title: JSR_055_U133_2


title: JSR_048_U133_2

status: Public on Oct 14 2014

type: RNA

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

description: Gene expression of T-ALL patient bone marrow sample

scan_protocol: Slides were scanned on the Affymetrix Genechip Scanner 3000 7G

data_processing: Normalization of microarray intensities was done using the variance stabilization and calibration (VSN) package in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

label_protocol: The gene expression profiling was performed at the IGBMC (www.igbmc.fr, Strasbourg, France) according to standardized procedures. The GeneChip® 3’ IVT Express Kit was used.

extract_protocol: Total RNA was harvested with the miRNeasy mini kit (Qiagen). The RNA quality was evaluated on the Agilent 2100 bioanalyzer.

tag: molecular subgroup

value: immature subgroup

tag: tissue

value: bone marrow


title: JSR_044_U133_2

hyb_protocol: The gene expression profiling was performed at the IGBMC (www.igbmc.fr, Strasbourg, France) according to standardized procedures.

value: immature, HOXA13-t subgroup


title: JSR_040_U133_2

description: Gene expression of T-ALL patient blood sample

source_name: blood

value: TAL-R subgroup

value: blood


title: JSR_037_U133_2


title: JSR_026_U133_2


title: JSR_036_U133_2


title: JSR_024_U133_2

value: CALM-AF10 subgroup


title: JSR_038_U133_2

value: HOX


title: JSR_033_U133_2

value: MLL-t subgroup


title: JSR_031_U133_2

value: TLX3 subgroup


title: JSR_029_U133_2


title: JSR_025_U133_2


title: JSR_039_U133_2


title: JSR_017_U133_2


title: JSR_013_U133_2


title: JSR_002_U133_2


title: JSR_001_U133_2


title: AML with normal karyotype (07-009076)

status: Public on Sep 27 2014

city: München

first: Torsten

last: Haferlach

address: Max-Lebsche-Platz 31

country: Germany

institute: MLL Munich leukemia laboratory

hyb_protocol: according MILE study target preparation SOP v1.11

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using Affymetrix default analysis settings.

extract_protocol: Isolation of total RNA was performed with the Qiagen RNeasy MinElute Cleanup Kit according to the manufacturer's instructions.

tag: gender

value: male

value: Bone Marrow

value: negative

tag: condition

value: AML with normal karyotype


title: AML with other chromosomal aberrations (07-009077)

label_protocol: according MILE study target preparation SOP v1.11

value: AML with other chromosomal aberrations


title: AML with t(11q23)/MLL, t(11;19), MLL-ELL, therapy-related (07-008641)

value: female


title: ALL with t(8;14) (07-013810)

value: not available

value: ALL with t(8;14)


title: AML with normal karyotype (07-008833)


title: AML with complex aberrant karyotype, untypical (07-008363)


title: AML with other chromosomal aberrations (07-008534)


title: AML with normal karyotype (07-008671)


title: AML with normal karyotype (07-008260)

value: positive


title: AML with normal karyotype (07-009227)


title: AML with normal karyotype (07-009817)


title: AML with inv(3)/t(3;3) (07-010229)

value: AML with inv(3)/t(3;3)


title: ALL with t(11q23)/MLL, t(4;11), MLL-AF4 (07-008434)

value: ALL with t(11q23)/MLL, t(4;11), MLL-AF4


title: AML with other chromosomal aberrations, trisomy 8, trisomy 13 (07-007861)


title: AML with complex aberrant karyotype, del(5q) (07-007627)


title: AML with normal karyotype (07-008752)


title: AML with t(11q23)/MLL, t(6;11), MLL-AF6 (07-007654)

value: AML with t(11q23)/MLL, t(6;11), MLL-AF6


title: AML with trisomy 8 sole (07-007456)

value: AML with trisomy 8 sole


title: AML with normal karyotype (07-008066)


title: AML with trisomy 13 sole (07-006475)

value: AML with trisomy 13 sole


title: AML with normal karyotype (07-007544)


title: AML with trisomy 13 sole (07-006077)


title: AML with normal karyotype (07-005823)


title: ALL with t(9;22), BCR-ABL, additional aberrations (07-006432)


title: AML with normal karyotype, therapy-related (07-004839)


title: AML with other chromosomal aberrations (07-005629)


title: AML with complex aberrant karyotype, del(5q) (07-005446)


title: AML with t(15;17), PML-RARA, FAB M3 (07-004755)

value: AML with t(15;17), PML-RARA, FAB M3


title: JSR_116_U133_2

description: Gene expression of T-ALL patient EM sample

source_name: EM

value: TAL-R subgroup

value: EM


title: AML with other chromosomal aberrations (07-003920)

value: male


title: AML with monosomy 7 sole (07-002226)

value: Bone Marrow

value: AML with monosomy 7 sole


title: AML with normal karyotype (07-002207)

value: AML with normal karyotype


title: AML with trisomy 13 sole (07-003707)

value: negative


title: AML with other chromosomal aberrations, trisomy 9, 13, 14, 21, 22 (07-004170)


title: AML with complex aberrant karyotype, del(5q) (07-000915)

value: female


title: ALL, B-lineage, aberrant karyotype hyperdiploid (07-001310)

value: Peripheral Blood

value: not available


title: AML with t(15;17), PML-RARA (07-001787)

value: positive

value: AML with t(15;17), PML-RARA


title: MDS with monosomy 7 sole, CMML-2 (07-003442)

value: MDS with monosomy 7 sole, CMML-2


title: AML with t(6;9) (07-001214)

value: AML with t(6;9)


title: AML with complex aberrant karyotype, del(5q) (07-001377)


title: AML with normal karyotype (07-000407)


title: AML with complex aberrant karyotype, del(5q) (07-000224)


title: AML with inv(16)/t(16;16) kryptic rearrangement, CBFB-MYH11 (07-004463)


title: AML with t(11q23)/MLL, t(9;11), MLL-AF9 (07-002809)

value: AML with t(11q23)/MLL, t(9;11), MLL-AF9


title: AML with del(5q) sole (07-000251)

value: AML with del(5q) sole


title: AML with other chromosomal aberrations, trisomy 6 sole (07-000861)


title: AML with normal karyotype (07-001019)


title: AML with normal karyotype (07-000067)


title: AML with t(15;17), PML-RARA, FAB M3 (07-000165)

value: AML with t(15;17), PML-RARA, FAB M3


title: AML with normal karyotype (07-000400)


title: AML with normal karyotype (07-000177)


title: AML with other chromosomal aberrations, trisomy 21 sole (07-000025)


title: AML with normal karyotype (06-013165)


title: AML with normal karyotype (06-013387)


title: AML with normal karyotype (07-000001)


title: ALL, B-lineage, aberrant karyotype (07-000250)

value: ALL, B-lineage, aberrant karyotype


title: AML with complex aberrant karyotype, del(5q) (06-013025)


title: AML with normal karyotype (06-012912)


title: AML with t(15;17), PML-RARA, FAB M3 (06-012777)


title: ALL, T-lineage, mature (06-013357)

value: ALL, T-lineage, mature


title: AML with other chromosomal aberrations, trisomy 13, monosomy 21 (06-012770)

value: male


title: MDS with trisomy 8 sole, CMML-2 (06-012690)

value: Bone Marrow

value: MDS with trisomy 8 sole, CMML-2


title: AML with complex aberrant karyotype, del(5q) (06-012349)


title: MDS with trisomy 8 sole, CMML-2 (06-011619)


title: MDS with normal karyotype, CMML-2 (06-010006)

value: MDS with normal karyotype, CMML-2


title: AML with normal karyotype, therapy-related (06-010996)

value: negative


title: AML with other chromosomal aberrations, therapy-related (06-009690)


title: AML with t(15;17), PML-RARA, FAB M3 (06-009387)

value: female


title: AML with other chromosomal aberrations, monosomy 7, del(20q) (06-012341)


title: AML with del(5q) sole (06-009517)


title: ALL with t(9;22), BCR-ABL (06-008977)

value: ALL with t(9;22), BCR-ABL


title: AML with normal karyotype (06-009604)

value: AML with normal karyotype


title: AML with complex aberrant karyotype, del(5q), RAEB-2/AML (06-010565)

value: not available


title: AML with complex aberrant karyotype, del(5q) (06-009508)


title: AML with t(8;21), AML1-ETO (06-010611)

value: AML with t(8;21), AML1-ETO


title: AML with normal karyotype (06-011100)

value: Peripheral Blood


title: ALL with t(9;22), BCR-ABL, additional aberrations (06-010430)


title: AML with normal karyotype (06-009483)


title: AML with other chromosomal aberrations, trisomy 8 (06-011056)


title: ALL, B-lineage, aberrant karyotype (06-008775)


title: AML with normal karyotype (06-008912)

value: positive


title: AML with normal karyotype (06-008546)


title: AML with complex aberrant karyotype, del(5q) (06-008664)


title: MDS with normal karyotype, CMML-2 (06-012485)


title: AML with normal karyotype (06-009222)


title: AML with normal karyotype (06-009728)


title: AML with normal karyotype (06-008562)


title: AML with complex aberrant karyotype, del(5q) (06-008808)


title: ALL with t(9;22), BCR-ABL, additional aberrations (06-008248)


title: AML with other chromosomal aberrations (06-008442)

value: AML with other chromosomal aberrations


title: JSR_022_U133_2

value: immature subgroup

value: blood


title: AML with normal karyotype (06-008973)


title: AML with normal karyotype (06-008204)


title: AML with normal karyotype (06-007813)


title: AML with t(8;21), AML1-ETO (06-007178)


title: AML with other chromosomal aberrations (06-006924)


title: ALL with t(8;14) (06-007651)

value: ALL with t(8;14)


title: AML with other chromosomal aberrations (06-007847)


title: AML with normal karyotype (06-008062)


title: AML with normal karyotype (06-006577)


title: AML with trisomy 8 sole (06-006741)

value: AML with trisomy 8 sole


title: MDS with normal karyotype, CMML-2 (06-007923)

value: male


title: AML with t(15;17), PML-RARA (06-006763)

value: AML with t(15;17), PML-RARA


title: AML with monosomy 7 sole (06-007812)

value: Bone Marrow

value: AML with monosomy 7 sole


title: AML with complex aberrant karyotype, untypical, independent clones (06-007275)

value: negative


title: AML with other chromosomal aberrations (06-006608)


title: AML with monosomy 7 sole (06-006315)

value: female


title: AML with normal karyotype (06-006431)


title: ALL, T-lineage, cortical (06-006250)

value: ALL, T-lineage, cortical


title: AML with inv(16)/t(16;16) kryptic rearrangement, CBFB-MYH11 (06-006744)


title: AML with complex aberrant karyotype, del(5q) (06-006457)


title: MDS with other chromosomal aberrations, CMML-2 (06-006326)


title: AML with normal karyotype (06-006397)

value: AML with normal karyotype


title: AML with complex aberrant karyotype, del(5q) (06-006493)


title: AML with complex aberrant karyotype, del(5q) (06-005962)


title: AML with monosomy 7 sole (06-005167)


title: ALL, B-lineage, hyperdiploid karyotype (06-005843)

value: not available

value: ALL, B-lineage, hyperdiploid karyotype


title: MDS with normal karyotype, CMML-1 (06-003959)

value: MDS with normal karyotype, CMML-1


title: AML with normal karyotype (06-011617)

value: positive


title: AML with t(8;21), AML1-ETO (06-005906)

value: AML with t(8;21), AML1-ETO


title: AML with t(1;3) (06-005327)

value: Peripheral Blood

value: AML with t(1;3)


title: MDS with normal karyotype, CMML-1 (06-005458)


title: MDS with normal karyotype, CMML-1 (06-002906)


title: MDS with trisomy 8 sole, CMML-2 (06-005104)

value: MDS with trisomy 8 sole, CMML-2


title: AML with other chromosomal aberrations, trisomy 13q (06-004792)


title: AML with complex aberrant karyotype, del(5q) (06-002850)


title: AML with trisomy 13 sole (06-002469)

value: AML with trisomy 13 sole


title: AML with normal karyotype (06-005560)

value: male


title: AML with normal karyotype (06-003528)


title: AML with t(15;17), PML-RARA, FAB M3 (06-005966)

value: AML with t(15;17), PML-RARA, FAB M3


title: AML with t(11q23)/MLL, t(9;11) (06-004437)


title: AML with trisomy 13 sole (06-002086)

value: Bone Marrow


title: MDS with complex aberrant karyotype, del(5q), CMML-2 (06-000892)


title: AML with inv(3)/t(3;3) (06-001216)

value: AML with inv(3)/t(3;3)


title: AML with t(15;17), PML-RARA (06-002218)

value: negative

value: AML with t(15;17), PML-RARA


title: AML with trisomy 8 sole (06-000894)

value: AML with trisomy 8 sole


title: ALL, T-lineage, immature (Pre) (06-001673)

value: ALL, T-lineage, immature (Pre)


title: ALL with t(8;14)+t(14;18) (06-001255)

value: female

value: not available


title: AML with trisomy 8 sole (06-000809)


title: AML with normal karyotype, FLT3-LM(5) (06-000867)

value: AML with normal karyotype, FLT3-LM(5)


title: AML with t(8;16), MOZ-CBP negative, therapy-related (06-002379)


title: MDS with trisomy 8 sole, CMML-1 (06-000806)

value: MDS with trisomy 8 sole, CMML-1


title: MDS with normal karyotype, CMML-1 (06-000688)

value: MDS with normal karyotype, CMML-1


title: AML with inv(16)/t(16;16), CBFB-MYH11 (06-000250)

value: Peripheral Blood

value: positive

value: AML with inv(16)/t(16;16), CBFB-MYH11


title: MDS with normal karyotype, CMML-1 (06-000080)


title: AML with trisomy 13 sole (06-000038)

value: AML with trisomy 13 sole


title: AML with other chromosomal aberrations (06-000158)

value: male

value: AML with other chromosomal aberrations


title: ALL, T-lineage, immature (Pre) (05-003324)

value: Bone Marrow


title: AML with t(8;21), AML1-ETO (05-000575)

value: AML with t(8;21), AML1-ETO


title: AML with inv(3)/t(3;3) (05-000623)

value: negative

value: AML with inv(3)/t(3;3)


title: ALL, T-lineage, cortical (05-003013)

value: ALL, T-lineage, cortical


title: AML with normal karyotype (05-001613)

value: AML with normal karyotype


title: AML with normal karyotype (05-000123)

value: female


title: ALL with t(9;22), BCR-ABL, additional aberrations (05-001591)

value: not available


title: ALL with t(9;22), BCR-ABL, additional aberrations (05-001350)


title: ALL, B-lineage, aberrant karyotype (05-003446)

value: ALL, B-lineage, aberrant karyotype


title: AML with trisomy 8 sole (05-002207)

value: AML with trisomy 8 sole


title: AML with t(15;17), PML-RARA (05-000973)

value: AML with t(15;17), PML-RARA


title: AML with t(8;21), AML1-ETO, therapy-related (05-000295)

value: Peripheral Blood


title: ALL with t(11q23)/MLL, t(4;11), MLL-AF4 (05-003264)

value: ALL with t(11q23)/MLL, t(4;11), MLL-AF4


title: MDS with other chromosomal aberrations, CMML-1 (05-001465)


title: AML with t(8;21), AML1-ETO (05-002903)


title: ALL with t(9;22), BCR-ABL, additional aberrations (05-000520)


title: AML with trisomy 8 sole (05-000297)

value: positive


title: ALL with t(9;22), BCR-ABL, additional aberrations (05-001500)


title: AML with monosomy 7, trisomy 11 (05-000153)

value: AML with monosomy 7, trisomy 11


title: RNA (diagnosis) from T-ALL patient ALL_145

status: Public on Sep 18 2013

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: Biotinylated cRNAs were hybridized to the gene chips for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: The GeneChips were then washed and stained using the Fluidics Station 450 and scanned using the GeneChip® Scanner 3000 7G

data_processing: The data was normalized using the robust multi-array average (RMA) method  (Irizarry et al. 2003)

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared from two micrograms of total RNA

growth_protocol: NA, primary cells

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Ficoll-isopaque centrifugation

value: Peripheral blood

tag: cell type

value: primary ALL (acute lymphoblastic leukemia) cells at diagnosis

tag: tumor subtype

value: T-ALL


title: RNA (diagnosis) from BCP-ALL patient ALL_148

source_name: Bone marrow

value: Bone marrow


title: RNA (diagnosis) from T-ALL patient ALL_144


title: AML with normal karyotype (05-000398)


title: RNA (diagnosis) from BCP-ALL patient ALL_130


title: RNA (diagnosis) from BCP-ALL patient ALL_140

value: undefined


title: RNA (diagnosis) from T-ALL patient ALL_72


title: RNA (diagnosis) from T-ALL patient ALL_42


title: RNA (diagnosis) from BCP-ALL patient ALL_50


title: RNA (diagnosis) from BCP-ALL patient ALL_10

value: HeH


title: RNA (diagnosis) from BCP-ALL patient ALL_43


title: RNA (diagnosis) from BCP-ALL patient ALL_27


title: RNA (diagnosis) from T-ALL patient ALL_38


title: RNA (diagnosis) from BCP-ALL patient ALL_149


title: RNA (diagnosis) from BCP-ALL patient ALL_47


title: RNA (diagnosis) from BCP-ALL patient ALL_1


title: RNA (diagnosis) from BCP-ALL patient ALL_7


title: RNA (diagnosis) from BCP-ALL patient ALL_5


title: 507202

status: Public on Oct 30 2013

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

country: USA

institute: Washington University School of Medicine

description: A study that used high-throughput sequencing of the bone marrow (tumor) and skin of acute myeloid leukemia patients.

hyb_protocol: according to manufacturer's protocol

data_processing: MAS5, scaled to array mean of 1500

source_name: AML bone marrow

label_protocol: according to manufacturer's protocol

extract_protocol: Trizol reagent standard protocol

value: AML bone marrow

tag: fab

tag: Sex

value: M

tag: race

value: C

tag: age on study

tag: karyotype

value: Normal


title: RNA (diagnosis) from  patient ALL_ 783


title: RNA (diagnosis) from  patient ALL_ 781


title: RNA (diagnosis) from BCP-ALL patient ALL_16


title: RNA (diagnosis) from  patient ALL_ 782


title: 767969


title: RNA (diagnosis) from  patient ALL_ 780


title: RNA (diagnosis) from T-ALL patient ALL_20


title: RNA (diagnosis) from BCP-ALL patient ALL_560


title: RNA (diagnosis) from BCP-ALL patient ALL_143


title: RNA (diagnosis) from  patient ALL_ 779


title: RNA (diagnosis) from  patient ALL_ 778


title: 635258

value: F

value: Complex


title: RNA (diagnosis) from BCP-ALL patient ALL_548


title: RNA (diagnosis) from  patient ALL_ 777


title: RNA (diagnosis) from T-ALL patient ALL_552


title: RNA (diagnosis) from BCP-ALL patient ALL_88


title: RNA (diagnosis) from BCP-ALL patient ALL_581


title: RNA (diagnosis) from BCP-ALL patient ALL_537


title: RNA (diagnosis) from BCP-ALL patient ALL_499


title: RNA (diagnosis) from BCP-ALL patient ALL_541


title: RNA (diagnosis) from BCP-ALL patient ALL_478


title: RNA (diagnosis) from BCP-ALL patient ALL_497


title: RNA (diagnosis) from BCP-ALL patient ALL_492


title: RNA (diagnosis) from BCP-ALL patient ALL_479


title: RNA (diagnosis) from BCP-ALL patient ALL_535


title: RNA (diagnosis) from T-ALL patient ALL_483


title: RNA (diagnosis) from BCP-ALL patient ALL_488

description: re-analysis of GSM661390


title: RNA (diagnosis) from BCP-ALL patient ALL_477


title: RNA (diagnosis) from T-ALL patient ALL_466


title: RNA (diagnosis) from T-ALL patient ALL_530


title: RNA (diagnosis) from BCP-ALL patient ALL_472

description: re-analysis of GSM661386


title: RNA (diagnosis) from BCP-ALL patient ALL_506


title: RNA (diagnosis) from BCP-ALL patient ALL_476


title: RNA (diagnosis) from T-ALL patient ALL_522


title: RNA (diagnosis) from T-ALL patient ALL_519


title: RNA (diagnosis) from BCP-ALL patient ALL_494

description: re-analysis of GSM661381


title: RNA (diagnosis) from BCP-ALL patient ALL_467

description: re-analysis of GSM661385


title: RNA (diagnosis) from T-ALL patient ALL_484

description: re-analysis of GSM661399


title: RNA (diagnosis) from BCP-ALL patient ALL_459

description: re-analysis of GSM661384


title: RNA (diagnosis) from BCP-ALL patient ALL_419


title: RNA (diagnosis) from BCP-ALL patient ALL_458

description: re-analysis of GSM661388


title: RNA (diagnosis) from T-ALL patient ALL_457

description: re-analysis of GSM661397


title: RNA (diagnosis) from T-ALL patient ALL_385


title: RNA (diagnosis) from BCP-ALL patient ALL_402


title: RNA (diagnosis) from BCP-ALL patient ALL_399


title: RNA (diagnosis) from BCP-ALL patient ALL_382


title: RNA (diagnosis) from BCP-ALL patient ALL_415


title: RNA (diagnosis) from T-ALL patient ALL_375


title: RNA (diagnosis) from T-ALL patient ALL_461


title: RNA (diagnosis) from BCP-ALL patient ALL_369

description: re-analysis of GSM661395


title: RNA (diagnosis) from BCP-ALL patient ALL_450


title: RNA (diagnosis) from T-ALL patient ALL_374


title: RNA (diagnosis) from BCP-ALL patient ALL_359

description: re-analysis of GSM661383


title: RNA (diagnosis) from T-ALL patient ALL_428


title: RNA (diagnosis) from T-ALL patient ALL_414


title: RNA (diagnosis) from BCP-ALL patient ALL_357


title: RNA (diagnosis) from BCP-ALL patient ALL_325


title: RNA (diagnosis) from BCP-ALL patient ALL_294


title: RNA (diagnosis) from BCP-ALL patient ALL_323


title: RNA (diagnosis) from T-ALL patient ALL_311


title: RNA (diagnosis) from BCP-ALL patient ALL_379


title: RNA (diagnosis) from BCP-ALL patient ALL_293

description: re-analysis of GSM661380


title: RNA (diagnosis) from BCP-ALL patient ALL_269


title: RNA (diagnosis) from BCP-ALL patient ALL_309


title: RNA (diagnosis) from BCP-ALL patient ALL_426


title: RNA (diagnosis) from BCP-ALL patient ALL_280


title: RNA (diagnosis) from BCP-ALL patient ALL_258


title: RNA (diagnosis) from BCP-ALL patient ALL_292


title: RNA (diagnosis) from T-ALL patient ALL_6


title: RNA (diagnosis) from T-ALL patient ALL_331


title: RNA (diagnosis) from T-ALL patient ALL_253


title: RNA (diagnosis) from BCP-ALL patient ALL_244


title: RNA (diagnosis) from BCP-ALL patient ALL_283


title: RNA (diagnosis) from T-ALL patient ALL_266


title: RNA (diagnosis) from T-ALL patient ALL_285


title: RNA (diagnosis) from BCP-ALL patient ALL_250


title: RNA (diagnosis) from BCP-ALL patient ALL_187


title: RNA (diagnosis) from  patient ALL_ 776


title: RNA (diagnosis) from BCP-ALL patient ALL_198


title: RNA (diagnosis) from BCP-ALL patient ALL_180


title: RNA (diagnosis) from T-ALL patient ALL_212


title: RNA (diagnosis) from T-ALL patient ALL_233


title: RNA (diagnosis) from BCP-ALL patient ALL_194


title: RNA (diagnosis) from BCP-ALL patient ALL_175


title: RNA (diagnosis) from  patient ALL_ 775


title: RNA (diagnosis) from BCP-ALL patient ALL_168

description: re-analysis of GSM661392


title: RNA (diagnosis) from BCP-ALL patient ALL_195


title: RNA (diagnosis) from BCP-ALL patient ALL_191


title: RNA (diagnosis) from T-ALL patient ALL_165


title: RNA (diagnosis) from BCP-ALL patient ALL_162


title: RNA (diagnosis) from BCP-ALL patient ALL_188


title: RNA (diagnosis) from T-ALL patient ALL_169


title: PML004

status: Public on Jul 02 2013

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

description:
JD0002-AMD-v5-U133A
t(15:17)-#01  (identifier used in PMID:15226186)

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

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

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

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram of total RNA (Expression Analysis Technical Manual 701025 rev1, 2001, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases

extract_protocol: Trizol

tag: disease state

value: AML

tag: subtype

value: PML-RARalpha

tag: cytogenetics

tag: kras status

value: KRAS wild type

tag: nras status

value: NRAS wild type


title: MLL007

description:
JD0301-AML-v5-U133A
Additional Array

value: MLLr


title: PML005

description:
JD0036-AMD-v5-U133A
t(15:17)-#03  (identifier used in PMID:15226186)


title: CD34_2

description:
JD-ALD624-v5-U133A
GSM706041 (Accession Number in GSE33315)

source_name: Adult normal bone marrow; CD34(+)

value: normal bone marrow sample

value: Not available


title: MLL008

description:
JD0336-AML-v5-U133A
Additional Array


title: CD34_3

description:
JD-ALD633-v5-U133A
GSM706042 (Accession Number in GSE33315)


title: PML006

description:
JD0053-AMD-v5-U133A
t(15:17)-#05  (identifier used in PMID:15226186)


title: 255421

status: Public on Sep 06 2013

city: St Louis

address: 4320 Forest Park Avenue, Suite 211

description: A study that used high-throughput re-sequencing of the kinase domains of 26 Tyrosine kinase genes that are expressed in most acute myeloid leukemia patients. Used genomic DNA from bone marrow (tumor).

tag: cytogenetic change

tag: flt3 d835

tag: flt3 itd

tag: nmp1 ins


title: MLL031

description:
JD0089-AMD-v5-U133A
Other-#37 (identifier used in PMID:15226186)


title: MLL030

description:
JD0095-AMD-v5-U133A
Other-#40 (identifier used in PMID:15226186)


title: CD34_1

description:
JD-ALD623-v5-U133A
GSM706040 (Accession Number in GSE33315)


title: MLL005

description:
JD0259-AML-v5-U133A
Additional Array


title: CD34_4

description:
JD-ALD634-v5-U133A
GSM706043 (Accession Number in GSE33315)


title: PML007

description:
JD0049-AMD-v5-U133A
t(15:17)-#04  (identifier used in PMID:15226186)


title: MLL002

description:
JD0227-AMD-v5-U133A
Additional Array


title: mis015

description:
JD0262-AML-v5-U133A
Additional Array


title: MLL003

description:
JD0240-AMD-v5-U133A
Additional Array


title: MLL006

description:
JD0085-AMD-v5-U133A
MLL-#16 (identifier used in PMID:15226186)


title: MLL015

description:
JD0059-AMD-v5-U133A
MLL-#13 (identifier used in PMID:15226186)


title: MLL001

description:
JD0097-AMD-v5-U133A
MLL-#18 (identifier used in PMID:15226186)


title: MLL013

description:
JD0050-AMD-v5-U133A
MLL-#10 (identifier used in PMID:15226186)


title: N020

description:
JD0282-AML-v5-U133A
Additional Array

value: normal or miscellaneous karyotype


title: MLL012

description:
JD0046-AMD-v5-U133A
MLL-#08 (identifier used in PMID:15226186)


title: N021

description:
JD0268-AML-v5-U133A
Additional Array


title: RNA (diagnosis) from BCP-ALL patient ALL_234

tag: tissue

value: Peripheral blood

value: primary ALL (acute lymphoblastic leukemia) cells at diagnosis


title: MLL009

description:
JD0026-AMD-v5-U133A
MLL-#01 (identifier used in PMID:15226186)


title: mis031

description:
JD0256-AML-v5-U133A
Additional Array


title: N015

description:
JD0034-AMD-v5-U133A
Other-#14 (identifier used in PMID:15226186)


title: N009

description:
JD0007-AMD-v5-U133A
Other-#04 (identifier used in PMID:15226186)


title: N003

description:
JD0222-AMD-v5-U133A
Additional Array


title: N007

description:
JD0289-AML-v5-U133A
Additional Array


title: N019

description:
JD0038-AMD-v5-U133A
Other-#15 (identifier used in PMID:15226186)


title: N018

description:
JD0062-AMD-v5-U133A
Other-#25 (identifier used in PMID:15226186)


title: mis006

description:
JD0233-AMD-v5-U133A
Additional Array


title: mis020

description:
JD0064-AMD-v5-U133A
Other-#26 (identifier used in PMID:15226186)


title: N012

description:
JD0012-AMD-v5-U133A
Other-#06 (identifier used in PMID:15226186)


title: N002

description:
JD0100-AMD-v5-U133A
Other-#43 (identifier used in PMID:15226186)


title: N013

description:
JD0028-AMD-v5-U133A
Other-#12 (identifier used in PMID:15226186)


title: N014

description:
JD0032-AMD-v5-U133A
Other-#13 (identifier used in PMID:15226186)


title: mis030

description:
JD0003-AMD-v5-U133A
Other-#01 (identifier used in PMID:15226186)


title: N006

description:
JD0078-AMD-v5-U133A
Other-#32 (identifier used in PMID:15226186)


title: mis004

description:
JD0099-AMD-v5-U133A
Other-#42 (identifier used in PMID:15226186)


title: MLL014

description:
JD0051-AMD-v5-U133A
MLL-#11 (identifier used in PMID:15226186)


title: mis016

description:
JD0041-AMD-v5-U133A
Other-#16 (identifier used in PMID:15226186)


title: mis032

description:
JD0291-AML-v5-U133A
Additional Array


title: N016

description:
JD0044-AMD-v5-U133A
Other-#17 (identifier used in PMID:15226186)


title: MLL004

description:
JD0069-AMD-NA-v5-U133A
MLL-#14 (identifier used in PMID:15226186)


title: mis010

description:
JD0082-AMD-v5-U133A
Other-#33 (identifier used in PMID:15226186)


title: N011

description:
JD0004-AMD-v5-U133A
Other-#02 (identifier used in PMID:15226186)


title: mis022

description:
JD0255-AML-v5-U133A
Additional Array


title: mis012

description:
JD0015-AMD-v5-U133A
Other-#08 (identifier used in PMID:15226186)


title: N017

description:
JD0018-AMD-v5-U133A
Other-#09 (identifier used in PMID:15226186)


title: mis023

description:
JD0329-AML-R-v5-U133A
Additional Array


title: N001

description:
JD0093-AMD-v5-U133A
Other-#39 (identifier used in PMID:15226186)


title: mis008

description:
JD0320-AML-v5-U133A
Additional Array


title: mis003

description:
JD0098-AMD-v5-U133A
Other-#41 (identifier used in PMID:15226186)


title: mis011

description:
JD0083-AMD-v5-U133A
Other-#34 (identifier used in PMID:15226186)


title: mis014

description:
JD0084-AMD-v5-U133A
Other-#35 (identifier used in PMID:15226186)


title: mis002

description:
JD0092-AMD-v5-U133A
Other-#38 (identifier used in PMID:15226186)


title: mis009

description:
JD0077-AMD-v5-U133A
Other-#31 (identifier used in PMID:15226186)


title: mis021

description:
JD0075-AMD-v5-U133A
Other-#30 (identifier used in PMID:15226186)


title: mis018

description:
JD0060-AMD-v5-U133A
Other-#23 (identifier used in PMID:15226186)


title: mis019

description:
JD0061-AMD-v5-U133A
Other-#24 (identifier used in PMID:15226186)


title: i16008

description:
JD0270-AML-v5-U133A
Additional Array


title: M7008

description:
JD0067-AMD-v5-U133A
Other-M7-#05 (identifier used in PMID:15226186)


title: M7009

description:
JD0068-AMD-v5-U133A
Other-M7-#06 (identifier used in PMID:15226186)


title: mis013

description:
JD0047-AMD-v5-U133A
Other-#19 (identifier used in PMID:15226186)


title: M7006

description:
JD0023-AMD-v5-U133A
Other-M7-#01 (identifier used in PMID:15226186)


title: M7001

description:
JD0243-AMD-v5-U133A
Additional Array


title: i16007

description:
JD0307-AML-v5-U133A
Additional Array


title: i16016

description:
JD0087-AMD-v5-U133A
inv16-#10 (identifier used in PMID:15226186)


title: i16004

description:
JD0211-AMD-v5-U133A
Additional Array


title: i16026

description:
JD0357-AML-v5-U133A
Additional Array


title: mis005

description:
JD0045-AMD-v5-U133A
Other-#18 (identifier used in PMID:15226186)


title: i16003

description:
JD0162-AMD-v5-U133A
inv16-#14 (identifier used in PMID:15226186)


title: i16006

description:
JD0242-AMD-v5-U133A
Additional Array


title: i16001

description:
JD0094-AMD-v5-U133A
inv16-#11 (identifier used in PMID:15226186)


title: M7002

description:
JD0216-AMD-v5-U133A
Additional Array


title: mis007

description:
JD0072-AMD-v5-U133A
Other-#29 (identifier used in PMID:15226186)


title: M7007

description:
JD0058-AMD-v5-U133A
Other-M7-#03 (identifier used in PMID:15226186)


title: i16015

description:
JD0079-AMD-v5-U133A
inv16-#08 (identifier used in PMID:15226186)


title: i16005

description:
JD0232-AMD-v5-U133A
Additional Array


title: i16012

description:
JD0081-AMD-v5-U133A
inv16-#09 (identifier used in PMID:15226186)


title: i16014

description:
JD0056-AMD-v5-U133A
inv16-#06 (identifier used in PMID:15226186)


title: i16011

description:
JD0013-AMD-v5-U133A
inv16-#03 (identifier used in PMID:15226186)


title: i16013

description:
JD0035-AMD-v5-U133A
inv16-#05 (identifier used in PMID:15226186)


title: i16010

description:
JD0006-AMD-v5-U133A
inv16-#02 (identifier used in PMID:15226186)


title: i16009

description:
JD0001-AMD-v5-U133A
inv16-#01 (identifier used in PMID:15226186)


title: AE007

description:
JD0292-AML-v5-U133A
Additional Array


title: AE009

description:
JD0296-AML-v5-U133A
Additional Array


title: AE014

description:
JD0145-AMD-v5-U133A
t(8:21)-#20 (identifier used in PMID:15226186)


title: AE006

description:
JD0260-AML-v5-U133A
Additional Array


title: AE004

description:
JD0163-AMD-v5-U133A
t(8:21)-#21 (identifier used in PMID:15226186)


title: AE005

description:
JD0231-AMD-v5-U133A
Additional Array


title: AE017

description:
JD0070-AMD-v5-U133A
t(8:21)-#08 (identifier used in PMID:15226186)


title: AE003

description:
JD0131-AMD-v5-U133A
t(8:21)-#18 (identifier used in PMID:15226186)


title: AE020

description:
JD0290-AML-v5-U133A
Additional Array


title: AE012

description:
JD0020-AMD-v5-U133A
t(8:21)-#04 (identifier used in PMID:15226186)


title: AE013

description:
JD0022-AMD-v5-U133A
t(8:21)-#05 (identifier used in PMID:15226186)


title: AE001

description:
JD0144-AMD-v5-U133A
t(8:21)-#19 (identifier used in PMID:15226186)


title: M7004

description:
JD0244-AMD-v5-U133A
Additional Array


title: AE011

description:
JD0016-AMD-v5-U133A
t(8:21)-#02 (identifier used in PMID:15226186)


title: AE010

description:
JD0011-AMD-v5-U133A
t(8:21)-#01 (identifier used in PMID:15226186)


title: AE015

description:
JD0030-AMD-v5-U133A
t(8:21)-#06 (identifier used in PMID:15226186)


title: MLL011

description:
JD0042-AMD-v5-U133A
MLL-#07 (identifier used in PMID:15226186)


title: AE008

description:
JD0086-AMD-v5-U133A
t(8:21)-#11 (identifier used in PMID:15226186)


title: healthy control H19

status: Public on Jul 01 2013

city: rotterdam

first: nico

middle: jm

last: van beveren

address: dr molewaterplein

department: psychiatry

country: Netherlands

institute: erasmus university medical center

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip© microarray containing 54,675 probe sets (Affymetrix Co).otinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).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:
Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
samples  A06 and A18 were excluded after signal processing due to outlying global signal intensities

source_name: healthy control

label_protocol: isolated RNA was biotinylated into cRNA using the One-Cycle Target Labeling and Control Reagents Kit (Affymetric Co) according to the manufacturer’s protocol. Before hybridisation RNA quality and integrity was assessed using the Agilent 2100 BioAnalyzer (Agilent). Biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip© microarray containing 54,675 probe sets (Affymetrix Co).otinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Cells were subsequently disrupted (Qiashredder kit; Qiagen), and RNA was isolated (RNeasy minikit; Qiagen) with an additional DNAse digestion step (RNase-free DNase set; Qiagen), all according to the manufacturer’s protocol, diluted in nuclease free water, and frozen at –80 C before use. Before freezing, RNA purity and quantity was assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

tag: cell type

value: PBMCs

value: healthy control

tag: gender

value: male


title: healthy control H25


title: remitted schizophrenia patient  S13

source_name: remitted schizophrenia patient

value: remitted schizophrenia patient


title: healthy control H29


title: remitted schizophrenia patient  S10


title: remitted schizophrenia patient  S09


title: acutely admitted, severely psychotic schizophrenia patient  A26


title: acutely admitted, severely psychotic schizophrenia patient  A18


title: healthy control H26


title: remitted schizophrenia patient  S16


title: remitted schizophrenia patient  S22


title: remitted schizophrenia patient  S14


title: remitted schizophrenia patient  S21


title: healthy control H28_2


title: remitted schizophrenia patient  S15


title: healthy control H27


title: acutely admitted, severely psychotic schizophrenia patient  A23


title: remitted schizophrenia patient  S11


title: acutely admitted, severely psychotic schizophrenia patient  A19


title: healthy control H30


title: acutely admitted, severely psychotic schizophrenia patient  A21


title: remitted schizophrenia patient  S18


title: healthy control H24


title: acutely admitted, severely psychotic schizophrenia patient  A25


title: remitted schizophrenia patient  S08


title: remitted schizophrenia patient  S19


title: acutely admitted, severely psychotic schizophrenia patient  A24


title: remitted schizophrenia patient  S20


title: remitted schizophrenia patient  S17


title: healthy control H23


title: healthy control H22


title: healthy control H18


title: healthy control H14


title: healthy control H21


title: healthy control H20


title: acutely admitted, severely psychotic schizophrenia patient  A11


title: remitted schizophrenia patient  S06


title: healthy control H12


title: healthy control H13


title: acutely admitted, severely psychotic schizophrenia patient  A13


title: healthy control H06


title: healthy control H01


title: healthy control H17


title: healthy control H15


title: acutely admitted, severely psychotic schizophrenia patient  A12


title: healthy control H03


title: remitted schizophrenia patient  S04


title: acutely admitted, severely psychotic schizophrenia patient  A15


title: remitted schizophrenia patient  S03


title: healthy control H10


title: remitted schizophrenia patient  S05


title: remitted schizophrenia patient  S01


title: remitted schizophrenia patient  S07


title: healthy control H08


title: healthy control H11


title: acutely admitted, severely psychotic schizophrenia patient  A09


title: healthy control H09


title: acutely admitted, severely psychotic schizophrenia patient  A16


title: acutely admitted, severely psychotic schizophrenia patient  A08


title: remitted schizophrenia patient  S02


title: healthy control H07


title: healthy control H05


title: acutely admitted, severely psychotic schizophrenia patient  A04


title: acutely admitted, severely psychotic schizophrenia patient  A10


title: healthy control H02


title: healthy control H04


title: acutely admitted, severely psychotic schizophrenia patient  A05


title: acutely admitted, severely psychotic schizophrenia patient  A02


title: acutely admitted, severely psychotic schizophrenia patient  A01


title: acutely admitted, severely psychotic schizophrenia patient  A06


title: COPD subject (25366B)

status: Public on May 06 2013

city: Denver

first: Grant

last: Hughes

state: CO

address: 1400 Jackson St

institute: University of Colorado/National Jewish

hyb_protocol: Expression of 54,675 transcripts was measured using Affymetrix Human Genome U133 plus 2.0 Gene Array

scan_protocol: RNA purity was assessed using the Thermo Scientific NanoDrop instrument.  As recommended by Affymetrix, only samples with A260/A280 absorbance ratios between 1.8 and 2.1 were considered acceptable.  RNA integrity was also assessed using an Agilent ioanalyzer. Only samples with an integrity number above 7 were used.

data_processing: Data quality assessment was conducted using the affyPLM package within the R statistical computing environment.  Data were filtered for present/absent frequency (only probe sets with present calls in all samples were used) and normalized using the RMA algorithm.  ComBat, an empirical Bayes batch effect adjustment algorithm, was implemented on the normalized data set.

source_name: COPD subject PBMC

label_protocol: RNA samples were hybridized in three separate batches using standard Affymetrix protocols. The batches were balanced with respect to GOLD stages.

extract_protocol: A minimum of 50 ml of blood was drawn from either the arm or the hand. Peripheral blood was drawn into a BD Vacutainer Cell Preparation Tube, which was processed within 60 minutes according to the manufacturer’s instructions. Upon centrifugation, lymphocytes and other mononuclear cells appeared in a distinct band and were isolated from the supernatant. RNA isolation was performed using Qiagen RNeasy RNA isolation spin-column kits and protocol combined with the fully-automated Qiagen QIAcube.

value: PBMC

tag: distwalked

tag: bmi

tag: parentalcopd

tag: smokcignow

tag: finalgold


title: COPD subject (25023X)


title: COPD subject (24902U)


title: COPD subject (25237Q)


title: COPD subject (24927K)


title: Control subject (24826E)

source_name: Control subject PBMC


title: COPD subject (24762E)


title: Control subject (25214E)


title: COPD subject (24811R)


title: Control subject (24716X)


title: Control subject (24718B)


title: Control subject (25036G)


title: COPD subject (25020R)


title: COPD subject (24931B)


title: COPD subject (24812T)


title: acutely admitted, severely psychotic schizophrenia patient  A07

tag: disease state


title: Control subject (25229R)


title: COPD subject (24745E)


title: acutely admitted, severely psychotic schizophrenia patient  A03


title: COPD subject (24918J)


title: COPD subject (24639F)


title: COPD subject (24670Z)


title: Control subject (24653Z)


title: Control subject (24514L)


title: COPD subject (24513J)


title: Control subject (24382U)


title: Control subject (24394B)


title: COPD subject (24438V)


title: COPD subject (24450L)


title: COPD subject (24449A)


title: COPD subject (24211T)


title: COPD subject (24429U)


title: COPD subject (24063E)


title: Control subject (23091E)


title: COPD subject (24456X)


title: Control subject (23744X)


title: Control subject (23575A)


title: Control subject (24344M)


title: COPD subject (24158P)


title: COPD subject (23124T)


title: COPD subject (23089R)


title: COPD subject (24309K)


title: Control subject (22951X)


title: Control subject (24580Y)


title: Control subject (23294S)


title: COPD subject (23090C)


title: COPD subject (24706U)


title: COPD subject (24678P)


title: Control subject (23611E)


title: Control subject (22753T)


title: COPD subject (22754V)


title: COPD subject (22986Q)


title: COPD subject (22752R)


title: COPD subject (22544K)


title: Control subject (22569A)


title: Control subject (22375N)


title: COPD subject (21731E_2)


title: Control subject (22602Y)


title: Control subject (22545M)


title: COPD subject (22721G)


title: Control subject (22225U)


title: Control subject (21929Z)


title: Control subject (21961V)


title: COPD subject (22691X)


title: Control subject (22363G)


title: COPD subject (22332V)


title: Control subject (22155Z)


title: COPD subject (22623G)


title: Control subject (22692Z)


title: COPD subject (21482J)


title: COPD subject (22723K)


title: COPD subject (22057Z)


title: COPD subject (21489X)


title: COPD subject (21710W)


title: COPD subject (21609H)


title: COPD subject (21556M)


title: COPD subject (20900W)


title: COPD subject (21520R)


title: COPD subject (21305N)


title: Control subject (21920H)


title: Control subject (21931M)


title: Control subject (21711Y)


title: COPD subject (20271R)


title: COPD subject (20542W)


title: COPD subject (20132D)


title: COPD subject (20370T)


title: COPD subject (20580E)


title: COPD subject (20815F)


title: COPD subject (20777X)


title: COPD subject (19370G)


title: COPD subject (19688L)


title: Control subject (12969K)


title: COPD subject (20738N)


title: COPD subject (12778D)


title: COPD subject (13959M)


title: COPD subject (18468S)


title: COPD subject (12900A)


title: COPD subject (12816L)


title: COPD subject (13672S)


title: COPD subject (13885J)


title: Control subject (20400C)


title: COPD subject (11805B)


title: COPD subject (20778Z)


title: COPD subject (11455A)


title: COPD subject (13012C)


title: COPD subject (11774Q)


title: COPD subject (11218M)


title: Control subject (12771P)


title: COPD subject (13686D)


title: COPD subject (20696X)


title: COPD subject (12593R)


title: COPD subject (11070G)


title: Control subject (11209L)


title: COPD subject (10458B)


title: COPD subject (10455V)


title: COPD subject (14303S)


title: Control subject (10465Y)


title: Control subject (10104S)


title: COPD subject (10166O)


title: Control subject (10136F)


title: COPD subject (10473X)


title: COPD subject (10328O)


title: COPD subject (10170F)


title: COPD subject (10300S)


title: COPD subject (10087S)


title: COPD subject (10544U)


title: COPD subject (10071D)


title: COPD subject (10182M)


title: COPD subject (10630N)


title: COPD subject (10245K)


title: Control subject (10391V)


title: COPD subject (10636Z)


title: COPD subject (10390T)


title: Control subject (10102O)


title: Control subject (10687Q)


title: COPD subject (10062C)


title: COPD subject (10138J)


title: COPD subject (10097V)


title: Altitude SP0126

status: Public on Apr 30 2013

city: Rochester

first: Nicole

last: Herman

state: MN - Minnesota

address: 200 1st St SW

institute: Mayo Clinic

hyb_protocol: Affymetrix GeneChip Human Genome U133 Plus 2 array.

scan_protocol: Affymetrix GeneChipScanner 3000 (Santa Clara CA)

data_processing: data were normalized with quantile normalization, without background correction and then summarized using Tukey’s median polish

source_name: Healthy volunteer

label_protocol: cDNA was generated from five micrograms of total RNA using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7 Oligo(dT) primer. Subsequently, the products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: frozen and thawed PBMC

extract_protocol: RNA was extracted using Rneasy MiniKits (Quiagen) and stored at -80°C.  Microarray analysis was performed using the

treatment_protocol: Blood samples were collected at McMurdo station and on the third day at the South Pole Station in PAXgene Blood RNA tubes (PreAnalytix). The tubes were then frozen at -40°C until returning to the US.

tag: location

value: Altitude


title: Altitude SP0044


title: Altitude SP0039


title: Altitude SP0027


title: Altitude SP0042


title: Altitude SP0033


title: Altitude SP0034


title: Altitude SP0038


title: Altitude SP0045


title: Altitude SP0024


title: Altitude SP0125


title: Altitude SP0023


title: Altitude SP0040


title: Altitude SP0035


title: Altitude SP0123


title: Altitude SP0043


title: Altitude SP0037


title: Altitude SP0017


title: Altitude SP0026


title: Altitude SP0021


title: Altitude SP0028


title: Altitude SP0020


title: Altitude SP0046


title: Altitude SP0036


title: Altitude SP0025


title: Altitude SP0019


title: Altitude SP0030


title: Altitude SP0014


title: Altitude SP0018


title: Altitude SP0016


title: Base Campe SP0126

value: Base camp


title: Base Campe SP0046


title: Altitude SP0010


title: Altitude SP0002


title: Altitude SP0012


title: Altitude SP0005


title: Base Campe SP0043


title: Altitude SP0007


title: Altitude SP0011


title: Altitude SP0001


title: Altitude SP0004


title: Altitude SP0006


title: Base Campe SP0040


title: Base Campe SP0125


title: Altitude SP0009


title: Base Campe SP0039


title: Base Campe SP0045


title: Altitude SP0003


title: Base Campe SP0044


title: Altitude SP0013


title: Altitude SP0008


title: Base Campe SP0038


title: Base Campe SP0042


title: Base Campe SP0035


title: Base Campe SP0034


title: Base Campe SP0036


title: Base Campe SP0123


title: Base Campe SP0033


title: Base Campe SP0037


title: Base Campe SP0026


title: Base Campe SP0021


title: Base Campe SP0025


title: Base Campe SP0016


title: Base Campe SP0014


title: Base Campe SP0013


title: Base Campe SP0020


title: Base Campe SP0023


title: Base Campe SP0019


title: Base Campe SP0028


title: Base Campe SP0017


title: Base Campe SP0027


title: Base Campe SP0030


title: Base Campe SP0024


title: Base Campe SP0012


title: Base Campe SP0010


title: Base Campe SP0009


title: Base Campe SP0008


title: Base Campe SP0003


title: Base Campe SP0011


title: Base Campe SP0018


title: Base Campe SP0006


title: Base Campe SP0005


title: Base Campe SP0007


title: Base Campe SP0002


title: Base Campe SP0001


title: Altitude SPO245


title: Altitude SPO243


title: Altitude SPO241


title: Altitude SPO238


title: Altitude SPO239


title: Altitude SPO236


title: Altitude SPO230


title: Altitude SPO226


title: Altitude SPO231


title: Altitude SPO222


title: Altitude SPO235


title: Altitude SPO227


title: Altitude SPO221


title: Altitude SPO223


title: Altitude SPO219


title: Altitude SPO234


title: Altitude SPO229


title: Altitude SPO220


title: Altitude SPO218


title: Altitude SPO207


title: Altitude SPO224


title: Altitude SPO206


title: Altitude SPO211


title: Altitude SPO209


title: Altitude SPO208


title: Altitude SPO213


title: Altitude SPO203


title: Altitude SPO204


title: Altitude SPO210


title: Altitude SPO200


title: Altitude SPO198


title: Altitude SPO191


title: Altitude SPO186


title: Altitude SPO196


title: Altitude SPO197


title: Altitude SPO170


title: Altitude SPO164


title: Altitude SPO185


title: Altitude SPO199


title: Altitude SPO184


title: Altitude SPO180


title: Altitude SPO183


title: Altitude SPO150


title: Altitude SPO188


title: Altitude SPO169


title: Altitude SPO181


title: Altitude SPO140


title: Altitude SPO148


title: Altitude SPO179


title: Altitude SPO165


title: Altitude SPO163


title: Altitude SPO142


title: Base camp SPO245


title: Base camp SPO241


title: Base camp SPO243


title: Altitude SPO143


title: Altitude SPO141


title: Base camp SPO239


title: Base camp SPO238


title: Base camp SPO234


title: Base camp SPO222


title: Altitude SPO144


title: Base camp SPO208


title: Base camp SPO218


title: Base camp SPO206


title: Base camp SPO211


title: Base camp SPO213


title: Base camp SPO204


title: Base camp SPO229


title: Base camp SPO236


title: Base camp SPO207


title: Base camp SPO210


title: Base camp SPO230


title: Base camp SPO220


title: Base camp SPO199


title: Base camp SPO226


title: Base camp SPO203


title: Base camp SPO221


title: Base camp SPO223


title: Base camp SPO227


title: Base camp SPO200


title: Base camp SPO219


title: Base camp SPO209


title: Base camp SPO231


title: Base camp SPO235


title: Base camp SPO224


title: Base camp SPO198


title: Base camp SPO188


title: Base camp SPO165


title: Base camp SPO185


title: Base camp SPO142


title: Base camp SPO163


title: Base camp SPO186


title: Base camp SPO196


title: Base camp SPO148


title: Base camp SPO184


title: Base camp SPO179


title: Base camp SPO191


title: Base camp SPO181


title: Base camp SPO140


title: Base camp SPO164


title: Base camp SPO183


title: Base camp SPO180


title: Base camp SPO143


title: Base camp SPO144


title: Base camp SPO169


title: Base camp SPO170


title: Base camp SPO150


title: Base camp SPO141


title: Base camp SPO197


title: Base Campe SP0004


title: Pediatric AML AML356 (A339)

status: Public on Apr 01 2013

city: Tokyo

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 plus 2.0 array (Affymetrix). Arrays were washed and stained in Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.3 (GCOS1.3, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Leukemic cells

label_protocol: Biotinylated cRNA was prepared from 20 ng of total RNA with a two-cycle cDNA synthesis kit and 3’-amplification reagents for IVT labeling (Affymetrix).

extract_protocol: Total RNA was prepared using an RNeasy Mini kit (Qiagen).

treatment_protocol: Mononuclear cells were collected from bone marrow or peripheral blood of pediatric AML patients at the time of diagnosis.

tag: fab subtype

tag: karyotype

tag: aml99 study no.


title: Pediatric AML AML361 (A411)


title: Pediatric AML AML357 (A326)

value: Others


title: Pediatric AML AML355 (A353)


title: Pediatric AML AML359 (A391)

value: Normal


title: Pediatric AML AML352 (A331)


title: Pediatric AML AML347 (A319)


title: Pediatric AML AML348 (A335)


title: Pediatric AML AML345 (A333)


title: Pediatric AML AML358 (A382)


title: Pediatric AML AML337 (A292)


title: Pediatric AML AML344 (A325)


title: Pediatric AML AML354 (A337)


title: Pediatric AML AML353 (A357)


title: Pediatric AML AML342 (A321)


title: Pediatric AML AML340 (A322)


title: Pediatric AML AML350 (A336)


title: Pediatric AML AML346 (A296)


title: Pediatric AML AML343 (A327)


title: Pediatric AML AML351 (A345)


title: Pediatric AML AML339 (A315)


title: Pediatric AML AML332 (A297)


title: Pediatric AML AML330 (A282)


title: Pediatric AML AML349 (A355)


title: Pediatric AML AML329 (A299)


title: Pediatric AML AML333 (A300)


title: Pediatric AML AML328 (A294)


title: Pediatric AML AML338 (A311)


title: Pediatric AML AML327 (A309)


title: Pediatric AML AML341 (A320)


title: Pediatric AML AML326 (A285)


title: Pediatric AML AML325 (A274)


title: Pediatric AML AML319 (A266)


title: Pediatric AML AML315 (A250)


title: Pediatric AML AML309 (A240)

value: ?/Down


title: Pediatric AML AML324 (A280)


title: Pediatric AML AML322 (A277)


title: Pediatric AML AML320 (A275)


title: Pediatric AML AML311 (A244)


title: Pediatric AML AML316 (A256)


title: Pediatric AML AML304 (A236)


title: Pediatric AML AML321 (A281)


title: Pediatric AML AML301 (A234)


title: Pediatric AML AML314 (A259)


title: Pediatric AML AML312 (A249)


title: Pediatric AML AML317 (A257)


title: Pediatric AML AML300 (A208)


title: Pediatric AML AML310 (A243)


title: Pediatric AML AML299 (A116)


title: Pediatric AML AML313 (A301)


title: Pediatric AML AML303 (A239)


title: Pediatric AML AML307 (A245)


title: Pediatric AML AML293 (A168)


title: Pediatric AML AML298 (A181)


title: Pediatric AML AML297 (A180)


title: Pediatric AML AML308 (A238)


title: Pediatric AML AML291 (A172)


title: Pediatric AML AML294 (A171)


title: Pediatric AML AML292 (A173)


title: Pediatric AML AML285 (A154)


title: Pediatric AML AML288 (A162)


title: Pediatric AML AML290 (A167)


title: Pediatric AML AML286 (A159)


title: Pediatric AML AML282 (A149)


title: Pediatric AML AML281 (A140)


title: Pediatric AML AML283 (A051)


title: Pediatric AML AML273 (A135)


title: Pediatric AML AML270 (A132)


title: Pediatric AML AML274 (A023)


title: Pediatric AML AML280 (A141)


title: Pediatric AML AML271 (A129)


title: Pediatric AML AML272 (A128)


title: Pediatric AML AML268 (A115)


title: Pediatric AML AML264 (A119)


title: Pediatric AML AML266 (A117)


title: Pediatric AML AML269 (A121)


title: Pediatric AML AML262 (A108)


title: Pediatric AML AML265 (A114)


title: Pediatric AML AML254 (A211)


title: Pediatric AML AML260 (A102)


title: Pediatric AML AML277 (A150)


title: Pediatric AML AML256 (A218)


title: Pediatric AML AML257 (A217)


title: Pediatric AML AML261 (A109)


title: Pediatric AML AML306 (A235)


title: Pediatric AML AML241 (A094)


title: Pediatric AML AML259 (A106)


title: Pediatric AML AML242 (A095)


title: Pediatric AML AML240 (A093)


title: Pediatric AML AML244 (A188)


title: Pediatric AML AML253 (A203)


title: Pediatric AML AML247 (A190)


title: Pediatric AML AML238 (A089)


title: Pediatric AML AML237 (A087)


title: Pediatric AML AML255 (A210)


title: Pediatric AML AML246 (A187)


title: Pediatric AML AML249 (A199)


title: Pediatric AML AML243 (A191)


title: Pediatric AML AML239 (A090)


title: Pediatric AML AML252 (A200)


title: Pediatric AML AML245 (A185)


title: Pediatric AML AML250 (A202)


title: Pediatric AML AML234 (A110)


title: Pediatric AML AML229 (A081)


title: Pediatric AML AML279 (A137)


title: Pediatric AML AML223 (A062)


title: Pediatric AML AML276 (A138)


title: Pediatric AML AML219 (A049)


title: Pediatric AML AML232 (A078)


title: Pediatric AML AML214 (A037)


title: Pediatric AML AML221 (A053)


title: Pediatric AML AML220 (A052)


title: Pediatric AML AML228 (A075)


title: Pediatric AML AML225 (A004)


title: Pediatric AML AML212 (A019)


title: Pediatric AML AML210 (A027)


title: Pediatric AML AML227 (A113)


title: Pediatric AML AML215 (A040)


title: Pediatric AML AML204 (A009)


title: Pediatric AML AML207 (A015)


title: Pediatric AML AML222 (A057)


title: Pediatric AML AML205 (A013)


title: Pediatric AML AML218 (A044)


title: Pediatric AML AML226 (A063)


title: Pediatric AML AML209 (A029)


title: Pediatric AML AML224 (A059)


title: Pediatric AML AML206 (A006)


title: Pediatric AML AML203 (A008)


title: Pediatric AML AML233 (A086)


title: VFP-0255_G7_DF [HG-U133Plus2]

status: Public on Jan 26 2013

city: silver spring

first: peifang

last: sun

address: 503 robert grant ave

institute: Naval Medical Research Center

hyb_protocol: The biotin-labeled and fragmented cRNA was hybridized to the HUGeneFL GeneChip array (Affymetrix) or to the TEST 3 array as described previously. Briefly, a 220-ml hybridization solution consisting of 1 M NaCl, 10 mM Tris (pH 7.6), 0.005% Triton X-100, 50 pM control Oligo B2 (59-bioGTCAAGATGCTACCGTTCAG-39) (Affymetrix), control cRNA cocktail (Bio B [150 pM], Bio C [500 pM], Bio D [2.5 nM], and Cre X [10 nM]; American Type Tissue Collection [Manassas, VA] and Lofstrand Laboratories [Gaithersburg, MD]), herring sperm DNA (0.1 mg/ml), and fragmented labeled sample cRNA (0.05 mg/ml) was heated to 95°C for 35 min, cooled to 40°C, and clarified by centrifugation. Hybridization was at 42°C in a rotisserie hybridization oven (model 320; Affymetrix) at 60 rpm or 16 hr. Following hybridization, the gene chip arrays were washed 10 times at 25°C with 63 SSPE-T buffer (1 M NaCl, 0.006 M EDTA, and 0.06 M Na3PO4) and 0.005% Triton X-100 (pH 7.6), using the automated fluidics station protocol. Gene chip arrays were incubated at 50°C in 0.53 SSPE-T and 0.005% Triton X-100 for 20 min at 60 rpm in the rotisserie oven. Gene chip arrays were stained for 15 min at room temperature and at 60 rpm, with streptavidin–phycoerythrin (Molecular probes, Eugene, OR) stain solution at a final concentration of 10 mg/ml in 63SSPE-T buffer and acetylated bovine serum albumin (1.0 mg/ml; Sigma).

scan_protocol: Gene chip arrays were washed twice at room temperature with 63 SSPE-T buffer. Gene chip arrays were scanned with an HP GeneArray scanner (Hewlett-Packard, Santa Clara, CA) controlled by GeneChip 3.1 software (Affymetrix).

data_processing:
Gene chips with a scaling factor >50 on dChip software (2005 version) were eliminated from further analysis [1, 2]. Gene chips were also examined by QA/QC functions built in the Partek software according to the company’s User’s Manual. Affymetrix CEL files were imported to Partek Genomics Suite Version 6.6 (Partek). Gene chips that failed by QC metrics and appeared as outliers on Principal Component Analysis (PCA) were eliminated for further analysis. CEL files were normalized at the probe level using the Robust Multi-chip Average (RMA) method built into in Partek Genomic Suite software. RMA is a method of normalization of microarray data that leverages gene expression assessments made on Affymetrix gene chips. For each probeset, the technique generates an estimated value for the probe and chip effects that result in the overall pattern of probe set values observed in the data set. RMA is comprised of 3 calculation applications that address background correction, normalization of quantiles, and median polish summarization. Gene expression data were expressed as log2 values. Data sets from the two gene chip platforms were first normalized individually and further analyzed independently.
Differentially expressed genes were analyzed using analysis of variance (ANOVA) built in the Partek software. Multi-way ANOVA was chosen based on the number of factors contributing to chip data variation. The following factors were taken in consideration as variation factors: subject #, scan date (date the gene chip experiment was done and the chip image was taken), infecting serotype, illness day (days of illness when sample was taken), and disease severity (samples associated with DF or DHF category). Genes considered being significant only by chance were defined by the false discovery rate (FDR≥5%) and were excluded from further analysis. In this study, genes with fold change of >2 or <-2 and a p value plus a FDR < 5% were counted to be significant. Heatmap and principal component analysis were used to visualize the most informative trends by showing the predominant gradients in the data set.

label_protocol:
Double-stranded cDNA was synthesized in two steps with the SuperScript Choice system (GIBCO-BRL, Rockville, MD) and the reverse transcription primer T7-(dt)24 (59-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(T)24-39] (Genset, La Jolla, CA). First-strand synthesis was carried out in a 20-ml reaction. Approximately 5 mg of total RNA or 1.0 mg of poly(A) RNA was annealed to 7 mg of T7-(dt)24 primer at 70°C for 10 min. Reverse transcription was carried out at 37°C for 1 hr in a final concentration of 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol(DTT), dATP, dCTP, dGTP, and dTTP (500 mM each), and SuperScript II reverse transcriptase (20,000 to 30,000 U/ml) and the reaction was terminated by placing the tube on ice. Second strand synthesis was carried out in 150 ml incorporating the entire 20-ml first-strand reaction mixture and the 130-ml second strand reaction mixture for a final concentration of 25 mM Tris-HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 10 mM (NH4)2SO4, 0.15 mM b-NAD1, dATP, dCTP, dGTP, and dTTP (250 mM each), 1.2 mM DTT, DNA ligase (65 U/ml), DNA polymerase I (250 U/ml), and RNase H (13 U/ml). The mixture was incubated at 16°C for 2 hr, whereupon 2 ml of T4 DNA polymerase at 5 U/ml was added and the incubation continued at 16°C for 5 min. To terminate the reaction, 10 ml of 0.5 M EDTA was added. The cDNA was purified with phenol–chloroform–isoamyl alcohol (24:23:1) saturated with 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA (Ambion, Austin, TX). The purified cDNA was precipitated with 5 M ammonium acetate and absolute ethanol at 220°C for 20 min. The pellet was resuspended in 7–9 ml of RNase-free water to achieve a final concentration of between 0.25 and 0.65 mg/ml.
Synthesis of biotin-labeled cRNA was carried out by in vitro transcription using the MEGAscript T7 in vitro transcription kit (Ambion). In accordance with the manufacturer’s instructions, 0.4–1.0 mg of double-stranded cDNA was placed into a 20-ml reaction mix, at room temperature, containing Ambion 13 reaction buffer and enzyme mix (proprietary). The labeling mix consisted of 7.5 mM ATP, 7.5 mM GTP, 5.6 mM UTP and 1.9 mM biotinylated UTP (Enzo Diagnostics, Farmingdale, NY), and 5.6 mM CTP and 1.9 mM biotinylated CTP (Enzo Diagnostics). The reaction was incubated at 37°C for 5 hr. The biotin-labeled cRNA was purified with RNeasy spin columns (Qiagen,Valencia, CA) according to the manufacturer’s protocol. The biotin-labeled cRNA was fragmented in a 40-ml reaction mixture containing 40 mM Tris–acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate, incubated at 94°C for 35 min, and then put on ice.

growth_protocol:
Peripheral blood mononuclear cells (PBMCs) were separated using Ficoll-paque according to manufacturer's instruction
Cells were frozen in 10%  dimethyl sulfoxide (DMSO) in -70  ͦC until use.

extract_protocol: The DMSO-cryopreserved cells were resuspended in 1 ml of TRI Reagent (Molecular Research Center, Woodlands, TX). The mixture was vortexed for 15 sec and allowed to stand at room temperature for 10 min. The manufacturer’s instructions for the preparation of total RNA were followed.

tag: patient no.

tag: Stage

tag: infecting serotype

tag: phase

value: Convalenscent

tag: severity

value: DF (dengue fever)

tag: fever days or defervescent (df) days

value: c

tag: scan date


title: VFP-0250_G4_DHF [HG-U133Plus2]

value: Late Acute

value: DHF (dengue hemorrhagic fever)


title: VFP-0255_G5_DF [HG-U133Plus2]


title: VFP-0255_G2_DF [HG-U133Plus2]

value: Early Acute


title: VFP-0250_G7_DHF [HG-U133Plus2]


title: VFP-0255_G3_DF [HG-U133Plus2]


title: VFP-0250_G6_DHF [HG-U133Plus2]


title: Pediatric AML AML235 (A085)


title: VFP-0249_G7_DHF [HG-U133Plus2]


title: VFP-0249_G3_DHF [HG-U133Plus2]


title: VFP-0240_G7_DHF [HG-U133Plus2]


title: VFP-0243_G7_DHF [HG-U133Plus2]


title: VFP-0243_G5_DHF [HG-U133Plus2]


title: VFP-0249_G6_DHF [HG-U133Plus2]


title: VFP-0240_G6_DHF [HG-U133Plus2]


title: VFP-0234_G7_DHF [HG-U133Plus2]


title: VFP-0243_G4_DHF [HG-U133Plus2]


title: VFP-0240_G3_DHF [HG-U133Plus2]


title: VFP-0234_G3_DHF [HG-U133Plus2]


title: VFP-0240_G4_DHF [HG-U133Plus2]


title: VFP-0243_G3_DHF [HG-U133Plus2]


title: VFP-0224_G6_DF [HG-U133Plus2]


title: VFP-0234_G5_DHF [HG-U133Plus2]


title: VFP-0249_G4_DHF [HG-U133Plus2]


title: VFP-0234_G2_DHF [HG-U133Plus2]


title: VFP-0224_G7_DF [HG-U133Plus2]


title: VFP-0224_G4_DF [HG-U133Plus2]


title: VFP-0224_G2_DF [HG-U133Plus2]


title: VFP-0220_G7_DHF [HG-U133Plus2]


title: VFP_0186_G4_DF [HG-U133Plus2]


title: VFP-0224_G1_DF [HG-U133Plus2]


title: VFP-0220_G4_DHF [HG-U133Plus2]


title: VFP-0213_G7_DF [HG-U133Plus2]


title: VFP-0161_G6_DHF [HG-U133Plus2]


title: VFP-0178_G3_DHF [HG-U133Plus2]


title: VFP-0178_G7_DHF [HG-U133Plus2]


title: VFP-0220_G2_DHF [HG-U133Plus2]


title: VFP_0213_G5_DF [HG-U133Plus2]


title: VFP-0213_G1_DF [HG-U133Plus2]


title: VFP_0220_G3_DHF [HG-U133Plus2]


title: VFP-0178_G6_DHF [HG-U133Plus2]


title: VFP-0220_G6_DHF [HG-U133Plus2]


title: VFP-0186_G7_DF [HG-U133Plus2]


title: VFP-0178_G5_DHF [HG-U133Plus2]


title: VFP-0186_G3_DF [HG-U133Plus2]


title: VFP-0186_G2_DF [HG-U133Plus2]


title: VFP-0131_G6(2)_DHF [HG-U133Plus2]


title: VFP-0178_G2_DHF [HG-U133Plus2]


title: VFP-0131_G7_DHF [HG-U133Plus2]


title: VFP-0213_G2_DF [HG-U133Plus2]


title: VFP-0161_G4_DHF [HG-U133Plus2]


title: VFP-0161_G7_DHF [HG-U133Plus2]


title: VFP-0161_G3_DHF [HG-U133Plus2]


title: VFP-0213_G3_DF [HG-U133Plus2]


title: VFP-0131_G3_DHF [HG-U133Plus2]


title: VFP-0129_G7_DF [HG-U133Plus2]


title: VFP-0127_G7_DHF [HG-U133Plus2]


title: VFP-0131_G6(1)_DHF [HG-U133Plus2]


title: VFP-0129_G4_DF [HG-U133Plus2]


title: VFP-0127_G6(1)_DHF [HG-U133Plus2]


title: VFP-0104_G7_DF [HG-U133Plus2]


title: VFP-0082_G7_DF [HG-U133Plus2]


title: VFP-0087_G3_DF [HG-U133Plus2]


title: VFP-0101_G3_DF [HG-U133Plus2]


title: VFP-0113_G6_DF [HG-U133Plus2]


title: VFP-0127_G5_DHF [HG-U133Plus2]


title: VFP-0104_G6_DF [HG-U133Plus2]


title: VFP-0111_G6_DF [HG-U133Plus2]


title: VFP-0131_G4_DHF [HG-U133Plus2]


title: VFP-0105_G6_DF [HG-U133Plus2]


title: VFP-0127_G6(2)_DHF [HG-U133Plus2]


title: VFP-0117_G6_DF [HG-U133Plus2]


title: VFP-0101_G4_DF [HG-U133Plus2]


title: VFP-0083_G7_DF [HG-U133Plus2]


title: VFP-0082_G5_DF [HG-U133Plus2]


title: VFP-0075_G7_DF [HG-U133Plus2]


title: VFP-0064_G6_DF [HG-U133Plus2]


title: VFP-0082_G4_DF [HG-U133Plus2]


title: VFP-0081_G6_DF [HG-U133Plus2]


title: VFP-0063_G3_DF [HG-U133Plus2]


title: VFP-0070_G4_DF [HG-U133Plus2]


title: VFP-0060_G4_DHF [HG-U133Plus2]


title: VFP-0075_G5_DF [HG-U133Plus2]


title: VFP-0057_G6_DF [HG-U133Plus2]


title: VFP-0057_G7_DF [HG-U133Plus2]


title: VFP-0057_G3_DF [HG-U133Plus2]


title: VFP-0053_G4_DF [HG-U133Plus2]


title: VFP-0039_G7_DF [HG-U133Plus2]


title: VFP-0047_G4_DHF [HG-U133Plus2]


title: VFP-0040_G4_DF [HG-U133Plus2]


title: VFP-0047_G7_DHF [HG-U133Plus2]


title: VFP-0041_G6_DF [HG-U133Plus2]


title: VFP-0011_G6_DHF [HG-U133Plus2]


title: VFP-0003_G3_DF [HG-U133Plus2]


title: VFP-0056_G6_DF [HG-U133Plus2]


title: VFP-0045_G5_DF [HG-U133Plus2]


title: VFP-0011_G4_DHF [HG-U133Plus2]


title: VFP-0003_G2_DF [HG-U133Plus2]


title: VFP-0047_G5_DHF [HG-U133Plus2]


title: VFP-0056_G4_DF [HG-U133Plus2]


title: Down-SNP-#21

status: Public on Dec 12 2012

first: Charles

middle: G

last: Mullighan

institute: St Jude Children's Research Hospital

hyb_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with CRLF2 rearrangement

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases at diagnosis.

extract_protocol: Total RNA extraction (Trizol)

tag: tissue

value: leukemic cells obtained from bone marrow or blood at diagnosis

tag: cell type

value: childhood ALL with CRLF2 rearrangement


title: Other-SNP-#127

scan_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/


title: Hyperdip>50-SNP-#126

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with high hyperdiploid karyotype

label_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/


title: E2A-PBX1-SNP-#23

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with TCF3-PBX1 rearrangement


title: VFP-0003_G7_DF [HG-U133Plus2]


title: Hyperdip>50-SNP-#164

value: childhood ALL with high hyperdiploid karyotype


title: Hyperdip>50-SNP-#108


title: VFP-0011_G7_DHF [HG-U133Plus2]


title: 680 pbmc

status: Public on Mar 28 2012

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

description: Sample from peripheral blood mononuclear cells taking during carotid endarterectomy

hyb_protocol: Hybridization was performed according to Affymetrix protocols for HG-U133 plus2 2.0 arrays, at the Bioinformatics and Expression Analysis core facility at the Karolinska Institute.

scan_protocol: Scanning was performed according to Affymetrix protocols for HG-U133 plus2 2.0 arrays, at the Bioinformatics and Expression Analysis core facility at the Karolinska Institute.

data_processing: cel files were preprocessed using RMA normalization, as implemented in the Affymetrix Power Tools 1.10.2 package apt-probeset-summarize. As part of the RMA normalization, all expression measurements were log2-transformed.

source_name: peripheral blood mononuclear cells

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

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (Qiagen) and treatment with the RNase-free DNase set (Qiagen) according to the manufacturer’s instructions. RNA quality was analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies Inc, Palo Alto, Calif), and RNA concentration was measured on a NanoDrop (Thermo Scientific). Low concentration and low quality samples were omitted.

treatment_protocol: Flash frozen directly after sampling.

tag: individual

tag: sample type

value: peripheral blood mononuclear cells

tag: age (y)

tag: ischemic time (days)

tag: ischemic event

value: FALSE


title: 669 pbmc

value: TRUE


title: 681 pbmc


title: 659 pbmc


title: 654 pbmc


title: 677 pbmc


title: 664 pbmc


title: 665 pbmc


title: 627 pbmc


title: Hyperdip>50-SNP-#127


title: 630 pbmc


title: 618 pbmc


title: 624 pbmc


title: 603 pbmc


title: 605 pbmc


title: 638 pbmc


title: 625 pbmc


title: 642 pbmc


title: 646 pbmc


title: 606 pbmc


title: 591 pbmc


title: 554 pbmc


title: 558 pbmc


title: 571 pbmc


title: 588 pbmc


title: 552 pbmc


title: 561 pbmc


title: 550 pbmc


title: T-ALL-SNP-#96

source_name: RNA extracted from T-lineage ALL

value: T-lineage ALL


title: 509 pbmc


title: 544 pbmc


title: 528 pbmc


title: 489 pbmc


title: 481 pbmc


title: 514 pbmc


title: 502 pbmc


title: 532 pbmc


title: 519 pbmc


title: 458 pbmc


title: 497 pbmc


title: 492 pbmc


title: 686 pbmc


title: 446 pbmc


title: 521 pbmc


title: 442 pbmc


title: 440 pbmc


title: 466 pbmc


title: 439 pbmc


title: 433 pbmc


title: 431 pbmc


title: 520 pbmc


title: 429 pbmc


title: 412 pbmc


title: 427 pbmc


title: 411 pbmc


title: 420 pbmc


title: 404 pbmc


title: 383 pbmc


title: 371 pbmc


title: 398 pbmc


title: 406 pbmc


title: 397 pbmc


title: 378 pbmc


title: 421 pbmc


title: 366 pbmc


title: 356 pbmc


title: 391 pbmc


title: 355 pbmc


title: 384 pbmc


title: 365 pbmc


title: 345 pbmc


title: 367 pbmc


title: 363 pbmc


title: 359 pbmc


title: 340 pbmc


title: 334 pbmc


title: 392 pbmc


title: 370 pbmc


title: 318 pbmc


title: 364 pbmc


title: 333 pbmc


title: 372 pbmc


title: 337 pbmc


title: 327 pbmc


title: 313 pbmc


title: 302 pbmc


title: 298 pbmc


title: 301 pbmc


title: 306 pbmc


title: 288 pbmc


title: 286 pbmc


title: 281 pbmc


title: 285 pbmc


title: 282 pbmc


title: 284 pbmc


title: 296 pbmc


title: 311 pbmc


title: 292 pbmc


title: 279 pbmc


title: SJETV092

status: Public on Jan 10 2012

address: 262 Danny Thomas Place, MS 342

description: ETV6-RUNX1 B-precursor ALL

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA

growth_protocol: No growth protocol. Cells were obtained from bone marrow or blood from children with acute lymphoblastic leukemia

value: tumor cells obtained at diagnosis

tag: subtype


title: SJETV090

description: ETV6-RUNX1 B-precursor ALL


title: SJETV077

description: ETV6-RUNX1 B-precursor ALL


title: SJETV083

description: ETV6-RUNX1 B-precursor ALL


title: SJETV084

description: ETV6-RUNX1 B-precursor ALL


title: SJETV091

description: ETV6-RUNX1 B-precursor ALL


title: SJETV085

description: ETV6-RUNX1 B-precursor ALL


title: SJHYPER090

description: High hyperdiploid B-precursor ALL


title: SJETV094

description: ETV6-RUNX1 B-precursor ALL


title: SJETV078

description: ETV6-RUNX1 B-precursor ALL


title: SJETV086

description: ETV6-RUNX1 B-precursor ALL


title: SJETV081

description: ETV6-RUNX1 B-precursor ALL


title: SJETV093

description: ETV6-RUNX1 B-precursor ALL


title: SJETV087

description: ETV6-RUNX1 B-precursor ALL


title: SJETV082

description: ETV6-RUNX1 B-precursor ALL


title: SJETV079

description: ETV6-RUNX1 B-precursor ALL


title: SJETV076

description: ETV6-RUNX1 B-precursor ALL


title: SJETV073

description: ETV6-RUNX1 B-precursor ALL


title: SJETV075

description: ETV6-RUNX1 B-precursor ALL


title: SJETV074

description: ETV6-RUNX1 B-precursor ALL


title: SJETV070

description: ETV6-RUNX1 B-precursor ALL


title: SJETV069

description: ETV6-RUNX1 B-precursor ALL


title: SJETV114

description: ETV6-RUNX1 B-precursor ALL


title: SJETV113

description: ETV6-RUNX1 B-precursor ALL


title: SJETV068

description: ETV6-RUNX1 B-precursor ALL


title: SJETV111

description: ETV6-RUNX1 B-precursor ALL


title: SJTALL032

description: T-lineage ALL


title: SJETV023

description: ETV6-RUNX1 B-precursor ALL


title: SJETV072

description: ETV6-RUNX1 B-precursor ALL


title: SJETV027

description: ETV6-RUNX1 B-precursor ALL


title: SJETV099

description: ETV6-RUNX1 B-precursor ALL


title: SJTALL083

description: T-lineage ALL


title: SJTALL034

description: T-lineage ALL


title: SJTALL033

description: T-lineage ALL


title: SJETV028

description: ETV6-RUNX1 B-precursor ALL


title: SJETV100

description: ETV6-RUNX1 B-precursor ALL


title: SJETV022

description: ETV6-RUNX1 B-precursor ALL


title: SJETV110

description: ETV6-RUNX1 B-precursor ALL


title: SJETV098

description: ETV6-RUNX1 B-precursor ALL


title: SJTALL029

description: T-lineage ALL


title: SJTALL007

description: T-lineage ALL


title: SJTALL028

description: T-lineage ALL


title: SJTALL031

description: T-lineage ALL


title: SJTALL085

description: T-lineage ALL


title: SJTALL014

description: T-lineage ALL


title: SJTALL221

description: T-lineage ALL


title: SJTALL010

description: T-lineage ALL


title: SJETV103

description: ETV6-RUNX1 B-precursor ALL


title: SJETV021

description: ETV6-RUNX1 B-precursor ALL


title: SJTALL009

description: T-lineage ALL


title: SJTALL030

description: T-lineage ALL


title: SJTALL035

description: T-lineage ALL


title: SJTALL006

description: T-lineage ALL


title: SJTALL026

description: T-lineage ALL


title: SJTALL002

description: T-lineage ALL


title: SJTALL216

description: T-lineage ALL


title: SJTALL025

description: T-lineage ALL


title: SJTALL218

description: T-lineage ALL


title: SJTALL005

description: T-lineage ALL


title: SJTALL215

description: T-lineage ALL


title: SJTALL048

description: T-lineage ALL


title: SJTALL055

description: T-lineage ALL


title: SJTALL056

description: T-lineage ALL


title: SJTALL040

description: T-lineage ALL


title: SJTALL074

description: T-lineage ALL


title: SJTALL081

description: T-lineage ALL


title: SJTALL024

description: T-lineage ALL


title: SJTALL008

description: T-lineage ALL


title: SJTALL087

description: T-lineage ALL


title: SJTALL004

description: T-lineage ALL


title: SJTALL086

description: T-lineage ALL


title: SJBALL059

description: B-precursor ALL with miscellaneous karyotype


title: SJBALL081


title: SJBALL210


title: SJBALL071


title: SJBALL205


title: SJTALL089


title: SJBALL058


title: SJBALL080


title: SJBALL082


title: SJBALL061


title: SJBALL057


title: SJBALL079


title: SJTALL222

description: T-lineage ALL


title: SJHYPER198

description: High hyperdiploid B-precursor ALL


title: SJHYPO106

description: B-precursor ALL with hypodiploid karyotype


title: SJBALL054


title: SJBALL055


title: SJBALL056


title: SJBALL052


title: SJERG012


title: SJBALL047


title: SJBALL049


title: SJBALL048


title: SJBALL046


title: SJBALL045


title: SJBALL053


title: SJBALL050


title: SJINF077


title: SJBALL038


title: SJBALL044


title: SJBALL041


title: SJERG011


title: SJMLL039

description: MLL-rearranged B-precursor ALL


title: SJBALL020


title: SJERG010


title: SJBALL043


title: SJBALL030


title: SJBALL121


title: SJBALL022


title: SJBALL118


title: SJBALL040


title: SJERG009


title: SJBALL021


title: SJBALL042


title: SJHYPO145


title: SJERG022


title: SJBALL119


title: SJBALL116


title: SJBALL117


title: SJBALL037


title: SJBALL105


title: SJBALL107


title: SJBALL115


title: SJHYPO143


title: SJHYPO126


title: SJBALL104


title: SJERG019


title: SJBALL111


title: SJBALL103


title: SJBALL099


title: SJERG020


title: SJBALL102


title: SJERG017


title: SJBALL098


title: SJHYPO140


title: SJERG018


title: SJERG016


title: SJBALL100


title: SJBALL095


title: SJBALL097


title: SJBALL092


title: SJERG015


title: SJERG014


title: SJBALL090


title: SJBALL089


title: SJBALL093


title: SJBALL094


title: SJBALL086


title: SJBALL087


title: SJBALL084


title: SJBALL012


title: SJMLL033

description: MLL-rearranged B-precursor ALL


title: SJBALL083


title: SJBALL088


title: SJERG013


title: SJHYPO123


title: SJMLL004

description: MLL-rearranged B-precursor ALL


title: SJBALL085


title: SJHYPO124


title: SJMLL032

description: MLL-rearranged B-precursor ALL


title: SJBALL014


title: SJMLL016

description: MLL-rearranged B-precursor ALL


title: SJINF055

description: MLL-rearranged B-precursor ALL


title: SJMLL024

description: MLL-rearranged B-precursor ALL


title: SJINF069

description: MLL-rearranged B-precursor ALL


title: SJMLL037

description: MLL-rearranged B-precursor ALL


title: SJMLL023

description: MLL-rearranged B-precursor ALL


title: SJHYPO129


title: SJMLL031

description: MLL-rearranged B-precursor ALL


title: SJMLL029

description: MLL-rearranged B-precursor ALL


title: SJBALL160


title: SJBALL162


title: SJHYPER201

description: High hyperdiploid B-precursor ALL


title: SJBALL208


title: SJBALL211


title: SJBALL155


title: SJBALL159


title: SJHYPER022

description: High hyperdiploid B-precursor ALL


title: SJHYPER023

description: High hyperdiploid B-precursor ALL


title: SJHYPER060

description: High hyperdiploid B-precursor ALL


title: SJHYPER086

description: High hyperdiploid B-precursor ALL


title: SJHYPER148

description: High hyperdiploid B-precursor ALL


title: SJHYPER149

description: High hyperdiploid B-precursor ALL


title: SJHYPER141

description: High hyperdiploid B-precursor ALL


title: SJHYPER143

description: High hyperdiploid B-precursor ALL


title: SJHYPER135

description: High hyperdiploid B-precursor ALL


title: SJHYPER145

description: High hyperdiploid B-precursor ALL


title: SJHYPER048

description: High hyperdiploid B-precursor ALL


title: SJHYPER065

description: High hyperdiploid B-precursor ALL


title: SJHYPER153

description: High hyperdiploid B-precursor ALL


title: SJHYPER146

description: High hyperdiploid B-precursor ALL


title: SJHYPER150

description: High hyperdiploid B-precursor ALL


title: SJHYPER130

description: High hyperdiploid B-precursor ALL


title: SJHYPER020

description: High hyperdiploid B-precursor ALL


title: SJHYPER131

description: High hyperdiploid B-precursor ALL


title: SJHYPER136

description: High hyperdiploid B-precursor ALL


title: SJHYPER129

description: High hyperdiploid B-precursor ALL


title: SJHYPER128

description: High hyperdiploid B-precursor ALL


title: SJHYPER127

description: High hyperdiploid B-precursor ALL


title: SJHYPER126

description: High hyperdiploid B-precursor ALL


title: SJHYPER137

description: High hyperdiploid B-precursor ALL


title: SJHYPER122

description: High hyperdiploid B-precursor ALL


title: SJHYPER124

description: High hyperdiploid B-precursor ALL


title: SJHYPER123

description: High hyperdiploid B-precursor ALL


title: SJHYPER120

description: High hyperdiploid B-precursor ALL


title: SJHYPER119

description: High hyperdiploid B-precursor ALL


title: SJHYPER118

description: High hyperdiploid B-precursor ALL


title: SJHYPER117

description: High hyperdiploid B-precursor ALL


title: SJHYPER125

description: High hyperdiploid B-precursor ALL


title: SJHYPER116

description: High hyperdiploid B-precursor ALL


title: SJHYPER108

description: High hyperdiploid B-precursor ALL


title: SJHYPER112

description: High hyperdiploid B-precursor ALL


title: SJHYPER104

description: High hyperdiploid B-precursor ALL


title: SJHYPER109

description: High hyperdiploid B-precursor ALL


title: SJHYPER110

description: High hyperdiploid B-precursor ALL


title: SJHYPER102

description: High hyperdiploid B-precursor ALL


title: SJHYPER092

description: High hyperdiploid B-precursor ALL


title: SJHYPER103

description: High hyperdiploid B-precursor ALL


title: SJHYPER101

description: High hyperdiploid B-precursor ALL


title: SJHYPER094

description: High hyperdiploid B-precursor ALL


title: SJHYPER106

description: High hyperdiploid B-precursor ALL


title: SJHYPER121

description: High hyperdiploid B-precursor ALL


title: SJHYPER096

description: High hyperdiploid B-precursor ALL


title: SJHYPER091

description: High hyperdiploid B-precursor ALL


title: SJHYPER100

description: High hyperdiploid B-precursor ALL


title: SJHYPER111

description: High hyperdiploid B-precursor ALL


title: SJHYPER089

description: High hyperdiploid B-precursor ALL


title: SJHYPER097

description: High hyperdiploid B-precursor ALL


title: SJHYPER093

description: High hyperdiploid B-precursor ALL


title: SJHYPER010

description: High hyperdiploid B-precursor ALL


title: SJE2A031

description: TCF3-PBX1 B-precursor ALL


title: SJE2A032

description: TCF3-PBX1 B-precursor ALL


title: SJE2A026

description: TCF3-PBX1 B-precursor ALL


title: SJE2A028

description: TCF3-PBX1 B-precursor ALL


title: SJE2A034

description: TCF3-PBX1 B-precursor ALL


title: SJE2A036

description: TCF3-PBX1 B-precursor ALL


title: SJE2A022

description: TCF3-PBX1 B-precursor ALL


title: SJE2A024

description: TCF3-PBX1 B-precursor ALL


title: SJE2A035

description: TCF3-PBX1 B-precursor ALL


title: SJE2A030

description: TCF3-PBX1 B-precursor ALL


title: SJDOWN014


title: SJE2A025

description: TCF3-PBX1 B-precursor ALL


title: SJE2A009

description: TCF3-PBX1 B-precursor ALL


title: SJDOWN010


title: SJE2A041

description: TCF3-PBX1 B-precursor ALL


title: SJDOWN012


title: SJE2A040

description: TCF3-PBX1 B-precursor ALL


title: SJDOWN011

description: ETV6-RUNX1 B-precursor ALL


title: SJE2A039

description: TCF3-PBX1 B-precursor ALL


title: SJPHALL015

description: BCR-ABL1 B-precursor ALL


title: SJPHALL016

description: BCR-ABL1 B-precursor ALL


title: Acute Myeloid Leukemia, sample 77

status: Public on Jan 05 2012

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

hyb_protocol: 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: The data were analyzed with MASv5 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: AML blasts from bone marrow (at diagnosis), wild-type NPM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: RNA was extracted directly from fresh AML blasts.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen).

value: AML blasts from bone marrow

tag: set

value: test

tag: npm status

value: wild-type

tag: fab classification

tag: flt3 status

value: WT


title: Acute Myeloid Leukemia, sample 78


title: SJPHALL014

description: BCR-ABL1 B-precursor ALL


title: SJPHALL013

description: BCR-ABL1 B-precursor ALL


title: SJPHALL012

description: BCR-ABL1 B-precursor ALL


title: Acute Myeloid Leukemia, sample 75

value: internal tandem duplication (ITD)


title: Acute Myeloid Leukemia, sample 73


title: Acute Myeloid Leukemia, sample 76


title: Acute Myeloid Leukemia, sample 74


title: Acute Myeloid Leukemia, sample 71


title: Acute Myeloid Leukemia, sample 72


title: Acute Myeloid Leukemia, sample 67

source_name: AML blasts from bone marrow (at diagnosis), mutated NPM

value: mutated

value: internal tandem duplication (ITD)/D835 mutation


title: Acute Myeloid Leukemia, sample 69


title: Acute Myeloid Leukemia, sample 59


title: Acute Myeloid Leukemia, sample 68


title: Acute Myeloid Leukemia, sample 60


title: Acute Myeloid Leukemia, sample 62


title: Acute Myeloid Leukemia, sample 70


title: Acute Myeloid Leukemia, sample 66


title: Acute Myeloid Leukemia, sample 64


title: Acute Myeloid Leukemia, sample 58


title: Acute Myeloid Leukemia, sample 65


title: Acute Myeloid Leukemia, sample 63


title: Acute Myeloid Leukemia, sample 56


title: Acute Myeloid Leukemia, sample 54


title: Acute Myeloid Leukemia, sample 61


title: Acute Myeloid Leukemia, sample 52


title: Acute Myeloid Leukemia, sample 53


title: Acute Myeloid Leukemia, sample 51


title: Acute Myeloid Leukemia, sample 45


title: Acute Myeloid Leukemia, sample 46

value: D835 mutation


title: Acute Myeloid Leukemia, sample 44


title: Acute Myeloid Leukemia, sample 50


title: Acute Myeloid Leukemia, sample 47


title: Acute Myeloid Leukemia, sample 43


title: SJE2A027

description: TCF3-PBX1 B-precursor ALL


title: Acute Myeloid Leukemia, sample 42


title: Acute Myeloid Leukemia, sample 41


title: Acute Myeloid Leukemia, sample 36

value: training


title: Acute Myeloid Leukemia, sample 34


title: Acute Myeloid Leukemia, sample 35


title: Acute Myeloid Leukemia, sample 40


title: Acute Myeloid Leukemia, sample 30


title: Acute Myeloid Leukemia, sample 29


title: Acute Myeloid Leukemia, sample 38


title: Acute Myeloid Leukemia, sample 48


title: Acute Myeloid Leukemia, sample 31


title: Acute Myeloid Leukemia, sample 39


title: Acute Myeloid Leukemia, sample 32


title: Acute Myeloid Leukemia, sample 33


title: Acute Myeloid Leukemia, sample 37


title: Acute Myeloid Leukemia, sample 26


title: Acute Myeloid Leukemia, sample 28


title: Acute Myeloid Leukemia, sample 27


title: Acute Myeloid Leukemia, sample 25


title: Acute Myeloid Leukemia, sample 22


title: Acute Myeloid Leukemia, sample 21


title: Acute Myeloid Leukemia, sample 24


title: Acute Myeloid Leukemia, sample 23


title: Acute Myeloid Leukemia, sample 19


title: Acute Myeloid Leukemia, sample 18


title: Acute Myeloid Leukemia, sample 20


title: Acute Myeloid Leukemia, sample 14


title: Acute Myeloid Leukemia, sample 16


title: Acute Myeloid Leukemia, sample 49


title: Acute Myeloid Leukemia, sample 12


title: Acute Myeloid Leukemia, sample 11


title: Acute Myeloid Leukemia, sample 3


title: Acute Myeloid Leukemia, sample 6


title: Acute Myeloid Leukemia, sample 7


title: Acute Myeloid Leukemia, sample 8


title: Acute Myeloid Leukemia, sample 13


title: Acute Myeloid Leukemia, sample 9


title: Acute Myeloid Leukemia, sample 10


title: Acute Myeloid Leukemia, sample 15


title: Acute Myeloid Leukemia, sample 2


title: Acute Myeloid Leukemia, sample 1


title: Acute Myeloid Leukemia, sample 5


title: Acute Myeloid Leukemia, sample 4


title: Acute Myeloid Leukemia, sample 57


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR12

status: Public on Jan 01 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: PBMC from K-CR group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: The labelled arrays were scanned with a Gene chip scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) 'affy' in R.2.9.1

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted from peripheral blood using the TRIzol method (Invitrogen, Cergy Pontoise, France). Genomic DNA was removed by DNase treatment (Roche, Indianapolis, IN, USA). RNA quality and quantity was determined using an Agilent 2100 BioAnalyzer (Palo Alto, CA, USA). RNA was reverse transcribed into cDNA using polydT oligonucleotide and Maloney leukemia virus reverse transcription (Invitrogen).

treatment_protocol: Ficoll PBMC isolation from peripheral blood

tag: immunotolerance group

value: K-CR

tag: outcome

value: Peripheral blood mononuclear cells


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR11

description: PBMC from K-CR group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR07

description: PBMC from K-CR group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL07

description: PBMC from L-NonTol group

value: L-NonTol

value: Liver recipients in whom drug weaning was attempted but this led to an acute rejection episode requiring reinstitution of immunosuppression


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL12

description: PBMC from L-NonTol group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL09

description: PBMC from L-NonTol group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR10

description: PBMC from K-CR group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL06

description: PBMC from L-NonTol group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR06

description: PBMC from K-CR group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR01

description: PBMC from K-CR group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL11

description: PBMC from L-Tol group

value: L-Tol

value: Liver recipients maintaining stable graft function in the absence of immunosuppressive therapy


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL04

description: PBMC from L-NonTol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL10

description: PBMC from L-Tol group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL03

description: PBMC from L-NonTol group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL11

description: PBMC from L-NonTol group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR03

description: PBMC from K-CR group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL05

description: PBMC from L-NonTol group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR05

description: PBMC from K-CR group


title: Acute Myeloid Leukemia, sample 55


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR02

description: PBMC from K-CR group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL08

description: PBMC from L-NonTol group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR04

description: PBMC from K-CR group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR08

description: PBMC from K-CR group


title: kidney recipients under standard immunosuppression with deteriorating kidney graft function KCR09

description: PBMC from K-CR group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL02

description: PBMC from L-NonTol group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL01

description: PBMC from L-NonTol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL09

description: PBMC from L-Tol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL12

description: PBMC from L-Tol group


title: liver recipients with attempted drug weaning that led to acute rejection and reinstitution of immunosuppression LNTOL10

description: PBMC from L-NonTol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL06

description: PBMC from L-Tol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL01

description: PBMC from L-Tol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL03

description: PBMC from L-Tol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL04

description: PBMC from L-Tol group


title: CD10CD19_4

status: Public on Oct 28 2011

description: Adult normal bone marrow; CD19 (+) CD10(+)

source_name: Adult normal bone marrow

value: sorted CD10(+) CD19(+) cells


title: T-ALL-SNP-#26

status: Public on Dec 12 2011

value: leukemic cells obtained from bone marrow or blood at diagnosis

value: T-lineage ALL


title: CD10CD19_2


title: Pseudodip-SNP-#09

source_name: RNA extracted from tumor with alteration of ERG

value: tumor with alteration of ERG


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL02

description: PBMC from L-Tol group


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL05

description: PBMC from L-Tol group


title: CD10CD19_3


title: TEL-AML1-SNP-#25

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: Pseudodip-SNP-#11

source_name: RNA extracted from B-precursor ALL with pseudodiploid karyotype


title: Hyperdip47-50-SNP-#14

value: childhood ALL with CRLF2 rearrangement


title: BCR-ABL-SNP-#07

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with BCR-ABL1 rearrangement


title: T-ALL-SNP-#25


title: Hyperdip47-50-SNP-#15


title: CD10CD19_1


title: Hyperdip>50-SNP-#18

value: childhood ALL with high hyperdiploid karyotype


title: Pseudodip-SNP-#10

value: B-precursor ALL with pseudodiploid karyotype


title: BCR-ABL-SNP-#06

value: childhood ALL with BCR-ABL1 rearrangement


title: MLL-SNP-#05

source_name: RNA extracted from tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement

value: childhood ALL with MLL rearrangement