title: WBM, BI12-000644

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Male

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000737

status: Public on Aug 31 2019

type: RNA

city: La Jolla

first: Samuel

last: Danziger

state: CA

address: 10300 Campus Point Dr

country: USA

institute: Celgene

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on human GeneChip. U133 plus 2.0 chips are washed and stained further in affymetrix fluidics station

scan_protocol: Chips were scanned using the HG-U133 Plus 2.0 v2.2 on a Affymetrix Genechip scanner

data_processing:
Gene-expression data were generated using the Affymetrix Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific) chips from WBM biopsies and CD138+-selected myeloma plasma cells. Risk status was assessed by ISS stage as defined by the International Myeloma Working Group (IMWG)25. CD138+ gene-expression data were used to generate the GEP-70 score55. A total of 1,360 Affymetrix Human Genome U133 Plus 2.0 gene-expression microarrays were derived from WBM biopsies from 461 samples from patients.
Unsupervised clustering of the top 10% most variable estimated non-tumor gene expression profiles (643 genes) across all time points was performed using the R package ConsensusClusterPlus (Bioconductor). Bayesian information criterion (BIC) was used to select the optimal number of clusters. The cluster centroids were calculated based on the median expression of each of the genes for the patient samples belonging to that cluster, and the sum of the squared distances was taken for the entire patient cluster. The residual sum squared distances across all clusters were used to calculate the BIC score, with the assumption of a Gaussian special case, as follows:  BIC = n × ln(RSS/n) + ln(n) × k, where n is the number of observations, RSS is the residual sum of squares, and k is the number of clusters. The maximum possible number of clusters was set to the square root of  the number of samples; thus, for the 867 patient samples, the optimal number of clusters determined by the algorithm was 13 out of a possible maximum of 29 clusters. Several of these microenvironment clusters were comprised of very few patient samples; therefore, we combined those micro-clusters defined as those containing less than a threshold of 5% of the samples.   For supervised machine learning survival analysis, cell-type estimates for cells with similar functions and gene expression signatures were added together to create 19 cell types for assessment.
The final signals correspond to probes that map to annotated genes as reported by Bioconductor's 'hgu133plus2.db' or BioMart repository ENSEMBL_MART_ENSEMBL with probes matching to 'LINC00597' added by hand.  Where multiple probes map to a particular gene, the median reported signal was used.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from200ng total RNA

extract_protocol: RNA extraction and isolation was performed with the AllPrep kit by Qiagen

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 3, 6 months follow-up

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

value: Confirmed CR

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: III

value: FALSE


title: WBM, BI14-000292

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Female

value: Black

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000621

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: FG-PostConsolidation

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Maintenance 1

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

value: VGPR

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI12-000743

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 3, 6 months follow-up

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: White / Caucasian

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Relapse

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000820

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 1

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: FALSE


title: WBM, BI14-000195

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000822

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, BI12-000759

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Female

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: VGPR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000642

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Extra Sample

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

value: Y

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI12-000757

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 2

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, BI13-000851

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 3

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

value: Confirmed NCR

tag: monthspfs

tag: albumin

tag: ldh

value: III


title: WBM, BI12-000623

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 1

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Male

value: Native American

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000617

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Female

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI14-000923

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: C1 48Hr Vel

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

value: II

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, RE12-000233

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: monthspfs

tag: albumin

tag: ldh


title: HM07

type: genomic

city: Chiba

first: Hirokazu

last: Usui

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Reproductive Medicine

country: Japan

institute: Graduate School of Medicine, Chiba University

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip array was scanned using the iScan (Illumina)

data_processing:
Data were processed using GenomeStudio V2011.1
Raw data files include: X Raw, Y Raw,  X, Y
Processed data files include: SNP Name, GC Score,  Allele1 - AB,  Allele2 - AB,  Theta,  R , B Allele Freq,   Log R Ratio

molecule: genomic DNA

source_name: androgenetic CHM

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted from MCT tissues using the Qiagen DNA Mini Kit.

tag: tissue

value: placenta

tag: diagnosis

value: hydatidiform mole

tag: placental sex

value: female


title: HM10


title: HM12


title: HM13

value: male


title: HM09


title: HM11


title: HM08


title: WBM, BI12-000616

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Extra Sample

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

value: Male

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progressive Disease

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000620

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, BI12-000732

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Black

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, BI14-000290

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Female

tag: race

tag: ageatsampledate

tag: numberoftransplants

value: VGPR

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI12-000641

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 2

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Male

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Not Evaluable

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P4415-01-bc14973-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh

value: III


title: WBM, P1186-04-BC15200-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Physician Request (Comment)

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: SD

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, BI14-000293

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Female

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI14-000301

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: HY

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

value: Male

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: HM06

tag: tissue

value: placenta

tag: diagnosis

value: hydatidiform mole

tag: placental sex

value: male


title: WBM, BI12-000739

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 2

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

value: Progression

tag: monthspfs

tag: albumin

tag: ldh

value: II


title: HM05

tag: tissue

tag: diagnosis

tag: placental sex


title: WBM, BI14-000406

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

value: Y

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

value: III

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, BI14-000134

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Female

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

value: VGPR

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI14-000587

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: tc

tag: datapulled

tag: datechip

value: Male

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P4434-01-BC14365-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: Native American

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, BI12-000755

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 1

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: tc

tag: datapulled

tag: datechip

value: White / Caucasian

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: HM03

tag: tissue

value: placenta

tag: diagnosis

value: hydatidiform mole

tag: placental sex

value: male


title: HM04


title: HM02

value: female


title: HM01


title: WBM, BI12-000428

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 2

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

value: Confirmed Response

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: II

value: FALSE


title: WBM, BI14-000400

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

value: Male

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progressive Disease

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000085

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Physician Request (Comment)

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

value: Progression

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, BI12-000440

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: FG-PostConsolidation

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, RE12-000235

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 1

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: FALSE


title: WBM, BI14-000404

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

value: Male

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000468

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh


title: 3D HepG2 day_28, replicate 3

city: Durham

first: Sreenivasa

middle: C

last: Ramaiahgari

state: NC

address: 111 TW Alexander drive

department: National Toxicology Program

institute: NIEHS

description: 3D cells cultured for 28 days

hyb_protocol: The fragmented cRNA with a concentration of 0.0375 µg/µl was utilized for the hybridization on the Affymetrix HT Human Genome U133+ PM array plate.  The Affymetrix HWS Kit (#901530) was used for the hybridization, washing and staining of the chips.

scan_protocol: Scanning  of  the  Array  Plates  was  performed  using  the  Affymetrix GeneTitan scanner.

data_processing: The software program Affymetrix GeneChip Command Console (v3.2) was used to operate the Affymetrix GeneTitan system which process the washing, staining and hybridization of the Array Plates. After scanning, the array images (DAT files) as well as the visual inspection of the correct alignment of the grid were inspected using the program Affymetrix Command Console Viewer software. The data Quality Control was performed in the program Affymetrix Expression Console v1.1 software to determine if all parameters are within quality specifications. A summarization step was performed prior to the performance of the data Quality Control. The Probe Logarithmic Intensity Error Estimation (PLIER) algorithm method is used for probe summarization. This step is only performed for quality control of the data set.

source_name: 3D HepG2 cells at day 28

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA.

growth_protocol: HepG2 cells in 2D were cultured in tissue culture flasks in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 25 U/mL penicillin/ 25 μg/mL streptomycin. For 3D culture cells were grown on top of matrigel with the same media used for 2D culture.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions; followed by clean up with RNeasy mini kit (Qiagen) as per manufacturer's instructions.

treatment_protocol: No treatments are involved; we looked at the basal-level gene expressionof cells in 2D culture at day 3 and cells in 3D culture at day 3, 7, 14, 21 and 28

tag: cell type

value: Human hepatocarcinoma

tag: cell line

tag: culture condition

tag: time point

value: 28 days


title: WBM, BI14-000124

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 5

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed NCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000451

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 1

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

value: Relapse from Complete Response (include only in disease-free survival analysis)

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: III


title: 3D HepG2 day_21, replicate 2

description: 3D cells cultured for 21 days

source_name: 3D HepG2 cells at day 21

tag: cell type

tag: cell line

tag: culture condition

tag: time point

value: 21 days


title: 3D HepG2 day_21, replicate 4

description: 3D cells cultured for 21 days


title: 3D HepG2 day_21, replicate 3

description: 3D cells cultured for 21 days


title: 3D HepG2 day_28, replicate 1

description: 3D cells cultured for 28 days


title: WBM, BI12-000443

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 2

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

value: Female

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, BI12-000434

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: BLANK

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh


title: 3D HepG2 day_28, replicate 4

description: 3D cells cultured for 28 days

tag: cell type

value: Human hepatocarcinoma

tag: cell line

tag: culture condition

tag: time point

value: 28 days


title: WBM, P2867-08-BC14474-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000449

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Extra Sample

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: I


title: WBM, BI12-000445

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, BI12-000453

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 2

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

value: sCR

tag: monthspfs

tag: albumin

tag: ldh

value: II


title: WBM, BI12-000433

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Off-Study, Other Than Relapse

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

value: Female

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: 3D HepG2 day_14, replicate 2

description: 3D cells cultured for 14 days

source_name: 3D HepG2 cells at day 14

tag: cell type

value: Human hepatocarcinoma

tag: cell line

tag: culture condition

tag: time point

value: 14 days


title: 3D HepG2 day_14, replicate 4

description: 3D cells cultured for 14 days


title: 3D HepG2 day_21, replicate 1

description: 3D cells cultured for 21 days

value: 21 days


title: 3D HepG2 day_28, replicate 2

description: 3D cells cultured for 28 days

value: 28 days


title: 3D HepG2 day_14, replicate 3

description: 3D cells cultured for 14 days


title: 3D HepG2 day_14, replicate 1

description: 3D cells cultured for 14 days


title: WBM, BI14-000071

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Annual

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Progression

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: III


title: WBM, BI14-000492

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Improvement

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: FALSE

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish

value: VDTACE (Vel / Dex / Thal / Adria / Cytoxan / Etop)


title: WBM, BI12-000436

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 2

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: sCR

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, RE12-000237

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: CDE-PostTransplant

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000481

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: II


title: WBM, BI14-000121

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Extra Sample

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

value: Female

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed NCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: 3D HepG2 day_7, replicate 2

description: 3D cells cultured for 7 days

source_name: 3D HepG2 cells at day 7

tag: cell type

value: Human hepatocarcinoma

tag: cell line

tag: culture condition

tag: time point

value: 7 days


title: 3D HepG2 day_3, replicate 4

description: 3D cells cultured for 3 days

source_name: 3D HepG2 cells at day 3

value: 3 days


title: WBM, BI14-000100

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 2

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh

value: FALSE


title: 3D HepG2 day_3, replicate 1

description: 3D cells cultured for 3 days

tag: cell type

tag: cell line

tag: culture condition

tag: time point


title: 3D HepG2 day_7, replicate 3

description: 3D cells cultured for 7 days


title: WBM, BI14-000480

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: FG-PostConsolidation

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Relapse / Progression

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: SD

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: 3D HepG2 day_3, replicate 2

description: 3D cells cultured for 3 days

tag: cell type

tag: cell line

tag: culture condition

tag: time point


title: 3D HepG2 day_7, replicate 1

description: 3D cells cultured for 7 days


title: WBM, BI13-000859

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Extra Sample

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Confirmed CR

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

value: III


title: WBM, BI13-000723

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

value: Female

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Not Evaluable

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000437

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: VGPR

tag: monthspfs

tag: albumin

tag: ldh

value: FALSE


title: WBM, BI14-000090

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Physician Request (Comment)

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

value: Male

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000585

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P4421-01-BC13546-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000930

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: C1 48Hr Vel

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: sCR

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: WBM, RE12-000145

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: 3D HepG2 day_7, replicate 4

description: 3D cells cultured for 7 days

tag: cell type

value: Human hepatocarcinoma

tag: cell line

tag: culture condition

tag: time point

value: 7 days


title: 2D HepG2 day_3, replicate 4

description: 2D cells cultured for 3 days

source_name: 2D HepG2 cells at day 3

value: 3 days


title: 2D HepG2 day_3, replicate 2

description: 2D cells cultured for 3 days


title: 3D HepG2 day_3, replicate 3

description: 3D cells cultured for 3 days


title: WBM, BI14-000109

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Off-Study, Other Than Relapse

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh


title: N1ICD, biological rep 3

city: Winnipeg

first: Afshin

last: Raouf

state: Manitoba

address: 471 Apotex centre, 750 McDermot Avenue

department: Immunology

country: Canada

institute: University of Manitoba

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Arrays. 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 Partek Genomics Suite using the RMA normalization method

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: 184-hTert cells were grown in DMEM:F12 1:1 media supplemented with 10ng EGF, 25 μg Insulin, 500μg hydrocortisone, 2.5ng sodium selenate, 400μg G418, 0.15U prolactin, 1.6 μg transferrin and 10nM isoproterenol and were subcultured every 2-3 days (before reaching confluency). Both the cell types were maintained in a humidified chamber at 37c and 5% CO2.

extract_protocol: RNA isolation was done using Trizol, according to the manufacturer's instructions.

treatment_protocol: Cells were lentivirally transduced and after 48 hours, the transduded cells expressing green fluorescent protein (GFP) are sorted via FACS for RNA isolation

tag: cell line


title: WBM, BI13-000720

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 2, 6 months follow-up

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: N3ICD, biological rep 3

tag: cell line


title: N1ICD, biological rep 2


title: Control, biological rep 3


title: N1ICD, biological rep 1


title: WBM, BI14-000563

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Relapse / Progression

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Progression

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: N3ICD, biological rep 1

tag: cell line


title: 2D HepG2 day_3, replicate 1

description: 2D cells cultured for 3 days

tag: cell type

tag: culture condition

tag: time point


title: N3ICD, biological rep 2


title: WBM, P4392-01-BC13695-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: C1 48Hr Vel

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: III

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: 2D HepG2 day_3, replicate 3

description: 2D cells cultured for 3 days

tag: cell type

value: Human hepatocarcinoma

tag: cell line

tag: culture condition

tag: time point

value: 3 days


title: WBM, BI14-000931

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, BI14-000583

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: FG-PostConsolidation

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Physician Request (Comment)

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000922

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: B-PostInduction

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: Control, biological rep 1

tag: cell line


title: WBM, BI13-000704

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Extra Sample

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

value: Female

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI14-000917

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: C1 48Hr Vel

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: sCR

tag: monthspfs

tag: albumin

tag: ldh

value: FALSE


title: WBM, BI14-000568

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

value: LB

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

value: Black

value: Y

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progressive Disease

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, RE12-000155

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: WBM, P4423-01-BC13447-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

tag: pointgroup

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: Control, biological rep 2

tag: cell line


title: WBM, BI13-000713

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: Signal Genetics

tag: pointgroup

value: H-PostMaintenance

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Maintenance Year 3

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: ASCs only 1

city: Shanghai

first: Zhihua Han

last: Han

state: Please select region, state or province

address: Xin Songjiang Road 650

department: Orthopedic Traumatology, Shanghai Trauma and Emergency Center

country: China

institute: Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: ASCs only

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: ASCs were isolated and then cultured in Dulbecco’s modified Eagle’s medium/F12 medium containing 10% fetal bovine serum (FBS) in 37°, 5% CO2 incubator. The medium was changed every 2-3 days.

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

treatment_protocol: Both ASCs and NPCs at passage 3 were co-cultured using non-direct cell-cell contact coculturing system for 7 days

tag: cell type

value: adipose-derived mesenchymal stem cells (ASCs)

tag: age

value: passage 3


title: ASCs only 2


title: WBM, P4431-01-BC13350-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datapulled

tag: datechip

value: Male

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish