title: 3038_20_858

description: Library name: MDX_3038_20_858_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma/Micropapillary carcinoma

tag: t

value: pT 1b(m)

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: P

tag: er irs

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: 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 (cycles)


title: 3038_20_846

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_846_LumA_node_positive

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.

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 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 4b

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

value: LumA

value: Y

value: Pleura, lung, liver

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: anthracycline (y/n)


title: 3038_20_838

description: Library name: MDX_3038_20_838_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

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

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: 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


title: 3038_20_831_excluded_subtype

description: Library name: MDX_3038_20_831_B_excluded_subtype

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

value: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma/Micropapillary carcinoma

tag: t

value: pT 2

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

value: LumB

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: anthracycline (y/n)

tag: anthracycline (cycles)


title: 3038_20_83

description: Library name: MDX_3038_20_83_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st 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(m)

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: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Y

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


title: 3038_20_826

description: Library name: MDX_3038_20_826_LumA_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th 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 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumA

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: anthracycline (y/n)


title: 3038_20_879

description: Library name: MDX_3038_20_879_LumA_node_negative

tag: tissue

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

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: P

tag: er irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Liver

tag: tc

tag: other

value: ET

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_823

description: Library name: MDX_3038_20_823_HER2_minus_LumB_node_negative

tag: tissue

tag: isolate

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 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: er negpos

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumB

value: N

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: anthracycline (y/n)


title: 3038_20_842

description: Library name: MDX_3038_20_842_LumA_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

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 irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_823_excluded_subtype

description: Library name: MDX_3038_20_823_excluded_subtype

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

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

value: P

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: anthracycline (y/n)


title: 3038_20_819_excluded_subtype

description: Library name: MDX_3038_20_819_excluded_subtype

tag: tissue

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/Invasive lobular carcinoma

tag: t

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er irs

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: Bone

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 (cycles)


title: 3038_20_816_healthy

description: Library name: MDX_3038_20_816_healthy

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

value: no tumor

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1a

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: 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: anthracycline (y/n)


title: 3038_20_856

description: Library name: MDX_3038_20_856_LumB_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

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: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_815

description: Library name: MDX_3038_20_815_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 1b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumA

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: anthracycline (y/n)


title: 3038_20_819

description: Library name: MDX_3038_20_819_LOB_LumB_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma/Invasive lobular carcinoma

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: 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: 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 (cycles)


title: 3038_20_824

description: Library name: MDX_3038_20_824_LumA_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

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: anthracycline (y/n)


title: 3038_20_827

description: Library name: MDX_3038_20_827_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

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: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_813

description: Library name: MDX_3038_20_813_LumB_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: male

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: Bone, lymph nodes, lung, liver

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: anthracycline (y/n)


title: 3038_20_811

description: Library name: MDX_3038_20_811_LumA_node_positive

tag: tissue

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

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_810

description: Library name: MDX_3038_20_810_LumA_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

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 4b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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

value: MCT

tag: anthracycline (y/n)


title: 3038_20_809

description: Library name: MDX_3038_20_809_LumA_node_positive

tag: tissue

value: breast

tag: isolate

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: Invasive ductal carcinoma

tag: t

value: pT 2(m)

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

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: 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


title: 3038_20_808

description: Library name: MDX_3038_20_808_LumB_node_negative

tag: tissue

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

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 1b(m)

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumB

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: anthracycline (y/n)


title: 3038_20_81

description: Library name: MDX_3038_20_81_LumB_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 postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_831

description: Library name: MDX_3038_20_831_A_LumB_node_positive

tag: tissue

value: breast

tag: isolate

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: Invasive ductal carcinoma/Micropapillary carcinoma

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 irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: anthracycline (y/n)

tag: anthracycline (cycles)


title: 3038_20_805

description: Library name: MDX_3038_20_805_LumB_node_positive

tag: tissue

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

value: Invasive lobular 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

value: P

tag: er irs

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: 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


title: 3038_20_802

description: Library name: MDX_3038_20_802_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

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

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumB

value: Liver, lung, pleura, lymph node, bone, brain, 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: anthracycline (y/n)

tag: anthracycline (cycles)


title: 3038_20_796

description: Library name: MDX_3038_20_796_TNBC_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

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

value: Invasive ductal carcinoma/Invasive lobular 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: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_801

description: Library name: MDX_3038_20_801_LumB_node_positive

tag: tissue

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: er negpos

value: P

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: anthracycline (y/n)


title: 3038_20_793

description: Library name: MDX_3038_20_793_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: N

tag: er irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_797

description: Library name: MDX_3038_20_797_LumA_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

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumA

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: anthracycline (y/n)


title: 3038_20_791

description: Library name: MDX_3038_20_791_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

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

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er irs

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: Y

tag: tc

tag: other

value: EC/MCT

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_790

description: Library name: MDX_3038_20_790_LumB_node_positive

tag: tissue

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

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: Liver

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: anthracycline (y/n)


title: 3038_20_79

description: Library name: MDX_3038_20_79_LumB_node_positive

tag: tissue

value: breast

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

tag: histopathological tumor_type

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 irs

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: Lung, pleura, bone, liver, brain

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


title: 3038_20_789

description: Library name: MDX_3038_20_789_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

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

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

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumA

value: Liver, lung, bone

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: anthracycline (y/n)


title: 3038_20_786

description: Library name: MDX_3038_20_786_LumA_node_negative

tag: tissue

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

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)

value: P

tag: er irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: 3038_20_784

description: Library name: MDX_3038_20_784_Her2_node_positive

tag: tissue

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 premenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: anthracycline (y/n)


title: 3038_20_78

description: Library name: MDX_3038_20_78_TNBC_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma, 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 irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: 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


title: 3038_20_778

description: Library name: MDX_3038_20_778_A_LumB_node_negative

tag: tissue

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

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumB

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: anthracycline (y/n)


title: 5xFADEif2ATRAP_snRNAseq

city: New York

first: Anna

last: Flury

state: NY

address: 85 St Nicholas Terrace

country: USA

institute: CUNY Graduate Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
.fastq files containing barcoded reads for single-nuclei sequencing were aligned to the mouse mm10 genome and processed into filtered feature barcode matrices (Market Exchange Format) using CellRanger Pipeline v7.1.0 with default parameters. To capture unspliced pre-mRNA in the single-nucleus RNA expression assay, intronic regions in the 10X Cell Ranger mm10 v1.2.0 reference were marked as exonic as suggested by 10X for pre-mRNA reference generation
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files as output by Cell Ranger

molecule: nuclear RNA

organism: Mus musculus

source_name: cortex

growth_protocol: not applicable

extract_protocol:
Microglial nuclei were isolated based on the eGFP-L10a fluorescence of newly formed ribosomes in the microglia nucleoli as described in Ayata et al. Briefly, one male and one female mouse for each sample were sacrificed by cervical dislocation. Brain regions were quickly dissected and homogenized in 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8 with a glass Dounce homogenizer (1984-10002, Kimble Chase, Vineland, NJ). The buffers were supplemented with 10 μl/ml RNasin, Superasin, and EDTA-free protease inhibitor cocktail (11836170001, Roche). The homogenate was then spun through a 29% iodixanol cushion. The resulting nuclear pellet was resuspended in 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine pH 7.8, supplemented with 10 μM DyeCycle Ruby (V10304, Invitrogen), and 10% donkey serum (017-000-121, Jackson Immunoresearch, West Grove, PA). Microglial nuclei were sorted in a BD FACS Aria cell sorter by gating for the lowest DyeCycle Ruby, which indicates nuclei singlets and a high GFP signal. For single nuclei RNA sequencing, isolated nuclei were used immediately for 10X sequencing
Libraries were constructed from isolated microglial nuclei (at least 5,000 nuclei) using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3′ gene expression (3′ GEX) V2 kit, using a targeted input of ~8,000 nuclei per sample. In brief, gel-bead in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher)

treatment_protocol:
Tamoxifen treatment: To activate Tamoxifen-inducible Cre-Ert2, all mice were gavaged at 4-6 weeks of age with six doses of 100 mg/kg of Tamoxifen (T5648, Sigma, St. Louis, MO) in corn oil (C8267, Sigma) with a separation of at least 48 hours between doses. Tamoxifen was dissolved directly in corn oil with 2 hours of incubation at 55°C.
VEGF/ASV treatment: Mice were injected with 1 μg/kg VEGF in 0.9% saline. 30 minutes after VEGF administration, we orally administered 5 mg/kg ASV in 1:9 DMSO:PEG300. This was repeated biweekly for 4 weeks. In iPKR mice, treatment started at 4-5 months of age, 5xFADTRAP mice at 5 months, and 5xFADiPKR at 5 months.

tag: tissue

value: cortex

tag: Sex

value: pooled male and female

tag: age (mpnths)

tag: cell type

value: microglia nuclei

tag: genotype

tag: treatment

value: tamoxifen


title: 5xFADiPKR_snRNAseq

description: 10X Genomics

value: tamoxifen and VEGF/ASV


title: 3038_20_777

description: Library name: MDX_3038_20_777_LumB_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

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

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

tag: deceased (y/n)

tag: relapse/metastasis

value: N

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: Y

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


title: 5xFADTRAP_snRNAseq

description: 10X Genomics

tag: tissue

tag: Sex

tag: age (mpnths)

tag: cell type

tag: genotype

tag: treatment


title: 3038_20_778_excluded_subtype

description: Library name: MDX_3038_20_778_B_excluded_subtype

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: sample category

value: extra ROI

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular 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

tag: organ relapse/metastasis

tag: incidence of_other_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: anthracycline (y/n)


title: 3038_20_774

description: Library name: MDX_3038_20_774_LumB_node_positive

tag: tissue

value: breast

tag: isolate

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

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

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

value: not applicable

tag: organ affected_by_tumorous_disease

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


title: 3038_20_772

description: Library name: MDX_3038_20_772_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

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)

value: P

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: 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: anthracycline (y/n)

tag: anthracycline (cycles)


title: 3038_20_770

description: Library name: MDX_3038_20_770_LumB_node_positive

tag: tissue

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

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

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: organ affected_by_tumorous_disease

value: Y

tag: tc

tag: other

value: 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: IRPT3 TEC

type: RNA

city: HOUSTON

first: IN HYUK

last: BANG

state: TX

address: 6431 Fannin St

department: Anesthesiology

institute: UThealth at Houston

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Gene chip from Clariom™ S Assay, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G System

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0.2.

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip WT PLUS Reagent Kit User Guide (Pub. No. MAN0018137 B.0)).

growth_protocol: Renal tubular epithelial cells were obtained from the kidnetys digested with Collagenase Type 2.

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

treatment_protocol: Mice were performed with 30 minutes of ischemia and 24 hours of reperfusion for vehicle- or PT2385 treated (10 mg/kg of PT2384 was injecteed at 16 hours before surgery, 1 hour, 8 hours and 20 hours after surgery) mice .Rnal tubular epithelial cells were isolated from the kidney.

tag: tissue

value: Renal tubular epithelial cell


title: IR3 TEC


title: f42_HSD_Day_50_Female_Progeny

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description:
Library name: f42
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.

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: IRPT1 TEC


title: IRPT2 TEC


title: 3038_20_77_excluded_subtype

description: Library name: MDX_3038_20_77_2_excluded_subtype

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

value: female

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

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: tc

tag: anthracycline (y/n)


title: 3038_20_77

description: Library name: MDX_3038_20_77_1_LumB_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

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

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: 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


title: 3038_20_782

description: Library name: MDX_3038_20_782_Her2_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

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2(m)

tag: n

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: tc

tag: anthracycline (y/n)


title: 3038_20_769

description: Library name: MDX_3038_20_769_LumB_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

value: inferred perimenopausal

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

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

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


title: f40_HFD_Day_50_Female_Progeny

description:
Library name: f40
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: Female

tag: day

tag: group


title: f43_HSD_Day_50_Female_Progeny

description:
Library name: f43
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: f39_HFD_Day_50_Female_Progeny

description:
Library name: f39
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_766

description: Library name: MDX_3038_20_766_LumB_node_negative

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

tag: histopathological tumor_type

value: NST

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

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: tc

value: weekly

tag: anthracycline (y/n)


title: f38_HFD_Day_50_Female_Progeny

description:
Library name: f38
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: IR1 TEC

value: Renal tubular epithelial cell


title: f37_HFD_Day_50_Female_Progeny

description:
Library name: f37
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds


title: f44_HSD_Day_50_Female_Progeny

description:
Library name: f44
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_760

description: Library name: MDX_3038_20_760_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

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)

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

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: 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


title: 3038_20_762

description: Library name: MDX_3038_20_762_Her2_node_positive

tag: tissue

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

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 4b

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

value: Y

value: Local recurrence

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: anthracycline (y/n)


title: f35_CD_Day_50_Female_Progeny

description:
Library name: f35
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: f36_HFD_Day_50_Female_Progeny

description:
Library name: f36
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: f34_CD_Day_50_Female_Progeny

description:
Library name: f34
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_757

description: Library name: MDX_3038_20_757_LumA_node_positive

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

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)

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

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: 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


title: 3038_20_755

description: Library name: MDX_3038_20_755_LumA_node_positive

tag: tissue

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

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

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: 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: anthracycline (y/n)


title: 3038_20_756

description: Library name: MDX_3038_20_756_LumA_node_negative

tag: tissue

value: breast

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

value: pT 1c

tag: n

value: pN 0

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: 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


title: f32_CD_Day_50_Female_Progeny

description:
Library name: f32
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_753

description: Library name: MDX_3038_20_753_LumA_node_negative

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

value: NST

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

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: anthracycline (y/n)


title: 3038_20_752

description: Library name: MDX_3038_20_752_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

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c(m)

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: Y

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


title: 3038_20_751

description: Library name: MDX_3038_20_751_LumA_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

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)

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: anthracycline (y/n)


title: f29_HSD_Day_10_Female_Progeny

description:
Library name: f29
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: Female

tag: day

tag: group


title: 3038_20_750

description: Library name: MDX_3038_20_750_TNBC_node_positive

tag: isolate

value: breast cancer patient

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

tag: t

value: pT 2

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: 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: 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


title: f28_HSD_Day_10_Female_Progeny

description:
Library name: f28
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: f26_HSD_Day_10_Female_Progeny

description:
Library name: f26
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_743

description: Library name: MDX_3038_20_743_LumA_node_positive

value: breast

tag: isolate

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 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

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: anthracycline (y/n)


title: 3038_20_741

description: Library name: MDX_3038_20_741_LumA_node_positive

tag: tissue

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

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

value: Y

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


title: 3038_20_758

description: Library name: MDX_3038_20_758_LumB_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: N

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: anthracycline (y/n)


title: f23_HFD_Day_10_Female_Progeny

description:
Library name: f23
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: Female

tag: day

tag: group


title: 3038_20_739

description: Library name: MDX_3038_20_739_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 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

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

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: 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


title: f27_HSD_Day_10_Female_Progeny

description:
Library name: f27
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

tag: day

tag: group


title: 3038_20_74

description: Library name: MDX_3038_20_74_A_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

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: NST

tag: t

value: pT 1a

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: anthracycline (y/n)


title: 3038_20_738

description: Library name: MDX_3038_20_738_LumB_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 postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 4

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

value: N

value: Y

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


title: f22_HFD_Day_10_Female_Progeny

description:
Library name: f22
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: Female

tag: day

tag: group


title: f33_CD_Day_50_Female_Progeny

description:
Library name: f33
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_74_excluded_subtype

description: Library name: MDX_3038_20_74_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 perimenopausal

tag: histopathological tumor_type

value: NST

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

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: anthracycline (y/n)


title: IR2 TEC

tag: tissue

value: Renal tubular epithelial cell


title: f31_CD_Day_50_Female_Progeny

description:
Library name: f31
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: f30_HSD_Day_10_Female_Progeny

description:
Library name: f30
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: f20_CD_Day_10_Female_Progeny

description:
Library name: f20
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_733

description: Library name: MDX_3038_20_733_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

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)

value: missing

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: 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: 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


title: 3038_20_736

description: Library name: MDX_3038_20_736_LumB_node_negative

tag: tissue

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 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: 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: anthracycline (y/n)


title: f19_CD_Day_10_Female_Progeny

description:
Library name: f19
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_732

description: Library name: MDX_3038_20_732_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

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

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: 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


title: f25_HFD_Day_10_Female_Progeny

description:
Library name: f25
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

tag: day

tag: group


title: 3038_20_748

description: Library name: MDX_3038_20_748_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

value: inferred postmenopausal

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)

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

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


title: f18_CD_Day_10_Female_Progeny

description:
Library name: f18
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: f24_HFD_Day_10_Female_Progeny

description:
Library name: f24
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_progeny.csv
DDS_kallisto_all.rds

value: Female


title: f17_CD_Day_10_Female_Progeny

description:
Library name: f17
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_729

description: Library name: MDX_3038_20_729_LumA_node_positive

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

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma/Invasive lobular carcinoma

tag: t

value: pT 1c(m)

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: 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: 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: f16_CD_Day_10_Female_Progeny

description:
Library name: f16
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_730

description: Library name: MDX_3038_20_730_LumB_node_negative

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 1b

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

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)

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: 3038_20_726

description: Library name: MDX_3038_20_726_LumA_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

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

value: N

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

tag: anthracycline (y/n)


title: f15_HSD_Day_0_Female_Progeny

description:
Library name: f15
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: Female

tag: day

tag: group


title: f14_HSD_Day_0_Female_Progeny

description:
Library name: f14
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_725

description: Library name: MDX_3038_20_725_LumB_node_positive

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

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other


title: f13_HSD_Day_0_Female_Progeny

description:
Library name: f13
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: f21_HFD_Day_10_Female_Progeny

description:
Library name: f21
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: f12_HSD_Day_0_Female_Progeny

description:
Library name: f12
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_724

description: Library name: MDX_3038_20_724_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b

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

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: f11_HSD_Day_0_Female_Progeny

description:
Library name: f11
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: Female

tag: day

tag: group


title: 3038_20_714

description: Library name: MDX_3038_20_714_LumB_node_positive

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 postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 3a

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

value: N

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: suspected 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_720

description: Library name: MDX_3038_20_720_PR_minus_LumB_node_positive

tag: tissue

value: breast

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 perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1

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: Sternum, liver, mediastinum, lung, bone

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: f9_HFD_Day_0_Female_Progeny

description:
Library name: f9
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: Female

tag: day

tag: group


title: 3038_20_713

description: Library name: MDX_3038_20_713_LumA_node_negative

tag: isolate

value: breast cancer patient

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/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

value: N

tag: her2 ihc

tag: her2 dna_fish

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Bone, adrenal glands, liver

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: f8_HFD_Day_0_Female_Progeny

description:
Library name: f8
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

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_711

description: Library name: MDX_3038_20_711_LumA_node_positive

value: breast

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

value: Invasive ductal carcinoma

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

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: Y

tag: organ relapse/metastasis

value: Bone, brain

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: 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_720_excluded_subtype

description: Library name: MDX_3038_20_720_excluded_subtype

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

value: extra ROI - invasive

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: Sternum, liver, mediastinum, lung, bone

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_708

description: Library name: MDX_3038_20_708_LumA_node_negative

tag: tissue

value: breast

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: Mucinous carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

value: N

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: 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: f7_HFD_Day_0_Female_Progeny

description:
Library name: f7
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: Female

tag: day

tag: group


title: 3038_20_705

description: Library name: MDX_3038_20_705_LumB_node_negative

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: 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

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: tc

tag: other


title: f4_CD_Day_0_Female_Progeny

description:
Library name: f4
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: CD

tag: condition

tag: gender

tag: day

tag: group


title: 3038_20_728

description: Library name: MDX_3038_20_728_LumA_node_positive

value: breast

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 lobular 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

tag: deceased (y/n)

value: Y

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)