title: KO Oct4 DE

data_processing:
Raw fastq files were mapped to mm9 genome using STAR allowing upto 3 mismatches. Only unique reads were consdiered for further analysis
Cuffdiff was used to identify the differentially expressed genes between shEV and shLrrc31 cells.
Cuffquant was used to perform gene counting. Cuffquant’s output cxb files were then utilized to generate the FPKM table using cuffnorm
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimeted table containing FPKM values of each gene in all the samples.

growth_protocol: E14 and D3 mouse ES cells were cultured on gelatin (0.1%) coated plates in mESC medium at 37°C with 5% CO2. The medium composition: 15% heat-inactivated ES-qualified fetal bovine serum (GIBCO), 2mM L-glutamine (GIBCO), 0.1mM nonessential amino acid (NEAA, GIBCO), 5000U/ml penicillin/streptomycin (GIBCO), 0.055mM β-mercaptoethanol (GIBCO) and 1000U/ml home-made leukemia inhibitory factor in Dulbecco’s modified Eagles’ medium (DMEM, Hyclone).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen). Contaminating DNA was removed by DNaseI (Ambion) treatment, and the RNA was further purified using QIAGEN RNeasy Kit.
Cellular RNA was extracted using the RNA extraction protocol mentioned in previous section. The quality of extracted RNA samples was accessed by qRT-PCR. mRNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101), following the manufacturer’s protocol.

treatment_protocol: mESCs were trypsinized for 5 minutes at 37 °C, counted by hemocytometer and 200,000 cells seeded into one well of 6 well plates. mESCs were transfected with 2.5 μg of sgRNA construct and 5 μl of Lipofectamine 2000 (Thermofisher). 1 μg/ml of puromycin was added to the mES medium 24 hours after transfection.

tag: condition

value: sgRNA Targeting Oct4 Distal Enhancer


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A4_ad004

status: Public on Sep 13 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: SSs

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A4_ad002


title: KO NT2

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

library_source: transcriptomic

molecule: total RNA

value: WT


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A4_ad012


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A4_ad006


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A3_ad001


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A5_ad006


title: minimal_lesion_IgAN_4

type: RNA

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio.

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cDNA was prepared with the Illumina WG-DASL asay.

extract_protocol: RNA was extracted with QIAGEN miRNeasy FFPE kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: M

tag: subject status

value: IgAN patient

tag: igan patient grpup

tag: tissue

value: FFPE_Kidney_biopsy specimen


title: minimal_lesion_IgAN_5


title: KO CRE210

value: sgRNA Targeting CRE210


title: KO NT1


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A3_ad004


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A3_ad006


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad001


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad012


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad007


title: minimal_lesion_IgAN_2


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad010


title: minimal_lesion_IgAN_1


title: 5391-sgPAK4

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
The sequences were aligned to the UCSC hg38 reference genome using RNA-Star (v2.4.2a) (https://github.com/alexdobin/STAR).
The gene expression was normalized and calculated as Fragments Per Kilobase Million (FPKM) values by Cufflinks (v2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) with Gencode v22 gene annotations (https://www.gencodegenes.org/releases/22.html).
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Comma-separated values file that includes FPKM values of all samples.

source_name: Human tumor (GBM) EC

growth_protocol: GBM-derived ECs were maintained in Endothelial Cell Medium (ECM, ScienCell, supplemented with VEGF-A) at 37 degrees Celcius with 5% CO2. All cells were used between passages two and five.

extract_protocol:
2 x 10e6 cells were lysed in 1 ml TRIzol (Thermo Fisher), followed by RNA extraction. The isolated RNA was purified with an RNeasy Plus Mini Kit (Qiagen).
The DNA library was constructed by using a RiboZero protocol with TapeStation (Agilent), and subjected to deep sequencing (125 PE, approximately 40 megabyte reads for each sample, Illumina HiSeq 2500) at the Children’s Hospital of Philadelphia/Beijing Genomics Institute core facility (CHOP/BGI).

treatment_protocol: The gRNA sequence (5’-GTGTTTGGGAAGAGGAAGAAG-3’) targeting PAK4 or control gRNA sequence was subcloned into lentiCRISPRv2 puro vector. ECs were transduced with the lenvirus expressing PAK4 sgRNA, followed by cell selection by incubation with medium containing 2 µg/ml puromycin.

tag: cell type

value: Human tumor (GBM) EC

tag: treatment


title: 5465-sgControl

value: sgControl


title: 5465-sgPAK4


title: 5391-sgControl


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad006


title: KO CRE18

value: sgRNA Targeting CRE18


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A3_ad012


title: 5377-sgPAK4


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad004


title: 5377-sgControl


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A3_ad010


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad002


title: KO CRE135

value: sgRNA Targeting CRE135


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A2_ad008


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A12_ad008


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A12_ad007


title: KO CRE111

value: sgRNA Targeting CRE111


title: KO CRE140

value: sgRNA Targeting CRE140


title: KO CRE4

value: sgRNA Targeting CRE4


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A12_ad001


title: minimal_lesion_IgAN_3


title: KO CRE77

value: sgRNA Targeting CRE77


title: KO CRE132

value: sgRNA Targeting CRE132


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad012


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad007


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad001


title: shEV Rep4

data_processing:
Raw fastq files were mapped to mm9 genome using STAR allowing upto 3 mismatches. Only unique reads were consdiered for further analysis
Cuffdiff was used to identify the differentially expressed genes between shEV and shLrrc31 cells.
Genome_build: mm9
Supplementary_files_format_and_content: Excel Worksheets containing the differential Gene Expression Data

treatment_protocol: Dharmacon siDESIGN center was used for the design of the shRNA sequences (http://dharmacon.gelifesciences.com/design-center/). shRNA sequences were ordered as DNA oligos from IDT and cloned into pSUPER-puro plasmid. mESCs were trypsinized for 5 minutes at 37 °C, counted by hemocytometer and 200,000 cells seeded into one well of 6 well plates. mESCs were transfected with 2.5 μg of shRNA construct and 5 μl of Lipofectamine 2000 (Thermofisher). 1 μg/ml of puromycin was added to the mES medium 24 hours after transfection. All the knockdown experiments were carried out in biological triplicates.


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad002


title: shEV Rep3


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad010


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A12_ad002


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad004


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad008


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad007


title: KO CRE32

value: sgRNA Targeting CRE32


title: shEV Rep1


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad008

value: SSs


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad004

value: male


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad002


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad006


title: shLrrc31-2 Rep2

value: Lrrc31 Knock-down


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad001


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad012


title: shEV Rep2

value: WT


title: shLrrc31-2 Rep1


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A11_ad010


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad010


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad007


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad004


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad002


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A1_ad008


title: shLrrc31-1 Rep2


title: shLrrc31-1 Rep1


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A10_ad001


title: shLrrc31-2 Rep3


title: Oct4DE_MEF

data_processing:
Fastq files were trimmed to remove 4C primer sequence using Cutadapt. Then the trimmed libraries were mapped to mm9 using STAR allowing upto 3 mismatches. Multimapped reads were removed.
Interaction regions were called by r3C-seq package using the bam files as input.
Genome_build: mm9
Supplementary_files_format_and_content: Tab Delimited tables containing the loci which interact with the studied CREs

extract_protocol:
In summary, 10 million E14 cells and MEF were lysed with cross-linked by 1% formaldehyde for 10 min at room temperature.
4C library were prepared using previously published protocol(Stadhouders et al., 2013). In summary, 10 million E14 cells and MEF were lysed with cross-linked by 1% formaldehyde for 10 min at room temperature. Cross-linked chromatin was digested with the primary restriction enzyme HindIII (CRE18, CRE111, CRE132, Oct4 DE; NEB), EcoRI(CRE 140; NEB); Next, 3C library was generated by proximity ligation using T4 DNA ligase (EL0013, Thermo Scientific) on HindIII digested DNA, followed by cross-link removal using Proteinase K (AM2546, Vivantis). The 3C libraries were then subjected to a second restriction enzyme digestion using DpnII (CRE132, Oct4 DE; NEB), NlaIII(CRE18; NEB), CviQI(CRE111, CRE140; NEB) followed by another ligation reaction using T4 DNA ligase. For each viewpoint, 3.2 μg of the resulting 4C templates was used to perform an inverse PCR. The PCR products were then run on 2% agarose gels. On the gel, smears from 200 to 600 bp were excised and unwanted PCR product bands were removed. DNA was then extracted from the cut-out gel pieces for next-generation sequencing on an Illumina Miseq. Interaction regions for each bait sequence was identified using r3Cseq package(Thongjuea et al., 2013).


title: Oct4DE_E14_BR2


title: Oct4DE_E14_BR1


title: shLrrc31-1 Rep3


title: CRE140_MEF


title: Fraction 7#2

city: Suita-shi

first: Takeshi

last: Inoue

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: pro-mem RNA-seq.txt

source_name: Fraction 7 B cells

growth_protocol: Bcl6-YFP B1-8hi naïve B cells were transferred into wild-type CD45.1+ mice. Mice were immunized i.p. (day 0) with NP-CGG/alum and NP-specific IgG1+ donor GC LZ (CD45.2+NP+CD138−IgG1+CD38−CD86hiCXCR4lo), Fr.2 (CD45.2+NP+CD138−IgG1+CD38−CD86hiCXCR4loBcl6-YFPhiCD69hi), Fr.3 (CD45.2+NP+CD138−IgG1+CD38−CD86hiCXCR4loBcl6-YFPhiCD69lo), Fr.5 (CD45.2+NP+CD138−IgG1+CD38+GL7−Bcl6-YFPhiEfnb1hi), Fr.6 (CD45.2+NP+CD138−IgG1+CD38+GL7−Bcl6-YFPloEfnb1hi), and Fr.7 (CD45.2+NP+CD138−IgG1+CD38+GL7−Bcl6-YFPloEfnb1lo) B cells were sorted from pooled splenocytes of 9 recipient mice on day 10.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
DNA library was constructed using an NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) from total RNA purified from 1~2 × 10^4 sorted cells.

value: spleen

tag: genotype

value: Bcl6-YFP(KI/+) B1-8hi(KI/+)

value: Fraction 7 B cells (mature memory B cells)


title: CRE140_E14_BR2


title: Fraction 7#1


title: CRE140_E14_BR1


title: Fraction 6#1

source_name: Fraction 6 B cells

value: Fraction 6 B cells (pre-memory B cells)


title: Fraction 6#2


title: Fraction 5#3

source_name: Fraction 5 B cells

value: Fraction 5 B cells (GC pro-memory B cells)


title: Fraction 7#3


title: CRE132_MEF


title: Fraction 5#2


title: Control-3

city: Stanford

first: Robert

middle: Wenchen

last: Hsieh

address: 265 Campus Drive

department: Stem Cell Institute

institute: Stanford University

description: MDA-MB231 transduced with Empty Vector, biological replicate 3

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings.

label_protocol: Affymetrix 3'IVT Plus protocol was used to generate biotinylated cRNA from 200 ngs of total RNA was used to generate biotinylated cRNA from 200 ngs of total RNA

growth_protocol: MDA-MB231 cells were infected with shRNA targeting CDK19, shRNA targeting CDK8, empty vector and grown in cell culture conditions for 96 hours.

extract_protocol: Total RNA was extracted from these cells by RNeasy plus micro kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: Cells were subsequently sorted by FACS to isolate transduced cells (which were RFP positive)

value: breast cancer cell line

tag: cell line

tag: subtype

value: Triple Negative


title: CDK8 KD-2

description: MDA-MB231 transduced with CDK8 shRNA, biological replicate 2


title: CDK8 KD-3

description: MDA-MB231 transduced with CDK8 shRNA, biological replicate 3


title: Fraction 5#1


title: Control-2

description: MDA-MB231 transduced with Empty Vector, biological replicate 2


title: Fraction 3#3

source_name: Fraction 3 B cells

value: Fraction 3 B cells (light zone GC B cells under selection)


title: CDK19 KD-3

description: MDA-MB231 transduced with CDK19 shRNA, biological replicate 3


title: Fraction 3#2


title: CDK19 KD-1

description: MDA-MB231 transduced with CDK19 shRNA, biological replicate 1


title: CEMBA181002_5C_5_CEMBA181002_5C_6_A3_ad008


title: CRE132_E14_BR2


title: CRE132_E14_BR1


title: Fraction 3#1


title: Control-1

description: MDA-MB231 transduced with Empty Vector, biological replicate 1


title: CRE18_MEF


title: LZ#3

source_name: GC LZ B cells

value: GC LZ B cells


title: LZ#1


title: CRE18_E14_BR2


title: Bach2(f/f)Prdm1(f/f) DZ#2

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Bach2(f/f)Prdm1(f/f) DZ

growth_protocol: Prdm1f/f ERT2cre B1-8hi or Bach2f/f Prdm1f/f ERT2cre B1-8hi naïve B cells were transferred independently into wild-type CD45.1/45.2 mice. After administration of tamoxifen (3 mg) for 3 days, mice were immunized i.p. (day 0) with NP-CGG/alum, and NP-specific donor GC DZ (CD45.1−CD45.2+NP+GL7+CD38−CD86loCXCR4hi) and LZ (CD45.1−CD45.2+NP+GL7+CD38−CD86hiCXCR4lo) B cells were sorted from pooled splenocytes of 5 recipient mice on day 10.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
DNA library was constructed using an NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) from total RNA purified from ~ 3 × 10^4 sorted cells.

tag: strain background

value: Bach2(f/f) Prdm1(f/f) ERT2cre(KI/+) B1-8hi(KI/+)

value: DZ GC B cells


title: CRE18_E14_BR1


title: CDK8 KD-1

description: MDA-MB231 transduced with CDK8 shRNA, biological replicate 1


title: Bach2(f/f)Prdm1(f/f) DZ#1


title: Fraction 2#1

source_name: Fraction 2 B cells

value: Fraction 2 B cells (recycling-prone GC B cells)


title: CDK19 KD-2

description: MDA-MB231 transduced with CDK19 shRNA, biological replicate 2


title: CRE111_MEF


title: CRE111_E14_BR2


title: Bach2(+/+)Prdm1(f/f) DZ#2

source_name: Bach2(+/+)Prdm1(f/f) DZ

value: Bach2(+/+) Prdm1(f/f) ERT2cre(KI/+) B1-8hi(KI/+)


title: Bach2(f/f)Prdm1(f/f) LZ#2

source_name: Bach2(f/f)Prdm1(f/f) LZ

value: LZ GC B cells


title: Bach2(+/+)Prdm1(f/f) LZ#2

source_name: Bach2(+/+)Prdm1(f/f) LZ


title: CRE111_E14_BR1


title: Bach2(f/f)Prdm1(f/f) LZ#1


title: Fraction 2#2


title: Bach2(+/+)Prdm1(f/f) LZ#1


title: The infection group of TgMe49 at 12h, repeat 1 [M12_1]

status: Public on Sep 12 2020

city: Wuhan

first: Yanqin

last: Zhou

state: Hubei province

address: No.1, Shizishan Street, Hongshan District

country: China

institute: Huazhong agricultural university

data_processing:
Illumina Casava 1.8 software was used for basecalling
Clean reads were obtained by removing low quality reads and reads containing adapter. The clean reads were aligned to toxoplasma gondii TgME49 genome or Sus scrofa genome through HISAT 2.0.4.
Genome_build: Sus scrofa reference genone for  alignment: ftp://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/ ;  Me49 reference genome for alignment: ftp://ftp.ensemblgenomes.org/pub/release-23/protists//fasta/toxoplasma gondii/dna/
Supplementary_files_format_and_content: Tab-delimited text files include read counts values for each sample

organism:
Toxoplasma gondii
Sus scrofa

source_name: TgMe49-porcine alveoalr macrophage

growth_protocol: The cells (pig alveolar macrophages and HFF cells) and 3 different T.gondii strains (TgRH, TgMe49 and TgHB1) were cultured in DMEM with 10% or 2% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 10μg/ml streptomycin, respectively. These all were maintained at 37℃ in 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted individually from mixture samples using Transzol UP Reagent (TransGen Biotech) according to the manufacturer’s protocol.
The RNA library was generated using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer’s recommendations.

treatment_protocol: Tachyzoites freshly egressed from HFFs were harvested and filtered through 3.0 um membrane filters (Whatman). Pig alveolar macrophage was infected with 3 type of different strain’ tachyzoites (TgRH, TgME49 and TgHB1) at MOI equal to 5 (the ratio of tachyzoite and macrophage). The parasites and macrophage were harvested together by 0.05% trypsin digestion at 6h, 12h and 24h time point respectively. Each experimental group had 3 biological replicates.

value: porcine alveoalr macrophage

tag: infection

value: TgMe49 at 12h

tag: infrection condition

value: maintained in HFFs in T25 tissue culture flask, about 12 h


title: The infection group of TgMe49 at 6h, repeat 3 [M6_4]

value: TgMe49 at 6h

value: maintained in HFFs in T25 tissue culture flask, about 6 h


title: The infection group of TgMe49 at 12h, repeat 3 [M12_4]


title: The infection group of TgMe49 at 24h, repeat 2 [M24_2]

value: TgMe49 at 24h

value: maintained in HFFs in T25 tissue culture flask, about 24 h


title: The infection group of TgMe49 at 24h, repeat 3 [M24_4]


title: The infection group of TgMe49 at 24h, repeat 1 [M24_1]


title: The infection group of TgMe49 at 12h, repeat 2 [M12_2]


title: The infection group of TgRH at 24h, repeat 3 [R24_4]

source_name: TgRH-porcine alveoalr macrophage

value: TgRH at 24h


title: The infection group of TgMe49 at 6h, repeat 1 [M6_1]


title: The infection group of TgMe49 at 6h, repeat 2 [M6_2]


title: LZ#2

value: spleen

value: Bcl6-YFP(KI/+) B1-8hi(KI/+)


title: The infection group of TgRH at 24h, repeat 2 [R24_2]


title: The infection group of TgRH at 24h, repeat 1 [R24_1]


title: The infection group of TgRH at 12h, repeat 3 [R12_4]

value: TgRH at 12h


title: Bach2(+/+)Prdm1(f/f) DZ#1


title: The infection group of TgRH at 12h, repeat 1 [R12_1]


title: The infection group of TgRH at 12h, repeat 2 [R12_2]


title: The infection group of TgRH at 6h, repeat 3 [R6_4]

value: TgRH at 6h


title: The infection group of TgRH at 6h, repeat 2 [R6_2]


title: The infection group of TgRH at 6h, repeat 1 [R6_1]


title: The infection group of TgHB1 at 24h, repeat 3 [H24_4]

source_name: TgHB1-porcine alveoalr macrophage

value: TgHB1 at 24h


title: The infection group of TgHB1 at 24h, repeat 1 [H24_1]


title: The infection group of TgHB1 at 12h, repeat 3 [H12_4]

value: TgHB1 at 12h


title: The infection group of TgHB1 at 24h, repeat 2 [H24_2]


title: The infection group of TgHB1 at 12h, repeat 2 [H12_2]


title: The infection group of TgHB1 at 6h, repeat 3 [H6_4]

value: TgHB1 at 6h


title: The infection group of TgHB1 at 12h, repeat 1 [H12_1]


title: The infection group of TgHB1 at 6h, repeat 2 [H6_2]


title: The infection group of TgHB1 at 6h, repeat 1 [H6_1]


title: The control of porcine alveoalr macrophages, repeat 3 [NC3]

organism: Sus scrofa

source_name: porcine alveoalr macrophage

tag: cell line/strain

value: at 70-80 %  confluency in T25 tissue culture flask, about 36 h


title: The control of porcine alveoalr macrophages, repeat 2 [NC2]


title: The control of porcine alveoalr macrophages, repeat 1 [NC1]


title: Human_SkMuscle

last: Xing

address: 3615 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

description:
circRNAs
isoCirc_hg19_12Tissues.isocirc.out.gz

data_processing: Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long-read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length < 30 bp or repeat copy number < 2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.

source_name: Human skeletal muscle tissue

growth_protocol: HEK293 cells were maintained at ~3×10^6 cells per plate at 37°C in humidified 10% CO2 atmosphere in MEM and 10% FBS, which had been filtered through a 0.2-um PES membrane filter (Nalgene Rapid-flow).

extract_protocol: Total RNA (commercial human total RNAs from Clontech) was enriched for circRNAs by removing rRNAs (RiboMinus Eukaryote Kit) and digesting using RNase R. Reverse transcription was performed with ProtoScript II reverse transcriptase. Circular DNA was precipitated and used as a template for RCA using the TempliPhi 100 Amplification Kit. Debranching was performed by annealing RCA products in a thermocycler using T7 Endonuclease I, followed by isopropanol precipitation. Fragments at 3-50 kb were used for library construction using the Oxford Nanopore Ligation Sequencing Kit (#SQK-LSK109).

value: skeletal muscle tissue


title: Human_prostate

data_processing: Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length < 30 bp or repeat copy number < 2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.

source_name: Human prostate tissue

value: prostate tissue


title: Human_adipose

source_name: Human adipose tissue

value: adipose tissue


title: Human_kidney

source_name: Human kidney tissue

value: kidney tissue


title: Human_heart

data_processing: Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long-read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length was <30 bp or repeat copy number was <2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.

source_name: Human heart tissue

value: heart tissue


title: Human_blood

data_processing: Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length was <30 bp or repeat copy number was <2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.

source_name: Human blood, peripheral leukocytes

value: blood, peripheral leukocytes


title: Human_SmMuscle

source_name: Human smooth muscle tissue

value: smooth muscle tissue


title: Nano-58

description:
circRNAs
isoCirc_hg19_HEK293_6reps.isocirc.out.gz

source_name: HEK293 cells

extract_protocol: Total RNA was extracted from cultured HEK293 cells using TRIzol and treated with DNase I. Total RNA was enriched for circRNAs by removing rRNAs using the RiboMinus Eukaryote Kit and digesting using RNase R. Reverse transcription was performed with ProtoScript II reverse transcriptase. Circular DNA was precipitated and used as a template for RCA using the TempliPhi 100 Amplification Kit. Debranching was performed by annealing RCA products in a thermocycler using T7 Endonuclease I, followed by isopropanol precipitation. Fragments at 3-50 kb were used for library construction using the Oxford Nanopore Ligation Sequencing Kit (#SQK-LSK109).

tag: cell  line

tag: passage


title: Nano-60


title: Nano-59


title: Human_liver

source_name: Human liver tissue

extract_protocol: Total RNA (commercial human total RNAs from Clontech) was enriched for circRNAs by removing rRNAs (RiboMinus Eukaryote Kit) and digesting using RNase R. Reverse transcription was performed with ProtoScript II reverse transcriptase. Circular DNA was precipitated and used as a template for rolling-chain amplification (RCA) using the TempliPhi 100 Amplification Kit. Debranching was performed by annealing RCA products in a thermocycler using T7 Endonuclease I, followed by isopropanol precipitation. Fragments at 3-50 kb were used for library construction using the Oxford Nanopore Ligation Sequencing Kit (#SQK-LSK109).

value: liver tissue


title: Human_adrenal

source_name: Human adrenal gland tissue

value: adrenal gland tissue


title: Nano-43

data_processing: Raw ONT long-read data (fast5 format) were base-called using the Guppy base-calling software (version 2.1.3). Tandem repeats in each long read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length was <30 bp or repeat copy number was <2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.

value: HEK293, Passage:27-29


title: Nano-44

data_processing: Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length was < 30 bp or repeat copy number was < 2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.


title: Nano-45

data_processing:
Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length < 30 bp or repeat copy number < 2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms.
Genome_build was hg19.
Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.


title: 26APR16-PacBio-HelaS3-unsyn

city: Worcester

first: Bastiaan

last: Dekker

state: Massachusetts

address: 368 Plantation street

department: Systems Biology

institute: University of Massachusetts Medical School

data_processing:
Library strategy: MC-3C
reads with a quality threshold over 80 were selected
reads were virtually cut at the sequence sites recognized by DpnII (GATC
cut reads were mapped using bwa-mem
cut reads had to align at least 85% to the DpnII Genomic fragment to be assigned
combined all replicates as final output
Genome_build: hg19
Supplementary_files_format_and_content: table with all interactions from c-walks represented as pairwise interactions (tab seperated)

source_name: DpnII MC-3C on Asynchronious cells

growth_protocol: Hela S3 cells were grown in DMEM media supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
For each MC-3C library 5 Million cells were crosslinked
MC-3C was performed as described in detail in supplemental methods.

tag: protocol

tag: enzyme

value: DpnII


title: 21SEP-PacBio-HelaS3-unsyn


title: MCF-SUM159-A3

type: genomic

city: TAMPA

first: Daria

last: Miroshnychenko

state: FL

address: 12902 USF Magnolia Drive

department: Cancer Physiology

institute: Moffitt Cancer Center

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
ChaS fostware (Affymetrix)
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

source_name: Hybrid between MCFDCIS and SUM159PT, subclone A3

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown in the corresponding media in standard conditions

extract_protocol: Quiagen DNAeasy

treatment_protocol: no treatment


title: MCF-SUM159-A1

source_name: Hybrid between MCFDCIS and SUM159PT, subclone A1


title: SUM159_rep2

source_name: SUM159PT, replicate 2


title: SUM159_rep1

source_name: SUM159PT, replicate 1


title: MCFDCIS


title: Human_testis

source_name: Human testis tissue

value: testis tissue


title: Human_brain

source_name: Human brain tissue

value: brain tissue


title: Hs578T_rep2

source_name: Hs578T, replicate 2


title: MDA231_rep1

source_name: MDA-MB-231, replicate 1


title: Hs578T-MDA231-B4

source_name: Hybrid between Hs578T and MDA-MB-231, subclone B4


title: Human_lung

source_name: Human lung tissue

extract_protocol: Total RNA (commercial human total RNAs from Clontech) was enriched for circRNAs by removing rRNAs using the RiboMinus Eukaryote Kit and digesting using RNase R. Reverse transcription was performed with ProtoScript II reverse transcriptase. Circular DNA was precipitated and used as a template for RCA using the TempliPhi 100 Amplification Kit. Debranching was performed by annealing RCA products in a thermocycler using T7 Endonuclease I, followed by isopropanol precipitation. Fragments at 3-50 kb were used for library construction using the Oxford Nanopore Ligation Sequencing Kit (#SQK-LSK109).

value: lung tissue


title: Hs578T-MDA231-A2

source_name: Hybrid between Hs578T and MDA-MB-231, subclone A2


title: P2

city: Marseille

first: Julia

last: Schaeffer

address: Parc Scientifique de Luminy

department: IBDM, CNRS UMR7288

country: France

institute: Aix-Marseille Université

data_processing:
For each sample, sequencing quality was visualized with FastQC (available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapters were trimmed as part of the Illumina sequencing pipeline. The quality control of the sequencing, performed using FastQC software, showed high quality base calls with an average Phred score > 28 for all samples, so no filtering was performed for the rest of the analysis.
Single-end sequence reads were aligned to Galgal4 chicken reference genome (Gallus_gallus-4.0 (GCA_000002315.2) downloaded from Ensembl (Aken et al., 2017)) using Tophat2 aligner (version 2.1.0) (Kim et al., 2013).
Identification of differentially expressed genes was performed using Cuffdiff (Cufflinks version 2.2.1) (Trapnell et al., 2013). Three replicates of A (A1, A2, A3) were compared to three replicates of P (P1, P2 and P3).
Genome_build: Galgal4
Supplementary_files_format_and_content: .txt - cuffdiff output A versus P (3 replicates each)

organism: Gallus gallus

source_name: posterior half-sclerotomes

growth_protocol: Wild type chick eggs were obtained from Winter Egg Farm. Eggs were delivered weekly and kept at 16-18°C until required. Eggs were incubated at 37.5°C until the embryos reached the required stage. The development of embryos was assessed according to Hamburger Hamilton (HH) stages. Dissection dishes were prepared using Sylgard® 184 silicone elastomer kit (Dow Corning). Anterior and posterior half-sclerotomes were dissected from chick embryos at embryonic day 3 (stage HH 18) in ice-cold Dulbecco's modified Eagle's medium (DMEM). The amnion was removed and the head cut. The embryo was pinned at each extremity of the neural tube, with the dorsal part facing up. A somite strip was isolated on one side of the embryo, by cutting it away from the neural tube and cutting the limb buds, and pinned. Half-sclerotomes from the anterior or the posterior side of each somite were dissected from the #11 most recent/caudal somite and up to 12 somites rostral to it. Anterior and posterior half-sclerotomes were washed once in ice-cod diethyl pyrocarbonate-treated PBS (DEPC-PBS), then pooled by type in Eppendorf tubes and immediately frozen on dry ice. The tissue was kept at -80°C until RNA extraction.

extract_protocol:
RNA extraction was done using High Pure RNA Isolation kit (Roche) and the concentration determined with NanoDrop ND-1000 Spectrophotometer (Labtech International).
cDNA libraries were prepared from about 200ng total RNA. RNA samples were polyA selected and single-end sequencing libraries were constructed with TruSeq Stranded mRNA HT Sample Prep kit (Illumina). Sequencing was performed at CRUK Cambridge Institute Core Genomics Illumina Sequening platforms. Sequencing was 50 base single-end.

tag: developmental stage

value: Hamburger Hamilton 18

value: sclerotome (11th to 23rd most recent)

tag: type

value: posterior

tag: number of half-sclerotomes


title: P1

tag: tissue


title: A2

source_name: anterior half-sclerotomes

value: anterior


title: P3


title: Hs578T-MDA231-A5

source_name: Hybrid between Hs578T and MDA-MB-231, subclone A5

tag: cell type


title: A3


title: A1


title: GG45

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
exposure.dhr.results.csv.gz
prostate.dhr.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window. The PBS and DMSO controls were added together into a single control goup for the exposure analyses.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. the gestating female rats treated were designated as the F0 generation. F1- F3 generation control and glyphosate lineages were housed in the same room and racks with lighting, food and water as previously described 3,6,7. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).

extract_protocol:
For each sample, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm.  The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing.   An appropriate amount of rat sperm suspension was used for DNA extraction. Previous studies have shown mammalian sperm heads are resistant to sonication unlike somatic cells 25,26. Somatic cells and debris were therefore removed by brief sonication (Fisher Sonic Dismembrator, model 300, power 25), then centrifugation and washing 1-2 times in 1xPBS. The resulting pellet was resuspended in 820 μL DNA extraction buffer and 80 μl 0.1M DTT added, then incubated at 65°C for 15 minutes. 80 μl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for 2-4 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 μl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500 rpm for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 μl of glycoblue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol. After incubation, the sample was spun at 13,500 x g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 μl of nuclease free water.  For the MeDIP procedure, genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with TE buffer to 400 μl, then heat-denatured for 10min at 95˚C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml), and incubated for 2-3 hours on a rotator at 55˚. DNA clean-up was performed using a Phenol-Chloroform-Isoamyalcohol extraction, and the supernatant precipitated with 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol in -20˚C freezer for one to several hours. The DNA precipitate was pelleted, washed with 70% ethanol, then dried and resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with the ssDNA kit (Molecular Probes Q10212).  For histone chromatin immunoprecipitation, individual rat sperm collections were generated. To remove any somatic cell contamination sperm samples from each animal were sonicated for 10 seconds using a Sonic Dismembrator Model 300 (Thermo Scientific Fisher, USA) then centrifuged 1800xg for 5 min at 4 °C then resuspended and counted individually on a Neubauer counting chamber (Propper manufacturing Co., Inc., New York, USA) prior to pooling. The sperm samples were reconstituted up to 1 ml with PBS (phosphate buffered saline). To reduce disulfide bonds, 50 µl of 1 M DTT was added to each sample and the samples were then incubated for 2 hours at room temperature under constant rotation. To quench any residual DTT (dithiothreitol, Fisher Scientific, NY USA) in the reaction, 120 µl of fresh 1 M NEM (N-Ethylmaleimide, Thermo Scientific, Rockford, USA) was then added and the samples were incubated for 30 min at room temperature under constant rotation. The sperm cells were pelleted at 450xg for 5 min at room temperature and the supernatant was discarded. Pellets were resuspended in PBS and then spun again at 450xg for 5 min at room temperature. The supernatant was discarded and resuspended in 130 µl of complete buffer supplemented with tergitol 0.5% and DOC 1%. The samples were then sonicated using the Covaris M220. Covaris was set to a 10 min “Chromatin shearing” program and the program was run for each tube in the experiment.  After the Covaris sonication, 10 µl of each sample was run on a 1.5% agarose gel to verify fragment size. Samples were then centrifuged at 12,500xg for 10 min at room temperature. The supernatant was transferred to a fresh microfuge tube. 65 µl of protease inhibitor cocktail (1 tablet dissolved in 500 µl, 20 × concentrated) (Roche, cat. no. 11 873 580 001) were added in each sample as well as 3 µl of antibody (anti-histone H3 pan-monoclonal antibody, cat no. 05–928, Millipore Corp, Temecula CA USA). The DNA-antibody mixture was incubated overnight on a rotator at 4 °C. The following day, magnetic beads (ChIP-Grade protein G magnetic beads, Cell Signaling 9006) were pre-washed as follows: the beads were resuspended in the vial, then 30 µl per sample was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 ml) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1–2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of IP buffer as the initial volume of beads. 30 µl of beads were added to each DNA-antibody mixture from the overnight incubation, then incubated for 2 h on a rotator at 4 °C. After the incubation, the bead-antibody-DNA complex was washed three times with IP buffer as follows: the tube was placed into a magnetic rack for 1–2 min and the supernatant was discarded, then washed with IP buffer 3 times. The washed bead-antibody-DNA solution was then resuspended in 300 µl of digestion buffer (1 M Tris HCI, pH 8.0, 0.5 M EDTA, 10% SDS) and 3 µl proteinase K (20 mg/ml). The sample was incubated for 3 h on a rotator at 56 °C. After incubation the samples were extracted with Phenol-Chloroform-Isoamylalcohol and precipitated with 2 µl of Glycoblue (20 mg/ml), a one-tenth volume of 3 M sodium acetate and two volumes of ethanol overnight at −20 °C.  The precipitate was centrifuged at 18,000xg for 30 min at 4 °C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 µl cold 70% ethanol, then centrifuged again at 18,000xg for 10 min at 4 °C and the supernatant was discarded. The tube was spun briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with a gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 min), then resuspended in 20 µl H20. DNA concentration was measured in the Qubit (Life Technologies) with the BR dsDNA kit (Molecular Probes Q32853).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step the MeDIP DNA, and starting with the ChIP DNA, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Timed-pregnant females on days 8 through 14 of gestation 2 were administered daily intraperitoneal injections of glyphosate (25 mg/kg BW/day dissolved in PBS) (Chem Service, Westchester PA) or dimethyl sulfoxide (DMSO) or Phosphate Buffered Saline (PBS), as previously described 3. Twenty-five mg/kg for glyphosate is 0.4% of rat oral LD50 and 50% of the NOAEL and considering glyphosate rapid metabolism approximately twice the occupational exposure 3-5 mg/kg per daily exposure 4,5. There was a founder effect observed in the offspring of a specific male from the control population treated with PBS, manifesting as abnormally high rates (80-100%) of obesity in descendants. Therefore, a portion of original control colony was excluded from the study due to the obesity founder effects identified. These animals were replaced with offspring from DMSO-treated controls from a concurrent study. Disease phenotypes were compared from both DMSO lineage and PBS lineage controls, with no significant differences observed with histopathology evaluations between the two populations.

tag: treatment

value: Glyphosate

tag: antibody

tag: disease

value: prostate

tag: matched sample name


title: GG44

description:
exposure.dhr.results.csv.gz
kidney.dhr.results.csv.gz

value: anti-histone H3 pan-monoclonal antibody, cat no. 05–928, Millipore Corp

value: kidney


title: GG42


title: GG40

description:
exposure.dhr.results.csv.gz
multiple.dhr.results.csv.gz

value: prostate, tumor


title: GG43

description:
exposure.dhr.results.csv.gz
obesity.dhr.results.csv.gz

value: obese


title: MDA231_rep2

source_name: MDA-MB-231, replicate 2


title: Hs578T_rep1

source_name: Hs578T, replicate 1


title: GG36


title: GG29


title: GG30

value: prostate, obese


title: GG38

description:
exposure.dhr.results.csv.gz
prostate.dhr.results.csv.gz
kidney.dhr.results.csv.gz
obesity.dhr.results.csv.gz
multiple.dhr.results.csv.gz


title: GG39


title: GG32


title: GG28

value: prostate, kidney, obese


title: GG26


title: GG34


title: GG33

description: exposure.dhr.results.csv.gz

value: testes


title: GG24


title: GG37


title: GG35


title: GG41


title: GG23


title: GG25

value: testes, kidney


title: GG22


title: GG21

value: testes, kidney, obese


title: GG20

value: testes, prostate, kidney


title: GG16


title: GG15


title: GG27


title: GG12


title: GG13

value: testes, prostate


title: GG14


title: GG11


title: GG9


title: GG8


title: GG18


title: GG17


title: GG7


title: GG6


title: GG4

description: exposure.dhr.results.csv.gz


title: GG5


title: GG3


title: GC12

description: exposure.dhr.results.csv.gz

value: PBS Control

value: puberty, tumor, lean


title: GC15

description: exposure.dhr.results.csv.gz


title: GG2


title: GG1


title: GC10

description: exposure.dhr.results.csv.gz

value: kidney, obese


title: GC4

description: exposure.dhr.results.csv.gz

value: testes, obese


title: GC6

description: exposure.dhr.results.csv.gz


title: GC9

description: exposure.dhr.results.csv.gz


title: GC5

description: exposure.dhr.results.csv.gz


title: GC7

description: exposure.dhr.results.csv.gz


title: GC8

description: exposure.dhr.results.csv.gz


title: GC3

description: exposure.dhr.results.csv.gz


title: GC2

description: exposure.dhr.results.csv.gz

value: kidney, lean


title: GC1

description: exposure.dhr.results.csv.gz


title: gly78

description: exposure.dmr.results.csv.gz

value: DMSO Control

value: monoclonal mouse anti 5-methyl cytidine, Diagenode #C15200006


title: LSK WT D1

first: David

last: Calcagno

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description:
single cell RNA
10X Genomics

data_processing:
Alignment, filtering, and barcode demultiplexing of fastq files were performed using 10X Genomics Cell Ranger analysis pipieline with standard configurations.
To account for variations in sequencing depth, total transcript count for each cell was scaled to 10,000 molecules, and raw counts for each gene were normalized to the total transcript count associated with that cell and then natural log transformed. Cells with between 200 and 2,500 uniquely expressed genes and < 5% mitochondrial counts were retained for further analysis. Highly variable genes across individual datasets were identified with the FindVariableFeatures method from the Seurat R package (version 3.0) by selecting 4,000 genes with the highest feature variance after variance-stabilizing transformation.
Integration of multiple single-cell RNA-seq datasets was performed in Seurat to enable harmonized clustering and downstream comparative analyses across conditions(32, 68, 69). Anchoring cell pairs between datasets were identified by Canonical Correlation Analysis (CCA) and the mutual nearest
After scaling and centering expression values for each variable gene, linear dimensionality reduction was performed on integrated data using principal component analysis (PCA). Clustering was performed using the shared nearest neighbor (SNN) clustering algorithm with the Louvain method for modularity optimization, as implemented in the Seurat FindNeighbors and FindClusters functions. To visualize data in two-dimensional space, Uniform Manifold Approximation and Projection (UMAP) dimensional reduction was performed. Differentially expressed genes between clusters were determined using a Wilcoxon Rank Sum test.
As the highly-variable differentially expressed genes (DEGs) which drive unsupervised clustering are primarily composed of cell-type specific marker genes, we utilized a sub-clustering technique to examine cell-state heterogeneity within cell types in an unbiased manner. This involved serially subsetting particular cell-type clusters, identifying a new set of DEGs within the subset, and re-clustering the subset based on the newly determined DEGs.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: counts matrices consisting of three files: matrix.mtx, features.tsv, barcodes.tsv.

source_name: Bone Marrow Immune Cells

extract_protocol:
Bone marrow cells were collected by flushing femurs with ice-cold PBS.  The resulting solution was filtered through a 40 µm nylon mesh and treated with red blood cell (RBC) lysis buffer (BioLegend).   Blood was collected by cardiac puncture.  The cellular fraction was collected into EDTA-containg tubes (Sigma), and erythrocytes were eliminated using RBC lysis.   Heart tissue was collected by incising the right atrium and perfusing 10 mL of ice-cold saline into the left ventricular apex. Heart tissue was then removed and used for one of several assays detailed below. To obtain single cell suspensions for surface immunostaining, flow cytometric analysis, FACS sorting, or single cell RNA-Seq, hearts were enzymatically digested for 1 hour under continuous agitation in 450 U/ml collagenase I, 125 U/ml collagenase XI, 60 U/ml DNase I, and 60 U/ml hyaluronidase (Sigma) for 1 hour at 37°C, and filtered through a 40 µm nylon mesh cell strainer in FACS buffer (DPBS with 2.5% bovine serum albumin) for enumeration by flow cytometry. For single cell RNA-Seq, the enzymatic digestion was limited to 45 minutes to minimize transcript degradation.
Single cell libraries were prepared according to 10X Genomics standard procedures.

value: Flushed Bone Marrow

tag: days post-mi

tag: strain

tag: genotype

value: WT

value: untreated


title: LSK WT D0

description:
single cell RNA
10X Genomics


title: gly77

description: exposure.dmr.results.csv.gz


title: BM Tet2-/- D0

description:
single cell RNA
10X Genomics


title: GC14

description: exposure.dhr.results.csv.gz

value: anti-histone H3 pan-monoclonal antibody, cat no. 05–928, Millipore Corp


title: gly76

description: exposure.dmr.results.csv.gz


title: BM Tet2-/- D2

description:
single cell RNA
10X Genomics


title: GC11

description: exposure.dhr.results.csv.gz

value: obese


title: gly74

description: exposure.dmr.results.csv.gz


title: gly75

description: exposure.dmr.results.csv.gz


title: BM Irf3-/- D2

description:
single cell RNA
10X Genomics


title: BM WT D2

description:
single cell RNA
10X Genomics


title: BM Irf3-/- D0

description:
single cell RNA
10X Genomics


title: gly73

description: exposure.dmr.results.csv.gz


title: gly72

description: exposure.dmr.results.csv.gz


title: gly71

description: exposure.dmr.results.csv.gz


title: BM WT D0

description:
single cell RNA
10X Genomics


title: Bld Irf3-/- D2

description:
single cell RNA
10X Genomics

source_name: Peripheral Blood Immune Cells

value: Peripheral Blood


title: gly68

description: exposure.dmr.results.csv.gz


title: gly70

description: exposure.dmr.results.csv.gz


title: Bld Irf3-/- D0

description:
single cell RNA
10X Genomics


title: Bld WT D2

description:
single cell RNA
10X Genomics


title: gly67

description: exposure.dmr.results.csv.gz

value: kidney


title: gly69

description: exposure.dmr.results.csv.gz


title: Bld WT D4

description:
single cell RNA
10X Genomics


title: Bld WT D1

description:
single cell RNA
10X Genomics


title: gly66

description: exposure.dmr.results.csv.gz


title: Bld WT D0

description:
single cell RNA
10X Genomics


title: gly65

description: exposure.dmr.results.csv.gz


title: Hrt WT D0

description:
single cell RNA
10X Genomics

source_name: Heart Immune Cells

value: Heart


title: Hrt Nrf2-/- D4 rep2

description:
single cell RNA
10X Genomics


title: BM WT D1

description:
single cell RNA
10X Genomics


title: gly64

description: exposure.dmr.results.csv.gz


title: gly63

description: exposure.dmr.results.csv.gz


title: gly62

description: exposure.dmr.results.csv.gz


title: Hrt Ifnar Ab D4 rep2

description:
single cell RNA
10X Genomics

value: Ifnar-Ab treated


title: gly61

description: exposure.dmr.results.csv.gz


title: gly60

description: exposure.dmr.results.csv.gz

value: prostate


title: Hrt Nrf2-/- D4 rep1

description:
single cell RNA
10X Genomics


title: gly59

description: exposure.dmr.results.csv.gz

value: PBS Control


title: gly58

description: exposure.dmr.results.csv.gz

value: puberty, prostate


title: gly57

description: exposure.dmr.results.csv.gz

value: puberty, tumor, lean


title: gly56

description: exposure.dmr.results.csv.gz


title: Hrt WT D4

description:
single cell RNA
10X Genomics


title: C2C12 myoblasts, 232 day 4 rep2

city: Saint Petersburg

first: Oksana

last: Ivanova

address: 2 Akkuratova street

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
Read quality was checked for each sample using FastQC v0.11.5.
Sequenced reads were mapped to the mouse genome using mapper STAR v2.6 with reference genome GRCm38 and annotation Gencode vM22.
Aligned reads were count with featureCounts program v1.6.4.
Further analysis were made using DESeq2 and fGSEA R packages, as well as MSigDB and phantasus online tools.
Genome_build: Genome Reference Consortium Mouse Build 38 primary assembly (GRCm38.p6)
Supplementary_files_format_and_content: tab-delimited text file includes matrix of raw counts for each of 27 Samples

source_name: C2C12 myoblast cell line

growth_protocol: Transgenic WT/G232E/R482L-hLMNA C2C12 myoblast cells were cultured in DMEM sup??plemented with 20% fetal bovine serum, 1% L?? glutamine, and 1% penicillin/strepto?? mycin mixture

extract_protocol:
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen, Russia)
Libraries were constructed using TruSeq Stranded mRNA library prep kit

treatment_protocol: Myogenic stimulation was induced in the differenti??ating medium consisting of DMEM supple??mented with 2% horse serum, 1% L??glutamine, and 1% penicillin/streptomycin mixture after the cells had reached the subconfluent state.

tag: cell line

value: C2C12 myoblast cell line

value: G232E-hLMNA C2C12

tag: time

value: differentiation day 4

tag: induction of differentiation

value: Horse serum


title: C2C12 myoblasts, 482 day 4 rep2

value: R482L-hLMNA C2C12


title: gly52

description: exposure.dmr.results.csv.gz

value: monoclonal mouse anti 5-methyl cytidine, Diagenode #C15200006


title: C2C12 myoblasts, 232 day 4 rep1


title: C2C12 myoblasts, 482 day 4 rep3


title: C2C12 myoblasts, WT day 4 rep2

value: WT-hLMNA C2C12


title: C2C12 myoblasts, WT day 4 rep3


title: C2C12 myoblasts, WT day 4 rep1


title: gly51

description: exposure.dmr.results.csv.gz

value: testes, obese


title: gly50

description: exposure.dmr.results.csv.gz


title: Hrt Ifnar Ab D4 rep1

description:
single cell RNA
10X Genomics

value: WT


title: C2C12 myoblasts, 482 day 2 rep3

value: differentiation day 2


title: gly49

description: exposure.dmr.results.csv.gz


title: C2C12 myoblasts, 482 day 4 rep1


title: C2C12 myoblasts, 482 day 2 rep2


title: C2C12 myoblasts, 232 day 2 rep3


title: gly53

description: exposure.dmr.results.csv.gz

value: kidney, obese


title: gly46

description: exposure.dmr.results.csv.gz


title: gly48

description: exposure.dmr.results.csv.gz


title: C2C12 myoblasts, 232 day 2 rep2


title: C2C12 myoblasts, 482 day 2 rep1


title: C2C12 myoblasts, 232 day 4 rep3


title: gly55

description: exposure.dmr.results.csv.gz


title: gly45

description:
exposure.dmr.results.csv.gz
prostate.dmr.results.csv.gz

value: Glyphosate


title: gly47

description: exposure.dmr.results.csv.gz

value: kidney, lean


title: gly54

description: exposure.dmr.results.csv.gz


title: gly44

description:
exposure.dmr.results.csv.gz
kidney.dmr.results.csv.gz

value: kidney


title: C2C12 myoblasts, WT day 2 rep3


title: C2C12 myoblasts, 232 day 2 rep1


title: gly43

description:
exposure.dmr.results.csv.gz
obesity.dmr.results.csv.gz

value: obese


title: gly41

value: prostate


title: C2C12 myoblasts, 482 control rep3

value: differentiation day 0

value: No


title: C2C12 myoblasts, WT day 2 rep1

value: C2C12 myoblast cell line


title: gly40

description:
exposure.dmr.results.csv.gz
multiple.dmr.results.csv.gz

value: prostate, tumor


title: C2C12 myoblasts, 482 control rep2


title: C2C12 myoblasts, 232 control rep3

value: G232E-hLMNA C2C12


title: gly38

description:
exposure.dmr.results.csv.gz
prostate.dmr.results.csv.gz
kidney.dmr.results.csv.gz
obesity.dmr.results.csv.gz
multiple.dmr.results.csv.gz


title: C2C12 myoblasts, 232 control rep2


title: gly37


title: gly36


title: C2C12 myoblasts, WT control rep3


title: C2C12 myoblasts, 232 control rep1


title: gly35


title: C2C12 myoblasts, WT day 2 rep2

value: Horse serum


title: gly33

description: exposure.dmr.results.csv.gz

value: monoclonal mouse anti 5-methyl cytidine, Diagenode #C15200006

value: testes


title: gly42


title: C2C12 myoblasts, WT control rep2

value: WT-hLMNA C2C12


title: gly34


title: gly31

value: prostate, obese


title: gly32


title: gly30


title: gly29


title: gly28

value: prostate, kidney, obese


title: gly39


title: C2C12 myoblasts, WT control rep1


title: C2C12 myoblasts, 482 control rep1

value: R482L-hLMNA C2C12


title: gly27

value: Glyphosate


title: gly26


title: PID 471

city: SAN DIEGO

first: Shaobo

last: Wang

state: California

address: 9500 Gilman Dr., La Jolla, San Diego

institute: University of California San Diego

data_processing:
scRNA-seq Mapping using CellRanger (v2.1; 10x Genomics). The scRNA-seq dataset was mapped against the human hg19 reference genome using CellRanger (v2.1; 10x Genomics). GRCh38-1.2.0 was used as a gene model for the alignment and was provided as part of the CellRanger pipeline as a compatible transcriptome reference.
Single-Cell Differential Gene Expression Analysis by Seurat (v.2.2.0). Secondary analysis on the raw counts generated from the Cell Ranger pipeline was performed using Seurat (v.2.2.0), an R package for single-cell genomics. The analysis was based on the pipeline presented in the Guided Clustering Tutorial by the Sajita Lab. First, the cells were filtered to exclude cells with a large number of genes or with a large amount of mitochondrial DNA. The data were then normalized using a global-scaling method known as “LogNormalize,” which normalizes gene expression measurements for each cell by total expression, multiplies the values by a scale factor, and log-transforms the results. The average expression for each gene was calculated to identify genes with highly variable expression and then scaled to remove background variation. Linear dimensional reduction principal component analysis was performed on the identified variable genes. Principal components were determined by the generated Jackstraw and Elbow plots and PC 10 was mostly used for our PBMC analysis. A graph-based clustering approach was used to cluster the cells by type. The resolution parameter was altered for each sample according to cell number. Typically, a resolution >0.8 was used to identify a large number of clusters so that even small cell populations could be identified. Clusters of the same cell type were recombined when the clusters were labeled. Non-linear dimension reduction (tSNE) was used to visualize the data, and the plots were color-coded by cell type.
Genes enriched in a specific cluster were identified by the mean expression of each gene across all cells in the cluster. Then the expression of each gene from the cluster was compared to the median expression of the same gene from cells in all other clusters. To identify cell clusters, Seurat Findclusters was utilized based on a graph-based clustering approach. Cells were clustered by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm. Then clusters were further characterized based on known markers. The cluster-specific markers were based on the top 20 genes after finding differentially expressed genes for each cluster. We defined the DEG by average expression fold change (avg_log FC) and percentage of expressing cells (pct.).
Genome_build: human hg19 reference genome
Supplementary_files_format_and_content: matrix.mtx, gene expression in single cells

source_name: peripheral blood mononuclear cell

growth_protocol: PBMCs were isolated and resuspended in complete RPMI 1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (Hyclone), and 100 U/ml DNase I (StemCell).

extract_protocol:
PBMCs was subjected to scRNA seq library construction on the 10X Genomics platform using Chromium™ Single Cell 3' v2 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol
scRNA seq library construction was performed according to the 10X Genomics's instructions

treatment_protocol: No treatment

value: peripheral blood mononuclear cell

tag: individual

value: PID 471

tag: disease state

value: HIV


title: gly25

value: testes, kidney


title: PID 168

value: PID 168


title: gly24

value: kidney


title: gly23

value: obese


title: PID 529

value: PID 529


title: PID 876

value: PID 876


title: gly20

value: testes, prostate, kidney


title: gly21

value: monoclonal mouse anti 5-methyl cytidine, Diagenode #C15200006

value: testes, kidney, obese


title: gly22


title: PID 630

value: PID 630


title: gly18


title: gly19


title: gly17


title: E_H_FMG6

city: Daegu

first: Youngji

last: Han

address: Daehakro 80

country: South Korea

institute: Kyungpook National University

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix)

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: Epididymal fat

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Four-week-old male C57BL/6J mice were obtained from Jackson Laboratory (Bar Harbor, ME, USA). All mice were individually housed under constant temperature (24 ◦C) and 12-h light/dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After a 1-week acclimation on a normal chow diet, the mice were then randomly divided into six groups, and each group was fed one of the following diets for 12 weeks: Normal diet (ND, 10% kcal from fat, n = 10); High fat diet (HFD, 40% of kcal from fat, n = 10); Bacilus Coagulans group (BC, HFD with 0.3% Bacilus Coagulans (w/w), n = 10); 0.3% Steamed grain group (SMG, HFD with 0.3% steamed grain (w/w), n = 10); Low-dose fermented mixed grain group (L-FMG, HFD with 0.3% fermented mixed grain (w/w)); High-dose fermented mixed grain group (H-FMG, HFD with 0.9 % fermented mixed grain (w/w)).

tag: Sex

value: male

value: Epididymal fat

tag: diet

value: HFD

tag: group


title: gly16

value: Glyphosate


title: E_L_FMG10

tag: tissue


title: SATB2 knockdown, biological rep2

city: Cleveland

first: weiwei

last: tao

state: OH

address: 9500 Euclid Avenue, NE30

department: Lerner Research Institute

institute: Cleveland Clinic

description: Gene expression data from glioblastoma stem cells transduced with lentiviral-mediated non-SATB2 shRNA, biological rep2

hyb_protocol: Following labeling procedure, cDNA were hybridized, washed and stained according to WT Array Hybridization-Cartridge array hybridization on the GeneChip® manual and according to GeneChip® Fluidics Station 450, GeneChip® Expression Wash guides.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 System according to manufacture's manual.

data_processing: The process of calculating expression values through RMA method in raw data was analyzed using Expression console v1.4.

label: Biotin

source_name: Glioblastoma stem cells

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Plus kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 3)

growth_protocol: Cells were cultured in Neurobasal-A medium supplemented with B27, 10 ng/ml EGF, 10 ng/ml bFGF, 2 mM L-glutamine and 1 mM sodium pyruvate.

extract_protocol: Total RNA was isolated using Thermo Fisher PureLink RNA mini extraction kit according to manufacturer's protocol

treatment_protocol: Cells were transduced with lentiviral-mediated non-targeting shRNA or SATB2 shRNA

value: Brain tumor

tag: tumor stage

value: Grade IV glioma

value: SATB2 knockdown


title: E_L_FMG8


title: control, biological rep1

description: Gene expression data from glioblastoma stem cells transduced with lentiviral-mediated non-targeting shRNA, biological rep1

value: control


title: E_H_FMG8


title: E_L_FMG4


title: E_H_FMG3


title: gly14

tag: treatment


title: HD1

tag: cell type

value: peripheral blood mononuclear cell


title: SATB2 knockdown, biological rep1

description: Gene expression data from glioblastoma stem cells transduced with lentiviral-mediated non-SATB2 shRNA, biological rep1


title: gly15

tag: antibody

tag: disease

value: prostate


title: PID 717

value: PID 717

value: HIV


title: gly13

value: testes, prostate


title: polyA-3

description:
polyA+ RNA
ciri2_SR_hg19_HEK293_output.txt

data_processing: Paired-end Illumina sequencing data with 101-bp read length were generated from RNase R-treated libraries and poly(A)-selected libraries. Reads from the 6 samples were pooled and aligned to the GRCh37/hg19 reference genome using BWA-MEM with '-T 19' and default settings. To increase sensitivity, BSJs were detected from alignment records of all reads, using CIRI2 with Ensembl GRCh37.87 annotation and default settings. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA BSJs identified from each sample.

source_name: HEK293 cells

extract_protocol: Total RNA was extracted from cultured HEK293 cells using TRIzol and treated using DNase I. Poly(A)-selected libraries were prepared using the TruSeq protocol (Illumina).

tag: cell  line

tag: passage


title: E_SMG12

tag: strain

value: SMG


title: E_SMG8


title: control, biological rep2

description: Gene expression data from glioblastoma stem cells transduced with lentiviral-mediated non-targeting shRNA, biological rep2

tag: genotype


title: gly12

value: monoclonal mouse anti 5-methyl cytidine, Diagenode #C15200006

value: obese


title: gly11


title: gly10


title: polyA-2


title: polyA-1


title: gly8

value: kidney


title: RNaseR-3

description:
circRNAs
ciri2_SR_hg19_HEK293_output.txt

extract_protocol: Total RNA was extracted from cultured HEK293 cells using TRIzol, treated using DNase I, and digested using RNase R. Libraries were prepared using the TruSeq protocol (Illumina).


title: gly7


title: gly5


title: gly4

description: exposure.dmr.results.csv.gz

value: testes


title: Retina WT 3

city: Guangzhou

first: Xiaowei

last: Yu

address: No.7 jinsui road

institute: Zhongshan ophthalmology center, Sun yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensembl_v96 (GRCm38) whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Ensembl_v96 (GRCm38)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Retina

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

tag: age

value: 8 weeks

value: WT


title: RNaseR-2


title: gly6

value: Glyphosate

value: testes, kidney, obese


title: gly3


title: RNaseR-1


title: gly2


title: E_RMG10

value: male

value: Epididymal fat

value: HFD

value: RMG


title: E_SMG5


title: NCD_2

city: Jinan

first: Shuai

last: Zong

address: Jingwu Road 324

institute: Shandong Provincial Hospital Affiliated to Shandong University

data_processing:
Sequencing data were mapped to the human reference genome (hg38) using HISAT2 v2.1.0. FPKM for each gene were calculated.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM files

source_name: lung adenocarcinoma

extract_protocol:
Total RNA of H1975 cells was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell line

value: control group


title: gly1


title: NCD_3


title: Retina WT 2


title: D52_3

value: FKBP4-depletion group


title: D52_2


title: Retina WT 1


title: E_BC11

value: BC


title: E_BC4


title: E_BC7


title: E_HFD7


title: Retina Myrf-kd 3

value: Myrf-kd


title: ID#11 cultured in QGel CN99®

city: Herlev

first: Ole

middle: Haagen

last: Nielsen

address: Borgmester Ib Juuls Vej 1

department: Dept. of Gastroenterology

country: Denmark

institute: Herlev Hospital

description: FPKM_refseq_hg38.txt [m2_p6_s12]

data_processing:
Raw reads from fastq files were trimmed with Trimmomatic (v0.32) using default settings except: ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:1:true HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Triimmed PE reads were aligned using STAR (v.2.5.1a) to the canonical chromosomes of the hg38 genome assembly with RefSeq gene annotation (refGene.txt from UCSC date-stamped: 2018-08-05) as guide. Default STAR settings except: --sjdbGTFfile <RefSeq GTF> --sjdbOverhang 139  --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16 --outFilterMismatchNmax 5
Aligned reads were assigned to genes using featureCounts (v1.5.1) with default settings except:  --primary -p -B -O -M --fraction -s 0 -J -a <RefSeq GTF>
FPKM values were calculated in R with the fpkm() function from the DESeq2 package
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values for each sample and RefSeq gene

source_name: colon organoids

growth_protocol: Colon organoids were cultured in either QGel® CN99 or Matrigel® using IntestiCult™ Organoid Growth Medium (Human, STEMCELL Technologies).

extract_protocol: Organoids were lysed in RP1 lysis buffer and subsequent RNA extraction was performed using NucleoSpin® TriPrep purification kit (Macherey-Nagel).

tag: matrix conditions

value: QGel CN99


title: E_RMG9


title: ID#10 cultured in QGel CN99®

description: FPKM_refseq_hg38.txt [m2_p5_s11]


title: E_HFD6


title: E_RMG4


title: Retina Myrf-kd 2


title: ID#9 cultured in QGel CN99®

description: FPKM_refseq_hg38.txt [m2_p4_s10]


title: Murine male liver sample 2 (M3)

city: Washington

first: Blythe

middle: D

last: Shepard

state: DC

address: 3700 Reservoir Road NW

department: Human Science

institute: Georgetown University

description: M3 liver

data_processing:
Cycle threshold (Ct) was determined for each sample (listed in matrix non-normalized template).  Delta Ct values were calculated using the average 18s ribosomal RNA Ct value (Ct target gene - Ct reference gene)
The delta Ct value was determined as Ct target gene - Ct reference gene

label: FAM

source_name: liver

label_protocol: 2ug of RNA was used to synthesize cDNA using the High Capacity RNA-to-cDNA kit (Applied Biosystems).  Each reservoir in the given TaqMan array microfluidic card was filled with 1000ng of cDNA and the array cards were run on the 7900 HT-PT-PCR system (Applied Biosystems) and analyzed using the SDS software.  Each gene was run in triplicate and delta Ct values for each receptor was calculated using 18s ribosomal RNA.

extract_protocol: RNA was isolated from male C57BL6 livers using phenol-chloroform extraction.  50mg of frozen liver was homogenized in 500ul Trizol and RNA was extracted using 100ul chloroform followed by ethanol precipitation.  Residual genomic DNA was removed using DNaseI (Qiagen).

tag: gender

value: liver


title: ID#8 cultured in QGel CN99®

description: FPKM_refseq_hg38.txt [m2_p3_s9]


title: WT 2

city: Eugene

first: Gabriel

last: Yette

state: Oregon

address: 1229 University of Oregon 1318 Franklin Blvd

department: Biology- Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling by Illumina Real-Time Analysis 2 (RTA2).
Sequence reads were mapped to GRCz11/danRer11 using TopHat2
Mapped reads were counted using HTSeq
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: Tab-delimited text files of HTSeq counts for each sample are provided

organism: Danio rerio

source_name: 96 hpa WT distal regenerate

extract_protocol:
Tissue was collected and immediately homogenized in TRIzol reagent. RNA was isolated following the manufacturer's instruction.
Libraries were prepared from 1 mg of isolated RNA using Kapa stranded mRNA-Seq kit and protocol.

value: wildtype

tag: transgene

value: regenerating caudal fin

tag: time

value: 96 hours post amputation


title: The control of TgMe49, repeat 3 [ME_3]

data_processing:
Illumina Casava 1.8 software was used for basecalling
Clean reads were obtained by removing low quality reads and reads containing adapter. The clean reads were aligned to toxoplasma gondii TgME49 genome or Sus scrofa genome through HISAT 2.0.4.
Genome_build: Sus scrofa reference genone for  alignment: ftp://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/ ;  Me49 reference genome for alignment: ftp://ftp.ensemblgenomes.org/pub/release-23/protists//fasta/toxoplasma gondii/dna/
Supplementary_files_format_and_content: Tab-delimited text files include read counts values for each sample

organism: Toxoplasma gondii

extract_protocol:
Total RNA was extracted individually from mixture samples using Transzol UP Reagent (TransGen Biotech) according to the manufacturer’s protocol.
The RNA library was generated using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer’s recommendations.

tag: cell line/strain

tag: infrection condition

value: maintained in HFFs in T25 tissue culture flask, about 48 h


title: ID#7 cultured in QGel CN99®

description: FPKM_refseq_hg38.txt [m2_p2_s8]


title: E_ND8

tag: Sex

tag: tissue

tag: diet

value: ND

tag: group


title: Murine male liver sample 1 (HF1)

description: HF1 liver


title: E_HFD4


title: E_ND9


title: The control of TgMe49, repeat 2 [ME_2]


title: WT 1


title: D52_1


title: Ren50M-4

city: L'HOSPITALET DE LLOBREGAT

first: ORIOL

last: CASANOVAS

address: AV. GRAN VIA, 199. 3 PL.

department: ProCURE, OncoBell

country: Spain

institute: CATALAN INSTITUTE OF ONCOLOGY - IDIBELL

data_processing:
Illumina Casava1.8 software was used for basecalling.
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the human genome (GRCh38/hg38) using STAR (version 2.5.1b) with ENCODE parameters for long RNA.
Genes were quantified using RSEM (version 1.2.28) and read counts were used as input for DESeq2 (version 1.10.1).
Gene expression was quantified as counts per million (CPM).
Genome_build: hg38
Supplementary_files_format_and_content: CPM data matrix of gene expression of each sample

source_name: Patient-derived orthoxenograft model (PDOX)

growth_protocol: Human cancer tissue samples from surgery or biopsy were implanted in the kidney of 6‐week‐old athymic NMRI‐Foxn1nu male mice and established for at least 10 passages.

extract_protocol:
Total RNA from tumor tissue was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using modified Illumina TruSeq Stranded Total RNA kit protocol

value: Tumor Tissue

tag: source

value: Kidney of nude mouse

tag: cell type

value: Human kidney cancer


title: The control of TgMe49, repeat 1 [ME_1]

last: Zhou

address: No.1, Shizishan Street, Hongshan District

institute: Huazhong agricultural university


title: Ren50M-3


title: lof 2

source_name: 96 hpa lof distal regenerate

value: longfin heterozygous


title: E_ND6

value: male

value: Epididymal fat


title: ID#11 cultured in Matrigel®

description: FPKM_refseq_hg38.txt [m1_p6_s6]

value: Matrigel


title: Retina Myrf-kd 1

value: retina

value: 8 weeks


title: The control of TgRH, repeat 3 [RH_3]

source_name: TgRH

value: TgRH


title: Ren50M-2


title: lof 1


title: The control of TgRH, repeat 2 [RH_2]


title: ID#10 cultured in Matrigel®

description: FPKM_refseq_hg38.txt [m1_p5_s5]


title: Ren50M-1


title: Ren13-3


title: The control of TgRH, repeat 1 [RH_1]


title: ID#8 cultured in Matrigel®

description: FPKM_refseq_hg38.txt [m1_p3_s3]


title: BMDBM+MPs

city: Nanjing

first: Yuxuan

last: Liu

address: NO1 Xikang Road

institute: HOHAI

data_processing:
Seurat package in R (version 3.5.2) was used to analyze the sequenced reads. Principal component analysis (PCA) was used for dimensionality reduction and a graph-based clustering was applied to cluster in PCA space. UMAP was used for the visualization of the clusters. The marker genes of each cluster were identified by FindMarkers function in the Seurat package. The clusters were annotated to a known cell type according to the Zebrafish Information Network (ZFIN) database and current literature
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: emberyo

extract_protocol:
After exposure, forty embryos collected from each group were transferred to 1 mL phosphate buffer saline (PBS) with 1% bovine serum albumin (BSA). After incubated in 0.5 mL Hank's balanced salt solution (HBSS) containing 0.6 U/mL of dispase (Yuanye Biotechnology, Shanghai, China) at 37 °C for 5 min, 100 µL of fetal bovine serum (FBS) was added to stop digestion. The cell suspension was filtered through a 40 µm filter and washed by 1% BSA-HBSS. The cells were finally transferred to 1 mL PBS in preparation for single-cell sequencing. The obtained cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, USA) to generate single-cell gel beads in the emulsion.
ScRNA-seq libraries were prepared using the GemCode Single Cell 3′ Gel Bead, Chip and Library Kits (10× Genomics, Pleasanton, USA).

tag: treatment

value: exposed to BMDBM and MPs

value: 12 hpf

value: wild type


title: MPs

value: exposed to MPs


title: The control of TgHB1, repeat 3 [HB_3]

first: Yanqin


title: BMDBM

value: exposed to BMDBM


title: ID#6 cultured in QGel CN99®

description: FPKM_refseq_hg38.txt [m2_p1_s7]

value: QGel CN99


title: Ren13-1


title: Ren13-2


title: The control of TgHB1, repeat 2 [HB_2]

value: maintained in HFFs in T25 tissue culture flask, about 48 h


title: ID#7 cultured in Matrigel®

description: FPKM_refseq_hg38.txt [m1_p2_s2]


title: The control of TgHB1, repeat 1 [HB_1]


title: ID#6 cultured in Matrigel®

description: FPKM_refseq_hg38.txt [m1_p1_s1]


title: GC13

description: exposure.dhr.results.csv.gz

source_name: Sperm

value: PBS Control

tag: antibody

value: anti-histone H3 pan-monoclonal antibody, cat no. 05–928, Millipore Corp

tag: disease

value: puberty, prostate

tag: matched sample name


title: NCD_1

tag: cell line

tag: genotype

value: control group


title: ID#9 cultured in Matrigel®

description: FPKM_refseq_hg38.txt [m1_p4_s4]

tag: matrix conditions


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H9_ad008

status: Public on Sep 11 2020

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

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

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: CP

value: male

tag: age

tag: strain


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H9_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H8_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H8_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H8_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H9_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H9_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H9_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H9_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H8_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H8_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad010


title: control

value: untreated


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H8_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H7_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H4_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H4_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H4_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H5_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H4_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H4_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H6_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H4_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad007


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H3_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H2_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H12_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad001


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad008


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad004


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad006


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H11_ad002


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H10_ad010


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad012


title: CEMBA180925_5E_7_CEMBA180925_5E_8_H1_ad010