title: f5_CD_Day_0_Female_Progeny

description:
Library name: f5
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_701

status: Public on Dec 23 2024

type: SRA

city: Bratislava

first: Evan

last: Paul

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

description: Library name: MDX_3038_20_701_LumA_node_negative

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: breast

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

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: f3_CD_Day_0_Female_Progeny

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description:
Library name: f3
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

data_processing:
The obtained reads were aligned and quantified using kallisto, with the organism's transcriptome FASTA files (Genome assembly BDGP6.46) used to build the index. Quantification was performed from the FASTQ files, and the resulting abundance.h5 files were imported into R (v. 4.2.0). Annotations from the genome assembly GTF file were added. The tximport (v. 1.24.0) and DESeq2 (v. 1.36.0) packages were used to create a SummarizedExperiment object (provided as processed file).
Assembly: BDGP6.46
Supplementary files format and content: countMatrix_mothers.csv => contains the kallisto based count Matrix for only the mothers
Supplementary files format and content: countMatrix_progeny.csv => contains the kallisto based count Matrix for progeny
Supplementary files format and content: DDS_kallisto_mothers.rds => is a DEseq Data set including sample and gene annotation next to count data for the mothers
Supplementary files format and content: DDS_kallisto_all.rds => is a DEseq Data set including sample and gene annotation next to count data for all the progeny

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Female flies were placed on one of three diets: CD (Control Diet), HSD (High Sugar Diet), or HFD (High Fat Diet) for 7 days, and mated with CD-fed male flies. The resulting offspring are CD-fed and raised under light/dark cycles in a climate-controlled incubator at 25°C.

extract_protocol:
The samples were thawed and homogenized using the Precellys®24 (Peqlab) system at 5000 RPM for 15 seconds, then centrifuged at 13,000 g for 30 seconds, and the supernatant was pipetted to a new tube to remove residual glass beads.
Total RNA was extracted from samples stored at -80 °C in Qiazol using the RNeasy UCP Micro Kit (Qiagen, 73934). Samples were homogenized with the Precellys®24 system, followed by phase separation with chloroform and RNA purification using RNeasy MinElute spin columns, including on-column DNase digestion. RNA quality was assessed with the Agilent RNA 6000 Pico Kit and Agilent 2100 Bioanalyzer, with RIN values calculated to evaluate integrity.

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_695

description: Library name: MDX_3038_20_695_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Left breast, right breast, liver, bone

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_692

description: Library name: MDX_3038_20_692_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: Local recurrence

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m45_HSD_Day_50_Male_Progeny

description:
Library name: m45
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m42_HSD_Day_50_Male_Progeny

description:
Library name: m42
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: 3038_20_690

description: Library name: MDX_3038_20_690_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: NST

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

value: P

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Right breast

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_693

description: Library name: MDX_3038_20_693_2_TNBC_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

value: Y

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: f2_CD_Day_0_Female_Progeny

description:
Library name: f2
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_685

description: Library name: MDX_3038_20_685_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b

tag: n

value: pN X

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: m44_HSD_Day_50_Male_Progeny

description:
Library name: m44
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

value: HSD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m43_HSD_Day_50_Male_Progeny

description:
Library name: m43
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: m40_HSD_Day_50_Male_Progeny

description:
Library name: m40
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: f10_HFD_Day_0_Female_Progeny

description:
Library name: f10
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: HFD


title: 3038_20_684_excluded_subtype

description: Library name: MDX_3038_20_684_B_excluded_subtype

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 2(m)

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m39_HFD_Day_50_Male_Progeny

description:
Library name: m39
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: m41_HSD_Day_50_Male_Progeny

description:
Library name: m41
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: 3038_20_679

description: Library name: MDX_3038_20_679_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: f6_HFD_Day_0_Female_Progeny

description:
Library name: f6
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

value: HFD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_684

description: Library name: MDX_3038_20_684_A_LumA_node_positive

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_680

description: Library name: MDX_3038_20_680_LumB_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: not applicable

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_704

description: Library name: MDX_3038_20_704_LumA_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_678

description: Library name: MDX_3038_20_678_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

value: weekly 3x


title: m35_CD_Day_50_Male_Progeny

description:
Library name: m35
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m36_HFD_Day_50_Male_Progeny

description:
Library name: m36
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: HFD


title: 3038_20_702

description: Library name: MDX_3038_20_702_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Tubular carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m34_CD_Day_50_Male_Progeny

description:
Library name: m34
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_674

description: Library name: MDX_3038_20_674_LumB_node_positive

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Lung, liver, thoracic wall, pelvic region, bone

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_677

description: Library name: MDX_3038_20_677_LumB_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Micropapillary carcinoma

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m33_CD_Day_50_Male_Progeny

description:
Library name: m33
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_671

description: Library name: MDX_3038_20_671_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

value: N

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: m32_CD_Day_50_Male_Progeny

description:
Library name: m32
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_67

description: Library name: MDX_3038_20_67_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

value: Y

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m30_HSD_Day_10_Male_Progeny

description:
Library name: m30
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m29_HSD_Day_10_Male_Progeny

description:
Library name: m29
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: m28_HSD_Day_10_Male_Progeny

description:
Library name: m28
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: m31_CD_Day_50_Male_Progeny

description:
Library name: m31
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: CD


title: 3038_20_668

description: Library name: MDX_3038_20_668_LumB_node_positive

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Bone

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

value: EC/MCT


title: 3038_20_665

description: Library name: MDX_3038_20_665_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2(m)

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

value: not applicable

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m27_HSD_Day_10_Male_Progeny

description:
Library name: m27
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m38_HFD_Day_50_Male_Progeny

description:
Library name: m38
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: HFD


title: 3038_20_658

description: Library name: MDX_3038_20_658_invasive_LumA_node_positive

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_662

description: Library name: MDX_3038_20_662_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: Y

value: Left axilla

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m26_HSD_Day_10_Male_Progeny

description:
Library name: m26
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m23_HFD_Day_10_Male_Progeny

description:
Library name: m23
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: HFD


title: 3038_20_656

description: Library name: MDX_3038_20_656_TNBC_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Metaplastic carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_654

description: Library name: MDX_3038_20_654_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_659

description: Library name: MDX_3038_20_659_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c(m)

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

value: Y

tag: tc

tag: other


title: 3038_20_652

description: Library name: MDX_3038_20_652_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: not applicable

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m22_HFD_Day_10_Male_Progeny

description:
Library name: m22
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_658_excluded_subtype

description: Library name: MDX_3038_20_658_excluded_subtype

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - no tumor

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 2(m)

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: m24_HFD_Day_10_Male_Progeny

description:
Library name: m24
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: m25_HFD_Day_10_Male_Progeny

description:
Library name: m25
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: 3038_20_651_excluded_subtype

description: Library name: MDX_3038_20_651_B_excluded_subtype

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: extra ROI - DCIS

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Local recurrence

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: m21_HFD_Day_10_Male_Progeny

description:
Library name: m21
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_651

description: Library name: MDX_3038_20_651_A_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_649

description: Library name: MDX_3038_20_649_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: male

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

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

value: Y - not specified

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: m20_CD_Day_10_Male_Progeny

description:
Library name: m20
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_646

description: Library name: MDX_3038_20_646_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Right breast, lung

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: 3038_20_645

description: Library name: MDX_3038_20_645_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

value: not applicable

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: m19_CD_Day_10_Male_Progeny

description:
Library name: m19
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_641

description: Library name: MDX_3038_20_641_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_643

description: Library name: MDX_3038_20_643_LumB_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_635

description: Library name: MDX_3038_20_635_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 2

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: P

value: N

value: LumA

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_634

description: Library name: MDX_3038_20_634_Her2_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Lymph nodes, lung, suspected left breast

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (cycles)


title: m17_CD_Day_10_Male_Progeny

description:
Library name: m17
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_633

description: Library name: MDX_3038_20_633_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_629

description: Library name: MDX_3038_20_629_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

value: not applicable

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_63

description: Library name: MDX_3038_20_63_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: anthracycline (y/n)


title: m18_CD_Day_10_Male_Progeny

description:
Library name: m18
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m16_CD_Day_10_Male_Progeny

description:
Library name: m16
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: 3038_20_632

description: Library name: MDX_3038_20_632_Her2_node_positive

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 3

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: P

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: f41_HSD_Day_50_Female_Progeny

description:
Library name: f41
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

value: HSD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_627

description: Library name: MDX_3038_20_627_LumA_node_positive

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: anthracycline (y/n)


title: m15_HSD_Day_0_Male_Progeny

description:
Library name: m15
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m14_HSD_Day_0_Male_Progeny

description:
Library name: m14
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: 3038_20_623

description: Library name: MDX_3038_20_623_LumB_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_647

description: Library name: MDX_3038_20_647_LumA_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: anthracycline (y/n)


title: m13_HSD_Day_0_Male_Progeny

description:
Library name: m13
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m12_HSD_Day_0_Male_Progeny

description:
Library name: m12
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: CLL_296, Chronic lymphocytic Leukemia;  biological replicate

type: RNA

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

country: USA

institute: University of Michigan

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize and fit log2 transformed expression values.

label: biotin

source_name: CD19+ cells sorted from human PBMCs

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN encore end-labeling module).

growth_protocol: no additional ex vivo growth or culture

extract_protocol: Total RNA was isolated from CD19+ sorted CLL cells and further purified using Qiagen RNAeasy columns

treatment_protocol: PBMCs isolated from the blood of CLL patients and cryopreserved and flow sorted using CD19

value: m

tag: cll-fish

tag: ighv status

value: no data

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_622

description: Library name: MDX_3038_20_622_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_617

description: Library name: MDX_3038_20_617_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_618

description: Library name: MDX_3038_20_618_LumB_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: Y

value: Local recurrence, bone, liver, brain

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: m10_HFD_Day_0_Male_Progeny

description:
Library name: m10
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: m11_HSD_Day_0_Male_Progeny

description:
Library name: m11
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: HSD


title: 3038_20_621

description: Library name: MDX_3038_20_621_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 2

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_620

description: Library name: MDX_3038_20_620_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 4d

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: Bone

value: not applicable

tag: fec, fec-t

value: ET/EC

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_610

description: Library name: MDX_3038_20_610_TNBC_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Metaplastic carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_612

description: Library name: MDX_3038_20_612_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_609

description: Library name: MDX_3038_20_609_LumA_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: P

value: N

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: anthracycline (y/n)


title: 3038_20_616

description: Library name: MDX_3038_20_616_Her2_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: m9_HFD_Day_0_Male_Progeny

description:
Library name: m9
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_605

description: Library name: MDX_3038_20_605_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other


title: 3038_20_602

description: Library name: MDX_3038_20_602_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: P

tag: her2 ihc

tag: her2 dna_fish

value: not applicable

value: Y

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)

tag: anthracycline (cycles)


title: CLL_295, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: no data

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_292, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_285, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_265, Chronic lymphocytic Leukemia;  biological replicate

value: M


title: m8_HFD_Day_0_Male_Progeny

description:
Library name: m8
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

value: Male

tag: day

tag: group


title: 3038_20_596

description: Library name: MDX_3038_20_596_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: m7_HFD_Day_0_Male_Progeny

description:
Library name: m7
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_586

description: Library name: MDX_3038_20_586_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_585

description: Library name: MDX_3038_20_585_B_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_584

description: Library name: MDX_3038_20_584_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxol dosage

tag: anthracycline (y/n)


title: m5_CD_Day_0_Male_Progeny

description:
Library name: m5
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_585_excluded_subtype

description: Library name: MDX_3038_20_585_A_excluded_subtype

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_260, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_581

description: Library name: MDX_3038_20_581_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_257, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

tag: ighv status

tag: snp 6.0 genomic lesion total

tag: cell type

tag: tissue

tag: disease state


title: 3038_20_598

description: Library name: MDX_3038_20_598_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

value: Y

tag: tc

tag: other

value: FEC/EC

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_261, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

tag: cll-fish

tag: ighv status

value: no data

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_287, Chronic lymphocytic Leukemia;  biological replicate


title: m4_CD_Day_0_Male_Progeny

description:
Library name: m4
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

value: Male

tag: day

tag: group


title: CLL_250, Chronic lymphocytic Leukemia;  biological replicate

value: m

tag: tp53 status

value: mutated

value: UM


title: CLL_252, Chronic lymphocytic Leukemia;  biological replicate

value: f


title: 3038_20_580_excluded_subtype

description: Library name: MDX_3038_20_580_2_excluded_subtype

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2(m)

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_591

description: Library name: MDX_3038_20_591_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

value: Y - Nolvadex (Tamoxifen)

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_580

description: Library name: MDX_3038_20_580_1_LumB_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: LumB

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_249, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: m6_HFD_Day_0_Male_Progeny

description:
Library name: m6
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

value: Male

tag: day

tag: group


title: m3_CD_Day_0_Male_Progeny

description:
Library name: m3
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: CD


title: 3038_20_587

description: Library name: MDX_3038_20_587_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b (multifokal)

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: m2_CD_Day_0_Male_Progeny

description:
Library name: m2
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_576

description: Library name: MDX_3038_20_576_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Bone

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_577

description: Library name: MDX_3038_20_577_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1b

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

value: Brain

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_579

description: Library name: MDX_3038_20_579_Her2_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: N

value: P

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_575_excluded_subtype

description: Library name: MDX_3038_20_575_B_excluded_subtype

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: extra ROI - LCIS

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: m1_CD_Day_0_Male_Progeny

description:
Library name: m1
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Male

tag: day

tag: group


title: 3038_20_575

description: Library name: MDX_3038_20_575_A_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_245, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_574_excluded_subtype

description: Library name: MDX_3038_20_574_B_excluded_subtype

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: extra ROI - DCIS

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: s15_HSD_Female_mother

description:
Library name: s15
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_572

description: Library name: MDX_3038_20_572_A_LumB_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

value: pT 1c(m)

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_572_excluded_subtype

description: Library name: MDX_3038_20_572_B_excluded_subtype

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: not applicable

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_247, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: s13_HSD_Female_mother

description:
Library name: s13
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

value: Female

tag: day

tag: group