title: S7: Formaldehyde Air 8-oxoG-Immunoprecipitated RNA

city: Austin

first: Lydia

middle: M

last: Contreras

address: 200 E Dean Keeton St,

department: Chemical Engineering

institute: University of Texas at Austin

description:
Immunoprecipitated RNA from formaldehyde air exposure
DESeq2-FA_IP.txt

data_processing:
Illumina HiSeq 4000 Real-Time Analysis (RTA v2) basecalling
Cutadapt was used to trim adaptor sequences from each pair and filter low quality sequences using option -q 30, followed by quality check using FastQC
STAR-2.6.0a was used for first pass mapping of trimmed pairs to the human genome GRCh38.94 using options --genomeLoad NoSharedMemory --outFilterIntronMotifs None --outSAMattrIHstart 0 --outSAMstrandField intronMotif  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate
STAR-2.6.0a was used for second pass mapping of trimmed pairs using all first pass maps as available splice junctions and options --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outBAMcompression 10 --quantTranscriptomeBAMcompression 10 --outFilterIntronMotifs None --outSAMattrIHstart 0 --outFilterType Normal --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
RSEM-1.2.25 calculate-expression was used to estimate the number of reads assigned to each splice variant using options --paired-end -p 24 --bam --output-genome-bam
Differential expression and 8-oxoG enrichment was performed using DESeq2 in R version 3.5.0.
Genome_build: GRCh38.94
Supplementary_files_format_and_content: isoform.results.txt files are tab-delimited text files containing TPM and FPKM values for each sample generated by RSEM.  DESeq2 files contain results of differential expression (Input) and oxidation enrichment values (CA_IP and FA_IP)

source_name: normal human bronchial epithelium cell line

growth_protocol: Normal human lung cell cultures of BEAS-2B (ATCC CRL-9609) were initiated from cryopreserved cells in 23 ml of complete Bronchial Epithelial Cell Growth medium (BEGM, Lonza, Walkersville, MD) with a seeding density of 225,000 cells at 37°C under an atmosphere containing 5% CO2 in a humidified incubator. Cells were incubated for 4 days until reaching 70% - 80% confluence with medium renewal 48h after seeding. Cells were then passaged to collagen-coated inserts (30 mm diameter, hydrophilic PTFE with pore size of 0.4 µm, EMD Millipore, Burlington, MA) housed in 6-well plates (Corning Costar Clear Multiple Well Plates, Corning, NY) with a seeding density of 200,000 cells and incubated for 24h with 0.8 ml and 1.1 ml of medium in the apical and basolateral side, respectively. Cell culture inserts were coated with 1 ml of 57 µg/ml of Bovine Collagen Type I (Advanced BioMatrix, Carlsbad, CA) in BEGM 24h before seeding. Two hours before exposure, the medium from the apical cell surface was completely removed, and the medium from the basolateral cell surface was renewed with fresh complete medium

extract_protocol:
TRIzol RNA extraction was conducted following TRIzol’s manufacturer instructions with freshly prepared ethanol (200 Proof, OmniPur, EMD Millipore, Burlington, MA), isopropanol (molecular biology grade, IBI Scientific, Dubuque, IA) and nuclease-free water (Ambion, Austin, TX) purged of oxygen with ultra-high purity N2. The purified RNA was incubated with DNAseI (New England Biolabs, Ipswich, MA) following the manufacturer’s protocol. RNA was then re-extracted with 200 µl of 25:24:1 mixture of phenol/chloroform/isoamyl alcohol (Fisher BioReagents, Hampton, NH) followed by a chloroform extraction and an isopropanol precipitation as described above. After DNase I treatment of RNA, ribosomal RNA (rRNA) was depleted using Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA) as described by the manufacturer’s protocol to produce the formaldehyde air and clean air input RNA samples (FAInput and CAInput).  Immunoprecipitations of 8-oxoG-containing RNA transcripts were performed in biological duplicates for CA and FA conditions. All buffers were prepared fresh from concentrated stocks on the day of pulldown experiments and purged of O2 as described above. A portion of the input RNA was incubated with 12.5 µg of 8-oxo-7,8-dihydrodeoxyguanosine (8-oxo-dG) monoclonal antibody (0.5 mg/ml, Clone 2E2, Trevigen, Gaithersburg, MD) in IP buffer (10 mM Tris pH 7.4, 150 mM NaCl, 0.1% IGEPAL, and 200 units/ml SUPERaseIn RNA inhibitor [Invitrogen, Carlsbad, CA]) in a 1 ml reaction volume for 2h at 4°C with rotation.  SureBeads Protein A magnetic beads (Biorad, Hercules, CA) were washed according to manufacturer’s protocol and blocked in IP buffer supplemented with 0.5 mg/ml bovine serum albumen (BSA) for two hours at room temperature. After washing beads twice in IP buffer, the beads were resuspended in IP buffer, mixed with the RNA-antibody reaction and incubated for 2h at 4°C with rotation. Next, the beads were washed three more times in IP buffer before two rounds of competitive elution were performed with free 8-oxo-dG nucleosides (Cayman Chemical, Ann Arbor, MI). Each elution consisted of incubation of the beads with 108 µg of 8-oxo-dG in IP buffer for 1h at 4°C with rotation. The elution volume was then cleaned up using the RNA Clean and Concentrator-5 kit (Zymo Research, Irvine, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
library strategy: 8-oxoG-Seq

treatment_protocol: Cells were placed in a chamber and exposed to a mix of 0.08 L/min CO2 and 1.52 L/min formaldehyde-containing air or 0.08 L/min CO2 and 1.52 L/min humidified clean air for two hours.  Media was then replaced, and cells were allowed to recover for 6 hours at 37˚C in a humidified incubator under an atmosphere containing 5% CO2.

value: BEAS-2B cells (ATCC CRL-9609)

value: Anti-8-oxo-dG Monoclonal Antibody (clone 15A3)

value: Formaldehyde Air

value: Lung, bronchus

tag: disease

value: Normal


title: S8: Formaldehyde Air 8-oxoG-Immunoprecipitated RNA

status: Public on Oct 13 2020

type: SRA

state: TX

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: antibody

tag: treatment

tag: tissue


title: S6: Clean Air 8-oxoG-Immunoprecipitated RNA

description:
Immunoprecipitated RNA from clean air exposure
DESeq2-CA_IP.txt

value: Clean Air


title: RNA-seq of nucleus after 0h of LPS treatment rep 1

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: Systems biology

country: South Korea

institute: Yonsei University

data_processing:
RNA-seq paired-end reads were mapped to UCSC mm10 Mus musculus genome using Tophat2
Exon-regions and intron-regions (GTF files) were identified using GenomicFeature R-package
The expression level of each gene was quantified as TPM using StringTie tool v2.1.3
RIP-seq paired-end reads were mapped to UCSC mm10 Mus musculus genome using Tophat2
The FPKM values of each gene (exon and intron, respectively) was quantified using StringTie tool v2.1.3
Genome_build: UCSC mm10 Mus musculus genome
Supplementary_files_format_and_content: tpm_all.200603.3.xlsx contains TPM values of each sample for exon and intron, respectively.

organism: Mus musculus

source_name: nucleoplasm

extract_protocol:
Cytoplasm, nucleoplasm, and nucleoli were extracted from LPS-stimulated macrophages as previously described (http://www.lamondlab.com/f5nucleolarprotocol.htm).  RNAs were purifed using RiboEx reagent and cleaned up using RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Raw264.7 cells

value: LPS 0h


title: TYV-1

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Sample_95717
T=total, Y=young, V=vehicle, biological replicate = 1

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to verify sample quality.
The Tuxedo Suite was used to align reads to the reference transcriptome using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure only high quality data
Two different methods were used for expression quantitation, normalization, and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was one method used for expression quantitation and differential expression analysis. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
HTSeq (version 0.6.1)   to count non-ambiguously mapped reads only. Data were pre-filtered to remove genes with 0 counts in all samples. DESeq2 (version 1.14.1) for normalization and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

molecule: polyA RNA

source_name: Preoptic area of the hypothalamus

growth_protocol: GnRH CRE (homozygote) male mice were bred to floxed-stop-floxed  L10a-GFP (homozygote) female mice to generate offspring that express GFP tagged ribosomal protein L10a in GnRH neurons.

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen; 74004) with on column DNasing and assessed for quantity and quality using the Pico or Nano Chip (Agilent).
SMARTer v4 Ultra low (poly A), fragment length 120nt.

treatment_protocol: Preoptic Area hypothalamic punches were collected from female  adult female (diestrous)  tissue collection from both sexes.

tag: genotype

value: GnRH CRE x Floxed L10a-GFP

value: Preoptic area of the hypothalamus

tag: rna fraction

value: GnRH Depleted Supernatant

tag: age

value: Young

tag: prenatal treatment

value: Vehicle


title: S5: Clean Air 8-oxoG-Immunoprecipitated RNA


title: KDsRNAseq_AGO1_III

city: Maale-AdumimJerusalem

first: Arie

last: Fridrich

state: Israel

department: EEB

country: Israel

institute: The Hebrew University of Jerusalem

description:
small RNA
sRNA-seq-Zamore-protocol

data_processing:
The data were pre-processed to remove the adapters using cutadapt
processed reads were analysed using miRDeep2 software
The gene models can be found here: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Genome_build: ASM20922v1, INSDC Assembly GCA_000209225.1, Sep 2007.
Supplementary_files_format_and_content: read counts
Supplementary_files_format_and_content: counts.tabular_tabular

organism: Nematostella vectensis

source_name: whole animals

extract_protocol: sRNA-seq-Zamore-protocol:Small RNA libraries were constructed as described in Phillip Zamore Lab Illumina TruSeq Small RNA Cloning Protocol April, 2014 (http://www.umassmed.edu/zamore/resources/protocols/).  sRNA-seq-modified-nebnext was carried out using NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (cat. no E7300, New Enagland Biolabs) according to the protocol described by: Plotnikova et al. Plant Cell 2019. mRNA sequensing was carried out with Lexogen Sense kit according to the manufacturer's instructions.

tag: developmental stage

value: Planula

tag: agent

value: Morpholino


title: 10-OVLT-36HWD-stim_to_cell_type_mapping

city: Dallas

first: Allan-Hermann

last: Pool

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

data_processing:
Gene-cell matrices were generated by mapping sequencing reads to mm10 based mouse pre-mRNA reference transcriptome with Cell Ranger 3.0.1
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are simple gene-cell matrices (genes as rows, cell indexes as columns).

source_name: Dissociated single cell suspensions from OVLT

extract_protocol:
Animals were anaesthetized with isoflurane. Brains were extracted and dissected in NMDG-ACSF. Tissue was digested with papain in trehalose-HEPES-ACSFand triturated to generate single cell suspensions. For stimulus to cell-type mapping experiments, actinomycin-D was included in NMDG-ACSF and trehalose-HEPES-ACSF to block artificial induction of immediate early genes.
Sequencing libraries were constructed following 10x Genomics 3' v2 (Samples 1, 2) or v3 )Samples 3-10) standard protocols.
3' Single-cell RNA-Seq

treatment_protocol: Samples 3, 7: water sated; Samples 4, 8: osmotic thirst (intraperitoneal (i.p.) injection of 2 M NaCl (5 μl/g bodyweight) followed by sacking 1 hour after injection); Samples 5, 9: hypovolemic thirst (i.p. injection of furosemide at a dose of 50 mg/kg bodyweight followed by sacking 4 hours after injection); Samples 6, 10: chronic water deprivation (36H water deprivation).

tag: strain

value: Vascular organ of the lamina terminalis (OVLT)

value: chronic water deprivation


title: 9-OVLT-hypovolemic_thirst-stim_to_cell_type_mapping

value: hypovolemic thirst


title: 8-OVLT-osmotic_thirst-stim_to_cell_type_mapping

value: osmotic thirst


title: S4: Formaldehyde Air Input RNA

description: total RNA from formaldehyde air exposure

value: BEAS-2B cells (ATCC CRL-9609)

value: Formaldehyde Air


title: S3: Formaldehyde Air Input RNA

value: Lung, bronchus

value: Normal


title: 7-OVLT-water_sated-stim_to_cell_type_mapping

value: water sated


title: S2: Clean Air Input RNA

description:
total RNA from clean air exposure
DESeq2-Input.txt

value: Clean Air


title: GF2

type: RNA

city: Shanghai

first: Zheyu

last: Zhang

address: Yueyang Road

country: China

institute: CAS

description: germ-free mice

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: mouse plasma sample

label_protocol: fter RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: sample type

value: plasma

tag: gender

value: male


title: GF3

description: germ-free mice


title: RNA-seq of nucleus after 0h of LPS treatment rep 2

value: Raw264.7 cells

value: LPS 0h


title: S1: Clean Air Input RNA


title: GF1

description: germ-free mice


title: 6-SFO-36HWD-stim_to_cell_type_mapping

source_name: Dissociated single cell suspensions from SFO

value: Subfornical organ (SFO)


title: Agg_8174_rnaseq

city: madrid

first: Paulina

middle: G.

last: Eusebi

state: madrid

address: Ave. Puerta del hierro

department: Animal Production

country: Spain

institute: Universidad Complutense de Madrid

data_processing:
Illumina Casava1.7 software used for de-multiplex individual reads
Read quality of the sixteen RNA-seq datasets was checked and trimmed using PRINSEQ v. 0.20.4
Trimmed reads were then mapped to the bovine reference genome (Bos taurus ARS.UCD 1.2) with STAR v.2.7.3a
The SAM files generated by STAR, which contains the count of reads per base aligned to each location across the length of the genome, were converted into a binary alignment/map (BAM) format and sorted using SAMTools v.0.1.18
The aligned RNA-seq reads were assembled into transcripts and their abundance in fragments per kilobase of exon per million fragments mapped (FKPM) was determined with Cufflinks v.2.2.1
Analysis of differential gene expression across aggressive and non-aggressive groups was performed using Cuffdiff
Genome_build: Bos_taurus_ARS.UCD 1.2
Supplementary_files_format_and_content: text files include  gene  transcript values for each Sample

organism: Bos taurus

source_name: Prefrontal cortex

extract_protocol:
PFC were removed, preserved with RNA-later and then RNA extacted with Rneasy Lipid tissue Mini kit, and RNApreserved with RNAstable, Illumina TruSeq stranded mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: breed

value: Lidia

tag: brain region

value: Prefrontal cortex

value: 4 years

value: aggressive

tag: Sex


title: GF-SPF 3

description: with fecal microbiota gavage transplantation (FMT) from specific pathogen free (SPF) mice into germ-free mice


title: Agg_8171_rnaseq

value: 3 years


title: 5-SFO-hypovolemic_thirst-stim_to_cell_type_mapping

value: hypovolemic thirst


title: iSTARR-seq_plasmid_rep2

city: Shenzhen

first: Chunhui

last: Hou

state: Guangdong

address: Nanshan distinct

institute: Southern University of Science and Technology

library_source: genomic

data_processing:
Library strategy: STARR-seq
For STARR-seq sequencing data, we used bowtie2 to align the reads to the Arabidopsis thaliana genome (TAIR10) with parameters “--no-discordant -X 2000”. Duplicate reads were removed by picard MarkDuplicates. Low quality reads were filtered by samtools view with parameters “-f 2 –q 5”. Two replicates of cDNA and plasmid were merged separately for subsequent peak calling. The correlation between replicates were calculated by deeptools. The fragment size and coverage of STARR-seq library were calculated by picard CollectInsertSizeMetrics and CollectWgsMetricsWithNonZeroCoverage. The merged bam files were converted into bigwig format for subsequent IGV visualization.
For iSTARR-seq sequencing data, cDNA library contained the reads with oligo dT (aSTs reads) and without oligo dT (dSTs reads). Because oligo dT sequences are located in 5’ end of pair-end read2. We cut the 20bp at 5’ end and 30bp low quality bases at 3’ end for both pair-end reads. Then we carried out the same mapping, filtering, merging as in STARR-seq data processing. iSTARR-seq plasmid library contains 6 sub-libraries marked by 6 different index in each replicate. Each index library’s reads were mapped and filtered separately. And then we merged these reads from 6 index libraries into one bam file. The correlation, fragment size and coverage were also calculated like in STARR-seq.
We used R package BasicSTARRseq to call enhancer with parameters “minQuantile = 0.9, peakWidth = 500, maxPval = 0.001”. We calculated FDR for each peak with ranked P values. The enrichment of peak were calculated by two ways: Peak coverage enrichment = (cDNA coverage of peak / total cDNA reads) / (plasmid coverage of peak / total plasmid reads); Peak summit enrichment = normalized cDNA summit signal of peak / normalized plasmid signal at cDNA summit site. Finally, we took the peaks with P value < 0.001, FDR < 0.001 and Peak summit enrichment >= 1.3 as enhancers.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files are generated from aligned bam files by deeptools bamCoverage

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The Arabidopsis seedlings were grown at 22°C with a relative humidity around 60%. The light/dark photoperiod is 16/8 h by using a bank of 400 W metal halide lamps. The light intensity is 400 µmol m–2s–1 at the plant height. We collected 2-week-old seedlings for the all experiments.

extract_protocol:
Reporter cDNA libraries construction for Illumina sequencing: 24hrs post-transfection, cells were washed in W5 solution twice and concentrated. Total RNA was extracted using TransZolTM Up Plus RNA Kit (ER501). polyA+ RNA fraction was isolated using VAHTS mRNA Capture Beads  (N401). 5U DNase I (NEB M0303S) was used to digest DNA at 37°C for 20 min. Synthesis of first strand cDNA was carried out with TransScript One-Step gDNA Removal and cDNA synthesis SuperMix (AU311 50°C for 30 min and 85°C for 5s) using a specific primer (GACTGGAGTTCAGACGTGTGCTCTTCCGATCTttttttttttttttttttNNNNNN)  and 8ul of RNA in 20 reactions.  All reactions were pooled. The total amount of reporter cDNA was amplified for Illumina sequencing by a 2-step nested PCR strategy using the TransStart® FastPfu Fly DNA Polymerase (AP231-12).
Transfected plasmid library construction for Illumina sequencing: When the PolyA RNA was capture, keep the total RNA (without mRNA) supernatant, add 10ul RNase A  TransGen® Biotech GE 101 20mg/ml at 37°C for 30-60min, and the plasmid was purified by GeneJET PCR Purification Kit and eluted in 50 ul EB. Purified plasmid as template for the second PCR (98°C for 2min; followed by 8-12 cycles of 98°C for 30s, 65°C for 30s, 72°C for 30s; and then 72 °C for 5min) with TransGen® Biotech FastPfu Fly DNA Polymerase and with VAHTSTM DNA Adapters for Illumina® (N302). PCR products were purified by GeneJET PCR Purification and eluted in 20-30 ul EB. All the libraries were sequenced on Illumine X Ten platform.

treatment_protocol: Protoplasts isolation is described below. Leaves tissues from 2-week-old seedlings were used. Seedlings were cut together into approximately 0.5 mm strips using sharp razors in 0.6M D-mannitol on Petri dishes. The strips were then digested (1.5% Cellulase RS, 0.6 M mannitol, 0.1% BSA, 0.75% Macerozyme R-10, 3.4mM CaCl2, 10 mM MES, pH 5.7), and then vacuumed at -50kPa in bottle for 30 min. After that, the bottle was put on oscillator for 4-5h in dark with gentle shaking (45rpm) at 22°C. After digestion, protoplasts were filtered through 300 micron nylon meshes and washed 3-5 times with W5 solution (125 mM CaCl2, 154 mM NaCl, 5 mM KCl, 2 mM MES, pH 5.7). Protoplasts were pelleted by centrifugation at 80g for 5min. After another two wash with W5 solution (equal volume), protoplasts were then resuspended in MMG solution (15 mM MgCl2, 0.6M mannitol, 4 mM MES, pH 5.7), and placed on ice for 30 min. Protoplasts were centrifuged at 80g again for 5 min and finally resuspended at a concentration of 1 × 107 cells per ml using the MMG solution, determined by using a hematocytometer. All procedures were carried out at room temperature.

tag: ecotype

tag: Stage

value: seedlings


title: iSTARR-seq_plasmid_rep1


title: GF-SPF 1


title: GF-SPF 2


title: Agg_8165_rnaseq


title: iSTARR-seq_cDNA_rep2


title: 4-SFO-osmotic_thirst-stim_to_cell_type_mapping

value: osmotic thirst


title: iSTARR-seq_cDNA_rep1


title: 3-SFO-water_sated-stim_to_cell_type_mapping


title: Agg_8162_rnaseq


title: 25.B replicate 2

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Standard Illumina base-calling pipeline.
HiCUP v0.5.3  (using Bowtie v1.1.0) mapped sequence reads to the relevant genome assembly and removed common Hi-C artefacts.
Hi-C contact maps quantified using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ) and subsequently Matlab.
Genome_build: S288C_reference_sequence_R64-1-1_20110203
Supplementary_files_format_and_content: Hi-C Contact Matrices: Each file contains the interaction data between restriction fragments. Each column or row corresponds to a restriction fragment and each entry in the matrix shows the number of contacts between corresponding fragments. Fragments are sorted according to their chromosome number and their position on chormosomes. Therefore, the first row and the first column are showing the first fragment in chromosome I, while the last row and the last column correspond to the last fragment in chromosome XVI.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Saccharomyces cerevisiae BY4742 was used for all experiments. Cells were inoculated from a frozen glycerol stock onto appropriate medium plates using inoculation loops. The plates were grown in an incubator (Heraeus) at 25°C for 3 consecutive days. A single colony was selected and grown overnight in 6 ml yeast peptone dextrose (YPD) medium at 25°C with shaking at 200 rpm in an incubator (Infors HT Multitron Pro). The starter culture was diluted back down to OD600=0.2 in a 100 ml intermediate culture and incubated o/n at 25°C with shaking at 200 rpm. The culture was diluted down to OD600=0.2 in 400 ml total culture volume and incubated at 25°C with shaking at 200 rpm until mid-log phase (OD600=0.4-0.6).   Cells were divided into two aliquots. One fixed with formaldehyde (Agar Scientific) at a final concentration of 3% for 20 minutes with shaking at 220 rpm at 25°C. The reaction was quenched with 2.5M glycine added to a final concentration of 0.35M and incubated for 5 minutes with shaking at 220 rpm, 25°C. The other group was shifted to heat-shock conditions by adding 1 vol. of fresh YPD, prewarmed to 49˚C, and grown with shaking at 37˚C for 15 minutes. Fixation was done with formaldehyde at 3% with shaking at 220 rpm, 37°C, then quenched with glycine at 0.35M final concentration and 5 min incubation at 37°C. Cells were centrifuged at 3000 rpm at 4°C for 5 minutes, washed in 100 ml sterile water, then re-centrifuged at 3000 rpm, 4°C for 5 minutes. The pellet was re-suspended in 5 ml 1x NEBuffer 2.

extract_protocol:
Cells were ground by mortar and pestle in liquid nitrogen for 10 minutes. Lysed cells were washed in 50 ml 1x NEBuffer 2 then centrifuged at 3000 rpm at 4°C for 5 minutes. The OD600 of the pellet was adjusted to 10.0 with 1x NEBuffer 2 followed by 2 volumes washes with 1x NEBuffer 2. Lysed cells were centrifuged at 4000 g at 4°C for 10 minutes and resuspended in 0.38 volume of the adjusted OD600=10.0 with 1x NEBuffer 2, SDS was added (0.1% final concentration) and the chromatin of mechanically lysed cells were incubated at 65˚C with shaking (950 rpm) for one hour. Triton X-100 was added at a final concentration of 0.95 % and incubated at 37˚C with shaking (950 rpm) for 10 minutes.
Restriction digest was performed overnight at 37˚C with HindIII (NEB; 1500 units per sample).  The restriction sites were then filled in with Klenow (NEB) using biotin-14-dATP (Life Technologies), dCTP, dGTP and dTTP (all at a final concentration of 0.28 µM) for 60 minutes at 37˚C. Filled-in chromatin was mixed with 0.93 volumes of ligation reaction mix at a final concentration of 1x ligation buffer (NEB), 0.1mg/ml bovine serum albumin (BSA), 25 units / sample T4 DNA ligase (Life Technologies) for 6 hours at 16˚C. Reverse crosslinking (65˚C overnight in the presence of Proteinase K (Roche)) was followed by RNase A (Roche) treatment at 37 ˚C for 60 minutes and two sequential phenol/chloroform extractions. The DNA was precipitated in the presence of sodium acetate 3 M pH 5.2 (1/10 volume) and ethanol (2.5 x volumes) 45 min at -20˚C. The DNA extraction was repeated with one phenol extraction followed by two sequential phenol/chloroform extractions then one chloroform extraction. The DNA was precipitated in the presence of sodium acetate 3 M pH 5.2 (1/10 volume) and absolute ethanol (2.5 x volumes) overnight at -20˚C. After three consecutive washes with 70% v/v ethanol, the DNA concentration was determined using Quant-iT Pico Green (Life Technologies). Each 5 µg of Hi-C library DNA were incubated with  0.1 mg/ml BSA, 1x NEBuffer 2 (NEB), 0.2 mM dATP, and 15 units T4 DNA polymerase (NEB) in a total volume of 100 μl for 4 hours at 20˚C to remove any biotin from non-ligated fragment ends, followed by DNA purification (Qiagen PCR purification kit). DNA was eluted in 130 μl double distilled water.  Sonication was performed to obtain DNA fragments with a size peak around 400 bp (Covaris E220 settings: duty factor: 10%; peak incident power: 140W; cycles per burst: 200; time: 110 seconds). The sonicated DNA was end-repaired (T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB)) for 30 minutes at 20˚C, followed by DNA purification (Qiagen PCR purification kit). dATP was added with Klenow exo- (NEB) for 30 minutes at 37˚C, and the enzyme was heat-inactivated (20 minutes at 65˚C). A double size selection using AMPure XP beads (Beckman Coulter) was performed: first, the ratio of AMPure XP beads solution volume to DNA sample volume was adjusted to 0.6:1. After incubation for 10 minutes at room temperature, the sample was transferred to a magnetic separator (DynaMag-2 magnet; Life Technologies), and the supernatant was transferred to a new Eppendorf tube. The ratio of AMPure XP beads solution volume to DNA sample volume was then adjusted to 0.9:1 final. After incubation for 10 minutes at room temperature, the sample was transferred to a magnet (DynaMag-2 magnet; Life Technologies). Following two washes with 70% v/v ethanol, the DNA was eluted in 300 µl of TLE (10 mM Tris-HCl pH 8.0; 0.1 mM EDTA). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Life Technologies) on a DynaMag-2 magnet (Life Technologies) in binding buffer (10 mM Tris-HCl pH8, 1mM EDTA, 2 M NaCl) for 15 minutes at room temperature with rotation, followed by one wash in washing buffer (5 mM Tris-HCl pH8.0, 0.5 mM EDTA, 1 M NaCl), and one wash in ligation buffer (NEB). TruSeq indexed adapters (Illumina) were ligated onto Hi-C ligation products bound to streptavidin beads for 2 hours at room temperature (T4 DNA ligase NEB, in ligation buffer, slowly rotating). After washes in wash buffer (5 mM Tris, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) and NEBuffer 2, the DNA-bound beads were resuspended in a final volume of 50µl NEBuffer 2. Bead-bound Hi-C DNA was amplified with 12 PCR amplification cycles using TruSeq primer PCR 1.0 and TruSeq primer PCR 2.0 primers (Illumina). The concentration and size distribution of Hi-C library DNA after PCR amplification was determined by Bioanalyzer profiles (Agilent Technologies). Hi-C libraries were sequenced using 50 bp paired-end sequencing on an Illumina HiSeq 2500 instrument in High Output mode, using Sequencing by Synthesis (SBS) v4 reagents.


title: 25.A replicate 1


title: 37.A replicate 1


title: 37.B replicate 2


title: GF3

description: germ-free mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse plasma sample,germ-free mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.


title: Agg_8324_rnaseq


title: M1KO_579

city: Baltimore

first: Guang

last: Wong

state: MD

address: 855 N Wolfe Street

department: School of Medicine

institute: The Johns Hopkins University

data_processing:
Illumina CASAVA performed base-calling of Illumina NovaSeq 6000 150bp paired-end data producing FASTQ files.
Data were filtered to remove reads containing adaptors, with N>10% of bases, or error rates > 0.02%.
STAR v2.5 performed mapping to mm10 with mismatch=2 and tne MMP option.
HTSeq v0.6.1, with -m union setting, quantified the reads to FPKM
DESeq2 v2_1.6.3 performed diffferential analysis using the negative binomial distribution, where FDR adjustment was by the Benjamini and Hochberg algorithm.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: Processed data supplementary file, Wong-May-20_Submission, is a .txt file of the FPKM values used in the DESeq2 differential analysis.  A sample's FPKM column name corresponds to the above "Sample name".

source_name: Kidney

growth_protocol: Both wild-type (WT) and knockout (KO) mice were on a C57BL6/J genetic background. All Ctrp1-KO (-/-) and WT (+/+) littermate controls were generated by intercrossing Ctrp1 heterozygous (+/-) mice. Male Ctrp1-KO mice and WT littermate controls were housed in polycarbonate cages on a 12-h light-dark photocycle with ad libitum access to water and food, with no more than five adult mice per cage. Mice were fed a high-fat diet (HFD; 60% kcal derived from fat; D12492, Research Diets) beginning at 6 weeks of age.

extract_protocol:
Whole kidneys from the anatomical left were immediately excised from euthanized WT and CTRP1-deficient mice and flash frozen in liquid nitrogen. Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific, Carlsbad, CA.)  per the manufacturer's protocol. RNA samples were subjected to DNASE I (New England Biolabs, Ipswwich, MA.) digestion to remove genomic DNA contamination using the manufacturer's protocol. A 3M (pH 5.2) sodium actetate (Quality Biological, Gaithersburg, MD.) precipation was performed after DNASE I digestion to purify RNA samples.  In brief, sodium acetate was added at 1/10 the volume of the sample followed by the addition of 2.5 volumes of ice cold 100% ethanol and mixed throroughly. The samples were incubated at -80 ° C overnight. The samples were centrifuged at 12,000 x g for 20 minutes at 4° C and the supernantant was decanted. The RNA pellets were washed twice using 1ml of ice cold 75% ethanol and centrifuged at 12,000 x g at 4° C. A quick spin was performed to removed any traces of residual ethanol in the pellet using a very fine pipette tip. The pellets were air dryed and reconsitituted in sterile filtered molecular biology grade water (Quality Biological, Gaithersburg, MD). The RNA quality number (RQN) of total RNA was determined for each sample before RNA-seq analysis was performed by Novogene.
Quality-controlled total RNA was purified to mRNA with poly-T magnetic beads, fragmented, and then reverse transcribed into cDNA.  Fragments of 150~200bp were selected and the library PCR amplified.

treatment_protocol: The Ctrp1 KO (-/-) mouse strain used for this research project (B6;129S5-C1qtnf1tm1Lex/Mmucd, identification number 032164-UCD) was obtained from the Mutant Mouse Regional Resource Center (MMRRC), an NCRR-NIH funded strain repository, and was donated to the MMRRC by Genentech, Inc. The Ctrp1 gene is located on mouse chromosome 11 and comprises 4 exons. The largest exon, exon 4 (which codes for 61% of the full-length protein), was targeted by homologous recombination. A total of 679 bp, spanning the coding region of exon 4 and a portion (162 bp) of the 3’UTR, was deleted. Heterozygous mice were recovered from cryo-preserved embryos. Since the ES cells were derived from the 129S5/Sv mouse strain, we backcrossed Ctrp1 KO mice to the C57BL/6J genetic background for >6 generations. All Ctrp1-KO (-/-) and WT (+/+) littermate controls used in this study were generated by intercrossing Ctrp1 heterozygous (+/-) mice. Male Ctrp1 KO mice and WT littermate controls were housed in polycarbonate cages on a 12-h light-dark photocycle with ad libitum access to water and food.

value: kidney

value: 40 weeks

tag: diet

value: high fat


title: Agg_8320_rnaseq


title: STARR-seq_plasmid_rep1


title: Agg_8312_rnaseq


title: GF2

description: germ-free mice

value: plasma


title: GF1

description: germ-free mice

value: male


title: M1WT_597

value: wild type


title: GF_SPF2

source_name: mouse plasma sample,with fecal microbiota gavage transplantation (FMT) from specific pathogen free (SPF) mice into germ-free mice


title: GF_SPF3


title: Non_agg_12_rnaseq

value: Wagyu

value: non-aggressive


title: U251TR Clone2

city: Shenyang

first: Wei

last: Wang

state: Liaoning

address: 155 Nanjing North Street

department: Department of Neurosurgery

institute: the First Affiliated Hospital of China Medical University

description:
Test
SAMPLE 5

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-Change worksheet reports test/control (U251TR/U251) ratios.

label: SYBR Green

source_name: U251TR Clone2

label_protocol: RT2 lncRNA qPCR Assay were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 1 mg RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: U251 obtained from from Cell Bank of Chinese Academy of Sciences (Shanghai, China) and was exposed to stepwise increasing temozolomide for over 12 months. The survival clones were subsequently passaged and grew under the same conditions for more than 20 passages with 100μM temozolomide. The temozolomide-adapted cells were defined as U251TR. Cells were grown in DMEM, supplemented with 10% FBS. All cell lines were maintained in a humidified incubator with 5% of CO2 and 95% air at 37°C.

extract_protocol: Total RNA was extracted by 1 mL TRIzol (Merck & Co., Inc., Kenilworth, NJ, USA)according to the manufacturer’s protocol.

tag: cell line

value: U251 glioma cell line

tag: phenotype

value: temozolomide-resistant cell line

tag: passage


title: Non_agg_9_rnaseq

tag: tissue

value: brain

value: Prefrontal cortex

tag: genotype


title: M1KO_594

tag: age


title: STARR-seq_plasmid_rep2


title: M1WT_631


title: M1WT_524


title: Non_agg_7_rnaseq


title: U251 Clone3

description:
Control
SAMPLE 3

source_name: U251 Clone3

value: parental cell line


title: M1KO_525


title: Agg_8314_rnaseq

value: Lidia

value: 3 years

value: aggressive


title: si-RECQL4#2

city: Qingdao

first: Li

last: Guo

state: China

address: N0.1 jiaozhou road

institute: Qingdao Municipal Hospital

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit
High-quality reads were mapped to the human reference genome hg19 using TopHat software with default parameters
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software
Genome_build: hg19

source_name: HEY

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEY

tag: cell type

value: serous ovarian cancer cell line

tag: transfection


title: STARR-seq_cDNA_rep2

value: seedlings


title: Non_agg_6_rnaseq


title: STARR-seq_cDNA_rep1


title: Non_agg_5_rnaseq


title: M1WT_572

tag: strain

value: kidney

value: 40 weeks

value: high fat


title: U251TR Clone3

description:
Test
SAMPLE 6

source_name: U251TR Clone3


title: si-RECQL4#1


title: U251 Clone1

description:
Control
SAMPLE 1

source_name: U251 Clone1


title: Non_agg_4_rnaseq

value: male


title: GF_SPF1

tag: sample type

value: plasma


title: variant F

city: Busan

first: Jungwook

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

data_processing:
Raw data derived from RNA-seq was filtered to a minimum phred quality score of 28 using FASTX-Toolkit.
The filtered reads were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bamtoreadcount.
Reads per kilobase of gene per million mapped sequence reads were calculated for normalization.
Genome_build: ASM14687v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Paenibacillus polymyxa

source_name: Bacterial culture, P. polymyxa E681, F

extract_protocol:
Total RNAs from ‘B’ and ‘F’ type cells of P. polymyxa E681 were isolated from 2-day-old cultures grown in TSA using the RNeasy mini kit with on-column DNase I treatment (Qiagen Inc., Hilden, Germany). After DNase I treatment, a MICROBExpress bacterial mRNA enrichment kit (Ambion, Carlsbad, CA) was used to remove bacterial rRNA from the total RNA sample.
RNA-sequencing libraries were prepared using an Illumina TruSeqTM RNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq2000 instrument using the reagents provided in the Illumina TruSeq PE Cluster kits (Illumina).

tag: genotype/variation

value: variant F

tag: morphology

value: Flat colony


title: wild-type B

source_name: Bacterial culture, P. polymyxa E681, B

value: wild-type

value: Bald colony


title: si-NC#1

value: si-NC


title: U251TR Clone1

description:
Test
SAMPLE 4

source_name: U251TR Clone1

value: U251 glioma cell line

value: temozolomide-resistant cell line


title: si-RECQL4#3


title: Non_agg_3_rnaseq

value: brain

tag: breed

value: Wagyu

tag: brain region

value: Prefrontal cortex

value: 3 years

value: non-aggressive


title: R18_rep1

status: Public on Oct 12 2020

city: Harbin

first: yan

last: yu

address: Nangang District

institute: Heilongjiang University

data_processing:
mRNA library construction and sequencing
Sequence and primary analysis
RNA-seq reads mapping
Transcript abundance estimation and differentially expressed testing
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000499845.1
Supplementary_files_format_and_content: counts, FPKM

organism: Phaseolus vulgaris

source_name: R18_somatic cells

growth_protocol: Climate chamber

extract_protocol:
RNA extraction kit
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.Approximately 10 ug of total RNArepresenting a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

treatment_protocol: No

tag: line

value: Renaya (a green bean line)

value: Leaf

value: Somatic cell


title: R18_rep3


title: R14_rep3

source_name: R14_somatic cells


title: R14_rep2


title: R18_rep2


title: R14_rep1


title: rep4

city: Buenos Aires

first: Gabriela

middle: Maia

last: Teplitz

address: Chorroarin 280

department: Histology and Embriology

country: Argentina

institute: Universidad de Buenos Aires

description: Biological replicates 4 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.

organism: Sus scrofa

source_name: blastocysts

label_protocol:
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).
The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)

value: Blastocyst from cumulus oocyte complexes madured in coculture with porcine luteal cells

value: Blastocyst from cumulus oocyte complexes in control


title: U251 Clone2

description:
Control
SAMPLE 2

source_name: U251 Clone2

value: parental cell line


title: rep2

description: Biological replicates 2 of 4


title: R10_rep1

source_name: R10_somatic cells


title: R10_rep2


title: A18_rep2

source_name: A18_somatic cells

value: A18-1 (a golden bean line)


title: rep1

description: Biological replicates 1 of 4


title: si-NC#3

value: HEY

value: serous ovarian cancer cell line


title: A18_rep3


title: M1KO_573

value: kidney

value: 40 weeks

value: high fat


title: R10_rep3


title: si-NC#2

value: si-NC


title: A14_rep3

source_name: A14_somatic cells


title: rep3

description: Biological replicates 3 of 4


title: Non_agg_1_rnaseq

source_name: Prefrontal cortex

value: brain

value: Wagyu

tag: Sex

value: male


title: A14_rep2


title: A14_rep1


title: A10_rep3

source_name: A10_somatic cells


title: A10_rep2


title: A10_rep1


title: A18_rep1


title: 1aK9_60min_BL_2_2

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

description: biological replicate 2, technical replicate 2

data_processing:
Illumina Casava-1.8 software used for basecalling.
Illumina reads were mapped to the EnsemblProtists release of the Phaeodactylum tricornutum genome using CLC workbench with default parameters.
The resulting raw read counts were used for downstream analyses.
Transcripts per million (TPM)  were reported for all transcripts
Supplementary_files_format_and_content: Excel sheet file (PtAureo1a_TPM_RR.xlsx) includes TPM values and read counts for every gene and every sample

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum tricornutum Pt4, UTEX#646

growth_protocol: Phaeodactylum strains were cultivated in Erlenmeyer flasks on an orbital shaker in an Algaetron incubation chamber (PSI, Czech Republic) under controlled conditions (14/10-h light/dark cycle, 20 °C, red light (28 µmol photons m-2 s-1, 659 ± 11 nm)).

extract_protocol:
Cells were harvested and immediately frozen in liquid nitrogen. RNA was isolated from filtered cells using PeqGOLD RNApure and PeqGOLD RNA extraction kits (VWR). Residues of DNA were removed by an on-column digest with the PeqGOLD DNase I digest kit (VWR). RNA integrity and fragment size were analyzed on a 2100 Bioanalyzer (Agilent).
Libraries were prepared from 1 µg RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).  Samples were multiplexed  and sequenced in paired-end mode (150 bp read length) on an Illumina HiSeq 2000 and HiSeq 3000 platform, respectively.

treatment_protocol: After 10 d red light incubation, cells were shifted to blue light (18 µmol photons m-2 s-1, 469 ± 10 nm). Besides the change in light condtions all other growth parameters were kept constant. Samples were taken before (0min_RL), 10 min (10min_BL) and 60 min (60min_BL) after shift to blue light.

tag: light condition

value: blue light (BL)

tag: time point

value: 60 min after shift to BL


title: 1aK9_10min_BL_1_2

description: biological replicate 1, technical replicate 2

value: 10 min after shift to BL


title: 1aK9_60min_BL_1_2


title: 1aK9_10min_BL_1_1

description: biological replicate 1, technical replicate 1


title: 1aK9_0min_RL_2_2

value: red light (RL)

value: 0 min (before shift to BL)


title: 1aK9_0min_RL_1_1


title: 1aK9_60min_BL_1_1


title: 1aK9_0min_RL_2_1

description: biological replicate 2, technical replicate 1


title: 1aK8_10min_BL_3

description: biological replicate 3


title: 1aK8_10min_BL_2

description: biological replicate 2


title: 1aK8_10min_BL_1

description: biological replicate 1


title: 1aK9_60min_BL_2_1


title: 1aK8_60min_BL_1

description: biological replicate 1


title: 1aK8_60min_BL_2

description: biological replicate 2


title: 1aK8_60min_BL_3

description: biological replicate 3


title: 1aK8_0min_RL_1

description: biological replicate 1


title: 1aK8_0min_RL_3

description: biological replicate 3


title: WT_60min_BL_3

description: biological replicate 3

value: wild type


title: WT_10min_BL_2

description: biological replicate 2


title: 1aK9_10min_BL_2_1


title: WT_60min_BL_2

description: biological replicate 2


title: WT_10min_BL_3

description: biological replicate 3


title: WT_10min_BL_1

description: biological replicate 1


title: WT_60min_BL_1

description: biological replicate 1


title: 1aK9_0min_RL_1_2


title: WT_0min_RL_1

description: biological replicate 1


title: WT_0min_RL_3

description: biological replicate 3


title: 1aK8_0min_RL_2

description: biological replicate 2


title: WT_0min_RL_2

description: biological replicate 2


title: 1aK9_10min_BL_2_2


title: S2_hEZHIP_5µM

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
H3K27me3 were normalized using ChIP-Rx (1000000/number of reads aligned to the exogenous refernce genome(mm9))
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig (genome wide enrichment), bed (peaks)

organism: Drosophila melanogaster

source_name: S2 cell line

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

extract_protocol:
Cells were crosslinked with 0.8% PFA for 8 min. Lysed in (15 mM Tris, 1 mM CaCl2, 0.25% TritonX-100), treated with Mnase to genrate mono-nucleosomes. Chromatin was dialyzed against RIPA buffer (10mM Tris, 1% TritonX-100, 0.1% SDS, 0.1% Na-DOC) and supernatant was incubated with antibody overnight. Antibody was caputred using dynabeads for 3 hours. IPed material was eluted by boiling the beads in 1% SDS buffer at 65 degree C, after washing 5 times.
Libraries were constructed according to NEB Next Ultra protocol

treatment_protocol: FLAG-tagged human EZHIP was cloned into the pMT-puro vector (Addgene #17923). Transfections were performed with 2 µg plasmid DNA, using Effectene Transfection Reagent (Qiagen), and cells were selected using 2 µg/ml puromycin for approximately three weeks. For induction, 5 µM or 10 µM copper sulfate was added to cells at one million cells/ ml density. Cells were incubated for 72 hours and harvested for immunoblot or ChIP.

tag: cell line

value: Cells containing human EZHIP

value: induced with 5uM Cu2+

tag: antibody

value: H3K27me3 (Cell signaling; Cat number:9733; lot number:NA, monoclonal)

tag: molecule subtype

value: Immunoprecipitated DNA


title: S2_hEZHIP_10µM

value: induced with 10uM Cu2+


title: S2_emptyVector_10µM

value: Cells containing empty vector


title: Parental strain, rep4

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

country: Japan

institute: RIKEN Quantitative Biology Center

description: Gene expression of E. coli cells at exponential growth phase.

hyb_protocol: After confirmation of yields (> 825 ng) and specific activities (> 15 pmol/μg) of the Cy3-labbeled cRNAs using NanoDrop ND-2000, 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to custom designed the Agilent 8× 60K arrays for E. coli W3110, E.coli_K12_Expression_Ver.1, for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_GX_1Color, Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: ExternalFullGEML_043017_D_F_20120907) to obtain background subtracted and spatially detrended Processed Signal intensities.
ORF level expression was calculated by median value of all probes corresponding to each ORF.

organism: Escherichia coli

label_protocol: 100 ng of purified total RNA samples were labelled using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) with Cyanine3 (Cy3) according to the manufacturer’s instructions.

growth_protocol: MDS42 and the evolved strains cells were inoculated from the frozen glycerol stock into 5 ml of modified M9 medium in test tubes and cultivated overnight at 34°C at 150 rpm. The overnight cultures were diluted to an OD600 of 0.1 into fresh modified M9 medium in test tubes and cultured.

extract_protocol: An equal volume of ice-cold ethanol containing 10% (w/v) phenol was added directly to the exponentially growing cultures to stabilize cellular RNA. The cells were harvested by centrifugation at 20,000 × g at 4°C for 5 min, and the pelleted cells were stored at –80°C before RNA extraction. Total cellular RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The purified RNA samples were stores at – 80°C before microarray experiments. The quality of the purified RNA was evaluated using Agilent 2100 Bioanalyzer with an RNA 6000 Nano kit (Agilent Technologies). Only purified RNAs that had RIN (RNA integrity number) of9.0 or more were utilized. The purified RNAs were stored at −80°C prior to transcriptome analysis.

treatment_protocol: Cells were inoculated from the frozen glycerol stock into 96-well microplates containing 200 µl of modified M9 medium without chemicals used for laboratory evolution and cultivated 24h at 34°C with agitation at 900 rotations/min. The precultures were diluted to an OD620 of 0.000033-0.0004 into 200 µl of fresh modified M9 medium in 96-well microplates and cultured. After 12 to 21 h incubation, the exponentially growing cultures (OD600 in the 0.072-0.135 range) were harvested for total RNA extraction.

tag: genetic background

tag: strain type

value: Parent

tag: resistance


title: GEMM26

type: genomic

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

description: Infinium type I or II probe

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Module. Average Beta values were calculated. The files Array-1-5-MethylationProfile.txt, Array-2-12-MethylationProfile.txt and Array-3-11-MethylationProfile.txt contain average beta and unmethylated and methylated signal. The file NormalizedMatrix_transposed.txt contains the transposed average beta values with additional measurements including Index, Detected CpG (0.01)  , Detected CpG (0.05), etc.

label: Cy3 and Cy5

source_name: pancreatic cancer

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: tissue

value: pancreatic cancer


title: GEMM15

description: Infinium type I or II probe


title: GEMM25

description: Infinium type I or II probe


title: 314010

description: Infinium type I or II probe

source_name: adjacent normal

value: adjacent normal pancreas


title: 314011

description: Infinium type I or II probe


title: 314008

description: Infinium type I or II probe

source_name: primary cancer associated fibroblasts

value: primary cancer associated fibroblasts


title: Parental strain, rep2


title: GEMM17

description: Infinium type I or II probe


title: GEMM27

description: Infinium type I or II probe


title: Control strain without stressor Line4

value: Evolved

value: Control


title: PH64A

description: Infinium type I or II probe


title: Parental strain, rep1


title: Parental strain, rep3


title: PH67A

description: Infinium type I or II probe


title: 314004

description: Infinium type I or II probe

source_name: juice circulating cancer cells

value: juice circulating cancer cells


title: Control strain without stressor Line3


title: 314002

description: Infinium type I or II probe


title: 314009

description: Infinium type I or II probe


title: 314012

description: Infinium type I or II probe


title: PH64B

description: Infinium type I or II probe


title: Control strain without stressor Line1


title: 314006

description: Infinium type I or II probe


title: PH67B

description: Infinium type I or II probe


title: GEMM22

description: Infinium type I or II probe


title: GEMM16

description: Infinium type I or II probe


title: GEMM21

description: Infinium type I or II probe


title: Vancomycin Hydrochloride (VCM) evolved strain Line5

value: VCM resistance


title: GEMM23

description: Infinium type I or II probe


title: Vancomycin Hydrochloride (VCM) evolved strain Line4


title: 314007

description: Infinium type I or II probe


title: 314001

description: Infinium type I or II probe


title: 314005

description: Infinium type I or II probe

source_name: primary culture cancer cells

value: primary culture cancer cells


title: PH70B

description: Infinium type I or II probe


title: 314003

description: Infinium type I or II probe


title: Control strain without stressor Line2


title: Vancomycin Hydrochloride (VCM) evolved strain Line6


title: Tetracycline (TET) evolved strain Line6

value: TET resistance


title: Tetracycline (TET) evolved strain Line2


title: Sulfisoxazole (SXZ) evolved strain Line1

value: SXZ resistance


title: Sulfisoxazole (SXZ) evolved strain Line4


title: Sodium salicylate (SS) evolved strain Line4

value: SS resistance


title: Sulfisoxazole (SXZ) evolved strain Line2


title: DL-Serine hydroxamate (SHX) evolved strain Line4

value: SHX resistance


title: Sodium salicylate (SS) evolved strain Line1


title: Sodium salicylate (SS) evolved strain Line6


title: GEMM18

description: Infinium type I or II probe


title: Sodium salicylate (SS) evolved strain Line2


title: GEMM9

description: Infinium type I or II probe


title: DL-Serine hydroxamate (SHX) evolved strain Line5


title: DL-Serine hydroxamate (SHX) evolved strain Line1


title: DL-Serine hydroxamate (SHX) evolved strain Line3


title: Sodium Dichromate Dihydrate (SDC) evolved strain Line3

value: SDC resistance


title: Sodium Dichromate Dihydrate (SDC) evolved strain Line2


title: Sodium Dichromate Dihydrate (SDC) evolved strain Line1


title: Sodium Dichromate Dihydrate (SDC) evolved strain Line6


title: Rifampicin (RFP) evolved strain Line2

value: RFP resistance


title: Sulfisoxazole (SXZ) evolved strain Line5


title: Tetracycline (TET) evolved strain Line4


title: Rifampicin (RFP) evolved strain Line3


title: Tetracycline (TET) evolved strain Line1


title: Puromycin Dihydrochloride (PUR) evolved strain Line5

value: PUR resistance


title: Rifampicin (RFP) evolved strain Line1


title: Rifampicin (RFP) evolved strain Line4


title: Promethazine Hydrochloride (PMZ) evolved strain Line1

value: PMZ resistance


title: Puromycin Dihydrochloride (PUR) evolved strain Line1


title: Puromycin Dihydrochloride (PUR) evolved strain Line3


title: Promethazine Hydrochloride (PMZ) evolved strain Line4


title: Puromycin Dihydrochloride (PUR) evolved strain Line2


title: Protamine Sulfate, from Salmon (PS) evolved strain Line4

value: PS resistance


title: Protamine Sulfate, from Salmon (PS) evolved strain Line2


title: Protamine Sulfate, from Salmon (PS) evolved strain Line6


title: Protamine Sulfate, from Salmon (PS) evolved strain Line5


title: Phleomycin (PLM) evolved strain Line1

value: PLM resistance


title: Promethazine Hydrochloride (PMZ) evolved strain Line2


title: Phleomycin (PLM) evolved strain Line6


title: Phleomycin (PLM) evolved strain Line5


title: Promethazine Hydrochloride (PMZ) evolved strain Line6


title: Phleomycin (PLM) evolved strain Line3


title: 1,10-Phenanthroline Monohydrate (PHEN) evolved strain Line1

value: PHEN resistance


title: 1,10-Phenanthroline Monohydrate (PHEN) evolved strain Line6


title: DL-3-hydroxynorvaline (NVA) evolved strain Line2

value: NVA resistance


title: 1,10-Phenanthroline Monohydrate (PHEN) evolved strain Line2

value: Evolved


title: DL-3-hydroxynorvaline (NVA) evolved strain Line5


title: 1,10-Phenanthroline Monohydrate (PHEN) evolved strain Line5


title: DL-3-hydroxynorvaline (NVA) evolved strain Line6


title: 4-Nitroquinoline 1-oxide (NQO) evolved strain Line4

value: NQO resistance


title: 4-Nitroquinoline 1-oxide (NQO) evolved strain Line6


title: 4-Nitroquinoline 1-oxide (NQO) evolved strain Line3


title: Vancomycin Hydrochloride (VCM) evolved strain Line2


title: Nitrofurantoin (NIT) evolved strain Line3

value: NIT resistance


title: Nitrofurantoin (NIT) evolved strain Line5


title: N-methyl-N-octylamine (NMNO) evolved strain Line4

value: NMNO resistance


title: N-methyl-N-octylamine (NMNO) evolved strain Line5


title: Nitrofurantoin (NIT) evolved strain Line1


title: Nickel(II) Chloride (NiCl) evolved strain Line3

value: NiCl resistance


title: N-methyl-N-octylamine (NMNO) evolved strain Line6


title: 4-Nitroquinoline 1-oxide (NQO) evolved strain Line5


title: N-methyl-N-octylamine (NMNO) evolved strain Line1


title: Norfloxacin (NFLX) evolved strain Line5

value: NFLX resistance


title: Nickel(II) Chloride (NiCl) evolved strain Line2


title: DL-3-hydroxynorvaline (NVA) evolved strain Line1


title: Nickel(II) Chloride (NiCl) evolved strain Line6


title: Nickel(II) Chloride (NiCl) evolved strain Line1


title: Nitrofurantoin (NIT) evolved strain Line2


title: Norfloxacin (NFLX) evolved strain Line6


title: Mitomycin C (MMC) evolved strain Line5

value: MMC resistance


title: Norfloxacin (NFLX) evolved strain Line1


title: Mitomycin C (MMC) evolved strain Line1


title: Mitomycin C (MMC) evolved strain Line4


title: Mitomycin C (MMC) evolved strain Line6


title: Norfloxacin (NFLX) evolved strain Line4


title: Mecillinam (MEC) evolved strain Line3

value: MEC resistance


title: Mecillinam (MEC) evolved strain Line2


title: Mecillinam (MEC) evolved strain Line6


title: L-Valine (LVAL) evolved strain Line3

value: LVAL resistance


title: L-Valine (LVAL) evolved strain Line4


title: L-Valine (LVAL) evolved strain Line5


title: L-Valine (LVAL) evolved strain Line6


title: Potassium Tellurite (IV) (KTe) evolved strain Line6

value: KTe resistance


title: Potassium Tellurite (IV) (KTe) evolved strain Line3


title: Potassium Tellurite (IV) (KTe) evolved strain Line2


title: Kanamycin Sulfate (KM) evolved strain Line4

value: KM resistance


title: Potassium Tellurite (IV) (KTe) evolved strain Line5


title: L-Homoserine (HSE) evolved strain Line1

value: HSE resistance


title: L-Homoserine (HSE) evolved strain Line4


title: Kanamycin Sulfate (KM) evolved strain Line5


title: Kanamycin Sulfate (KM) evolved strain Line6


title: L-Homoserine (HSE) evolved strain Line3


title: L-Homoserine (HSE) evolved strain Line2


title: Mecillinam (MEC) evolved strain Line5


title: Hydrogen peroxide (H2O2) evolved strain Line2

value: H2O2 resistance


title: Hydrogen peroxide (H2O2) evolved strain Line3


title: Hydrogen peroxide (H2O2) evolved strain Line6


title: Hydrogen peroxide (H2O2) evolved strain Line5


title: L-Glutamic acid γ-hydrazide (GAH) evolved strain Line4

value: GAH resistance


title: L-Glutamic acid γ-hydrazide (GAH) evolved strain Line1


title: Furaltadone (FTD) evolved strain Line3

value: FTD resistance


title: L-Glutamic acid γ-hydrazide (GAH) evolved strain Line2


title: L-Glutamic acid γ-hydrazide (GAH) evolved strain Line3


title: Furaltadone (FTD) evolved strain Line2


title: Fosfomycin disodium salt (FOS) evolved strain Line1

value: FOS resistance


title: Furaltadone (FTD) evolved strain Line4


title: Furaltadone (FTD) evolved strain Line1


title: Kanamycin Sulfate (KM) evolved strain Line1


title: Fosfomycin disodium salt (FOS) evolved strain Line5


title: Fosfomycin disodium salt (FOS) evolved strain Line6


title: Fosfomycin disodium salt (FOS) evolved strain Line3


title: Erythromycin (EM) evolved strain Line2

value: EM resistance


title: Erythromycin (EM) evolved strain Line6

value: Evolved


title: Erythromycin (EM) evolved strain Line1


title: Erythromycin (EM) evolved strain Line3


title: Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA) evolved strain Line3

value: EDTA resistance


title: D-Cycloserine (DCS) evolved strain Line4

value: DCS resistance


title: D-Cycloserine (DCS) evolved strain Line2


title: Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA) evolved strain Line1


title: D-Cycloserine (DCS) evolved strain Line3


title: D-Valine (DVAL) evolved strain Line5

value: DVAL resistance


title: D-Cycloserine (DCS) evolved strain Line5


title: D-Valine (DVAL) evolved strain Line6


title: D-Valine (DVAL) evolved strain Line1


title: D-Valine (DVAL) evolved strain Line2


title: Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA) evolved strain Line6


title: Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA) evolved strain Line2


title: Chloramphenicol (CP) evolved strain Line3

value: CP resistance


title: Cefmetazole sodium salt (CMZ) evolved strain Line6

value: CMZ resistance


title: Chloramphenicol (CP) evolved strain Line6


title: Chloramphenicol (CP) evolved strain Line2


title: Chloramphenicol (CP) evolved strain Line5


title: Cefmetazole sodium salt (CMZ) evolved strain Line1


title: Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) evolved strain Line6

value: CCCP resistance


title: Cefmetazole sodium salt (CMZ) evolved strain Line4


title: Cefmetazole sodium salt (CMZ) evolved strain Line3


title: Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) evolved strain Line3


title: Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) evolved strain Line5


title: Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) evolved strain Line4


title: Carbenicillin Sodium Salt (CBPC) evolved strain Line3

value: CBPC resistance


title: Carbenicillin Sodium Salt (CBPC) evolved strain Line1


title: Benserazide Hydrochloride (BZ) evolved strain Line4

value: BZ resistance


title: Carbenicillin Sodium Salt (CBPC) evolved strain Line5


title: Benserazide Hydrochloride (BZ) evolved strain Line6


title: Blasticidine S hydrochloride (BSD) evolved strain Line2

value: BSD resistance


title: Aztreonam (AZT) evolved strain Line4

value: AZT resistance


title: Blasticidine S hydrochloride (BSD) evolved strain Line4


title: Benserazide Hydrochloride (BZ) evolved strain Line2


title: Amitriptyline Hydrochloride (ATP) evolved strain Line1

value: ATP resistance


title: β-Chloro-L-alanine hydrochloride (B.Cl.Ala) evolved strain Line1

value: B.Cl.Ala resistance


title: Aztreonam (AZT) evolved strain Line3


title: Benserazide Hydrochloride (BZ) evolved strain Line1


title: Amitriptyline Hydrochloride (ATP) evolved strain Line6


title: Amitriptyline Hydrochloride (ATP) evolved strain Line5


title: Blasticidine S hydrochloride (BSD) evolved strain Line5


title: β-Chloro-L-alanine hydrochloride (B.Cl.Ala) evolved strain Line2


title: Blasticidine S hydrochloride (BSD) evolved strain Line6


title: Aztreonam (AZT) evolved strain Line6


title: Aztreonam (AZT) evolved strain Line5


title: Acriflavine (AF) evolved strain Line3

value: AF resistance


title: DL-2-Aminobutyric acid (ABU) evolved strain Line3

value: ABU resistance


title: β-Chloro-L-alanine hydrochloride (B.Cl.Ala) evolved strain Line6


title: Acriflavine (AF) evolved strain Line2


title: β-Chloro-L-alanine hydrochloride (B.Cl.Ala) evolved strain Line4


title: Amitriptyline Hydrochloride (ATP) evolved strain Line3


title: Acriflavine (AF) evolved strain Line4


title: Carbenicillin Sodium Salt (CBPC) evolved strain Line2


title: DL-2-Aminobutyric acid (ABU) evolved strain Line6


title: DL-2-Aminobutyric acid (ABU) evolved strain Line4


title: Acriflavine (AF) evolved strain Line6


title: 6-Mercaptopurine monohydrate (6.MP) evolved strain Line4

value: 6.MP resistance


title: DL-2-Aminobutyric acid (ABU) evolved strain Line5


title: 6-Mercaptopurine monohydrate (6.MP) evolved strain Line5


title: 6-Mercaptopurine monohydrate (6.MP) evolved strain Line3


title: 6-Mercaptopurine monohydrate (6.MP) evolved strain Line6


title: 5-Fluorouracil (5.FU) evolved strain Line2

value: 5.FU resistance


title: 5-Fluoroorotic Acid Monohydrate (5.FOA) evolved strain Line2

value: Evolved

value: 5.FOA resistance


title: 5-Fluoroorotic Acid Monohydrate (5.FOA) evolved strain Line3


title: 3-Amino-1,2,4- triazole (3.AT) evolved strain Line4

value: 3.AT resistance


title: 5-Fluoroorotic Acid Monohydrate (5.FOA) evolved strain Line6


title: 5-Fluorouracil (5.FU) evolved strain Line3


title: 5-Fluorouracil (5.FU) evolved strain Line1


title: 5-Fluorouracil (5.FU) evolved strain Line4


title: 3-Amino-1,2,4- triazole (3.AT) evolved strain Line3


title: 5-Fluoroorotic Acid Monohydrate (5.FOA) evolved strain Line4


title: 3-Amino-1,2,4- triazole (3.AT) evolved strain Line1


title: 3-Amino-1,2,4- triazole (3.AT) evolved strain Line5


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snm3C-seq
Reads were trimed with Cutadapt for adapters and low-quality bases (Phred score >= 20)
The trimmed fastq files were mapped to in-silico bisulfite converted mm10 reference genome using Bismark with bowtie1
The umapped reads were split into the first 40bp, middle segment, and the final 40bp, and split reads were mapped to the reference genome using Bismark with bowtie1
The BAM files were filtered using Samtools by MAPQ > 10 and PCR duplicates were removed using Picard
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls were generated with in-house developed package with the filtered BAM files
Two ends of reads from separated BAM files were paired, and chromosome contacts were extracted with in-house pipeline
Genome_build: mm10
Supplementary_files_format_and_content: ALLC files: tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column; HIC files: The single cell contact file contains eight columns, corresponding to the short format for Juicer tools pre (https://github.com/aidenlab/juicer/wiki/Pre). Specifically, each row represents a contact, including the columns of read1_strand, read1_chromosome, read1_position, read1_fragment, read2_strand, read2_chromosome, read2_position, read2_fragment. We did not use the information of restriction fragment, so read1_fragment and read2_fragment were set to be 0 and 1, respectively. The contact files for single cells could be merged by “sort -m -k2,2 -k6,6” to generate the contact file of a cell type, which could be used as the input to Juicer tools pre to generate .hic file of the cell type.

source_name: C57BL/6J Male P56 Mouse Brain

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

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Lee, Dong-Sung, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, et al. 2019. “Simultaneous Profiling of 3D Genome Structure and DNA Methylation in Single Human Cells.” Nature Methods 16 (10): 999–1006.

value: Hippocampus

value: male

tag: age

tag: strain


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H9_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H9_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H9_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H9_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H7_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H8_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H7_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H7_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H6_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H5_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H7_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H7_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H5_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H4_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H6_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H4_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H4_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H3_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H4_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H5_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H3_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H4_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H12_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H1_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H11_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H1_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H6_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H6_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H11_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H4_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H3_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H12_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H3_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H1_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H11_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H12_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H10_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H11_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H12_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H1_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H1_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H2_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H11_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H10_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G9_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H10_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H10_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G9_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G9_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G8_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G7_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G4_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G7_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G7_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G7_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G7_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G9_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G4_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G4_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-H10_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G6_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G6_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G4_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G3_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G6_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G5_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G1_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G3_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G4_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G2_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G1_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G3_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G8_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G3_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G1_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G2_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G6_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G12_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G2_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G11_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G11_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G12_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G5_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G11_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G12_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G10_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G1_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G10_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F9_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G11_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G3_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G10_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G10_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F8_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F8_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F9_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F8_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F9_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F7_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F8_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F7_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F8_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-G11_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F6_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F6_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F6_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F5_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F6_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F5_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F5_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F3_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F9_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F4_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F3_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F4_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F3_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F1_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F3_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F4_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F7_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E7_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F2_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F2_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F12_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F11_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F1_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F6_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F11_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F1_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F10_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F12_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F10_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F10_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F10_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F2_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F10_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-F2_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E9_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E5_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E7_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E9_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E9_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E8_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E8_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E8_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E7_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E7_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E5_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E6_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E6_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E6_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E5_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E3_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E3_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E3_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E3_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E6_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E11_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E7_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E12_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E1_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E11_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E2_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E4_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E2_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E2_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E12_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E11_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E2_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E12_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E3_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E4_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E1_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E1_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E11_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E10_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E10_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E10_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E10_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D9_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E10_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E10_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-E4_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D9_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D9_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D9_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D8_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D8_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D7_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D8_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D9_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D5_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D6_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D5_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D7_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D3_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D8_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D4_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D6_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D4_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D3_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D4_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D3_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D6_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D5_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D5_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D6_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D5_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D6_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D7_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D4_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D2_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D1_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D2_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D2_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D1_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D2_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D11_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D12_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C9_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D12_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C9_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C8_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D11_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C7_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C9_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C8_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D3_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C9_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C9_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D10_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D12_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C7_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C8_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D10_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C8_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C7_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C7_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C7_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C7_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C3_ad004


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C4_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C5_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C5_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C6_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C5_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C5_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C2_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C1_ad012


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C1_ad006


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C2_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C5_ad001


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C12_ad008


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C11_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C11_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C4_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C12_ad007


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C10_ad010


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-C2_ad002


title: 191217-CEMBA-mm-P56-CEMBA191127-11F-5-CEMBA191126-HCV-9-D5_ad001