title: 3038_20_571

description: Library name: MDX_3038_20_571_LumB_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

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: 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: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_240, Chronic lymphocytic Leukemia;  biological replicate

status: Public on Dec 23 2024

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

molecule: total RNA

organism: Homo sapiens

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: f

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_57_2_excluded_subtype

type: SRA

city: Bratislava

first: Evan

last: Paul

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

description: Library name: MDX_3038_20_57_2_excluded_subtype

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

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: 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: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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)

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)


title: 3038_20_57_1_excluded_subtype

description: Library name: MDX_3038_20_57_1_excluded_subtype

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

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage


title: 3038_20_57

description: Library name: MDX_3038_20_57_3_LumB_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_569

description: Library name: MDX_3038_20_569_TNBC_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: TNBC

value: Bone, paravertebral area

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: s11_HSD_Female_mother

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description:
Library name: s11
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

organism: Drosophila melanogaster

source_name: whole organism

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

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

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HSD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_567

description: Library name: MDX_3038_20_567_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: s10_HFD_Female_mother

description:
Library name: s10
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

value: HFD

tag: condition

tag: gender

tag: day

tag: group


title: s14_HSD_Female_mother

description:
Library name: s14
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds


title: s12_HSD_Female_mother

description:
Library name: s12
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds


title: 3038_20_560

description: Library name: MDX_3038_20_560_Her2_node_negative

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

value: Y

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_239, 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

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_227, Chronic lymphocytic Leukemia;  biological replicate

value: m


title: 3038_20_559

description: Library name: MDX_3038_20_559_B_Her2_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1b(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: P

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Left breast

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_226, 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: 3038_20_56

description: Library name: MDX_3038_20_56_LumA_node_positive

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

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: 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: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: s8_HFD_Female_mother

description:
Library name: s8
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_556

description: Library name: MDX_3038_20_556_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred 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

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_555

description: Library name: MDX_3038_20_555_LumA_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

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: not applicable

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: s7_HFD_Female_mother

description:
Library name: s7
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_551

description: Library name: MDX_3038_20_551_LumA_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

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)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_230, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: s6_HFD_Female_mother

description:
Library name: s6
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: strain

tag: genotype

tag: diet

tag: condition

tag: day

tag: group


title: CLL_223, Chronic lymphocytic Leukemia;  biological replicate

value: normal


title: 3038_20_550

description: Library name: MDX_3038_20_550_LumA_node_negative

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: 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)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_220, 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

tag: tissue

tag: disease state


title: 3038_20_559_excluded_subtype

description: Library name: MDX_3038_20_559_A_excluded_subtype

value: breast

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: extra ROI - DCIS

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1b(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Left breast

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: fec, fec-t

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_548

description: Library name: MDX_3038_20_548_LumA_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: LumA

value: Liver, suspected brain

tag: ec, ec-t,_etc

tag: tc

tag: other

value: ET

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_207, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_213, Chronic lymphocytic Leukemia;  biological replicate

value: normal

value: M


title: s9_HFD_Female_mother

description:
Library name: s9
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: HFD

tag: condition

value: Female

tag: day

tag: group


title: CLL_218, Chronic lymphocytic Leukemia;  biological replicate

value: f


title: CLL_211, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_541

description: Library name: MDX_3038_20_541_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c(m)

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

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Lung, liver, bone, peritoneum

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_204, 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: CLL_210, Chronic lymphocytic Leukemia;  biological replicate

value: normal


title: CLL_201, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_540

description: Library name: MDX_3038_20_540_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_200, 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

tag: tissue

tag: disease state


title: 3038_20_537

description: Library name: MDX_3038_20_537_LumA_node_positive

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

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)

value: Y

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_206, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_532

description: Library name: MDX_3038_20_532_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 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_535

description: Library name: MDX_3038_20_535_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 1b

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

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: not applicable

value: Y

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_209, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: s5_CD_Female_mother

description:
Library name: s5
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

value: Female

tag: day

tag: group


title: 3038_20_521_S143

description: Library name: MDX_3038_20_521_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_52

description: Library name: MDX_3038_20_52_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: s2_CD_Female_mother

description:
Library name: s2
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

value: whole organism

tag: strain

tag: genotype

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: 3038_20_524

description: Library name: MDX_3038_20_524_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_534

description: Library name: MDX_3038_20_534_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Micropapillary carcinoma

tag: t

value: pT 1c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: s4_CD_Female_mother

description:
Library name: s4
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

tag: strain

tag: genotype

tag: diet

tag: condition

tag: gender

tag: day

tag: group


title: CLL_199, Chronic lymphocytic Leukemia;  biological replicate

value: f

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

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_517

description: Library name: MDX_3038_20_517_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

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

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_513

description: Library name: MDX_3038_20_513_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_510

description: Library name: MDX_3038_20_510_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

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: LumA

value: Y

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: L3mbt_OSC_renilla_siRNA_rep2

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: renilla siRNA in l3mbt knockout OSC

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.
Assembly: dm6
Supplementary files format and content: tab-delimited text files showing 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

source_name: OSC

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).
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: Sense and anti-sense siRNA sequences (21 nt) for target genes were designed using the DSIR tool (http://biodev.cea.fr/DSIR/DSIR.html). The designed sequences were ordered from IDT and resuspended in 400 μl RNase-free water. Equal volumes of the resuspended sense and antisense siRNA were mixed then added to an equal amount of 2x annealing buffer (60 mM potassium acetate; 200 mM HEPES, pH 7.5). The mix was boiled for 5 min. at 75 °C, then ramped down to 25 °C (-0.1 °C/second) to anneal the siRNA sequences into the siRNA duplex (100 μM final concentration =200 pmoles). 2 μL of the final 100 μM siRNA duplex was mixed with 100 μL of Nucleofection solution V (VVCA-1003, Lonza) and transfected into 10 million cells using NucleofectorTM 2b Device (T-029 program) (Lonza). Cells were plated into 12-well plates and the media was changed after 24 hr. RNA was harvested at 48 hr.

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment


title: L3mbt_OSC_renilla_siRNA_rep1

description: renilla siRNA in l3mbt knockout OSC


title: 3038_20_505

description: Library name: MDX_3038_20_505_LumA_node_negative

tag: tissue

tag: isolate

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

value: NST

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

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: L3mbt_OSC_renilla_siRNA_rep3

description: renilla siRNA in l3mbt knockout OSC

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 3038_20_518

description: Library name: MDX_3038_20_518_LumA_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_508

description: Library name: MDX_3038_20_508_Her2_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2(m)

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Lung, lymph node, sternum

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_51

description: Library name: MDX_3038_20_51_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Mucinous 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)

value: P

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

value: not applicable

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: taxol dosage


title: 3038_20_519

description: Library name: MDX_3038_20_519_LumB_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

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: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: 3038_20_502

description: Library name: MDX_3038_20_502_TNBC_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

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: taxol dosage


title: L3mbt_OSC_ovo_siRNA_rep3

description: ovo siRNA in l3mbt knockout OSC

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment


title: s1_CD_Female_mother

description:
Library name: s1
within csv, colnames carry the library names for identification; rds object contains the DEseq Data Set
countMatrix_mothers.csv
DDS_kallisto_mothers.rds

tag: tissue

value: whole organism

tag: strain

value: white mutant

tag: diet

value: CD

tag: condition

tag: gender

value: Female

tag: day

tag: group


title: CLL_196, Chronic lymphocytic Leukemia;  biological replicate

value: m

tag: cll-fish

value: normal

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_501

description: Library name: MDX_3038_20_501_LumA_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: L3mbt_OSC_ovo_siRNA_rep2

description: ovo siRNA in l3mbt knockout OSC

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment


title: CLL_192, 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

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_500

description: Library name: MDX_3038_20_500_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

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

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_50

description: Library name: MDX_3038_20_50_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: CLL_183, 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_182, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_187, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: normal


title: L3mbt_OSC_ovo_siRNA_rep1

description: ovo siRNA in l3mbt knockout OSC

tag: cell line

value: OSC

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment


title: 3038_20_498

description: Library name: MDX_3038_20_498_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 5th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_493

description: Library name: MDX_3038_20_493_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

tag: t

value: pT 2

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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

value: Y

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_490

description: Library name: MDX_3038_20_490_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

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: other

tag: taxane (y/n)

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

tag: taxol dosage


title: CLL_195, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: WCE_OSC_ectopic_ovo_rep1

library_source: genomic

data_processing:
The paired-end reads were trimmed of adapter sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT using Cutadapt tool (v1.18; default parameters).
Burrows-Wheeler Aligner (BWA) (v0.7.17, bwa aln) was used to align the trimmed paired reads to 2014 (BDGP Release 6 + ISO1 MT/dm6) assembly of the D. melanogaster genome.
SAMtools (v1.9) was used for sorting, indexing, and merging.
ChIP-seq peaks were called using MACS3 (v3.0.0a6) callpeak command (-q 0.01) with data from ChIP input (the whole cell extract) used as the control (-c)
The RPKM normalized bigWig files were generated using bamCoverage tool in deepTools (v3.5.1) with the parameter (--extendReads 120) specified. The input-normalized bigWig files were generated using the bamCompare tool in the deepTools (v3.5.1). Signals from bigWig files were quantified using the multiBigwigSummary tool in deepTools (v3.5.1)
Assembly: dm6
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 ChIP-seq peaks from MACS3

molecule: genomic DNA

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:
>30 million OSCs were nucleofected with ovo-B-FLAG construct (0.5-0.8 μg per million cells; Nucleofector Kit V, VVCA-1003; NucleofectorTM 2b Device, T-029 program, Lonza) and crosslinked 48 hours later by covering cells in 1% formaldehyde (FA) solution (50mM Hepes-KOH, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% FA) for 10 min at room temperature. Cell lysis was performed as described in Schmidt, D. et al. 2009. Sonication was performed with 15-18 cycles of 10 s ON and 60 s OFF (Fisherbrand™ Q705 Sonicator, 418-21 probe) in 3 mL of LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine; in 7 ml conical polypropylene tube) to shear DNA into 100-500 bp fragments. Chromatin immunoprecipitation was performed using 5-10 μg of primary mouse monoclonal ANTI-FLAG® M2 antibody (F1804-200UG; Merck) (in 250 μL LB3 with 1% Triton X-100) overnight at 4 °C. Crosslinks were reversed by incubation at 65 °C for 16 h. Proteins and RNA were enzymatically digested. DNA purification was performed using phenol-chloroform extraction and ethanol precipitation.
The purified ChIP DNA and 220 ng of whole cell extract DNA were used to prepare ChIP-seq libraries using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S; with PCR amplifications carried out for 16 cycles) and sequenced in NovaSeq 6000 System with 2 × 150 bp reads on SP flow cell.

tag: treatment

value: OSCs were nucleofected with ovo-B-FLAG construct for enforced ovo expression for 48 hr

tag: cell line

value: OSC

value: ovarian somatic cell

tag: antibody

value: 5-10 ug of primary mouse monoclonal ANTI-FLAG M2 antibody (F1804-200UG; Merck)

tag: Sex

value: female


title: WCE_OSC_ectopic_ovo_rep2


title: 3038_20_49

description: Library name: MDX_3038_20_49_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

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 lobular carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: CLL_178, 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


title: ChIP_OSC_ectopic_ovo_rep2

tag: treatment

value: OSCs were nucleofected with ovo-B-FLAG construct for enforced ovo expression for 48 hr

tag: cell line

value: OSC

value: ovarian somatic cell

tag: antibody

value: 5-10 ug of primary mouse monoclonal ANTI-FLAG M2 antibody (F1804-200UG; Merck)

tag: Sex


title: CLL_173, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: Chronic Lymphocytic leukemia


title: 3038_20_481

description: Library name: MDX_3038_20_481_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

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 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

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: Lymph node

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_485

description: Library name: MDX_3038_20_485_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 1a

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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_483

description: Library name: MDX_3038_20_483_LumB_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular 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: 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_489

description: Library name: MDX_3038_20_489_LumB_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd 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 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

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_478

description: Library name: MDX_3038_20_478_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

value: P

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: ChIP_OSC_ectopic_ovo_rep1

tag: treatment

value: OSCs were nucleofected with ovo-B-FLAG construct for enforced ovo expression for 48 hr

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: antibody

value: 5-10 ug of primary mouse monoclonal ANTI-FLAG M2 antibody (F1804-200UG; Merck)

tag: Sex


title: 3038_20_574

description: Library name: MDX_3038_20_574_A_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

value: Austria:Graz 4th shipment

value: female

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_497

description: Library name: MDX_3038_20_497_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: not applicable

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: 3038_20_473

description: Library name: MDX_3038_20_473_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

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

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

value: TAC/FEC

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: l3mbtOSC_control_48h_rep3 (RNA-seq)

description:
l3mbt_empty_vector_48h_rep3
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
l3mbt_empty_vector_48h_merged_rpkm_forward.bw
l3mbt_empty_vector_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

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: l3mbt knockout

tag: treatment

value: empty vector 48 hours

tag: Sex


title: 3038_20_472

description: Library name: MDX_3038_20_472_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

value: Austria:Graz 4th shipment

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

value: N

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: 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_171, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: l3mbtOSC_control_48h_rep2 (RNA-seq)

description:
l3mbt_empty_vector_48h_rep2
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
l3mbt_empty_vector_48h_merged_rpkm_forward.bw
l3mbt_empty_vector_48h_merged_rpkm_reverse.bw

tag: cell line

value: OSC

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment

tag: Sex


title: CLL_165, Chronic lymphocytic Leukemia;  biological replicate

value: normal

value: M


title: 3038_20_47

description: Library name: MDX_3038_20_47_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 1st shipment

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

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

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_168, 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_170, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_471

description: Library name: MDX_3038_20_471_TNBC_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: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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)

tag: ac, ac-t,_tac

tag: cmf

tag: other

tag: taxane (y/n)

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

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_181, 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

tag: tissue

tag: disease state


title: CLL_156, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_157, Chronic lymphocytic Leukemia;  biological replicate

tag: tp53 status


title: 3038_20_474

description: Library name: MDX_3038_20_474_LumA_node_positive

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

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

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

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: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_469

description: Library name: MDX_3038_20_469_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 2nd shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

value: Y

value: Lymph node, liver, suspected bone marrow

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: other

value: Navelbine / Caelyx (x6)

tag: taxane (y/n)

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

tag: taxol dosage

tag: anthracycline (y/n)


title: l3mbtOSC_control_48h_rep1 (RNA-seq)

description:
l3mbt_empty_vector_48h_rep1
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
l3mbt_empty_vector_48h_merged_rpkm_forward.bw
l3mbt_empty_vector_48h_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment

value: empty vector 48 hours

tag: Sex

value: female


title: l3mbtOSC_ovo_48h_rep2 (RNA-seq)

description:
l3mbt_ovo_48h_rep2
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
l3mbt_ovo_48h_merged_rpkm_forward.bw
l3mbt_ovo_48h_merged_rpkm_reverse.bw

value: Ovo overexpression 48 hours


title: l3mbtOSC_ovo_48h_rep3 (RNA-seq)

description:
l3mbt_ovo_48h_rep3
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
l3mbt_ovo_48h_merged_rpkm_forward.bw
l3mbt_ovo_48h_merged_rpkm_reverse.bw


title: 3038_20_460

description: Library name: MDX_3038_20_460_LumA_node_negative

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

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

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

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: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: CLL_161, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_449

description: Library name: MDX_3038_20_449_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 4th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

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: other

tag: taxane (y/n)

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

tag: taxol dosage

tag: anthracycline (y/n)


title: l3mbtOSC_ovo_48h_rep1 (RNA-seq)

description:
l3mbt_ovo_48h_rep1
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
l3mbtKO_OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
l3mbt_ovo_48h_merged_rpkm_forward.bw
l3mbt_ovo_48h_merged_rpkm_reverse.bw

tag: cell line

value: OSC

tag: cell type

value: ovarian somatic cell

tag: genotype

value: l3mbt knockout

tag: treatment

value: Ovo overexpression 48 hours

tag: Sex


title: 3038_20_441

description: Library name: MDX_3038_20_441_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

value: missing

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 3

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Bone, peritoneum, stomach, colon

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_464

description: Library name: MDX_3038_20_464_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

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: Lung

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: other

tag: taxane (y/n)

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

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_448

description: Library name: MDX_3038_20_448_LumB_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

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

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: axillary lymph node

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_445

description: Library name: MDX_3038_20_445_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred 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

value: N

value: LumA

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: other

value: TAC/FEC

tag: taxane (y/n)

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

tag: taxol dosage

tag: anthracycline (y/n)


title: OSC_control_48h_rep3 (RNA-seq)

description:
OSC_empty_vector_48h_rep3
OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
OSC_empty_vector_48h_merged_rpkm_forward.bw
OSC_empty_vector_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: empty vector 48 hours

tag: Sex

value: female


title: 3038_20_454

description: Library name: MDX_3038_20_454_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 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 1 c(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

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: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)


title: 3038_20_438

description: Library name: MDX_3038_20_438_LumB_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

value: G2 und G3

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

value: LumB

value: Soft tissue, bone, liver, peritoneum

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: other

tag: taxane (y/n)

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

tag: taxol dosage


title: 3038_20_434

description: Library name: MDX_3038_20_434_LumA_node_positive

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

value: pN 2a

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)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Liver, bone

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: OSC_control_48h_rep2 (RNA-seq)

description:
OSC_empty_vector_48h_rep2
OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
OSC_empty_vector_48h_merged_rpkm_forward.bw
OSC_empty_vector_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: empty vector 48 hours

tag: Sex


title: 3038_20_437

description: Library name: MDX_3038_20_437_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

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: 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: other

tag: taxane (y/n)

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

tag: taxol dosage


title: CLL_142, 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: CLL_155, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: UM


title: OSC_control_48h_rep1 (RNA-seq)

description:
OSC_empty_vector_48h_rep1
OSC_ovoFLAG_vs_empty_vector_Deseq2_normalized_counts.txt
OSC_ovoFLAG_vs_empty_vector_Deseq2_fold_changes.txt
OSC_empty_vector_48h_merged_rpkm_forward.bw
OSC_empty_vector_48h_merged_rpkm_reverse.bw

tag: cell line

value: OSC

value: ovarian somatic cell

tag: genotype

value: wild type

tag: treatment

value: empty vector 48 hours

tag: Sex

value: female


title: CLL_140, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_139, Chronic lymphocytic Leukemia;  biological replicate


title: 3038_20_43

description: Library name: MDX_3038_20_43_LumB_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st 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

value: pT 1 c

tag: n

value: pN 1

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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)

value: Y

tag: ac, ac-t,_tac

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

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

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

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: anthracycline (y/n)


title: OSC_ovo_48h_rep3 (RNA-seq)

description:
OSC_ovo_48h_rep3
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

tag: treatment

value: Ovo overexpression 48 hours

tag: Sex


title: CLL_147, 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