title: 3038_20_436

description: Library name: MDX_3038_20_436_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_428

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_428_LumA_node_negative

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: breast

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

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Papillary carcinoma

tag: t

value: pT 1 a(m)

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

value: Y

tag: organ relapse/metastasis

value: Bone, liver, cervical lymph node, lung

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_430

description: Library name: MDX_3038_20_430_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: taxol dosage

tag: anthracycline (y/n)


title: CLL_138, Chronic lymphocytic Leukemia;  biological replicate

type: RNA

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

country: USA

institute: University of Michigan

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

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

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

label: biotin

source_name: CD19+ cells sorted from human PBMCs

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

growth_protocol: no additional ex vivo growth or culture

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

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

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_424

description: Library name: MDX_3038_20_424_LumA_node_positive

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 postmenopausal

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

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: Bone, pleura

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: OSC_ovo_48h_rep1 (RNA-seq)

city: Cambridge

first: Azad

last: Alizada

state: Cambridgeshire

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description:
OSC_ovo_48h_rep1
OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
OSC_ovo_48h_merged_rpkm_forward.bw
OSC_ovo_48h_merged_rpkm_reverse.bw

data_processing:
The reads were trimmed of adapter sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT using Cutadapt tool (v1.18; -m 1 specified to not have reads trimmed to zero).
The trimmed reads were aligned to the genome assemblies using the RNA-seq aligner STAR (v2.7.3a).
Gene counts were calculated with the featureCounts tool (Subread package v1.5.3; -s 2 for stranded libraries prepared by dUTP method). D. mel gene annotations were taken from Drosophila_melanogaster.BDGP6.28.100.gtf in the Ensembl genome database.
Differential gene expression analysis was performed using DESeq2 (v1.30.1) package.
The RPKM normalized bigWig files were generated for each strand using bamCoverage tool (--filterRNAstrand specified for dUTP stranded libraries) in deepTools (v3.5.1).
Assembly: dm6
Supplementary files format and content: tab-delimited text files showing DESeq2-normalized gene counts for each sample
Supplementary files format and content: tab-delimited text files for differential RNA-seq analysis showing DESeq2-computed fold-change values between the contrasted samples
Supplementary files format and content: RPKM-normalized bigWig files for each sample (separate files for forward and reverse strands) and RPKM-normalized bigWig files of merged biological replicates (separate files for forward and reverse strands)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: Cells were cultured at 26 °C in Shields and Sang M3 Insect Medium supplemented with 10% fetal bovine serum, 10% fly extract (purchased from DGRC), 0.6 mg/mL glutathione, and 10 mU/mL human insulin

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Cat. No. 74106, QIAGEN) with RNase-Free DNase Set (Cat. No. 79254, QIAGEN) for DNase digestion during RNA purification as per manufacturer’s instruction. Reverse transcription was performed with 100 ng to 1 µg RNA using SuperScript™ IV Reverse Transcriptase (Cat. No. 18090010, Thermo Fisher Scientific).
For total RNA-seq, ribosomal depletion was performed using riboPOOLs (siTOOLs Biotech) for Drosophila melanogaster (Cambridge Bioscience) using 500 ng of total RNA as input. For mRNA-seq, poly(A) selection was done using Poly(A) mRNA Magnetic Isolation Module (NEB # E7490) with 500 ng of total RNA as input. Libraries were prepared using The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (#E7420L). Library quality was assessed using Agilent 2100 bioanalyzer (High Sensitivity DNA Kit).

treatment_protocol: The Ovo overexpression constructs (treatment) or the empty vector (control) were transfected into cells with Nucleofector Kit V (VVCA-1003, Lonza) using NucleofectorTM 2b Device (Lonza).

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: wild type

tag: treatment

value: Ovo overexpression 48 hours

tag: Sex


title: vasGFPminus_rep3 (RNA-seq)

description:
GFP_minus_rep3
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_normalized_counts.txt
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_fold_changes.txt
vasGFP-_merged_rpkm_forward.bw
vasGFP-_merged_rpkm_reverse.bw

source_name: ovary

growth_protocol: Flies were kept at 25°C on standard cornmeal food or propionic food.

treatment_protocol: Flies were fed with yeast extract 2-3 days before the dissections. Ovaries from the transgenic vas-GFP flies were dissected in ice-cold PBS and cells were dissociated using 5 mg/mL trypsin and 2.5 mg/mL collagenase-A in Ringer's solution (600 µL for 148 ovaries) for 1 hr. at 800 rpm (30°C) in a thermomixer and passed through a 100μm cell strainer followed by addition of 400 µL of Schneider's Medium (Gibco™) containing 10% FBS and centrifuged at 500 g (4°C) for 5 min. The supernatant was discarded and 600 µL of PBS was added to the pellet to wash cells by centrifugation at 500 g (4°C) for 5 min. The cells were resuspended in 500 µL PBS and sorted into GFP-positive and GFP-negative populations using FACS Aria cell sorter (BD Biosciences).

tag: tissue

value: ovary

value: somatic cells (ovary)

value: FACS-sorted vas-GFP_negative

tag: strain

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]

tag: strain source

value: vas-EGFP fly strain obtained from Bloomington Drosophila Stock Center (# 76126)


title: 3038_20_423

description: Library name: MDX_3038_20_423_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

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

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: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_415

description: Library name: MDX_3038_20_415_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

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

value: LumB

value: not applicable

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: 3038_20_429

description: Library name: MDX_3038_20_429_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

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: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Ovary

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: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_425

description: Library name: MDX_3038_20_425_LumB_node_negative

tag: tissue

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

tag: histopathological tumor_type

value: Apocrine carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: OSC_ovo_48h_rep2 (RNA-seq)

description:
OSC_ovo_48h_rep2
OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
OSC_ovo_48h_merged_rpkm_forward.bw
OSC_ovo_48h_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: wild type

tag: treatment

value: Ovo overexpression 48 hours

tag: Sex


title: 3038_20_418

description: Library name: MDX_3038_20_418_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma, Invasive lobular carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

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: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_130, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

value: normal

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_419

description: Library name: MDX_3038_20_419_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

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

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: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_132, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

tag: tissue

tag: disease state


title: s3_CD_Female_mother

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description:
Library name: s3
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

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

source_name: whole organism

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

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

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

value: Female

tag: day

tag: group


title: vasGFPminus_rep1 (RNA-seq)

description:
GFP_minus_rep1
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_normalized_counts.txt
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_fold_changes.txt
vasGFP-_merged_rpkm_forward.bw
vasGFP-_merged_rpkm_reverse.bw

value: ovary

value: somatic cells (ovary)

tag: treatment

value: FACS-sorted vas-GFP_negative

tag: Sex

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]

tag: strain source

value: vas-EGFP fly strain obtained from Bloomington Drosophila Stock Center (# 76126)


title: 3038_20_414

description: Library name: MDX_3038_20_414_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_411

description: Library name: MDX_3038_20_411_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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


title: CLL_146, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_123, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: M


title: CLL_115, Chronic lymphocytic Leukemia;  biological replicate

value: normal


title: 3038_20_410

description: Library name: MDX_3038_20_410_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: missing

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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

value: not applicable

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_122, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

tag: snp 6.0 genomic lesion total

tag: cell type

tag: tissue

tag: disease state


title: vasGFPplus_rep3 (RNA-seq)

description:
GFP_plus_rep3
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_normalized_counts.txt
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_fold_changes.txt
vasGFP+_merged_rpkm_forward.bw
vasGFP+_merged_rpkm_reverse.bw

value: ovary

value: germline cells (ovary)

tag: treatment

value: FACS-sorted vas-GFP_positive

tag: Sex

tag: strain

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]

tag: strain source

value: vas-EGFP fly strain obtained from Bloomington Drosophila Stock Center (# 76126)


title: 3038_20_406

description: Library name: MDX_3038_20_406_TNBC_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Metaplastic carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

value: weekly? 2x


title: vasGFPminus_rep2 (RNA-seq)

description:
GFP_minus_rep2
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_normalized_counts.txt
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_fold_changes.txt
vasGFP-_merged_rpkm_forward.bw
vasGFP-_merged_rpkm_reverse.bw

tag: tissue

tag: cell type

value: somatic cells (ovary)

tag: treatment

value: FACS-sorted vas-GFP_negative

tag: Sex

value: female

tag: strain

tag: strain source


title: 3038_20_401

description: Library name: MDX_3038_20_401_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

tag: menopausal status

value: missing

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)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_111, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

value: normal

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: vasGFPplus_rep2 (RNA-seq)

description:
GFP_plus_rep2
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_normalized_counts.txt
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_fold_changes.txt
vasGFP+_merged_rpkm_forward.bw
vasGFP+_merged_rpkm_reverse.bw

value: ovary

value: germline cells (ovary)

tag: treatment

value: FACS-sorted vas-GFP_positive

tag: Sex

value: female

tag: strain

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]

tag: strain source

value: vas-EGFP fly strain obtained from Bloomington Drosophila Stock Center (# 76126)


title: 3038_20_4

description: Library name: MDX_3038_20_4_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

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 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)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Bone, lymph node

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: 3038_20_394

description: Library name: MDX_3038_20_394_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: ac, ac-t,_tac

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_391

description: Library name: MDX_3038_20_391_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: LumA

value: Bone

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_395

description: Library name: MDX_3038_20_395_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

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

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Bone, liver

tag: incidence of_other_tumorous_disease

tag: ac, ac-t,_tac

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: fGSOSS_rep4 (RNA-seq)

description:
fGSOSS_rep4
cell_lines_Deseq2_normalized_counts.txt
fGSOSS_vs_OSC_Deseq2_fold_changes.txt
fGSOSS_merged_rpkm_forward.bw
fGSOSS_merged_rpkm_reverse.bw

source_name: fGS/OSS

growth_protocol: Cells were cultured at 26 °C in Shields and Sang M3 Insect Medium supplemented with 10% fetal bovine serum, 10% fly extract (purchased from DGRC), 0.6 mg/mL glutathione, and 10 mU/mL human insulin. The fGS/OSS cells were cultured using 25% medium from the old culture and passaged before reaching 50% confluency.

tag: cell line

value: fGS/OSS

tag: cell type

value: mix of female germ-line stem cells/ovarian somatic sheet

tag: genotype

value: wild type

tag: treatment

tag: Sex

value: female


title: 3038_20_39

description: Library name: MDX_3038_20_39_LumB_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

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: LumB

value: N

value: not applicable

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CLL_110, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_385_excluded_subtype

description: Library name: MDX_3038_20_385_1_excluded_subtype

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

value: extra ROI - invasive

tag: menopausal status

value: inferred postmenopausal

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

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_387

description: Library name: MDX_3038_20_387_LumB_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

value: LumB

value: not applicable

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CLL_108, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_106, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_384

description: Library name: MDX_3038_20_384_LumA_node_negative

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: fGSOSS_rep3 (RNA-seq)

description:
fGSOSS_rep3
cell_lines_Deseq2_normalized_counts.txt
fGSOSS_vs_OSC_Deseq2_fold_changes.txt
fGSOSS_merged_rpkm_forward.bw
fGSOSS_merged_rpkm_reverse.bw

tag: cell line

value: fGS/OSS

tag: cell type

value: mix of female germ-line stem cells/ovarian somatic sheet

tag: genotype

value: wild type

tag: treatment

tag: Sex

value: female


title: fGSOSS_rep1 (RNA-seq)

description:
fGSOSS_rep1
cell_lines_Deseq2_normalized_counts.txt
fGSOSS_vs_OSC_Deseq2_fold_changes.txt
fGSOSS_merged_rpkm_forward.bw
fGSOSS_merged_rpkm_reverse.bw


title: vasGFPplus_rep1 (RNA-seq)

description:
GFP_plus_rep1
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_normalized_counts.txt
VasGFPfly_ovary_sorted_GFP_plus_vs_GFP_minus_cells_Deseq2_fold_changes.txt
vasGFP+_merged_rpkm_forward.bw
vasGFP+_merged_rpkm_reverse.bw

tag: tissue

value: ovary

value: germline cells (ovary)

value: FACS-sorted vas-GFP_positive

tag: strain

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]

tag: strain source

value: vas-EGFP fly strain obtained from Bloomington Drosophila Stock Center (# 76126)


title: 3038_20_376

description: Library name: MDX_3038_20_376_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: 3038_20_374

description: Library name: MDX_3038_20_374_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Tubular carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: LumA

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_372

description: Library name: MDX_3038_20_372_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: 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: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_371_excluded_subtype

description: Library name: MDX_3038_20_371_excluded_subtype

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - LCIS

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma, Invasive lobular carcinoma

tag: t

value: pT 1 a(m)

tag: n

tag: node status

tag: g

value: G2 und G3

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: l3mbtKO_OSC_rep3 (RNA-seq)

description:
l3mbtKO_rep3
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
l3mbt_merged_rpkm_forward.bw
l3mbt_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment

tag: Sex


title: 3038_20_371

description: Library name: MDX_3038_20_371_invasive_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: 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: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_38

description: Library name: MDX_3038_20_38_TNBC_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 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: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: l3mbtKO_OSC_rep4 (RNA-seq)

description:
l3mbtKO_rep4
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
l3mbt_merged_rpkm_forward.bw
l3mbt_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

tag: treatment

tag: Sex


title: CLL_104, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_101, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: UM


title: CLL_102, Chronic lymphocytic Leukemia;  biological replicate

value: normal


title: CLL_089, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_385

description: Library name: MDX_3038_20_385_2_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: CLL_097, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_103, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: UM


title: 3038_20_383

description: Library name: MDX_3038_20_383_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular 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

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: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: fGSOSS_rep2 (RNA-seq)

description:
fGSOSS_rep2
cell_lines_Deseq2_normalized_counts.txt
fGSOSS_vs_OSC_Deseq2_fold_changes.txt
fGSOSS_merged_rpkm_forward.bw
fGSOSS_merged_rpkm_reverse.bw

tag: cell line

value: fGS/OSS

tag: cell type

value: mix of female germ-line stem cells/ovarian somatic sheet

tag: genotype

value: wild type

tag: treatment

tag: Sex


title: l3mbtKO_OSC_rep2 (RNA-seq)

description:
l3mbtKO_rep2
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
l3mbt_merged_rpkm_forward.bw
l3mbt_merged_rpkm_reverse.bw

value: OSC

value: ovarian somatic cell

value: l3mbt knockout


title: 3038_20_369

description: Library name: MDX_3038_20_369_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

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

value: pN 2a

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: Bone

value: not applicable

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: l3mbtKO_OSC_rep1 (RNA-seq)

description:
l3mbtKO_rep1
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
l3mbt_merged_rpkm_forward.bw
l3mbt_merged_rpkm_reverse.bw

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: Sex

value: female


title: 3038_20_370

description: Library name: MDX_3038_20_370_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: WT_OSC_rep4 (RNA-seq)

description:
OSC_rep4
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
OSC_merged_rpkm_forward.bw
OSC_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: wild type

tag: treatment

tag: Sex


title: 3038_20_357

description: Library name: MDX_3038_20_357_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: 3038_20_354

description: Library name: MDX_3038_20_354_LumA_node_negative

tag: tissue

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

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

value: not applicable

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_355

description: Library name: MDX_3038_20_355_LumA_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: Lymph node, suspected bone

tag: incidence of_other_tumorous_disease

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: WT_OSC_rep3 (RNA-seq)

description:
OSC_rep3
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
OSC_merged_rpkm_forward.bw
OSC_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: wild type

tag: treatment

tag: Sex


title: 3038_20_364

description: Library name: MDX_3038_20_364_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

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 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: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CLL_087, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_35

description: Library name: MDX_3038_20_35_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: Y

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: WT_OSC_rep2 (RNA-seq)

description:
OSC_rep2
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
OSC_merged_rpkm_forward.bw
OSC_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: wild type

tag: treatment

tag: Sex


title: 3038_20_361

description: Library name: MDX_3038_20_361_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Mucinous 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

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: 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: ec, ec-t,_etc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_343

description: Library name: MDX_3038_20_343_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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


title: WT_OSC_rep1 (RNA-seq)

description:
OSC_rep1
cell_lines_Deseq2_normalized_counts.txt
l3mbt_KO_vs_WT_OSC_Deseq2_fold_changes.txt
OSC_merged_rpkm_forward.bw
OSC_merged_rpkm_reverse.bw

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: Sex


title: CLL_081, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_349

description: Library name: MDX_3038_20_349_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

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

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_339

description: Library name: MDX_3038_20_339_LumB_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

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

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: Y

tag: other

tag: taxane (y/n)

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

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

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


title: 3038_20_334

description: Library name: MDX_3038_20_334_Her2_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_084, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: vasGFP_strain_dmel_10_ovaries (ATAC-seq)

description:
ATAC_dmel_ovary_vasGFP_strain_biomerge.narrowPeak
ATAC_dmel_ovary_vasGFP_strain_biomerge.bw

library_source: genomic

data_processing:
The paired-end reads were trimmed of adapter sequences TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG and GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa mem -M -t 4) was used to align the trimmed paired reads to 2014 (BDGP Release 6 + ISO1 MT/dm6) assembly of the D. melanogaster genome.
Duplicates were marked using Picard tool (v2.9.0) (MarkDuplicates, validation stringency=lenient). SAMtools (v1.9) was used for indexing and filtering. The quality metrics for the aligned ATAC-seq reads were assessed using ataqv (v1.0.0)
The ATAC-seq peaks were called with MACS2 (v2.1.1.20160309) using --nomodel --shift -37 --extsize 73 parameters and FDR cut-off q ≤ 0.05
Differential accessibility analysis was performed using DiffBind package (v3.0.15). RPKM normalized bigWig files were generated using deepTools (v3.5.1, bamCoverage).
Assembly: dm6
Supplementary files format and content: tab-delimited text file of differential ATAC-seq regions between the wild-type ovarian somatic cells (OSC) and the l(3)mbt-knockout OSCs showing the DiffBind-computed fold-change values
Supplementary files format and content: RPKM-normalized bigWig files for each sample and RPKM-normalized bigWig files of merged biological replicates
Supplementary files format and content: narrowPeak files of ATAC-seq peaks from MACS2

molecule: genomic DNA

growth_protocol: Flies were kept at 25°C on standard cornmeal food or propionic food. Flies were fed with yeast extract 2-3 days before the dissections.

extract_protocol:
For the cell lines, the omni-ATAC-seq protocol was performed using 50,000 cells as described before. For the ovaries, the freshly dissected instact ovaries were directly lysed in ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and washed out with cold ATAC-RSB containing 0.1% Tween-20.
The transposition reaction was performed with 25 μl 2x TD buffer from and 2.5 μl transposase (100nM final) from Illumina Tagment DNA Enzyme and Buffer Small Kit (Illumina 20034197), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O at 37°C for 30 minutes in a thermomixer with 1000 RPM mixing. Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) was used for a clean-up. The transposed fragments were amplified for 5 cycles [72 °C for 5 min, 98 °C for 30 s (98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min) × 5] using NEBNext 2x MasterMix and primer pairs of the universal primer Ad1 and the index primers Ad2. This was followed by qPCR amplification to determine additional cycle number. Amplified DNA was purified using Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and eluted in 20 μl H2O. AMPure XP beads (Beckman Coulter) were used for double-sided bead purification. 100-600 bp fragments were selected using Blue Pippin (Sage Science).

value: ovary

tag: Sex

tag: strain

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]


title: 3038_20_330

description: Library name: MDX_3038_20_330_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

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

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: Bone, pleura, lymph nodes

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: taxane (y/n)

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

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

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


title: vasGFP_strain_dmel_6_ovaries (ATAC-seq)

tag: tissue

tag: Sex

value: female

tag: strain


title: 3038_20_332

description: Library name: MDX_3038_20_332_TNBC_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Apocrine carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: Y

tag: fec, fec-t

tag: tc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: w1118_dmel_6_ovaries_rep2 (ATAC-seq)

description:
ATAC_dmel_ovary_w1118_biomerge.narrowPeak
ATAC_dmel_ovary_w1118_biomerge.bw

tag: tissue

value: ovary

tag: Sex

tag: strain

value: w1118 strain


title: CLL_078, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_316

description: Library name: MDX_3038_20_316_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

value: male

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(m)

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

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: Bone

tag: incidence of_other_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: taxane (y/n)

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

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

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


title: CLL_077, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

tag: tissue

tag: disease state


title: 3038_20_325

description: Library name: MDX_3038_20_325_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma, Invasive lobular carcinoma

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: 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: fec, fec-t

tag: tc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_313

description: Library name: MDX_3038_20_313_LumB_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: LumB

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: taxane (y/n)

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

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

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


title: w1118_dmel_6_ovaries_rep1 (ATAC-seq)

tag: tissue

value: ovary

tag: Sex

tag: strain

value: w1118 strain


title: CLL_076, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

value: normal

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

value: no data

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_340

description: Library name: MDX_3038_20_340_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: female

tag: sample category

tag: menopausal status

value: missing

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

value: G2 und G3

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

value: N

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_312

description: Library name: MDX_3038_20_312_LumB_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b(m)

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: Y

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: taxane (y/n)

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

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

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

value: weekly

tag: anthracycline (y/n)


title: CLL_074, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_310_excluded_subtype

description: Library name: MDX_3038_20_310_A_excluded_subtype

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: extra ROI - invasive

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive ductal carcinoma, Micropapillary carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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: fec, fec-t

tag: tc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: l3mbtKO_OSC_rep2 (ATAC-seq)

description:
ATAC_l3mbt_biomerge.narrowPeak
ATAC_l3mbt_biomerge.bw
l3mbt_KO_vs_WT_OSC_DiffBind_differential_ATAC_regions.txt

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: Sex


title: 3038_20_335

description: Library name: MDX_3038_20_335_LumB_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: other

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_327

description: Library name: MDX_3038_20_327_LumA_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

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: 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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: l3mbtKO_OSC_rep1 (ATAC-seq)

tag: cell line

tag: cell type

tag: genotype

tag: Sex


title: 3038_20_324

description: Library name: MDX_3038_20_324_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

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: cp combo

tag: ec, ec-t,_etc

tag: other

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_31

description: Library name: MDX_3038_20_31_LumA_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

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: 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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_310

description: Library name: MDX_3038_20_310_B_LumA_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma, Micropapillary carcinoma

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

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: cp combo

tag: ec, ec-t,_etc

tag: other

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: CLL_068, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

value: normal

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_309

description: Library name: MDX_3038_20_309_LumA_node_positive

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma, Invasive lobular carcinoma

tag: t

tag: n

value: pN 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 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Liver, suspected lung metastasis, bone

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_306

description: Library name: MDX_3038_20_306_LumA_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: LumA

value: not applicable

tag: incidence of_other_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: other

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: WT_OSC_rep1 (ATAC-seq)

description:
ATAC_OSC_biomerge.narrowPeak
ATAC_OSC_biomerge.bw
l3mbt_KO_vs_WT_OSC_DiffBind_differential_ATAC_regions.txt

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: wild type

tag: Sex

value: female


title: 3038_20_305

description: Library name: MDX_3038_20_305_LumB_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: sample category

tag: menopausal status

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: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_304

description: Library name: MDX_3038_20_304_LumB_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2(m)

tag: n

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: incidence of_other_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: other

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: Ta_infiltration_AvrStb6-1E4_6h_3

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

data_processing:
Reads were mapped to Triticum aestivum IWGSC transcriptome reference (release 41 on https://plants.ensembl.org/, accessed November 2018) and to the Z. tritici transcriptome (Accession number PRJNA290690 on https://www.ncbi.nlm.nih.gov/, accessed November 2018) using Kallisto v0.44.0 with default parameters
Read counts were summarized using tximport v1.2.0
Read abundance normalization and differential gene expression analysis were performed with the R package DESeq2 and EdgeR
Assembly: Triticum_aestivum.IWGSC.cdna.all
Supplementary files format and content: tab-delimited txi.kallisto abundance counts for all samples
Supplementary files format and content: tab-delimited txi.kallisto abundance counts for all samples

organism: Triticum aestivum

source_name: Triticum aestivum; AvrStb6-1E4 purified protein infiltration

extract_protocol:
Samples were homogenized with zirconium beads (1.4 mm diameter) using a Bead Ruptor equipped with a cooling unit (Omni International, Kennesaw, GA, USA). Total RNA isolation was performed using GENEzol reagent (Geneaid Biotech, Taipei, Taiwan) following the manufacturer's instructions. DNA contamination was removed using the on-column DNase treatment of the RNase-Free Nase Set (Qiagen GmbH, Hilden, Germany). Concentration and quality were measured by Qubit fluorometer (Life Technologies) and Tapestation (Agilent).
Ribosomal RNA was depleted by poly-A enrichment and DNA libraries were sequenced.
The library preparation was performed with Illumina’s TruSeq Stranded mRNA kit using 500 ng of total RNA as input amount.

treatment_protocol: Chinese Spring wheat plants (12 days post sowing) were treated with 3D7-GFP, 3D7-GFP expressing AvrStb61E4 (3D7-GFP+AvrStb61E4) or mock solution (0.1% (v/v) Tween 20 solution), as described for the infection assays. Samples were collected at 3 and 6 days post infection (dpi). For each treatment, the top 3 cm from the leave tips were discarded, three second leaves (from independent plants) were pooled and flash-frozen in liquid N2. oncurrently, 13-day old Chinese Spring leaves were infiltrated with 176 mg mL-1 of AvrStb6 purified protein (see Protein production in P. pastoris) or with PBS buffer. Infiltrated areas were marked and collected at 1, 2 and 5 hours after infiltration and flash-frozen in liquid N2.

tag: tissue

value: Leaves infiltrated with AvrStb6-1E4 purified protein

tag: time

tag: genotype

value: Chinese Spring

tag: treatment


title: 3038_20_302

description: Library name: MDX_3038_20_302_LumA_node_positive

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 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: 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: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_303

description: Library name: MDX_3038_20_303_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 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

tag: her2 ihc

tag: her2 dna_fish

tag: incidence of_other_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: other

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: CLL_063, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_067, Chronic lymphocytic Leukemia;  biological replicate

value: f

tag: tp53 status

value: mutated

value: UM


title: CLL_066, Chronic lymphocytic Leukemia;  biological replicate

value: normal


title: CLL_060, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_061, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_298_excluded_subtype

description: Library name: MDX_3038_20_298_B_excluded_subtype

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

value: female

tag: sample category

value: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

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

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Ta_infiltration_AvrStb6-1E4_6h_2

tag: tissue

value: Leaves infiltrated with AvrStb6-1E4 purified protein

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: AvrStb6-1E4 purified protein infiltration


title: 3038_20_298

description: Library name: MDX_3038_20_298_A_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: other

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: CLL_058, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_059, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: normal


title: WT_OSC_rep2 (ATAC-seq)

tag: cell line

value: OSC

value: ovarian somatic cell

tag: genotype

value: wild type

tag: Sex

value: female


title: vasGFP_strain_dmel_30_ovaries (ATAC-seq)

description:
ATAC_dmel_ovary_vasGFP_strain_biomerge.narrowPeak
ATAC_dmel_ovary_vasGFP_strain_biomerge.bw

value: ovary

tag: strain

value: transgenic vas-EGFP fly strain:w[*]; TI{TI}vas[AID:EGFP]


title: 3038_20_291

description: Library name: MDX_3038_20_291_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 2

tag: n

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

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Ta_infiltration_AvrStb6-1E4_4h_3

tag: tissue

value: Leaves infiltrated with AvrStb6-1E4 purified protein

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: AvrStb6-1E4 purified protein infiltration