title: _ILC_A066

description: Gene expression data from human breast cancer tissue A066

tag: Alter = 78, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = 1A, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 2, Diagnosis = ILC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 40, OS_Months = 40, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = NA, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA

tag: common reference sample


title: Rhesus kidney 1 (replicate a)

status: Public on Sep 17 2008

type: RNA

city: Chicago

first: Ran

last: Blekhman

state: IL

country: USA

institute: University of Chicago

description: Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle.

hyb_protocol: Nimblegen hybridization protocol (www.nimblegen.com)

scan_protocol: Microarrays were scanned using an Axon scanner

data_processing: Raw data was extracted from the images using the NimbleScan software (version 2.4). We performed background correction using the normexp function in limma with an offset of 32, and normalization using an adaptation of the quantile normalization approach.

molecule: total RNA

organism: Macaca mulatta

source_name: kidney

label_protocol: Nimblegen RNA labeling protocol (www.nimblegen.com)

extract_protocol: total RNA was extracted using Trizol

tag: Rhesus kidney 1 (replicate a)


title: _IDC-mixed_A064

city: Heidelberg

first: Alberto

last: Calabro

address: INF 580

country: Germany

institute: DKFZ

description: Gene expression data from human breast cancer tissue A064

hyb_protocol: ch1 and ch2 together are solved in 50 ul 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt's solution and 2 ng/ul Cot1-DNA (Invitrogen); sample was denaturated at 65C for 2min, hybridzation of arrays were performed in Corning chambers 17h at 39C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: Hybridized arrays were scanned with the GenePix 4000B microarray scanner (Axon Instruments, Union City, CA)

data_processing: log2 ratios (Cy5/Cy3)

organism: Homo sapiens

source_name: human breast cancer tumor tissue

label_protocol: Labelled cRNA were prepared according to the TacKle protocol [Schlingemann et al. Nucleic Acids Res. 2005]

extract_protocol: total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturers' instructions.

treatment_protocol: tumor tissue samples from surgically treated patients were collected intraoperatively, snap-frozen and stored at -80 C. All samples underwent a careful analysis of the histopathology, estimation of tumor and stromal content and subsequent macro-dissection of the tumor regions before enrollment into the microarray experiments.

tag: Alter = 67, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 11, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC-mixed, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 16.59, OS_Months = 28.58, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 1, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no

source_name: Universal human reference RNA (Stratagene), one round amplified

extract_protocol: 2ug total RNA was amplified one round based on T7 RNA Polymerase (Ambion Message Amplification Kit Reagents, 6h IVT)


title: _IDC_A063

description: Gene expression data from human breast cancer tissue A063

tag: Alter = 75, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 134, OS_Months = 161, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = NA, Her2neu_DAKO = 1+, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: Chimp kidney 5 (replicate b)

organism: Pan troglodytes

tag: Chimp kidney 5 (replicate b)


title: _IDC_A062

description: Gene expression data from human breast cancer tissue A062

tag: Alter = 72, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 1BII, pM = 0, Number_of_asported_lymphnodes = 15, Number_of_positive_lyphnodes = 6, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 30.32, OS_Months = 50.17, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp kidney 2 (replicate a)

tag: Chimp kidney 2 (replicate a)


title: Human kidney 6 (replicate B)

tag: Human kidney 6 (replicate B)


title: _medullar_A061

description: Gene expression data from human breast cancer tissue A061

tag: Alter = 68, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 1BIV, pM = 0, Number_of_asported_lymphnodes = 15, Number_of_positive_lyphnodes = 3, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 1, Diagnosis = medullar, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 108.25, OS_Months = 145.61, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp kidney 1 (replicate A)

tag: Chimp kidney 1 (replicate A)


title: Chimp kidney 2 (replicate b)

tag: Chimp kidney 2 (replicate b)


title: Human kidney 4 (replicate B)

tag: Human kidney 4 (replicate B)


title: _IDC_A059

description: Gene expression data from human breast cancer tissue A059

tag: Alter = 59, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 20, Number_of_positive_lyphnodes = 11, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 9.36, OS_Months = 14.92, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = yes


title: Human kidney 6 (replicate A)

tag: Human kidney 6 (replicate A)


title: Human kidney 5 (replicate B)

tag: Human kidney 5 (replicate B)


title: Human kidney 1 (replicate A)

tag: Human kidney 1 (replicate A)


title: _IDC_A056

description: Gene expression data from human breast cancer tissue A056

tag: Alter = 65, Year_of_Diagnosis = 1989, Gender = f, pT = 2, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 15, OS_Months = 15, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: _IDC_A058

description: Gene expression data from human breast cancer tissue A058

tag: Alter = 56, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 1BI, pM = 0, Number_of_asported_lymphnodes = 13, Number_of_positive_lyphnodes = 1, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 18.17, OS_Months = 35.38, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 2, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no

tag: common reference sample


title: Chimp kidney 1 (replicate b)

tag: Chimp kidney 1 (replicate b)


title: _IDC_A057

description: Gene expression data from human breast cancer tissue A057

tag: Alter = 43, Year_of_Diagnosis = 1991, Gender = f, pT = X, pN = 0, pM = 0, Number_of_asported_lymphnodes = 16, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = 0, Status = lost_for_follow_up, Reason_of_death = NA, DFS_Months = 133.26, OS_Months = 133.26, , Epithel_Percentage = 70, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Human kidney 4 (replicate A)

tag: Human kidney 4 (replicate A)


title: Human kidney 2 (replicate B)

tag: Human kidney 2 (replicate B)


title: Human kidney 3 (replicate B)

tag: Human kidney 3 (replicate B)


title: Human kidney 5 (replicate A)

tag: Human kidney 5 (replicate A)


title: _IDC_A053

description: Gene expression data from human breast cancer tissue A053

tag: Alter = 46, Year_of_Diagnosis = 1990, Gender = f, pT = 1C, pN = 0, pM = 0, Number_of_asported_lymphnodes = 11, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = dead, Reason_of_death = tumoral, DFS_Months = 29.96, OS_Months = 104.64, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Human kidney 3 (replicate A)

tag: Human kidney 3 (replicate A)


title: _IDC_A054

description: Gene expression data from human breast cancer tissue A054

tag: Alter = 67, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 1BIV, pM = 0, Number_of_asported_lymphnodes = 13, Number_of_positive_lyphnodes = 12, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 6.08, OS_Months = 32.69, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _ILC_A050

description: Gene expression data from human breast cancer tissue A050

tag: Alter = 79, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 2, Diagnosis = ILC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 46, OS_Months = 126, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: _IDC_A051

description: Gene expression data from human breast cancer tissue A051

tag: Alter = 70, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = X, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 161, OS_Months = 161, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = NA, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: Rhesus Liver 6 (replicate A)

source_name: liver

tag: Rhesus Liver 6 (replicate A)


title: _IDC_A046

description: Gene expression data from human breast cancer tissue A046

tag: Alter = 50, Year_of_Diagnosis = 1992, Gender = f, pT = 1C, pN = 0, pM = 0, Number_of_asported_lymphnodes = 22, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = 0, Status = alive, Reason_of_death = NA, DFS_Months = 136, OS_Months = 136, , Epithel_Percentage = 80, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A049

description: Gene expression data from human breast cancer tissue A049

tag: Alter = 61, Year_of_Diagnosis = 1991, Gender = f, pT = X, pN = 0, pM = 0, Number_of_asported_lymphnodes = 14, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = 2, Status = lost_for_follow_up, Reason_of_death = NA, DFS_Months = 118, OS_Months = 118, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A052

description: Gene expression data from human breast cancer tissue A052

tag: Alter = 48, Year_of_Diagnosis = 1991, Gender = f, pT = 4D, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 14, Number_of_positive_lyphnodes = 12, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 1, Diagnosis = IDC, Lymphocyte_infiltration = 1, Status = dead, Reason_of_death = tumoral, DFS_Months = 4, OS_Months = 35, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 1, Neoadjuvant_PCT_with_Anthracyclin = yes, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = yes, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A047

description: Gene expression data from human breast cancer tissue A047

tag: Alter = 70, Year_of_Diagnosis = 1993, Gender = f, pT = 2, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 22, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 1, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = alive, Reason_of_death = NA, DFS_Months = 136.57, OS_Months = 136.57, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 6 (replicate B)

description: Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle.

tag: Rhesus Liver 6 (replicate B)


title: _IDC-mixed_A045

description: Gene expression data from human breast cancer tissue A045

tag: Alter = 47, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = 0, pM = 0, Number_of_asported_lymphnodes = 8, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC-mixed, Lymphocyte_infiltration = 1, Status = dead, Reason_of_death = tumoral, DFS_Months = 34.27, OS_Months = 92.16, , Epithel_Percentage = 70, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = yes, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = yes, Adjuvant_PCT_without_Anthracyclin = no

tag: common reference sample


title: _IDC_A044

description: Gene expression data from human breast cancer tissue A044

tag: Alter = 70, Year_of_Diagnosis = 1989, Gender = f, pT = 1C, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 48, OS_Months = 48, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: Rhesus Liver 4 (replicate A)

tag: Rhesus Liver 4 (replicate A)


title: _IDC-mixed_A043

description: Gene expression data from human breast cancer tissue A043

tag: Alter = 71, Year_of_Diagnosis = 1991, Gender = f, pT = X, pN = 2, pM = 0, Number_of_asported_lymphnodes = 13, Number_of_positive_lyphnodes = 13, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC-mixed, Lymphocyte_infiltration = 2, Status = dead, Reason_of_death = tumoral, DFS_Months = 38.8, OS_Months = 52.96, , Epithel_Percentage = 70, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 3 (replicate A)

tag: Rhesus Liver 3 (replicate A)


title: Human kidney 2 (replicate A)

tag: Human kidney 2 (replicate A)


title: Rhesus Liver 5 (replicate A)

tag: Rhesus Liver 5 (replicate A)


title: _IDC_A039

description: Gene expression data from human breast cancer tissue A039

tag: Alter = 59, Year_of_Diagnosis = 1992, Gender = f, pT = 1C, pN = 1BII, pM = 0, Number_of_asported_lymphnodes = 26, Number_of_positive_lyphnodes = 4, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = lost_for_follow_up, Reason_of_death = NA, DFS_Months = 163, OS_Months = 163, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 5 (replicate B)

tag: Rhesus Liver 5 (replicate B)


title: Chimp kidney 3 (replicate b)

tag: Chimp kidney 3 (replicate b)


title: _IDC_A038

description: Gene expression data from human breast cancer tissue A038

tag: Alter = 70, Year_of_Diagnosis = 1993, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 13, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = 1, Status = alive, Reason_of_death = NA, DFS_Months = 139, OS_Months = 139, , Epithel_Percentage = 60, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A040

description: Gene expression data from human breast cancer tissue A040

tag: Alter = 76, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = X, pM = 0, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 10, OS_Months = 15, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = NA, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: _IDC_A036

description: Gene expression data from human breast cancer tissue A036

tag: Alter = 63, Year_of_Diagnosis = 1994, Gender = f, pT = 4B, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 9, Number_of_positive_lyphnodes = 4, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 13.37, OS_Months = 62.49, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = yes, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = yes, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 4 (replicate B)

tag: Rhesus Liver 4 (replicate B)


title: Chimp Liver 6 (replicate B)

tag: Chimp Liver 6 (replicate B)


title: _IDC_A037

description: Gene expression data from human breast cancer tissue A037

tag: Alter = 50, Year_of_Diagnosis = 1990, Gender = f, pT = 2, pN = 1BII, pM = 0, Number_of_asported_lymphnodes = 28, Number_of_positive_lyphnodes = 8, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 1.77, OS_Months = 63.87, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 3, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 3 (replicate B)

tag: Rhesus Liver 3 (replicate B)


title: _IDC_A035

description: Gene expression data from human breast cancer tissue A035

tag: Alter = 71, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 2, pM = 0, Number_of_asported_lymphnodes = 6, Number_of_positive_lyphnodes = 4, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = not_tumoral_Bronchopneumonie, DFS_Months = 71.29, OS_Months = 128, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 1, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no

tag: common reference sample


title: _ILC_A042

description: Gene expression data from human breast cancer tissue A042

tag: Alter = 56, Year_of_Diagnosis = 1996, Gender = f, pT = 3, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 25, Number_of_positive_lyphnodes = 25, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 2, Diagnosis = ILC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 14.92, OS_Months = 35.71, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 1, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A033

description: Gene expression data from human breast cancer tissue A033

tag: Alter = 84, Year_of_Diagnosis = 1992, Gender = f, pT = 1C, pN = 1A, pM = 0, Number_of_asported_lymphnodes = 16, Number_of_positive_lyphnodes = 1, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = 1, Status = dead, Reason_of_death = tumoral, DFS_Months = 103.26, OS_Months = 103.26, , Epithel_Percentage = 30, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = brusterhaltend_(Quadrantenresektion), Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 2 (replicate A)

tag: Rhesus Liver 2 (replicate A)


title: _IDC_A032

description: Gene expression data from human breast cancer tissue A032

tag: Alter = 45, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = 1BI, pM = 0, Number_of_asported_lymphnodes = 9, Number_of_positive_lyphnodes = 1, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 64.16, OS_Months = 176, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = yes


title: Rhesus Liver 1 (replicate B)

tag: Rhesus Liver 1 (replicate B)


title: Human kidney 1 (replicate B)

tag: Human kidney 1 (replicate B)


title: _IDC_A027

description: Gene expression data from human breast cancer tissue A027

tag: Alter = 67, Year_of_Diagnosis = 1992, Gender = f, pT = 1B, pN = 1BI, pM = 0, Number_of_asported_lymphnodes = X, Number_of_positive_lyphnodes = 1, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 26.87, OS_Months = 33.25, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 1, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _medullar_A030

description: Gene expression data from human breast cancer tissue A030

tag: Alter = 57, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = medullar, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 40, OS_Months = 140, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = NA, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: Rhesus Liver 1 (replicate A)

tag: Rhesus Liver 1 (replicate A)


title: _IDC_A026

description: Gene expression data from human breast cancer tissue A026

tag: Alter = 48, Year_of_Diagnosis = 1990, Gender = f, pT = 2, pN = 1BII, pM = X, Number_of_asported_lymphnodes = 13, Number_of_positive_lyphnodes = 6, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 29, OS_Months = 93, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = yes, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = yes, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC-mixed_A031

description: Gene expression data from human breast cancer tissue A031

tag: Alter = 43, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 1BII, pM = 0, Number_of_asported_lymphnodes = 14, Number_of_positive_lyphnodes = 13, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC-mixed, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 108.02, OS_Months = 156, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A025

description: Gene expression data from human breast cancer tissue A025

tag: Alter = 61, Year_of_Diagnosis = 1989, Gender = f, pT = 2, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 192, OS_Months = 192, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: _IDC_A024

description: Gene expression data from human breast cancer tissue A024

tag: Alter = 61, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 10, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 20.8, OS_Months = 47.54, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 3, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Rhesus Liver 2 (replicate B)

description: Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle.

tag: Rhesus Liver 2 (replicate B)


title: _IDC-mixed_A023

description: Gene expression data from human breast cancer tissue A023

tag: Alter = 78, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC-mixed, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 79, OS_Months = 245, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = NA, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = NA, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: Chimp Liver 4 (replicate B)

tag: Chimp Liver 4 (replicate B)


title: Chimp Liver 4 (replicate A)

tag: Chimp Liver 4 (replicate A)


title: Chimp Liver 6 (replicate A)

tag: Chimp Liver 6 (replicate A)


title: Chimp Liver 2 (replicate A)

tag: Chimp Liver 2 (replicate A)


title: _IDC_A022

description: Gene expression data from human breast cancer tissue A022

tag: Alter = 52, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 9, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = 1, Status = alive, Reason_of_death = NA, DFS_Months = 51.48, OS_Months = 148, , Epithel_Percentage = 40, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no

tag: common reference sample


title: _IDC_A021

description: Gene expression data from human breast cancer tissue A021

tag: Alter = 67, Year_of_Diagnosis = 1993, Gender = f, pT = 4, pN = 2, pM = 0, Number_of_asported_lymphnodes = 24, Number_of_positive_lyphnodes = 24, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 0.99, OS_Months = 8.11, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = yes, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A019

description: Gene expression data from human breast cancer tissue A019

tag: Alter = 61, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = 1BI, pM = 0, Number_of_asported_lymphnodes = 9, Number_of_positive_lyphnodes = 2, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 122.58, OS_Months = 150.77, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp Liver 2 (replicate B)

tag: Chimp Liver 2 (replicate B)


title: _IDC_A018

description: Gene expression data from human breast cancer tissue A018

tag: Alter = 46, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 18, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = 1, Status = lost_for_follow_up, Reason_of_death = NA, DFS_Months = 124.06, OS_Months = 124.06, , Epithel_Percentage = 70, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp Liver 5 (replicate A)

tag: Chimp Liver 5 (replicate A)


title: _IDC-mixed_A017

description: Gene expression data from human breast cancer tissue A017

tag: Alter = 70, Year_of_Diagnosis = 1992, Gender = f, pT = 1C, pN = 1BI, pM = 0, Number_of_asported_lymphnodes = 7, Number_of_positive_lyphnodes = 4, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 1, Diagnosis = IDC-mixed, Lymphocyte_infiltration = 0, Status = dead, Reason_of_death = tumoral, DFS_Months = 16.82, OS_Months = 34.3, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp Liver 3 (replicate B)

tag: Chimp Liver 3 (replicate B)


title: ML_35DAS_2

city: Rehovot

first: Idan

middle: D.

last: Efroni

address: Weizmann

country: Israel

institute: Weizmann Institute

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Values obtained using MAS5. Median was normalized to 50.

label: Standard affymetrix protocol

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana mature leaves

label_protocol: Standard affymetrix protocol

growth_protocol: Soil grown at short days

extract_protocol: Using qiagen RNAEasy kit, according to manufacturer protocol

tag: Ecotype

value: Ler


title: _IDC_A016

description: Gene expression data from human breast cancer tissue A016

tag: Alter = 52, Year_of_Diagnosis = 1991, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 14, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 13.67, OS_Months = 21.26, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A020

description: Gene expression data from human breast cancer tissue A020

tag: Alter = 51, Year_of_Diagnosis = 1992, Gender = f, pT = 2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 19, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = 0, Status = lost_for_follow_up, Reason_of_death = NA, DFS_Months = 116, OS_Months = 149, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp Liver 5 (replicate B)

tag: Chimp Liver 5 (replicate B)


title: _IDC_A015

description: Gene expression data from human breast cancer tissue A015

tag: Alter = 62, Year_of_Diagnosis = 1993, Gender = f, pT = 2, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 21, Number_of_positive_lyphnodes = 3, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 39.26, OS_Months = 68.86, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 3, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: ML_35DAS_1


title: _mucinous_A012

description: Gene expression data from human breast cancer tissue A012

tag: Alter = 65, Year_of_Diagnosis = 1993, Gender = f, pT = 2, pN = 1BI, pM = 0, Number_of_asported_lymphnodes = 18, Number_of_positive_lyphnodes = 1, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 2, Diagnosis = mucinous, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 48.76, OS_Months = 116.7, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = yes, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Chimp Liver 3 (replicate A)

tag: Chimp Liver 3 (replicate A)


title: human liver 6 (replicate A)

tag: human liver 6 (replicate A)


title: EL_14DAS_2

source_name: Arabidopsis thaliana expanding leaves 1+2


title: Chimp Liver 1 (replicate B)

tag: Chimp Liver 1 (replicate B)


title: EL_14DAS_1


title: _IDC_A014

description: Gene expression data from human breast cancer tissue A014

tag: Alter = 48, Year_of_Diagnosis = 1991, Gender = f, pT = 1B, pN = 1BIV, pM = 0, Number_of_asported_lymphnodes = 19, Number_of_positive_lyphnodes = 3, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = 0, Status = lost_for_follow_up, Reason_of_death = NA, DFS_Months = 169, OS_Months = 169, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = postmenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no

tag: common reference sample


title: _IDC-mixed_A009

description: Gene expression data from human breast cancer tissue A009

tag: Alter = 47, Year_of_Diagnosis = 1991, Gender = f, pT = 1C, pN = 0, pM = 0, Number_of_asported_lymphnodes = 8, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC-mixed, Lymphocyte_infiltration = 1, Status = dead, Reason_of_death = tumoral, DFS_Months = 34.27, OS_Months = 92.16, , Epithel_Percentage = 70, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = yes, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = yes, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC-mixed_A013

description: Gene expression data from human breast cancer tissue A013

tag: Alter = 39, Year_of_Diagnosis = 1993, Gender = f, pT = 1C, pN = 0, pM = 0, Number_of_asported_lymphnodes = 27, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC-mixed, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 39.66, OS_Months = 133.52, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = 0, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = yes


title: _IDC_A007

description: Gene expression data from human breast cancer tissue A007

tag: Alter = 51, Year_of_Diagnosis = 1994, Gender = f, pT = 1C, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 26, Number_of_positive_lyphnodes = 5, Level_Estrogen_receptor_IHC = 2, Level_Progesteron_receptor_IHC = 2, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 39.49, OS_Months = 120, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 1, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = yes


title: human liver 5 (replicate B)

tag: human liver 5 (replicate B)


title: _IDC_A004

description: Gene expression data from human breast cancer tissue A004

tag: Alter = 67, Year_of_Diagnosis = 1995, Gender = f, pT = 2, pN = 1BIV, pM = 0, Number_of_asported_lymphnodes = 17, Number_of_positive_lyphnodes = 15, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 4.96, OS_Months = 21.75, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 3, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = no, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A006

description: Gene expression data from human breast cancer tissue A006

tag: Alter = 68, Year_of_Diagnosis = 1994, Gender = f, pT = 1C, pN = 0, pM = 0, Number_of_asported_lymphnodes = 17, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = tumoral, DFS_Months = 11.93, OS_Months = 15.21, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = 2, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A003

description: Gene expression data from human breast cancer tissue A003

tag: Alter = 35, Year_of_Diagnosis = 1991, Gender = f, pT = 4B, pN = 1BIII, pM = 0, Number_of_asported_lymphnodes = 17, Number_of_positive_lyphnodes = 15, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = 1, Status = dead, Reason_of_death = tumoral, DFS_Months = 3.78, OS_Months = 12.91, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: _IDC_A005

description: Gene expression data from human breast cancer tissue A005

tag: Alter = 77, Year_of_Diagnosis = 1990, Gender = f, pT = 2, pN = 0, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 0, Level_Progesteron_receptor_IHC = 0, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 90, OS_Months = 90, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = brusterhaltend_(Quadrantenresektion),_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA


title: _IDC_A002

description: Gene expression data from human breast cancer tissue A002

tag: Alter = 43, Year_of_Diagnosis = 1990, Gender = f, pT = 1C-2, pN = 0, pM = 0, Number_of_asported_lymphnodes = 12, Number_of_positive_lyphnodes = 0, Level_Estrogen_receptor_IHC = 1, Level_Progesteron_receptor_IHC = 1, Diagnosis = DIC, Lymphocyte_infiltration = 1, Status = dead, Reason_of_death = tumoral, DFS_Months = 33.58, OS_Months = 35.12, , Epithel_Percentage = 90, Menopausal_status_at_First_Tumor_Diagnosis = premenopausal, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = no, Neoadjuvant_PCT_without_Anthracyclin = no, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = no, Adjuvant_PCT_with_Anthracyclin = no, Adjuvant_PCT_without_Anthracyclin = no


title: Apex_14DAS_2

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label: Standard Affymetrix protocol

source_name: Arabidopsis thaliana vegetative apices, 14DAS

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA extracted using Qiagen RNAEasy kit according to manufacturer protocol

tag: Ecotype


title: Apex_14DAS_1

growth_protocol: Soil grown in short days

extract_protocol: RNA extracted with Qiagen RNAEasy kit according to manufacturer protocol


title: human liver 5 (replicate A)

description: Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle.

tag: human liver 5 (replicate A)


title: S288c (wt) stationary (growth) Replicate 1

status: Public on Sep 16 2008

city: Cambridge

first: Kevin

middle: J.

last: Verstrepen

state: MA

address: 52 Oxford Street

department: Harvard FAS Center for Systems Biology

institute: Harvard University

description: no additional information

hyb_protocol: Hybridization was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Basic analysis was carried out using the Affymetrix GCOS software package.

label: biotin

organism: Saccharomyces cerevisiae

label_protocol: Labeling was performed according to the Affymetrix protocol.

growth_protocol: Fresh cultures were inoculated for pre-cultures and samples were taken after 24 hours of growth. YPGal medium contained 2% raffinose, 2% galactose, 2% peptone and 1% yeast extract.

extract_protocol:
Total RNA was prepared using a standard phenol-chloroform extraction method. Samples were purified using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase
(Qiagen).

tag: S288c strain (wt)

tag: YPGal medium

tag: Stationary growth

tag: Biological replicate 1


title: S288c pGAL-FLO1 (mut) stationary (growth) Replicate 1

description: no additional information

tag: S288c strain FLO1 (mut)


title: Anther 1.0mm ND101 msca1-mut Rep3

city: Stanford

first: John

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description: compare msca1 fertile sib to mutant at Anther 1.0mm stage

hyb_protocol: 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software.

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, median intensity values were normalized using loess method in limma R package (within arrays) and then with the quantile method (between arrays).  Values were normalized again to the median intensity of hybridized probes on an array by array basis.

organism: Zea mays

source_name: Anther 1.0mm ND101 msca1-mut X9-111E

label_protocol: Total RNA (500 ng) was amplified & labeled with either Cy5 or Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were dissected after growth outdoors at the Stanford summer field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

tag: background


title: human liver 4 (replicate B)

tag: human liver 4 (replicate B)


title: Chimp Liver 1 (replicate A)

tag: Chimp Liver 1 (replicate A)


title: _IDC_A001

description: Gene expression data from human breast cancer tissue A001

tag: Alter = 72, Year_of_Diagnosis = 1990, Gender = f, pT = 1C, pN = 1BI, pM = X, Number_of_asported_lymphnodes = NA, Number_of_positive_lyphnodes = NA, Level_Estrogen_receptor_IHC = 3, Level_Progesteron_receptor_IHC = 3, Diagnosis = IDC, Lymphocyte_infiltration = NA, Status = NA, Reason_of_death = NA, DFS_Months = 111, OS_Months = 111, , Epithel_Percentage = NA, Menopausal_status_at_First_Tumor_Diagnosis = NA, Surgical_method = MRM,_axill._Lymphadenektomie, Her2neu_DAKO = NA, Neoadjuvant_PCT_with_Anthracyclin = NA, Neoadjuvant_PCT_without_Anthracyclin = NA, Postoperative_Radiation = yes, Postop_adjuvant_Hormontherapy = NA, Adjuvant_PCT_with_Anthracyclin = NA, Adjuvant_PCT_without_Anthracyclin = NA

tag: common reference sample


title: Anther 1.5mm ND101 msca1-mut Rep3

description: compare msca1 fertile sib to mutant at Anther 1.5mm stage

source_name: Anther 1.5mm ND101 msca1-mut X9-11F


title: human liver 6 (replicate B)

tag: human liver 6 (replicate B)


title: S288c pGAL-FLO1 (mut) stationary (growth) Replicate 2

description: no additional information

tag: Biological replicate 2


title: human liver 4 (replicate A)

tag: human liver 4 (replicate A)


title: Anther 1.5mm ND101 msca1-mut Rep2

source_name: Anther 1.5mm ND101 msca1-mut X9-59F


title: human liver 3 (replicate A)

tag: human liver 3 (replicate A)


title: Anther 2.0mm ND101 msca1-fs Rep2

description: compare msca1 fertile sib to mutant at Anther 2.0mm stage

source_name: Anther 2.0mm ND101 msca1-fs X9-46G


title: Spikelets ND101 msca1-fs Rep3

description: compare msca1 fertile sib to mutant at Spikelets stage

source_name: Spikelets ND101 msca1-fs X9-88D


title: Anther 2.0mm ND101 msca1-fs Rep1

source_name: Anther 2.0mm ND101 msca1-fs X9-54G


title: Anther 1.5mm ND101 msca1-fs Rep1

source_name: Anther 1.5mm ND101 msca1-fs X9-71F


title: human liver 3 (replicate B)

tag: human liver 3 (replicate B)


title: Anther 1.0mm ND101 msca1-fs Rep2

source_name: Anther 1.0mm ND101 msca1-fs X9-50E


title: Spikelets ND101 msca1-mut Rep2

source_name: Spikelets ND101 msca1-mut X9-67D


title: Anther 2.0mm ND101 msca1-mut Rep3

source_name: Anther 2.0mm ND101 msca1-mut X9-172G


title: Spikelets ND101 msca1-mut Rep1

source_name: Spikelets ND101 msca1-mut X9-63D


title: Anther 1.0mm ND101 msca1-fs Rep1

source_name: Anther 1.0mm ND101 msca1-fs X9-36E


title: Anther 2.0mm ND101 ms23-mut Rep3

description: compare ms23 fertile sib to mutant at Anther 2.0mm stage

source_name: Anther 2.0mm ND101 ms23-mut X14-63G5


title: Anther 2.0mm ND101 ms23-fs Rep2

source_name: Anther 2.0mm ND101 ms23-fs X14-20G2


title: Anther 1.5mm ND101 ms23-fs Rep3

description: compare ms23 fertile sib to mutant at Anther 1.5mm stage

source_name: Anther 1.5mm ND101 ms23-fs X14-106F3


title: Anther 2.0mm ND101 ms23-fs Rep1

source_name: Anther 2.0mm ND101 ms23-fs X14-87G1


title: Spikelets ND101 ms23-fs Rep3

description: compare ms23 fertile sib to mutant at Spikelets stage

source_name: Spikelets ND101 ms23-fs X14-95_D5


title: Anther 1.0mm ND101 ms23-fs Rep1

description: compare ms23 fertile sib to mutant at Anther 1.0mm stage

source_name: Anther 1.0mm ND101 ms23-fs X14-87E1


title: Anther 1.5mm ND101 ms23-mut Rep2

source_name: Anther 1.5mm ND101 ms23-mut X14-109F3


title: Anther 1.5mm ND101 ms23-mut Rep1

source_name: Anther 1.5mm ND101 ms23-mut X14-4F1


title: Anther 1.0mm ND101 ms23-mut Rep3

source_name: Anther 1.0mm ND101 ms23-mut X16-42_E5


title: Spikelets ND101 ms23-mut Rep2

source_name: Spikelets ND101 ms23-mut X14-100_D2


title: human liver 2 (replicate A)

source_name: liver

tag: human liver 2 (replicate A)


title: human liver 2 (replicate B)

tag: human liver 2 (replicate B)


title: Spikelets ND101 ms23-mut Rep1

source_name: Spikelets ND101 ms23-mut X16-7_D1


title: Anther 2.0mm A619 mac1-fs Rep3

description: compare mac1 fertile sib to mutant at Anther 2.0mm stage

source_name: Anther 2.0mm A619 mac1-fs X35-28G


title: human liver 1 (replicate A)

tag: human liver 1 (replicate A)


title: Anther 1.0mm ND101 ms23-fs Rep2

source_name: Anther 1.0mm ND101 ms23-fs X14-94E2


title: Anther 1.5mm A619 mac1-mut Rep1

description: compare mac1 fertile sib to mutant at Anther 1.5mm stage

source_name: Anther 1.5mm A619 mac1-mut X28-1F


title: human liver 1 (replicate B)

tag: human liver 1 (replicate B)


title: Anther 1.5mm A619 mac1-mut Rep2

source_name: Anther 1.5mm A619 mac1-mut X28-25F


title: Anther 1.0mm A619 mac1-fs Rep3

description: compare mac1 fertile sib to mutant at Anther 1.0mm stage

source_name: Anther 1.0mm A619 mac1-fs X28-37E3


title: Anther 1.5mm A619 mac1-fs Rep3

source_name: Anther 1.5mm A619 mac1-fs X28-4F3


title: Anther 1.0mm A619 mac1-mut Rep2

source_name: Anther 1.0mm A619 mac1-mut X27-9E


title: Spikelets A619 mac1-mut Rep3

description: compare mac1 fertile sib to mutant at Spikelets stage

source_name: Spikelets A619 mac1-mut X28-11D


title: Spikelets A619 mac1-mut Rep1

source_name: Spikelets A619 mac1-mut X28-1D


title: Anther 1.0mm A619 mac1-fs Rep1

source_name: Anther 1.0mm A619 mac1-fs X28-28E2


title: Spikelets A619 mac1-fs Rep2

source_name: Spikelets A619 mac1-fs X28-28D


title: Anther 1.5mm ND101 msca1-fs Rep2

source_name: Anther 1.5mm ND101 msca1-fs X9-50F


title: Anther 1.5mm ND101 msca1-mut Rep1

source_name: Anther 1.5mm ND101 msca1-mut X9-172F


title: Anther 2.0mm A619 mac1-mut Rep1

source_name: Anther 2.0mm A619 mac1-mut X35-21G


title: Anther 2.0mm ND101 msca1-mut Rep2

source_name: Anther 2.0mm ND101 msca1-mut X9-11G


title: Anther 1.5mm ND101 msca1-fs Rep3

source_name: Anther 1.5mm ND101 msca1-fs X9-42F


title: Anther 2.0mm ND101 msca1-fs Rep3

source_name: Anther 2.0mm ND101 msca1-fs X9-62G


title: Anther 2.0mm ND101 ms23-fs Rep3

source_name: Anther 2.0mm ND101 ms23-fs X14-79G5


title: Anther 2.0mm ND101 msca1-mut Rep1

source_name: Anther 2.0mm ND101 msca1-mut X9-59G


title: Anther 2.0mm A619 mac1-fs Rep2

source_name: Anther 2.0mm A619 mac1-fs X27-14G


title: Anther 1.0mm ND101 msca1-mut Rep1

source_name: Anther 1.0mm ND101 msca1-mut X9-8E


title: Anther 1.0mm ND101 msca1-fs Rep3

source_name: Anther 1.0mm ND101 msca1-fs X9-71E


title: S288c (wt) stationary (growth) Replicate 2

description: no additional information

label: biotin (Bio 11 CTP and Bio 11 UTP)

tag: S288c strain (wt)

tag: YPGal medium

tag: Stationary growth


title: Spikelets ND101 msca1-mut Rep3

source_name: Spikelets ND101 msca1-mut X9-94D

tag: background


title: Spikelets ND101 msca1-fs Rep2

source_name: Spikelets ND101 msca1-fs X9-68D


title: Anther 1.0mm ND101 msca1-mut Rep2

source_name: Anther 1.0mm ND101 msca1-mut X9-59E


title: Spikelets ND101 msca1-fs Rep1

source_name: Spikelets ND101 msca1-fs X9-55D


title: Anther 2.0mm ND101 ms23-mut Rep2

source_name: Anther 2.0mm ND101 ms23-mut X14-33G3


title: Anther 1.5mm ND101 ms23-mut Rep3

source_name: Anther 1.5mm ND101 ms23-mut X16-39F4


title: Anther 2.0mm ND101 ms23-mut Rep1

source_name: Anther 2.0mm ND101 ms23-mut X14-2G1


title: Anther 1.5mm ND101 ms23-fs Rep2

source_name: Anther 1.5mm ND101 ms23-fs X14-94F2


title: Anther 1.5mm ND101 ms23-fs Rep1

source_name: Anther 1.5mm ND101 ms23-fs X14-87F1


title: Anther 1.0mm ND101 ms23-fs Rep3

source_name: Anther 1.0mm ND101 ms23-fs X14-106E3


title: Anther 1.0mm A619 mac1-mut Rep3

source_name: Anther 1.0mm A619 mac1-mut X28-11E


title: Anther 1.5mm A619 mac1-mut Rep3

source_name: Anther 1.5mm A619 mac1-mut X28-11F


title: Anther 1.0mm ND101 ms23-mut Rep2

source_name: Anther 1.0mm ND101 ms23-mut X14-147_E3


title: Anther 1.0mm ND101 ms23-mut Rep1

source_name: Anther 1.0mm ND101 ms23-mut X14-100_E1


title: Spikelets ND101 ms23-mut Rep3

source_name: Spikelets ND101 ms23-mut X14-67_D3


title: Anther 1.0mm A619 mac1-fs Rep2

source_name: Anther 1.0mm A619 mac1-fs X28-19E1


title: Spikelets ND101 ms23-fs Rep2

source_name: Spikelets ND101 ms23-fs X14-69_D3


title: Anther 1.5mm A619 mac1-fs Rep1

source_name: Anther 1.5mm A619 mac1-fs X28-19F1


title: Anther 1.5mm A619 mac1-fs Rep2

source_name: Anther 1.5mm A619 mac1-fs X28-28F2


title: Anther 2.0mm A619 mac1-mut Rep3

source_name: Anther 2.0mm A619 mac1-mut X35-27G


title: Anther 1.0mm A619 mac1-mut Rep1

source_name: Anther 1.0mm A619 mac1-mut X27-1E


title: Spikelets A619 mac1-fs Rep1

source_name: Spikelets A619 mac1-fs X28-19D


title: Spikelets A619 mac1-mut Rep2

source_name: Spikelets A619 mac1-mut X28-8D


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred - rep2

type: genomic

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Plants grown in glasshouse for 2 weeks.

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

molecule: genomic DNA

source_name: leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred)

label_protocol: BioPrime DNA labeling system for AFLP

growth_protocol: Growth Description:  glasshouse

extract_protocol: Amplified fragment length polymorphism (AFLP)

tag: CML69 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007071 2.02 main shoot and axillary shoots visible at two nodes (Development Stage); 2 week old (Age); Scotts MetroMix 200 (Growth Media).


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred)

tag: B73 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007071 2.02 main shoot and axillary shoots visible at two nodes (Development Stage); 2 week old (Age); Scotts MetroMix 200 (Growth Media).


title: Spikelets ND101 ms23-fs Rep1

source_name: Spikelets ND101 ms23-fs X14-94_D2


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: Anther 2.0mm A619 mac1-mut Rep2

source_name: Anther 2.0mm A619 mac1-mut X27-9G


title: Spikelets A619 mac1-fs Rep3

source_name: Spikelets A619 mac1-fs X28-4D


title: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Methylation filtration (MF) - genotype: CML69 maize inbred)

label_protocol: BioPrime DNA labeling system for CF/MF

extract_protocol: Methylation Filtration (MF)


title: Anther 2.0mm A619 mac1-fs Rep1

source_name: Anther 2.0mm A619 mac1-fs X28-15G


title: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred)

tag: Mo17 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007071 2.02 main shoot and axillary shoots visible at two nodes (Development Stage); 2 week old (Age); Scotts MetroMix 200 (Growth Media).


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred)


title: tg95

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: total RNA was subjected to two rounds of linear amplification to obtain sufficient RNA to hybridize via the messageAmp kit from Ambion.

hyb_protocol: Hybridization was carried out using a Lucidea Slide Pro machine. All wash solutions were made using Ambion Pre-Made Solutions (Nuclease-free Water, 20% SDS and 20XSSC) and filtered sterilized with a 500ml, 0.22uM filter unit. All C. elegans arrays from the Washington University in St. Louis Genomic Sequencing Center arrive pretreated; no blocking step was necessary. To prepare the aRNA sample for hybridization, the labeled aRNA sample was brought up to a volume with Nuclease-free water and Dextran Sulfate/ Hybe Buffer mix was added to the aRNA sample. The mixture was warmed to 50°C. Using a Hamilton syringe the labeled sample was loaded into the Lucidea chamber. The hybridization program was run for 16hrs at 42°C with a cycling speed of 10µl/sec every 30 minutes. The array was then washed at a speed of 50Î¼l/sec with the following wash buffers in succession: 2X SSC +0.1% SDS (warmed to 42°C for 1st wash solution), 2X SSC, 0.2XSSC, and a 95% ethanol drying step.

scan_protocol: The array slide was loaded into a Perkin Elmer Scan Array Express 2-Laser Scanner. A QuickScan was performed, which scans the first 3-4 rows of the array. A surface calibration was then performed using the Spot Report control spots on the array. After surface calibration, the PMT and POW settings were adjusted to have the control spots match in intensity. The array was then scanned. Images were quantitated using GenePix 5.0 software package which overlays the GAL file (provided by the Washington University in St. Louis Genomic Sequencing Center) on the two array TIFF images (Cy3 and Cy5).  Pixels per spot, per channel were counted by the software and a gpr file was generated.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003), see Golden et al., 2008.

organism: Caenorhabditis elegans

source_name: Individual C. elegans, age: 4 days old

label_protocol: Each sample, including the reference pool, was subjected to two rounds of linear amplification using the MessageAmpTM kit from Ambion for the first round and the Amino Allyl Message Amplification II kit from Ambion for the second round. After amplification, each sample was assessed for yield and overall quality via Bioanlayzer™(Amersham). Samples that did not pass QC were discarded, and not used in the final analysis. Post Labeling Reactive Dyes (Cy3 and Cy5) from Amersham were used in conjunction with the reagents and protocol from the Ambion Amino Allyl Message Amplification II Kit to label the aRNA.  5μg of aRNA plus aRNA spike were labeled (aRNA Spike: equal amounts of the 10 Stratagene Spot Repot Spikes were combined and then amplified 1 round, to make an aRNA Spot Report Spike mix). All controls were labeled with the Cy3 dye and all experimental samples were labeled with the Cy5 dye. The Cy3 and Cy5 sample pairs were combined and purified.

growth_protocol: Wild type (N2) C. elegans were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR).  The worm population was initiated with a two-hour timed lay.  Worms were cultured at 20°C on nematode growth media (NGM) plates seeded with OP50 bacteria.  Seven plates containing 100 nematodes each were maintained; plates were checked at least every other day, live and dead worms were counted, and live worms moved to fresh plates to avoid contamination by progeny.  All seven plates had virtually identical survival curves.  At the specified ages, 20 individuals were picked at random from the seven plates.  Each individual was placed on an NGM plate without an OP50 lawn and filmed.  The worm was then picked into a tube containing 5µl of nuclease-free water and flash-frozen and stored at 80°C until RNA was prepared.

extract_protocol: Total RNA was extracted from individual worms using the AbsolutelyRNATM Nanoprep kit from Stratagene.  Reference RNA was a pool of RNA from15 four-day-old nematodes.

tag: 4 day old N2 raised under standard conditions at 20°C

source_name: Pool of 15 4 day old N2 nematodes

tag: Pool of 15 4 day old N2 nematodes


title: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: tg94

source_name: Individual C. elegans, age: 14 days old

tag: 14 day old N2 raised under standard conditions at 20°C


title: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: tg97

source_name: Individual C. elegans, age: 20 days old

tag: 20 day old N2 raised under standard conditions at 20°C


title: protocol: Methylation filtration (MF) - genotype: B73 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Methylation filtration (MF) - genotype: B73 maize inbred)


title: tg96

source_name: Individual C. elegans, age: 12 days old

tag: 12 day old N2 raised under standard conditions at 20°C


title: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Cot filtration (CF) - genotype: CML69 maize inbred)

extract_protocol: Cot Filtration (CF)


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: tg92


title: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Methylation filtration (MF) - genotype: B73 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.


title: tg98


title: protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Methylation filtration (MF) - genotype: B73 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: tg93


title: tg88

source_name: Individual C. elegans, age: 16 days old

tag: 16 day old N2 raised under standard conditions at 20°C


title: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.  Array data is low quality. The data has low correlation (0.5) with other Mo17-CF arrays.

source_name: leaf (protocol: Cot filtration (CF) - genotype: Mo17 maize inbred)


title: tg91


title: tg87


title: tg89

source_name: Individual C. elegans, age: 8 days old

tag: 8 day old N2 raised under standard conditions at 20°C


title: tg85


title: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.


title: protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep3

description: Plants grown in glasshouse for 2 weeks.

source_name: leaf (protocol: Cot filtration (CF) - genotype: B73 maize inbred)


title: tg90


title: tg86


title: protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep1

description: Plants grown in glasshouse for 2 weeks.


title: tg77


title: tg82


title: protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep2

description: Plants grown in glasshouse for 2 weeks.


title: tg83


title: tg79


title: protocol: mRNA - genotype: CML69 maize inbred - rep2

description: Plants grown in glasshouse for 4-weeks (April to May). No supplemental lighting.

source_name: leaf (protocol: mRNA - genotype: CML69 maize inbred)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Total RNA Isolation in Maize

tag: CML69 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007088 2.04 main shoot and axillary shoots visible at four nodes (Development Stage); 4 week old (Age); Scotts MetroMix 200 (Growth Media).


title: protocol: mRNA - genotype: CML69 maize inbred - rep1


title: tg76


title: tg75


title: protocol: mRNA - genotype: CML69 maize inbred - rep3


title: protocol: mRNA - genotype: Mo17 maize inbred - rep3

source_name: leaf (protocol: mRNA - genotype: Mo17 maize inbred)

tag: Mo17 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007088 2.04 main shoot and axillary shoots visible at four nodes (Development Stage); 4 week old (Age); Scotts MetroMix 200 (Growth Media).


title: tg61


title: tg62


title: tg58


title: tg54


title: tg59

source_name: Individual C. elegans, age: 24 days old

tag: 24 day old N2 raised under standard conditions at 20°C


title: protocol: mRNA - genotype: Mo17 maize inbred - rep1


title: protocol: mRNA - genotype: B73 maize inbred - rep2

source_name: leaf (protocol: mRNA - genotype: B73 maize inbred)

tag: B73 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007088 2.04 main shoot and axillary shoots visible at four nodes (Development Stage); 4 week old (Age); Scotts MetroMix 200 (Growth Media).


title: tg60


title: protocol: mRNA - genotype: B73 maize inbred - rep1


title: protocol: mRNA - genotype: Mo17 maize inbred - rep2


title: tg8


title: tg64


title: protocol: mRNA - genotype: B73 maize inbred - rep3


title: tg6


title: tg56


title: tg67


title: tg57


title: tg52


title: tg48


title: tg49


title: tg53


title: tg43


title: tg46


title: tg50


title: tg51


title: tg41


title: tg38


title: tg44


title: tg24


title: tg33


title: tg35


title: tg32


title: tg47


title: tg26


title: tg45


title: tg39


title: tg42


title: tg37


title: tg20


title: tg31


title: tg28


title: tg14


title: tg29


title: tg36


title: tg34


title: tg40


title: tg23


title: tg136


title: tg138


title: tg137


title: tg30


title: tg133


title: tg139


title: tg135


title: tg134


title: Chromosome 9 Replacement alpha-type Cell Replicate 1

city: Taipei

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

country: Taiwan

institute: Academia Sinica

description: The S. cerevisiae hybrid karyotypes were analyzed by array-CGH to identify small regions of duplication or homeologous chromosomal exchange occurring during the strain construction.

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

scan_protocol: Arrays were scanned for F635(cy5) and F532(Cy3) fluoresence intensities using AXON 4000B ( Molecular Device , sunnyvale , CA )

data_processing: Subtracted background. Dividing by ch2 (control) was used to transform data (Agilent GeneSpring 7.3.1 software)

source_name: S. cerevisiae chromosome 9 replacement alpha-type cells

label_protocol: fragmentation protocol：4.5 µg total genomic DNA were digested by 1 µl Dnase I (0.05 U) at 37 degree for 5 minutes and at 100 degree, 15 minutes for enzyme inactivation. The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)

growth_protocol: Yeast cells were grown in YPD medium, at 30 degree

extract_protocol: Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit

treatment_protocol: S. bayanus were crossed to S. cerevisiae to generate F1 hybrid cells. The hybrid diploids were induced to sporulate and viable spores were backcrossed to S. cerevisiae to construct chromosome replacement lines

tag: strain

value: W303；S. cerevisiae chromosome 9 was replaced by S. bayanus chromosome 9

source_name: S. cerevisiae alpha-type cells


title: tg131


title: Chromosome 9 Replacement alpha-type Cell Replicate 2


title: Chromosome 8+15 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 8+15 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 8+15 was replaced by S. bayanus chromosome 8+15


title: Chromosome 8+15 Replacement alpha-type Cell Replicate 1


title: Chromosome 7 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 7 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 7 was replaced by S. bayanus chromosome 7


title: Parental Yeast alpha-type Cell Replicate 2

organism: Saccharomyces bayanus

source_name: S. bayanus alpha-type cells

value: S. bayanus#180


title: tg123

source_name: Individual C. elegans, age: 4 days old

source_name: Pool of 15 4 day old N2 nematodes


title: Parental Yeast alpha-type Cell Replicate 1


title: Chromosome 7 Replacement alpha-type Cell Replicate 1


title: tg132

source_name: Individual C. elegans, age: 12 days old


title: tg121

source_name: Individual C. elegans, age: 20 days old


title: tg129


title: tg128

source_name: Individual C. elegans, age: 16 days old


title: tg124


title: tg122


title: Chromosome 6+10 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 6+10 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 6+10 was replaced by S. bayanus chromosome 6+10


title: tg119


title: tg127

source_name: Individual C. elegans, age: 8 days old


title: tg126

source_name: Individual C. elegans, age: 14 days old


title: tg130


title: tg125


title: tg120


title: Chromosome 5+7 Replacement alpha-type Cell Replicate 1

source_name: S. cerevisiae chromosome 5+7 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 5+7 was replaced by S. bayanus chromosome 5+7


title: Chromosome 5+7 Replacement alpha-type Cell Replicate 2


title: Chromosome 6+10 Replacement alpha-type Cell Replicate 1


title: tg118


title: tg117


title: Chromosome 3 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 3 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 3 was replaced by S. bayanus chromosome 3


title: Chromosome 16 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 16 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 16 was replaced by S. bayanus chromosome 16


title: Chromosome 16 Replacement alpha-type Cell Replicate 1


title: Chromosome 12 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 12 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 12 was replaced by S. bayanus chromosome 12


title: Chromosome 13 Replacement alpha-type Cell Replicate 1

source_name: S. cerevisiae chromosome 13 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 13 was replaced by S. bayanus chromosome 13


title: tg115


title: Chromosome 11 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 11 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 11 was replaced by S. bayanus chromosome 11

source_name: S. cerevisiae alpha-type cells


title: Parental Yeast a-type Cell Replicate 1

source_name: S. bayanus a-type cells

source_name: S. cerevisiae a-type cells


title: Chromosome 11 Replacement alpha-type Cell Replicate 1


title: Chromosome 1 Replacement alpha-type Cell Replicate 2

source_name: S. cerevisiae chromosome 1 replacement alpha-type cells

value: W303；S. cerevisiae chromosome 1 was replaced by S. bayanus chromosome 1


title: Chromosome 9 Replacement a-type Cell Replicate 1

source_name: S. cerevisiae chromosome 9 replacement a-type cells


title: Chromosome 12 Replacement alpha-type Cell Replicate 1


title: Parental Yeast a-type Cell Replicate 2


title: Chromosome 8+15 Replacement a-type Cell Replicate 1

source_name: S. cerevisiae chromosome 8+15 replacement a-type cells


title: Chromosome 8+15 Replacement a-type Cell Replicate 2


title: Chromosome 9 Replacement a-type Cell Replicate 2


title: Chromosome 7 Replacement a-type Cell Replicate 1

source_name: S. cerevisiae chromosome 7 replacement a-type cells


title: Chromosome 7 Replacement a-type Cell Replicate 2


title: tg116

source_name: Individual C. elegans, age: 20 days old

source_name: Pool of 15 4 day old N2 nematodes


title: tg113

source_name: Individual C. elegans, age: 16 days old


title: Chromosome 1 Replacement alpha-type Cell Replicate 1


title: tg11

source_name: Individual C. elegans, age: 14 days old


title: Chromosome 3 Replacement alpha-type Cell Replicate 1


title: tg114

source_name: Individual C. elegans, age: 24 days old


title: Chromosome 13 Replacement alpha-type Cell Replicate 2


title: tg112

source_name: Individual C. elegans, age: 8 days old


title: tg111

source_name: Individual C. elegans, age: 4 days old


title: tg106


title: tg110


title: Chromosome 6+10 Replacement a-type Cell Replicate 2

source_name: S. cerevisiae chromosome 6+10 replacement a-type cells


title: tg108


title: Chromosome 6+10 Replacement a-type Cell Replicate 1


title: Chromosome 5+7 Replacement a-type Cell Replicate 2

source_name: S. cerevisiae chromosome 5+7 replacement a-type cells


title: tg105


title: Chromosome 5+7 Replacement a-type Cell Replicate 1


title: Chromosome 3 Replacement a-type Cell Replicate 2

source_name: S. cerevisiae chromosome 3 replacement a-type cells


title: Chromosome 3 Replacement a-type Cell Replicate 1


title: Chromosome 16 Replacement a-type Cell Replicate 1

source_name: S. cerevisiae chromosome 16 replacement a-type cells


title: tg103


title: Chromosome 16 Replacement a-type Cell Replicate 2


title: Chromosome 11 Replacement a-type Cell Replicate 2

source_name: S. cerevisiae chromosome 11 replacement a-type cells


title: Chromosome 1 Replacement a-type Cell Replicate 2

source_name: S. cerevisiae chromosome 1 replacement a-type cells

source_name: S. cerevisiae a-type cells


title: Chromosome 12 Replacement a-type Cell Replicate 1

source_name: S. cerevisiae chromosome 12 replacement a-type cells


title: Chromosome 12 Replacement a-type Cell Replicate 2


title: Chromosome 1 Replacement a-type Cell Replicate 1


title: Chromosome 11 Replacement a-type Cell Replicate 1


title: tg102


title: Chromosome 13 Replacement a-type Cell Replicate 2

source_name: S. cerevisiae chromosome 13 replacement a-type cells


title: Chromosome 13 Replacement a-type Cell Replicate 1


title: tg104


title: tg10


title: tg101


title: tg100


title: tg109


title: MEN2 20080829_hv32420_59M16

status: Public on Sep 15 2008

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Human Pheochromocytoma

hyb_protocol: 200 picomoles of Cy3 and 100 picomoles of Cy5 labeled cRNAs are put in a total volume of 24 ul (qsp with DEPC H20) and 6 microliter of 5x fragmentation buffer from Affymetrix. the mixture is incubated at 94 øC for 15 minutes. Then, 25 ul of 2X  hybridization buffer (250 _l Formamide, 250 _l 20xSSC and 20 _l 10%SDS). The mixture is then denatured for 2 minutes and applied on the Maui (BioMicro Systems, Inc) hybridization chamber/ array slide sandwich. The hybridization is performed at 45 degre for 20 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray software, lowess normalization

label_protocol: 0.5-1.0 microgram of total RNA was reverse transcribed with T7 Oligo-dT, followed by a second strand synthesis and overhight in vitro transcription in the presence of  Aminoallyl UTPs using the Amino Allyl MessageAmp_ II aRNA Amplification kit from Ambion (Kit Cat#1753). The Aminoallyl UTP labeled cRNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cRNAs are then purified with columns and reagents provided by the Kit (Cat#1753).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: Human pheochromocytoma

source_name: Normal human adrenal RNA

tag: Normal human adrenal RNA


title: MEN2 20080829_hv32444_82M06

description: Human Pheochromocytoma


title: VHL 20080829_hv32485_34V01

description: Human Pheochromocytoma

source_name: VHL


title: VHL 20080829_hv32473_20V02

description: Human Pheochromocytoma


title: VHL 20080829_hv32422_62V17

description: Human Pheochromocytoma


title: MEN2 20080829_hv32495_43M05

description: Human Pheochromocytoma


title: MEN2 20080829_hv32457_2M7

description: Human Pheochromocytoma


title: VHL 20080829_hv32493_41V11

description: Human Pheochromocytoma


title: MEN2 20080829_hv32528_67M15

description: Human Pheochromocytoma


title: MEN2 20080829_hv32468_14M5

description: Human Pheochromocytoma


title: VHL 20080829_hv32531_117V19

description: Human Pheochromocytoma


title: MEN2 20080829_hv32537_84M8A

description: Human Pheochromocytoma


title: VHL 20080829_hv32545_25V12

description: Human Pheochromocytoma


title: MEN2 20080829_hv32474_22M7

description: Human Pheochromocytoma


title: MEN2 20080829_hv32536_86M9A

description: Human Pheochromocytoma


title: VHL 20080829_hv32552_45V08

description: Human Pheochromocytoma


title: MEN2 20080829_hv32549_97B3

description: Human Pheochromocytoma


title: XEN_rep3_ChIP-chip (microarray 1 of 2)

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis Street

department: Stem Cell and Developmental Biology

country: Singapore

institute: GIS

description: Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages_XEN_3

hyb_protocol: 4 μg of each labeled sample was blocked with mouse Cot-1 DNA (Invitogen) and blocking agent (Agilent), and hybridized to DNA microarrays (G4490A, Agilent) for 40 h at 65oC. The microarrays were washed and stabilized with acetonitrile (Sigma), followed by stabilization and drying solution (Agilent).

scan_protocol: The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (G2567AA, version 9.1).

data_processing: Probe features were extracted using the default 2-color dye normalization (i.e., linear normalization) that is encoded in the  Feature Extraction Software (G2567AA, version 9.1).

organism: Mus musculus

label_protocol: 2 μg of each amplified sample were labeled with Cy5 for IP DNA, and Cy3 for input DNA using CGH labeling kit (Invitrogen).

extract_protocol: Cells were cross-linked with 1 % formaldehyde for 10 min at room temperature and formaldehyde was then inactivated by the addition of 125 mM glycine. Chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using antibodies. Approximately 5x107 cells and 10ug of anti-Sall4 antibodies were used for each ChIP reaction. Immunoprecipitated (IP) DNA was blunted with T4 polymerase and ligated to linkers with T4 DNA ligase. For DNA reference, 200 ng of input DNA was used. Ligated DNA was amplified with two rounds of PCR cycles.

tag: XEN-GIS


title: MEN2 20080829_hv32569_114M17A

description: Human Pheochromocytoma


title: HP4(Rex-1-/-)#2(251147218926)

status: Public on Sep 13 2008

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: TRIZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used.1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using pipette tips. The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 4 degree. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at room temperature for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 4 degree. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 4 degree. 6. REDISSOLVING THE RNA At the end of the procedure, briefly drying the RNApellet.

tag: embryonic stem cell

tag: Individual Identifier

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: eutopic endometrium, biological rep2

city: Paris

first: Bruno

last: Borghese

address: 24, rue du Faubourg Saint-Jacques

department: Genetics and Development

country: France

institute: Institut Cochin

description: cDNA prepared from 6-patients pools, where the same patient provided both eutopic and ectopic endometrium (endometriomas)

hyb_protocol: Samples were shipped to NimbleGen Inc. in Reykjavic and thus hybridization were performed overthere according to NimbleGen protocols

scan_protocol: Samples were shipped to NimbleGen Inc. in Reykjavic and thus scanning were performed overthere according to NimbleGen protocols

data_processing: We normalize expression data using quantile normalization. See Bolstad B, et al. (2003), A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics, 19:185-193. Gene calls are generated using the Robust Multichip Average (RMA) algorithm. See Irizarry R. et al. (2003), Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264.

source_name: eutopic endometrium

label_protocol: Samples were shipped to NimbleGen Inc. in Reykjavic and thus labelling were performed overthere according to NimbleGen protocols

growth_protocol: liquid nitrogen

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

tag: Pool of endometriums from 12 caucasian patients in luteal phase


title: VHL 20080829_hv32567_112V15

description: Human Pheochromocytoma


title: XEN_rep2_ChIP-chip (microarray 1 of 2)

description: Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages_XEN_2


title: HP3(rex-1-/-)-#2(251147218920)


title: ectopic endometrium, biological rep2

source_name: ectopic endometrioma

tag: Pool of endometriotic lesions (endometriomas) from 6 of the 12 patients used for E1 and E2


title: HP3(rex-1-/-)-#1(251147218919)


title: XEN_rep1_ChIP-chip (microarray 1 of 2)

description: Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages_XEN_1


title: HP4(Rex-1-/-)#1(251147218925)


title: E14_rep3_ChIP-chip (microarray 2 of 2)

description: Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages_E14_3

tag: Embryonic stem cells E14


title: ectopic endometrium, biological rep 1


title: HP4(Rex-1-/-)#3(251147218927)


title: HP3(rex-1-/-)-#3(251147218921)


title: MEN2 20080829_hv32583_96M4

description: Human Pheochromocytoma


title: RKPG9(Rex-1+/-)-#3(251147218918)


title: eutopic endometrium, biological rep1


title: E14_rep1_ChIP-chip (microarray 2 of 2)

description: Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages_E14_1


title: XEN_rep2_ChIP-chip (microarray 2 of 2)


title: E14_rep3_ChIP-chip (microarray 1 of 2)


title: VHL 20080829_hv32564_108V5

description: Human Pheochromocytoma


title: XEN_rep3_ChIP-chip (microarray 2 of 2)


title: E14_rep2_ChIP-chip (microarray 1 of 2)

description: Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages_E14_2


title: E14_rep1_ChIP-chip (microarray 1 of 2)


title: VHL 20080829_hv32559_103V10

description: Human Pheochromocytoma


title: VHL 20080829_hv32547_105V20

description: Human Pheochromocytoma


title: XEN_rep1_ChIP-chip (microarray 2 of 2)


title: E14_rep2_ChIP-chip (microarray 2 of 2)


title: RKPG9(Rex-1+/-)-#2(251147218917)


title: EB5-#3(251147218914)


title: EB5-#2(251147218913)


title: EB5-#1(251147218912)


title: S. japonicum sporocysts life cycle replicate 1 of 3

status: Public on Sep 12 2008

city: Herston

first: Dr Geoffrey

middle: N

last: Gobert

state: QLD

address: 300 Herston road

department: Infectious Diseases / Molecular Parasitology

country: Australia

institute: Queensland Institute of Medical Research

description: S. japonicum sporocysts

hyb_protocol: One-color Microarray-Based gene expression version 5.5 February 2007

scan_protocol: Microarrays were scanned using the Aglient DNA microarray scanner

data_processing: Agilent Feature Extraction software version 9.5.3.1

organism: Schistosoma japonicum

source_name: S. japonicum sporocysts

label_protocol: Agilent Low RNA Input linear amplification kit

extract_protocol: Trizol / QIAGEN RNeasy isolated total RNA

tag: S. japonicum sporocysts


title: S. japonicum ovary laser microdissection microarray replicate 2 of 2

description: S. japonicum ovary

source_name: S. japonicum ovary

tag: S. japonicum ovary


title: S. japonicum control laser microdissection microarray replicate 2 of 2

description: S. japonicum control

source_name: S. japonicum control

tag: S. japonicum control


title: S. japonicum gut laser microdissection microarray replicate 1 of 2

description: S. japonicum gut

source_name: S. japonicum gut

tag: S. japonicum gut