title: 191216-CEMBA-mm-P56-CEMBA191127-10F-3-CEMBA191127-10F-4-C3_ad002


title: 191216-CEMBA-mm-P56-CEMBA191127-10F-3-CEMBA191127-10F-4-C2_ad012

status: Public on Oct 12 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: snm3C-seq
Reads were trimed with Cutadapt for adapters and low-quality bases (Phred score >= 20)
The trimmed fastq files were mapped to in-silico bisulfite converted mm10 reference genome using Bismark with bowtie1
The umapped reads were split into the first 40bp, middle segment, and the final 40bp, and split reads were mapped to the reference genome using Bismark with bowtie1
The BAM files were filtered using Samtools by MAPQ > 10 and PCR duplicates were removed using Picard
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls were generated with in-house developed package with the filtered BAM files
Two ends of reads from separated BAM files were paired, and chromosome contacts were extracted with in-house pipeline
Genome_build: mm10
Supplementary_files_format_and_content: ALLC files: tab-delimited 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; HIC files: The single cell contact file contains eight columns, corresponding to the short format for Juicer tools pre (https://github.com/aidenlab/juicer/wiki/Pre). Specifically, each row represents a contact, including the columns of read1_strand, read1_chromosome, read1_position, read1_fragment, read2_strand, read2_chromosome, read2_position, read2_fragment. We did not use the information of restriction fragment, so read1_fragment and read2_fragment were set to be 0 and 1, respectively. The contact files for single cells could be merged by “sort -m -k2,2 -k6,6” to generate the contact file of a cell type, which could be used as the input to Juicer tools pre to generate .hic file of the cell type.

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 Lee, Dong-Sung, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, et al. 2019. “Simultaneous Profiling of 3D Genome Structure and DNA Methylation in Single Human Cells.” Nature Methods 16 (10): 999–1006.

tag: brain region

value: Hippocampus

tag: Sex

value: male

tag: age

tag: strain


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title: 191216-CEMBA-mm-P56-CEMBA191127-10F-1-CEMBA191127-10F-2-G5_ad012


title: 191216-CEMBA-mm-P56-CEMBA191127-10F-1-CEMBA191127-10F-2-G6_ad010


title: 191216-CEMBA-mm-P56-CEMBA191127-10F-1-CEMBA191127-10F-2-G7_ad002


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title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E1_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E1_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E12_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E12_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E12_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E12_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E1_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E12_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E12_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G1_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G1_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G1_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E1_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E2_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E2_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-3-CEMBA191126-9J-4-E1_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F9_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G1_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F9_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G10_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F9_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G12_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F9_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-G11_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F8_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F6_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F6_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F6_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F6_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F6_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F5_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F7_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F1_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F1_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F4_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F1_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F1_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F2_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F1_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F1_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F12_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F12_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F12_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F11_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F12_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F11_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F12_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F12_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F11_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F3_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F11_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E9_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E9_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E9_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E7_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F11_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E8_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E7_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E7_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E7_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E7_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-F10_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E9_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E5_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E9_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E5_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E5_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E5_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E5_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E5_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E9_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E1_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E2_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E2_ad012


title: SW620_pos_3

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

library_source: transcriptomic

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg19) by STAR (version 2.5.2b).
The number of fragments in each known gene from GENCODE (version 25) was quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Genome_build: hg19
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are raw counts for all the samples.

molecule: total RNA

organism: Homo sapiens

source_name: Colon cancer cell line.

growth_protocol: SW620 cells were cultured in RPMI1640 medium containing 10% FBS, streptomycin and penicillin. Cells were treated with vehicle control or doxycycline.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR. Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R. Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).

tag: cell line

tag: cell type

value: Carcinoma

tag: genotype


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E1_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E1_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E2_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E3_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E6_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E1_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E1_ad008


title: SW620_neg_2

treatment_protocol: Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E12_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad012


title: SW620_neg_3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E2_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E4_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad004


title: OB_17_0312_1

city: San Diego

first: Zhengyan

last: Kan

address: 10770 Science Center Drive

department: Computational Biology, Oncology Research & Development

institute: Pfizer

data_processing:
RNA-Seq data was analyzed using the RSEM42 pipeline with hg19 as the genome reference
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix with gene expression by samples in TPM units

source_name: Primary Tumor

extract_protocol: For RNA-Seq, sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (RS-122-2001 and RS-122-2002, Illumina). Sequencing of the RNA libraries was performed on an Illumina HiSeq2500 in 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit.

tag: gender

value: Female

value: Premenopausal

value: No

value: Not Detected

value: Invasive ductal carcinoma

value: AC+T

tag: bilaterality

tag: multiplicity

value: LumA

value: ER+

tag: time


title: OB_17_0312_2


title: OB_17_0294_2

value: Yes

value: Detected

value: Basal

value: TN


title: OB_17_0294_1


title: OB_17_0290_1


title: OB_17_0286_2

value: Postmenopausal

value: AC+T+Trastuzumab


title: SW620_pos_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad006

value: Hippocampus


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad010

value: male


title: OB_17_0286_1


title: OB_17_0275_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E11_ad002


title: OB_17_0275_1


title: SW620_neg_1

value: Carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D9_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad006


title: OB_17_0266_1

value: Female


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D9_ad010


title: OB_17_0257_1

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D8_ad002


title: OB_17_0249_1

value: No


title: OB_17_0257_2

value: Not Detected


title: OB_17_0255_2

value: Premenopausal

value: Invasive ductal carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad002


title: OB_17_0234_3

value: AC+T


title: OB_17_0234_2

value: LumA


title: OB_17_0230_2

value: Yes

value: Normal

value: ER+


title: OB_17_0230_1

value: Basal

value: TN


title: OB_17_0234_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D9_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D9_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D9_ad002


title: OB_17_0266_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D8_ad004


title: OB_17_0202_1

value: Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D8_ad007

value: Hippocampus


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad001

value: male


title: OB_17_0181_2

value: Postmenopausal

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D8_ad010


title: OB_17_0183_1

value: Female

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D9_ad008


title: OB_17_0171_1

value: No

value: Not Detected


title: OB_17_0181_1

value: Invasive ductal carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D8_ad001


title: OB_17_0171_2

value: Premenopausal

value: AC+T


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D8_ad012


title: OB_17_0166_2

value: Yes

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D7_ad012


title: OB_17_0179_2


title: OB_17_0166_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D7_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D7_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-E10_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D6_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D7_ad006


title: OB_17_0179_1


title: OB_17_0169_1


title: OB_17_0155_3


title: OB_17_0155_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D6_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D7_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D6_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D6_ad010


title: OB_17_0134_1


title: OB_17_0155_1


title: OB_17_0128_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D5_ad006


title: OB_17_0134_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D6_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D6_ad006


title: OB_17_0127_2


title: OB_17_0127_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D5_ad010


title: OB_17_0128_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D5_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D5_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D5_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad008


title: OB_17_0100_1

value: ER+


title: OB_17_0084_2

value: Positive

value: Negative


title: OB_17_0169_2


title: OB_17_0084_1


title: OB_17_0066_1

value: Basal

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad007

value: Hippocampus

value: male


title: OB_17_0058_2

value: Postmenopausal

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D5_ad007


title: OB_17_0058_1

value: Female


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad002


title: OB_17_0045_1

value: No

value: TCHP

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D4_ad001


title: OB_17_0050_1

value: Invasive ductal carcinoma


title: OB_17_0038_2

value: Premenopausal

value: AC+T


title: OB_17_0038_3

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad010


title: OB_17_0099_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad012


title: OB_17_0038_1

value: ER+


title: OB_17_0018_2

value: Yes

value: Not Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad006


title: OB_17_0001_2

value: Negative

value: Basal


title: OB_17_0001_3

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad002

value: Hippocampus

value: male


title: OB_17_0001_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D3_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D2_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D2_ad010


title: OB_16_0364_2


title: OB_16_0364_3


title: OB_16_0361_1

value: Postmenopausal

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D2_ad012


title: OB_16_0359_2

value: Female

value: No


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D2_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D1_ad010


title: OB_16_0355_2

value: Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D2_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D2_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D1_ad006


title: OB_16_0348_2

value: Invasive ductal carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D1_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D1_ad002


title: OB_16_0347_2


title: OB_16_0347_1


title: OB_16_0344_3

value: Premenopausal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad010


title: OB_16_0341_2

value: AC+T

value: Positive


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D1_ad001


title: OB_16_0344_1

value: Normal

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad012


title: OB_16_0344_2

value: Not Detected


title: OB_16_0341_1

value: Negative

value: LumB


title: OB_16_0355_1

value: Basal

value: TN


title: OB_16_0359_1


title: OB_16_0336_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad008

value: Hippocampus

value: male


title: OB_16_0336_1

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad006


title: OB_16_0320_1

value: Female

value: Yes


title: OB_16_0317_1

value: No

value: Detected


title: OB_16_0348_1

value: Postmenopausal

value: Invasive ductal carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad010


title: OB_16_0283_2

value: Premenopausal

value: AC+T

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad007


title: OB_16_0269_2

value: Not Detected


title: OB_16_0315_3

value: Positive

value: Negative

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad002


title: OB_16_0259_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad012


title: OB_16_0253_1

value: Normal


title: OB_16_0244_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad004

value: Hippocampus


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D11_ad002

value: male


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad010


title: OB_16_0243_1

value: AC+T+Trastuzumab

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad006


title: OB_16_0243_2

value: Female


title: OB_16_0315_2

value: No


title: OB_16_0315_1


title: OB_16_0240_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D10_ad012


title: OB_16_0237_1

value: Basal

value: TN


title: OB_16_0269_1

value: Invasive ductal carcinoma


title: OB_16_0234_2

value: Premenopausal

value: TCHP


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C8_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C8_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-D12_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C7_ad007


title: OB_16_0221_1

value: Yes

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C8_ad002


title: OB_16_0215_1

value: Not Detected

value: AC+T

value: Positive


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C8_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C8_ad007


title: OB_16_0207_2


title: OB_16_0207_1


title: OB_16_0240_2

value: Negative

value: ER+


title: OB_16_0199_1

value: Postmenopausal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad002

value: Hippocampus

value: male


title: OB_16_0192_1

value: Female

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C9_ad007


title: OB_16_0191_3

value: No


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C8_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C7_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C6_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C7_ad010


title: OB_16_0234_1


title: OB_16_0188_2


title: OB_16_0184_2

value: Mucinous carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C6_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C6_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C7_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C6_ad010


title: OB_16_0175_2

value: Detected

value: Equivocal

value: Invasive ductal carcinoma

value: Others

value: Basal

value: TN


title: OB_16_0184_1

value: Premenopausal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C6_ad004


title: OB_16_0215_2

value: Not Detected

value: AC+T

value: Positive

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad010

value: Hippocampus


title: OB_16_0192_2

value: Postmenopausal

value: Negative


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad012

value: male


title: OB_16_0168_3

value: Female

value: No

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad008


title: OB_16_0173_1

value: TCHP


title: OB_16_0175_1

value: Yes

value: Detected

value: Equivocal

value: Invasive ductal carcinoma


title: OB_16_0168_2

value: Premenopausal


title: OB_16_0168_1

value: Not Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad006


title: OB_16_0163_3

value: AC+T


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad004


title: OB_16_0163_1

value: Positive

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C7_ad001

value: Hippocampus


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C4_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C4_ad006


title: OB_16_0153_2

value: Basal

value: TN


title: OB_16_0156_1

value: AC+T+Trastuzumab

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C3_ad007

value: male


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C6_ad008


title: OB_16_0149_1

value: Female

value: No

value: Mucinous carcinoma with signet ring cell differentiation


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C4_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C5_ad001


title: OB_16_0147_1

value: Detected

value: Negative


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C4_ad008


title: OB_16_0131_1

value: Equivocal

value: Invasive ductal carcinoma

value: ER+


title: OB_16_0115_2

value: Postmenopausal

value: Not Detected

value: AC+T


title: OB_16_0115_3


title: OB_16_0108_1

value: Premenopausal

value: Yes

value: Invasive carcinoma with lobular feature

value: Positive


title: OB_16_0102_1

value: Others

value: Basal

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C4_ad002

value: Hippocampus

value: male


title: OB_16_0102_2

value: Female

value: No


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C3_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C2_ad008


title: OB_16_0163_2

value: Negative

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C4_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C2_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C3_ad006


title: OB_16_0081_1

value: Invasive ductal carcinoma


title: OB_16_0156_2

value: AC+T+Trastuzumab


title: OB_16_0123_2

value: TCHP

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad012


title: OB_16_0123_1

value: Premenopausal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C2_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C3_ad001


title: OB_16_0101_3

value: Not Detected


title: OB_16_0101_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C2_ad001


title: OB_16_0100_2


title: OB_16_0100_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad006


title: OB_16_0095_2

value: Detected

value: Equivocal

value: AC+T

value: ER+


title: OB_16_0095_3

value: Basal

value: TN


title: OB_16_0089_1


title: OB_16_0080_3

value: Positive


title: OB_16_0096_2

value: Female

value: Normal


title: OB_16_0080_2

value: No

value: Negative


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad010

value: Hippocampus

value: male


title: OB_16_0118_2

value: Postmenopausal

value: Invasive ductal carcinoma

value: AC+T+Trastuzumab

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad007


title: OB_16_0080_1

value: Premenopausal

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad007


title: OB_16_0078_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad002


title: OB_16_0070_1

value: TCHP


title: OB_16_0096_1

value: Detected

value: Not Detected

value: AC+T


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C1_ad004


title: OB_16_0051_1

value: Positive

value: Basal

value: ER+

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad006


title: OB_16_0047_1

value: Female

value: No

value: Negative


title: OB_16_0039_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad008

value: Hippocampus

value: male


title: OB_16_0095_1

value: Equivocal

value: Invasive ductal carcinoma

value: Normal


title: OB_16_0034_1

value: Premenopausal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad004


title: OB_16_0032_1

value: LumB


title: OB_16_0030_1

value: TCHP


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad012


title: OB_16_0026_1

value: Not Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad002


title: OB_16_0011_1

value: INVASIVE MICROPAPILLARY CARCINOMA

value: Others


title: OB_16_0078_1

value: Postmenopausal

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad001


title: OB_16_0006_2

value: Invasive carcinoma, POORLY DIFFERENTIATED

value: TN


title: OB_16_0006_1

value: Female

value: No

value: Basal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C10_ad001

value: Hippocampus

value: male


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C10_ad006


title: OB_16_0005_2

value: Invasive ductal carcinoma

value: AC+T

value: Positive

value: Negative

value: LumA

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C10_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C11_ad008


title: OB_16_0005_1

value: Premenopausal

value: Not Detected

value: LumB


title: OB_15_0294_2

value: Equivocal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C10_ad004


title: OB_15_0259_2

value: Postmenopausal

value: Others


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C10_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad010


title: OB_15_0294_1

value: Female

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad004


title: OB_15_0253_2

value: No

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C12_ad001

value: Hippocampus

value: male


title: OB_15_0253_1

value: Invasive ductal carcinoma


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-C10_ad012


title: OB_15_0237_1

value: AC+T

value: Basal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B8_ad012


title: OB_15_0237_2

value: Negative

value: Normal


title: OB_15_0202_1

value: Premenopausal


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B6_ad010


title: OB_15_0222_2

value: Not Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad001


title: OB_15_0135_2

value: LumA


title: OB_15_0131_1

value: Equivocal


title: OB_15_0069_3

value: Yes


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B8_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B8_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B8_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B9_ad007


title: OB_15_0237_3

value: Postmenopausal


title: OB_15_0058_3

value: Female

value: Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B8_ad001


title: OB_15_0066_3

value: No


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad010


title: OB_15_0053_1

value: Others

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad007

value: Hippocampus

value: male


title: OB_16_0033_1

value: Invasive ductal carcinoma

value: AC+T


title: OB_16_0029_2

value: Negative

value: LumB

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B6_ad006


title: OB_16_0029_1

value: Premenopausal

value: Not Detected

value: Basal


title: OB_16_0012_1

value: AC+T+Trastuzumab

value: Positive


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B6_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad001


title: OB_16_0012_2

value: Female


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B7_ad006


title: OB_15_0306_2

value: LumA


title: OB_15_0304_2

value: Postmenopausal

value: No


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B6_ad004


title: OB_15_0299_2

value: Yes


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad001

value: Hippocampus


title: OB_15_0299_3


title: OB_15_0299_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad002

value: male


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B6_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad007


title: OB_15_0298_2

value: Equivocal

value: Invasive ductal carcinoma

value: TN


title: OB_15_0298_1

value: AC+T

value: Negative


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B6_ad001


title: OB_15_0286_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad012


title: OB_15_0281_1

value: Others


title: OB_15_0295_1

value: Premenopausal


title: OB_15_0281_2

value: Not Detected

value: Normal


title: OB_15_0273_3

value: cT4N3M1(m/contralateral axillary LNs)

value: Positive

value: LumB

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad010


title: OB_15_0273_1

value: Female

value: No

value: Basal


title: OB_15_0273_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad008

value: Hippocampus

value: male


title: OB_15_0261_3

value: Postmenopausal

value: Invasive ductal carcinoma


title: OB_15_0261_2

value: AC+T

value: TN


title: OB_15_0261_1

value: Negative


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B4_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B4_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B4_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B4_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad012


title: OB_15_0246_2

value: Premenopausal

value: Equivocal

value: AC+T+Trastuzumab


title: OB_15_0251_1

value: LumA


title: OB_15_0246_1

value: Not Detected

value: Positive


title: OB_15_0243_2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B5_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B4_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad010


title: OB_15_0238_2

value: Yes


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad004


title: OB_15_0235_3

value: Female

value: Invasive carcinoma with lobular feature

value: ER+


title: OB_15_0238_1

value: LumB


title: OB_15_0243_1

value: No


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad002

value: Hippocampus

value: male


title: OB_15_0235_2

value: AC+T


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B2_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad001


title: OB_15_0235_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B2_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B1_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B4_ad007


title: OB_15_0234_2

value: Postmenopausal

value: Invasive ductal carcinoma


title: OB_15_0201_3

value: Premenopausal

value: Negative


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B2_ad006


title: OB_15_0208_1

value: Basal

value: TN


title: OB_15_0234_1

value: AC+T+Trastuzumab


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B2_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B2_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B2_ad002


title: S2_ATAC_2

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
Adapter sequences were trimmed from raw sequence reads using NGmerge
Reads were aligned to the D. melanogaster genome using Bowtie2 using the following parameters: --very-sensitive, --no-mixed, --no-discordant, -X 5000, -k 2
Aligned reads were filtered to include only reads with a mapping quality score > 30. Reads aligning to scaffolds or the mitochondrial genome were discarded. To identify fragments that likely originated from nucleosome-free regions, fragments were filtered to include only those < 100 bp.
To call peaks on accessible fragments, accessible fragments from both replicates were merged and MACS2 was used with the following parameters: -f BAMPE, --keep-dup all, -g 1.2e8, --call-summits
Genome_build: dm6
Supplementary_files_format_and_content: bigwigs were generated using deeptools. Scores represent sequencing depth in 10bp bins.
Supplementary_files_format_and_content: narrowPeak file contains peaks as called by MACS2

organism: Drosophila melanogaster

source_name: S2 cell line

growth_protocol: S2 cells in this study were cultured at 25°C in Schneider’s Media (Thermo Fisher) containing 10% FBS (Omega Scientific), and 1% antibiotic/antimycotic (Thermo Fisher).

extract_protocol:
ATAC was performed on 2x10^6 S2 cells using Tn5 transposase (Illumina 15027865)
Tagmented DNA was amplified for 12 PCR cycles using unique dual index primers

tag: molecule subtype

value: tagmented DNA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B3_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B1_ad006


title: OB_15_0201_1

value: Not Detected

value: Positive


title: S2_ATAC_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B1_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B1_ad010


title: OB_15_0197_2

value: Female

value: LumA


title: OB_15_0197_1

value: LumB

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B12_ad004

value: Hippocampus


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B12_ad008

value: male


title: OB_15_0190_3

value: Yes

value: AC+T


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B1_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B12_ad012