title: T126

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T122

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: For pathology key, see pathology_consensus_key.xlsx

library_source: transcriptomic

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing using the Picard ExtractIlluminaBarcodes algorithm.
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 hg19 RepeatMasker track (downloaded March 14, 2011).
Remaining reads are aligned using TopHat2 2.0.5 (default parameters except for --mate-inner-dist (average size with adapters 355, range 268-465, measured for each sample individually) --mate-std-dev 100 --library-type fr-firststrand --keep-fasta-order --no-coverage-search) to the human genome reference GRCh37/hg19 (with b37 masked chromosome Y and hs37d5 decoy sequences) together with 80,883 transcript annotations from the UCSC knownGenes table (downloaded September 10, 2012).
Gene expression data in FPKM were generated using cufflinks 2.1.1 and pre-processed by collapsing on 27,979 unique gene symbols (sum of FPKM values of each matching transcript), keeping 18,802 NCBI RefSeq NM-category (mRNA) gene symbols and adding to each expression measurement 0.1 FPKM, 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.
Genome_build: Human genome reference GRCh37/hg19 (with b37 masked chromosome Y and hs37d5 decoy sequences).
Supplementary_files_format_and_content: FPKM gene expression 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 instrument.

tag: tissue

value: breast tumor

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3

value: LumA


title: T121

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T140

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T120

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T138

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T116

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype

value: LumB


title: T117

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T115

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype

value: Basal


title: T114

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T113

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T111

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T132

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T110

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T109

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T108

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T107

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T106

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T105

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T104

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T103

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T102

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T101

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T100

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T119

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T95

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T96

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T99

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T97

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T92

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T98

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T91

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3

value: Normal


title: T93

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T94

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T118

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T90

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T88

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T89

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T112

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T86

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T87

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T84

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T82

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T83

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T81

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T80

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T79

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T78

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T76

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T77

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T75

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T73

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T72

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T74

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T71

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T70

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T63

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T68

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T69

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T64

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T67

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T60

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T59

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T65

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T66

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T85

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T61

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T56

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T58

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T62

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T55

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T53

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T50

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T54

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T52

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T48

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T51

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T47

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T49

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T46

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T45

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T43

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T44

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T42

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T57

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T40

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T41

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T39

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T38

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T31

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T32

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T29

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T37

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T36

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T33

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T34

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T27

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T35

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T28

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T30

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T25

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T22

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T21

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T26

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T20

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T23

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T18

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T17

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T19

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T16

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T15

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T14

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T13

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T11

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T9

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T12

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T10

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T8

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T7

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T3

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T24

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T1

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T2

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T6

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: T5

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: her2 consensus

tag: ki67 reading 1

tag: ki67 reading 2

tag: ki67 reading 3

tag: ki67 consensus

tag: nhg reading 1 tubular

tag: nhg reading 1 pleomorph

tag: nhg reading 1 mitotic

tag: nhg reading 2 tubular

tag: nhg reading 2 pleomorph

tag: nhg reading 2 mitotic

tag: nhg reading 3 tubular

tag: nhg reading 3 pleomorph

tag: nhg reading 3 mitotic

tag: nhg consensus

tag: pam50 subtype


title: T4

tag: tissue

tag: er ihc routinestain clinical reading

tag: er ihc routinestain reading 2

tag: er ihc routinestain reading 3

tag: er ihc restain reading 1

tag: er ihc restain reading 2

tag: er ihc restain reading 3

tag: er consensus

tag: pgr ihc routinestain clinical reading

tag: pgr routinestain reading 2

tag: pgr routinestain reading 3

tag: pgr restain reading 1

tag: pgr restain reading 2

tag: pgr restain reading 3

tag: pgr consensus

tag: her2 ihc clinreading

tag: her2 ihc reading 2

tag: her2 ihc reading 3

tag: her2 clinical status

tag: her2 sish reading 1

tag: her2 sish reading 2

tag: her2 sish reading 3


title: 16_Th17

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

country: USA

institute: University of Pittsburgh

description:
Th17
processed data file: FPKM_values_all_Revu.txt

data_processing:
Analysis was performed on Illumina NextSeq500.
Raw sequence reads were cleaned for adapter sequences using Trimmomatic (Bolger et al., 2014) with default parameters.
Trimmed reads were mapped onto human genome build GRCh38 using TopHat2.1.1 and gene expression FPKM values were calculated using Cufflinks 2.2.1 (Trapnell et al., 2012).
Data (heat maps) generated from FPKM values normalized relative to mean expression for that gene for each of two independent donors.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM_values_all_Revu.txt: Tab-delimited text file includes FPKM values for individual samples.

molecule: total RNA

source_name: Buffy coat

growth_protocol: Cells were cultured for 5 days in Complete RPMI containing (10% FBS, 2mm L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 50µM 2-_x001F_β-mercaptoethanol, HEPES and Na pyruvate)  in 96 well tissue culture plate.

extract_protocol:
Total RNA was isolated according to the manufacturer instructions using RNeasy mini purification kit (Qiagen, Hilden, Germany).
Libraries were prepared using ultra DNA library prep kits.

treatment_protocol: Cells were activated on plate bound aCD3 in the presence or absence of soluble IL23+IL1β and anti-CD28.

tag: disease status

value: Healthy

tag: cell type

value: Peripheral blood mononuclear cells (PBMCs)

tag: cell population

value: Negatively selected CD4 naive T cells

tag: growth condition

value: anti-CD3, IL-23 and IL-1b

tag: donor


title: 16_Th17CD28_2

description:
Th17CD28
processed data file: FPKM_values_all_Revu.txt

value: anti-CD3, anti-CD28, IL-23 and IL-1b


title: 16_Th0CD28_1

description:
Th0CD28
processed data file: FPKM_values_all_Revu.txt

value: anti-CD3 and anti-CD28


title: 16_Th0CD28_2


title: 15_Th17_2


title: 15_Th0CD28_1


title: 16_Th0

description:
Th0
processed data file: FPKM_values_all_Revu.txt


title: 15_Th0CD28_2


title: 15_Th0


title: 15_Th17_1


title: 15_Th17CD28_2


title: H3K27ac_MOLM13_SIK3TQ_HG

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Sequencing reads were mapped into reference human genome hg19 using Bowtie2
Peakcalling was done using MACS2 FDR cut off 5% with broad peak and narrow peak option for H3K27ac and MEF2C, respectively
The H3K27ac peaks in knockout experiment or HG-9-91-01 treatment experiment were merged with corresponding control ChIP-seq using BEDtools
Normalized tag count was calculated using Bamliquidator package
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: actue myeloid luekemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin.

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end-repaired, 3’-adenylated, and then ligated with indexed adaptor. These DNA was size selected (200-400 bp) via agarose gel electrophoresis, and PCR amplified. Final products were purified using AMPure XP beads.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout, or treated with DMSO or 100 nM HG-9-91-01 for 2 hrs

tag: cell line

value: MOLM-13 cell expressing SIK3T142Q

tag: treatment

value: 2 hr treatment of 100 nM HG-9-91-01

tag: chip antibody

value: H3K27ac (abcam, ab4729)


title: 15_Th17CD28_1


title: H3K27ac_MOLM13_empty_HG

value: MOLM-13 cell harboring empty vector


title: H3K27ac_MOLM13_empty

value: 2 hr treatment of 0.1% DMSO


title: Input_MOLM13_SIK3TQ_HG


title: Input_MOLM13_empty


title: H3K27ac_HEL_sgSIK3e4

value: HEL cell

value: day 5 after sgSIK3e4 guideRNA infection

value: H3K27ac (abcam ab4729)


title: Input_MOLM13_for MEF2C

value: MOLM-13 cell


title: MEF2C_MOLM13

value: MEF2C (Cell Signaling Technologies, 5030S)


title: Input_HEL_sgLKB1e2

value: day 5 after sgLKB1e2 guideRNA infection


title: Input_HEL_sgSIK3e4


title: H3K27ac_HEL_sgNeg2

value: day 5 after sgNeg2 guideRNA infection


title: 16_Th17CD28_1

value: Healthy

value: Peripheral blood mononuclear cells (PBMCs)


title: H3K27ac_MOLM13_sgSIK3e4


title: Input_HEL_sgNeg2


title: Input_MOLM13_sgNeg2


title: Input_MOLM13_sgLKB1e2


title: MOLM13_sgSIK3e4_sgHDAC4e20

data_processing:
Sequencing reads were mapped into reference human genome hg19 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: txt, normalized RPKM

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

value: day 5 after sgSIK3e4 & sgHDAC4e20 guideRNAs co-infection


title: Input_MOLM13_sgSIK3e4


title: H3K27ac_MOLM13_sgNeg2


title: MOLM13_sgSIK3e1_sgHDAC4e19

value: day 5 after sgSIK3e1 & sgHDAC4e19 guideRNAs co-infection


title: MOLM13_empty_HG


title: MOLM13_SIK3TQ_HG


title: MOLM13_sgLKB1e3

value: day 5 after sgLKB1e3 guideRNA infection


title: MOLM13_SIK3TQ_DMSO

value: MOLM-13 cell expressing SIK3T142Q


title: F3265repl

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

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.

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.

tag: scan-b external id

tag: instrument model

value: NextSeq 500

tag: age at diagnosis

tag: tumor size

tag: lymph node group

value: NodeNegative

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

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: F3250repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status


title: Input_MOLM13_empty_HG

tag: cell line

value: MOLM-13 cell harboring empty vector

tag: treatment

value: 2 hr treatment of 100 nM HG-9-91-01

tag: chip antibody


title: H3K27ac_HEL_sgLKB1e2

value: HEL cell

value: H3K27ac (abcam, ab4729)


title: F3127repl

tag: ki67 status

tag: nhg

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


title: F3058repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: NodePositive

tag: er status

tag: pgr status

value: LumB

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F3006repl

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc


title: F3028repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype


title: H3K27ac_MOLM13_sgLKB1e2

tag: cell line

value: MOLM-13 cell

tag: treatment

value: day 5 after sgLKB1e2 guideRNA infection

tag: chip antibody

value: H3K27ac (abcam ab4729)


title: F2921repl

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

value: Basal

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F2974repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

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: F2384repl

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F2871repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1580repl

tag: lymph node status

tag: er status

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: F1519repl

tag: scan-b external id

tag: instrument model

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F1438repl

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1497repl

tag: scan-b external id

tag: instrument model

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: F1214repl

tag: age at diagnosis

tag: tumor size

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F1439repl

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: er status

value: Normal

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1156repl

tag: age at diagnosis

tag: tumor size

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: MOLM13_empty_DMSO

tag: cell line

tag: treatment

value: 2 hr treatment of 0.1% DMSO