title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B8_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B3_AD004_indexed

status: Public on Aug 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: ACA,PL,ILA

tag: Sex

value: male

tag: age

tag: strain


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B7_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B5_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B4_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B3_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B3_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B4_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B4_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B3_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B1_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B2_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_C10_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B12_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B3_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B12_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B2_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B2_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B11_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B2_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B2_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B12_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B3_AD002_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B1_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_B11_AD002_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_A10_AD012_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H8_AD001_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_A10_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H6_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H6_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H6_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H7_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_3_CEMBA180206_4A_4_A10_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H6_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180206_4A_1_CEMBA180206_4A_2_H6_AD007_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A8_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A9_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A8_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_B10_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A4_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A7_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A4_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A4_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A4_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A4_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A5_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A6_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A12_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A4_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A12_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A12_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A3_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A11_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A9_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A2_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD001_indexed


title: BPM_0354

type: genomic

city: Campinas

first: Cristiane

middle: de Souza

last: Rocha

state: São Paulo

address: Av Tessália Vieira de Camargo, 126 Cidade Universitária "Zeferino Vaz"

department: Medical Genetics

country: Brazil

institute: Unicamp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). The genotype were called from fluorescent signals by the CRLMM package in R software.

label: biotin

organism: Homo sapiens

source_name: reference individual

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: The genomic DNA for the samples was obtained from peripheral blood via the phenol-chloroform procedure. The quantification and quality of each DNA sample was evaluated with a Qubit® 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and an Epoch 2 microplate spectrophotometer (BioTek Instruments Inc., Winooski, VT, USA).

tag: tissue

value: blood


title: BPM_0355


title: BPM_0357


title: BPM_0358


title: BPM_0353


title: BPM_0352


title: WT MS rep1

city: Haikou

first: Pingjuan

last: Zhao

address: XueYuan Road 4

department: Institute of Tropical Bioscience and Biotechnology

country: China

institute: Chinese Academy of Tropical Agricultural Sciences

library_source: transcriptomic

data_processing:
Seqtk used for filter data
Hisat2 version:2.0.4 used for mapping genome
Stringtie version:1.3.0 used for Standardization of gene expression
Genome_build: Mesculenta_305_v6
Supplementary_files_format_and_content: excel files include FPKM values for each Gene ...

molecule: total RNA

organism: Manihot esculenta

source_name: leaf

growth_protocol: 2-month-old WT seedlings were cultured by stem segment cuttings  in MS medium and sterile bottle for two months.

extract_protocol: leaves were removed, flash frozen on dry ice, and RNA was harvested using  RNAplant Plus Reagent (Tiangen, DP441) .

treatment_protocol: For ABA and PEG treatments, a certain amount of ABA and PEG6000 solution was added into the medium grow 60-day-old WT cassava seedlings to a final concentration of 50 μmol of ABA and 7% PEG. The mature leaves were collected at  48 h after treatment. The collected samples were used to extract total RNA.

tag: treatment

value: 2-month-old seedlings in MS medium

tag: genotype/variation

value: wild type


title: WT ABA rep2

value: 2-month-old seedlings in MS +ABA medium


title: WT ABA rep1


title: BPM_0351


title: BPM_0350


title: WT MS rep2


title: BPM_0347


title: BPM_0349


title: BPM_0346


title: BPM_0348


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_A10_AD004_indexed


title: BPM_0343


title: BPM_0342


title: WT ABA rep3


title: BPM_0345


title: BPM_0341


title: BPM_0339


title: BPM_0344


title: BPM_0338


title: BPM_0336


title: BPM_0337


title: BPM_0356


title: BPM_0335


title: BPM_0331


title: BPM_0334


title: BPM_0332


title: BPM_0333


title: BPM_0329


title: BPM_0328


title: BPM_0330


title: BPM_0323


title: BPM_0322


title: BPM_0327


title: BPM_0326


title: BPM_0320


title: BPM_0317


title: BPM_0316


title: BPM_0340


title: BPM_0318


title: BPM_0314


title: BPM_0313


title: BPM_0310


title: BPM_0312


title: BPM_0309


title: BPM_0308


title: BPM_0307


title: BPM_0304


title: BPM_0321


title: BPM_0324


title: BPM_0302


title: BPM_0325


title: BPM_0306


title: BPM_0301


title: BPM_0305


title: BPM_0300


title: BPM_0298


title: BPM_0297


title: BPM_0296


title: BPM_0295


title: BPM_0299


title: BPM_0294


title: BPM_0293


title: BPM_0292


title: BPM_0311


title: BPM_0290


title: BPM_0291


title: BPM_0288


title: BPM_0289


title: BPM_0287


title: BPM_0286


title: BPM_0285


title: BPM_0284


title: BPM_0283


title: BPM_0303


title: BPM_0282


title: BPM_0280


title: BPM_0279


title: BPM_0281


title: BPM_0278


title: BPM_0277


title: BPM_0275


title: BPM_0274


title: BPM_0272


title: BPM_0271


title: BPM_0267


title: BPM_0266


title: BPM_0264


title: BPM_0263


title: BPM_0269


title: BPM_0268


title: BPM_0265


title: BPM_0261


title: BPM_0259


title: BPM_0256


title: BPM_0255


title: BPM_0258


title: BPM_0262


title: BPM_0276


title: BPM_0251


title: BPM_0254


title: BPM_0252


title: BPM_0250


title: BPM_0253


title: BPM_0248


title: BPM_0249


title: BPM_0273


title: BPM_0270


title: BPM_0319


title: BPM_0246


title: BPM_0247


title: BPM_0243


title: BPM_0245


title: BPM_0242


title: BPM_0240


title: BPM_0241


title: BPM_0260


title: BPM_0244


title: BPM_0238


title: BPM_0239


title: BPM_0237


title: BPM_0257


title: BPM_0236


title: BPM_0235


title: BPM_0232


title: BPM_0234


title: BPM_0231


title: BPM_0233


title: BPM_0230


title: BPM_0226


title: BPM_0229


title: BPM_0228


title: BPM_0225


title: BPM_0227


title: BPM_0224


title: BPM_0223


title: BPM_0222


title: BPM_0221


title: BPM_0220


title: BPM_0216


title: BPM_0218


title: BPM_0215


title: BPM_0209


title: BPM_0214


title: BPM_0212


title: BPM_0210


title: BPM_0213


title: BPM_0211


title: BPM_0208


title: BPM_0205


title: BPM_0202


title: BPM_0204


title: BPM_0201


title: BPM_0197


title: BPM_0198


title: BPM_0194


title: BPM_0203


title: BPM_0219


title: BPM_0206


title: BPM_0196


title: BPM_0315


title: BPM_0193


title: BPM_0217


title: BPM_0192


title: BPM_0200


title: BPM_0191


title: BPM_0190


title: BPM_0189


title: BPM_0188


title: BPM_0207


title: BPM_0185


title: BPM_0184


title: BPM_0187


title: BPM_0186


title: BPM_0183


title: BPM_0182


title: BPM_0195


title: BPM_0181


title: BPM_0179


title: BPM_0180


title: BPM_0177


title: BPM_0199


title: BPM_0176


title: BPM_0178


title: BPM_0172


title: BPM_0175


title: BPM_0173


title: BPM_0174


title: BPM_0171


title: BPM_0169


title: BPM_0168


title: BPM_0166


title: BPM_0167


title: BPM_0165


title: BPM_0164


title: BPM_0163


title: BPM_0161


title: BPM_0162


title: NeuCs-XL +LPS rep1

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

country: Japan

institute: Keio University

data_processing:
Bcl2fastq (v2.17.1.14) was used to process the original image data for base calling and preliminary quality analysis.
The Illumina built-in software determined whether to keep or discard each of the sequencing fragments (namely reads) based on the quality of the first 25 bases.
The raw data (Pass Filter Data) obtained from this step was stored in FASTQ format, which contains the base sequence and the corresponding sequencing quality information.
Data filtering was performed by Cutadapt software (version 1.9.1), and the alignment of the clean data to the reference genome was performed using Hisat2 (v2.0.1) with default parameters.
Gene expression calculation was performed to calculate FPKM (Fragments per kilobases per million reads) based on read counts.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx, fpkm

source_name: Neutrophil-like cells with LPS

growth_protocol: Neutrophil progenitors were generated from iPSC-derived hematopoietic progenitor cells (HPC) by the doxycycline-inducible induction of c-Myc, BMI-1 and BCL-XL. Then, neutrophil-like cells were generated four days after the withdrawal of doxycycline.

extract_protocol:
RNA was harvested using RNAeasy reagents (QIAGEN), then reverse transcription was performed with ReverTra Ace qPCR RT Master Mix (TOYOBO).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample 7-9 were LPS treated for 24 hours.

tag: cell type

value: iPSC-derived neutrophil-like cells

value: four days after the withdrawal of dox with 24-hour LPS stimulation


title: NeuCs-XL rep1

source_name: Neutrophil-like cells

value: four days after the withdrawal of dox


title: NeuCs-XL rep2


title: BPM_0170


title: NeuCs-XL +LPS rep2


title: NeuCs-XL +LPS rep3


title: NeuCs-XL rep3


title: BPM_0159


title: BPM_0158


title: NeuPs-XL rep1

source_name: Neutrophil progenitors

value: iPSC-derived neutrophil progenitors

value: with doxycycline


title: BPM_0157


title: BPM_0160


title: KP8966 AML-MSCs

type: RNA

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

hyb_protocol: Hybridization of Affymetrix ClariomS mouse microarrays was performed as recommenden by the manufacturer

scan_protocol: The microarrays were washed and stained in an Affymetrix Fluidics station and scanned in a GC3000 scanner with G7 update, as recommended by Affymetrix

data_processing: Signal summarization was done in Partek Genomics Suite using the RMA algorithm

source_name: Endosteal stroma of the bone marrow, transplanted with AML cells

label_protocol: Total RNA samples (~10 pg) were amplified and labelled using the  Affymetrix WT Pico Reagent Kit

growth_protocol: 3 mice which are KP8201, KP8203 and KP8966, were transplanted with BM transduced with MLL-AF9 while 3 mice which are KP1820, KP8816 and TU1777, were transplanted with normal BM cells. When the mice became sick, they were killed and the MSCs from the crushed bones were sorted for RNA study.

extract_protocol: Extraction and purification of RNA were performed using spin columen (RNeasy Mini kit, Qiagen) according to the manifacturer's instructions

treatment_protocol: No treatment

value: bone marrow

value: Mesenchymal stromal cells

tag: disease state

value: AML


title: TU1777 Ctrl-MSCs

source_name: Endosteal stroma of the bone marrow, transplanted with normal BM cells

value: normal BM


title: KP8816 Ctrl-MSCs


title: KP8203 AML-MSCs


title: KP8201 AML-MSCs


title: BPM_0156


title: BPM_0155


title: KP1820 Ctrl-MSCs

value: female


title: NeuPs-XL rep3


title: NeuPs-XL rep2


title: BPM_0153


title: BPM_0154


title: BPM_0152


title: P3NT1_20_Region2_2_Proximal

city: Beijing

first: Qiming

last: Zhou

address: No. 30, Shuangqing Road, Haidian District

institute: Tsinghua University

data_processing:
Clean data obtained from Annoroad company
Adaptor removal and reads filtering by trim_galore
filtered pair-end fastq files were then mapped to human reference genome (GRCh38.p13) by STAR
Duplication removal by PICARD
Raw transcript read counts were measured by HTSeq-count and merge to gene-based read count
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Human non-tumor liver biospecimen

extract_protocol:
Tissue blocks were obtained in 0.2 ml PCR tube by LMD7000 (Leica, Germany). Buffer RLT (Qiagen, Germany) with DTT (Sigma, USA) were added and shaken vigorously for tissue lysis and RNA release. RNA Clean beads (Vazyme, China) 1.8x were added to isolate total RNA.
Prepare annealing procedure in the same tube with 3ul H2O, 1ul dNTP, 1ul Oligo(dT) and 0.5ul RNase Inhibitor (RI) (Life Technologies, USA). Incubated at 72 degree 3min and immediately transfer in ice for 2min. Prepare reverse transcription reaction in same tube with 2ul 5x RT buffer, 0.5ul DTT, 0.5ul RI, 0.5ul Template Switch Oligo (TSO, Sangon Biotech, China), 1ul Maxima reverse transcriptase (Life Technologies, USA). Incubate with 50 degree with 1 hour and deactivate reverse transcriptase with 85 degree for 5 min. Amplified the first strand product with 12.5ul 2x KAPA HIFI HotStart ReadyMix (Sigma, USA), 0.5ul TSO-PCR primer (Sangon Biotech, China) and 2ul H2O. Reaction condition was 95 degree 3min, 98 degree 20s, 67 degree 15s, 72 degree 6min for 21 cycles and 72 degree for 5min. PCR product was purified with 0.8x DNA Clean beads (Vazyme, China). Next generation sequecning library was then constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, China). Libraries were sequenced by Illumina Xten Pair-end 150bp by Annoroad

value: Liver

tag: group

value: Hepa69-high (Proximal)


title: P3NT1_24_Region3_2_Distal

value: Hepa69-low (Distal)


title: P3NT1_19_Region1_2_FB

value: Fibrotic region (FB)


title: P3NT1_23_Region3_2_Proximal


title: P3NT1_15_Region3_1_Distal


title: P3NT1_18_Region1_2_Distal


title: BPM_0151

value: blood


title: P3NT1_10_Region2_1_FB


title: P3NT1_9_Region2_1_Distal


title: P3NT1_11_Region3_1_Proximal


title: BPM_0149


title: BPM_0147


title: BPM_0146


title: BPM_0145


title: P3NT1_14_Region4_1_Proximal


title: BPM_0148


title: P3NT1_5_Region1_1_Proximal


title: P3NT1_6_Region1_1_Distal


title: P3NT1_7_Region1_1_FB


title: BPM_0144


title: BPM_0143


title: TC_1_IFNr_2

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts and normalized counts

growth_protocol: Cells were growth in RPMI with 10% FBS and 1% penicillin/streptomycin. For 72 hours, IFN-gamma treated group was treated with 20ng/ml murine recombinant interferon-gamma and control group was untreated.

extract_protocol:
RNA was extracted from cells with TRIzol RNA isolation reagents.
Poly(A) RNA Selection + SMARTer stranded RNA-Seq kit HT
QuantSeq 3' mRNA-Seq Library Prep Kit FWD

treatment_protocol: 20ng/ml IFN-gamma for 72 hours.

tag: cell line

value: lung adenocarcinoma cell line

value: IFN-gamma


title: TC_1_IFNr_3


title: BPM_0141


title: BPM_0140


title: BPM_0142


title: TC_1_Ct_2

value: Untreated


title: TC_1_Ct_3


title: P3NT1_8_Region2_1_Proximal


title: BPM_0139


title: BPM_0137


title: TC_1_Ct_1


title: MCMV-IL-15-3

source_name: MCMV-infected mouse with IL-15

growth_protocol: Control group was uninfected and MCMV-infected group was infected with MCMV 1x10^6 pfu i.p. 30 days after infection, 0.5 million TC-1 cells diluted in 100ul of PBS were injected through mouse tail vein. After 7 days of injection, 2ug of IL-15 were injected to intra-peritoneal twice with interval of 2 days. At day 21, mouse lung was harvested and dissociated into single cells with mechanical and enzymatic digestion. Epithelial cells were seperated from those single cells by MACS cell sorter with EpCAM positive and CD45, CD31 negative.

treatment_protocol: 1 x 10^6 PFU of MCMV / 2ug of IL-15 (twice)

value: Mouse lung epithelial cells


title: BPM_0136


title: MCMV-IL-15-4


title: MCMV-IL-15-1


title: BPM_0133


title: MCMV-PBS-1

source_name: MCMV-infected mouse without IL-15

value: MCMV-infected-PBS


title: BPM_0132


title: MCMV-PBS-3


title: BPM_0134


title: MCMV-PBS-2


title: TC_1_IFNr_1


title: BPM_0129


title: P3NT1_22_Region2_2_FB


title: BPM_0138


title: Ct-IL-15-2

source_name: Naive mouse with IL-15


title: BPM_0131


title: BPM_0127


title: BPM_0128


title: Ct-IL-15-1


title: BPM_0135


title: BPM_0126


title: Ct-PBS-1

source_name: Naive mouse without IL-15

value: Uninfected-PBS


title: BPM_0124


title: Ct-PBS-3


title: BPM_0123


title: Ct-IL-15-3


title: BPM_0122


title: PLAC-seq F123 KO-POLII POL2-S5P

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing:
Library strategy: PLAC-Seq
CAP-C, BL-CAP-C, in-situ Hi-C and PLAC-seq: Each read end sequenced from the proximity ligated libraries was aligned independently to either the mm10, hg19 or dm3 reference genome using BWA-MEM (v 0.7.12). Singletons and chimeric reads were removed. PCR duplicates, unligated reads and reads with a contact distance less than 1Kb were also filtered. PCR duplicates were removed using Picard Tools (v 2.2.2). Unligated reads were defined as both read ends mapping onto the same MboI fragment. A pre-formatted text file was prepared before converting it into a .hic format file with the following resolutions (0.5 Kb, 1 Kb, 2 Kb, 5 Kb, 10 Kb, 25 Kb, 40 Kb, 50 Kb, 100 Kb, 250 Kb, 500 Kb, 1 Mb and 2.5 Mb). Finally, a MAPQ>=1 and MAPQ>=30 .hic file was then generated for each sample. To generate a CAP-C merge file, all G3, G5 and G7 primary and replicated libraries in the pre-formatted text file were concatenated and merged-sorted before using Juicer Tools (v 0.7.0) to convert it into a .hic formatted file.
BL-CAP-C: For DNase I fragmentation-based libraries, we have additional pre-processing steps to be performed prior to the instructions listed in the CAP-C data processing section listed above. We first used SeqPrep to merge overlapping read pairs (2×150 bp). For the resulting merged and unmerged read pairs, cutadapt was used to trim the bridge linker adaptor (ACGCGATATCTTATCTGACT, both forward and reverse-complementary) off the read from the 5’ (-g) and 3’ (-a) direction. Up to 1 adaptor count per read (-n) was used, and a minimum overlap length of 10 threshold (--overlap) between the linker and read was used. Only read pairs where the length of at least one read was too short (<15bp) or merged read pairs that failed to possess a linker were removed (Supplementary Table 2). Because DNase I was used to fragment BL-CAP-C datasets, no restriction cut site annotation files was done to annotate the paired reads.
CAP-C, BL-CAP-C and in-situ Hi-C: Compartments were called using the Eigenvector module of Juicer (v 0.7.0). Peaks/Loops were called using HiCCUPs. Domains were called using Arrowhead. Strength around the ends of the domain boundary or a region of interest was measured by computing the values of the directionality index metric. Aggregate Peak Analysis (APA) was performed on low-resolution contact maps using the APA module of Juicer.
ChIP-seq: ChIP-seq libraries were aligned to the mm10 or hg19 reference genome using BWA-MEM (v 0.7.12). PCR duplicates were removed using Picard Tools (v 2.2.2). Peak calling was performed using MACS2 (Zhang et al.) with both treated and control BAM files, or just the IP sample alone using the following parameters: -q 0.05 –f BAM (–g mm | -g hs). We used bedtools (v 2.27) to create bedGraph files of depth-normalized RPM or FPM values before converting them to bigWig files using UCSC bedGraphToBigWig.
Genome_build: mm10,hg19,dm3
Supplementary_files_format_and_content: Merged primary and replicate samples are labeled with a B0* instead of an S0* or R0*.

source_name: mouse embryonic stem cells

growth_protocol: F123 mouse embryonic stem cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (85% High Glucose DMEM, 15% Knockout Serum Replacement, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM Glutamine, LIF 500U/mL, +P/S). Before harvesting for CAP-C; ChIP-Seq; PLAC-Seq or in-situ Hi-C, F123 mESCs were passaged onto feeder free 0.2% gelatin coated plates for at least 2 passages to rid the culture of feeder cells.

extract_protocol:
For all PLAC-Seq experiment, after crosslinking, restriction enzyme digestion and proximal ligation, DNA bound protein was striped away by proteinase K and DNA was extracted by ethanol precopitation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment ( exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 11 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were grown in medium containing 500 uM auxin to deplete CTCF for 48 hours. Medium with auxin was changed every 24 hours. 6-8 hours before havesting, cells were treated with 1uM flavopiridol for 6-8 hours.

value: embyonic stem cells

tag: chip antibody

value: Mouse Monoclonal anti-Phospho RNA Polymerase II CTD (Ser5) (Abcam, ab5408)


title: PLAC-seq F123 POLII POL2-S5P

treatment_protocol: Cells were treated with 1uM flavopiridol for 6-8 hours before harvesting


title: PLAC-seq F123 POLII-hexanediol POL2-S5P

treatment_protocol: Cells were treated with of 5% (v/v) 1,6-hexanediol at room temperature for 10 minbefore harvesting


title: BPM_0130


title: PLAC-seq F123 WT POL2-S5P


title: BPM_0125


title: BPM_0121


title: PLAC-seq F123 KO POL2-S5P

treatment_protocol: Cells were grown in medium containing 500 uM auxin to deplete CTCF for 48 hours. Medium with auxin was changed every 24 hours.


title: BPM_0120


title: BPM_0119


title: ChIP-seq BL-CAP-C F123 CTCF-AID WT Pol2-S5P

data_processing:
CAP-C, BL-CAP-C, in-situ Hi-C and PLAC-seq: Each read end sequenced from the proximity ligated libraries was aligned independently to either the mm10, hg19 or dm3 reference genome using BWA-MEM (v 0.7.12). Singletons and chimeric reads were removed. PCR duplicates, unligated reads and reads with a contact distance less than 1Kb were also filtered. PCR duplicates were removed using Picard Tools (v 2.2.2). Unligated reads were defined as both read ends mapping onto the same MboI fragment. A pre-formatted text file was prepared before converting it into a .hic format file with the following resolutions (0.5 Kb, 1 Kb, 2 Kb, 5 Kb, 10 Kb, 25 Kb, 40 Kb, 50 Kb, 100 Kb, 250 Kb, 500 Kb, 1 Mb and 2.5 Mb). Finally, a MAPQ>=1 and MAPQ>=30 .hic file was then generated for each sample. To generate a CAP-C merge file, all G3, G5 and G7 primary and replicated libraries in the pre-formatted text file were concatenated and merged-sorted before using Juicer Tools (v 0.7.0) to convert it into a .hic formatted file.
BL-CAP-C: For DNase I fragmentation-based libraries, we have additional pre-processing steps to be performed prior to the instructions listed in the CAP-C data processing section listed above. We first used SeqPrep to merge overlapping read pairs (2×150 bp). For the resulting merged and unmerged read pairs, cutadapt was used to trim the bridge linker adaptor (ACGCGATATCTTATCTGACT, both forward and reverse-complementary) off the read from the 5’ (-g) and 3’ (-a) direction. Up to 1 adaptor count per read (-n) was used, and a minimum overlap length of 10 threshold (--overlap) between the linker and read was used. Only read pairs where the length of at least one read was too short (<15bp) or merged read pairs that failed to possess a linker were removed (Supplementary Table 2). Because DNase I was used to fragment BL-CAP-C datasets, no restriction cut site annotation files was done to annotate the paired reads.
CAP-C, BL-CAP-C and in-situ Hi-C: Compartments were called using the Eigenvector module of Juicer (v 0.7.0). Peaks/Loops were called using HiCCUPs. Domains were called using Arrowhead. Strength around the ends of the domain boundary or a region of interest was measured by computing the values of the directionality index metric. Aggregate Peak Analysis (APA) was performed on low-resolution contact maps using the APA module of Juicer.
ChIP-seq: ChIP-seq libraries were aligned to the mm10 or hg19 reference genome using BWA-MEM (v 0.7.12). PCR duplicates were removed using Picard Tools (v 2.2.2). Peak calling was performed using MACS2 (Zhang et al.) with both treated and control BAM files, or just the IP sample alone using the following parameters: -q 0.05 –f BAM (–g mm | -g hs). We used bedtools (v 2.27) to create bedGraph files of depth-normalized RPM or FPM values before converting them to bigWig files using UCSC bedGraphToBigWig.
Genome_build: mm10,hg19,dm3
Supplementary_files_format_and_content: Merged primary and replicate samples are labeled with a B0* instead of an S0* or R0*.

extract_protocol:
For all ChIP-Seq experiment, after formaldehyde crosslinking, chromatins were sheared by sonication and DNA bound with protein of interest was enriched by antibodies. DNA protein complexes were revese crosslinked and extracted by phenol:chloroform.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment ( exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 11 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: ChIP-seq BL-CAP-C CTCF-AID WT Rad21

value: Rabbit Polyclonal anti-RAD21 (Abcam, ab992)


title: ChIP-seq BL-CAP-C F123 CTCF-AID WT Pol2-S2P

value: Mouse Monoclonal anti-Phospho RNA Polymerase II CTD (Ser2) (MAB Institute, Inc, MABI0602)


title: Ct-PBS-2


title: ChIP-seq BL-CAP-C F123 CTCF-AID POLII Rad21


title: ChIP-seq BL-CAP-C F123 CTCF-AID WT Ctcf

value: Rabbit Polyclonal anti-CTCF (Abcam, ab70303)


title: BPM_0117


title: BPM_0115


title: BPM_0114


title: BPM_0113


title: BPM_0116


title: ChIP-seq BL-CAP-C F123 CTCF-AID POLII Pol2-S2P


title: BPM_0112


title: ChIP-seq BL-CAP-C F123 CTCF-AID POLII Pol2-S5P


title: BPM_0110


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO Pol2-S5P


title: ChIP-seq BL-CAP-C F123 CTCF-AID POLII Ctcf


title: BPM_0108


title: BPM_0111


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO Pol2-S2P


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO Ctcf


title: BPM_0109


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO-POLII Pol2-S5P


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO-POLII Rad21


title: BPM_0107


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO Rad21


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO-POLII Ctcf


title: BPM_0106


title: BPM_0105


title: BPM_0104


title: BPM_0118


title: BPM_0103


title: BPM_0102


title: NfkB2-/- RelB 0h 2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Single-end reads were generated by Illumina sequencer and were demultiplexed.
Adapters, if present were removed by cutadapt and bad quality bases (Q<20) were removed.
The cleaned FASTQ files were aligned against mm9 genome using bowtie with "--best --strata" options and unique alignments were reported.
Peaks were called using cisGenome using a window size of 200 bases and a cutoff of 4 reads in total (2 reads from each strand), FDR<0.1 and Fold change >2
KO_Input was used for NfkB2-/- KO samples.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file contain the rank ordered list of peaks with enrichment values.

growth_protocol: MEF cells were cultured in DMEM medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen)

extract_protocol:
Cell nuclei were isolated and lysed. The crosslinked chromatin was subjected to fragmentation by sonication (Branson Sonicator). Chromatin immunoprecipitation (ChIP) was performed using anti-RelA antibody (Santa Cruz, sc-372) or anti-RelB antibody (sc-226) bound to 50μl Protein A Dynabeads (Invitrogen).
ChIP seq library were prepared using Nugen Ovation Ultra-low library preparation kit version 2 according to the manufacturer’s protocol (Nugen, San Carlo, CA).  The libraries were sequenced on Illumina NextSeq 500 for single end reads

treatment_protocol: For activation, cells were exposed to 10ng/ml of TNF (R&D) for 0 and 6 h

value: MEF

value: 10ng/ml of TNF for 0h

value: RelB Antibody (sc-226, Santa Cruz)


title: BPM_0101


title: NfkB2-/- RelB 6h 1

value: 10ng/ml of TNF for 6h


title: NfkB2-/- p65 6h 2

value: p65 Antibody (sc-372, Santa Cruz)


title: BPM_0099

value: blood


title: BPM_0100


title: BPM_0098


title: BPM_0097


title: NfkB2-/- p65 6h 1


title: BPM_0096


title: NfkB2-/- p65 0h 2


title: NfkB2-/- p65 0h 1


title: BPM_0094


title: ChIP-seq BL-CAP-C F123 CTCF-AID KO-POLII Pol2-S2P


title: F123 input DNA

data_processing:
CAP-C and in-situ Hi-C: Each read end sequenced from the CAP-C and in-situ Hi-C libraries was aligned independently to the mm10 reference genome using BWA-MEM (v 0.7.12). Singletons and chimeric reads were removed. PCR duplicates, unligated reads and reads with a contact distance less than 1Kb were also filtered. PCR duplicates were removed using Picard Tools (v 2.2.2). Unligated reads were defined as both read ends mapping onto the same MboI fragment. A pre-formatted text file was prepared before converting it into a .hic format file with the following resolutions (0.5 Kb, 1 Kb, 2 Kb, 5 Kb, 10 Kb, 25 Kb, 40 Kb, 50 Kb, 100 Kb, 250 Kb, 500 Kb, 1 Mb and 2.5 Mb). Finally, a MAPQ>=1 and MAPQ>=30 .hic file was then generated for each sample. To generate a CAP-C merge file, all G3, G5 and G7 primary and replicated libraries in the pre-formatted text file were concatenated and merged-sorted before using Juicer Tools (v 0.7.0) to convert it into a .hic formatted file.
CAP-C and in-situ Hi-C: Compartments were called using the Eigenvector module of Juicer (v 0.7.0). Peaks/Loops were called using HiCCUPs. Domains were called using Arrowhead. Strength around the ends of the domain boundary or a region of interest was measured by computing the values of the directionality index metric. Aggregate Peak Analysis (APA) was performed on low-resolution contact maps using the APA module of Juicer.
ChIP-seq: Top2b ChIP-seq and control datasets was aligned to the mm10 reference genome using BWA-MEM (v 0.7.12). PCR duplicates were removed using Picard Tools (v 2.2.2). Peak calling was performed using MACS2 (Zhang et al.) with both treated and control BAM files and the following parameters: -q 0.05 –f BAM –g mm. We used bedtools (v 2.27) to create bedGraph files of depth-normalized RPM or FPM values before converting them to bigWig files using UCSC bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: Merged primary and replicate samples are labeled with a B0* instead of an S0*. CAP-C merge .hic files are comprised of G3, G5 and G7 CAP-C libraries.

growth_protocol: F123 mouse embryonic stem cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (85% High Glucose DMEM, 15% Knockout Serum Replacement, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM Glutamine, LIF 500U/mL, +P/S). Before harvesting for CAP-C and in-situ Hi-C, F123 mESCs were passaged onto feeder free 0.2% gelatin coated plates for at least 2 passages to rid the culture of feeder cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and top2b-DNA complexes were isolated with antibody.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment ( exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 11 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: F123 Top2b ChIPSeq

value: Top2b (A-12) (Santa Cruz sc-365071 lot #G1916)


title: BPM_0093


title: F123 CAP-C No proteinase K

data_processing:
Library strategy: DNA-Seq
CAP-C and in-situ Hi-C: Each read end sequenced from the CAP-C and in-situ Hi-C libraries was aligned independently to the mm10 reference genome using BWA-MEM (v 0.7.12). Singletons and chimeric reads were removed. PCR duplicates, unligated reads and reads with a contact distance less than 1Kb were also filtered. PCR duplicates were removed using Picard Tools (v 2.2.2). Unligated reads were defined as both read ends mapping onto the same MboI fragment. A pre-formatted text file was prepared before converting it into a .hic format file with the following resolutions (0.5 Kb, 1 Kb, 2 Kb, 5 Kb, 10 Kb, 25 Kb, 40 Kb, 50 Kb, 100 Kb, 250 Kb, 500 Kb, 1 Mb and 2.5 Mb). Finally, a MAPQ>=1 and MAPQ>=30 .hic file was then generated for each sample. To generate a CAP-C merge file, all G3, G5 and G7 primary and replicated libraries in the pre-formatted text file were concatenated and merged-sorted before using Juicer Tools (v 0.7.0) to convert it into a .hic formatted file.
CAP-C and in-situ Hi-C: Compartments were called using the Eigenvector module of Juicer (v 0.7.0). Peaks/Loops were called using HiCCUPs. Domains were called using Arrowhead. Strength around the ends of the domain boundary or a region of interest was measured by computing the values of the directionality index metric. Aggregate Peak Analysis (APA) was performed on low-resolution contact maps using the APA module of Juicer.
ChIP-seq: Top2b ChIP-seq and control datasets was aligned to the mm10 reference genome using BWA-MEM (v 0.7.12). PCR duplicates were removed using Picard Tools (v 2.2.2). Peak calling was performed using MACS2 (Zhang et al.) with both treated and control BAM files and the following parameters: -q 0.05 –f BAM –g mm. We used bedtools (v 2.27) to create bedGraph files of depth-normalized RPM or FPM values before converting them to bigWig files using UCSC bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: Merged primary and replicate samples are labeled with a B0* instead of an S0*. CAP-C merge .hic files are comprised of G3, G5 and G7 CAP-C libraries.

extract_protocol:
For all CAP-C experiment, after dendrimer crosslinking, DNA bound protein was striped away by proteinase K and DNA was extracted by ethanol precopitation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment ( exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 11 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: BPM_0092


title: BPM_0090


title: BPM_0089


title: BPM_0088


title: F123 CAP-C G7 rep2


title: BPM_0091


title: F123 CAP-C G5 rep2


title: BPM_0095


title: BPM_0087


title: F123 CAP-C G7 rep1


title: BPM_0085


title: ChIP-seq BL-CAP-C HCT116 WT SMC3

source_name: human colon

value: colon cells

value: Rabbit Polyclonal anti-SMC3 (Abcam, ab9263)


title: NfkB2-/- RelB 0h 1


title: F123 CAP-C G3 rep2


title: NfkB2-/- Input

value: none (input)


title: BPM_0082


title: F123 CAP-C No UV


title: BPM_0080


title: F123 CAP-C G3 rep1


title: BPM_0081


title: ChIP-seq BL-CAP-C HCT116 Induction SMC3

treatment_protocol: Cells were treated with 500 nM DAC for 72h. DAC containing medium was refreshed every 24 hours.


title: BPM_0079


title: WT PEG rep3

value: 2-month-old seedlings in MS +PEG medium

value: wild type


title: ChIP-seq BL-CAP-C HCT116 WT Pol2-S5P


title: F123 CAP-C No dendrimer

value: embyonic stem cells


title: ChIP-seq BL-CAP-C HCT116 Induction Pol2-S5P

value: Mouse Monoclonal anti-Phospho RNA Polymerase II CTD (Ser5) (Abcam, ab5408)


title: ChIP-seq BL-CAP-C HCT116 WT CTCF


title: F123 CAP-C G5 rep1


title: ChIP-seq BL-CAP-C HCT116 Induction H3K4me3

value: Rabbit Polyclonal anti-H3K4me3 (Abcam, ab8580)


title: WT PEG rep2


title: ChIP-seq BL-CAP-C HCT116 Induction CTCF


title: BPM_0078


title: BPM_0086


title: BPM_0077


title: ChIP-seq BL-CAP-C HCT116 WT H3K4me3


title: NfkB2-/- RelB 6h 2


title: WT MS rep3

value: 2-month-old seedlings in MS medium


title: BPM_0076


title: BPM_0075


title: BPM_0074


title: Acenaphthene_biorep_4

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

data_processing:
Fastq files resulting from sequencing were trimmed by quality using Trimmomatic and characterized using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, accessed on: 25th Jan 2018).
Transcript-level count estimates of sequence reads were accomplished using Salmon against Danio rerio Zv9 transcripts maintained by Ensembl
Experimental metrics across samples, encompassing trimming and pseudoalignment rates, were aggregated using MultiQC
Transcript level counts were summed to the gene level using tximport. Raw counts for each sample were then normalized with DESeq2.
Genome_build: Danio rerio Zv9 transcripts maintained by Ensembl
Supplementary_files_format_and_content: csv file of log 2 normalized expression values

organism: Danio rerio

source_name: whole 48 hpf embryo

growth_protocol: Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf, they were placed into 96 well plates with 100 μL E2 embryo medium per well. Following the chemical exposure procedure, wells were covered in parafilm and animals were maintained in the dark at 28.5˚C.

extract_protocol:
Total RNA was extracted from 48 hpf whole embryos using RNAzol (Molecular Research Center, Inc; Cincinnati, OH) and a bullet blender with 0.5 mM zirconium oxide beads (Next Advance, Averill Park, New York) as recommended by the manufacturer. The RNA was purified using the Direct-zol MiniPrep kit (Zymo Research; Irvine, CA) and included an in-column DNase 1 digestion. RNA quality and quantity was assessed using a SynergyMix microplate reader with the Gen5 Take3 module. RNA integrity was confirmed (RIN score > 8) with an Agilent Bioanalyzer 2100.
Total RNA samples were sent to Oregon State University Center for Genome Research and Biocomputing Core facilities for library preparation and sequencing. Samples were prepared using the Robotic PolyA Enrichment Library Prep and Robotic Stranded RNA Library Prep Kits (WaferGen, Fremont, CA).
Libraries were multiplexed and randomized across 6 lanes and sequenced with 100bp single-end reads using the Illumina HiSeq 3000. Raw sequence reads were quality checked prior to processing.

treatment_protocol: Static chemical exposures (1% DMSO or PAH with EC80 final concentrations) started at 6-8 hpf and were performed using a Hewlett-Packard D500e chemical dispenser in 96-well plates. After covering with parafilm and foil, plates were placed on an automated shaker overnight at 28.5˚C.

value: Tropical 5D line

value: whole 48 hpf embryo

tag: agent

value: 50 µM acenaphthene


title: Acenaphthene_biorep_2


title: Acenaphthene_biorep_3


title: BPM_0073


title: BPM_0150


title: BPM_0072


title: Acenaphthene_biorep_1


title: WT PEG rep1


title: MCMV-IL-15-2

value: female

value: Mouse lung epithelial cells