title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD012

value: SSp


title: Mus musculus I-C

status: Public on Nov 20 2020

type: RNA

city: Chiyoda-ku

first: Kento

last: Mio

state: Tokyo

address: 12 Sanban-cho

department: Studies in Human Life Sciences

country: Japan

institute: Otsuma Womenʼs University

description: Gene expression data of ileum extracted from Mus musculus fed a cellulose diet.

hyb_protocol: cDNA were hybridized to the GeneArray Mouse 2.0ST Array. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific, Inc.) according to the manufacturer’s recommendations.

data_processing: Expression values were generated using Expression Console software, version 1.3 (Thermo Fisher Scientific, Inc.) with default robust multichip analysis parameters.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: ileum in Mus musculus fed cellulose diet

label_protocol: The resultant single-strand cDNA was fragmented and labeled with biotin.

extract_protocol: Total RNA in each organs were extracted by using protocol of RNeasy Mini kit (Qiagen, Hilden, Germany).

tag: strain

tag: tissue

value: ileum

tag: dietary fiber

value: cellulose


title: Mus musculus A-C

description: Gene expression data of adipocytes extracted from Mus musculus fed a cellulose diet.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific, Inc.) according to the manufacturer’s recommendations.

source_name: adipocytes in Mus musculus fed cellulose diet

value: adipocytes


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD010

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: age

value: brain

tag: source

tag: target

value: ACA

tag: gender

value: female


title: Mus musculus I-B

description: Gene expression data of ileum extracted from Mus musculus fed a barley diet.

source_name: ileum in Mus musculus fed barley diet

value: barley


title: RNAseq_6wk_hippocampus_input_rep2

city: Atlanta

first: Andrew

last: Shafik

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_6wk_hippocampus_called_peaks.xls

library_source: transcriptomic

data_processing:
Reads were aligned to mouse genome (mm9) or human genome (hg38) using Bowtie v2.2.4. Mapping parameters were set to local, sensitive and non-deterministic mode.
m6A peaks were identified using MACS2 with parameters:  –nomodel,–extsize 150, -p 5e-2
High-confidence peaks found in both biological replicates were annotated by ChiPSeeker
Differential methylation (DM) in m6A-RIP-seq data was analyzed by MACS2 bdgdiff
BAM files were converted to tiled data files (TDF) for the Integrative Genomics Viewer (IGV) using igvtools.
The genome-wide coverage data were normalized by 1,000,000/total read count for visualization in IGV.
TPM values were calculated by TPMCalculator.
Genome_build: mm9/hg38
Supplementary_files_format_and_content: xls files containing coordinate, gene name information of called m6A peaks. This was achieved using MACS2 callpeak; the input serves as the background.

source_name: Hippocampus

extract_protocol:
Trizol was used to extract total RNA from all samples.
Total RNA was fragmented to ~100 bp using chemical fragmentation. The input libraries were generated from approximatley 50 ng of poly(A) + mRNA. For the m6A libraries, total RNA was immunoprecipated using m6A antibody. Libraries were then constructed using the Illumina Truseq RNA Library Preparation kit v2, according to the manufacturer's protcol. An Agilent 2100 BioAnalyzer and DNA1000 kit were used to determine the concentration and quality of the final amplified cDNA libraries.

tag: developmental stage

value: 6 week old

value: wild type

tag: m6a antibody


title: OID_f0_Rep2

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.3.4.1 with parameters --sensitive-local -p 4 -q
miRNA and GtRNA GTF files were acquired from UCSC genome browser. Raw reads were generated from R package GenomicAlignment and GenomicFeatures.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix for DESeq2 normalized counts for each sample

source_name: mature sperm cells

growth_protocol: CO and OID-fed males (F0) and their male offspring (F1) were euthanized and their caudal epididymis dissected for sperm collection. The epididymis was collected, punctured, and transferred to tissue culture dish containing M2 media (M2 Medium-with HEPES, without penicillin and streptomycin, liquid, sterile-filtered, suitable for mouse embryo, SIGMA, product #M7167) where it was incubated for 1 hour at 37°C

extract_protocol:
Total RNA was isolated from sperm using Qiagen’s miRNeasy extraction kit, according to the manufacturer’s instructions.
Samples were barcoded, pooled, precipitated and separated  on a 15% polyacrylamide gel (PAGE). The gel was stained with SYBR® gold dye and the small non-coding RNA segment corresponding to transfer RNA fragments or tRFs (30-45 nucleotides) excised and purified using a cDNA library preparation method

treatment_protocol: Sperm samples were isolated and purified from somatic cells. Briefly, the samples were washed with PBS, and then incubated with SCLB (somatic cell lysis buffer, 0.1% SDS, 0.5% TX-100 in Diethylpyrocarbonate water) for 1 hour.  SCLB was rinsed off with 2 washes of PBS and the somatic cell-free purified spermatozoa sample pelleted and used for RNA extraction.

tag: diet

value: obesity-inducing diet

tag: generation


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD008

value: male


title: HEK.KO1.4.2_RNA-seq

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: Total RNA-seq

data_processing:
Trim_galore! was used to remove Illumina adaters.
TopHat2 (v 2.1.0) was used to align the reads to the hg38 reference genome using Gencode v23 gene models.
Ribo-seq reads were firstly aligned to a set of known rRNA and tRNAs (selected from the UCSC RepeatMasker tracks), followed by alignment of all unmapped reads to the reference genome.
FeatureCounts (with Gencode v23 gene models) was used to count the number of reads per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing counts for each gene and sample

organism: Homo sapiens

source_name: human embryonic kidney 293 cells

growth_protocol: The human embryonic stem cell (hESC) line Hues9 (H9) was obtained from the Wicell Research Institute (Madison, WI) and maintained in Essential 8 media (Thermo Fisher Scientific) on hESC-Qualified Matrigel (Corning) coated plates. Media was refreshed daily and the cultures were dissociated in clumps every 4 days using 0.5mM EDTA in PBS. HEK293 (HEK) cells were obtained from ATCC and grown in DMEM Media (Thermo Fisher Scientific) supplemented with 1mM Glutamax (Thermo Fisher Scientific), 10% heat inactivated FBS (Thermo Fisher Scientific). All cells were grown at 37°C, 5 % CO2.

extract_protocol:
Total RNA extraction by non ionic detergent-based cell lysis was performed for both H9 and HEK293 cells.
Libraries for H9 WT and NSun6 KO cells (at least 4 replicates each) were performed as described before (Bornelov et al, 2019, Blanco et al. 2016). For the RNA seq samples, we used the NEB ultra-directional library prep kit (NEB). Ribosomal profiling samples were made into libraries using the Illumina Truseq small RNA kit (Illumina). HEK293 WT and NSun6 KO libraries (4 replicates each) were prepared using the Illumina TruSeq Ribo Profile kit; the Total RNA libraries were depleted of ribosomal RNAs using the Illumina Ribo-Zero rRNA removal kit.

tag: cell line

tag: genotype

value: Nsun6 knockout (Clone 1 nucleotide indel)

tag: batch


title: HEK.KO1.4.3_RNA-seq

description: Total RNA-seq


title: HEK.KO1.4.1_RNA-seq

description: Total RNA-seq


title: OID_f0_Rep3


title: RNAseq_6wk_hippocampus_m6AIP_rep2

value: Synaptic systems m6A antibody 202003


title: OID_f0_Rep1


title: RNAseq_6wk_hippocampus_input_rep1


title: CO_f1_Rep4

value: control


title: RNAseq_6wk_hippocampus_m6AIP_rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD004

value: MOp


title: CO_f1_Rep3


title: RNAseq_6wk_hypothalamus_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_6wk_hypothalamus_called_peaks.xls

source_name: Hypothalmus


title: CO_f1_Rep2


title: CO_f1_Rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD002


title: MRC5-RRBS-UV-3 hr rep2

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

country: China

institute: Guangzhou medical university

data_processing:
The sequencing reads were first trimmed by Trimmomatic-0.36 (slidingwindow:4:15; leading:3; trailing:3; mismatch 2; illuminaclip: adapter. fa: 2:30:10) to filter out low quality reads and adapters.
Reads were mapped to the computationally bisulfite-converted human genome (hg38) using Bismark-0.19.0 (--score_min L,0,-0.2).
The methylation levels of covered cytosine sites were calculated by dividing the number of reported C with the total number of reported C and T.
Differentially methylated regions were identified by using swDMR.
Genome_build: hg38

source_name: Fibroblast cells

growth_protocol: MRC5 cells were routinely maintained in DMEM supplemented with 10% FBS at 37°C in a 5% CO2 water-saturated environment.

extract_protocol:
High-molecular-weight genomic DNA was extracted from fibroblast cells using the Genomic DNA extraction kit (Takara) according to the manufacturer’s protocol and spiked with control DNA (unmethylated lambda DNA, Promega).
Genomic DNA was digested overnight with MspI restriction enzyme (recognition site C^CGG, NEB) at 37°C. After purification, single A nucleotides were added to the 3’-end UTR, followed by ligation to methylated adapter with T overhang. After 2% agarose gel purification to select fragments of size 40-220 bp, samples were subjected to bisulfite conversion with a ZYMO EZ DNA Methylation-Gold™ Kit. The final libraries were generated by PCR amplification using standard Illumina protocols.

treatment_protocol: Cells were treated with 12J/m2 UV-C light and recovered for the indicated time in the study.

tag: cell type

value: normal lung tissue-derived fibroblast cells

tag: treatment

value: treated with 12J/m2 UV-C and recovered for 3 hours


title: MRC5-RRBS-UV-24 hr rep2

value: treated with 12J/m2 UV-C and recovered for 24 hours


title: MRC5-RRBS-UV-24 hr rep1


title: RNAseq_6wk_hypothalamus_m6AIP_rep2


title: MRC5-RRBS-UV-3 hr rep1


title: RNAseq_6wk_hypothalamus_m6AIP_rep1


title: MRC5-RRBS-UV-30 min rep2

value: treated with 12J/m2 UV-C and recovered for 30 minutes


title: RNAseq_6wk_hypothalamus_input_rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD007

value: SSp


title: CO_f0_Rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD012

value: brain


title: MRC5-RRBS-UV-30 min rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD008

value: ACA


title: CO_f0_Rep1


title: RNAseq_6wk_cerebellum_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_6wk_cerebellum_called_peaks.xls

source_name: Cerebellum


title: RNAseq_6wk_cerebellum_m6AIP_rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD007


title: MRC5-RRBS-CON rep2

value: untreated


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B2_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD006

value: female


title: Tfh_Tfr_WT_3

city: New Haven

first: Jiawei

state: CT

address: 300 George St, Suite 503

institute: Yale University

data_processing:
STAR (version 2.5.3a) is used for alignment and mapping sequencing reads to genome.
featureCounts (version 1.5.3) is used to count gene expression counts from bam files.
Gene names are matched with Ensembl IDs with R package biomaRt.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mLN

extract_protocol:
Cells were isolated from the mediastinal lymph nodes of infected animals.
The library was constructed at the Yale Center for Genomic Analysis and low input library prep was performed.

treatment_protocol: Animals were infected with influenza virus strain PR8

value: Tfh cells

tag: condition

value: post infection day 8


title: MRC5-RRBS-CON rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD004

tag: strain


title: MRC5-ATAC-UV-24 hr

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2).
The reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13).
All peak calling was performed with macs2 using 'macs2 callpeak --nomodel --keepdup all --call-summits'. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Genome_build: hg38

extract_protocol:
ATAC-seq was performed as previously reported (Buenrostro et al., 2013). Briefly, nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 minutes.
Equimolar Adapter 1 and Adapter 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) accordinig to the manufactuer's instructions.


title: CO_f0_Rep3


title: RNAseq_6wk_cerebellum_input_rep1

value: 6 week old

value: wild type


title: RNAseq_6wk_cerebellum_m6AIP_rep1


title: Tfh_Tfr_WT_1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD010

tag: tissue


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD002

value: male


title: RNAseq_6wk_cortex_input_rep2

description:
Peaks are calculated by compared the IP sample to the background input. Only one called peaks file is submitted for each brain region, which reports the consensus peaks from both replicates.
m6A_6wk_cortex_called_peaks.xls

source_name: Cortex


title: Tfh_Tfr_KO_3


title: MRC5-ATAC-UV-3 hr


title: Tfh_Tfr_KO_2


title: RNAseq_6wk_cortex_m6AIP_rep2

value: Synaptic systems m6A antibody 202003


title: RNAseq_6wk_cortex_input_rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B1_AD001


title: MRC5-ATAC-CON


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD012


title: Tfh_Tfr_KO_1


title: RNAseq_6wk_cortex_m6AIP_rep1


title: HA+_GC B_Tfr_ WT_2

value: GC B cells

value: post infection day 36

value: Tfr WT


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD008


title: Vector U3

last: Luo

address: 107 Yanjiang West Avenue,Yuexiu district

department: General Surgery

institute: Sun yat-sen Memorial Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:hg38）using Hisat2（version:2.0.4）.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Anders S, et al., Bioinformatics 2015, 31(2):166-169 and Robinson MD, et al. Genome Biol 2010, 11(3):R25. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: bladder cancer cell UM-UC-3

growth_protocol: The human bladder cancer cell lines UM-UC-3, T24 and 5637 were purchased from American Type Culture Collection and cultured in an incubator with 5% CO2 at 37℃. UM-UC-3 cells were cultured in Dulbecco's modified eagle's medium while T24 and 5637 cells were cultured in RPMI 1640. All media contained 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions.

treatment_protocol: After 72 hr transfection, the viral supernatants of 293T cells were collected. Lentiviral particles were concentrated using a LentiX™ Concentrator overnight at 4°C. UM-UC-3, T24 and 5637 cells (5×105 cells per well) were seeded in six-well culture plates and infected with lentivirus and polybrene for 24 hr. Cells were infected by lentivirus with the presence of polybrene and selected by puromycin for 2 weeks to obtain stable expression cell lines.

value: Negative control

tag: treatment protocol

value: UM-UC-3 cells were infected by lentivirus using vector to obtain stable expression cell  lines.


title: ELNAT1 U3

value: ELNAT1 was overexpressed in UM-UC-3 cells

value: UM-UC-3 cells were infected by lentivirus using pcDNA3.1 ELNAT1 to obtain stable expression cell  lines.


title: Tfh_Tfr_WT_2


title: HA+_GC B_Tfr_ WT_1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD006

tag: age

value: brain

value: MOp


title: Skin_Fibroblast_sh_HuR3

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

institute: Jiangsu Jiangyin People's Hospital

data_processing:
A total amount of 1 μg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected. clusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Human skin fibroblast

extract_protocol:
RNA  was isolated using TRIZOL.RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA).RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0  Flurometer.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human skin fibroblast cells were treated with high expression of HUR and low expression

value: Human skin fibroblast

tag: genotype/variation

value: HUR gene interference treatment 3


title: Skin_Fibroblast_sh_HuR2

value: HUR gene interference treatment 2


title: HA+_GC B_Tfr_KO_2

value: Tfr KO


title: ELNAT1 T24

source_name: bladder cancer cell T24

value: ELNAT1 was overexpressed in T24 cells

value: T24 cells were infected by lentivirus using pcDNA3.1 ELNAT1 to obtain stable expression cell  lines.


title: Vector 5637

source_name: bladder cancer cell 5637

value: 5637 cells were infected by lentivirus using Vector to obtain stable expression cell  lines.


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD004

tag: source

tag: target

value: ACA

value: female


title: MRC5-ATAC-UV-30 min

value: normal lung tissue-derived fibroblast cells

value: treated with 12J/m2 UV-C and recovered for 30 minutes


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD002

tag: gender

value: male


title: KO5

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
Basecalling was performed using the Illumina default pipeline
Reads were trimmed to remove adapter sequences using Trim Galore
Quality of sequencing data was assessed using FastQC
Reads aligning to ribosomal RNA (Gene ID: 100861531) and immunoglobulin loci (Gene IDs: 111507, 243469, 111519) were filtered out
Reads were mapped to mouse genome using Tophat2 (version 2.0.12)
Reads aligning to genes were counted using HTSeq-count (version 0.10.0)
differentially expressed genes was identified using the DESeq2 (version 1.10.1)
FPKM values were calculated for individual samples using Cuffnorm (version 2.2.1)
Genome_build: GRCm38.80/mm10
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each sample.

source_name: Activated CD19+ B cells

growth_protocol: Fo CD19+ B cells were isolated from pooled peripheral and mesenteric lymph nodes using the negative depletion with biotin-conjugated antibodies against CD5, CD43, Mac and Ter119 followed by DynaBeads-Streptavidin   All samples are from individual female mice

extract_protocol:
RNA-seq libraries were prepared using an ARTseq Ribosome Profiling Kit (Epicentre, Illumina) according to the manufacturer’s instructions for preparing libraries from total (not nuclease treated) RNA
RNA-seq libraries were prepared using an ARTseq Ribosome Profiling Kit (Epicentre, Illumina), pooled and sequenced on two lanes of Illumina HiSeq 2500.

treatment_protocol: B cells were cultured for 48 hours in RPMI-1640 containing 10% FCS, 1mM Na-pyruvate, 2mM GlutaMAX, penicillin/streptomycin, 50 µM β-mercaptoethanol and activated with 10µg/ml LPS, 10ng/ml IL4, 10ng/ml IL5

value: Zfp36l1(fl/fl) CD79a-cre cKO

value: 8 to 11 weeks

tag: Sex

value: Female

tag: number of mice

value: Peripheral and mesenteric LN

value: LN CD19+ B cells


title: HA+_GC B_Tfr_KO_1

value: GC B cells

value: post infection day 36


title: Skin_Fibroblast_sh_NC3

value: Human skin fibroblast

value: Interference control 3


title: Skin_Fibroblast_sh_HuR1

value: HUR gene interference treatment 1


title: Skin_Fibroblast_sh_NC2

value: Interference control 2


title: KO4


title: Skin_Fibroblast_sh_NC1

value: Interference control 1


title: ELNAT1 5637

value: ELNAT1 was overexpressed in 5637 cells

value: 5637 cells were infected by lentivirus using pcDNA3.1 ELNAT1 to obtain stable expression cell  lines.


title: Skin_Fibroblast_OE_HuR3

value: HUR gene overexpression treatment3


title: Vector T24

value: Negative control

value: T24 cells were infected by lentivirus using vector to obtain stable expression cell  lines.


title: KO2

value: Zfp36l1(fl/fl) CD79a-cre cKO


title: KO3

value: 8 to 11 weeks


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B11_AD008

value: brain

value: SSp

value: ACA

value: male


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B11_AD007


title: Skin_Fibroblast_OE_HuR2

value: HUR gene overexpression treatment2


title: KO1

value: Female

value: Peripheral and mesenteric LN

value: LN CD19+ B cells


title: WT6

value: Zfp36l1(fl/fl) control


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B11_AD012

value: female


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B11_AD006

value: MOp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B11_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B12_AD001


title: HSC_day6_ctrl_set3

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

description: CD34+ cells sorted by flow cytometry

data_processing:
The quality of single-end reads with FASTQC (version 0.11.8) was first evaluated to remove adapters, known artifacts
quality trimmed (PHRED quality score <10) reads with BBDUK from BBTOOLS (version 37.53) were filtered
Reads that became too short after trimming (N<60 bp) were discarded
Transcript-level quantification of cleaned mRNA-seq data was estimated using SALMON (version 1.0.0) by a quasi-mapping on the human reference gene annotation GDC.h38 GENCODE v22
Genome_build: GDC.h38 GENCODE v22
Supplementary_files_format_and_content: SALMON - format - .sf - TMM and read counts

source_name: Umbilical Cord blood

growth_protocol: CD34+ hematopoietic stem cell are culture for 6 days with Stemline II media (sigma) and Thrombopoietin(100ng/ml), FLT-3(100ng/ml), IL-3(50ng/ml), SCF(150ng/ml)

extract_protocol:
Cultured cells were harvested, and CD34+ cells were sorted by flow cytometry. Total RNA was isolated  using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols with Ribozero depletion

treatment_protocol: CD34+ hematopoietic stem cells wer cultured in the absence or presence of valproic acid (VPA)

value: CD34+ hematopoietic stem cell

tag: culture condition

value: Stemline II media (Millipore Sigma)

tag: cytokine cocktail

tag: valproic acid 1mm stimulation


title: HSC_day6 _vpa_set3

description: CD34+ cells sorted by flow cytometry

value: Thrombopoietin(100ng/ml), FLT-3(100ng/ml), IL-3(50ng/ml), SCF(150ng/ml)


title: HSC_day6 _vpa_set2

description: CD34+ cells sorted by flow cytometry


title: HSC_day6 _vpa_set1

description: CD34+ cells sorted by flow cytometry


title: WT5

tag: genotype


title: Skin_Fibroblast_OE_NC3

value: Human skin fibroblast

value: Overexpression control 3


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B11_AD002


title: Skin_Fibroblast_OE_NC2

value: Overexpression control 2


title: HSC_day6_ctrl_set2

description: CD34+ cells sorted by flow cytometry

tag: cell type


title: HSC_day6_ctrl_set1

description: CD34+ cells sorted by flow cytometry


title: WT4

value: 8 to 11 weeks


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B10_AD008

value: brain

value: SSp


title: Skin_Fibroblast_OE_NC1

value: Overexpression control 1


title: WT2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B10_AD007

value: ACA

value: male


title: MRC5-UV-24hr-IP rep2

data_processing:
Library strategy: meRIP-Seq
Clean reads were mapped to the human genome hg38 by using Bowtie2.
After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 2.8.0, an exome-based peak-calling algorithm) with default parameters (P < 1 x 10-5, FDR < 1 x 10-3, Fold Enrichment ≥ 2).
HOMER software (version 4.10) was used to de novo identify consensus motifs from the enriched m6A modification sites.
For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using BEDTools and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
Genome_build: hg38

extract_protocol:
Total RNA was extracted using Rneasy mini kit (Qiagen).
Following the instructions of the Magna MeRIP™ m6A Kit (Merck, Darmstadt, Germany), the total RNA was fragmented into ~100-nt-long oligonucleotides using fragmentation buffer under elevated temperature and validated by an Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Kit. The Magna ChIP Protein A/G Magnetic Beads were incubated for 30 min at room temperature with m6A-specific antibody in immunoprecipitation buffer. The mixture was then incubated with the MeRIP reaction mixture for 2 h at 4°C.

tag: cell line

value: normal lung tissue-derived fibroblast cells

tag: treatment

value: treated with 12J/m2 UV-C and recovered for 24 hours


title: N-RV4

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-ended reads were mapped to human hg19 genome using Tophat V2.1.1, along with the human reference annotation file from RefSeq.
Cufflinks V2.2.1 was used to assemble the transcriptome and cuffcompare was used to annotate the transcripts. DESeq2 was used to normalize the raw read counts.
Genome_build: hg19

source_name: non-disease human heart RV

extract_protocol:
Non-disease human heart RV tissue frozen in liquid nitrigen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: heart right ventricle


title: Skin_Fibroblast_OE_HuR1

value: HUR gene overexpression treatment1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B10_AD006

source_name: C57BL/6J P56 Mouse Brain

tag: strain

value: MOp

value: female


title: MRC5-UV-24hr-input rep2


title: MAF4

city: Tel Aviv Yaffo

first: Neta

last: Erez

address: Haim Levanon

department: Pathology

country: Israel

institute: Tel Aviv University

description: processed data file: Normalized_counts_RNAseq_data_2019.xlsx

data_processing:
Sequencing was performed on the Illumina HiSeq 2500 sequencer (Illumina, Inc.)
Reads were aligned to the mouse genome (mm9) using TopHat2.
Gene expression counts were calculated using HTseq-count using Gencode annotations.
Only genes that got at least 20 counts in at least one sample were included in subsequent analysis (12,105 genes).
Differential expression analysis was carried out using DESeq2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Normalized_counts_RNAseq_data_2019.xlsx: Excel file, 12105 genes included for subsequent analysis.

source_name: Macro metastasis bearing lung fibroblasts

growth_protocol: All animals were maintained within the Tel Aviv University specific pathogen free (SPF) facility.

extract_protocol:
Trizol LS reagent (Life Technologies; 10296-028) and RNA was isolated according to the manufacturer’s instructions.
Transcriptomic sequencing of RNA was performed using NEBNext® rRNA Depletion Kit (New England Biolabs, Inc.; E6310S) and SMARTer Stranded Total RNA-Seq Kit - Pico Input (Clontech; 635005).

value: Lung fibroblasts

tag: metastatic stage

value: Macro-metastasis


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B10_AD004

tag: tissue


title: MAF3


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B10_AD002

tag: age


title: MRC5-UV-24hr-IP rep1


title: MRC5-UV-24hr-input rep1


title: N-RV1


title: N-LV6

source_name: non-disease human heart LV

extract_protocol:
Non-disease human heart LV tissue frozen in liquid nitrigen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: heart left venticle


title: MAF2

tag: genotype/variation


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_B10_AD001

tag: source


title: MRC5-UV-3hr-IP rep2

value: treated with 12J/m2 UV-C and recovered for 3 hours


title: N-LV5


title: MAF1


title: MRC5-UV-3hr-input rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A9_AD012

tag: target


title: MIF3

source_name: Micro metastasis bearing lung fibroblasts

value: Micro-metastasis


title: N-LV4


title: N-RV5


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A9_AD008

tag: gender


title: MRC5-UV-3hr-IP rep1


title: WT1

value: Zfp36l1(fl/fl) control

value: 8 to 11 weeks

tag: Sex

value: Female

value: Peripheral and mesenteric LN

value: LN CD19+ B cells


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A9_AD007

value: brain

value: SSp

value: ACA

value: male


title: N-RV3

value: heart right ventricle


title: MIF2


title: N-LV3


title: MRC5-UV-3hr-input rep1

value: normal lung tissue-derived fibroblast cells


title: MIF1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A9_AD006

value: MOp

value: female


title: N-LV2


title: NLF4

source_name: Normal lung fibroblasts

value: Lung fibroblasts

value: Normal


title: N-LV1

value: heart left venticle


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A9_AD002


title: MRC5-UV-30min-input rep2

value: treated with 12J/m2 UV-C and recovered for 30 minutes


title: NLF3


title: MRC5-UV-30min-input rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A9_AD001


title: NLF2


title: pie1-MNase-2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
MNase-reads were aligned to the TAIR10 genome assembly using bowtie1 version 1.1.1 with parameters -v 2 -m 1  -3 42
nucleosome reads were generated by the midpoint of insertion segment
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

organism: Arabidopsis thaliana

source_name: 147bp DNA digested by Mnase enzyme

growth_protocol: seeds were grown on MS plates with a 16 h light/8 h dark photoperiod at 22ºC for 12 days and harvested for the next-step experiment

extract_protocol:
12-day-old seedling were collected. Nucleosome were extracted and cut by Mnase enzyme. 147bp DNA were extracted for library construction.
libraries were prepared for MNase-seq

value: Arabidopsis seedlings


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A8_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A8_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A8_AD006


title: MRC5-CON-IP rep1

source_name: Fibroblast cells

value: untreated


title: mbd9-MNase-1


title: MRC5-CON-input rep2


title: MRC5-CON-input rep1


title: MRC5-UV-30min-IP rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A7_AD008


title: N-RV2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A7_AD007


title: WT-MNase-2

value: wild type


title: MRC5-UV-30min-IP rep1


title: chr1117-MNase-2


title: WT-MNase-1


title: MRC5-CON-IP rep2


title: pie1-MNase-1


title: HEK.rep3_miCLIP

description: miCLIP

data_processing:
miCLIP reads with identical random barcodes (position 1-3, 8-10), representing PCR products, were filtered.
The adapter sequence ‘AGATCGGAAGAGCGGTTCAG’ was removed using cutadapt (options -O 4 -e 0.06). Only reads with a minimal length of 18 nt were retained.
miCLIP reads were mapped to the human reference genome (hg19/GRCh37) by using bowtie with parameters -m 1 -v 1 --best --strata to select uniquely mapping reads allowing one mismatch.
Methylation sites were inferred from miCLIP read truncation positions by assigning the read counts to the closest cytosine within +/- 2 nt of the truncation site.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with miCLIP stop positions

source_name: human embryonic kidney 293 cells

extract_protocol:
For miCLIP, myc-tagged NSun6 constructs were transfected into HEK293 cells which were harvested 24 hours post-transfection. Cells were then lysed in lysis buffer and treated with high concentration of DNase and low concentration of RNaseI to partially fragment RNAs. Lysates were incubated with proteinG dynabeads in the presence of anti-myc antibody to isolate NSUN-RNA complexes. Libraries were then prepared following isolation of RNAs from the protein-RNA complexes.
Libraries were prepared using Illumina TruSeq RNA prep kits

value: Control (Wild-type)

tag: rip antibody

value: anti c-myc 9E10

tag: rip antibody manufacturer

value: Sigma; catalog number M4439


title: NLF1


title: MRC5-RNA-UV_3 hr rep2

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, poly-N and low quality reads.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

extract_protocol:
Total RNA was harvested using RNeasy mini kit (Qiagen). NEBNext® Ultra™ RNA Library Prep Kit (Cat#E7530L) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: treated with 12J/m2 UV-C and recovered for 3 hours


title: chr1117-MNase-1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A7_AD002

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: brain

value: ACA


title: mbd9-MNase-2


title: MRC5-RNA-UV_3 hr rep1


title: HEK.rep2_miCLIP

description: miCLIP


title: HEK.rep1_miCLIP

description: miCLIP


title: MRSA stimulated aza-derivative rep2

city: Padova

first: PAOLA

last: BRUN

state: PD

address: via Gabelli

department: Molecular Medicine

country: Italy

institute: Università di Padova

data_processing:
100 nucleotides of sequence was determined from both ends of each cDNA fragment using the NextSeq platform (Illumina)
Sequencing reads were annotated and aligned to the USA300 MRSA reference genome using TopHat.
results produced were checked against the Uniprot Knowledge base (https://www.uniprot.org)
Genome_build: USA300
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample, table with log2FoldChanges

organism: Staphylococcus aureus

growth_protocol: 1x10^6 CFU/ml bacteria were grown for 16 hours

extract_protocol:
Bacteria were collected by centrifugation (3000 rpm, 5 min) and total RNA was isolated and purified from the bacterial pellets using the GRS Total RNA Kit – Bacteria (#GK16.0100, GRISP Research Solution) following the manufacturer’s instructions. RNA-seq libraries were prepared with the TruSeq RNASample Prep kit (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: control samples were incubated for 16 hrs with DMSO 0.05%; stimulated samples were incubated with aza-derivative 100 microM for 16 hrs

value: aza-derivative 100 microM, 16 hrs


title: MRSA stimulated aza-derivative rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A7_AD001

value: male


title: MRC5-RNA-UV_24 hr rep2

value: normal lung tissue-derived fibroblast cells

value: treated with 12J/m2 UV-C and recovered for 24 hours


title: MRSA control rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD012

value: SSp

value: female


title: MRC5-RNA-UV_30 min rep1


title: MRC5-RNA-UV_30 min rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD010


title: MRSA control rep1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A7_AD004

value: MOp


title: Total RNA-seq sgNSD3 Sample 3

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

institute: University of Macau

data_processing:
RNA-seq: Hisat2, FeatureCounts
Cut&Run Seq: CUT&RUNtools, ngs.plot
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2_normalized_log2_exp.txt, cut_run_geneobody_peak_norm.txt

source_name: tumor-derived cells with sgNSD3

growth_protocol: Mose tumor-derived cells were growed in DMEM media complemented with 10% FBS and 1% Pen-Strep on coated culture dishes. Cells were passaged at 1:8 ratio every 3 days.

extract_protocol:
Mnase-digested DNA from specific antibody bound nucleosmes in native state were released by diffusion.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: Mouse tumor-derived cells were treated with either control sgRNA or sgRNA against NSD3

value: mouse tumor-derived cells

tag: passages


title: MRC5-RNA-UV_24 hr rep1


title: SgControl_IgG

data_processing:
Library strategy: CUT&RUN
Hisat2
FeatureCounts
CUT&RUNtools
Genome_build: mm10
Supplementary_files_format_and_content: text file. DEGs of Control vs. KO.

source_name: tumor-derived cells with sgControl

tag: antibody


title: SgNSD3_IgG


title: MRC5-RNA-CON rep2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD007


title: MRC5-RNA-CON rep1


title: Total RNA-seq sgNSD3 Sample 2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD006


title: F - Differentiating CD34+ cells

city: Aurora

first: George

middle: Devon

last: Trahan

state: CO

address: 1635 Aurora Ct

department: The Department of Pediatrics Section of Hematology, Oncology and Bone Marrow Transplantation

institute: University of Colorado Anschutz Medical Campus

data_processing:
Basecalls performed using RTA v3.3.3
Reads were aligned to the GRCh38 transcriptome assembly using STAR aligner via Cell Ranger v2.0.0
Cell barcodes were filtered by removing cells with less than 250 unique genes
Samples were aggregated and processed further within an R environment via Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: Gzipped tar archives containing the results (count matrices, barcode lists, and feature lists) produced by Cell Ranger

source_name: Cord blood CD34+ cells

growth_protocol: The CD34+ cells (purity, >95%) were suspended (5x104 cells/ml) in Stemspan II cell culture media (Stemcell) supplemented with 1% penicillin + streptomycin, stem cell factor (SCF, 100 ng/ml, R&D), FMS-like tyrosine kinase 3 (Flt3L, 100 ng/ml, Stemcell), thrombopoietin (TPO, 50 ng/ml, R&D) and low density lipoprotein (LDL, 10 µg/ml, Stemcell) and cultured in 24 well plates for 5 days of expansion. After 5 days of culture, the expanded cells were considered for up to 23 dys of differentiation, cells were cultured in B0 differentiation media (as previously described (25)), supplemented with SCF (20 ng/ml, R&D Systems), IL-3 (5 ng/ml, Stemcell), IL-7 (20 ng/ml, R&D), IL-15 (10 ng/ml, NIH), IL-23 (10 ng/ml, R&D) and Flt3L (10 ng/ml, Stemcell).

extract_protocol:
5 days expanded CD34+ HSCs were FACS sorted into 4 different subsets including CD34+α4β7+CD48+/- and CD34+α4β7+CD48+CD52+/- for scRNAseq. The CD34+α4β7+CD48-CD52+ and CD34+α4β7+CD48+CD52+ were also differentiated into NK cells followed by scRNA seq of FACS sorted CD56+CD94+ NK cells. scRNA seq was also performed on differentiating CD34+ cells.
Libraries were prepared according to 10x Genomics Chromium Single Cell 3' Reagent Kits v2 documentation

value: Cord blood CD34 derived progenitors, ILCs and NK cells

tag: days of differentiation

tag: culture

value: in vitro differentiated


title: D - Differentiating CD34+ cells

tag: cell type


title: E14 vs E18 tooth molar germ

city: Kobe

first: Masato

last: Nakagawa

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

hyb_protocol: Array hybridization were performed according to standard protocols at the DNA Chip Research Inc using Agilent Gene Expression Wash Pack.

scan_protocol: Scanned on an Agilent DNA MicroArray scanner.

data_processing: Agilent Feature Extraction Software was used.

source_name: pooled whole mouse molar E14

label_protocol: Labeling were performed according to standard protocols at the DNA Chip Research Inc.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Samples were isolated from the first molar of the mandible at E11, 12, 14, 16, 18.

tag: day

value: whole embryic molar germ

source_name: pooled whole mouse molar E18


title: Total RNA-seq sgControl Sample 3

tag: strain

value: sgControl


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD001

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A6_AD002


title: E - Differentiating CD34+ cells


title: Total RNA-seq sgNSD3 Sample 1


title: Total RNA-seq sgControl Sample 2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD012


title: B - Differentiating CD34+ cells


title: Total RNA-seq sgControl Sample 1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD010


title: E14 vs E12 tooth molar germ

source_name: pooled whole mouse molar E12


title: C - Differentiating CD34+ cells


title: CD34+α4β7+CD48-CD52+-derived CD56+CD94+ NK cells

value: Cord blood CD34 derived NK cells


title: H3K36me2A sgNSD3 Sample 2

data_processing:
library strategy: Cut&Run Seq
RNA-seq: Hisat2, FeatureCounts
Cut&Run Seq: CUT&RUNtools, ngs.plot
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2_normalized_log2_exp.txt, cut_run_geneobody_peak_norm.txt


title: H3K36me2A sgNSD3 Sample 1


title: E14 vs E16 tooth molar germ

source_name: pooled whole mouse molar E16


title: CP20, replicate 2

city: San Juan

first: Pablo

middle: E

last: Vivas-Mejía

state: PR

address: Medical Sciences Campus

department: Cancer Medicine

country: Puerto Rico

institute: University of Puerto Rico Cancer Center

hyb_protocol: Array hybridization and analysis was performed by the Genomics Core Facility at Brown University.

scan_protocol: Affymetrix

data_processing: Analysis was conducted on Partek's Genomics Suite 6.6 version software.

source_name: CP20 cell line

label_protocol: Total RNA was biotin-labeled following the FlashTag Biotin HSR RNA labeling kit manufacturer’s instructions.

growth_protocol: Cells were grown on RPMI1640 supplemented with 10% FBS and 1% antibiotics. All cells were kept at 37°C and 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from ovarian cancer cells using the mirVana miRNA Isolation Kit.

value: Cisplatin-resistant ovarian cancer cell


title: CP20, replicate 1


title: E14 vs E11 tooth molar germ

source_name: pooled whole mouse molar E11


title: PARP-inhibitor sensitive AsPC vs resistant AsPC  (2369S vs 2367R)

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Normalized log10 ratio (Cy3/Cy5) representing test/reference for samples 2301 R  –  2354 S, 2351 R  –  2309 S, 2317 R  –  2314 S, 2343 R  –  2284 S, 2343 R  –  2284 S, 2358 R  –  2355 S, and 2367 R  –  2369 S; normalized log10 ratio (Cy5/Cy3) representing test/reference for samples 2354 S  –  2301 R, 2309 S  –  2351 R, 2314 S  –  2317 R, 2284 S  –  2343 R, 2355 S  –  2358 R, and 2369 S  –  2367 R

source_name: AsPC 2369 sensitive cell line

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: AsPCs were grown in ovarian surface epithelial (OSE) growth medium (representing 1:1 mix of Media 199 (Sigma-Aldrich, St. Louis, MS, USA) and MCDB 105 (Sigma-Aldrich, St. Louis, MS, USA), with the addition of 25 μg/mL gentamicin and 2.5 μg/ml fungizone, and supplemented with 10% heat inactivated fetal bovine serum. Cells were grown as spheroids cells n hanging drop plates and left in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: AsPCs spheroids in hanging drops were exposed to increasing concentrations of either olaparib (AZD-2281)-(AstraZeneca, Wilmington, DE, USA) or niraparib (MK4827)-(Merck, Kenilworth, NJ, USA) at the following concentrations (0 μM, 10 μM, 50 μM and 100 μM). The AsPCs were incubated with the drugs for 72 h and  toxicity (thus sensitivity or resistance) was determined using the WST-1 assay for the hanging drop (spheroid) model.

value: ascites-derived human ovarian cancer cells

tag: phenotype

value: sensitive

source_name: AsPC 2367 resistant cell line

value: resistant


title: PARP-inhibitor resistant AsPC vs sensitive AsPC  (2367R vs 2369S)


title: PARP-inhibitor sensitive AsPC vs resistant AsPC  (2284S vs 2343R)

source_name: AsPC 2284 sensitive cell line

source_name: AsPC 2343 resistant cell line


title: CD34+α4β7+CD48+CD52+-derived CD56+CD94+ NK cells


title: PARP-inhibitor sensitive AsPC vs resistant AsPC  (2355S vs 2358R)

source_name: AsPC 2355 sensitive cell line

source_name: AsPC 2358 resistant cell line


title: PARP-inhibitor resistant AsPC vs sensitive AsPC  (2343R vs 2284S)


title: CD34+a4b7+CD48-CD52+ progenitor cells

value: Cord blood CD34 derived progenitors


title: PARP-inhibitor resistant AsPC vs sensitive AsPC  (2358R vs 2355S)


title: PARP-inhibitor sensitive AsPC vs resistant AsPC  (2314S vs 2317R)

source_name: AsPC 2314 sensitive cell line

source_name: AsPC 2317 resistant cell line


title: CIS, replicate 2

source_name: CIS cell line


title: H3K36me2A sgControl Sample 2

source_name: tumor-derived cells with sgControl


title: H3K36me2A sgControl Sample 1


title: CD34+a4b7+CD48-CD52- progenitor cells

source_name: Cord blood CD34+ cells


title: CD34+a4b7+CD48+CD52+ progenitor cells


title: A - Differentiating CD34+ cells


title: H3K27me3 sgControl

value: H3K27me3:Thermo MA5-11198


title: H3K27me3 sgNSD3

source_name: tumor-derived cells with sgNSD3


title: Rad16_0hrUV_600J_UVDEseq_rep1_A4

status: Public on Nov 19 2020

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Replicate 1

data_processing:
Library strategy: UVDE-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
FASTA file of lesion-containing dinucleotide sequence extracted using BEDTOOLS2 fastaFromBed
Damage-containing dinucleotide sequences counted using custom perl script

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures (BY4741) were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and dissolved in sterile deionized H2O.
UVDE-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444) and our own CPD-seq method. Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were repaired using purified E. coli CPD photolyase. All other UV-induced lesions were cleaved with purified T. thermophilus UVDE. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 8 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O. 20mL of BY4741 and MP072 collected for unirradiated samples. 20mL BY4741 and MP072 irradiated with 600 J/m2 UVC. After UV irradiation, cells were spun down and kept at -80˚C until genomic DNA isolation.

tag: genotype

tag: treatment

value: UV irradiated 600 J/m2

tag: repair time

value: 0 hr


title: [delta]fumAB MMS+ [alpha]-Ketoglutarate-3

city: Jerusalem

first: Ophry

last: Pines

address: Ein Kerem Campus

department: Microbiology and Molecular Genetics

institute: Hebrew university of Jerusalem

data_processing:
good quality reads were mapped using bwa(7.16v) software
the gene expression of mRNA were quantified using Stringtie tool, values were computed as: read counts, FPKM and TPM
Differential expression (DE) analysis was performed using DESeq2 tool to compare expression levels of all mRNA under different experimental conditions and the expression fold change between each comparison group was calculated and log-transformed.
mRNA with expression fold change ≥2 and p-adjusted <0.01 were selected as statistically significant differentially expressed.
Genome_build: using BWA v7.6 tool, quality filtered sequences were then mapped to Escherichia coli BW251153 (WT) reference genome (accession number: CP009273) obtained from GenBank.
Supplementary_files_format_and_content: FPKM    TPM     read_count

organism: Escherichia coli

source_name: DfumAB MMS+ α-Ketoglutarate-3

growth_protocol: Bacteria were grown to early exponential phase (OD600nm=0.3) in LB medium or LB medium supplemented with 25mM α-Ketoglutaric acid with phosphate buffer (PH=6.8)

extract_protocol:
total RNA purification kit from Norgen Biotek Corp followed by Ribo-zero bacteria and mRNA library prep kit
according to the manufacturer’s instructions

treatment_protocol:
0.35% [v/v] MMS, 30 min, 37*C, 200rpm
or 0.35% [v/v] MMS+25mM α-Ketoglutaric acid, 30 min, 37*C, 200rpm

value: [delta]fumAB

value: treated-0.35% methylmethansulfonate+ 25mM [alpha]-Ketoglutaric acid


title: [delta]fumA MMS+ [alpha]-Ketoglutarate-3

source_name: DfumA MMS+ α-Ketoglutarate-3

value: [delta]fumA


title: BW25113 (WT) MMS+ [alpha]-Ketoglutarate-3

source_name: BW25113 (WT) MMS+ α-Ketoglutarate-3


title: [delta]fumB MMS+ [alpha]-Ketoglutarate-3

source_name: DfumB MMS+ α-Ketoglutarate-3

value: [delta]fumB


title: CIS, replicate 1


title: CD34+a4b7+CD48+CD52- progenitor cells


title: PARP-inhibitor resistant AsPC vs sensitive AsPC  (2317R vs 2314S)


title: [delta]fumAB-3

value: untreated


title: WT rep1

city: Jinan

first: Xueying

last: Gao

address: Jingliu Rd.

institute: Shandong University

data_processing:
We used Bowtie2 (v1.2.8) to  align the clean data to the reference gene sequences and the gene  expression levels were quantified by RSEM (v1.2.8).
Differentially  expressed genes (DEGs) were identified using DEGseq2.
Genome_build: GRCh38

source_name: starved NCI-H295R cells

extract_protocol:
Total RNA was extracted from cultured NCI-H295R cells grown  under serum starvation and NAM conditions using TRIzol Reagent  according to the manufacturer's instructions (Takara Bio).
RNA   was then enriched using Oligo (dT) magnetic beads (Invitrogen).  Following fragment screening, library building, and PCR product  purification, the samples were sequenced on a BGISEQ-500  platform at the BGI Bioinformatics Corporation

tag: cells

value: adrenocortical cells

value: distilled water


title: WT rep2


title: NAM rep2

value: NAM


title: PARP-inhibitor sensitive AsPC vs resistant AsPC  (2309S vs 2351R)

source_name: AsPC 2309 sensitive cell line

source_name: AsPC 2351 resistant cell line


title: PARP-inhibitor resistant AsPC vs sensitive AsPC  (2351R vs 2309S)


title: PARP-inhibitor resistant AsPC vs sensitive AsPC  (2301R vs 2354S)

source_name: AsPC 2301 resistant cell line

source_name: AsPC 2354 sensitive cell line


title: PARP-inhibitor sensitive AsPC vs resistant AsPC  (2354S vs 2301R)


title: A2780, replicate 2

source_name: A2780 cell line

value: Cisplatin-sensitive ovarian cancer cell


title: [delta]fumB-3


title: NAM rep1


title: [delta]fumACB MMS+ [alpha]-Ketoglutarate-2

source_name: DfumACB MMS+ α-Ketoglutarate-2

value: [delta]fumACB


title: [delta]fumAB MMS+ [alpha]-Ketoglutarate-2

source_name: DfumAB MMS+ α-Ketoglutarate-2


title: Rad16_NoUV_UVDEseq_rep1_A3

description: Replicate 1


title: BW25113 (WT) MMS+ [alpha]-Ketoglutarate-2

source_name: BW25113 (WT) MMS+ α-Ketoglutarate-2


title: WT_0hrUV_600J_UVDEseq_rep1_A2

description: Replicate 1

value: Wild-type


title: WT_NoUV_UVDEseq_rep1_A1

description: Replicate 1


title: [delta]fumACB MMS+ [alpha]-Ketoglutarate-3

source_name: DfumACB MMS+ α-Ketoglutarate-3


title: [delta]fumACB MMS-2

source_name: DfumACB MMS-2

value: treated-0.35% methylmethansulfonate


title: [delta]fumB MMS-2

source_name: DfumB MMS-2


title: [delta]fumB-2


title: [delta]fumA-2


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A7_AD010

city: La Jolla

first: Joseph

last: Ecker

source_name: C57BL/6J P56 Mouse Brain

tag: age

tag: tissue

value: brain

tag: source

value: SSp

tag: target

value: ACA

value: female


title: [delta]fumACB MMS-3

source_name: DfumACB MMS-3


title: [delta]fumAB MMS-3

source_name: DfumAB MMS-3


title: A2780, replicate 1


title: [delta]fumB MMS-3

source_name: DfumB MMS-3


title: BW25113 (WT) MMS-3


title: BW25113 (WT)-2


title: [delta]fumACB-3


title: [delta]fumA MMS+ [alpha]-Ketoglutarate-2

source_name: DfumA MMS+ α-Ketoglutarate-2


title: [delta]fumAB MMS+ [alpha]-Ketoglutarate-1

source_name: DfumAB MMS+ α-Ketoglutarate-1


title: [delta]fumA MMS+ [alpha]-Ketoglutarate-1

source_name: DfumA MMS+ α-Ketoglutarate-1


title: [delta]fumA-3


title: BW25113 (WT)-3


title: BW25113 (WT) MMS-1


title: [delta]fumACB MMS-1

source_name: DfumACB MMS-1


title: [delta]fumA MMS-1

source_name: DfumA MMS-1


title: [delta]fumAB MMS-2

source_name: DfumAB MMS-2


title: [delta]fumB MMS+ [alpha]-Ketoglutarate-2

source_name: DfumB MMS+ α-Ketoglutarate-2


title: [delta]fumA MMS-2

source_name: DfumA MMS-2


title: [delta]fumA-1


title: [delta]fumA MMS-3

source_name: DfumA MMS-3


title: BW25113 (WT)-1


title: BW25113 (WT) MMS-2


title: [delta]fumACB-2


title: [delta]fumAB-2


title: BW25113 (WT) MMS+ [alpha]-Ketoglutarate-1

source_name: BW25113 (WT) MMS+ α-Ketoglutarate-1


title: WTCD8N

city: Xi’an

first: Anjun

last: Jiao

state: Shaanxi

address: No. 28, Xianning West Road, Xi'an City, Shaanxi Province

institute: Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University

data_processing:
After filtering the raw reads containing adapters or low quality bases, 50 bp paired-end ATAC-Seq clean reads from each sample were aligned to the ensemble mouse genome (GRCm38) with bowtie using Bowtie2 (version 2.2.8)
For all data files duplicates were removed using Picard. ATAC-SEQ peak regions were called by MACS (version 2.1.2) with parameters “--nomodel --shift -100 --extsize 200 -B -q 0.05” and filtered to remove putative copy number altered regions
Genome_build: Ensembl release87
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: peak text files

source_name: Naïve CD8+T cells

extract_protocol:
Purified cells were washed in cold PBS and lysed using ATAC-Seq lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and NP-40) on ice for 10 min. Nuclei suspensions were incubated in transposition mix buffer including 2.5μl Nextera Tn5 transposase at 37°C for 30 min
Immediately following transposition, the transposed DNA fragments were purified using a QIAGEN minielute kit, sequenced using Illumina HiSeqTM 4000 with 30 million pairs.

treatment_protocol: 5×104 naïve CD8+ T cells (CD44-CD62+) were sorted from CD4Cre+Dhx9f/f mice and wild-type littermates. 5×104 effector CD8+ T cells (CD44+CD62-) were sorted from LCMV-Armstrong-infected CD4Cre+Dhx9f/f mice and wild-type littermates on day 8 post-infection

value: spleen

value: Naive CD8+T cells

value: wildtype


title: KOCD8E

source_name: Effector CD8+T cells

value: CD8 T cells from the spleens 8 days post infection


title: DHX_2

description: CD8 T cells from the spleens 8 days post infection

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36)
ChIP-seq reads were aligned to the mm9 genome assembly using STAR software (version 2.5.3a) with default parameters
The RSeQC（version 2.6）was used for reads distribution analysis
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The Homer（version 4.10）was used for motifs analysis
Genome_build: mm9
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: peak bam files
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: peak text files

source_name: CD8+T cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: CD44+CD62- effector CD8+ T cells were sorted from the spleens of LCMV-Armstrong-infected CD4Cre+Dhx9 f/f mice and wild-type littermates

value: CD8+T cells


title: DHX_1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD007

source_name: C57BL/6J P56 Mouse Brain

tag: gender

value: male


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD004

value: MOp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD008


title: wt_colon

city: Zürich

first: Michael

middle: David

last: Brügger

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zürich

data_processing:
The sequencing libraries were de-multiplexed, aligned to the mouse transcriptome (mm10) and unique molecular identifiers (UMI) were counted using Cell Ranger (10x Genomics) version 3.0.1
Further data analysis was performed using the Seurat package version 3.1 (Butler et al., 2018) in R version 3.6.2.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are read abundance measurements in tab-delimited txt format with genes and barcode sequences corresponding to row and column indices

molecule: polyA RNA

source_name: Intestinal mesenchymal and epithelial cells

extract_protocol:
Colonic tissue was harvested, minced into small pieces (2mm) and subsequently washed with PBS. Tissue pieces were then incubated in Gentle Cell Dissociation Reagent (STEMCELL Technologies) for 30 minutes at room temperature to detach the epithelium. The epithelial fraction was then filtered through a Falcon 70 µm cell strainer (Corning), washed with plain ADMEM/F12 and incubated for 5 minutes at 37 °C in prewarmed TrypLE express (Gibco), followed by single cell dissociation using the m_intestine program on the gentleMACS Octo Dissociator (Miltenyi Biotec). The epithelial single cell suspension was then filtered through a Falcon 40 µm cell strainer (Corning) and stored on ice in ADMEM/F12 (supplemented with 10% FBS). After the detachment of the epithelium the remaining tissue pieces were digested for 1 hour at 37°C under 110 rpm shaking conditions in DMEM supplemented with 2mg/mL collagenase D (Roche) and 0.4 mg/mL Dispase (Gibco). The mesenchymal fraction was then filtered through a Falcon 70 µm cell strainer (Corning), washed with plain ADMEM/F12 and subsequently filtered through a Falcon 40 µm cell strainer (Corning). Both epithelial and mesenchymal cells were stained for 30 minutes on ice with anti-CD45-PE (1:500, eBioscience) and anti-CD326(EpCAM)-FITC (1:500, eBioscience) in ADMEM/F12 (supplemented with 10% FBS). Prior to cell sorting, all cells were stained for 5 minutes on ice with Zombie Violet Fixable Viability Kit in PBS (1:1000, Biolegend). In the case of mesenchymal cell isolation from PdgfraH2BeGFP mice only staining with Zombie Violet Fixable Viability Kit was performed. Cells were detected and sorted at the Cytometry Facility at the University of Zürich using a FACSAria III cell sorter (Gates visible in corresponding Figures) (BD Biosciences).
Library preparation was performed according to the manufacturer’s indications (Chromium Next GEM Single Cell 3ʹ Reagent Kits v2 (PdgfraEGFP) or v3 (wt_colon) protocol)

value: colon

tag: celltype

value: mesenchymal & epithelial


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD001

department: Genomic Analysis Laboratory


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD007


title: [delta]fumACB MMS+ [alpha]-Ketoglutarate-1

source_name: DfumACB MMS+ α-Ketoglutarate-1

value: treated-0.35% methylmethansulfonate+ 25mM [alpha]-Ketoglutaric acid


title: [delta]fumB MMS+ [alpha]-Ketoglutarate-1

source_name: DfumB MMS+ α-Ketoglutarate-1

value: [delta]fumB


title: pdgfraegfp_colon

source_name: Intestinal mesenchymal cells

value: mesenchymal


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD004


title: [delta]fumAB MMS-1

source_name: DfumAB MMS-1

value: [delta]fumAB

value: treated-0.35% methylmethansulfonate


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A2_AD007

value: brain

value: SSp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A2_AD006

value: ACA

value: female


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A2_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A1_AD010


title: [delta]fumB MMS-1

source_name: DfumB MMS-1


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A1_AD012


title: [delta]fumAB-1

value: untreated


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A1_AD008


title: [delta]fumB-1


title: WTCD8E

value: spleen

value: wildtype


title: KOCD8N

value: Naive CD8+T cells


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A12_AD007

value: male


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A12_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A1_AD001

value: MOp


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A12_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A12_AD002


title: Input_2

value: CD8+T cells

tag: antibody


title: Input_1


title: [delta]fumACB-1

value: [delta]fumACB


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A4_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A2_AD008


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A1_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A2_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A1_AD002


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H9_AD007

value: AI


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H9_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H9_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A12_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A2_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A12_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD012


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD004


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H7_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H9_AD010


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD007


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD001


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD006


title: 180503_CEMBA_mm_P56_P63_RS2_180503_P1_180503_P2_A11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H2_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H2_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H12_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_H10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_G10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F3_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F3_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F3_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F3_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F12_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F12_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F11_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F11_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F10_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD007


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F10_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E8_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD002


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_F10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E6_AD008


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E6_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E6_AD001


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E5_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E5_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E4_AD007


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E3_AD008


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E3_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E3_AD001


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E12_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P7_180419_P8_E12_AD004