title: 180822_P3-180822_P4-D5-AD008

value: P


title: Serum, patient 613, BRCA Mutated

status: Public on May 02 2023

type: SRA

city: Łódź

first: Zuzanna

last: Nowicka

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Łódź

description: QIAseq

library_source: transcriptomic

data_processing:
All miRNA sequencing data were mapped to the reference miRNA database (miRBase version 22.1) using nf-core/smrnaseq version 1.1.0.
The sequencing protocol was set as QIAseq, Illumina or Nextflex, as appropriate for each sample. All parameters of the pipeline were kept at the default values recommended by the code authors.
After voom normalization and mean variance trend removal (model formula used for voom: ~0 + brcaStatus + havingOvaries + group), ComBat was used to combine data from all subject groups, with the UPenn group serving as reference (model formula used for ComBat: ~brcaStatus + havingOvaries)
miRNAs were filtered for species detected in at least 33% of the samples in each group at a minimum detection threshold of >=10 transcripts per million (TPM).
Assembly: Reads unmapped to miRbase were subsequently mapped to human genome GRCh38.
Supplementary files format and content: processed_raw.xlsx - spreadsheet containing raw miRNA counts of all samples
Supplementary files format and content: processed_log2tpm.xlsx -spreadsheet containing log2(TPM)-transformed miRNA counts of all samples

molecule: total RNA

organism: Homo sapiens

source_name: Serum

extract_protocol:
Libraries were prepared using NEBNEXT library generation kit (New England Biolabs Inc.) according to the manufacturer’s instructions.
Total RNA was extracted from serum using the miRCURY™ RNA isolation kit - biofluids.

tag: tissue

value: Serum

tag: brca1/2 mutation_status

value: Mutated

tag: control type

value: Healthy

tag: Sex

value: Female

tag: menopausal status

value: Postmenopausal

tag: having ovaries_at_testing

value: yes

tag: platform

value: ILLUMINA


title: Serum, patient 614, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-D5-AD007

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

molecule: genomic DNA

organism: Mus musculus

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: THl

tag: target

value: male


title: 180822_P3-180822_P4-D5-AD006

value: THm

value: ACA

value: female


title: 180822_P3-180822_P4-D4-AD012

value: THp


title: 180822_P3-180822_P4-D5-AD001

value: SSp


title: Serum, patient 619, BRCA Mutated

description: QIAseq

value: Premenopausal


title: Serum, patient 611, BRCA Mutated

description: QIAseq


title: Serum, patient 610, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-D5-AD010

value: P


title: Serum, patient 609, BRCA Mutated

description: QIAseq

value: Serum


title: 180822_P3-180822_P4-D4-AD007


title: 180822_P3-180822_P4-D4-AD002


title: Serum, patient 608, BRCA Mutated

description: QIAseq

value: Mutated


title: Serum, patient 604, BRCA Mutated

description: QIAseq

value: Healthy


title: Serum, patient 607, BRCA Mutated

description: QIAseq

value: Female


title: 180822_P3-180822_P4-D4-AD010


title: Serum, patient 603, BRCA Mutated

description: QIAseq

value: Postmenopausal


title: 180822_P3-180822_P4-D4-AD001


title: Serum, patient 605, BRCA Mutated

description: QIAseq

value: yes


title: 180822_P3-180822_P4-D3-AD010


title: 180822_P3-180822_P4-D3-AD008


title: 180822_P3-180822_P4-D3-AD002


title: 180822_P3-180822_P4-D3-AD001


title: Serum, patient 602, BRCA Mutated

description: QIAseq

value: ILLUMINA


title: Serum, patient 612, BRCA Mutated

description: QIAseq


title: Serum, patient 601, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-D2-AD010

value: brain


title: Serum, patient 625, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-D2-AD012


title: Serum, patient 599, BRCA Mutated

description: QIAseq

value: Other cancer in the future


title: 180822_P3-180822_P4-D3-AD012


title: Serum, patient 598, BRCA Mutated

description: QIAseq


title: Serum, patient 606, BRCA Mutated

description: QIAseq


title: Serum, patient 597, BRCA Mutated

description: QIAseq


title: Serum, patient 600, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-D2-AD007

value: THl

value: male


title: 180822_P3-180822_P4-D2-AD008

value: female


title: Serum, patient 595, BRCA Mutated

description: QIAseq

value: Breast cancer in the past


title: Serum, patient 596, BRCA Mutated

description: QIAseq


title: Serum, patient 594, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-D12-AD010

value: THp


title: 180822_P3-180822_P4-D2-AD001

value: THm

value: SSp


title: 180822_P3-180822_P4-D12-AD012

value: P


title: Serum, patient 593, BRCA Mutated

description: QIAseq

value: Serum

value: Mutated

value: Premenopausal


title: 180822_P3-180822_P4-D12-AD007


title: 180822_P3-180822_P4-D12-AD008


title: 180822_P3-180822_P4-D12-AD001


title: Serum, patient 592, BRCA Mutated

description: QIAseq

value: Healthy

value: Female

value: Postmenopausal


title: Serum, patient 590, BRCA Mutated

description: QIAseq

value: yes

value: ILLUMINA


title: 180822_P3-180822_P4-D12-AD002

value: brain


title: Serum, patient 591, BRCA Mutated

description: QIAseq

value: Other cancer in the future


title: Serum, patient 589, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-D11-AD012

value: female


title: 180822_P3-180822_P4-D11-AD010

value: male


title: Serum, patient 588, BRCA Mutated

description: QIAseq


title: Serum, patient 587, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D2-AD002


title: Serum, patient 585, BRCA Wild-type

description: QIAseq


title: Serum, patient 586, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D11-AD004

value: ACA


title: 180822_P3-180822_P4-D11-AD006

value: THm


title: Serum, patient 584, BRCA Wild-type

description: QIAseq


title: Serum, patient 583, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D11-AD002

value: SSp


title: 180822_P3-180822_P4-D10-AD012

value: THp

value: P


title: Serum, patient 582, BRCA Wild-type

description: QIAseq

value: Serum


title: 180822_P3-180822_P4-D11-AD001


title: 180822_P3-180822_P4-D10-AD010


title: 180822_P3-180822_P4-D10-AD007

value: THl


title: Serum, patient 579, BRCA Wild-type

description: QIAseq

value: Healthy

value: Premenopausal


title: Serum, patient 580, BRCA Wild-type

description: QIAseq

value: Female


title: 180822_P3-180822_P4-D11-AD008


title: Serum, patient 577, BRCA Wild-type

description: QIAseq

value: yes


title: Serum, patient 576, BRCA Wild-type

description: QIAseq

value: Postmenopausal

value: ILLUMINA


title: 180822_P3-180822_P4-D10-AD002

value: brain


title: 180822_P3-180822_P4-C9-AD010


title: 180822_P3-180822_P4-C9-AD008


title: 180822_P3-180822_P4-D1-AD001


title: 180822_P3-180822_P4-D11-AD007


title: Serum, patient 575, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-C9-AD007


title: 180822_P3-180822_P4-C9-AD004


title: Serum, patient 572, BRCA Wild-type

description: QIAseq


title: Serum, patient 574, BRCA Wild-type

description: QIAseq


title: Serum, patient 570, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C8-AD010


title: 180822_P3-180822_P4-C8-AD012

value: female


title: Serum, patient 573, BRCA Wild-type

description: QIAseq


title: Serum, patient 571, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C9-AD002


title: Serum, patient 569, BRCA Wild-type

description: QIAseq


title: Serum, patient 581, BRCA Wild-type

description: QIAseq


title: Serum, patient 568, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D10-AD001

value: male


title: Serum, patient 578, BRCA Wild-type

description: QIAseq


title: Serum, patient 567, BRCA Wild-type

description: QIAseq


title: Serum, patient 566, BRCA Wild-type

description: QIAseq


title: Serum, patient 565, BRCA Wild-type

description: QIAseq


title: Serum, patient 563, BRCA Wild-type

description: QIAseq


title: Serum, patient 562, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C8-AD006

value: ACA


title: Serum, patient 561, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C8-AD002

value: THm


title: 180822_P3-180822_P4-C7-AD012


title: 180822_P3-180822_P4-C7-AD010


title: 180822_P3-180822_P4-C7-AD008


title: 180822_P3-180822_P4-C7-AD007


title: 180822_P3-180822_P4-C7-AD004


title: Serum, patient 560, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C7-AD001

value: SSp


title: Serum, patient 558, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C6-AD012

value: THp


title: 180822_P3-180822_P4-C8-AD008

value: P


title: 180822_P3-180822_P4-C8-AD007


title: 180822_P3-180822_P4-C6-AD010


title: Serum, patient 557, BRCA Wild-type

description: QIAseq

value: Serum


title: Serum, patient 555, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C8-AD001


title: Serum, patient 554, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C6-AD007

value: THl


title: 180822_P3-180822_P4-C6-AD004


title: Serum, patient 556, BRCA Wild-type

description: QIAseq

value: Healthy


title: 180822_P3-180822_P4-C6-AD008


title: Serum, patient 564, BRCA Wild-type

description: QIAseq

value: Premenopausal


title: 180822_P3-180822_P4-C6-AD002


title: Serum, patient 553, BRCA Wild-type

description: QIAseq

value: Female


title: Serum, patient 552, BRCA Wild-type

description: QIAseq

value: yes


title: 180822_P3-180822_P4-C6-AD001


title: Serum, patient 551, BRCA Wild-type

description: QIAseq

value: Postmenopausal


title: 180822_P3-180822_P4-C5-AD012


title: Serum, patient 550, BRCA Wild-type

description: QIAseq

value: ILLUMINA


title: Serum, patient 549, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C5-AD010

value: brain


title: 180822_P3-180822_P4-C5-AD008


title: Serum, patient 559, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-C5-AD001


title: 180822_P3-180822_P4-C3-AD012

value: female


title: Serum, patient 546, BRCA Wild-type

description: QIAseq


title: Serum, patient 544, BRCA Wild-type

description: QIAseq


title: Serum, patient 547, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C3-AD010

value: male


title: Serum, patient 545, BRCA Wild-type

description: QIAseq


title: Serum, patient 548, BRCA Wild-type

description: QIAseq


title: Serum, patient 543, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C3-AD007


title: Serum, patient 542, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C3-AD002


title: Serum, patient 541, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C2-AD012


title: 180822_P3-180822_P4-C2-AD010


title: Serum, patient 540, BRCA Wild-type

description: QIAseq


title: Serum, patient 539, BRCA Wild-type

description: QIAseq


title: Serum, patient 537, BRCA Wild-type

description: QIAseq


title: Serum, patient 538, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C2-AD007


title: 180822_P3-180822_P4-C2-AD002


title: Serum, patient 536, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C12-AD012


title: Serum, patient 535, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C12-AD010


title: Serum, patient 534, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C5-AD002


title: 180822_P3-180822_P4-C12-AD008


title: Serum, patient 533, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C3-AD008


title: Serum, patient 530, BRCA Wild-type

description: QIAseq


title: Serum, patient 532, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C12-AD002


title: 180822_P3-180822_P4-C12-AD006

value: ACA


title: 180822_P3-180822_P4-C12-AD007


title: Serum, patient 529, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C11-AD012


title: Serum, patient 528, BRCA Wild-type

description: QIAseq


title: Serum, patient 527, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C11-AD010


title: 180822_P3-180822_P4-C2-AD008


title: 180822_P3-180822_P4-C11-AD008


title: Serum, patient 526, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C11-AD002

value: THm


title: Serum, patient 522, BRCA Wild-type

description: QIAseq


title: Serum, patient 524, BRCA Wild-type

description: QIAseq


title: Serum, patient 523, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C11-AD001

value: SSp


title: 180822_P3-180822_P4-C10-AD012

value: THp


title: 180822_P3-180822_P4-C10-AD010

value: P


title: Serum, patient 531, BRCA Wild-type

description: QIAseq

value: Serum


title: Serum, patient 521, BRCA Wild-type

description: QIAseq

value: Benign


title: 180822_P3-180822_P4-C10-AD008

value: THl


title: Serum, patient 520, BRCA Wild-type

description: QIAseq


title: Serum, patient 518, BRCA Wild-type

description: QIAseq

value: Premenopausal


title: 180822_P3-180822_P4-C12-AD001


title: 180822_P3-180822_P4-C10-AD007


title: Serum, patient 519, BRCA Wild-type

description: QIAseq

value: Female


title: 180822_P3-180822_P4-C10-AD006


title: Serum, patient 517, BRCA Wild-type

description: QIAseq

value: yes


title: Serum, patient 516, BRCA Wild-type

description: QIAseq

value: Postmenopausal


title: Serum, patient 515, BRCA Wild-type

description: QIAseq

value: ILLUMINA


title: 180822_P3-180822_P4-C10-AD004

value: brain


title: 180822_P3-180822_P4-C10-AD001


title: 180822_P3-180822_P4-C1-AD010


title: 180822_P3-180822_P4-C11-AD007


title: Serum, patient 525, BRCA Wild-type

description: QIAseq

value: Wild-type

value: Healthy


title: Serum, patient 513, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C1-AD007

value: male


title: Serum, patient 512, BRCA Wild-type

description: QIAseq


title: Serum, patient 510, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C1-AD002

value: female


title: 180822_P3-180822_P4-C1-AD006

value: THm

value: ACA


title: Serum, patient 511, BRCA Wild-type

description: QIAseq


title: Serum, patient 509, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-C1-AD001

value: SSp


title: 180822_P3-180822_P4-B9-AD012

value: THp

value: P


title: Serum, patient 508, BRCA Wild-type

description: QIAseq

value: Serum

value: Benign


title: Serum, patient 507, BRCA Wild-type

description: QIAseq

value: Premenopausal


title: 180822_P3-180822_P4-B9-AD010


title: Serum, patient 506, BRCA Wild-type

description: QIAseq

value: Female


title: 180822_P3-180822_P4-C10-AD002


title: Serum, patient 504, BRCA Wild-type

description: QIAseq

value: yes


title: Serum, patient 505, BRCA Wild-type

description: QIAseq

value: Postmenopausal


title: 180822_P3-180822_P4-C1-AD012


title: Serum, patient 503, BRCA Wild-type

description: QIAseq

value: ILLUMINA


title: 180822_P3-180822_P4-B9-AD008

value: brain

value: THl


title: Serum, patient 514, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-B9-AD006


title: 180822_P3-180822_P4-B9-AD002


title: 180822_P3-180822_P4-B9-AD007

value: male


title: 180822_P3-180822_P4-B8-AD012

value: female


title: 180822_P3-180822_P4-B9-AD001

value: THm


title: Serum, patient 502, BRCA Wild-type

description: QIAseq

value: Healthy


title: Serum, patient 501, BRCA Wild-type

description: QIAseq


title: Serum, patient 500, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B8-AD010


title: 180822_P3-180822_P4-B8-AD007


title: 180822_P3-180822_P4-B8-AD004

value: ACA


title: Serum, patient 498, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B8-AD001

value: SSp


title: Serum, patient 497, BRCA Wild-type

description: QIAseq


title: Serum, patient 496, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B8-AD002


title: Serum, patient 495, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B7-AD012

value: THp

value: P


title: 180822_P3-180822_P4-B7-AD010


title: Serum, patient 493, BRCA Wild-type

description: QIAseq

value: Serum


title: 180822_P3-180822_P4-B7-AD008


title: Serum, patient 494, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B7-AD007


title: Serum, patient 491, BRCA Wild-type

description: QIAseq

value: Premenopausal


title: 180822_P3-180822_P4-B7-AD002


title: Serum, patient 492, BRCA Wild-type

description: QIAseq

value: Female


title: 180822_P3-180822_P4-B7-AD001


title: 180822_P3-180822_P4-B6-AD012


title: 180822_P3-180822_P4-B6-AD008


title: Serum, patient 486, BRCA Wild-type

description: QIAseq

value: Benign

value: yes


title: Serum, patient 487, BRCA Wild-type

description: QIAseq

value: ILLUMINA


title: Serum, patient 490, BRCA Wild-type

description: QIAseq


title: Serum, patient 489, BRCA Wild-type

description: QIAseq

value: Postmenopausal


title: Serum, patient 499, BRCA Wild-type

description: QIAseq


title: Serum, patient 488, BRCA Wild-type

description: QIAseq


title: Serum, patient 485, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B6-AD007

value: brain

value: THl


title: 180822_P3-180822_P4-B5-AD012


title: Serum, patient 484, BRCA Wild-type

description: QIAseq

value: Wild-type


title: Serum, patient 483, BRCA Wild-type

description: QIAseq


title: Serum, patient 482, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B5-AD007

value: male


title: Serum, patient 481, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B5-AD002

value: THm

value: female


title: 180822_P3-180822_P4-B5-AD001


title: Serum, patient 480, BRCA Wild-type

description: QIAseq


title: Serum, patient 479, BRCA Wild-type

description: QIAseq

value: Healthy


title: Serum, patient 478, BRCA Wild-type

description: QIAseq


title: Serum, patient 477, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B4-AD012


title: Serum, patient 476, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B4-AD007


title: 180822_P3-180822_P4-B4-AD010


title: 180822_P3-180822_P4-B4-AD008


title: 180822_P3-180822_P4-B4-AD004

value: ACA


title: Serum, patient 475, BRCA Wild-type

description: QIAseq


title: Serum, patient 473, BRCA Wild-type

description: QIAseq


title: Serum, patient 474, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-B4-AD002

value: SSp


title: 180822_P3-180822_P4-B3-AD012

value: THp

value: P


title: 180822_P3-180822_P4-B4-AD001


title: Serum, patient 472, BRCA Wild-type

description: QIAseq

value: Serum

value: Premenopausal


title: 180822_P3-180822_P4-B5-AD008


title: 180822_P3-180822_P4-B5-AD010


title: Serum, patient 471, BRCA Mutated

description: QIAseq

value: Mutated

value: Female

value: Unknown


title: Serum, patient 470, BRCA Mutated

description: QIAseq

value: yes

value: ILLUMINA


title: 180822_P3-180822_P4-B3-AD008

value: brain

value: THl


title: 180822_P3-180822_P4-B3-AD010

value: male


title: 180822_P3-180822_P4-B3-AD007


title: 180822_P3-180822_P4-B3-AD002

value: THm


title: Serum, patient 467, BRCA Mutated

description: QIAseq


title: Serum, patient 468, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-B2-AD012

value: female


title: Serum, patient 466, BRCA Mutated

description: QIAseq

value: Healthy


title: 180822_P3-180822_P4-B2-AD010


title: 180822_P3-180822_P4-B2-AD008


title: 180822_P3-180822_P4-B6-AD010


title: Serum, patient 465, BRCA Mutated

description: QIAseq


title: Serum, patient 461, BRCA Mutated

description: QIAseq

value: Breast cancer in the future


title: 180822_P3-180822_P4-B12-AD012


title: Serum, patient 460, BRCA Mutated

description: QIAseq


title: Serum, patient 462, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-B2-AD007


title: 180822_P3-180822_P4-B2-AD002

value: SSp


title: 180822_P3-180822_P4-B12-AD010

value: THp


title: Serum, patient 459, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-B12-AD008

value: P


title: 180822_P3-180822_P4-B12-AD002


title: Serum, patient 469, BRCA Mutated

description: QIAseq

value: Serum


title: Serum, patient 458, BRCA Wild-type

description: NEXTFLEX

extract_protocol:
Libraries were prepared using NEXTflex® Small RNA-Seq v3 Automation Kit according to the manufacturer’s instructions.
Total RNA was extracted from serum using the miRCURY™ RNA isolation kit - biofluids.

value: Wild-type


title: 180822_P3-180822_P4-B12-AD007


title: 180822_P3-180822_P4-B12-AD001


title: 180822_P3-180822_P4-B3-AD001


title: Serum, patient 456, BRCA Wild-type

description: NEXTFLEX


title: 180822_P3-180822_P4-B11-AD008


title: 180822_P3-180822_P4-B11-AD007


title: Serum, patient 455, BRCA Wild-type

description: NEXTFLEX

value: Premenopausal


title: Serum, patient 453, BRCA Mutated

description: Illumina

value: Mutated

value: Female


title: Serum, patient 457, BRCA Wild-type

description: NEXTFLEX

value: Postmenopausal

value: yes


title: Serum, patient 454, BRCA Wild-type

description: NEXTFLEX

value: Unknown

value: ILLUMINA


title: 180822_P3-180822_P4-B11-AD002

value: brain


title: Serum, patient 464, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-B11-AD001

value: THm

value: male


title: 180822_P3-180822_P4-B10-AD012

value: female


title: 180822_P3-180822_P4-B10-AD010


title: Serum, patient 449, BRCA Mutated

description: Illumina

value: Healthy

value: no


title: Serum, patient 451, BRCA Mutated

description: Illumina


title: Serum, patient 448, BRCA Mutated

description: Illumina


title: Serum, patient 450, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-B10-AD006

value: ACA


title: 180822_P3-180822_P4-B10-AD007

value: THl

value: P


title: Serum, patient 446, BRCA Mutated

description: Illumina

value: Serum


title: Serum, patient 447, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-B10-AD002

value: SSp


title: 180822_P3-180822_P4-B11-AD012

value: THp


title: Serum, patient 444, BRCA Mutated

description: Illumina

value: Mutated

value: Female


title: Serum, patient 443, BRCA Mutated

description: Illumina

value: yes


title: 180822_P3-180822_P4-B1-AD012


title: Serum, patient 445, BRCA Mutated

description: Illumina

value: Unknown


title: 180822_P3-180822_P4-B10-AD001


title: Serum, patient 442, BRCA Mutated

description: Illumina

value: ILLUMINA


title: 180822_P3-180822_P4-B1-AD008

value: brain


title: Serum, patient 441, BRCA Mutated

description: Illumina


title: Serum, patient 440, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-B1-AD007


title: Serum, patient 452, BRCA Mutated

description: Illumina


title: Serum, patient 439, BRCA Mutated

description: Illumina


title: Serum, patient 463, BRCA Mutated

description: QIAseq

value: Breast cancer in the future


title: 180822_P3-180822_P4-B1-AD002

value: THm


title: 180822_P3-180822_P4-B10-AD008

value: female


title: Serum, patient 438, BRCA Mutated

description: Illumina

value: Healthy


title: 180822_P3-180822_P4-A9-AD012


title: 180822_P3-180822_P4-A9-AD010

value: male


title: 180822_P3-180822_P4-A9-AD007


title: Serum, patient 437, BRCA Mutated

description: Illumina


title: Serum, patient 436, BRCA Mutated

description: Illumina


title: Serum, patient 435, BRCA Mutated

description: Illumina

value: no


title: Serum, patient 434, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A9-AD001


title: 180822_P3-180822_P4-A9-AD002


title: 180822_P3-180822_P4-A8-AD012


title: Serum, patient 433, BRCA Mutated

description: Illumina


title: Serum, patient 430, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A8-AD002


title: Serum, patient 431, BRCA Mutated

description: Illumina


title: Serum, patient 429, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A8-AD001


title: 180822_P3-180822_P4-A7-AD012


title: 180822_P3-180822_P4-A7-AD010


title: 180822_P3-180822_P4-A7-AD002


title: Serum, patient 428, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-B1-AD010


title: Serum, patient 426, BRCA Mutated

description: Illumina


title: Serum, patient 427, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A6-AD010


title: Serum, patient 424, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A6-AD008

value: THl


title: Serum, patient 422, BRCA Mutated

description: Illumina


title: Serum, patient 432, BRCA Mutated

description: Illumina


title: Serum, patient 423, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A7-AD001


title: Serum, patient 425, BRCA Mutated

description: Illumina


title: Serum, patient 421, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A6-AD007

value: P


title: Serum, patient 420, BRCA Mutated

description: Illumina

value: Serum


title: Serum, patient 418, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A7-AD008


title: 180822_P3-180822_P4-A5-AD010


title: 180822_P3-180822_P4-A5-AD008


title: 180822_P3-180822_P4-A7-AD006

value: ACA


title: Serum, patient 416, BRCA Mutated

description: Illumina


title: 180822_P3-180822_P4-A4-AD012

value: THp


title: Serum, patient 417, BRCA Mutated

description: Illumina

value: Mutated


title: Serum, patient 419, BRCA Mutated

description: Illumina

value: Female


title: 180822_P3-180822_P4-A5-AD002

value: SSp


title: 180822_P3-180822_P4-A7-AD007


title: Serum, patient 415, BRCA Mutated

description: Illumina

value: Unknown

value: yes


title: 180822_P3-180822_P4-A4-AD010

value: brain


title: Serum, patient 413, BRCA Mutated

description: Illumina

value: ILLUMINA


title: 180822_P3-180822_P4-A4-AD008


title: 180822_P3-180822_P4-A4-AD007


title: 180822_P3-180822_P4-A6-AD001

value: THm


title: 180822_P3-180822_P4-A6-AD002

value: female


title: 180822_P3-180822_P4-A4-AD004


title: Serum, patient 409, BRCA Mutated

description: QIAseq

value: Healthy


title: 180822_P3-180822_P4-A4-AD002


title: Serum, patient 410, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A4-AD001

value: male


title: 180822_P3-180822_P4-A3-AD012


title: Serum, patient 407, BRCA Mutated

description: QIAseq

value: Breast cancer in the future

value: no


title: 180822_P3-180822_P4-A3-AD006


title: Serum, patient 406, BRCA Mutated

description: QIAseq

value: Breast cancer in the past


title: Serum, patient 405, BRCA Mutated

description: QIAseq

value: Serum


title: 180822_P3-180822_P4-A3-AD001


title: Serum, patient 404, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A3-AD002


title: 180822_P3-180822_P4-A2-AD012

value: P


title: Serum, patient 403, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A2-AD010

value: THp


title: Serum, patient 402, BRCA Mutated

description: QIAseq

value: Mutated


title: Serum, patient 414, BRCA Mutated

description: Illumina

value: Female


title: 180822_P3-180822_P4-A4-AD006

value: ACA


title: Serum, patient 412, BRCA Mutated

description: QIAseq

value: Unknown


title: Serum, patient 411, BRCA Mutated

description: QIAseq


title: Serum, patient 400, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A2-AD008

value: THl


title: 180822_P3-180822_P4-A2-AD007

value: brain


title: Serum, patient 399, BRCA Mutated

description: QIAseq

value: yes

value: ILLUMINA


title: Serum, patient 408, BRCA Mutated

description: QIAseq


title: Serum, patient 398, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A2-AD004

value: THm


title: Serum, patient 397, BRCA Mutated

description: QIAseq

value: Healthy


title: 180822_P3-180822_P4-A2-AD001

value: SSp

value: male


title: 180822_P3-180822_P4-A12-AD012

value: female


title: 180822_P3-180822_P4-A2-AD002


title: Serum, patient 396, BRCA Mutated

description: QIAseq

value: no


title: 180822_P3-180822_P4-A12-AD010


title: Serum, patient 395, BRCA Mutated

description: QIAseq

value: Serum

value: Breast cancer in the past


title: Serum, patient 394, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A12-AD007

value: P


title: Serum, patient 392, BRCA Mutated

description: QIAseq

value: Mutated


title: Serum, patient 393, BRCA Mutated

description: QIAseq

value: Female


title: Serum, patient 401, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-A12-AD008


title: Serum, patient 391, BRCA Wild-type

description: QIAseq

value: Wild-type

value: Benign

value: Postmenopausal


title: 180822_P3-180822_P4-A12-AD001

value: brain


title: Serum, patient 390, BRCA Wild-type

description: QIAseq

value: Premenopausal

value: yes


title: 180822_P3-180822_P4-A11-AD008

value: THl


title: Serum, patient 388, BRCA Wild-type

description: QIAseq

value: ILLUMINA


title: 180822_P3-180822_P4-A11-AD007


title: Serum, patient 386, BRCA Wild-type

description: QIAseq


title: Serum, patient 389, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A10-AD012

value: THp


title: Serum, patient 385, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A11-AD001

value: THm

value: SSp

value: male


title: Serum, patient 384, BRCA Wild-type

description: QIAseq

value: Serum


title: Serum, patient 383, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A10-AD008

value: female


title: 180822_P3-180822_P4-A10-AD007

value: P


title: Serum, patient 382, BRCA Wild-type

description: QIAseq


title: Serum, patient 381, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A10-AD001


title: 180822_P3-180822_P4-A11-AD012


title: 180822_P3-180822_P4-A12-AD002


title: 180822_P3-180822_P4-A10-AD002


title: Serum, patient 379, BRCA Wild-type

description: QIAseq


title: Serum, patient 378, BRCA Wild-type

description: QIAseq


title: Serum, patient 380, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A1-AD010


title: 180822_P3-180822_P4-A1-AD012


title: Serum, patient 387, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A1-AD008


title: Serum, patient 376, BRCA Wild-type

description: QIAseq


title: Serum, patient 375, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A1-AD002


title: Serum, patient 374, BRCA Wild-type

description: QIAseq


title: Serum, patient 373, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-A1-AD001


title: 180822_P3-180822_P4-A10-AD010


title: 180822_P1-180822_P2-H9-AD010

value: ACA


title: Serum, patient 372, BRCA Wild-type

description: QIAseq

value: Female


title: 180822_P1-180822_P2-H9-AD008


title: Serum, patient 371, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-A11-AD002


title: 180822_P3-180822_P4-A1-AD007


title: 180822_P1-180822_P2-H9-AD004


title: Serum, patient 369, BRCA Wild-type

description: QIAseq

value: Benign


title: Serum, patient 368, BRCA Wild-type

description: QIAseq

value: Postmenopausal


title: 180822_P1-180822_P2-H8-AD010

value: brain


title: 180822_P1-180822_P2-H9-AD001


title: Serum, patient 377, BRCA Wild-type

description: QIAseq

value: Premenopausal


title: 180822_P1-180822_P2-H9-AD002


title: Serum, patient 367, BRCA Wild-type

description: QIAseq

value: yes


title: 180822_P1-180822_P2-H8-AD008

value: THl


title: Serum, patient 365, BRCA Wild-type

description: QIAseq

value: ILLUMINA


title: 180822_P1-180822_P2-H8-AD004

value: THp


title: Serum, patient 366, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H8-AD002


title: Serum, patient 364, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H8-AD001


title: Serum, patient 363, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H7-AD010


title: Serum, patient 362, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H9-AD007


title: 180822_P1-180822_P2-H7-AD008


title: Serum, patient 360, BRCA Wild-type

description: QIAseq


title: Serum, patient 361, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H7-AD007


title: 180822_P1-180822_P2-H7-AD004


title: Serum, patient 359, BRCA Wild-type

description: QIAseq


title: Serum, patient 358, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H7-AD002


title: Serum, patient 370, BRCA Wild-type

description: QIAseq


title: Serum, patient 356, BRCA Wild-type

description: QIAseq


title: Serum, patient 357, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H7-AD001


title: 180822_P1-180822_P2-H6-AD010


title: 180822_P1-180822_P2-H6-AD008


title: 180822_P1-180822_P2-H6-AD007


title: Serum, patient 353, BRCA Wild-type

description: QIAseq


title: Serum, patient 352, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H6-AD004


title: Serum, patient 354, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H6-AD002


title: Serum, patient 351, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H6-AD001


title: Serum, patient 349, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H5-AD012


title: Serum, patient 348, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H7-AD006


title: 180822_P1-180822_P2-H5-AD010


title: Serum, patient 350, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H5-AD008


title: 180822_P1-180822_P2-H5-AD002


title: Serum, patient 346, BRCA Wild-type

description: QIAseq


title: Serum, patient 345, BRCA Wild-type

description: QIAseq

value: Healthy


title: Serum, patient 347, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H5-AD001

value: SSp


title: 180822_P1-180822_P2-H4-AD012


title: Serum, patient 344, BRCA Wild-type

description: QIAseq


title: Serum, patient 355, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H4-AD010

value: male


title: Serum, patient 343, BRCA Wild-type

description: QIAseq

value: Serum


title: Serum, patient 342, BRCA Wild-type

description: QIAseq


title: Serum, patient 341, BRCA Wild-type

description: QIAseq


title: Serum, patient 340, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H4-AD008

value: female


title: 180822_P1-180822_P2-H4-AD006


title: Serum, patient 339, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H4-AD002


title: 180822_P1-180822_P2-H4-AD001


title: 180822_P1-180822_P2-H3-AD010


title: Serum, patient 338, BRCA Wild-type

description: QIAseq


title: Serum, patient 337, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H3-AD006


title: Serum, patient 336, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H3-AD004


title: 180822_P1-180822_P2-H3-AD002


title: Serum, patient 335, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H3-AD001


title: Serum, patient 333, BRCA Wild-type

description: QIAseq


title: Serum, patient 331, BRCA Wild-type

description: QIAseq


title: Serum, patient 332, BRCA Wild-type

description: QIAseq


title: Serum, patient 330, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H2-AD010


title: 180822_P1-180822_P2-H2-AD007


title: 180822_P1-180822_P2-H4-AD007


title: 180822_P1-180822_P2-H2-AD008


title: Serum, patient 329, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H2-AD006


title: Serum, patient 327, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H2-AD004


title: 180822_P1-180822_P2-H2-AD001


title: 180822_P1-180822_P2-H12-AD010


title: 180822_P1-180822_P2-H12-AD008


title: Serum, patient 325, BRCA Wild-type

description: QIAseq


title: Serum, patient 323, BRCA Wild-type

description: QIAseq


title: Serum, patient 334, BRCA Wild-type

description: QIAseq


title: Serum, patient 322, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H12-AD006


title: 180822_P1-180822_P2-H2-AD002


title: Serum, patient 321, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H12-AD007


title: 180822_P1-180822_P2-H12-AD004


title: Serum, patient 320, BRCA Wild-type

description: QIAseq


title: Serum, patient 324, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H12-AD002


title: Serum, patient 319, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H11-AD010


title: Serum, patient 318, BRCA Wild-type

description: QIAseq


title: Serum, patient 328, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H11-AD008


title: Serum, patient 316, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H11-AD007


title: Serum, patient 326, BRCA Wild-type

description: QIAseq


title: Serum, patient 315, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H11-AD004


title: 180822_P1-180822_P2-H11-AD001


title: 180822_P1-180822_P2-H11-AD002


title: Serum, patient 314, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H10-AD008


title: Serum, patient 312, BRCA Wild-type

description: QIAseq


title: Serum, patient 311, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H10-AD006


title: 180822_P1-180822_P2-H10-AD004


title: Serum, patient 310, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H10-AD002


title: Serum, patient 309, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H10-AD001


title: Serum, patient 308, BRCA Wild-type

description: QIAseq


title: Serum, patient 307, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H1-AD010


title: Serum, patient 317, BRCA Wild-type

description: QIAseq


title: Serum, patient 306, BRCA Wild-type

description: QIAseq


title: Serum, patient 305, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H12-AD001


title: Serum, patient 304, BRCA Wild-type

description: QIAseq


title: Serum, patient 303, BRCA Wild-type

description: QIAseq


title: Serum, patient 313, BRCA Wild-type

description: QIAseq


title: Serum, patient 302, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H1-AD007


title: 180822_P1-180822_P2-H1-AD006


title: 180822_P1-180822_P2-H1-AD008


title: Serum, patient 301, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-H1-AD002


title: Serum, patient 300, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G9-AD012


title: 180822_P1-180822_P2-H10-AD007


title: 180822_P1-180822_P2-H1-AD001


title: Serum, patient 299, BRCA Wild-type

description: QIAseq


title: Serum, patient 298, BRCA Wild-type

description: QIAseq


title: Serum, patient 297, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G9-AD004


title: Serum, patient 296, BRCA Wild-type

description: QIAseq


title: Serum, patient 295, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G9-AD001


title: 180822_P1-180822_P2-G8-AD010


title: Serum, patient 294, BRCA Wild-type

description: QIAseq


title: Serum, patient 292, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G8-AD007


title: 180822_P1-180822_P2-G8-AD006


title: 180822_P1-180822_P2-G8-AD004


title: Serum, patient 291, BRCA Wild-type

description: QIAseq


title: Serum, patient 289, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G8-AD001


title: Serum, patient 290, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G8-AD002


title: 180822_P1-180822_P2-G9-AD008


title: Serum, patient 287, BRCA Wild-type

description: QIAseq


title: Serum, patient 288, BRCA Wild-type

description: QIAseq


title: Serum, patient 286, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G9-AD002


title: 180822_P1-180822_P2-G7-AD007


title: 180822_P1-180822_P2-G7-AD008


title: 180822_P1-180822_P2-G7-AD006


title: Serum, patient 285, BRCA Wild-type

description: QIAseq


title: Serum, patient 284, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G7-AD004


title: 180822_P1-180822_P2-G7-AD002


title: Serum, patient 283, BRCA Wild-type

description: QIAseq


title: Serum, patient 293, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G9-AD007


title: 180822_P1-180822_P2-G7-AD001


title: 180822_P1-180822_P2-G6-AD010


title: Serum, patient 281, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G6-AD008


title: 180822_P1-180822_P2-G6-AD007


title: Serum, patient 279, BRCA Wild-type

description: QIAseq


title: Serum, patient 280, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G6-AD006


title: 180822_P1-180822_P2-G7-AD010


title: Serum, patient 278, BRCA Wild-type

description: QIAseq


title: Serum, patient 275, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G6-AD004


title: Serum, patient 277, BRCA Wild-type

description: QIAseq


title: Serum, patient 276, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G6-AD001


title: 180822_P1-180822_P2-G6-AD002


title: Serum, patient 274, BRCA Wild-type

description: QIAseq


title: Serum, patient 273, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G5-AD006


title: 180822_P1-180822_P2-G5-AD010


title: Serum, patient 282, BRCA Wild-type

description: QIAseq


title: Serum, patient 272, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G5-AD004


title: Serum, patient 270, BRCA Wild-type

description: QIAseq


title: Serum, patient 271, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G5-AD002


title: Serum, patient 269, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G5-AD001


title: 180822_P1-180822_P2-G4-AD012


title: Serum, patient 268, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G4-AD010


title: Serum, patient 267, BRCA Wild-type

description: QIAseq


title: Serum, patient 266, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G4-AD006


title: Serum, patient 265, BRCA Wild-type

description: QIAseq


title: Serum, patient 263, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G4-AD001


title: Serum, patient 262, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G3-AD010


title: 180822_P1-180822_P2-G5-AD008


title: Serum, patient 264, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G4-AD004


title: Serum, patient 261, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G3-AD007


title: 180822_P1-180822_P2-G3-AD006


title: Serum, patient 258, BRCA Wild-type

description: QIAseq


title: Serum, patient 256, BRCA Wild-type

description: QIAseq


title: Serum, patient 259, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G3-AD008


title: 180822_P1-180822_P2-G3-AD001


title: Serum, patient 260, BRCA Wild-type

description: QIAseq


title: Serum, patient 255, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G2-AD012


title: Serum, patient 254, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G2-AD010


title: 180822_P1-180822_P2-G4-AD007


title: 180822_P1-180822_P2-G2-AD008


title: Serum, patient 252, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G4-AD002


title: Serum, patient 250, BRCA Wild-type

description: QIAseq


title: Serum, patient 249, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G2-AD007


title: Serum, patient 251, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G2-AD004


title: 180822_P1-180822_P2-G2-AD006


title: Serum, patient 248, BRCA Wild-type

description: QIAseq


title: Serum, patient 247, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G3-AD002


title: 180822_P1-180822_P2-G2-AD001


title: 180822_P1-180822_P2-G3-AD004


title: 180822_P1-180822_P2-G12-AD008


title: 180822_P1-180822_P2-G12-AD007


title: Serum, patient 257, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G12-AD006


title: Serum, patient 245, BRCA Wild-type

description: QIAseq


title: Serum, patient 243, BRCA Wild-type

description: QIAseq


title: Serum, patient 244, BRCA Wild-type

description: QIAseq


title: Serum, patient 253, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G12-AD002


title: Serum, patient 242, BRCA Wild-type

description: QIAseq


title: 180822_P1-180822_P2-G12-AD001


title: 180822_P1-180822_P2-G11-AD010


title: Serum, patient 241, BRCA Mutated

description: QIAseq

value: Mutated

value: Unknown


title: Serum, patient 240, BRCA Mutated

description: QIAseq

value: Female


title: 180822_P1-180822_P2-G11-AD002


title: 180822_P1-180822_P2-G2-AD002


title: 180822_P1-180822_P2-G11-AD004


title: Serum, patient 239, BRCA Mutated

description: QIAseq


title: Serum, patient 238, BRCA Mutated

description: QIAseq


title: Serum, patient 236, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G11-AD001


title: Serum, patient 246, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P1-180822_P2-G10-AD010

value: ACA


title: 180822_P1-180822_P2-G10-AD008


title: Serum, patient 235, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G10-AD004


title: Serum, patient 234, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G10-AD007


title: Serum, patient 232, BRCA Mutated

description: QIAseq


title: Serum, patient 233, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G10-AD001


title: 180822_P1-180822_P2-G1-AD010


title: Serum, patient 230, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G1-AD012


title: 180822_P1-180822_P2-G10-AD002


title: Serum, patient 231, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G1-AD008


title: 180822_P1-180822_P2-G1-AD007


title: Serum, patient 237, BRCA Mutated

description: QIAseq


title: Serum, patient 228, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G1-AD006


title: Serum, patient 226, BRCA Mutated

description: QIAseq


title: Serum, patient 227, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-G1-AD002


title: Serum, patient 225, BRCA Mutated

description: QIAseq


title: Serum, patient 224, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F9-AD010


title: 180822_P1-180822_P2-F9-AD007


title: Serum, patient 223, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F9-AD008


title: 180822_P1-180822_P2-F9-AD004


title: Serum, patient 222, BRCA Mutated

description: QIAseq

value: Breast cancer in the future


title: Serum, patient 221, BRCA Mutated

description: QIAseq


title: Serum, patient 229, BRCA Mutated

description: QIAseq


title: Serum, patient 220, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F9-AD002

value: brain


title: Serum, patient 218, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F9-AD001


title: Serum, patient 216, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F8-AD010


title: 180822_P1-180822_P2-F8-AD007


title: 180822_P1-180822_P2-F8-AD008


title: 180822_P1-180822_P2-G1-AD001


title: Serum, patient 217, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F8-AD006


title: Serum, patient 213, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F8-AD004


title: 180822_P1-180822_P2-F8-AD001


title: Serum, patient 214, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F8-AD002


title: Serum, patient 212, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F7-AD012


title: 180822_P1-180822_P2-F7-AD010


title: Serum, patient 219, BRCA Mutated

description: QIAseq


title: Serum, patient 210, BRCA Mutated

description: QIAseq


title: Serum, patient 211, BRCA Mutated

description: QIAseq


title: Serum, patient 209, BRCA Mutated

description: QIAseq


title: Serum, patient 208, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F7-AD007


title: 180822_P1-180822_P2-F7-AD008


title: Serum, patient 207, BRCA Mutated

description: QIAseq


title: Serum, patient 206, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F7-AD004


title: Serum, patient 205, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F6-AD012


title: Serum, patient 215, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F7-AD001


title: Serum, patient 203, BRCA Mutated

description: QIAseq


title: Serum, patient 202, BRCA Wild-type

description: NEXTFLEX


title: 180822_P1-180822_P2-F6-AD010


title: Serum, patient 204, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-F6-AD004


title: Serum, patient 201, BRCA Wild-type

description: NEXTFLEX


title: 180822_P1-180822_P2-F6-AD002


title: 180822_P1-180822_P2-F6-AD007


title: Serum, patient 198, BRCA Wild-type

description: NEXTFLEX


title: 180822_P1-180822_P2-F5-AD008


title: Serum, patient 200, BRCA Wild-type

description: NEXTFLEX

value: Premenopausal


title: 180822_P1-180822_P2-F5-AD007


title: Serum, patient 197, BRCA Wild-type

description: NEXTFLEX

value: yes


title: Serum, patient 196, BRCA Wild-type

description: NEXTFLEX


title: 180822_P1-180822_P2-F5-AD006


title: 180822_P1-180822_P2-F7-AD002

value: THl


title: Serum, patient 199, BRCA Wild-type

description: NEXTFLEX

value: ILLUMINA


title: 180822_P1-180822_P2-F5-AD002


title: 180822_P1-180822_P2-F5-AD001


title: 180822_P1-180822_P2-F4-AD012

value: THp


title: Serum, patient 193, BRCA Wild-type

description: NEXTFLEX

value: Healthy


title: Serum, patient 192, BRCA Wild-type

description: NEXTFLEX

value: Postmenopausal


title: Serum, patient 194, BRCA Wild-type

description: NEXTFLEX


title: Serum, patient 191, BRCA Wild-type

description: NEXTFLEX


title: 180822_P1-180822_P2-F4-AD008


title: 180822_P1-180822_P2-F5-AD010

value: male


title: Serum, patient 190, BRCA Wild-type

description: NEXTFLEX

value: Serum


title: Serum, patient 188, BRCA Wild-type

description: NEXTFLEX


title: 180822_P1-180822_P2-F4-AD007


title: Serum, patient 189, BRCA Wild-type

description: NEXTFLEX


title: Serum, patient 187, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F3-AD012

value: female


title: 180822_P1-180822_P2-F4-AD001

value: SSp


title: 180822_P1-180822_P2-F4-AD002


title: Serum, patient 186, BRCA Mutated

description: Illumina

value: Mutated

value: Unknown


title: 180822_P1-180822_P2-F3-AD007


title: 180822_P1-180822_P2-F3-AD006


title: Serum, patient 185, BRCA Mutated

description: Illumina

value: Female

value: no


title: Serum, patient 195, BRCA Wild-type

description: NEXTFLEX

value: Wild-type


title: Serum, patient 184, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F3-AD002

value: brain


title: Serum, patient 183, BRCA Mutated

description: Illumina


title: Serum, patient 182, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F3-AD001


title: 180822_P1-180822_P2-F2-AD010

value: ACA


title: Serum, patient 181, BRCA Mutated

description: Illumina

value: yes


title: Serum, patient 179, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F2-AD006


title: 180822_P1-180822_P2-F2-AD007

value: THl


title: Serum, patient 180, BRCA Mutated

description: Illumina

value: ILLUMINA


title: Serum, patient 178, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F2-AD008


title: 180822_P1-180822_P2-F2-AD004

value: THp


title: Serum, patient 176, BRCA Mutated

description: Illumina

value: Healthy


title: 180822_P1-180822_P2-F2-AD001


title: Serum, patient 175, BRCA Mutated

description: Illumina


title: Serum, patient 174, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F12-AD008


title: 180822_P1-180822_P2-F3-AD004


title: Serum, patient 173, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F12-AD010


title: 180822_P1-180822_P2-F2-AD002


title: Serum, patient 172, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F12-AD004


title: 180822_P1-180822_P2-F12-AD002


title: Serum, patient 170, BRCA Mutated

description: Illumina


title: Serum, patient 171, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F12-AD006


title: Serum, patient 169, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F11-AD010


title: Serum, patient 168, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F11-AD008


title: Serum, patient 166, BRCA Mutated

description: Illumina


title: Serum, patient 167, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F11-AD004


title: 180822_P1-180822_P2-F11-AD006


title: 180822_P1-180822_P2-F11-AD002


title: Serum, patient 165, BRCA Mutated

description: Illumina


title: Serum, patient 164, BRCA Mutated

description: Illumina


title: Serum, patient 163, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F10-AD007


title: Serum, patient 161, BRCA Mutated

description: Illumina


title: Serum, patient 162, BRCA Mutated

description: Illumina


title: Serum, patient 159, BRCA Mutated

description: Illumina


title: Serum, patient 160, BRCA Mutated

description: Illumina


title: Serum, patient 158, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F12-AD001


title: 180822_P1-180822_P2-F10-AD002


title: 180822_P1-180822_P2-F1-AD012


title: Serum, patient 155, BRCA Mutated

description: Illumina


title: Serum, patient 156, BRCA Mutated

description: Illumina


title: Serum, patient 154, BRCA Mutated

description: Illumina


title: Serum, patient 153, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F1-AD007


title: Serum, patient 152, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F1-AD010


title: Serum, patient 177, BRCA Mutated

description: Illumina


title: Serum, patient 150, BRCA Mutated

description: Illumina


title: Serum, patient 151, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F10-AD008


title: Serum, patient 149, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F1-AD006


title: Serum, patient 148, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F1-AD004


title: Serum, patient 147, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F10-AD001


title: Serum, patient 146, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-F1-AD001


title: Serum, patient 144, BRCA Mutated

description: Illumina


title: Serum, patient 157, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E9-AD010


title: 180822_P1-180822_P2-E9-AD007


title: Serum, patient 142, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E9-AD006


title: Serum, patient 139, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E9-AD004


title: Serum, patient 138, BRCA Mutated

description: Illumina


title: Serum, patient 141, BRCA Mutated

description: Illumina


title: Serum, patient 140, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E9-AD002


title: Serum, patient 135, BRCA Mutated

description: Illumina


title: Serum, patient 136, BRCA Mutated

description: Illumina


title: Serum, patient 137, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E8-AD012


title: 180822_P1-180822_P2-E8-AD007


title: 180822_P1-180822_P2-E8-AD008


title: Serum, patient 145, BRCA Mutated

description: Illumina


title: Serum, patient 133, BRCA Mutated

description: Illumina


title: Serum, patient 130, BRCA Mutated

description: Illumina


title: Serum, patient 132, BRCA Mutated

description: Illumina


title: Serum, patient 143, BRCA Mutated

description: Illumina


title: Serum, patient 129, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E8-AD004


title: 180822_P1-180822_P2-E8-AD002


title: Serum, patient 127, BRCA Mutated

description: Illumina


title: Serum, patient 126, BRCA Mutated

description: Illumina


title: Serum, patient 128, BRCA Mutated

description: Illumina


title: Serum, patient 125, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E8-AD001


title: Serum, patient 124, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD012


title: 180822_P1-180822_P2-F4-AD010


title: Serum, patient 121, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD010


title: Serum, patient 120, BRCA Mutated

description: Illumina


title: Serum, patient 119, BRCA Mutated

description: Illumina


title: Serum, patient 131, BRCA Mutated

description: Illumina


title: Serum, patient 134, BRCA Mutated

description: Illumina


title: Serum, patient 122, BRCA Mutated

description: Illumina


title: Serum, patient 118, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD007


title: Serum, patient 117, BRCA Mutated

description: Illumina


title: Serum, patient 116, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD006


title: Serum, patient 115, BRCA Mutated

description: Illumina


title: Serum, patient 114, BRCA Mutated

description: Illumina


title: Serum, patient 113, BRCA Mutated

description: Illumina


title: Serum, patient 112, BRCA Mutated

description: Illumina


title: Serum, patient 110, BRCA Mutated

description: Illumina


title: Serum, patient 111, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD004


title: Serum, patient 123, BRCA Mutated

description: Illumina


title: Serum, patient 108, BRCA Mutated

description: Illumina


title: Serum, patient 109, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD002


title: Serum, patient 107, BRCA Mutated

description: Illumina


title: Serum, patient 106, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E7-AD001


title: Serum, patient 105, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD008


title: Serum, patient 104, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD007


title: Serum, patient 101, BRCA Mutated

description: Illumina


title: Serum, patient 103, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD006


title: Serum, patient 99, BRCA Mutated

description: Illumina


title: Serum, patient 102, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD004


title: Serum, patient 98, BRCA Mutated

description: Illumina


title: Serum, patient 97, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD002


title: Serum, patient 96, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD010


title: Serum, patient 94, BRCA Mutated

description: Illumina


title: Serum, patient 95, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E6-AD001


title: 180822_P1-180822_P2-E5-AD010


title: 180822_P1-180822_P2-E5-AD008


title: Serum, patient 93, BRCA Mutated

description: Illumina


title: Serum, patient 90, BRCA Mutated

description: Illumina


title: Serum, patient 92, BRCA Mutated

description: Illumina


title: Serum, patient 89, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E5-AD007


title: Serum, patient 88, BRCA Mutated

description: Illumina


title: Serum, patient 87, BRCA Mutated

description: Illumina


title: Serum, patient 100, BRCA Mutated

description: Illumina


title: Serum, patient 86, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E5-AD004


title: Serum, patient 85, BRCA Mutated

description: Illumina


title: Serum, patient 83, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E5-AD002


title: 180822_P1-180822_P2-E5-AD001


title: Serum, patient 82, BRCA Mutated

description: Illumina


title: Serum, patient 81, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E4-AD012


title: Serum, patient 80, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E4-AD008


title: Serum, patient 91, BRCA Mutated

description: Illumina


title: Serum, patient 78, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E4-AD007


title: Serum, patient 75, BRCA Mutated

description: Illumina


title: Serum, patient 76, BRCA Mutated

description: Illumina


title: Serum, patient 74, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E4-AD004


title: Serum, patient 72, BRCA Mutated

description: Illumina


title: Serum, patient 73, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E4-AD002


title: 180822_P1-180822_P2-E4-AD006


title: Serum, patient 84, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E5-AD006


title: Serum, patient 69, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E4-AD001


title: Serum, patient 68, BRCA Mutated

description: Illumina


title: Serum, patient 67, BRCA Mutated

description: Illumina


title: Serum, patient 79, BRCA Mutated

description: Illumina


title: Serum, patient 64, BRCA Mutated

description: QIAseq

value: Breast cancer in the past


title: Serum, patient 66, BRCA Mutated

description: QIAseq


title: Serum, patient 63, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E3-AD007

value: male


title: Serum, patient 65, BRCA Mutated

description: QIAseq

value: Serum

value: Breast cancer in the future


title: 180822_P1-180822_P2-E3-AD006

value: SSp

value: female


title: 180822_P1-180822_P2-E3-AD008


title: Serum, patient 61, BRCA Mutated

description: QIAseq

value: Mutated

value: Unknown


title: Serum, patient 62, BRCA Mutated

description: QIAseq

value: Female

value: no


title: Serum, patient 77, BRCA Mutated

description: Illumina


title: 180822_P1-180822_P2-E3-AD004

value: brain


title: Serum, patient 59, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E3-AD002


title: Serum, patient 70, BRCA Mutated

description: Illumina


title: Serum, patient 71, BRCA Mutated

description: Illumina


title: Serum, patient 57, BRCA Mutated

description: QIAseq


title: Serum, patient 55, BRCA Mutated

description: QIAseq


title: Serum, patient 56, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E3-AD001


title: Serum, patient 54, BRCA Mutated

description: QIAseq


title: Serum, patient 53, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E2-AD012

value: ACA


title: Serum, patient 51, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E2-AD010


title: 180822_P1-180822_P2-E2-AD008


title: Serum, patient 52, BRCA Mutated

description: QIAseq


title: Serum, patient 49, BRCA Mutated

description: QIAseq

value: yes


title: Serum, patient 50, BRCA Mutated

description: QIAseq


title: Serum, patient 48, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E2-AD006


title: Serum, patient 47, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E2-AD002

value: THl


title: Serum, patient 60, BRCA Mutated

description: QIAseq

value: ILLUMINA


title: Serum, patient 44, BRCA Mutated

description: QIAseq


title: Serum, patient 58, BRCA Mutated

description: QIAseq


title: Serum, patient 43, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E12-AD010

value: THp


title: Serum, patient 42, BRCA Mutated

description: QIAseq


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P5_190321_P6_E9_ad010

value: VISp


title: Serum, patient 41, BRCA Mutated

description: QIAseq

value: Breast cancer in the past


title: 180822_P1-180822_P2-E2-AD001

value: male


title: 180822_P1-180822_P2-E12-AD008


title: Serum, patient 37, BRCA Mutated

description: QIAseq

value: Serum


title: Serum, patient 39, BRCA Mutated

description: QIAseq

value: Healthy


title: Serum, patient 36, BRCA Mutated

description: QIAseq


title: Serum, patient 35, BRCA Mutated

description: QIAseq

value: Breast cancer in the future


title: 180822_P1-180822_P2-E12-AD006

value: SSp

value: female


title: 180822_P1-180822_P2-E12-AD007


title: Serum, patient 38, BRCA Mutated

description: QIAseq

value: Mutated

value: Unknown


title: Serum, patient 40, BRCA Mutated

description: QIAseq

value: Female


title: Serum, patient 33, BRCA Mutated

description: QIAseq


title: Serum, patient 34, BRCA Mutated

description: QIAseq


title: Serum, patient 31, BRCA Mutated

description: QIAseq

value: no


title: Serum, patient 46, BRCA Mutated

description: QIAseq


title: Serum, patient 30, BRCA Mutated

description: QIAseq


title: Serum, patient 32, BRCA Mutated

description: QIAseq


title: Serum, patient 45, BRCA Mutated

description: QIAseq


title: Serum, patient 29, BRCA Mutated

description: QIAseq


title: Serum, patient 28, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E12-AD001

value: brain


title: Serum, patient 27, BRCA Mutated

description: QIAseq

value: yes


title: Serum, patient 25, BRCA Mutated

description: QIAseq


title: Serum, patient 26, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E11-AD006


title: Serum, patient 24, BRCA Mutated

description: QIAseq


title: Serum, patient 23, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E11-AD004


title: Serum, patient 22, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E12-AD004


title: Serum, patient 19, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E10-AD010

value: ACA


title: Serum, patient 21, BRCA Mutated

description: QIAseq

value: ILLUMINA


title: 180822_P1-180822_P2-E11-AD002

value: THl


title: Serum, patient 17, BRCA Mutated

description: QIAseq


title: Serum, patient 20, BRCA Mutated

description: QIAseq


title: Serum, patient 16, BRCA Mutated

description: QIAseq


title: Serum, patient 18, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E11-AD010

value: THp


title: Serum, patient 15, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E11-AD008


title: 180822_P1-180822_P2-E10-AD008


title: 180822_P1-180822_P2-E11-AD001


title: Serum, patient 14, BRCA Mutated

description: QIAseq


title: Serum, patient 13, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E10-AD001


title: Serum, patient 11, BRCA Mutated

description: QIAseq


title: Serum, patient 10, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E1-AD012


title: Serum, patient 8, BRCA Mutated

description: QIAseq


title: Serum, patient 7, BRCA Mutated

description: QIAseq

value: Breast cancer in the past


title: 180822_P1-180822_P2-E10-AD004

value: male


title: Serum, patient 6, BRCA Mutated

description: QIAseq

value: Serum


title: 180822_P1-180822_P2-E1-AD008


title: Serum, patient 5, BRCA Mutated

description: QIAseq

value: Healthy


title: Serum, patient 3, BRCA Mutated

description: QIAseq


title: Serum, patient 4, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E1-AD007


title: 180822_P1-180822_P2-E1-AD006


title: Serum, patient 2, BRCA Mutated

description: QIAseq


title: 180822_P1-180822_P2-E1-AD004


title: Serum, patient 1, BRCA Mutated

description: QIAseq


title: 3LWbrain, 12xWT, F, rep2

city: Chapel Hill

first: Gregory

last: Matera

state: North Carolina

address: Genome Science Building

institute: University of North Carolina at Chapel Hill

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk (parameters: ktrim=r, k=23, rcomp=t, tbo=t, tpe=t, hdist=1, mink=11). BBMap v38.67.
Dm6 genome files for use with the STAR aligner were generated using parameters: sjdbOverhang 99. Paired-end sequencing reads were aligned using STAR v2.7.7a with default parameters.
Bam files were indexed and sorted using samtools v1.9.
Bam files were converted to bed files using bbtools bamtobed with default parameters (bedtools v2.26).
Bam files were converted to bigwig files using deeptools v3.2.0. Samples were RPGC normalization, and a bin size of 10 was used. A genome size of 137547960 was used.
featureCounts (subread v2.0.1) was used for read summarization with parameters: T=4, t = exon.
DESeq2 (v1.34.0) was used to identify differentially expressed genes.
Assembly: dm6
Supplementary files format and content: DESeq2 output text file including log2FoldChange, lfcSE, stat, pvalue, padj, baseMean.log, and Log10padj data for all genes.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: third instar larval brain

extract_protocol:
25 brains were dissected from wandering 3rd instar larvae and homogenized in Trizol solution. RNA was isolated from the Trizol aqueous phase using the Zymo RNA Clean and Concentrator-5 kit (Genesee Scientific #11-352) including treatment with DNAse I, as per the manufacturer’s instructions.
Libraries were prepared from polyA selected RNA using the KAPA stranded mRNA kit (Roche # 07962207001)

value: third instar larval brain

tag: genotype


title: 3LWbrain, 12xWT, F, rep3


title: 3LWbrain, 12xWT, M, rep3

value: Male


title: 3LWbrain, 12xWT, F, rep1


title: 180822_P1-180822_P2-D9-AD007


title: 180822_P1-180822_P2-E1-AD001

value: SSp


title: 180822_P1-180822_P2-D9-AD006

value: female


title: 180822_P1-180822_P2-D9-AD010


title: 3LWbrain, 12xWT, M, rep2


title: 180822_P1-180822_P2-D9-AD004


title: 180822_P1-180822_P2-E10-AD002


title: 3LWbrain, 12xWT, M, rep1


title: Serum, patient 12, BRCA Mutated

description: QIAseq

value: Mutated

value: Unknown


title: Serum, patient 9, BRCA Mutated

description: QIAseq

value: Female


title: 180822_P1-180822_P2-D9-AD008

value: brain


title: 3LWbrain, yw, M, rep1

value: yw


title: 3LWbrain, yw, F, rep2


title: 180822_P1-180822_P2-D9-AD002


title: 3LWbrain, yw, F, rep1


title: 180822_P1-180822_P2-D9-AD001


title: 180822_P1-180822_P2-D8-AD012

value: ACA


title: S2-WT_aGrh_input_rep2 b

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
Bowtie2 version 2.4.4 was used to align ChIP-seq reads to the Drosophila melanogaster genome (version dm6) with the following non-default parameters: -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Aligned reads were filtered to include only reads with a mapping quality score > 30. Reads mapping to unplaced scaffolds or the mitochondrial genome were discarded.
. Peak calling was performed using MACS2 version 2.2 with parameters -g dm --call-summits. Only peaks that were detected in all replicates were considered in downstream analysis.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigwig file: contains z-score normalized read depth for each sample. Reads from two biological replicates were combined prior to generation of bigWig.
Supplementary files format and content: narrowPeak files: contain MACS2 peaks for ChIP samples.

growth_protocol: Drosophila S2 cells were cultured at 27°C in Schneider's medium supplemented with 10% fetal bovine serum  and antibiotic/antimycotic.

extract_protocol:
For each ChIP experiment, ~50 million cells were crosslinked by adding methanol-free formaldehyde directly to the cell culture medium to a final concentration of 0.8%. Cells were rotated on a nutator for 7 minutes at room temperature (RT) before quenching of crosslinking by adding glycine to 125 mM. Crosslinked cells were pelleted by centrifugation at 600 × g for 3 minutes. Cells were washed twice with 1X PBS. Cells were lysed by resuspending in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X 100) with protease inhibitors (Pierce) and incubating on ice for 10 minutes. The resulting chromatin was pelleted for 5 minutes at 1500 × g and resuspended in RIPA buffer. Chromatin was sonicated in a Covaris S220 Ultrasonicator (5 cycles of 120 seconds with 60 second delay, 170 peak power, 10% duty factor, 200 cycles/burst). Sonicated chromatin was centrifuged for 10 minutes at 10,000 × g to pellet insoluble material. 5% of the supernatant was set aside as input, and the remainder was incubated at 4°C overnight with antibodies (6 µL anti-Zld, 8 µL anti-Grh, 10 µg anti-Twi, 7.5 µL anti-HA). 20 µL protein A beads (Dynabeads Protein A, ThermoFisher Scientific) blocked with BSA were added and samples were incubated at 4°C for 4 hours. Beads were separated on a magnet and washed 3× with low salt wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton-X 100, 150 mM NaCl), 2× high salt wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton-X 100, 300 mM NaC), 2× LiCl wash buffer (0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate), and 1× with TE buffer with NaCl (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). Beads were resuspended in elution buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) and incubated at 65°C for 10 minutes. The IP and input samples were treated with 4.5 µL RNAse A for 30 minutes. 5 µL Proteinase K was added and samples were incubated overnight at 65°C to reverse crosslinking. DNA was isolated by phenol:chloroform extraction, precipitated with EtOH, and resuspended in 20 µL H2O.
Preparation of sequencing libraries was performed using NEBNext Ultra II kit (NEB) with 7 PCR cycles for library amplification. Sequencing was performed on the Illumina Hi-Seq4000 using 50bp single-end reads, or on the Illumina NovaSeq 6000 using 150bp paired-end reads.

treatment_protocol: Transcription factor expression was induced by adding CuSO4 to the cell culture media. For all induction experiments, cells were plated at 1×10^6 cells per mL. Experiments were performed with cells harvested 48 hours after induction.

tag: cell line

tag: treatment

value: 100 uM CuSO4

tag: antibody

value: anti-Grh


title: S2-WT_aGrh_input_rep1 a


title: S2-WT_aGrh_input_rep1 b


title: S2-WT_aGrh_input_rep2 a


title: 180822_P1-180822_P2-D8-AD008

value: THl


title: 180822_P1-180822_P2-D8-AD006

value: THp


title: 3LWbrain, yw, M, rep2


title: 180822_P1-180822_P2-D8-AD007

value: male


title: S2-Zld_aZld_IP_rep2

description:
S2-Zld_aZld_IP.bw
S2-Zld_aZld_IP.narrowPeak

value: 1000 uM CuSO4

value: anti-Zld


title: S2-WT_aZld_input_rep1


title: 180822_P1-180822_P2-D8-AD004


title: S2-WT_aZld_input_rep2


title: S2-WT_aGrh_IP_rep2

description:
S2-WT_aGrh_IP.bw
S2-WT_aGrh_IP.narrowPeak


title: S2-WT_aGrh_IP_rep1


title: S2-Zld_aIgG_input_rep1

value: anti-IgG


title: S2-Grh_aIgG_input_rep1


title: 180822_P1-180822_P2-D8-AD001


title: 180822_P1-180822_P2-D8-AD002


title: S2-Grh_aGrh_IP_rep2

description:
S2-Grh_aGrh_IP.bw
S2-Grh_aGrh_IP.narrowPeak


title: S2-WT_aZld_IP_rep1

description:
S2-WT_aZld_IP.bw
S2-WT_aZld_IP.narrowPeak


title: S2-Zld_aZld_IP_rep1


title: S2-Grh_aGrh_IP_rep1


title: 180822_P1-180822_P2-D7-AD008


title: 180822_P1-180822_P2-D7-AD007


title: S2-Grh_DMSO_IgG_rep2

data_processing:
The percentage of reads containing barcoded Epicypher nucleosomes was calculated and 1 divided by this percentage was used as the scaling factor for spike-in normalization. The z-score normalized read depth was multiplied by these scaling factors to generate spike-in normalized bigWigs.
Raw CUT&RUN reads were trimmed to remove adapter sequences using NGmerge version 0.3
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded.
Peak calling was performed using MACS2 with parameters –broad -f BAMPE –keep-dup all -g dm.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-scoore normalized read depth of merged replicates
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed using EpiCypher reagents according to the manufacturer protocol. 2×105 cells were used for each CUT&RUN reaction. Overnight incubation with antibodies was performed in antibody buffer containing 0.05% digitonin. 0.5 µL anti-H3K27me3 (Cell signaling technologies) or rabbit IgG were used for CUT&RUN. Prior to addition of antibody, a 1:5 dilution of K-MetStat Panel spike-in nucleosomes (EpiCypher, cat. # 19-1002) was added to each reaction.
Libraries were prepared using the NEBNext Ultra II kit (NEB). During library preparation, cleanup steps were performed using a 1.1X ratio of Axygen paramagnetic beads, as recommended by EpiCypher. PCR amplification was performed with the following conditions: 98°C for 45 seconds, then 14 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and a final extension of 72°C for 1 minute.

value: IgG

value: DMSO


title: S2-Zld_DMSO_IgG_rep2


title: S2-HA-Twi_Taz_aH3K27me3_rep2

value: Taz


title: S2-HA-Twi_DMSO_IgG_rep2


title: 180822_P1-180822_P2-D7-AD006

value: SSp

value: female


title: S2-Grh_Taz_aH3K27me3_rep2


title: S2-HA-Twi_DMSO_aH3K27me3_rep2


title: S2-WT_aZld_IP_rep2


title: 180822_P1-180822_P2-D7-AD004


title: S2-Zld_Taz_aH3K27me3_rep2


title: S2-Grh_DMSO_aH3K27me3_rep2


title: 180822_P1-180822_P2-D7-AD002


title: 180822_P1-180822_P2-D7-AD001


title: S2-HA-Twi_DMSO_aH3K27me3_rep1


title: S2-Zld_DMSO_aH3K27me3_rep2


title: S2-Grh_DMSO_IgG_rep1


title: S2-HA-Twi_DMSO_IgG_rep1


title: S2-HA-Twi_Taz_aH3K27me3_rep1


title: 180822_P1-180822_P2-D6-AD010


title: 180822_P1-180822_P2-D6-AD007


title: S2-Zld_DMSO_IgG_rep1


title: S2-Grh_DMSO_aH3K27me3_rep1


title: S2-Grh_IgG_48H_rep2

tag: time point


title: S2-Zld_DMSO_aH3K27me3_rep1


title: 180822_P1-180822_P2-D6-AD004


title: 180822_P1-180822_P2-D6-AD006


title: S2-Grh_IgG_48H_rep1

data_processing:
Raw CUT&RUN reads were trimmed to remove adapter sequences using NGmerge version 0.3
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded.
Peak calling was performed using MACS2 with parameters –broad -f BAMPE –keep-dup all -g dm.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-scoore normalized read depth of merged replicates
Library strategy: CUT&RUN


title: S2-Zld_Taz_aH3K27me3_rep1


title: 180822_P1-180822_P2-D6-AD002


title: S2-Grh_aGrh_48H_rep2

value: aGrh


title: S2-Grh_aGrh_24H_rep2


title: S2-Grh_aGrh_12H_rep1


title: S2-Grh_aGrh_12H_rep2


title: 180822_P1-180822_P2-D6-AD001

value: brain


title: 180822_P1-180822_P2-D5-AD012


title: S2-Grh_aGrh_4H_rep2


title: S2-Grh_aGrh_48H_rep1


title: 180822_P1-180822_P2-D5-AD010


title: S2-Grh_aGrh_0H_rep2


title: S2-Zld_IgG_48H_rep1


title: S2-Grh_Taz_aH3K27me3_rep1


title: S2-Grh_aGrh_0H_rep1


title: 180822_P1-180822_P2-D5-AD007


title: 180822_P1-180822_P2-D5-AD008


title: S2-Zld_aZld_24H_rep1

value: aZld


title: S2-Zld_aZld_24H_rep2


title: S2-Zld_aZld_48H_rep2


title: S2-Zld_aZld_12H_rep2


title: S2-Zld_aZld_12H_rep1


title: S2-Zld_IgG_48H_rep2


title: 180822_P1-180822_P2-D5-AD004


title: 180822_P1-180822_P2-D5-AD006


title: 180822_P1-180822_P2-D5-AD002


title: S2-Grh_aGrh_4H_rep1


title: S2-Zld_aZld_48H_rep1


title: S2-Grh_aGrh_24H_rep1


title: S2-Zld_aZld_4H_rep2


title: S2-Zld_aZld_4H_rep1


title: S2-Zld_aZld_0H_rep1


title: S2-Zld_aZld_0H_rep2


title: titration_S2-HA-Twi_40uM_rep2

description:
titration_S2-HA-Twi_40uM_small.bw
S2-HA-Twi-titration_ATACseq_peaks.narrowPeak

data_processing:
Raw ATAC-seq reads were trimmed to remove adapter sequences using NGmerge version 0.3.
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded. Only fragments < 100bp were considered for downstream analysis.
Reads were combined across all replicates and peak calling was performed using MACS2 with parameters -f BAMPE --keep-dup all -g dm --call-summits.
featureCounts was used to count the number of reads aligning within 200bp (100bp upstream or downstream) of peak summits.
Differential accessibility analysis was performed using DESeq2. Regions with an adjusted p-value < 0.05 were considered differentially accessible.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-score normalized read depth for merged replicates. Only small fragments (< 100bp) are included.
Supplementary files format and content: narrowPeak files: MACS2 peaks called on combined replicates for all samples within each experiment.

extract_protocol:
2×10^5 cells were harvested for ATAC-seq by centrifugation at 600 × g for 3 minutes at RT. Cells were washed once in 100 µL 1X PBS and resuspended in 100 µL ATAC lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2,0.1% NP-40). Cells were centrifuged at 600 × g for 10 minutes at 4°C. Supernatant was removed and pellet was resuspended in 47.5 µL buffer TD (Illumina). 2.5 uL of Tagment DNA Enzyme (Illumina) was added and samples were incubated at 37°C for 30 minutes. Tagmented DNA was purified using MinElute Reaction Cleanup Kit (Qiagen) and eluted in 10 µL of buffer EB.
DNA was PCR amplified for 12 cycles with the following conditions:72°C for 5 minutes, 98°C for 30 seconds, then 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Amplified libraries were purified using a 1.2X ratio of Axygen paramagnetic beads.

value: 40uM CuSO4


title: titration_S2-HA-Twi_10uM_rep2

description:
titration_S2-HA-Twi_10uM_small.bw
S2-HA-Twi-titration_ATACseq_peaks.narrowPeak

value: 10uM CuSO4


title: 180822_P1-180822_P2-D4-AD008

value: ACA


title: 180822_P1-180822_P2-D4-AD010


title: 180822_P1-180822_P2-D4-AD012


title: 180822_P1-180822_P2-D4-AD006


title: titration_S2-HA-Twi_0uM_rep2

description:
titration_S2-HA-Twi_0uM_small.bw
S2-HA-Twi-titration_ATACseq_peaks.narrowPeak

value: 0uM CuSO4


title: 180822_P1-180822_P2-D4-AD004

value: THp


title: titration_S2-Grh_100uM_rep2

description:
titration_S2-Grh_100uM_small.bw
S2-Grh-titration_ATACseq_peaks.narrowPeak

value: 100uM CuSO4


title: titration_S2-Grh_25uM_rep2

description:
titration_S2-Grh_25uM_small.bw
S2-Grh-titration_ATACseq_peaks.narrowPeak

value: 25uM CuSO4


title: titration_S2-Grh_400uM_rep2

description:
titration_S2-Grh_400uM_small.bw
S2-Grh-titration_ATACseq_peaks.narrowPeak

value: 400uM CuSO4


title: titration_S2-Grh_0uM_rep2

description:
titration_S2-Grh_0uM_small.bw
S2-Grh-titration_ATACseq_peaks.narrowPeak


title: 180822_P1-180822_P2-D3-AD012


title: 180822_P1-180822_P2-D5-AD001

value: THl

value: male


title: titration_S2-Zld_0uM_rep2

description:
titration_S2-Zld_0uM_small.bw
S2-Zld-titration_ATACseq_peaks.narrowPeak


title: 180822_P1-180822_P2-D4-AD002


title: titration_S2-Zld_1000uM_rep2

description:
titration_S2-Zld_1000uM_small.bw
S2-Zld-titration_ATACseq_peaks.narrowPeak

value: 1000uM CuSO4


title: titration_S2-Zld_1500uM_rep2

description:
titration_S2-Zld_1500uM_small.bw
S2-Zld-titration_ATACseq_peaks.narrowPeak

value: 1500uM CuSO4


title: 180822_P1-180822_P2-D3-AD008


title: titration_S2-HA-Twi_160uM_rep1

description:
titration_S2-HA-Twi_160uM_small.bw
S2-HA-Twi-titration_ATACseq_peaks.narrowPeak

value: 160uM CuSO4


title: 180822_P1-180822_P2-D3-AD007


title: titration_S2-HA-Twi_160uM_rep2


title: 180822_P1-180822_P2-D3-AD002

value: SSp

value: female


title: titration_S2-Grh_400uM_rep1


title: titration_S2-Grh_100uM_rep1


title: 180822_P1-180822_P2-D3-AD001

value: brain


title: titration_S2-Grh_25uM_rep1


title: 180822_P1-180822_P2-D2-AD010


title: titration_S2-HA-Twi_0uM_rep1


title: titration_S2-Zld_1000uM_rep1


title: titration_S2-Zld_1500uM_rep1


title: titration_S2-Grh_0uM_rep1


title: titration_S2-Zld_500uM_rep2

description:
titration_S2-Zld_500uM_small.bw
S2-Zld-titration_ATACseq_peaks.narrowPeak

value: 500uM CuSO4


title: titration_S2-Zld_500uM_rep1


title: 180822_P1-180822_P2-D2-AD008


title: titration_S2-Zld_0uM_rep1


title: 180822_P1-180822_P2-D2-AD007


title: DBD_ATAC_S2-WT_100uM_rep2

description:
DBD_ATAC_S2-WT_100uM_small.bw
S2-Zld-DBD_ATACseq_peaks.narrowPeak


title: S2-Zld-DBD_100uM_rep2

description:
S2-Zld-DBD_100uM_small.bw
S2-Zld-DBD_ATACseq_peaks.narrowPeak


title: S2-Grh-DBD_20uM_rep2

description:
S2-Grh-DBD_20uM_small.bw
S2-Grh-DBD_ATACseq_peaks.narrowPeak

value: 20uM CuSO4


title: 180822_P1-180822_P2-D2-AD004


title: titration_S2-HA-Twi_10uM_rep1

value: 10uM CuSO4


title: DBD_ATAC_S2-WT_100uM_rep1


title: S2-Zld-DBD_100uM_rep1


title: titration_S2-HA-Twi_40uM_rep1

value: 40uM CuSO4


title: DBD_ATAC_S2-WT_20uM_rep2

description:
DBD_ATAC_S2-WT_20uM_small.bw
S2-Grh-DBD_ATACseq_peaks.narrowPeak


title: DBD_ATAC_S2-WT_20uM_rep1


title: 180822_P1-180822_P2-D2-AD001


title: S2-Grh-DBD_20uM_rep1


title: 180822_P1-180822_P2-D12-AD012

value: ACA


title: 180822_P1-180822_P2-D12-AD008


title: 180822_P1-180822_P2-D12-AD010

value: THp


title: S2-Twi_40uM_rep1

description:
S2-Twi_40uM_small.bw
S2-Twi_ATACseq_peaks.narrowPeak


title: S2-Zld_1000uM_rep1

description:
S2-Zld_1000uM_small.bw
S2-Zld_ATACseq_peaks.narrowPeak


title: S2-WT_1000uM_rep1

description:
S2-WT_1000uM_small.bw
S2-Zld_ATACseq_peaks.narrowPeak


title: S2-WT_1000uM_rep2


title: 180822_P1-180822_P2-D12-AD006


title: S2-Twi_40uM_rep2


title: Twi_ATAC_S2-WT_40uM_rep2

description:
Twi_ATAC_S2-WT_40uM_small.bw
S2-Twi_ATACseq_peaks.narrowPeak


title: S2-Grh_100uM_rep1

description:
S2-Grh_100uM_small.bw
S2-Grh_ATACseq_peaks.narrowPeak

value: 100uM CuSO4


title: 180822_P1-180822_P2-D12-AD007


title: 180822_P1-180822_P2-D12-AD002


title: S2-Grh_100uM_rep2


title: FL_ATAC_S2-WT_100uM_rep2

description:
FL_ATAC_S2-WT_100uM_small.bw
S2-Grh_ATACseq_peaks.narrowPeak


title: 180822_P1-180822_P2-D2-AD006


title: FL_ATAC_S2-WT_100uM_rep1


title: S2-Zld_1000uM_rep2


title: 180822_P1-180822_P2-D11-AD008


title: 180822_P1-180822_P2-D11-AD010


title: Colon newborn

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

country: China

institute: Zhejiang University

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: ARS-USD1.2 cattle reference genome
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Bos taurus

source_name: Colon

extract_protocol:
After removed the outer muscle layers, the adult (AD) duodenum, jejunum, cecum, and colon samples were chopped into 1 mm pieces and treated with different enzymes for different durations：the duodenum and cecum samples were dissociated using the Lamina Propria Dissociation Kit (Miltenyi biotec, Bergisch Gladbach, Germany) for 30 min at 37℃; the jejunum and colon samples were dissociated using the Multi Tissue Dissociation Kit 2 (Miltenyi biotec, Bergisch Gladbach, Germany) for 41 min at 37℃. Then, the digestion was stopped by adding 10% of FBS, followed by a filtration step with 40 μm sieve. Next, after centrifuged at 300 × g for 5 min at 4°C and washed with 1× DPBS containing 2% FBS and 0.2 mM EDTA, the samples were treated with Red Blood Cell Lysis Solution (Miltenyi Biotech, Bergisch Gladbach, Germany) for 2 min. The samples were washed with 1× DPBS containing 2% FBS and 0.2 mM EDTA, centrifuged at 300 × g for 5 min at 4°C, and re-suspended in 1× DPBS containing 10% FBS and 0.2 mM EDTA.  For the NB reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum samples, we firstly removed the outer muscle layers of samples, and then minced samples into 10 × 0.5 mm2 pieces. The samples were incubated with 20 mM EDTA for 30 min at 37℃, and then rinsed with DPBS and chopped into 1 mm pieces. Tissue pieces were incubated in a 37℃ water bath for 5 min with 0.25% Trypsin-EDTA (Gibco) and then the centrifuge tube containing tissue pieces was inserted into ice for 2 min, and the digestion was stopped by adding the pre-chilled HBSS. The supernatant was discarded after centrifuged at 300 × g for 2 min at 4℃, and samples were washed twice with cold HBSS. Samples were incubated with different dissociation enzymes for different durations. For NB reticulum, omasum, and abomasum samples, the multiple enzymes (1.5 mg/ml collagenase I, 1.5 mg/ml collagenase IV, 100 U/ml hyaluronidase, 1.5 mg/ml dispase, and 50 U/ml DNase I) were added and treated for 30 min at 37℃. For the NB duodenum, jejunum, ileum, cecum, colon, and rectum samples, the multiple enzymes in the Propria Dissociation Kit (Miltenyi biotec, Bergisch Gladbach, Germany) were added and treated for 30 min at 37℃. The 10% FBS was added to stop the digestion, followed by a filtration step through 70 μm and 30 μm SmartStrainer (Miltenyi biotec, Bergisch Gladbach, Germany). After centrifuged at 300 × g for 5 min at 4℃, samples were then re-suspended in 2 mL of HBSS. Then, samples were centrifuged at 300 × g for 5 min at 4℃ and washed twice with 1×PBS with 0.04% BSA. Finally, samples were centrifuged at 300 × g for 5 min at 4℃ and re-suspended in 1×PBS with 0.04% BSA.   For the NB liver sample, the isolated sample was transferred into cold DPBS, minced into 1mm pieces, and then incubated with 1.5mg/ml Collagenase I, 20U/ml papain, and 50U/ml DNase I for 20 min at 37℃. The dissociated cells were then passed through 70 μm and 30 μm SmartStrainer, centrifuged at 300 × g for 5 min at 4℃, and then re-suspended in 2 mL of cold HBSS. After centrifuged at 300 × g for 5 min, dissociated cells were washed twice with 1×PBS with 0.04% BSA at 4℃ and then re-suspended in 1×PBS with 0.04% BSA.  For the NB salivary gland sample, the isolated sample from parotid gland was transferred into cold 1×PBS. The blood and fat of the sample were removed, and then the sample was chopped into 0.5 mm pieces. After incubated with 1.5mg/ml collagenase II, 1.5mg/ml dispase, and 50U/ml DNase I for 20 min at 37℃, the sample was passed through 70 μm and 30 μm SmartStrainers, and then centrifuged at 300 × g for 5 min at 4℃. Dissociated cells were re-suspended in 300 μL of RPMI 1640 medium (Gibco), and 3mL of Red Blood Cell Lysis Solution wad added for 3 min. Dissociated cells were then centrifuged at 300 × g for 5 min at 4℃ and re-suspended in 2 mL of RPMI 1640 medium. After centrifuged at 300 × g for 5 min, dissociated cells were washed twice with 1×PBS with 0.04% BSA at 4℃ and then re-suspended in 1×PBS with 0.04% BSA.
The single-cell RNA-seq library preparation was performed using the Chromium Single Cell 3' Reagent Kits v3.

tag: breed

value: Holstein dairy cows

value: colon

tag: developmental stage

value: newborn


title: Rectum newborn

source_name: Rectum

value: rectum


title: Liver newborn

source_name: Liver

value: liver


title: Cecum newborn

source_name: Cecum

value: cecum


title: 180822_P1-180822_P2-D12-AD001

value: THl

value: male


title: SalivaryGland newborn

source_name: Salivary Gland

value: salivary gland


title: Colon adult

value: adult


title: 180822_P1-180822_P2-D11-AD007

value: brain


title: 180822_P1-180822_P2-D11-AD006

value: SSp

value: female


title: Ileum newborn

source_name: Ileum

value: ileum


title: 180822_P1-180822_P2-D10-AD010

value: ACA


title: 180822_P1-180822_P2-D11-AD002


title: 180822_P1-180822_P2-D11-AD001


title: Jejunum newborn

source_name: Jejunum

value: jejunum


city: Boston

first: Ting

last: Zhang

address: 181 longwood Ave

institute: BWH

description:
Lm3
RawCounts_Lm.txt
Liver of Listeria monocytogenes infected mouse 3
Library 15

data_processing:
For data analysis, reads were trimmed using Trim Galore with automatic adapter sequence detection.
Then, trimmed reads were mapped to the mouse reference genome (mm10) and annotated using STAR v2.7.3a with default parameter.
The number of mapped reads to each gene were counted by featureCounts of the Subread package using mouse GENCODE annotation M25 (GRCm38.p6).
Assembly: mm10
Supplementary files format and content: Feature counts table

source_name: liver

extract_protocol:
RNAs were extracted from the liver samples using Trizol (Thermo Fisher).
RNA-seq libraries were prepared by KAPA RNA Hyperprep Kit (Roche).

value: Listeria monocytogenes infected mouse

tag: strain


title: Reticulum newborn

source_name: Reticulum

value: Holstein dairy cows

tag: tissue

value: reticulum


title: Jejunum adult


description:
Lm2
RawCounts_Lm.txt
Liver of Listeria monocytogenes infected mouse 2
Library 14


title: Abomasum newborn

source_name: Abomasum

value: abomasum

value: newborn


description:
Lm1
RawCounts_Lm.txt
Liver of Listeria monocytogenes infected mouse 1
Library 13

value: liver


title: 180822_P1-180822_P2-D10-AD007


title: Duodenum newborn

source_name: Duodenum

value: duodenum


title: 180822_P1-180822_P2-D10-AD006

value: THp


description:
Lm_Ctrl2
RawCounts_Lm.txt
Liver of uninfected mouse 2 (control group in Listeria monocytogenes experiment)
Library 11

value: uninfected mouse (control group in Listeria monocytogenes experiment)


description:
Lm_Ctrl3
RawCounts_Lm.txt
Liver of uninfected mouse 3 (control group in Listeria monocytogenes experiment)
Library 12


title: 180822_P1-180822_P2-D10-AD004

value: male