title: CEMBA181022_6B_1_CEMBA181022_6B_2_F4_ad012


title: CEMBA181022_6B_1_CEMBA181022_6B_2_F3_ad010

status: Public on Sep 22 2020

type: SRA

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:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 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
Genome_build: 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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

tag: Sex

value: male

tag: age

tag: strain


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_C6_ad001


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_C3_ad002


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_B9_ad002


title: CEMBA181022_6B_1_CEMBA181022_6B_2_B9_ad001


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_A12_ad004


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_A10_ad012


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_A10_ad010


title: CEMBA181022_6B_1_CEMBA181022_6B_2_A1_ad010


title: CEMBA181022_6B_1_CEMBA181022_6B_2_A1_ad007


title: CEMBA181022_6B_1_CEMBA181022_6B_2_A1_ad008


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_A1_ad006


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title: CEMBA181022_6B_1_CEMBA181022_6B_2_A11_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H9_ad004

value: PAL


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H9_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H9_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H9_ad012


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title: CEMBA181016_5H_3_CEMBA181016_5H_4_H8_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H9_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H8_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H8_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H8_ad001


title: CEMBA181022_6B_1_CEMBA181022_6B_2_A1_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H7_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H7_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H7_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_H7_ad008


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title: CEMBA181016_5H_3_CEMBA181016_5H_4_E8_ad007


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title: CEMBA181016_5H_3_CEMBA181016_5H_4_B3_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B5_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B3_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B3_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B3_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B10_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B10_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B2_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B10_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B10_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B10_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B12_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A8_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A8_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A8_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A8_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B11_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B10_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A8_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A8_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A6_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A9_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A4_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A3_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A2_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A2_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A2_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A2_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A2_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A5_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A10_ad004


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad008


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad012


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad002


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad006


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A12_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad001


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A2_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H9_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad007


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A1_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H8_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H5_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H7_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H6_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H2_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H2_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H3_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H4_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H2_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H2_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad002


title: BC6872: primary breast cancer patient 454

type: RNA

city: Mainz

first: Marcus

last: Schmidt

address: Langenbeckstr. 1

department: Universitäres Centrum für Tumorerkrankungen

country: Germany

institute: Universitätsmedizin Mainz

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
CEL file not available for this patient
Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturerâ€™s instructions

extract_protocol: Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For all tumors, samples were snap frozen and stored at -80°C. Tumor cell content exceeded 40% in all samples.

tag: tissue

value: primary breast cancer

tag: node

tag: grade

tag: t-size (mm)

tag: adjuvant treatment

value: adj chemo

tag: intrinsic subtype


title: CEMBA181016_5H_3_CEMBA181016_5H_4_B1_ad012


title: BC6871: primary breast cancer patient 453


title: BC6876: primary breast cancer patient 456


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad001


title: BC6883: primary breast cancer patient 460


title: BC6870: primary breast cancer patient 452


title: BC6880: primary breast cancer patient 459


title: BC6875: primary breast cancer patient 455


title: BC6884: primary breast cancer patient 461


title: BC6879: primary breast cancer patient 458


title: BC6868: primary breast cancer patient 450


title: BC6878: primary breast cancer patient 457


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad008


title: BC6869_2: primary breast cancer patient 451


title: BC6865: primary breast cancer patient 447


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H11_ad002


title: BC6863: primary breast cancer patient 446


title: BC6860: primary breast cancer patient 445


title: BC6857: primary breast cancer patient 443


title: BC6866: primary breast cancer patient 448


title: BC6867: primary breast cancer patient 449


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H12_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H11_ad010


title: CEMBA181016_5H_3_CEMBA181016_5H_4_A7_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H11_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H11_ad008


title: BC6856: primary breast cancer patient 442


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H11_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H11_ad006


title: BC6855: primary breast cancer patient 441


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad007


title: BC6844: primary breast cancer patient 433


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad001


title: BC6846: primary breast cancer patient 434


title: BC6848: primary breast cancer patient 436


title: BC6859: primary breast cancer patient 444


title: BC6847: primary breast cancer patient 435


title: BC6849: primary breast cancer patient 437


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H10_ad002


title: BC6852_2: primary breast cancer patient 438


title: BC6853: primary breast cancer patient 439


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad007


title: BC6843: primary breast cancer patient 432


title: BC6854: primary breast cancer patient 440


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad004


title: BC6836: primary breast cancer patient 427


title: BC6840: primary breast cancer patient 429


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad008


title: BC6841: primary breast cancer patient 430


title: BC6842: primary breast cancer patient 431


title: BC6837: primary breast cancer patient 428


title: BC6833: primary breast cancer patient 424


title: BC6834: primary breast cancer patient 425


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G9_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G9_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G9_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G9_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G9_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G9_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_H1_ad001


title: BC6835: primary breast cancer patient 426


title: BC6831: primary breast cancer patient 422


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad010


title: BC6828: primary breast cancer patient 419


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad008


title: BC6824: primary breast cancer patient 416


title: BC6827: primary breast cancer patient 418


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad001


title: BC6823: primary breast cancer patient 415


title: BC6830: primary breast cancer patient 421


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad004


title: BC6829: primary breast cancer patient 420


title: BC6826: primary breast cancer patient 417


title: BC6832: primary breast cancer patient 423


title: BC6819: primary breast cancer patient 414


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad002


title: BC6814: primary breast cancer patient 411


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad001


title: BC6815: primary breast cancer patient 412


title: BC6813: primary breast cancer patient 410


title: BC6818: primary breast cancer patient 413


title: BC6810: primary breast cancer patient 408


title: BC6809: primary breast cancer patient 407


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad006


title: BC6807: primary breast cancer patient 406


title: BC6806: primary breast cancer patient 405


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad007


title: BC6804: primary breast cancer patient 404


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G8_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad008


title: BC6803: primary breast cancer patient 403


title: BC6811: primary breast cancer patient 409


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad010


title: BC6238_2: primary breast cancer patient 400

value: tamoxifen


title: BC6802: primary breast cancer patient 402


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G7_ad008


title: BC6233: primary breast cancer patient 399


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad012


title: BC6801: primary breast cancer patient 401


title: BC6232: primary breast cancer patient 398

data_processing: Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)


title: BC6231: primary breast cancer patient 397


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G6_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad001


title: BC6230: primary breast cancer patient 396


title: BC6224: primary breast cancer patient 394


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad002


title: BC6220: primary breast cancer patient 392


title: BC6218: primary breast cancer patient 390


title: BC6219: primary breast cancer patient 391


title: BC6217: primary breast cancer patient 389


title: BC6227_2: primary breast cancer patient 395


title: BC6214: primary breast cancer patient 387


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad004


title: BC6216: primary breast cancer patient 388


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G4_ad006


title: BC6211: primary breast cancer patient 385


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G4_ad012


title: BC6221: primary breast cancer patient 393


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G4_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G4_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G5_ad010


title: BC6212: primary breast cancer patient 386


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G4_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G4_ad002


title: BC6210: primary breast cancer patient 384


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad002


title: BC6207: primary breast cancer patient 382


title: BC6208: primary breast cancer patient 383


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad010


title: BC6204: primary breast cancer patient 380


title: BC6205: primary breast cancer patient 381


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad004


title: BC6200: primary breast cancer patient 377


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad012


title: BC6199: primary breast cancer patient 376


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G3_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad004


title: BC6198: primary breast cancer patient 375


title: BC6197: primary breast cancer patient 374


title: BC6193: primary breast cancer patient 372


title: BC6201_E: primary breast cancer patient 378


title: BC6192: primary breast cancer patient 371


title: BC6203: primary breast cancer patient 379


title: BC6196: primary breast cancer patient 373


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad001


title: BC6188: primary breast cancer patient 367


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G2_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad004


title: BC6190: primary breast cancer patient 369


title: BC6189: primary breast cancer patient 368


title: BC6185: primary breast cancer patient 364


title: BC6191_E: primary breast cancer patient 370


title: BC6187: primary breast cancer patient 366


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad001


title: BC6186: primary breast cancer patient 365


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad012


title: BC6182: primary breast cancer patient 361


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G12_ad008


title: BC6183_E: primary breast cancer patient 362


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad008


title: BC6181: primary breast cancer patient 360


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad001


title: BC6180: primary breast cancer patient 359


title: BC6179: primary breast cancer patient 358


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad002


title: BC6184: primary breast cancer patient 363


title: BC6177: primary breast cancer patient 356


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G11_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad010


title: BC6171: primary breast cancer patient 352


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad002


title: BC6170: primary breast cancer patient 351


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad007


title: BC6174: primary breast cancer patient 354


title: BC6166: primary breast cancer patient 349


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad001


title: BC6173: primary breast cancer patient 353


title: BC6167: primary breast cancer patient 350


title: BC6178: primary breast cancer patient 357


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad001


title: BC6176_E_wdh: primary breast cancer patient 355


title: BC6161wdh: primary breast cancer patient 344


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad008


title: BC6165: primary breast cancer patient 348


title: BC6162wdh: primary breast cancer patient 345


title: BC6164wdh: primary breast cancer patient 347


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad004


title: BC6163: primary breast cancer patient 346


title: BC6158: primary breast cancer patient 342


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G10_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad012


title: BC6156: primary breast cancer patient 340


title: BC6157: primary breast cancer patient 341


title: BC6155: primary breast cancer patient 339


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad010


title: BC6153: primary breast cancer patient 337


title: BC6154: primary breast cancer patient 338


title: CEMBA181016_5H_1_CEMBA181016_5H_2_G1_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad007


title: BC6159: primary breast cancer patient 343


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad008


title: BC6152: primary breast cancer patient 336


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad002


title: BC6151wdh: primary breast cancer patient 335


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F9_ad010


title: BC6148: primary breast cancer patient 333


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad012


title: BC6150_E: primary breast cancer patient 334


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad010


title: BC6145: primary breast cancer patient 330


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad001


title: BC6147: primary breast cancer patient 332


title: BC6146wdh: primary breast cancer patient 331


title: BC6144: primary breast cancer patient 329


title: BC6141: primary breast cancer patient 327


title: BC6140_E: primary breast cancer patient 326


title: BC6139: primary breast cancer patient 325


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad006


title: BC6142: primary breast cancer patient 328


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F8_ad008


title: BC6134: primary breast cancer patient 322


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad004


title: BC6131: primary breast cancer patient 319


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad001


title: BC6130: primary breast cancer patient 318


title: BC6133: primary breast cancer patient 321


title: BC6132: primary breast cancer patient 320


title: BC6136_E: primary breast cancer patient 323


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F7_ad010


title: BC6127: primary breast cancer patient 316


title: BC6129: primary breast cancer patient 317


title: BC6138: primary breast cancer patient 324


title: BC6120: primary breast cancer patient 311


title: BC6119: primary breast cancer patient 310


title: BC6126wdh: primary breast cancer patient 315


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad001


title: BC6125_E: primary breast cancer patient 314


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad007


title: BC6117_E_wdh: primary breast cancer patient 308


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad002


title: BC6118: primary breast cancer patient 309


title: BC6116wdh: primary breast cancer patient 307


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F6_ad004


title: BC6122: primary breast cancer patient 313


title: BC6110: primary breast cancer patient 302


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad008


title: BC6111_E: primary breast cancer patient 303


title: BC6121: primary breast cancer patient 312


title: BC6112: primary breast cancer patient 304


title: BC6115: primary breast cancer patient 306


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad006


title: BC6114: primary breast cancer patient 305


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F4_ad006


title: BC6108: primary breast cancer patient 300


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F4_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F4_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F4_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad002


title: BC6104: primary breast cancer patient 296


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad007


title: BC6106: primary breast cancer patient 298


title: BC6102: primary breast cancer patient 294


title: BC6107: primary breast cancer patient 299


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F4_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad012


title: BC6105_E: primary breast cancer patient 297


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F4_ad008


title: BC6098: primary breast cancer patient 290


title: BC6097_E: primary breast cancer patient 289


title: BC6095: primary breast cancer patient 287


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad001


title: BC6094_E: primary breast cancer patient 286


title: BC6103: primary breast cancer patient 295


title: BC6109: primary breast cancer patient 301


title: BC6101wdh: primary breast cancer patient 293


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad006


title: BC6099: primary breast cancer patient 291


title: BC6100: primary breast cancer patient 292


title: BC6092: primary breast cancer patient 284


title: BC6096: primary breast cancer patient 288


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F3_ad006


title: BC6091_E: primary breast cancer patient 283


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad008


title: BC6085: primary breast cancer patient 278


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F2_ad008


title: BC6086: primary breast cancer patient 279


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad006


title: BC6089: primary breast cancer patient 282


title: BC6083: primary breast cancer patient 276


title: BC6093: primary breast cancer patient 285


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad004


title: BC6084: primary breast cancer patient 277


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad010


title: BC6087_E: primary breast cancer patient 280


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F12_ad012


title: BC6081_E: primary breast cancer patient 274


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad002


title: BC6088: primary breast cancer patient 281


title: BC6080: primary breast cancer patient 273


title: BC6079_E: primary breast cancer patient 272


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad010


title: BC6078: primary breast cancer patient 271


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F5_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F11_ad007


title: BC6082: primary breast cancer patient 275


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad010


title: BC6077: primary breast cancer patient 270


title: BC6073_E: primary breast cancer patient 266


title: BC6071: primary breast cancer patient 264


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad006


title: BC6070: primary breast cancer patient 263


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F10_ad001


title: BC6069: primary breast cancer patient 262


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F1_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F1_ad004


title: BC6065: primary breast cancer patient 258


title: BC6068_E: primary breast cancer patient 261


title: BC6067: primary breast cancer patient 260


title: BC6064_2: primary breast cancer patient 257


title: BC6075: primary breast cancer patient 268


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F1_ad012


title: BC6066wdh: primary breast cancer patient 259


title: BC6062wdh: primary breast cancer patient 255


title: BC6060wdh: primary breast cancer patient 253


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F1_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F1_ad010


title: BC6058: primary breast cancer patient 251


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E9_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_F1_ad007


title: BC6057: primary breast cancer patient 250


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E9_ad004


title: BC6061: primary breast cancer patient 254


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E8_ad012


title: BC6055: primary breast cancer patient 248


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E9_ad001


title: BC6059: primary breast cancer patient 252


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E9_ad007


title: BC6056wdh: primary breast cancer patient 249


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E8_ad007


title: BC6052: primary breast cancer patient 245


title: BC6051_2: primary breast cancer patient 244


title: BC6053: primary breast cancer patient 246


title: BC6048: primary breast cancer patient 241


title: BC6050: primary breast cancer patient 243


title: BC6049: primary breast cancer patient 242


title: BC6046_E: primary breast cancer patient 239


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E8_ad004


title: BC6047: primary breast cancer patient 240


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E8_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E9_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E9_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E8_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E8_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E7_ad008


title: BC6045: primary breast cancer patient 238


title: BC6044: primary breast cancer patient 237


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E7_ad004


title: Pflourescens_-Fe_rep4

city: Corvallis, OR

first: Rene

middle: M

last: Boiteau

state: OR

address: 104 CEOAS Administration Building

institute: Oregon State University

library_source: transcriptomic

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Brachypodium reads were aligned using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). using parameters -local, --sensitive-local
Pseudomonas reads were aligned using TMAP (https://github.com/iontorrent/TS/tree/master/Analysis/TMAP) using the 'map4' command with parameters --softclip-type 0, --aln-output-mode 1
Aligned reads were mapped to genes using htseq-count (https://pubmed.ncbi.nlm.nih.gov/25260700/) with parameters -a=1, --mode="union".
Genome_build: Brachypodium distachyon 3.1: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Bdistachyon
Genome_build: Pseudomonas fluorescens: https://www.ncbi.nlm.nih.gov/genome/150?genome_assembly_id=154324
Supplementary_files_format_and_content: read counts per gene

organism: Pseudomonas fluorescens

source_name: Brachypodium rhizosphere

growth_protocol: Brachypodium distachyon was grown in sterile conditions in a light box operating at 14:10 sunlight at 50% relative humidity and 20C. Plants were watered with 1/4 strength Hoagland solution containing every 3-4 days. After 28 days of growth, plants were cut between the roots and shoots and immediately frozen in natural craft bags in liquid nitrogen and stored at -80°C prior to RNA extraction. Two plants from the same container were pooled to obtain 5 biological replicates for each condition. Then the nutrient solution was agitated to wash bacterial cells off of the bead matrix, transferred to a 15mL centrifuge tube, and centrifuged at 4500rpm for 5 minutes at 4°C to obtain a bacterial pellet for RNA analysis (5 biological replicates for +Fe and -Fe conditions with bacterial inoculation).

extract_protocol:
RNA from Brachypodium roots was extracted using Qiagen Mini RNeasy kits, followed by genomic DNA removal using Qiagen RNase-Free DNase Set kit. Integrity of the RNA samples was assessed using an Agilent 2100 Bioanalyzer. TruSeq stranded mRNA was used to generate cDNA libraries for sequencing (Illumina NextSeq550 sequencer). RNA from the bacterial pellet was extracted using Trizol followed by clean-up using Qiagen Mini RNeasy kits and Qiagen RNase-Free Dnase sets.
For Brachypodium, TruSeq Stranded Total RNA (cat#20020596) is used to generate the cDNA library for illumina NextSeq550 platform according to the manufacturer's protocol. Single-read sequencing of the cDNA libraries with a read length of 150 is performed on NextSeq 550 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles
For Pseudomonas, the SMARTerR Universal Low RNA kit was used to generate full length cDNA template library according to the instruction manual, follow by the Ion Plus fragment library kit (Thermo Fisher Scientific) to fragment cDNA and barcode adapter ligation for template prep.  The template library was quantified using the Ion Library TaqMan Quantitation kit (Thermo Fisher Scientific). Emulsion clonal bead amplification was used to generate bead templates for the Ion Torrent platform using the Ion PI™ Hi-Q™ Chef Kit with Ion PI™ Chip Kit v3 on the Ion Chef System (Thermo Fisher Scientific).

treatment_protocol: After 14 days of establishing growth under the same conditions, each container received one of four treatments: (1) no change in watering conditions (sterile, +Fe), (2) Fe deprivation by exclusion of Fe-EDTA from the watering solution (sterile, -Fe ), (3) inoculation with P. fluorescens ( +Fe), (4) inoculation with Pseudomonas fluorescens and Fe deprivation ( -Fe). Plants that were inoculated with P. fluorescens were watered one time with bacteria containing Hoagland solution on day 14 of growth. For -Fe treatments, Fe was omitted from the 1/4 strength Hoagland watering solution beginning on day 16 of growth for the remainder of the experiment.

tag: bacterial treatment

tag: iron

value: no


title: Pflourescens_-Fe_rep3


title: Pflourescens_-Fe_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E7_ad002


title: Pflourescens_+Fe_rep5

value: yes


title: Pflourescens_-Fe_rep5


title: Pflourescens_-Fe_rep1


title: BC6063: primary breast cancer patient 256


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E7_ad001


title: BC6042: primary breast cancer patient 235


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E7_ad006


title: BC6043: primary breast cancer patient 236


title: Pflourescens_+Fe_rep3


title: Pflourescens_+Fe_rep4


title: BC6040: primary breast cancer patient 233


title: BC6054: primary breast cancer patient 247


title: BC6041: primary breast cancer patient 234


title: BC6037: primary breast cancer patient 231


title: BC6039: primary breast cancer patient 232


title: Pflourescens_+Fe_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E7_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E6_ad006


title: BC6036: primary breast cancer patient 230


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E6_ad001


title: Pflourescens_+Fe_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad008


title: BC6033: primary breast cancer patient 228


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad001


title: BC6035: primary breast cancer patient 229


title: BC6032: primary breast cancer patient 227


title: PBMC CR-L replicate 13

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 4*44K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

organism: Rattus norvegicus

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). We selected 5 random samples per genotype for Cy3 labelling as basis for the reference pool.

extract_protocol: Total RNA was isolated from peripheral blood mononuclear cells (PBMC) using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: Sixteen rats were mated and the dams continued pregnancy (controls) or were subsequently caloric restricted (CR) for 20% during days 1-12. Control female/male offspring continued normal lactation, while offspring of CR-treated dams received either normal lactation (CR group) or received during lactation until PN21 leptin supplementation at an average level of five times the amount in mother's milk (CR-L group). After four months ad libitum feeding with chow, a blood sample was drawn and PBMC were isolated and snap frozen in liquid nitrogen.

tag: cell type

value: Rat PBMC

source_name: PBMC, reference pool of all samples


title: PBMC CR-L replicate 08

source_name: peripheral blood mononuclear cells (PBMC)


title: DFAT_rep1

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

country: Japan

institute: Nihon University College of Bioresource Sciences

description: Gene expression data from DFAT grew to semiconfluence

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Mouse Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The data were analyzed with RMA using R/Bioconductor.

source_name: AC were dedifferentiated during ceiling culture, and grown to semiconfluence.

label_protocol: 5 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: Dedifferentiated mus musculus mature adipocytes (DFAT)


title: AC_rep2

description: Gene expression data from AC derived from fat tissue

source_name: AC derived from fat tissue of mus musculus

value: Mus musculus adipocytes


title: AC_rep3


title: PBMC CR-L replicate 07


title: BC6030: primary breast cancer patient 225


title: BC6031: primary breast cancer patient 226


title: PBMC CR-L replicate 11


title: PBMC CR-L replicate 10


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad002


title: AC_rep1


title: BC6028_3: primary breast cancer patient 223


title: PBMC CR-L replicate 12


title: PBMC CR-L replicate 09


title: BC6029_E: primary breast cancer patient 224


title: BC6027: primary breast cancer patient 222


title: PBMC CR-L replicate 06


title: PBMC CR-L replicate 05


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad004


title: BC6072: primary breast cancer patient 265


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E5_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad007


title: BC6076: primary breast cancer patient 269


title: PBMC CR-L replicate 03


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad006


title: PBMC CR-L replicate 04


title: DFAT_rep2


title: BC6025: primary breast cancer patient 220


title: BC6026: primary breast cancer patient 221


title: PBMC CR replicate 10


title: PBMC CR replicate 11


title: BC6022: primary breast cancer patient 218


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad004


title: PBMC CR replicate 08


title: PBMC CR-L replicate 02


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad012


title: PBMC CR replicate 07


title: PBMC CR-L replicate 01


title: BC6021: primary breast cancer patient 217


title: PBMC CR replicate 05


title: PBMC CR replicate 06


title: PBMC CR replicate 03


title: PBMC CR replicate 09


title: BC6020: primary breast cancer patient 216


title: DFAT_rep3


title: BC6019: primary breast cancer patient 215


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E4_ad008


title: BC6074: primary breast cancer patient 267


title: PBMC WT replicate 06


title: PBMC CR replicate 02


title: PBMC WT replicate 07


title: BC6016: primary breast cancer patient 213


title: PBMC CR replicate 01


title: BC6024: primary breast cancer patient 219


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E3_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_E3_ad004