title: DPeP300_07 [S447.07]

value: fetal testis

value: Sprague Dawley

value: wild type

value: 300 mg/kg/d DPeP


title: RMS_ESC_B

status: Public on Jan 16 2025

type: SRA

city: Houston

first: Eric

last: Van Nostrand

state: TX

address: 1 Baylor Plaza Rm T334

department: Therapeutic Innovation Center

country: USA

institute: Baylor College of Medicine

description: RiboMeth-seq from mouse embryonic stem cells, biological replicate 2

library_source: transcriptomic

data_processing:
Adapter trimming was performed using either trim_galore or cutadapt.
Mapping was performed using bowtie2 with --end-to-end -k 1 options.
Mapped bam files were converted to bed using bedtools bamtobed then 5' and 3' end counting was performed using "awk '{print $2}' RMS_${sample}.bed | sort | uniq -c | awk '{print $2, $1}' | sort -n > RMS_${sample}.5count.txt" and "awk '{print $3}' RMS_${sample}.bed | sort | uniq -c | awk '{print $2, $1}' | sort -n > {.}.3count.txt"
RMS meth score was calculated considering weighted 5' or 5'+3' counts of neighboring 12 nucleotides as described in Birkedal et al. 2014.
Assembly: Reads were mapped to 45S rRNA (NR_046233.2) and U2 snRNA (NR_004414.1).
Supplementary files format and content: Tab delimited text file containing end counts (5' only or 5' and 3') and the calculated RMS score at each nucleotide position in 45S rRNA or U2 snRNA for each of the replicate RMS libraries. Mean RMS scores are also provided.
Library strategy: RiboMeth-seq

molecule: total RNA

organism: Mus musculus

source_name: ESC

growth_protocol: mESCs were maintained on plates pre-coated with 0.2% gelatin in DMEM (Thermo) supplemented with 10 mM HEPES (Thermo), 0.11 mM β-mercaptoethanol (Sigma), 1X nonessential amino acids (Corning), 2 mM L-glutamine (Corning), 15% fetal bovine serum (Cytivia), and 1000 U/mL leukemia inhibitory factor (LIF; Sigma).

extract_protocol:
Total RNA was extracted using Trizol.
150 to 250 ng of DNase-treated RNA was hydrolyzed in 50 mM sodium bicarbonate buffer (pH 9.2) for 1 to 12 minutes. The hydrolysis reaction was quenched in 1 mL EtOH containing 10 uL 3 M NaOAc, pH 5.2 (Thermo) and 15 ug Glycoblue coprecipitant (Thermo) and submerged in liquid nitrogen. Hydrolyzed RNA was then precipitated and washed in 80% EtOH. The intended fragment size of around 50-100 bp was verified on the TapeStation 4200 system (Agilent). RNA was dephosphorylated by Antarctic Phosphatase (New England Biolabs) for 30 minutes at 37°C, and end-repaired by T4 PNK (New England Biolabs) in the presence of 1 mM ATP (New England Biolabs) for 1 hour at 37°C. End-repaired RNA was purified using RNA Clean & Concentrator-5 columns (Zymo). Illumina libraries were then prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (New England Biolabs) and purified on NucleoSpin® Gel and PCR Clean-up columns (Takara Bio).

treatment_protocol: For ASO experiments, mESC were first subject to in vitro neuron differentiated followed by free uptake of ASO, as follows. mESC were cultured for 24 hours on gelatin-coated plates in neuron differentiation media [BrainPhys neuronal medium (Stem Cell Technologies) supplemented with 1X NeuroCult SM1 (Stem Cell Technologies), 1X N2 supplement (Thermo), 20 ng/mL brain-derived neurotrophic factor (Stem Cell Technologies)] containing 1 μg/mL doxycycline (Sigma) to induce Ngn2 expression. Then, cells were re-plated onto 0.1% PEI coated dishes in neuron differentiation media containing 1 ug/mL doxycycline (Sigma). Within 24 hours of re-plating, 5-10-5 MOE gapmer ASOs (IDT) were added to the culture media at a final concentration of 10 uM to allow for free uptake by the neurons. RNA was extracted 72 to 96 hours after addition of the ASO using TRIzol (Thermo). The ASO sequences were Snord101 ASO 5’-GGGTATCCGACAATTCAAGT-3’ and Snord89 ASO 5’-TGACTCGCTTCAGGAGGTTT-3’.

tag: cell line

value: ESC

tag: cell type

tag: treatment


title: ISO_SON_2

city: Nijmegen

first: Dyah

middle: Winiarty

last: Karjosukarso

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp v0.23.2
The trimmed reads were mapped to the human GRCh38.p13  (Homo_sapiens.GRCh38.dna.primary_assembly.fa) reference provided in the References directory. The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (STAR2 v2.7.10) with default settings.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v2.0.2. T
Differential expression analysis was performed using DESeq2 v1.39.8)
Differential splicing analysis was carried out by utilizing Leafcutter v0.2.9.
Assembly: hg38
Supplementary files format and content: tab delimited file of counts

organism: Homo sapiens

source_name: retinal organoids

extract_protocol:
Total RNA was isolated using Nucleospin RNA Mini kit (Macherey Nagel) following manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The  sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep  Kit for Illumina" (NEB #E7760S/L). Briefly, rRNA was depleted from total RNA using the Qiagen fast select kit  (#334376). After fragmentation of the rRNA reduced RNA, a cDNA synthesis was performed. This was used for  ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield  after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the  resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: retinal organoids

tag: genotype

value: SON


title: Treg.spleen#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Spleen

extract_protocol: For freshly-isolated samples, 500-1000 cells were double-sorted into 5ul TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich). For whole-tissue RNA-seq  , the tissues were harvested and lysed in QIAzol followed by RNA isolation according to the manufacturer's protocol and 2 ng RNA were resuspended in 5 microliters of TCL buffer containing 1% 2-mercaptoethanol. Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

tag: tissue

value: Spleen

value: Treg cell


title: PAT_SON_1

value: ABCA4 c.768T


title: Female.Tregs#1

source_name: Meninges

value: Meninges


title: RMS_ESC_A

description: RiboMeth-seq from mouse embryonic stem cells, biological replicate 1


title: DPeP1_09 [S447.09]

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

data_processing:
The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Sequence reads were trimmed using Trimmomatic v0.36 and mapped using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
The Voom Normalize module in GenePattern was used to normalize the entire dataset for downstream analysis in BMDExpress2.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files with read counts

organism: Rattus norvegicus

source_name: fetal testis

growth_protocol: Rat fetal testes obtained from timed pregnant Sprague Dawley rats on gestational day (GD) 21.

extract_protocol:
Total RNA was extracted using the Zymo Research Quick-RNA MicroPrep Kit per manufacturer's instructions, including DNase treatment. 1-2 testes from fetuses in the same litter were pooled for each RNA sample.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA), with polyA selection for mRNA enrichment.

treatment_protocol: Timed pregnant rats were treated with dipentyl phthalate (DPeP) at doses of 1, 11, 100, or 300 mg/kg/d, or vehicle control (corn oil), a 2.5 mL/kg solution of corn oil, by oral gavage.

tag: strain

value: 1 mg/kg/d DPeP


title: GMI-24h-1

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: A549, lung cancer cells

data_processing:
The original image data were analyzed using Bcl2fastq (v2.17.1.14) for base calling and preliminary quality analysis.
Quality reads (Q20) were filtered and processed by Cutadapt (version 1.9.1).
Short-read aligment was carried out using Hisat2 (v 2.0.1) with default parameters.
Gene expression was analyzed to calculate FPKM (Fragments per kilo bases per million reads) based on read counts from HT-seq (v 0.6.1)
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include Gene_ID, Gene Symbol and FPKM value for each sample were provided.

source_name: lung cancer cell lines

growth_protocol: A549 cells were cultured in DMEM supplemented with 10 % fetal bovine serum.

extract_protocol:
Cells were washed by PBS and total RNA of each samples was extraced using Trizol reagent.
Total RNA of each sample was qualified by Agilent 2100 Bioanalyzer  (Agilent Technologies, Palo Alto, CA, USA). 1 μg total RNA with RIN value above 7 was used for library preparation with the NEBNext®  UltraTM RNA Library Prep Kit for Illumina®.

treatment_protocol: Cells were treated with GMI (0.6 μM) for 24 h.

tag: disease

value: lung cancer

tag: disease subtype

value: NSCLC

value: GMI (0.6 uM) for 24 h


title: ISO_SON_1


title: Fibrillarin IP chimeric eCLIP in mouse ESCs

data_processing:
Remove 10nt UMI from 5' end of read: umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
First adapter trimming: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.1 --quality-cutoff 6 -m 34 -a file:/storage/vannostrand/software/eclip/data/se.2.round.adapters.fasta -O 1 - --report minimal
Second adapter trimming (removes additional adapter-concatamers): cutadapt -j 8 -u -10  -o ${SampleID}.trim.gz
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping and peak calling, in order to reduce peak artifacts): STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/repbase/species_specific/homo_sapiens_repbase_v2 --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.repeat.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesCommand zcat --readFilesIn ${SampleID}.trim.fastq.gz
Unique genomic mapping (takes repeat-removed reads and maps to the genome to remove nonchimeric reads): STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.genome.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesIn ${SampleID}.trim.unmap.fastq
snoRNA mapping (takes genome-removed reads and maps to the snoRNA sequence to find putative snoRNA chimeric reads). bowtie2-build --quiet --offrate 2 /directory/snoRNA.txt.fa snoRNA.bowtie2.index 2> /dev/null. bowtie2 -D 20 -R 3 -N 0 -L 16 --local --norc -i S,1,0.50 --score-min L,16,0 --ma 1 --np o --mp 2,2 --rdg 5,1 --rfg 5,1 -p 8 --no-unal -x snoRNA.bowtie2.index -f -U ${SampleID}.mask.fasta -a -S ${SampleID}.mask.map.to.snoRNA.sam 2> ${SampleID}.mask.map.to.snoRNA.log
find putative target(takes the reads mapped to snoRNAs from previous step, if the remaining non-snoRNA fragment is longer than 18, save remaining non-snoRNA fragment to fastq files as putative target regions). We run this step with python script "split_source_map_sam" and "find_putiative_target"."split_source_map_sam" is used to split output sam file from previous step to 25 sub files, which could save the analysis duration and space occupation. find_putative_target ${SampleID}.mask.map.to.snoRNA.*.bam ZS89-IP-NOLC1.mask.map.to.snoRNA.*.target.fasta snoRNA False. All output fasta files from 25 sub sam files will then be merged together into one fasta file.
second snoRNA mapping (takes the fasta file from previous step and maps to snoRNA reference again to remove the reads led by snoRNA:snoRNA ligation). bowtie2 -D 20 -R 3 -N 0 -L 16 --local --norc -i S,1,0.50 --score-min L,12,0 --ma 1 --np o --mp 2,2 --rdg 5,1 --rfg 5,1 -p 8 --no-unal -x snoRNA.bowtie2.index -f -U ${SampleID}.mask.fasta -a -S ${SampleID}.mask.map.to.snoRNA.target.back.map.sam 2> ${SampleID}.mask.map.to.snoRNA.target.back.map.log
rRNA target mapping (takes the sam file from previous step and maps the putative target fragment to rRNA to identify rRNA interactions). bowtie-build --quiet --offrate 2 /directory/rRNA.fa rRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x rRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.rRNA.sam --un ${SampleID}.snoRNA.rRNA.unmap.fasta 2>${SampleID}.snoRNA.rRNA.log
snRNA target mapping(takes the sam file from previous step and maps the putative target fragment to snRNA). bowtie-build --quiet --offrate 2 /directory/snRNA.fa snRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x snRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.snRNA.sam --un ${SampleID}.snoRNA.snRNA.unmap.fasta 2>${SampleID}.snoRNA.snRNA.log
tRNA target mapping(takes the sam file from previous step and maps the putative target fragment to tRNA). bowtie-build --quiet --offrate 2 /directory/tRNA.fa tRNA.bowtie.index 2> /dev/null. bowtie -a --best --strata -e 35 -q -l 8 -n 1 -p 8 -x tRNA.bowtie.index --no-unal --norc -f ${SampleID}.mask.map.to.snoRNA.true.target.fasta --sam ${SampleID}.snoRNA.tRNA.sam --un ${SampleID}.snoRNA.tRNA.unmap.fasta 2>${SampleID}.snoRNA.tRNA.log
merge all unmaped fastq (takes the putative target reads that cannot mapped above reference sequence, saved as unmap.fasta in previous step, and merge them into one fasta file)
hg19 mapping (takes above merged unmap reads and maps to human genome, hg19, to capture snoRNA targets on other location). STAR --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndRemove --outBAMcompression 10 --outFileNamePrefix ${SampleID}.genome.map/ --outFilterMatchNminOverLread 0.66 --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterScoreMinOverLread 0.66 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype SAM --outSAMunmapped None --outStd Log --readFilesIn ${SampleID}.snoRNA.RNA.unmap.fasta --runMode alignReads --runThreadN 8
identify snoRNA chimeric reads (identifies the real chimeric reads if the target RNA fragments from above step meet the criteria and removes PCR duplicates.) The criteria is that the length of mapped target RNA fragment is longer than 16nt and the gap between snoRNA and target RNA is less than 4nt.  We run this step with python script "identify_chimeric_reads". command: identify_chimeric_read ${SampleID}.snoRNA.rRNA.bam snoRNA.rRNA.scaRNA.snRNA.tRNA.chimeras.count.tsv ${SampleID}.snoRNA.rRNA.chimeras.bam
parse indivudal snoRNA chimeras into single bam file (takes the chimeric bam file that mapped to each targets and split the bam files into per-snoRNA chimeric reads), we run this step with python script "parse_individual_chimeras", parse_individual_chimeras ${SampleID}.snoRNA.${target_RNA}.chimeras.bam --uid ${SampleID} --tag ${target_RNA} --cpus 8 --minimum_chimeras 1 --count_output individual.chimeras.count.tsv
call peaks on bam files mapped to human genome, hg19: clipper --species hg19 --processors 8 --bam ${SampleID}.chimeras.bam -o ${SampleID}.chimeras.bam.peaks.bed
Assembly: UCSC version hg19
Supplementary files format and content: bigwig files and tab-separated text files include read counts and RPM value for RNAs.
Library strategy: chimeric eCLIP

growth_protocol: 293T (Clontech), K562 (ATCC) and HepG2 (ATCC) cell lines were cultured in proper medium supplemented with 10% FBS (Cytivia) and antibiotics and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
For each 10cm plate (~15 million cells), cells were washed once with cold phosphate buffered saline, and then UV crosslinked (254 nm, 400 mJ/cm2) on ice. Cells were then spun down, supernatant removed, and washed with cold phosphate buffered saline. Cell pellets were flash frozen on dry ice and stored at -80°C.
Chimeric eCLIP was based off the previously described chimeric eCLIP protocol (Manakov et al. https://doi.org/10.1101/2022.02.13.480296). Lysis was performed in eCLIP lysis buffer, followed by sonication and digestion with RNase I (Ambion). Immunoprecipitation of snoRNA-associated RBPs-RNA complexes was achieved with a primary antibody using magnetic beads pre-coupled to the secondary antibody (typically 200 ul M-280 Sheep Anti-Rabbit IgG Dynabeads, Thermo Fisher Scientific). Where indicated, 2% of each immunoprecipitated (IP) sample was saved as input control. RNA fragments was dephosphorylated with FastAP (Thermo Fisher) and T4 PNK (NEB), followed by 5’ end phosphorylation of cleaved target RNAs with T4 polynucleotide kinase (PNK, 3' -phosphatase minus, NEB)). Chimeric ligation was then performed with T4 RNA ligase (NEB) without adapters. After additional dephosphorylation steps (FastAP, T4 PNK), phosphorylated RNA adapter was ligated to the 3’ end (T4 RNA Ligase, NEB). Samples were then denatured with 1X NuPage buffer (Life Technologies) and DTT, run on 4%–12% Bis-Tris protein gels and transferred to nitrocellulose membranes(GE Amersham). The region from the observed protein size to 75kD above (corresponding to ~250 nt RNA) was then isolated from membrane by razor blade, and RNA was isolated by Proteinase K (NEB) treatment followed by column purification (Zymo). RNA was then reverse transcribed with SuperScript IV Reverse Transcriptase (Invitrogen) using manganese chloride-based buffer to enhance read-through of modified nucleotides [[ref]]. Excess primers were removed with ExoSAP-IT (Thermo Fisher), and RNA was degraded by alkaline hydrolysis, followed by RNA purification (MyOne Silane beads, Thermo Fisher). Next, a 5’ Illumina DNA adapter (/5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGT/3SpC3)  was ligated to the 3’ end of cDNA fragment with T4 RNA ligase HC enzyme on beads overnight. After beads cleanup, an aliquot of each sample was proceeded for qPCR to identify the proper PCR cycles. The remainder of the samples were amplified with barcoded Illumina primers (Q5, NEB) and size selected via AMPure XP beads and 2% agarose gel (195-350bp). Samples were then quantified by Agilent TapeStation and sequenced either on the Illumina NextSeq (150 bp SE) or NovaSeq X Plus (150 bp PE) platforms.


title: ISO_AON_2

value: AON


title: Fibrillarin chimeric eCLIP Input in mouse ESCs


title: Treg.meninges#2


title: Treg.spleen#3


title: static

city: Neuherberg

first: Sandra

last: Wiedenmann

state: Bavaria

address: Ingolstädter Landstraße 1

department: Helmholtz Pioneer Campus

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic single cell

data_processing:
Raw sequencing data files were demultiplexed, aligned (reference genome hg38_ensrel96), filtered, barcodes and UMIs counted, and subjected to a quality filter with CellRanger (10xGenomics).
The pre-processing and downstream analysis were performed with the package ‘Scanpy62 API’88  (version 1.9.1) in python with default parameters, if not stated differently
For velocity analysis, alignment files (bam) were analyized by samtools ( version 1.16) and then "velocyto run" command was applied on sorted barcodes in Cell Ranger. The generated loom files were then analyzed together with the filtered,normalized and cluster annotated scRNAseq analysis file with the basic anaylsis pipeline of scvelo package(version  0.2.5)
Assembly: hg38_ensrel96
Supplementary files format and content: compressed matrix files

molecule: polyA RNA

source_name: hiPSCs

growth_protocol: HiPSCs (HMGUi001-A) were differentiated to endothelial cells in a 3D shaking culture approach and sorted for CD31+ cells on day 6 as described before. SC-ECs were cultured on fibronectin-coated plates (Sigma, 5 µg/ml final concentration) in StemPro-34 (LIFE Technologies), with 15% FBS, VEGFA and FGF2 (100 ng/ml each) with medium change every other day

extract_protocol:
For RNA single cell sequencing, chips were washed with PBS. To ensure that only cells growing in the hydrogel were collected, inlet and outlet ports were blocked with 3% agarose. After solidification of the agarose, cells were treated with a 1:1 mix of Collagenase P (18 U final concentration, Roche 11213857001) and Accutase and incubated for 30 min at 37°C. Pipette tips and tubes were washed with PBS + 2% BSA before usage to reduce cell loss. Successfully dissolved hydrogels and a single cell suspension was confirmed under the microscope before harvesting the cells in PBS + 10% FBS. The cells were centrifuged at 300 x g for 3 min, washed with PBS + 2% BSA and filtered with a 20 µm cell Pluristrainer (pluriSelect, 43-50020-023). Cells were counted with TrypanBlue (Sigma) and a cell vitality of over 70% was confirmed.
RNA libraries were generated using Chromium Single Cell 3’ library and gel bead kit v3.1 (10x Genomics).
The amplified cDNA library was sequenced on a NovaSeq SP flow cell from Illumina.

treatment_protocol: Endothelial cells were seeded into a pre-molded lumen which is embedded in a Collagen I hydrogel environmenton an microfluidic Vesssel-on-Chip platform. Either lumen were perfused by gravity driven flow on a shaker (25°, 2 min interval) or left in static condition for total 3 days. After seeding, EGM-2 (Sigma Aldrich, C-22011) medium was added to all chambers. Media change was performed every day.

value: hiPSCs

value: endothelial

value: wt

value: static


title: E14.5 fetal ovary, cKO, rep4

city: Brisbane

first: Josephine

last: Bowles

state: Queensland

address: The University of Queensland

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

description:
cKO4
BRPC_cKO4

data_processing:
Paired end 150bp reads were trimmed for adaptor / low quality sequence using Trimmomatic v0.39 with the following options "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36".
Trimmed reads were checked for quality using FastQC v0.11.9.
Trimmed reads were mapped to the Mus musculus genome (mm10, UCSC) using STAR v2.5.2, with the "--quantMode GeneCounts" option to obtain the number of reads per gene. Annotation GTF was from UCSC (mm10.refGene.gtf).
Normalisation and differential gene expression was conducted using edgeR, with the GLM approach. Low-expression genes with an average logCPM (aveLogCPM)<0 were excluded from the analysis.
Assembly: mm10
Supplementary files format and content: *.counts.txt: tab-delimited text files include raw counts for each Sample.
Supplementary files format and content: BRPC_CPM.txt: tab-deliminted text file includes log2-transformed CPM values for each Sample.

source_name: ovary

growth_protocol: Bmpr1a fl/fl females were time-mated with Bmpr1a fl/fl; Oct4-Cre Cre/WT studs to obtain embryos for this study. All mice were kept on a C57BL/6 background.

extract_protocol:
Fetal ovaries were collected from 8 x E14.5 Bmpr1a fl/fl; Oct4-Cre Cre/wt (Bmpr1a cKO) embryos and 8 x Bmpr1a fl/fl (control) littermates across 6 litters; gonad pairs were pooled into eight samples (n=4 each of cKO and control). Total RNA was isolated using the RNeasy Micro Kit (#74004, Qiagen) including on-column DNase treatment.
For each sample, 500ng total RNA was used for cDNA library construction. Strand-specfic paired-end libraries were constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (#E7760S, NEB), optimised for an approximate final library size of 520 bp, following manufacturer's protocols.

treatment_protocol: Pregnant females were injected intraperitoneally with 1mg 4-hydroxy tamoxifen (4OHT) and 0.5mg progesterone at 9.5, 10.5, 11.5 dpc to induce germ cell-specific CRE-dependent recombination of Bmpr1a in the embryos.

value: ovary

value: Bmpr1a fl/fl; Oct4-Cre Cre/WT (Bmpr1a cKO)

value: Embryos were exposed to 4-hydroxy tamoxifen and progesterone at E9.5 - E11.5.

tag: Sex

value: female

tag: developmental stage


title: NOP56 IP chimeric eCLIP in mouse ESCs

value: ESC


title: Control-24h-2

description: A549, lung cancer cells

value: control


title: Treg.spleen#2

value: Spleen

value: Treg cell


title: VEH_15 [S447.15]

value: fetal testis

value: Sprague Dawley

value: wild type

value: corn oil


title: Control-24h-1

description: A549, lung cancer cells

value: lung cancer

value: NSCLC


title: PAT_AON_1

value: retinal organoids

value: ABCA4 c.768T

value: AON


title: Treg.meninges#1

value: Meninges


title: NOP56 chimeric eCLIP Input in mouse ESCs


title: E14.5 fetal ovary, cKO, rep3

description:
cKO3
BRPC_cKO3

value: ovary

value: Bmpr1a fl/fl; Oct4-Cre Cre/WT (Bmpr1a cKO)


title: GMI-24h-2

description: A549, lung cancer cells

value: GMI (0.6 uM) for 24 h


title: Treg.meninges#3


title: DPeP300_13 [S447.13]

value: 300 mg/kg/d DPeP


title: E14.5 fetal ovary, cKO, rep2

description:
cKO2
BRPC_cKO2

value: Embryos were exposed to 4-hydroxy tamoxifen and progesterone at E9.5 - E11.5.

value: female


title: E14.5 fetal ovary, cKO, rep1

description:
cKO1
BRPC_cKO1


title: MDA-MB-231 cell line, Small

type: RNA

city: CAMBRIDGE

first: Satomi

last: Hirose

address: 500 Technology Square

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

description: SAMPLE 3

data_processing:
Relative gene expression was calculated using the 2−ΔΔCt method, with the mRNA levels of the target genes normalized to those of peptidylprolyl isomerase A (PPIA) as a housekeeping gene.
Outlier value was defined by Gribbs test (p<0.05)

label: TB Green

source_name: MDA-MB-231 cell line

label_protocol: Following the product manual, the RT-PCR reaction was performed in 20 μL of reaction buffer containing 10 μL of TB green Premix Ex Taq II (RR82WR; Takara), 1 μL of 10 μM forward primer, 1 μL of 10 μM reverse primer, 1 μL of 5 µg mL−1 cDNA, and 7 μL of water.

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (11995065; Gibco) supplemented with 10% fetal bovine serum (FBS; 26140079; Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (P4333; Sigma-Aldrich).

extract_protocol: Total RNA was extracted from each cell group cultured on cell culture dishes using the RNeasy Plus Mini Kit (74134; Qiagen) and converted to cDNA using the Verso cDNA Synthesis Kit (AB1453A; Thermo Fisher Scientific).

tag: sorted for

value: Smaller nuclei

tag: group

value: Control


title: E14.5 fetal ovary, control, rep3

description:
WT3
BRPC_WT3

value: Bmpr1a fl/fl (control)


title: E14.5 fetal ovary, control, rep4

description:
WT4
BRPC_WT4


title: Dnmt3a-Tg Female Old Gastro_7

city: Kyoto

first: Yasutomi

last: Kamei

address: 1-5 Shimogamo-Hangicho, Sakyo-ku

country: Japan

institute: Kyoto Prefectural University

description: Gene expression in skeletal muscle (gastrocnemius, 7 weeks of age)

hyb_protocol: cRNA was prepared according to the standard Agilent protocol. Agilent platform Agilent-028005 Whole Mouse Genome Microarray 8 × 60K G4858A was used.

scan_protocol: Arrays were scanned on an Agilent Microarray Scanner to detect Cy3 fluorescence.

data_processing: The scanned images were analyzed using Feature Extraction Software 9.5 (Agilent) with default parameters (protocol: GE1_1100_Jul11 and Grid: 028005_D_F_20150604) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction Software as Non-uniform outliers were excluded.

source_name: Dnmt3a-Tg Female Old Gastro

label_protocol: Cy3-labeled cRNA (1.65 μg) was mixed and fragmented according to the Agilent Technologies protocol.

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of wild-type control young mice (3 months of age, female, N=4), wild-type control old mice (26 months of age, female, N=8), Dnmt3a Tg young mice (3 months of age, female, N=4), and Dnmt3a Tg old mice (26 months of age, female, N=8). RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany).

value: gastrocnemius

tag: gender

tag: age

value: 26 months


title: DPeP11_17 [S447.17]

value: fetal testis

value: Sprague Dawley

value: wild type

value: 11 mg/kg/d DPeP


title: hippocampal glutamatergic neurons, DLK WT (cKO sib), biol rep 4

city: La Jolla

first: Yishi

last: Jin

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

description:
DfRV28
CKO_gene_counts.txt

data_processing:
Read quality was checked using FastQC (version 0.11.8).  Reads were mapped to the mouse reference genome (mm10) using STAR galaxy version 2.6.0b-1 with default settings. Mapped reads were assigned to genes using featureCounts version 1.6.3. Differential gene expression analysis was conducted using DESeq2 galaxy version 2.11.40.2 with genotype, sex, and batch included as factors in the analysis.
Assembly: mm10
Supplementary files format and content: Tab delimited file contains raw gene counts for each sample. Separated into DLK(iOE) and WT sibs or DLK(cKO) and WT sibs as separate files.
Library strategy: Ribo-seq

source_name: hippocampal

growth_protocol: Mice of desired genotypes were maintained under standard conditions until postnatal day 15.

extract_protocol:
HA tagged ribosomes were immunoprecipitated from homogenized tissue using the anti-HA antibody ( Roche, Cat#11867423001), following the protocol described in Sanz et al., 2019. RNA was extracted following manufacturer’s instructions in the RNAeasy Minikit (Qiagen).
Library preparation and sequencing for ribosome associated mRNAs were performed by the UCSD IGM Genomics Center using Illumina Stranded mRNA Prep.

treatment_protocol: Hippocampi were dissected in ice cold PBS

value: hippocampal

value: hippocampal glutamatergic neurons

value: Female

tag: batch


title: DPeP100_19 [S447.19]

value: 100 mg/kg/d DPeP


title: Rbp4,M,Saline,48hrs,rep5,b4

city: Berkeley

first: Andrea

middle: M

last: Gomez

address: 163 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Library name: AG-8175

data_processing:
Data quality assessment and sequence read primer trimming were performed by FastQC v0.11.9 and Cutadapt 3.5, respectively. We considered trim_galore version 0.6.7 with --phred33 parameter. The data was then aligned to a mouse reference genome build (Mus musculus; GRCm39: RefSeq assembly accession = GCF_000001635.27) using RSEM v1.3.1. Bowtie2 version 2.4.4 aligner index was created using rsem-prepare-reference --bowtie2 command and a gene-level read count matrix was generated using rsem-calculate-expression --bowtie2 command. Gene-level counts of each sample were combined using rsem-generate-data-matrix command.
For alternative splicing analysis, we first applied the same procedures for assessing data quality and sequence read primer trimming. The reads were then aligned to a mouse reference genome build (Mus musculus; GRCm39) using STAR 2.7.10a.
Assembly: Mus musculus; GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include raw counts for all samples combined

source_name: mouse prefrontal cortex

extract_protocol:
RNA purification from RiboTag mice were modified from previously published protocols (see methods for details). RNA purification was performed using a RNeasy Mini kit following the manufacturer’s instructions.
Samples with RNA integrity number (RIN) values >7 were used for library prep. 50 ng of RNA was used for library preparation with TruSeq stranded RNA library prep kit with poly-A enrichment. The libraries were sequenced 150bp paired-end on a NovaSeq 6000 platform for DOI samples, and X Plus for psilocybin samples, at 200 million reads per sample.

treatment_protocol: DOI (2mg/kg), psilocybin (2mg/kg) or saline were injected intraperitoneally (IP).

value: mouse prefrontal cortex

tag: cre line

value: male

tag: replicate

tag: time

value: Saline


title: MDA-MB-231 cell line, Large

description: SAMPLE 4

tag: cell line

value: Larger nuclei

value: Test


title: MDA-MB-231 cell line, EGFP-negative

description: SAMPLE 2

value: H2B-EGFP expression negative


title: hippocampal glutamatergic neurons, DLK WT (cKO sib), biol rep 3

description:
DfRV16
CKO_gene_counts.txt

tag: cell type


title: MDA-MB-231 cell line, EGFP-positive

description: SAMPLE 1

value: H2B-EGFP expression positive

value: Control


title: E14.5 fetal ovary, control, rep2

description:
WT2
BRPC_WT2

value: ovary

tag: genotype

value: Bmpr1a fl/fl (control)

tag: treatment

value: Embryos were exposed to 4-hydroxy tamoxifen and progesterone at E9.5 - E11.5.

value: female


title: VEH_08 [S446.08]

tag: tissue

value: fetal testis

tag: strain

value: Sprague Dawley

value: wild type

value: corn oil


title: E14.5 fetal ovary, control, rep1

description:
WT1
BRPC_WT1


title: Dnmt3a-Tg Female Old Gastro_8

value: gastrocnemius

value: 26 months


title: WT Female Old Gastro_8

source_name: WT Female Old Gastro


title: DPeP1_10 [S446.10]

value: 1 mg/kg/d DPeP


title: iNeuron, replicate 5, gRNA enrichment

city: Chapel Hill

first: Hyejung

last: Won

state: North Carolina

address: 116 Manning Dr, # 6110

department: Genetics and Molecular Biology

institute: UNC Chapel Hill

description:
gRNA enrichment; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In5_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In5_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In5_matrix.mtx.gz

data_processing:
scRNA-seq and gRNA library sequencing files were processed using the cellranger count 7.0.0 pipeline for demultiplexing, barcoded processing, gene counting and aggregation.
Assembly: hg38
Supplementary files format and content: Tab-separated value files, matrices, comma-separated values and cloupe files.

source_name: hiPSC-derived neuron

growth_protocol: We differentiated WTC11 i3Neuron dCas9-KRAB hiPSCs (iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background, SF2019-227, obtained from Kampmann Lab) into glutamatergic neurons following the iNeuron pre-differentiation & differentiation protocol from Tian et al., 2019. Briefly, cells were seeded at 7.5x105 cells/well in 6-well plates on day –3 for ‘pre-differentiation’ into neural progenitor cells (NPCs), with half media changes with N2 pre-differentiation media performed every day until day 0. On day 0, cells were re-plated in Poly-D-Lysine (PDL)-coated 10-cm dishes at 7x106 cells/well for differentiation into neurons.

extract_protocol:
Briefly, on the day of collection, papain (Worthington, cat. no. LK003153) was resuspended in 5 mL 1X HBSS (Thermo, cat. no. 2277417) for a concentration of 20 U/mL. A resuspension solution of DMEM (Thermo, cat. no. 10313039) with 10% FBS was also prepared and both solutions were warmed at 37°C for at least 10 minutes. From the plate of neurons, conditioned media (i.e., the media in which the cells were cultured) was separately collected from lentivirus-treated cells as well as the untreated cells. Additionally, 10 µM Y-27632 dihydrochloride ROCK inhibitor (Tocris, cat. no. 1254) and 2% FBS was added to each tube of conditioned media to ensure cell survival and to prevent aggregation in preparation for FACS. Immediately before use, DNase (Worthington, cat. no. LK003153) at 5 μg/mL and Magnesium Chloride (Thermo, cat. no. AM9530G) at 5 mM were added to the papain solution. The cell culture media was aspirated and washed with DPBS (Thermo, cat. no. 14190144), and the papain dissociation solution was added at 500 uL per well. The plate was then placed in the 37°C incubator for 10 minutes, and gently agitated to ensure neuron sheet dissociation. The papain dissociation solution was then quenched in 5 volumes of DMEM and 10% FBS solution, and the neuron sheet was then gently triturated with a P1000 pipette. The lentivirus-treated and untreated cells were then separately transferred to 15 mL conical tubes and centrifuged at 200g for 10 minutes. The supernatant was then carefully removed, and cells were resuspended by slow vortexing in conditioned media solution containing ROCK inhibitor and 2% FBS in preparation for FACS. Live, RFP-expressing cells were FACS isolated by the UNC Advanced Analytics (AA) Core. After FACS, RFP+ cells were immediately processed by the UNC AA Core using the Chromium 10x Genomics 3' v3.1 Dual Index workflow for single cell RNA-seq library generation.
Library preparation was done by UNC AA Core according to manufacturer instructions (Chromium 10x Genomics 3' v3.1 Dual Index Workflow).

value: hiPSC-derived neuron


title: Dnmt3a-Tg Female Old Gastro_6


title: Rbp4,M,Psilocybin,48hrs,rep5,b4

description: Library name: AG-8172

value: mouse prefrontal cortex

value: male

value: Psilocybin


title: Dnmt3a-Tg Female Old Gastro_5


title: hippocampal glutamatergic neurons, DLK WT (cKO sib), biol rep 2

description:
DfRV49
CKO_gene_counts.txt

value: hippocampal

value: hippocampal glutamatergic neurons

value: Male


title: hippocampal glutamatergic neurons, DLK WT (cKO sib), biol rep 1

description:
DfRV46
CKO_gene_counts.txt


title: iNeuron, replicate 4, gRNA enrichment

description:
gRNA enrichment; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In4_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In4_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In4_matrix.mtx.gz


title: iNeuron, replicate 3, gRNA enrichment

description:
gRNA enrichment; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In3_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In3_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In3_matrix.mtx.gz


title: hippocampal glutamatergic neurons, DLK(cKO), biol rep 4

description:
DfRV29
CKO_gene_counts.txt

value: Female


title: WT Female Old Gastro_6


title: iNeuron, replicate 1, gRNA enrichment

description:
gRNA enrichment; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In1_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In1_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In1_matrix.mtx.gz


title: iNeuron, replicate 2, gRNA enrichment

description:
gRNA enrichment; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In2_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In2_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In2_matrix.mtx.gz


title: hippocampal glutamatergic neurons, DLK(cKO), biol rep 2

description:
DfRV50
CKO_gene_counts.txt


title: PV,M,Psilocybin,48hrs,rep4,b4

description: Library name: AG-8127

value: PV


title: Cux2ERT,F,Psilocybin,48hrs,rep4,b4

description: Library name: AG-8067

value: female


title: hippocampal glutamatergic neurons, DLK(cKO), biol rep 3

description:
DfRV13
CKO_gene_counts.txt


title: WT Female Old Gastro_7


title: hippocampal glutamatergic neurons, DLK(cKO), biol rep 1

description:
DfRV47
CKO_gene_counts.txt


title: Dnmt3a-Tg Female Old Gastro_4


title: WT Female Old Gastro_5


title: iNeuron, replicate 4, scRNA-seq

description:
10x Genomics; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In4_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In4_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In4_matrix.mtx.gz


title: Cux2ERT,M,Saline,48hrs,rep4,b4

description: Library name: AG-8065

value: Saline


title: Dnmt3a-Tg Female Old Gastro_3


title: hippocampal glutamatergic neurons, DLK WT (iOE sib), biol rep 3

description:
DRV65
OE_gene_counts.txt


title: Rbp4,F,Psilocybin,48hrs,rep4,b4

description: Library name: AG-8171


title: Dnmt3a-Tg Female Old Gastro_2


title: iNeuron, replicate 3, scRNA-seq

description:
10x Genomics; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In3_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In3_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In3_matrix.mtx.gz


title: hippocampal glutamatergic neurons, DLK WT (iOE sib), biol rep 2

description:
DRV44
OE_gene_counts.txt


title: Rbp4,F,Psilocybin,48hrs,rep2,b4

description: Library name: AG-8057


title: PV,M,Psilocybin,48hrs,rep5,b4

description: Library name: AG-8128


title: Dnmt3a-Tg Female Old Gastro_1


title: iNeuron, replicate 2, scRNA-seq

description:
10x Genomics; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In2_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In2_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In2_matrix.mtx.gz


title: Cux2ERT,M,Saline,48hrs,rep3,b4

description: Library name: AG-8055


title: WT Female Old Gastro_4


title: PI3

city: Yantai

first: Dong

last: Wang

state: --- Select One ---

address: Binzhou Medica University, No. 346 Guanhai Road, Binhai Road Street, Laishan District, Yantai, Shandong Province

country: China

institute: Binzhou Mecical University

data_processing:
1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), cut the adapter;
2. Filter read length: if the length of the sequencing read is less than 150 bp, discard the entire read;
3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read,discard the entire read;
4. Filter low-quality data: if the bases with a quality value of less than 20 in the sequencing read account for 40.0% or more of the entire read, discard the entire read;
5. Obtain Clean reads: the output read quality value system is set to Phred+33.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: skin

extract_protocol:
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. PCR amplification and purification;
7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: skin


title: Cux2ERT,M,Psilocybin,48hrs,rep2,b4

description: Library name: AG-8051


title: hippocampal glutamatergic neurons, DLK(iOE), biol rep 3

description:
DRV64
OE_gene_counts.txt


title: iNeuron, replicate 5, scRNA-seq

description:
10x Genomics; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In5_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In5_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In5_matrix.mtx.gz


title: WT Female Old Gastro_3


title: Rbp4,M,Psilocybin,48hrs,rep3,b4

description: Library name: AG-8061


title: H3K4me3_Nt.CviPII (Size Selection)

city: Ipswich

first: Sriharsa

last: Pradhan

address: 240 County Road

institute: New England Biolabs

library_source: genomic

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
NEED-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using samtools. Open chromatin regions were identified by calling narrow peaks and Closed chromatin were identified by calling broad peaks using MACS2.
EM-seq: Trimmed read pairs were mapped to the reference genome (human: hg38) using Bwa-meth. PCR duplicates and mitochondrial reads were removed using samblaster and samtools.
ChIP-seq: Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using samtools.  Open chromatin regions were identified by calling narrow peaks and Closed chromatin were identified by calling broad peaks using MACS2 where Input were used as control
Hi-C: HiC data were analysed using HicPro.
Assembly: hg38
Supplementary files format and content: Bigwigs were generated using bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM
Library strategy: NEED-seq

molecule: genomic DNA

growth_protocol: HT1080 and HCT116 cells were grown in 6 well plates until 70-80% confluency. After one wash with 1XPBS, cells were crosslinked in 1XPBS with 4% formaldehyde (Thermo Fisher Scientific # 28908) for 10 min at RT. K562 crosslinked cells with 4% formaldehyde were decrosslinked overnight at 58°C in 1X PBS. Cytoplasmic extraction was performed for 30 min with end-over-end mixing at 4°C. After 300 g centrifugation at 4°C for 5 min, cell pellet was washed once with 1X PBS and nuclei concentration was defined using Luna automated cell counter.

extract_protocol:
Cells were fixed with 1% and 4% formaldehyde
HT1080 and HCT116 cells were grown in 6 well plates until 70-80% confluency. After one wash with 1X PBS (GIBCO # 770011-044), cells were crosslinked in 1X PBS with 4% formaldehyde (Thermo Fisher Scientific # 28908) for 10 min at room temperature (RT). In some crosslinking conditions, 1% formaldehyde was used. Crosslink was quenched using 0.25 M Glycine for 5 min at RT. Cells were de-crosslinked overnight at 58°C in 1X PBS. Cytoplasm was extracted for 10-30 min on ice using cytosolic buffer (15mM Tris-HCl, pH7.5, 5mM MgCl2, 60mM KCl, 0.5mM DTT, 15mM NaCl, 300mM sucrose, and 1% NP40) with occasional agitation. After 1X PBS wash, cells were incubated with 1X PBS / 5% BSA / 0.3% Triton™ X-100 for 1 hr at RT with gentle rocking. Primary antibodies were added (1/400 dilution per well) and incubated overnight at 4°C with gentle rocking. After 3 washes with 1X T-PBS (PBS + 0.1% Tween 20) for 5 min at RT, secondary antibodies were added , Alexa Fluor® 488 conjugated goat anti-Mouse IgG (H+L) Superclonal™ or goat anti-Rabbit IgG (H+L) Superclonal™ (corresponding to species of primary antibody; Thermo Fisher # A-28175 and A-27034 respectively) at a dilution of 1:1000 in PBS / 0.3% Triton™ X-100/ 5% BSA for 1 hr at RT with gentle rocking. After 3 washes with 1X T-PBS for 5 min at RT, cells were incubated for 1 hr at RT with 1 µl of Nt.CviPII-pGL (NEB, 0.5 units) in 800 µl binding buffer per well (20 mM potassium phosphate pH 7.0, 20 mM NaCl, 0.3% Triton™ X-100). In some experiments, heparin (Sigma-Aldrich # H3149) was added at different concentrations to prevent non-specific DNA binding. Plates were then washed 3 times with washing buffer (20 mM potassium phosphate buffer  pH 7.0, 500 mM NaCl, 0.3% Triton™ X-100) for 15 min at RT. Cells were incubated with 10 units of DNA Polymerase I (NEB # M0209S), 5 mM of dNTP mix including Biotin-14-dCTP (Thermo Fisher # 19518018), 5-methyl-dCTP (NEB # N0356S), dATP, dTTP and dGTP for 1 hr at 37°C in 800 µl of 1X NEBuffer 2 per well to allow nick translation to occur. Plates were then washed 3 times with washing buffer (20 mM potassium phosphate buffer, pH 7.0, 500 mM NaCl, 0.3% Triton™ X-100) for 15 min at RT with an additional wash with 1X PBS. Cells were then covered with 100 µl of 1X PBS and DNA was extracted using Monarch genomic DNA purification kit (NEB # T3010S) according to manufacturer’s recommendations. After DNA purification, 100-500 ng of genomic DNA was fragmented using 2 units of Nt.CviPII (NEB # R0626S) in 500  µl of 1X NEBuffer 2 at 37°C overnight. Nt.CviPII was inactivated at 65°C for 20 min. NaCl 5M stock was added to reach 1 M final concentration along with 30 µl of Streptavidin magnetic beads (NEB # S1420S) for 2 hrs with end-over-end mixing at 4°C to capture biotinylated DNA fragments. Streptavidin bound DNA beads were washed twice with 1X TE buffer supplemented with 2 M NaCl and 0.05 % Triton™ X-100. A third wash was performed with 1X TE buffer. Beads were resuspended in 50 µl of TE buffer and libraries were made on beads using NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® (NEB # E7645S) according to manufacturer’s protocol. 8 to 12 PCR cycles were used to amplify barcoded DNA. NEED-seq protocol described above was used with some modifications. Briefly, K562 crosslinked cells with 4% formaldehyde were decrosslinked overnight at 58°C in 1X PBS. Cytoplasmic extraction was performed for 30 min with end-over-end mixing at 4°C. After 300 x g centrifugation at 4°C for 5 min, cell pellet was washed once with 1X PBS and nuclei number was calculated using Luna automated cell counter. Nuclei resuspended in 1X PBS were then captured by adding 10 µl of preactivated Concanavalin A magnetic beads (Cell Signaling Technology # 93569) for 10 min with end-over-end mixing at RT. Bead-bound nuclei were incubated with 1X PBS including 0.3 % Triton X-100 and 5% BSA for 1 hr at RT. Primary antibodies were added (1/400 final dilution) and incubated overnight with end-over-end mixing at 4°C. After 3 washes with 1X T-PBS for 5 min at RT, blocking buffer was added with anti-mouse IgG or anti-rabbit IgG coupled with Alexa 488 for 1h at RT with gentle rocking. After 3 washes with 1X T-PBS for 5 min at RT, beads were resuspended in 1 ml binding buffer (as described above) including 1 l of fusion enzyme Nt.CviPII-pGL (NEB) for 1 hr at RT. Beads were then washed 3 times with washing buffer (as described above) for 15 min at RT. After 1 wash with 1X PBS, beads were incubated with 10 units of DNA Polymerase I, 5 M of dNTP mix including Biotin-14-dCTP, 5-methyl-dCTP, dATP, dTTP and dGTP for 1 hr at 37°C in 800 µl of 1X NEBuffer 2 with end-over-end mixing. After 3 washes with washing buffer for 15 min at RT, beads were resuspended in 50 mM Tris-Cl, pH 7.5, 1 % SDS, 200 mM NaCl and 2 µl of proteinase K (NEB # P8107S) and incubated overnight at 65°C to lyse nuclei bound to the beads and DNA was extracted using phenol-chloroform and precipitated using glycogen. 200 ng of DNA was fragmented using Nt.CviPII and used to make libraries as described above. For low number of cells, barcoded DNA was amplified using ~18 PCR cycles. To determine the dynamic range of NEED-seq, cells were serially diluted after the labeling reaction. In this modified NEED-seq method, HT1080 cells were grown on 6 well plate to 80% confluency. Cells were incubated for 10 min at 4°C using CSK buffer (10 mM PIPES pH 6.8, 300 mM sucrose, 100 mM NaCl, 1.5 mM MgCl2 and 0.5 % Triton X-100) followed by crosslinking with 4% formaldehyde for 10 min at RT. Glycine was used to quench formaldehyde for 5 min at RT (final concentration 0.25M). After 1X PBS wash, blocking buffer was added to cells for 1h at RT (5% BSA, 1X PBS and 0.3% Triton X-100). Different antibodies (see Table S2) were then added at dilutions recommended by the manufacturer and incubated with cells for 16 hrs at 4°C. After 3 washes with T-PBS (PBS with 0.1 % Tween 20) for 5 min at RT, blocking buffer was added with anti-mouse IgG or anti-rabbit IgG coupled with Alexa 488 for 1h at RT. After 3 washes with T-PBS for 5 min at RT, NEED-seq binding buffer (20 mM KPO4, 150 mM NaCl and 0.3% TritonX-100) was added along with Nt.CviPII-pGL enzyme (1 unit per well) for 1h at 37°C. After 3 washes with NEED-seq washing buffer (20 mM KPO4, 500 mM NaCl and 1% TritonX-100) for 15 min at RT, 1X NEBuffer2.1 was added for 1h at 37°C to allow Nt.CviPII-pGL activity to fragment the targeted DNA. After 1 wash with 1X PBS, genomic DNA extraction was performed using Monarch genomic DNA purification kit (6 wells pooled per antibody) according to NEB recommendations with a minor modification which included a lysis step at 56°C for 1h instead of 10 min to reverse DNA crosslinking. 0.1 to 1 µg of genomic DNA was used for size selection using first 0.4x volume of NEBNext Sample Purification beads with 10 min incubation at RT. Supernatant containing 200-500 bp DNA sizes was separated from beads using 12-tube magnetic separation rack (NEB # S1509S) and collected. An additional 0.4x volume of NEBNext Sample Purification beads was added to the supernatant and incubated for 10 min at RT. After 2 washes with 80% EtOH, DNA was eluted form beads with 50 µl of low TE buffer and DNA libraries were prepared using NEBNext Ultra II DNA Library Prep (NEB # E7103L) with some modifications. Briefly, end repair/dA tailing was performed on size selected DNA and NEBNext Illumina adaptor (1/10 dilution) were ligated for 2 hrs at RT. USER enzyme (NEB # E7103L) was incubated for 20 min at 37°C and another round of library size selection was performed as described above. The library was amplified using 13 PCR cycles. PCR products were purified using 0.9x volume of NEBNext Sample Purification beads. 1 nM of size selected DNA library was sequenced on Novaseq 6000. HT1080 cells (0.5x10e6) were crosslinked with 4% formaldehyde for 10 min at RT and quenched with 1.5 M Tris-HCl (pH 8) for 5 min at RT. After 1X PBS wash, cells were permeabilized with Hi-C lysis buffer (10 mM Tris-HCl (pH 8), 10 mM NaCl and 0.2% NP40) for 30 min at 4°C, washed with 1X NEBuffer2 and incubated for 10 min at 58°C with 1X NEBuffer2, 0.3% SDS and 1 mM DTT. To quench SDS, Triton X-100 was added (1% final concentration per well) for 15 min at 37°C. 400 U of MboI (NEB # R0147M) were added and incubated for 16 hrs at 37°C. Enzyme was inactivated at 58°C for 20 min. Supernatant was discarded and DNA polymerase I mix containing  NEBuffer2.1 1X (NEB # B7002S), 30 µM of dNTPs (including dCTP/dGTP/dTTP (NEB # N0441S/ N0442S/N0443S respectively) with biotin-14-dATP (ThermoFisher Scientific # 19524016)) and 50 U of DNA polymerase I (NEB # M0210M) was added and incubated for 4 hrs at RT. Ligase mix was added and incubated for 16 hrs at RT. Ligase mix contains 2000 U of T4 DNA ligase (M0202M NEB), 140 µg of recombinant albumin (NEB # B9200S),  1X T4 DNA ligase buffer (NEB # B0202S) and 1 % Triton X-100. After ligation, supernatant was discarded, and cells were washed using 1X PBS. Genomic DNA was extracted from the wells using Monarch Genomic DNA purification Kit (NEB # T3010L). To remove biotin from un-ligated DNA ends, 10 µg of genomic DNA was incubated with 30 U of T4 DNA Polymerase (NEB # M0203L), 25 µM dATP/dGTP (NEB # N0440S/N0442S respectively) in 1X NEBuffer2 for 4 hrs at 20°C. Enzyme was inactivated for 20 min at 75°C. DNA was purified using 1X volume of NEBNext Sample Purification beads (NEB # E6178S) and sheared to 300 bp using Covaris (program : repeat/iterations # 7; repeat process treatment duration 10s; peak power 50W; duty factor 20%; cycles per burst 1000; total treatment time per sample 70s). To capture biotinylated DNA, DNA was incubated with NEB Magnetic Streptavidin beads (NEB # S1420S) for 30 min at RT in 10 mM Tris-HCl (pH 7.5) supplemented with 1 M NaCl. Beads were washed once with 10 mM Tris-HCl (pH 7.5) supplemented with 1 M NaCl and once with low TE buffer. Beads were resuspended in 50 µl of low TE buffer and DNA libraries were prepared on beads using NEBNext Ultra II DNA Library Prep (NEB # E7103L) with some modifications. Briefly, end repair/dA tailing was performed on beads and NEBNext Illumina adaptor (1/10 dilution) were ligated for 2 hrs at RT. 3 µl of USER (NEB # E7103L) was added for 20 min at 37°C. Beads were then washed once with 10 mM Tris-HCl (pH 7.5) supplemented with 1 M of NaCl and once with low TE. Beads were resuspended in 15 µl of low TE. 14 PCR cycles were performed. Supernatant containing PCR products were separated from beads using 12-tube magnetic separation rack (NEB # S1509S) and purified using 0.9x volume of NEBNext Sample Purification beads. 1 nM of DNA Hi-C library was loaded on Novaseq 6000.

value: fibrosarcoma cells

tag: condition


title: PI2


title: iNeuron, replicate 1, scRNA-seq

description:
10x Genomics; iPSC line with inducible Ngn2 + inducible CRISPRi, WTC11 background
CD_crop_4-4-24-WTC11_Neuron_In1_barcodes.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In1_features.tsv.gz
CD_crop_4-4-24-WTC11_Neuron_In1_matrix.mtx.gz


title: Cux2ERT,M,Psilocybin,48hrs,rep3,b4

description: Library name: AG-8052

tag: Sex


title: hippocampal glutamatergic neurons, DLK(iOE), biol rep 1

description:
DRV35
OE_gene_counts.txt


title: WT Female Old Gastro_1


title: PI1


title: non-PI3


title: Rbp4,F,Saline,48hrs,rep4,b4

description: Library name: AG-8002


title: Dnmt3a-Tg Female Young Gastro_4

source_name: Dnmt3a-Tg Female Young Gastro

value: 3 months


title: Rbp4,F,Saline,48hrs,rep3,b4

description: Library name: AG-8001


title: WT Female Old Gastro_2

value: gastrocnemius


title: Cerebella of Prrc2a flox/flox (control) mice

city: Beijing

first: Zengqiang

last: yuan

address: No. 27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

data_processing:
Single-cell sequencing datasets were analysed by package CellRanger (v6.0.0, 10× Genomics) and Seurat (v4.1.0). The 10× Genomics pre-built mouse genome for mm10-3.0.0 was used as reference.
Assembly: mm10
Supplementary files format and content: cell barcodes (tab-separated text file)
Supplementary files format and content: cell features (tab-separated text file)
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (MEX Format)
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (HDF5 Format)

source_name: Cerebellum

extract_protocol:
7-day-old Prrc2a f/f and Prrc2a cKO mice (6 mice in each group) were euthanized, after perfusion with cold saline, cerebella were dissected for sample preparation. Single-cell suspensions were attained using the Neural Tissue Dissociation Kit-Postnatal Neurons (130-094-802, Miltenyi Biotec).
Following the removal of red blood cells and dead cells, cell libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics), and subsequently sequenced on the Novaseq 6000 (Illumina).

value: Cerebellum

value: Prrc2a flox/flox


title: Cerebella from mice with microglial-Prrc2a deletion

value: Prrc2a flox/flox; Cx3cr1-CreER


title: non-PI2


title: hippocampal glutamatergic neurons, DLK(iOE), biol rep 2

description:
DRV52
OE_gene_counts.txt


title: hippocampal glutamatergic neurons, DLK WT (iOE sib), biol rep 1

description:
DRV43
OE_gene_counts.txt


title: non-PI1


title: CD11b_PBS

city: Dresden

first: Marko

last: Barovic

state: Saxony

address: Fetscherstr. 74

department: Institute for Clinical Chemistry and Laboratory Medicine

institute: TU Dresden

data_processing:
The raw sequencing data was processed with the ‘count’ command of the Cell Ranger software (v7.0.0) provided by 10X Genomics. To build the reference for Cell Ranger, mouse genome (GRCm39) as well as gene annotation (Ensembl 104) were downloaded from Ensembl. Genome and annotation were processed following the build steps provided by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#mm10_2020A) to build the appropriate Cellranger reference.
Assembly: GRCm39
Supplementary files format and content: tsv
Supplementary files format and content: matrix

source_name: synovial

extract_protocol:
The cell concentration was adjusted to 1000-1600 cells per ul and approximately 10 000 cells per sample were loaded on the Chromium Next GEM Single Cell 3' v3.1 dual-index kit (10x Genomics).
Library construction was performed according to the manufacturer's instructions.

treatment_protocol: Beta-glucan- and PBS-treated mice underwent arthritis induction by i.v. injection of 1.5mg arthritogenic mAbs (Arthrogen-CIA 5-Clone Cocktail kit; Chondrex) followed by i.p. injection of 50ug Lipopolysaccharide on day 3. Synovial CD45+CD11b+ cells were FACS sorted at day 17 post arthritis induction.

value: synovial

value: myeloid cells CD45+CD11b+

value: PBS


title: Cux2ERT,M,Saline,48hrs,rep2,b4

description: Library name: AG-7930

value: mouse prefrontal cortex

value: male


title: Dnmt3a-Tg Female Young Gastro_3


title: CD11b_BGL

value: BGL


title: Cux2ERT,M,Psilocybin,48hrs,rep1,b4

description: Library name: AG-7932

value: Psilocybin


title: Dnmt3a-Tg Female Young Gastro_2


title: L3_Syp_SMI_R2

city: Oxford

first: Jeffrey

middle: Y

last: Lee

address: Dorothy Hodgkin Road

country: United Kingdom

institute: University of Oxford

description: Third instar (L3, 96 hours after larval hatching), Dissected brain, iCLIP size-matched input for Syp, rep2

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed and adapter trimmed.
Reads were aligned to reference Drosophila melanogaster genome, BDGP6.28 (Ensembl version 99), using STAR.
Crosslink position and counts were extracted using Bedtools and converted to BigWig files.
Significant RNA binding sites of Imp and Syp were determined using iCount and the R package DESeq2.
Assembly: BDGP6.28
Supplementary files format and content: BigWig file of crosslinked nucelotide positions (counts)
Supplementary files format and content: Bed file of significant RNA binding sites (considering both immunoprecipitated and size-matched input libraries) of Imp and Syp.

organism: Drosophila melanogaster

source_name: Dissected brain

growth_protocol: Imp::GFSTF or Syp::eGFP flies were staged on apple juice plate to appropirate developmental stage with a 2 hour collection window.

extract_protocol:
Whole larval and larval head samples were frozen and ground into find powder in liquid nitrogen. These samples were crosslinked with four rounds of 0.2 J/cm2 UV light irradiation at 254 nm. Dissected brains were crosslinked with four rounds of 0.15 J/cm2 UV light in PBS. Lysates were prepared in iCLIP lysis buffer (Buchbender et al. 2020) supplemented with AEBSF and RVC.
Libraries were constructed using iCLIP2 procotol (Buchbender et al. 2020)

treatment_protocol: Whole first instar larvae were collected and washed in room temperature PBS. Second instar larval heads were collected by cutting the head with micro-scissors in PBS. Third instar brains were dissected in PBS.

value: Dissected brain

value: Syp::eGFP (Titlow et al. 2020)

tag: antibody used

value: N/A (input)

tag: developmental stage


title: PV,M,Psilocybin,48hrs,rep3,b4

description: Library name: AG-8047

value: PV


title: WT Female Young Gastro_4

source_name: WT Female Young Gastro

value: female


title: Rbp4,M,Saline,48hrs,rep2,b4

description: Library name: AG-7910

value: Saline


title: UP_Del_No_Alopecia_CD45neg

city: Bethesda

first: Keisuke

last: Nagao

state: MD

address: 10 Center Dr, Bldg 10, 12N240B

institute: National Institutes of Health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v 7.1.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole skin

extract_protocol:
Whole skins from WT and Up_del mice with and without alopecia female adult mice were harvested after shaving with an electric clipper. The hypodermal layers were removed by scraping from the dermis with forceps. The rest of the skin containing dermis and epidermis was minced with scissors and digested for 2 hrs at 37°C in RPMI containing 0.25mg/mL of Liberase T-Flex and 1ug/mL of DNAse I followed by the addition of 0.25 % Trypsin-1mM EDTA for 10 min. Cells were isolated and immunostained with anti-CD45 and Sytox-Green (SG) before being FACS sorted as live CD45+ and CD45-. Sorted live CD45+ and CD45- cell counts were adjusted and captured as per 10X genomics protocol using 5'-HTv2 kit for single cell RNA sequencing.
Library construction was performed in accordance with 10X Genomics protocol (Chromium Next GEM Single Cell 5' HT Gene expression (GEX) library protocol, CGOOO423, Rev C).

value: Whole skin

value: 17-18 weeks old

value: No treatment


title: Dnmt3a-Tg Female Young Gastro_1

value: gastrocnemius

value: 3 months


title: L3_Syp_SMI_R1

description: Third instar (L3, 96 hours after larval hatching), Dissected brain, iCLIP size-matched input for Syp, rep1


title: UP_Del_No_Alopecia_CD45pos

description: 10x Genomics


title: WT Female Young Gastro_3


title: Rbp4,F,Psilocybin,48hrs,rep1,b4

description: Library name: AG-7907


title: L3_Syp_IP_R3

description: Third instar (L3, 96 hours after larval hatching), Dissected brain, iCLIP immunoprecipiated for Syp, rep3

value: anti-GFP


title: PV,M,Psilocybin,48hrs,rep2,b4

description: Library name: AG-7870


title: UP_Del_Alopecia_CD45neg

description: 10x Genomics


title: L3_Syp_IP_R2

description: Third instar (L3, 96 hours after larval hatching), Dissected brain, iCLIP immunoprecipiated for Syp, rep2


title: PV,M,Psilocybin,48hrs,rep1,b4

description: Library name: AG-7868


title: UP_Del_Alopecia_CD45pos

description: 10x Genomics


title: WT Female Young Gastro_1


title: PV,M,Saline,48hrs,rep5,b4

description: Library name: AG-7871


title: WT_CD45neg

description: 10x Genomics


title: WT Female Young Gastro_2


title: L3_Syp_IP_R1

description: Third instar (L3, 96 hours after larval hatching), Dissected brain, iCLIP immunoprecipiated for Syp, rep1


title: L2_Syp_SMI_R3

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP size-matched input for Syp, rep3

source_name: Larval head

value: Larval head

value: Imp::GFSTF (BDSC:60237)


title: L2_Syp_SMI_R2

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP size-matched input for Syp, rep2


title: Usp17l-KD9

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

data_processing:
Raw reads were processed using trim-galore and clean reads were mapped to mm10 from UCSC genome by Hisat2 with default parameters .
Uniquely mapped reads annotated in Gencode vM17 were calculated by Featurecounts , with default parameters.
Raw counts were normalized by library size via transcripts per kilobase of exon model per million mapped reads (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols manufacturer's protocols.

value: mouse embryonic stem cells

value: Usp17l knockdown

value: Cell lines were cultured normally

value: P 7


title: Dnmt3a transgenic male

description: Gene expression in skeletal muscle (gastrocnemius, 7 weeks of age)

source_name: Gastrocnemius_Dnmt3a Tg male

extract_protocol: RNA was isolated from the gastrocnemius skeletal muscle of control mice (7 weeks of age, male) and Dnmt3a Tg mice (7 weeks of age, male and female). RNA was purified using the RNeasy Mini kit (Qiagen, Hilden, Germany). Samples from wild-type and Dnmt3a Tg mice (N = 3 for each group) were pooled before use.

value: male


title: MCF7_ARC_6

city: Buffalo

first: Jianxin

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description: Library name: MCF7_ARC_6

data_processing:
Data was processed by an external company Cellecta (Mountain View, CA) using propriatry pipelines.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files, contains  gene and raw read counts.

growth_protocol: MB157 and MCF7 cells  were grown in DMEM medium, supplemented with 10% FBS. HCC1806 cells were grown in RPMI supplemented with 10%FBS

extract_protocol:
RNA was extracted using Quiagen Rneasy plus mini Kit.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The cells were treated with 0.1% DMSO and INX-31 (100 nM) up to 48 hours


title: PV,M,Saline,48hrs,rep3,b4

description: Library name: AG-6902

value: mouse prefrontal cortex


title: Dnmt3a transgenic female

source_name: Gastrocnemius_Dnmt3a Tg female


title: WT_CD45pos

description: 10x Genomics


title: MCF7_ARC_5

description: Library name: MCF7_ARC_5


title: L2_Syp_SMI_R1

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP size-matched input for Syp, rep1

value: N/A (input)


title: Wildtype control male

source_name: Gastrocnemius_wildtype male


title: Rbp4,F,Saline,48hrs,rep1,b4

description: Library name: AG-6252

value: female


title: L2_Syp_IP_R3

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP immunoprecipiated for Syp, rep3

value: anti-Syp


title: Usp17l-Control 1

value: E3 transfected with the empty vector


title: MCF7_ARC_4

description: Library name: MCF7_ARC_4


title: Usp17l-KD4


title: L2_Syp_IP_R2

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP immunoprecipiated for Syp, rep2


title: PV,F,Saline,48hrs,rep2,b4

description: Library name: AG-6218

value: PV

value: Saline


title: MCF7_DMSO_3

description: Library name: MCF7_DMSO_3


title: L2_Syp_IP_R1

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP immunoprecipiated for Syp, rep1


title: Cux2ERT,M,Saline,48hrs,rep1,b4

description: Library name: AG-5859


title: MCF7_DMSO_2

description: Library name: MCF7_DMSO_2


title: PV,F,Saline,48hrs,rep4,b4

description: Library name: AG-6905


title: L2_Imp_SMI_R3

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP size-matched input for Imp, rep3


title: WT_Tg replicate 3

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

data_processing:
Reads were mapped on mixed reference of human genome hg19 and lammbda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport
Assembly: Mouse mm10
Supplementary files format and content: bedGraph

source_name: Skeletal muscle, iibialis anterior

growth_protocol: Mice were housed at a constant temperature of 24°C under artificial light (12-h light/dark cycle) with ad libitum access to food (CE-2, CLEA, Japan) and water. Skeletal muscle (tibialis anterior) of Dnmt3a-KO and age-matched WT mice (male, 4 months old), and Dnmt3a-Tg and age-matched WT mice (male, 3 months old) were used.

extract_protocol:
Protease K treated muscle tissues are extracted with phenol, phenol/chloroform, and chloroform. DNA was ethanol precipitated, dissolved in 10 mM Tris-buffer (pH8.0)
tPBAT method as described in Miura F et al (2019), NAR, 47, e85

treatment_protocol: To compare genotype differences, mice were treated similarly. Excised skeletal muscle tissue was rapidly frozen in liquid nitrogen.

value: Skeletal muscle, iibialis anterior

value: Wildtype


title: MCF7_DMSO_1

description: Library name: MCF7_DMSO_1


title: WT_Tg replicate 2


title: WT young replicate 4

description: WT 3mo Gastro 6

source_name: Skeletal muscle, gastrocnemius

growth_protocol: Mice were housed at a constant temperature of 24°C under artificial light (12-h light/dark cycle) with ad libitum access to food (CE-2, CLEA, Japan) and water. Skeletal muscle (gastrocnemius) of Dnmt3a-Transgenic (3 months old, 26 months old), and age-matched  (3 months old, 26 months old) WT mice  were used.

extract_protocol:
Protease K treated muscle tissues are extracted with phenol, phenol/chloroform, and chloroform. DNA was ethanol precipitated, dissolved in 10 mM Tris-buffer (pH8.0)
Improved PBAT protocol using single-strand DNA ligase (sPBAT), which will be published elsewhere

value: Skeletal muscle, gastrocnemius

value: 3 months


title: WT_KO replicate 3


title: L2_Imp_SMI_R2

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP size-matched input for Imp, rep2

value: Larval head

value: Imp::GFSTF (BDSC:60237)


title: HCC1806-WT_ARC_6

description: Library name: HCC1806-WT_ARC_6


title: HCC1806-WT_ARC_5

description: Library name: HCC1806-WT_ARC_5


title: L2_Imp_SMI_R1

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP size-matched input for Imp, rep1


title: WT_Tg replicate 1


title: PV,M,Saline,48hrs,rep1,b4

description: Library name: AG-6037


title: WT_KO replicate 1


title: WT young replicate 1

description: WT 3mo Gastro 1


title: WT_KO replicate 2


title: HCC1806-WT_ARC_4

description: Library name: HCC1806-WT_ARC_4


title: HCC1806-WT_DMSO_3

description: Library name: HCC1806-WT_DMSO_3


title: WT young replicate 2

description: WT 3mo Gastro 3


title: L2_Imp_IP_R2

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP immunoprecipiated for Imp, rep2

value: anti-FLAG M2


title: Dnmt3a-Tg replicate 3

value: Transgenic


title: L2_Imp_IP_R3

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP immunoprecipiated for Imp, rep3


title: Dnmt3a-Tg replicate 2


title: L2_Imp_IP_R1

description: Second instar (L2, 48 hours after larval hatching), Larval head, iCLIP immunoprecipiated for Imp, rep1


title: WT old replicate 5

description: WT 26mo Gastro 7

value: 26 months


title: HCC1806-WT_DMSO_2

description: Library name: HCC1806-WT_DMSO_2


title: L1_Imp_SMI_R3

description: First instar (L1, 24 hours after larval hatching), Whole larva, iCLIP size-matched input for Imp, rep3

source_name: Whole larva

value: Whole larva


title: HCC1806-WT_DMSO_1

description: Library name: HCC1806-WT_DMSO_1


title: MB157-RB-_ARC_12

description: Library name: MB157-RB-_ARC_12


title: Dnmt3a-Tg replicate 1


title: Dnmt3a-KO replicate 3

value: Knockout


title: L1_Imp_SMI_R1

description: First instar (L1, 24 hours after larval hatching), Whole larva, iCLIP size-matched input for Imp, rep1

value: N/A (input)


title: WT young replicate 3

description: WT 3mo Gastro 4


title: WT old replicate 2

description: WT 26mo Gastro 2


title: WT old replicate 4

description: WT 26mo Gastro 5


title: Dnmt3a-KO replicate 2


title: MB157-RB-_ARC_10

description: Library name: MB157-RB-_ARC_10


title: L1_Imp_IP_R3

description: First instar (L1, 24 hours after larval hatching), Whole larva, iCLIP immunoprecipiated for Imp, rep3


title: WT old replicate 6

description: WT 26mo Gastro 8


title: WT old replicate 3

description: WT 26mo Gastro 4


title: L1_Imp_IP_R1

description: First instar (L1, 24 hours after larval hatching), Whole larva, iCLIP immunoprecipiated for Imp, rep1


title: Dnmt3a-KO replicate 1


title: L1_Imp_IP_R2

description: First instar (L1, 24 hours after larval hatching), Whole larva, iCLIP immunoprecipiated for Imp, rep2


title: Dnmt3a-Tg old  replicate 5

description: Dnmt3a-Tg 26mo Gastro 5


title: Hippocampus DTRpos, scRNA-seq

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Before extracting any tissue, the mice were intracardially perfused with at least 40 mL of cold PBS. Tissues were harvested and digested  decribed in the Methods section of the paper. Alive cells of interest were sorted using a FACS Aria cell sorter and MoFlo Astrios EQ cell sorter according to gating strategy stablished with the same tissue the day before the sorting: for CD4+ T cells the gating was  CD45+ CD3+ CD4+ cells; for the hippocampus CD45- Thy1 - cells. In the hippocampus for each condition (DTR- and DTR+), two mice were pulled together.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Hippocampus

value: Neurons and glia

value: Diphtheria toxin


title: Dnmt3a-Tg old  replicate 6

description: Dnmt3a-Tg 26mo Gastro 6


title: Hippocampus DTRneg, scRNA-seq


title: L1_Imp_SMI_R2

description: First instar (L1, 24 hours after larval hatching), Whole larva, iCLIP size-matched input for Imp, rep2


title: WT old replicate 1

description: WT 26mo Gastro 1


title: Dnmt3a-Tg old  replicate 3

description: Dnmt3a-Tg 26mo Gastro 3


title: MB157-RB-_DMSO_7

description: Library name: MB157-RB-_DMSO_7


title: Arabidopsis, leaf, well-watered, fixed_digested, rep2

city: Gent

first: Marieke

last: Dubois

address: Technologiepark 71

country: Belgium

institute: PSB, Vlaams Instituut voor Biotechnologie (VIB)

data_processing:
The data was processed using Galaxy. Reads were mapped on the Arabidopsis genome (TAIR 10) using the RNA-seq aligner tool STAR (Dobin et al., 2013). Statistical analysis was performed using the DESEQ package (Anders and Huber, 2010).
Assembly: TAIR10
Supplementary files format and content: The Excel file contains the normalized counts for each sample.

organism: Arabidopsis thaliana

source_name: Third true leaf at 14 days after stratification

growth_protocol: Arabidopsis Col-0 was grown under a long-day regime (intensity 110–120 μmol m−2s−1) at 21 °C on the WIWAM platform (http://www.wiwam.be). Five seedlings were grown per pot in order to obtain 80 seedlings per conditions (well-watered or mild drought, see later), per biological replicate. The seeds were sown in 85±1 g of Saniflor compost (Van Isreal N.V., Geraardsbergen, Belgium) with an average absolute water content of 70%. Plants were watered daily until 8 days after stratification (DAS) with a well‐watered regime of soil relative water content (RWC) 69% (2.2 gwater/gsoil). At 9 DAS, half of the pots (randomized) were not watered (MD) until harvest (14 DAS) while the other half kept the well-watered (WW) regime. The biological replicates were harvested as follows: a first experiment was performed to generate all "Rep1" samples and a second, fully independent experiment was performed six months later. All "Rep2" and "Rep3" samples were harvested from that experiment, from independently treated pots.

extract_protocol:
Total RNA was isolated using the ReliaPrep RNA extraction kit (Promega) according to the manufacturer’s instructions.
All samples were further processed by BGI TECH SOLUTIONS (Poland), where the RNA integrity was verified prior to library preparation. The library was sequenced on the DNBseq platform, and around 30M 150 bp pair-end reads were aimed for. After initial filtering by BGI, the number of reads retrieved for each sample was around 20M.

treatment_protocol: Per condition and per biological replicate, 5-6 third true leaves were pooled and immediatly frozen in liquid nitrogen for the "Undigested leaf" samples. For the digested samples (either without ("digested") or with fixation("fixed, digested")), ~80 third true leaves were harvested with a tweezer and pooled for tissue digestion by cell wall degradation. Tissue digestion protocol was adapted from (Ryu et al., 2019). The tissue was chopped and incubated in 1 ml cell wall digestion solution (0.4 M mannitol, 10 mM CaCl2, 20 mM MES, 20 mM KCl, 2% (wt/vol) cellulase and 0.5% (wt/vol) macero enzyme) and subsequently transferred to a 70-μm cell strainer placed in a 6-well plate. Extra cell wall digestion solution was added up to 5 ml. For the samples in which transcription had to be inhibited, Actinomycin D (ActD) was added to a concentration of 35 μM. Cell wall digestion was done by constantly shaking for 75 min at room temperature. After a 7-min centrifugation at 100 g, the pellet was resuspended in 1 ml washing solution (0.4 M mannitol, 10 mM CaCl2, 20 mM MES and 20 mM KCl).

value: Whole leaf, digested in presence of RNA fixative

value: Well-watered


title: MB157-RB-_DMSO_8

description: Library name: MB157-RB-_DMSO_8


title: Arabidopsis, leaf, mild drought, fixed_digested, rep1

value: Third true leaf at 14 days after stratification

value: Mild drought


title: Meninges replicate2, scCITE-seq

source_name: Meninges

value: Meninges

tag: hashid

value: CD4+ T cell


title: Meninges replicate2, scRNA-seq


title: Dnmt3a-Tg old  replicate 4

description: Dnmt3a-Tg 26mo Gastro 4

value: Skeletal muscle, gastrocnemius


title: Arabidopsis, leaf, well-watered, fixed_digested, rep1


title: MB157-RB+_ARC_6

description: Library name: MB157-RB+_ARC_6


title: Dnmt3a-Tg old replicate 1

description: Dnmt3a-Tg 26mo Gastro 1


title: MB157-RB-_ARC_11

description: Library name: MB157-RB-_ARC_11


title: Meninges replicate2, scTcr-seq


title: MB157-RB+_ARC_5

description: Library name: MB157-RB+_ARC_5


title: MB157-RB+_ARC_4

description: Library name: MB157-RB+_ARC_4


title: MB157-RB-_DMSO_9

description: Library name: MB157-RB-_DMSO_9


title: Meninges replicate1, scCITE-seq


title: Arabidopsis, leaf, mild drought, digested, rep2

value: Whole leaf, digested


title: Arabidopsis, leaf, mild drought, fixed_digested, rep2


title: Dnmt3a-Tg young replicate 4

description: Dnmt3a-Tg 3mo Gastro 8

value: 3 months


title: MB157-RB+_DMSO_3

description: Library name: MB157-RB+_DMSO_3


title: Arabidopsis, leaf, mild drought, digested, rep1


title: Meninges replicate1, scTcr-seq


title: Meninges replicate1, scRNA-seq


title: Dnmt3a-Tg young replicate 2

description: Dnmt3a-Tg 3mo Gastro 5

value: Transgenic


title: TKO cells with 602 mutant Dnmt1, day 7

data_processing:
Reads were mapped with BMap
Alignments were summerized with MPTC
Methylation levels and read coverage were exported with MetExport in bedGraph format
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Dnmt1/3a/3b triple knockout embryonic stem cells

growth_protocol: Embryonic stem cells (Day 0) were cultured in MEM medium containing 10% FBS and LIF, and cell differentiation was induced by 3-day adherent cell culture of 1-day-old embryoid bodys in culture medium without LIF . The Day 4 cells were then cultured in 10% KSR-containing medium with Activin A for 3 days (Day 7).

extract_protocol:
The genomic DNA was isolated by standard protocols using phenol/chloroform extraction and ethanol precipitation.
The tPBAT protocol described in Miura F et al., Nucleic Acids Research (2019), 47, e85

treatment_protocol: The cells were recovered with Trypsin-EDTA treatment.

tag: exogenous expression

value: 602-aa N-terminal deletion Dnmt1 mutant

tag: differentiation day

value: Day 7 after induction of differentiation

value: embryonic stem cells


title: Dnmt3a-Tg old  replicate 2

description: Dnmt3a-Tg 26mo Gastro 2

tag: age

value: 26 months


title: Arabidopsis, leaf, well-watered, digested, rep2


title: TKO cells with 602 mutant Dnmt1, day 4

value: Dnmt1/3a/3b triple knockout embryonic stem cells

value: Day 4 after induction of differentiation


title: TKO cells with 602 mutant Dnmt1, day 0

value: Before differentiation(UD, undifferentiated cells)


title: HEK293_N_rep3

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

data_processing:
Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19
Mapped reads were narrowed to their 3’ most nucleotide and converted to bigwig files for positive and negative strands and reads per million normalized bigwig files for positive and negative strands.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files of reads narrowed to their 3’ most nucleotide for positive and negative strands and reads per million normalized  bigwig files for positive and negative strands.

source_name: HEK293 cell line

growth_protocol: Cells were cultured in a 37°C incubator with 5 % CO2 to 80-90 % confluency before harvesting

extract_protocol:
Subcellular fractionation into nuclear and cytoplasmic fractions followed by RNA isolation using Triazol reagent (Fischl et al., 2020).
The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit (Lexogen)

tag: subcellular fraction

value: Nuclear


title: Dnmt3a-Tg young replicate 1

description: Dnmt3a-Tg 3mo Gastro 3


title: Brevibacillus brevis, PLA Treated 3

city: Jeonju-si

first: Jaeyoung

last: Yu

address: Baekje-daero

country: South Korea

institute: Jeonbuk National University

description: Processeddatafile.xlsx

data_processing:
the raw reads were trimmed using Trimmomatic (v0.39) by filtering out adaptor-only nucleotides with a minimum length of 75 bp.
Trimmed reads were aligned to the reference genome (GCF_900637055.1) using HISAT2 software (v2-2.1.0).
Reads were also aligned without using the ‘--rna-strandness RF’ option to compare reads with and without strand information. We used FeatureCounts to quantify mapped reads.
DEGs were confirmed using the Bioconductor package (edgeR, v3.36.0) based on the generalized linear model used for RNA-Seq data analysis by considering gene expression as negative binomial.
To decrease the influence of outlier genes, the edgeR-robust method was used. We used a false discovery rate (FDR) < 0.05 significance cutoff for DEGs.
Assembly: GCF_900637055.1
Supplementary files format and content: Processed data excel file includes CPM values for each sample. All data is organized in one file.
Supplementary files format and content: Genes that do not match the Uniprot DB are filtered out. Filtered data can also be checked in Excel. Control mean Brevibacillus brevis grown without the PLA film, and PLA means B. brevis grown in the presence of the PLA film.

organism: Brevibacillus brevis

source_name: prokaryotes

growth_protocol: B. brevis KACC10857 were grown in minimal synthetic media (MSM) (1 g L-1 K2HPO4, 0.2 g L-1 MgSO4·7H2O, 0.15 g L-1 KCl, 0.1 g L-1 CaCl2·2H2O, 1.09 mg L-1 FeSO4·7H2O, 1 mg L-1 ZnSO4·7H2O, 1.07 mg L-1 MnSO4·H2O) at 30 °C and 150 rpm. 0.5wt% soytone and 0.1wt% gelatin were added to MSM.

extract_protocol:
Total RNA integrity was assessed using the Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) and RiboGreen dye.
Libraries for RNA-Seq were obtained from total RNA using the TruSeq Stranded mRNA Sample Preparation Kit. Poly A+ RNA was purified by AMPure XP beads and fragmented to 200 ~ 700 bp. cDNA was synthesized with reverse transcriptase (SuperScript II) and random primers. The strand-specific RNA-Seq library was obtained by the dUTP second-strand marking method. Double-stranded DNA was ligated to barcoded TruSeq adapters for library preparation. PCR was carried out on the size of fragments selected for library amplification. Libraries were sequenced on a NovaSeq 6000 System (Illumina) using a paired-end run (2 × 101 bases).

treatment_protocol:
PLA films were formed by solvent casting method. 0.5 g PLA was dissolved in 10 mL chloroform. The solution was stirred at room temperature for 24 hours and transferred onto a silicon mold with a size of 8 × 8 cm. Then, it was dried overnight in a fume hood. After drying, the PLA films were dried in a vacuum oven at 40 °C for 2 days. The PLA films were cut into 1 × 3 cm for the biodegradation test. The thickness of the film was approximately 100 μm. The PLA films were treated in a UV lamp with a wavelength of 365 nm (KCHS-04; KJUV co., Incheon, Korea) for 30 mins to induce partial photolysis and to simulate natural weathering exposed to the sun before weighing. For the biodegradation test, PLA films were sterilized with 70% ethanol for 15 minutes, washed with distilled water, and then air-dried for 15 minutes on a laminar flow hood.
20 mL of bacteria were added to a 50 mL Erlenmeyer flask containing the prepared PLA film. The PLA film was biodegraded in an incubator at 30 °C and 150 rpm.

value: prokaryotes

value: B. brevis KACC10857

value: stationary

value: grown on PLA


title: Arabidopsis, leaf, well-watered, digested, rep1

value: Third true leaf at 14 days after stratification

value: Well-watered


title: Arabidopsis, leaf, mild drought, undigested, rep3

value: Whole leaf, undigested

value: Mild drought


title: Arabidopsis, leaf, mild drought, undigested, rep2


title: TKO cells with full-length Dnmt1, day 7

value: full-length Dnmt1


title: Arabidopsis, leaf, mild drought, undigested, rep1


title: HEK293_N_rep2


title: Brevibacillus brevis, PLA Treated 2

description: Processeddatafile.xlsx


title: HEK293_N_rep1


title: Brevibacillus brevis, PLA Treated 1

description: Processeddatafile.xlsx


title: TKO cells with full-length Dnmt1, day 4


title: HEK293_C_rep3

value: Cytoplasmic


title: Arabidopsis, leaf, well-watered, undigested, rep3


title: Dnmt3a-Tg young replicate 3

description: Dnmt3a-Tg 3mo Gastro 7

value: Skeletal muscle, gastrocnemius

value: 3 months

value: Transgenic


title: MB157-RB+_DMSO_2

description: Library name: MB157-RB+_DMSO_2


title: HEK293_C_rep2


title: TKO cells with full-length Dnmt1, day 0

value: Dnmt1/3a/3b triple knockout embryonic stem cells

value: embryonic stem cells


title: Brevibacillus brevis, Control 2

description: Processeddatafile.xlsx

value: control


title: MB157-RB+_DMSO_1

description: Library name: MB157-RB+_DMSO_1


title: Brevibacillus brevis, Control 3

description: Processeddatafile.xlsx


title: Arabidopsis, leaf, well-watered, undigested, rep1


title: HEK293_C_rep1


title: Arabidopsis, leaf, well-watered, undigested, rep2


title: Brevibacillus brevis, Control 1

description: Processeddatafile.xlsx


title: WJF7

status: Public on Jan 15 2025

first: Jinfang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

description: genomic DNA with in-vitro-expressed ClNAC56 protein

data_processing:
Library strategy: DAP-Seq
The DAP-seq reads were aligned reference genome using bowtie2
After sorting and indexing, the duplicated reads were removed using Picard (http://broadinstitute.github.io/picard/) with default parameters
The peaks were called using MACS2, and the peaks of the three replicates were merged using bedtools
T1 peaks contain data WJF5, while T2 to WJF6, and T3 to WJF7.
Supplementary_files_format_and_content: peaks

organism: Citrullus lanatus

source_name: leaves

extract_protocol:
The purified in-vitro-expressed ClNAC56 protein combinded with DNA library. The protein-DNA complexs was obtained by washing buffer (PBS+0.1%CA630)
Libraries were prepared according to Illumina's NEBNext Ultra DNA Library Prep Kit (E7370S).

tag: tissues

value: leaves


title: WJF6


title: WJF2-2

description: genomic DNA with in-vitro-expressed MBP protein (control)


title: WJF2


title: WJF1


title: clnor 42 dap-1

data_processing:
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
TPM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Genome_build: http://cucurbitgenomics.org/organism/21;
Supplementary_files_format_and_content: exp_detail_20210325_105822.txt  (text file includes TPM values for each Sample)

source_name: flesh

growth_protocol: The wild type (WT) and clnor mutant fruits were harveseted at 10 DAP,18 DAP,26 DAP, 34 DAP and 42 DAP (days after pollination)

extract_protocol:
RNA was extracted from WT and clnor mutant fruits at 10,18,26,34 and 42 DAP with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed
The 30 libraries were built by TruseqTM RNA sample prep kit (Illumina, USA).

value: 42 days after pollination

value: clnor mutant

value: flesh


title: clnor 42 dap-2


title: WT 42 dap-3

value: wild type


title: WT 42 dap-2


title: WT 42 dap-1


title: clnor 34 dap-3

value: 34 days after pollination


title: clnor 34 dap-1


title: WT 34 dap-3


title: clnor 34 dap-2


title: WT 34 dap-2


title: WT 34 dap-1


title: clnor 26 dap-3

value: 26 days after pollination


title: clnor 26 dap-1


title: WT 26 dap-1


title: WT 26 dap-2


title: WT 26 dap-3


title: clnor 26 dap-2


title: clnor 18 dap-3

value: 18 days after pollination


title: TKO cells

value: Before differentiation(UD, undifferentiated cells)


title: WT 18 dap-3


title: WJF5


title: clnor 18 dap-1


title: WT 18 dap-2


title: clnor 18 dap-2


title: WT 18 dap-1


title: clnor 10 dap-3

value: 10 days after  pollination


title: clnor 42 dap-3


title: clnor 10 dap-2


title: clnor 10 dap-1


title: WT 10 dap-2


title: WT 10 dap-1

value: 10 days after pollination


title: WT 10 dap-3