title: Non-Tobacco_User_replicate_29

status: Public on Feb 20 2017

hyb_protocol: Following fragmentation, cRNA was hybridized using SeqWright SOP LAB.58.15 according to Affymetrix protocols.  GeneChips were washed and stained in the Affymetrix Fluidics Station F450.

scan_protocol: The raw image was acquired by scanning the arrays using Affymetrix 7G Plus Scanner as per SeqWright SOPs LAB.58.16 and Multiple files were generated and exported by Affymetrix’s software Command console and Expression Console as per SeqWright SOP LAB.58.17.

data_processing: The Affymetrix .CEL files were imported and analyzed using Partek’s Genomics Suite software. All data were normalized using the Robust Multi-array Analysis expression statistical analysis (RMA).

label_protocol: One hundred ng of total RNA from each sample was used for double-stranded cDNA synthesis,using Affymetrix 3' IVT Express kit.

growth_protocol: PBMCs were isolated from the fresh blood collected from subjects by standard density gradient centrifugation by using Isolymph (CTL Scientific  Supply Corp., Deer Park, NY).

extract_protocol: The total RNA was isolated from frozen cell lysate using the Qiagen RNeasy Plus Mini kit (Qiagen Cat. No. 74134) as per SeqWright SOP LAB.50.16.

treatment_protocol: The three cohorts in this study were Cigarette Smokers (Smk), Moist snuff consumers (MSC) and Non-tobacco consumers (NTC).

tag: subject status

value: generally healthy

tag: gender

value: male

tag: sample group

value: Peripheral blood mononuclear cells (PBMCs)


title: Non-Tobacco_User_replicate_28

type: RNA

city: Winston-Salem

first: Gaddamanugu

middle: L

last: Prasad

state: NC

country: USA

institute: RAI Services Company

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: age

tag: cell type


title: Non-Tobacco_User_replicate_37


title: Non-Tobacco_User_replicate_39


title: Non-Tobacco_User_replicate_32


title: Non-Tobacco_User_replicate_25


title: Non-Tobacco_User_replicate_30


title: Non-Tobacco_User_replicate_23


title: Non-Tobacco_User_replicate_31


title: Non-Tobacco_User_replicate_34


title: Non-Tobacco_User_replicate_26


title: Non-Tobacco_User_replicate_24


title: Non-Tobacco_User_replicate_21


title: Non-Tobacco_User_replicate_38


title: Non-Tobacco_User_replicate_36


title: Non-Tobacco_User_replicate_35


title: Non-Tobacco_User_replicate_33


title: Non-Tobacco_User_replicate_27


title: Non-Tobacco_User_replicate_22


title: Non-Tobacco_User_replicate_18


title: Non-Tobacco_User_replicate_16


title: Non-Tobacco_User_replicate_19


title: Non-Tobacco_User_replicate_13


title: Non-Tobacco_User_replicate_15


title: Non-Tobacco_User_replicate_17


title: Non-Tobacco_User_replicate_11


title: Non-Tobacco_User_replicate_10


title: Non-Tobacco_User_replicate_8


title: Non-Tobacco_User_replicate_12


title: Non-Tobacco_User_replicate_9


title: Non-Tobacco_User_replicate_7


title: Non-Tobacco_User_replicate_6


title: Non-Tobacco_User_replicate_5


title: Moist_Snuff_User_replicate_40


title: Non-Tobacco_User_replicate_1


title: Non-Tobacco_User_replicate_14


title: Non-Tobacco_User_replicate_2


title: Non-Tobacco_User_replicate_4


title: Moist_Snuff_User_replicate_39


title: Moist_Snuff_User_replicate_32


title: Moist_Snuff_User_replicate_37


title: Moist_Snuff_User_replicate_35


title: Non-Tobacco_User_replicate_3


title: Moist_Snuff_User_replicate_33


title: Moist_Snuff_User_replicate_24


title: Moist_Snuff_User_replicate_31


title: Moist_Snuff_User_replicate_36


title: Moist_Snuff_User_replicate_38


title: Moist_Snuff_User_replicate_25


title: Moist_Snuff_User_replicate_21


title: Moist_Snuff_User_replicate_28


title: Moist_Snuff_User_replicate_29


title: Moist_Snuff_User_replicate_19


title: Moist_Snuff_User_replicate_23


title: Moist_Snuff_User_replicate_26


title: Moist_Snuff_User_replicate_34


title: Moist_Snuff_User_replicate_22


title: Moist_Snuff_User_replicate_20


title: Moist_Snuff_User_replicate_27


title: Moist_Snuff_User_replicate_18


title: Moist_Snuff_User_replicate_30


title: Non-Tobacco_User_replicate_20


title: Moist_Snuff_User_replicate_17


title: Moist_Snuff_User_replicate_16


title: Moist_Snuff_User_replicate_9


title: Moist_Snuff_User_replicate_13


title: Moist_Snuff_User_replicate_12


title: Moist_Snuff_User_replicate_15


title: Moist_Snuff_User_replicate_7


title: Moist_Snuff_User_replicate_10


title: Moist_Snuff_User_replicate_8


title: Moist_Snuff_User_replicate_5


title: Cigarette_Smoker_replicate_39


title: Moist_Snuff_User_replicate_2


title: Moist_Snuff_User_replicate_3


title: Moist_Snuff_User_replicate_4


title: Cigarette_Smoker_replicate_37


title: Moist_Snuff_User_replicate_1


title: Moist_Snuff_User_replicate_6


title: Cigarette_Smoker_replicate_40


title: Cigarette_Smoker_replicate_35


title: Cigarette_Smoker_replicate_36


title: Cigarette_Smoker_replicate_38


title: Cigarette_Smoker_replicate_34


title: Cigarette_Smoker_replicate_31


title: Cigarette_Smoker_replicate_33


title: Cigarette_Smoker_replicate_30


title: Cigarette_Smoker_replicate_32


title: Cigarette_Smoker_replicate_13


title: Cigarette_Smoker_replicate_26


title: Cigarette_Smoker_replicate_22


title: Cigarette_Smoker_replicate_29


title: Cigarette_Smoker_replicate_12


title: Cigarette_Smoker_replicate_20


title: Cigarette_Smoker_replicate_28


title: Cigarette_Smoker_replicate_17


title: Cigarette_Smoker_replicate_16


title: Cigarette_Smoker_replicate_21


title: Cigarette_Smoker_replicate_15


title: Cigarette_Smoker_replicate_14


title: Cigarette_Smoker_replicate_27


title: Cigarette_Smoker_replicate_18


title: Cigarette_Smoker_replicate_25


title: Cigarette_Smoker_replicate_24


title: Cigarette_Smoker_replicate_11


title: Cigarette_Smoker_replicate_19


title: Cigarette_Smoker_replicate_9


title: Moist_Snuff_User_replicate_11


title: Moist_Snuff_User_replicate_14


title: Cigarette_Smoker_replicate_7


title: Cigarette_Smoker_replicate_10


title: Cigarette_Smoker_replicate_6


title: Sample36889 (array)

status: Public on Nov 30 2016

city: Duarte

first: Susan

last: Neuhausen

state: California

address: 1500 E duarte road

department: Population Sciences

institute: City of hope

description: Gene expresssion data, FFPE samples

scan_protocol: scanned beadchips using the iScan software on the HiScan

data_processing:
Raw Illumina HumanHT-12 WG-DASL V4.0 gene expression values were produced using GenomeStudio with background correction.  Exported gene-level expression values were then quantile normalized and batch-corrected using ComBat.
GenomeStudio processed log2 signal intensity, annotated using HumanHT-12_V4_0_R2_15002873_B_WGDASL.bgx

source_name: FFPE prostatectomy

growth_protocol: clinical samples

extract_protocol: RecoverAll™ Total Nucleic Acid Isolation kit (Life Technology Inc.)

treatment_protocol: untreated

tag: patientid

tag: tissue

value: tumor

tag: Stage

tag: gleason

tag: psa

tag: race

value: White

tag: ethnicity

value: Non-Hispanic


title: Sample36853 (array)

description: Gene expresssion data, FFPE samples


title: Sample36904 (array)

description: Gene expresssion data, FFPE samples

value: normal


title: Cigarette_Smoker_replicate_8


title: Sample36929 (array)

description: Gene expresssion data, FFPE samples


title: Sample36922 (array)

description: Gene expresssion data, FFPE samples


title: Sample36925 (array)

description: Gene expresssion data, FFPE samples


title: Sample36923 (array)

description: Gene expresssion data, FFPE samples


title: Sample36863 (array)

description: Gene expresssion data, FFPE samples

value: African-American


title: Cigarette_Smoker_replicate_4


title: Sample36928 (array)

description: Gene expresssion data, FFPE samples


title: Sample36903 (array)

description: Gene expresssion data, FFPE samples


title: Sample36947 (array)

description: Gene expresssion data, FFPE samples


title: Cigarette_Smoker_replicate_2


title: Sample36854 (array)

description: Gene expresssion data, FFPE samples


title: Sample36890 (array)

description: Gene expresssion data, FFPE samples


title: Cigarette_Smoker_replicate_5


title: Sample36948 (array)

description: Gene expresssion data, FFPE samples


title: Cigarette_Smoker_replicate_1


title: Sample36973 (array)

description: Gene expresssion data, FFPE samples


title: Sample36851 (array)

description: Gene expresssion data, FFPE samples


title: Sample36855 (array)

description: Gene expresssion data, FFPE samples


title: Sample36926 (array)

description: Gene expresssion data, FFPE samples

value: Hispanic


title: Sample36914 (array)

description: Gene expresssion data, FFPE samples


title: Sample36974 (array)

description: Gene expresssion data, FFPE samples


title: Sample36927 (array)

description: Gene expresssion data, FFPE samples


title: Sample36864 (array)

description: Gene expresssion data, FFPE samples


title: Sample36862 (array)

description: Gene expresssion data, FFPE samples


title: Sample36924 (array)

description: Gene expresssion data, FFPE samples


title: Sample36858 (array)

description: Gene expresssion data, FFPE samples


title: Cigarette_Smoker_replicate_3


title: Sample36856 (array)

description: Gene expresssion data, FFPE samples


title: Sample36915 (array)

description: Gene expresssion data, FFPE samples


title: Sample36967 (array)

description: Gene expresssion data, FFPE samples


title: Sample36869 (array)

description: Gene expresssion data, FFPE samples


title: Sample36852 (array)

description: Gene expresssion data, FFPE samples


title: Sample36860 (array)

description: Gene expresssion data, FFPE samples


title: Sample36857 (array)

description: Gene expresssion data, FFPE samples


title: Sample36961 (array)

description: Gene expresssion data, FFPE samples


title: Sample36902 (array)

description: Gene expresssion data, FFPE samples


title: Sample36861 (array)

description: Gene expresssion data, FFPE samples


title: Sample36870 (array)

description: Gene expresssion data, FFPE samples


title: Sample36950 (array)

description: Gene expresssion data, FFPE samples

value: Asian


title: Sample36900 (array)

description: Gene expresssion data, FFPE samples


title: Sample36959 (array)

description: Gene expresssion data, FFPE samples


title: Sample36867 (array)

description: Gene expresssion data, FFPE samples


title: Sample36969 (array)

description: Gene expresssion data, FFPE samples


title: Sample36874 (array)

description: Gene expresssion data, FFPE samples


title: Cigarette_Smoker_replicate_23


title: Sample36873 (array)

description: Gene expresssion data, FFPE samples


title: Sample36872 (array)

description: Gene expresssion data, FFPE samples


title: Sample36875 (array)

description: Gene expresssion data, FFPE samples


title: Sample36866 (array)

description: Gene expresssion data, FFPE samples


title: Sample36930 (array)

description: Gene expresssion data, FFPE samples


title: Sample36955 (array)

description: Gene expresssion data, FFPE samples


title: Sample36871 (array)

description: Gene expresssion data, FFPE samples


title: Sample36931 (array)

description: Gene expresssion data, FFPE samples


title: Sample36956 (array)

description: Gene expresssion data, FFPE samples


title: Sample36958 (array)

description: Gene expresssion data, FFPE samples


title: Sample36953 (array)

description: Gene expresssion data, FFPE samples


title: Sample36935 (array)

description: Gene expresssion data, FFPE samples


title: Sample36919 (array)

description: Gene expresssion data, FFPE samples


title: Sample36934 (array)

description: Gene expresssion data, FFPE samples


title: Sample36906 (array)

description: Gene expresssion data, FFPE samples


title: Sample36918 (array)

description: Gene expresssion data, FFPE samples


title: Sample36932 (array)

description: Gene expresssion data, FFPE samples


title: Sample36942 (array)

description: Gene expresssion data, FFPE samples


title: Sample36881 (array)

description: Gene expresssion data, FFPE samples


title: Sample36920 (array)

description: Gene expresssion data, FFPE samples


title: Sample36908 (array)

description: Gene expresssion data, FFPE samples


title: Sample36882 (array)

description: Gene expresssion data, FFPE samples


title: Sample36916 (array)

description: Gene expresssion data, FFPE samples


title: Sample36901 (array)

description: Gene expresssion data, FFPE samples


title: Sample36917 (array)

description: Gene expresssion data, FFPE samples


title: Sample36921 (array)

description: Gene expresssion data, FFPE samples


title: Sample36877 (array)

description: Gene expresssion data, FFPE samples


title: Sample36907 (array)

description: Gene expresssion data, FFPE samples


title: Sample36880 (array)

description: Gene expresssion data, FFPE samples


title: Sample36878 (array)

description: Gene expresssion data, FFPE samples


title: Sample36943 (array)

description: Gene expresssion data, FFPE samples


title: Sample36905 (array)

description: Gene expresssion data, FFPE samples


title: Sample36884 (array)

description: Gene expresssion data, FFPE samples


title: Sample36885 (array)

description: Gene expresssion data, FFPE samples


title: Sample36910 (array)

description: Gene expresssion data, FFPE samples


title: Sample36966 (array)

description: Gene expresssion data, FFPE samples


title: Sample36965 (array)

description: Gene expresssion data, FFPE samples


title: Sample36891 (array)

description: Gene expresssion data, FFPE samples


title: Sample36893 (array)

description: Gene expresssion data, FFPE samples


title: Sample36895 (array)

description: Gene expresssion data, FFPE samples


title: Sample36887 (array)

description: Gene expresssion data, FFPE samples


title: Sample36894 (array)

description: Gene expresssion data, FFPE samples


title: Sample36888 (array)

description: Gene expresssion data, FFPE samples


title: Sample36886 (array)

description: Gene expresssion data, FFPE samples


title: Sample36892 (array)

description: Gene expresssion data, FFPE samples


title: Sample36909 (array)

description: Gene expresssion data, FFPE samples


title: Sample36896 (array)

description: Gene expresssion data, FFPE samples


title: Sample36883 (array)

description: Gene expresssion data, FFPE samples


title: Sample36939 (array)

description: Gene expresssion data, FFPE samples


title: Sample36876 (array)

description: Gene expresssion data, FFPE samples


title: Sample36941 (array)

description: Gene expresssion data, FFPE samples


title: Sample36898 (array)

description: Gene expresssion data, FFPE samples


title: Sample36938 (array)

description: Gene expresssion data, FFPE samples


title: Sample36936 (array)

description: Gene expresssion data, FFPE samples


title: Sample36897 (array)

description: Gene expresssion data, FFPE samples


title: 49525hg133a11

status: Public on Sep 17 2016

city: Portland

first: Byung

last: Park

state: Oregon

address: 3181 SW Sam Jackson Park Rd. CR145

institute: Oregon Health & Science University

description: Expression data from mononuclear cells from bone marrow and peripheral blood

hyb_protocol: Sample pre-processing and array hybridization were performed according to the manufacturer’s directions.  The detailed protocol is available at the following url: http://www.affymetrix.com/support/technical/manuals.affx.

scan_protocol: Array were scanned using GeneArray Laser Scanner (Affymetrix).

data_processing: The data were normalized using RMA.

source_name: PRE B-ALL (Set A)

label_protocol:
Each RNA sample was labeled by synthesizing complementary cDNA and converted to labeled complementary RNA using T7 RNA polymerase in the presence of biotinylated UTP (Affymetrix).
This cRNA is used as the target for microarray fragmentation and hybridization.

growth_protocol: The samples were obtained fresh in the operating room

extract_protocol: Approximately 10X106  cells per case were used for the extraction of total RNA by RNeasy Micro kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: All blood and bone marrow have been subjected to ficoll density centrifugation and frozen viable cells were prepared in DMSO+FCS+RPMI and stored over liquid nitrogen. Tissue samples have been minced and a cell suspension was prepared.  Cell suspension was then stored as frozen viable cells in DMSO+FCS+RPMI and stored in liquid nitrogen

value: Bone marrow

tag: risk group

value: PRE B-ALL


title: 52564hg133a11

source_name: T-ALL (Set A)

value: T-ALL


title: 52576hg133a11

value: Peripheral blood


title: 52566hg133a11


title: 101286hg133a11


title: 52567hg133a11


title: 101284hg133a11


title: 53837hg133a11


title: 52573hg133a11


title: 52565hg133a11


title: 53835hg133a11


title: 101289hg133a11


title: 101288hg133a11


title: 52568hg133a11


title: 101287hg133a11


title: 52572hg133a11


title: 101285hg133a11


title: 49526hg133a11


title: 52571hg133a11


title: 101290hg133a11


title: 52577hg133a11


title: 49524hg133a11


title: 101292hg133a11


title: 101280hg133a11


title: 101281hg133a11


title: 101282hg133a11


title: 101283hg133a11


title: 49523hg133a11


title: Sample36933 (array)

description: Gene expresssion data, FFPE samples


title: 101279hg133a11


title: 58858hg133a21

source_name: MDS (Set A)

value: MDS


title: 58856hg133a11


title: 54079hg133a11

source_name: CML (Set A)

value: CML


title: 58851hg133a11


title: 53832hg133a11


title: 54075hg133a11


title: 58854hg133a11


title: 58849hg133a11


title: 58850hg133a11


title: 52590hg133a11


title: 58852hg133a11


title: 58853hg133a11


title: 52592hg133a11


title: 54077hg133a11


title: 52588hg133a11


title: 54072hg133a11


title: 54069hg133a11


title: 54076hg133a11


title: 52582hg133a11


title: 52580hg133a11


title: 52586hg133a11


title: 58857hg133a11


title: 104902hg133a11


title: 58855hg133a11


title: 104900hg133a11


title: 52581hg133a11


title: 54080hg133a11


title: 53833hg133a11


title: 53834hg133a11


title: 103849hg133a11


title: 58224hg133a11

source_name: BCLL (Set A)

value: BCLL


title: 104897hg133a11


title: 58220hg133a11


title: 58222hg133a11


title: 103853hg133a11


title: 57708hg133a11


title: 58219hg133a11


title: 57712hg133a11


title: 58218hg133a11


title: 57702hg133a11


title: 49537hg133a11


title: 57709hg133a11


title: 57706hg133a11


title: 57699hg133a11


title: 49535hg133a11


title: 49531hg133a11


title: 49534hg133a11


title: 57707hg133a11


title: 57697hg133a11


title: 49536hg133a11


title: 49529hg133a11


title: 57700hg133a11


title: 49083hg133a11


title: 49082hg133a11


title: 49086hg133a31


title: 49084hg133a11


title: 49085hg133a11


title: 49080hg133a11


title: 49530hg133a11


title: 49087hg133a11


title: 49528hg133a11


title: 49079hg133a11


title: 103847hg133a11

value: Lymph Node


title: 49074hg133a11


title: 49075hg133a11


title: 57711hg133a11


title: 49081hg133a11


title: 103619hg133a11


title: 53819hg133a11

source_name: AML (Set A)

value: AML


title: 110528hg133a11


title: 48868hg133a11


title: 48867hg133a11


title: 48860hg133a11


title: 48873hg133a11


title: 48859hg133a11


title: 48872hg133a11


title: 48866hg133a11


title: 48864hg133a11


title: 48861hg133a21


title: 48865hg133a21


title: 48857hg133a11


title: 48862hg133a11


title: 48871hg133a11


title: 48863hg133a11


title: 48870hg133a11


title: 48856hg133a11


title: 104912hg133a11


title: 40615hg133a11


title: 40617hg133a21


title: 104913hg133a11


title: 104914hg133a11


title: 57710hg133a11


title: 48858hg133a11


title: 46883hg133a11


title: 40613hg133a11


title: 49076hg133a11


title: 49532hg133a11


title: 48854hg133a11


title: 48855hg133a11


title: 40614hg133a11


title: 104911hg133a11


title: orkin-00383: AML003

status: Public on Jun 17 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

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

source_name: PB

tag: sample

tag: ds

value: non-DS

tag: class

value: AML M4

value: 14 years

tag: source

value: PB

tag: %blast

tag: gata-1 sequence

value: nd


title: orkin-00383: DSTMD148

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

value: DS

value: DS TMD

value: 4 days

tag: Sex

value: M

tag: consequence

value: fs, translation from codon 84

tag: cytogenetics


title: orkin-00383: AML004

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

source_name: BM

tag: age

value: 42 months

value: BM


title: orkin-00383: DSTMD058

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

value: 2 days

value: F


title: 104907hg133a11

tag: tissue

value: Bone marrow


title: orkin-00383: AML002

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

value: 13 months


title: orkin-00383: AML005

value: 15 years


title: orkin-00383: AML006

value: non-DS

value: AML M5

value: 11 years


title: orkin-00383: AML009

value: 20 months

value: PB


title: orkin-00383: AML007

value: 5 years

value: nd


title: orkin-00383: DSTMD053

value: DS

value: DS TMD

value: 6 days


title: orkin-00383: AML001

value: AML M4

value: 20 years


title: orkin-00383: DSTMD052

value: 4 days

value: M

value: BM

value: fs, translation from codon 84


title: 104905hg133a11

value: Bone marrow

value: AML


title: 103855hg133a11


title: orkin-00383: DSTMD013


title: 104904hg133a11


title: orkin-00383: DSTMD017

value: 2 days


title: 104910hg133a11


title: orkin-00383: DSTMD012

value: 3 days

value: 173 del CT


title: orkin-00383: AMKL063

value: DS AML

value: 24 months

value: F

value: PB


title: orkin-00383: AMKL060

value: DS

value: first ATG deleted


title: orkin-00383: DSAMKL130

value: DS AMKL

value: 36 months


title: orkin-00383: DSAMKL132

value: 11 months

value: 285 del C, 285 ins 5 nt


title: 104909hg133a11


title: orkin-00383: DSAMKL133

value: 15 months

value: M


title: 104906hg133a11

value: Bone marrow


title: orkin-00383: DSAMKL128

value: nd


title: orkin-00383: DSAMKL127

value: 22 months

value: fs, translation from codon 84


title: orkin-00383: DSAMKL122

value: 23 months

value: 169 ins G


title: orkin-00383: DSAMKL126

value: 25 months

value: BM


title: orkin-00383: DSAMKL124

value: 16 months

value: F

value: PB

value: 158 ins G


title: orkin-00383: DSAMKL125

value: DS

value: DS AMKL

value: 27 months


title: orkin-00383: DSAMKL020

value: 8 months

value: 93 A to G

value: mutates first ATG


title: orkin-00383: DSAMKL120

value: 14 months

value: several del and ins


title: orkin-00383: DSAMKL121

value: 30 months

value: M

value: nd


title: orkin-00383: DSAMKL030

value: 18 months

value: 201del AG, 285 C to T

value: fs, translation from codon 84


title: orkin-00383: DSAMKL070

value: 20 months

value: F

value: 196 G to T

value: generates stop codon, translation from codon 84


title: orkin-00383: DSAMKL068

value: DS

value: DS AMKL

value: 26 months

value: PB

value: 262 ins C, 112 A to G

value: mutates first ATG, frame shift


title: orkin-00383: DSAMKL011

value: 10 months

value: BM


title: orkin-00383: DSAMKL129

value: 28 months


title: orkin-00383: AMKL057

value: 1 month

value: M

value: nd


title: orkin-00383: DSAMKL018

value: 13 months

value: 141 G to A


title: orkin-00383: DSAMKL019

value: 11 months

value: F


title: orkin-00383: DSAMKL015

value: 14 months


title: orkin-00383: AMKL069

value: non-DS

value: AMKL +21

value: 1 day

value: 112 A to G

value: mutates first ATG

value: trisomy 21, see note


title: orkin-00383: DSAMKL016

value: DS

value: DS AMKL

value: 15 months


title: orkin-00383: AMKL085

value: 1 month

value: BM

value: 264 ins GTGTG


title: orkin-00383: AMKL067

value: 19 months

value: M

value: PB

value: nd


title: orkin-00383: AMKL032

value: 2 months

value: wt


title: orkin-00383: AMKL039

value: non-DS

value: AMKL +21

value: 58 years


title: orkin-00383: AMKL025

value: 6 years

tag: notes

value: RBM15-MKL1 RT PCR neg

value: hypotetraploid 68~69,XXYY mit t(1;22)(p13;q13)


title: orkin-00383: AMKL042


title: orkin-00383: AMKL026

value: 3 months


title: orkin-00383: AMKL070

value: AMKL

value: 67 years

value: not available


title: orkin-00383: AMKL074

value: 76 years

value: F

value: Add(3q) detected on 3 mitosis


title: orkin-00383: AMKL096

value: 14 months

value: M

value: PB

value: same as 97


title: orkin-00383: AMKL097

value: non-DS

value: BM

value: nd

value: same as 96


title: orkin-00383: AMKL094

value: 70 years


title: orkin-00383: AMKL073

value: 56 years

value: monosomy 7


title: orkin-00383: AMKL086

value: AMKL

value: 6 years

value: normal


title: orkin-00383: AMKL072

value: 47 years

value: complex aberrations


title: orkin-00383: AMKL047

value: 38 months

value: not available


title: orkin-00383: AMKL066

value: 14 months

value: F

value: wt


title: orkin-00383: AMKL054

value: non-DS

value: 40 years


title: orkin-00383: AMKL082

value: 45 years.

value: M

value: BM


title: orkin-00383: AMKL044

value: 8 months


title: orkin-00383: AMKL041

value: 7 months


title: orkin-00383: AMKL045

value: AMKL

value: 3 months


title: orkin-00383: AMKL049

value: 11 months


title: orkin-00383: AMKL050

value: 18 month

value: normal


title: orkin-00383: AMKL036

value: 30 months

value: PB

value: same as 49, relapse


title: orkin-00383: AMKL037

value: 36 months


title: orkin-00383: AMKL040

value: 20 months

value: F

value: nd


title: orkin-00383: AMKL035

value: non-DS

value: wt


title: orkin-00383: AMKL033

value: 16 months

value: M

value: BM


title: orkin-00383: AMKL038

value: AMKL

value: 24 months


title: 104908hg133a11

value: Bone marrow

value: AML


title: orkin-00383: AMKL083

value: 22 months

value: not available


title: orkin-00383: AMKL031

value: 13 months


title: orkin-00383: AMKL029

value: 11 years


title: orkin-00383: AMKL046

value: 26 years


title: orkin-00383: AMKL048

value: 62 years


title: orkin-00383: AMKL028

value: 8 months

value: F

value: normal


title: orkin-00383: AMKL024

value: non-DS

value: 51 months

value: PB

value: nd

value: random aberration


title: orkin-00383: DSTMD014

value: DS

value: DS TMD

value: 9 days

value: BM

value: fs, translation from codon 84


title: orkin-00383: AMKL084

value: AMKL

value: 38 years

value: M

value: wt

value: not available


title: Patient #215, Day 8

status: Public on May 26 2016

city: Singapore

first: Allen Eng Juh

last: Yeoh

address: 14 Medical Drive, MD6 #09-02

department: Paediatrics

country: Singapore

institute: National University of Singapore

description: gene expression data at Day 8

hyb_protocol: Hybridization step was performed according to the Affymetrix 3' IVT PLUS Reagent Kit User Manual. Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A or -U133 Plus 2.0 array.

scan_protocol: Arrays were washed and stained using the Affymetrix Fluidics Station 450, and scanned using the GeneChip Scanner 3000 7G accroding to the manufacturer's instruction.

data_processing: Gene expression signal intensities were interrogated using the Affymetrix Expression Console software. Expression values were scaled to the target of 500 within the 22,277 probe sets that are common to both platforms. To reduce noise, a probe set was only retained if it is present in >30% of the samples. The remaining probe sets were then log transformed and quantile normalized.

source_name: bone marrow sample from child with acute lymphoblastic leukemia

label_protocol: Labeling step was performed according to the Affymetrix 3' IVT PLUS Reagent Kit User Manual.

extract_protocol: Total RNA was isolated using TRIzol reagent and purified using RNeasy Mini Kit according to respective manufacturer's instruction.

value: bone marrow

tag: time point

value: Day 8

tag: patient id

tag: dataset

value: Test set


title: Patient #220, Day 8

description: gene expression data at Day 8


title: Patient #215, Day 0

description: gene expression data at Day 0

value: Day 0


title: Patient #212, Day 0

description: gene expression data at Day 0


title: Patient #219, Day 8

description: gene expression data at Day 8


title: Patient #220, Day 0

description: gene expression data at Day 0


title: Patient #212, Day 8

description: gene expression data at Day 8


title: Patient #216, Day 8

description: gene expression data at Day 8


title: Patient #213, Day 0

description: gene expression data at Day 0


title: Patient #217, Day 0

description: gene expression data at Day 0


title: Patient #218, Day 8

description: gene expression data at Day 8


title: Patient #214, Day 0

description: gene expression data at Day 0


title: Patient #211, Day 8

description: gene expression data at Day 8


title: Patient #218, Day 0

description: gene expression data at Day 0


title: Patient #214, Day 8

description: gene expression data at Day 8


title: Patient #213, Day 8

description: gene expression data at Day 8


title: Patient #216, Day 0

description: gene expression data at Day 0


title: Patient #211, Day 0

description: gene expression data at Day 0


title: Patient #219, Day 0

description: gene expression data at Day 0


title: Patient #210, Day 0

description: gene expression data at Day 0


title: Patient #217, Day 8

description: gene expression data at Day 8


title: Patient #208, Day 0

description: gene expression data at Day 0


title: Patient #209, Day 8

description: gene expression data at Day 8


title: Patient #209, Day 0

description: gene expression data at Day 0


title: Patient #210, Day 8

description: gene expression data at Day 8


title: Patient #208, Day 8

description: gene expression data at Day 8


title: Patient #207, Day 8

description: gene expression data at Day 8


title: Patient #207, Day 0

description: gene expression data at Day 0


title: orkin-00383: AML008

value: non-DS

value: AML M5

value: 5 years

value: PB


title: Patient #203, Day 8

description: gene expression data at Day 8


title: Patient #203, Day 0

description: gene expression data at Day 0


title: Patient #204, Day 8

description: gene expression data at Day 8


title: Patient #206, Day 0

description: gene expression data at Day 0


title: Patient #201, Day 8

description: gene expression data at Day 8


title: Patient #199, Day 0

description: gene expression data at Day 0


title: Patient #198, Day 8

description: gene expression data at Day 8


title: Patient #198, Day 0

description: gene expression data at Day 0


title: Patient #202, Day 8

description: gene expression data at Day 8


title: Patient #197, Day 0

description: gene expression data at Day 0


title: Patient #200, Day 8

description: gene expression data at Day 8


title: Patient #204, Day 0

description: gene expression data at Day 0


title: Patient #200, Day 0

description: gene expression data at Day 0


title: Patient #195, Day 0

description: gene expression data at Day 0


title: Patient #202, Day 0

description: gene expression data at Day 0


title: Patient #194, Day 8

description: gene expression data at Day 8


title: Patient #196, Day 0

description: gene expression data at Day 0


title: Patient #205, Day 8

description: gene expression data at Day 8


title: Patient #201, Day 0

description: gene expression data at Day 0


title: Patient #193, Day 8

description: gene expression data at Day 8


title: Patient #196, Day 8

description: gene expression data at Day 8


title: Patient #193, Day 0

description: gene expression data at Day 0


title: Patient #192, Day 0

description: gene expression data at Day 0


title: Patient #195, Day 8

description: gene expression data at Day 8


title: Patient #194, Day 0

description: gene expression data at Day 0


title: Patient #197, Day 8

description: gene expression data at Day 8


title: Patient #206, Day 8

description: gene expression data at Day 8


title: Patient #110, Day 8

description: gene expression data at Day 8

tag: diagnosis

value: acute lymphoblastic leukemia

value: Training set


title: Patient #192, Day 8

description: gene expression data at Day 8


title: Patient #205, Day 0

description: gene expression data at Day 0


title: Patient #88, Day 0

description: gene expression data at Day 0


title: Patient #94, Day 8

description: gene expression data at Day 8


title: Patient #87, Day 0

description: gene expression data at Day 0


title: Patient #87, Day 8

description: gene expression data at Day 8


title: Patient #88, Day 8

description: gene expression data at Day 8


title: Patient #65, Day 0

description: gene expression data at Day 0


title: Patient #94, Day 0

description: gene expression data at Day 0


title: Patient #63, Day 8

description: gene expression data at Day 8


title: Patient #63, Day 0

description: gene expression data at Day 0


title: Patient #65, Day 8

description: gene expression data at Day 8


title: Patient #57, Day 0

description: gene expression data at Day 0


title: Patient #64, Day 8

description: gene expression data at Day 8


title: Patient #64, Day 0

description: gene expression data at Day 0


title: Patient #57, Day 8

description: gene expression data at Day 8


title: Patient #37, Day 8

description: gene expression data at Day 8


title: Patient #44, Day 0

description: gene expression data at Day 0


title: Patient #51, Day 0

description: gene expression data at Day 0


title: Patient #51, Day 8

description: gene expression data at Day 8


title: Patient #33, Day 8

description: gene expression data at Day 8


title: Patient #32, Day 8

description: gene expression data at Day 8


title: Patient #37, Day 0

description: gene expression data at Day 0


title: Patient #32, Day 0

description: gene expression data at Day 0


title: Patient #33, Day 0

description: gene expression data at Day 0


title: Patient #20, Day 8

description: gene expression data at Day 8


title: Patient #44, Day 8

description: gene expression data at Day 8


title: Patient #31, Day 8

description: gene expression data at Day 8


title: Patient #20, Day 0

description: gene expression data at Day 0


title: Patient #31, Day 0

description: gene expression data at Day 0


title: Patient #19, Day 0

description: gene expression data at Day 0


title: Patient #19, Day 8

description: gene expression data at Day 8


title: Patient #18, Day 8

description: gene expression data at Day 8


title: Patient #18, Day 0

description: gene expression data at Day 0


title: Patient #11, Day 8

description: gene expression data at Day 8


title: Patient #11, Day 0

description: gene expression data at Day 0


title: Patient #9, Day 0

description: gene expression data at Day 0


title: Patient #10, Day 0

description: gene expression data at Day 0


title: Patient #10, Day 8

description: gene expression data at Day 8


title: Patient #9, Day 8

description: gene expression data at Day 8


title: T_ALL_patient_63 [GPL570]

status: Public on Feb 26 2016

city: Berlin

first: Lars

last: Fransecky

address: Hindenburgdamm 30

department: Hematology and Oncology

country: Germany

institute: Charité University Hospital Berlin

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization.

source_name: bone marrow mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from bone marrow (BM) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using TRIzol (Life Technologies, Grand Island, NY, USA). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute T-cell lymphoblastic leukemia (T-ALL)

tag: patient age at diagnosis

tag: all type

value: pre T-ALL


title: T_ALL_patient_70 [GPL570]


title: T_ALL_patient_75 [GPL570]

value: thymic T-ALL


title: T_ALL_patient_77 [GPL570]


title: T_ALL_patient_67 [GPL570]


title: T_ALL_patient_72 [GPL570]


title: T_ALL_patient_83 [GPL570]


title: T_ALL_patient_79 [GPL570]


title: T_ALL_patient_74 [GPL570]


title: T_ALL_patient_82 [GPL570]


title: T_ALL_patient_71 [GPL570]


title: T_ALL_patient_73 [GPL570]


title: Patient #199, Day 8

description: gene expression data at Day 8


title: T_ALL_patient_69 [GPL570]


title: T_ALL_patient_64 [GPL570]


title: T_ALL_patient_65 [GPL570]


title: T_ALL_patient_81 [GPL570]


title: T_ALL_patient_76 [GPL570]


title: T_ALL_patient_62 [GPL570]


title: T_ALL_patient_78 [GPL570]


title: T_ALL_patient_80 [GPL570]


title: T_ALL_patient_68 [GPL570]

value: mature T-ALL


title: T_ALL_patient_60 [GPL570]


title: T_ALL_patient_61 [GPL570]


title: T_ALL_patient_59 [GPL570]


title: T_ALL_patient_58 [GPL570]


title: T_ALL_patient_57 [GPL570]


title: T_ALL_patient_56 [GPL570]


title: T_ALL_patient_55 [GPL570]


title: T_ALL_patient_66 [GPL570]


title: T_ALL_patient_52 [GPL570]


title: T_ALL_patient_51 [GPL570]


title: T_ALL_patient_54 [GPL570]


title: T_ALL_patient_46 [GPL570]


title: T_ALL_patient_49 [GPL570]


title: T_ALL_patient_53 [GPL570]


title: T_ALL_patient_48 [GPL570]


title: T_ALL_patient_50 [GPL570]


title: 143210hp133a11

status: Public on Jan 12 2016

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

hyb_protocol: 3.75ug of biotin labelled cDNA was hybridised to HG_Plus_2.0 GeneChips (Affymetrix, Santa Clara, CA, USA) following standard procedures.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 and fluorescent intensity for each feature on the array was obtained by using GeneChip Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: CEL files from both studies were processed together with RMA as implemented in the expresso function from the affy R package (version 1.48.0 ) with the parameters bgcorrect.method=rma, normalize.method=quantiles,pmcorrect.method=pmonly,summary.method=medianpolish). Prior to network analysis, gene expression values were centered and normalized by their standard error (signal to ratio).

source_name: ECLIPSE_whole blood

label_protocol: RNA samples were adjusted to 10ng/ul, and 50ng of total RNA was labelled using the Nugen Ovation RNA Amplification v2 procedure following manufacturer’s instructions.

extract_protocol: Paxgene extraction was performed (see PMID 25265030)

tag: gender

tag: packs

tag: cohort

value: ECLIPSE


title: 143221HP133A11


title: 143203hp133a11


title: 143217HP133A11


title: 143220HP133A11


title: 143215HP133A11


title: 143208hp133a11


title: T_ALL_patient_47 [GPL570]


title: 143212HP133A11


title: 143219HP133A11


title: 143209hp133a11


title: 143213HP133A11


title: 143222HP133A11


title: 143216HP133A11


title: 143218HP133A11


title: 143223HP133A11


title: 143207hp133a11


title: 143211HP133A11


title: 143204HP133A11


title: 143205HP133A11


title: 143206hp133a11


title: 143202hp133a11


title: 143214HP133A11


title: 143199hp133a11


title: 143196hp133a11


title: 143201hp133a11


title: 143200hp133a11


title: 143195hp133a11


title: 143189hp133a11


title: 143193hp133a11


title: 143197hp133a11


title: 143185hp133a11


title: 143182hp133a11


title: 143175hp133a11


title: 143177hp133a11


title: 143184hp133a11


title: 143180hp133a11


title: 143181hp133a11


title: 143174hp133a11


title: 143176hp133a11


title: 143190hp133a11


title: 143178hp133a11


title: 143179hp133a11


title: 143173hp133a11


title: 143166hp133a11


title: 143186hp133a11


title: 143172hp133a11


title: 143169hp133a11


title: 143188hp133a11


title: 143194hp133a11


title: 143171hp133a11


title: 143167hp133a11


title: 143164hp133a11


title: 143165HP133A11


title: 143183hp133a11


title: 143170hp133a11


title: 143161hp133a11


title: 143168hp133a11


title: 143187hp133a11


title: 143160hp133a11


title: 143198hp133a11


title: 143156HP133A11


title: 143152HP133A11


title: 143157HP133A11


title: 143153HP133A11


title: 143151HP133A11


title: 143147HP133A11


title: 143154HP133A11


title: 143146HP133A11


title: 143158HP133A11


title: 143155HP133A11


title: 143150HP133A11


title: 143159hp133a11


title: 143138HP133A11


title: 143136HP133A11


title: 143137HP133A11


title: 143135HP133A11


title: 143148HP133A11


title: 143142HP133A11


title: 143145HP133A11


title: 143144HP133A11


title: 143149HP133A11


title: 143143HP133A11


title: 143139HP133A11


title: 143134HP133A11


title: 143141HP133A11


title: 143132HP133A11


title: 143131HP133A11


title: 143128HP133A11


title: 143121HP133A11


title: 143119HP133A11


title: 143120HP133A11


title: 143127HP133A11


title: 143130HP133A11


title: 143140HP133A11


title: 143123HP133A11


title: 143122HP133A11


title: 143125HP133A11


title: 143133HP133A11


title: 143126HP133A11


title: 143113HP133A11


title: 143191hp133a11


title: 143110HP133A11


title: 143111HP133A11


title: 143116HP133A11


title: 143105HP133A11


title: 143103HP133A11


title: 143112HP133A11


title: 143115HP133A11


title: 143109HP133A11


title: 143114HP133A11


title: 143106HP133A11


title: 143100HP133A11


title: 143107HP133A11


title: 143101HP133A11


title: 143102HP133A11


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title: 143096HP133A11


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title: 143085HP133A11


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title: 143068hp133a11


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title: 143054hp133a11


title: 143065hp133a11


title: 143056HP133A11


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title: 143047HP133A11


title: 143048HP133A11


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title: 143046HP133A11


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title: 143040HP133A11


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title: 143036HP133A11


title: 143032HP133A11


title: 143030HP133A11


title: 143118HP133A11


title: 143025HP133A11


title: 143117HP133A11


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title: 143024HP133A11


title: 143022HP133A11


title: 143021HP133A11


title: 143023HP133A11


title: 143020HP133A11


title: 143016HP133A11


title: 143027HP133A11


title: 143017HP133A11


title: 143014HP133A11


title: 143018HP133A11


title: 143013HP133A11


title: 143042hp133a11


title: 143012HP133A11


title: 143006HP133A11


title: 143009HP133A11


title: 142999HP133A11


title: 142995HP133A11


title: 143008HP133A11


title: 143005HP133A11


title: 143010HP133A11


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title: 142998HP133A11


title: 142988HP133A11


title: 143003HP133A11


title: 142992HP133A11


title: 143001HP133A11


title: 143015HP133A11


title: 142993hp133a12


title: 142996HP133A11


title: 143000HP133A11


title: 142991HP133A11


title: 143007HP133A11


title: 142986HP133A11


title: 142984hp133a11


title: 143004HP133A11


title: 143002hp133a12


title: 142997HP133A11


title: 142989HP133A11


title: 142987HP133A11


title: 142982HP133A11


title: 142990HP133A11


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title: 142979HP133A11


title: 142977HP133A11


title: 143019hp133a12


title: 142976HP133A11


title: 142975hp133a11


title: SU056 LPC 28

status: Public on Jan 04 2016

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

description: Leukemic progenitor cell (LPC)

hyb_protocol: Performed according to manufacturer's instructions

scan_protocol: Scanning was done using an Affymetrix Gene Chip 3000 scanner, and processed into CEL files using Affymetrix GCOS software

data_processing: Raw CEL data were normalized in R/bioconductor using MAS5 with custom CDF (brainarray) version 16.0 of ENTREZG

source_name: Bone marrow of AML patient

label_protocol: Standard Affymetrix IVT labeling protocol

extract_protocol: Total RNA was extracted according to the manufacturer's protocol

tag: surface markers

tag: cell type

value: Leukemic progenitor cell (LPC)


title: SU059 LPC 31

description: Leukemic progenitor cell (LPC)


title: SU266 LPC

description: Leukemic progenitor cell (LPC)


title: SU044 LSC 17

description: Leukemic stem cell (LSC)

value: Leukemic stem cell (LSC)


title: SU267 LSC

description: Leukemic stem cell (LSC)


title: SU266 Blast

description: Leukemic blast (Blast)

value: Leukemic blast (Blast)


title: SU056 LSC 29

description: Leukemic stem cell (LSC)


title: SU306 LSC

description: Leukemic stem cell (LSC)


title: SU042 LPC 19

description: Leukemic progenitor cell (LPC)


title: SU046 Blast 13

description: Leukemic blast (Blast)


title: SU267 LPC

description: Leukemic progenitor cell (LPC)


title: SU302 LPC

description: Leukemic progenitor cell (LPC)


title: SU302 LSC

description: Leukemic stem cell (LSC)


title: SU306 Blast

description: Leukemic blast (Blast)


title: SU266 LSC

description: Leukemic stem cell (LSC)


title: SU044 LPC 16

description: Leukemic progenitor cell (LPC)


title: SU056 Blast 27

description: Leukemic blast (Blast)


title: SU267 Blast

description: Leukemic blast (Blast)


title: SU046 LPC 14

description: Leukemic progenitor cell (LPC)


title: SU059 LSC 32

description: Leukemic stem cell (LSC)


title: SU042 LSC 20

description: Leukemic stem cell (LSC)


title: SU068 Blast 33

description: Leukemic blast (Blast)


title: SU068 LPC 34

description: Leukemic progenitor cell (LPC)


title: SU042 Blast 18

description: Leukemic blast (Blast)


title: SU306 LPC

description: Leukemic progenitor cell (LPC)


title: SU059 Blast 30

description: Leukemic blast (Blast)


title: SU302 Blast

description: Leukemic blast (Blast)


title: SU044 Blast 15

description: Leukemic blast (Blast)


title: SU037 LSC 47

description: Leukemic stem cell (LSC)


title: SU068 LSC 35

description: Leukemic stem cell (LSC)


title: SU037 Blast 45

description: Leukemic blast (Blast)


title: SU037 LPC 46

description: Leukemic progenitor cell (LPC)


title: SU032 LSC 9

description: Leukemic stem cell (LSC)


title: SU008 LSC 3

description: Leukemic stem cell (LSC)


title: SU008 Blast 1

description: Leukemic blast (Blast)


title: SU009 LSC 38

description: Leukemic stem cell (LSC)


title: SU036 LPC 11

description: Leukemic progenitor cell (LPC)


title: SU035 LSC 23

description: Leukemic stem cell (LSC)


title: SU009 LPC 37

description: Leukemic progenitor cell (LPC)


title: SU014 Blast 4

description: Leukemic blast (Blast)


title: SU036 Blast 10

description: Leukemic blast (Blast)


title: SU029 LSC 26

description: Leukemic stem cell (LSC)


title: SU014 LSC 6

description: Leukemic stem cell (LSC)


title: SU029 LPC 25

description: Leukemic progenitor cell (LPC)


title: SU011 LSC 44

description: Leukemic stem cell (LSC)


title: SU036 LSC 12

description: Leukemic stem cell (LSC)


title: SU011 LPC 43

description: Leukemic progenitor cell (LPC)


title: SU029 Blast 24

description: Leukemic blast (Blast)


title: SU006 Blast 48

description: Leukemic blast (Blast)


title: SU006 LSC 50

description: Leukemic stem cell (LSC)


title: SU002 LSC 41

description: Leukemic stem cell (LSC)


title: SU035 LPC 22

description: Leukemic progenitor cell (LPC)


title: SU035 Blast 21

description: Leukemic blast (Blast)


title: SU014 LPC 5

description: Leukemic progenitor cell (LPC)


title: SU011 Blast 42

description: Leukemic blast (Blast)


title: SU032 LPC 8

description: Leukemic progenitor cell (LPC)


title: SU008 LPC 2

description: Leukemic progenitor cell (LPC)


title: SU009 Blast 36

description: Leukemic blast (Blast)


title: SU006 LPC 49

description: Leukemic progenitor cell (LPC)


title: SU002 LPC 40

description: Leukemic progenitor cell (LPC)


title: SU002 Blast 39

description: Leukemic blast (Blast)


title: SU032 Blast 7

description: Leukemic blast (Blast)


title: BM2806 MEP 92

description: Megakarocyte-erythroid progenitor (MEP)

source_name: Bone marrow of healthy donor

value: Megakarocyte-erythroid progenitor (MEP)


title: BM2793 CMP 78

description: Common myeloid progenitor (CMP)

value: Common myeloid progenitor (CMP)


title: BM2793 MEP 80

description: Megakarocyte-erythroid progenitor (MEP)


title: BM2806 HSC 87

description: Hematopoietic stem cell (HSC)

value: Hematopoietic stem cell (HSC)


title: BM2794 MPP 82

description: Multipotent progenitor (MPP)

value: Multipotent progenitor (MPP)


title: BM2793 GMP 79

description: Granulocyte-macrophage progenitor

value: Granulocyte-macrophage progenitor


title: BM2806 L MPP 89

description: Lymphoid-primed multipotent progenitor (LMPP)


title: BM2770 HSC 69

description: Hematopoietic stem cell (HSC)


title: BM2806 MPP 88

description: Multipotent progenitor (MPP)


title: BM2770 GMP 73

description: Granulocyte-macrophage progenitor


title: BM2794 MEP 86

description: Megakarocyte-erythroid progenitor (MEP)


title: BM2793 HSC 75

description: Hematopoietic stem cell (HSC)


title: BM2770 MEP 74

description: Megakarocyte-erythroid progenitor (MEP)


title: BM2794 GMP 85

description: Granulocyte-macrophage progenitor


title: BM2770 MPP 70

description: Multipotent progenitor (MPP)


title: BM2806 GMP 91

description: Granulocyte-macrophage progenitor


title: BM2770 L MPP 71

value: Lymphoid-primed multipotent progenitor (LMPP)


title: BM2806 CMP 90

description: Common myeloid progenitor (CMP)


title: BM2793 MPP 76

description: Multipotent progenitor (MPP)


title: BM2794 L MPP 83


title: BM2793 L MPP 77


title: BM2770 CMP 72

description: Common myeloid progenitor (CMP)


title: BM2794 HSC 81

description: Hematopoietic stem cell (HSC)


title: BM2768 MPP 64

description: Multipotent progenitor (MPP)


title: BM2794 CMP 84

description: Common myeloid progenitor (CMP)


title: BM2768 GMP 67

description: Granulocyte-macrophage progenitor


title: BM2768 MEP 68

description: Megakarocyte-erythroid progenitor (MEP)


title: BM2768 L MPP 65


title: BM2768 HSC 63

description: Hematopoietic stem cell (HSC)


title: BM2768 CMP 66

description: Common myeloid progenitor (CMP)


title: BM2761 CMP 60

description: Common myeloid progenitor (CMP)


title: BM2759 CMP 54

description: Common myeloid progenitor (CMP)


title: BM2759 MPP 52

description: Multipotent progenitor (MPP)


title: BM2761 MPP 58

description: Multipotent progenitor (MPP)


title: BM2761 HSC 57

description: Hematopoietic stem cell (HSC)


title: BM2759 GMP 55

description: Granulocyte-macrophage progenitor


title: BM2761 L MPP 59


title: BM2761 GMP 61

description: Granulocyte-macrophage progenitor


title: BM2761 MEP 62

description: Megakarocyte-erythroid progenitor (MEP)


title: BM2759 MEP 56

description: Megakarocyte-erythroid progenitor (MEP)


title: BM2759 L MPP 53


title: BM2759 HSC 51

description: Hematopoietic stem cell (HSC)


title: ALL - bone marrow - Relapse -19

status: Public on Dec 31 2015

city: Rotterdam

first: Vincent

middle: HJ

last: van der Velden

address: Wytemaweg 80

department: Immunology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Ten micrograms of fragmented cRNA was  hybridized for 16 h to Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: After washing and staining, the arrays were scanned in a Hewlett-Packard/Affymetrix scanner at 570 nm.

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.

source_name: ALL - bone marrow - Relapse

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

growth_protocol: ALL cells from BM samples were sorted to >95% purity as described previously and subsequently used for RNA extraction. Given the relatively low cell numbers and generally high percentages of ALL cells in CSF, ALL cells in CSF were directly processed for RNA extraction

extract_protocol: RNA was extracted from the ALL cells using Qiagen RNeasy isolation kit according to the manufacturer’s instruction (Qiagen, Hilden, Germany).

value: m

tag: age at diagnosis

tag: wbc at diagnosis (10e9/l)

tag: side of relapse

value: bone marrow

value: relapse


title: ALL - bone marrow - Relapse -2


title: ALL - bone marrow - Relapse -20

value: f


title: ALL - bone marrow - Relapse -15


title: ALL - bone marrow - Relapse -1


title: ALL - bone marrow - Relapse -18


title: ALL - bone marrow - Relapse -3


title: ALL - bone marrow - Relapse -16


title: ALL - bone marrow - Relapse -7


title: ALL - bone marrow - Relapse -5


title: ALL - bone marrow - Relapse -13


title: ALL - bone marrow - Relapse -14


title: ALL - bone marrow - Relapse -4


title: ALL - bone marrow - Relapse -17


title: ALL - bone marrow - Relapse -11


title: ALL - bone marrow - Diagnosis -21

source_name: ALL - bone marrow - Diagnosis

value: diagnosis


title: ALL - bone marrow - Relapse -9


title: ALL - bone marrow - Diagnosis -8


title: ALL - bone marrow - Relapse -10


title: ALL - bone marrow - Diagnosis -19


title: ALL - bone marrow - Relapse -8

value: v


title: ALL - bone marrow - Diagnosis -10


title: ALL - bone marrow - Diagnosis -20


title: ALL - bone marrow - Diagnosis -3


title: ALL - bone marrow - Diagnosis -11


title: ALL - bone marrow - Relapse -12


title: ALL - bone marrow - Diagnosis -1


title: ALL - bone marrow - Diagnosis -6


title: ALL - bone marrow - Diagnosis -5


title: ALL - bone marrow - Diagnosis -7


title: ALL - bone marrow - Relapse -6


title: ALL - bone marrow - Diagnosis -4


title: ALL - bone marrow - Diagnosis -16


title: ALL - bone marrow - Diagnosis -2


title: semen-BTHO5

status: Public on Nov 04 2015

type: genomic

city: Beltsville

first: Derek

middle: Martens

last: Bickhart

address: Building 005, Rm 318, BARC-West 10300 Baltimore Ave

department: BARC

institute: USDA ARS

description: Processed data files are bed file coordinates for probe locations. Columns 4 and 5 indicate the normalized aCGH copy number value and the rCV value, respectively

hyb_protocol: Hybridization was performed by the third party provider, Nimblegen. Dye swap experiments with the Dominette reference sample were performed to test probe quality

scan_protocol: Scanning was performed by the third party provider, Nimblegen

data_processing:
Data processing was performed similar to Sudmant et al. 2010 's single channel aCGH methodology. In short, single channel array intensities were transformed into integer copy number estimates by using normalized reference signal intensity derived from all tested array samples.
Median reference signal intensity normalized log2 ratios, and rCV estimates of probe sequence copy number fluctuation.

molecule: genomic DNA

organism: Bos taurus

source_name: frozen semen stock

label_protocol: Labeling was performed by the third party provider, Nimblegen

extract_protocol: DNA was extracted from semen using a Qiagen DNEasy tissue and blood kit

value: male

tag: breed

value: Holstein

source_name: L1 Dominette whole blood DNA extract

value: female

value: Hereford


title: semen-BTHO2


title: semen-BTHO3


title: ALL - bone marrow - Diagnosis -18


title: ALL - bone marrow - Diagnosis -9


title: ALL - bone marrow - Diagnosis -22


title: semen-BTHO1


title: ALL - bone marrow - Diagnosis -14


title: semen-BTHO4


title: ALL - bone marrow - Diagnosis -15


title: ALL - bone marrow - Diagnosis -17


title: ALL - bone marrow - Diagnosis -12


title: ALL - bone marrow - Diagnosis -13


title: Sirt2+/+ (untreated) 1

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile method with the Illumina function provided by beadarray Bioconductor package

organism: Mus musculus

source_name: MEFs

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer’s protocol and starting with 150 ng of total RNA

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) per the manufacturer’s instructions. Quantity and quality of each RNA sample was assessed using Nanodrop and Bioanalyzer (Agilent)

treatment_protocol: 4 hours treatment with mouse IFNβ (2500 IU/ml)

value: mouse embryonic fibroblasts (MEFs)

tag: genotype


title: Sirt2+/+ (untreated) 3

description: replicate 3


title: Sirt2+/+ + IFNβ 3

description: replicate 3


title: Sirt2-/- (untreated) 2

description: replicate 2


title: Sirt2-/- (untreated) 1

description: replicate 1


title: Sirt2+/+ + IFNβ 2

description: replicate 2


title: Sirt2-/- (untreated) 3

description: replicate 3


title: Sirt2-/- + IFNβ 1

description: replicate 1


title: Sirt2-/- + IFNβ 3

description: replicate 3


title: Sirt2-/- + IFNβ 2

description: replicate 2


title: Sirt2+/+ (untreated) 2

description: replicate 2


title: semen-BTHO6


title: Sirt2+/+ + IFNβ 1

description: replicate 1


title: EXP-608: Blood_TCGA-AB-2803

status: Public on May 14 2015

source_name: Primary Blood Derived Cancer

tag: age

tag: french-american-british classification

tag: Sex

value: FEMALE

tag: organism part

value: Blood

tag: cytogenetic

value: Normal

value: BONE MARROW


title: EXP-608: Blood_TCGA-AB-2977


title: EXP-608: Blood_TCGA-AB-2816


title: EXP-608: Blood_TCGA-AB-2864

value: Trisomy 8


title: EXP-608: Blood_TCGA-AB-2926


title: EXP-608: Blood_TCGA-AB-2916

value: [Not Available]


title: EXP-608: Blood_TCGA-AB-2848

value: MALE


title: EXP-608: Blood_TCGA-AB-2854


title: EXP-608: Blood_TCGA-AB-2857


title: EXP-608: Blood_TCGA-AB-2893


title: EXP-608: Blood_TCGA-AB-2819


title: EXP-608: Blood_TCGA-AB-2905


title: EXP-608: Blood_TCGA-AB-2829


title: EXP-608: Blood_TCGA-AB-2855

value: Complex (greater than or equal to 3 distinct abnormalities)


title: EXP-608: Blood_TCGA-AB-2827


title: EXP-608: Blood_TCGA-AB-3002


title: EXP-608: Blood_TCGA-AB-2853


title: EXP-608: Blood_TCGA-AB-2845


title: EXP-608: Blood_TCGA-AB-2813


title: EXP-608: Blood_TCGA-AB-2846


title: EXP-608: Blood_TCGA-AB-2814

value: M0 Undifferentiated


title: EXP-608: Blood_TCGA-AB-2807


title: EXP-608: Blood_TCGA-AB-3001


title: EXP-608: Blood_TCGA-AB-2847


title: EXP-608: Blood_TCGA-AB-2833


title: EXP-608: Blood_TCGA-AB-2806


title: EXP-608: Blood_TCGA-AB-2997


title: EXP-608: Blood_TCGA-AB-2835


title: EXP-608: Blood_TCGA-AB-2838


title: EXP-608: Blood_TCGA-AB-2999


title: EXP-608: Blood_TCGA-AB-2920


title: EXP-608: Blood_TCGA-AB-2808


title: EXP-608: Blood_TCGA-AB-2820


title: EXP-608: Blood_TCGA-AB-2860


title: EXP-608: Blood_TCGA-AB-3012


title: EXP-608: Blood_TCGA-AB-2851


title: EXP-608: Blood_TCGA-AB-3005


title: EXP-608: Blood_TCGA-AB-2805


title: EXP-608: Blood_TCGA-AB-2868


title: EXP-608: Blood_TCGA-AB-2990


title: EXP-608: Blood_TCGA-AB-2968


title: EXP-608: Blood_TCGA-AB-2888


title: EXP-608: Blood_TCGA-AB-2914


title: EXP-608: Blood_TCGA-AB-2861


title: EXP-608: Blood_TCGA-AB-2877


title: EXP-608: Blood_TCGA-AB-2836


title: EXP-608: Blood_TCGA-AB-2974


title: EXP-608: Blood_TCGA-AB-2875


title: EXP-608: Blood_TCGA-AB-2824


title: EXP-608: Blood_TCGA-AB-3009

value: BLOOD


title: EXP-608: Blood_TCGA-AB-2840


title: EXP-608: Blood_TCGA-AB-3011


title: EXP-608: Blood_TCGA-AB-2828


title: EXP-608: Blood_TCGA-AB-2832


title: EXP-608: Blood_TCGA-AB-2826


title: EXP-608: Blood_TCGA-AB-2895


title: EXP-608: Blood_TCGA-AB-2862


title: EXP-608: Blood_TCGA-AB-2989


title: EXP-608: Blood_TCGA-AB-2863


title: EXP-608: Blood_TCGA-AB-2817


title: EXP-608: Blood_TCGA-AB-2859


title: EXP-608: Blood_TCGA-AB-2957


title: EXP-608: Blood_TCGA-AB-2843


title: EXP-578: 0232_L07

status: Public on May 13 2015

source_name: Pediatric B-Precursor High-Risk Acute Lymphoblastic Leukemia

tag: diagnosis


title: EXP-578: 0232_F18

value: Pediatric B-Precursor High-Risk Acute Lymphoblastic Leukemia


title: EXP-578: 0232_E14


title: EXP-578: 0232_P18


title: EXP-608: Blood_TCGA-AB-2812


title: EXP-578: 0232_J03


title: EXP-578: 0232_G10


title: EXP-578: 0232_I22


title: EXP-608: Blood_TCGA-AB-2810


title: EXP-608: Blood_TCGA-AB-2837


title: EXP-608: Blood_TCGA-AB-2841


title: EXP-608: Blood_TCGA-AB-2844


title: EXP-608: Blood_TCGA-AB-2994


title: EXP-608: Blood_TCGA-AB-3008


title: EXP-608: Blood_TCGA-AB-2822


title: EXP-608: Blood_TCGA-AB-2963


title: EXP-608: Blood_TCGA-AB-2881


title: EXP-608: Blood_TCGA-AB-2866


title: EXP-578: 0232_E22


title: EXP-608: Blood_TCGA-AB-2821


title: EXP-608: Blood_TCGA-AB-2858


title: EXP-578: 0232_F21


title: EXP-578: 0232_A20


title: EXP-608: Blood_TCGA-AB-2880


title: EXP-578: 0232_E06


title: EXP-608: Blood_TCGA-AB-2865


title: EXP-578: 0232_O15


title: EXP-578: 0232_P10


title: EXP-578: 0232_F19


title: EXP-578: 0232_H13


title: EXP-578: 0232_L15


title: EXP-578: 0232_I21


title: EXP-578: 0232_K03


title: EXP-578: 0232_C24


title: EXP-578: 0232_A17


title: EXP-578: 0232_H03


title: EXP-578: 0232_K19


title: EXP-578: 0232_H15


title: EXP-578: 0232_G03


title: EXP-578: 0232_L23


title: EXP-578: 0232_P05


title: EXP-578: 0232_D08


title: EXP-578: 0232_K15


title: EXP-578: 0232_D09


title: EXP-578: 0232_E03


title: EXP-578: 0232_M23


title: EXP-578: 0232_K06


title: EXP-578: 0232_B10


title: EXP-578: 0232_H10


title: EXP-578: 0232_M04


title: EXP-578: 0232_K08


title: EXP-578: 0232_P06


title: EXP-578: 0232_P09


title: EXP-578: 0232_A19


title: EXP-578: 0232_E17


title: EXP-578: 0232_A12


title: EXP-578: 0232_H07


title: EXP-578: 0232_C16


title: EXP-578: 0232_A14


title: EXP-578: 0232_K23


title: EXP-578: 0232_B11


title: EXP-578: 0232_F24


title: EXP-578: 0232_A11


title: EXP-578: 0232_A05


title: EXP-578: 0232_A18


title: EXP-578: 0232_B02


title: EXP-578: 0232_L18


title: EXP-578: 0232_N06


title: EXP-578: 0232_B09


title: EXP-578: 0232_F22


title: EXP-578: 0232_G23


title: EXP-578: 0232_B07


title: EXP-578: 0232_A22


title: EXP-578: 0232_G06


title: EXP-578: 0232_E20


title: EXP-578: 0232_B24


title: EXP-578: 0232_D22


title: EXP-578: 0232_A03


title: EXP-578: 0232_G20


title: EXP-578: 0232_D06


title: EXP-578: 0232_C02


title: EXP-578: 0232_G24


title: EXP-578: 0232_K02


title: EXP-578: 0232_P22


title: EXP-578: 0232_J10


title: EXP-608: Blood_TCGA-AB-2830


title: EXP-578: 0232_D01


title: EXP-578: 0232_D04


title: EXP-578: 0232_I16


title: EXP-578: 0232_O05


title: EXP-578: 0232_L04


title: EXP-578: 0232_B12


title: EXP-578: 0232_J06


title: EXP-578: 0232_C05


title: EXP-578: 0232_B21


title: EXP-578: 0232_O07


title: EXP-578: 0232_K01


title: EXP-578: 0232_J11


title: EXP-578: 0232_K05


title: EXP-578: 0232_B03


title: EXP-578: 0232_G18


title: EXP-578: 0232_C17


title: EXP-578: 0232_L19


title: EXP-578: 0232_K20


title: EXP-578: 0232_L08


title: EXP-578: 0232_C08


title: EXP-578: 0232_G01


title: EXP-578: 0232_C13


title: EXP-578: 0232_H22


title: EXP-578: 0232_G09


title: EXP-578: 0232_C01


title: EXP-578: 0232_I14


title: EXP-608: Blood_TCGA-AB-2818


title: EXP-578: 0232_B19


title: EXP-578: 0232_E09


title: EXP-578: 0232_F07


title: EXP-578: 0232_L21


title: EXP-578: 0232_E23


title: EXP-578: 0232_D14


title: EXP-578: 0232_B17


title: EXP-578: 0232_D11


title: EXP-578: 0232_H06


title: EXP-578: 0232_G11


title: EXP-578: 0232_C03


title: EXP-578: 0232_I07


title: EXP-578: 0232_I03


title: EXP-578: 0232_B23


title: EXP-578: 0232_F14


title: EXP-578: 0232_L17


title: EXP-578: 0232_M10


title: EXP-578: 0232_M19


title: EXP-578: 0232_K14


title: EXP-578: 0232_M08


title: EXP-578: 0232_L06


title: EXP-578: 0232_F04


title: EXP-578: 0232_H05


title: EXP-578: 0232_M14


title: EXP-578: 0232_I15


title: EXP-578: 0232_C22


title: EXP-578: 0232_N14


title: EXP-578: 0232_G05


title: EXP-578: 0232_G14


title: EXP-578: 0232_F23


title: EXP-578: 0232_G12


title: EXP-578: 0232_L09


title: EXP-578: 0232_F17


title: EXP-578: 0232_I06


title: EXP-578: 0232_M11


title: EXP-578: 0232_P03


title: EXP-578: 0232_P04


title: EXP-578: 0232_O19


title: EXP-578: 0232_M07


title: EXP-578: 0232_A10


title: EXP-578: 0232_D20


title: EXP-578: 0232_G13


title: EXP-578: 0232_I23


title: EXP-578: 0232_A24


title: EXP-578: 0232_A04


title: EXP-578: 0232_I04


title: EXP-578: 0232_N07


title: EXP-578: 0232_A06


title: EXP-578: 0232_E13


title: EXP-578: 0232_A13


title: EXP-578: 0232_E24


title: EXP-578: 0232_A02


title: EXP-578: 0232_A08


title: EXP-578: 0232_B14


title: EXP-578: 0232_J04


title: EXP-578: 0232_C09


title: EXP-578: 0232_D18


title: EXP-578: 0232_H18


title: EXP-578: 0232_G07


title: EXP-578: 0232_O10


title: EXP-578: 0232_B01


title: EXP-578: 0232_M16


title: EXP-578: 0232_B15


title: EXP-578: 0232_K12


title: EXP-578: 0232_C12


title: EXP-578: 0232_G02


title: EXP-578: 0232_B18


title: EXP-578: 0232_G08


title: EXP-578: 0232_H08


title: EXP-578: 0232_D21


title: EXP-578: 0232_E10


title: EXP-578: 0232_L24


title: EXP-578: 0232_C19


title: EXP-578: 0232_P13


title: EXP-578: 0232_H17


title: EXP-578: 0232_K18


title: EXP-578: 0232_J13


title: EXP-578: 0232_H12


title: EXP-578: 0232_K10


title: EXP-578: 0232_B08


title: EXP-578: 0232_D13


title: EXP-578: 0232_H11


title: EXP-578: 0232_C20


title: EXP-578: 0232_E04


title: EXP-578: 0232_P21


title: EXP-578: 0232_D12


title: EXP-578: 0232_E19


title: EXP-578: 0232_C07


title: EXP-578: 0232_G15


title: EXP-578: 0232_L03


title: EXP-578: 0232_C04


title: EXP-578: 0232_H20


title: EXP-578: 0232_H14


title: EXP-578: 0232_F13


title: EXP-578: 0232_L05


title: EXP-578: 0232_M17


title: EXP-578: 0232_K21


title: EXP-578: 0232_F16


title: EXP-578: 0232_J14


title: EXP-578: 0232_O06


title: EXP-578: 0232_J16


title: EXP-578: 0232_J19


title: EXP-578: 0232_M06


title: EXP-578: 0232_O01


title: EXP-578: 0232_K24


title: EXP-578: 0232_P14


title: EXP-578: 0232_O04


title: EXP-578: 0232_D03


title: EXP-578: 0232_M12


title: EXP-578: 0232_C21


title: EXP-578: 0232_J05


title: EXP-578: 0232_E16


title: EXP-578: 0232_A15


title: EXP-578: 0232_J01


title: EXP-578: 0232_B16


title: EXP-578: 0232_M09


title: EXP-578: 0232_L20


title: EXP-578: 0232_D17


title: EXP-578: 0232_K16


title: EXP-578: 0232_P08


title: EXP-578: 0232_E02


title: EXP-578: 0232_H23


title: EXP-578: 0232_I12


title: EXP-578: 0232_E15


title: EXP-578: 0232_L01


title: EXP-578: 0232_N01


title: EXP-578: 0232_K04


title: EXP-578: 0232_J08


title: EXP-578: 0232_F15


title: EXP-578: 0232_E07


title: EXP-578: 0232_G22


title: EXP-578: 0232_C06


title: EXP-578: 0232_L11


title: EXP-578: 0232_J09


title: EXP-578: 0232_D07


title: EXP-578: 0232_F06


title: EXP-578: 0232_J02


title: EXP-578: 0232_J21


title: EXP-578: 0232_E12


title: EXP-578: 0232_N09


title: EXP-578: 0232_F10


title: EXP-578: 0232_L13


title: EXP-578: 0232_A07


title: EXP-578: 0232_G17


title: EXP-578: 0232_L22


title: EXP-578: 0232_F11


title: EXP-578: 0232_E18


title: EXP-578: 0232_M24


title: EXP-578: 0232_O08


title: EXP-578: 0232_C14


title: EXP-578: 0232_F20


title: EXP-578: 0232_O18


title: EXP-578: 0232_M21


title: EXP-578: 0232_N08


title: EXP-578: 0232_K13


title: EXP-578: 0232_E11


title: EXP-578: 0232_M01


title: EXP-578: 0232_N11


title: EXP-578: 0232_M18


title: EXP-578: 0232_B06


title: EXP-578: 0232_E08


title: EXP-578: 0232_H21


title: EXP-578: 0232_A01


title: EXP-578: 0232_A23


title: EXP-578: 0232_I10


title: EXP-578: 0232_H19


title: EXP-578: 0232_D15


title: EXP-578: 0232_B05


title: EXP-578: 0232_D24


title: EXP-578: 0232_A16


title: EXP-578: 0232_M05


title: EXP-578: 0232_D10


title: EXP-578: 0232_I08


title: EXP-578: 0232_G16


title: EXP-578: 0232_M13


title: EXP-578: 0232_B04


title: EXP-578: 0232_C10


title: EXP-578: 0232_O09


title: EXP-578: 0232_P15


title: EXP-578: 0232_K09


title: EXP-578: 0232_H09


title: EXP-578: 0232_I09


title: EXP-578: 0232_N02


title: EXP-578: 0232_K11


title: EXP-578: 0232_L14


title: EXP-578: 0232_G04


title: willm-00140: 9906_257

status: Public on May 12 2015

source_name: Childhood Precursor B-Lymphoblastic Leukemia

tag: disease state


title: willm-00140: 9906_259

value: Childhood Precursor B-Lymphoblastic Leukemia

value: Bone Marrow


title: willm-00140: 9906_251


title: willm-00140: 9906_271


title: willm-00140: 9906_249


title: willm-00140: 9906_272


title: willm-00140: 9906_256


title: willm-00140: 9906_243


title: willm-00140: 9906_254


title: willm-00140: 9906_258


title: willm-00140: 9906_265


title: willm-00140: 9906_262


title: willm-00140: 9906_247


title: willm-00140: 9906_248


title: willm-00140: 9906_246


title: willm-00140: 9906_264


title: willm-00140: 9906_255


title: willm-00140: 9906_241


title: willm-00140: 9906_245


title: willm-00140: 9906_240


title: willm-00140: 9906_253


title: willm-00140: 9906_244


title: willm-00140: 9906_242


title: willm-00140: 9906_267


title: willm-00140: 9906_260


title: willm-00140: 9906_261


title: willm-00140: 9906_239


title: willm-00140: 9906_238


title: willm-00140: 9906_235


title: willm-00140: 9906_233


title: willm-00140: 9906_228


title: willm-00140: 9906_229


title: willm-00140: 9906_232


title: willm-00140: 9906_224


title: willm-00140: 9906_230


title: willm-00140: 9906_227


title: willm-00140: 9906_236


title: willm-00140: 9906_234


title: willm-00140: 9906_222


title: willm-00140: 9906_216


title: willm-00140: 9906_215


title: willm-00140: 9906_225


title: willm-00140: 9906_218


title: willm-00140: 9906_221


title: willm-00140: 9906_217


title: willm-00140: 9906_214


title: willm-00140: 9906_219


title: willm-00140: 9906_220


title: willm-00140: 9906_210


title: willm-00140: 9906_213


title: willm-00140: 9906_207


title: EXP-578: 0232_D05


title: willm-00140: 9906_200


title: willm-00140: 9906_206


title: willm-00140: 9906_205


title: willm-00140: 9906_196


title: willm-00140: 9906_209


title: willm-00140: 9906_199


title: willm-00140: 9906_201


title: willm-00140: 9906_202


title: willm-00140: 9906_189


title: willm-00140: 9906_190


title: willm-00140: 9906_195


title: willm-00140: 9906_198


title: willm-00140: 9906_187


title: willm-00140: 9906_192


title: willm-00140: 9906_184


title: willm-00140: 9906_185


title: willm-00140: 9906_179


title: willm-00140: 9906_263


title: willm-00140: 9906_188


title: willm-00140: 9906_176


title: willm-00140: 9906_180


title: willm-00140: 9906_183


title: willm-00140: 9906_186


title: willm-00140: 9906_174


title: willm-00140: 9906_175


title: willm-00140: 9906_171


title: willm-00140: 9906_177


title: willm-00140: 9906_172


title: willm-00140: 9906_166


title: willm-00140: 9906_173


title: willm-00140: 9906_160


title: willm-00140: 9906_161


title: willm-00140: 9906_158


title: willm-00140: 9906_156


title: willm-00140: 9906_159


title: willm-00140: 9906_157


title: willm-00140: 9906_163


title: willm-00140: 9906_152


title: willm-00140: 9906_167


title: willm-00140: 9906_155


title: willm-00140: 9906_148


title: willm-00140: 9906_153


title: willm-00140: 9906_145


title: willm-00140: 9906_146


title: willm-00140: 9906_147


title: willm-00140: 9906_151


title: willm-00140: 9906_144


title: willm-00140: 9906_141


title: willm-00140: 9906_168


title: willm-00140: 9906_170


title: willm-00140: 9906_150


title: willm-00140: 9906_142


title: willm-00140: 9906_143


title: willm-00140: 9906_139


title: willm-00140: 9906_138


title: willm-00140: 9906_136


title: willm-00140: 9906_135


title: willm-00140: 9906_132


title: willm-00140: 9906_137


title: willm-00140: 9906_129


title: willm-00140: 9906_133


title: willm-00140: 9906_123


title: willm-00140: 9906_116


title: willm-00140: 9906_124


title: willm-00140: 9906_113


title: willm-00140: 9906_117


title: willm-00140: 9906_112


title: willm-00140: 9906_115


title: willm-00140: 9906_120


title: willm-00140: 9906_109


title: willm-00140: 9906_108


title: willm-00140: 9906_122


title: willm-00140: 9906_119


title: willm-00140: 9906_110


title: willm-00140: 9906_111


title: willm-00140: 9906_107


title: willm-00140: 9906_118


title: willm-00140: 9906_102


title: willm-00140: 9906_106


title: willm-00140: 9906_101


title: willm-00140: 9906_114


title: willm-00140: 9906_099


title: willm-00140: 9906_121


title: willm-00140: 9906_097


title: willm-00140: 9906_094


title: willm-00140: 9906_098


title: willm-00140: 9906_095


title: willm-00140: 9906_093


title: willm-00140: 9906_071


title: willm-00140: 9906_096


title: willm-00140: 9906_085


title: willm-00140: 9906_074


title: willm-00140: 9906_083


title: willm-00140: 9906_090


title: willm-00140: 9906_069


title: willm-00140: 9906_066


title: willm-00140: 9906_076


title: willm-00140: 9906_092


title: willm-00140: 9906_091


title: willm-00140: 9906_082


title: willm-00140: 9906_060


title: willm-00140: 9906_084


title: willm-00140: 9906_079


title: willm-00140: 9906_058


title: willm-00140: 9906_073


title: willm-00140: 9906_080


title: willm-00140: 9906_062


title: willm-00140: 9906_086


title: willm-00140: 9906_061


title: willm-00140: 9906_065


title: willm-00140: 9906_063


title: willm-00140: 9906_064


title: willm-00140: 9906_128


title: willm-00140: 9906_055


title: willm-00140: 9906_043


title: willm-00140: 9906_048


title: willm-00140: 9906_050


title: willm-00140: 9906_045


title: willm-00140: 9906_052


title: willm-00140: 9906_046


title: willm-00140: 9906_041


title: willm-00140: 9906_031


title: willm-00140: 9906_042


title: willm-00140: 9906_027


title: willm-00140: 9906_034


title: willm-00140: 9906_033


title: willm-00140: 9906_024


title: willm-00140: 9906_028


title: willm-00140: 9906_030


title: willm-00140: 9906_039


title: willm-00140: 9906_037


title: willm-00140: 9906_032


title: willm-00140: 9906_049


title: willm-00140: 9906_023


title: willm-00140: 9906_038


title: willm-00140: 9906_022


title: willm-00140: 9906_047


title: willm-00140: 9906_020


title: willm-00140: 9906_019


title: willm-00140: 9906_018


title: willm-00140: 9906_036


title: willm-00140: 9906_021


title: willm-00140: 9906_126


title: willm-00140: 9906_017


title: willm-00140: 9906_051


title: willm-00140: 9906_005


title: EXP-520: P9407_M02

source_name: infant ALL case

value: PBL

tag: gender

value: Male

tag: race

value: BLACK

tag: ethnicity

value: Not Hispanic or Latino

tag: gene

tag: pg

tag: karyotype

tag: treatment

value: COHORT 3


title: EXP-520: P9407_M09

value: BM

value: Female

value: WHITE

tag: cohort


title: EXP-520: P9407_K11

value: ENL

value: COHORT 2


title: willm-00140: 9906_004


title: EXP-520: P9407_K13

value: Unknown(Individuals not reporting ethnicity)


title: willm-00140: 9906_008

value: Blood


title: willm-00140: 9906_006


title: willm-00140: 9906_012


title: EXP-520: P9407_K10

value: Hispanic or Latino


title: EXP-520: P9407_K12


title: willm-00140: 9906_009


title: EXP-520: P9407_K03


title: EXP-520: P9407_I07


title: EXP-520: P9407_K07


title: willm-00140: 9906_002


title: EXP-520: P9407_M05

value: OTHER MLL

value: NOT AF4, AF9 OR ENL; PARTNER UNKNOWN


title: EXP-520: P9407_K01

value: COHORT 1


title: EXP-520: P9407_K08


title: EXP-520: P9407_K02


title: EXP-520: P9407_K05


title: willm-00140: 9906_001

value: Childhood Precursor B-Lymphoblastic Leukemia

value: Bone Marrow


title: EXP-520: P9407_K06

value: Male


title: willm-00140: 9906_003


title: EXP-520: P9407_I05

value: PBL


title: EXP-520: P9407_H11

value: Not Hispanic or Latino


title: EXP-520: P9407_H10

value: COHORT 3


title: EXP-520: P9407_I04

value: ASIAN


title: EXP-520: P9407_H08

value: Female


title: EXP-520: P9407_H09

value: WHITE


title: EXP-520: P9407_G12


title: EXP-520: P9407_H02


title: EXP-520: P9407_H04

value: MORE THAN ONE RACE


title: EXP-520: P9407_H07

value: BM

value: ENL


title: EXP-520: P9407_H06


title: EXP-520: P9407_H03


title: EXP-520: P9407_G11


title: EXP-520: P9407_H01


title: EXP-520: P9407_I01


title: EXP-520: P9407_H05

value: BLACK

value: Unknown(Individuals not reporting ethnicity)


title: EXP-520: P9407_G10

value: Hispanic or Latino


title: EXP-520: P9407_F09


title: EXP-520: P9407_G03


title: EXP-520: P9407_G08

value: OTHER MLL


title: EXP-520: P9407_G09


title: EXP-520: P9407_F07

value: UNKNOWN


title: EXP-520: P9407_G01

value: NOT AF4, AF9 OR ENL; PARTNER UNKNOWN


title: EXP-520: P9407_F10


title: EXP-520: P9407_F06


title: EXP-520: P9407_F05


title: EXP-520: P9407_F03


title: EXP-520: P9407_E10


title: EXP-520: P9407_F04


title: EXP-520: P9407_F01


title: EXP-520: P9407_F02


title: EXP-520: P9407_E11


title: EXP-520: P9407_D11


title: willm-00140: 9906_013

value: Childhood Precursor B-Lymphoblastic Leukemia

value: Bone Marrow


title: EXP-520: P9407_E08

value: PBL

value: Male

value: AMERICAN INDIAN


title: EXP-520: P9407_E03

value: Not Hispanic or Latino

value: COHORT 3


title: willm-00140: 9906_007


title: EXP-520: P9407_D12

value: WHITE


title: EXP-520: P9407_D08

value: Female


title: EXP-520: P9407_E09


title: EXP-520: P9407_E01


title: EXP-520: P9407_D10


title: EXP-520: P9407_D07


title: EXP-520: P9407_E12

value: BM


title: EXP-520: P9407_D06

value: ENL


title: EXP-520: P9407_D03


title: EXP-520: P9407_D05


title: EXP-520: P9407_F12


title: EXP-520: P9407_D09


title: EXP-520: P9407_D01


title: EXP-520: P9407_D02

value: BLACK


title: EXP-520: P9407_B12

value: ASIAN


title: EXP-520: P9407_B05


title: EXP-520: P9407_C05


title: EXP-520: P9407_C01

value: Hispanic or Latino


title: EXP-520: P9407_C03


title: EXP-520: P9407_B02


title: EXP-520: P9407_B09


title: EXP-520: P9407_B08


title: EXP-520: P9407_C04

value: OTHER MLL


title: EXP-520: P9407_B11


title: EXP-520: P9407_C02


title: EXP-520: P9407_B07


title: EXP-520: P9407_E07

value: Unknown(Individuals not reporting ethnicity)


title: EXP-520: P9407_C11


title: EXP-520: P9407_B01


title: EXP-520: P9407_C10


title: EXP-520: P9407_C09


title: EXP-520: P9407_C07


title: EXP-520: P9407_B10


title: EXP-520: P9407_I06


title: EXP-520: P9407_A10

value: NOT AF4; PARTNER UNKNOWN

value: COHORT 2


title: EXP-520: P9407_A07

value: OTHER


title: EXP-520: P9407_A04


title: EXP-520: P9407_A05

value: PBL


title: EXP-520: P9407_A11

value: Male

value: UNKNOWN


title: EXP-520: P9407_B04

value: Not Hispanic or Latino


title: EXP-520: P9407_I03

value: COHORT 3


title: EXP-520: P9407_C12

value: WHITE


title: EXP-520: P9407_A03


title: EXP-520: P9407_A02


title: EXP-520: P9407_A06


title: EXP-520: P9407_A01

value: Female


title: PBMC, Healthy control,Biological replicate 7

status: Public on Apr 07 2015

city: Buffalo

first: kaiyu

last: Jiang

state: NY

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Affymetrix Human U133 Plus 2.0 GeneChips following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner

data_processing: CHP files were generated by Affymetrix expression console software using the 3' exp array -RMA program

label: Biotin

source_name: PBMC RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA)

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated from granulocytes and red blood cells by density-gradient centrifugation. Red cells were removed from granulocytes by hypotonic lysis. PBMC and granulocytes were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

tag: cell type

value: PBMC

value: Healthy control


title: PBMC, Healthy control,Biological replicate 12


title: PBMC, Healthy control,Biological replicate 2


title: PBMC, Healthy control,Biological replicate 8


title: PBMC, Pauciarticular,Biological replicate 8

value: Pauciarticular JIA


title: PBMC, Healthy control,Biological replicate 9


title: PBMC, Healthy control,Biological replicate 5


title: PBMC, Healthy control,Biological replicate 6


title: PBMC, Pauciarticular,Biological replicate 5


title: PBMC, Pauciarticular,Biological replicate 1


title: PBMC, Healthy control,Biological replicate 10


title: PBMC, Polyrticular,Biological replicate 12

value: Polyrticular JIA


title: PBMC, Pauciarticular,Biological replicate 6


title: PBMC, Healthy control,Biological replicate 11


title: PBMC, Polyrticular,Biological replicate 13


title: PBMC, Healthy control,Biological replicate 15


title: PBMC, Healthy control,Biological replicate 1


title: PBMC, Polyrticular,Biological replicate 14


title: PBMC, Healthy control,Biological replicate 13


title: PBMC, Healthy control,Biological replicate 14


title: PBMC, Polyrticular,Biological replicate 10


title: PBMC, Pauciarticular,Biological replicate 4


title: PBMC, Healthy control,Biological replicate 4


title: PBMC, Pauciarticular,Biological replicate 2


title: PBMC, Pauciarticular,Biological replicate 3


title: PBMC, Pauciarticular,Biological replicate 7


title: PBMC, Polyrticular,Biological replicate 11


title: PBMC, Polyrticular,Biological replicate 9


title: PBMC, Polyrticular,Biological replicate 7


title: PBMC, Polyrticular,Biological replicate 5


title: PBMC, Polyrticular,Biological replicate 8


title: PBMC, Polyrticular,Biological replicate 2


title: PBMC, Polyrticular,Biological replicate 1


title: PBMC, Polyrticular,Biological replicate 4


title: PBMC, Polyrticular,Biological replicate 3


title: SAM622028 SLE

status: Public on Mar 31 2015

city: South San Francisco

first: Michael

last: Townsend

address: 1 DNA Way

department: ITGR Diagnostics Discovery

institute: Genentech

description: Gene expression from SLE PBMCs

hyb_protocol: Samples were hybridized to GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Inc.).  Arrays were washed and stained in the Affymetrix Fluidics station and scanned on a GeneChip® scanner 3000

scan_protocol: GeneChip® scanner 3000

data_processing: Expression signals were obtained using the Affymetrix GeneChip® operating system and analysis software. The data was MAS 5.0 normalized in R and probesets filtered using Bioconductor geneFilter package.

source_name: PBMCs

extract_protocol: RNeasy minikit (Qiagen Inc., Valencia, CA)

tag: disease status

value: SLE


title: SAM622031 SLE

description: Gene expression from SLE PBMCs


title: SAM622033 SLE

description: Gene expression from SLE PBMCs


title: SAM622027 SLE

description: Gene expression from SLE PBMCs


title: SAM622029 SLE

description: Gene expression from SLE PBMCs


title: PBMC, Healthy control,Biological replicate 3


title: SAM622032 SLE

description: Gene expression from SLE PBMCs


title: SAM616389 SLE

description: Gene expression from SLE PBMCs


title: SAM622030 SLE

description: Gene expression from SLE PBMCs


title: SAM622026 SLE

description: Gene expression from SLE PBMCs


title: SAM615872 SLE

description: Gene expression from SLE PBMCs


title: SAM615871 SLE

description: Gene expression from SLE PBMCs


title: SAM622023 SLE

description: Gene expression from SLE PBMCs


title: SAM622022 SLE

description: Gene expression from SLE PBMCs


title: SAM622024 SLE

description: Gene expression from SLE PBMCs


title: SAM622025 SLE

description: Gene expression from SLE PBMCs


title: SAM621338 SLE

description: Gene expression from SLE PBMCs


title: SAM616388 SLE

description: Gene expression from SLE PBMCs


title: SAM616390 SLE

description: Gene expression from SLE PBMCs


title: PBMC, Polyrticular,Biological replicate 6


title: SAM615869 SLE

description: Gene expression from SLE PBMCs


title: SAM615873 SLE

description: Gene expression from SLE PBMCs


title: SAM615237 Control

description: Gene expression from SLE PBMCs

value: Control


title: SAM615238 Control

description: Gene expression from SLE PBMCs


title: SAM615239 Control

description: Gene expression from SLE PBMCs


title: SAM613838 SLE

description: Gene expression from SLE PBMCs


title: SAM615240 Control

description: Gene expression from SLE PBMCs


title: SAM622021 SLE

description: Gene expression from SLE PBMCs


title: SAM613443 SLE

description: Gene expression from SLE PBMCs


title: SAM613431 SLE

description: Gene expression from SLE PBMCs


title: SAM615870 SLE

description: Gene expression from SLE PBMCs


title: SAM613442 SLE

description: Gene expression from SLE PBMCs


title: SAM613326 SLE

description: Gene expression from SLE PBMCs


title: SAM613328 SLE

description: Gene expression from SLE PBMCs


title: SAM613322 SLE

description: Gene expression from SLE PBMCs


title: SAM613325 SLE

description: Gene expression from SLE PBMCs


title: SAM613321 SLE

description: Gene expression from SLE PBMCs


title: SAM613318 SLE

description: Gene expression from SLE PBMCs


title: SAM613319 SLE

description: Gene expression from SLE PBMCs


title: SAM613320 SLE

description: Gene expression from SLE PBMCs


title: SAM613444 SLE

description: Gene expression from SLE PBMCs


title: SAM613323 SLE

description: Gene expression from SLE PBMCs


title: SAM613331 SLE

description: Gene expression from SLE PBMCs


title: SAM613316 SLE

description: Gene expression from SLE PBMCs


title: SAM613317 SLE

description: Gene expression from SLE PBMCs


title: SAM613313 SLE

description: Gene expression from SLE PBMCs


title: SAM613330 SLE

description: Gene expression from SLE PBMCs


title: SAM613315 SLE

description: Gene expression from SLE PBMCs


title: SAM613324 SLE

description: Gene expression from SLE PBMCs


title: SAM613314 SLE

description: Gene expression from SLE PBMCs


title: SAM613312 SLE

description: Gene expression from SLE PBMCs


title: SAM613311 SLE

description: Gene expression from SLE PBMCs


title: SAM613310 SLE

description: Gene expression from SLE PBMCs


title: SAM610532 SLE

description: Gene expression from SLE PBMCs


title: SAM610531 SLE

description: Gene expression from SLE PBMCs


title: SAM610530 SLE

description: Gene expression from SLE PBMCs


title: SAM613329 SLE

description: Gene expression from SLE PBMCs


title: SAM610528 SLE

description: Gene expression from SLE PBMCs


title: SAM608877 Control

description: Gene expression from SLE PBMCs


title: SAM608880 Control

description: Gene expression from SLE PBMCs


title: SAM608879 Control

description: Gene expression from SLE PBMCs


title: SAM608212 Control

description: Gene expression from SLE PBMCs


title: SAM610526 SLE

description: Gene expression from SLE PBMCs


title: SAM608208 Control

description: Gene expression from SLE PBMCs


title: SAM608876 Control

description: Gene expression from SLE PBMCs


title: SAM608426 Control

description: Gene expression from SLE PBMCs


title: SAM608215 SLE

description: Gene expression from SLE PBMCs


title: SAM608213 SLE

description: Gene expression from SLE PBMCs


title: SAM608211 Control

description: Gene expression from SLE PBMCs


title: SAM608878 Control

description: Gene expression from SLE PBMCs


title: SAM608214 SLE

description: Gene expression from SLE PBMCs


title: SAM608872 SLE

description: Gene expression from SLE PBMCs


title: SAM607438 Control

description: Gene expression from SLE PBMCs


title: SAM608207 Control

description: Gene expression from SLE PBMCs


title: SAM608209 Control

description: Gene expression from SLE PBMCs


title: SAM608206 Control

description: Gene expression from SLE PBMCs


title: SAM607439 Control

description: Gene expression from SLE PBMCs


title: SAM607442 SLE

description: Gene expression from SLE PBMCs


title: SAM608074 SLE

description: Gene expression from SLE PBMCs


title: SAM607440 Control

description: Gene expression from SLE PBMCs


title: SAM607441 SLE

description: Gene expression from SLE PBMCs


title: SAM608210 Control

description: Gene expression from SLE PBMCs


title: CLL-2_US-24h mRNA

status: Public on Feb 10 2015

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: Gene expression data from CLL cells-unstimulated-24h

hyb_protocol: Detailed protocol for sample preparations is available from Affymetrix (http://www.affymetrix.com/support/technical/manual/expression manual.affx)

data_processing: RMA normalized values

source_name: Peripheral blood from CLL patient-unstimulated-24h

growth_protocol: Peripheral blood mononuclear cells isolated from untreated CLL samples were enriched in CD19+ B cells (≥98%) and subsequently cultured and stimulated with a F(ab')2 anti-human IgM

extract_protocol: RNA extraction with TRIzol reagent followed by isopropanol precipitation.

treatment_protocol: Stimulation with a F(ab')2 anti-human IgM.

tag: tissue

value: Peripheral blood

tag: tp53 status

value: WT

tag: FISH analysis

tag: binet stage

value: A

value: Progressive

tag: ighv status

value: M

tag: ighv gene

tag: age


title: CLL-21_US-24h mRNA

scan_protocol: Detailed protocol for sample preparations is available from Affymetrix (http://www.affymetrix.com/support/technical/manual/expression manual.affx)

value: UM

tag: gender

value: F


title: CLL-2_S-24h mRNA

description: Gene expression data from CLL cells-Stimulated with a F(ab')2 anti-human IgM-24h

source_name: Peripheral blood from CLL patient-Stimulated with a F(ab')2 anti-human IgM-24h

label_protocol: Detailed protocol for sample preparations is available from Affymetrix (http://www.affymetrix.com/support/technical/manual/expression manual.affx)


title: CLL-15_S-24h mRNA

value: Negative

value: B


title: CLL-25_US-48h mRNA

description: Gene expression data from CLL cells-unstimulated-48h

source_name: Peripheral blood from CLL patient-unstimulated-48h

value: Stable


title: CLL-20_S-24h mRNA


title: CLL-20_US-24h mRNA


title: CLL-21_S-24h mRNA


title: CLL-14_US-24h mRNA


title: CLL-14_S-24h mRNA


title: CLL-25_US-24h mRNA


title: CLL-23_US-24h mRNA


title: CLL-14_S-48h mRNA

description: Gene expression data from CLL cells-Stimulated with a F(ab')2 anti-human IgM-48h

source_name: Peripheral blood from CLL patient-Stimulated with a F(ab')2 anti-human IgM-48h


title: CLL-2_US-48h mRNA


title: CLL-25_S-48h mRNA


title: CLL-14_US-48h mRNA


title: CLL-19_US-24h mRNA


title: CLL-15_S-48h mRNA


title: CLL-2_S-48h mRNA


title: CLL-25_S-24h mRNA


title: CLL-15_US-24h mRNA


title: CLL-19_S-24h mRNA


title: CLL-15_US-48h mRNA


title: CLL-23_S-24h mRNA


title: CLL-22_US-24h mRNA


title: CLL-16_S-24h mRNA


title: CLL-9_S-48h mRNA


title: CLL-22_S-24h mRNA


title: CLL-16_US-24h mRNA


title: CLL-9_US-24h mRNA


title: CLL-9_US-48h mRNA


title: CLL-9_S-24h mRNA


title: CLL-7_S-24h mRNA


title: CLL-12_S-48h mRNA


title: CLL-26_S-48h mRNA


title: CLL-7_S-48h mRNA


title: SAM613327 SLE

description: Gene expression from SLE PBMCs


title: CLL-11_US-24h mRNA


title: CLL-5_S-48h mRNA


title: CLL-12_S-24h mRNA


title: CLL-5_S-24h mRNA


title: CLL-7_US-48h mRNA


title: CLL-12_US-48h mRNA


title: CLL-6_US-48h mRNA


title: CLL-26_US-48h mRNA


title: CLL-7_US-24h mRNA


title: CLL-11_US-48h mRNA


title: CLL-12_US-24h mRNA


title: CLL-26_S-24h mRNA


title: CLL-11_S-48h mRNA


title: CLL-5_US-24h mRNA


title: CLL-5_US-48h mRNA


title: CLL-24_US-24h mRNA


title: CLL-6_S-48h mRNA


title: CLL-26_US-24h mRNA


title: CLL-11_S-24h mRNA


title: CLL-18_US-24h mRNA


title: CLL-24_S-24h mRNA


title: CLL-17_S-24h mRNA


title: CLL-18_S-24h mRNA


title: CLL-17_US-24h mRNA


title: CLL-10_S-24h mRNA


title: CLL-10_S-48h mRNA


title: CLL-10_US-48h mRNA


title: T-ALL_9105 B

status: Public on Nov 03 2014

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation 12.5ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and target value scaling as normalization method. The trimmed mean target intensity of each array was set to a value of 200.

source_name: Bone marrow

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix One Cycle Protocol

extract_protocol: Trizol RNA isolation, phenol chloroform isoamylalcohol purification, isopropanol precipitation

treatment_protocol: no treatment applied, diagnostic initial leukemia samples

tag: disease state

value: T-cell acute lymphoblastic leukemia (T-ALL)

tag: t-all source

value: Bone marrow


title: T-ALL_9083 B

source_name: peripheral blood

value: peripheral blood


title: T-ALL_9919


title: T-ALL_9858


title: T-ALL_9963


title: T-ALL_704 B


title: T-ALL_9577


title: T-ALL_9012


title: T-ALL_1632 B


title: T-ALL_9323


title: T-ALL_9989


title: T-ALL_9243


title: T-ALL_9316


title: T-ALL_9421


title: T-ALL_9827


title: T-ALL_9830


title: CLL-10_US-24h mRNA


title: T-ALL_9938


title: T-ALL_9757


title: T-ALL_2229 B


title: T-ALL_9696


title: T-ALL_9376


title: T-ALL_9247


title: T-ALL_8815


title: T-ALL_9226


title: T-ALL_9928


title: T-ALL_9160


title: T-ALL_9194


title: T-ALL_9027


title: T-ALL_8628


title: T-ALL_8577


title: T-ALL_8639


title: T-ALL_6897 T17


title: T-ALL_749


title: T-ALL_750


title: T-ALL_491


title: T-ALL_321


title: T-ALL_6515 T79


title: T-ALL_585


title: T-ALL_492


title: T-ALL_6333 T11


title: T-ALL_6155 T55


title: T-ALL_3037


title: T-ALL_759


title: T-ALL_378


title: T-ALL_2669


title: T-ALL_6640 T32


title: T-ALL_2794


title: T-ALL_2911


title: T-ALL_3028


title: T-ALL_3044


title: T-ALL_2436


title: T-ALL_2805


title: T-ALL_230


title: T-ALL_577


title: T-ALL_2691


title: T-ALL_2322


title: T-ALL_2509


title: T-ALL_2486


title: T-ALL_2252


title: T-ALL_222


title: T-ALL_1964


title: T-ALL_2130


title: T-ALL_1842


title: T-ALL_2120 opnieuw


title: T-ALL_1815


title: T-ALL_1509


title: T-ALL_1701


title: T-ALL_1132


title: T-ALL_1032


title: T-ALL_1524


title: T-ALL_10030


title: T-ALL_10110


title: T-ALL_167


title: T-ALL_1113


title: T-ALL_1446


title: T-ALL_1570


title: T-ALL_1753


title: T-ALL_10138


title: T-ALL_10111


title: JSR_148_U133_2

status: Public on Oct 14 2014

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

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, HOXA13-t subroup

value: bone marrow


title: JSR_115_U133_2

description: Gene expression of T-ALL patient blood sample

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

source_name: blood

value: TAL-R subgroup

value: blood


title: JSR_125_U133_2

value: TLX3 subgroup


title: JSR_118_U133_2


title: JSR_149_U133_2


title: JSR_112_U133_2


title: JSR_124_U133_2


title: JSR_088_U133_2


title: JSR_086_U133_2


title: JSR_133_U133_2


title: JSR_090_U133_2


title: JSR_128_U133_2

value: MLL-t subgroup


title: JSR_114_U133_2


title: JSR_087_U133_2

value: immature subgroup


title: JSR_120_U133_2

value: TLX1 subgroup


title: JSR_089_U133_2


title: JSR_119_U133_2


title: JSR_123_U133_2


title: JSR_127_U133_2


title: JSR_075_U133_2

value: unknown, clusters with MLL but does not express HOXA genes


title: JSR_082_U133_2


title: JSR_073_U133_2


title: JSR_068_U133_2


title: JSR_070_U133_2


title: JSR_066_U133_2


title: JSR_071_U133_2


title: JSR_074_U133_2


title: JSR_079_U133_2


title: JSR_080_U133_2


title: JSR_077_U133_2


title: JSR_064_U133_2


title: JSR_061_U133_2


title: JSR_062_U133_2


title: JSR_058_U133_2


title: JSR_059_U133_2


title: JSR_060_U133_2


title: JSR_041_U133_2


title: JSR_054_U133_2


title: JSR_056_U133_2


title: JSR_057_U133_2


title: JSR_051_U133_2


title: JSR_053_U133_2

value: HOXA of unknown mechanism subgroup


title: JSR_052_U133_2


title: JSR_047_U133_2