title: WBM, P1331-01-BS3722-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

tag: samexclude

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tag: posttransplantnomaintenance

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tag: poststartmaintenance

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tag: sorting

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tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

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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

value: I


title: WBM, P1339-02-BS3884-U133Plus-2

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

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tag: descprotocol

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tag: batch

value: MIRT

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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: 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

value: Y

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, P1323-00-BS3577-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

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tag: posttransplantpreconsolidation

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tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

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tag: isexpress

tag: sampletype

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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

value: Hispanic

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Remission

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1341-02-BS3678-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

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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: 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: 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, P1307-03-BS3498-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

tag: daysafterbasesample

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tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

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tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

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tag: polypc

tag: ifn

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tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

tag: race

value: Asian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1307-00-BS3626-U133Plus-2

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: C1 48Hr VDTPACE

tag: cluster

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tag: wnt

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tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1081-08-BS3628-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

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

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation 1

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

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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

value: Progression

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1323-05-BS3765-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

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tag: posttransplantnomaintenance

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tag: sampleID

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tag: sorting

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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: Y

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: WBM, P1366-04-BS3840-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

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tag: sorting

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value: Baseline

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value: PR

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tag: ifn

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tag: protocolsample

tag: celname

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tag: gender

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tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Possible Relapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1337-03-BS4006-U133Plus-2

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

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tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

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, P1314-04-BS3295-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

value: A-BeforeTreatment

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tag: samexclude

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tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

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tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

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tag: sampleID

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tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MF

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tag: polypc

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tag: centrosomeindex

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tag: transplant

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tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: WBM, P1296-07-BS3323-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

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tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

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tag: sampletype

value: RNBX-Random Biopsy

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tag: responselast

value: SD

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tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1338-02-BS3856-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

tag: pointgroup

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tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

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tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

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tag: isexpress

tag: sampletype

tag: sorting

tag: sampleprotocol

tag: point

tag: cluster

value: MS

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tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

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tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: datapulled

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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: Confirmed NCR

tag: monthspfs

tag: albumin

tag: ldh


title: Sample_RR_HsDm_IgG_IgG-

type: SRA

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

library_source: transcriptomic

data_processing:
Library strategy: CUT&RUN
We aligned reads to both human genome hg38 and spike-in genome dm6 using Bowtie2-2.2.6 with the following comment: bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
We used an in-house R package, domainCalling (https://github.com/TapscottLab/domainCalling), to perform spike-in factor normalization and binding domain (board peaks) detection.
The algorithm started by counting reads overlapping with a sliding window throughout the genome for non-background (DUX+) and background (IgG or DUX-) samples
We normalized counts for each windows by spike-in factor and filtered out un-interesting windows whose average abundance was not exceed three fold change to the background .
We merged retained window with neighbors within 2kbp distance and filtered out merged windows of less than 500 bp width.
Genome_build: hg38
Supplementary_files_format_and_content: XYPlusVsIgG in both BED and RDA format is the called XY binding domains in DUX+ samples with IgG+ as background.
Supplementary_files_format_and_content: XYPlusVsMinus in both BED and RDA format is the called XY binding domains in DUX+ samples with DUX- as background.

molecule: polyA RNA

source_name: MB135iDUX4 myoblast

growth_protocol: MB135iDUX4 cells were grown in F10 medium supplemented with 10% FBS, 1% pen/strep, 10pg/mL fgf, 1uM dexamethasone, and 2ug/mL puromycin

extract_protocol:
cells were trypsinized and counted; 5 million cells were used per CUT and RUN reaction
described in Skene and Henikoff, 2017 eLife

treatment_protocol: cells were treated with 1ug/mL doxycycline for 16 hours

tag: tissue

value: MB135iDUX4 myoblast

tag: treatment

value: IgG/No DUX4 induction

tag: median fragment

tag: genome


title: WBM, P1309-06-BS3601-U133Plus-2

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

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

value: Female

value: White / Caucasian

value: Y

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Onset Response

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: FALSE

tag: iss

value: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1291-01-BS3367-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

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: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh

value: II


title: WBM, P1314-05-BS3578-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

value: RNBX-Random Biopsy

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: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1296-05-BS3450-U133Plus-2

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

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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: SD

tag: monthspfs

tag: albumin

tag: ldh


title: Sample_RR_HsDm_3_DUX-

tag: tissue

value: MB135iDUX4 myoblast

tag: treatment

value: No DUX4 induction

tag: median fragment

tag: genome


title: WBM, P1271-02-BS3149-U133Plus-2

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: 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

value: Female

value: White / Caucasian

value: Y

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, P1305-04-BS3474-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

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: datesamplernbx

tag: gender

value: Male

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Confirmed NCR

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, P1389-02-BS3438-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

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: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: Sample_RR_HsDm_2_DUX-

tag: tissue

value: MB135iDUX4 myoblast

tag: treatment

value: No DUX4 induction

tag: median fragment

tag: genome


title: WBM, BI13-000029

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: Off-Study, Other Than Relapse

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

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1259-02-BS3102-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

value: Y

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progression

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: III

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, RE12-000457

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 1

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: SD

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1248-04-BS2916-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

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

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: Sample_RR_HsDm_1_DUX-

tag: tissue

value: MB135iDUX4 myoblast

tag: treatment

value: No DUX4 induction

tag: median fragment

tag: genome


title: WBM, P1228-02-BS3007-U133Plus-2

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: 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

tag: dateebmtrelapse

value: Remission

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1263-05-BS3151-U133Plus-2

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: 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

value: Y

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: Sample_RR_HsDm_IgG_IgG+

tag: tissue

tag: treatment

value: IgG/DUX4 induction

tag: median fragment

tag: genome


title: WBM, P1271-03-BS3181-U133Plus-2

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

tag: datapulled

tag: datechip

tag: protocolsample

tag: celname

tag: datesamplernbx

tag: gender

value: Female

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh

value: III

value: FALSE


title: Sample_RR_HsDm_3_DUX+

tag: tissue

tag: treatment

value: DUX4 induction

tag: median fragment

tag: genome


title: WBM, P1239-05-BS2918-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

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

tag: protocolsample

tag: celname

value: Male

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Improvement

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, RE12-000364

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 Transplant 2

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: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Confirmed CR

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, P1224-03-BS2977-U133Plus-2

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: 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

value: Black

value: Y

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, BI12-000167

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 Consolidation 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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh

value: II

value: FALSE


title: Sample_RR_HsDm_2_DUX+

tag: tissue

value: MB135iDUX4 myoblast

tag: treatment

value: DUX4 induction

tag: median fragment

tag: genome


title: Sample_RR_HsDm_1_DUX+


title: WBM, P1228-03-BS3069-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

value: Male

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Remission

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

value: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI12-000042

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

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Transplant 2

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: datesamplernbx

tag: gender

value: Female

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Confirmed CR

tag: monthspfs

tag: albumin

tag: ldh

value: I


title: WBM, P1232-02-BS2672-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

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

value: Y

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progression

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: Mature 3

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

data_processing:
Align reads to Human Genome and Output concordant aligned reads as fastq - HiSat2  (v2.0.3) : hisat2  -x "UCSC_hg38"  --al-conc  "output"  --rna-strandness R  --no-mixed --no-discordant.
Align concordant human aligned reads to Mouse Genome and output unaligned reads as fastq - HiSat2  (v2.0.3) : hisat2  -x "UCSC_mm10" --un-conc "output"   --rna-strandness R  --no-mixed --no-discordant.
Align Human Specific Reads to Human Genome and output concordant aligned reads as BAM - HiSat2  (v2.0.3) : hisat2  -x "UCSC_hg38"  --rna-strandness R  --no-mixed --no-discordant. Output concordant aligned reads as BAM
Generate Human specific read counts for each gene - HTSeq-count  (v0.6.1) : htseq-count --mode=union --stranded=reverse --minaqual=255 --type='exon'
Differential Expression Analysis - DESeq2 (v1.12.4) : DESeq  (test = "Wald", fitType= "parametric")
Genome_build: Homo_sapiens_UCSC_hg38 & Mus_musculus_UCSC_mm10
Supplementary_files_format_and_content: tab-delimited text files containing feature counts (htCount)

organism:
Homo sapiens
Mus musculus

source_name: hES cell graft in rodent brain

growth_protocol: Human PSCs were seeded on Laminin-521 (10ug/ml; StemCell Technologies) in the presence of dual SMAD inhibitors (SB431542, 10uM, 0-5 days in vitro (DIV), R&D systems; and LDN193189, 200nM, 0-11DIV, Stemgent) to promote neural induction. Sonic hedgehog C25II (100ng/ml; R&D systems) and Purmorphamine (2uM; Stemgent) were supplemented into the media from day 1-7DIV to promote ventralisation, in addition to the caudalizing Wnt agonist, CHIR 99021 (3uM; Stemgent, 3-11DIV). From 13DIV, cells were cultured in a ‘maturation media’ consisting of NBB27 supplemented with GDNF (20ng/ml; R&D systems), BDNF (20ng/ml, R&D system), TGFβ3 (1 ng/ml; PeproTech), DAPT (10 μM, Sigma-Aldrich), ascorbic acid (200nM; Sigma-Aldrich) and dibutyryl cAMP (0.05mM; Tocris Bioscience). At 21 DIV differentiating cultures were dissociated in Accutase (Innovative Cell Technologies) to a single-cell suspension and fluorescent activated cell sorting (FACS) performed on a MoFlo cell sorter (Beckman Coulter, MoFlo to isolate LMX1A-GFP expressing progenitors, as previously described (de Luzy et al., 2018). The FACS-isolated cell fraction was resuspended at 100,000 cells/µL in maturation media containing ROCK inhibitor (Y27632, 40uM, Sigma) and stored on ice until the time of implantation.

extract_protocol:
The striatum (containing the transplant) were rapidly dissected from the host brain and flash frozen. The isolated tissue was homogenised using a TissueLyser LT (Qiagen) and total RNA extracted using the RNeasy Mini Kit (Qiagen) including DNase treatment.
Mixed species cDNA libraries were prepared using TruSeq stranded mRNA sample preparation kit (Illumina).

tag: graft type

value: Ventral midbrain

tag: transplant time

value: 5 Months

tag: host

value: Athymic (Foxn1nu) nude mice


title: Mature 2


title: WBM, P1239-04-BS3067-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: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Improvement

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: Mature 1

tag: graft type

tag: transplant time

tag: host


title: WBM, P1224-05-BS3044-U133Plus-2

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: C1 48Hr VDTPACE

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: celname

value: Black

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: WBM, RE12-000362

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 Transplant 2

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: protocolsample

tag: datesamplernbx

tag: gender

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

value: I


title: WBM, BI12-000010

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

tag: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, P1248-05-BS3066-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

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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, RE12-000611

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 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: celname

value: Male

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, P1119-03-BS2997-U133Plus-2

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: C1 48Hr Vel

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: protocolsample

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

value: II


title: Immature3

tag: graft type

value: Ventral midbrain

tag: transplant time

value: 1 Month

tag: host

value: Athymic (Foxn1nu) nude mice


title: WBM, RE12-000352

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: celname

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: III

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1225-03-BS2994-U133Plus-2

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: refchip

tag: fyprimary

tag: qyconverted

tag: protocolsample

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Progression

tag: monthspfs

tag: albumin

tag: ldh

value: I

value: FALSE


title: Immature2

tag: graft type

tag: transplant time

tag: host


title: WBM, P1189-05-BS2699-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: descprotocol

tag: ftprotocolbase

tag: batch

value: MIRT

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

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: celname

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, P1158-04-BS2912-U133Plus-2

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: 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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Complete Response

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: WBM, P1177-04-BS2660-U133Plus-2

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: 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

tag: celname

value: Male

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Stable

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1263-04-BS2878-U133Plus-2

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: refchip

tag: fyprimary

tag: qyconverted

tag: protocolsample

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Confirmed CR

tag: monthspfs

tag: albumin

tag: ldh

value: II


title: WBM, BI12-000849

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

tag: tc

tag: datapulled

tag: datechip

tag: celname

value: Female

value: Y

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: Immature1

tag: graft type

value: Ventral midbrain

tag: transplant time

value: 1 Month

tag: host

value: Athymic (Foxn1nu) nude mice


title: WBM, P1169-05-BS2751-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

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: C1 48Hr VDTPACE

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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Complete Response

tag: monthspfs

tag: albumin

tag: ldh

value: FALSE


title: WBM, P1189-00-BS2791-U133Plus-2

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

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: celname

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progression

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1178-02-BS2753-U133Plus-2

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: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: Undiff 2

tag: graft type

value: Undifferentiated

tag: transplant time

tag: host


title: WBM, P1184-02-BS2658-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

tag: celname

value: Y

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, RE12-000521

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

value: RNBX-Random Biopsy

tag: sorting

tag: sampleprotocol

tag: point

value: Pre Consolidation 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: protocolsample

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh

value: II


title: Undiff 1

tag: graft type

tag: transplant time

value: 1 Month

tag: host

value: Athymic (Foxn1nu) nude mice


title: WBM, P1174-03-BS2702-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

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: celname

value: Female

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, P1182-00-BS2610-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

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: protocolsample

tag: datesamplernbx

tag: gender

value: Male

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, P1186-00-BS2601-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

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: tc

tag: datapulled

tag: datechip

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: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, BI13-000017

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

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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1195-02-BS2632-U133Plus-2_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

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: celname

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed NCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: I

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: Undiff 3

tag: graft type

value: Undifferentiated

tag: transplant time

value: 1 Month

tag: host

value: Athymic (Foxn1nu) nude mice


title: WBM, P1171-03-BS2613-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

value: C1 48Hr VDTPACE

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: datesamplernbx

tag: gender

value: Female

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: WBM, P1188-00-BS2690-U133Plus-2

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: celname

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: WBM, P1176-00-BS2578-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

tag: cluster

value: HY

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: datesamplernbx

tag: gender

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh

value: III


title: WBM, P1182-04-BS2718-U133Plus-2

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: C1 48Hr Vel

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: celname

value: Male

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progression

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, P0521-04-BS2569-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: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: sCR

tag: monthspfs

tag: albumin

tag: ldh

value: II


title: WBM, P1132-07-BS2517-U133Plus-2

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

tag: refchip

tag: fyprimary

tag: qyconverted

tag: celname

value: Female

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1176-03-BS2614-U133Plus-2

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: C1 48Hr VDTPACE

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: datesamplernbx

tag: gender

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh

value: III


title: WBM, P1174-00-BS2558-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: celname

value: White / Caucasian

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish


title: WBM, P1167-00-BS2508-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

value: C1 48Hr Vel

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

tag: protocolsample

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1178-03-BS2524-U133Plus-2

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: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Complete Response

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1130-02-BS2473-U133Plus-2

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

tag: protocolsample

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Confirmed CR

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh


title: WBM, P1169-04-BS2505-U133Plus-2

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: 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: celname

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, P1187-02-BS2688-U133Plus-2

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

tag: protocolsample

tag: datesamplernbx

tag: gender

value: Female

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: SD

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1166-00-BS2357-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

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: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Onset PR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1196-00-BS2288-U133Plus-2

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: Baseline

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: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Progressive Disease

tag: monthspfs

tag: albumin

tag: ldh

value: FALSE


title: WBM, P1145-00-BS2271-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

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: celname

value: Male

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, P1173-03-BS2435-U133Plus-2

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: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1100-00-BS2287-U133Plus-2

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: 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: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Confirmed CR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

value: TRUE

tag: iss

tag: sampledatetime

tag: hyperdiploidclinicalfish


title: WBM, P1003-07-BS2472-U133Plus-2_3

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

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: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: Relapse

tag: monthspfs

tag: albumin

tag: ldh

value: III


title: WBM, P1132-01-BS2383-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

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: celname

value: Female

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, P1145-04-BS2313-U133Plus-2

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: 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: tc

tag: datapulled

tag: datechip

tag: protocolsample

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

value: SD

tag: monthspfs

tag: albumin

tag: ldh


title: WBM, P1093-04-BS2217-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

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: celname

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: No Response

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish