title: Multiple Myeloma Plasmacells, S2


title: Monocytes-derived Macrophages M1-Day 3 Replicate 1

status: Public on Dec 24 2024

type: SRA

city: Chicago

first: Afsar

middle: Raza

last: Naqvi

state: Illinois

address: 801 S Pauline

department: Periodontics

country: USA

institute: University of Illinois

description:
Library name: Group B_FPKM.M1_Day3_1
FPKM.M1_Day3_1
Group B
Total RNA-seq

library_source: transcriptomic

data_processing:
Transcripts Assembly: Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Tophat2 to map reads to the genome of Homo sapiens (Version: GRCh38). The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from 37 samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare (https://github.com/gpertea/gffcompare/). After the ﬁnal transcriptome was generated, StringTie and Ballgown were used to estimate the expression levels of all transcripts.
lncRNA identification: First, transcripts that overlapped with known mRNAs, known lncRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts with class code (I, j, o, u, x) were considered as lncRNAs.
Different expression analysis of transcripts: StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown.
Target gene prediction and functional analysis of lncRNAs: To explore the function of lncRNAs, we predicted the cis-target genes of lncRNAs. lncRNAs may play a cis role acting on neighboring target genes. In this study, coding genes in 100,000 upstream and downstream were selected by perl script. Then, we showed functional analysis of the target genes for lncRNAs by using the scripts in house. Signiﬁcance was expressed as a p value < 0.05.
Localization of lncRNAs on genome: Two diagrams were generated to show the localization and abundance of lncRNAs in genome using the program Circos. One diagram showed lncRNA expression level in different samples. The lncRNAs in the other diagram were subdivided into five categories according to their class code generated by StringTie: (i) a transfrag falling entirely within a reference intron (intronic); (j) potentially novel isoform or fragment at least one splice junction is shared with a reference transcript; (o) generic exonic overlap with a reference transcript; (u) unknown, intergenic transcript (intergenic); (x) Exonic overlap with reference on the opposite strand (antisense).
Assembly: GRCh38
Supplementary files format and content: Processed_data_macrophages_LncRNAs.xlsx: Excel file

molecule: total RNA

organism: Homo sapiens

source_name: Healthy buffy coats

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to remove ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribo-minus RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the pair-end 2×150bp sequencing on an Illumina Hiseq 4000 platform housed in the LC Sciences (Hangzhou, China) following the vendor's recommended protocol.

tag: tissue

value: Healthy buffy coats

tag: cell type

value: Monocytes-derived macrophages M1

tag: time point

value: Day 3


title: RPE1-hTERT TP53-/- PACKO Cas9 ZRANB3-/- T18_A

city: toronto

first: Sumin

last: Feng

address: 600 University Avenue

country: Canada

institute: The Lunenfeld-Tanenbaum Research Institute

library_source: genomic

data_processing:
Count tables of sgRNA created from fastq files using mageck's (v0.5.9.5) count command
Gene essentiality scores calculated as median of 10 iterations of Bagel2 (v2.115), and from CrisprCountsAnalysis (CCA) using default parameters
Custom R script to plot Bagel and CCA results (scatter_bagel_cca_SF202306.R)
Assembly: Toronto KnockOut (TKO) CRISPR Library - Version 3
Supplementary files format and content: XML-based file format xlsx file includes readcount for each sample

molecule: genomic DNA

extract_protocol:
DNA was harvested by QIAamp Blood Maxi Kit (QIAGEN)
Genome-integrated sgRNA sequences were amplified by PCR using Q5 Mastermix (NEB Next UltraII, New Endland Biolabs, M0544S). i5 and i7 multiplexing barcodes were introduced in a second round of PCR
CRISPR screens

tag: cell line

value: retinal pigment epithelial

tag: genotype

tag: treatment

value: NO


title: SW016789 6h N=1

city: Indianapolis

first: Michael

middle: A

last: Kalwat

state: IN

address: 1210 Waterway Blvd Suite 2000

department: Lilly Diabetes Center of Excellence

institute: Indiana Biosciences Research Institute

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC mm10
Supplementary_files_format_and_content: processed data is a combined Excel table. Sheet 1 contains the mapping statistics. Sheet 2 contains Gene identifier information, log2(FPKM), TPM, and raw counts for all samples.

organism: Mus musculus

source_name: MIN6 beta cells

growth_protocol: Mouse MIN6 beta cells were cultured in 12 well dishes in complete medium (DMEM containin 25mM glucose, 10% FBS, 50uM beta-mercaptoethanol, antibiotics).

extract_protocol:
RNA extraction was done with Invitrogen Purelink RNA mini kit with on-column DNAse digestion.
KAPA RNA Hyperprep Kit (KK8581) and QIAseq FastSelect HMR rRNA Removal Kit.

treatment_protocol: Cells were treated with DMSO (0.1%), SW016789 (5uM), or thapsigargin (100nM) for 0, 1, 2, 6, and 24 h. Treatment addition times were staggered such that all samples were collected at the same time at the end of the experiment.

value: insulinoma

tag: time (h)


title: Monocytes-derived Macrophages M1-18h Replicate 4

description:
Library name: Group A_FPKM.M1_18h_4
FPKM.M1_18h_4
Group A
Total RNA-seq


title: RPE1-hTERT TP53-/- PACKO Cas9 ZRANB3-/- T0


title: Multiple Myeloma Plasmacells, S1

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
Sequence reads were trimmed using Trimmomatic (v0.39)
Trimmed sequence reads were aligned using Tophat 2.1.1
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Multiple Myeloma Plasmacells

growth_protocol: CD138-positive tumoral plasma cells were purified through an immunomagnetic procedure and immediately frozen as a dry pellet. Following this, RNA was extracted for RNA sequencing analysis.

extract_protocol:
RNA was extracted with the Qiagen miRNeasy advanced cell/tissue kit, quality controlled using the TapeStation system (Agilent) and quantity controlled with the NanoDrop system (Invitrogen).
Ribosomal RNA depletion was done with RiboCop depletion kit (Lexogen) and RNA-seq libraries were produced using the CORALL total RNA seq Library Prep kit (Lexogen) following manufacturer's protocols.

treatment_protocol: No cell treatment

value: Multiple Myeloma Plasmacells


title: SW016789 2h N=1


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/- T18_B


title: RPE1-hTERT TP53-/- PACKO Cas9 HLTF-/- T18_A


title: Monocytes-derived Macrophages M1-18h Replicate 3

description:
Library name: Group A_FPKM.M1_18h_3
FPKM.M1_18h_3
Group A
Total RNA-seq


title: Monocytes-derived Macrophages M1-18h Replicate 2

description:
Library name: Group A_FPKM.M1_18h_2
FPKM.M1_18h_2
Group A
Total RNA-seq


title: DMSO 24h N=1

value: DMSO


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/- T18_A


title: RPE1-hTERT TP53-/- PACKO Cas9 SMARCAL1-/- T0


title: DMSO 6h N=1


title: Monocytes Replicate 3

description:
Library name: Control_FPKM.Mon_7
FPKM.Mon_7
Control
Total RNA-seq

value: Monocytes


title: RPE1-hTERT TP53-/- PACKO Cas9 WT T18_B

value: RPE1-hTERT TP53-/- PACKO Cas9 WT T18_B


title: DMSO 2h N=1


title: WT2_PP

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

description: Library name: WT2_PP_scRNA-seq

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq data were processed with bcl2fastq v2.20 to demultiplex samples and convert .bcl files to .fastq format. For initial data processing and some basic analyses 10xGenomics Cell Ranger pipelines and Seurat R package were used.
The nfcore/atacseq bioinformatic pipeline (https://nf-co.re/atacseq/2.1.2/ ) was used for the ATAC-seq data analysishttps://nf-co.re/atacseq/2.1.2/. Briefly, after adapter trimming the reads were mapped to the human genome (hg38) using Bowtie2 with default paired-end settings. Next, all non-nuclear reads, and unmapped paired reads were discarded. Duplicated reads were removed with picard MarkDuplicates. Filtering to remove unmapped regions, mitochondrial DNA and blacklisted regions was done using SAMtools. Macs2 was used for broad peak calling and HOMER for peak annotation (annotatePeaks.pl). Motif enrichment analysis was conducted with Homer (findMotifsGenome.pl). The normalized bigWig files, scaled to 1 million mapped reads, were created with BEDTools. Differential accessibility analysis was carried out using DESeq2. IGV platform was used for visualization of bigWig tracks, peaks and differential sites.
Assembly: hg38
Supplementary files format and content: tap-separated values files and matrix files

source_name: cell line

extract_protocol:
hPSC derived WT and ETV1 KO PP spheroids, were dispersed with Tripsin, washed with 0.1% saponin – 1% BSA – PBS, filtered through 30 μm mesh filter. Afterwards cells were counted using Countess and adjusted to 700-1,200 cells/μl.
The scRNA-seq was performed with 10xGenomics platform and Illumina according to the manufacturer's protocol. Libraires were pair-end sequenced with depth of 40,000 reads per cell.
ATAC-seq: The WT, KO and tKO hPSCs or PPs were dispersed to single cells using TrypLE. The 5 x 104 cells were resuspended in 50 µl of cold ATAC-RSB buffer (10mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2,, 0.1% Tween-20, 0.1% NP-40). For nuclei extraction, the cells were incubated with 0.1% digitonin for 3 min at 4 °C and centrifuged at 500 x g for 10 min at 4 °C with the addition of 1 ml ATAC-RSB. The supernatant was discarded, and nuclei were prepared for the transposition reaction. The solution containing transposed fragments was purified using the Zymo DNA Clean & Concentrator (Zymo Research, USA) and the transposed DNA was eluted in 20 μl H2O and stored in -20 °C. Barcoded adapters were added to the transposed fragments by PCR with the NEBNext Ultra II Q5 2x Master Mix (New England Biolabs, USA), according to the producer protocol and after purified with the AMPure XP beads. The samples were 150 bp paired-end sequenced on the NovaSeqX platform.

value: cell line

value: HUES8 derived pancreatic progenitors

value: Pancreatic progenitors, stage 4, day 12

value: WT


title: WT1_PP

description: Library name: WT1_PP_scRNA-seq


title: Monocytes-derived Macrophages M1-18h Replicate 1

description:
Library name: Group A_FPKM.M1_18h_1
FPKM.M1_18h_1
Group A
Total RNA-seq
The R2 fastq file for this Sample is not available.


title: KO_2_PP_ATAC

description: Library name: KO_2_PP_ATAC

value: KO


title: DMSO 1h N=1


title: Monocytes Replicate 2

description:
Library name: Control_FPKM.Mon_6
FPKM.Mon_6
Control
Total RNA-seq


title: RPE1-hTERT TP53-/- PACKO Cas9 WT T18_A

value: RPE1-hTERT TP53-/- PACKO Cas9 WT T18_A


title: WT_2_PP_ATAC

description: Library name: WT_2_PP_ATAC


title: SRR8731962_m_0_0_pe

city: Beijing

first: Yi

last: Zheng

address: No. 7, Beinong Road, Huilongguan Town, Changping District

country: China

institute: Beijing University of Agriculture

description: Library name: Sample 1

data_processing:
RNA-Seq reads were processed with FastQC (v0.11.9), trimmed with Trimmomatic, aligned using STAR (v2.7.10b), and normalized to FPKM values.
Assembly: GCA_014183005.1
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Castanea mollissima

source_name: mix 1

extract_protocol:
Plant Total RNA Extraction Kit
Directional RNA Library Prep Kit for Illumina following the manufacturer’s protocols.

value: mix 1


title: KO_1_PP_ATAC

description: Library name: KO_1_PP_ATAC


title: RPE1-hTERT TP53-/- PACKO Cas9 WT-T0

value: RPE1-hTERT TP53-/- PACKO Cas9 WT-T0


title: SW016789 1h N=1


title: WT_1_PP_ATAC

description: Library name: WT_1_PP_ATAC


title: SRR17139643_r_3m_0_pe

description: Library name: Sample 6

source_name: root 6

value: root 6


title: SRR17139642_r_3m_0_pe

description: Library name: Sample 5

source_name: root 5

value: root 5


title: SRR10479852_e_0_yh_pe

description: Library name: Sample 7

source_name: embryo 7

value: embryo 7


title: KO2_PP

description: Library name: KO2_PP_scRNA-seq


title: tKO_2_pluri_ATAC

description: Library name: tKO_2_pluri_ATAC

value: hESC

value: tKO


title: KO1_PP

description: Library name: KO1_PP_scRNA-seq


title: Monocytes Replicate 1

description:
Library name: Control_FPKM.Mon_C
FPKM.Mon_C
Control
Total RNA-seq

value: Healthy buffy coats


title: Baseline 0h N=1

value: insulinoma

value: not treated


title: KO_2_pluri_ATAC

description: Library name: KO_2_pluri_ATAC


title: SRR17140806_r_1m_0_pe

description: Library name: Sample 3

source_name: root 3

value: root 3


title: SRR10479851_e_0_ys_pe

description: Library name: Sample 5

source_name: embryo 5

value: embryo 5


title: SRR17140805_r_1m_0_pe

description: Library name: Sample 2

source_name: root 2

value: root 2


title: 2 hours tunicamycin biol rep 2

city: Istanbul

first: Ozgur

last: Cakir

address: Vezneciler

country: Turkey

institute: Istanbul University

data_processing:
Trimmomatic (v 0.40) for filtering low quality reads
cufflink-cummeRbund for identifying DEGs
Supplementary files format and content: tab-delimited .xlsx files include fold change and FDR values for each Sample

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
RNA samples are extracted manually using trizol reagent
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep Kit (NEB, USA) following manufacturer's protocols.

value: leaf

value: tunicamycin

value: 2 hours


title: 6 hours tunicamycin biol rep 1

value: 6 hours


title: SRR17139641_r_3m_0_pe

description: Library name: Sample 4

source_name: root 4

value: root 4


title: 6 hours tunicamycin biol rep 2


title: 6 hours control biol rep 2

value: control


title: SRR10479853_e_0_ys_pe

description: Library name: Sample 6

source_name: embryo 6

value: embryo 6


title: tKO_1_pluri_ATAC

description: Library name: tKO_1_pluri_ATAC

value: cell line


title: SRR17140804_r_1m_0_pe

description: Library name: Sample 1

source_name: root 1

value: root 1


title: 2 hours tunicamycin biol rep 1


title: 6 hours control biol rep 1


title: WT_2_pluri_ATAC

description: Library name: WT_2_pluri_ATAC

value: hESC

value: WT


title: Wild-Type, scRNA-seq

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

country: Japan

institute: keio university

description: 10x Genomics

data_processing: Sequencing is performed on an MGI tech DNBSEQ-G400 at Azenta Japan Corp. Cell Ranger v3.1 (10× Genomics) software with mouse mm10 reference sequence in prebuild Cell Ranger reference packages was used for initial data processing. After initial data processing, all processing steps were performed using Seurat v3.

source_name: kidney cortex

extract_protocol:
The digestion buffer was a mixture of Dulbecco PBS with collagenase type II (3 mg/ml, Worthington), ProNase E (1.5 mg/ml, Millipore), DNAse (62.5 U/mL, Takara), and 5 mM calcium chloride. Kidneys were harvested, minced into 1 mm3 cubes, and digested using digestion buffer with shaking at 37 °C for 20 minutes. Then, the digestion mixture was incubated in a thermomixer for 5 minutes at 37 °C with shaking at 1200 RPM. The solution was successively passed through 70- and 30-μm cell strainers. The solution was then centrifuged at 300 ×g for 5 minutes, and the resulting cell pellet was diluted with DMEM– high-glucose media (Gibco) with 10% FBS (Sigma‒Aldrich). The solution was passed through 30-μm cell strainers three times, and a single-cell suspension was obtained. The single-cell suspension was loaded onto a chip on the 10× Chromium Single Cell instrument (10× Genomics).
Barcoding and cDNA amplified were performed using Chromium Single Cell 3’ Reagent Kits v3.1 (10× Genomics) according to the manufacturer’s instructions.

value: kidney cortex

tag: age

value: 16 weeks old


title: WT_1_pluri_ATAC

description: Library name: WT_1_pluri_ATAC


title: SRR10479848_e_0_ys_pe

description: Library name: Sample 3

source_name: embryo 3

value: embryo 3


title: 2 hours control biol rep 2


title: SRR10350465_e_0_ys_pe

description: Library name: Sample 1

source_name: embryo 1

value: embryo 1


title: SRR10350466_e_0_ys_pe

description: Library name: Sample 2

source_name: embryo 2

value: embryo 2


title: Msm/KOmsoA rep3

status: Public on Dec 23 2024

city: Nanning

first: Hao

last: Li

state: Guangxi

address: No. 100, University East Road, Xixiangtang District

department: College of Life Science and Technology

institute: Guangxi University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCF_000015005.1_ASM1500v1_genomic.fna
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Mycolicibacterium smegmatis

source_name: Mycolicibacterium smegmatis

growth_protocol: The strains were grown for overnight in 7H9 medium at 37℃ shaker incubator. Cells were grown to mid-logarithmic phase, and each culture was diluted in 100 ml of fresh 7H9 broth. The cultures were then allowed to grow further at 37℃ with shaking at 160 rpm.The bacterial cells of mid-logarithmic phase were harvested and washed using fresh 7H9 medium. Then we divide the bacteria into tubes with the same biomass

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies,USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrityof total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA),and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing. One micrograms of RNA were used as input material for the RNA sample preparations
RNA-seq strand-specific libraries were constructed using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit (Vazyme, China) according to the manufacturer’s instructions. Briefly, RNA was purified by magnetic beads after removal of rRNA. Then RNA was fragmented into small pieces using divalent cations for 8 min at 94℃. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. These cDNA fragments then go through the end repair process, addition of a single ‘A’ base, and ligation of the adapters. The products were purified and enriched by PCR to create the final cDNA library. Purified  ibraries were quantified and validated by Qubit® 3.0 Fluorometer and Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot after the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA).

tag: strain

value: KOmsoA

tag: time

value: logarithmic phase


title: SRR10479849_e_0_ys_pe

description: Library name: Sample 4

source_name: embryo 4

value: embryo 4


title: Msm/WT rep3


title: Msm/KOmsoA rep2


title: PT-I_Ppo-1, scRNA-seq

description: 10x Genomics


title: T cells, FM

city: Xiamen

first: Yipeng

last: Rao

address: Xiangan Campus, Xiamen University, Xiangan Road, Xiangan District, Xiamen City, Fujian Province, China

institute: national insititute of diagnostics and vaccine development in infectious diseases（xiamen university）

description: Library name: Fresh Medium

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis  GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG.  KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: spleen

growth_protocol: Freshly purified mouse T cells were grown in RPMI 1640 medium supplemented with 10% FBS, 100 µg/ml penicillin-streptomycin, 1 mM sodium pyruvate, 50 µM 2-mercaptoethanol, and 50 U/ml recombinant IL-2. Huh-7 cells were cultured in DMEM medium supplemented with 10% FBS and 100 µg/ml penicillin-streptomycin.

extract_protocol:
RNA samples were extracted using the Trizol method. 1 μg total RNA was used for following library preparation
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: T cells were activated with anti-CD3/CD28-coated beads (Thermo Fisher Scientific, 11452D) and cultured with fresh medium or tumor supernatants for 72 hours. The Huh-7 cells were infected with a control and SLC3A2 knockdown lentivirus.

value: spleen

value: T-cell

value: immune cells

value: T cells treated with fresh culture medium

tag: batch


title: T cells, SUP-LYS

description: Library name: SUP+Lysine

value: T cells treated with Hepa1-6 cell supernatant supplemented with lysine


title: KO_1_pluri_ATAC

description: Library name: KO_1_pluri_ATAC

source_name: cell line

value: cell line

value: KO


title: T cells, SUP

description: Library name: Supernatant

value: T cells treated with Hepa1-6 cell supernatant


title: 2 hours control biol rep 1

value: leaf

value: control

value: 2 hours


title: Msm/WT rep1

value: WT


title: Msm/WT rep2


title: Msm/KOmsoA rep1


title: PBMC Ctrl, Lgr3,Tg,TPO patient4

city: Kyoto

first: GENKI

last: KOBAYASHI

address: Kamugyoku, Kajii-cho 465

institute: Kyoto Prefectural university of medicine

description: Library name: Sample7

data_processing:
The sequencing-derived FASTQ files were processed using the BD Rhapsody Targeted Analysis Pipeline with V(D)J processing (BD Biosciences) via the Seven Bridges Platform (https://www.sevenbridges.com/d). Initially, low-quality read pairs were filtered out based on factors such as read length, average base quality score, and single-base frequency. High-quality R1 reads were then utilized to identify cell labels and unique molecular identifiers (UMIs). High-quality R2 reads were aligned to the reference sequences, including 399 targeted genes, BD AbSeq 30 markers, and BCR gene segments, using the Bowtie2 program and BCR gene data from the International ImMunoGeneTics Information System® (IMGT.org). IGBlast was used to determine CDR3 regions. Reads with matching cell labels, UMI sequences, and genes were collapsed into single molecules.
Assembly: GRAF™(Seven Bridges Platform (https://www.sevenbridges.com/d))
Supplementary files format and content: tsv,mtx

source_name: blood mononucler cells

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation. Intrathyroidal blood mononuclear cells were also isolated by density gradient centrifugation , using surgically excised thyroid tissue. They were resuspended in 650 μL of cold sample buffer for loading on a BD Rhapsody cartridge.
Targeted scRNA-seq with BCR analysis was performed using the BD Rhapsody Express system (BD Biosciences, NJ, USA). Cell capture and library preparation were performed using the BD Rhapsody Targeted mRNA and AbSeq Reagent Kit (BD Biosciences). Briefly, cells from each sample were captured in a microwell plate with beads. This was followed by cell lysis, bead retrieval, cDNA synthesis, template switching, Klenow extension, and library preparation (targeted gene library using human B-cell expression panel and BCR gene library) following the BD Rhapsody VDJ CDR3 protocol. The final pooled libraries were spiked with 20% PhiX control DNA to increase the sequence complexity and subsequently sequenced (75 bp × 225 bp paired-end) on a HiSeq X Ten/ Illumina NovaSeq X sequencer (Illumina, San Diego, CA).

value: blood mononucler cells


title: PBMC Ctrl, Lgr3,Tg,TPO patient6

description: Library name: Sample5


title: Thyroid Ctrl,Lgr3,Tg,TPO patient6

description: Library name: Sample6


title: PBMC Ctrl, Lgr3,Tg,TPO patient8

description: Library name: Sample9


title: PBMC Ctrl, Lgr3,Tg,TPO patient7

description: Library name: Sample8


title: Thyroid Ctrl  patient8

description: Library name: Sample10


title: TFEB_Torin1_Input biol rep 2

city: Berkeley

first: Meagan

middle: Nicole

last: Esbin

state: California

address: 475 Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California Berkeley

description:
Library name: Sample 16
Input control

data_processing:
Raw data were assessed using FastQC
Cutadapt was used to trim 5' and 3' adapter sequences from reads using the settings (-j 0 --pair-filter=any --minimum-length=20)
FASTQ files were aligned to the human genome (hg38 assembly) using Bowtie2 (version 2.3.4.1) with options –local –very-sensitivelocal –no-unal –no-mixed –no-discordant -p10 -I 50 -X 1000.
Samtools (Li et al. 2009) (version 1.8) was used to create, sort, and index bam files.
Peaks were called with MACS2 version 2.1.0.20140616 (-f BAMPE –nomodel) using either the input or IgG DNA as controls. Similar numbers of peaks were called against each control, so the peaks called against the IgG sample were used in further analysis
Bam files were converted to bigWig files with read numbers normalized to 1× sequencing depth, obtaining read coverage per 50 bp bins across the whole genome, using bamCoverage (-of bigwig –binSize 50 –normalizeTo1x 2913022398 –extendReads –ignoreDuplicates).
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak (for FLAG IP samples, all compared to IgG control for each Sample)

source_name: BeWo

growth_protocol: BeWo cells (ATCC CCL-98) were cultured at 37°C and 5% CO2 in F-12K medium (Corning or ATCC) supplemented with 10% fetal bovine serum and 10 U/mL penicillin–streptomycin. Cells were passaged by trypsinization every 2–4 days and split at a ratio of 1:3–1:5. Media was changed completely every 24–36 h.

extract_protocol:
After treatment, media on each 15 cm plate was changed to 20 mL of serumfree F-12K media containing 1% formaldehyde and incubated with shaking for 5 min. Cross-linking was then quenched by adding 10 mL of 0.125 M glycine in PBS and shaking for an additional 5 min. Media was then poured off, and plates were rinsed twice with ice-cold PBS. Finally, 5 mL of PBS plus protease inhibitors (0.25μM PMSF, 10 μg/mL aprotinin) was added to each plate, and cells were scraped on ice, collected in 15 mL conical tubes, and centrifuged at 1200 rpm for 10 min at 4°C. The supernatant was aspirated, and cell pellets were flash-frozen in liquid nitrogen and stored at −80°C until further processing. Plating, treatment, and fixation of cells were repeated twice for two biological replicates of each condition. Cell pellets were thawed on ice, resuspended in 2 mL of cell lysis buffer (5 mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40; 1 mL/15 cm plate) with protease inhibitors and incubated for 10 min on ice. During incubation, the lysates were pipetted up and down every 5 min. Lysates were then centrifuged at 4000 rpm for 10 min. Nuclear pellets were resuspended in 6 vol of sonication buffer (50 mM Tris-HCl at pH 8.1, 10 mM EDTA, 0.1% SDS) with protease inhibitors, incubated on ice, and sonicated to obtain DNA fragments <1000 bp in length (Covaris S220 sonicator: 20% duty factor, 200 cycles/burst, 150 peak incident power, six to eight cycles of 30 sec on and 30 sec off). Sonicated lysates were cleared by centrifugation, and chromatin (400 μg/antibody) was diluted in RIPA buffer (10 mM Tris-HCl at pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-1000, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 mg/mL and precleared with magnetic Protein G Dynabeads (Thermo Fisher 10009D) for 2 h at 4°C. Precleared lysates were then immunoprecipitated overnight with 4 mg of normal antimouse IgG (Jackson ImmunoResearch 211-032-171) and anti-FLAG [M2] (Sigma Aldrich F1804). About 4% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with Qiagen QIAquick PCR purification kit (Qiagen 28106) and eluted in 40 μL of 0.1× TE (1 mM Tris-HCl at pH 8.0, 0.01 mM EDTA). Samples were checked by qPCR together with 2% of the input chromatin and then used in ChIP-seq library preparation.
ChIP-seq libraries were prepared independently from two ChIP biological replicates using the NEBNext Ultra II DNA library preparation kit (New England Biolabs E6177L) according to the manufacturer’s instructions with a few modifications. As starting material, 20 ng of ChIP input DNA (as measured by NanoDrop) and 20 μL of the immunoprecipitated DNA (spiked with 5 μL of 10 ng/mL sheared Drosophila melanogaster DNA) was used. The recommended reagents’ volumes were cut in half. The NEBNext Adaptor for Illumina was diluted 1:10 in Tris/NaCl (pH 8.0; 10 mM Tris-HCl at pH 8.0, 10 mM NaCl), and the ligation step was extended to 30min. A single purification step with 0.9× vol of Agencourt AMPure XP PCR purification beads (Beckman Coulter A63880) was performed after ligation. DNA was eluted in 22 μL of 10 mM Tris-HCl (pH 8.0), and 20 μL of the eluted DNA was used for the library enrichment step. Library samples were enriched with 11 cycles of PCR amplification in 50 μL of total reaction volume (10 μL of 5× KAPA buffer, 1.5 μL of 10 mM dNTPs, 0.5 μL of 10 mM NEB Universal PCR primer, 0.5 μL of 10 mM index primers, 1 mL of KAPA polymerase, 16.5 μL of nuclease-free water, 20 μL of sample). After amplification, PCR samples were again purified with 0.9× vol of AMPure XP PCR amplification beads and eluted in 33 μL of 10 mM Tris-HCl (pH 8.0). Library concentration was assessed using Qubit dsDNA HS assay kit (Invitrogen Q32851)

treatment_protocol: Stably expressing L30 3xFLAG-Halo-TFEB IRES Puro BeWo cells (passage ∼10) were scaled up to two 15 cm plates per condition. Cells were grown to ∼50% confluence, and the media was changed to 0.1% DMSO or 20 μM Forskolin and treated for 48 h, changing media at 24 h. For Torin1-treated samples, cells were treated with 0.1% DMSO for 46 h and changed to media containing 250nM Torin1 for 2 h before being fixed with paraformaldehyde.

tag: chip antibody

value: BeWo

value: choriocarcinoma

value: L30 Halo-TFEB IRES Puro stable BeWo cell line

value: 250nM Torin1 for 2hrs


title: TFEB_FSK_Input biol rep 2

description:
Library name: Sample 13
Input control

value: 20uM FSK for 48hrs


title: TFEB_FSK_mIgG biol rep 2

description:
Library name: Sample 15
mIgG immunoprecipitation control

value: anti-mouse IgG (Jackson ImmunoResearch 211-032-171)


title: TFEB_Torin1_mIgG biol rep 2

description:
Library name: Sample 18
mIgG immunoprecipitation control


title: TFEB_FSK_mFlag biol rep 2

description:
Library name: Sample 14
mFLAG immunoprecipitation

value: FLAG M2 (Sigma Aldrich F1804)


title: HEK293T-Tet-FLAG-DUX4 cells, ChIP, repeat-1

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

description: Library name: sample 3

data_processing:
The raw sequencing data were processed using Fastp (v0.23.1) for quality control and data filtering, and the clean reads were mapped to the reference genome using STAR (v.2.7.6a). Peak calling was performed using MACS2 in narrow peak mode . HOMER software was used to extract sequences from the identified peak regions, scan for shared motifs, and visualize the motifs. Differential peak analysis between groups was conducted using the csaw package within the edgeR framework .
Assembly: hg38
Supplementary files format and content: tab-delimited bigwig file includes raw counts for each sample

extract_protocol:
DNA was purified by phenol-chloroform extraction
Perform end repair and A-tailing on the DNA from the IP. Add sequencing adapters to the repaired and A-tailed DNA. Use magnetic beads to recover target-sized fragments, followed by PCR amplification to generate the sequencing library

value: Epithelial cells

value: HSV-1 infection


title: HEK293T-Tet-FLAG-DUX4 cells, Input, repeat-1

description: Library name: sample 1


title: HEK293T-Tet-FLAG-DUX4 cells, Input, repeat-2

description: Library name: sample 2


title: U2OS cells, Mock

description: Library name: sample 1

data_processing:
The raw sequencing data were processed using trim-galore (v.0.6.10) to remove adapters and low-quality reads. Subsequently, the genome index was prepared with bismark_genome_preparation (v.0.24.0) , specifying the path to Bowtie2 (v.2.5.4) and the genome folder .  The bisulfite-converted sequencing reads were aligned to the reference genome using the bismark algorithm. The output files (BAM) containing aligned reads, aong with a comprehensive report detailing various statistical metrics and methylation data. Methylation information was extracted from the BAM files by using the bismark_methylation_extractor command.
Assembly: hg38
Supplementary files format and content: tab-delimited bedGraph file includes raw counts for each sample

extract_protocol:
genomic DNA was extracted using TIANamp Genomic DNA Kit (TIANGEN, Beijing). Bisulfite conversion of DNA was performed using the EpiArt DNA methylation bisulfite kit (Vazyme, Nanjing, China).
Illumina sequencing libraries were constructed by PCR

value: Osteosarcoma cells

value: mock infection


title: HEK293T-Tet-FLAG-DUX4 cells, ChIP, repeat-2

description: Library name: sample 4


title: TFEB_Torin1_mIgG biol rep 1

description:
Library name: Sample 9
mIgG immunoprecipitation control


title: TFEB_DMSO_mIgG biol rep 2

description:
Library name: Sample 12
mIgG immunoprecipitation control

value: 0.1% DMSO for 48hrs


title: PBMC Ctrl, Lgr3,Tg,TPO patient1

description: Library name: Sample4


title: TFEB_Torin1_mFlag biol rep 1

description:
Library name: Sample 8
mFLAG immunoprecipitation


title: TFEB_DMSO_mFlag biol rep 2

description:
Library name: Sample 11
mFLAG immunoprecipitation


title: TFEB_Torin1_Input biol rep 1

description:
Library name: Sample 7
Input control


title: TFEB_DMSO_Input biol rep 2

description:
Library name: Sample 10
Input control


title: TFEB_FSK_mIgG biol rep 1

description:
Library name: Sample 6
mIgG immunoprecipitation control


title: TFEB_FSK_mFlag biol rep 1

description:
Library name: Sample 5
mFLAG immunoprecipitation


title: TFEB_FSK_Input biol rep 1

description:
Library name: Sample 4
Input control


title: TFEB_DMSO_mIgG biol rep 1

description:
Library name: Sample 3
mIgG immunoprecipitation control


title: TFEB_DMSO_mFlag biol rep 1

description:
Library name: Sample 2
mFLAG immunoprecipitation


title: TFEB_DMSO_Input_biol rep 1

description:
Library name: Sample 1
Input control


title: U2OS cells, HSV-1

description: Library name: sample 2


title: TFEB_Torin1_mFlag biol rep 2

description:
Library name: Sample 17
mFLAG immunoprecipitation


title: DNMT3A_overexpresion_2_RNASeq

city: Shenzhen

first: Aixia

last: Zhai

state: Guangdong

address: 92 Fuhua Road, Futian District

department: The Eighth Affiliated Hospital

institute: Sun Yat-sen University

description: Library name: pLV_EGFP_DN_2

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: HepG2 cell line overexpressing DNMT3A was constructed by lentivirus

value: Human hepatocellular carcinoma cells

value: DNMT3A overexpression


title: DNMT3A_overexpresion_3_RNASeq

description: Library name: pLV_EGFP_DN_3


title: DNMT3A_overexpresion_4_RNASeq

description: Library name: pLV_EGFP_DN_4


title: control_4_RNASeq

description: Library name: pLV_EGFP_NC_4


title: control_2_RNASeq

description: Library name: pLV_EGFP_NC_2


title: control_3_RNASeq

description: Library name: pLV_EGFP_NC_3


title: control_1_RNASeq

description: Library name: pLV_EGFP_NC_1


title: DNMT3A_overexpresion_1_RNASeq

description: Library name: pLV_EGFP_DN_1


title: posMIX_36

city: Bratislava

first: Evan

last: Paul

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

description: Library name: posMIX_36

data_processing:
The bioinformatics pipeline for RNA sequencing is outlined below. 1) FASTQC (v0.11.9) – used for initial quality check of raw sequencing data 2) Cutadapt (v3.4) – removal of adapters and filtering for sequence quality and length. 3) STAR (v2.7.7a) – alignment 4) SAMtools (v1.16.1) – indexing 5) UMI-tools (v1.0.0) – deduplicating bam files based on unique molecular identifiers introduced during library preparation. 6) FeatureCounts (v1.5.2)
Assembly: GRCh38.104
Supplementary files format and content: quantification table generated by featureCounts tool of a Subread package

source_name: breast

extract_protocol:
The Macherey Nagel NucleoSpin total RNA FFPE XS kit was used for RNA isolation. After RNA isolation, RNA quantity was measured using the Qubit RNA HS (High Sensitivity) Assay Kit with a Qubit 4 Fluorometer and RNA quality using the Agilent High Sensitivity RNA ScreenTape with an Agilent 4150 TapeStation. The DV200 value of the sample (i.e., the percentage of fragments more than 200 bases in length) was calculated as recommended by Illumina. Samples with DV200 values over 15% were considered viable samples for library preparation.
We used the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit to prepare total RNA-SEQ libraries following the manufacturer's instructions. We included a single natural positive control sample in each library preparation batch and a synthetic spike-in control in each sample to control for batch library preparation effects. Following library preparation, the quantity and fragment size range of the library was assessed using both the Qubit dsDNA HS kit (Qubit 4 Fluorometer) and the Agilent High Sensitivity DNA ScreenTape kit (Agilent 4150 TapeStation). Successfully prepared libraries contained sufficient library to pool on an Illumina NovaSeq 6000 sequencing instrument and fragment range spanning 200 - 1,000 bp, with a local maximum of 250 - 350 bp. Depending on pool size, individual sequencing libraries were pooled and sequenced on an Illumina NovaSeq 6000 using SP, S1, S2, or S4 flow cells. Pooled libraries were spiked with 10% PhiX as recommended by both Illumina and Takara for low-complexity libraries sequenced on patterned flow cells. Paired-end sequencing (2 x 100 bp) was conducted to obtain approximately 100 million reads per sample.

value: breast

tag: isolate

value: not applicable

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: positive control

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_5

description: Library name: posMIX_5

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_7

description: Library name: posMIX_7

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_38

description: Library name: posMIX_38

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_9

description: Library name: posMIX_9

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_31b

description: Library name: posMIX_31b

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_33

description: Library name: posMIX_33

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_4

description: Library name: posMIX_4

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_8

description: Library name: posMIX_8

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_32

description: Library name: posMIX_32

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_28

description: Library name: posMIX_28

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_35

description: Library name: posMIX_35

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_37

description: Library name: posMIX_37

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_26

description: Library name: posMIX_26

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_22

description: Library name: posMIX_22

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_30

description: Library name: posMIX_30

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_24

description: Library name: posMIX_24

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_25

description: Library name: posMIX_25

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_39

description: Library name: posMIX_39

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_3

description: Library name: posMIX_3

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_27

description: Library name: posMIX_27

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_23

description: Library name: posMIX_23

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_21

description: Library name: posMIX_21

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_29

description: Library name: posMIX_29

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_34

description: Library name: posMIX_34

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_6

description: Library name: posMIX_6

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_20

description: Library name: posMIX_20

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_2

description: Library name: posMIX_2

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_19

description: Library name: posMIX_19

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_18

description: Library name: posMIX_18

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_15

description: Library name: posMIX_15

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_16

description: Library name: posMIX_16

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_17b

description: Library name: posMIX_17b

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_14

description: Library name: posMIX_14

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: posMIX_10

description: Library name: posMIX_10

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: posMIX_11

description: Library name: posMIX_11

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease


title: MDX_3181

description: Library name: MDX_3181_Her2_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

value: Germany:sample source OF, PATH 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

value: N

value: P

value: missing

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3190

description: Library name: MDX_3190_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source RE, PATH 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Medullary carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac


title: MDX_3188_excluded

description: Library name: MDX_3188_excluded_non_invasive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: no tumor

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

value: not applicable

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3185

description: Library name: MDX_3185_TNBC_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac


title: posMIX_1

description: Library name: posMIX_1

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: positive control

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3182

description: Library name: MDX_3182_Her2_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

value: N

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: P

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3187

description: Library name: MDX_3187_Her2_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source RE, PATH 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma, DCIS

tag: t

tag: n

value: pN 1mic

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: missing

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: poMIX_12

description: Library name: poMIX_12

tag: tissue

tag: isolate

value: not applicable

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac


title: MDX_3183

description: Library name: MDX_3183_TNBC_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: MDX_3189

description: Library name: MDX_3189_Her2_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac


title: MDX_3191

description: Library name: MDX_3191_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

value: P

tag: her2 dna_fish

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3186_excluded_subtype

description: Library name: MDX_3186_A_excluded_subtype

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 4b

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

value: Paclitaxel


title: MDX_3186

description: Library name: MDX_3186_B_Her2_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

value: missing

value: not applicable

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3179

description: Library name: MDX_3179_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: premenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac


title: MDX_3177

description: Library name: MDX_3177_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

value: Y

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: MDX_3176

description: Library name: MDX_3176_Her2_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: P

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: epirubicin (y/n)


title: MDX_3184

description: Library name: MDX_3184_TNBC_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

value: Germany:sample source OF, PATH 5th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: MDX_3171

description: Library name: MDX_3171_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: missing

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Bones, Liver, Brain

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: epirubicin (y/n)


title: MDX_3174

description: Library name: MDX_3174_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: MDX_3180

description: Library name: MDX_3180_TNBC_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive papillary carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: epirubicin (y/n)


title: MDX_3169

description: Library name: MDX_3169_Her2_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma, DCIS

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

value: P

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: MDX_3170

description: Library name: MDX_3170_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac


title: posMIX_13

description: Library name: posMIX_13

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: positive control

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: pr negpos

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3168

description: Library name: MDX_3168_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: er irs

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3166

description: Library name: MDX_3166_TNBC_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: TNBC

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3167

description: Library name: MDX_3167_TNBC_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Lung

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3164

description: Library name: MDX_3164_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3163

description: Library name: MDX_3163_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: perimenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

value: missing

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3165_healthy

description: Library name: MDX_3165_healthy

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: no tumor

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma, DCIS

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: not applicable

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3150

description: Library name: MDX_3150_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source MR, PATH 2nd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

value: N

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)

tag: epirubicin (y/n)


title: MDX_3162_DCIS

description: Library name: MDX_3162_DCIS

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

value: Germany:sample source OF, PATH 5th shipment

tag: Sex

tag: sample category

value: DCIS

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: TNBC

value: Y

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3157

description: Library name: MDX_3157_TNBC_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Germany:sample source OF, PATH 3rd shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

value: missing

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: MDX_3160

description: Library name: MDX_3160_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: chest wall/breast

value: not applicable

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: docetaxel (taxotere,_taxan)_(y/n)

tag: docetaxel (taxotere,_taxan)_(cycles)

tag: paclitaxel (abraxane)_(y/n)

tag: paclitaxel (abraxane)_(cycles)


title: MDX_3156

description: Library name: MDX_3156_TNBC_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: PATH biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)