title: S000428

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000477

status: Public on May 09 2022

type: SRA

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description: ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high

library_source: transcriptomic

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC RepeatMasker track (downloaded March 14, 2011).
Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38.
Remaining reads were aligned using HISAT2 v 2.1.0 to the human genome reference GRCh38/hg38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014) using the GENCODE release 27 transcriptome model, with default parameters except --no-unal --non-deterministic --novel-splicesite-outfile ${SPLICEFILE}  --rna-strandness RF. HISAT2 indexes were created using the --snp parameter and dbSNP build 150.
Gene expression data in FPKM ( fragments per kilobase of transcript per million mapped reads) were generated using StringTie v1.3.3b (default parameters including --rf -e) using protein coding transcripts from GENCODE release 27 as transcriptome model. Novel transcripts were discarded. An FPKM gene expression matrix was generated from .ctab files using tximport and subsequently transformed to TPM values adding to each expression measurement 0.1, followed by log2 transformation.
PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect to available clinical characteristics. Before subtyping tumors in this study, gene expression of the PAM50 genes for each tumor was centered to the reference set separately using custom R scripts.
Spearman rank correlation was used to determine correlations between expression of ESR1 and ESR2. Kruskal-Wallis non-parametric test and Wilcoxon rank sum test were used to compare and plot expression of the ESR1 and ESR2 genes in various clinical groups such as PAM50 subtype and age groups in the SCAN-B cohort. Transformed ESR2 expression data was divided into tertiles, with the first tertile defined as ESR2-high, and the bottom two tertiles at ESR2-low. Mann Whitney U test and Fisher’s exact test were used to evaluate significant differences in the clinicopathological variables for the ESR2-high and ESR2-low groups. Survival analysis was performed by Kaplan-Meier and Cox regression survival analyses. All analysis was performed for a cohort of 3207 samples from patients enrolled in the SCAN-B study.
Assembly: Human genome reference GRCh38/hg38.
Supplementary files format and content: Gene expression in TPM in CSV format.

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 or NextSeq 500 instrument.

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tag: lymph node status

value: NodeNegative

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tag: clinical groups

tag: histopathological type

value: Lobular

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: S000422

tag: er status

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value: Ductal

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tag: esr2 expression


title: S000448

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title: S000405

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tag: overall survival years

tag: overall survival event

tag: relapse free interval days


title: S000437

value: NX

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

value: LumB

value: Other

tag: relapse free interval years

tag: relapse free interval event


title: S000402

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tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S000419

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

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tag: chemo treated

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tag: overall survival years


title: S000412

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000426

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

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tag: relapse free interval event


title: S000424

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title: S000396

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tag: overall survival days

tag: overall survival years


title: S000406

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title: S000411

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title: S000403

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title: S000401

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tag: overall survival years


title: S000408

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value: Basal

tag: clinical groups

value: TNBC

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title: S000413

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tag: her2 status

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value: Normal

tag: relapse free interval years

tag: relapse free interval event


title: S000397

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title: S000385

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title: S000389

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title: S000379

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title: S000392

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tag: overall survival days

tag: overall survival years


title: S000374

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tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000387

value: SubMicroMet

tag: pam50 subtype

tag: clinical groups

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tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000420

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000377

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000393

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

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tag: relapse free interval days


title: S000386

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tag: relapse free interval event


title: S000372

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title: S000366

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tag: overall survival years


title: S000373

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tag: overall survival event

tag: relapse free interval days


title: S000365

tag: scanb external id

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tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000394

tag: pam50 subtype

tag: clinical groups

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tag: esr2 expression


title: S000378

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tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000390

tag: scanb external id

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tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000399

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000363

tag: er status

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tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000375

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000352

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival event

tag: relapse free interval days


title: S000347

tag: er status

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tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S000349

tag: scanb external id

tag: age at diagnosis

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tag: lymph node group

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tag: esr1 expression

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title: S000381

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tag: clinical groups

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tag: chemo treated

tag: overall survival days

tag: overall survival years


title: S000345

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000340

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000359

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000364

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000371

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000354

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000337

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000335

tag: scanb external id

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tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000336

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tag: relapse free interval days


title: S000333

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tag: relapse free interval event


title: S000362

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S000361

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years


title: S000355

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000342

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000367

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000344

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000334

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000325

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000322

tag: er status

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tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000330

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000315

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival event

tag: relapse free interval days


title: S000328

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S000310

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S000324

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years


title: S000309

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000308

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000319

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000323

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000327

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000299

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000300

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000321

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000314

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival event

tag: relapse free interval days


title: S000294

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval years

tag: relapse free interval event


title: S000292

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S000312

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years


title: S000313

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000289

tag: scanb external id

tag: age at diagnosis

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tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000318

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

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tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000316

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000283

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000287

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000282

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000288

tag: scanb external id

tag: age at diagnosis

tag: tumor size

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tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000326

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival event

tag: relapse free interval days


title: S000295

tag: er status

tag: pgr status

tag: her2 status

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tag: nhg

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tag: relapse free interval event


title: S000275

tag: scanb external id

tag: age at diagnosis

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tag: lymph node group

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tag: esr1 expression

tag: esr2 expression


title: S000303

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tag: clinical groups

tag: histopathological type

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tag: overall survival days

tag: overall survival years


title: S000307

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tag: relapse free interval days


title: S000280

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tag: relapse free interval event


title: S000317

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title: S000297

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tag: overall survival days

tag: overall survival years


title: S000273

tag: scanb external id

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tag: overall survival event

tag: relapse free interval days


title: S000304

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tag: clinical groups

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tag: relapse free interval event


title: S000272

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tag: esr2 expression


title: S000285

tag: scanb external id

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tag: overall survival days

tag: overall survival years


title: S000291

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title: S000284

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value: Unclassified

tag: relapse free interval years

tag: relapse free interval event


title: S000320

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S000290

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tag: clinical groups

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tag: chemo treated

tag: overall survival days

tag: overall survival years


title: S000260

tag: er status

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tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000298

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000261

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: esr1 expression

tag: esr2 expression


title: S000258

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000254

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000293

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval years

tag: relapse free interval event


title: S000257

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000253

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: overall survival years


title: S000274

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

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tag: overall survival event

tag: relapse free interval days


title: S000251

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tag: relapse free interval years

tag: relapse free interval event


title: S000306

tag: scanb external id

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tag: esr1 expression

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title: S000252

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tag: clinical groups

tag: histopathological type

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tag: chemo treated

tag: overall survival days

tag: overall survival years


title: S000271

tag: er status

tag: pgr status

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tag: nhg

tag: overall survival event

tag: relapse free interval days


title: S000277

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval years

tag: relapse free interval event


title: S000245

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

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tag: esr1 expression

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title: S000267

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: overall survival years


title: S000239

tag: scanb external id

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tag: tumor size

tag: lymph node group

tag: lymph node status

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title: S000264

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title: S000256

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title: S000263

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title: S000237

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title: S000247

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tag: nhg

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title: S000235

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title: S000249

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title: S000250

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tag: nhg

tag: overall survival days

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title: S000248

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title: S000231

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title: S000236

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title: S000228

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tag: lymph node group

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title: S000229

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tag: clinical groups

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title: S000227

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tag: relapse free interval days


title: S000226

tag: scanb external id

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tag: lymph node group

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title: S000225

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tag: clinical groups

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title: S000221

tag: er status

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tag: her2 status

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tag: nhg

tag: overall survival days

tag: overall survival years


title: S000220

tag: scanb external id

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tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival event

tag: relapse free interval days


title: S000224

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

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tag: relapse free interval event


title: S000216

tag: er status

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tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: S000219

tag: scanb external id

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title: S000214

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title: S000215

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title: S000213

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title: S000210

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tag: histopathological type

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title: S000208

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title: S000203

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tag: nhg

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title: S000198

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tag: relapse free interval days


title: S000196

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title: S000167

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title: S000162

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title: S000164

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tag: overall survival days

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title: S000166

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title: S000159

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title: S000200

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title: S000156

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title: S000185

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title: S000146

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title: S000173

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title: S000138

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tag: overall survival days

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title: S000133

tag: er status

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title: S000135

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title: S000127

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title: S000117

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title: S000119

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title: S000114

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tag: esr1 expression

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title: S000149

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tag: overall survival days

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title: S000125

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title: S000112

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title: S000121

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title: S000126

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title: S000107

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title: S000098

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title: S000099

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title: S000093

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title: S000097

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title: S000096

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title: S000088

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title: S000083

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title: S000118

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title: S000077

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title: S000073

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title: S000063

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title: S000062

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title: S000064

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title: S000058

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title: S000067

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title: S000060

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title: S000065

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title: S000054

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title: S000053

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title: S000057

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title: S000056

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title: S000048

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title: S000022

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title: S000012

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tag: relapse free interval days


title: S000011

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title: S000001

tag: er status

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title: S000003

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tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: overall survival years


title: CFPAC1.IRF1-KO #03

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: Illumina Truseq. The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to human genome build GRCh38/hg38 using using START version 2.6.0c. Only uniquely mapped reads were retained
Gene expression counts were estimated using featureCounts  v0.6.1 (Rsubread version 1.6.1) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCh38/hg38

molecule: total RNA

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

treatment_protocol: See additional columns of the SAMPLES section

tag: cell type

value: Pool of CFPAC1 genome-edited clonal cell line

tag: growth protocol

tag: treatment

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting IRF1 gene


title: CFPAC1.IRF1-KO #02

extract_protocol: Illumina Truseq. The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

value: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: S000037

tag: er status

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: CFPAC1.WT #03 (IRF1-KO control)

value: Pool of CFPAC1 clonal cell lines

value: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)


title: S000021

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

value: NodeNegative

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: esr1 expression

tag: esr2 expression


title: CFPAC1.IRF1-KO #01

tag: cell type

tag: growth protocol

tag: treatment


title: CFPAC1.WT #01 (IRF1-KO control)


title: CFPAC1.WT #02 (IRF1-KO control)


title: H3K27ac_CFPAC1_IRF1KO_clone_2

description: Chromatin IP against H3K27ac

library_source: genomic

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

molecule: genomic DNA

growth_protocol: See additional columns of the SAMPLES section

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by AMPure XP SPRI (Beckman Coulter) and quantified using Quantifluor (Promega). ChIP DNA was prepared for HiSeq2000 or NextSeq500 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: CFPAC1 clonal cell line

tag: antibody

value: Anti H3K27ac (Abcam, ab4729)


title: L929 cells, TNF-α 2

city: Nanjing

first: Ruiyu

last: Xiang

department: Institute of Dermatology

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus Musculus(GRCm38/mm10) whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

growth_protocol: L929 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were fed with DMEM supplemented with 10% FBS, TNF-α of 10ng/ml（Peprotech）,  and actinomycin d of 1μg/ml（Selleck） for 12 hours.

tag: cell line

value: Fibroblast

tag: genotype

value: WT

value: TNF-alpha of 10ng/ml and actinomycin d of 1microg/ml.


title: S000002

tag: lymph node status

tag: er status

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

value: Ductal

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: liver Tet1 KO YAP Tg input rep 2

city: Dallas

first: Duojia

last: Pan

state: Texas

address: 6001 Forest Park

department: Physiology

country: USA

institute: UT Southwestern Medical Center

data_processing:
reads were aligned with Bowtie2 to the mm10 mouse genome and duplicates were removed from the mapped data using PICARD.
for methylation, bigwig data were generated by subtrating with input
for ChIP, signal were normalized with spike in control
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Liver tissue

extract_protocol: For ChIP-seq, ChIP was performed with Magna ChIP HiSens chromatin immunoprecipitation kit (Millipore Sigma) according to the manufacturer’s protocols. Briefly, 100 mg mouse liver was pulverized with liquid nitrogen, and cross-linked in 1% methanol-free formaldehyde at room temperature for 10 minutes. Fixed cells were collected and lysed in Nuclei Isolation Buffer for 15 minutes. Then, cells were homogenized 10 times in a Dounce homogenizer (loose pestle). Extracted nuclei were fragmented by sonication to an average size of 200-700 bp (S2 Focused-ultrasonicator, Covaris). 10 μg fragmented chromatin was subjected to overnight incubation at 4 °C with specific antibody pre-conjugated beads. For ChIP normalization, 10 ng spike-in Drosophila chromatin (Active Motif, 53083) and 1 ug spike-in antibody (Active Motif, 61686) were added in each reaction before overnight incubation. After serial washing, the beads were incubated with ChIP elution buffer, Proteinase K at 65 °C for 2 hours and at 95°C for 15 minutes. The released DNA was purified using MinElute PCR Purification Kit (Qiagen). 5 ng of ChIP eluent were prepared using KAPA HTP Library Preparation Kit according to the manufacturer’s protocols. PCR amplified libraries were purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer for quality control.

tag: strain

tag: tissue

value: Liver

tag: treatment

value: Doxycycline

value: Tet1 -/- YAP Tg

tag: mbd/chip antibody


title: S000017

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

value: LumB

tag: esr1 expression

tag: esr2 expression


title: L929 cells, TNF-α 1

tag: cell line

tag: cell type

tag: genotype

value: TNF-alpha of 10ng/ml and actinomycin d of 1microg/ml


title: liver Tet1 KO YAP Tg input rep 1

tag: strain

tag: tissue


title: liver Tet1 KO YAP Tg MBD-seq rep 2

extract_protocol: For MBD-seq, 5 μg genomic DNA was first fragmented by sonication to an average size of 400 bp (Peak: 400; Intensity: 4; Duty cycle: 10%; Cycles per Burst: 200; Treatment Time: 55s; sample volume:130 μl) (S2 Focused-ultrasonicator, Covaris). Methylated DNA was captured and eluted from 1 μg fragmented DNA according to the manufacturer’s protocols. The released DNA was purified using MinElute PCR Purification Kit (Qiagen). 5ng of input DNA and methylated DNA were then prepared using KAPA HTP Library Preparation Kit according to the manufacturer’s protocols. PCR amplified libraries were purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer for quality control.

tag: treatment

tag: mbd/chip antibody

value: MethylMiner Methylated DNA Enrichment Kit (ThermoFisher)


title: L929 cells, Control 2

value: Control


title: liver decitabine treated Tet1 KO YAP Tg MBD-seq rep 2

value: Doxycycline+Decitabine


title: L929 cells, TNF-α 3


title: liver YAP Tg MBD-seq rep 1

value: YAP Tg


title: liver YAP Tg input rep 2


title: liver YAP Tg input rep 1


title: L929 cells, Control 1


title: liver Control input_rep 1

value: wild type


title: liver decitabine treated Tet1 KO YAP Tg MBD-seq rep 1


title: liver Control input rep 2


title: liver YAP Tg MBD-seq rep 2


title: liver Tet1 KO YAP Tg MBD-seq rep 1


title: liver Control MBD-seq rep 2


title: liver Control MBD-seq rep 1


title: liver YAP Tg rep 2

description:
liver YAP Tg rep 2
YAP2

data_processing:
Data was mapped to the mouse geneome using TopHat2 and the UCSC mm10 mouse genome as reference.
Count data were generated using featureCounts, and differential gene expression analysis was carried out by edgeR R package.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized gene counts for every gene and every sample

extract_protocol:
Liver total RNA was extracted using TRIzol Plus RNA Purification Kit (Invitrogen) and further cleaned up by TURBO DNA-free Kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Doxycycline treatment, 1-month-old mice or nursing mothers of newborn pups were fed with 50 mg/L Doxycycline (LKT Laboratories, Inc.) in drinking water for the indicated time. For decitabine administration, 1-month-old mice were kept on 50 mg/L Dox, injected intraperitoneally with 0.5 mg/kg decitabine (Cayman Chemical) daily for 10 days.


title: L929 cells, Control 3


title: liver Tet1 KO YAP Tg rep 2

description:
liver Tet1 KO YAP Tg rep 2
AH2


title: liver YAP Tg rep 3

description:
liver YAP Tg rep 3
YAP3


description:
liver decitabine treated Tet1 KO YAP Tg rep 1
DAC1


title: liver Tet1 KO YAP Tg rep 3

description:
liver Tet1 KO YAP Tg rep 3
AH3


description:
liver decitabine treated Tet1 KO YAP Tg rep 2
DAC2


title: liver Tet1 KO YAP Tg rep 1

description:
liver Tet1 KO YAP Tg rep 1
AH1


title: liver Control rep 3

description:
liver Control rep 3
WT3


title: liver Control rep 2

description:
liver Control rep 2
WT2


title: mESC derived_NMP_ Hoxb1 null3

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

country: Germany

institute: TU Dresden

data_processing:
bcl2fastq: bcl2fastq 1.8.2/1.8.4
alignment: Fastq files were alignment with gsnap (2014-12-17) to the mm10 reference which was obtained from Ensembl. Additionally Ensembl annotation version 69 from mm10 was used to support splicesite detection for gsnap (-d mm10 --gunzip -A sam -n 1 -s EnsemblGene-69.ss.mm10.iit -N 1)
fragment counting: FeatureCounts (1.4.6) was used to count fragments per gene. Ensembl annotation version 69 as gtf file was used to detect genomic coordinates of genes (-s 2 -Q 1 -T 8)
Genome_build: mm10
Supplementary_files_format_and_content: tab separated file where the first columns provide details about the genes (ID, start, end, chromosome, strand) which is followed by the counts per gene per sample

source_name: mESC derived NMPs

growth_protocol: Refer to M&M section of Pazur et al

extract_protocol:
Qiagen Rneasy Method
Total RNA was used. mRNA was isolated from 1-2 ug total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation custom adaptors were used 1: (Adaptor-Oligo 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligaton adapters were depleted by an XP bead purification (Beckman Coulter) adding bead in a ratio of 1:1. Indexing was done during the following PCR enrichment (15 cycles) using custom amplification primers carring the index sequence indicated with ‘NNNNNN’. (Primer1: Oligo_Seq AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T, primer2: GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T, primer3: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNN GTG ACT GGA GTT. After two more XP beads purifications (1:1) libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen).

value: ES-derived neuromesodermal  progenitors

tag: treatments

value: differentiation as described

value: Hoxb1 null


title: mESC derived_NMP_wt3

value: wildtype


title: mESC derived_NMP_ Hoxb1 null1


title: liver Control rep 1

description:
liver Control rep 1
WT1


title: mESC derived_NMP_ Hoxb1 null2


description:
liver decitabine treated Tet1 KO YAP Tg rep 3
DAC3


title: liver YAP Tg rep 1

description:
liver YAP Tg rep 1
YAP1


title: mESC derived neural progenitors Hoxb1 2

source_name: mESC derived neural progenitors

value: ES-derived neural progenitor cells

value: differentiation as described+DOX

value: expressing Hoxb1


title: mESC derived neural progenitors Hoxb1 3


title: mESC derived neural progenitors 3

value: not expressing Hoxb1


title: mESC derived neural progenitors 1


title: mESC derived neural progenitors Hoxb1 1


title: mESC derived neural progenitors 2


title: mESC derived_NMP_wt2


title: mESC derived neural progenitors Hoxb1 + SAG 3

value: differentiation as described + SAG+DOX


title: mESC derived neural progenitors Hoxb1 + SAG 1


title: mESC derived neural progenitors Hoxb1 + SAG 2


title: mESC derived neural progenitors + SAG 2

value: differentiation as described + SAG


title: mESC derived neural progenitors + SAG 3


title: mESC derived neural progenitors + SAG 1


title: mESC derived NMP_wt1


title: R3_C59

city: Cambridge

first: Bryan

middle: B

last: Bryson

state: MA

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Data preprocessing and count matrix construction was performed using the Smart-seq2 Multi-Sample v2.2.0 Pipeline (RRID:SCR_018920)
Paired-end FASTQ files were individually processed using the Smart-seq2 Single Sample v5.1.1 Pipeline (RRID:SCR_021228).
Reads were aligned to the GENCODE transcriptome using HISAT2 v2.1.0.
Assembly: hg38
Supplementary files format and content: loom file containing counts
Supplementary files format and content: tab-delimited text files including counts and metadata for each Sample

source_name: blood

growth_protocol: Primary human monocyte-derived macrophages were cultured for 7 days in RPMI + 10% FBS in the presence of 25 ng/mL GM-CSF.

extract_protocol:
RNA was harvested in RLT + 1% BME lysis buffer and extracted using RNA-SPRI beads.
RNA-seq libraries were generated using Smart-seq2 protocol

treatment_protocol: Macrophages were treated with various ligands described in the metadata at listed concentrations for 24 hours.

value: blood

value: primary monocyte-derived macrophages

value: macrophages

tag: condition

value: VEGFA

tag: ligand

tag: ligand concentration

tag: lps stimulated

value: FALSE

tag: lps concentration

value: 10 ng/mL

tag: donor

value: C

tag: plate

tag: time

value: 24 hours


title: R3_C55


title: R3_C58

value: TSLP


title: R3_C56


title: R3_C61

value: FASLG


title: R3_C61_L

value: TRUE


title: R3_C54


title: R3_C62_L


title: R3_C57

value: TNF


title: R3_C60


title: R3_C53


title: R3_C52_L


title: R3_C52


title: R3_C51_L


title: R3_C49


title: R3_C48

value: PLAU


title: R3_C45


title: R3_C44

value: PBS-BSA


title: R3_C62


title: R3_C43

value: ox-LDL


title: R3_C46


title: R3_C47


title: R3_C42

value: OSM


title: R3_C41

value: NAMPT


title: R3_C38

value: blood

value: INHBB


title: R3_C51

value: primary monocyte-derived macrophages

value: macrophages


title: R3_C37

value: FALSE


title: R3_C33

value: 10 ng/mL


title: R3_C36

value: C


title: R3_C32

value: 24 hours


title: R3_C34


title: R3_C35


title: R3_C27


title: R3_C28


title: R3_C31_L


title: R3_C26


title: R3_C25


title: R3_C39

value: LPA


title: R3_C21


title: R3_C30


title: R3_C19


title: R3_C18_L

value: EPO


title: R3_C40_L

value: TRUE


title: R3_C22


title: R3_C40


title: R3_C18


title: R3_C19_L


title: R3_C31


title: R3_C23


title: R3_C16_L


title: R3_C30_L


title: R3_C16


title: R3_C29


title: R3_C14


title: R3_C09


title: R3_C11


title: R3_C17_L


title: R3_C15


title: R3_C24

value: IFNG


title: R3_C21_L


title: R3_C07


title: R3_C08


title: R3_C11_L


title: R3_C10


title: R3_C08_L


title: R3_C12


title: R3_C12_L


title: R3_C13


title: R3_C10_L


title: R3_C04_L

value: APOE


title: R3_C06_L


title: R3_C09_L


title: R3_C17


title: R3_C05_L

value: ATRA


title: R3_C04


title: R3_C03_L


title: R3_C06


title: R3_C05


title: R3_C14_L


title: R3_C15_L


title: R3_C13_L


title: R3_C02_L

value: ADIPOQ


title: R3_C02


title: R3_C03


title: R3_B25

value: B


title: R3_C07_L


title: R3_B23


title: R3_A25

value: A


title: R3_C01_L

value: blood


title: R3_B24


title: R3_C01


title: R3_A23


title: R3_B22


title: R3_A22


title: R2_C58_L

value: TSLP


title: R2_C57_L

value: primary monocyte-derived macrophages

value: TNF


title: R3_A24

value: macrophages

value: FALSE


title: R2_C56_L

value: 10 ng/mL

value: C


title: R2_C59_L

value: VEGFA

value: 24 hours


title: R2_C54_L

value: TRUE


title: R2_C60_L


title: R2_C49_L


title: R2_C45_L


title: R2_C43_L

value: ox-LDL


title: R2_C46_L


title: R2_C53_L


title: R2_C44_L

value: PBS-BSA


title: R2_C48_L

value: PLAU


title: R2_C47_L


title: R2_C42_L

value: OSM


title: R2_B59

value: B


title: R2_B62


title: R2_B60


title: R2_B57


title: R2_B58


title: R2_B54


title: R2_B56


title: R2_C55_L


title: R2_B55


title: R2_B53


title: R2_B51


title: R2_B48


title: R2_B49


title: R2_B41

value: NAMPT


title: R2_B40

value: blood


title: R2_B43


title: R2_B47


title: R2_B45


title: R2_B42


title: R2_B46


title: R2_B44


title: R2_B39

value: LPA


title: R2_B34

value: primary monocyte-derived macrophages


title: R2_B38

value: INHBB


title: R2_B36

value: macrophages


title: R2_B37

value: FALSE


title: R2_B35

value: 10 ng/mL


title: R2_B33


title: R2_B32


title: R2_B52


title: R2_B30


title: R2_B31


title: R2_B27


title: R2_B28


title: R2_B29


title: R2_B26


title: R2_B22


title: R2_B21_L


title: R2_B23


title: R2_B18_L

value: EPO


title: R2_B24

value: IFNG


title: R2_B25

value: 24 hours


title: R2_B16_L

value: TRUE


title: R2_B16


title: R2_B15


title: R2_B19_L


title: R2_B14_L


title: R2_B19


title: R2_B17_L


title: R2_B15_L


title: R2_B12


title: R2_B14


title: R2_B13_L


title: R2_B12_L


title: R2_B11_L


title: R2_B18


title: R2_B11


title: R2_B08


title: R2_B10


title: R2_B07_L


title: R2_B09_L


title: R2_B09


title: R2_B05

value: ATRA


title: R2_B07


title: R2_B02

value: ADIPOQ


title: R2_B06_L


title: R2_B02_L


title: R2_B13


title: R2_B01_L


title: R2_B05_L


title: R2_B03


title: R2_B17


title: R2_B10_L


title: R2_B01


title: R2_B06


title: R2_B04

value: APOE


title: R2_B21


title: R2_B08_L


title: CK_Control;C

city: Buncrana

first: Breedge

last: Conwell

address: Cromore rd

country: United Kingdom

institute: Ulster university

data_processing:
Intensity correction and base calling (into BCL files), FASTQ files were generated using appropriate bcl2fastq software (Illumina Inc.) which includes quality scoring of each individual base in a read.
Data was separated for paired end reads to determine whether the second read significantly differs from the first in terms of overall quality. Data analysis was performed by Exiqon (Exiqon, Denmark).
NGS RNA-Seq analysis pipeline include Bowtie2 (v.2.2.2), Tophat (v2.0.11) and Cufflinks (v2.2.1).
As we were comparing groups, Cuffdiff, normally used for unpaired samples to calculate FPKM (number of fragments per kilobase per million mapped fragments) was replaced with featureCounts.
FeatureCounts was used to calculate the counts of mapped reads in specific genes when groups with paired samples were compared, and generalised linear model likelihood ratio test (glmLRT) implemented by edgeR was used to test differential expression across submitted samples using featureCounts input. Post processing of Cufflinks and Cuffdiff was performed using CummeRbund and Bioconductor software to generate visual representations of sequencing results.
Assembly: h.sapiens, hg19 / GRC37, UCSC Genome Browser

source_name: Human Trabecular Meshwork

extract_protocol:
RNA was isolated using the Qiagen Universal All Prep, as per standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human donor trabecular meshwork cells were treated with TGFB2 for 24hrs (or vehicle control).

value: Ocular

value: Trabecular meshwork

tag: disease state

value: Non-POAG (Normal)

value: Control


title: TK_Treated;B

value: TGFB2 Treated


title: R2_B04_L

value: blood

tag: cell line

value: primary monocyte-derived macrophages

value: B


title: S006771

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

value: High

tag: nhg

tag: pam50 subtype

value: LumA

tag: clinical groups

tag: histopathological type

value: Lobular

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression

tag: esr2 expression


title: S006751

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: NodeNegative

tag: er status

tag: pgr status

value: LumB

value: Ductal


title: CK_Control;B

tag: tissue

tag: cell type

tag: disease state

tag: treatment


title: CK_Control;E


title: TK_Treated;C


title: TK_Treated;A


title: TK_Treated;D


title: TK_Treated;E


title: CK_Control;D


title: R2_B03_L

tag: cell line

value: macrophages

tag: condition

tag: ligand

tag: ligand concentration

tag: lps stimulated

value: TRUE

tag: lps concentration

value: 10 ng/mL

tag: donor

tag: plate

tag: time

value: 24 hours


title: S006737

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: her2 status

tag: ki67 status

value: Low

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression

tag: esr2 expression


title: CK_Control;A

tag: tissue

value: Ocular

tag: cell type

value: Trabecular meshwork

tag: disease state

value: Non-POAG (Normal)

tag: treatment


title: S006686

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype


title: S006666

value: Unclassified

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression


title: S006665

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: esr2 expression


title: S006706

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: clinical groups

tag: histopathological type


title: S006652

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years


title: S006667

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S006626

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: esr2 expression


title: S006623

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event


title: S006597

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S006549

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S006569

tag: pam50 subtype

value: Basal

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S006486

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S006622

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S006441

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S006465

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S006570

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S006391

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S006422

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: Other

tag: relapse free interval event

tag: esr1 expression


title: S006491

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

value: High

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S006523

tag: pam50 subtype

tag: clinical groups

value: TNBC

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S006321

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: Normal

tag: relapse free interval days

tag: relapse free interval years


title: S006352

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

value: LumA

value: Lobular

tag: relapse free interval event

tag: esr1 expression


title: S006531

value: NodeNegative

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

value: Ductal

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S006695

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S006372

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S006414

tag: pam50 subtype

value: LumB

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S006320

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S006442

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S006439

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S006314

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S006506

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S006447

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S006440

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S006444

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S006358

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S006313

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S006174

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S006191

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S006190

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S006262

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S006291

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S006109

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S006071

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S006251

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S005989

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S005893

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S006157

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S005958

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S006090

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S005782

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S005839

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S005636

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S006156

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S006150

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S005595

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S006012

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S006552

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S005520

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S005690

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S005514

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S006009

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S006105

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S005467

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S005458

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S005446

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S005433

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S005402

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S005624

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S005388

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S005375

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S005856

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S005703

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S005373

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S006193

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S005829

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S005947

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S005372

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S005608

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S005441

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S005605

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S005598

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S005288

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S005894

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S005241

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S005239

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S005376

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S005400

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S005362

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S005183

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S005393

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S005157

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S005182

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S005544

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S005270

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S005253

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S005184

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival years

tag: overall survival event


title: S005293

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S005399

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S005351

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S005353

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S005158

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S005139

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S005097

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression


title: S004750

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival years

tag: overall survival event


title: S004781

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval days

tag: relapse free interval years


title: S005151

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval event

tag: esr1 expression


title: S004867

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: esr2 expression


title: S004725

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: SubMicroMet

tag: overall survival years

tag: overall survival event


title: S004954

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: relapse free interval days

tag: relapse free interval years


title: S004782

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval event

tag: esr1 expression


title: S004778

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: overall survival days

tag: esr2 expression


title: S004731

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival years

tag: overall survival event


title: S004734

tag: pam50 subtype

tag: clinical groups

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: relapse free interval days

tag: relapse free interval years


title: S004703

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: relapse free interval event

tag: esr1 expression


title: S004649

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: overall survival days

tag: esr2 expression