title: F780

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F778

status: Public on Mar 12 2018

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
processed data file:
gene_expression_3273_samples_and_136_replicates_transformed.csv
transcript_expression_3273_samples_and_136_replicates.csv

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 TopHat2 2.0.12 or 2.0.13 (default parameters except for --mate-inner-dist X (estimated in previous step), --mate-std-dev Y (estimated in previous step), --library-type fr-firststrand, --no-coverage-search, --max-insertion-length 20, --max-deletion-length 20, --read-gap-length 20, --read-edit-dist 22) to the human genome reference GRCh38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014).
Gene expression data in FPKM were generated using cufflinks 2.2.1 (default parameters except –GTF, --frag-bias-correct GRCh38.fa, --multi-read-correct, --library-type fr-firststrand, --total-hits-norm, --max-bundle-frags 10000000). The resulting data was was post-processed by collapsing on 30,865 unique gene symbols (sum of FPKM values of each matching transcript), adding to each expression measurement 0.1 FPKM, and performing a 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.
Single-gene classifiers (SGCs) and multi-gene classifiers (MGCs) were trained for ER, PgR, HER2, Ki67 (SGC and MGC) and NHG (MGC only) on the expression of the single underlying gene (ESR1, PGR, ERBB2 or MKI67) or multiple genes (5000 most varying genes across all samples) of a 405 sample cohort using consensus pathology scores as labels. Classifier training was performed by selecting expression thresholds that maximize prediction concordance to the consensus scores (SGCs) and nearest shrunken centroids using the pamr R package (MGCs). The classifiers were used to predict the biomarker status in a validation cohort of 3273 samples from patients enrolled in the SCAN-B study.
Genome_build: Human genome reference GRCh38/hg38.
Supplementary_files_format_and_content: Gene expression in FPKM 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.

value: HiSeq 2000

tag: age at diagnosis

tag: tumor size

value: NodeNegative

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

value: LumA

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F784

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

value: Basal


title: F781

tag: age at diagnosis

tag: tumor size

value: NodePositive

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

value: Normal


title: F799

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F800

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


title: F783

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F779

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

value: LumB

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F773

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F776

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F775

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F774

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


title: F772

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F771

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F788

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F787

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F770

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F769

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


title: F782

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F767

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F764

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F768

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F765

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F762

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


title: F766

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F761

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F777

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F760

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F763

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F755

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


title: F758

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F754

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F751

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F753

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F759

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F752

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


title: F750

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F749

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F747

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F748

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F745

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F746

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


title: F744

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F743

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F742

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F757

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F738

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F740

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


title: F739

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F756

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F741

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F737

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F732

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F734

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


title: F735

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F730

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F731

tag: scan-b external id

tag: instrument model

tag: lymph node group

value: SubMicroMet

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F733

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F728

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F729

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


title: F723

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F722

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F726

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F719

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F721

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F727

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


title: F715

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F718

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F710

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F713

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F736

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F712

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


title: F714

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F717

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F716

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F707

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F711

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F709

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


title: F704

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F703

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F706

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F705

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F698

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F701

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


title: F700

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F697

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F699

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F702

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F696

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F694

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


title: F695

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F691

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F692

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F693

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F689

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F690

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


title: F687

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F685

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F686

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F683

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F681

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F684

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


title: F680

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F682

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F677

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F679

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F676

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F678

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


title: F675

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F673

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F674

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F671

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F669

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F668

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


title: F670

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F667

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F688

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F666

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F665

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F664

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


title: F661

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F663

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F660

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F662

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F659

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F656

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


title: F658

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F651

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F657

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F652

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F654

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F655

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


title: F653

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F672

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F650

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F649

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F648

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F644

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


title: F645

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F647

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F646

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F640

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F641

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F636

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


title: F637

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F642

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F639

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F632

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F633

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F638

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


title: F631

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F635

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F643

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F629

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F630

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F627

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


title: F624

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F623

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F621

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F626

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F628

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F622

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


title: F617

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F620

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F619

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F618

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F613

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F614

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


title: F615

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F616

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F610

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F611

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F612

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F605

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


title: F606

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F600

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F602

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F609

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F604

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F603

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


title: F607

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F595

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F590

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F591

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F592

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F593

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


title: F597

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F589

tag: age at diagnosis

tag: tumor size

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F587

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg


title: F608

tag: age at diagnosis

tag: tumor size

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F588

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F601

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


title: 76_SL220773

status: Public on Jan 13 2018

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

country: USA

institute: Virginia Tech

data_processing:
Sequences were trimmed of their adapters
Reads were aligned to the bovine genome , and sequences aligning to multiple places on the genome, with 5 or more mismatches were filtered out. The sequences were then marked for duplicates, and non-duplicated reads were used for gene expression study
Genome_build: UMD3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples
Supplementary_files_format_and_content: tab-delimited text files include count reads

molecule: total RNA

organism: Bos taurus

source_name: Peripheral white blood cells

extract_protocol:
Total RNA was then isolated from PWBCs of 23 heifers using TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol
Libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina, Inc., San Diego, CA) following manufacturer’s instructions

tag: station

value: Station A

tag: pregnancy outcome


title: 85_SL220775


title: 82_SL220774


title: 91_SL220767


title: 88_SL220765


title: 89_SL220766


title: 70_SL220768


title: F596

tag: scan-b external id

tag: instrument model

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc


title: F599

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F594

tag: scan-b external id

tag: instrument model

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc


title: 66_SL220764

tag: station

tag: pregnancy outcome


title: 71_SL220769


title: 73_SL220771


title: CV_input

status: Public on Mar 27 2017

city: Durham

first: John

middle: F

last: Rawls

state: NC

address: 213 Research Drive

institute: Duke University School of Medicine

library_source: genomic

data_processing:
For ChIP-seq, peaks were called using MACS2 Galaxy version 2.1.0.20151222.0 with FDR < 5% and using the same condition's input as background; for Dnase-seq, peaks were called using MACS (version 2.1.0.20140616) with FDR < 1%
bigWig files were generated using bamCoverage (Galaxy verion 2.2.3.0) using RPKM normalization
Genome_build: mm9
Supplementary_files_format_and_content: bigWig and peak files

molecule: genomic DNA

organism: Mus musculus

source_name: Jejunal intestinal epithelial cells

extract_protocol:
Mice were euthanized under CO2 and cervical dislocation and placed on a chilled wax dissection pad.  The small intestine was removed from the mouse and the jejunum was excised from the duodenum and ileum (Duodenum was defined as the anterior 5 cm of the midgut and ileum was defined as posterior 6 cm of midgut as described (Camp, et al 2014).  Adipose and vasculature were removed from the tissue.  The jejunum was opened longitudinally along the length of the tissue, exposing the lumen and epithelial cell layer.  Luminal debris was washed away from the epithelia with ice cold sterile PBS.  The tissue was temporarily stored in 10 ml of ice cold sterile PBS with 1x Protease Inhibitor (Complete EDTA-Free, Roche 1187350001) and 10 uM Y-27632 (ROCK I inhibitor, Selleck Chemicals S1049) to inhibit spontaneous apoptosis.  The jejunum was moved into a 15 ml conical tube containing 3 mM EDTA in PBS with 1x protease inhibitor and 10 uM Y-27632.  The tissue was placed on a nutator in a cold room for 15 minutes.  The jejunum was removed from the 3 mM EDTA and placed on an ice cold glass petri dish with PBS containing 1mM MgCl2 and 2 mM CaCl2 with protease inhibitors and 10 uM Y-27632.  Villi were scraped off of the tissue using a sterile plastic micropipette and placed into a new 15 ml conical tube.  The isolated IECs were then pelleted at 250 x g at 4°C for 5 minutes, resuspended in 15 ml of ice cold PBS containting 10 uM Y-27632 and 1x protease inhibitors and pelleted again at 250 x g at 4°C.  The cell pellet was used for chromatin immunoprecipitation or for nuclear extractions.
[ChIP-seq] Frozen sonicated chromatin was thawed on ice.  Thawed and fresh chromatin samples were diluted in 1 mL of ChIP dilution buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl (pH 8.1), and 150 mM NaCl) containing 1x protease inhibitor and precleared with washed protein G Dynabeads for 3 hours at 4°C on a nutator.  Precleared chromatin was incubated with ChIP grade antibodies [4 ug H3K4me1 (Rabbit anti-H3K4me1, Abcam ab8895), 4 ug H3K27ac (Rabbit anti-H3K27ac, Abcam ab4729), 8 ug Hnf4a (Mouse anti-Hnf4a, Abcam 41898), 8 ug Hnf4g (Goat anti-Hnf4g, Santa Cruz sc-6558X), 8 ug CTCF (Rabbit anti-CTCF, Active Motif, 61311)] overnight at 4°C on a nutator.  Antibody-chromatin complexes were pulled down with washed protein G dynabeads for 4 hours at 4°C on a nutator.  The beads were washed 5x for 3 minutes with ice cold LiCl wash buffer (100 mM Tris-Cl (pH 7.5), 500 mM LiCl, 1% IGEPAL, 1% sodium deoxycholate)) and 1x with ice cold TE buffer at 4°C on a nutator.  Washed beads were resuspended in 100 uL of ChIP elution buffer (1% SDS and 0.1 M sodium bicarbonate)) and placed in a thermomixer heated to 65°C and programed to vortex at 2000 RPM for 15 seconds, rest for 2 minutes for a total of 30 minutes.  The beads were pelleted, placed on a magnet, and the supernatant was moved to a new tube.  This elution process was repeated once and corresponding elutions were combined for a total of 200 uL.  To reverse crosslink immunoprecipitated chromatin, 8 uL of 5 M NaCl was added to each 200 uL ChIP elution and elutions were incubated at 65°C overnight.  Immunoprecipitated chromatin was isolated using a QIAquick PCR quick preparation kit (Qiagen 28104), quantified using a Qubit 2.0 flourometer and stored at -80°C until library preparations and amplification.  Libraries were always prepared within 3 days of the immunoprecipitation with the NEBNextUltra DNA Library Prep Kit for Illumina (New England Biolabs E7370S).  Prepared libraries were quantified using a Qubit 2.0 fluorometer and submitted to Hudson Alpha Genomic Services Laboratory for 50 bp single end sequencing on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.
[RNA-seq] Mouse jejunum intestinal epithelial cells were collected as mentioned above.  Prior to crosslinking, 1/50 of the isolated IECs were suspended in 1 ml TRIzol and stored at -80°C.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12,000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column-based RNA-isolation kit (Ambion Cat 12183018A) with an on column DNase I (RNase-free) treatment (New England Biolabs M0303L) to remove DNA contamination.  RNA was eluted off the column in nuclease-free water, quantified using a Qubit 2.0 and stored at -80°C until submission to the Duke Sequencing and Genomic Technologies Core.  RNA-seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.
[Dnase-seq] DNase hypersensitivity was performed as described (Camp et al., 2014) with the following modifications: IECs were isolated as above from jejunum and subjected to endogenous DNase activity to digest chromatin.  DNase-seq libraries were constructed as previously described, with “Oligo 1b” phosphorylated at the 5’-end to enhance ligation efficiency (Song and Crawford, 2010).  Libraries were sequenced by Illumina HiSeq 2000 with 50 bp single end reads with 3 samples per lane.
[Input] Germ free or conventionalized chromatin for input normalization was generated using the same protocol as above except no antibody was used during the overnight antibody incubation; instead, chromatin was incubated at 4°C with gentle agitation.  Bead incubation, reverse-crosslinking and library preparations for these samples were performed using the same protocol

treatment_protocol: All mouse husbandry was performed as described in (Camp et al., 2014) using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine with the following exceptions. All mice used in this study were 10 – 12 week old male C57BL/6J, housed on Alpha-dri bedding (Shepherd) and fed 2020SX diet (Envigo) ad libitum.  To generate conventionalized mice, germ-free mice were colonized with a conventional microbiota from by receiving a 200 uL oral gavage of 20% glycerol stock containing 1:1 w/v fecal sample collected from adult SPF C57BL/6J mice collected over 2 weeks and homogenized in reduced PBS

tag: strain

tag: condition

value: CV

tag: cell type

value: Jejunal intestinal epithelial cells

tag: chip antibody


title: CV_RNA-seq_2


title: GF_input

value: GF


title: CV_RNA-seq_1


title: Fibroblasts_Healthy_Control_8

status: Public on Jan 03 2018

type: RNA

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

country: Italy

institute: University of Brescia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hours at 45 °C on GeneChip HumanGene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics FS 450.

scan_protocol: The GeneChip was scanned and data extracted using GeneChip scanner 3000 7G (Affimetrix, Santa Clara, CA).

data_processing: The raw data were analyzed with Expression Console™ Software using Affymetrix default analysis settings and Robust Multichip Analysis (RMA). The resulting CEL files were processed using Partek® Genomics Suite software, version 6.6 Copyright©; 2014 (Partek Inc., St. Louis, MO, USA). To detect differentially expressed genes (DEGs) between vEDS vs control cells, a one-way ANOVA analysis was used as a criterion for the selection of DEGs. To assess significant differences in the gene expression profile in vEDS fibroblasts, we selected the genes that had more than a 1.5-fold change and p-value <0.05. Multiple testing correction was applied to control the false-discovery rate (FDR) using the Benjamini–Hochberg (BH) procedure. Genes with a FDR <0.05 were selected as differentially expressed and retained for further analysis.

label: Biotin

source_name: Skin fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Skin fibroblasts, derived from vEDS patients and healthy donors, were cultured in Eagle's minimum essential (MEM) supplemented with 10% FBS, 100 mg/mL streptomycin, 100 U/mL penicillin and incubated at 37° C in a humidified chamber with 5% CO2. Cells were harvested once they reached confluence by treating with trypsin (0.05% trypsin with 0.25% EDTA).

extract_protocol: Total RNA was extracted from skin fibroblasts of three vEDS patients and nine unrelated healthy individuals using the Qiagen RNeasy kit according to manufacturer's instructions (Qiagen, Hilden, Germany).

tag: disease

value: healthy


title: Fibroblasts_Healthy_Control_7


title: Fibroblasts_Healthy_Control_6


title: Fibroblasts_Healthy_Control_3


title: Fibroblasts_Healthy_Control_5


title: CV_Dnase_3


title: CV_ChIP-seq_Hnf4g_1

value: Hnf4g (Santa Cruz sc-6558X)


title: Fibroblasts_Healthy_Control_2


title: 75_SL220772


title: Fibroblasts_Healthy_Control_9


title: GF_RNA-seq_1


title: CV_ChIP-seq_Hnf4g_3


title: GF_ChIP-seq_Hnf4g_4


title: CV_ChIP-seq_Hnf4g_4


title: Fibroblasts_vEDS_P3

value: vascular Ehlers Danlos syndrome


title: CV_ChIP-seq_Hnf4g_2


title: Fibroblasts_vEDS_P1


title: GF_Dnase_2


title: CV_Dnase_1


title: Fibroblasts_Healthy_Control_1


title: GF_RNA-seq_2


title: Fibroblasts_Healthy_Control_4


title: GF_ChIP-seq_Hnf4g_3


title: Fibroblasts_vEDS_P2


title: GF_Dnase_1


title: CV_Dnase_2


title: GF_ChIP-seq_Hnf4g_2


title: GF_ChIP-seq_Hnf4g_1


title: CV_ChIP-seq_Hnf4a_3

value: Hnf4a (Abcam ab41898)


title: CV_ChIP-seq_Hnf4a_2


title: CV_ChIP-seq_Hnf4a_1


title: GF_ChIP-seq_Hnf4a_2


title: GF_ChIP-seq_Hnf4a_1


title: CV_ChIP-seq_H3K4me1_3

value: H3K4me1 (Abcam ab8895)


title: CV_ChIP-seq_H3K4me1_1


title: GF_ChIP-seq_Hnf4a_3


title: GF_ChIP-seq_H3K4me1_3


title: CV_ChIP-seq_H3K4me1_2


title: CV_ChIP-seq_H3K27ac_1

value: H3K27ac (Abcam ab4729)


title: GF_ChIP-seq_H3K4me1_1


title: CV_ChIP-seq_H3K27ac_2


title: WTCV_1

data_processing:
Zebrafish RNA-seq reads were aligned to the zebrafish genome (danRer7) using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping (default TopHat settings)
bam files were normalized by sequencing depth to generate bigWigs
Genome_build: DanRer7 (zv9)
Supplementary_files_format_and_content: bigWig

organism: Danio rerio

source_name: zebrafish digestive tracts

extract_protocol:
Zebrafish digestive tracts (n = 13 – 20 per condition per genotype) were removed by microdissection and resuspended in 1 mL TRIzol (Ambion/Invitrogen/ThermoFisher Scientific 15596026).  Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each.  200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature.  The samples were incubated at room temperature for 2 minutes and centrifuged at 12,000 x g for 15 minutes at 4°C.  The top aqueous layer was removed and added to equal volume of isopropanol.  The nucleic acids were isolated using a column-based RNA-isolation kit (Ambion Cat 12183018A) with an on column DNase I (RNase-free) treatment (New England Biolabs M0303L) to remove DNA contamination.  RNA was eluted off the column in nuclease-free water, quantified using a Qubit 2.0 and stored at -80°C until submission to the Duke Sequencing and Genomic Technologies Core.
RNA-seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.

treatment_protocol: Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described (Westerfield, 2000). Production, colonization, maintenance, and sterility testing of gnotobiotic zebrafish were performed as described (Pham et al., 2008).

tag: genotype

value: WT (hnf4a+/+)

tag: tissue

value: Larval digestive tract


title: WTGF_3


title: MutCV_1

value: Mutant (hnf4a-/-)


title: WTGF_2


title: WTGF_1


title: WTCV_2


title: MutCV_2


title: MutGF_1


title: GF_ChIP-seq_H3K4me1_2


title: WTCV_3


title: MutGF_2


title: GF_ChIP-seq_H3K27ac_2


title: ChIP-seq, Islet_Input

status: Public on Dec 31 2016

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
ChIP-seq: To obtain enough read depth, all the biological replicates were pooled together by selecting unique reads for Isl1 and Ldb1 respectively. Peak calling was performed using ‘findPeak’ command in Homer. Peaks within ENCODE blacklist regions were discarded. BigWig files for stack height profiles were generated by 1bp-resolution & RPM scale.
RNA-seq: RNA-seq library sequencing and preprocessing were performed by the Functional Genomics Core at the University of Pennsylvania. Reads were aligned to UCSC mouse genome mm9 and gene expression level were quantified using RUM pipeline. Differential gene expression analysis was done using edgeR and genes with FDR < 0.01 were selected as differentially expressed genes upon KO.
Genome_build: mm9
Supplementary_files_format_and_content: Compressed peak file in BED format with RPM-normalized peak height in 5th column. ChIP-seq stack height profile in bigWig format. Differential gene expression analysis results in excel file.

source_name: Isolated whole islets

extract_protocol:
For RNA-Seq: Islets were enzymatically isolated from the pancreas and separated from residual exocrine debris. Isolated islets were dispersed into single-cell suspensions using trypsin. Lineage-tracing positive cells were enriched using MoFlo Astrios directly into TRIzol. Total RNA was extracted using RNAeasy Micro columns then DNAse-treated with the TURBO DNA-free Kit and purified by RNAeasy Micro column. For ChIP-Seq: Islets were enzymatically isolated from the pancreas and separated from residual exocrine debris. Isolated islets were fixed and nuclear lysates were created. Chromatin was sheared and immunoprecipitated
RNA-Seq Libraries: ScriptSeq Complete Gold – Low Input (Illumina, SCL6G); and ChIP-Seq Libraries: NEBNext Ultra DNA Libray Prep Kit for Illumina (NEB, E7370S)

treatment_protocol: At P28, male mice received 5 oral gavages of tamoxifen (Tm) (Sigma, T5648) prepared at 50mg/ml in 90% sun flower seed oil, 10% EtOH (v/v) and given at 150µg/g bodyweight at 24-hour intervals under inhaled isoflurane anesthesia. Repeated at P35. For Isl1L/L; Rosa26LsLeYFP/ LsLeYFP; MIP-CreERTm mice the dosage was lowered to 100µg/g and not repeated at P35.

value: WT

tag: antibody


title: ChIP-seq, Islet_Isl1

value: Anti-Islet 1 antibody [EP4182] (Abcam, ab109517)


title: GF_ChIP-seq_H3K27ac_1


title: ISL1 ChIP-seq

status: Public on Apr 25 2016

city: Beijing

first: Yang

last: Wang

state: Beijing

address: Xueyuan Road 38#

department: Molecular Biology and Biochemistry

country: China

institute: Peking University Health Science Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and aligned to the mm9 genome assembly using Bowtie version 2.2.4 with the following configurations: -p 5 --sensitive.
reads from two biological replicates at each conditions were merged with samtools: samtools merge rep1.bam rep2.bam merged.bam.
peaks were called using MACS version 1.4.2 with the following setting:--pvalue-1E-05 --diag --wig.
peaks were annotated using PeakAnalyzer version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: Excel file is generated by MACS, representing ISL1 peaks or JMJD3 peaks; Bed file is generated by PeakAnalyzer to annotate peaks associated nearest transcription start sites.

source_name: Cardiac progenitor cells

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
Libraries were prepared according to manufacturer’s instructions (Illumina). Briefly, immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicentre), tailed with deoxyadenine using Klenow exo minus (NEB), and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 350 ± 50 bp were size-selected using Agencourt AMPure XP beads, and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 DNA polymerase (NEB). Libraries were quantified by qPCR using primers annealing to the adaptor sequence and sequenced at a concentration of 10 pM on an Illumina HiSeq 2000.

value: E14 mES-derived cardiac progenitor cells

tag: chip-antibody

value: ISL1 Abcam ab109517


title: Input ChIP-seq

value: Non


title: tp_stv_h24_r01

status: Public on Nov 30 2015

city: La Jolla

first: Raffaela

last: Abbriano

state: CA

address: 9500 Gilman Dr

department: Scripps Institution of Oceanography

institute: University of California San Diego

data_processing:
Demultiplexing Custom perl script
Alignment Tophat2  tophat2   --b2-sensitive --solexa1.3-quals  --read-realign-edit-dist 0  --no-coverage-search  --library-type fr-firststrand  --min-intron-length 40 --max-intron-length 2000
Raw counts HTSeq 0.6.1p1 htseq-count --stranded
Normalized counts  DESeq2_1.6.3 padj was calculated using the likelihood ratio test with deviance between biological replicates as the reduced model (dds <- DESeq(dds, test = "LRT", reduced = ~replicate))
Genome_build: Thaps3_chromosomes_assembly_chromosomes_repeatmasked.fasta,  Thaps3_bd_unmapped_assembly_scaffolds_repeatmasked.fasta  (http://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=Thaps3)
Supplementary_files_format_and_content: csv file containing deseq2 normalized count data for each sample

organism: Thalassiosira pseudonana

source_name: cell culture

growth_protocol: Axenic 8L cultures of Thalassiosira pseudonana (CCMP1335) were grown in artificial seawater medium (NEPC, http://www3.botany.ubc.ca/cccm/NEPCC/esaw.html) at 18C under continuous light (150 μmol/m^2/sec) to a concentration of approximately1x10^6 cells/ml, harvested by centrifugation for 12 min at 3100 x g, and then placed in 8L of silicon free medium in a polycarbonate bottle at a concentration of approximately 1x10^6 cells/ml. Cultures were stirred and bubbled with air under continuous light, and sampled at 0, 4, 8, 12, 18, and 24 hours following inoculation into silicic acid free medium. The -2 hour timepoint was taken two hours prior to silicon starvation.

extract_protocol:
Total RNA was extracted from cell pellets using TriReagent as described in Hildebrand & Dahlin, 2000.
cDNA libraries were prepared from 4 µg of total RNA for each sample using the Illumina TruSeq Stranded mRNA Sample Prep kit (Illumina, San Diego, CA) according to manufacturer's protocols (Rev. D), which includes a poly-A purification step. The resulting libraries were evaluated for size on an Agilent DNA High Sensitivity chip following the manufacturer's instructions, and quantified by quantitative PCR according to Illumina's protocols. Each library was diluted to 2 nM with 10 mM Tris-Cl, 0.1% Tween 20. Bar-coded libraries were then pooled (10 or 11 per pool), and sequenced on an Illumina HiSeq 2000 with 100 nt paired end reads.

treatment_protocol: 750 ml of culture was removed, treated with cycloheximide (final concentration, 20 μg ml-1) and harvested by filtration. Cells were pelleted and stored at -80° C.

value: CCMP 1335

value: T=24 silicon starvation

tag: replicate


title: tp_stv_h24_r02


title: tp_stv_h18_r02

value: T=18 silicon starvation


title: Fibroblasts Control 1

status: Public on Aug 05 2016

hyb_protocol: Labeled RNA was hybridized for 16 hr at 45° C on GeneChip miRNA 3.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affimetrix, SantanClara, CA).

data_processing: The data were analyzed with Expression Console™ Software using Affymetrix default analysis settings and Robust Multichip Analysis (RMA).   Analyses to identify differentially expressed miRNAs were performed with Partek® Genomics Suite software version 6.6 (Partek Inc., St. Louis, MO).

label_protocol: 250 ng of total RNA was labeled using the Flash Tag Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays according to the manufacturer's instructions.

growth_protocol: Skin fibroblasts from EDS-HT/JHS patients and healthy controls were cultured in Eagle's minimum essential (MEM) supplemented with 10% FBS, 100 µg/mL streptomycin, 100 U/mL penicillin and incubated at 37° C in a humidified chamber with 5% CO2. Cells were harvested once they reached confluence by treating with trypsin (0.05% trypsin with 0.25% EDTA).

extract_protocol: Total RNA was extracted from skin fibroblasts of five EDS-HT/JHS patients and six unrelated controls using the Qiagen RNeasy kit according to manufacturer's instructions (Qiagen, Hilden, Germany).

tag: disease state

value: healthy


title: Fibroblasts Control 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45° C on GeneChip HumanGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics FS 450.

data_processing: The data were analyzed with Expression Console™ Software using Affymetrix default analysis settings and Robust Multichip Analysis (RMA). The resulting CEL files were analyzed using Partek® Genomics Suite software, version 6.6 Copyright©; 2014 (Partek Inc., St. Louis, MO, USA). Analysis of variance (ANOVA) was used to identify the differentially expressed genes between EDS-HT/JHS patients and controls.

growth_protocol: Skin fibroblasts from EDS-HT/JHS patients and sex-matched healthy controls were cultured in Eagle's minimum essential (MEM) supplemented with 10% FBS, 100 µg/mL streptomycin, 100 U/mL penicillin and incubated at 37° C in a humidified chamber with 5% CO2. Cells were harvested once they reached confluence by treating with trypsin (0.05% trypsin with 0.25% EDTA).

extract_protocol: Total RNA was extracted from skin fibroblasts of 5 EDS-HT/JHS patients and 6 unrelated controls using the Qiagen RNeasy kit according to manufacturer’s instructions (Qiagen, Hilden, Germany).


title: Fibroblasts_EDS-HT/JHS_P2

value: EDS-HT/JHS


title: Fibroblasts Control 1


title: Fibroblasts Control 4


title: Fibroblasts Control 3


title: Fibroblasts_EDS-HT_P4


title: Fibroblasts Control 5


title: Fibroblasts_EDS-HT/JHS_P3


title: Fibroblasts Control 6


title: Fibroblasts_EDS-HT/JHS_P5


title: Fibroblasts_EDS-HT/JHS_P1


title: Fibroblasts Control 5


title: tp_stv_h18_r01


title: Fibroblasts Control 2


title: tp_stv_h12_r01

value: T=12 silicon starvation


title: Fibroblasts Control 3


title: tp_stv_h12_r02


title: Fibroblasts Control 2


title: Fibroblasts_EDS-HT_P1


title: Fibroblasts Control 6


title: Fibroblasts_EDS-HT/JHS_P4


title: Fibroblasts_EDS-HT_P3


title: tp_stv_h04_r02

value: T=4 silicon starvation


title: tp_stv_h00_r02

value: T=0 silicon starvation


title: tp_stv_h00_r01


title: tp_stv_h-2_r02

value: exponential growth


title: Fibroblasts_EDS-HT_P2


title: Fibroblasts_EDS-HT_P5


title: tp_stv_h08_r02

value: T=8 silicon starvation


title: tp_stv_h08_r01


title: Forelimb_Input_DNA

status: Public on Oct 01 2015

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

data_processing:
Basecalls were performed CASAVA version 1.8.2.
Illumina reads were aligned to the mouse genome (mm9) or green anole genome (anoCar2) with Bowtie version 1.1.0 with the options "--best --sam -t -l 28 -n 3 -m 1".
ChIP-Seq data quality and fragment size was assessed from aligned reads for each sample using phantompeaktools (https://code.google.com/p/phantompeakqualtools/).
Regions of H3K27ac enrichment were determined using macs2 (version 2.0.10.20130501) with the options “--bdg --SPMR --nomodel --qvalue=0.05”. Extension size was determined for each sample based on the cross-correlation profile of the aligned reads.
BigWig files of H3k27ac signal visualized as fold enrichment compared to background were generated from treatment and control bedGraph files using macs2 bdgcmp with the options " --tdepth=1 --cdepth=1 --method=FE". BedGraph files were converted to BigWig using BEDtools slopBed command and the bedClip and bedGraphToBigWig from UCSC Kent Utilities as implemented in the bdg2bw script by Tao Liu (https://gist.github.com/taoliu/2469050).
Genome_build: mm9 (Mus musculus); anoCar2 (Anolis carolinensis)
Supplementary_files_format_and_content: BigWig files were generated from treatment and control signal files created by macs2 and represent the fold enrichment of the ChIP sample versus the input DNA control. Bed files were created from the first 6 columns of the narrowPeak format files created by macs2 and represent regions with significant H3K27ac enrichment compared to background signal from input DNA controls with a qvalue cutoff of 0.05.

source_name: embryonic forelimb

growth_protocol: Normal gestation

extract_protocol:
After cross-linking in 1% formaldehyde in PBS for 30 minutes, tissues were rinsed and treated with trypsin for 5 minutes to generate a single cell suspension. Samples were then pre-disrupted with a Branson 450 Sonifier, and then sheared with a Bioruptor (Diagenode) to generate a chromatin size range of 200–600 bp. PureProteome Protein G Magnetic Beads (Millipore) were pre-incubated with H3k27ac antibody before incubating overnight with 100-200 μg of sheared chromatin. After washing, immune complexes were eluted from the beads, and protein-DNA crosslinks were reversed by incubating at 65˚C overnight. After treatment with RNase followed by proteinase K, samples were purified with the QIAquick PCR Purification Kit (Qiagen).
ChIP and input chromatin control libraries were produced using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England BioLabs) as directed by the manufacturer with Illumina-compatible adapters. Libraries were sequenced with 50 bp single-end runs on an Illumina HiSeq 2000 at the HudsonAlpha Institute for Biotechnology.

value: ICR

value: embryonic forelimb

tag: developmental stage

value: wild type


title: Hindlimb_Input_DNA

source_name: embryonic hindlimb

value: embryonic hindlimb


title: GenitalTubercle_Input_DNA

source_name: embryonic genital tubercle

value: embryonic genital tubercle


title: Forelimb_H3K27ac_Replicate2

value: H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294)


title: Hindlimb_H3K27ac_Replicate1


title: Forelimb_H3K27ac_Replicate1


title: tp_stv_h04_r01


title: tp_stv_h-2_r01


title: Hindlimb_H3K27ac_Replicate2


title: Fibroblasts_Control_1

status: Public on Sep 21 2015

data_processing: The data were analyzed with Expression Console™ Software using Affymetrix default analysis settings and Robust Multichip Analysis (RMA). Subsequently analyses for differentially expressed genes cathegorization were performed with Partek® Genomics Suite software version 6.6 (Partek Inc., St. Louis, MO).

growth_protocol: Fibroblast cells were cultured in Eagle's minimum essential (MEM) supplemented with 10% FBS, 100 mg/mL streptomycin, 100 U/mL penicillin and incubated at 37° C in a humidified chamber with 5% CO2. Cells were harvested once they reached confluence by treating with trypsin (0.05% trypsin with 0.25% EDTA).

extract_protocol: Total RNA was extracted from skin fibroblasts of 3 ATS patients and 3 unrelated controls using the Qiagen RNeasy kit according to manufactures’ instructions (Qiagen, Hilden, Germany).

value: skin fibroblast

value: control


title: Fibroblasts_Control_2


title: Fibroblasts_ATS_P2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45° C on GeneChip HumanGene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics FS 450.

scan_protocol: The GeneChip was scanned and data extracted using GeneChip scanner 3000 7G (Affimetrix, SantanClara, CA).

tag: diagnosis

value: arterial tortuosity syndrome (ATS)


title: Fibroblasts_Control_1


title: Fibroblasts_ATS_P3

value: arterial tortuosity syndrome


title: Fibroblasts_ATS_P1


title: Fibroblasts_Control_3


title: Fibroblasts_ATS_P3


title: Fibroblasts_Control_3

value: healthy


title: Fibroblasts_ATS_P2


title: Fibroblasts_Control_2


title: 16 hour norepinephrine-treated CD8+ Tcm 72 Hours post-activation Replicate 1

status: Public on Mar 01 2015

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

description:
Sample name: NE72_rep1
16-hour norepinephrine treated CD8+ Tcm cells collected 72 hours after stimulation with CD3/CD28 beads

hyb_protocol: Samples were hybridized onto whole human genome 8x60K array slides for 17 hours at 65°C in a rotator oven secured in Agilent hybridization chambers followed by washing with appropriate wash buffers (Agilent) per manufacturer's instructions.

scan_protocol: Scanned on Agilent SureScan Scanner G2600D

data_processing:
Agilent Feature Extraction Software (v 9) was used for background subtraction and normalization. Custom analysis program was used to combine (all of the separate files to yield a file with test/reference values), normalize (if there is low correlation between the two channels, then output levels are adjusted slightly to compensate), and log-transform the resulting data into a single data file, which was used for further analysis.
Additional batch normalization was conducted for some further analyses (see supplementary file linked to the Series record.)

source_name: CD8+ Tcm

label_protocol: 100µg of total RNA from the sample and human universal references RNA was labeled using the Low Input Quick Amp Labeling Kit based on the manufacturer's instructions. Probes were quantified by NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Cells were examined at resting state (0 hour), and 24 and 72 hours after stimulation with CD3/28 antibodies in a 24-well plate with RPMI1640 with 10% FBS and pelicillin (10U/ml)/streptomycin(10µg/ml)

extract_protocol: Total RNA extracted using Qiacube per manufacturer's instructions

treatment_protocol: Control CD8 Tcm cells were untreated. Treated CD8 Tcm cells were treated with norepinephrine twice: 16 hours and 30 minutes before stimulation with CD3/28 antibodies.

value: CD8 T central memory (Tcm) cell

tag: treatment

value: NE

tag: activation

value: activation with CD3/28 antibodies

tag: time (hours after cd3/cd28 activation)

source_name: Agilent Universal Human Reference RNA

extract_protocol: Universal Human Reference RNA purchased from Agilent

tag: sample type

value: Universal Reference


title: 16 hour norepinephrine-treated CD8+ Tcm Pre-activation Replicate 3

description:
Sample name: NE0_rep3
16-hour norepinephrine treated CD8+ Tcm cells collected prior to stimulation with CD3/CD28 beads

value: unactivated control


title: 16 hour norepinephrine-treated CD8+ Tcm Pre-activation Replicate 2

description:
Sample name: NE0_rep2
16-hour norepinephrine treated CD8+ Tcm cells collected prior to stimulation with CD3/CD28 beads


title: 16 hour norepinephrine-treated CD8+ Tcm 72 Hours post-activation Replicate 2

description:
Sample name: NE72_rep2
16-hour norepinephrine treated CD8+ Tcm cells collected 72 hours after stimulation with CD3/CD28 beads


title: 16 hour cultured CD8+ Tcm Pre-activation Replicate 1

description:
Sample name: WT0_rep1
16 hour cultured CD8+ Tcm cells collected prior to stimulation with CD3/CD28 beads

value: untreated control


title: 16 hour cultured CD8+ Tcm 24 Hours post-activation Replicate 2

description:
Sample name: WT24_rep2
16 hour cultured CD8+ Tcm cells collected 24 hours after stimulation with CD3/CD28 beads


title: Fibroblasts_ATS_P1


title: 16 hour cultured CD8+ Tcm 72 Hours post-activation Replicate 1

description:
Sample name: WT72_rep1
16 hour cultured CD8+ Tcm cells collected 72 hours after stimulation with CD3/CD28 beads


title: 16 hour norepinephrine-treated CD8+ Tcm 24 Hours post-activation Replicate 3

description:
Sample name: NE24_rep3
16-hour norepinephrine treated CD8+ Tcm cells collected 24 hours after stimulation with CD3/CD28 beads


title: 16 hour norepinephrine-treated CD8+ Tcm 24 Hours post-activation Replicate 2

description:
Sample name: NE24_rep2
16-hour norepinephrine treated CD8+ Tcm cells collected 24 hours after stimulation with CD3/CD28 beads


title: 16 hour cultured CD8+ Tcm 24 Hours post-activation Replicate 3

description:
Sample name: WT24_rep3
16 hour cultured CD8+ Tcm cells collected 24 hours after stimulation with CD3/CD28 beads


title: 16 hour cultured CD8+ Tcm Pre-activation Replicate 3

description:
Sample name: WT0_rep3
16 hour cultured CD8+ Tcm cells collected prior to stimulation with CD3/CD28 beads


title: 16 hour cultured CD8+ Tcm Pre-activation Replicate 2

description:
Sample name: WT0_rep2
16 hour cultured CD8+ Tcm cells collected prior to stimulation with CD3/CD28 beads


title: 16 hour cultured CD8+ Tcm 72 Hours post-activation Replicate 2

description:
Sample name: WT72_rep2
16 hour cultured CD8+ Tcm cells collected 72 hours after stimulation with CD3/CD28 beads


title: 16 hour norepinephrine-treated CD8+ Tcm 24 Hours post-activation Replicate 1

description:
Sample name: NE24_rep1
16-hour norepinephrine treated CD8+ Tcm cells collected 24 hours after stimulation with CD3/CD28 beads


title: Fibroblasts_SEMDJL1_P1

status: Public on Jun 10 2014

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip HumanGene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics FS 450.

data_processing: The data were analyzed with Expression Console™ Software using Affymetrix default analysis settings and Robust Multichip Analysis (RMA). Subsequently analyses for differentially expressed genes categorization were performed with Partek® Genomics Suite software version 6.6 (Partek Inc., St. Louis, MO).

extract_protocol: Total RNA was extracted from dermal fibroblasts of both SEMDJL1 patients and 3 unrelated controls using the Qiagen RNeasy kit according to manufactures’ instructions (Qiagen, Hilden, Germany).

value: skin

value: fibroblasts

tag: disease status

value: GalT-II deficiency


title: Fibroblasts_Control_2


title: Fibroblasts_Control_3


title: Fibroblasts_SEMDJL1_P2


title: Hippocampus_male_42yrs_indiv86

status: Public on Oct 09 2008

city: Irvine

first: Nicole

middle: Claudia

last: Berchtold

address: 1226 Gillespie Neuroscience Facility

department: Institute for Memory Impairments and Neurological Disorders

institute: UC Irvine

description: Brain from cognitively intact individual.

hyb_protocol: Using a robotics system (Biomek FX MicroArray Plex SA System; Beckman Coultier) to optimize consistency in processing and minimize handling variability, each fragmented, biotin-labeled cRNA sample (30 mg) was individually hybridized to an Affymetrix Hg-U133 plus 2.0 chip for 16 hours and rotated at 13 rpm at 50C.

scan_protocol: The chips were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: GC-RMA expression values were obtained from CEL files using GeneSpring 7.3.1 software.  PLIER expression values were obtained using Expression Console software using default settings.  PLIER and GC-RMA data were processed using GeneSpring 7.0 software, with default normalizations (Data transformation:set values<0.01 to 0.01; per chip: normalize to 50th percentile; per gene: normalize to median).

label: biotin

source_name: brain, hippocampus, male, 42 years

label_protocol: Total RNA (10 ug) from each sample was used to generate first strand cDNA using a T7-linked-(dT)24 primer, followed by in vitro transcription using the ENZO BioArray High-Yield RNA transcript labeling kit (ENZO Farmingdale, NY) to generate biotin-labeled cRNA target.

extract_protocol: Total RNA was extracted from 10-200 mg of frozen, unfixed tissue using Trizol reagent (Invitrogen, Carlsbad CA), and purified using quick spin columns (Qiagen, Valencia CA).  RNA quality was assessed using the Agilent BioAnalyzer (Agilent Technologies, Palo Alto, CA) and UV spectrophotometer for the presence of sharp peaks and 28S/18S RNA.

tag: individual

tag: brain region

value: hippocampus

tag: gender

value: male

tag: age (yrs)


title: Fibroblasts_Control_1

tag: cell type


title: Hippocampus_male_33yrs_indiv84

source_name: brain, hippocampus, male, 33 years


title: Hippocampus_female_26yrs_indiv76

source_name: brain, hippocampus, female, 26 years

value: female


title: 16 hour cultured CD8+ Tcm 24 Hours post-activation Replicate 1

description:
Sample name: WT24_rep1
16 hour cultured CD8+ Tcm cells collected 24 hours after stimulation with CD3/CD28 beads


title: Hippocampus_male_28yrs_indiv29

source_name: brain, hippocampus, male, 28 years


title: Hippocampus_male_22yrs_indiv85

source_name: brain, hippocampus, male, 22 years


title: Hippocampus_female_34yrs_indiv35

source_name: brain, hippocampus, female, 34 years


title: DEV

status: Public on Sep 17 2012

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: 500-1000 FACS-sorted living cells

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Most bioinformatics analyses were performed using GeneSpring 7.3.1 software (Agilent Technologies) with GC-RMA preprocessing of the raw expression data (CEL files). Further statistical analysis was done with the computing environment R. Additional software packages (affy, geneplotter) were taken from the Bioconductor project.

source_name: lymphocyte-predominant Hodgkin lymphoma (lpHL) cell line sample

label_protocol: The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).

growth_protocol:
PRIMARY TUMOR SAMPLES: Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
CELL LINE SAMPLES: In vitro growing cell cultures were cooled at 4°C and 500-1000 living cells were immediately subjected to fluorescence-activated cell sorting directly into Purescript lysis buffer (Gentra).

extract_protocol: The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.

tag: cell line

value: DEV

value: Cultured lymphocyte-predominant Hodgkin lymphoma (lpHL) cells

tag: isolated by

value: fluorescence-activated cell sorting


title: Hippocampus_female_37yrs_indiv45

source_name: brain, hippocampus, female, 37 years


title: GenitalTubercle_H3K27ac_Replicate1

tag: strain

value: ICR

tag: tissue

value: embryonic genital tubercle

tag: genotype

value: wild type

tag: chip antibody

value: H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294)


title: 16 hour norepinephrine-treated CD8+ Tcm Pre-activation Replicate 1

description:
Sample name: NE0_rep1
16-hour norepinephrine treated CD8+ Tcm cells collected prior to stimulation with CD3/CD28 beads

value: CD8 T central memory (Tcm) cell

value: NE


title: GenitalTubercle_H3K27ac_Replicate2

tag: developmental stage