title: 3038_20_296

description: Library name: MDX_3038_20_296_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

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: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_292

status: Public on Dec 23 2024

type: SRA

city: Bratislava

first: Evan

last: Paul

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

description: Library name: MDX_3038_20_292_Her2_node_positive

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: breast

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

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

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: N

tag: er irs

tag: pr negpos

tag: pr irs

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (cycles)


title: Ta_infiltration_AvrStb6-1E4_6h_1

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

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

organism: Triticum aestivum

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

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

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

tag: tissue

value: Leaves infiltrated with AvrStb6-1E4 purified protein

tag: time

tag: genotype

value: Chinese Spring

tag: treatment


title: CLL_055, Chronic lymphocytic Leukemia;  biological replicate

type: RNA

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

country: USA

institute: University of Michigan

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

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

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

label: biotin

source_name: CD19+ cells sorted from human PBMCs

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

growth_protocol: no additional ex vivo growth or culture

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

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

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_284

description: Library name: MDX_3038_20_284_LumB_node_positive

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: Liver

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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


title: 3038_20_286

description: Library name: MDX_3038_20_286_TNBC_node_negative

tag: tissue

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

value: not applicable

value: Y

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_285

description: Library name: MDX_3038_20_285_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1 c(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: LumA

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: taxane (y/n)

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

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

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


title: 3038_20_282

description: Library name: MDX_3038_20_282_LumA_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_283

description: Library name: MDX_3038_20_283_LumB_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1

tag: n

value: pN 2a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: LumB

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: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CLL_054, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_281

description: Library name: MDX_3038_20_281_Her2_node_positive

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Brain

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Ta_infiltration_AvrStb6-1E4_2h_3

tag: tissue

value: Leaves infiltrated with AvrStb6-1E4 purified protein

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: AvrStb6-1E4 purified protein infiltration


title: CLL_051, 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: disease state


title: 3038_20_461

description: Library name: MDX_3038_20_461_TNBC_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 3rd shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: NST

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

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: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CLL_052, 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: CLL_057, Chronic lymphocytic Leukemia;  biological replicate

value: m


title: 3038_20_277

description: Library name: MDX_3038_20_277_LumA_node_positive

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2(m)

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: 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: cmf

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Ta_infiltration_AvrStb6-1E4_2h_2

tag: tissue

value: Leaves infiltrated with AvrStb6-1E4 purified protein

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: AvrStb6-1E4 purified protein infiltration


title: Ta_infiltration_AvrStb6-1E4_4h_1


title: 3038_20_274

description: Library name: MDX_3038_20_274_LumB_node_positive

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Lung

tag: ac, ac-t,_tac

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: Ta_infiltration_AvrStb6-1E4_4h_2

tag: tissue

tag: time

tag: genotype

tag: treatment


title: CLL_050, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

value: normal

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: Ta_infiltration_AvrStb6-1E4_2h_1

value: Leaves infiltrated with AvrStb6-1E4 purified protein


title: 3038_20_269

description: Library name: MDX_3038_20_269_TNBC_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

value: pT 1c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CLL_053, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: tp53 status

value: mutated

tag: ighv status

tag: snp 6.0 genomic lesion total

tag: cell type

tag: tissue

tag: disease state


title: 3038_20_266

description: Library name: MDX_3038_20_266_LumA_node_positive

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: NST

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

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: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_262

description: Library name: MDX_3038_20_262_LumB_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_264

description: Library name: MDX_3038_20_264_LumA_node_positive

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

value: N

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: fec, fec-t

tag: taxane (y/n)

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

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

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


title: Ta_infiltration_PBS_6h_3

source_name: Triticum aestivum; PBS buffer

tag: tissue

value: Leaves infiltrated with PBS buffer

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: PBS buffer infiltration


title: 3038_20_257

description: Library name: MDX_3038_20_257_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_045, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: Ta_infiltration_PBS_6h_2

tag: time

tag: genotype

tag: treatment


title: 3038_20_256_healthy

description: Library name: MDX_3038_20_256_healthy

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

value: no tumor

tag: menopausal status

value: inferred postmenopausal

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

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: taxane (y/n)

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

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

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


title: Ta_infiltration_PBS_6h_1

tag: tissue

value: Leaves infiltrated with PBS buffer

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: PBS buffer infiltration


title: 3038_20_275

description: Library name: MDX_3038_20_275_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

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 1

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)

value: Y

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Pleura

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_254

description: Library name: MDX_3038_20_254_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 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c(m)

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: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CLL_048, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

value: normal

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: 3038_20_253

description: Library name: MDX_3038_20_253_TNBC_node_negative

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 b

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: Brain

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CLL_042, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

tag: cll-fish

tag: ighv status

tag: snp 6.0 genomic lesion total

tag: cell type

tag: tissue

tag: disease state


title: Ta_infiltration_PBS_4h_3

value: Leaves infiltrated with PBS buffer

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: PBS buffer infiltration


title: 3038_20_248

description: Library name: MDX_3038_20_248_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Tubular carcinoma

tag: t

value: pT 1 c(m)

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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


title: 3038_20_247

description: Library name: MDX_3038_20_247_TNBC_node_negative

tag: tissue

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 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: Y

tag: ac, ac-t,_tac

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_249

description: Library name: MDX_3038_20_249_LumA_node_positive

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Mucinous carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 1mi

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_246

description: Library name: MDX_3038_20_246_LumB_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Lymph node, bone, suspected lung and suspected liver

value: Y - letrozole

tag: ac, ac-t,_tac

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CLL_040, 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: Ta_infiltration_PBS_4h_2

value: Leaves infiltrated with PBS buffer

tag: time

tag: genotype

value: Chinese Spring

tag: treatment

value: PBS buffer infiltration


title: CLL_044, Chronic lymphocytic Leukemia;  biological replicate

value: UM


title: CLL_037, Chronic lymphocytic Leukemia;  biological replicate

tag: tp53 status

value: mutated


title: 3038_20_244

description: Library name: MDX_3038_20_244_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: 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: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: Ta_infiltration_PBS_4h_1

tag: tissue

value: Leaves infiltrated with PBS buffer

tag: time

tag: genotype

tag: treatment


title: 3038_20_237

description: Library name: MDX_3038_20_237_TNBC_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

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

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)

value: Y

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Ta_mock_3D7-AvrStb6_infection_6dpi_2

organism:
Triticum aestivum
Zymoseptoria tritici

source_name: Triticum aestivum; Zymoseptoria tritici

tag: tissue

value: Infected leaves

tag: time

value: Day 6

tag: genotype

value: Chinese Spring

tag: treatment

value: Zymoseptoria tritci infection


title: 3038_20_241

description: Library name: MDX_3038_20_241_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

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: neoadjuvant treatment_(y/n)_-_and_type

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CLL_035, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

value: normal

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_243

description: Library name: MDX_3038_20_243_LumB_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c(m)

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Y

tag: organ relapse/metastasis

value: 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: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Ta_mock_3D7-AvrStb6_infection_6dpi_3

tag: tissue

value: Infected leaves

tag: time

value: Day 6

tag: genotype

value: Chinese Spring

tag: treatment

value: Zymoseptoria tritci infection


title: CLL_036, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

value: normal

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: Ta_infiltration_PBS_2h_3

value: Leaves infiltrated with PBS buffer

value: PBS buffer infiltration


title: Ta_infiltration_PBS_2h_2


title: Ta_mock_3D7-AvrStb6_infection_6dpi_1


title: Ta_mock_3D7-AvrStb6_infection_3dpi_3

value: Day 3


title: Ta_infiltration_PBS_2h_1


title: 3038_20_231

description: Library name: MDX_3038_20_231_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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


title: PBMC and Thyroid Control  patients3,4

city: Kyoto

first: GENKI

last: KOBAYASHI

address: Kamugyoku, Kajii-cho 465

country: Japan

institute: Kyoto Prefectural university of medicine

description: Library name: Sample2

library_source: transcriptomic single cell

data_processing:
The sequencing-derived FASTQ files were processed using the BD Rhapsody Targeted Analysis Pipeline with V(D)J processing (BD Biosciences) via the Seven Bridges Platform (https://www.sevenbridges.com/d). Initially, low-quality read pairs were filtered out based on factors such as read length, average base quality score, and single-base frequency. High-quality R1 reads were then utilized to identify cell labels and unique molecular identifiers (UMIs). High-quality R2 reads were aligned to the reference sequences, including 399 targeted genes, BD AbSeq 30 markers, and BCR gene segments, using the Bowtie2 program and BCR gene data from the International ImMunoGeneTics Information System® (IMGT.org). IGBlast was used to determine CDR3 regions. Reads with matching cell labels, UMI sequences, and genes were collapsed into single molecules.
Assembly: GRAF™(Seven Bridges Platform (https://www.sevenbridges.com/d))
Supplementary files format and content: tsv,mtx

source_name: blood mononucler cells

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation. Intrathyroidal blood mononuclear cells were also isolated by density gradient centrifugation , using surgically excised thyroid tissue. They were resuspended in 650 μL of cold sample buffer for loading on a BD Rhapsody cartridge.
Targeted scRNA-seq with BCR analysis was performed using the BD Rhapsody Express system (BD Biosciences, NJ, USA). Cell capture and library preparation were performed using the BD Rhapsody Targeted mRNA and AbSeq Reagent Kit (BD Biosciences). Briefly, cells from each sample were captured in a microwell plate with beads. This was followed by cell lysis, bead retrieval, cDNA synthesis, template switching, Klenow extension, and library preparation (targeted gene library using human B-cell expression panel and BCR gene library) following the BD Rhapsody VDJ CDR3 protocol. The final pooled libraries were spiked with 20% PhiX control DNA to increase the sequence complexity and subsequently sequenced (75 bp × 225 bp paired-end) on a HiSeq X Ten/ Illumina NovaSeq X sequencer (Illumina, San Diego, CA).

tag: cell type

value: blood mononucler cells


title: CLL_033, 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

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_034, Chronic lymphocytic Leukemia;  biological replicate


title: CLL_032, Chronic lymphocytic Leukemia;  biological replicate


title: PBMC and Thyroid Control  patients5,6

description: Library name: Sample3


title: 3038_20_230

description: Library name: MDX_3038_20_230_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 2nd shipment

tag: Sex

value: male

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

value: pN 3a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

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

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: tc

tag: other

value: MCT

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: Ta_mock_3D7-AvrStb6_infection_3dpi_2

tag: tissue

value: Infected leaves

tag: time

value: Day 3

tag: genotype

value: Chinese Spring

tag: treatment

value: Zymoseptoria tritci infection


title: AL

city: Wuhan

first: qiwen

last: man

state: Hubei

address: Luyu road

country: China

institute: wuhan university

data_processing:
Basecalls performed using bcl2fastq V2.19.
equenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Assembly: GRCh38
Supplementary files format and content: .txt file contains mitochondrial content statistics
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx) in tar archive

molecule: polyA RNA

source_name: ameloblastoma  tissue

extract_protocol:
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

treatment_protocol: The tissue pieces were digested with 2 ml GEXSCOPE® Tissue Dissociation Solution at 37℃ for 15 min

value: ameloblastoma  tissue

value: Untreated

tag: age

tag: Sex

value: Male


title: 3038_20_229

description: Library name: MDX_3038_20_229_TNBC_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

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: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: taxane (y/n)

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

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

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


title: PBMC and Thyroid Control  patients1,2

description: Library name: Sample1

tag: cell type

value: blood mononucler cells


title: AB67894

tag: tissue

tag: treatment

tag: age

tag: Sex


title: CLL_024, 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

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: Ta_mock_3D7-AvrStb6_infection_3dpi_1

value: Infected leaves

tag: time

value: Day 3

tag: genotype

value: Chinese Spring

value: Zymoseptoria tritci infection


title: 3038_20_215

description: Library name: MDX_3038_20_215_LumB_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: NST

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_22

description: Library name: MDX_3038_20_22_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 perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: taxane (y/n)

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

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

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


title: Ta_mock_3D7_infection_6dpi_2

tag: tissue

value: Infected leaves

tag: time

value: Day 6

tag: genotype

value: Chinese Spring

tag: treatment

value: Zymoseptoria tritci infection


title: Ta_mock_3D7_infection_6dpi_1


title: 3038_20_236

description: Library name: MDX_3038_20_236_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 2nd shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular carcinoma

tag: t

value: pT 1 c

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: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CLL_029, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: f

tag: cll-fish

value: normal

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_027, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: M


title: Ta_mock_3D7_infection_6dpi_3

value: Infected leaves

tag: time

value: Day 6

tag: genotype

value: Chinese Spring

tag: treatment

value: Zymoseptoria tritci infection


title: PJS6

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

data_processing:
Illumina Casava1.7 software used for basecalling.
Collected reads were trimmed by Trimmomatic, and clean reads were aligned by HISAT2 (version 2.2.1.0)
The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) values were calculated by StringTie (version 2.1.1) for statistical analysis
The samtools jointly with bcftools were employed to identify genomic variants from the RNA-seq data
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with TPM for every gene and every sample

source_name: PJS polyps

extract_protocol:
colorectal tissue was removed, flash frozen on dry ice, and total RNA was harvested by mirVanaTM miRNA Isolation kit (Invitrogen, AM1561)
The libraries were constructed using the TruSeq Stranded mRNA LTSample Prep Kit (Illumina, RS-122-2101,San Diego, CA, USA) with 4ug total RNA

value: STK16 gene mutation

value: PJS


title: 3038_20_216

description: Library name: MDX_3038_20_216_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 2nd shipment

tag: 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 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

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: taxane (y/n)

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

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

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


title: AB100851

tag: tissue

value: ameloblastoma  tissue

tag: treatment

value: Untreated

tag: age

tag: Sex

value: Male


title: CLL_022, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: UM

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: Ta_mock_3D7_infection_3dpi_3

value: Infected leaves

tag: time

value: Day 3

tag: genotype

value: Chinese Spring

value: Zymoseptoria tritci infection


title: PJS5

value: STK15 gene mutation

value: PJS


title: 3038_20_213

description: Library name: MDX_3038_20_213_TNBC_node_positive

value: breast

tag: isolate

value: breast cancer patient

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

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 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: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: Ta_mock_3D7_infection_3dpi_2

tag: tissue

value: Infected leaves

tag: time

value: Day 3

tag: genotype

value: Chinese Spring

tag: treatment

value: Zymoseptoria tritci infection


title: 3038_20_214

description: Library name: MDX_3038_20_214_LumA_node_positive

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 perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 b(m)

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: taxane (y/n)

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

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

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


title: 3038_20_212

description: Library name: MDX_3038_20_212_LumA_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive lobular 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: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: PJS4

tag: genotype

value: STK14 gene mutation

tag: disease state

value: PJS


title: Ta_mock_3D7_infection_3dpi_1

tag: tissue

value: Infected leaves

tag: time

value: Day 3

value: Chinese Spring

tag: treatment

value: Water spray


title: Ta_mock_water_spray_6dpi_3

value: Day 6


title: PJS3

value: STK13 gene mutation


title: CLL_014, 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

value: PBMCs isolated from blood

value: Chronic Lymphocytic leukemia


title: CLL_020, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: M


title: 3038_20_210

description: Library name: MDX_3038_20_210_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 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

value: Y

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CLL_018, Chronic lymphocytic Leukemia;  biological replicate

tag: gender

value: m

tag: cll-fish

tag: ighv status

value: M

tag: snp 6.0 genomic lesion total

tag: cell type

value: CD19+ cells sorted from PBMCs

tag: tissue

value: PBMCs isolated from blood

tag: disease state

value: Chronic Lymphocytic leukemia


title: CLL_017, Chronic lymphocytic Leukemia;  biological replicate

value: f

value: normal

value: UM


title: CLL_013, Chronic lymphocytic Leukemia;  biological replicate


title: PJS1

tag: genotype

value: STK11 gene mutation

value: PJS


title: PJS2

value: STK12 gene mutation


title: Ta_mock_water_spray_6dpi_2

value: Infected leaves

tag: time

value: Day 6

value: Chinese Spring

tag: treatment

value: Water spray


title: CLL_012, Chronic lymphocytic Leukemia;  biological replicate


title: FAP9

source_name: FAP polyps

value: APC gene mutation

value: FAP


title: Ta_mock_water_spray_3dpi_3

value: Day 3


title: 3038_20_21

description: Library name: MDX_3038_20_21_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 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: Tubular 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

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: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 3038_20_208_excluded_subtype

description: Library name: MDX_3038_20_208_B_excluded_subtype

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

value: extra ROI - no tumor

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CLL_010, 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: FAP8

tag: genotype

value: APC gene mutation

value: FAP


title: Ta_mock_water_spray_3dpi_2

value: Infected leaves

tag: time

value: Day 3

value: Chinese Spring

tag: treatment

value: Water spray


title: 3038_20_209

description: Library name: MDX_3038_20_209_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 2nd shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 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

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: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: Ta_mock_water_spray_6dpi_1

tag: tissue

value: Infected leaves

tag: time

value: Day 6

tag: genotype

tag: treatment


title: 3038_20_211

description: Library name: MDX_3038_20_211_LumA_node_negative

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Tubular carcinoma

tag: t

value: pT 1a(m)

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: FAP7

tag: genotype

value: APC gene mutation

tag: disease state

value: FAP


title: Ta_mock_water_spray_3dpi_1

tag: tissue

tag: time

value: Day 3

value: Chinese Spring

tag: treatment

value: Water spray


title: CSCC_373_T2b_B4_RNA

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description: Library name: CSCC_373_T2b_B4_RNA

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

source_name: skin

growth_protocol: Patient samples

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

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

value: skin

tag: group

value: Primary Tumor


title: 3038_20_208

description: Library name: MDX_3038_20_208_A_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: 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 1 c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

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: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: FAP6

tag: genotype

value: APC gene mutation

tag: disease state

value: FAP


title: CSCC_349_T3_B4_RNA

description: Library name: CSCC_349_T3_B4_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: CSCC_359_T2a_B4_RNA

description: Library name: CSCC_359_T2a_B4_RNA


title: 3038_20_200

description: Library name: MDX_3038_20_200_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_201

description: Library name: MDX_3038_20_201_Her2_node_positive

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

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: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: CSCC_374_T2b_B4_RNA

description: Library name: CSCC_374_T2b_B4_RNA

tag: tissue

tag: group

value: Primary Control


title: FAP4

tag: genotype

value: APC gene mutation

tag: disease state

value: FAP


title: CLL_005, 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

value: PBMCs isolated from blood

value: Chronic Lymphocytic leukemia


title: Aqp5-/- -2

city: Qingdao

first: Peng

last: Chen

address: 308 Ningxia road, Qingdao

institute: Qingdao University

description: Library name: Sample 5

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
Assembly: MM10
Supplementary files format and content: tab -delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.
the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions

value: liver


title: Aqp5-/- -3

description: Library name: Sample 6


title: Aqp5-/- -1

description: Library name: Sample 4


title: CSCC_346_T3_B4_RNA

description: Library name: CSCC_346_T3_B4_RNA

value: skin


title: CLL_007, Chronic lymphocytic Leukemia;  biological replicate

value: m

value: normal

value: M


title: Aqp5+/+-3

description: Library name: Sample 3

value: Wild type


title: FAP3


title: 3038_20_20

description: Library name: MDX_3038_20_20_1_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: 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)

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

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: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: 3038_20_20_excluded_subtype

description: Library name: MDX_3038_20_20_2_excluded_subtype

tag: tissue

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

tag: sample category

value: extra ROI - invasive

tag: menopausal status

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Aqp5+/+-2

description: Library name: Sample 2

tag: tissue

value: liver

tag: genotype

value: Wild type


title: CSCC_339_T2b_B4_RNA

description: Library name: CSCC_339_T2b_B4_RNA

value: skin

tag: group

value: Primary Control


title: FAP2

value: APC gene mutation

tag: disease state

value: FAP


title: 3038_20_202

description: Library name: MDX_3038_20_202_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 6th 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 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

value: LumA

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: FAP1

tag: genotype

tag: disease state


title: CLL_004, 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

value: Chronic Lymphocytic leukemia


title: 3038_20_199

description: Library name: MDX_3038_20_199_LumB_node_negative

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 perimenopausal

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)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

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: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CSCC_335_T2a_B4_RNA

description: Library name: CSCC_335_T2a_B4_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: FAP5

tag: genotype

value: APC gene mutation

tag: disease state

value: FAP


title: 3038_20_196

description: Library name: MDX_3038_20_196_LumA_node_negative

value: breast

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 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: LumA

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CSCC_338_T2b_B4_RNA

description: Library name: CSCC_338_T2b_B4_RNA

tag: tissue

tag: group


title: CSCC_331_T1-T_B4_RNA

description: Library name: CSCC_331_T1-T_B4_RNA


title: CT14LKO2

city: YANGLING

first: Guohao

last: Han

address: NWAFU

institute: NWAFU

description: Library name: CT14LKO2

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

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

value: liver

tag: genotype

value: LKO

tag: time point


title: ConB4

source_name: sporadic polyps

tag: disease state

value: sporadic polyps


title: CT14LKO3

description: Library name: CT14LKO3


title: 3038_20_19

description: Library name: MDX_3038_20_19_LumA_node_negative

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 perimenopausal

tag: histopathological tumor_type

tag: t

value: pT 1 c

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: N

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

value: not applicable

tag: organ affected_by_tumorous_disease

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_190

description: Library name: MDX_3038_20_190_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 2nd 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

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: relapse/metastasis

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: CSCC_326_T3_B4_RNA

description: Library name: CSCC_326_T3_B4_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: 3038_20_188

description: Library name: MDX_3038_20_188_LumA_node_negative

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

value: Invasive lobular carcinoma

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: LumA

tag: deceased (y/n)

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: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: Aqp5+/+-1

description: Library name: Sample 1

tag: tissue

value: liver

tag: genotype

value: Wild type


title: ConB2

tag: disease state

value: sporadic polyps


title: CT2LKO3

description: Library name: CT2LKO3

value: LKO

tag: time point


title: CSCC_308_T2b_B4_RNA

description: Library name: CSCC_308_T2b_B4_RNA

tag: group


title: CT14LKO1

description: Library name: CT14LKO1


title: 093-T2a_B2_RNA

description: Library name: 093-T2a_B2_RNA


title: CT2LKO1

description: Library name: CT2LKO1


title: 3038_20_180_excluded_subtype

description: Library name: MDX_3038_20_180_B_excluded_subtype

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

value: extra ROI - DCIS

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: relapse/metastasis

tag: organ relapse/metastasis

value: not applicable

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: 3038_20_181

description: Library name: MDX_3038_20_181_LumA_node_negative

tag: tissue

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

value: female

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)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumA

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: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: ConA9

source_name: colonic mucosae

tag: disease state

value: colorectal cancer


title: 3038_20_184

description: Library name: MDX_3038_20_184_LumA_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: 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: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: ConB5

tag: disease state

value: sporadic polyps


title: CT2LKO2

description: Library name: CT2LKO2

tag: tissue

value: liver

tag: genotype

value: LKO

tag: time point


title: ConB3


title: CSCC_316_T2b_B4_RNA

description: Library name: CSCC_316_T2b_B4_RNA

value: skin

tag: group

value: Primary Tumor


title: CSCC_331_T1-C_B4_RNA

description: Library name: CSCC_331_T1-C_B4_RNA

value: Primary Control


title: 085-T2a_B2_RNA

description: Library name: 085-T2a_B2_RNA


title: ConB1


title: CT14KO3

description: Library name: CT14KO3

value: KO


title: 3038_20_180

description: Library name: MDX_3038_20_180_A_TNBC_node_negative

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

tag: Sex

tag: sample category

tag: menopausal status

value: inferred perimenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 b

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

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

value: not applicable

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: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: 3038_20_18

description: Library name: MDX_3038_20_18_LumB_node_negative

tag: tissue

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

value: Austria:Graz 6th shipment

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

value: pT 2

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

value: LumB

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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

tag: anthracycline (y/n)


title: ConA7

tag: disease state

value: colorectal cancer


title: CT14KO1

description: Library name: CT14KO1

tag: tissue

value: liver

tag: genotype

value: KO

tag: time point


title: CT14KO2

description: Library name: CT14KO2


title: 072-T2b_B2_RNA

description: Library name: 072-T2b_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: ConA6


title: CT2KO3

description: Library name: CT2KO3


title: 073-T2a_B2_RNA

description: Library name: 073-T2a_B2_RNA


title: 3038_20_179

description: Library name: MDX_3038_20_179_Her2_node_positive

tag: isolate

value: breast cancer patient

tag: age

tag: biomaterial provider

value: GRAZ biobank

tag: geo loc_name

value: Austria:Graz 1st shipment

tag: Sex

tag: sample category

tag: menopausal status

value: inferred premenopausal

tag: histopathological tumor_type

value: Invasive ductal carcinoma

tag: t

value: pT 1 c

tag: n

value: pN 1a

tag: node status

tag: g

tag: lymphatic invasion_(l)

value: missing

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

tag: deceased (y/n)

tag: relapse/metastasis

tag: overall survival_(months)

tag: progression free_survival_(months)

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

tag: chemotherapy (y/n)

tag: ac, ac-t,_tac

tag: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage


title: CSCC_367_T2a_B4_RNA

description: Library name: CSCC_367_T2a_B4_RNA

tag: tissue

tag: group

value: Primary Control


title: ConA4

tag: disease state


title: 3038_20_177

description: Library name: MDX_3038_20_177_LumB_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

tag: t

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: Y

tag: organ relapse/metastasis

value: Pleura, bone, lung

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

value: not applicable

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CT2KO2

description: Library name: CT2KO2

tag: tissue

value: liver

tag: genotype

value: KO

tag: time point


title: ConA8

tag: disease state

value: colorectal cancer


title: ConA3


title: 205-T2b_B2_RNA

description: Library name: 205-T2b_B2_RNA

value: skin

tag: group

value: Primary Tumor


title: ConA2


title: CSCC_301_T2b_B4_RNA

description: Library name: CSCC_301_T2b_B4_RNA


title: 3038_20_172_excluded_subtype

description: Library name: MDX_3038_20_172_B_excluded_subtype

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

tag: sample category

value: extra ROI - DCIS

tag: menopausal status

value: missing

tag: histopathological tumor_type

value: NST

tag: t

value: pT 1c

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

value: LumB

tag: deceased (y/n)

tag: relapse/metastasis

value: Lymph node

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: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: ConA1

tag: disease state


title: 203-T2b_B2_RNA

description: Library name: 203-T2b_B2_RNA

tag: tissue

tag: group


title: 3038_20_176

description: Library name: MDX_3038_20_176_TNBC_node_negative

value: breast

tag: isolate

tag: age

tag: biomaterial provider

tag: geo loc_name

tag: Sex

value: female

tag: sample category

value: invasive breast cancer sample

tag: menopausal status

value: inferred postmenopausal

tag: histopathological tumor_type

value: Metaplastic carcinoma

tag: t

value: pT 2

tag: n

value: pN 0

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: N

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

tag: her2 dna_fish

tag: ihc surrogate_subtype

value: TNBC

tag: deceased (y/n)

tag: organ relapse/metastasis

tag: incidence of_other_tumorous_disease

tag: organ affected_by_tumorous_disease

tag: cmf

tag: fec, fec-t

tag: tc

tag: taxane (y/n)

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

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

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


title: CT14F2

description: Library name: CT14F2

tag: tissue

value: liver

tag: genotype

value: F

tag: time point


title: 3038_20_172

description: Library name: MDX_3038_20_172_A_LumB_node_negative

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

tag: sample category

tag: menopausal status

tag: histopathological tumor_type

tag: t

tag: n

tag: node status

tag: g

tag: lymphatic invasion_(l)

tag: residual tumor_(path_only)

tag: er negpos

value: P

tag: er irs

tag: pr negpos

tag: pr irs

tag: her2 negpos

tag: her2 ihc

value: Y

tag: 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: cp combo

tag: ec, ec-t,_etc

tag: other

tag: paclitaxel (abraxane)_(cycles)

tag: taxol (y/n)

tag: taxol dosage

tag: anthracycline (y/n)


title: 201-T2b_B2_RNA

description: Library name: 201-T2b_B2_RNA

tag: tissue

value: skin

tag: group

value: Primary Tumor


title: CT14F3

description: Library name: CT14F3

tag: genotype

tag: time point


title: 200-T2b_B2_RNA

description: Library name: 200-T2b_B2_RNA


title: CT14F1

description: Library name: CT14F1


title: ConA5

tag: disease state

value: colorectal cancer


title: IEC, B6J wt uninfected, d25, Biol. Rep2

city: Aachen

first: Mathias

last: Hornef

address: Pauwelstr. 30

department: Institute for Medical Microbiology

country: Germany

institute: University Hospital RWTH Aachen

description:
Library name: Sample 6
10X genomics

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

source_name: small intestine

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

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

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

value: small intestine

tag: strain

value: wt spf

tag: cell type

value: epithelial cells

tag: age

tag: treatment

value: uninfected


title: IEC, B6J wt uninfected, d25, Biol. Rep1

description:
Library name: Sample 5
10X genomics


title: CT2F3

description: Library name: CT2F3