title: Berti’s Lymphoma, P230, scRNA-seq


title: Berti’s Lymphoma, P195, scRNA-seq

status: Public on Oct 24 2024

type: SRA

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids); filtered_contig_annotations.csv and clonotypes.csv (information about TCR sequencing)
Supplementary files format and content: *filtered_contig_annotations.csv (TCR alpha beta clonotypes file )
Supplementary files format and content: *clonotypes.csv (TCR alpha beta clonotypes file )
Supplementary files format and content: *filtered_contig_annotations_gd.csv (TCR gamma delta clonotypes file )
Supplementary files format and content: *clonotypes_gd.csv (TCR gamma delta clonotypes file )

molecule: total RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 and v2 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

tag: tissue

value: Skin

tag: cell type

value: mixture of skin cells

tag: condition

value: Berti’s Lymphoma


title: CD4 MF, PGS, scRNA-seq

value: CD4 MF


title: HepG2_Taze_1, ATAC-seq

city: Cheongju-si

first: Jaehyun

last: Lee

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological Science and Biotechnology

country: South Korea

institute: Chungbuk National University

library_source: genomic

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
To ensure data quality, the raw files were trimmed using Trim Galore (version 0.6.6, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters.
These trimmed reads were then aligned to the human genome (hg38 assembly) using Bowtie2 (version 2.3.5.1) with default parameters.
To identify peaks over background signals, the makeTagDirectory and findPeaks commands from HOMER (version 4.11.1) were utilized.
A FDR cutoff of 0.05 was employed. The total number of mapped reads for each sample was normalized to 10 million mapped reads. Differential peak analysis for the ATAC-seq data was performed using the getDifferentialPeaks command.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: peaks.txt

molecule: genomic DNA

source_name: Liver

growth_protocol: HepG2 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Tazemetostat (EPZ-6438)-treated 50,000 of HepG2 cells were pretreated with 200 U/ml DNase (Worthington) for 30 minutes at 37 °C to remove free-floating DNA and digest DNA from dead cells. The cells were then washed, resuspended in cold phosphate-buffered saline (PBS). Cells were harvested from culture plate using TrypLE (12604013; Gibco) and resuspended in 1 mL of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.5 (15567-027; Invitrogen), 10 mM NaCl (AM9759; Invitrogen), and 3 mM MgCl2 (AM9530G; Invitrogen) in nuclease-free water), Cells were centrifuged at 500 relative centrifugal force (RCF) for 5 minutes in a pre-chilled (4 °C) fixed-angle centrifuge. After centrifugation, the supernatant was carefully aspirated to avoid the cell pellet, and the cells were then resuspended in 50 μl of RSB containing 0.1% NP40 (11332473001; Roche), 0.1% Tween-20 (11332465001; Roche), and 0.01% digitonin (G9441; Promega). This cell lysis reaction was incubated on ice for 3 minutes. After lysis, 1 ml of RSB containing 0.1% Tween-20 (without NP40 or Digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 minutes at 500 RCF in a pre-chilled (4 °C) fixed-angle centrifuge. The supernatant was removed, and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl transposase26 (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water). The transposition reactions were incubated at 37 °C for 30 minutes in a thermomixer with shaking at 1,000 revolutions per minute (RPM). Reactions were cleaned up with MinElute Reaction Cleanup Kit (28206; Qiagen).
Reactions were pre-amplified for 5 cycles using NEBNext High-Fidelity 2x PCR MasterMix (M0541L; NEB) with adapter primers. The amplification profiles were manually assessed to determine the number of additional cycles to amplify as previously described 52. The final amplified library samples were stored at -80 °C for ATAC-seq after library purification with AMPure XP (A63880; Beckman). Libraries were validated using the Agilent High Sensitivity D1000 kit (5067-5584, 5067-5585; Agilent) and were subjected to high-throughput sequencing using the Illumina HiSeq 2500 Sequencer.

treatment_protocol: HepG2 cells were stabilized for 24 h and 5 μM Tazemetostat (MCE) dissolved in DMSO was treated for 48 h.

value: Liver

tag: cell line

value: Epithelial cell

tag: genotype

value: WT

tag: treatment

value: Tazemetostat treatment


title: CD4 MF, P303, scRNA-seq


title: Berti’s Lymphoma, P218, scRNA-seq


title: Gammadelta MF, P318A, scRNA-seq

value: Gammadelta MF


title: CD4 MF, P311, scRNA-seq


title: FRO-cont2

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

institute: CHA university

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: ATC cell line

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: ATC cell line

value: FRO

value: anaplastic thyroid cancer

value: DMSO


title: FRO-cont-1


title: CD4 MF, P204, scRNA-seq


title: HepG2_Ctrl_2, ATAC-seq

value: Untreated


title: CD4 MF, P171, scRNA-seq


title: control vigorous:M. sylvestris_2 phloem 60dabb

city: Qingdao

first: Yanjing

last: Shi

state: Shandong

address: 53# Zhengzhou Road

country: China

institute: Qingdao university of Science & Technology

description: FPKM of M_syl.txt

data_processing:
Raw data (raw reads) were processed using Trimmomatic， . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
clean reads were mapped to reference genome using hisat2
FPKM[3] value of each gene was calculated using cufflinks[4]
, and the read counts of each gene
were obtained by htseq-count，
Assembly: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=491
Supplementary files format and content: tabdelimited text files include FPKM of each sample

organism: Malus sylvestris

source_name: phloem

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion)
The libraries  were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,  CA, USA) according to the manufacturer’s instruction

value: phloem

tag: phenotype

value: vigorous


title: CD4 MF, P76, scRNA-seq


title: FRO-3μM-2

value: Auranofin


title: FRO-3μM-1


title: 8505c-cont-2


title: Healthy control skin, P116, scRNA-seq

value: Skin

value: Healthy control skin


title: Healthy control skin, P121, scRNA-seq

value: mixture of skin cells


title: Healthy control skin, P115, scRNA-seq


title: HepG2_Taze_2, ATAC-seq


title: Phloem  of PYTC at bud break stage replicate3

data_processing:
Raw data (raw reads) were processed using Trimmomatic， . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
Assembly: hista2 clean read map to genome downloaded from https://data.jgi.doe.gov/refine-download/phytozome?genome_id=491
Supplementary files format and content: budbreakstage_FPKM.txt
Supplementary files format and content: tabdelimited text files include FPKM of each sample

molecule: polyA RNA

organism: Malus hupehensis


title: VIM-AS1 KD Fibroblasts Bio rep3

city: Evry

first: Nicolas

last: FORTUNEL

address: 2 Rue Gaston Cremieux

country: France

institute: CEA

data_processing:
Read Quality: For patients RNA-seq: reads were preprocessed by trimming the adapters using cutadapt v. 1.134  and quality filtered (QV > 15) check on fastqc tool v. 0.11.7.5 For VIM-AS1 knockdown: reads were trimmed with TrimGalore v0.6.7, and the overall quality of raw sequencing data was checked using FastQC v0.11.9.5
Pseudoaligment and quantification: The clean Fastq files were used as an input of Salmon tool v 1.6.0.6 The human transcriptome GRCh37 v32 (for RNA-seq from patients) and  GRCh38.p13 v43 (for RNA-seq from VIM-AS1 KD) fasta files from GENCODE were used to generate the Salmon index. Transcript expression quantification was performed for each sample using Salmon tool (parameters: --numBootstraps, --validateMappings).
Gene filtering: batch effects were adjusted using the ComBat function from the R package sva version 3.36.0,7 all genes lowly expressed were removed using filterByExpr function on edgeR package version 3.30.3  (Patients RNA-seq) and 3.42.4 (VIM-AS1 KD).
Normalization: We applied normalisation by the method of trimmed mean of M-values (TMM). This method is performed using the calcNormFactors function from edgeR package version 3.30.3 (Patients RNA-seq) and 3.42.4 (VIM-AS1 KD).
Differential expression analysis: Mean-variance relationship was estimated using the estimateDisp function from the EdgeR package. Moderated p values were calculated by fitting a quasi-likelihood negative binomial generalized log-linear model to the count data using the empirical Bayes method (glmQLFit function from the EdgeR package). RNAs satisfying the following criteria were tagged as differentially expressed (DE): |fold-change| > 1.5 and Pvalue < 0.05.
Assembly: GRCh37 v32 (for RNA-seq from patients) and GRCh38.p13 v43 (for RNA-seq from VIM-AS1 KD)
Supplementary files format and content: TXT files includes raw counts (raw_counts)  and cpm values (norm_counts) for each sample from patients and VIM-AS1 KD sets

source_name: skin

growth_protocol: For patients RNA-seq: Fibroblasts were derived from skin explants issued from patient forearm after local anesthesia with a standardized dermatologic punch. For VIM-AS1 KD: A strain of primary dermal fibroblasts from a healthy female donor  (skin fibroblasts) was obtained at CEA from a breast skin surgical sample. All fibroblasts were cultured in Dulbecco’s Modified Eagle Medium – Glutamax medium (Thermo Fisher Scientific Inc) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific Inc) and 1% penicillin/streptomycin (Thermo Fisher Scientific Inc) in a 5% CO2 humid 37°C incubator.

extract_protocol:
Total RNA from fibroblast strains was isolated and purified using the RNeasy Plus Mini kit (Qiagen), according to the manufacturer’s instructions. Total amount and integrity of RNA samples were evaluated by NanoDrop One (Thermo Fisher Scientific) and Bioanalyzer System (Agilent technologies). The integrity criteria were values between 1.8 and 2.2 (A 260/280), >1.8 (A260/230), and RIN ≥ 8.
RNA sequencing of patient fibroblasts was performed at the CEA Genomic Center (CNRGH, Evry, France). RNA libraries were prepared using the Illumina Truseq RNA Library Preparation Kit V2 according to the manufacturer's instructions. Paired-end RNA sequencing was performed on HiSeq4000 (Illumina) with an input of 1 µg, with 100 bp paired-end reads. A single sequencing run was performed per patient. For sequencing after VIM-AS1 knockdown, RNA sequencing was performed at the Curie Institute NGS/Bioinformatics core facilities. An Illumina Stranded mRNA Prep Kit was used for library preparation, followed by paired-end RNA sequencing on an Illumina NovaSeq System, with an input of 1 µg, with 100 bp paired-end reads.  A single sequencing run was performed per biological replicate.

treatment_protocol: For VIM-AS1 KD: Primary skin fibroblasts obtained from a healthy donor were cultured in a DMEM complete medium containing 10% FBS and treated with 25 nM of custom-designed Antisense LNA GapmeRs-ASOs or scramble LNA-GapmeRs (Qiagen) using Lipofectamine 3000 (Thermo Fisher Scientific Inc) at a final concentration of 1 µL/mL and incubated for 24 hours. Cells were then starved in a DMEM medium containing 1% FBS for another 24 hours, and stimulated with TGFB1 10 ng/mL for another 72 hours, for a total of 120 hours of treatment

value: skin

value: Fibroblasts

value: VIM-AS1 knockdown

value: TGFB 10ng/mL


title: VIM-AS1 KD Fibroblasts Bio rep4


title: 8505c-cont-1


title: Phloem  of PYTC at bud break stage replicate2

value: WT


title: Healthy control skin, P112, scRNA-seq


title: 6-12

city: Washington, DC

first: Max

last: Stevenson

state: DC

address: 3970 Reservoir Rd. NW

country: USA

institute: Georgetown University

description:
NILAD-006-M12
NILAD-006-M12

data_processing:
Data analysis was performed using Partek Flow software to identify differentially expressed microRNAs. An optimized workflow was used to perform quality assessment, alignment, quantification, normalization, and different analysis. Quality assessment of data in fastq format was performed in Partek flow and reads containing the adapters or low-quality bases (Qscore ≤5) were removed. The trimmed reads were then aligned to the hg38 reference genome using the Bowtie method. The aligned reads were then quantified to the miRBase reference to obtain the total miRNA read count for each sample.
Assembly: hg38
Supplementary files format and content: Excel

source_name: CSF

extract_protocol:
Cell-free total RNA was isolated from 200 μl of CSF using the Qiagen miRNAeasy extraction kit
Samples were normalized to an input volume of 5 μl RNA eluate to prepare miRNAseq libraries using Qiagen QiaSeq miRNA-seq library preparation kit

treatment_protocol: AD patients were randomized to placebo for 12 months or nilotinib,150 mg for 6 months followed by nilotinib, 300 mg, for another 6 months

value: CSF

tag: disease

value: AD

tag: time point

value: Placebo


title: VIM-AS1 KD Fibroblasts Bio rep2


title: CD4 MF, P312, scRNA-seq

value: CD4 MF


title: HepG2_Ctrl_1, ATAC-seq

value: Liver

value: Epithelial cell


title: Phloem  of PYTC at bud break stage replicate1

value: phloem


title: VIM-AS1 KD Fibroblasts Bio rep1


title: 8505c- 3μM-2

value: ATC cell line

value: anaplastic thyroid cancer


title: 8505c- 3μM-1

value: Auranofin


title: Phloem  of QZ1 at bud break stage replicate3

value: Columnal


title: control vigorous:M. sylvestris_1 phloem 60dabb

description: FPKM of M_syl.txt

value: vigorous


title: Scrambled Fibroblasts Bio rep 3

value: skin

value: Scramble


title: Scrambled Fibroblasts Bio rep 2

value: Fibroblasts


title: Phloem  of QZ1 at bud break stage replicate2


title: Scrambled Fibroblasts Bio rep 1

value: TGFB 10ng/mL


title: KB-052

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v2.10)
Trimmed reads aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.8a)
featureCounts (v2.0.2)[3] was used to count the number of mapped reads to each gene.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: Comma delimited file includes CPM values for each sample

source_name: Adipose

extract_protocol:
Frozen adipose tissue was disrupted using the Qiagen TissueRuptor (VA and PLHIV cohorts) or ceramic beads and grinder system (MP Biomedicals LLC FastPrep-24 5G and Lysing Matrix D tubes with 1.4mm Ceramic beads for the discovery cohort) in Qiazol Lysis Reagent. RNA was purified using the Qiagen RNEasy Plus Mini kit. An on-column DNAse digestion was performed for the discovery and VA cohorts.
NEBNext Ultra II RNA Library Prep Kit (NEB) per manufacturer’s instructions

value: Adipose

tag: bmi

tag: age

tag: Sex

value: Female


title: KB-051

value: Male


title: Hu3112_v_3_RNAPolIIS2_ChIP_seq

city: Huddinge

first: Shengyuan

last: Zeng

state: Stockholm

address: Blickagången 16

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: the read counts gene list with start and end position for TSS and ORF, the read count results for the genes for all ChIP sample, and difference analyzed by DeSeq2

data_processing:
Raw sequencing data from Nextseq 2000 (Bcl files) were converted and demulti-plexed to fastq files using the bcl2fastq v2.20.0.422 program. The bwa 0.7.17 and Samtools 1.17 were used for alignment and file convert. Later, we used deeptools 3.3.2 to compute pairwise Spearman correlation coefficients, normalized the bigwig files, count the reads. The graphs were performed by using R. For Volcano plots and Bubble plots batch effects were removed using DEseq2 .
Assembly: ASM294v2
Supplementary files format and content: we count all genes at TSS region and ORF region, and analyzed the read count by DeSeq2

organism: Schizosaccharomyces pombe

growth_protocol: Fission yeast cells were grown in PMG (Pombe Minimal Glutamate medium) media at 30°C, 200 rpm until cells reached mid-log phase. Vegetative cells (V cells) were harvested at mid-log phase. For quiescence experiments, the mid-log phase cells were washed three times with PMG without nitrogen (PMG-N) media to completely remove the nitrogen, and then switched to PMG-N media and incubated for 24 hours before harvesting the quiescent cells (Q cells).

extract_protocol:
After immunoprecipitation, three washing steps were performed using low salt wash buffer (20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 2 mM EDTA (pH 8.0), 1% (w/v) Triton X-100, 0.1% SDS), high salt wash buffer (20 mM Tris-HCl (pH 8.0), 500 mM NaCl, 2 mM EDTA (pH 8.0), 1% (w/v) Triton X-100, 0.1% SDS), and LiCl wash buffer (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA (pH 8.0), 1% IGEPAL CA-630, 0.1% sodium deoxycholate) successively. ChIP-DNA was extracted using the ChIP DNA Clean & Concentrator kit (ZYMO RESEARCH, D5205), and DNA concentration was measured using the Qubit dsDNA HS assay kit (ThermoFisher, Q33231).
The sequencing library was prepared using the ThruPLEX DNA-Seq kit (TaKaRa, R400676) with the DNA HT Dual Index Kit – 96N Set A (TaKaRa, R400660). Sequencing was performed using the Illumina Nextseq 2000 platform with the P3 v3 50 kit (36 + 8 + 8 + 36 cycles, single-end sequencing) at the BEA facility (Huddinge, Sweden).

treatment_protocol: The mid-log phase vegetative cells (growing in PMG media) and quiescent cells (after switch to PMG-N media for 24 hours) were cross-linked with a final concentration of 1% formaldehyde solution (Sigma, 252549) at 25°C for 30 minutes and then quenched by a final concentration of 125 mM Glycine at 25°C for 5 minutes. The cross-linked cells were washed twice with cold 1 ´ PBS and snap-frozen using dry ice. The frozen cell pellets were thawed and re-washed with ChIP lysis buffer (50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 1% (w/v) Triton X-100, 0.1% (w/v) SDS and 0.1 sodium deoxycholate). After the final wash, the cell solution was transferred into pre-cooled Sarstedt screw-cap tubes containing 500 µl of 0.5 mm Zirconia/Silica Beads (Techtum, 11079105z). Cell lysis was performed using a FastPrep-24 machine (MP) until more than 90% of the cells were broken. After puncturing the bottom of the Sarstedt screw-cap tube and performing a low-speed centrifuge, the bottom part of the solution was collected, avoiding any beads. The solution was then transferred into 1.5 ml Bioruptor microtubes (Diagenode, C30010016) and sonicated using a Bioruptor apparatus. After determining the chromatin concentration and fragment size, the ideal sheared chromatin (chromatin fragment sizes were around 500 base pairs) was stored at -80°C.

value: wild type

value: mat1-M smt-0 pht1-myc

value: anti RNA pol II S2, vegetative


title: Hu3112_v_3_MyC_ChIP_seq

value: anti H2A.Z, vegetative


title: Phloem  of QZ1 at bud break stage replicate1

value: phloem


title: phloem of A1d at bud break stage replicate3

value: partial  GA insenstity


title: KB-050


title: KB-049


title: KB-048


title: phloem of A1d at bud break stage replicate2


title: KB-047


title: Hu3112_v_3_H3K9me3_ChIP_seq

value: anti H3K9me3, vegetative


title: Hu3112_v_3_H3K9me2_ChIP_seq

value: anti H3K9me2, vegetative


title: KB-046


title: Scrambled Fibroblasts Bio rep 4


title: phloem of A1d at bud break stage replicate1


title: Hu3112_v_3_H3K9ac_ChIP_seq

value: anti H3K9ac, vegetative


title: Hu3112_v_3_RNAPolIIS5_ChIP_seq

value: anti RNA pol II S5, vegetative


title: KB-044


title: KB-045


title: control vigorous :PYTC_2 phloem 60dabb

description: FPKM of 4 samples -67DABB.TXT

value: vigorous

value: WT


title: KB-043


title: KB-042


title: KB-041


title: Hu3112_v_3_H3K4me3_ChIP_seq

value: anti H3K4me3, vegetative


title: dwarfing Apple rootstock phloem：A1d_2 60dabb

description: FPKM of 4 samples -61DABB.TXT

value: dwarfing

value: GA insensitive mutant


title: Hu3112_v_3_H3_ChIP_seq

value: anti H3, vegetative


title: KB-039

value: Adipose

value: Male


title: Hu3112_v_2_RNAPolIIS5_ChIP_seq

value: wild type

value: mat1-M smt-0 pht1-myc


title: KB-038

value: Female


title: dwarfing Apple rootstock phloem：A1d_1 60dabb

description: FPKM of 4 samples -60DABB.TXT

value: phloem


title: KB-034


title: KB-037


title: KB-035


title: Hu3112_v_2_MyC_ChIP_seq

value: anti H2A.Z, vegetative


title: KB-033


title: Defender2-Rep2

city: Guangzhou

first: Weixing

last: Zhang

address: 135 Xingang west road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
The Paired-end raw reads were mapped to the human reference genome (hg19) with Bowtie2 after adapter sequences were trimmed.
The reads were then filtered for mitochondrial reads, low-quality reads, PCR duplicates, and black list regions. The peak calling of each sample was performed by MACS2.
Peak counts were combined into an N × M matrix and then be normalized by R package DiffBind, where N represents called peaks, M represents the samples, and each value Di,j represents the peak intensity for respective peak i in sample j.
The HOMER's promoter analysis was used to identify enriched motifs for differential peak set. The differential analysis was conducted using Wilcoxon's-test.
Assembly: hg19
Supplementary files format and content: counts

organism: Apis mellifera

source_name: Antennae

growth_protocol: All MDA-MB-231 cell lines were grown in DMEM medium (HyClone) with 10% FBS (ExCell Bio) and 1% penicillin-streptomycin (Gibco).

extract_protocol:
ATAC–seq of HOTAIR-Ctrl, HOTAIR-OE, HOTAIR-Ctrl YTHDF3-KO and HOTAIR-OE YTHDF3-KO cells were performed as previously described (Corces et al., 2017). Briefly, 50000 cells were pelleted, resuspended in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40, and immediately centrifuged at 500g for 10 min at 4 °C. The nuclei pellets were resuspended in 50 μl of transposition buffer (25 μl of 2× TD buffer, 22.5 μl of distilled water, 2.5 μl of Illumina Tn5 transposase) and incubated at 37 °C for 30 min. Transposed DNA was purified with the DNA Clean & Concentrator-5 kit (Zymo Research), and eluted in 10 μl of EB buffer.
Library fragments were amplified using NEBnext PCR master mix as previously described (Corces et al., 2017)

value: Antennae


title: KB-032


title: KB-031


title: Hu3112_v_2_H3K9me3_ChIP_seq

value: anti H3K9me3, vegetative


title: Defender1-Rep1


title: KB-030


title: control vigorous :PYTC_1 phloem 60dabb

description: FPKM of 4 samples -66DABB.TXT


title: KB-029


title: Hu3112_v_2_H3K9me2_ChIP_seq

value: anti H3K9me2, vegetative


title: Hu3112_v_2_H3K9ac_ChIP_seq

value: anti H3K9ac, vegetative


title: KB-040


title: KB-026


title: Forager3-Rep3


title: Forager2-Rep2


title: KB-027


title: KB-024


title: KB-023


title: Hu3112_v_2_RNAPolIIS2_ChIP_seq

value: anti RNA pol II S2, vegetative


title: Hu3112_v_2_H3K4me3_ChIP_seq


title: Hu3112_v_1_RNAPolIIS5_ChIP_seq

value: anti RNA pol II S5, vegetative


title: Hu3112_v_2_H3_ChIP_seq


title: KB-020


title: Forager1-Rep2


title: Nurse3-Rep3


title: KB-022


title: Defender3-Rep3


title: KB-016


title: Nurse2-Rep2


title: KB-019


title: Nurse1-Rep2


title: KB-017


title: KB-015


title: Hu3112_v_1_MyC_ChIP_seq


title: Newly_emerged_worker3-Rep3


title: KB-014


title: KB-013


title: KB-012


title: Newly_emerged_worker2-Rep2


title: KB-011


title: Hu3112_v_1_Input_ChIP_seq

value: Input, vegetative


title: KB-010


title: Newly_emerged_worker1-Rep1


title: Hu3112_v_1_H3K9me3_ChIP_seq


title: KB-009


title: Hu3112_v_1_H3K9me2_ChIP_seq


title: KB-007


title: KB-008


title: HSALR mouse RNA-Seq 3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

data_processing:
Reads were subject to adapter clipping and quality filtering using BBDUK2 from BBMap version 37.02
rRNA-mapped reads were discarded with Bowtie 2 version 2 2.4.4
Gene expression levels were calculated with RSEM version 1.3.1; ENSEMBL 111 annotations were applied
Assembly: GRCm39
Supplementary files format and content: Tab-delimited default output files of RSEM, with the following columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

organism: Mus musculus

source_name: skeletal muscles, quadriceps

extract_protocol:
TRIzol Reagent isolation; 0.5ug of total RNA was used for libraries preparation
TruSeq totalRNA stranded with RiboZero Human/Mouse/Rat Gold

value: skeletal muscles, quadriceps

value: transgenic mice expressing a human skeletal actin gene containing a CTG repeat expansion of approximately 220 repeats


title: Hu3112_v_1_H3K9ac_ChIP_seq


title: KB-004


title: KB-003


title: Hu3112_v_1_RNAPolIIS2_ChIP_seq


title: HSALR mouse RNA-Seq 2


title: Hu3112_v_1_H3K4me3_ChIP_seq

value: anti H3K4me3, vegetative


title: KB-002

value: Adipose


title: HSALR mouse RNA-Seq 1


title: Hu3112_v_1_H3_ChIP_seq

value: anti H3, vegetative


title: KB-028


title: Hu3112_G0_3_RNAPolIIS5_ChIP_seq

value: wild type

value: anti RNA pol II S5, nitrogen starvation for 24 hours


title: WT mouse RNA-Seq 2

value: WT


title: WT mouse RNA-Seq 3


title: KB-036

value: Male


title: KB-018


title: KB-025


title: Hu3112_G0_3_RNAPolIIS2_ChIP_seq

value: mat1-M smt-0 pht1-myc

value: anti RNA pol II S2, nitrogen starvation for 24 hours


title: RT-19


title: Hu3112_G0_3_H3K9me3_ChIP_seq

value: anti H3K9me3, nitrogen starvation for 24 hours


title: KB-006


title: Hu3112_G0_3_MyC_ChIP_seq

value: anti H2A.Z, nitrogen starvation for 24 hours


title: RT-20


title: RT-18


title: HSALR mouse smallRNA-Seq 2

library_source: other

data_processing:
Raw reads, with adapters already clipped by a provider of sequencing services, were turned into a FASTA format using fastq_to_fasta utility from FASTX_Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Reads were counted with fastx_collapser utility from FASTX_Toolkit
Assembly: GRCm39
Supplementary files format and content: FASTA files with a header in the following format: a consecutive sequence ID, followed by a "-", followed by a raw read count (e.g. >4-750152)

molecule: other

extract_protocol:
TRIzol Reagent isolation; 1ug of total RNA was used for libraries preparation
NebNext small RNA library with selection 18-35bp
smallRNA seq


title: KB-005


title: RT-17

value: Female


title: HSALR mouse smallRNA-Seq 3


title: Hu3112_G0_3_H3K9me2_ChIP_seq

value: anti H3K9me2, nitrogen starvation for 24 hours


title: RT-16


title: KB-001


title: HSALR mouse smallRNA-Seq 1


title: Hu3112_G0_3_H3K9ac_ChIP_seq

value: anti H3K9ac, nitrogen starvation for 24 hours


title: RT-14


title: WT mouse smallRNA-Seq 3


title: WT mouse RNA-Seq 1


title: Hu3112_G0_3_H3K4me3_ChIP_seq

value: anti H3K4me3, nitrogen starvation for 24 hours


title: Zfp36l1/Zfp36l2 dKO 3

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
The quality of RNA-sequencing data was assessed using FastQC (0.11.9; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed using Trim Galore (0.6.6) and mapped to mouse genome GRCm38 using HiSat2 (2.1.0).
Raw counts were calculated with SeqMonk (1.48.0; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), using the GRCm38.90 annotation release.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing gene names and IDs, together with raw read counts for all samples, generated using Seqmonk

source_name: Peripheral LN

growth_protocol: For inducible germinal centre B cell culture (iGCB), 3T3 cells expressing mouse CD40L and human BAFF (40LB cells) were irradiated (~120Gγ) and seeded at 100×10^3 cells per well in a 12-well plate. One day later, 40×10^3 naive B cells were isolated from peripheral lymph nodes using the B cell isolation kit (Miltenyi Biotec), and added to 40LB cells in the presence of 2ng/ml mIL-4. On day 4, B cells were harvested and re-seeded on freshly irradiated 40LB cells in the presence of 5 ng/ml recombinant mouse IL-21 (PeproTech).

extract_protocol:
On day 7, 0.5x10^6 CD19+ B220hi CD138- TACI- iGCB cells were FACS-sorted, washed twice with ice-cold PBS and cell pellets were snap frozen in liquid nitrogen. RNA was extracted using the RNeasy Micro Kit (Qiagen) and its quality was assessed on a 2100 Bioanalyser (Agilent). RNA integrity numbers > 8 of total RNA were used to generate cDNA.
Opposing strand-specific RNA-sequencing libraries were generated using the NEB PolyA kit (E7490) and the NEB Ultra II stranded kit (E7760) with NEB dual index, according to the manufacturer's instructions, and sequenced on an Illumina NovaSeq 6000 using 50bp paired-end reads.

tag: strain

value: Peripheral LN

value: B cells

value: Zfp36l1fl/fl Zfp36l2fl/fl CD23cre

value: Induced germinal center B cell culture, day 7

value: 13 weeks


title: WT mouse smallRNA-Seq 2

value: skeletal muscles, quadriceps


title: RT-13

value: Adipose


title: Zfp36l1/Zfp36l2 dKO 1


title: Hu3112_G0_3_H3_ChIP_seq

value: wild type

value: anti H3, nitrogen starvation for 24 hours


title: RT-12


title: Hu3112_G0_2_RNAPolIIS5_ChIP_seq

value: mat1-M smt-0 pht1-myc

value: anti RNA pol II S5, nitrogen starvation for 24 hours


title: WT mouse smallRNA-Seq 1

value: WT


title: Ctrl 3

value: Zfp36l1fl/fl Zfp36l2fl/fl


title: Ctrl 2

value: Female


title: W.24.F.3.Sp.1

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
RNA extracted from 24 week old WKY female spleen replicate 3
Rat spleen

data_processing: Initial quality control included melt-curve analysis and removal of samples and genes with >60% failed reactions. Genes with >60% working reactions were used to generate a median expression level across all samples. Raw Ct values were normalized against this median expression level to obtain DCt values. DCt values were generated for each gene according to the following equation: DCt_gene = Ct_gene - (median sample Ct). The median across all samples within a gene was then used to calculate -DDCt from DCt values by use of the following equation: -DDCt_gene = -(DCt_gene - DCt_median_across_samples).

label: Evagreen

organism: Rattus norvegicus

label_protocol: The reverse transcriptase reaction was performed using SuperScript VILO Master Mix (Thermo Fisher Scientific, Waltham, MA). cDNA samples were processed for 12 cycles of specific target amplification of 96 genes using TaqMan PreAmp Master Mix as per the manufacturer’s protocol (Applied Biosystems, Foster City, CA, USA) followed by real-time PCR using Evagreen intercalated dye-based approach to detect the PCR-amplified product. Intron-spanning PCR primers were designed for every assay using Primer3 and BLAST. Real-time PCR reactions were performed using 96x96 BioMark Dynamic Arrays (Fluidigm, South San Francisco, CA, USA) of 150 samples and 96 genes enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions. Each run consisted of 30 amplification cycles (15 s at 95C, 5 s at 70C, 60 s at 60C). Two 96x96 BioMark Arrays were used to measure gene expression across all the 150 samples before QC. The same serial dilution sample set was included in each chip to verify reproducibility and test for technical variability. This 6-point dilution series also serves to detect any over-amplification that may lead to a bias in the data. Samples from each animal were run across the two chips to obtain data on 96 genes per sample. Each set of chip runs contained overlapping assays that served as technical replicates to evaluate chip-to-chip variability.

extract_protocol: Direct-Zol miniprep kit from Zymo Research

value: Wistar-Kyoto rat (WKY)

value: 24 weeks

tag: organ

value: Spleen


title: Ctrl 1

value: Peripheral LN


title: RT-10

value: Male


title: Hu3112_G0_2_MyC_ChIP_seq

value: anti H2A.Z, nitrogen starvation for 24 hours


title: W.24.F.1.Sp.1

description:
RNA extracted from 24 week old WKY female spleen replicate 1
Rat spleen


title: RT-9


title: RT-15


title: Hu3112_G0_2_RNAPolIIS2_ChIP_seq

value: anti RNA pol II S2, nitrogen starvation for 24 hours


title: W.24.F.2.Sp.1

description:
RNA extracted from 24 week old WKY female spleen replicate 2
Rat spleen


title: RT-8


title: S.24.F.3.Sp.1

description:
RNA extracted from 24 week old SHR female spleen replicate 3
Rat spleen

value: Spontaneously Hypertensive rat (SHR)


title: RT-7


title: Hu3112_G0_2_H3K9me3_ChIP_seq

value: anti H3K9me3, nitrogen starvation for 24 hours


title: Zfp36l1/Zfp36l2 dKO 2

value: B cells

value: Zfp36l1fl/fl Zfp36l2fl/fl CD23cre

value: Induced germinal center B cell culture, day 7

value: 13 weeks


title: RT-6

value: Adipose


title: Hu3112_G0_2_H3K9me2_ChIP_seq

value: wild type

value: mat1-M smt-0 pht1-myc

value: anti H3K9me2, nitrogen starvation for 24 hours


title: RT-5


title: Hu3112_G0_2_H3K4me3_ChIP_seq

value: anti H3K4me3, nitrogen starvation for 24 hours


title: Hu3112_G0_2_H3_ChIP_seq

value: anti H3, nitrogen starvation for 24 hours


title: Hu3112_G0_2_H3K9ac_ChIP_seq

value: anti H3K9ac, nitrogen starvation for 24 hours


title: W.16.F.3.Sp.1

description:
RNA extracted from 16 week old WKY female spleen replicate 3
Rat spleen

value: Female

value: Wistar-Kyoto rat (WKY)

value: 16 weeks

value: Spleen


title: W.16.F.2.Sp.1

description:
RNA extracted from 16 week old WKY female spleen replicate 2
Rat spleen


title: LPS_PMMA3

city: Shijiazhuang

first: Weiye

last: Fan

address: No. 139 Ziqiang Road, Qiaoxi District

institute: Department of Orthopaedic Surgery, Hebei Medical University Third Hospital

data_processing:
CLC Genomics Workbenchv 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

source_name: Abdominal cavity

growth_protocol: RAW264.7 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 mg/mL streptomycin (complete medium). The incubation conditions for the cells were maintained at 37 °C and 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 .3 ug of total RNA was used for the construction of sequencing libranies
RNA lilbraies for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

treatment_protocol: RAW264.7 cells were induced by LPS for 24 hours, and then the culture medium was changed to different bone cement extract medium for further culture.

value: Abdominal cavity

value: Macrophages


title: LPS_ES_PMMA2


title: LPS_PMMA1


title: LPS_PMMA2


title: LPS_ES_PMMA3


title: RT-11

value: Male


title: W.16.F.1.Sp.1

description:
RNA extracted from 16 week old WKY female spleen replicate 1
Rat spleen


title: RT-3


title: Hu3112_G0_1_RNAPolIIS2_ChIP_seq

value: anti RNA pol II S2, nitrogen starvation for 24 hours


title: RT-4


title: LPS_ES_PMMA1


title: RT-2


title: S.24.F.1.Sp.1

description:
RNA extracted from 24 week old SHR female spleen replicate 1
Rat spleen

value: Spontaneously Hypertensive rat (SHR)

value: 24 weeks


title: S.24.F.2.Sp.1

description:
RNA extracted from 24 week old SHR female spleen replicate 2
Rat spleen


title: S.16.F.3.Sp.1

description:
RNA extracted from 16 week old SHR female spleen replicate 3
Rat spleen


title: S.16.F.2.Sp.1

description:
RNA extracted from 16 week old SHR female spleen replicate 2
Rat spleen


title: B16F10 PD-L1 KO sEVs treated RAW264.7 cells, replicate 2, RNA-seq

city: Wuhan

first: He-jing

address: Guangba Rd.

institute: Wuhan university

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

growth_protocol: RAW264.7 (murine macrophage cell) cells were cultured in DMEM medium (Gibco). The culture mediums were supplemented with 10% (v/v) FBS, 100 U/ml penicillin G, and 100 μg/ml streptomycin. The cells were incubated at 37°C with 95% air/5% CO2 in a humidified atmosphere.

extract_protocol:
Total RNA was extracted from cultured cells using Trizol (Takara) following the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer's protocols.

treatment_protocol: LPS-activated murine macrophage RAW264.7 cells incubated with 20 μg/ml control B16-F10-derived sEVs (TEVs) or PD-L1 KO TEVs for 12 h.

value: macrophage cell line

value: WT

value: B16F10 PD-L1 KO sEVs


title: B16F10 PD-L1 KO sEVs treated RAW264.7 cells, replicate 3, RNA-seq


title: Hu3112_G0_1_Input_ChIP_seq

value: wild type

value: mat1-M smt-0 pht1-myc

value: Input, nitrogen starvation for 24 hours


title: Hu3112_G0_1_MyC_ChIP_seq

value: anti H2A.Z, nitrogen starvation for 24 hours


title: S.16.F.1.Sp.1

description:
RNA extracted from 16 week old SHR female spleen replicate 1
Rat spleen

value: Female


title: B16F10 PD-L1 KO sEVs treated RAW264.7 cells, replicate 1, RNA-seq


title: 194 – LPD8

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin Biopsy

tag: subject id

value: 194 – LPD8

tag: clinical diagnosis

value: Large-patch dermatitis

tag: molecular condition

value: Parapsoriasis

tag: chemistry

value: Single Cell 5' PE


title: B16F10 control sEVs treated RAW264.7 cells, replicate 3, RNA-seq

tag: cell type

value: B16F10 control sEVs


title: Hu3112_G0_1_H3K9me3_ChIP_seq

value: anti H3K9me3, nitrogen starvation for 24 hours


title: W.12.F.3.Sp.1

description:
RNA extracted from 12 week old WKY female spleen replicate 3
Rat spleen

value: Wistar-Kyoto rat (WKY)

value: 12 weeks

value: Spleen


title: 163 – LPD7

tag: tissue

value: 163 – LPD7

value: Mycosis fungoides


title: B16F10 control sEVs treated RAW264.7 cells, replicate 2, RNA-seq

tag: cell line

value: macrophage cell line

value: WT


title: W.12.F.2.Sp.1

description:
RNA extracted from 12 week old WKY female spleen replicate 2
Rat spleen


title: 150 – LPD6

value: 150 – LPD6


title: Hu3112_G0_1_H3K9me2_ChIP_seq

value: wild type

tag: genotype

value: mat1-M smt-0 pht1-myc

value: anti H3K9me2, nitrogen starvation for 24 hours


title: S.12.F.3.Sp.1

description:
RNA extracted from 12 week old SHR female spleen replicate 3
Rat spleen

value: Female

value: Spontaneously Hypertensive rat (SHR)


title: 143 – LPD2

value: Skin Biopsy

value: 143 – LPD2

value: Large-patch dermatitis

value: Parapsoriasis


title: RRBS36_TP50.1_WT_F_01ppm_inHB

city: Leuven

first: Lehua

last: Chen

address: Herestraat 49

country: Belgium

institute: KU Leuven

description:
01ppm_WT.filt.bw
WT.01vs3ppm.hyper.DMR.bed
WT.01vs3ppm.hypo.DMR.bed
KOvsWT.01ppm.hyper.DMR.bed

data_processing:
Processing of the raw reads was done according to the instructions of RRBS-library preparation kit (Tecan/Nugen). Reads were first trimmed for quality and presence of the adaptor using TrimGalore (v0.6.10) with the following command: “trim_galore --paired -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC”, followed by removal of the diversity-adaptors using a custom Python script provided by Tecan/Nugen (“-b” flag is specified due to double digestion with both MspI and TaqI). Subsequently, the trimmed reads were aligned to GENCODE mm10GRCm38.p6 using Bismark (v0.24.1) (Krueger and Andrews 2011) with a maximum insert size of 500 bp. The Tecan/Nugen kit implements a UMI as the last 6 bp of I1 read, thus the aligned reads were deduplicated using UMI-tools (Smith et al. 2017), followed by methylation extraction with the bismark methylation-extractor (v0.24.1). On average, we reached a coverage of 8.7X and detected 2.6*106 CpGs with a minimal coverage of 5X per library, covering roughly 13% of mm10. Differentially methylated regions (DMRs) were called based on two different strategies (Mulholland et al 2020) for every pair-wise comparison using MethylKit (v1.26.0) in R (v4.3.1) (Akalin et al. 2012). First, differentially methylated CpGs were called (q-value < 0.05, Δ5mC < 10%) with a minimal coverage of 5X and were merged together (distance ≤ 250 bp, width ≥ 100 bp) . Secondly, differential methylation scores (q-value < 0.05, Δ5mC < 10%) were calculated for covered regions, based on the UCSC annotation of promoters, CpG islands, CpGi shores, CpGi shelves and 1kb tiles with a 500 bp sliding window, containing at least 3 measured CpGs. From both strategies, regions that were overlapping were merged, filtered for minimally ≥ 2 differentially methylated CpGs and separated into hyper and hypo methylated DMRs. Per pairwise comparison, we only statistically tested CpGs that have an overall standard deviation of 2% methylation rates within all samples (Akalin et al. 2012). DMRs were annotated using AnnotatR (v1.26.0) and ChIPseeker (v1.36.0). Genes were associated with DMRs using the rGREAT (v2.2.0) package and GO term enrichment was performed using Cluster Profiler (4.8.1). DMR subsets were made using bedtools (v2.31.0). Profile plots were made using DeepTools (v3.5.5).
Assembly: mm10
Supplementary files format and content: .meth files of individual samples
Supplementary files format and content: bigwig files of CpG methylation of pooled samples
Supplementary files format and content: bed file with hyperDMRs
Supplementary files format and content: bed file with hypoDMRs

source_name: embryonic brain

extract_protocol:
Genomic DNA (gDNA) was extracted from embryonic brains using the Purelink Genomic DNA mini kit (Invitrogen, K182001) from individual E11.5 brains . DNA quality was assessed with NanoDdrop One (Thermo Fisher) , and absence of RNA contamination was confirmed with a 0.8% agarose gel stained with SYBR Safe.
RRBS libraries were prepared to include oxidative bisulfite (oxBS) conversion using the Ovation RRBS Methyl-Seq kit (Tecan/Nugen, 0553-32), according to the manufacturer's instructions. Per sample, 100 ng of gDNA as input was processed through the oxBS workflow to map true 5mC. To increase the coverage, we performed double digestion using MspI (Supplied with the Nugen Kit) and TaqI (NEB, R0149S) in each sample, first with MspI digestion at 37°C for 60 min, followed by TaqI digestion at 65°C for another 60 min. After digestion, each library was ligated to custom single-indexed sequencing adapter   (8 bp barcodes from the 96-Plex Adaptor Plate, Tecan, S02223) followed by final repair. Before oxidation and bisulfite conversion, libraries were purified and washed 3× with 80% acetonitrile to get rid of any residual ethanol, followed by incubation at 37°C for 5 min with denaturing buffer provided with the kit. Libraries were oxidized by the addition of TrueMethyl oxidant solution incubating at 40°C for 10 min. Immediately after the oxidation, each library was converted with bisulfite reagent solution, following the bisulfite conversion thermal cycler program in the instruction. Bisulfite converted DNA was then desulfonated at RT for 5 min, following 2× washing with 70% ethanol. For each library, the optimal amplification was determined using qPCR, in which 1/5th of the libraries was added to amplification master mix containing SYBR Green and run on an Applied Biosystems StepOnePlus Real-Time PCR system for 30 cycles. Relative log-fluorescence vs amplification cycle was plotted out to manually determine the appropriate amplification cycles, selected within the middle to late exponential phase of amplification. Based on the optimization, libraries were amplified between 8 and 13 cycles. Following amplification, libraries were purified with a final 1× clean-up using AMPure (Agencourt) beads. The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). The libraries were sequenced on NovaSeq S4 (GenomeScan, NL)  to obtain minimally 20 million PE150 reads per sample.

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

tag: treatment


title: S.12.F.2.Sp.1

description:
RNA extracted from 12 week old SHR female spleen replicate 2
Rat spleen

value: 12 weeks

value: Spleen


title: 127 – LPD1

value: 127 – LPD1

value: Mycosis fungoides

value: Single Cell 5' PE


title: 107 – LPD5

value: 107 – LPD5


title: RRBS35_TP57.5_KO_M_3ppm_NTD

description:
3ppm_KO.filt.bw
KO.01vs3ppm.hyper.DMR.bed
KOvsWT.3ppm.hyper.DMR.bed

value: KO


title: S.12.F.1.Sp.1

description:
RNA extracted from 12 week old SHR female spleen replicate 1
Rat spleen


title: Hu3112_G0_1_H3_ChIP_seq

description: the read counts gene list with start and end position for TSS and ORF, the read count results for the genes for all ChIP sample, and difference analyzed by DeSeq2

value: wild type

value: mat1-M smt-0 pht1-myc

value: anti H3, nitrogen starvation for 24 hours


title: 90 – LPD4

value: Skin Biopsy

value: 90 – LPD4


title: RT-1

value: Adipose

value: Male


title: W.10.F.3.Sp.1

description:
RNA extracted from 10 week old WKY female spleen replicate 3
Rat spleen

value: Female

value: Wistar-Kyoto rat (WKY)

value: 10 weeks


title: 65 – LPD3

value: 65 – LPD3

value: Large-patch dermatitis


title: mSpleen B Cell Fraction B

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Drukier Institute

institute: Weill Cornell Medicine

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, vdj)
Assembly: GRCm38
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

source_name: Spleen

extract_protocol:
10x Genomics CG000424_C
10x Genomics CG000424_C

value: Spleen

value: B cell

value: 6-8w/o (at infection)

value: Influenza NL09 34wpi


title: mSpleen B Cell Fraction C

description: 10X Genomics


title: RRBS33_TP42.9_KO_M_3ppm_inHB

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: KO


title: 149 – SPD7

value: Skin Biopsy

value: 149 – SPD7

value: Small-patch dermatitis

value: Parapsoriasis

value: Single Cell 5' PE


title: mSpleen B Cell Fraction D

description: 10X Genomics


title: B16F10 control sEVs treated RAW264.7 cells, replicate 1, RNA-seq

value: macrophage cell line

value: WT

value: B16F10 control sEVs


title: RRBS32_TP43.7_WT_M_30ppm_norm

description:
30ppm_WT.filt.bw
WT.30vs3ppm.hyper.DMR.bed
KOvsWT.30ppm.hyper.DMR.bed


title: 144 – SPD6

value: 144 – SPD6


title: S.10.F.3.Sp.1

description:
RNA extracted from 10 week old SHR female spleen replicate 3
Rat spleen

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 10 weeks

value: Spleen


title: Hu3112_G0_1_H3K9ac_ChIP_seq

value: wild type

value: mat1-M smt-0 pht1-myc

value: anti H3K9ac, nitrogen starvation for 24 hours


title: W.10.F.1.Sp.1

description:
RNA extracted from 10 week old WKY female spleen replicate 1
Rat spleen

value: Wistar-Kyoto rat (WKY)


title: Hu3112_G0_1_H3K4me3_ChIP_seq

value: anti H3K4me3, nitrogen starvation for 24 hours


title: Hu3112_G0_1_RNAPolIIS5_ChIP_seq

value: anti RNA pol II S5, nitrogen starvation for 24 hours


title: IP dnmnatOE after injury replicate 3

city: Onna, Kunigami District

first: Marco

last: Terenzio

state: Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology

data_processing:
Fastq files were trimmed using Trimmomatic for adaptor sequences/unpaired reads (parameter: slidingwindow:5:20 minlen:75)
Trimmed reads were aligned to the D. melanogaster genome (dmel-all-chromosome_r6.43_FB2021_06) using Hisat2 (parameter: -q -p 80 --phred33 --rna-strandness RF --no-mixed --no-discordant)
Aligned files were sorted, indexed and converted to .bam files using SamTools
Read counts were extracted from sorted and indexed .bam files using HTSeq-count (parameter: -f bam -r pos -s reverse -t exon -i gene_id)
Library normalization and statistical analysis of differentially expressed genes (DEG) using DESeq2
Assembly: dmel-all-chromosome_r6.43_FB2021_06
Supplementary files format and content: Text Document (.txt) files containing raw read counts for each sample

organism: Drosophila melanogaster

source_name: fly head

extract_protocol:
The homogenized heads were incubated with magnetic agarose GFP-Trap beads to pulldown ribosomes with associated mRNAs. RNA was extracted from ribosomes bound to the beads according to the NucleoSpin RNA (input) and RNA Plus XS (pulldowns) kit manufacturer’s recommendations. Each sample was then processed in three technical replicates for RNA sequencing (RNA-seq).
The library preparation was performed with poly-A purification for input samples and  skipped poly-A for the pulldowns, both without rRNA depletion.

treatment_protocol: For each genotype and condition (before and after injury), 300 adult animals were collected to perfom Translation Ribosome Affinity Purification (TRAP)

value: fly head

value: olfactory sensory neurons

value: 7 days after injury


title: RRBS30_TP41.8_KO_F_30ppm_norm

description:
30ppm_KO.filt.bw
KO.30vs3ppm.hyper.DMR.bed
KOvsWT.30ppm.hyper.DMR.bed

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: KO


title: S.10.F.2.Sp.1

description:
RNA extracted from 10 week old SHR female spleen replicate 2
Rat spleen

value: Female


title: S.10.F.1.Sp.1

description:
RNA extracted from 10 week old SHR female spleen replicate 1
Rat spleen

value: Spontaneously Hypertensive rat (SHR)


title: mSpleen B Cell Fraction A

description: 10X Genomics

value: B cell

value: 6-8w/o (at infection)

value: Influenza NL09 34wpi


title: RRBS29_TP41.4_KO_M_30ppm_inHB


title: 138 – SPD5

city: Vienna

first: Natalia

address: Währinger Gürtel 18-20

institute: Medical University of Vienna

value: Skin Biopsy

value: 138 – SPD5

value: Small-patch dermatitis

value: Mycosis fungoides

value: Single Cell 5' PE


title: IP dnmnatOE after injury replicate 2

value: fly head


title: RRBS34_TP57.3_WT_M_3ppm_norm

description:
3ppm_WT.filt.bw
WT.30vs3ppm.hyper.DMR.bed
WT.01vs3ppm.hyper.DMR.bed
WT.01vs3ppm.hypo.DMR.bed
KOvsWT.3ppm.hyper.DMR.bed
HETvsWT.3ppm.hyper.DMR.bed
HETvsWT.3ppm.hypo.DMR.bed

value: WT


title: RRBS28_TP54.8_KO_M_01ppm_norm

description:
01ppm_KO.filt.bw
KO.01vs3ppm.hyper.DMR.bed
KOvsWT.01ppm.hyper.DMR.bed


title: W.10.F.2.Sp.1

description:
RNA extracted from 10 week old WKY female spleen replicate 2
Rat spleen

value: Wistar-Kyoto rat (WKY)

value: 10 weeks

value: Spleen


title: 88 – SPD3

value: 88 – SPD3

value: Parapsoriasis


title: RRBS31_TP43.4_KO_M_30ppm_norm

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: KO


title: IP dnmnatOE after injury replicate 1

value: olfactory sensory neurons

value: 7 days after injury


title: RRBS27_TP54.7_HET_M_01ppm_norm

description:
01ppm_HET.filt.bw
HET.01vs3ppm.hyper.DMR.bed

value: HET


title: W.8.F.3.Sp.1

description:
RNA extracted from 8 week old WKY female spleen replicate 3
Rat spleen

value: Female

value: 8 weeks


title: IP wild type after injury replicate 3

value: w; orco-Gal4/+; 5xUAS-GFP::RpL10Ab/+;


title: 78 – SPD1

value: Skin Biopsy

value: 78 – SPD1

value: Small-patch dermatitis

value: Single Cell 5' PE


title: W.8.F.1.Sp.1

description:
RNA extracted from 8 week old WKY female spleen replicate 1
Rat spleen

value: Wistar-Kyoto rat (WKY)

value: Spleen


title: RRBS25_TP50.3_KO_F_01ppm_NTD


title: IP wild type after injury replicate 2

value: fly head


title: RRBS24_TP45.8_KO_F_3ppm_norm

value: embryonic brain


title: IP wild type after injury replicate 1


title: 96 –  AD5 (re-analysis)

value: 96 –  AD5

value: Atopic dermatitis


title: S.8.F.3.Sp.1

description:
RNA extracted from 8 week old SHR female spleen replicate 3
Rat spleen

value: Spontaneously Hypertensive rat (SHR)


title: IP background after injury replicate 3

value: olfactory sensory neurons

value: w; orco-Gal4/+; ;


title: RRBS26_TP50.5_KO_F_01ppm_NTD

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: KO


title: 102 – SPD4

value: 102 – SPD4

value: Parapsoriasis


title: 81 –  AD4 (re-analysis)

value: Skin Biopsy

value: 81 –  AD4


title: S.8.F.2.Sp.1

description:
RNA extracted from 8 week old SHR female spleen replicate 2
Rat spleen

value: Female

value: 8 weeks


title: RRBS23_TP45.6_HET_F_3ppm_norm

description:
3ppm_HET.filt.bw
HET.01vs3ppm.hyper.DMR.bed
HETvsWT.3ppm.hyper.DMR.bed
HETvsWT.3ppm.hypo.DMR.bed

value: HET


title: S.8.F.1.Sp.1

description:
RNA extracted from 8 week old SHR female spleen replicate 1
Rat spleen

value: Spleen


title: 77 –  AD3 (re-analysis)

value: 77 –  AD3

value: Single Cell 5' PE


title: RRBS22_TP45.3_WT_F_3ppm_norm

value: embryonic brain

value: WT


title: IP background after injury replicate 2

value: fly head

value: olfactory sensory neurons

value: 7 days after injury


title: W.24.F.3.Lu.1

description:
RNA extracted from 24 week old WKY female lung replicate 3
Rat lung

value: Wistar-Kyoto rat (WKY)

value: 24 weeks

value: Lung


title: W.8.F.2.Sp.1

description:
RNA extracted from 8 week old WKY female spleen replicate 2
Rat spleen


title: 75 –  AD2 (re-analysis)

value: 75 –  AD2

value: Atopic dermatitis


title: IP background after injury replicate 1

value: w; orco-Gal4/+; ;


title: 79 – SPD2

value: Skin Biopsy

value: 79 – SPD2

value: Small-patch dermatitis

value: Parapsoriasis


title: W.24.F.2.Lu.1

description:
RNA extracted from 24 week old WKY female lung replicate 2
Rat lung

value: Female


title: IP dnmnatOE before injury replicate 3

value: before injury


title: RRBS21_TP40.10_KO_M_3ppm_norm

description:
3ppm_KO.filt.bw
KO.01vs3ppm.hyper.DMR.bed
KOvsWT.3ppm.hyper.DMR.bed

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: KO


title: 74 –  AD1 (re-analysis)

value: 74 –  AD1

value: Single Cell 5' PE


title: RRBS20_TP41.3_WT_F_30ppm_norm

description:
30ppm_WT.filt.bw
WT.30vs3ppm.hyper.DMR.bed
KOvsWT.30ppm.hyper.DMR.bed

value: WT


title: IP dnmnatOE before injury replicate 2

value: fly head

value: olfactory sensory neurons


title: 121 – HC4 (re-analysis)

value: Healthy control skin


title: W.24.F.1.Lu.1

description:
RNA extracted from 24 week old WKY female lung replicate 1
Rat lung

value: Wistar-Kyoto rat (WKY)

value: 24 weeks

value: Lung


title: 116 – HC3 (re-analysis)

value: Skin Biopsy


title: IP wild type before injury replicate 3

value: w; orco-Gal4/+; 5xUAS-GFP::RpL10Ab/+;


title: S.24.F.3.Lu.1

description:
RNA extracted from 24 week old SHR female lung replicate 3
Rat lung

value: Female

value: Spontaneously Hypertensive rat (SHR)


title: IP wild type before injury replicate 2

value: before injury


title: RRBS17_TP38.6_KO_M_30ppm_NTD

description:
30ppm_KO.filt.bw
KO.30vs3ppm.hyper.DMR.bed
KOvsWT.30ppm.hyper.DMR.bed

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>


title: RRBS16_TP35.4_KO_F_01ppm_inHB

description:
01ppm_KO.filt.bw
KO.01vs3ppm.hyper.DMR.bed
KOvsWT.01ppm.hyper.DMR.bed

value: E11.5 brain

value: KO


title: IP dnmnatOE before injury replicate 1


title: S.24.F.2.Lu.1

description:
RNA extracted from 24 week old SHR female lung replicate 2
Rat lung


title: 115 – HC2 (re-analysis)

value: Single Cell 5' PE


title: IP wild type before injury replicate 1


title: S.24.F.1.Lu.1

description:
RNA extracted from 24 week old SHR female lung replicate 1
Rat lung


title: 12Z_Myrrh-treated [M3]

city: Yangsan

first: Ki-Tae

last: Ha

address: Busandaehak-ro 49

institute: Pusan National University

data_processing:
Reads were mapped to the GRCh38 reference using STAR (Spliced Transcripts Alignment to a Reference, ver. 2.7.8a). Read counts for each gene were obtained by RSEM (ver.1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Reproductive

growth_protocol: 12Z cells were maintained in DMEM/F12 supplemented with 10% charcoal-stripped fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were extracted using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA library prep kit (illumina) following manufacturer's protocols.

treatment_protocol: 12Z cells were treated with 100 ug/mL Myrrh extract diluted in DMSO for 12 hrs. As control, DMSO was used.

value: Reproductive

value: Immotalized Human Endometriotic Cell

value: Wild type

value: Myrrh


title: W.16.F.3.Lu.1

description:
RNA extracted from 16 week old WKY female lung replicate 3
Rat lung

value: Wistar-Kyoto rat (WKY)

value: 16 weeks


title: RRBS14_TP34.5_KO_M_01ppm_norm


title: W.16.F.2.Lu.1

description:
RNA extracted from 16 week old WKY female lung replicate 2
Rat lung

value: Lung


title: IP background before injury replicate 3

value: fly head

value: olfactory sensory neurons

value: w; orco-Gal4/+; ;


title: 12Z_Myrrh-treated [M1]


title: 12Z_Myrrh-treated [M2]


title: RRBS19_TP41.2_HET_M_30ppm_norm

value: HET


title: IP background before injury replicate 1

value: before injury


title: RRBS13_TP34.3_WT_M_01ppm_norm

description:
01ppm_WT.filt.bw
WT.01vs3ppm.hyper.DMR.bed
WT.01vs3ppm.hypo.DMR.bed
KOvsWT.01ppm.hyper.DMR.bed

value: embryonic brain

value: WT


title: W.16.F.1.Lu.1

description:
RNA extracted from 16 week old WKY female lung replicate 1
Rat lung

value: Female


title: 12Z_vehicle-treated [C3]

value: DMSO


title: S.16.F.3.Lu.1

description:
RNA extracted from 16 week old SHR female lung replicate 3
Rat lung

value: Spontaneously Hypertensive rat (SHR)


title: IP background before injury replicate 2


title: RRBS18_TP38.7_HET_M_30ppm_inHB

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain


title: RRBS12_TP40.5_KO_F_3ppm_norm

value: KO


title: Input dnmnatOE after injury replicate 3

value: 7 days after injury


title: 12Z_vehicle-treated [C2]

value: Reproductive

value: Immotalized Human Endometriotic Cell

value: Wild type


title: 12Z_vehicle-treated [C1]


title: Input dnmnatOE after injury replicate 2

value: fly head


title: RRBS11_TP40.3_WT_F_3ppm_norm

description:
3ppm_WT.filt.bw
WT.30vs3ppm.hyper.DMR.bed
WT.01vs3ppm.hyper.DMR.bed
WT.01vs3ppm.hypo.DMR.bed
KOvsWT.3ppm.hyper.DMR.bed
HETvsWT.3ppm.hyper.DMR.bed
HETvsWT.3ppm.hypo.DMR.bed


title: Input dnmnatOE after injury replicate 1

value: olfactory sensory neurons


title: RRBS15_TP35.2_HET_F_01ppm_norm

description:
01ppm_HET.filt.bw
HET.01vs3ppm.hyper.DMR.bed


title: W.12.F.3.Lu.1

description:
RNA extracted from 12 week old WKY female lung replicate 3
Rat lung

value: Wistar-Kyoto rat (WKY)

value: 12 weeks

value: Lung


title: CD34-RARG, IgG, CUT&Tag, replicate 2

city: Suzhou

first: meng

last: shan

address: shizi street

institute: Soochow university

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: enriched CD34+ cells form mobilized peripheral blood cells

extract_protocol:
CUT&Tag assay was performed as described previously with modifications(Hatice et al., 2019 ). Briefly，100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail).
To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: primary cells

value: hematopoietic stem and progenitor cells

value: RARG overexpression

value: cultured in myeloid medium for 15 days

tag: antibody

value: mouse IgG (Millipore, #12-371)


title: S.16.F.2.Lu.1

description:
RNA extracted from 16 week old SHR female lung replicate 2
Rat lung

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 16 weeks


title: CD34-RARG, IgG, CUT&Tag, replicate 1

value: enriched CD34+ cells form mobilized peripheral blood cells


title: W.12.F.2.Lu.1

description:
RNA extracted from 12 week old WKY female lung replicate 2
Rat lung


title: RRBS8_TP36.7_KO_F_30ppm_NTD

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: KO


title: W.12.F.1.Lu.1

description:
RNA extracted from 12 week old WKY female lung replicate 1
Rat lung


title: CD34-RARG, flag antibody, CUT&Tag, replicate 2

value: flag (Sigma, #F3165)


title: Input wild type after injury replicate 2

value: fly head

value: olfactory sensory neurons

value: w; orco-Gal4/+; 5xUAS-GFP::RpL10Ab/+;

value: 7 days after injury


title: RRBS7_TP36.6_KO_F_30ppm_inHB


title: CD34-RARG, flag antibody, CUT&Tag, replicate 1

value: primary cells

value: hematopoietic stem and progenitor cells


title: 112 – HC1 (re-analysis)

last: Alkon

value: Skin Biopsy

value: Healthy control skin

value: Single Cell 5' PE


title: S.12.F.3.Lu.1

description:
RNA extracted from 12 week old SHR female lung replicate 3
Rat lung

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 12 weeks

value: Lung


title: RRBS6_TP36.4_HET_F_30ppm_inHB

value: embryonic brain

value: 129S6.cg Tet1<tm1Koh>

value: HET


title: S.12.F.2.Lu.1

description:
RNA extracted from 12 week old SHR female lung replicate 2
Rat lung


title: Input wild type after injury replicate 1


title: Input background after injury replicate 2

value: w; orco-Gal4/+; ;


title: RRBS5_TP36.3_WT_F_30ppm_norm

description:
30ppm_WT.filt.bw
WT.30vs3ppm.hyper.DMR.bed
KOvsWT.30ppm.hyper.DMR.bed

value: E11.5 brain

value: WT


title: CD34-CRS, IgG, CUT&Tag, replicate 2

value: enriched CD34+ cells form mobilized peripheral blood cells

value: CRS overexpression

value: cultured in myeloid medium for 15 days

value: mouse IgG (Millipore, #12-371)


title: RRBS10_TP40.2_WT_M_3ppm_norm


title: CD34-CRS, IgG, CUT&Tag, replicate 1

value: primary cells

value: hematopoietic stem and progenitor cells


title: S.16.F.1.Lu.1

description:
RNA extracted from 16 week old SHR female lung replicate 1
Rat lung

value: 16 weeks


title: RRBS9_TP40.1_HET_F_3ppm_norm

description:
3ppm_HET.filt.bw
HET.01vs3ppm.hyper.DMR.bed
HETvsWT.3ppm.hyper.DMR.bed
HETvsWT.3ppm.hypo.DMR.bed


title: Input background after injury replicate 1

value: fly head

value: olfactory sensory neurons

value: 7 days after injury


title: CD34-CRS, flag antibody, CUT&Tag, replicate 2

value: flag (Sigma, #F3165)


title: RRBS4_TP34.1_HET_M_01ppm_norm

value: embryonic brain


title: Input wild type after injury replicate 3

value: w; orco-Gal4/+; 5xUAS-GFP::RpL10Ab/+;


title: W.10.F.3.Lu.1

description:
RNA extracted from 10 week old WKY female lung replicate 3
Rat lung

value: Female

value: Wistar-Kyoto rat (WKY)

value: 10 weeks

value: Lung


title: RRBS3_TP42.1_HET_M_3ppm_norm

description:
3ppm_HET.filt.bw
HET.01vs3ppm.hyper.DMR.bed
HETvsWT.3ppm.hyper.DMR.bed

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: HET


title: CD34-CRS flag antibody, CUT&Tag, replicate 1

value: enriched CD34+ cells form mobilized peripheral blood cells

value: CRS overexpression

value: cultured in myeloid medium for 15 days


title: W.10.F.2.Lu.1

description:
RNA extracted from 10 week old WKY female lung replicate 2
Rat lung


title: RRBS2_TP38.3_HET_M_30ppm_norm


title: Input background after injury replicate 3

value: w; orco-Gal4/+; ;


title: CD34-CRL, IgG, CUT&Tag, replicate 2

value: primary cells

value: hematopoietic stem and progenitor cells

value: CRL overexpression

value: mouse IgG (Millipore, #12-371)


title: RRBS1_TP36.2_HET_F_30ppm_norm

value: embryonic brain


title: Input dnmnatOE before injury replicate 2

value: fly head

value: olfactory sensory neurons

value: before injury


title: W.10.F.1.Lu.1

description:
RNA extracted from 10 week old WKY female lung replicate 1
Rat lung

value: Female

value: Wistar-Kyoto rat (WKY)

value: 10 weeks


title: Input dnmnatOE before injury replicate 1


title: S.10.F.3.Lu.1

description:
RNA extracted from 10 week old SHR female lung replicate 3
Rat lung

value: Spontaneously Hypertensive rat (SHR)

value: Lung


title: CD34-CRL, IgG, CUT&Tag, replicate 1

value: enriched CD34+ cells form mobilized peripheral blood cells


title: S.10.F.2.Lu.1

description:
RNA extracted from 10 week old SHR female lung replicate 2
Rat lung


title: Input dnmnatOE before injury replicate 3


title: CD34-CRL, flag antibody, CUT&Tag, replicate 1

value: flag (Sigma, #F3165)


title: Input wild type before injury replicate 3

value: w; orco-Gal4/+; 5xUAS-GFP::RpL10Ab/+;


title: CD34-CRL, flag antibody, CUT&Tag, replicate 2

value: cultured in myeloid medium for 15 days


title: S.12.F.1.Lu.1

description:
RNA extracted from 12 week old SHR female lung replicate 1
Rat lung

value: 12 weeks


title: sample 20, Irradiated d+1

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

institute: IRSN

data_processing:
After quality control using FastQC, the reads were mapped to the Ensembl GRCm38 reference mouse genome with the STAR aligner software (v2.7.9a) using the quantMode GeneCounts option to generate read counts.
Assembly: GRCm38
Supplementary files format and content: tab-delimitated files include raw counts for each sample

source_name: Aorta

extract_protocol:
Total RNA was extracted from abdominal aortas using a RNAEasy Kit (Qiagen), then mRNA was selected by polyA selection.
RNA-sequence libraries were prepared with the TruSeq Stranded mRNA Prep Kit (Illumina, San Diego, CA, USA).

value: Aorta

value: Apoe-/-


title: sample 19, Irradiated d+1


title: sample 18, Irradiated d+1


title: Input wild type before injury replicate 1


title: W.8.F.1.Lu.1

description:
RNA extracted from 8 week old WKY female lung replicate 3
Rat lung

value: 8 weeks


title: S.10.F.1.Lu.1

description:
RNA extracted from 10 week old SHR female lung replicate 1
Rat lung


title: CD34+ cells, empty vector, replicate 3

data_processing:
FastQC softwae was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample.
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample.

source_name: enriched CD34+ cells form human cord blood cells

extract_protocol:
The totla RNA was extracted  for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard Illumina protocols

value: primary cells

value: hematopoietic stem and progenitor cells

value: wild type

value: myeloid differentaition

tag: time

value: day 15


title: CD34+ cells, empty vector, replicate 2

value: enriched CD34+ cells form human cord blood cells


title: W.8.F.3.Lu.1

description:
RNA extracted from 8 week old WKY female lung replicate 2
Rat lung

value: Female

value: Wistar-Kyoto rat (WKY)


title: Input background before injury replicate 3

value: fly head

value: olfactory sensory neurons

value: w; orco-Gal4/+; ;

value: before injury


title: Input background before injury replicate 2


title: W.8.F.2.Lu.1

description:
RNA extracted from 8 week old WKY female lung replicate 1
Rat lung

value: Lung


title: S.8.F.3.Lu.1

description:
RNA extracted from 8 week old SHR female lung replicate 3
Rat lung

value: Spontaneously Hypertensive rat (SHR)


title: CD34+ cells, CRS expression, replicate 3


title: Input background before injury replicate 1


title: CD34+ cells, empty vector, replicate 1


title: sample 15, Irradiated d-3

value: Aorta


title: Knockout_RiboSeq

first: Hao

last: Peng

state: Guangdong

address: Zhongshan 2nd Road, Guangzhou, 510080, China

department: Department of Breast Cancer

institute: Guangdong General Hospital

description: small RNA

data_processing:
Library strategy: Ribo-seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
Supplementary_files_format_and_content: The txt files of RNA-seq and Ribo-seq include the FPKM values for every gene.

source_name: Nasopharyngeal carcinoma 5-8F cells

growth_protocol: Human 5-8F cells were maintained in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: METTL5 was knocked out by sgRNA.

value: METTL5 knockout

value: Nasopharyngeal carcinoma 5-8F cells


title: Input wild type before injury replicate 2

value: w; orco-Gal4/+; 5xUAS-GFP::RpL10Ab/+;


title: CD34+ cells, CRS expression, replicate 2

value: primary cells

value: hematopoietic stem and progenitor cells


title: S.8.F.2.Lu.1

description:
RNA extracted from 8 week old SHR female lung replicate 2
Rat lung

value: 8 weeks


title: sample 13, Irradiated d-3

value: Apoe-/-


title: CD34+ cells, CRS expression, replicate 1

value: enriched CD34+ cells form human cord blood cells

value: wild type

value: myeloid differentaition

value: day 15


title: S.8.F.1.Lu.1

description:
RNA extracted from 8 week old SHR female lung replicate 1
Rat lung

value: Female


title: Vector_RiboSeq

description: small RNA

value: Wild type


title: W.24.F.3.Li.1

description:
RNA extracted from 24 week old WKY female liver replicate 3
Rat liver

value: Wistar-Kyoto rat (WKY)

value: 24 weeks

value: Liver


title: sample 12, Irradiated d-3

value: Aorta


title: Knockout_Input_for_RiboSeq

description: PolyA mRNA+lncRNA

value: METTL5 knockout


title: W.24.F.2.Li.1

description:
RNA extracted from 24 week old WKY female liver replicate 2
Rat liver


title: sample 17, Irradiated d+1


title: sample 11, Irradiated d-3


title: CD34+ cells, CRL expression, replicate 3


title: Vector_Input_for_RiboSeq

description: PolyA mRNA+lncRNA

value: Nasopharyngeal carcinoma 5-8F cells


title: WT Ctrl 3

data_processing:
iCLIP data were processed using the iCLIP analysis pipeline on the iMaps platform (https://imaps.goodwright.com/ when performed; now hosted on the flow platform: https://app.flow.bio/)
In brief, reads were deduplicated based on their barcodes, trimmed using Cutadapt (v2.4) and mapped to the GRCm38 mouse genome build using STAR (v2.7.0f). Significant crosslink sites were then determined using iCount.
Following iMaps analysis, the gene and feature type to which each cross-link site was assigned were determined by considering all transcript isoforms from the Ensembl Mus_musculus. GRCm38.90 annotation. If multiple genes or feature types were overlapped, the most likely was chosen by a hierarchy of feature types: 3’UTR > CDS > 5’UTR > intron > non-coding exon > non-coding intron.
Assembly: GRCm38
Supplementary files format and content: Bedgraph-format files showing the raw coverage of crosslinks (following deduplication), mapped to the mouse GRCm38 genome build. Generated using the iCLIP analysis pipeline from iMaps.

extract_protocol:
On day 7, iCLIP experiments were performed as described (doi: https://doi.org/10.1101/2021.08.27.457890). Briefly, iGCB cells were irradiated 1x with ultraviolet (UV) light for cross-linkage of protein-RNA (150 mJ/cm2; Stratalinker 2400). After washing cells in ice-cold PBS, cell pellets were snap-frozen in liquid nitrogen and stored at -80C.  Next, cells were lysed with 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% Igepal CA-630 (Sigma), 0.1% SDS, and 0.5% sodium deoxycholate lysis buffer, and sonicated (3x 15’’). For each mCherry-ZFP36L1 sample, cell lysates from two age- and sex-matched mice were pooled together, which were selected to match total iGCB cell numbers to WT controls. Total protein concentration from extract supernatants was measured by Pierce BCA protein assay and 1.5mg protein were treated for 3 min at 37 °C with 4U Turbo DNAse (Ambion) and 0.4U RNase I (ThermoFisher Scientific). mCherryZFP36L1-RNA complexes were immunoprecipitated with 20μl RFP-Trap magnetic particles M-270 (Chromotek), which were previously washed 3x in lysis buffer, and rotating overnight at 4°C. Immunoprecipitates were separated by SDS-PAGE. RNA-protein complexes were transferred to a nitrocellulose membrane and isolated after cutting the areas from ~100 to ~140 kDa where mCherryZFP36L1 was expected to be cross-linked to RNAs.
After protein digestion, RNA isolation and cDNA library preparation was carried out as described (doi: https://doi.org/10.1101/2021.08.27.457890) using the L3-IR-App adapter to visualize and retrotranscribe the RNA cross-linked to mCherryZFP36L1. Amplification of iCLIP cDNA libraries was done with 21 PCR cycles.

value: Peripheral LN

value: B cells

value: WT

value: Induced germinal center B cell culture, day 7

tag: ip

value: RFP-Trap

tag: 5' barcode

value: NNNNCCTGCWWW


title: W.24.F.1.Li.1

description:
RNA extracted from 24 week old WKY female liver replicate 1
Rat liver

tag: age


title: CD34+ cells, CRL expression, replicate 1

value: enriched CD34+ cells form human cord blood cells

value: primary cells

value: hematopoietic stem and progenitor cells

value: wild type


title: sample 10, Irradiated d-3

value: Apoe-/-


title: sample 16, Irradiated d-3


title: BL-115_VDJ

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

description:
10x Genomics
tumor_vdj.tsv.gz
barcodes.tsv.gz

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8. The files for each sample can be analyzed and de-multiplexed directly using the 10X Genomics CellRanger software.
Gene expression and VDJ data were mapped to the human genome (GRCh38) and processed together using the 10X Genomics CellRanger v6.0.0 multi pipeline.
Assembly: grch38
Supplementary files format and content: Gene expression consists of UMI counts for cells/genes. Barcodes.tsv is a summary that contains cell ids, from which sample they originated, and whether they are classified as “tumor” or “not tumor”. tumor_vdj.tsv contains VDJ information for the tumor cells.

source_name: Tumor mass

extract_protocol:
Burkitt lymphoma diagnostic specimens, including pleural or abdominal effusions and nodal tumor masses, were collected at diagnosis and frozen as viable single cell suspensions. Upon thawing, cell suspensions were subject to Ficoll density centrifugation to remove dead cells and diluted at the concentration of 1,000 cells/ul.
Single cells were captured and analyzed in a Chromium Controller (10x Genomics) using the Chromium Next GEM Single Cell 5’ kit v2 and the Chromium Next GEM Single Cell V(D)J Enrichemtn Human B cell Kit following manufacturer's instructions (10x Genomics).

value: Tumor mass

value: Burkitt lymphoma


title: sample 14, Irradiated d-3


title: WT Ctrl 2

value: NNNNCAGGGWWW


title: sample 9, Non irradiated

value: Aorta


title: S.24.F.3.Li.1

description:
RNA extracted from 24 week old SHR female liver replicate 3
Rat liver

tag: Sex

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: 24 weeks

value: Liver


title: WT Ctrl 1

tag: strain

value: Peripheral LN

value: B cells

value: WT

value: NNNNCATACWWW


title: sample 6, Non irradiated


title: BL-113_VDJ


title: S.24.F.2.Li.1

description:
RNA extracted from 24 week old SHR female liver replicate 2
Rat liver

tag: organ


title: mCherry-ZFP36L1 3

value: Induced germinal center B cell culture, day 7

value: RFP-Trap

value: NNNNGTAACWWW


title: S.24.F.1.Li.1

description:
RNA extracted from 24 week old SHR female liver replicate 1
Rat liver


title: sample 8, Non irradiated


title: W.16.F.3.Li.1

description:
RNA extracted from 16 week old WKY female liver replicate 3
Rat liver

value: Wistar-Kyoto rat (WKY)

value: 16 weeks


title: sample 5, Non irradiated

value: Apoe-/-


title: BL-110-E_VDJ

source_name: Ascites

value: Ascites

value: Burkitt lymphoma


title: W.16.F.2.Li.1

description:
RNA extracted from 16 week old WKY female liver replicate 2
Rat liver


title: mCherry-ZFP36L1 2

value: NNNNGATCGWWW


title: sample 4, Non irradiated

value: Aorta


title: BL-109_VDJ

value: Tumor mass


title: mCherry-ZFP36L1 1

value: NNNNTCCACWWW


title: BL-108_VDJ


title: W.16.F.1.Li.1

description:
RNA extracted from 16 week old WKY female liver replicate 1
Rat liver

value: Female

value: Liver


title: sample 3, Irradiated d+1


title: sample 2, Irradiated d+1


title: Zfp36l1 fl/fl Zfp36l2 fl/fl CD23cre, replicate 1

description: TrAEL-seq adaptor 5

data_processing:
Sequencing data was processed with a custom script (TrAELseq_preprocessing_UMIplusBarcode.py; https://github.com/s-andrews/TrAEL-seq/) to demultiplex based on the in-line sample barcodes (4bp) and transfer these, together with the first 8bp of each sequence (UMI, unique molecular identifier) to the readID of the FastQ file. In addition, up to and including 3 T bases were removed from the 5'-end following the UMI clipping. The read lengths in the submitted FastQ files thus vary by up to 3bp, and the end of the readID comprises: Illumina barcode (6N):Sample barcode (4N):UMI (8N)
The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified by correcting for total read counts per million reads mapped.
Assembly: GRCm38
Supplementary files format and content: Worksheet contains TrAEL-seq read density, indicating where replications forks are located in replicating cells across the genome. These values for each biological replicate are running windows of 100,000 bp with step size of 10,000 bp using Read Count Quantification of All reads corrected for total read counts per million reads mapped.
Library strategy: TrAEL-seq

growth_protocol: Naive B cells were isolated from the peripheral lymph nodes of mice using the B cell isolation kit (Miltenyi Biotec), and cultured in Dutch-modified RPMI-1640 media supplemented with 8% FBS, 1x GlutaMAX (Gibco), 50µM 2-mercaptoethanol, 100units/ml penicillin and 100μg/ml streptomycin (both ThermoFisher Scientific)

extract_protocol:
Half an agarose plug of 2x10^6 cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µlof indicated TrAEL-seq adaptor (eg. TrAEL-seq adaptor 1 [App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT)) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs with different TrAEL-seq adaptors were pooled into one eppendorf tube (as indicated in Sample description), equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. One third of this solution from ascynhronously dividing wild type cells were spiked into each pool (i.e. T0, T1 and T2 pools). DNA was then ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5 µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2 µl 10 mM dNTPs and 1 µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: For inducible germinal centre B cell culture (iGCB), 3T3 cells expressing mouse CD40L and human BAFF (40LB cells33) were irradiated (~120Gγ) and seeded at 100×10^3 cells per well in a 12-well plate. One day later (day 0), 40×10^3 naive B cells were added to 40LB cells in the presence of 2ng/ml mIL-4. On day 4, B cells were harvested and re-seeded on freshly irradiated 40LB cells in the presence of 5 ng/ml recombinant mouse IL-21 (PeproTech). Cells were harvested on day 7.

value: Peripheral LN

value: B cell

value: Zfp36l1 fl/fl Zfp36l2 fl/fl CD23cre

value: Male

value: 15 weeks


title: S.16.F.3.Li.1

description:
RNA extracted from 16 week old SHR female liver replicate 3
Rat liver

value: Spontaneously Hypertensive rat (SHR)


title: Zfp36l1 fl/fl Zfp36l2 fl/fl CD23cre, replicate 2

description: TrAEL-seq adaptor 6

value: Induced germinal center B cell culture, day 7


title: BL-107_VDJ

source_name: Pleural Effusion

value: Pleural Effusion


title: sample 1, Irradiated d+1

value: Apoe-/-


title: BL-103b_VDJ


title: BL-112_VDJ


title: Zfp36l1 fl/fl Zfp36l2 fl/fl, replicate 2

description: TrAEL-seq adaptor 3

value: Zfp36l1 fl/fl Zfp36l2 fl/fl


title: S.16.F.2.Li.1

description:
RNA extracted from 16 week old SHR female liver replicate 2
Rat liver

value: 16 weeks


title: PyMT sgIl1a-CAS9 untreated tumor (multiplexing capture library)

city: Tampa

first: Xiaoxian

last: Liu

state: FL

address: 13131 USF Magnolia Drive

institute: Moffitt Cancer Center

description: 10X Genomics

data_processing:
The Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v7.1.0 software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary tumor

extract_protocol:
Tumors from mice were harvested 14 days after implantation. Tumors were first minced using scissors and then digested in 25 ml glass bottles with a magnetic stirrer in 5-10 ml of DMEM with Collagenase A at 1 mg/ml (Sigma-Aldrich) and DNase I at 50 U/ml (Roche Life Sci) for 45 min in a 36° C water bath. Cell suspension was then passed through 100 μm cell strainer. Each of the tumor cell suspensions per group were then stained with anti-CD45.2-APC (Biolegend; Clone 104; Cat.No 109814) including the respective barcoded TotalSeq™-B anti-mouse Hashtag antibody in sorting buffer (DPBS +2%FBS) for 30 min on ice. Cell suspensions were then washed twice with sorting buffer before resuspended in sorting buffer including DAPI (1 μg/ml) as a viability stain. Live CD45+ cells were then sorted on a BD FACSAria for each sample, washed twice with resuspension buffer DPBS (+0.04% sterile filtered BSA) and resuspended in 30-50 μl resuspension buffer. TotalSeq™ hashtag antibodies From Biolegend Inc (San Deiego, CA, USA) were used in the experiments to multiplex samples, increase sample throughput, and improve the identification of multiples. The cell viability and counts were obtained by AO/PI dual fluorescent staining and visualization on the Nexcelom Cellometer K2 (Nexcelom Bioscience LLC, Lawrence, MA). Cells were then loaded onto the 10X Genomics Chromium Single Cell Controller at a concentration of 3,000 cells/µl in order to encapsulate 10000 cells per sample. Single cells, reagents, and 10X Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs), and reverse transcription of poly-adenylated mRNA was performed inside each droplet at 53°C.
The scRNA-Seq libraries were prepared following the protocol provided by the 10X genomics. The cDNA libraries were completed in a single bulk reaction using the 10X Genomics Chromium NextGEM Single Cell 3’ Reagent Kit v3.1.  50,000 sequencing reads per cell for scRNA-seq were generated on the Illumina NovaSeq6000 instrument.

value: Mammary tumor

value: C57 PyMT

value: mammary carcinoma

value: untreated


title: CD34+ cells, CRL expression, replicate 2

value: enriched CD34+ cells form human cord blood cells

value: primary cells

value: hematopoietic stem and progenitor cells

value: wild type

value: myeloid differentaition

value: day 15


title: BL-103a_VDJ

value: Burkitt lymphoma


title: PyMT sgIl1a-CAS9 untreated tumor (gene expression library)

description: 10X Genomics


title: BL-110_VDJ

value: Tumor mass


title: S.16.F.1.Li.1

description:
RNA extracted from 16 week old SHR female liver replicate 1
Rat liver

value: Female

value: Spontaneously Hypertensive rat (SHR)

value: Liver


title: S.12.F.3.Li.1

description:
RNA extracted from 12 week old SHR female liver replicate 3
Rat liver

value: 12 weeks


title: S.12.F.2.Li.1

description:
RNA extracted from 12 week old SHR female liver replicate 2
Rat liver


title: PyMT sgNTC-CAS9 untreated tumor (gene expression library)

description: 10X Genomics


title: PyMT sgNTC-CAS9 untreated tumor (multiplexing capture library)

description: 10X Genomics


title: BL-102b_VDJ

value: Pleural Effusion


title: BL-102a_VDJ