title: golub-00299: NSCLC_A549ATCC

value: Adenocarcinoma

value: Lung

value: Epithelial Cell


title: golub-00327: 5500024030401071707289.H11

status: Public on May 16 2015

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cell

tag: cosmic id

tag: disease state

value: carcinoma

tag: disease location

value: pancreas

tag: organism part

value: Pancreas

tag: sample

tag: cell line code

tag: supplier

value: ECCC

tag: crna plate


title: golub-00299: NSCLC_NCIH226

scan_protocol: See mage-tab files linked to series entry for additional details

source_name: cell

value: Squamous Cell Carcinoma

tag: cell type

tag: cell line


title: golub-00327: 5500024035100021608461.C09

data_processing: See mage-tab files linked to series entry for additional details

value: large cell carcinoma

value: lung

value: RIKEN


title: golub-00327: 5500024052603032009483.H05

label_protocol: See mage-tab files linked to series entry for additional details


title: golub-00299: CNS_SF295

extract_protocol: See mage-tab files linked to series entry for additional details

value: Glioblastoma

value: Brain


title: golub-00299: MELAN_SKMEL28

value: Melanoma

value: Skin


title: golub-00327: 5500024034290101707049.G08

value: osteosarcoma

value: femur

value: Bone

value: HSRRB


title: golub-00327: 5500024031722092907496.D08

value: #N/A

value: plasma cell myeloma

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: ATCC


title: golub-00299: NSCLC_HOP92

value: Large Cell Carcinoma

value: Lung

value: Epithelial Cell


title: golub-00299: BREAST_HS578T

value: Carcinosarcoma

value: Breast


title: golub-00327: 5500024052603032009483.E05

value: bone


title: golub-00299: RENAL_CAKI1

value: Carcinoma

value: Kidney


title: golub-00299: COLON_HCT116

value: Colon


title: golub-00327: 5500024032848101507998.C10

value: hepatocellular carcinoma

value: liver

value: Liver


title: golub-00299: BREAST_MDAMB435


title: golub-00327: 5500024032848101507998.E10

value: HSRRB


title: golub-00327: 5500024030401071707289.E11

value: carcinoma

value: bile duct

value: BiliaryTract


title: golub-00299: CNS_SF539

value: Glioblastoma

value: Brain


title: golub-00299: LEUK_HL60

value: Myeloid Leukemia

value: Blood


title: golub-00299: CNS_SNB19


title: golub-00327: 5500024034290101707049.F08


title: golub-00299: NSCLC_EKVX

value: Adenocarcinoma

value: Lung

value: Epithelial Cell


title: golub-00327: 5500024034290101707049.C08

value: cervix

value: Cervix

value: ATCC


title: golub-00327: 5500024034290101707049.D08

value: adenocarcinoma

value: colon

value: Colorectal

value: ECCC


title: golub-00299: LEUK_K562

value: Chronic Myelogenous Leukemia


title: golub-00299: NSCLC_HOP62


title: golub-00327: 5500024034290101707049.H08

value: plasma cell myeloma

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: HSRRB


title: golub-00299: RENAL_A498

value: Kidney


title: golub-00327: 5500024032848101507998.A12

value: duodenum

value: Stomach


title: golub-00299: LEUK_RPMI8226

value: Plasma Cell Myeloma

value: Blood


title: golub-00299: OVAR_OVCAR4

value: Adenocarcinoma

value: Ovary

value: Epithelial Cell


title: golub-00299: RENAL_ACHN

value: Carcinoma


title: golub-00327: 5500024052861011409506.G02

value: carcinoma

value: colon

value: DTP


title: golub-00299: COLON_HT29

value: Colon


title: golub-00327: 5500024034290101707049.B08

value: transitional cell carcinoma

value: bladder

value: Urinary tract

value: ATCC


title: golub-00327: 5500024034290101707049.A08


title: golub-00327: 5500024035100021608461.D03

value: small cell carcinoma

value: lung

value: Lung

value: ICLC


title: golub-00299: MELAN_MALME3M

value: Melanoma

value: Skin


title: golub-00327: 5500024052603032009483.A11


title: golub-00327: 5500024031722092907496.A09

value: B cell lymphoma unspecified

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00327: 5500024032848101507998.C09

value: fibrosarcoma

value: Connective and Soft Tissue


title: golub-00327: 5500024034290101707049.E08

value: carcinoma

value: thyroid

value: Thyroid Gland

value: RIKEN


title: golub-00299: COLON_KM12

value: Adenocarcinoma

value: Colon

value: Epithelial Cell


title: golub-00299: NSCLC_NCIH23


title: golub-00327: 5500024052861011409506.D07

value: squamous cell carcinoma

value: tongue

value: Head and Neck

value: HSRRB


title: golub-00327: 5500024052861011409506.A08


title: golub-00327: 5500024035100021608461.G10

value: mouth


title: golub-00299: NSCLC_H460

value: Large Cell Carcinoma

value: Lung


title: golub-00327: 5500024032848101507998.D10

value: malignant melanoma

value: skin

value: Skin

value: ATCC


title: golub-00299: CNS_SF268

value: Glioblastoma

value: Brain


title: golub-00327: 5500024032848101507998.B09

value: ductal carcinoma

value: pancreas

value: Pancreas


title: golub-00299: RENAL_7860

value: Adenocarcinoma

value: Kidney

value: Epithelial Cell


title: golub-00327: 5500024035100021608461.A08

value: squamous cell carcinoma

value: Head and Neck


title: golub-00327: 5500024032848101507998.E09

value: osteosarcoma

value: bone

value: Bone


title: golub-00299: COLON_SW620

value: Carcinoma

value: Colon


title: golub-00327: 5500024052603032009483.H06

value: large cell carcinoma

value: lung

value: Lung

value: DTP


title: golub-00299: LEUK_MOLT4

value: Precursor Lymphoblastic Leukemia

value: Blood


title: golub-00327: 5500024052861011409506.E02

value: adenocarcinoma


title: golub-00236: SR2000042216AA

source_name: renal cell carcinoma

value: renal cell carcinoma


title: golub-00236: SR2000042215AA

description: Renal Carcinoma 6727

value: Kidney


title: golub-00236: SR2000042213AA


title: golub-00327: 5500024032848101507998.D09

value: mouth roof

value: DSMZ


title: golub-00236: SR2000042212AA

source_name: uterine adenocarcinoma

value: uterine adenocarcinoma

value: Uterus


title: golub-00236: SR2000042210AA


title: golub-00327: 5500024032848101507998.G09

value: hepatocellular carcinoma

value: liver

value: Liver

value: HSRRB


title: golub-00236: SR2000042209AA


title: golub-00327: 5500024052603032009483.C03

value: M3 acute myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00327: 5500024052603032009483.D04

value: carcinoma

value: breast

value: Breast

value: DTP


title: golub-00236: SR2000042208AA

source_name: bladder transitional cell carcinoma

value: bladder transitional cell carcinoma

value: Bladder


title: golub-00299: OVAR_OVCAR8

value: Carcinoma

value: Ovary

value: Epithelial Cell


title: golub-00327: 5500024031722092907496.H08

value: Adult T-Cell Leukemia/Lymphoma

value: ATCC


title: golub-00236: SR2000042207AA

value: uterine adenocarcinoma

value: Uterus


title: golub-00236: SR2000042206AA


title: golub-00327: 5500024032848101507000.G01

value: M6 acute myeloid leukemia

value: HSRRB


title: golub-00236: SR2000042205AA


title: golub-00327: 5500024030401071707289.G05

value: chondrosarcoma

value: extraskeletal

value: Bone

value: ECCC


title: golub-00327: 5500024032848101507998.F09

value: adenocarcinoma

value: endometrium

value: Endometrium


title: golub-00236: SR2000042204AA

value: renal cell carcinoma

value: Kidney


title: golub-00327: 5500024052861011409506.E07

value: Hodgkin lymphoma

value: lymph node

value: Lymphoma

value: DSMZ


title: golub-00236: SR2000042203AA

value: uterine adenocarcinoma


title: golub-00236: SR2000042202AA

value: Uterus


title: golub-00299: CNS_SNB75

value: Glioblastoma

value: Brain


title: golub-00327: 5500024052861011409506.G11

value: M6 acute myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: HSRRB


title: golub-00236: SR2000042201AA

value: bladder transitional cell carcinoma

value: Bladder


title: golub-00327: 5500024034290101707049.H07

value: adenocarcinoma

value: cervix

value: Cervix

value: ATCC


title: golub-00327: 5500024052603032009483.C08

value: carcinoma

value: stomach

value: Stomach

value: RIKEN


title: golub-00236: SR1999121604AA

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: Lung


title: golub-00236: MG2000033107AA

source_name: normal Brain

value: normal

value: Brain


title: golub-00327: 5500024035100021608461.E09

value: Hodgkin lymphoma

value: lymph node

value: Lymphoma

value: DSMZ


title: golub-00327: 5500024052861011409506.F02

value: colon

value: Colorectal

value: DTP


title: golub-00327: 5500024035100021608461.C03

value: squamous cell carcinoma

value: buccal mucosa

value: Head and Neck

value: HSRRB


title: golub-00236: MG1999112206AA


title: golub-00327: 5500024032848101507998.D08

value: ductal carcinoma

value: breast

value: Breast

value: ATCC


title: golub-00327: 5500024034290101707049.G07

value: esophagus

value: Oesophagus

value: Unspecified


title: golub-00236: MG2000033106AA

value: normal

value: Brain


title: golub-00327: 5500024030401071707289.F07

value: sinus

value: RIKEN


title: golub-00236: MG1999101304AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S97_27534_G_

source_name: large B-cell lymphoma

value: large B-cell lymphoma

value: Lymphoid Tissue


title: golub-00236: MG1999112201AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S93_04233_Y_

value: Lymphod Tissue


title: golub-00236: MG1999100702AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S94_22323_G_


title: golub-00327: 5500024052861011409506.B02

value: adenocarcinoma

value: colon

value: Colorectal

value: DTP


title: golub-00327: 5500024032848101507998.H12

value: ductal carcinoma

value: breast


title: golub-00236: MG1999100506AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S94_6696_G_

source_name: large-Bcell lymphoma

value: large-Bcell lymphoma


title: golub-00236: SR1999121605AA

source_name: colorectal adenocarcinoma

value: colorectal adenocarcinoma

value: Colon


title: golub-00327: 5500024032848101507998.G12

value: Breast

value: ATCC


title: golub-00236: MG1999100104AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S94_17150_R_


title: golub-00327: 5500024052603032009483.F12

value: Hodgkin lymphoma

value: lymph node

value: Lymphoma

value: DSMZ


title: golub-00236: MG1999090202AA

source_name: glioblastoma

value: glioblastoma

value: Brain


title: golub-00327: 5500024032848101507998.B12


title: golub-00236: MG1999090201AA


title: golub-00327: 5500024030401071707289.E07

value: malignant melanoma

value: skin

value: Skin

value: RIKEN


title: golub-00236: MG1999081810AA


title: golub-00236: MG1999081807AA


title: golub-00236: MG1999081806AA


title: golub-00327: 5500024034290101707049.F07

value: ductal carcinoma


title: golub-00327: 5500024035100021608461.D07

value: breast


title: golub-00327: 5500024032848101507998.C12


title: golub-00236: MG1999081803AA


title: golub-00327: 5500024052603032009483.A08


title: golub-00236: MG1999081804AA


title: golub-00327: 5500024032848101507998.H08

value: squamous cell carcinoma


title: golub-00327: 5500024030401071707289.D02

value: hairy cell leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00236: MG1999070205AA

source_name: Follicular lymphoma

value: Follicular lymphoma

value: Lymphoid Tissue


title: golub-00327: 5500024032848101507998.E12

value: Breast

value: ATCC


title: golub-00327: 5500024035100021608461.C06

value: Acute Lymphoblastic Leukemia


title: golub-00327: 5500024032848101507998.A09

value: adenocarcinoma

value: stomach

value: Stomach


title: golub-00327: 5500024032848101507998.F12


title: golub-00327: 5500024032848101507998.E08

value: glioma

value: central nervous system

value: Brain


title: golub-00327: 5500024052603032009483.G04

value: RIKEN


title: golub-00327: 5500024032848101507998.F08

value: Mycosis Fungoides and Sezary Syndrome

value: skin

value: Lymphoma


title: golub-00236: MG1999070201AA


title: golub-00327: 5500024032848101507998.G08

value: colon

value: Colorectal

value: ECCC


title: golub-00236: MG1999081805AA

value: glioblastoma


title: golub-00327: 5500024032848101507998.D12

value: ductal carcinoma

value: breast

value: Breast


title: golub-00236: MG1999070105AA

value: Follicular lymphoma

value: Lymphoid Tissue


title: golub-00236: MG1999062903AA


title: golub-00236: MG1999081802AA


title: golub-00236: MG1999062409AA

source_name: medulloblastoma

value: medulloblastoma


title: golub-00236: MG1999081801AA


title: golub-00236: MG1999062408AA


title: golub-00327: 5500024032848101507998.H07

value: adenocarcinoma


title: golub-00236: MG1999070203AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S98_17557_R_

value: large B-cell lymphoma


title: golub-00327: 5500024035100021608461.B03

value: renal cell carcinoma

value: kidney

value: Kidney

value: Unspecified


title: golub-00236: MG1999060209AA

value: Brain


title: golub-00236: MG1999052819AA


title: golub-00327: 5500024030401071707289.E08

value: neuroblastoma

value: autonomic ganglia

value: Autonomic Ganglion

value: HSRRB


title: golub-00236: MG1999062407AA


title: golub-00327: 5500024035100021608461.F12

value: glioblastoma multiforme

value: brain

value: DSMZ


title: golub-00236: MG1999052820AA


title: golub-00236: MG1999052809AA


title: golub-00327: 5500024030401071707289.G03

value: ICLC


title: golub-00236: MG1999052806AA


title: golub-00236: MG1999052801AA


title: golub-00327: 5500024030401071707289.F05

value: M4 acute myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00236: MG1999052404AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S98_12569_R_

value: large B-cell lymphoma

value: Lymphoid Tissue


title: golub-00327: 5500024030401071707289.E02

value: adenocarcinoma

value: stomach

value: Stomach

value: RIKEN


title: golub-00236: MG1999052403AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S98_8825_Y_


title: golub-00236: MG1999052110AA

value: Follicular lymphoma


title: golub-00327: 5500024034290101707049.E07

value: neuroblastoma

value: autonomic ganglia


title: golub-00327: 5500024032848101507998.B08

value: malignant fibrous histiocytoma-pleomorphic sarcoma

value: Connective and Soft Tissue

value: ATCC


title: golub-00327: 5500024031722092907496.G02

value: rhabdoid tumor

value: kidney

value: Kidney


title: golub-00327: 5500024031722092907496.E02

value: Burkitt lymphoma

value: Hematopoietic and Lymphoid Tissue


title: golub-00236: MG1999052108AA

description: Follicular Lymphoma FSCC_S99_5073_1


title: golub-00327: 5500024032848101507998.C08

value: glioma

value: central nervous system

value: Brain

value: DSMZ


title: golub-00236: MG1999052107AA

description: Large B-cell Lymphoma L_B_CELL_S98_1217_R

value: large B-cell lymphoma

value: Lymphod Tissue


title: golub-00327: 5500024034290101707049.D07

value: Leukemia


title: golub-00327: 5500024032848101507998.G07

value: gliosarcoma

value: brain

value: RIKEN


title: golub-00236: MG1999052102AA

value: Follicular lymphoma

value: Lymphoid Tissue


title: golub-00236: MG1999052105AA

description: Large_B-Cell__Lymphoma_L_B_CELL_S98_12453_R_


title: golub-00327: 5500024052861011409506.A07

value: malignant melanoma

value: skin

value: Skin

value: ATCC


title: golub-00236: MG1999052004AA


title: golub-00327: 5500024030401071707289.G02

value: follicular carcinoma

value: thyroid

value: Thyroid Gland

value: ICLC


title: golub-00236: MG1999052003AA


title: golub-00327: 5500024032848101507000.F08

value: squamous cell carcinoma

value: hypopharynx

value: Head and Neck


title: golub-00236: MG1999052001AA


title: golub-00327: 5500024035100021608461.F07

value: Ewings sarcoma-peripheral primitive neuroectodermal tumor

value: bone

value: Bone

value: Unspecified


title: golub-00327: 5500024052603032009483.G10


title: golub-00236: MG1999030904AA

value: renal cell carcinoma

value: Kidney


title: golub-00236: MG1999030902AA


title: golub-00327: 5500024035100021608461.G06


title: golub-00327: 5500024034290101707049.B07


title: golub-00236: LG2000100309AA

source_name: normal Blood

value: normal

value: Blood


title: golub-00236: LG2000100308AA


title: golub-00236: MG1999021109AA

description: AML (2,PK) BM

source_name: acute myeloid leukemia

value: acute myeloid leukemia

value: Bone Marrow


title: golub-00236: LG2000100306AA


title: golub-00327: 5500024035100021608461.C07


title: golub-00327: 5500024034290101707049.A07


title: golub-00327: 5500024035100021608461.H06


title: golub-00236: LG2000100304AA


title: golub-00236: MG1999030901AA


title: golub-00236: MG1999030903AA


title: golub-00327: 5500024034290101707049.H06


title: golub-00327: 5500024035100021608461.H07


title: golub-00236: CL2000100335AA

source_name: melanoma

value: melanoma

value: Skin


title: golub-00236: LG2000100305AA


title: golub-00327: 5500024034290101707049.G06


title: golub-00327: 5500024035100021608461.A07


title: golub-00327: 5500024032848101507000.B01

value: carcinoma

value: breast

value: Breast

value: DSMZ


title: golub-00236: CL2000100333AA

source_name: normal Kidney


title: golub-00327: 5500024031722092907496.B03

source_name: Cell

value: adenocarcinoma

value: bile duct

value: BiliaryTract

value: RIKEN


title: golub-00236: CL2000091228AA

value: Brain


title: golub-00327: 5500024032848101507998.F07

value: malignant melanoma

value: skin

value: HSRRB


title: golub-00236: CL2000091227AA

source_name: normal Ovary

value: normal

value: Ovary


title: golub-00327: 5500024030401071707289.F11

value: carcinosarcoma-malignant mesodermal mixed tumor

value: endometrium

value: Endometrium


title: golub-00236: CL2000091226AA

value: Kidney


title: golub-00327: 5500024034290101707049.E06

value: Ewings sarcoma-peripheral primitive neuroectodermal tumor

value: bone

value: Bone

value: Unspecified


title: golub-00236: CL2000091225AA

source_name: normal Uterus

value: Uterus


title: golub-00236: CL2000091224AA

source_name: normal Bladder

value: Bladder


title: golub-00236: CL2000091223AA

source_name: normal Lung

value: Lung


title: golub-00327: 5500024034290101707049.D06


title: golub-00236: CL2000091214AA


title: golub-00236: CL2000091215AA

value: Brain


title: golub-00327: 5500024034290101707049.H05


title: golub-00327: 5500024034290101707049.C06


title: golub-00236: CL2000091213AA


title: golub-00327: 5500024034290101707049.F06


title: golub-00236: CL2000091211AA

source_name: normal Colon

value: Colon


title: golub-00236: CL2000091210AA


title: golub-00236: CL2000091209AA


title: golub-00236: CL2000091212AA


title: golub-00236: CL2000091222AA


title: golub-00327: 5500024034290101707049.A06


title: golub-00327: 5500024052861011409506.F10

value: chronic eosinophilic leukemia-hypereosinophilic syndrome

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: RIKEN


title: golub-00236: SR2000042214AA

source_name: uterine adenocarcinoma

value: uterine adenocarcinoma


title: golub-00236: CL2000091207AA

source_name: normal Breast

value: normal

value: Breast


title: golub-00327: 5500024031722092907496.C02

value: blast phase chronic myeloid leukemia

value: DSMZ


title: golub-00236: CL2000090549AA

source_name: normal Brain


title: golub-00327: 5500024030401071707289.G10

value: Micropapillary Serous Carcinoma

value: ovary

value: Ovary


title: golub-00327: 5500024031722092907496.D01

value: adenocarcinoma

value: bile duct

value: BiliaryTract


title: golub-00327: 5500024052603032009483.G02


title: golub-00327: 5500024052861011409506.H10

value: lung

value: Lung

value: DTP


title: golub-00327: 5500024052603032009483.F05

value: squamous cell carcinoma


title: golub-00327: 5500024030401071707289.H04

value: mucinous carcinoma


title: golub-00327: 5500024032848101507000.E08

value: ductal carcinoma

value: breast


title: golub-00327: 5500024052603032009483.H02


title: golub-00236: CL2000090547AA

value: normal

value: Brain


title: golub-00236: CL2000090546AA


title: golub-00327: 5500024052603032009483.F04

value: chronic lymphocytic leukemia-small lymphocytic lymphoma

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00236: CL2000090548AA


title: golub-00236: CL2000090545AA


title: golub-00327: 5500024052603032009483.B06

value: small cell adenocarcinoma

value: stomach

value: Stomach

value: RIKEN


title: golub-00327: 5500024031722092907496.C03

value: Burkitt lymphoma

value: ATCC


title: golub-00327: 5500024031722092907496.F02

value: carcinoma

value: esophagus

value: Oesophagus


title: golub-00327: 5500024031722092907496.E08

value: small cell carcinoma

value: gastrointestinal tract (site indeterminate)


title: golub-00327: 5500024034290101707049.F05


title: golub-00327: 5500024030401071707289.F12


title: golub-00327: 5500024031722092907496.D03

value: adenocarcinoma

value: lung

value: Lung

value: DSMZ


title: golub-00236: CL2000090543AA

source_name: normal Pancreas

value: normal

value: Pancreas


title: golub-00236: CL2000090541AA

value: Kidney


title: golub-00236: CL2000090542AA


title: golub-00236: CL2000090544AA

value: Ovary


title: golub-00236: CL2000090539AA


title: golub-00236: CL2000090537AA

value: Uterus


title: golub-00236: CL2000090536AA


title: golub-00236: CL2000090534AA


title: golub-00327: 5500024030401071707289.A09

value: ductal carcinoma

value: breast

value: Breast


title: golub-00236: CL2000090535AA


title: golub-00327: 5500024030401071707289.E12

value: carcinoma

value: bladder

value: Urinary tract

value: Unspecified


title: golub-00327: 5500024052861011409506.D02

value: prostate

value: Prostate

value: DTP


title: golub-00236: CL2000090532AA

value: Bladder


title: golub-00327: 5500024035100021608461.G09

value: diffuse large B cell lymphoma

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: DSMZ


title: golub-00327: 5500024034290101707049.D05

value: epithelial dysplasia

value: mouth

value: Head and Neck

value: ECCC


title: golub-00236: CL2000090531AA

value: normal


title: golub-00327: 5500024030401071707289.H03

value: small cell carcinoma

value: lung

value: Lung


title: golub-00327: 5500024035100021608461.D12


title: golub-00327: 5500024052603032009483.B04

value: ATCC


title: golub-00327: 5500024052861011409506.A12

value: ductal carcinoma

value: breast

value: Breast


title: golub-00327: 5500024052861011409506.H11


title: golub-00236: CL2000090540AA

value: Kidney


title: golub-00236: CL2000090527AA

value: Colon


title: golub-00327: 5500024032848101507998.E07


title: golub-00236: CL2000090528AA


title: golub-00236: CL2000090526AA


title: golub-00236: CL2000090523AA


title: golub-00236: CL2000090529AA


title: golub-00236: CL2000090525AA


title: golub-00236: CL2000090524AA


title: golub-00236: CL2000090522AA


title: golub-00236: CL2000090533AA

value: Uterus


title: golub-00236: CL2000090521AA


title: golub-00327: 5500024030401071707289.H06

value: lymphoid neoplasm

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00327: 5500024052603032009483.H04

value: malignant trichilemmal cyst

value: skin

value: Skin

value: RIKEN


title: golub-00327: 5500024034290101707049.E05

value: carcinoma

value: cervix

value: Cervix


title: golub-00236: CL2000090530AA

value: normal

value: Bladder


title: golub-00327: 5500024052861011409506.G08

value: glioblastoma multiforme

value: parietal lobe

value: Brain

value: DSMZ


title: golub-00236: CL2000090520AA

value: Lung


title: golub-00327: 5500024052861011409506.C02

value: colon

value: Colorectal

value: DTP


title: golub-00327: 5500024031722092907496.F08

value: diffuse large B cell lymphoma

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: ATCC


title: golub-00327: 5500024030401071707289.H02

value: small cell carcinoma

value: lung

value: ECCC


title: golub-00236: CL2000090519AA

source_name: normal Prostate

value: normal

value: Prostate


title: golub-00327: 5500024052861011409506.B05

value: Burkitt lymphoma


title: golub-00236: CL2000090518AA


title: golub-00327: 5500024031722092907496.E03


title: golub-00327: 5500024031722092907496.D02


title: golub-00327: 5500024031722092907496.A03

value: glioblastoma multiforme

value: brain


title: golub-00327: 5500024031722092907496.G08

value: desmoplastic

value: posterior fossa

value: Brain


title: golub-00236: CL2000090517AA


title: golub-00236: CL2000090516AA


title: golub-00327: 5500024035100021608461.G08

value: astrocytoma

value: Unspecified


title: golub-00236: CL2000090515AA


title: golub-00327: 5500024031722092907496.H02

value: carcinoma

value: pharynx

value: Head and Neck


title: golub-00236: CL2000090514AA


title: golub-00236: CL2000090513AA

value: Breast


title: golub-00236: CL2000090511AA


title: golub-00236: CL2000090512AA


title: golub-00327: 5500024034290101707049.G04


title: golub-00327: 5500024035100021608461.B09


title: golub-00236: CL2000090509AA

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma


title: golub-00236: CL2000090507AA


title: golub-00236: CL2000090508AA


title: golub-00236: CL2000090506AA


title: golub-00327: 5500024034290101707049.A05


title: golub-00327: 5500024034290101707049.H04


title: golub-00327: 5500024034290101707049.B05

value: glioma


title: golub-00236: CL2000090501AA

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: Lung


title: golub-00327: 5500024034290101707049.F04


title: golub-00327: 5500024034290101707049.D04


title: golub-00236: CL2000090503AA


title: golub-00327: 5500024034290101707049.C04


title: golub-00327: 5500024034290101707049.B04


title: golub-00236: CL2000090502AA


title: golub-00236: CL2000090504AA


title: golub-00327: 5500024030401071707289.D05

value: central nervous system

value: ATCC


title: golub-00327: 5500024035100021608461.B06


title: golub-00327: 5500024034290101707049.E04


title: golub-00236: CL2000080301AA

source_name: breast adenocarcinoma

value: breast adenocarcinoma


title: golub-00327: 5500024034290101707049.C05

value: brain


title: golub-00327: 5500024032848101507998.F04

value: acute myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: DSMZ


title: golub-00327: 5500024034290101707049.H03

value: astrocytoma

value: Brain

value: Unspecified


title: golub-00327: 5500024032848101507998.F05

value: carcinoma

value: colon

value: Colorectal

value: RIKEN


title: golub-00327: 5500024052603032009483.F11

value: B cell lymphoma unspecified


title: golub-00236: CL2000080142AA

value: normal

value: Kidney


title: golub-00236: CL2000080141AA


title: golub-00236: CL2000080140AA


title: golub-00327: 5500024034290101707049.A04


title: golub-00236: CL2000080139AA


title: golub-00327: 5500024035100021608461.C12


title: golub-00236: CL2000080302AA

description: Melanoma MGH 7974

value: melanoma

value: Skin


title: golub-00327: 5500024030401071707289.C07


title: golub-00327: 5500024052603032009483.E06


title: golub-00236: CL2000080138AA


title: golub-00236: CL2000080137AA


title: golub-00236: CL2000080130AA

description: Melanoma MGH 8907


title: golub-00236: CL2000080116AA

value: prostate adenocarcinoma

value: Prostate


title: golub-00327: 5500024032848101507000.A04

value: small cell carcinoma

value: lung

value: Lung


title: golub-00236: CL2000080114AA

source_name: bladder transitional cell carcinoma

value: bladder transitional cell carcinoma

value: Bladder


title: golub-00236: CL2000080129AA

description: Melanoma MGH 11511

source_name: melanoma


title: golub-00236: CL2000080115AA


title: golub-00327: 5500024035100021608461.A03

value: malignant melanoma

value: skin

value: Unspecified


title: golub-00236: CL2000080112AA


title: golub-00236: CL2000080109AA


title: golub-00236: CL2000080111AA


title: golub-00327: 5500024032848101507998.G06

value: ECCC


title: golub-00327: 5500024035100021608461.F02


title: golub-00327: 5500024032848101507998.G05


title: golub-00327: 5500024035100021608461.H02


title: golub-00236: CL2000080107AA

source_name: ovarian adenocarcinoma

value: ovarian adenocarcinoma

value: Ovary


title: golub-00327: 5500024030401071707289.G04

source_name: Cell

value: adenocarcinoma


title: golub-00327: 5500024052861011409506.G06


title: golub-00327: 5500024052861011409506.E05


title: golub-00327: 5500024052861011409506.F06

value: large cell carcinoma


title: golub-00327: 5500024032848101507000.B04

value: carcinoma

value: breast

value: Breast

value: DSMZ


title: golub-00236: CL2000080106AA


title: golub-00236: CL2000080113AA


title: golub-00236: CL2000080104AA


title: golub-00327: 5500024030401071707289.A06

value: colon

value: Colorectal

value: ICLC


title: golub-00236: CL2000080105AA


title: golub-00327: 5500024052603032009483.A01

value: Skin


title: golub-00327: 5500024032848101507000.E10

value: small cell carcinoma

value: lung

value: Lung


title: golub-00236: CL2000080103AA


title: golub-00236: CL2000080101AA

value: breast adenocarcinoma


title: golub-00236: CL2000080110AA

value: bladder transitional cell carcinoma

value: Bladder


title: golub-00327: 5500024030401071707289.H01

value: #N/A

value: ovary

value: Ovary

value: ECCC


title: golub-00236: CL2000071418AA

source_name: medulloblastoma

value: medulloblastoma

value: Brain


title: golub-00327: 5500024032848101507998.G04

value: adenocarcinoma

value: endometrium

value: Endometrium


title: golub-00327: 5500024032848101507998.E05

value: carcinoma

value: colon

value: Colorectal

value: DSMZ


title: golub-00236: CL2000071417AA

source_name: Follicular lymphoma

value: Follicular lymphoma

value: Lymphoid


title: golub-00236: CL2000071416AA

value: normal

value: Pancreas


title: golub-00327: 5500024052861011409506.H12


title: golub-00327: 5500024034290101707049.G03

value: small cell carcinoma

value: lung

value: Lung


title: golub-00327: 5500024052861011409506.B07

value: malignant melanoma

value: skin

value: Skin

value: RIKEN


title: golub-00236: CL2000071415AA


title: golub-00236: CL2000071413AA

value: prostate adenocarcinoma

value: Prostate


title: golub-00236: CL2000071412AA

value: bladder transitional cell carcinoma

value: Bladder


title: golub-00236: CL2000072034AA


title: golub-00236: CL2000071409AA


title: golub-00236: CL2000071408AA

description: Melanoma MGH 10427

value: melanoma


title: golub-00236: CL2000071407AA

source_name: pancreatic adenocarcinoma

value: pancreatic adenocarcinoma


title: golub-00236: CL2000071404AA


title: golub-00327: 5500024052861011409506.G01

value: adenocarcinoma

value: colon

value: Colorectal

value: DTP


title: golub-00236: CL2000071401AA

value: ovarian adenocarcinoma

value: Ovary


title: golub-00236: CL2000071414AA

value: Pancreas


title: golub-00236: CH2000031319AA

description: Bladder TCC 104-64931


title: golub-00236: CH2000031318AA


title: golub-00327: 5500024032848101507000.G04

value: blast phase chronic myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: DSMZ


title: golub-00327: 5500024032848101507998.C07

value: ATCC


title: golub-00236: CH2000031315AA

source_name: colorectal adenocarcinoma

value: colorectal adenocarcinoma

value: Colon


title: golub-00327: 5500024032848101507998.B07

value: neuroblastoma

value: autonomic ganglia

value: Autonomic Ganglion

value: RIKEN


title: golub-00327: 5500024032848101507998.H04

value: M7 acute myeloid leukemia


title: golub-00236: CL2000071406AA

source_name: normal Bladder

value: normal

value: Bladder


title: retina/RPE_wildtype_1year_rep4

city: Santa Barbara

first: Steven

middle: K

last: Fisher

state: CA

address: BLDG. 571 Lagoon Rd.

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

description: Gene expression of age matched wildtype

hyb_protocol: Samples with an RNA Integrity Number (RIN) greater or equal to 8.0 were deemed acceptable and used for microarray anaylsis.  Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Kit v6.0. An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA.  Samples were subsequently hybridized on Agilent SurePrint G3 Mouse GE 8 X 60K Microarray (Design ID: 028005)

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner at a 3um scanning resolution

data_processing: Data was processed with Agilent Feature Extraction 11.0.1.1.  Processed signal was normalized using Agilent GeneSpring 12.0

organism: Mus musculus

label_protocol: RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples with an RNA Integrity Number (RIN) greater or equal to 8.0 were deemed acceptable and used for microarray anaylsis.  Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Kit v6.0

extract_protocol: Wild-type and nm3342 mice at P30 and P365 (n = 4/timepoint) were sacrificed, after which mRNA was isolated from both retinas and RPE using a mirVana RNA isolation kit (Life Technologies, Carlsbad, CA).

tag: strain background

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 1 year

tag: tissue

value: Retina/Retinal Pigmented Epithelium


title: golub-00327: 5500024034290101707049.F03


title: golub-00327: 5500024032848101507998.A06

value: malignant melanoma

value: skin

value: Skin


title: golub-00236: CH2000031316AA

description: Melanoma 96 I 166

value: melanoma


title: golub-00327: 5500024032848101507998.H06

value: carcinoma

value: lung

value: Lung

value: ATCC


title: retina/RPE_wildtype_1year_rep1

description: Gene expression of age matched wildtype


title: retina/RPE_wildtype_1year_rep2

description: Gene expression of age matched wildtype


title: retina/RPE_wildtype_1year_rep3

description: Gene expression of age matched wildtype


title: golub-00327: 5500024032848101507998.A05

value: follicular carcinoma

value: thyroid

value: Thyroid Gland

value: DSMZ


title: golub-00327: 5500024032848101507000.H04

value: neuroblastoma

value: autonomic ganglia

value: Autonomic Ganglion

value: RIKEN


title: golub-00236: CH2000031313AA

value: colorectal adenocarcinoma

value: Colon


title: golub-00327: 5500024030401071707289.C03

value: ductal carcinoma

value: pancreas

value: Pancreas

value: ECCC


title: retina/RPE_wildtype_1month_rep3

description: Gene expression of age matched wildtype

value: wild type

value: male

value: 1 month

value: Retina/Retinal Pigmented Epithelium


title: retina/RPE_wildtype_1month_rep2

description: Gene expression of age matched wildtype


title: retina/RPE_wildtype_1month_rep4

description: Gene expression of age matched wildtype


title: golub-00236: CH2000031317AA


title: golub-00236: CH2000031310AA

description: Melanoma 94 I 191

value: melanoma

value: Skin


title: golub-00327: 5500024032848101507000.C04

value: squamous cell carcinoma

value: esophagus

value: Oesophagus

value: DSMZ


title: golub-00236: CH2000031309AA


title: golub-00236: CH2000031308AA


title: retina/RPE_wildtype_1month_rep1

description: Gene expression of age matched wildtype


title: golub-00327: 5500024032848101507000.C03

value: M4 acute myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: ATCC


title: retina/RPE_mutant_1year_rep4

description: Gene expression after 1 year of serous retinal detachment

value: nm3342 (mutant)

value: 1 year


title: golub-00236: CH2000031312AA

value: pancreatic adenocarcinoma

value: Pancreas


title: golub-00327: 5500024052603032009483.G03

value: Acute Lymphoblastic Leukemia

value: DTP


title: golub-00236: CH2000031311AA


title: golub-00236: CH2000031303AA

description: Breast Adeno 93 I 192

value: breast adenocarcinoma

value: Breast


title: golub-00236: CH2000031304AA

value: normal


title: golub-00327: 5500024052861011409506.C07

value: carcinoma

value: cervix

value: Cervix


title: Lung cancer cell H661 with SALL4 shRNA , rep3

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: Gene expression data from H661 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using RMA in the bioconducter and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 8.

source_name: Cells (#3)  isolated from H661 lung cell line with SALL4 knockdown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lung cancer H661 cells were cultured in RPMI medium supplemented with 10% FBS in a 37°C incubator with 5% CO2 atmosphere

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

treatment_protocol: Lung cancer H661 cells were treated with either scrambled or SALL4 shRNA.

value: Human lung carcinoma cell line


title: retina/RPE_mutant_1month_rep4

description: Gene expression after 1 month of serous retinal detachment

value: male

value: 1 month

value: Retina/Retinal Pigmented Epithelium


title: golub-00236: CH2000031301AA

description: Ovary Adeno HCTN 19120

value: ovarian adenocarcinoma

value: Ovary


title: retina/RPE_mutant_1year_rep1

value: nm3342 (mutant)

value: 1 year


title: retina/RPE_mutant_1year_rep2


title: golub-00236: CH2000031306AA

value: pancreatic adenocarcinoma

value: Pancreas


title: golub-00236: CH2000031106AA


title: golub-00327: 5500024030401071707289.B01

value: glioblastoma multiforme

value: brain

value: Brain

value: ECCC


title: golub-00327: 5500024034290101707049.E03

value: #N/A

value: adenocarcinoma

value: pancreas

value: DSMZ


title: Lung cancer cell H661 with SALL4 shRNA , rep1

description: Gene expression data from H661 cells

source_name: Cells (#1)  isolated from H661 lung cell line with SALL4 knockdown

value: Human lung carcinoma cell line


title: golub-00236: CH2000031305AA

description: Melanoma 93 I 262

value: melanoma

value: Skin


title: retina/RPE_mutant_1year_rep3

value: male

value: Retina/Retinal Pigmented Epithelium


title: Lung cancer cell H661 with scrambled control , rep3

description: Gene expression data from H661 cells

source_name: Cells (#3)  isolated from H661 lung cell line with scrambled control


title: golub-00327: 5500024035100021608461.E02

value: rectum

value: Colorectal

value: HSRRB


title: retina/RPE_mutant_1month_rep3

value: nm3342 (mutant)

value: 1 month


title: Lung cancer cell H661 with SALL4 shRNA , rep2

description: Gene expression data from H661 cells

source_name: Cells (#2)  isolated from H661 lung cell line with SALL4 knockdown


title: golub-00236: CH2000031302AA

value: breast adenocarcinoma

value: Breast


title: golub-00327: 5500024032848101507998.E06

value: glioblastoma multiforme

value: brain

value: Brain

value: ICLC


title: retina/RPE_mutant_1month_rep2


title: golub-00236: CH2000031105AA

description: Lung Adeno 95 I 117

value: lung adenocarcinoma

value: Lung


title: Lung cancer cell H661 with scrambled control , rep2

description: Gene expression data from H661 cells

source_name: Cells (#2)  isolated from H661 lung cell line with scrambled control

value: Human lung carcinoma cell line


title: retina/RPE_mutant_1month_rep1


title: golub-00236: CH2000031104AA

value: ovarian adenocarcinoma

value: Ovary


title: golub-00327: 5500024034290101707049.C03

value: adenocarcinoma

value: ovary

value: ATCC


title: golub-00327: 5500024034290101707049.D03

value: ductal carcinoma

value: pancreas

value: Pancreas

value: DSMZ


title: golub-00327: 5500024032848101507998.D05


title: golub-00392: Ir2.5uM_3d_3

source_name: PrimaryPatient7, Iressa-treated

value: Acute Myeloid Leukemia

tag: aml fab classification


title: golub-00236: CH2000031103AA

value: breast adenocarcinoma

value: Breast


title: Lung cancer cell H661 with scrambled control , rep1

description: Gene expression data from H661 cells

source_name: Cells (#1)  isolated from H661 lung cell line with scrambled control


title: golub-00327: 5500024034290101707049.B03

value: carcinoma

value: breast


title: golub-00236: CH2000031024AA

value: pancreatic adenocarcinoma


title: golub-00327: 5500024032848101507000.A03

value: lung

value: Lung


title: golub-00236: CH2000031023AA

source_name: normal Breast

value: normal


title: golub-00392: DMSO_3d_2

source_name: PrimaryPatient7, DMSO-treated control


title: golub-00392: DMSO_3d_1


title: golub-00327: 5500024032848101507000.B03


title: golub-00236: CH2000031021AA

description: Mesothelioma 74 T6

source_name: mesothelioma

value: mesothelioma

value: Mesothelium


title: golub-00236: CH2000031022AA

description: Mesothelioma 228 T4


title: golub-00392: Ir5uM_24hr_3


title: golub-00392: Ir5uM_24hr_2


title: golub-00236: CH2000031020AA

description: Pancreas Adeno 97 I 077


title: golub-00392: Ir2.5uM_3d_1


title: golub-00236: CH2000031019AA

description: Mesothelioma 165 T5


title: golub-00327: 5500024032848101507000.H02

value: mucoepidermoid carcinoma


title: golub-00392: Ir2.5uM_3d_2


title: golub-00236: CH2000031101AA

source_name: breast adenocarcinoma


title: golub-00327: 5500024052861011409506.F08

source_name: Cell


title: golub-00392: Ir2.5uM_24hr_3


title: golub-00236: CH2000031017AA

description: Mesothelioma 215 T5


title: golub-00327: 5500024032848101507998.B06


title: golub-00392: Ir2.5uM_24hr_2


title: golub-00327: 5500024052861011409506.C09

value: Osteoblastic Osteosarcoma

value: bone

value: Bone


title: golub-00327: 5500024052603032009483.C02


title: golub-00392: DMSO_3d_3


title: golub-00327: 5500024034290101707049.A03

value: renal cell carcinoma

value: kidney

value: Kidney


title: golub-00327: 5500024032848101507998.A07

value: anaplastic carcinoma

value: thyroid

value: Thyroid Gland

value: DSMZ


title: golub-00236: CH2000031016AA

description: Melanoma 0-9652

source_name: melanoma

value: melanoma

value: Skin


title: golub-00392: Ir2.5uM_24hr_1

value: Acute Myeloid Leukemia


title: golub-00236: CH2000031015AA

description: Mesothelioma 224 T5


title: golub-00236: CH2000031014AA

description: Mesothelioma 31 T10


title: golub-00392: DMSO_24hr_3


title: golub-00392: DMSO_24hr_2


title: golub-00327: 5500024034290101707049.H02

value: carcinoma

value: breast

value: Breast


title: golub-00392: DMSO_24hr_1


title: golub-00236: CH2000031011AA

description: Melanoma 94 I 149


title: golub-00236: CH2000031013AA

value: colorectal adenocarcinoma

value: Colon


title: golub-00392: Ir5uM_24hr_1


title: golub-00236: CH2000031018AA

description: Mesothelioma 235 T6

value: mesothelioma

value: Mesothelium


title: golub-00392: Ir5uM_6hr_3


title: golub-00236: CH2000031010AA

description: Mesothelioma 166 T4


title: golub-00327: 5500024034290101707049.G02

value: squamous cell carcinoma

value: vulva

value: Vulva


title: golub-00392: Ir5uM_6hr_2


title: golub-00236: CH2000031008AA

value: pancreatic adenocarcinoma

value: Pancreas


title: golub-00392: Ir5uM_6hr_1


title: golub-00327: 5500024034290101707049.E02

value: ductal carcinoma


title: golub-00327: 5500024032848101507998.C06

value: tongue

value: Head and Neck

value: DSMZ


title: golub-00327: 5500024034290101707049.F02

value: Unspecified


title: golub-00327: 5500024032848101507998.B05

value: Non-Small Cell Carcinoma

value: lung

value: Lung


title: golub-00236: CH2000031006AA

value: colorectal adenocarcinoma


title: golub-00392: Ir2.5uM_6hr_3

value: Acute Myeloid Leukemia


title: golub-00327: 5500024032848101507000.B10

value: carcinoma

value: breast

value: Breast


title: golub-00392: Ir2.5uM_6hr_2


title: golub-00236: CH2000031005AA

source_name: normal  Pancreas

value: normal


title: golub-00327: 5500024030401071707289.H12

value: squamous cell carcinoma

value: gingiva

value: HSRRB


title: golub-00392: Ir2.5uM_6hr_1


title: golub-00236: CH2000031004AA

description: Mesothelioma 169 T7

value: mesothelioma

value: Mesothelium


title: golub-00327: 5500024052861011409506.H01

value: clear cell renal cell carcinoma

value: kidney

value: Kidney

value: DTP


title: golub-00392: DMSO_6hr_3


title: golub-00236: CH2000031001AA

description: Mesothelioma 161 T6


title: golub-00236: CH2000030521AA

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma

value: Prostate


title: golub-00236: CH2000030520AA

value: breast adenocarcinoma


title: golub-00327: 5500024032848101507998.H05

value: Burkitt lymphoma

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: ATCC


title: golub-00392: DMSO_6hr_1

value: Acute Myeloid Leukemia


title: golub-00236: CH2000030516AA

description: Colorectal Adeno 95 I 175

source_name: colorectal adenocarcinoma

value: colorectal adenocarcinoma

value: Colon


title: golub-00392: mono3

source_name: mono3, no treatment

value: normal


title: golub-00392: DMSO_6hr_2


title: golub-00327: 5500024052861011409506.G12

value: hepatocellular carcinoma

value: liver

value: Liver


title: golub-00327: 5500024032848101507000.F02

value: carcinoma

value: cervix

value: Cervix


title: golub-00392: mono2

source_name: mono2, no treatment


title: golub-00392: mono1

source_name: mono1, no treatment


title: golub-00236: CH2000030515AA

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: Lung


title: golub-00327: 5500024032848101507000.G02


title: golub-00327: 5500024030401071707289.E01

value: Adult T-Cell Leukemia/Lymphoma

value: ECCC


title: golub-00327: 5500024052861011409506.B09


title: golub-00236: CH2000030509AA

value: breast adenocarcinoma

value: Breast


title: golub-00392: poly3

source_name: poly3, no treatment


title: golub-00392: poly2

source_name: poly2, no treatment


title: golub-00236: CH2000030508AA

source_name: renal cell carcinoma

value: renal cell carcinoma

value: Kideny


title: golub-00392: poly1

source_name: poly1, no treatment


title: golub-00236: CH2000030507AA

value: colorectal adenocarcinoma


title: golub-00236: CH2000030504AA

source_name: pancreatic adenocarcinoma

value: pancreatic adenocarcinoma

value: Pancreas


title: golub-00327: 5500024032848101507998.E04

value: ATCC


title: golub-00327: 5500024035100021608461.D02

value: malignant melanoma

value: skin

value: Skin


title: golub-00392: AML9

source_name: AML9, no treatment

value: Acute Myeloid Leukemia


title: golub-00327: 5500024032848101507998.F06

value: adenocarcinoma

value: colon

value: Colorectal


title: golub-00236: CH2000030424AA

source_name: normal Prostate

value: normal

value: Prostate


title: golub-00327: 5500024032848101507000.E04

value: blast phase chronic myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: DSMZ


title: golub-00392: AML8

source_name: AML8, no treatment


title: golub-00236: CH2000030415AA

source_name: ovarian adenocarcinoma

value: ovarian adenocarcinoma

value: Ovary


title: golub-00392: AML7

source_name: AML7, no treatment


title: golub-00236: CH2000030511AA

source_name: breast adenocarcinoma

value: breast adenocarcinoma

value: Breast


title: golub-00327: 5500024052603032009483.E04

source_name: Cell

value: papillary ductal carcinoma

value: breast

value: DTP


title: golub-00236: CH2000030413AA

source_name: uterine adenocarcinoma

value: uterine adenocarcinoma

value: Uterus


title: golub-00327: 5500024034290101707049.C02

value: hyperplasia

value: prostate


title: golub-00236: CH2000030411AA


title: golub-00392: AML5

source_name: AML5, no treatment

value: Acute Myeloid Leukemia


title: golub-00392: AML6

source_name: AML6, no treatment


title: golub-00236: CH2000030409AA

value: lung adenocarcinoma

value: Lung


title: golub-00327: 5500024034290101707049.D02

value: carcinoma

value: ATCC


title: golub-00392: AML4

source_name: AML4, no treatment


title: golub-00392: AML3

source_name: AML3, no treatment


title: golub-00236: CH2000031314AA

source_name: normal Pancreas

value: normal

value: Pancreas


title: golub-00236: CH2000030408AA

source_name: colorectal adenocarcinoma

value: colorectal adenocarcinoma

value: Colon


title: golub-00327: 5500024030401071707289.F01

value: hairy cell leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: DSMZ


title: golub-00392: AML2

source_name: AML2, no treatment


title: golub-00392: AML1

source_name: AML1, no treatment


title: golub-00327: 5500024030401071707289.A01

value: pancreas

value: ECCC


title: golub-00327: 5500024032848101507998.D06

value: Burkitt lymphoma


title: golub-00236: CH2000030403AA

value: breast adenocarcinoma

value: Breast


title: golub-00327: 5500024034290101707049.B02

value: squamous cell carcinoma

value: cervix

value: Cervix

value: HSRRB


title: golub-00236: CH2000030401AA

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: Lung


title: golub-00392: Pt_C_5uM_Iressa-1

source_name: PrimaryPatient2, Iressa-treated

value: Acute Myeloid Leukemia


title: golub-00327: 5500024052861011409506.A09


title: golub-00236: CH1999121701AA


title: golub-00236: CH2000030407AA


title: golub-00327: 5500024032848101507998.D04


title: golub-00236: CH1999111202AA

description: ALL (87_52) BM

source_name: T-cell ALL

value: T-cell ALL

value: Bone Marrow


title: golub-00236: CH1999101507AA

description: ALL (92_571) BM


title: golub-00392: Pt_C_DMSO-1

source_name: PrimaryPatient2, DMSO-treated control


title: golub-00236: CH2000030405AA

source_name: prostate adenocarcinoma

value: prostate adenocarcinoma

value: Prostate


title: golub-00392: 3d_DMSO1

source_name: PrimaryPatient1, DMSO-treated control


title: golub-00392: Pt_C_5uM_Iressa-2


title: golub-00327: 5500024035100021608461.D09

value: anaplastic carcinoma

value: thyroid

value: Thyroid Gland

value: DSMZ


title: golub-00236: CH1999021520AA

description: ALL (9186)  BM


title: golub-00392: 3d_iressa3

source_name: PrimaryPatient1, Iressa-treated


title: golub-00236: CH1999021515AA

description: ALL (19769)  BM

source_name: B-cell ALL

value: B-cell ALL


title: golub-00327: 5500024034290101707049.A02

source_name: Cell

value: head neck

value: Head and Neck


title: golub-00236: CH1999090803AA

description: Lung Adeno LT14


title: golub-00392: 3d_iressa2


title: golub-00236: CH1999021516AA

description: AML (1,PK) BM

source_name: acute myeloid leukemia

value: acute myeloid leukemia


title: golub-00392: 3d_iressa1


title: golub-00392: Pt_C_DMSO-2


title: golub-00236: CH1999021514AA

description: AML (16,PK) BM


title: golub-00327: 5500024032848101507998.H03

value: carcinoma

value: kidney

value: Kidney


title: golub-00327: 5500024052603032009483.E12

value: papillary transitional cell carcinoma

value: brain

value: Urinary tract


title: golub-00327: 5500024032848101507998.C04

value: lung

value: Lung


title: golub-00392: Kas_24h_Ir10uM_3

source_name: Kasumi_1, Iressa-treated

value: Acute Myeloid Leukemia


title: golub-00327: 5500024035100021608461.B12


title: golub-00327: 5500024052603032009483.C05

value: Acute Lymphoblastic Leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: golub-00327: 5500024052603032009483.E01

value: glioblastoma multiforme

value: Brain

value: HSRRB


title: golub-00327: 5500024052861011409506.A06


title: golub-00327: 5500024052861011409506.H08

value: B cell lymphoma unspecified

value: ATCC


title: golub-00392: 3d_DMSO2


title: golub-00236: CH1999021511AA

description: ALL (23953)  BM

value: B-cell ALL

value: Bone Marrow


title: golub-00236: CH1999021508AA

description: ALL (14749) BM


title: golub-00392: Kas_24h_Ir10uM_1


title: golub-00392: Kas_24h_Ir10uM_2


title: golub-00236: CH1999021507AA

description: ALL (28373)  BM


title: golub-00236: CH1999021322AA

description: ALL (20414)  BM


title: golub-00392: Kas_6h_Ir10uM_2


title: golub-00392: Kas_6h_Ir10uM_1


title: golub-00236: CH1999021321AA

description: ALL (19183)  BM


title: golub-00236: CH1999021320AA

description: AML (14,PK) BM

value: acute myeloid leukemia


title: golub-00392: Kas_24h_DMSO3

source_name: Kasumi_1, DMSO-treated control


title: golub-00327: 5500024034290101707049.H01

value: papillary carcinoma

value: thyroid

value: Thyroid Gland

value: Unspecified


title: golub-00392: Kas_24h_DMSO2


title: golub-00236: CH1999021319AA

description: AML (12,PK) BM


title: golub-00392: Kas_24h_DMSO1


title: golub-00327: 5500024035100021608461.C02

value: renal cell carcinoma

value: kidney

value: Kidney


title: golub-00392: Kas_6h_DMSO2

value: Acute Myeloid Leukemia


title: golub-00236: CH1999021312AA

description: ALL (9335)  BM


title: golub-00392: Kas_6h_DMSO1


title: golub-00236: CH1999021314AA

description: ALL (17281) BM


title: golub-00327: 5500024035100021608461.B02

value: squamous cell carcinoma

value: head neck

value: Head and Neck


title: golub-00236: CH1999021311AA

description: AML (7,PK) BM


title: golub-00392: HL60_10uM_Iressa_24hr-3

source_name: HL60, Iressa-treated


title: golub-00236: CH1999021309AA

description: ALL(14402)  BM

value: T-cell ALL


title: golub-00327: 5500024032848101507998.B04

value: astrocytoma

value: brain

value: Brain

value: HSRRB


title: golub-00236: CH1999021310AA

description: ALL (17269)  BM

value: Bone Marrow


title: golub-00392: HL60_10uM_Iressa_24hr-1


title: golub-00327: 5500024032848101507998.G03

value: B cell lymphoma unspecified

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: ATCC


title: golub-00327: 5500024035100021608461.A02

value: Unspecified


title: golub-00327: 5500024052861011409506.C06

value: plasma cell myeloma


title: golub-00392: HL60_10uM_Iressa_24hr-2


title: golub-00327: 5500024032848101507998.F03

value: B Acute Lymphoblastic Leukemia

value: RIKEN


title: golub-00236: CH1999021306AA

description: ALL (16415) BM


title: golub-00327: 5500024032848101507000.C02

value: carcinoma

value: pancreas

value: Pancreas


title: golub-00327: 5500024032848101507000.B02

value: L1 Acute T-Cell Lymphoblastic Leukemia


title: golub-00236: CH1999021305AA

description: ALL (9723)  BM

value: T-cell ALL


title: golub-00327: 5500024032848101507000.D02

value: adenocarcinoma

value: endometrium

value: Endometrium


title: golub-00392: HL60_DMSO_24hr-1

source_name: HL60, DMSO-treated control

value: Acute Myeloid Leukemia


title: golub-00392: HL60_DMSO_24hr-2


title: golub-00236: CH1999021111AA

description: ALL (21302)  BM

value: B-cell ALL

value: Bone Marrow


title: golub-00236: CH1999021109AA

description: ALL (9692)  BM


title: golub-00392: HL60_DMSO_24hr-3


title: golub-00236: CH1999021108AA

description: AML (5,PK) BM

value: acute myeloid leukemia


title: golub-00327: 5500024032848101507998.B03

value: glioblastoma multiforme

value: brain

value: Brain

value: HSRRB


title: golub-00392: HL60_10uM_Iressa_6hr-2


title: golub-00327: 5500024034290101707049.G01

value: M5 acute myeloid leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia

value: ATCC


title: golub-00327: 5500024032848101507998.D03

value: Acute Lymphoblastic Leukemia

value: ICLC


title: golub-00236: CH1999021107AA

description: AML (6,PK) BM


title: golub-00327: 5500024034290101707049.F01

value: adenocarcinoma

value: stomach

value: Stomach


title: golub-00327: 5500024052861011409506.G10


title: golub-00392: HL60_10uM_Iressa_6hr-1

value: Acute Myeloid Leukemia


title: golub-00236: CH1999021106AA

description: AML (3,PK) BM


title: golub-00392: HL60_DMSO_6hr-2


title: golub-00392: HL60_DMSO_6hr-3


title: golub-00236: CH1999021105AA

description: AML (13,PK) BM


title: golub-00236: CH1999021101AA

description: ALL (17638)  BM

value: T-cell ALL


title: golub-00392: HL60_DMSO_6hr-1


title: golub-00236: CH1999021103AA

description: ALL (19881)  BM

value: Bone Marrow


title: golub-00327: 5500024052861011409506.A02

value: renal cell carcinoma

value: kidney

value: Kidney

value: DTP


title: golub-00392: HL60_10uM_Iressa_6hr-3


title: golub-00327: 5500024030401071707289.F02

value: neuroblastoma

value: autonomic ganglia

value: Autonomic Ganglion


title: golub-00327: 5500024052861011409506.C11


title: golub-00327: 5500024030401071707289.G12


title: golub-00327: 5500024052861011409506.D01

value: carcinoma

value: lung

value: Lung


title: golub-00327: 5500024032848101507998.A03

value: rhabdomyosarcoma

value: striated muscle

value: Muscle

value: ATCC


title: golub-00327: 5500024032848101507998.G02

value: stomach

value: Stomach

value: HSRRB


title: golub-00327: 5500024052861011409506.H06

value: malignant melanoma

value: skin

value: Skin


title: golub-00327: 5500024032848101507000.A10


title: golub-00327: 5500024052861011409506.H04

value: adenocarcinoma

value: ovary

value: Ovary

value: ICLC


title: golub-00327: 5500024034290101707049.E01

value: squamous cell carcinoma

value: DSMZ


title: golub-00327: 5500024035100021608461.H08

value: mucoepidermoid carcinoma

value: submaxillary

value: Head and Neck


title: golub-00327: 5500024052861011409506.E06


title: golub-00327: 5500024052861011409506.D06

value: lung

value: Lung


title: golub-00327: 5500024052603032009483.F03

value: carcinoma

value: kidney

value: Kidney

value: DTP


title: golub-00327: 5500024032848101507998.C03

value: rhabdomyosarcoma

value: striated muscle

value: Muscle

value: ATCC


title: WT_MIR  replicate 4

city: Frederick

first: Xavier

last: Bofill-De Ros

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

label_protocol: 100ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the LowInputQuick Amp Labeling kit  (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: adult

value: hippocampus

tag: condition

value: euploid

tag: transduction


title: golub-00327: 5500024032848101507998.F02

tag: cosmic id

tag: disease state

value: glioblastoma multiforme

value: frontal lobe

value: Brain

value: DSMZ


title: TS_MIR  replicate 4

value: trisomic


title: Rosette_TCP15EARvsWT_BiolRep1

city: Santa Fe

first: Agustin

middle: Lucas

last: Arce

state: Santa Fe

address: Ciudad Universitaria

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

hyb_protocol: Hybridization was performed at 10 rpm for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B-C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sept09). Normexp background subtraction was applied followed by a loess normalization.

organism: Arabidopsis thaliana

source_name: Rosette, wild type

label_protocol: The labelling protocol used was GE2 v6.5.

growth_protocol: Plants were grown on soil at 22-24ºC under a long-day photoperiod (16 h of illumination by a mixture of cool-white and GroLux fluorescent lamps) at an intensity of approximately 100 µE m-2 s-1.

extract_protocol: RNA was prepared using the RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: Complete rosettes were taken 25 days after germination.

tag: ecotype

value: wild type

value: rosette

value: 25 days

tag: biological replicate

source_name: Rosette, P15::TCP15-EAR

tag: genotype

value: P15::TCP15-EAR (transgenic)


title: WT_GFP  replicate 4

value: Lv-Control


title: Rosette_TCP15EARvsWT_BiolRep2


title: golub-00327: 5500024034290101707049.D01

value: anaplastic carcinoma

tag: disease location

value: thyroid

tag: organism part

value: Thyroid Gland

tag: sample

tag: cell line code

tag: supplier

value: HSRRB


title: TS_MIR  replicate 5

value: adult


title: golub-00327: 5500024032848101507998.H02

value: brain

value: ATCC

tag: crna plate


title: golub-00327: 5500024032848101507000.E02

value: carcinoma

value: lung

value: Lung


title: TS_GFP  replicate 3

value: hippocampus


title: golub-00327: 5500024032848101507998.E03

value: malignant melanoma

value: skin

value: Skin


title: Rosette_control_BiolRep1

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sept09). Normexp background subtraction was applied followed by a quantile normalization.

label_protocol: The labelling protocol used was GE1 v6.5.

tag: genotype/variation

value: wild type

value: rosette

value: 25 days


title: WT_MIR replicate 3

tag: age

value: euploid


title: siSCR + E2 Replicate 3

city: Newcastle Upon Tyne

first: Mark

middle: A

last: Wade

state: Tyne and Wear

address: Paul O'Gorman Building, Framlington Place

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

description: Array 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed and analysed using R statistical software and BioConductor packages. Background corrected signal intensities were variance-stabilized and normlized using the 'vsn' package (Huber, W, von Heydebreck, A., Sueltmann, H.,  Poustka, A., and Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics: Vol. 18 suppl. 1 S96-S104 (2002)) .

source_name: siSCR + E2 Replicate 3

label_protocol: According to manufacturer (Illumina) specifications.

extract_protocol: RNA was extracted with TRIzol reagent (Ambion, Life Technologies) following manufacturers instructions. Quality control was performed with Agilent Bioanalyser.

tag: transfection

value: siSCR

tag: agent

value: 10 nM E2

tag: cell type

value: Human breast adenocarcinoma cell line

tag: cell line


title: WT_MIR replicate 2

value: adult

tag: tissue

tag: condition

tag: transduction


title: golub-00327: 5500024030401071707289.C10

tag: cosmic id

tag: disease state

value: transitional cell carcinoma

value: bladder

value: Urinary tract

value: DSMZ


title: golub-00327: 5500024052861011409506.D05

tag: disease location


title: siKDM3A-B - E2 Replicate 3

description: Array 2

source_name: siKDM3A-B - E2 Replicate 3

value: vehicle


title: TS_MIR  replicate 3

value: hippocampus

value: trisomic


title: golub-00327: 5500024032848101507998.E02

value: clear cell renal cell carcinoma

value: kidney

tag: organism part

value: Kidney

value: Unspecified


title: golub-00327: 5500024030401071707289.D04

value: ureter

tag: sample


title: siSCR + E2 Replicate 2

description: Array 1

source_name: siSCR + E2 Replicate 2


title: Rosette_TCP15EAR_BiolRep1

tag: ecotype

value: P15::TCP15-EAR (transgenic)

value: rosette

value: 25 days

tag: biological replicate


title: golub-00327: 5500024052861011409506.E01

tag: cell line code

tag: supplier

value: DTP

tag: crna plate


title: golub-00327: 5500024032848101507998.D02

value: adenocarcinoma

value: stomach

value: Stomach


title: siKDM3A-B + E2 Replicate 2

description: Array 1

source_name: siKDM3A-B + E2 Replicate 2

tag: transfection

value: 10 nM E2

value: Human breast adenocarcinoma cell line


title: siKDM3A-B - E2 Replicate 2

description: Array 1

source_name: siKDM3A-B - E2 Replicate 2

tag: agent

value: vehicle


title: TS_GFP  replicate 2

tag: age

value: adult

value: hippocampus

value: Lv-Control


title: WT_GFP  replicate 3

value: euploid


title: TS_MIR  replicate 2

value: trisomic


title: siSCR - E2 Replicate 2

description: Array 1

source_name: siSCR - E2 Replicate 2

value: siSCR

tag: cell type

tag: cell line


title: golub-00327: 5500024052603032009483.A09

value: carcinoma

value: bladder

value: Urinary tract

value: ATCC


title: siKDM3A-B + E2 Replicate 1

description: Array 1

source_name: siKDM3A-B + E2 Replicate 1


title: golub-00327: 5500024035100021608461.H01

value: prostate

value: Prostate

value: DSMZ


title: siSCR - E2 Replicate 3

description: Array 2

source_name: siSCR - E2 Replicate 3


title: siSCR + E2 Replicate 1

description: Array 1

source_name: siSCR + E2 Replicate 1


title: siKDM3A-B - E2 Replicate 1

description: Array 1

source_name: siKDM3A-B - E2 Replicate 1


title: TS_MIR  replicate 1

tag: tissue

tag: condition


title: golub-00327: 5500024034290101707049.A01

source_name: Cell

tag: cosmic id

value: NS Acute Lymphoblastic Leukemia

value: Hematopoietic and Lymphoid Tissue

value: Leukemia


title: WT_GFP  replicate 2

tag: transduction


title: TS_GFP  replicate 1


title: WT_MIR replicate 1


title: WT_GFP  replicate 1


title: A549-lung adenocarcinoma-CUL3-Neg-rep2

status: Public on May 15 2015

city: Minneapolis

first: Casey

last: Dorr

state: MN

address: 701 Park Avenue

institute: Minneapolis Medical Research Foundation

description:
CUL3 knockdown replicate 2
SAMPLE 5

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: A549 stage 2 lung adenocarcinoma

label_protocol: Standard Illumina protocol

growth_protocol: To make stable CUL3 knockdown cells, CUL3 specific shRNA encoding lentivirus was used to transduce A549 cells. Open-Biosystems lentiviral packaging mix with Non-silencing, CUL3 2702, CUL3 32413, or CUL3 351781 shRNA plasmids were used to produce lentivirus that harbors CUL3 specific shRNA sequence. Cells were transfected according to the Open Biosystems' lentivirus production protocol.The cells were then grown under puromycin selection in RPMI. A549 cells with stable CUL3 knockdown, or expressing the non-silencing control, were then transfected with SABiosciences SureSilencing shRNA plasmids for human PTEN (catalog number KH00327H) or with the negative shRNA encoding plasmid control. The cells were maintained in RPMI with 1 X Penicillin, Streptomycin, 10% fetal bovine serum, 1 μg/ml Puromycin and 32 μg/ml Hygromycin at 37°C and 5% CO2. All microarray experiemnts were conducted by the University of Minnesota's Genomics Center

extract_protocol: RNA was isoated using Trizol and Qiagen RNeasy QIA shredder

tag: treatment

value: CUL3 knockdown


title: A549-lung adenocarcinoma-NS-Neg-rep3

description:
Control replicate 3
SAMPLE 3

value: Control


title: A549-lung adenocarcinoma-NS-PTEN-rep3

description:
PTEN knockdown replicate 3
SAMPLE 9

value: PTEN knockdown


title: A549-lung adenocarcinoma-CUL3-PTEN-rep3

description:
CUL3 and PTEN knockdown replicate 3
SAMPLE 12

value: CUL3 and PTEN knockdown


title: A549-lung adenocarcinoma-CUL3-PTEN-rep1

description:
CUL3 and PTEN knockdown replicate 1
SAMPLE 10


title: A549-lung adenocarcinoma-NS-PTEN-rep1

description:
PTEN knockdown replicate 1
SAMPLE 7


title: A549-lung adenocarcinoma-CUL3-PTEN-rep2

description:
CUL3 and PTEN knockdown replicate 2
SAMPLE 11


title: Replicate 1 - CDB4124

city: PHILADELPHIA

first: Chirayu

middle: Pankaj

last: Goswami

state: PA

address: 110 S 11TH STREET

department: MOLECULAR DIAGNOSTIC LABORATORY

institute: THOMAS JEFFERSON UNIVERSITY HOSPITAL

description: replicate 1

data_processing: Background Correction and Quantile Normalization using 'lumi' package in R

source_name: T47D breast cancer cells

label_protocol: Standard Illumina label protocol was used.

growth_protocol: The cells were starved overnight in phenol red free MEM (Minimal Essential Medium) containing 5% charcoal-stripped fetal bovine serum with NEAA (non-essential amino acids), L-glutamine , sodium bicarbonate, penicillin, streptomycin and Fungizone.

extract_protocol: RNA was extracted followed by clean-up and DNase I treatment using the DNA-Free RNA Kit (Zymo Research) in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: The cells were treated with vehicle, R5020 [10nM], TPA [1µM] or R5020 [10mM] + TPA [1µM] in fresh media [as given in growth protocol] for 24 hours.

value: Telpristone [1µM]


title: A549-lung adenocarcinoma-NS-Neg-rep2

description:
Control replicate 2
SAMPLE 2


title: A549-lung adenocarcinoma-NS-PTEN-rep2

description:
PTEN knockdown replicate 2
SAMPLE 8


title: Replicate 3 - Vehicle

description: replicate 3

value: contol


title: A549-lung adenocarcinoma-NS-Neg-rep1

description:
Control replicate 1
SAMPLE 1


title: golub-00327: 5500024035100021608461.G01

tag: disease state

value: L2 Acute Lymphoblastic Leukemia

tag: disease location

tag: organism part


title: Replicate 2 - R5020

description: replicate 2


title: Replicate 3 - R5020+CDB4124

description: replicate 3

value: R5020 [10nM] + Telapristone [1µM]


title: A549-lung adenocarcinoma-CUL3-Neg-rep3

description:
CUL3 knockdown replicate 3
SAMPLE 6


title: Replicate 1 - R5020

description: replicate 1


title: Replicate 1 - R5020+CDB4124

description: replicate 1


title: siSCR - E2 Replicate 1

description: Array 1

source_name: siSCR - E2 Replicate 1

value: siSCR

value: vehicle

value: Human breast adenocarcinoma cell line


title: A549-lung adenocarcinoma-CUL3-Neg-rep1

description:
CUL3 knockdown replicate 1
SAMPLE 4


title: Replicate 3 - CDB4124

description: replicate 3


title: Replicate 2 - R5020+CDB4124

description: replicate 2


title: Replicate 3 - R5020

description: replicate 3


title: Replicate 2 - CDB4124

description: replicate 2


title: Replicate 1 - Vehicle

description: replicate 1


title: EA_Control5_CD20

city: Rochester

first: Timothy

last: Niewold

address: 1216 2nd St SW

department: Rheumatology

institute: Mayo Clinic Rochester MN

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Quantile normalization followed log2 transformation using Partek Genomics Suite (v.6.6).; Only the probes with average signal intensity value greater than 0.1 and a detection p value less than 0.05 were considered present in this study. The raw data was then filtered by this cretieria.  Of the 44,589 probes on the bead-arrays, 38,932 probes were present in at least one of 208 samples (the PALO list). Thus the raw data from these 38,932 probes had been processed and analyzed in present study.

label: Biotin

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit

treatment_protocol: 1: PBMCs were isolated after the blood draw and kept in RPMI and 10% FBS overnight in 37°C incubator. 2: Next day, cells were stained and sorted by flow cytometry.

tag: ancestral background

value: European-American (EA)

tag: gender

value: Female

tag: subject condition

value: healthy control

value: Peripheral blood

tag: surface markers used in facs

value: CD20 positive B cells


title: Replicate 2 - Vehicle

description: replicate 2


title: EA_Control1_CD20


title: EA_Control4_CD20


title: AA_Control1_CD20

value: African-American (AA)


title: AA_Control3_CD20


title: AA_Control2_CD20


title: EA_Control2_CD20


title: AA_Control5_CD20


title: EA_Case20_CD20

value: Systemic lupus erythematosus (SLE) patient


title: EA_Case19_CD20


title: EA_Control3_CD20


title: EA_Case18_CD20


title: EA_Case16_CD20


title: EA_Case21_CD20


title: EA_Case15_CD20


title: EA_Case4_CD20


title: EA_Case7_CD20


title: EA_Case8_CD20


title: EA_Case2_CD20


title: EA_Case13_CD20


title: EA_Case9_CD20


title: EA_Case1_CD20


title: EA_Case3_CD20


title: AA_Control4_CD20


title: EA_Case17_CD20


title: AA_Case15_CD20


title: AA_Case16_CD20


title: AA_Case12_CD20


title: AA_Case8_CD20


title: AA_Case9_CD20


title: EA_Case5_CD20


title: AA_Case21_CD20


title: AA_Case11_CD20


title: EA_Case12_CD20


title: EA_Case10_CD20


title: AA_Case19_CD20


title: AA_Case13_CD20


title: EA_Case6_CD20


title: AA_Case18_CD20


title: AA_Case5_CD20


title: AA_Case10_CD20


title: EA_Case14_CD20


title: AA_Case17_CD20


title: AA_Case7_CD20


title: EA_Case11_CD20


title: AA_Case14_CD20


title: AA_Case20_CD20


title: AA_Case4_CD20


title: AA_Case6_CD20


title: AA_Case3_CD20


title: AA_Case2_CD20


title: EA_Control4_CD14

value: CD14 positive monocytes


title: EA_Control1_CD14


title: AA_Case1_CD20


title: EA_Control2_CD14


title: EA_Control3_CD14


title: EA_Case16_CD14


title: EA_Case18_CD14


title: AA_Control2_CD14


title: AA_Control3_CD14


title: EA_Case19_CD14


title: AA_Control5_CD14


title: EA_Case20_CD14


title: EA_Case17_CD14


title: AA_Control1_CD14


title: EA_Control5_CD14


title: EA_Case21_CD14


title: AA_Control4_CD14


title: EA_Case8_CD14


title: EA_Case9_CD14


title: EA_Case14_CD14


title: EA_Case5_CD14


title: EA_Case7_CD14


title: EA_Case6_CD14


title: EA_Case4_CD14


title: EA_Case12_CD14


title: EA_Case10_CD14


title: EA_Case15_CD14


title: EA_Case3_CD14


title: EA_Case11_CD14


title: EA_Case2_CD14


title: EA_Case13_CD14


title: EA_Case1_CD14


title: AA_Case20_CD14


title: AA_Case13_CD14


title: AA_Case21_CD14


title: AA_Case12_CD14


title: AA_Case18_CD14


title: AA_Case15_CD14


title: AA_Case14_CD14


title: AA_Case16_CD14


title: AA_Case9_CD14


title: EA_Control4_CD8

value: CD8 positive T cells


title: AA_Case11_CD14


title: AA_Case17_CD14


title: AA_Case5_CD14


title: AA_Case10_CD14


title: EA_Control5_CD8


title: AA_Case2_CD14


title: AA_Case3_CD14


title: EA_Control1_CD8


title: AA_Case8_CD14


title: AA_Case4_CD14


title: AA_Case1_CD14


title: EA_Control3_CD8


title: AA_Case7_CD14


title: EA_Control2_CD8


title: AA_Control5_CD8


title: AA_Control2_CD8


title: AA_Control4_CD8


title: AA_Case6_CD14


title: AA_Case19_CD14


title: EA_Case15_CD8


title: EA_Case10_CD8


title: EA_Case16_CD8


title: EA_Case17_CD8


title: EA_Case18_CD8


title: EA_Case14_CD8


title: EA_Case19_CD8


title: EA_Case20_CD8


title: EA_Case7_CD8


title: EA_Case13_CD8


title: EA_Case12_CD8


title: EA_Case4_CD8


title: EA_Case5_CD8


title: EA_Case6_CD8


title: AA_Control1_CD8


title: EA_Case9_CD8


title: EA_Case21_CD8


title: EA_Case1_CD8


title: EA_Case3_CD8


title: EA_Case8_CD8


title: EA_Case11_CD8


title: AA_Case18_CD8


title: AA_Control3_CD8


title: AA_Case21_CD8


title: AA_Case20_CD8


title: AA_Case16_CD8


title: EA_Case2_CD8


title: AA_Case17_CD8


title: AA_Case15_CD8


title: AA_Case19_CD8


title: Group 4: Combined radiation and burn injury mouse, biological rep 6

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

description: Serum exosomal microRNA gene expression data in mouse with combined radiation and burn injury

hyb_protocol: 21.5ul of each high-quality biotin-labeled miRNA sample was hybridized to Affymetrix Gene-Chip®  miRNA 2.0 Array for 16 hours according  to Affymetrix protocol. The arrays were washed and stained on the Affymetrix Fluidics station 400.

scan_protocol: The arrays were scanned with a Hewlett Packard G2500A gene Array Scanner.

data_processing: Gene expression values were obtained using Affymetrix Expression Console software, checked on Quality Control,  normalized and analyzed using RMA-DABG option (Affymetrix, Santa Clara, CA).

source_name: Mouse with combined radiation and burn injury

label_protocol: Exosomal RNA samples, containing low molecular weight RNA, were biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit. The quality of the biotin labeling process was confirmed by using Enzyme Linked Oligosorbent Assay (ELOSA) protocol (Affymetrix, Santa Clara, CA).

growth_protocol: B6D2F1/J female mice will be obtained from The Jackson Laboratory, Bar Harbor, Maine.

extract_protocol: Mouse 200ul serum samples were subjected to total RNA isolation procedure using SeraMir Exosome RNA Amplification kit (System Biosciences, Mountain View, CA) according to manufacturer’s instructions. Concentration of each RNA sample was determined by NanoDrop® spectrophotometer ND-1000 (NanoDrop Technologies, Wilmington, DE). The quality of RNA samples was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

treatment_protocol: All radiation and burn injuries will be performed at AFRRI Radiation and Animal facility as per IACUC approved protocols. 30 days following combined radiation and burn injuries arterial blood will be harvested from euthanized mice for genomic microRNA analysis.

tag: strain

value: Serum

value: 10-12 weeks

tag: weigh

tag: Sex

value: female

value: radiation and burn injury


title: AA_Case12_CD8

tag: cell type


title: Group 4: Combined radiation and burn injury mouse, biological rep 5

tag: age


title: AA_Case10_CD8

tag: tissue


title: AA_Case9_CD8


title: EA_Control3_CD4

value: CD4 positive T cells


title: AA_Case1_CD8


title: Group 4: Combined radiation and burn injury mouse, biological rep 2


title: EA_Control4_CD4


title: AA_Case8_CD8


title: Group 4: Combined radiation and burn injury mouse, biological rep 4


title: Group 4: Combined radiation and burn injury mouse, biological rep 3


title: Group 4: Combined radiation and burn injury mouse, biological rep 1


title: Group 3: Radiation injury mouse, biological rep 6

description: Serum exosomal microRNA gene expression data in mouse with radiation injury

source_name: Mouse with radiation injury

value: radiation injury


title: EA_Control1_CD4


title: AA_Case4_CD8


title: AA_Control5_CD4


title: AA_Case14_CD8


title: AA_Case3_CD8


title: AA_Case2_CD8


title: AA_Control2_CD4


title: AA_Case11_CD8


title: AA_Case6_CD8


title: AA_Case13_CD8


title: AA_Control3_CD4


title: AA_Control4_CD4


title: EA_Control2_CD4


title: AA_Case7_CD8


title: AA_Case5_CD8


title: EA_Control5_CD4


title: Group 3: Radiation injury mouse, biological rep 4


title: Group 3: Radiation injury mouse, biological rep 1


title: Group 2: Skin burn injury mouse, biological rep 6

description: Serum exosomal microRNA gene expression data in mouse with skin burn injury

source_name: Mouse with skin burn injury

value: skin burn injury


title: Group 2: Skin burn injury mouse, biological rep 5


title: Group 3: Radiation injury mouse, biological rep 3


title: Group 2: Skin burn injury mouse, biological rep 4


title: AA_Control1_CD4


title: Group 2: Skin burn injury mouse, biological rep 3


title: Group 3: Radiation injury mouse, biological rep 2


title: Group 2: Skin burn injury mouse, biological rep 2


title: Group 2: Skin burn injury mouse, biological rep 1


title: EA_Case19_CD4


title: Group 1: Mouse control 6, biological rep 6

description: Serum exosomal microRNA gene expression data in control mouse

source_name: Control mouse, without injury


title: EA_Case16_CD4


title: Group 1: Mouse control 5, biological rep 5


title: EA_Case21_CD4


title: Group 1: Mouse control 4, biological rep 4


title: EA_Case17_CD4


title: EA_Case18_CD4


title: EA_Case14_CD4


title: EA_Case20_CD4


title: Group 1: Mouse control 3, biological rep 3


title: EA_Case13_CD4


title: EA_Case10_CD4


title: EA_Case11_CD4


title: EA_Case9_CD4


title: EA_Case12_CD4


title: EA_Case15_CD4


title: EA_Case5_CD4


title: EA_Case7_CD4


title: EA_Case4_CD4


title: EA_Case3_CD4


title: AA_Case19_CD4


title: AA_Case20_CD4


title: EA_Case2_CD4


title: EA_Case6_CD4


title: AA_Case17_CD4


title: EA_Case8_CD4


title: AA_Case14_CD4


title: AA_Case16_CD4


title: EA_Case1_CD4


title: AA_Case15_CD4


title: AA_Case21_CD4


title: AA_Case18_CD4


title: AA_Case9_CD4


title: AA_Case11_CD4


title: AA_Case13_CD4


title: AA_Case8_CD4


title: AA_Case12_CD4


title: AA_Case10_CD4


title: 24 h following CLP 2

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: CLP 24h-3

hyb_protocol: The pre-hybridization of MRmiOA v3 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on MRmiOA v3 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520-550 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1).  We ﬁltered out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling normalization method.
The Matrix value is normalized intensities. Based on the normalized intensities, we calculate average ratios and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: 24 h following CLP

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy3, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

extract_protocol: RNA extraction by RNeasy Protect Animal Blood Kit (QIAGEN Cat. no. 73224). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: the whole blood samples were obtained from C57BL/6 mice at 4, 8, and 24 h following CLP for miRNA expression analysis

tag: sample group

value: 24 h following CLP

value: whole blood


title: 24 h following CLP 3

description: CLP 24h A


title: 24 h following CLP 4

description: CLP 24h B


title: 24 h following CLP 1

description: CLP 24h-2


title: 8 h following CLP 4

description: CLP 8h

source_name: 8 h following CLP

value: 8 h following CLP


title: 8 h following CLP 2

description: CLP 8h-3


title: 8 h following CLP 3

description: CLP 8h-4


title: AA_Case7_CD4

value: Female


title: 4 h following CLP 3

description: CLP 4h A

source_name: 4 h following CLP

value: 4 h following CLP


title: Sham operation control 3

description: CLP CTL2

source_name: Sham operation control

value: Sham operation control


title: 4 h following CLP 2

description: CLP 4h-4


title: 8 h following CLP 1

description: CLP 8h-1


title: 4 h following CLP 1

description: CLP 4h-3


title: Sham operation control 2

description: CLP CTL1


title: Sham operation control 1


title: geral-00143: AD_U133A_VI-453-CSFBS-EtOH72hr

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass A

tag: er(-)subclass

value: A

tag: progesteronereceptorstatus

value: negative

tag: estrogenreceptorstatus

value: incubated in stripped media for 48 h and then exposed to vehicle control for 48 h followed by RNA extraction

tag: organismpart

value: breast

tag: strainorline

value: breast carcinomas


title: AA_Case6_CD4

value: African-American (AA)

value: Systemic lupus erythematosus (SLE) patient

value: Peripheral blood


title: geral-00143: AD_U133A_V-453-CSFBS-androgen72hr

tag: treatment

value: incubated in stripped media for 48 h and then exposed to 1nM R-1881 for 48 h followed by RNA extraction

tag: disease state


title: Sham operation control 4

description: CLP CTL3


title: AA_Case5_CD4

tag: ancestral background

tag: gender

value: CD4 positive T cells


title: AA_Case3_CD4

tag: subject condition

tag: surface markers used in facs


title: geral-00143: AD_U133A_III-453-CSFBS-EtOH48hr

value: stripped media with 1 nM R-1881


title: geral-00143: AD_U133A_II-453-CSFBS48hr

value: charcoal-stripped media supplemented with vehicle control


title: AA_Case1_CD4


title: AA_Case2_CD4


title: WT vs. Brpf1-deficient E8.75 embryo 1

city: Montreal

first: Xiang-Jiao

state: Quebec

address: 1160 Pine Ave W

department: Medicine

country: Canada

institute: McGill University

description: Pair 1

hyb_protocol: 825 ng each of  Cy3-labelled (WT) and Cy5-labelled (MUT) aRNA samples were co-hybridised in duplicate on Agilent whole mouse genome arrays (catalogue number G4852A; Agilent Technologies).

scan_protocol: The microarray slides were washed according to the manufacturer’s instructions and scanned using an Agilent dual-laser scanner.  Feature extraction was performed using Agilent Feature Extraction software (version 9.5.3.1).

data_processing: Limma package (Smyth, 2004) was used to normalize and determine the modulated genes from microarray data. Signal background correction was carried out using normexp method and offset = 50 as suggested by Limma. To determine the modulated genes between a mutant and its wild type, we applied the two-‐channel normalization. Within-‐array normalization was carried out using loess method while between-‐array normalization was performed using a quantile method (Li et al., 2010). Empirical Bayes statistics was applied to determine the differential expression of the genes. The data from the three sets were averaged to generate the normalized gene list (Gene list A Aug 26 2014, attached).

source_name: Wild-type E8.75 embryo

label_protocol: 350 ng of total RNA was subjected to a single round of amplification using the Amino Allyl MessageAmpTM II aRNA kit (catalogue number AM1753; Ambion/Life Technologies,  Burlington, Ontario, Canada) according to the manufacturere's instructions, and the amplified product was labelled using a CyDye Post-Labeling Reactive Dye Pack (GE Healthcare Life Sciences, Baie d'Urfé, Quebec, Canada ).

growth_protocol: The pregnant mice were sacrificed at E8.75 to recover embryos.

extract_protocol: RNA was isolated from the wild-type and mutant embryos. RNA quality was assessed using a Bioanalyzer microfluidics workstation (Agilent Technologies, Mississaugo, Ontario, Canada) and quantitated using a NanoDrop spectrophotometer (Thermo Scientific, Wilminton , DE).

treatment_protocol: There was no treatment applied to the embryos.

value: E8.75 embryo

tag: genotype/variation

value: Wild-type

source_name: Brpf1-deficient E8.75 embryo


title: 4 h following CLP 4

description: CLP 4h B

tag: strain

value: whole blood


title: WT vs. Brpf1-deficient E8.75 embryo 3

description: Pair 3


title: WT vs. Brpf1-deficient E8.75 embryo 2

description: Pair 2


title: geral-00143: SL_U133A_B9-Trep

source_name: estrogen receptor-positive ER(+) breast cancer

value: positive


title: geral-00143: SL_U133A_B7-T

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass B

value: B


title: geral-00143: AD_U133A_IV-453-CSFBS-Androgen-Flut48hr

value: A

value: stripped media with 1 nM R-1881 and 10mM flutamide


title: geral-00143: SL_U133A_B4-T

value: negative


title: Group 3: Radiation injury mouse, biological rep 5

value: Serum

value: 10-12 weeks

tag: weigh

tag: Sex

value: female

value: radiation injury


title: geral-00143: SL_U133A_B32-T

value: breast

value: breast carcinomas


title: geral-00143: SL_U133A_B8-T


title: geral-00143: SL_U133A_B6-T


title: geral-00143: SL_U133A_B3-T


title: geral-00143: SL_U133A_B33-T


title: geral-00143: SL_U133A_B29-T


title: geral-00143: SL_U133A_B28-T


title: geral-00143: SL_U133A_B31-T


title: geral-00143: SL_U133A_B26-T


title: geral-00143: SL_U133A_B27-Trep


title: geral-00143: SL_U133A_B5-T


title: geral-00143: SL_U133A_B24-T


title: geral-00143: SL_U133A_B23-T


title: Maternal-Grandmother_S1_S2

type: genomic

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description: Genomic DNA of family member: maternal grandmother of siblings S1 and S2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA), with the exception that the fragmentation step was shortened from 20-24h to 7h and the hybridization step was shortened from 16-20h to 6h for the rapid protocol.

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing: The genotypes, B allele frequencies and LogR values were extracted by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75 in GenCall.

molecule: genomic DNA

source_name: Blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The embryos were in vitro cultured in Life Global medium (Life Global, Canada) or Quinns Advantage Protein Plus Medium (Cooper Surgical, USA). On day 2 and 3 after fertilization, embryo development was evaluated for the number of blastomeres, the percentage of fragmentation and the symmetry of the blastomeres. All ≥ 6 cell stage embryos that had less than 25% fragmentation on day 3 after fertilization were biopsied using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Germany) coupled to an inverted microscope, after first being incubated in Ca2+/Mg2+ free medium. One or two blastomeres were gently aspirated from each embryo for the conventional FISH- or PCR-based PGD.  The embryos were immediately transferred to fresh medium; while the aspirated blastomeres were separately washed twice with Ca2+/Mg2+ free medium to remove possible oil remnants.

extract_protocol: Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with GenomiPhiV2 (GE Healthcare, USA). The MDA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer). Single-cell amplifications yielding less than 2 µg DNA were not further used.

treatment_protocol: The embryos that were not suitable for transfer on day 4 were dissociated and single blastomeres were collected for further analysis. The zona pellucida was removed by incubation in a droplet of Tyrode's solution (Sigma-Aldrich, USA). The acid was and consequently washed away and the embryos were dissociated in a droplet of Ca2+/Mg2+ free medium (Life Global, Canada).

tag: tissue

value: Blood

tag: dna sample

value: Multi cell

tag: wga

tag: hybridization protocol

value: Conventional


title: Mother_S1_S2_24h

description: Genomic DNA of family member: mother of siblings S1 and S2.

value: Rapid


title: Maternal-Grandfather_S1_S2

description: Genomic DNA of family member: maternal grandfather of siblings S1 and S2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: AA_Case4_CD4

value: African-American (AA)

value: Female

value: Systemic lupus erythematosus (SLE) patient

value: Peripheral blood

tag: cell type

value: CD4 positive T cells


title: geral-00143: SL_U133A_B18-T

tag: er(-)subclass

tag: progesteronereceptorstatus

value: positive

tag: estrogenreceptorstatus

tag: organismpart


title: geral-00143: SL_U133A_B2-T

value: B

value: negative

tag: treatment

tag: strainorline

tag: disease state


title: geral-00143: AD_U133A_I-453-FBS48hr

value: A

value: incubated cells in media containing 10% FBS


title: geral-00143: SL_U133A_B17-T


title: geral-00143: SL_U133A_B16-T


title: S2_ebv07_mda_24h

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S2. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2.

source_name: EBV-transformed lymphoblast

value: EBV-transformed lymphoblast

value: Single cell

value: MDA


title: S2_ebv09_mda_24h


title: S2_ebv10_picoplex_24h

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S2. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used.

value: PicoPlex


title: Father_S1_S2_24h

description: Genomic DNA of family member: father of siblings S1 and S2.

value: Blood

value: Multi cell


title: S2_ebv11_picoplex

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S2. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used. The sample was processed according to the manual of Infinium II assay (Illumina, USA).

value: Conventional


title: S2_ebv11_picoplex_24h

value: Rapid


title: S2_ebv09_mda

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S2. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: Father_S1_S2

description: Genomic DNA of family member: father of siblings S1 and S2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: S2_ebv08_mda


title: S2_MC_24h

description: Multi-cell control DNA from sibling S2.


title: Mother_S1_S2

description: Genomic DNA of family member: mother of siblings S1 and S2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: geral-00143: SL_U133A_B15-T

value: breast

value: breast carcinomas


title: geral-00143: SL_U133A_B14-T


title: geral-00143: SL_U133A_B12-T


title: S2_ebv10_picoplex


title: S1_ebv04_picoplex_24h

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S1. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used.


title: S2_MC

description: Multi-cell control DNA from sibling S2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: geral-00143: SL_U133A_B10-Trep


title: S2_ebv07_mda


title: geral-00143: SL_U133A_B1-T


title: geral-00143: MD_U133A_B99T


title: geral-00143: MD_U133A_B98T