title: DDX1 KD replicate 3

description: rRNA-depleted total RNA

tag: cell line

value: A549-ACE2 shDDX1 induced

value: SARS2 virus infection at 0.1 MOI 24hpi (strain hCoV-19/England/02/2020 (Public Health England propagated viral isolate Feb 2020, EPI_ISL_407073) ); DDX1 KD via doxycyclin induction of pLKO-Tet-On with shRNA sequence GATGTGGTCTGAAGCTATTAA


title: DDX1 KD replicate 2

status: Public on May 29 2021

type: SRA

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: rRNA-depleted total RNA

library_source: transcriptomic

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Reads were aligned to a combined human (GRCh38.99) and SARS2 (NC_045512.2) reference genomes in a splice-site aware fashion using STAR aligner (2.7.3a) (Dobin et al. 2013).
Uniquely mapping reads were assigned to exonic regions of genes using htseq-count (0.11.3) (Anders et al. 2015) in a strand-specific fashion, counting only uniquely assigning reads.
Genome_build: GRCh38.99 (human) and NC_045512.2 (SARS2)
Supplementary_files_format_and_content: Tab-delimited tables with counts for each gene

molecule: total RNA

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

growth_protocol: Cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
24hpi cells were detached and lysed in Trizol LS, total RNA extraction was performed following manufacturers recommendation
RNA sequencing libraries were prepared using the Illumina Total RNA Prep with Ribo-Zero Plus library kit (Cat# 20040525) according to manufacturers guidelines. Briefly, 100ng of total RNA was first depleted of the abundant ribosomal RNA present in the samples by rRNA targeted DNA probe capture followed by enzymatic digestion. Samples were then purified by Beckman Coulter RNAClean XP beads (Cat #A63987). Obtained rRNA-depleted RNA was fragmented, reverse transcribed, converted to dsDNA, end repaired and A-tailed. The A-tailed DNA fragments were ligated to anchors allowing for PCR amplification with Illumina dual indexing primers (Cat#20040553). Libraries were pooled in equimolar concentrations and sequenced on an Illumina NextSeq 500 sequencer using a high-output cartridge (Cat# 20024907), generating single 150bp long reads.

treatment_protocol: Knockdown was induced by treatment with 1ug/ml Doxycyclin; Cells were seeded into 2.5x10^5/well into 24well plates and infected at MOI=0.1 for 24hpi

tag: treatment


title: SP2_rep1

status: Public on May 30 2021

city: Wuhan

first: Ying

last: Wang

state: Hubei

address: No. 299 bayi road

department: College of Life Sciences

country: China

institute: Wuhan University

data_processing:
Raw reads of RNA-seq were aligned to the O.sativa Nipponbare release 7 of the MSU Rice Genome Annotation Project reference using HISAT2 with default parameters.
lncRNA analysis: The transcriptome was assembled using the StringTie (1.3.1) based on the reads mapped to the reference genome. The assembled transcripts were annotated using the gffcompare program.The unknowntranscripts were used to screen for putative lncRNAs. Three computational approaches include CPC/CNCI/Pfam/CPAT were combined to sort non-protein codingRNA candidates from putative protein-coding RNAs in the unknown transcripts.Putative protein-coding RNAs were filtered out using aminimum length and exon number threshold . Transcripts with lengths more than 200 nt and have more than two exons were selected as lncRNA candidates and further screened using CPC/CNCI/Pfam/CPAT that have the power to distinguish the protein-coding genes from the non-coding genes. As well as the different types of lncRNAs include lincRNA,introniclncRNA, anti-sense lncRNA ,sense lncRNA were selected using cuffcompare.
CircRNA analysis: The reads that could not be mapped to the genomes were obtained to screening the putative cicRNAs. For these unmapped reads, the 20-nt anchors were first extracted from both ends and aligned independently to the rice reference genomes to identify the unique anchor positions using the find_circ software. The reversed orientation of the aligned anchors suggested circRNA splicing. Then, the anchor alignments were extended to generate the GU/AG splice sites flanking the complete read alignments and breakpoints. Finally, a candidate circRNA was identified if it had at least two distinct back-spliced reads.
StringTie (1.3.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample . Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: MSU7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: Sterility male of WXS at PMC formation stage

growth_protocol: During summer in 2017, WXS rice was grown in the experimental field of Wuhan University (30°54′ N, 114°37′ E), Wuhan, Hubei province of China.

extract_protocol:
Total RNA was extracted using TRIzol reagent. A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Under natural conditions, with daily average temperatures that were higher than 24 ℃ and average day lengths that were longer than 12 h, WXS could produce male-sterility rice (WXS (S)) that did not form pollen. When the panicle length was approximately 1 cm, some of the rice plants were transferred into a fully intelligent artificial climate plant incubator for a short period of sunshine treatment under short lighting (12 h light/12 h dark) at low day average temperatures (approximately 21 °C) for 3-4 weeks. These WXS plants treated with short sunshine and low temperatures would become male-fertile rice (WXS (F)), with a normal anther morphology. The young panicles of WXS (S) and WXS (F) were harvested upon formation of the pollen mother cell (PMC) (P2), meiosis of the PMC (P3) and formation of the microspore (P4) stages, and correspondingly designated as SP2, SP3, SP4, FP2, FP3 and FP4, respectively. Immediately upon harvesting, the panicles were frozen in liquid nitrogen and stored at -80 °C.

tag: tissue

value: panicle

tag: Stage

value: PMC formation


title: DDX1 KD replicate 1

description: rRNA-depleted total RNA


title: HBCC-WZX

type: RNA

city: Hangzhou

first: Wenbiao

last: Chen

address: Zhejiang University, Hangzhou

institute: Zhejiang University

hyb_protocol: Agilent surehyb is used for hybridization experiments

scan_protocol: Agilent DNA microarray scanner was used for scanning, agilent feature extraction software (v11.0.1.1) was used to collect chip probe signal value, and agilent genespring software was used for chip standardization

data_processing:
Agilent genespring GX V12.2 software was used to select differentially expressed lncRNA and mNRA, and the differentially expressed mrnas were analyzed by GO and KEGG
Differentially expressed lncRNAs and mRNAs with statistical significance between two groups were identified through plot filtering with a threshold of fold-change (test/control)>2 and P<0.05

organism: Homo sapiens

source_name: HBV-related Hepatocellular carcinoma

label_protocol: Arraystar RNA flash labeling kit is used for labeling samples

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The tumor was removed surgically in patients with liver cancer

tag: disease state

value: hepatocellular carcinoma

value: liver


title: HNCC-WYZ

source_name: no HBV-related Hepatocellular carcinoma


title: WT replicate 2

description: rRNA-depleted total RNA

value: A549-ACE2 shDDX1 uninduced

value: SARS2 virus infection at 0.1 MOI 24hpi (strain hCoV-19/England/02/2020 (Public Health England propagated viral isolate Feb 2020, EPI_ISL_407073) )


title: HBCC-GHZ


title: WT replicate 1

description: rRNA-depleted total RNA


title: HNCC-BSG


title: HBCC-CZL


title: HNCC-ZGX


title: HNCC-BSY


title: HNCC-CFL


title: HBCC-WYG


title: t_72hr_SCOV2_S26

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

country: USA

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Homo sapiens genome reference (GRCh38/hg38) using STAR and per transcript reads were counted with  HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow, using DREAM methodology for multiple measures modeling.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text file includes ENSEMBL id and raw read counts for each transcript, in each sample

growth_protocol: Primary human bronchial epithelial cells (HBECs) were cultured on air-liquid interface (ALI) to generate a pseudostratified airway epithelium . Briefly, 1 x 10^5 cells in 100 µl of BronchiaLifeTM epithelial airway medium (BLEAM) (Cat# LL-0023, Lifeline® Cell Technology, Oceanside, CA, USA) were seeded in the apical chamber of a 0.4 µm pore-sized Transwell® insert (Cat# 3470, Corning®, Corning, NY, USA) pre-coated with human type IV collagen (Cat# C7521, Sigma Aldrich, St. Louis, MO, USA) with 1 ml of BLEAM in the basolateral chamber (ALI day -2). The following day, fresh BLEAM media was replaced in the apical and basolateral chambers (100 µl and 1 ml, respectively). Following two days of submerged culture, media from the apical chamber was removed to expose the cells to air (ALI day 0), and 1 ml of HBTEC ALI differentiation medium (Cat# LM-0050, Lifeline® Cell Technology) supplemented with Penicillin (100 I.U./ml) - Streptomycin (100 µg/ml) was added to the basolateral chamber. The media was replaced every other day and the cells allowed to differentiate for up to 29-31 days.

extract_protocol:
Total RNA was extracted via direct lysis of cells in the ALI well using the PureLinkTM RNA mini kit (Cat# 12183018A, Thermo Scientific, Waltham, MA, USA) and included DNase treatment (Cat# 12185-010, Thermo Scientific) on the column to remove contaminating genomic DNA. RNA concentrations were measured with a NanoPhotometer® N60 (Implen, Westlake Village, CA, USA)
RNA-sequencing was performed on a NextSeq 500 Flowcell, High SR75 (Illumina, San Diego, CA, USA) following library preparation using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). The library preparation and sequencing were performed by the Clinical Genomics Core at the Oklahoma Medical Research Foundation

treatment_protocol: Differentiated ALI cultures (ALI day 29-31) were infected with SARS-CoV-2 (average of 1.45 x 10^4 PFU per ALI well) via the apical chamber of the transwell insert at a multiplicity of infection (MOI) of 0.1 calculated based on the total number of cells per ALI well at the time of infection. The cells were either mock infected (uninfected) or infected with SARS-CoV-2 in HBTEC media by adding 100 μl of inoculum to the apical chamber. Mock infected cells received an equal volume of media used for preparing the SARS-CoV-2 inoculum added to the HBTEC media. After a 2hr incubation at 370C with 5% CO2, the inocula were removed from the apical chamber to expose the cells to air for the remainder of the experiment. At each time point post-infection (24hr, 48hr, 72hr and 96hr) the samples were harvested to collect RNA.

tag: cell type

value: bronchial epithelial cells

tag: donor

value: Donor 3 (Male, 67 years old)

value: SARS-CoV-2 infected

tag: time

value: 72 hours


title: HNCC-HJD


title: HBCC-JAP


title: 404943: PTSD53M

type: genomic

city: Kelvin Grove

first: Divya

last: Mehta

state: Australia

address: 60 Musk Avenue

country: Australia

institute: Queensland University Of Technology

hyb_protocol: Illumina

scan_protocol: Illumina EPIC

data_processing: background and control-normalized using the Bioconductor MINFI package

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Bisulphite

extract_protocol: Blood-derived DNA

tag: age

tag: Sex

value: M

tag: zygosity

tag: pheno

value: discPTSD

tag: ptsd

value: PTSD

value: blood


title: HNCC-SQX


title: t_96hr_SCOV2_S36

value: Donor 4 (Female, 69 years old)

value: 96 hours


title: HBCC-WRT


title: t_48hr_SCOV2_S34

value: 48 hours


title: t_72hr_SCOV2_S35


title: Bulk S2 cells not-induced

city: Utrecht

first: Wessel

middle: van

last: Leeuwen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
tRNA genes and pseudogenes were identified using tRNAscan-SE (version 2.0.7)
Adapter and homopolymer sequences were first trimmed from read 2 using cutadapt (version 3.2)
Trimmed reads were depleted of rRNA sequences by aligning to a ribosomal reference using bwa aln (version 0.7.17-r1188) and bwa mem, and discarding any read that aligned using either method
Depleted reads were then two-pass aligned to the reference genome using STARSolo (version 2.7.7a)
Aligned reads were deduplicated with UMI-tools (version 1.1.1)
Variant identification followed the GATK RNA-seq short variant discovery best-practices workflow using GATK (version 4.1.9.0)
Allele frequency and statistics were determined using an in-house written script
Genome_build: BDGP6

organism: Drosophila melanogaster

source_name: S2 cell

extract_protocol:
Direct-zol RNA microprep kit (Zymo)
See Muraro et al. 2016

treatment_protocol: S2 cells were treated with CuSO4 to induce protein expression, neuron expression was induced by RU486. Cells were stressed with 0.5mM sodium arsenite

value: S2 cells

value: 4h Schneider's followed by 4h Schneider's


title: HBCC-LJG

value: hepatocellular carcinoma


title: t_72hr_uninfected_S31

value: Uninfected


title: t_24hr_uninfected_S29

value: 24 hours


title: t_48hr_uninfected_S30


title: 407506: con31M

value: con


title: 402337: PTSD47M


title: t_0_uninfected_S28

value: bronchial epithelial cells

value: 0 hours


title: 404942: con53M


title: t_24hr_SCOV2_S24

value: Donor 3 (Male, 67 years old)

value: SARS-CoV-2 infected


title: 407507: PTSD31M

value: M


title: t_48hr_SCOV2_S16

value: Donor 2 (Male, 69 years old)


title: 417563: con51F

value: F

value: discPTSD


title: 401048: con34M

value: blood


title: 416810: con44M


title: t_96hr_SCOV2_S27

value: 96 hours


title: t_48hr_SCOV2_S25

value: 48 hours


title: t_48hr_uninfected_S12


title: t_96hr_uninfected_S14


title: t_72hr_uninfected_S13

value: 72 hours


title: t_96hr_uninfected_S32

value: Donor 4 (Female, 69 years old)


title: t_0_uninfected_S10


title: 416811: PTSD44M

value: PTSD


title: 417562: PTSD51F


title: t_72hr_SCOV2_S8

value: Donor 1 (Female, 67 years old)


title: t_72hr_SCOV2_S17


title: 401049: PTSD34M


title: t_96hr_uninfected_S23

value: Uninfected


title: t_72hr_uninfected_S4


title: 402336: con47M

value: con


title: t_0_uninfected_S1

value: bronchial epithelial cells


title: t_72hr_uninfected_S22


title: Splenic tTreg cRel-/- rep 1

city: Melbourne

first: Thomas

last: Fulford

state: Vic

address: 792 Elizabeth St

department: DMI

institute: University of Melbourne

data_processing:
The RNAsik pipeline was used (version 1.4.6) to process the raw data (e.g RNAsik -align star -fqDir /path_to_fastq_files/ -outDir run_x -fastaRef /path_to_reference_genome/Mus_musculus.GRCm38.dna_sm.primary_assembly.fa.gz -count -gtfFile /path_to_reference_annotation/Mus_musculus.GRCm38.84.gtf.gz -prePro  -fastqc -multiqc -exonicRate -threads 20 )
It uses STAR (ver 2.5.2) to align raw fastq files to the reference genome, producing bam files which are then sorted and duplicate reads are marked using Picard (ver 2.9.0)
FeatureCounts (Subread version 1.5.2)  uses the marked duplicate bam files to assign aligned reads to an annotated feature (gene)
The counts file produced by featureCounts is then uploaded to the Degust web tool for differential gene expression analysis (DGE)
Degust implements voom and limma by default for differential testing
Genome_build: GRCm38 (ensembl, release 84)
Supplementary_files_format_and_content: Csv files with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Spleen

extract_protocol:
pre-Tregs and Tregs were isolated from cRel+/+Foxp3rfp or cRel-/-Foxp3rfp mice by magnetic enrichment for CD4 T cells followed by FACS sorting. RNA was extracted using Qiagen RNAeasy micro kit following manufacturer's instructions
Libraries were constructed following Illumina protocols.

tag: genotype

value: tTreg cells

tag: strain


title: t_48hr_uninfected_S21

value: Donor 3 (Male, 67 years old)


title: Splenic tTreg WT rep 2


title: Thymic de novo Treg cRe-/- rep 1

source_name: Thymus

value: de novo Treg cells


title: Thymic de novo Treg cRe-/- rep 2


title: Pre-Treg cRel-/- rep 1

value: pre-Treg cells


title: Pre-Treg cRel-/- rep 2


title: Pre-Treg WT rep 2


title: t_0_uninfected_S19

value: 0 hours


title: t_24hr_uninfected_S20

value: 24 hours


title: t_96hr_SCOV2_S18

value: Donor 2 (Male, 69 years old)

value: SARS-CoV-2 infected


title: T-152

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

data_processing:
Raw fastq files were processed by the miRMaster platform (July 2019, miRBase v22), using its default settings. MiRMaster performs adapter trimming, quality filtering, and sequence alignment to the hg38 assembly.
Predicted novel miRNA precursor sequences were excluded if not classified by miRMaster as ‘novel’.
For putative novel mature miRNA sequences that could be derived from multiple different miRNA precursors, reads from each precursor were averaged, but only the precursor with the highest probability (as assigned by miRmaster) of being a true precursor is reported.
Genome_build: hg38
Supplementary_files_format_and_content: nov-miR files: Sequence (of the putative mature miRNA sequence), Chromosome, Strand, Start (nucleotide position of the start of the putative miRNA precursor), Stop (nucleotide position of the end of the putative miRNA precursor), RPM (expression of the putative mature miRNA, normalized to reads-per-million); kno-miR files: precursor, miRNA, RPM (expression of miRNA, normalized to reads-per-million); supplementary file: Reference (for kno-miRs, has the format precursor|mature miRNA; for novel miRNAs, has the format chromosome|strand|start|stop|sequence), Subtype (kno-miR or nov-miR), subsequent columns denote reads-per-million expression in different samples.

source_name: lung adenocarcinoma tumour

extract_protocol:
Fresh-frozen LUAD tumour and patient matched non-malignant lung parenchymal tissues were collected from treatment naive patients. Tissue microdissection was guided by a lung pathologist to ensure >80% tumor cell or >80% non-malignant cell content. Total RNA was extracted using TRIzol reagent (Life Technologies, Carlsbad, CA, USA/ThermoFisher, MA).
Full description of library construction and sequencing are as previously described [TCGA: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70].

value: lung

tag: tumour stage

tag: gender

value: F

tag: smoking status

value: EX


title: T-123

value: I

value: CS


title: T-154

value: M


title: t_24hr_SCOV2_S15

tag: treatment


title: T-120

tag: tissue


title: t_24hr_uninfected_S11

value: Uninfected


title: T-141

value: T2a, N0


title: T-116

value: IIB

value: NS


title: t_96hr_SCOV2_S9

value: bronchial epithelial cells

value: Donor 1 (Female, 67 years old)

value: 96 hours


title: T-125

value: IV


title: T-113

value: IIIA


title: T-107

value: IA


title: t_48hr_SCOV2_S7

value: SARS-CoV-2 infected

value: 48 hours


title: t_24hr_SCOV2_S6

value: 24 hours


title: t_48hr_uninfected_S3


title: t_24hr_uninfected_S2


title: Splenic tTreg cRel-/- rep 2

value: tTreg cells


title: Thymic de novo Treg WT rep 1

value: de novo Treg cells


title: Pre-Treg cRel-/- rep 3

value: pre-Treg cells


title: Splenic tTreg WT rep 1


title: t_96hr_uninfected_S5


title: T-95

value: lung

value: IB

value: F

value: CS


title: T-94

value: NS


title: T-153

value: EX


title: Pre-Treg WT rep 1


title: Thymic de novo Treg WT rep 2


title: T-89

value: IIB


title: T-90


title: T-114

value: M


title: T-117

value: I


title: T-115


title: T-83


title: T-126

value: IIA


title: T-96

value: IA


title: T-91


title: T-102


title: T-87


title: t_24hr_SCOV2_S33

value: bronchial epithelial cells

value: Donor 4 (Female, 69 years old)

value: SARS-CoV-2 infected


title: T-86

value: IIIB


title: T-84


title: T-85

value: IIIA


title: T-81


title: T-99


title: T-80


title: T-54


title: T-61


title: T-66


title: T-57


title: T-73


title: T-70


title: T-69


title: T-67


title: T-79


title: T-55


title: T-50


title: T-63


title: T-60


title: T-47


title: T-46


title: T-78


title: T-44


title: T-36


title: T-37


title: T-45


title: T-52


title: T-38


title: T-33


title: T-26


title: T-30


title: T-25


title: T-18


title: T-23


title: T-19


title: T-17


title: T-7


title: T-13


title: N-141

source_name: non-malignant lung parenchymal tissue from a lung adenocarcinoma patient

value: T2a, N0


title: N-126

value: lung


title: T-4


title: N-152


title: N-123


title: N-125

value: IV


title: N-120

value: F


title: N-115


title: N-113


title: N-116


title: N-102

value: IB

value: CS


title: N-105

value: NS


title: N-96


title: N-112


title: N-117

value: EX


title: N-99


title: N-94


title: N-91


title: N-154

value: M


title: N-89

value: IIB


title: N-86


title: N-85


title: N-87


title: N-81


title: N-90


title: N-79


title: N-78


title: N-84


title: N-80


title: N-73


title: N-66


title: N-95


title: N-60


title: N-55


title: N-63


title: N-52


title: N-61


title: N-67


title: N-54


title: N-57


title: N-44


title: N-47


title: N-50


title: N-37


title: N-46


title: N-83


title: N-38


title: N-70


title: N-42


title: N-32

value: IIA


title: N-31


title: N-33


title: N-35


title: N-25


title: N-23

value: IA


title: N-24


title: N-21


title: N-20


title: N-45


title: N-19


title: N-36


title: N-18


title: N-153


title: N-17


title: N-14


title: N-16


title: N-22


title: N-12


title: N-13


title: N-10


title: N-8


title: N-29


title: N-7


title: N-9


title: N-3


title: N-11


title: F-22

source_name: fetal lung

extract_protocol:
Tissue was obtained from chromosomally normal (46XX / 46XY) fetuses in their second trimester (17-24 weeks gestation), after elective terminations for medical reasons. TRIzol reagent (Life Technologies, Carlsbad, CA, USA/ThermoFisher, MA) was used to isolate total RNA from frozen tissue samples.
Full description of library construction and sequencing are as previously described [TCGA: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70].


title: F-24


title: F-23


title: F-25


title: N-4


title: F-21


title: HeLa lib2 T8 150 mM NaCl C

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Raw sequencing reads from CRISPR-Cas9 samples were aligned to the sgRNAs sequences of the Toronto KnockOut Library v1 (TKO) [Hart et al., 2015, Cell] (available at http://tko.ccbr.utoronto.ca/) using Bowtie (v1.2.1.1; parameters used: -m 1 -v 2)[Langmead, Trapnell, Pop & Salzberg, 2009, Genome Biology]. Read counts for each sgRNA were tabulated and used for downstream analyses.
Genome_build: Toronto KnockOut Library (TKO) v1 [Hart et al., 2015, Cell] (available at http://tko.ccbr.utoronto.ca/)
Supplementary_files_format_and_content: Raw read counts in tabular text format

source_name: HeLa cells

growth_protocol: HeLa hCas9 cells were maintained in Dulbecco’s Modified Eagle’s Medium containing 10% fetal calf serum supplemented with 1 mM sodium pyruvate and 100 U/ml penicillin, and cultured in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
genomic DNA was extracted from cell pellets (20.106 cells) using the QIAamp Blood Maxi Kit (Qiagen).
gRNA inserts were amplified via PCR using primers harboring Illumina TruSeq adapters with i5 and i7 barcodes and the resulting libraries were sequenced on an Illumina HiSeq2500. Each read was completed with standard primers for dual indexing with Rapid Run V1 reagents. The first 20 cycles of sequencing were "dark cycles" or base additions without imaging. The actual 26-bp read began after the dark cycles and contained two index reads, reading the i7 sequences first, followed by i5.

treatment_protocol: 150 mM NaCl for 24h

tag: cell line

value: HeLa

value: Cervix

value: Epithelial

value: 150 mM NaCl


title: N-15


title: HeLa lib2 T8 150 mM NaCl B


title: HeLa lib2 T8 150 mM NaCl A


title: F-19


title: F-18


title: F-17


title: HeLa lib2 T8B Control

value: untreated


title: HeLa lib2 T8C Control


title: HeLa lib1 T8 150 mM NaCl A


title: HeLa lib1 T8 150 mM NaCl B


title: F-15


title: HeLa lib2 T8A Control


title: F-13


title: F-14


title: HeLa lib1 T8C Control


title: ReCrzA-3

city: QingDao

first: Kaili

last: Zhao

address: National Glycoengineering Research Center, Shandong University, No. 72 Binhai Road

institute: ShanDong University

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: CrzA recover strain  in glucose

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% strach as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% strach as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.  After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CrzA recover strain

tag: medium

value: Modified Mendal’s medium with 2% starch as carbon resource

tag: culture time

value: 18h after transferring washed mycelia to the new medium

value: Fungal mycelia


title: F-12

value: lung


title: ReCrzA-2


title: HeLa lib1 T8 150 mM NaCl C

tag: cell type


title: F-20


title: F-11


title: HeLa lib1 T8B Control


title: HeLa lib2 T0


title: ReCrzA-1


title: F-16


title: DCrzA-2

source_name: CrzA deletion strain in glucose

value: CrzA deletion strain


title: HeLa lib1 T0


title: F-9


title: DCrzA-3


title: F-10


title: F-8


title: miRNA Hcy, biological rep2

city: Philadelphia

first: Hong

state: PA

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: Pre-processing of microarray data was performed with Partek® Genomics Suite v6.5 (Partek Inc., St. Louis, MO) using a robust multi-array average (RMA) algorithm to interpret the raw signal.

label: biotin

source_name: Human Aortic Endothelial  Cells

label_protocol: standard Affymetrix protocols

growth_protocol: HAEC were grown in M199 medium (Thermo Scientific, Waltham, MA) containing 20% fetal calf serum (Thermo Scientific), 50μg/mL endothelial cell growth supplement (BD Biosciences, San Jose, CA), and 50μg/mL heparin. Cells from passage 6 were used for experiments.

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

treatment_protocol: Cells were cultured to 80% confluence and then treated for 48h with 500μM L-Hcy to mimic severe HHcy seen in homocystinuria patients with CBS deficiencyvor with control medium.

value: Hyperhomocysteinemia


title: HeLa lib1 T8A Control


title: RNA Hcy, biological rep2

hyb_protocol: standard Affymetrix Protocol

scan_protocol: standard Affymetrix Protocol

label_protocol: standard Affymetrix Protocol


title: DCrzA-1


title: miRNA Hcy, biological rep3


title: RNA Control, biological rep2

value: control


title: WT-3

source_name: Wild type strain in glucose

value: 114-2(wild type)


title: RNA Hcy, biological rep3


title: RNA Control, biological rep3


title: F-7


title: WT-2


title: T-31

value: IB

value: M

value: CS


title: RNA Hcy, biological rep1


title: miRNA Control, biological rep3


title: RNA Control, biological rep1


title: WT-1


title: miRNA Hcy, biological rep1


title: miRNA Control, biological rep2


title: Neu 2' Biological Replicate 2

city: Miami

first: Harrys Kishore

last: Charles Jacob

state: Florida

address: 1501 NW 10th Ave BRB 542E

department: Surgery

institute: University of Miami, Miller SOM

description: Gene Expression data of Naïve Neutrophils Control 2 minutes

hyb_protocol: GeneTitan™ Hybridization, Wash and Stain Kit for 3' Array Plates was done

scan_protocol: Following hybridization, the Clariom S arrays are washed, stained, and scanned using a GeneChip Scanner 3000 (Thermo Fisher, MA, USA). T

data_processing: he microarrays were processed at the Microarray Research Services Laboratory (MRSL) at Thermo Fisher Scientific,( Thermo Fisher, Santa Clara, USA). The quality of the experiment was assessed based on the values of pos vs. neg auc and pm mean, which were calculated using the Affymetrix® Expression Console software (Thermo Fisher, MA, USA). CEL files were processed for each replicate and experimental condition using the Affymetrix® Transcriptome Analysis Console software 4.0 (Thermo Fisher, MA, USA). The CEL files were then subjected to normalization using the Signal Space Trans-formation-Robust Multiarray Analysis (SST-RMA) method [27] to generate CHP files. To analyze significantly differentially expressed gene (fold change ≥ ± 2, p value < 0.05). There was no significant difference between the neutrophils collected over different time points, so all comparisons were done against the 2-min time point of neutrophils treated with PBS. Neutrophil sample collected at time point 2-min is represented as 2′, while neutro-phils treated with EVs and collected at time points 10′, 30′, and 60′ are, respectively, rep-resented as EV10′, EV30′, and EV60′.

label: Biotin

source_name: Naïve Neutrophils

label_protocol: Extracted RNA samples undergo the stepwise process of first-strand cDNA synthesis us-ing reverse transcriptase of the RNA, cleanup of excess primers, 3’ adaptor synthesis, pre-IVT amplification, cRNA amplification, cRNA purification, 2nd-cycle ds-cDNA syn-thesis, template RNA removal, ds-cDNA purification and quantification, fragmentation and terminal Biotin labeling, and finally hybridization to the array.

growth_protocol: Naïve neutrophils were freshly isolated from two donors using the MACSExpress neutrophil isolation kit from whole blood

extract_protocol: RNA was extracted from different samples using the using the RNeasy UCP Micro kit (Qiagen, Germantown, USA), quantified and processed on Clariom S (Thermo Fisher, MA, USA) arrays using IVT Pico kit (Thermo Fisher, MA, USA).

treatment_protocol: 10^8 neutrophils were treated with extracellular vesicles (EVs) from Caucasian Male  61 years old (CM61) Circulating Tumor Cell lines from culture and samples were collected at 10, 30 and 60 minutes. Untreated naïve neutrophils collected at 2 minutes were used as controls.

value: Naïve Neutrophils Control 2 minutes


title: F-5


title: F-6


title: F-4


title: Dermal Treg

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

data_processing:
Fastq files generated from bcl files and analzyed by Cell Ranger (Epidermal/Dermal: 4.0.0; Lymph node: 2.2.0) with default parameters to generate filtered feature matrices
Genome_build: mm10
Supplementary_files_format_and_content: processed data files are the cellranger output filtered feature bc matrix files

source_name: dermis

extract_protocol:
Epidermis/Dermis Tregs: Skin layers were separated with thermolysin, and dermis was collagenase digested. Lymph node was mashed. Cells were FACS purified and sorted for Foxp3-expressing Tregs (GFP+ CD4+ CD3+ CD45+ cells)
10x Single Cell 3' v3 chemistry (Epidermal/Dermal Tregs) and 10x Single Cell 3' v2 chemistry (Lymph Node Tregs)

value: FOXP3-EGFP (C.Cg-Foxp3tm2Tch/J)


title: F-3


title: Epidermal Treg

source_name: epidermis


title: F-2

description: pooled sample; total RNA obtained from Biocat GmbH (Heidelberg, Germany)

extract_protocol:
Total RNA was obtained from Biocat GmbH (Heidelberg, Germany).
Full description of library construction and sequencing are as previously described [TCGA: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70].


title: F-1


title: miRNA Control, biological rep1


title: Lymph Node Treg

source_name: lymph node


title: Control MSN01-03R-CM Rep 1

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The scRNA sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 4.0, 10x Genomics) pipeline with the provided GRCh38 reference genome to produce the read counts matrix with the corresponding reference gene features and cell barcodes for each sample which then are combined into a single data table.
Genome_build: Homo sapiens (human) genome assembly GRCh38 (hg38)
Supplementary_files_format_and_content: A compressed TAR file containing a numerical read counts table file, reference gene feature file, and cell barcode file for each cell sample.
Supplementary_files_format_and_content: A compressed TSV file containing a combined read counts table of each reference gene across all sequenced cells for each cell sample.

source_name: primary dermal fibroblasts

growth_protocol: Cultured under growth conditions with mTeSR1 Basal Medium  (see the Section 8. Splitting/expansion of induced pluripotent stem cells (MEF/feeder-free) of the SOP document DToxS SOP CE-7.0 Reprogramming Human Fibroblasts to Human Induced Pluripotent Stem.pdf)

extract_protocol: 10x Genomics Chromium platform

treatment_protocol: Fully confluent and differentiated cells were treated with  vehicle (DMSO) for 24 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)

tag: source organ

value: skin

value: induced pluripotent stem cell-derived cardiomyocytes

tag: passage number

tag: sample id


title: Control MSN02-04R-CM Rep 1


title: Control MSN09-04R-CM Rep 1


title: Neu 2' Biological Replicate 1


title: Control MSN08-13R-CM Rep 1


title: HSF-KO_T0-1

status: Public on May 28 2021

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

data_processing:
Illumina Casava software used for basecalling.
RNAseq trimmed reads alignment performed by Hisat2 in PE mode and sorted with samtools 1.9.
Duplicated reads were removed with Picard MarkDuplicates 1.115 tool.
Survived reads counted by htseq-count (HTSeq 0.6.0) with “--nonunique none” option. TPM normalized and shown as mean value. Differential expression analysis and clustering done in R (edgeR, hclust).
For motif analysis, the promoter regions with the 1000bp (+/- 500bp from TSS or TSS predicted by CAGE if available) of each cluster were submitted into Fimo of MEME Suite 5.0.2 with default settings and  JASPAR2018 CORE motifs collection (MA0486.1, MA0486.2, MA0770.1 and MA0771.1 - for HSF binding motif)
Domains were annotated with InterproScan
Genome_build: Pv11_5.2
Supplementary_files_format_and_content: tab-delimited text file with mean TPM values, HFS motif binding sites, domain annotation, Blast results, expression clusters

organism: Polypedilum vanderplanki

growth_protocol: Pv11 cells and all clonal cell lines were cultured in IPL-41 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 2.6 g/L tryptone phosphate broth (Becton, Dickinson and Company, Franklin Lakes, NJ), 10% (v/v) fetal bovine serum (MP Biomedicals, Santa Ana, CA), and 0.05% (v/v) of an antibiotic and antimycotic mixture (penicillin, amphotericin B, and streptomycin; Merck KGaA, Darmstadt, Germany).

extract_protocol:
Total RNA extracted with a RNA Plus (Takara Bio, Shiga, Japan) and genomic DNAs were digested with a TURBO DNase (Invitrogen)
NGS library preparation done by using a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Cells were treated with 400 µg/mL zeocin or 200 µg/mL blasticidin at a density of 1 × 10^5 cells per mL five days after vector transfection. One week after the treatment, the medium was changed to normal IPL-41 medium, then the cells were cultured two weeks.

value: anhydrobiotic insect cell line

tag: genotype/variation

tag: condition

value: normal condition (before trehalose treatment)


title: EV 30' Biological Replicate 2

description: Gene Expression data of Neutrophils treated with EVs 30 minutes

source_name: Neutrophils

value: EVs 30 minutes


title: HSF-KO_T48-2

value: 48h of trehalose treatment


title: EV 60' Biological Replicate 1

description: Gene Expression data of Neutrophils treated with EVs  60 minutes

value: EVs 60 minutes


title: Pv11_T48-3

value: WT (normal Pv11)


title: HSF-KO_T0-2


title: HSF-KO_T48-1


title: EV 60' Biological Replicate 2


title: Pv11_T48-1


title: HSF-KO_T48-3


title: Pv11_T0-3


title: Pv11_T0-2


title: HSF-KO_T0-3


title: EV 10' Biological Replicate 1

description: Gene Expression data of Neutrophils treated with EVs  10 minutes

value: EVs 10 minutes


title: EV 10' Biological Replicate 2


title: EV 30' Biological Replicate 1

description: Gene Expression data of Neutrophils treated with EVs  30 minutes


title: HSF-KI_T48-2

value: Hsf1-/-; Hsf1-HaloTag/BlaR


title: HSF-KI_T48-1


title: HSF-KI_T0-2


title: HSF-KI_T0-3


title: HSF-KI_T0-1


title: Halo-Bla_T0-3

value: Hsf1-/- HaloTag/BlaR


title: Halo-Bla_T48-2


title: Halo-Bla_T0-1


title: Pv11_T48-2


title: Halo-Bla_T48-3


title: Pv11_T0-1


title: HSF-KI_T48-3


title: Halo-Bla_T0-2


title: Halo-Bla_T48-1


title: TGTT_0183

first: Fara

last: Brasó-Maristany

state: Barcelona

address: C/Casanova 143

department: Medical Oncology

institute: Institut d'Investigacions Biomediques August Pi I Sunyer

hyb_protocol: Hybridation was performed as per manufacturer's protocol

scan_protocol: Analysed in the nCounter FLEX Digital Analyzer

data_processing: Expression counts were then normalized using custom scripts in R 3.6.3.

source_name: metastatic breast cancer

label_protocol: Fluorescent barcode

extract_protocol: RNA was extracted using the High Pure FFPET RNA isolation kit (Roche, Indianapolis, IN, USA) following manufacturer’s protocol. One to five 10-μm FFPE slides depending on tumor cellularity were used for each tumor sample, and macrodissection was performed, when needed, to avoid normal tissue contamination. A minimum of 100 ng of total RNA was analyzed at the nCounter platform using the Breast Cancer 360 Panel.

tag: organ

value: Skin

tag: Sex

value: female

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

value: locoregional

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

value: no

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group

value: TNBC

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0161

tag: organ

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

value: Yes

value: No


title: TGTT_0181

value: Bone

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0182

tag: organ

value: Lung

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: her2 ihc

tag: her2 ish

tag: ihc group

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0163

value: Breast

value: postmenopausal

tag: site of metastatic biopsy

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy


title: TGTT_0158

tag: organ

tag: Sex

value: female

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0177

value: premenopausal

tag: site of metastatic biopsy

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: her2 ihc

tag: her2 ish

tag: ihc group

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0169

tag: organ

value: Skin

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy


title: TGTT_0179

value: Lymph node

tag: site of metastatic biopsy

value: locoregional

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0172

tag: organ

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: ≥3

value: yes

value: no

tag: her2 ihc

tag: her2 ish

tag: ihc group

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0180

value: Liver

tag: site of metastatic biopsy

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: NEG

value: TNBC


title: TGTT_0176

tag: organ

tag: Sex

tag: pre-post menopausal

value: unknown

tag: de novo metastasis vs relapsed

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0171

tag: site of metastatic biopsy

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: her2 ihc

tag: her2 ish

tag: ihc group

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0170

tag: organ

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy


title: TGTT_0175

tag: site of metastatic biopsy

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0164

tag: organ

value: Lung

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: Yes

value: No

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0166

value: Breast

value: female

value: postmenopausal

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0167

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0168

value: Skin

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0160

tag: organ

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0173

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0165

tag: organ

value: Brain

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0178

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: locoregional

value: yes

value: no

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0174

tag: organ

value: Pleura

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: NEG

value: TNBC


title: TGTT_0157

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: locorregional

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: Yes

value: No

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0159

tag: organ

value: female

value: postmenopausal

tag: metastatic spread

tag: number of metastatic sites

value: unknown

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0162

value: Breast

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0155

tag: organ

value: Lung

tag: metastatic spread

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0156

value: Brain

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0184

tag: organ

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0147

value: Skin

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: de novo

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group

value: TNBC


title: TGTT_0154

tag: organ

value: Pleura

value: female

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

value: Yes

tag: immunotherapy

value: No

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0136

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0139

tag: organ

value: Breast

value: locoregional

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0135

value: Bone

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0148

tag: organ

value: distant

tag: metastatic spread

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0152

value: Peritoneum

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: unknown

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0153

tag: organ

value: Skin

value: female

value: premenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: TNBC

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0149

value: Breast

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

value: locorregional

value: Yes

value: No

tag: everolimus

tag: pi3k inhibitors

value: Yes BKM120

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0151

tag: organ

value: distant

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0146

value: Pleura

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

value: no

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0138

tag: organ

value: Bone

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS

value: NEG


title: TGTT_0130

value: Ovary

tag: Sex

value: female

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0132

tag: organ

value: Lymph node

value: postmenopausal

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0133

value: Lung

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: de novo

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0137

tag: organ

value: Liver

value: relapsed

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0141

value: Brain

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: unknown

tag: site of metastatic biopsy

value: Bone only:no

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: TNBC

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0140

tag: organ

value: Bone

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: NEG

value: POS


title: TGTT_0145

value: Skin

tag: Sex

value: female

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: No

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0143

tag: organ

value: Lymph node

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0144

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0131

tag: organ

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0129

value: Breast

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: de novo

tag: site of metastatic biopsy

value: locoregional

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0128

tag: organ

value: Liver

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0134

value: Ovary

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: no

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0150

tag: organ

value: female

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

value: Yes

tag: immunotherapy

value: TNBC

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0127

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0126

tag: organ

value: Brain

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0142

value: Skin

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: No

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0103

tag: organ

value: Lymph node

value: relapsed

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0099

value: Lung

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: no

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0116

tag: organ

value: Bone

value: female

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: NEG

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0123

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: unknown

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0118

tag: organ

tag: metastatic spread

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: POS

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0122

value: Brain

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0117

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0120

value: Skin

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0121

tag: organ

value: Liver

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0124

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: TNBC


title: TGTT_0119

tag: organ

value: Lymph node

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0102

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

value: no

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0104

tag: organ

value: Breast

value: female

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0125

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

value: de novo

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0101

tag: organ

value: postmenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: unknown

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0108

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

value: yes

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0105

tag: organ

value: Brain

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: POS

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0110

value: Bone

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0114

tag: organ

value: relapsed

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: TNBC


title: TGTT_0107

value: Lymph node

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: locoregional

value: Bone only:no

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0115

tag: organ

value: female

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0113

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0106

tag: organ

value: premenopausal

tag: metastatic spread

value: Bone only:yes

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0112

value: Lung

tag: Sex

value: male

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0111

tag: organ

value: postmenopausal

value: unknown

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0097

value: Breast

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: de novo

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: yes

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0100

tag: organ

value: Liver

value: relapsed

value: distant

tag: metastatic spread

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: POS

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0109

value: Bone

tag: Sex

value: female

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: TNBC


title: TGTT_0096

tag: organ

value: Skin

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

value: no

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0098

value: Brain

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0095

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0094

value: Breast

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0089

tag: organ

value: Lung

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0092

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: unknown

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0093

tag: organ

value: Liver

value: de novo

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0091

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

value: distant

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: POS

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0090

tag: organ

value: female

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0077

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0078

tag: organ

value: Skin

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

value: no

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0080

value: Bone

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0079

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0073

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0083

tag: organ

value: Pleura

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0071

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: yes

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0084

tag: organ

value: Brain

value: postmenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: unknown

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: TNBC

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0086

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0072

tag: organ

value: Liver

value: de novo

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0067

tag: Sex

value: female

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

value: ≥3

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: POS

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0081

tag: organ

value: premenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0070

value: Bone

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:yes

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0074

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0087

value: Brain

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0082

tag: organ

value: Breast

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0068

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0085

tag: organ

value: Liver

value: relapsed

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0088

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

value: unknown

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0075

tag: organ

value: female

value: de novo

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: NEG

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0076

value: Pleura

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0069

tag: organ

value: Bone

value: premenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: no

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0066

value: Lymph node

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0064

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0062

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0063

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0059

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0060

tag: organ

value: Skin

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0061

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0057

tag: organ

value: Breast

value: postmenopausal

tag: metastatic spread

value: Bone only:yes

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0055

value: Liver

tag: Sex

value: female

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0056

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: NEG

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0054

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0053

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0052

value: Bone

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0058

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0042

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0045

tag: organ

value: Pleura

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0046

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0050

tag: organ

value: Peritoneum

tag: metastatic spread

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0051

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0044

tag: organ

value: de novo

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: TNBC


title: TGTT_0049

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0047

tag: organ

value: Liver

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0041

tag: Sex

value: female

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0048

tag: organ

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0039

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: NEG

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0040

tag: organ

value: Skin

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0065

tag: Sex

tag: pre-post menopausal

value: premenopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: no

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0038

tag: organ

value: Pleura

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0037

value: Muscle

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: yes

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0035

tag: organ

tag: metastatic spread

tag: number of metastatic sites

value: ≥3

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0036

value: Ovary

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0034

tag: organ

value: postmenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0043

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

value: locoregional

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0030

tag: organ

value: Lung

value: female

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0031

value: Brain

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0033

tag: organ

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0029

value: Bone

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0023

tag: organ

tag: metastatic spread

value: Bone only:yes

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0028

value: Liver

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: no

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0025

tag: organ

value: Lymph node

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0024

value: Pleura

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0022

tag: organ

value: postmenopausal

value: relapsed

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0027

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0017

tag: organ

value: locoregional

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0014

tag: Sex

value: female

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0015

tag: organ

value: de novo

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0018

value: Ovary

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: distant

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0019

tag: organ

value: Bone

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0020

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: Bone only:no

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0026

tag: organ

tag: metastatic spread

value: Bone only:yes

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: POS


title: TGTT_0016

value: Liver

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

value: no

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0009

tag: organ

value: Lymph node

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: yes

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0013

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: ≥3

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0011

tag: organ

value: Skin

value: postmenopausal

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0012

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: locoregional

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0008

tag: organ

value: female

value: relapsed

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0032

value: Brain

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0010

tag: organ

value: Muscle

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0021

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: NEG


title: TGTT_0006

tag: organ

value: Bone

value: de novo

tag: metastatic spread

value: Bone only:no

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0005

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

value: POS

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: TGTT_0004

tag: organ

tag: metastatic spread

value: Bone only:yes

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

value: no

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr


title: TGTT_0002

value: Lung

tag: Sex

tag: pre-post menopausal

tag: de novo metastasis vs relapsed

tag: site of metastatic biopsy

value: yes

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: TGTT_0003

tag: organ

value: Lymph node

tag: metastatic spread

tag: number of metastatic sites

tag: neoadjuvant or adjuvant treatment?

tag: anti-her2 treatment? yes vs not?

tag: chemotherapy? yes vs not

tag: immunotherapy

tag: ose

tag: os (months) since dxmet

tag: age (years)


title: BR rep1

city: Fuzhou

first: wenfei

state: Fujian

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

department: Haixia Institute of Science and Technology

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data filtering steps contain removing reads containing adapter, reads containing ploy-N and low quality reads to obtain clean reads. Meanwhile, Q20, Q30 and GC content the clean data were calculated.
Paired-end clean reads were aligned to Glycine max whole genome using Hisat2 v2.0.5 software.
FeatureCounts v1.5.0-p3 was used to calculate the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was used by DESeq2 software.
Genome_build: Glycine_max_Wm82.a4.v1.gtf
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Glycine max

source_name: 0.01 nM BL_treatment_Root

growth_protocol: Soybean seeds for RNA-seq were germinated in vermiculite for 3 days. Then seedlings were transferred into modified half-strength Hoagland's nutrient solution under long-day conditions (16 h light / 8 h dark) at 24 °C for 7 and a half days

extract_protocol:
Total RNA  isolated of soybean seedlings root tips(1 cm) by using RNAprep pure Plant Kit (TIANGEN, China).
RNA degradation and contamination was detection on 1% agarose gels. The purity of RNA was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. RNA libraries were constructed by 1 μg total RNA per sample.

treatment_protocol: 3-day-old soybean seedlings were transferred to hydroponics medium for 5 days, then treated with 0.1 μM PPZ and mock for another 2.5 days. Meanwhile, 3-day-old soybean seedlings were transferred to hydroponics medium for 7 days, then treated with 0.01 nM BL and mock for another 0.5 days.

tag: cultivar

tag: age

value: ten and a half days seedlings

tag: treatment

value: 0.01 nM BL treatment

tag: tissue

value: 1 cm of the root tip


title: PPZ rep3

source_name: 0.1 μM PPZ_treatment_Root

value: 0.1 μM PPZ treatment


title: PPZ_BR rep2

source_name: 0.1 μM PPZ after 0.01 nM BL treatment_Root

value: 0.1 μM PPZ after 0.01 nM BL treatment


title: PPZ_BR rep1


title: Mock rep3

value: Mock treatment


title: Mock rep1


title: PPZ rep2


title: BR rep3


title: PPZ rep1


title: BR rep2


title: PR1729_378-L1-4

first: Rajanikanth

last: Vadigepalli

address: 1020 Locust St, 314C

department: Pathology

institute: Jefferson University

description:
Single Neuron excised from Right Atrial Ganglionic Plexus (RAGP) of the heart
Neuron Identified using Cresyl violet flourescent signal collected using Laser Capture microdissection
BioMark-qRTPCR

data_processing: none provided by the submitter

label: EvaGreen

organism: Sus scrofa

source_name: RAGP of Pig Heart

label_protocol: none provided by the submitter

extract_protocol: Cell Lysates were directly processed for Reverse Transcription

tag: gender

value: female

tag: breed

value: Yucatan mini pig

tag: animal id

tag: sample flourecent label

value: Cresyl violet

tag: sample san (sino-atrial node) projecting/san non-projecting


title: PR1729_378-L1-2


title: PR1729_366-L1-4


title: PR1729_366-L1-7


title: PR1729_366-L1-5


title: PR1729_366-L1-3


title: PR1729_378-L1-1


title: PR1729_366-L1-6


title: TGTT_0007

tag: organ

tag: Sex

tag: pre-post menopausal

value: postmenopausal

tag: de novo metastasis vs relapsed

value: relapsed

tag: site of metastatic biopsy

value: distant

tag: metastatic spread

tag: number of metastatic sites

tag: number of lines of treatment?

tag: endocrine therapy? yes vs not

tag: cdk treatment? yes vs not

tag: everolimus

tag: pi3k inhibitors

tag: akt inhibitor

tag: bevacizumab

tag: parp inhibitors

tag: hr

value: NEG

tag: her2 ihc

tag: her2 ish

tag: ihc group


title: Mock rep2

tag: cultivar

tag: age

tag: treatment

tag: tissue