title: 3038_20_162

description: Library name: MDX_3038_20_162_LumB_node_negative

value: breast

tag: isolate

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

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_163

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_163_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

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: NST

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

value: LumA

tag: deceased (y/n)

value: not applicable

value: Y

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CT2KO1

city: YANGLING

first: Guohao

last: Han

address: NWAFU

country: China

institute: NWAFU

description: Library name: CT2KO1

data_processing:
Clean data were processed using fastp v0.23.2 to remove low quality score reads, sequencing adapters, and reads containing more than 10% “N”. The clean data were then mapped to the Mus musculus GRCm39 genome from Ensembl release-110 using HISAT2 v2.2.1. Gene counts and Transcripts Per Kilobase of exon model per Million mapped reads (TPMs) in each sample were calculated using StringTie v1.3.1.
Assembly: Mus musculus GRCm39 genome from Ensembl release-110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was isolated from liver samples of WT, Bmal1 KO, F, and L-Bmal1 KO mice, collected at CT2 and CT14, using a Versatile RNA Library Kit (QIAGEN, GERMANY).
The RNA samples were converted into Illumina sequencing libraries according to the TruSeq Stranded mRNA Sample Preparation Guide (Illumina, AMERICA).

tag: tissue

value: liver

tag: genotype

value: KO

tag: time point


title: CT2F2

description: Library name: CT2F2

value: F


title: 169-T2a_B2_RNA

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

country: USA

institute: Mayo Clinic

description: Library name: 169-T2a_B2_RNA

data_processing:
Illumina Casava software used for basecalling.
We aligned the reads to the NCBI Build 38 reference genome (hg38) using MAPRSeq 3.0.
Gene expression levels were obtained for 39,436 genes/transcripts annotated in the RefSeq database.
Assembly: NCBI Build 38 reference genome (hg38)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: skin

growth_protocol: Patient samples

extract_protocol:
RNA was isolated from FFPE tissue using the RNeasy FFPE kit (Qiagen) following manufacturer recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) tissue

value: skin

tag: group

value: Primary Tumor


title: 3038_20_16

description: Library name: MDX_3038_20_16_TNBC_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

value: TNBC

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CT2F1

description: Library name: CT2F1

tag: tissue

tag: genotype

tag: time point


title: 167-T2a_B2_RNA

description: Library name: 167-T2a_B2_RNA

tag: group


title: IEC, B6J wt infected, d5, Biol. Rep1

city: Aachen

first: Mathias

last: Hornef

address: Pauwelstr. 30

department: Institute for Medical Microbiology

country: Germany

institute: University Hospital RWTH Aachen

description:
Library name: Sample 3
10X genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cellranger v3.1.0
Assembly: mm10-3.0.0
Supplementary files format and content: comma-delimited Excel files for the barcodes and features files
Supplementary files format and content: matrix files

source_name: small intestine

growth_protocol: First, intestinal epithelial cells were first isolated from murine small intestinal tissue following incubations in EDTA and then single EPCAM+, CD45-, DAPI- epithelial cells were FACS sorted

extract_protocol:
GEM generation, barcoding and cDNA amplification were performed using the Chromium single cell 3’ reagent kit v2 and the Chromium controller (10x Genomics) following manufacturer's instructions
cDNA libraries were prepared using the Chromium single cell 3’ reagent kit v2 (10x Genomics)following manufacturer's instructions

treatment_protocol: 1-day-old newborn mice were orally infected with 100-200 CFUs Salmonella Typhimurium (in PBS). Small intestinal epithelial cells were isolated 4 days post-infection.

value: small intestine

tag: strain

value: wt spf

tag: cell type

value: epithelial cells

tag: age

tag: treatment

value: infected


title: 3038_20_159

description: Library name: MDX_3038_20_159_LumB_node_negative

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: 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: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 165-T2a_B2_RNA

description: Library name: 165-T2a_B2_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: IEC, B6J wt uninfected, d5, Biol. Rep1

description:
Library name: Sample 2
10X genomics

tag: strain

tag: genotype

tag: cell type

tag: age

tag: treatment

value: uninfected


title: CT14WT2

description: Library name: CT14WT2

value: liver

value: WT

tag: time point


title: 3038_20_171

description: Library name: MDX_3038_20_171_LumA_node_negative

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_158

description: Library name: MDX_3038_20_158_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 1st 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 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: Bone, lymph node, suspected lung

tag: chemotherapy (y/n)

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CT14WT3

description: Library name: CT14WT3

tag: tissue

value: liver

tag: genotype

value: WT

tag: time point


title: 3038_20_157

description: Library name: MDX_3038_20_157_LumB_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

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

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: IEC, B6J wt uninfected, d1, Biol. Rep1

description:
Library name: Sample 1
10X genomics

tag: tissue

value: small intestine

tag: strain

tag: genotype

value: wt spf

tag: cell type

value: epithelial cells

tag: age

tag: treatment

value: uninfected


title: 163-T2a_B2_RNA

description: Library name: 163-T2a_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: 171-T2a_B2_RNA

description: Library name: 171-T2a_B2_RNA


title: CT14WT1

description: Library name: CT14WT1

value: liver

tag: time point


title: 159-T2a_B2_RNA

description: Library name: 159-T2a_B2_RNA


title: 3038_20_156

description: Library name: MDX_3038_20_156_TNBC_node_negative

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: Left Breast

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: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CSCC_363_T2a_B4_RNA

description: Library name: CSCC_363_T2a_B4_RNA

tag: tissue

tag: group


title: 3038_20_15

description: Library name: MDX_3038_20_15_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: 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

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

value: Liver

value: not applicable

tag: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CT2WT3

description: Library name: CT2WT3

tag: tissue

value: liver

tag: genotype

value: WT

tag: time point


title: CT2WT2

description: Library name: CT2WT2


title: IEC, B6J wt uninfected, d10, Biol. Rep1

description:
Library name: Sample 4
10X genomics

value: small intestine

tag: strain

value: wt spf

tag: cell type

value: epithelial cells

tag: age

tag: treatment

value: uninfected


title: IEC, B6J, SPF, Uninfected, d25, Biol. Rep1

description: Library name: Sample 15

data_processing:
Sequence reads were trimmed for adapter/low quality reads using Cutadapt v4.4
Trimmed sequences were mapped to the murine genome GRCm38.102 using STAR v2.7.10a
Read count matrix was created using feaureCounts function from Rsubread v2.14.2
Assembly: GRCm38.102
Supplementary files format and content: comma-delimited Excel file including raw counts for each sample

growth_protocol: Intestinal epithelial cells were isolated from murine small intestinal tissue using EDTA.

extract_protocol:
Total RNA was isolated from small intestinal epithelial cells using TRIzol reagent following manufacturer's instructions.
cDNA libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina in combination with the NEBNext poly(A) mRNA magnetic isolation module (New England Biolabs) following manufacturer's instructions.

tag: mouse background

tag: housing condition

value: spf

value: control


title: CT2WT1

description: Library name: CT2WT1


title: IEC, B6J, SPF, Uninfected, d25, Biol. Rep3

description: Library name: Sample 17


title: IEC, B6J, SPF, Uninfected, d25, Biol. Rep2

description: Library name: Sample 16


title: 157-T2a_2_B2_RNA

description: Library name: 157-T2a_2_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: 155-T2a_B2_RNA

description: Library name: 155-T2a_B2_RNA


title: 3038_20_152

description: Library name: MDX_3038_20_152_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

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: missing

tag: histopathological tumor_type

value: NST

tag: t

value: pT 2

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

value: Y - FEC (5-fluorouracil, Epirubicin, Cyclophosphamide) und Taxotere (Docetaxel) bzw.Taxan and Radiotherapy

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_148

description: Library name: MDX_3038_20_148_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2(m)

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

value: Bone

value: not applicable

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: IEC, B6N, GF, Uninfected, d10, Biol. Rep4

description: Library name: Sample 30

tag: tissue

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

value: gf

tag: age

tag: treatment

value: control


title: IEC, B6J, SPF, Uninfected, d10, Biol. Rep1

description: Library name: Sample 12

value: spf


title: IEC, B6J, SPF, Uninfected, d10, Biol. Rep2

description: Library name: Sample 13


title: 3038_20_146

description: Library name: MDX_3038_20_146_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

value: LumB

tag: organ relapse/metastasis

value: Sternum

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

value: N

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 153-T2a_B2_RNA

description: Library name: 153-T2a_B2_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: IEC, B6N, GF, Uninfected, d10, Biol. Rep3

description: Library name: Sample 29

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

tag: age

tag: treatment


title: CSCC_304_T2b_B4_RNA

description: Library name: CSCC_304_T2b_B4_RNA


title: IEC, B6N, GF, Uninfected, d10, Biol. Rep2

description: Library name: Sample 28

value: gf

value: control


title: 151-T2a_B2_RNA

description: Library name: 151-T2a_B2_RNA


title: 3038_20_143

description: Library name: MDX_3038_20_143_TNBC_node_negative

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: IEC, B6N, GF, Uninfected, d10, Biol. Rep1

description: Library name: Sample 27

tag: tissue

tag: cell type

tag: mouse background

tag: housing condition

tag: age

tag: treatment


title: IEC, B6J, SPF, Uninfected, d5, Biol. Rep2

description: Library name: Sample 6

value: spf


title: CSCC_306_T2a_B4_RNA

description: Library name: CSCC_306_T2a_B4_RNA

tag: group


title: 3038_20_142

description: Library name: MDX_3038_20_142_LumB_node_negative

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: 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: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: IEC, B6J, SPF, Uninfected, d10, Biol. Rep3

description: Library name: Sample 14

tag: tissue

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

tag: age

tag: treatment

value: control


title: IEC, B6N, GF, Uninfected, d5, Biol. Rep4

description: Library name: Sample 26

value: gf


title: 109-T2a_B2_RNA

description: Library name: 109-T2a_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: IEC, B6J, SPF, Uninfected, d1, Biol. Rep3

description: Library name: Sample 3

value: spf


title: IEC, B6N, GF, Uninfected, d5, Biol. Rep2

description: Library name: Sample 24


title: IEC, B6N, GF, Uninfected, d5, Biol. Rep3

description: Library name: Sample 25


title: 3038_20_139_excluded_subtype

description: Library name: MDX_3038_20_139_B_excluded_subtype

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred premenopausal

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: N

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)

value: Y

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (cycles)


title: CSCC_321_T2a_B4_RNA

description: Library name: CSCC_321_T2a_B4_RNA

tag: tissue

tag: group

value: Primary Control


title: CSCC_320_T2a_B4_RNA

description: Library name: CSCC_320_T2a_B4_RNA


title: IEC, B6J, SPF, Uninfected, d1, Biol. Rep1

description: Library name: Sample 1

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

tag: age

tag: treatment

value: control


title: IEC, B6N, GF, Uninfected, d5, Biol. Rep1

description: Library name: Sample 23

value: gf


title: CSCC_322_T2b_B4_RNA

description: Library name: CSCC_322_T2b_B4_RNA

value: skin

value: Primary Tumor


title: 3038_20_139

description: Library name: MDX_3038_20_139_A_Her2_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: P

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_145

description: Library name: MDX_3038_20_145_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

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

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

value: Axillary lymph nodes, bone, liver

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

tag: chemotherapy (y/n)

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_136

description: Library name: MDX_3038_20_136_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

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: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Retroperitoneum, uterus

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: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_135

description: Library name: MDX_3038_20_135_Her2_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

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 1 c(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: Chest wall, lung

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

tag: chemotherapy (y/n)

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: B6J, SPF, d25, intestinal villus, Biol. Rep3

description: Library name: Sample 24

data_processing:
Sequence reads were trimmed for adapter/low quality reads using cutadapt v3.4
Trimmed sequences were mapped to the murine reference genome GRCm38.102 using STAR v2.7.9a
Read count matrix was created using featureCounts function from Rsubread v2.0.3
Assembly: GRCm38.102
Supplementary files format and content: comma-delimited Excel file including raw counts for each sample

extract_protocol:
Total RNA was isolated from microdissected material using RNeasy micro kit (Qiagen) following manufacturer's instructions.
Libraries were prepared using QuantSeq 3'mRNA-Seq library prep kit FWD for Illumina following manufacturer's instructions.
3'mRNA-Seq

treatment_protocol: Small intestine from 1-, 5-, 10- and 25-day-old SPF mice were isolated, rolled and snap-frozen in liquid nitrogen. 10µm-thick cryosections were stained with cresyl violet and 1 to 2 million µm² crypts or villi were microdissected.

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: age

tag: localization

value: villus


title: B6J, SPF, d25, intestinal villus, Biol. Rep2

description: Library name: Sample 23


title: IEC, B6N, GF, Uninfected, d1, Biol. Rep3

description: Library name: Sample 21

tag: cell type

value: epithelial cells

tag: housing condition

value: gf

tag: treatment

value: control


title: 101-T2a_B2_RNA

description: Library name: 101-T2a_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: 3038_20_140

description: Library name: MDX_3038_20_140_LumB_node_positive

tag: isolate

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

value: male

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Brain

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: IEC, B6J, SPF, Uninfected, d1, Biol. Rep2

description: Library name: Sample 2

tag: tissue

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

value: spf

tag: age

tag: treatment


title: 3038_20_127

description: Library name: MDX_3038_20_127_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

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

tag: chemotherapy (y/n)

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: IEC, B6N, GF, Uninfected, d1, Biol. Rep1

description: Library name: Sample 19

tag: tissue

tag: cell type

tag: mouse background

tag: housing condition

value: gf

tag: age

tag: treatment

value: control


title: B6J, SPF, d25, intestinal crypt, Biol. Rep3

description: Library name: Sample 21

value: C57Bl/6J wt spf

tag: localization

value: crypt


title: 097-T2a_B2_RNA

description: Library name: 097-T2a_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: B6J, SPF, d25, intestinal crypt, Biol. Rep2

description: Library name: Sample 20

value: small intestine


title: B6J, SPF, d25, intestinal villus, Biol. Rep1

description: Library name: Sample 22

value: villus


title: 3038_20_126

description: Library name: MDX_3038_20_126_LumB_node_positive

value: breast

tag: isolate

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

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)

value: N

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CSCC_303_T2a_B4_RNA

description: Library name: CSCC_303_T2a_B4_RNA

tag: tissue

tag: group

value: Primary Control


title: 3038_20_119

description: Library name: MDX_3038_20_119_LumA_node_negative

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

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: LumA

tag: deceased (y/n)

value: not applicable

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

tag: chemotherapy (y/n)

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: IEC, B6N, GF, Uninfected, d1, Biol. Rep4

description: Library name: Sample 22

tag: tissue

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

value: gf

tag: age

tag: treatment

value: control


title: CSCC_302_T2a_B4_RNA

description: Library name: CSCC_302_T2a_B4_RNA

value: skin

tag: group

value: Primary Tumor


title: IEC, B6J, SPF, Salmonella, d5, Biol. Rep2

description: Library name: Sample 10

value: spf

value: infected


title: B6J, SPF, d10, intestinal villus, Biol. Rep3

description: Library name: Sample 18

value: C57Bl/6J wt spf

tag: localization

value: villus


title: IEC, B6J, SPF, Salmonella, d5, Biol. Rep1

description: Library name: Sample 9


title: B6J, SPF, d25, intestinal crypt, Biol. Rep1

description: Library name: Sample 19

value: crypt


title: CSCC_53C_RNA

description: Library name: CSCC_53C_RNA

value: Primary Control


title: 3038_20_134

description: Library name: MDX_3038_20_134_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st 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

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

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: IEC, B6N, GF, Uninfected, d1, Biol. Rep2

description: Library name: Sample 20

tag: tissue

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

value: gf

tag: age

tag: treatment

value: control


title: B6J, SPF, d10, intestinal villus, Biol. Rep2

description: Library name: Sample 17

value: C57Bl/6J wt spf

tag: localization

value: villus


title: IEC, B6J, SPF, Uninfected, d5, Biol. Rep4

description: Library name: Sample 8

value: spf


title: CSCC_310_T2a_B4_RNA

description: Library name: CSCC_310_T2a_B4_RNA

value: skin

tag: group

value: Primary Tumor


title: CSCC_52_RNA

description: Library name: CSCC_52_RNA


title: 3038_20_115

description: Library name: MDX_3038_20_115_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd 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

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: LumA

tag: deceased (y/n)

value: Y

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_114

description: Library name: MDX_3038_20_114_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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: Bone, brain

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J, SPF, Uninfected, d1, Biol. Rep4

description: Library name: Sample 4

tag: tissue

value: small intestine

tag: cell type

value: epithelial cells

tag: mouse background

tag: housing condition

value: spf

tag: age

tag: treatment

value: control


title: B6J, SPF, d10, intestinal villus, Biol. Rep1

description: Library name: Sample 16

value: C57Bl/6J wt spf

tag: localization

value: villus


title: CSCC_48_RNA

description: Library name: CSCC_48_RNA

value: skin

tag: group

value: Primary Tumor


title: IEC, B6J, SPF, Salmonella, d5, Biol. Rep3

description: Library name: Sample 11

value: infected


title: CSCC_42T_RNA

description: Library name: CSCC_42T_RNA


title: 3038_20_118

description: Library name: MDX_3038_20_118_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

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

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_111

description: Library name: MDX_3038_20_111_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Tubular carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J wt SPF, d25, distal, Biol. Rep3

description:
Library name: Sample 36
dist_d25_5

data_processing:
Sequence reads were trimmed for adapter/low quality reads using Cutadapt v4.4
Trimmed sequences were mapped to the murine genome GRCm38.102 using STAR v2.7.10a
Read count matrix was created using feaureCounts function from Rsubread v2.16
Assembly: GRCm38.102
Supplementary files format and content: comma-delimited Excel file including raw counts for each sample

growth_protocol: Intestinal epithelial cells were isolated from murine small intestinal tissue using EDTA

extract_protocol:
Total RNA was isolated from small intestinal epithelial cells using TRIzol reagent following manufacturer's instructions
cDNA libraries were prepared using the NEBNext ultra II directional RNA library kit for Illumina in combination with the NEBNext poly(A) mRNA magnetic isolation module (New England Biolabs) following manufacturer's instructions

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: distal


title: IEC, B6J wt SPF, d25, distal, Biol. Rep2

description:
Library name: Sample 35
dist_d25_4


title: CSCC_42C_RNA

description: Library name: CSCC_42C_RNA

value: skin

tag: group

value: Primary Control


title: B6J, SPF, d10, intestinal crypt, Biol. Rep1

description: Library name: Sample 13

value: crypt


title: B6J, SPF, d10, intestinal crypt, Biol. Rep3

description: Library name: Sample 15


title: B6J, SPF, d5, intestinal villus, Biol. Rep3

description: Library name: Sample 12

value: villus


title: 3038_20_106

description: Library name: MDX_3038_20_106_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

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: Invasive ductal carcinoma

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

value: LumA

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_104

description: Library name: MDX_3038_20_104_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

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: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CSCC_39T_RNA

description: Library name: CSCC_39T_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: IEC, B6J wt SPF, d25, distal, Biol. Rep1

description:
Library name: Sample 34
dist_d25_2

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: distal


title: IEC, B6J wt SPF, d25, medial, Biol. Rep3

description:
Library name: Sample 33
med_d25_5

value: medial


title: CSCC_39C_RNA

description: Library name: CSCC_39C_RNA

value: Primary Control


title: 3038_20_103

description: Library name: MDX_3038_20_103_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

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: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: LumA

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Suspected tibial metastasis, bone, brain, liver, bone marrow

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: B6J, SPF, d5, intestinal villus, Biol. Rep2

description: Library name: Sample 11

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: age

tag: localization

value: villus


title: IEC, B6J wt SPF, d25, medial, Biol. Rep2

description:
Library name: Sample 32
med_d25_4

tag: cell type

value: epithelial cells

value: medial


title: CSCC_30C_RNA

description: Library name: CSCC_30C_RNA

value: skin

tag: group

value: Primary Control


title: IEC, B6J, SPF, Uninfected, d5, Biol. Rep3

description: Library name: Sample 7

tag: housing condition

value: spf

tag: treatment

value: control


title: 3038_20_1

description: Library name: MDX_3038_20_1_TNBC_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st 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 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

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: IEC, B6J wt SPF, d25, medial, Biol. Rep1

description:
Library name: Sample 31
med_d25_2

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: medial


title: B6J, SPF, d5, intestinal villus, Biol. Rep1

description: Library name: Sample 10

value: villus


title: CSCC_29_RNA

description: Library name: CSCC_29_RNA

value: skin

tag: group

value: Primary Tumor


title: B6J, SPF, d10, intestinal crypt, Biol. Rep2

description: Library name: Sample 14

value: crypt


title: IEC, B6J wt SPF, d25, proximal, Biol. Rep3

description:
Library name: Sample 30
prox_d25_5

value: proximal


title: 3038_20_11

description: Library name: MDX_3038_20_11_TNBC_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 22G_1930_healthy

description: Library name: MDX_22G_1930_healthy

tag: tissue

tag: isolate

value: healthy individual

tag: age

tag: biomaterial provider

value: Precision for Medicine

tag: geo loc_name

value: missing

tag: Sex

tag: sample category

value: true healthy samples

tag: menopausal status

tag: histopathological tumor_type

value: healthy

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: progression free_survival_(months)

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

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)


title: 22G_1916_healthy

description: Library name: MDX_22G_1916_healthy

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: 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: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CSCC_28C_RNA

description: Library name: CSCC_28C_RNA

tag: tissue

value: skin

tag: group

value: Primary Control


title: B6J, SPF, d5, intestinal crypt, Biol. Rep3

description: Library name: Sample 9

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: age

tag: localization

value: crypt


title: IEC, B6J wt SPF, d25, proximal, Biol. Rep2

description:
Library name: Sample 29
prox_d25_4

tag: cell type

value: epithelial cells

value: proximal


title: B6J, SPF, d5, intestinal crypt, Biol. Rep2

description: Library name: Sample 8


title: CSCC_27_RNA

description: Library name: CSCC_27_RNA

value: Primary Tumor


title: 22G_1905_healthy

description: Library name: MDX_22G_1905_healthy

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: 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: progression free_survival_(months)

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

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)


title: B6J, SPF, d5, intestinal crypt, Biol. Rep1

description: Library name: Sample 7

tag: tissue

tag: mouse background

tag: age

tag: localization


title: CSCC_24_RNA

description: Library name: CSCC_24_RNA

tag: group


title: IEC, B6J wt SPF, d10, distal, Biol. Rep3

description:
Library name: Sample 27
dist_d10_3

tag: cell type

value: distal


title: IEC, B6J wt SPF, d25, proximal, Biol. Rep1

description:
Library name: Sample 28
prox_d25_2


title: B6J, SPF, d1, intestinal villus, Biol. Rep2

description: Library name: Sample 5

value: villus


title: B6J, SPF, d1, intestinal villus, Biol. Rep3

description: Library name: Sample 6


title: 22G_1894_healthy

description: Library name: MDX_22G_1894_healthy

tag: isolate

value: healthy individual

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: not applicable

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CSCC_23_RNA

description: Library name: CSCC_23_RNA

tag: tissue

tag: group


title: IEC, B6J wt SPF, d10, distal, Biol. Rep2

description:
Library name: Sample 26
dist_d10_2

tag: mouse background

tag: cell type

tag: age

tag: localization


title: 22G_12522_healthy

description: Library name: MDX_22G_12522_healthy

tag: isolate

tag: biomaterial provider

value: Precision for Medicine

tag: geo loc_name

value: missing

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: progression free_survival_(months)

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

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)


title: CSCC_18_RNA

description: Library name: CSCC_18_RNA

tag: tissue

tag: group


title: B6J, SPF, d1, intestinal villus, Biol. Rep1

description: Library name: Sample 4

tag: mouse background

tag: age

tag: localization


title: IEC, B6J wt SPF, d10, distal, Biol. Rep1

description:
Library name: Sample 25
dist_d10_1

tag: cell type


title: 22G_12520_healthy

description: Library name: MDX_22G_12520_healthy

tag: isolate

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: true healthy samples

tag: menopausal status

tag: histopathological tumor_type

value: healthy

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CSCC_19_RNA

description: Library name: CSCC_19_RNA

tag: tissue

value: skin

tag: group

value: Primary Control


title: CSCC_17_RNA

description: Library name: CSCC_17_RNA


title: 22G_12375_healthy

description: Library name: MDX_22G_12375_healthy

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: progression free_survival_(months)

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

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)


title: IEC, B6J wt SPF, d10, medial, Biol. Rep2

description:
Library name: Sample 23
med_d10_2

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

tag: age

tag: localization

value: medial


title: 21G_19879_healthy

description: Library name: MDX_21G_19879_healthy

tag: isolate

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: B6J, SPF, d1, intestinal crypt, Biol. Rep3

description: Library name: Sample 3

tag: tissue

tag: mouse background

tag: age

tag: localization

value: crypt


title: IEC, B6J wt SPF, d10, medial, Biol. Rep1

description:
Library name: Sample 22
med_d10_1

tag: cell type

value: epithelial cells


title: IEC, B6J wt SPF, d10, medial, Biol. Rep3

description:
Library name: Sample 24
med_d10_3


title: B6J, SPF, d1, intestinal crypt, Biol. Rep2

description: Library name: Sample 2


title: 22G_1898_healthy

description: Library name: MDX_22G_1898_healthy

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: progression free_survival_(months)

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

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)


title: CSCC_16_RNA

description: Library name: CSCC_16_RNA

tag: tissue

tag: group

value: Primary Tumor


title: CSCC_323_T2b_B4_RNA

description: Library name: CSCC_323_T2b_B4_RNA


title: CSCC_15_RNA

description: Library name: CSCC_15_RNA


title: 5xFADiPKR_rep4

city: New York

first: Anna

last: Flury

state: NY

address: 85 St Nicholas Terrace

institute: CUNY Graduate Center

description: RNA-seq

data_processing:
Quality control was performed on raw sequencing reads with Trim Galore
Reads were aligned to the mouse genome (mm10) with HISAT2 (version 2.2.1) using default parameters
featureCounts (version 2.0.3) was used to obtain the raw read counts per gene against the mm10 GENCODE annotation
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts per gene per sample
Supplementary files format and content: tab-delimited file includes RPKM values for each gene per sample

source_name: cortex

growth_protocol: not applicable

extract_protocol:
The brain tissue was thawed in an ice-cold  glass homogenizer containing 1 mL cell-lysis buffer. After manually homogenizing the samples with 3-5 gentle strokes, samples were  homogenized in a motor-driven overhead stirrer. A post-nuclear supernatant was prepared by centrifugation. Post-mitochondrial supernatant was prepared by centrifugation after NP40 and DHPC treatment. GFP-antibod-coated beads were added to each supernatant. After overnight incubation, the polysome-bound beads were washed with the high-salt buffer. RNA clean-up was performed using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
libraries were constructed using SMART-Seq® mRNA LP (Takara, 634768), multiplexed using Unique Dual Index Kit 1–96 (Takara, 634752), and size-selected using NucleoMag® NGS Clean-up and Size Select beads (Takara 744970.5) as per the manufacturer’s recommendations.

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.
VEGF/vehicle treatment: Vehicle-treated animals received an intraperitoneal VEGF administration followed by 1:9 DMSO:PEG300 at 10ml/kg. In iPKR mice, treatment started at 4-5 months of age.

value: cortex

tag: age (months)

tag: Sex

value: F

tag: batch

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: CSCC_14_RNA

description: Library name: CSCC_14_RNA


title: 5xFADiPKR_rep3

description: RNA-seq


title: 08T9

description: Library name: MDX_08T9_LumA

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Mixed infiltrating carcinoma (ductal and lobular)

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J wt SPF, d10, proximal, Biol. Rep2

description:
Library name: Sample 20
prox_d10_2

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: proximal


title: IEC, B6J wt SPF, d10, proximal, Biol. Rep3

description:
Library name: Sample 21
prox_d10_3


title: CSCC_13_RNA

description: Library name: CSCC_13_RNA

value: skin

tag: group

value: Primary Control


title: 08T8

description: Library name: MDX_08T8_LumA

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: missing

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: 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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)


title: IEC, B6J wt SPF, d10, proximal, Biol. Rep1

description:
Library name: Sample 19
prox_d10_1

tag: tissue

tag: mouse background

tag: cell type

tag: age

tag: localization


title: CSCC_12_RNA

description: Library name: CSCC_12_RNA

tag: group

value: Primary Tumor


title: 09T1

description: Library name: MDX_09T1_LumA

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

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)

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: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: 5xFADiPKR_rep2

description: RNA-seq

tag: tissue

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: B6J, SPF, d1, intestinal crypt, Biol. Rep1

description: Library name: Sample 1

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: age

tag: localization

value: crypt


title: 5xFADiPKR_rep1

description: RNA-seq

value: F


title: CSCC_10T_RNA

description: Library name: CSCC_10T_RNA

value: skin

tag: group


title: 08T6

description: Library name: MDX_08T6_LumA

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

value: missing

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: paclitaxel (abraxane)_(cycles)


title: iPKR_ASV_rep5

description: RNA-seq

tag: tissue

tag: age (months)

tag: Sex

tag: batch

tag: cell type

tag: genotype

tag: treatment


title: IEC, B6J wt SPF, d5, distal, Biol. Rep2

description:
Library name: Sample 17
dist_d5_2

tag: mouse background

value: epithelial cells

tag: age

tag: localization

value: distal


title: IEC, B6J wt SPF, d5, distal, Biol. Rep3

description:
Library name: Sample 18
dist_d5_3


title: CSCC_10C_RNA

description: Library name: CSCC_10C_RNA

tag: group

value: Primary Control


title: 08T5

description: Library name: MDX_08T5_LumA

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J wt SPF, d5, distal, Biol. Rep1

description:
Library name: Sample 16
dist_d5_1

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

tag: age

tag: localization


title: iPKR_ASV_rep3

description: RNA-seq

value: cortex

tag: age (months)

tag: Sex

value: F

tag: batch

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: 08T4

description: Library name: MDX_08T4_LumA

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

value: missing

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

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: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: paclitaxel (abraxane)_(cycles)


title: CSCC_8_RNA

description: Library name: CSCC_8_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: CSCC_9_RNA

description: Library name: CSCC_9_RNA

value: Primary Control


title: 08T7

description: Library name: MDX_08T7_LumA

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: ec, ec-t,_etc

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: 08T3

description: Library name: MDX_08T3_LumA

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

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er 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: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: paclitaxel (abraxane)_(cycles)


title: IEC, B6J wt SPF, d5, medial, Biol. Rep2

description:
Library name: Sample 14
med_d5_2

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: medial


title: iPKR_ASV_rep2

description: RNA-seq

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: 08T2

description: Library name: MDX_08T2_LumA

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

value: missing

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Mixed infiltrating carcinoma (ductal and lobular)

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: 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: ec, ec-t,_etc

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J wt SPF, d5, medial, Biol. Rep1

description:
Library name: Sample 13
med_d5_1

tag: tissue

tag: mouse background

tag: cell type

tag: age

tag: localization


title: iPKR_ASV_rep1

description: RNA-seq

tag: age (months)

tag: Sex

tag: batch

tag: genotype

tag: treatment


title: CSCC_6_RNA

description: Library name: CSCC_6_RNA

value: skin

tag: group

value: Primary Tumor


title: IEC, B6J wt SPF, d5, proximal, Biol. Rep3

description:
Library name: Sample 12
prox_d5_3

value: small intestine

value: proximal


title: CSCC_5_RNA

description: Library name: CSCC_5_RNA

value: Primary Control


title: 08T15

description: Library name: MDX_08T15_Her2

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

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)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: paclitaxel (abraxane)_(cycles)


title: Control_iPKR_vehicle_rep2

description: RNA-seq

tag: tissue

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/PEG:DMSO


title: CSCC_4_RNA

description: Library name: CSCC_4_RNA

tag: group


title: IEC, B6J wt SPF, d5, proximal, Biol. Rep1

description:
Library name: Sample 10
prox_d5_1

tag: mouse background

value: C57Bl/6J wt spf

value: epithelial cells

tag: age

tag: localization


title: CSCC_7_RNA

description: Library name: CSCC_7_RNA

value: skin


title: IEC, B6J wt SPF, d5, proximal, Biol. Rep2

description:
Library name: Sample 11
prox_d5_2


title: 08T13

description: Library name: MDX_08T13_LumA

value: breast

tag: isolate

tag: biomaterial provider

tag: geo loc_name

value: missing

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: 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: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J wt SPF, d5, medial, Biol. Rep3

description:
Library name: Sample 15
med_d5_3

tag: tissue

value: small intestine

tag: mouse background

tag: cell type

tag: age

tag: localization

value: medial


title: 08T16

description: Library name: MDX_08T16_LumA

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: 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: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

tag: paclitaxel (abraxane)_(cycles)


title: Control_iPKR_vehicle_rep4

description: RNA-seq

tag: tissue

value: cortex

tag: age (months)

tag: Sex

value: F

tag: batch

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/PEG:DMSO


title: Eif2ATRAP_rep4

description: RNA-seq

value: tamoxifen


title: 08T12

description: Library name: MDX_08T12_LumA

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: missing

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

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

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

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

tag: taxol (y/n)

tag: taxol dosage


title: IEC, B6J wt SPF, d1, distal, Biol. Rep3

description:
Library name: Sample 9
dist_d1_3

tag: tissue

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: distal


title: iPKR_ASV_rep4

description: RNA-seq

tag: age (months)

tag: Sex

value: M

tag: batch

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: IEC, B6J, SPF, Uninfected, d5, Biol. Rep1

description: Library name: Sample 5

tag: housing condition

value: spf

value: control


title: IEC, B6J wt SPF, d1, distal, Biol. Rep2

description:
Library name: Sample 8
dist_d1_2


title: Control_iPKR_vehicle_rep3

description: RNA-seq

value: cortex


title: Eif2ATRAP_rep3

description: RNA-seq

value: microglia


title: Sdr5a2 kd - stress biol rep 4

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
10X genomics
21225X20

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1)
Assembly: R_norvegicus_Mar_2012
Supplementary files format and content: csv - counts and metadata - xlsx

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Dissected prefrontal cortex was flash frozen in LN2 and preserved at -80C until processing. The specimens were gently thawed in 2 ml of ice-cold phosphate-buffered saline (PBS, devoid of Ca2+ and Mg2+). This solution was supplemented with various compounds to preserve the quality of the sample: 0.54 μM Nectostatin (Inc. #J65341, ThermoFisher Scientific Chemicals, Waltham, MA), 1 μM HPN-07 (SML2163, Sigma-Aldrich), 0.32 μM sodium hydroxybutyrate (A1161314, ThermoFisher Scientific Chemicals), 78 nM Q-VD-Oph (SML0063, Sigma-Aldrich), and 0.2 U/ml of Ribolock RNase inhibitor (EO0381, Life Technologies Corporation, Carlsbad, CA). The tissue, held over dry ice in a 60-mm Petri dish, was methodically minced into fragments smaller than 2 mm using a razor blade. Subsequently, this tissue was transitioned to a 2 ml Dounce homogenizer containing 1.5 ml of nuclei extraction buffer (130-128-024, Miltenyi Biotec, Bergisch Gladbach, Germany) along with 0.2 U/ml Ribolock RNase inhibitor.  Samples were then centrifuged at 600×g for 5 min, resuspended in 400 μL of PBS enriched with 2% BSA, passed through a 70-μm FLOWMI for clarification, and strained via a 40-μm FLOWMI. Specimens were then entrusted to the Hunstman Cancer Institute High Throughput Genomics Core for 10X Genomics library construction and sequencing.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing (these six samples were sequenced on a lane of an S4 flowcell).

treatment_protocol: Stress was introduced with the forced swim test. Rats were plunged individually into a vertical plexiglass cylinder (diameter: 30 cm; height: 45.7 cm) containing 30 cm of water maintained at 25°C. After 10 min in the cylinder, they were removed and allowed to dry for 15 min in a heated enclosure (32°C) before being returned to their cages. Environmental light was kept at 300 lux. Animals were video recorded, and the latency to immobility (s) and the duration of immobility (s) during the first 5 minutes were measured. When the FST was used as an acute stress paradigm, animals were sacrificed immediately or 30 minutes after the test.

value: brain

tag: brain region

value: prefrontal cortex

value: Srd5a2 knockdown

value: stress


title: Sdr5a2 kd - stress biol rep 3

description:
10X genomics
21225X19


title: IEC, B6J wt SPF, d1, distal, Biol. Rep1

description:
Library name: Sample 7
dist_d1_1


title: 08T1_D_excluded_subtype

description: Library name: MDX_08T1_D_excluded_subtype

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

value: missing

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: paclitaxel (abraxane)_(cycles)


title: KON_siLINC02154

type: RNA

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: KON cells with LINC02154 siRNA

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

source_name: KON cells

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: KON cells were cultured in RPMI 1640 medium with 10% fetal bovine serum at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: KON cells were transfected with  DsiRNA targeting LINC02154 or a  negative control DsiRNA (Integrated DNA Technologies Inc.).

tag: sirna

value: LINC02154 siRNA

tag: cell line

value: KON


title: Eif2ATRAP_rep2

description: RNA-seq

tag: tissue

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

tag: cell type

tag: genotype

tag: treatment

value: tamoxifen


title: KON_siCtrl

description: KON cells with control siRNA

value: control siRNA


title: Sdr5a2 kd - stress biol rep 2

description:
10X genomics
21225X18

value: brain

tag: brain region

value: prefrontal cortex

value: Srd5a2 knockdown


title: 08T1_B_excluded_subtype

description: Library name: MDX_08T1_B_excluded_subtype

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

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

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

tag: taxol (y/n)


title: Sdr5a2 kd - stress biol rep 1

description:
10X genomics
21225X17

tag: tissue

tag: brain region

tag: genotype

tag: treatment

value: stress


title: IEC, B6J wt SPF, d1, medial, Biol. Rep2

description:
Library name: Sample 5
med_d1_2

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization

value: medial


title: Eif2ATRAP_rep1

description: RNA-seq

tag: age (months)

tag: Sex

value: F

tag: batch

value: microglia


title: 5xFADEif2ATRAP_rep3

description: RNA-seq

value: cortex

value: M


title: 08T1_A_excluded_subtype

description: Library name: MDX_08T1_A_excluded_subtype

tag: isolate

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

value: missing

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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

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: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: paclitaxel (abraxane)_(cycles)


title: Sdr5a2 knockdown biol rep 5

description:
10X genomics
21225X15

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: genotype

value: Srd5a2 knockdown

tag: treatment

value: control


title: IEC, B6J wt SPF, d1, medial, Biol. Rep1

description:
Library name: Sample 4
med_d1_1

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

tag: cell type

value: epithelial cells

tag: age

tag: localization


title: IEC, B6J wt SPF, d1, proximal, Biol. Rep3

description:
Library name: Sample 3
prox_d1_3

value: proximal


title: 5xFADEif2ATRAP_rep2

description: RNA-seq

value: cortex

tag: age (months)

tag: Sex

tag: batch

value: microglia

value: tamoxifen


title: Sdr5a2 knockdown biol rep 4

description:
10X genomics
21225X14


title: 07T8

description: Library name: MDX_07T8_LumB

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

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)

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: docetaxel (taxotere,_taxan)_(cycles)

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

tag: taxol (y/n)

tag: taxol dosage


title: 08T10

description: Library name: MDX_08T10_LumA

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: missing

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: 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: tc

tag: other

tag: taxane (y/n)

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

tag: paclitaxel (abraxane)_(cycles)


title: 5xFADEif2ATRAP_rep1

description: RNA-seq

tag: tissue

tag: age (months)

tag: Sex

value: F

tag: batch

tag: cell type

tag: genotype

tag: treatment


title: IEC, B6J wt SPF, d1, proximal, Biol. Rep2

description:
Library name: Sample 2
prox_d1_2

value: small intestine

tag: mouse background

value: C57Bl/6J wt spf

value: epithelial cells

tag: age

tag: localization

value: proximal


title: Sdr5a2 knockdown biol rep 3

description:
10X genomics
21225X13

value: brain

tag: brain region

value: prefrontal cortex

value: Srd5a2 knockdown

value: control


title: 07T7_healthy

description: Library name: MDX_07T7_healthy

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: hospital (Malaga)

tag: geo loc_name

value: Spain

tag: sample category

value: no tumor

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive tubular carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

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

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

tag: taxol (y/n)


title: 5xFADTRAP_rep4

description: RNA-seq

tag: tissue

value: cortex

tag: age (months)

tag: Sex

value: M

tag: batch

tag: cell type

value: microglia

tag: genotype

tag: treatment

value: tamoxifen and VEGF/ASV


title: Sdr5a2 knockdown biol rep 2

description:
10X genomics
21225X12

tag: brain region