title: WBM, MGUS, BI14-000331

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

value: Relapse / Progression

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI14-000374

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 the  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.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MGUS Patients

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

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

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: Signal Genetics

tag: pointgroup

value: AMM

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

value: RNBX-Random Biopsy

value: Baseline

value: MS

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue

value: whole bone marrow (WBM)


title: PBMC_25.4_NK

type: SRA

city: London

first: Harry

last: Pickering

state: Greater London

address: LSHTM, Keppel Street

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

library_source: transcriptomic

data_processing:
trim low quality tails, polyA tails and adapters (bbmap): k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 int=f
align to human genome (hg38)  (STAR aligner): --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
indexed BAM files (samtools)
counted reads per sample (HTSeq-count)
normalised counts by variance stabilising transformation (DESeq2)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated ensembl transcript and read count per sample (.txt)

source_name: PBMC

growth_protocol: Human PBMC purified by gradient centrifugation, stimulated in vitro for 18 hours with 0.75ng/ml recombinant human IL-15

extract_protocol:
RNA was extracted from cell pellets using Norgen RNA/DNA purification kits
Library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

tag: cell fraction

value: NK cell enriched

tag: stimulation condition

value: IL-15 (18 hours)

tag: time point

value: 30 days post-vaccination


title: WBM, MGUS, BI14-000267

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

value: Physician Request (Comment)

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI14-000317

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

value: SWOG 0120

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: 3 Yr Follow-Up

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI14-000304

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI14-000348

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: MGUS

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: MF

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: PBMC_37.4_NK

tag: cell fraction

tag: stimulation condition

tag: time point


title: WBM, MGUS, BI14-000330

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

value: MGUS, Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI14-000402

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: First - Untreated Patient

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: PBMC_19.1_NK

tag: cell fraction

tag: stimulation condition

tag: time point

value: Baseline (pre-vaccination)


title: WBM, MGUS, BI14-000344

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

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: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI14-000265

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: AMM

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: RNBX-Random Biopsy

value: 2 Yr Follow-Up

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI14-000422

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

value: whole bone marrow (WBM)


title: WBM, MGUS, BI14-000230

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI14-000136

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: PBMC_16.4_NK

tag: cell fraction

value: NK cell enriched

tag: stimulation condition

value: IL-15 (18 hours)

tag: time point


title: WBM, MGUS, BI14-000037

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

value: Baseline

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI14-000104

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

value: Extra Sample

tag: cluster

value: PR

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000205

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

value: SWOG 0120

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000194

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI14-000153

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: MGUS

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

value: Physician Request (Comment)

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000190

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000202

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: PBMC_16.1_NK

tag: cell fraction

tag: stimulation condition

tag: time point


title: PBMC_19.4_NK

value: 30 days post-vaccination


title: WBM, MGUS, BI13-000184

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000183

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000167

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI12-000333

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: First - Untreated Patient

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000157

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: Signal Genetics

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000163

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, P2403-01-BC3155-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: MIRT

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000169

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: AMM

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: RNBX-Random Biopsy

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, P2631-02-BC4345-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

value: whole bone marrow (WBM)


title: WBM, MGUS, BI13-000168

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000166

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, P2628-02-BC4270-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: First - Treated patient

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, P2598-04-BC4245-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, P2319-02-BC2369-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000164

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

value: MS

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000182

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000159

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, P2321-02-BC2367-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: Relapse / Progression

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000174

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000181

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, P2288-02-BC1954-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI13-000161

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, P2402-01-BC3219-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

value: MGUS, Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, BI12-000612

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, P2387-01-BC2847-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

value: Waldenstrom, Baseline

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, P2419-01-BC2387-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

value: SWOG 0120

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI13-000171

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: WBM, MGUS, P2633-02-BC3970-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

value: PR

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue


title: WBM, MGUS, BI12-000200

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

value: HY

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc


title: SKOV3_sh3: SKOV_SFPQ_replicate3_Ovarian Cancer cells

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

country: Italy

institute: CRO Aviano

description: Constitutive Gene expression of EOC cells.

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: epithelial ovarian cancer cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Accordinf ATCC guidelines

extract_protocol: Total RNA was extracted from ovarian cancer cell lines using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: tissue

value: ovarian cancer

tag: histotype

value: epithelial


title: WBM, MGUS, P1533-02-BS5514-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: WBM, MGUS, P1706-02-BS7589-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: tissue


title: WBM, MGUS, P2233-01-BC1627-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

value: MF

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: WBM, MGUS, P1540-02-BS4498-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: MGUS

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: tissue


title: WBM, MGUS, P2281-02-BC2107-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: MIRT

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: WBM, MGUS, P1819-02-BS8246-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: AMM

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

value: 3 Mo Follow-Up

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: tissue


title: SKOV3_sh2: SKOV_SFPQ_replicate2_Ovarian Cancer cells

tag: cell line

tag: histotype


title: WBM, MGUS, P2186-02-BC1432-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

value: RNBX-Random Biopsy

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

value: whole bone marrow (WBM)


title: WBM, MGUS, P1255-02-BS3024-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: tissue


title: WBM, MGUS, P2242-02-BC1658-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: WBM, MGUS, P2234-01-BC1639-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: posttransplantpremaintenance

tag: posttransplantnomaintenance

tag: sampleID

tag: chiptype

tag: isexpress

tag: sampletype

tag: sorting

tag: point

tag: cluster

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: tissue


title: WBM, MGUS, P2089-02-BS1148-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

tag: postconsolidationpremaintenance

tag: postconsolidationnomaintenance

tag: poststartmaintenance

tag: eventid

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: SKOV3_sh_cnt: SKOV_cnt1_Ovarian Cancer cells

tag: cell line

tag: tissue

tag: histotype


title: human patient blood mRNA 5

city: beijing

first: Yang

last: Zou

address: Xicheng District road 95 Yongan

country: China

institute: Beijing Friendship Hospital Affiliated to the Capital University of Medical Sciences.

description: mRNA expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: human patient blood mRNA

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

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

tag: subject status

value: Chinese imported falciparum malaria patient

tag: age (years)

tag: gender

value: male

value: blood

tag: parasitemia (%)

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: WBM, MGUS, P2285-02-BC2161-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: 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: datepulled

tag: chipdate

tag: protocolsample


title: MDAH_sh_cnt: MDAH_cnt1_Ovarian Cancer cells

tag: cell line

value: MDAH

tag: tissue

tag: histotype


title: human patient blood mRNA 6

description: mRNA expression

tag: subject status

tag: age (years)

tag: gender

tag: parasitemia (%)

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: SKOV3_sh_cnt: SKOV_cnt2_Ovarian Cancer cells


title: MDAH_sh_cnt: MDAH_cnt2_Ovarian Cancer cells


title: WBM, MGUS, P1851-02-BS8590-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: 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: datepulled

tag: chipdate

tag: celname


title: WBM, MGUS, P1018-02-BS1464-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

value: MGUS, Baseline

tag: cluster

tag: risk

tag: protocolsample

tag: tissue


title: WBM, MGUS, P1198-00-BS2533-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

value: Relapse / Progression

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: datepulled

tag: chipdate

tag: celname


title: WBM, MGUS, P1811-03-BS8348-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

value: SWOG 0120

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

tag: cluster

tag: risk

tag: protocolsample

tag: tissue


title: human patient blood mRNA 3

description: mRNA expression

tag: subject status

tag: age (years)

tag: gender

tag: parasitemia (%)

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: human patient blood mRNA 4

description: mRNA expression


title: MDAH_sh2: MDAH_SFPQ_replicate2_Ovarian Cancer cells

tag: cell line

value: ovarian cancer

tag: histotype


title: human patient blood mRNA 2

description: mRNA expression


title: MDAH_sh3: MDAH_SFPQ_replicate3_Ovarian Cancer cells

value: epithelial


title: Leaf_PI344123

city: Ann Arbor

first: Sonal

last: Gupta

state: Michigan

address: 1121 Maiden Lane, Apt 106

department: Ecology and Evolutionary Biology

data_processing:
Base calling using bcl2fastq - 2.17.1.14 (convert bcl to fastq files); HCS - 2.2.68 (HiSeq Control Software); RTA - 1.18.66.3 (Real-Time-Analysis, generation of .bcl files); Flowcell - version 4 (flowcell and chemistry)
Sequenced reads were adapter trimmed (cutadapt v1.4), quality controlled (trimmomatic v0.36) and corrected for bases (rcorrector).
Two individuals chosen at random (SampleID 81504 and 81512) were used to constuct de-novo transcriptome assembly, using a single k-mer approach (Trinity) with k=25, and multi k-mer approach (Velvet/Oases) with k-mer ranging from 23-41 and 93-99 with a step-size of 2. The EvidentialGene tr2aacds pipeline (http://arthropods.eugenes.org/EvidentialGene/trassembly.html) was used to merge the all the assemblies to remove redundancy and to get biologically most useful set of transcripts; all transcripts with length less than 200 bases were not considered for further analysis.
Cleaned reads from all samples were mapped back to the reference transcriptome using bwa mem v0.7.15 with default parameter.
Read counts for all transcripts per sample were estimated for only the uniquely mapped reads using samtools v1.9(samtools view -F 0x904 -f 0x40 -b ; samtools idxstats), which were used for differential  expressions analysis using edgeR (version 3.18.1) in R
Genome_build: de-novo assembled transcriptome GHHM01000000 (within Bioproject PRJNA525886)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

organism: Ipomoea batatas

source_name: Young leaf

growth_protocol: The plants were grown in the greenhouse (16 hrs light/8 hrs night cycle)

extract_protocol:
Qiagen RNeasy Plant mini kit with the optional DNase digestion step.
TruSeq Stranded mRNA Sample Preparation protocol (LS protocol)

treatment_protocol: Flash frozen in liquid Nitrogen

tag: developmental stage

tag: leaf shape trait

value: High AR

value: Young leaf


title: Leaf_PI566617

tag: tissue


title: Leaf_PI318848

value: Low AR


title: Leaf_PI531122


title: WBM, MGUS, P1002-02-BS1566-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: MIRT

tag: pointgroup

value: MGUS

tag: daysafterbasesample

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: point

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: WBM, MGUS, P0833-01-BS0651-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

tag: cluster

tag: risk

tag: proindex

tag: tissue

value: whole bone marrow (WBM)


title: human normal blood mRNA 6

description: mRNA expression

source_name: human normal blood mRNA

tag: subject status

value: normal, healthy subject

tag: age (years)

tag: gender

value: male

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: Leaf_PI599392

tag: developmental stage

tag: leaf shape trait


title: human normal blood mRNA 3

description: mRNA expression

value: blood


title: human normal blood mRNA 5

description: mRNA expression


title: WBM, MGUS, P0407-02-BS0006-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

tag: cluster

value: PR

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: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: WBM, MGUS, P0904-03-BS1370-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

tag: daysafterbasesample

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: point

value: Baseline

tag: cluster

tag: risk

tag: proindex

tag: tissue


title: WBM, MGUS, P0987-02-BS1751-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

tag: pointgroup

value: AMM

tag: daysafterbasesample

tag: beforetreatment

tag: posttreatmentpretransplant

tag: posttransplantpreconsolidation

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: datepulled

tag: chipdate

tag: protocolsample

tag: celname


title: human normal blood mRNA 4

description: mRNA expression

tag: subject status

tag: age (years)

tag: gender

tag: tissue

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: human patient blood mRNA 1

description: mRNA expression

value: Chinese imported falciparum malaria patient

tag: parasitemia (%)


title: Leaf_PI566638

tag: developmental stage

tag: leaf shape trait


title: Leaf_PI208886


title: Leaf_PI564154


title: P3876.01.L092.U133Plus.2

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.

source_name: CD138+-selected plasma cell RNA from patients from patients

tag: fnpatid

tag: datesamplernbx

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

tag: iss

value: I

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish

tag: hyperdiploidcyto

tag: imids

value: Thalidomide

tag: inregimenstep

value: Transplant 1 (L):Fractionated MEL + VDT

tag: imidpostresponse

tag: imidimproved

tag: imidgiven

tag: monthsobs

tag: recrev

tag: celfilernbx

tag: celfilernas

tag: maxpfs

tag: gepprocesslocation

tag: issr


title: WBM, MGUS, P0870-05-BS1049-U133Plus-2

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: MIRT

tag: pointgroup

value: MGUS

tag: daysafterbasesample

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: point

value: Extra Sample

tag: cluster

value: MF

tag: risk

tag: proindex

tag: nfkbscore

tag: polypc

tag: ifn

tag: cmyc

tag: wnt

tag: centrosomeindex

tag: pcscorebiopsy

tag: wmprob

tag: refchip

tag: fyprimary

tag: qyconverted

tag: tc

tag: datepulled

tag: chipdate

tag: protocolsample

tag: celname

tag: tissue

value: whole bone marrow (WBM)


title: human normal blood mRNA 2

description: mRNA expression

tag: subject status

value: normal, healthy subject

tag: age (years)

tag: gender

value: male

value: blood

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: human normal blood mRNA 1

description: mRNA expression


title: human patient blood miRNA 5

description: miRNA expression

source_name: human patient blood miRNA

value: Chinese imported falciparum malaria patient

tag: parasitemia (%)


title: Leaf_PI566613

tag: developmental stage

tag: leaf shape trait

value: Entire (High Circularity)

value: Young leaf


title: P3903.01.L211.U133Plus.2

tag: fnpatid

tag: datesamplernbx

value: Female

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: VGPR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: monthspfs

value: TRUE

tag: albumin

tag: ldh

tag: iss

value: II

tag: sampledatetime

tag: hyperdiploidclinicalfish

tag: hyperdiploidcyto

tag: imids

tag: inregimenstep

tag: imidpostresponse

value: SD

tag: imidimproved

tag: imidgiven

tag: monthsobs

tag: recrev

tag: celfilernbx

tag: celfilernas

tag: maxpfs

tag: gepprocesslocation

tag: issr


title: WT Wing imaginal disc 10x scRNA-seq

city: Hong Kong

first: Yan

last: Yan

address: Clear Water Bay

department: LIFS

institute: HKUST

data_processing:
Raw data mapping and primary analysis was performed in the Cell Ranger pipeline.
Secondary analysis for marker gene expression pattern was performed with Seurat (Butler et al., 2018).
Genome_build: GCF_000001215.4
Supplementary_files_format_and_content: csv files include normalized abundance measurements for each Sample

organism: Drosophila melanogaster

source_name: Imaginal wing disc

growth_protocol: Around 50 embryos collected within 3 hours were put in an individual vial of fly food to avoid crowding and the larvae were raised at 25-degree incubator for appropriate lengths of time before dissection.

extract_protocol:
The wing imaginal discs were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation.
Construction of 10x single cell libraries and sequencing on Illumina Hiseq platform were performed by Novogene.

tag: strain

tag: tissue

value: Wing imaginal disc

tag: age

value: 96 Hour After Egg Laying

tag: genotype


title: Leaf_PI585054

tag: developmental stage

tag: leaf shape trait


title: P3814.01.K863.U133Plus.2

tag: fnpatid

tag: datesamplernbx

tag: gender

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: monthspfs

tag: albumin

tag: ldh

tag: iss

value: III

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish

tag: hyperdiploidcyto

tag: imids

value: Thalidomide

tag: inregimenstep

value: Transplant 1 (L):Fractionated MEL + VDT

value: MIRT


title: Leaf_PI592993

tag: developmental stage

tag: leaf shape trait

value: Entire (High Circularity)

tag: tissue

value: Young leaf


title: P3841.01.K970.U133Plus.2

tag: fnpatid

tag: datesamplernbx

tag: gender

value: Male

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Post Transplant 1 bridging

tag: imidpostresponse

tag: imidimproved

tag: imidgiven

tag: monthsobs

tag: recrev

tag: celfilernbx

tag: celfilernas

tag: maxpfs

tag: gepprocesslocation

tag: issr


title: P3823.01.K884.U133Plus.2

tag: fnpatid

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

value: Progressive Disease

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: monthspfs

tag: albumin

tag: ldh

tag: iss

value: I

tag: sampledatetime

tag: hyperdiploidclinicalfish

tag: hyperdiploidcyto

tag: imids

tag: inregimenstep

value: PR


title: P3676.01.K733.U133Plus.2

tag: fnpatid

tag: datesamplernbx

tag: gender

tag: race

tag: ageatsampledate

tag: numberoftransplants

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: TRUE

value: II

value: Consolidation 1 (S):VTDPACE3

tag: imidpostresponse

value: CR

tag: imidimproved

tag: imidgiven

tag: monthsobs

tag: recrev

tag: celfilernbx

tag: celfilernas

tag: maxpfs

tag: gepprocesslocation

tag: issr


title: Leaf_PI585108

tag: developmental stage

tag: leaf shape trait

tag: tissue


title: Leaf_PI612701


title: human patient blood miRNA 3

description: miRNA expression

tag: subject status

value: Chinese imported falciparum malaria patient

tag: age (years)

tag: gender

value: male

value: blood

tag: parasitemia (%)

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: human patient blood miRNA 6

description: miRNA expression


title: Leaf_PI595868


title: human patient blood miRNA 4

description: miRNA expression


title: Leaf_PI634379

value: Lobed (Low Circularity)


title: P3674.01.K730.U133Plus.2

tag: fnpatid

tag: datesamplernbx

value: Female

tag: race

value: Black

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: sCR

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: monthspfs

tag: albumin

tag: ldh

tag: iss

tag: sampledatetime

value: FALSE

tag: hyperdiploidclinicalfish

tag: hyperdiploidcyto

tag: imids

value: Thalidomide

tag: inregimenstep

value: Induction Mel 10 VTDPACE

tag: imidpostresponse

tag: imidimproved

tag: imidgiven

tag: monthsobs

tag: recrev

tag: celfilernbx

tag: celfilernas

tag: maxpfs

tag: gepprocesslocation

value: MIRT


title: Leaf_PI573318

tag: developmental stage

tag: leaf shape trait

tag: tissue

value: Young leaf


title: P3669.01.K706.U133Plus.2

tag: fnpatid

tag: datesamplernbx

tag: gender

value: Male

tag: race

value: White / Caucasian

tag: ageatsampledate

tag: numberoftransplants

tag: transplant

value: Y

tag: ftprotocol

tag: dateenrolled

tag: dateebmtrelapse

tag: dateimwgrelapse

tag: datedeath

tag: datelastcontact

tag: datelastresponse

tag: responselast

value: Progressive Disease

tag: dateprogress

tag: censorforosdate

tag: monthsos

tag: censorforpfsdate

tag: monthspfs

tag: albumin

tag: ldh

tag: iss

value: I

tag: sampledatetime

value: Transplant 1 (L):Fractionated MEL + VDT

value: PR

tag: issr


title: human patient blood miRNA 2

description: miRNA expression

tag: subject status

value: Chinese imported falciparum malaria patient

tag: age (years)

tag: gender

value: male

tag: tissue

value: blood

tag: parasitemia (%)

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: human normal blood miRNA 3

description: miRNA expression

source_name: human normal blood miRNA

value: normal, healthy subject


title: human normal blood miRNA 5

description: miRNA expression


title: Leaf_PI599387

tag: developmental stage

tag: leaf shape trait

value: Lobed (Low Circularity)


title: Leaf_PI585061

value: Lobed (Low Circularity); high AR


title: Leaf_PI585067


title: human normal blood miRNA 4

description: miRNA expression


title: human normal blood miRNA 1

description: miRNA expression


title: human normal blood miRNA 6

description: miRNA expression


title: human normal blood miRNA 2

description: miRNA expression


title: IL4 1

city: Pittsburgh

first: Jun

last: Chen

state: PA

address: 200 Lothrop Street

department: Neurology

institute: University of Pittsburgh

hyb_protocol: Following overnight (16h) hybridization to the Affymetrix Clariom S rat array at 45oC with rotational mixing at 60 RPM, arrays were processed on a GeneChip 450 Fluidics Station using manufacturer specified protocols.

scan_protocol: GeneChips were scanned using the GeneArray 3000 scanner.

data_processing:
First level image analysis was performed using Affymetrix Expression Console. Data were subjected to subsequent analysis using Transcriptome Analysis Console (Affymetrix).
Transcriptome Analysis Console 4.0
Array Type: Clariom_S_Rat
Analysis Type: Expression (Gene)
Analysis Version: version 1
Summarization Method: Gene Level - SST-RMA
Pos vs Neg AUC Threshold: 0.7
Genome Version: rn6 (Rattus norvegicus)
Annotation: Clariom_S_Rat.na36.rn6.transcript.csv

organism: Rattus norvegicus

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

growth_protocol: Primary oligodendrocyte progenitor cell (OPC) cultures were prepared from brains of postnatal day 1-2 mixed-sex Sprague Dawley rat pups. OPCs were maintained for 3 days in a serum-free basal defined medium (BDM: DMEM, 0.1% bovine serum albumin, 50 μg/mL human apo-transferrin, 50 μg/mL insulin, 30 nM sodium selenite, 10 nM D-biotin, 10 nM hydrocortisone).

treatment_protocol: Primary OPCs were treated with PBS or IL-4 (20 ng/mL) for 3 days.

tag: strain

value: Sprague Dawley

tag: age

value: postnatal day 1-2

value: brain

tag: cell type

tag: treatment

value: IL-4 (20 ng/mL) for 3 days


title: IL4 2

value: Primary oligodendrocyte progenitor cell (OPC)


title: Control ChIP-seq from CH12.LX (ENCLB734NDR)

status: Public on Aug 30 2019

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000ERS/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on mouse CH12 produced by the Snyder lab
experiment encode accession: ENCSR000ERS
assay title: Control ChIP-seq
assembly: mm9, mm10
encode release date: 2011-09-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB734NDR
fragmentation methods: see document

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B10.H-2aH-4bp/Wts CH12.LX immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f710178a-26e4-4afa-b925-37e6c9dbad34/@@download/attachment/wgEncodeSydhTfbs.release4.html.pdf

tag: antibody

value: rabbit-IgG-control

tag: line

value: cell line

tag: description

value: B-cell lymphoma

tag: biosample encode accession

value: unknown

tag: dev stage

tag: Sex

value: female

tag: health state

tag: lab

value: Michael Snyder, Stanford

tag: link

value: ENCBS912CAS at ENCODE; https://www.encodeproject.org/ENCBS912CAS/

value: Derived from ENCODE donor ENCDO324YEK; https://www.encodeproject.org/ENCDO324YEK/

value: ENCODE dbxrefs Cellosaurus CVCL_0211; http://web.expasy.org/cellosaurus/CVCL_0211

value: ENCODE dbxrefs CH12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CH12


title: Control ChIP-seq from ES-E14 (ENCLB073ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000ADJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on mouse ES-E14 produced by the Snyder lab
experiment encode accession: ENCSR000ADJ
assay title: Control ChIP-seq
assembly: mm9, mm10
encode release date: 2012-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB073ZZZ
fragmentation methods: sonication (generic)
size range: 150-350

source_name: Mus musculus strain 129/Ola ES-E14 stem cell male embryo

extract_protocol:
general protocol: https://www.encodeproject.org/documents/302689be-b110-40b6-8912-cc9d934b002e/@@download/attachment/mouse.wgEncodeSydhHist.txt
extraction method: see document
general protocol: https://www.encodeproject.org/documents/302689be-b110-40b6-8912-cc9d934b002e/@@download/attachment/mouse.wgEncodeSydhHist.txt

value: Control

value: mouse embryonic stem cell line E14

value: embryonic

value: male

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: TF ChIP-seq from HepG2 (ENCLB604YZW)

description:
https://www.encodeproject.org/experiments/ENCSR854JES/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2G ChIP-seq on HepG2
experiment encode accession: ENCSR854JES
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR975KJI
encode release date: 2018-01-18
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB604YZW
size range: 200-400

source_name: Homo sapiens HepG2 cell line

value: cell line

value: POLR2G ChIP-seq on HepG2 cells

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: ENCBS926EJR at ENCODE; https://www.encodeproject.org/ENCBS926EJR/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: TF ChIP-seq from HepG2 (ENCLB608BDL)

description:
https://www.encodeproject.org/experiments/ENCSR854JES/
***************
biological replicate number: 2
technical replicate number: 1
description: POLR2G ChIP-seq on HepG2
experiment encode accession: ENCSR854JES
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR975KJI
encode release date: 2018-01-18
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB608BDL
size range: 200-400

value: ENCBS466ZIX at ENCODE; https://www.encodeproject.org/ENCBS466ZIX/


title: IL4 3

value: Sprague Dawley

value: postnatal day 1-2

tag: tissue

value: brain

value: Primary oligodendrocyte progenitor cell (OPC)

value: IL-4 (20 ng/mL) for 3 days


title: Histone ChIP-seq from skeletal muscle myoblast (ENCLB738UWZ)

description:
https://www.encodeproject.org/experiments/ENCSR596NOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR596NOF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000ANN
encode release date: 2016-03-22
lab: Bradley Bernstein, Broad
library encode accession: ENCLB738UWZ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (22 years) skeletal muscle myoblast primary cell

value: skeletal muscle myoblast

value: primary cell

value: male

value: adult

value: 22 year

value: Bradley Bernstein, Broad

value: ENCBS034BMX at ENCODE; https://www.encodeproject.org/ENCBS034BMX/

value: Derived from ENCODE donor ENCDO341XKY; https://www.encodeproject.org/ENCDO341XKY/


title: TF ChIP-seq from K562 (ENCLB663NBH)

description:
https://www.encodeproject.org/experiments/ENCSR814AJH/
***************
biological replicate number: 1
technical replicate number: 1
description: SRSF9 ChIP-seq in K562
experiment encode accession: ENCSR814AJH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB663NBH
size range: 200-400

source_name: Homo sapiens K562 cell line

value: cell line

value: SRSF9 ChIP-seq in K562

value: female

value: 53 year

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS958AOA at ENCODE; https://www.encodeproject.org/ENCBS958AOA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Histone ChIP-seq from skeletal muscle myoblast (ENCLB971DWL)

description:
https://www.encodeproject.org/experiments/ENCSR596NOF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR596NOF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000ANN
encode release date: 2016-03-22
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971DWL
fragmentation methods: none
size range: 200-600
nucleic acid starting quantity: 72
nucleic acid starting quantity units: ng

value: ENCBS914GNL at ENCODE; https://www.encodeproject.org/ENCBS914GNL/


title: TF ChIP-seq from K562 (ENCLB629NVI)

description:
https://www.encodeproject.org/experiments/ENCSR814AJH/
***************
biological replicate number: 2
technical replicate number: 1
description: SRSF9 ChIP-seq in K562
experiment encode accession: ENCSR814AJH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB629NVI
size range: 200-400

value: ENCBS331LZB at ENCODE; https://www.encodeproject.org/ENCBS331LZB/


title: TF ChIP-seq from K562 (ENCLB827GPZ)

description:
https://www.encodeproject.org/experiments/ENCSR506KWJ/
***************
biological replicate number: 2
technical replicate number: 1
description: XRCC5 ChIP-seq in K562
experiment encode accession: ENCSR506KWJ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR464FDA
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB827GPZ
size range: 200-400

value: XRCC5 ChIP-seq in K562

value: ENCBS957QHW at ENCODE; https://www.encodeproject.org/ENCBS957QHW/


title: IL4 4

value: Sprague Dawley

value: postnatal day 1-2

value: brain

value: Primary oligodendrocyte progenitor cell (OPC)

value: IL-4 (20 ng/mL) for 3 days


title: TF ChIP-seq from HepG2 (ENCLB163NSL)

description:
https://www.encodeproject.org/experiments/ENCSR247XFV/
***************
biological replicate number: 1
technical replicate number: 1
description: KIAA1967 ChIP-seq on HepG2
experiment encode accession: ENCSR247XFV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254UDV
encode release date: 2018-01-22
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB163NSL
size range: 200-400

value: cell line

value: DBC1 ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS982JDZ at ENCODE; https://www.encodeproject.org/ENCBS982JDZ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: TF ChIP-seq from K562 (ENCLB988UUL)

description:
https://www.encodeproject.org/experiments/ENCSR189YMA/
***************
biological replicate number: 4
technical replicate number: 1
description: eGFP-VEZF1 ChIP-seq on human K562
experiment encode accession: ENCSR189YMA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR529YPZ
encode release date: 2017-11-08
lab: Kevin White, UChicago
library encode accession: ENCLB988UUL
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-VEZF1

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to VEZEF1

value: female

value: adult

value: 53 year

value: Kevin White, UChicago

tag: passage number

value: chronic myelogenous leukemia (CML)

value: ENCBS545PWB at ENCODE; https://www.encodeproject.org/ENCBS545PWB/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control 3

value: Sprague Dawley

value: postnatal day 1-2

value: brain

value: Primary oligodendrocyte progenitor cell (OPC)

value: PBS for 3 days


title: TF ChIP-seq from HepG2 (ENCLB203FAM)

description:
https://www.encodeproject.org/experiments/ENCSR151NQL/
***************
biological replicate number: 2
technical replicate number: 1
description: AGO2 ChIP-seq in HepG2
experiment encode accession: ENCSR151NQL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB203FAM
size range: 200-400

value: cell line

value: EIF2C2 ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ENCBS623OHX at ENCODE; https://www.encodeproject.org/ENCBS623OHX/


title: Histone ChIP-seq from mammary epithelial cell (ENCLB245XTI)

description:
https://www.encodeproject.org/experiments/ENCSR016JWS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR016JWS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMN
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB245XTI
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens mammary epithelial primary cell female (50 years)

value: mammary epithelial cell

value: primary cell

value: mammary epithelial cells

value: 50 year

value: unknown

value: female

value: Bradley Bernstein, Broad

value: ENCBS091ENC at ENCODE; https://www.encodeproject.org/ENCBS091ENC/

value: Derived from ENCODE donor ENCDO830BUW; https://www.encodeproject.org/ENCDO830BUW/

value: ENCODE dbxrefs HMEC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HMEC


title: TF ChIP-seq from K562 (ENCLB518BGC)

description:
https://www.encodeproject.org/experiments/ENCSR018MSO/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF148 ChIP-seq on human K562
experiment encode accession: ENCSR018MSO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR745QMZ
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB518BGC
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 cell line stably expressing C-terminal eGFP-tagged eGFP-ZNF148

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF148

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS538KOD at ENCODE; https://www.encodeproject.org/ENCBS538KOD/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Histone ChIP-seq from mammary epithelial cell (ENCLB585PYO)

description:
https://www.encodeproject.org/experiments/ENCSR016JWS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR016JWS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMN
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585PYO
fragmentation methods: none
size range: 200-600
nucleic acid starting quantity: 103
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (50 years) mammary epithelial primary cell

value: mammary epithelial cell

value: primary cell

value: HMEC Mammary Epithelial Primary Cells

value: ENCBS045GHW at ENCODE; https://www.encodeproject.org/ENCBS045GHW/


title: TF ChIP-seq from K562 (ENCLB333WBP)

description:
https://www.encodeproject.org/experiments/ENCSR764OXF/
***************
biological replicate number: 1
technical replicate number: 1
description: RBM39 ChIP-seq in K562
experiment encode accession: ENCSR764OXF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2018-01-22
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB333WBP
size range: 200-400

value: RBM39 ChIP-seq in K562

value: female

value: Xiang-Dong Fu, UCSD

value: ENCBS670BDF at ENCODE; https://www.encodeproject.org/ENCBS670BDF/


title: TF ChIP-seq from K562 (ENCLB611XRG)

description:
https://www.encodeproject.org/experiments/ENCSR598GER/
***************
biological replicate number: 1
technical replicate number: 1
description: CCAR2 ChIP-seq in K562
experiment encode accession: ENCSR598GER
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB611XRG
size range: 200-400

value: DBC1 ChIP-seq in K562

value: ENCBS559ERW at ENCODE; https://www.encodeproject.org/ENCBS559ERW/


title: TF ChIP-seq from K562 (ENCLB303KPA)

description:
https://www.encodeproject.org/experiments/ENCSR764OXF/
***************
biological replicate number: 2
technical replicate number: 1
description: RBM39 ChIP-seq in K562
experiment encode accession: ENCSR764OXF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2018-01-22
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB303KPA
size range: 200-400

value: cell line

value: ENCBS352EMA at ENCODE; https://www.encodeproject.org/ENCBS352EMA/


title: TF ChIP-seq from K562 (ENCLB740DEA)

description:
https://www.encodeproject.org/experiments/ENCSR581CVA/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPH1 ChIP-seq in K562
experiment encode accession: ENCSR581CVA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB740DEA
size range: 200-400

value: HNRNPH1 ChIP-seq in K562

value: adult

value: 53 year

value: ENCBS142DQA at ENCODE; https://www.encodeproject.org/ENCBS142DQA/


title: TF ChIP-seq from K562 (ENCLB513XZP)

description:
https://www.encodeproject.org/experiments/ENCSR598GER/
***************
biological replicate number: 2
technical replicate number: 1
description: CCAR2 ChIP-seq in K562
experiment encode accession: ENCSR598GER
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB513XZP
size range: 200-400

value: chronic myelogenous leukemia (CML)

value: ENCBS686VDZ at ENCODE; https://www.encodeproject.org/ENCBS686VDZ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Histone ChIP-seq from tibial artery (ENCLB829EXR)

description:
https://www.encodeproject.org/experiments/ENCSR535GFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR535GFO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR819JOI
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB829EXR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) tibial artery tissue

value: tibial artery

value: tissue

value: EnTEX:Artery - Tibial

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS646JZQ at ENCODE; https://www.encodeproject.org/ENCBS646JZQ/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: TF ChIP-seq from K562 (ENCLB103GBI)

description:
https://www.encodeproject.org/experiments/ENCSR581CVA/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPH1 ChIP-seq in K562
experiment encode accession: ENCSR581CVA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB103GBI
size range: 200-400

value: cell line

value: female

value: Xiang-Dong Fu, UCSD

value: ENCBS290ACU at ENCODE; https://www.encodeproject.org/ENCBS290ACU/


title: Histone ChIP-seq from tibial artery (ENCLB664YSJ)

description:
https://www.encodeproject.org/experiments/ENCSR535GFO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR535GFO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR819JOI
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB664YSJ
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: ENCBS736PQK at ENCODE; https://www.encodeproject.org/ENCBS736PQK/


title: TF ChIP-seq from K562 (ENCLB009HHE)

description:
https://www.encodeproject.org/experiments/ENCSR506KWJ/
***************
biological replicate number: 1
technical replicate number: 1
description: XRCC5 ChIP-seq in K562
experiment encode accession: ENCSR506KWJ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR464FDA
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB009HHE
size range: 200-400

value: XRCC5 ChIP-seq in K562

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS876FQG at ENCODE; https://www.encodeproject.org/ENCBS876FQG/


title: TF ChIP-seq from body of pancreas (ENCLB621OUU)

description:
https://www.encodeproject.org/experiments/ENCSR572DUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR572DUJ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR888RBQ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB621OUU
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens body of pancreas tissue male adult (37 years)

value: CTCF

value: body of pancreas

value: tissue

value: 37 year

value: ENCBS869MHP at ENCODE; https://www.encodeproject.org/ENCBS869MHP/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Control 4

value: Sprague Dawley

value: postnatal day 1-2

value: brain

value: Primary oligodendrocyte progenitor cell (OPC)

value: PBS for 3 days


title: human patient blood miRNA 1

description: miRNA expression

tag: subject status

value: Chinese imported falciparum malaria patient

tag: age (years)

tag: gender

value: male

value: blood

tag: parasitemia (%)

tag: concentration of hemoglobin (g/l)

tag: platelets (×10^9/l)

tag: lymphocytes (×10^9/l)

tag: lymphocyte (%)

tag: neutrophils (×10^9/l)

tag: neutrophils (%)

tag: monocytess (×10^9/l)

tag: monocyte (%)


title: TF ChIP-seq from HepG2 (ENCLB358KBN)

description:
https://www.encodeproject.org/experiments/ENCSR247XFV/
***************
biological replicate number: 2
technical replicate number: 1
description: KIAA1967 ChIP-seq on HepG2
experiment encode accession: ENCSR247XFV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR254UDV
encode release date: 2018-01-22
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB358KBN
size range: 200-400

tag: antibody

tag: line

value: cell line

tag: description

value: DBC1 ChIP-seq on HepG2 cells

tag: biosample encode accession

tag: Sex

tag: dev stage

value: child

tag: age

value: 15 year

value: Xiang-Dong Fu, UCSD

tag: health state

value: hepatocellular carcinoma

value: ENCBS121QNT at ENCODE; https://www.encodeproject.org/ENCBS121QNT/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: TF ChIP-seq from K562 (ENCLB458AQJ)

description:
https://www.encodeproject.org/experiments/ENCSR462QZZ/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF395 ChIP-seq on human K562
experiment encode accession: ENCSR462QZZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR625UIZ
encode release date: 2017-12-04
lab: Kevin White, UChicago
library encode accession: ENCLB458AQJ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-ZNF395

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF395

value: female

value: adult

value: 53 year

tag: lab

value: Kevin White, UChicago

tag: passage number

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS366PAP at ENCODE; https://www.encodeproject.org/ENCBS366PAP/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control 2

tag: strain

value: Sprague Dawley

value: postnatal day 1-2

tag: tissue

value: brain

tag: cell type

value: Primary oligodendrocyte progenitor cell (OPC)

tag: treatment

value: PBS for 3 days


title: Control 1


title: TF ChIP-seq from K562 (ENCLB825UYD)

description:
https://www.encodeproject.org/experiments/ENCSR283ZRI/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2G ChIP-seq in K562
experiment encode accession: ENCSR283ZRI
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB825UYD
size range: 200-400

value: cell line

value: POLR2G ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: ENCBS964WYU at ENCODE; https://www.encodeproject.org/ENCBS964WYU/


title: TF ChIP-seq from K562 (ENCLB154PTI)

description:
https://www.encodeproject.org/experiments/ENCSR283ZRI/
***************
biological replicate number: 2
technical replicate number: 1
description: POLR2G ChIP-seq in K562
experiment encode accession: ENCSR283ZRI
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB154PTI
size range: 200-400

value: ENCBS083VWQ at ENCODE; https://www.encodeproject.org/ENCBS083VWQ/


title: TF ChIP-seq from HepG2 (ENCLB894EHB)

description:
https://www.encodeproject.org/experiments/ENCSR151NQL/
***************
biological replicate number: 1
technical replicate number: 1
description: AGO2 ChIP-seq in HepG2
experiment encode accession: ENCSR151NQL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-12-01
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB894EHB
size range: 200-400

value: EIF2C2 ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS561LQQ at ENCODE; https://www.encodeproject.org/ENCBS561LQQ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: TF ChIP-seq from K562 (ENCLB551NZK)

description:
https://www.encodeproject.org/experiments/ENCSR462QZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF395 ChIP-seq on human K562
experiment encode accession: ENCSR462QZZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR625UIZ
encode release date: 2017-12-04
lab: Kevin White, UChicago
library encode accession: ENCLB551NZK
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF395

value: female

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS819JKS at ENCODE; https://www.encodeproject.org/ENCBS819JKS/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Muscle_NS-212

city: Boston

first: Steven

middle: A

last: Greenberg

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133A Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using GCRMA normalization.

source_name: Nonspecific myositis_muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen).

tag: disease state

value: Nonspecific myositis

value: Muscle


title: Muscle_NS-221


title: TF ChIP-seq from H1 (ENCLB160OTT)

description:
https://www.encodeproject.org/experiments/ENCSR160ZLP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human H1-hESC KDM5A
experiment encode accession: ENCSR160ZLP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2012-03-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB160OTT
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens H1-hESC stem cell male embryo

value: cell line

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS952IPA at ENCODE; https://www.encodeproject.org/ENCBS952IPA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: Muscle_NS-160


title: Muscle_NS-139


title: Muscle_NS-102


title: Muscle_NM-292

source_name: Necrotizing myopathy_muscle

value: Necrotizing myopathy


title: Muscle_NM-291


title: Muscle_PM-197

value: Polymyositis


title: Muscle_NM-284


title: Muscle_NS-086


title: Muscle_NS-299


title: Muscle_NS-277


title: Muscle_PM-229


title: Muscle_PM-016


title: TF ChIP-seq from K562 (ENCLB349LZT)

description:
https://www.encodeproject.org/experiments/ENCSR189YMA/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-VEZF1 ChIP-seq on human K562
experiment encode accession: ENCSR189YMA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR529YPZ
encode release date: 2017-11-08
lab: Kevin White, UChicago
library encode accession: ENCLB349LZT
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to VEZEF1

value: female

value: adult

value: ENCBS410RUZ at ENCODE; https://www.encodeproject.org/ENCBS410RUZ/


title: Muscle_NS-250


title: Muscle_NS-236


title: Muscle_NS-096


title: Muscle_NS-182


title: Muscle_PM-156


title: Muscle_PM-080


title: Muscle_NS-295


title: Muscle_PM-164


title: Muscle_NS-243


title: Muscle_PM-017


title: Muscle_NM-263


title: Muscle_NM-126


title: TF ChIP-seq from K562 (ENCLB068BIS)

description:
https://www.encodeproject.org/experiments/ENCSR158RYZ/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZBTB40 ChIP-seq on human K562
experiment encode accession: ENCSR158RYZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR861LKS
encode release date: 2017-12-01
lab: Kevin White, UChicago
library encode accession: ENCLB068BIS
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting eGFP-ZBTB40

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB40

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS136FFT at ENCODE; https://www.encodeproject.org/ENCBS136FFT/


title: WBM, MGUS, P0980-02-BS1344-U133Plus-2

source_name: MGUS Patients

tag: datesample

tag: fnpatid

tag: datebasesample

tag: sampleprotocol

tag: batch

value: MIRT

tag: pointgroup

value: MGUS

tag: daysafterbasesample

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: point

value: MGUS, 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: datepulled

tag: chipdate

tag: protocolsample

tag: celname

value: whole bone marrow (WBM)