reference-#46-250knsp

description: Acute myeloid leukemia in remission

source_name: Bone marrow or peripheral blood

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at remission

treatment_protocol: Samples were obtained at different stages of disease

tag: Bone marrow or peripheral blood


title: Acute myeloid leukemia in remission Reference-#44-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#47-250knsp

description: Acute myeloid leukemia in remission


title: Acute leukemia cell line 380-250knsp

description: Acute leukemia cell line


title: Acute myeloid leukemia in remission Reference-#48-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#38-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#42-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#37-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#43-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#40-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#36-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#35-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#49-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#31-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#29-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#30-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#34-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#32-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#28-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#41-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#45-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#27-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#23-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#26-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#25-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#24-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#22-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#20-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#21-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#53-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#17-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#16-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#18-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#15-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#14-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#51-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#12-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#19-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#52-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#9-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#6-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#5-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#50-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#4-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#13-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#2-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#60-250knsp

description: Acute myeloid leukemia in remission


title: Chronic myeloid leukemia CML-#23-BC-GL-250knsp

description: Chronic myeloid leukemia

source_name: Blast crisis

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at diagnosis, during disease progression, or after treatment. Blast crisis samples were flow sorted prior to DNA extraction.

extract_protocol: Qiagen DNA blood mini or phenol chloroform

tag: Bone marrow, flow sorted


title: Acute myeloid leukemia in remission Reference-#1-250knsp

description: Acute myeloid leukemia in remission


title: Acute myeloid leukemia in remission Reference-#62-250knsp

description: Acute myeloid leukemia in remission


title: Chronic myeloid leukemia CML-#22-BC-GL-250knsp

description: Chronic myeloid leukemia

source_name: Germline


title: Chronic myeloid leukemia CML-#22-CP-250knsp

description: Chronic myeloid leukemia

source_name: Chronic phase

tag: Bone marrow


title: Chronic myeloid leukemia CML-#23-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#21-CP2-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#22-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#20-AP-250knsp

description: Chronic myeloid leukemia

source_name: Accelerated phase


title: Chronic myeloid leukemia CML-#20-BC-250knsp

description: Chronic myeloid leukemia


title: Acute myeloid leukemia in remission Reference-#7-250knsp

description: Acute myeloid leukemia in remission


title: Chronic myeloid leukemia CML-#19-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#20-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#19-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#17-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#16-BC-GL-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#17-AP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#19-BC-GL-250knsp

description: Chronic myeloid leukemia


title: Acute myeloid leukemia in remission Reference-#58-250knsp

description: Acute myeloid leukemia in remission


title: Chronic myeloid leukemia CML-#23-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#16-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#18-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#14-Rem-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#13-CP2-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#15-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#13-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#16-CP2-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#16-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#15-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#11-AP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#11-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#21-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#15-CP2-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#12-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#9-BC-GL-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#12-AP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#10-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#7-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#8-AP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#14-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#6-BC-GL-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#6-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#5-BC-GL-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#6-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#5-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#12-CP2-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#4-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#5-Rem-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#4-Rem-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#7-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#10-AP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#9-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#1-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#8-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#4-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#3-BC-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#2-CP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#3-AP-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#2-CP2-250knsp

description: Chronic myeloid leukemia


title: Chronic myeloid leukemia CML-#1-BC-250knsp

description: Chronic myeloid leukemia


title: Diagnostic_acute_leukemia MLL-SNP-#23-250knsp

source_name: Diagnostic acute leukemia blasts

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at diagnosis

tag: Tissue

value: acute lymphoblastic leukemia


title: Diagnostic_acute_leukemia Other-SNP-#24-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#23-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#25-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#17-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#21-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#39-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#16-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#26-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#11-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#50-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#49-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#48-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#47-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#46-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#7-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#22-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#16-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#21-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#15-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#10-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#38-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#20-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#48-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#15-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#45-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#21-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#20-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#19-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#8-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#44-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#18-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#45-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#47-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#9-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#14-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#19-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#37-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#41-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#44-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#20-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#46-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#43-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#9-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#10-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#17-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#43-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#20-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#36-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#14-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#42-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#40-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#18-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#39-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#9-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#42-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#13-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#35-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#20-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#22-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#34-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#33-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#12-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#38-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#19-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#19-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#11-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#40-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#31-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#41-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#12-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#8-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#32-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#17-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#21-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#40-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#37-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#36-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#13-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#11-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#39-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#35-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#18-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#30-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#33-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#15-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#34-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#7-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#16-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#10-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#10-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#36-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#6-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#27-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#38-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#37-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#8-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#29-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#32-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#26-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#35-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#34-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#16-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#13-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#28-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#32-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#31-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#31-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#24-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#14-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#29-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#25-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#5-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#8-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#9-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#33-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#17-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#17-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#18-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#16-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#15-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#30-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#19-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#24-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#23-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#23-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#14-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#30-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#12-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#18-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#13-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#22-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#11-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#43-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#10-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#42-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#37-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#38-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#41-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#40-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#36-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#39-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#35-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#32-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#31-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#33-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#27-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#29-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#25-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#26-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#30-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#12-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#24-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#17-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#23-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#7-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#23-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#29-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#22-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#27-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#7-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#28-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#34-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#28-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#28-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#24-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#27-250knsp


title: Diagnostic_acute_leukemia Other-SNP-#6-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#9-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#6-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#20-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#11-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#25-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#10-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#19-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#26-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#26-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#21-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#25-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#15-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#24-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#14-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#9-250knsp


title: BC5117cc

type: RNA

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

hyb_protocol: see Affymetrix standard protocols

scan_protocol: see Affymetrix standard protocols

data_processing: RMA. Controls were removed, like all genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples. Data were then log2 transformed.

label: biotin

molecule: total RNA

source_name: Breast cancer

label_protocol: see Affymetrix standard protocols

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

tag: center

value: IPC

tag: type

value: IBC

tag: age of diagnosis (year)

tag: molecular subtype

value: LuminalA

tag: histology

tag: pt

tag: pn

value: pos

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

value: neg

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfs

tag: mfsdel (month)


title: BC5521cc

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#23-250knsp

tag: Tissue


title: BC5437cc

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status


title: BC17609

value: NIBC

value: DUC

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status


title: BC14972

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: mfs

tag: mfsdel (month)


title: BC13716

value: Tunis

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status


title: BC13744

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status


title: Diagnostic_acute_leukemia Pseudodip-SNP-#8-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia Other-SNP-#5-250knsp


title: BC13708

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#18-250knsp


title: BC13742

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: mfs

tag: mfsdel (month)


title: BC13723

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#5-250knsp

tag: Tissue


title: BC13675

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status


title: BC13681

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: foxa1 ihc status

tag: mfs


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#22-250knsp


title: BC13682

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#13-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia T-ALL-SNP-#24-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#17-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#12-250knsp


title: BC9822

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: erbb2p ihc status

tag: igf1r ihc status

tag: egfr ihc status


title: BC12115

tag: histology

value: MIX

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: top2a ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia MLL-SNP-#16-250knsp


title: BC9737

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: mfs


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#21-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia T-ALL-SNP-#23-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#20-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#11-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#10-250knsp


title: BC11041

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: erbb2p ihc status

tag: igf1r ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia T-ALL-SNP-#22-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#9-250knsp


title: BC2352

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: egfr ihc status

tag: top2a ihc status


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#8-250knsp


title: BC9296

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#8-250knsp

tag: Tissue


title: BC10172

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: erbb2p ihc status

tag: igf1r ihc status

tag: mfs


title: BC9077

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: egfr ihc status

tag: mfsdel (month)


title: BC15120

value: Normal

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status


title: BC12851

tag: center

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

value: other

tag: erbb2p ihc status

tag: foxa1 ihc status


title: BC17253

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: igf1r ihc status

tag: mfs


title: BC14481

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: egfr ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#4-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia Other-SNP-#4-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#16-250knsp


title: BC7462

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status


title: BC16989

tag: molecular subtype

value: Basal

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2p ihc status

tag: foxa1 ihc status


title: BC12781

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: mfs


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#18-250knsp

tag: Tissue


title: BC3220

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: mfsdel (month)


title: BC13329

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2p ihc status

tag: top2a ihc status


title: Diagnostic_acute_leukemia MLL-SNP-#4-250knsp


title: BC10797

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#17-250knsp

tag: Tissue


title: BC5520

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: mfs


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#7-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#15-250knsp


title: BC8504

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: grade sbr

tag: erbb2p ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia Other-SNP-#3-250knsp


title: BC8584

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status


title: BC8484

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: foxa1 ihc status


title: BC9991

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: erbb2.tab ihc status

tag: mfs


title: Diagnostic_acute_leukemia MLL-SNP-#3-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia T-ALL-SNP-#21-250knsp


title: BC9317

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: erbb2p ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#19-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#7-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#14-250knsp


title: BC9725

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: top2a ihc status


title: BC12652

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#16-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia Other-SNP-#2-250knsp


title: BC9983

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: erbb2p ihc status

tag: mfs


title: BC2163cc

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: mfsdel (month)


title: BC11348

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status


title: BC2933

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia T-ALL-SNP-#20-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#15-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#13-250knsp


title: BC7780

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: mfs


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#6-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#6-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#3-250knsp


title: BC5836

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: erbb2.ht ihc status

tag: egfr ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia T-ALL-SNP-#19-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#5-250knsp


title: BC12710

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status


title: BC13591

tag: center

tag: type

tag: age of diagnosis (year)

tag: ki67 ihc status

tag: erbb2p ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia T-ALL-SNP-#17-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia Pseudodip-SNP-#7-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#18-250knsp


title: BC13008

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: erbb2.ht ihc status

tag: igf1r ihc status

tag: mfs


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#12-250knsp


title: 3D-cultured chondrocytes from OA donor 2

city: Berlin

first: Tilo

last: Dehne

state: Berlin

address: Tucholskystraße 2

department: Rheumatology and Clinical Immunology

country: Germany

institute: Charité - University Medicine Berlin

description:
OA_2_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from OA donor 2

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de).

source_name: human subcultured chondrocytes (passage 2) from OA donors maintained for 14 days in scaffold culture

label_protocol: 2 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: Human chondrocytes obtained from non-weight bearing area of 3 donors undergoing ACT treatment (normal donor) and from biopsies of 3 donors undergoing total knee replacement (OA donors) were expanded by cultivation in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages,  3D cultured in Hyaff-11 scaffolds for 14 days in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin

extract_protocol: Total RNA from chondrocytes cultured in monolayer (passage 2) was isolated applying protocols for animal tissues of the RNeasy Mini Kit (Qiagen, Hilden, Germany). For scaffold cultures, an 8 mm punch was prepared, snap-frozen in liquid nitrogen, and stored at -80°C until further use. Frozen samples were transferred to 1 ml TriReagent (Sigma-Aldrich) and mechanically homogenized. Subsequently, 133 µl 1-Bromo-3-chloro-propane (Sigma-Aldrich) was admixed followed by centrifugation for 45 min at 13000xg. The aqueous phase was collected and nucleic acids were precipitated by addition of an equal volume ice-cold isopropanol. After 30 min incubation the precipitated nucleic acids were pelletized and resolved in 350 µl RLT buffer (Qiagen). Further purification was performed according to protocols for animal tissues of the RNeasy Mini Kit (Qiagen). RNA from each donor was separately handled; no pooling was done at any stage.

treatment_protocol: Human chondrocytes were isolated by enzymatic digestion. Minced cartilage was digested for 16 hours in a spinner bottle in 10 ml of culture medium containing clostridial collagenase (1 mg per milliliter [150 U per liter]) and deoxyribonuclease I (0.1 mg per milliliter [25,000 U per liter]). . For scaffold culture, 2x106 chondrocytes of passage 2 were per cm2 were seeded in Hyaff-11 and were maintained under serum-free chondotions in presence of TGFbeta 1.

tag: disease group

value: osteoarthritis

tag: cell type

value: chondrocytes

tag: cell culture


title: Diagnostic_acute_leukemia MLL-SNP-#1-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#5-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#6-250knsp


title: 3D-cultured chondrocytes from OA donor 1

description:
OA_1_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from OA donor 1


title: 3D cultured chondrocytes from OA donor 3

description:
OA_3_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from OA donor 3


title: monolayer chondrocytes from OA donor 3

description:
OA_3_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from cartilage biopsies from patients undergoing total knee replacement, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from OA donor 3

source_name: human subcultured chondrocytes (passage 2) from OA donors

value: monolayer


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#10-250knsp


title: BC9948

tag: center

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: erbb2.tab ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#14-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia T-ALL-SNP-#15-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#4-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#15-250knsp


title: BC9934

tag: type

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2p ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia Hypodip-SNP-#5-250knsp


title: monolayer chondrocytes from OA donor 2

description:
OA_2_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from cartilage biopsies from patients undergoing total knee replacement, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from OA donor 2

tag: disease group

tag: cell type

tag: cell culture


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#11-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#14-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#4-250knsp


title: Diagnostic_acute_leukemia MLL-SNP-#2-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#12-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#3-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#16-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#9-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#2-250knsp


title: monolayer chondrocytes from normal donor 2

description:
ND_2_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage, undergoing ACT treatment)
human chondrocytes isolated from the non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from normal donor 2

source_name: human subcultured chondrocytes (passage 2) from normal donors

value: normal


title: monolayer chondrocytes from OA donor 1

description:
OA_1_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from cartilage biopsies from patients undergoing total knee replacement, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from OA donor 1


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#13-250knsp

value: acute lymphoblastic leukemia


title: Diagnostic_acute_leukemia Hypodip-SNP-#3-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#13-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#11-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#7-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#6-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#6-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#10-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#5-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#8-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#9-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#5-250knsp


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#4-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#12-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#8-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#10-250knsp


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#2-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#11-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#4-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#22-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#7-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#9-250knsp


title: BC17609

description: Raw signal intensities are included in linked supplementary (txt) file.

hyb_protocol: see Agilent CGH 244k standard protocols

scan_protocol: see Agilent CGH 244k standard protocols

data_processing: CBS (DNAcopy R package)

source_name: Breast tumor sample

label_protocol: see Agilent CGH 244k standard protocols

tag: center

value: IPC

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: p53 ihc status

tag: erbb2.tab ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: mfs


title: BC5117cc

tag: type

value: IBC

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: ki67 ihc status

tag: top2a ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia Pseudodip-SNP-#4-250knsp

tag: Tissue


title: BC5521cc

tag: center

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2.ht ihc status

tag: erbb2p ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia Pseudodip-SNP-#3-250knsp


title: Diagnostic_acute_leukemia T-ALL-SNP-#6-250knsp


title: BC13723

tag: type

tag: pr ihc status

tag: p53 ihc status

tag: erbb2.tab ihc status

tag: igf1r ihc status

tag: egfr ihc status

tag: mfs


title: BC5437cc

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: ki67 ihc status

tag: top2a ihc status


title: BC12115

tag: center

value: LuminalA

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2.ht ihc status

tag: mfsdel (month)


title: BC13742

tag: type

tag: pr ihc status

tag: p53 ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia T-ALL-SNP-#5-250knsp

tag: Tissue


title: BC13675

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: igf1r ihc status

tag: egfr ihc status

tag: mfs


title: Diagnostic_acute_leukemia Hypodip-SNP-#2-250knsp


title: BC13716

tag: center

tag: pn

value: pos

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: ki67 ihc status

tag: top2a ihc status


title: BC13744

tag: type

value: neg

tag: pr ihc status

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: mfsdel (month)


title: BC13681

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: igf1r ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#3-250knsp

tag: Tissue


title: BXD34B Myeloid batch3

status: Public on Sep 12 2009

city: Haren

first: Bruno

last: Tesson

address: Kerklaan 30

department: Groningen Bioinformatics Center

country: Netherlands

institute: University of Groningen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization was applied on log2 transformed data.

organism: Mus musculus

source_name: Myeloid

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s specifications starting with 100 ng total RNA

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol.

tag: mouse id

tag: bxd strain

tag: cell type

tag: array batch


title: BC14972

tag: center

tag: type

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: ki67 ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: mfs


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#8-250knsp


title: BC9822

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: foxa1 ihc status

tag: mfsdel (month)


title: BC9737

tag: center

tag: type

value: NIBC

tag: pn

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status


title: BC13708

tag: age of diagnosis (year)

tag: pr ihc status

tag: ki67 ihc status

tag: egfr ihc status

tag: top2a ihc status

tag: mfs


title: BC9296

tag: molecular subtype

tag: histology

value: DUC

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status


title: Diagnostic_acute_leukemia T-ALL-SNP-#4-250knsp

tag: Tissue


title: BC10172

tag: center

tag: type

tag: pn

tag: erbb2p ihc status

tag: igf1r ihc status

tag: foxa1 ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia T-ALL-SNP-#3-250knsp


title: BC13682

value: Tunis

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: ki67 ihc status

tag: egfr ihc status


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#6-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#7-250knsp


title: BC9077

tag: molecular subtype

tag: histology

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: top2a ihc status

tag: mfs


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#3-250knsp

tag: Tissue


title: BC3220

tag: center

tag: type

tag: pn

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia E2A-PBX1-SNP-#1-250knsp


title: BC2352

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: ki67 ihc status

tag: mfsdel (month)


title: BC13528

tag: molecular subtype

tag: histology

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: egfr ihc status

tag: top2a ihc status


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#5-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia MLL-SNP-#13-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#2-250knsp


title: BC12836

tag: center

tag: type

tag: pn

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: mfs


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#2-250knsp


title: Diagnostic_acute_leukemia BCR-ABL-SNP-#1-250knsp


title: Diagnostic_acute_leukemia Hypodip-SNP-#1-250knsp


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#2-250knsp


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#4-250knsp


title: BC11041

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: ki67 ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#3-250knsp


title: BC12048

tag: molecular subtype

tag: histology

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: egfr ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia T-ALL-SNP-#2-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia T-ALL-SNP-#1-250knsp


title: BC15120

tag: center

tag: type

tag: pn

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: top2a ihc status


title: BC14481

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: ki67 ihc status

tag: mfs


title: BC12851

tag: molecular subtype

tag: histology

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: egfr ihc status

tag: foxa1 ihc status


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#2-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia TEL-AML1-SNP-#1-250knsp


title: BC16989

tag: center

tag: type

tag: pn

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia Other-SNP-#1-250knsp


title: BC8584

tag: age of diagnosis (year)

value: MIX

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: pr ihc status

tag: ki67 ihc status

tag: top2a ihc status


title: BC13329

tag: molecular subtype

tag: histology

tag: pt

tag: p53 ihc status

tag: erbb2.ht ihc status

tag: egfr ihc status

tag: mfs


title: BC12781

tag: center

tag: type

tag: pn

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: foxa1 ihc status


title: BC9725

tag: age of diagnosis (year)

value: Normal

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: igf1r ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia Hyperdip50-SNP-#1-250knsp

tag: Tissue


title: Diagnostic_acute_leukemia MLL-SNP-#12-250knsp


title: BC9983

tag: molecular subtype

tag: histology

tag: pt

tag: pr ihc status

tag: p53 ihc status

tag: ki67 ihc status

tag: top2a ihc status


title: BC9991

tag: center

tag: type

tag: pn

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: egfr ihc status

tag: mfs


title: BC9317

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

tag: foxa1 ihc status


title: BC7462

tag: molecular subtype

tag: histology

tag: pt

tag: pr ihc status

tag: p53 ihc status

tag: mfsdel (month)


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#1-250knsp

tag: Tissue


title: BC8484

tag: center

tag: type

tag: pn

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status


title: BC2933

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2p ihc status

tag: egfr ihc status

tag: mfs


title: Diagnostic_acute_leukemia Other-SNP-#21-250knsp


title: Diagnostic_acute_leukemia Pseudodip-SNP-#1-250knsp


title: BC8504

tag: molecular subtype

tag: histology

tag: pt

tag: pr ihc status

tag: p53 ihc status

tag: igf1r ihc status

tag: foxa1 ihc status


title: BC5520

tag: center

tag: type

tag: pn

tag: ki67 ihc status

tag: erbb2.ht ihc status

tag: mfsdel (month)


title: BC11348

tag: age of diagnosis (year)

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status


title: RNA_1

status: Public on Sep 01 2009

city: Princeton

first: yirchung

last: Liu

state: NJ

address: 220 Carl Icahn Laboratory

department: Molecular Biology

institute: Princeton University

description:
RNA_1
Each raw data file represents a biological replicate.

hyb_protocol: The FS450_0002 washing protocol (Affymetrix) was used. Briefly, this includes two post-hybridization washes, a streptavidin-phycoerythrin stain, a post-stain wash, an antibody amplification stain, a second streptavidin-phycoerythrin stain, a final wash, and addition of holding buffer to the microarray.

scan_protocol: After completion of the wash cycle, the microarrays were scanned a single time at room temperature on a Affymetrix GeneChip Scanner 3000.

data_processing: We developed in-house computational and statistical analysis tools for use with the E. coli tiling array.  We used a previous study (Choe et al., 2005) as a model for perfect match adjustment on single arrays.  Analysis scripts were written in Perl, MatLab, and R to standardize the statistical manipulations across all data sets. The output file from the scanning process is a CEL file. The raw CEL data were used as the basis for the manuscript; no processed data are available.

organism: Escherichia coli

source_name: MG1655 RNA

label_protocol: DNA labeling: Two ug of the DNA isolated from DNA-protein complexes was used in a labeling reaction with the Enzo Terminal Labeling kit (P/N 42630). The labeling reactions were assembled according to the manufacturer’s instructions; the labeling reaction was incubated at 37 ˚C for 30 minutes to 1 hour.  RNA expression profiling: RNA samples were reverse-transcribed to DNA using the SuperScript system from Invitrogen (P/N 18053017). Ten ug of RNA was incubated with 5 ug random hexamer primer at 70 °C for 10 minutes, then mixed with 8 uL SuperScript buffer, 4 uL DTT, 2 uL 10 uM dNTP mix, 3 uL DEPC-treated water, 1 uL RNasin and 2 uL of SuperScript II Enzyme.  The samples was incubated at 25 °C for 10 minutes, and 42 °C for 2.5 hours, then moved to 95 °C for 5 minutes to terminate the reaction. To fragment the RNA template, 2 uL 1N NaOH was added, and the samples were placed at 65 °C for 15 minutes. At room temperature, the pH was readjusted by adding 2 uL 1N HCl. The cDNA was cleaned using the Qiagen QiaQuick Nucleotide Removal Kit (P/N 28304).

growth_protocol: Batch cultures of E. coli MG1655 were grown at 37°C with shaking in Luria-Bertani medium (0.1% Bacto Tryptone, 0.05% yeast extract, 0.05% NaCl).

extract_protocol: Genomic DNA Extraction: Genomic DNA was extracted according to Current Protocols in Molecular Biology.  Protein-DNA complex isolation: Protein-DNA complexes were isolated by phenol extraction with 150 μL 10 mM Tris and 500 μL 25:24:1 phenol : chloroform : isoamyl alcohol.  A white disk was readily discernible at the aqueous/organic interface. To purify this interface, all aqueous and organic liquid was removed by pipetting. A second extraction was performed by adding 500 μL 10 mM Tris and 450 μL 24:1 chloroform: isoamyl alcohol, vortexing and centrifuging.  Again, all liquid was removed from the interface by pipetting, and residual liquid was removed. For cross-link reversal: the interface was suspended in 500 μL 10 mM Tris and 50 μL 10% SDS, and placed at ~100 ˚C for 30 minutes. The tubes were placed on ice, then moved to 65 ˚C for 3 hours following addition of 5 μL proteinase K (20 mg/mL). After heat treatment, the solutions were phenol/chloroform extracted and ethanol precipitated in the presence of glycogen to purify the DNA.  RNA extraction: the Qiagen RNeasy kit (P/N 74104) was used to isolate total cellular RNA. Immediately following elution in RNase-free water, residual DNA was removed by treatment with DNaseI at 37 °C for 15 minutes. The samples were treated again using the RNeasy kit, resuspended in 40 μl RNase-free water, and stored at -20 °C.

treatment_protocol: For cross-linking, 30 mL of cells were mixed with 300 uL 1M sodium phosphates (pH 7.6) and 810 uL 37% formaldehyde. Cross-linking was quenched by addition of 2 mL 2M glycine. Protein-DNA complexes were isolated from cells grown to early (2.4 x 10^7 CFU/ml) or late (2.4 x 10^8 CFU/ml) exponential phase.  Batch cultures of E. coli MDS42 were grown to early exponential phase.  To obtain tiling-resolution RNA measures across the E. coli genome, wild-type cells were grown in biological duplicate in LB to early exponential phase. The cultures were moved to ice, and the Qiagen RNeasy kit (P/N 74104) was used to isolate total cellular RNA.

tag: strain


title: BC17253

tag: molecular subtype

tag: histology

value: other

tag: pt

tag: pr ihc status

tag: erbb2p ihc status

tag: egfr ihc status

tag: mfs


title: RNA_2

description:
RNA_2
Each raw data file represents a biological replicate.


title: BC2163cc

tag: center

tag: type

tag: pn

tag: p53 ihc status

tag: ki67 ihc status

tag: igf1r ihc status

tag: foxa1 ihc status


title: IPOD_late_log_2

description:
IPOD_late_log_2
Each raw data file represents a biological replicate.

source_name: MG1655 DNA isolated from late-phase DNA-protein complexes


title: CAFs, 4m, biological repetition 2

city: San Francisco

first: Neta

last: Erez

state: CA

address: 513 Parnassus Ave.

institute: UCSF

description: CAFs, 4m, biological repetition 2

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on 430 2.0 Affymetrix mouse genome arrays. . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G3000.

data_processing: The data were analyzed with Affymetrix GeneChip Operating System (GCOS)software using Affymetrix default analysis settings and RMA as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: CAFs: Dysplastic skin fibroblasts from HPV16 mice

label_protocol: Biotinylated cRNA were prepared with the WT-Ovation kit (NuGEN) according to the manufacturer's instructions.

growth_protocol: Fibroblasts were FACS sorted from single cell suspensions of 4 months old HPV or FVBn mouse ears.

extract_protocol: RNA was isolated by the Qiagen RNAeasy Kit and amplified once by the WT-Ovation RNA Amplification Kit.

treatment_protocol: PDGFRα+ fibroblasts were sorted by flow cytometry using BD FACSAria cell sorting system from single cell suspensions prepared from ears of fifteen K14-HPV16 mice with visible dysplastic tissue or from ears of fifteen age matched non transgenic FVB/n mice.

tag: tissue

value: dysplastic ear

tag: gender

value: male


title: IPOD_MDS42

description:
IPOD_MDS42
Each raw data file represents a biological replicate.

source_name: MDS42 DNA isolated from early-phase DNA-protein complexes

tag: strain


title: NDFs, 4m, biological repetition 1

description: NDFs, 4m, biological repetition 1

source_name: NDFs: Normal dermal fibroblasts

value: normal ear

value: FVBn


title: IPOD_late_log_1

description:
IPOD_late_log_1
Each raw data file represents a biological replicate.


title: CAFs, 4m, biological repetition 3

description: CAFs, 4m, biological repetition 3


title: BC7780

tag: age of diagnosis (year)

tag: molecular subtype

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status

tag: mfsdel (month)


title: NDFs, 4m, biological repetition 3

description: NDFs, 4m, biological repetition 3


title: BC10797

tag: center

tag: type

tag: histology

tag: pt

tag: pn

tag: pr ihc status

tag: erbb2p ihc status

tag: egfr ihc status

tag: mfs


title: BC12710

tag: age of diagnosis (year)

tag: molecular subtype

tag: p53 ihc status

tag: ki67 ihc status

tag: igf1r ihc status

tag: foxa1 ihc status


title: CAFs, 4m, biological repetition 1

description: CAFs, 4m, biological repetition 1

tag: tissue

tag: gender

tag: strain


title: NDFs, 4m, biological repetition 2

description: NDFs, 4m, biological repetition 2


title: BC5836

tag: center

tag: type

tag: grade sbr

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status

tag: mfsdel (month)


title: BC9934

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: pr ihc status

tag: erbb2p ihc status

tag: egfr ihc status

tag: mfs


title: genomic_ref4

description:
genomic_ref4
Each raw data file represents a biological replicate.

source_name: MG1655 genomic DNA

tag: strain


title: IPOD_early_log_1

description:
IPOD_early_log_1
Each raw data file represents a biological replicate.

source_name: MG1655 DNA isolated from early-phase DNA-protein complexes


title: BC13591

tag: center

tag: type

tag: grade sbr

tag: p53 ihc status

tag: ki67 ihc status

tag: igf1r ihc status

tag: foxa1 ihc status


title: genomic_ref5

description:
genomic_ref5
Each raw data file represents a biological replicate.


title: genomic_ref3

description:
genomic_ref3
Each raw data file represents a biological replicate.


title: BC12652

tag: age of diagnosis (year)

tag: erbb2 ihc status

tag: er ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: top2a ihc status

tag: mfsdel (month)


title: genomic_ref6

description:
genomic_ref6
Each raw data file represents a biological replicate.


title: IPOD_early_log_2

description:
IPOD_early_log_2
Each raw data file represents a biological replicate.


title: genomic_ref1

description:
genomic_ref1
Each raw data file represents a biological replicate.


title: genomic_ref2

description:
genomic_ref2
Each raw data file represents a biological replicate.


title: BC11979

tag: molecular subtype

tag: histology

tag: pt

tag: pn

tag: pr ihc status

tag: erbb2p ihc status

tag: egfr ihc status


title: BC13008

tag: center

tag: type

tag: grade sbr

tag: p53 ihc status

tag: ki67 ihc status

tag: mfs


title: Pm70_CTC_rep1

city: Mississippi state

first: Bindu

last: Nanduri

state: MS

address: Box 6100 Spring Street

department: Basic Sciences

institute: Mississippi State University

description: P. multocida cultured to mid-log phase (A600 of 0.8) in BHI growth medium

hyb_protocol: Hybridization and washes were conducted by NimbleGen SystemsInc.  Detection of hybridized biotin-labeled probe used Fluorolink Cy3 Labeled Streptavidin (Amersham Pharmacia). Detection of hybridized biotin-labeled probe used Fluorolink Cy3 Labeled Streptavidin (Amersham Pharmacia) by Nimblegen systems Inc.

scan_protocol: Scan was performed by Nimblegen Systems, Inc

data_processing: Raw intensity data (single channel) was log transformed, and normalied using quantile normalization and gene calls generated using  RMA algorithm

organism: Pasteurella multocida subsp. multocida str. Pm70

label_protocol: Samples were labeled by Nimblegen Systems, Inc (www.nimblegen.com) using their SOPs. Briefly, three independent RNA samples (10 ug each) from untreated and antibiotic treated Pm70 were reverse transcribed using Random Hexamer (Gibco) and SuperScript II Reverse Transcriptase (Invitrogen).  Biotin end-labeling of cDNA utilized Terminal Deoxynucleotidyl Transferase (Promega) with Biotin-N6-ddATP (Perkin Elmer)

growth_protocol: P. multocida Pm70 was cultivated in brain heart infusion broth (BHI) at 37 ˚C with rotary aeration. Stationary phase cultures of Pm70 were used to inoculate 50 ml BHI to an initial A600 of 0.05; antibiotic treated cultures contained ¼ MIC of AMX, CTC, or ENR, and control cultures were grown without antibiotics. All cultures were grown in triplicate to mid-log phase (A600 of 0.8). RNAprotect (Qiagen) was added to culture samples and harvested by centrifugation (10,000 x g, 10 min, 4 ºC). Pellets were stored at -80ºC.

extract_protocol: Total RNA from three biological replicate cultures (for untreated control culture as well as antibiotic treated cultures) was isolated using Qiagen RNeasy kit using manufacturer’s protocol. The quality and concentration of RNA was determined by Agilent Bioanalyzer. 10 µg total RNA was used by Nimblegen systems for carrying out cDNA labeling and hybridization using their standard protocols

treatment_protocol: Minimum inhibitory concentrations (MICs) of amoxicillin (AMX), chlortetracycline (CTC) and enrofloxacin (ENR) for Pm70 are 0.5 µg/ml, 4 µg /ml, and 0.031 µg /ml, respectively. Growth kinetics of Pm70 in the presence of 1/4 MIC of the three antibiotics were previously described (Nanduri et al, 2006 JPR). Antibiotic treated cultures contained ¼ MIC of AMX, CTC, or ENR, and control cultures were grown without antibiotics.

tag: Gram-negative, serotype 3 capsular type A strain isolated from a case of cholera in chickens, opportunistic pathogen that causes a range of infections in humans and animals.


title: Pm70_ENR_rep1


title: Pm70_ENR_rep3


title: A549 48 hours mifepristone 6 hours dexamethasone (2)

city: Pasadena

first: Peter

last: Dervan

address: 1200 East California Blvd

institute: California Institute of Technology

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

source_name: A549 lung adenocarcinoma epithelial cells

label_protocol: standard Affymetrix protocol

growth_protocol: Media:  F12K, 10% charcoal-treated FBS, 4mM penn/strep

extract_protocol: RNA isolated using Qiagen Rneasy kit following manufacturer's instructions

tag: cell line


title: A549 48 hours mismatch polyamide 6 hours dexamethasone (3)


title: Pm70_ENR_rep2


title: Pm70_CTC_rep2


title: A549 48 hours mismatch polyamide 6 hours dexamethasone (2)


title: Pm70_CTC_rep3


title: Pm70_AMX_rep2


title: A549 48 hours mismatch polyamide 6 hours dexamethasone (1)


title: A549  6 hours dexamethasone (1)

treatment_protocol: 6 hours dexamethasone


title: Pm70_AMX_rep3


title: A549 48 hours match polyamide 6 hours dexamethasone (3)


title: A549 48 hours match polyamide 6 hours dexamethasone (2)


title: Pm70_AMX_rep1


title: A549 48 hours mifepristone 6 hours dexamethasone (1)


title: A549  6 hours dexamethasone (2)


title: A549 48 hours match polyamide 6 hours dexamethasone (1)


title: A549 non-treated control (1)

treatment_protocol: non-treated control


title: A549 48 hours mifepristone 6 hours dexamethasone (3)


title: A549 non-treated control (3)


title: A549  6 hours dexamethasone (3)


title: A549 non-treated control (2)


title: si-RL Treg

city: Baltimore

first: Fan

last: Pan

state: MD

address: 1650 Orleans St CRB I Room 424

department: Oncology

institute: Johns Hopkins Medical Institions, School of Medicine

description: Gene expression of si-RL Natrual Treg

hyb_protocol: Samples were hybridized to separate Agilent 4x 44K whole mouse genome microarray chips at 65ºC for 17hrs

scan_protocol: Expression array Chips were scanned using Agilent Scanner controlled by Agilent Scan Control 7.0 Software and data was extracted using Agilent Feature Extraction 9.5.3.1 software.

data_processing:
Agilent FE processed signal intensities were imported into Genespring GX 9.0.1 (Agilent Technologies).
Log2 transformation and Cross-array quartile normalization was carried out on all intensities higher than 5.

source_name: si-RL GFP + CD4+CD25+ T cells

label_protocol: Standard labeling using Cyanine-3 Labeled CTPs was carried out after cDNA was synthesized using the Low RNA input Fluorescent linear Amplification kit ( Agilent Technologies) according to the manufacturers protocol.

growth_protocol: CD4 T cells were isolated from Balb/C mice and enriched for CD25+ and CD25- populations using Miltenyi’s magnetically labeled beads before sorting. Cells were maintained in Complete RPMI 1640.

extract_protocol: Sorted cells were pelleted suspended in Trizol and stored at -80ºC prior to RNA extraction using the Trizol reagent according to the manufacturer's instructions. RNA integrity was analyzed using an Agilent 2100 Bioanalyzer, the RNA 6000 Pico, and Nano Kits (Agilent Technologies).

treatment_protocol: Natural Tregs enriched for CD25+ using Miltenyi’s magnetically labeled beads, transduced with lentivirus containined Eos or Renilla luciferase gene specific shRNAs, and incubated for 60 hrs in Human IL-2 supplemented complete RPMI. GFP+ cells were sorted out for Gene Expression analysis using the FACSAria I.

tag: cell type

value: natural Tregs

tag: transfection protocol

value: control shRNA knockdown

tag: strain

value: Balb/C

tag: secondary lymphoid tissue

value: Spleen and Lymph nodes


title: Pm70_control_rep3


title: Pm70_control_rep1


title: Pm70_control_rep2


title: naïve

description: Gene Expression of Naïve T cells

source_name: CD4+CD25-CD62Lhi Tcells

value: naive  T cells

value: untransfected control


title: si-Eos Treg

description: Gene Expression of si-Eos Natural Treg

source_name: si-Eos GFP + CD4+CD25+ T cells

value: Eos shRNA knockdown


title: Stat3flx/flx/NIC ID # 819

city: Montreal

first: Solmaz

last: Shahalizadeh

state: Quebec

address: 3649 Prom. Sir-William-Osler, Room 435

department: McGill Centre for Bioinformatics

country: Canada

institute: McGill University

hyb_protocol: Dye-labeled RNA was hybridized onto a Whole Mouse Genome Oligo 4x44K Microarray platform (Agilent) against a universal mouse reference RNA (Stratagene)

scan_protocol: The resulting arrays were scanned using a Microarray Scanner (Model G2565BA, Agilent Technologies)

data_processing: The arrays were processed using Feature Extraction software (Agilent). Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.

source_name: mammary epithelial tumor

label_protocol: RNA samples were labeled using an Amino Allyl MessageAmp II aRNA Amplification Kit (Applied Biosystems) and Cy5 dye (Amersham Biosciences)

extract_protocol: Total RNA was extracted from flash frozen mammary tumor samples using a Qiagen Rneasy Midi Kit

tag: tissue

value: mammary epithelial tumor

tag: gender

value: female

tag: parity

value: virgin

tag: tumor stage

value: 6 weeks post palpation

source_name: Stratagene universal mouse reference

tag: reference

value: Stratagene universal mouse reference


title: Stat3wt/wt/NIC Pool 3


title: F24M_1

status: Public on Aug 29 2009

city: Reno

first: Claus

last: Tittiger

state: NV

address: Mail Stop 330

department: Biochemistry and Molecular Biology

institute: University of Nevada, Reno

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data processing was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

organism: Dendroctonus ponderosae

source_name: 30 pooled midguts/fatbodies

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Beetles were collected from Pinus ponderosae bolts from Little Valley, Nevada

extract_protocol: Qiagen plant midiprep followed by RNase-free DNase digestion

value: midguts/fatbodies

tag: status

value: fed with males 24 h


title: Stat3flx/flx/NIC ID # 2130


title: Stat3flx/flx/NIC ID # 2122


title: Stat3flx/flx/NIC ID # 1487


title: F48U_2

source_name: 20 pooled midguts/fatbodies

value: unfed (starved) 48 h


title: F48M_1

value: fed alone for 24 h, then with males 24 h


title: Stat3wt/wt/NIC Pool 2


title: Larv_1

source_name: 20 pooled whole bodies

value: whole bodies

value: unknown

value: multiple instars


title: F24M_2


title: Larv_3


title: Fpre_1

value: teneral (pre-emerged)


title: Stat3wt/wt/NIC Pool 1


title: Treg

description: Gene Expression of Natural Treg

source_name: CD4+CD25+ T cells

value: natural Tregs

value: Balb/C

value: Spleen and Lymph nodes


title: Larv_4


title: F24M_4


title: F24M_3


title: Pupa_4

value: pupae


title: Stat3flx/flx/NIC  ID # 260

value: mammary epithelial tumor


title: Pupa_3


title: Pupa_2


title: BC9948

source_name: Breast tumor sample

tag: center

value: IPC

tag: type

value: IBC

tag: age of diagnosis (year)

tag: molecular subtype

tag: histology

value: DUC

tag: pt

tag: pn

tag: erbb2 ihc status

value: pos

tag: er ihc status

tag: pr ihc status

tag: erbb2.ht ihc status

tag: erbb2.tab ihc status

tag: erbb2p ihc status

tag: igf1r ihc status

value: neg

tag: egfr ihc status

tag: top2a ihc status

tag: foxa1 ihc status

tag: mfsdel (month)


title: Larv_2

tag: tissue

tag: gender

tag: status


title: Fpre_2

value: midguts/fatbodies

value: female


title: Fpre_3


title: Mpre_3

value: male


title: Fpre_4


title: Mpre_2


title: M24F_3

value: fed alone for 24 h, then with females 24 h


title: M24U_2

value: unfed (starved) 24 h


title: M24F_2


title: M24F_4


title: Mpre_1


title: Mpre_4


title: M24U_3


title: M24U_4


title: F48U_1

value: unfed (starved) 48 h


title: M24U_1


title: F48U_3


title: Pupa_1

value: whole bodies

value: unknown


title: M24F_1


title: F24A_1

value: fed alone for 24 h


title: F48M_2

value: fed alone for 24 h, then with males 24 h


title: F48M_4


title: F48U_4


title: F48M_3


title: F24A_3


title: Sample NA19238_R

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: F24U_2


title: Sample NA19239


title: Sample NA19240


title: Sample NA19194


title: Sample NA19192


title: miR-24 HepG2 T Duplicate

status: Public on Aug 27 2009

city: Boston

first: Ashish

last: Lal

state: MA

address: 260 WAB, 200 Longwood Ave

institute: Harvard University

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The normalization process discards those genes for which the detection p-value is not significant.

source_name: HepG2 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type


title: Sample NA19193


title: Sample NA19160


title: F24A_4


title: Sample NA19173


title: miR-24 HepG2 T


title: Sample NA19171


title: Control HepG2 T


title: F24A_2


title: F24U_3


title: F24U_1


title: GM00144

status: Public on Aug 21 2009

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: GM00144 fibroblast cell line

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: fibroblasts were cultured in DMEM supplemented with 10% fetal calf serum, L-glutamine, penicillin, and streptomycin

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

tag: age

tag: sex

value: F

tag: race

value: cau

value: Skin


title: Sample NA19161


title: Sample NA19159


title: Sample NA19143


title: F24U_4


title: Sample NA19145


title: Sample NA19142


title: Sample NA19138


title: Sample NA19172


title: Sample NA19139


title: Sample NA19140


title: Sample NA19129


title: Sample NA19120


title: Sample NA19119


title: Sample NA19092


title: Sample NA19144


title: Sample NA19094


title: Sample NA19093


title: Sample NA19238


title: Sample NA19003


title: GM02767

description: GM02767 fibroblast cell line


title: Sample NA18999


title: Sample NA18987


title: Sample NA18965


title: Sample NA18972


title: Sample NA18968


title: Sample NA18960


title: Sample NA19141


title: Sample NA18952


title: Sample NA19137


title: Sample NA18953


title: Sample NA18978


title: Sample NA18956


title: Sample NA18971


title: Sample NA18951_R


title: Sample NA18855


title: Sample NA18856_R


title: Sample NA18949


title: Sample NA18856


title: Sample NA18992


title: Sample NA18857


title: Sample NA18853


title: Sample NA18994


title: Control HepG2 T Duplicate


title: Sample NA19116


title: Sample NA18854


title: Sample NA18852


title: Sample NA18612


title: Sample NA18609_R


title: Sample NA18609


title: Sample NA18577


title: Sample NA18576


title: Sample NA18608


title: Sample NA18593


title: Sample NA18951


title: Sample NA18555


title: Sample NA18558


title: Sample NA18944


title: GM06944

description: GM06944 fibroblast cell line


title: Sample NA18542


title: Sample NA18550


title: Sample NA18547


title: Sample NA18517


title: Sample NA18529


title: Sample NA18502


title: Sample NA18516


title: Sample NA12892


title: Sample NA12875


title: Sample NA18537


title: Sample NA12865


title: Sample NA12874


title: Sample NA12812


title: Sample NA12801


title: Sample NA18515


title: Sample NA12891


title: Sample NA18507


title: Sample NA12750


title: Sample NA12239


title: Sample NA12264


title: Sample NA12740


title: Sample NA12248_R


title: Sample NA12236


title: Sample NA12248


title: Sample NA12813


title: Sample NA12249


title: Sample NA12156


title: Sample NA12146


title: Sample NA12043


title: Sample NA12044


title: Sample NA12057


title: Sample NA12154


title: Sample NA11995


title: Sample NA11994


title: Sample NA11993_R


title: Sample NA11992


title: Sample NA12234


title: Sample NA11993


title: Sample NA11882


title: Sample NA12056


title: Sample NA11881


title: Sample NA10860


title: Sample NA10861


title: Sample NA10857


title: Sample NA10859


title: Sample NA10835


title: Sample NA10851


title: Sample NA10830


title: Sample NA07357


title: Sample NA07348


title: Sample NA07029


title: Sample NA06993_R


title: Sample NA06993


title: Sample NA07000


title: Sample NA06994


title: Sample NA10847


title: Sample NA06991


title: Sample NA06985


title: Sample NA12878


title: Sample NA12751


title: Sample NA10863


title: CDC220726

status: Public on Jun 15 2009

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

description:
Data from triplicate probes was averaged.  For each probe, see raw data which is supplied as a supplementary file.
We routinely scanned arrays hybridized with Cy5 labeled DNA using both 635 and 532 wavelengths.  The Cy3 channel data in the raw data files for these samples can be deleted as it was not used in any data analysis.

hyb_protocol: Labeled DNA was hybridized to arrays for 14 hrs at 42C.

scan_protocol: The arrays were scanned with a GenePix 4000B

data_processing: The log10 (average 635 nm median signal intensity for triplicate probes/average signal intensity of all empty spots on array) was determined.

organism: Clostridium botulinum

source_name: Clostridium botulinum, strain CDC220726

label_protocol: 1 ug of genomic DNA was labeled with Cy5 random primers using Klenow fragment

extract_protocol: Epicenter MasterPure DNA Purification kit (Madison, WI)

tag: toxin subtype


title: CDC36955

source_name: Clostridium botulinum, strain CDC36955


title: CDC2171

source_name: Clostridium botulinum, strain CDC2171


title: 69A

source_name: Clostridium botulinum, strain 69A


title: CDC36924

source_name: Clostridium botulinum, strain CDC36924


title: CDC36923

source_name: Clostridium botulinum, strain CDC36923


title: CDC36956

source_name: Clostridium botulinum, strain CDC36956


title: 62A

source_name: Clostridium botulinum, strain 62A


title: Sample NA07345


title: CDC51303

source_name: Clostridium botulinum, strain CDC51303


title: CDC42961

source_name: Clostridium botulinum, strain CDC42961

value: A(B)


title: CDC220727

source_name: Clostridium botulinum, strain CDC220727


title: 73A

source_name: Clostridium botulinum, strain 73A


title: mRNA_Reprogrammed iPSC line 1

status: Public on Jul 10 2009

city: Los Angeles

first: Mark

middle: H.

last: Chin

address: 650 Charles E. Young Dr

department: Human Genetics

institute: UCLA

description: mRNA_Reprogrammed iPSC line 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on human expression arrays

scan_protocol: Gene chips were analyzed using GeneChip® Scanner 3000.

data_processing:
The raw data was processed using the RMA algorithm and was implemented using R (Bioconductor).
The data is presented as a summary of the highest confidence probesets for each given RefSeq identifier. (See Materials and Methods, Chin, et al. Cell Stem Cell, 2009)

source_name: hiPSC line 1 (p61)

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

growth_protocol: Cell lines were cultured in ES cell media (Lowry, et al. PNAS, 2008)

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

treatment_protocol: Reprogrammed Cell lines were created as described in Lowry, et al. (PNAS, 2008)

value: induced pluripotent somatic cells

tag: cell line

value: clone line 1

tag: passages


title: CDC40234

source_name: Clostridium botulinum, strain CDC40234


title: CDC657

source_name: Clostridium botulinum, strain CDC657


title: FRI-H1A2

source_name: Clostridium botulinum, strain FRI-H1A2


title: ATCC 3502

organism: Clostridium botulinum A str. ATCC 3502

source_name: Clostridium botulinum, strain ATCC 3502


title: CDC21547

source_name: Clostridium botulinum, strain CDC21547


title: mutated non-IGVH3-23 repl 22

status: Public on Jun 13 2009

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description: Biological replicate 22 of 22.

hyb_protocol: The Hybridization was performed acording to Ambion protocol

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile

source_name: mutated non-IGVH323 purified cell of CLL

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy5-labeled reference aRNA (according to Agilent protocol)

extract_protocol: Total RNA was extracted according to TRIZOL reagent protocol

value: Mutated non-IGVH 323 purified cell of CLL

source_name: aRNA from pooled normal PB B cells of healthy donors

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol)

tag: reference


title: mutated non-IGVH3-23 repl 19

description: Biological replicate 19 of 22.

value: aRNA from pooled normal PB B cells of healthy donors


title: mRNA_Reprogrammed iPSC line 2

description: mRNA_Reprogrammed iPSC line 2

source_name: hiPSC line 2 (p54)

value: clone line 2


title: mRNA_Reprogrammed iPSC line 18 (p56)

description: mRNA_Reprogrammed iPSC line 18 (p56)

source_name: hiPSC line 18 (p56)

value: clone line 18


title: mutated non-IGVH3-23 repl 21

description: Biological replicate 21 of 22.


title: mutated non-IGVH3-23 repl 14

description: Biological replicate 14 of 22.


title: mutated non-IGVH3-23 repl 17

description: Biological replicate 17 of 22.


title: mutated non-IGVH3-23 repl 11

description: Biological replicate 11 of 22.


title: mutated non-IGVH3-23 repl 15

description: Biological replicate 15 of 22.


title: mutated non-IGVH3-23 repl 16

description: Biological replicate 16 of 22.


title: mutated non-IGVH3-23 repl 13

description: Biological replicate 13 of 22.


title: mutated non-IGVH3-23 repl 12

description: Biological replicate 12 of 22.


title: mutated non-IGVH3-23 repl 18

description: Biological replicate 18 of 22.


title: mutated non-IGVH3-23 repl 7

description: Biological replicate 7 of 22.


title: mutated non-IGVH3-23 repl 3

description: Biological replicate 3 of 22.


title: mutated non-IGVH3-23 repl 4

description: Biological replicate 4 of 22.


title: mutated non-IGVH3-23 repl 6

description: Biological replicate 6 of 22.


title: mutated non-IGVH3-23 repl 20

description: Biological replicate 20 of 22.


title: mutated non-IGVH3-23 repl 10

description: Biological replicate 10 of 22.


title: mutated non-IGVH3-23 repl 1

description: Biological replicate 1 of 22.


title: mutated non-IGVH3-23 repl 5

description: Biological replicate 5 of 22.


title: mutated non-IGVH3-23 repl 2

description: Biological replicate 2 of 22.


title: mutated non-IGVH3-23 repl 8

description: Biological replicate 8 of 22.


title: mutated non-IGVH3-23 repl 9

description: Biological replicate 9 of 22.


title: MC31

status: Public on Nov 01 2008

city: Houston

first: Federico

middle: A

last: Monzon

state: TX

address: 6565 Fannin St., MS205

institute: The Methodist Hospital Research Institute

hyb_protocol: Affymetrix Mapping 10K Xba 2.0 Assay

scan_protocol: Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner

data_processing: Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0

label: Biotinilated - Fragmented PCR products

source_name: Renal Neoplasm, Unclassified, DNA from Paraffin Embedded Tissue

label_protocol: Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, 2008 Mar;17(1):3-13)

extract_protocol: Deparaffinization followed by Qiagen DNaasy Mini kit by manufacturer's instructions

value: M

tag: agedecade

tag: tumor size

tag: furhman nuclear grade

tag: tnm stage

value: T1a Nx Mx

tag: lymphovascular invasion

value: N


title: MC29


title: MC24


title: MC19

value: T1b(5) Nx Mx


title: MC27

value: T3b Nx Mx


title: MC22

value: T2 Nx Mx


title: MC28


title: MC16

value: n


title: MC15


title: MC12

value: T3b N2 Mx

value: Y


title: MC30

value: F


title: MC02


title: MC01


title: MC25


title: MC18

value: T1b Nx Mx


title: MC26

value: T3a N0 Mx


title: MC21

value: T3a Nx Mx


title: MC13


title: MC11


title: MC14


title: MRCC09

source_name: Renal Cell Carcinoma, Papillary Type, DNA from Paraffin Embedded Tissue


title: MC20

value: UNK


title: MC10


title: MC06


title: MC23


title: MRCC14

data_processing: Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.1


title: MC09


title: RAD22

source_name: Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue


title: RAD10


title: RAD14


title: CUMC02


title: RAD20


title: CRCC6


title: MRCC02


title: RAD08


title: CUMC07


title: CUMC03


title: MRCC10

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep9

source_name: Renal Cell Carcinoma, Chromophobe Type, DNA from Paraffin Embedded Tissue


title: CRCC01


title: CUMC04


title: DES03


title: CHRCC03

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep6


title: CUMC06


title: CUMC09


title: PRCC02


title: CUMC05


title: ONC03

source_name: Renal Oncocytoma, DNA from Paraffin Embedded Tissue


title: MRCC01

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep8


title: MONC01


title: OC01


title: DES05


title: ONC02


title: CUMC01


title: DES08

description: RenalCellCarcinoma_Chromophobe_FFPE_Rep7


title: Sample ID 05_128 normal stroma from patient with localized prostate cancer

status: Public on Aug 17 2008

city: Seattle

first: Ilona

middle: N

last: Holcomb

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: On microgram each of tumor and reference DNA labeled with Cy5 and Cy3, respectively, were combined and briefly dried by Speedvac. The samples were resuspended in hybridization mix (50% formamide, 10% dextran sulfate, 3x SSC, 1.5% SDS) and heated to 70°C for 10 minutes, followed by 1-hour incubation at 37°C to allow blocking of repetitive sequences by human Cot-1 DNA. After incubation, samples were applied to the microarray under a coverslip and hybridized at 37°C for 18 hours. After hybridization, the arrays were then washed in 50% formamide and 2x SSC (pH 7.0) for 20 minutes at 45°C, followed by a 7-minute wash at room temperature in 0.1 mol/L NaPO4 (pH 8.0) and 0.1% NP40. After washing, the arrays were dried by centrifugation at 600 rpm for 5 minutes.

scan_protocol: Arrays were scanned with a GenePix 4000A scanner (Axon Instruments, Inc., Union City, CA); fluorescence data were processed with GenePix 3.0 image analysis software (Axon Instruments, Inc.). For each spot, log2 ratio = log2(Cy5/Cy3) and average log2 intensity = [log2(Cy5) + log2(Cy3)]/2 were calculated, where Cy5 and Cy3 refer to the median foreground fluorescent signals of the tumor and reference DNA, respectively. Background subtraction was not used because it conferred no benefit in tests run on cell lines with varying numbers of X chromosome copies.

data_processing: The log2 ratios on each array were normalized and corrected for intensity-based location adjustment with a block-level loess algorithm (as described in Yang YH, Dudoit S, Luu P, Speed TP Normalization for cDNA microarray Bittner ML Chen Y Dorsel AN Dougherty ER eds. . Microarrays: optical technologies and informatics 2001141-52. SPIE, Society for Optical Engineering Bellingham, WA).

source_name: Normal stromal sample collected from prostate.

label_protocol: Array CGH bioprime kit (Invitrogen)

extract_protocol: The area selected for molecular analysis was from normal prostate stroma. Cells were isolated by laser-capture microdissection (LCM), as described previously (Lin DW, Coleman IM, Hawley S, et al. Influence of surgical manipulation on prostate gene expression: implications for molecular correlates of treatment effects and disease prognosis. J Clin Oncol 2006;24:3763-70). Two to four thousand cells were collected. DNA was isolated by the QIAamp DNA Micro Kit (Qiagen, CA). DNA was then amplified by ligation mediated pcr (as per method described in Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR and Riethmuller G. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A 1999;96: 4494-4499).

tag: tissue

value: This sample was part of a set of five normal-cell samples that were used for defining thresholds of chromosomal loss and gain for primary tumor arrays.

source_name: normal female reference DNA

extract_protocol: DNA was isolated using a QIAamp DNA Blood Mini Kit (Qiagen)

value: Female peripheral blood


title: Sample ID 05_055 normal stroma from patient with localized prostate cancer


title: Roots of chickpea plants grown in soil at normal conditions

status: Public on Sep 26 2008

type: SAGE

anchor: NlaIII

city: Dijon

first: Carlos

middle: Mauricio

last: Molina

state: Bourgogne

address: 17 Rue Sully

department: UMRLEG

institute: INRA

description: Supersage libraries of chickpea roots were developed in control as well as 6h dehydration conditions

molecule: polyA RNA

organism: Cicer arietinum

extract_protocol: CTAB method with LiCl precipitation

tag: chickpea variety

value: ICC588 (drought tolerant)

tag: treatment

value: No treatment

tag: growth conditions

value: Greenhouse


title: Sample ID 05_132 normal stroma from patient with localized prostate cancer


title: CHRCC02

value: M


title: Sample ID 04_141 normal stroma from patient with localized prostate cancer


title: Sample ID 05_047 normal stroma from patient with localized prostate cancer