title: Mouse GV oocytes

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: mm10
Supplementary_files_format_and_content: CSV for the position, coverage, and methylation level for the samples

growth_protocol: Oocytes were obtained from the ovaries or oviducts of 7 to 8 week-old C57BL/6J female mice. GV oocytes were harvested from the minced ovaries 48 hours after the mice were administered 10 IU of pregnant mares’ serum gonadotrophin (PMSG, Solarbio, P9970) intraperitoneally. To obtain MII oocytes, mice were administered 5 IU human chorionic gonadotrophin (hCG, Univ, 230734) intraperitoneally, 44 - 48 hours after injection of 10 IU of PMSG (Solarbio, P9970). 12 hours later, the MII oocytes were picked under a microscope by fallopian tube dissection. One-cell embryos were collected from 7 to 8 week-old C57BL/6J females mated with C57BL/6J males, and ovulation was induced as described above. The embryo was flushed from the reproductive tract 24 hours after hCG administration. For all samples collected, the zona pellucida (ZP) was removed by treatment of 10 IU/ml Hyaluronidase (Sigma, H6254).

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT  100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

tag: genotype

tag: Sex

value: female

value: GV oocytes


title: HepG2-1

status: Public on Feb 27 2022

type: SRA

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

library_source: transcriptomic

data_processing:
The sequence reads were aligned to the human reference genome assembly (Ensemble GRCh38) and UMI counts of genes were calculated with the celseq2 pipeline (https://github.com/yanailab/celseq2).
The fastq files were demultiplexed with the bc_demultiplex program in the celseq2 pipeline package. UMIs of each sequence are indicated in the header of the fastq files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-delimited text files include raw count values of all samples

molecule: total RNA

organism: Homo sapiens

source_name: Human hepatocarcinomas

growth_protocol: In monolayer culture, iLCCs were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10-7 M dexamethasone, 10 mM nicotinamide, 2mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 1 µM A83-01, and 5 µM Y27632. HepG2 cells, HuH7 cells, and Huh6 cells were cultured in DMEM containing 10% FBS, 2mM L-glutamine, and penicillin/streptomycin. HuCCT1 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
RNA was extracted using the Isogen II (Nippongene)
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".

treatment_protocol: We purchased HUVECs on the market. To generate iLCCs, HUVECs were electroporated with episomal plasmids expressing the genes encoding transcription factors indicated above.

tag: tissue

value: liver

tag: cell type

value: Human hepatocarcinomas

tag: transfection

value: non-treated

tag: Stage

value: in vitro monolayer culture condition


title: ATAC-Seq OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 rep1

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

country: USA

institute: The University of Texas Health Science Center at Houston

library_source: genomic

data_processing:
ATAC-seq raw reads were mapped to the hg19 human reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses.
Bigwig files were build from bam files using deeptools  with options “-binSize 50 and --normalizeUsing RPGC”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: OCI-AML3 NPM1c degron2 cell line

growth_protocol: All human leukemia cell lines are maintained in RPMI-1640 medium with 10% FBS and 1% Pen/Strep, mouse progenitor cell lines are maintained in RPMI-1640 medium with 1% CHO-SCF condidtion medium and 1uM betaestrodial

extract_protocol:
50,000 cells were harvested and permeabilized in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The transposition reaction was carried out at 37°C for 30 min with agitation in 50 μL volume containing 25 μL of 2× TD buffer and 2.5 μL of Nextera Tn5 transposase. DNA was purified with Qiagen MinElute PCR purification kit. Library amplification was done with KAPA HiFi HotStart ReadyMix PCR kit, and the resulting libraries were purified with Qiagen MinElute PCR Purification Kit. Libraries were sequenced in the Illumina HiSeq 4000 platform to generate paired-end reads of 2 × 150 bp.
Library construction protocol is described in Himadewi. et al. [PMID: 34585664]

treatment_protocol: 500nM dTag-13 was used to treat cells for 24hrs.

tag: drug treatment

value: 500nM dTag-13 treated OCI-AML3 NPM1c-degron2 cells


title: HepG2-2


title: Mouse 1-Cell embryos

city: Guangzhou

first: Rui

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were firstly mapped to genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only. Unmapped reads were mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with customized script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts. Additional 6 bases at the ends of reads were ignored.
Customized scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at C-cutoff=3 and (v) one-side binomial P value (probability equals gene-specific non-conversion rate) < 0.001
Genome_build: mm10
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

molecule: polyA RNA

organism: Mus musculus

source_name: early embryo

growth_protocol: Pre-implantation embryos were collected from 7 to 8 week-old C57BL/6J females mated with C57BL/6J males. To induce ovulation, females were administered 5 IU of hCG (Univ, 230734) intraperitoneally, 44 - 48 hours after injection of 5 IU of PMSG (Solarbio, P9970). One-cell embryo was flushed from the reproductive tract at 24 hours after hCG administration in M2 medium (Sigma, M7167). The zona pellucida of embryos selected by cell number or morphology was gently removed by treatment of 10 IU/ml Hyaluronidase (Sigma, H6254) for several minutes. The embryos were then manually picked and total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit (Zymo research, R2051).

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: 1-Cell embryos

value: wildtype


title: RNA-Seq - OCI-AML3 NPM1c degron2 cell line treated with DMSO rep2

data_processing:
RNA-seq raw reads were mapped to the human genome (hg19)  or mouse genome mm9 using STAR-2.6.1 with default parameters. Transcript levels were calculated as TPM and count using RSEM . Those genes having a count greater than 5 in at least 50% of the samples were kept for further examination. The DESeq2 R package was used to perform differential gene expression analysis between groups . Significantly differentially expressed genes were defined as those with a log2fold change (LFC) value of > 1 and a false discovery rate (FDR) of < 0.05.
Genome_build: hg19 mm9
Supplementary_files_format_and_content: RSEM transcript count

extract_protocol:
RNA was extracted with Qiagen RNeasy micro
NEBNext Ultra II RNA-seq library kit was used to construct to library of mouse hematopietic progenitors. Swiftbio's rapid RNA-seq kit was used to construct the library for human AML cells.

treatment_protocol: For dTag-13 treatment, OCI-AML3-NPM1c-degron cells were treated with DMSO or 500nM dTag-13 for 24 hrs. For Selinexor treatment, OCI-AML3 cells were treated with 25nM Selinexor for 24 hrs.

value: DMSO control for dTag-13 for 24hr

tag: genome type


title: TFEB_E_3

city: Tampa

first: Mario

last: Fernandez

address: 12902 Magnolia Dr.

department: Tumor Biology

institute: Moffitt Cancer Center

description:
B-cell lymphoma transduced with bicistronic vector expressing TFEB-ERT2 and puromycin and treated with vehicle replicate 3
BBF139-T-E-3

data_processing:
Sequencing reads were subjected to adaptor trimming, series of quality assessment before being aligned with STAR-2.5.3 against mouse reference genome mm10.
Quantification of read counts aligned to the region associated with each gene was performed using HTSeq v0.6.1 based on National Center for Biotechnology information (NCBI) RefSeq gene model.
Read counts of all samples were normalized using the median-of-ratios method implemented in R/Bioconductor package DESeq2 v1.6.3.
Differential expression analysis between the two groups was performed by serial dispersion estimation and statistical model fitting procedures implemented in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Text file of normalized gene abundance

source_name: Lymph Node

growth_protocol: Eµ-Myc;Eµ-rtTA transgenic B-Cell Lymphoma maintained in 1:1 mix of IMDM/DMEM containing 4 mM L-Glutamine, 1 mM Sodium Pyruvate, 1% Penicillin/Streptomycin,  27.5 μM β-mercaptoethanol, 10% fetal bovine serum, and 10 ng/mL IL-7 and split every 3-4 days

extract_protocol:
Cells were washed with 1x PBS twice and cell pellets were lysed and total RNA extracted using the MACHEREY-NAGEL NucleoSpin RNA Mini Kit for RNA purification (REF 740955.50)
Nugen_Ovation_Mouse RNASeq Kit protocol

treatment_protocol: Lymphomas were treated with vehicle or 250 nM 4-OHT for 4 days

tag: cell line

value: Eu-Myc;Eu-rtTA transgenic B-Cell Lymphoma

tag: strain

tag: gene insert

tag: treatment

value: Vehicle


title: iLCC195-10

source_name: Human umbilical vein endothelial cells

value: umbilical vein

value: Human umbilical vein endothelial cells

value: transduced with HNF1A, FOXA3, LMYC, LIN28B, HNF1B, and KLF5


title: OCI-AML3 NPM1c degron2 cell line treated with 25nM Selinexor rep2

description:
BrUTP labeled RNA
Bru-seq-Selinexor-2

data_processing:
Library strategy: BRU-Seq
Bru-seq raw reads were mapped to the hg19 human reference genome using Bowtie2 (version 2.3.4) . Quality control for the alignment BAM files was performed by samtools, allowing only uniquely mapped reads to be retained and then PCR duplicates were removed by Picard (http://broadinstitute.github.io/picard/) using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses.
Bigwig files were build from bam files using deeptools  with options “-binSize 50 and --normalizeUsing RPGC”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
After the indicated treatment time, BrU was added to the culture medium to label the nascent transcripted RNA for 30 mins. Cells were lysed in Trizol buffer and RNA was extracted.
Library construction protocol is described in Paulsen. et al. [PMID: 23345452]

treatment_protocol: 500nM dTag-13 was used to treat cells for 12hrs, 25nM Selinexor was used to treat cells for 12hrs

value: Selinexor treated replicate 2


title: TFEB_4OHT_1

description:
B-cell lymphoma transduced with a bicistronic vector expressing TFEB-ERT2 and puromycin and treated with 250 nM 4-OHT replicate 1
BBF139-T-4OHT-1


title: HeLa Noc 72h

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: hg19
Supplementary_files_format_and_content: CSV for the position, coverage, and methylation level for the samples

source_name: HeLa

value: wild-type

value: HeLa

tag: time point


title: OCI-AML3 NPM1c degron2 cell line treated with 25nM Selinexor rep1

description:
BrUTP labeled RNA
Bru-seq-Selinexor-1

value: Selinexor treated replicate 1


title: OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 rep2

description:
BrUTP labeled RNA
Bru-seq-dTag-2

value: dTag-13 treated replicate 2


title: Mouse MII oocytes

source_name: oocyte

value: female

value: MII oocytes


title: HeLa Noc 24h


title: TFEB_E_2

description:
B-cell lymphoma transduced with bicistronic vector expressing TFEB-ERT2 and puromycin and treated with vehicle replicate 2
BBF139-T-E-2


title: Vec_4OHT_3

description:
B-cell lymphoma transduced with an empty bicistronic vector expressing puromycin and treated with 250 nM 4-OHT replicate 3
BBF139-V-4OHT-3

value: Empty


title: iLCC196-9

value: in vitro monolayer culture condition


title: Huh6

source_name: Human hepatoblastomas

value: liver

value: Human hepatoblastomas

value: non-treated


title: HeLa KO Mouse NSUN2

value: NSUN2 KO


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO rep1

description:
BrUTP labeled RNA
Bru-seq-DMSO-1

value: DMSO treated replicate 1


title: N2

city: Leeds

first: Patricija

last: van Oosten-Hawle

state: --Select State--

address: Woodhouse Lane

department: Molecular and Cell Biology

country: United Kingdom

institute: UNIVERSITY OF LEEDS

data_processing:
Library strategy: WGS
The resulting sequences were stored as fastq files and mapped to the WBCel235 version of the C. elegans genome using BWA software (v0.7.12-r1039) and duplicate paired end reads were removed using SAMtools software.
Each sequenced genome was compared to the N2 reference genome (WBCel235) to identify the frequency and nature of single-nucleotide polymorphisms (SNPs). Detection of SNPs was performed using GATK software and annotation of transcripts in which each SNP occurred was performed with ANNOVAR software.
Genome_build: WBCel235
Supplementary_files_format_and_content: *.xlsx: Excel files of SNPs identified in this study.

organism: Caenorhabditis elegans

source_name: Whole organism C. elegans

growth_protocol: 10 parental (P0) mutagenized animals were placed in each of 200 founder P0 plates and allowed to lay eggs overnight (F1 generation). P0 adults were removed and F1 eggs were allowed to mature to gravid adult stage and lay eggs (F2 generation). F2 generation were screened under a stereomicroscope equipped with a fluorescent light source and individual mutant animals were picked to establish mutant lines.

extract_protocol:
Genomic DNA was extracted using the Gentra PureGene Tissue Kit.
A DNA sequencing library was prepared using a NEBNext DNA Library Prep Kit (NEB, USA).
Whole-genome sequencing was performed on a Illumina Hi-Seq 150 platform using paired-end sequencing with 150 bp reads.

treatment_protocol: Each mutant strain (mutant 1-4), the control strains (hsp90control and N2) and the founder strain (hsp-90int) were crossed to CB4856 Hawaiian males and F1 cross progeny was singled. 50 F2 progeny was singled and then pooled.

value: Whole body


title: iLCC196-12

value: umbilical vein

value: Human umbilical vein endothelial cells


title: TFEB_E_1

description:
B-cell lymphoma transduced with bicistronic vector expressing TFEB-ERT2 and puromycin and treated with vehicle replicate 1
BBF139-T-E-1

value: Eu-Myc;Eu-rtTA transgenic B-Cell Lymphoma

value: Vehicle


title: HeLa Noc 48h

value: wild-type

value: HeLa


title: C4

value: PVH122 (mutant 4)

value: mutant 4; CB4856; sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry); pccIs002 (vha-6p::daf-21 RNAi::unc-54 3'-UTR)


title: Vec_4OHT_1

description:
B-cell lymphoma transduced with an empty bicistronic vector expressing puromycin and treated with 250 nM 4-OHT replicate 1
BBF139-V-4OHT-1


title: scADT_mESC_K562

city: Stanford

first: Amy

last: Chen

state: CA

address: 279 Campus Drive West

institute: Stanford University

description: sequencing of antibody-derived tags

data_processing:
Library strategy: ADT
For ADT and HTO processing, raw sequencing data were converted to fastq format using bcl2fastq (Illumina). ADTs and HTOs were then assigned to individual cells and antibodies based on cell and antibody barcode sequences. Counts for each antibody were tabulated by counting UMIs. In the barnyard experiment, cells with fewer than 200 ADT+HTO UMIs were excluded from analysis. In the CD4 T cell experiment, cells with fewer than 75 HTO UMIs or 100 ADT UMIs were excluded.
For the mouse-human mixture, raw ATAC-seq and RNA-seq data were converted to fastq format, and aligned to a chimeric hg38 and mm10 reference genome using cellranger-ARC v1.0.1 from 10x Genomics. First, we filtered droplets for high-quality cells, based on >7,500 RNA UMIs, >10,000 unique ATAC fragments, and TSS enrichment > 10. TSS enrichment was calculated using the combined set of mouse + human TSS coordinates and the default parameters of ArchR’s TSS enrichment.
For CD4 T cell scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. Fragment files were then loaded into ArchR (v1.0.2) using the createArrowFiles function.
For CD4 T cell scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. For each lane, the gene expression matrix from the filtered_feature_bc_matrix was used to create a Seurat object using Seurat v3.2.1. The two lanes of CD4 memory T cell data were then merged into one Seurat object and filtered for cells used in the scATAC-seq analysis.

molecule: other

organism:
Homo sapiens
Mus musculus

source_name: ESCs, K562 mixture

growth_protocol: Mouse V6.5 ESCs were cultured on gelatin-coated plates in Knockout DMEM (Thermo Fisher #10829018) supplemented with 7.5% ES-qualified serum (Applied Stem Cell #ASM-5017), 7.5% Knockout Serum replacement (Thermo Fisher #10828-028), 2mM L-glutamine (Gibco #35050061), 10mM HEPES (Gibco #15630080), 100 units/mL penicillin/streptomycin (Gibco #151401222), 0.1mM non-essential amino acids (Gibco #11140050), 0.1mM beta-mercaptoethanol (Gibco #21985023), and LIF. The human chronic myeloid leukemia cell line, K562, was purchased from ATCC and cultured in RPMI 1640 medium (Gibco #11875119) containing 15% FBS and 100 units/mL penicillin/streptomycin. HEK 293T cells were cultured in DMEM with GlutaMAX (Gibco #10566024) containing 10% FBS and 100 units/mL penicillin/streptomycin.

extract_protocol:
Single nuclei were stained and loaded onto a 10x Genomics Chromium controller for generation of NEAT-seq libraries
Antibody-stained cells in 1X Nuclei buffer were processed using the 10X Genomics Multiome kit as indicated in the standard protocol (Rev A) to generate ATAC-seq and RNA-seq libraries. During the pre-amplification step, Truseq read 2 (CAGACGTGTGCTCTTCCGATC) and Nextera read 2 (GGCTCGGAGATGTGTATAAGAGACAG) primers were spiked in at 0.2uM final concentration to amplify ADT and HTO oligos. To generate ADT and HTO libraries, 35ul of pre-amplification product from step 4.3p was amplified with indexing primers using 2X NEB Next High-Fidelity PCR Master Mix (M0541). A double-sided SPRI bead clean up was performed using 0.6X SPRI beads (retaining supernatant) and then adding additional SPRI beads to a final concentration of 1.2X, washing with 80% ethanol, and eluting ADT or HTO libraries from beads using EB buffer.

tag: neat-seq antibodies

value: GATA1, OCT4, SOX2, NPC


title: Positive-HGC_FN1_3UTR

city: Shenyang

first: Funan

last: Liu

state: Liaoning

address: Nanjing Street 155

institute: first affiliated hospital of china medical university

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change. Differentially expressed miRNA between two groups were filtered by Fold Change and P-value. Top 10 miRNA targets were predicted by self-developed software based on miranda and targetscan, and the GO and KEGG pathway analysis were performed based on the target genes.
Genome_build: hg38
Supplementary_files_format_and_content: Enriched peaks and were normalized into TPM.
Supplementary_files_format_and_content: miRNA_expression_counts.txt: Tab-delimited text file
Supplementary_files_format_and_content: miRNA_expression_TPM_normalized.txt: Tab-delimited text file

source_name: human gastric cancer cell line

growth_protocol: HGC27 cells were cultured in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and were incubated at 37 °C in a humidified incubator at 5% CO2. AGS cells were cultured in DMEM/F12 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and were incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
RNA pulldown assays were performed with Pierce Magnetic RNA-Protein Pull-Down Kit (Thermo Fisher) according to the instructions. In vitro transcribed (IVT) RNA probes for pull-down assays were prepared with AmpliScribe™ T7 High Yield Transcription Kit (Epicentre). In brief, 10^7 cells were collected and washed in ice-cold phosphate-buffered saline. The cell pellets lysed in 1ml IP lysis buffer, and centrifuged at 12000 g for 15 minutes at 4°C to collect the supernatant. Second, 50 μl washed streptavidin magnetic beads incubated with 5 μg biotinylated IVT lncRNA or its antisense RNA for 30 minutes at room temperature with agitation. Then, probes coated beads incubated with 500 μl cell lysis supernatant for 1 hour. The beads were washed briefly with wash buffer for five times and elutioned. The bound protein or RNA in the pull-down materials were purified for further analysis.
High-throughput sequencing service was provided by CloudSeq Biotech (Shanghai, China). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina Novaseq 6000 sequencer following the manufacturer's instructions.

treatment_protocol: FN1 3' UTR was stably overexpressed in HGC27 and AGS cells by lentiviral transfection.

value: FN1 3' UTR overexpression

tag: probe

value: Positive RNA probe to FN1 3' UTR sequence


title: HeLa KO Zebrafish NSUN2

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were firstly mapped to genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only. Unmapped reads were mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with customized script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts. Additional 6 bases at the ends of reads were ignored.
Customized scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at C-cutoff=3 and (v) one-side binomial P value (probability equals gene-specific non-conversion rate) < 0.001
Genome_build: hg19
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

tag: vector

value: Zebrafish NSUN2


title: Vec_4OHT_2

description:
B-cell lymphoma transduced with an empty bicistronic vector expressing puromycin and treated with 250 nM 4-OHT replicate 2
BBF139-V-4OHT-2

value: Empty


title: Negative-AGS_FN1_3UTR

value: AGS

value: Negative RNA probe to FN1 3' UTR sequence


title: Vec_E_3

description:
B-cell lymphoma transduced with an empty bicistronic vector expressing puromycin and treated with vehicle replicate 3
BBF139-V-E-3


title: Vec_E_1

description:
B-cell lymphoma transduced with an empty bicistronic vector expressing puromycin and treated with vehicle replicate 1
BBF139-V-E-1


title: OCI-AML3 NPM1c degron2 cell line treated with DMSO rep2

description:
BrUTP labeled RNA
Bru-seq-DMSO-2

value: DMSO treated replicate 2


title: C3

value: PVH121 (mutant 3)

value: mutant 3; CB4856; sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry); pccIs002 (vha-6p::daf-21 RNAi::unc-54 3'-UTR)

value: Whole body


title: N2_B2

data_processing:
Bowtie software v2.3.3 was used to build an index of the WBCel235 version of the C. elegans genome, to which reads were mapped using TopHat v2.0.12.
The number of reads mapped to each gene was counted using HTSeq v0.6.1 and was used to calculate FKPM for each gene.
Differential expression analysis was performed using the DESeq package v1.18.0.
Genome_build: WBCel235 was used as a reference genome.
Supplementary_files_format_and_content: readcount.txt: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: Eggs were synchronized to L1 larvae overnight in M9 and 10000 larvae were grown to Day 1 adulthood on NGM seeded with OP50-1.

extract_protocol:
RNA was extracted using TriZol and then purified using the Direct-Zol RNA Miniprep kit (Zymo-research, Cambridge Biosciences). RNA quality was measured using an Agilent Technologies 2200 TapeStation. All samples had an RNA integrity number of > 9.5.
cDNA libraries were prepared from >1.5 μgs of total RNA using the Illumina Hi-Seq PE150 platform (Illumina).

treatment_protocol: PVH1, PVH2, AM994 and N2 were grown at 20C on NGM seeded with OP50-1 bacteria. Animals were collected and washed three times with M9 media to remove bacteria. Worms were then snap frozen in liquid nitrogen.

value: N2 Bristol

value: WT

tag: age

value: Day 1 adult


title: Vec_E_2

description:
B-cell lymphoma transduced with an empty bicistronic vector expressing puromycin and treated with vehicle replicate 2
BBF139-V-E-2

value: Eu-Myc;Eu-rtTA transgenic B-Cell Lymphoma

value: Vehicle


title: Positive-AGS_FN1_3UTR

tag: genotype


title: C2

value: PVH120 (mutant 2)

value: mutant 2; CB4856; sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry); pccIs002 (vha-6p::daf-21 RNAi::unc-54 3'-UTR)


title: wt-PNS-adventitia-78-weeks-1

type: RNA

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

hyb_protocol: Staining with Fluidic Station 400 Protocol: EukGe-WS2v4

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin

source_name: adventitia of abdominal aorta

label_protocol:
ENZO T7 High Yield Transcript Labelling Kit, 24h IVT
Biotin/SAPE with Anti Streptavidin signal amplification

growth_protocol:
Mice from the Jackson Laboratory, USA.
Maintained under normal mouse chow (ND)

extract_protocol: Qiagen RNEasy Lipid Tissue Mini kit, standard protocol

treatment_protocol: Fresh-frozen aorta adventitia tissues were isolated by laser capture microdissection and taken up in Trizol

value: adventitia of abdominal aorta

tag: gender

value: male

value: 78 weeks


title: wt-SNS-Ganglion-78-weeks-4

source_name: peripheral nervous system

treatment_protocol: Fresh-frozen ganglion tissues were isolated by laser capture microdissection and taken up in Trizol

tag: tissue

value: sympathetic ganglia

value: wild-type


title: wt-SNS-Ganglion-78-weeks-5


title: C1

value: PVH119 (mutant 1)

value: mutant 1; CB4856; sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry); pccIs002 (vha-6p::daf-21 RNAi::unc-54 3'-UTR)


title: wt-PNS-adventitia-78-weeks-3


title: wt-SNS-Ganglion-78-weeks-1


title: wt-SNS-Ganglion-78-weeks-2


title: apoE-SNS-Ganglion-78-weeks-5

value: apoE-/-


title: apoE-SNS-Ganglion-78-weeks-6


title: Mg-Ecs_IP_Cy5

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

description: ECs-Mg(IP,Normalized)

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar human m6A-mRNA&lncRNA Epitranscriptomic Microarray (v1, Arraystar).

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

label_protocol: Briefly, the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: All cell lines were cultured under an atmosphere of 5% CO2 at 37°C. Human Coronary Artery Endothelial Cells (HCAEC) purchased from ScienCellTM (San Diego, California) were cultured in Endothelial Cell Medium (ScienCellTM). The medium package consists of 500 ml of basal medium, 25 ml of fetal bovine serum (ScienCellTM), 5 ml of endothelial cell growth supplement (ECGS, ScienCellTM) and 5 ml of penicillin/streptomycin solution (P/S, ScienCellTM).

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

treatment_protocol: HCAECs cultued on Magnesium-based alloy discs 24h, and static cultured HCAECs were used as control

tag: cell type

value: Primary Human Coronary Artery Endothelial Cells (HCAEC)

tag: passage

value: Magnesium-based alloy discs 24h

tag: ip antibody

value: anti-N6-methyadenosine (m6A) antibody

tag: molecule subtype

value: immunoprecipitated RNA


title: ANn_B3

value: PVH1 (hsp-90neuro)

value: Day 1 adult

value: Whole body


title: apoE-SNS-Ganglion-78-weeks-4


title: Control_IP_Cy5

description: ECs-Control(IP,Normalized)


title: wt-SNS-Ganglion-78-weeks-3


title: Negative-HGC_FN1_3UTR

value: FN1 3' UTR overexpression

value: Negative RNA probe to FN1 3' UTR sequence


title: ANn_B2


title: ANint


title: ANn_B1


title: HGC27_FN1_3'UTR overexpression_rep1

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster, resulting in 65,536 clusters. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment were performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Homo sapiens using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: *.RPKM.txt: Tab-delimited text files include RPKM values for each Sample.

growth_protocol: HGC27 cells were cultured in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco) and were incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski et al. (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: FN1 3' UTR was stably overexpressed in HGC27 cells by lentiviral transfection.


title: apoE-SNS-Ganglion-78-weeks-3


title: Control_supernatant_Cy3

description: ECs-Control(Sup,Normalized)

value: supernatant RNA


title: HGC27_FN1_3'UTR overexpression_rep3


title: lung cancer radioresistance cell line A549-RR_rep3

first: Jiaxin

last: Feng

address: No.151 Yanjiang West Road, Yuexiu District, Guangzhou , Guangdong Province

institute: The First Affiliated Hospital of Guangzhou Medical University

description: Gene expression after obtain radiation resistance characteristics

hyb_protocol: 1 μg of each labeled RNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled RNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the mRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: radioresistance cell line A549-RR

label_protocol: Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

growth_protocol: Cells were cultured in RPMI medium containing 10%FBS

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.

treatment_protocol: The lung cancer cell line A549 in logarithmic growth phase was irradiated with 4 Gy for the first time and cultured for subculture. After cell adherence growth, the cells were irradiated again with 4 Gy, with a total dose of 60Gy. The radiotherapy resistance cell line A549-RR was obtained by further culture.

value: radioresistance cell line A549-RR


title: AN

value: PVH67 (hsp-90control; CB4856)


title: lung cancer radioresistance cell line A549-RR_rep2


title: HGC27_Control_rep3

value: Control


title: N2_B3

value: N2 Bristol

value: WT


title: HGC27_Control_rep1


title: AN_B3

value: AM994 (hsp-90control)

value: sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry)


title: Ripk1_KO1_CD4_Ctrl

city: Yokohama

first: Takayuki

last: Imanishi

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences (IMS)

description: total RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: helper T cell

extract_protocol:
RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: 43 weeks


title: scRNA_CD4+CD45RO+_lane 2

description: single cell RNA-seq

data_processing:
For ADT and HTO processing, raw sequencing data were converted to fastq format using bcl2fastq (Illumina). ADTs and HTOs were then assigned to individual cells and antibodies based on cell and antibody barcode sequences. Counts for each antibody were tabulated by counting UMIs. In the barnyard experiment, cells with fewer than 200 ADT+HTO UMIs were excluded from analysis. In the CD4 T cell experiment, cells with fewer than 75 HTO UMIs or 100 ADT UMIs were excluded.
For the mouse-human mixture, raw ATAC-seq and RNA-seq data were converted to fastq format, and aligned to a chimeric hg38 and mm10 reference genome using cellranger-ARC v1.0.1 from 10x Genomics. First, we filtered droplets for high-quality cells, based on >7,500 RNA UMIs, >10,000 unique ATAC fragments, and TSS enrichment > 10. TSS enrichment was calculated using the combined set of mouse + human TSS coordinates and the default parameters of ArchR’s TSS enrichment.
For CD4 T cell scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. Fragment files were then loaded into ArchR (v1.0.2) using the createArrowFiles function.
For CD4 T cell scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. For each lane, the gene expression matrix from the filtered_feature_bc_matrix was used to create a Seurat object using Seurat v3.2.1. The two lanes of CD4 memory T cell data were then merged into one Seurat object and filtered for cells used in the scATAC-seq analysis.

source_name: primary CD4 memory T cells

value: Tbet, RORgT, GATA3, FOXP3, Helios, NPC


title: MB231_Ctrl

city: wuhan

first: Mengna

state: State...

address: Donghu Road, No. 115, Wuchang District

institute: wuhan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

extract_protocol:
RNA was harvested using Trizol reagent. KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast

tag: disease state

value: cancer

value: control


title: N2_B1

value: Day 1 adult

value: Whole body


title: Standard_Multiome_GM12878_ATAC

data_processing:
For ADT and HTO processing, raw sequencing data were converted to fastq format using bcl2fastq (Illumina). ADTs and HTOs were then assigned to individual cells and antibodies based on cell and antibody barcode sequences. Counts for each antibody were tabulated by counting UMIs. In the barnyard experiment, cells with fewer than 200 ADT+HTO UMIs were excluded from analysis. In the CD4 T cell experiment, cells with fewer than 75 HTO UMIs or 100 ADT UMIs were excluded.
For the mouse-human mixture, raw ATAC-seq and RNA-seq data were converted to fastq format, and aligned to a chimeric hg38 and mm10 reference genome using cellranger-ARC v1.0.1 from 10x Genomics. First, we filtered droplets for high-quality cells, based on >7,500 RNA UMIs, >10,000 unique ATAC fragments, and TSS enrichment > 10. TSS enrichment was calculated using the combined set of mouse + human TSS coordinates and the default parameters of ArchR’s TSS enrichment.
For CD4 T cell scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. Fragment files were then loaded into ArchR (v1.0.2) using the createArrowFiles function.
For CD4 T cell scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. For each lane, the gene expression matrix from the filtered_feature_bc_matrix was used to create a Seurat object using Seurat v3.2.1. The two lanes of CD4 memory T cell data were then merged into one Seurat object and filtered for cells used in the scATAC-seq analysis.
For GM12878 scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics.
For GM12878 scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics.
Genome_build: hg38
Supplementary_files_format_and_content: fragments file; RNA counts file

tag: sample prep

value: Processed using standard 10X Multiome protocol

tag: cell line


title: Ripk1_WT1_CD4_Ctrl

description: total RNA

tag: strain

value: wild type


title: HGC27_Control_rep2


title: wt-PNS-adventitia-78-weeks-2

value: adventitia of abdominal aorta

value: male

value: 78 weeks


title: lung cancer cell line A549_ctrl_rep2

description: Gene expression of parent cell line


title: Mg-Ecs_supernatant_Cy3

description: ECs-Mg(Sup,Normalized)

value: Primary Human Coronary Artery Endothelial Cells (HCAEC)

tag: treatment

value: Magnesium-based alloy discs 24h

value: supernatant RNA


title: HGC27_FN1_3'UTR overexpression_rep2

value: FN1 3' UTR overexpression


title: lung cancer cell line A549_ctrl_rep1

description: Gene expression of parent cell line


title: MB231_FMF_H


title: scATAC_CD4+CD45RO+_lane 2

description: single cell ATAC-seq


title: Ripk1_KO2_CD4_Ctrl

description: total RNA

value: spleen


title: MB231_FMF_L


title: ANi_B2

value: PVH2 (hsp-90int)

value: sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry); pccIs002 (vha-6p::daf-21 RNAi::unc-54 3'-UTR)


title: Orbital adipose/connective tissue from normal person_excised_rep1

city: Shanghai

first: Zifan

last: Yue

address: No. 415 Fengyang Road, Hangpu District

department: Ophthalmology

institute: Shanghai Changzheng Hospital

data_processing:
The Raw Reads obtained by sequencing may contain unqualified Reads with low overall quality, sequencing primers, low end quality, etc. These unqualified Reads are likely to have a certain impact on the quality of the analysis, so they must be filtered to obtain Clean Reads that can be used for data analysis, apply fastx (version: 0.0.13) for filtering.
For the clean reads of each sample, select the reads within a certain length range (18-40nt) for statistics.
We use the program written by Shanghai Biotechnology Corporation to compare all reads with the known TRF database (TRFdb) according to the principle of 100% matching, and compare the base distribution of the first site of TRF with different lengths and the bases of each TRF site. Base distribution statistics.
In order to make the TRF expression levels between different TRFs and between different samples comparable, the number of reads compared to each TRF is normalized by the TMM (trimmed mean of M values) method, and then converted into TPM (Transcripts per million, the formula is: the number of reads on a certain TRFx10^6/total number of reads) to standardize the amount of TRF expression.
Use edgeR to perform TRF analysis of differences between samples. After obtaining the p-value, perform multiple hypothesis testing and correction. By controlling the FDR (False Discovery Rate) to determine the p-value threshold, the corrected p-value is the q-value. At the same time, we calculate the multiple of differential expression based on the TPM value, that is, Fold-change.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: TRF_expression.txt: Tab-delimited text file includes counts and TPM values.

source_name: Orbital adipose/connective tissue from the tissue remains of healthy people after plastic surgery

growth_protocol: Liquid nitrogen quick freezing, -80 degrees refrigerator storage.

extract_protocol:
Use mirVana™ miRNA Isolation Kit (Cat #. AM1561, Austin TX, US) and perform total RNA extraction of samples according to the standard operating procedures provided by the manufacturer. Standby after passing the quality inspection of electrophoresis.
Perform 3' end adapter connection, 5' end adapter connection, reverse transcription, amplification, cDNA library size selection, purification and other steps on the purified Total RNA to complete the sequencing sample library construction. The constructed library uses Qubit® 2.0 Fluorometer to detect the concentration, and the Agilent 2100 detects the size of the library.

tag: diagnosis

value: Healthy

value: Orbital adipose/connective tissue

value: Female

tag: Stage

value: Stable period


title: Standard_Multiome_GM12878_RNA


title: apoE-SNS-Ganglion-78-weeks-2

value: sympathetic ganglia

value: apoE-/-


title: B_MxCre

city: Aachen

first: Ronghui

last: Li

address: Pauwelsstr. 19

institute: RWTH Aachen

data_processing:
Cell Ranger Software (Version 2.1.1) was used to process sequencing data
Seurat (Version 3.1.0) was used to integrate data
mm10
Genome_build: matrix: In hdf4 format. The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
Supplementary_files_format_and_content: Molecule Info : The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: Summary : The cellranger pipeline outputs a summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. Rarely, an issue may also be detected during the pipeline run leading to an alert also appearing on this page, and more information about these is provided in the troubleshooting documentation.

source_name: Bone marrow

growth_protocol: We isolated hematopoietic cells from fresh mouse bone marrow, extracted by flushing and crushing femur, tibia, pelvis and spine

extract_protocol: Single Cell 3′ Reagent Kits (v2) User Guide (manual part no. CG00052, Rev D). All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://suppo

treatment_protocol: Whole bone marrow cells were brought into single cell suspension and FACS sorted to isolate alive Lin-/Ckit+/Sca1+/cells.

value: Bone marrow


title: lung cancer cell line A549_ctrl_rep3

description: Gene expression of parent cell line


title: Orbital adipose/connective tissue from patients_excised_rep2

source_name: Orbital adipose/connective tissue from orbital decompression surgery

value: Thyroid-associated ophthalmopathy (TAO)

value: Male


title: lung cancer radioresistance cell line A549-RR_rep1

value: radioresistance cell line A549-RR


title: apoE-SNS-Ganglion-78-weeks-1

value: male

value: 78 weeks


title: ANi_B3

value: Day 1 adult

value: Whole body


title: scRNA_CD4+CD45RO+_lane 1

description: single cell RNA-seq

tag: neat-seq antibodies

value: Tbet, RORgT, GATA3, FOXP3, Helios, NPC


title: ANi_B1

value: PVH2 (hsp-90int)


title: Ripk1_WT2_CD4_Ctrl

description: total RNA

value: spleen

value: 43 weeks

value: wild type


title: Orbital adipose/connective tissue from normal person_excised_rep3

value: Healthy

value: Orbital adipose/connective tissue

value: Female


title: AN_B2

value: AM994 (hsp-90control)

value: sid-1 (pk3321); rmIs288 (myo-2p::CFP; C12C8.1p::mCherry)


title: Orbital adipose/connective tissue from normal person_excised_rep2

value: Stable period


title: D_Csnk

value: Bone marrow


title: MxCre_35_2LSK


title: XT stage0 5ng

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: Xenbase XT 9.1
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

organism: Xenopus tropicalis

source_name: early embryo

extract_protocol:
~200 embryos were used for RNA isolation.  Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: early embryo

tag: developmental stage

value: stage 0

tag: input


title: AN_B1

tag: genotype

tag: age


title: C_Csnk

tag: tissue


title: scHTO_CD4+CD45RO+_lane 2

description: sequencing of hash tag oligos

data_processing:
Library strategy: HTO
For ADT and HTO processing, raw sequencing data were converted to fastq format using bcl2fastq (Illumina). ADTs and HTOs were then assigned to individual cells and antibodies based on cell and antibody barcode sequences. Counts for each antibody were tabulated by counting UMIs. In the barnyard experiment, cells with fewer than 200 ADT+HTO UMIs were excluded from analysis. In the CD4 T cell experiment, cells with fewer than 75 HTO UMIs or 100 ADT UMIs were excluded.
For the mouse-human mixture, raw ATAC-seq and RNA-seq data were converted to fastq format, and aligned to a chimeric hg38 and mm10 reference genome using cellranger-ARC v1.0.1 from 10x Genomics. First, we filtered droplets for high-quality cells, based on >7,500 RNA UMIs, >10,000 unique ATAC fragments, and TSS enrichment > 10. TSS enrichment was calculated using the combined set of mouse + human TSS coordinates and the default parameters of ArchR’s TSS enrichment.
For CD4 T cell scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. Fragment files were then loaded into ArchR (v1.0.2) using the createArrowFiles function.
For CD4 T cell scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. For each lane, the gene expression matrix from the filtered_feature_bc_matrix was used to create a Seurat object using Seurat v3.2.1. The two lanes of CD4 memory T cell data were then merged into one Seurat object and filtered for cells used in the scATAC-seq analysis.


title: scHTO_CD4+CD45RO+_lane 1

description: sequencing of hash tag oligos


title: Orbital adipose/connective tissue from patients_excised_rep3

value: Thyroid-associated ophthalmopathy (TAO)

tag: gender

value: Male


title: XT stage0 20ng


title: A_MxCre

tag: cell type


title: XT stage0 rep1


title: XT stage0 10ng


title: scADT_CD4+CD45RO+_lane 2

description: sequencing of antibody-derived tags


title: scATAC_CD4+CD45RO+_lane 1

description: single cell ATAC-seq


title: HB_41

status: Public on Feb 26 2022

type: genomic

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

institute: Institute of Neuropathology Münster, Germany

description: CNS hemangioblastoma

hyb_protocol: Bisulphite converted DNA was hybridised to the MethylationEPIC BeadChip array.

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

data_processing: Processed data are beta values.

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed paraffin-embedded tumor samples using the Maxwell 16 FFPE Tissue LEV DNA Purification Kit (Promega).

value: female

tag: syndrome

value: sporadic

tag: location

value: cerebellum

value: hemangioblastoma

tag: sample type

value: cancer tissue

tag: donor id


title: Orbital adipose/connective tissue from patients_excised_rep1


title: iLCC-derived tumor-2

description: Sample 2

data_processing:
The sequence reads were aligned to human (hg38) and mouse (mm10) genomes separately using tophat2 program (v2.1.1) with the default settings. Then, human-derived reads were specifically extracted from the whole aligned reads using bamcmp program. The read counts of each gene were estimated from the processed reads using StringTie (v2.1.7) and featureCounts program in Subread package (v2.0.1) with the default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-delimited text file includes raw count values of all samples

source_name: umbilical vein

growth_protocol: Prior to transplantation of iLCCs, the recipient NSG mice (3 weeks old) were administered 40 mg/kg retrorsine by intraperitoneal injection and subsequently administered 80 mg/kg retrorsine twice every other week. One week after the last injection of retrorsine, the recipient mice (6 weeks old) received 70% partial hepatectomy, followed by intrasplenic injection of 1 × 10^6 iLCCs.

extract_protocol:
RNA was extracted using the Isogen II (Nippongene)
RNA-seq libraries were prepared using an NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: At two months after transplantaiton of iLCCs, the mouse were sacrificed and the liver tumors were collected.

value: Human umbilical vein endothelial cells

value: umbilical vein

tag: transfection

value: transduced with HNF1A, FOXA3, LMYC, LIN28B, HNF1B, and KLF5

value: tumor composed of human cells arising in immunodeficient mouse liver


title: HB_34

description: CNS hemangioblastoma

value: brainstem


title: HB_32

description: CNS hemangioblastoma


title: Csnk_35_4LSK

tag: strain


title: XT stage0 rep2


title: iLCC-derived tumor-1

description: Sample 1


title: Csnk_35_3LSK


title: HB_40

description: CNS hemangioblastoma

value: VHL

value: spinal


title: HB_38

description: CNS hemangioblastoma

value: male


title: HB_30_2

description: CNS hemangioblastoma


title: scADT_CD4+CD45RO+_lane 1

description: sequencing of antibody-derived tags

data_processing:
Library strategy: ADT
For ADT and HTO processing, raw sequencing data were converted to fastq format using bcl2fastq (Illumina). ADTs and HTOs were then assigned to individual cells and antibodies based on cell and antibody barcode sequences. Counts for each antibody were tabulated by counting UMIs. In the barnyard experiment, cells with fewer than 200 ADT+HTO UMIs were excluded from analysis. In the CD4 T cell experiment, cells with fewer than 75 HTO UMIs or 100 ADT UMIs were excluded.
For the mouse-human mixture, raw ATAC-seq and RNA-seq data were converted to fastq format, and aligned to a chimeric hg38 and mm10 reference genome using cellranger-ARC v1.0.1 from 10x Genomics. First, we filtered droplets for high-quality cells, based on >7,500 RNA UMIs, >10,000 unique ATAC fragments, and TSS enrichment > 10. TSS enrichment was calculated using the combined set of mouse + human TSS coordinates and the default parameters of ArchR’s TSS enrichment.
For CD4 T cell scATAC-seq data, raw sequencing data were converted to fastq format and aligned to the hg38 reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. Fragment files were then loaded into ArchR (v1.0.2) using the createArrowFiles function.
For CD4 T cell scRNA-seq data, raw sequencing data were converted to fastq format and aligned to the reference genome using cellranger-ARC v.1.0.1 from 10X Genomics. For each lane, the gene expression matrix from the filtered_feature_bc_matrix was used to create a Seurat object using Seurat v3.2.1. The two lanes of CD4 memory T cell data were then merged into one Seurat object and filtered for cells used in the scATAC-seq analysis.

value: Tbet, RORgT, GATA3, FOXP3, Helios, NPC


title: HB_37

description: CNS hemangioblastoma


title: HB_36

description: CNS hemangioblastoma


title: HB_42

description: CNS hemangioblastoma


title: HB_28

description: CNS hemangioblastoma


title: HB_35

description: CNS hemangioblastoma


title: HB_29_1

description: CNS hemangioblastoma


title: HB_33

description: CNS hemangioblastoma


title: HB_24

description: CNS hemangioblastoma


title: HB_27

description: CNS hemangioblastoma


title: HB_23

description: CNS hemangioblastoma


title: HB_31

description: CNS hemangioblastoma


title: HB_21

description: CNS hemangioblastoma


title: HB_22

description: CNS hemangioblastoma


title: HB_29_2

description: CNS hemangioblastoma


title: HB_19

description: CNS hemangioblastoma


title: HB_30_1

description: CNS hemangioblastoma


title: HB_26

description: CNS hemangioblastoma


title: HB_25

description: CNS hemangioblastoma


title: HB_39

description: CNS hemangioblastoma


title: HB_20

description: CNS hemangioblastoma

value: cerebrum


title: HB_18

description: CNS hemangioblastoma


title: HB_15

description: CNS hemangioblastoma


title: HB_16

description: CNS hemangioblastoma


title: HB_17

description: CNS hemangioblastoma


title: HB_14

description: CNS hemangioblastoma


title: HB_13_2

description: CNS hemangioblastoma


title: HB_10

description: CNS hemangioblastoma


title: HB_07

description: CNS hemangioblastoma


title: HB_13_1

description: CNS hemangioblastoma


title: HB_11

description: CNS hemangioblastoma


title: HB_05

description: CNS hemangioblastoma


title: HB_12

description: CNS hemangioblastoma


title: HB_08

description: CNS hemangioblastoma


title: HB_03

description: CNS hemangioblastoma


title: HB_09

description: CNS hemangioblastoma


title: HB_04

description: CNS hemangioblastoma


title: HB_06_2

description: CNS hemangioblastoma


title: HB_06_3

description: CNS hemangioblastoma


title: HB_06_1

description: CNS hemangioblastoma


title: HB_02

description: CNS hemangioblastoma


title: EVT-PE-6

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

description: Case

data_processing:
Normalization was performed using the arithmetic mean of 2 or more housekeeping genes,including ACTB, B2M, GAPDH and RPLP0
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_HKG − Ct_Target)]
Fold change calculations performed using 2^deltadeltaCt.

label: SYBR Green

source_name: Extravillous trophoblast cells - sample 5

label_protocol: Samples were analyzed using the Epithelial-Mesenchymal Transition (EMT) RT2 Profile PCR Array (Cat. #PAHS-090Z, Qiagen) using an ABI 7900 HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA) under cycling conditions recommended for the PCR Array

extract_protocol: RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. cDNA was transcribed from 10 ng of RNA using the RT2 First Strand Kit (Qiagen) according to the manufacturer’s instructions.

value: preeclampsia


title: HB_01

description: CNS hemangioblastoma


title: EVT-PE-3

description: Case

source_name: Extravillous trophoblast cells - sample 2


title: EVT-PE-4

description: Case

source_name: Extravillous trophoblast cells - sample 3


title: EVT-PE-5

description: Case

source_name: Extravillous trophoblast cells - sample 4


title: CTB-PE-1

description: Case

source_name: Cytotrophoblast cells - sample 1


title: CTB-PE-2

description: Case

source_name: Cytotrophoblast cells - sample 2


title: CTB-PE-4

description: Case

source_name: Cytotrophoblast cells - sample 4


title: EVT-PE-2

description: Case

source_name: Extravillous trophoblast cells - sample 1


title: EVT-PE-1

description: Case


title: CTB-PE-3

description: Case

source_name: Cytotrophoblast cells - sample 3


title: EVT-CTRL-3

description: Control

value: placenta previa


title: EVT-CTRL-7

description: Control


title: EVT-CTRL-8

description: Control


title: ab57_AGO1IP_Rep3_sRNA

city: Shenzhen

first: Xuemei

state: Guangdong

address: Nanhai Road 3688

institute: Shenzhen University

data_processing:
The data analysis was performed the pRNASeqTools pipeline (https://github.com/grubbybio/pRNASeqTools).
The raw reads were aligned to the TAIR10 genome using ShortStack.
Normalization was performed by calculating the RPMR (reads per million of 45S rRNA reads) value.
For AGO1 IP sRNA-Seq, normalization was performed by calculating the reads per million mapped reads (RPM)
Differentially expressed genes (DEGs) were identified between amiR-SUL and amiR-SUL ab57 mutant samples with 1.5 fold-change cutoff as well as P<0.01 by DESeq2. All DEGs were plotted using the value of log2 (RPMR).
Differentially expressed genes (DEGs) were identified among Col_input,ab57_input, Col-AGO1 IP and ab57_AGO1 IP samples with 1.5 fold-change cutoff as well as P<0.01 by DESeq2. All DEGs were plotted using the value of log2 (RPM).
Genome_build: Arabidopsis thaliana (assembly TAIR10)
Supplementary_files_format_and_content: wig, bw

organism: Arabidopsis thaliana

source_name: ab57_AGO1IP_15d-old seedlings

growth_protocol: All seeds were grown on petri dishes containing 1/2 Murashige and Skoog Basal Medium (Sigma-Aldrich, M5519) plus 2% Sucrose and 0.8% Agar. All plants were grown under 16 h light (22°C)/8 h dark (18°C) period in growth chambers at a light intensity of 120–150 μmolm−2 s−1.

extract_protocol:
Total RNAs were isolated from 15-day-old seedlings with TRI reagent (Molecular Research Center, TR118).
Total RNA extracted from 15-day-old seedlings of both wild type and mutants. For library construction, 30μg total RNA were resolved on a 15% polyacrylamide gel with 8M urea. Small RNAs in the 15-40 nt size range were recovered as described (Liu et al., 2012). Small RNA libraries were prepared using the library preparation kit (NEB, E7100), and sequenced with an Illumina HiSeq2500 platform at BerryGenomics, China. For AGO1 IP, 1g of 15-day-old seedlings were grinded in liquid nitrogen and IP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% NP-40, 1x cocktail and 1x PMSF) was added with incubating for 20 min with gently shaking at 4°C. Before immunoprecipitation, the supernatant was incubated with 100μL of dynabeads (Invitrogen, 10002D) for 2h at 4°C. After centrifuge and filtered, the supernatant was used for IP. 50 ul was taken out as input, the rest were incubated with AGO1 antibody (Agrisera, AS09527) for 2 h at 4 ℃. The beads were washed with wash buffer (IP buffer with 0.5% NP-40), 1/10 volume was added 2x SDS-loading buffer for western blots and 9/10 volume was for RNA isolation. And the small RNA libraries were prepared using the library preparation kit (NEB, E7100), and sequenced with an illumina Nextseq platform at BerryGenomics, China.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: 15-day-old seedlings


title: CTB-CTRL-3

description: Control


title: EVT-CTRL-6

description: Control


title: Col_AGO1IP_Rep3_sRNA

source_name: Col_AGO1IP_15d-old seedlings

value: wild type


title: EVT-CTRL-2

description: Control


title: ab57_AGO1IP_Rep1_sRNA


title: ab57_AGO1IP_Rep2_sRNA


title: EVT-CTRL-5

description: Control


title: ab57 input_Rep3_sRNA

source_name: ab57 input_15d-old seedlings


title: ab57 input_Rep1_sRNA


title: EVT-CTRL-4

description: Control


title: CTB-CTRL-4

description: Control


title: EVT-CTRL-1

description: Control


title: D 124 high concentrate feeding replicate 3

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

description:
D 124 high concentrate feeding rep 3
4631_435_D124

data_processing:
Ion torrent Small RNAseq, base-calling and adapter-trimming.
StrandNGS, quality control for pre- and post-alignment quality
StrandNGS, alignment to genome using defalt parameters
StrandNGS, Quantile algorithm used for sample normalization
StrandNGS, ANOVA preformed to determine differential expression
Genome_build: bosTau4
Supplementary_files_format_and_content: Text file of normalized read counts for all miRNA features for all samples

organism: Bos taurus

source_name: Longissimus muscle

extract_protocol:
Extraction of total RNA was extracted with Trizol according to manufactures specifications. Qantificatioon and qualification were checked by  NanoPhotometer spectrophotometer and Agilent Bioanalyzer 2100 system.
cDNA libraries were constructed using Ion Total RNA-Seq Kit v2 according to the manufacturer.

value: Longissimus muscle

tag: breed

value: angus-cross

tag: days on high concentrate diet

tag: replicate


title: D 124 high concentrate feeding replicate 2

description:
D 124 high concentrate feeding rep 2
4630_430_D124


title: s20

city: Leicester

first: Marcin

last: Wozniak

address: Leicester

institute: University of Leicester

data_processing:
The sequencing data were quality-checked with Fastqc v0.11.5, aligned to miRBase 21 using bowtie2 and quantified using Cufflinks. FPKM quantities were analyzed for differen_x0002_tial expression using limma R-package
Quantitative real-time PCR was carried on Qiagen’s Rotor-Gene machines using TaqMan Advanced miRNA assays
Genome_build: miRBase 21
Supplementary_files_format_and_content: counts matrix

source_name: urine

extract_protocol:
Blood was collected before surgery and 6-12, 24, 48, 72 and 96hrs after surgery (citrate and serum). Urine was collected before surgery and 24hrs after surgery. EV concentrations and size distributions were tested with NanoSight NS500. EV’s RNA was isolated from 1ml urine with an exoRNeasy kit (Qiagen) according to the manufacturer’s recommendations
Illumina single-end multiplexed sequencing 75bp

value: urine extracellular vesicles

tag: subject status

value: cardiac surgery patient

tag: remarks

value: not applicable

tag: aki

value: No

tag: time point

value: post

tag: molecule type

value: Total exosome


title: D 124 high concentrate feeding replicate 4

description:
D 124 high concentrate feeding rep 4
4632_746_D124

tag: tissue


title: CTB-CTRL-2

description: Control


title: D 92 high concentrate feeding replicate 2

description:
D 92 high concentrate feeding rep 2
4626_430_D90


title: s17


title: CTB-CTRL-1

description: Control


title: s15

value: Yes


title: Col_AGO1IP_Rep2_sRNA


title: ab57 input_Rep2_sRNA


title: Col_AGO1IP_Rep1_sRNA


title: Col input_Rep3_sRNA

source_name: Col input_15d-old seedlings


title: Col input_Rep2_sRNA


title: D 0 high concentrate feeding replicate 2

description:
D 0 high concentrate feeding rep 2
4622_430_D0


title: D 0 high concentrate feeding replicate 3

description:
D 0 high concentrate feeding rep 3
4623_435_D0


title: D 124 high concentrate feeding replicate 1

description:
D 124 high concentrate feeding rep 1
4629_30_D124


title: mutant comK-2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
adaptor clipping and quality trimming: cutadapt
read mapping: READemptin align / segemehl
coverage calculation: READemptin coverage
Genome_build: NC_009641.1
Supplementary_files_format_and_content: wiggle

organism: Staphylococcus aureus

source_name: Laboratory Cultures

growth_protocol: TSB cultures in stationary phase

extract_protocol:
Under the specific growth conditions explained in greater detailed in the main text, cells were harvested and immediately incubated with RNA-protect (Qiagen), or, when derived from cell-line infections, with trizol (Thermo Scientific, USA). Total RNA was isolated using the RNeasy kit (Qiagen). To remove all traces of DNA, RNA samples were treated with DNase I (New England Biolabs). RNA purity and quality were determined by Nanodrop (Thermo Scientific, USA).
cDNA was fragmented using Bioruptor (Diagenode, NJ, USA), profiled using Agilent Tapestation, and subjected to Beckman Biomek FXp (Biomek 6000, Beckman Coulter) fully automatic workstation and a Beckman HT library kit (SPRIworks HT, Beckman Coulter, USA) to generate fragment libraries.

value: Newman

tag: genotype

value: comK mutant


title: D 92 high concentrate feeding replicate 4

description:
D 92 high concentrate feeding rep 4
4628_746_D90


title: CTB-CTRL-5

description: Control


title: s19


title: D 92 high concentrate feeding replicate 3

description:
D 92 high concentrate feeding rep 3
4627_435_D90


title: wild type WT-1

treatment_protocol: cells were harvested and immediately incubated with RNA-protect (Qiagen),

value: Wild type


title: s11


title: s18


title: D 92 high concentrate feeding replicate 1

description:
D 92 high concentrate feeding rep 1
4625_30_D90


title: s16


title: 32261_cornea  [Sample_58]

city: Wauwatosa

first: Iris

last: Kassem

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

data_processing:
Filtering and trimming with SOAPnuke software version 1.5.2 using parameters: -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G found at: https://github.com/BGIflexlab/SOAPnuke
Alignment using HISAT2 v2.0.4, using parameters: -p 8 --phred33 --sensitive -I 1 -X 1000 found at http://www.ccb.jhu.edu/software/hisat
Clean reads mapped to the reference genome using Bowtie v2.2.5 Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Gene expression levels calculated with RSEM v1.2.12
Genome_build: GCF_000003625.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Oryctolagus cuniculus

source_name: cornea

extract_protocol:
Tissues were homogenized using a Mini-Bead beater 16 (Biospec Products) at 10 °C. Samples were homogenized for approximately 90 seconds and then cooled for 90 seconds on ice for three rounds. Following homogenization, RNA was extracted using a RNeasy Extraction kit (Qiagen, Germantown, MD), according to the manufacturer’s protocol, with an additional wash step of 500 microliters of Buffer RPE prior to adding the RNAse-free water. Following this step, 50 microliters of RNAse-free water was added to the spin-column membrane to extract the total RNA. Total RNA samples were sent to BGI Group for quality control verification and library preparation.
Library constructed by BGI using DNBseq platform.

value: New Zealand white rabbit

value: cornea

tag: age

value: 5 weeks

tag: tissue treatment

value: unoperated


title: s10

value: pre


title: s14


title: Col input_Rep1_sRNA

value: Columbia

value: wild type

value: 15-day-old seedlings


title: s13

value: urine extracellular vesicles

value: cardiac surgery patient


title: D 0 high concentrate feeding replicate 4

description:
D 0 high concentrate feeding rep 4
4624_746_D0

value: Longissimus muscle

value: angus-cross


title: WT_CK_22C_3

city: Kunming

first: Jiajia

last: Han

state: Yunnan

address: Yunnan University (Chenggong Campus)

institute: Yunnan University

data_processing:
Messenger RNA was isolated from 1μg of total RNA according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer.
Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).
Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol  sequencing with NovaSeq 6000 sequencer at Shanghai Majorbio Bio-pharm Technology Co.,Ltd.
Genome_build: tair10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: The aboveground parts of seedlings

growth_protocol: Arabidopsis was grown on half-strength MS medium with 1.2% sucrose (½MS). The seeds were stratified at 4°C for 3 days and then first grown at 22°C under short-day growth condition (12 h: 12 h, day: night photoperiod, 7000 LX light) in growth chambers. Serendipita indica (syn. Piriformospora indica, DSM11827) fungus were grown and conserved in PDA medium (200 g L-1 potato, 20 g L-1 dextrose and 20 g L-1 agar).

extract_protocol:
Total RNA was extracted using TRIzol® Reagent from the Si and CK samples grown at 22℃,25℃or 28℃. There were three biological replicates for each group.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.

treatment_protocol: For cocultivation with S. indica, 9-day-old Arabidopsis seedlings were inoculated with S. indica in PNM medium plates. S. indica-incubated (Si) and control (CK) samples were grown at 22°C, 25°C or 28°C under short-day growth condition.

tag: treatment

value: 22 degrees C for 7 days

value: aboveground parts of seedlings


title: WT_CK_22C_2


title: D 0 high concentrate feeding replicate 1

description:
D 0 high concentrate feeding rep 1
4621_30_D0


title: mutant comK-1

value: Newman


title: s12

value: not applicable

value: Yes

value: post

value: Total exosome


title: WT_Si_22C_2

value: Si-incubated at 22 degrees C for 7 days


title: wild type WT-2

value: Wild type


title: 32261_iris  [Sample_57]

source_name: iris & ciliary body

value: New Zealand white rabbit

value: iris & ciliary body

value: 5 weeks

value: unoperated


title: WT_Si_22C_3

value: wild type


title: WT_CK_25C_2

value: 25 degrees C for 7 days


title: s9

value: urine extracellular vesicles

value: cardiac surgery patient

value: No

value: pre


title: 32260_cornea  [Sample_56]

value: cornea

value: operated


title: 32259_cornea  [Sample_54]


title: 32260_iris  [Sample_55]


title: s7

value: not applicable


title: WT_CK_25C_1

value: aboveground parts of seedlings


title: WT_CK_25C_3


title: 32259_iris  [Sample_53]


title: s6

value: Total exosome


title: WT_Si_25C_1

value: Si-incubated at 25 degrees C for 7 days


title: WT_Si_25C_2


title: WT_CK_22C_1

value: 22 degrees C for 7 days


title: s5

value: Yes


title: s4


title: WT_Si_22C_1

value: Si-incubated at 22 degrees C for 7 days


title: WT_CK_28C_2

value: 28 degrees C for 7 days


title: 32258_iris  [Sample_51]

value: New Zealand white rabbit

value: iris & ciliary body

value: 6 months

value: unoperated


title: s8

value: urine extracellular vesicles

value: cardiac surgery patient


title: 32257_cornea  [Sample_50]


title: s3

value: pre


title: 32257_iris  [Sample_49]


title: WT_Si_28C_2

value: Si-incubated at 28 degrees C for 7 days

value: wild type


title: WT_Si_28C_1


title: s2

value: not applicable


title: WT_Si_28C_3

value: aboveground parts of seedlings


title: s1

value: Total exosome


title: 32256_cornea  [Sample_48]

value: cornea


title: 32256_iris  [Sample_47]


title: Inguinal fat, FNIP1-AKO biological rep2

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

description: Inguinal fat from FNIP1-AKO mouse

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped)  were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

source_name: Inguinal fat from 8-week-old FNIP1-AKO mouse

extract_protocol:
Inguinal fat were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Inguinal fat

value: 8 weeks


title: 32258_cornea  [Sample_52]


title: WT_CK_28C_1


title: Inguinal fat, FNIP1-AKO biological rep1

description: Inguinal fat from FNIP1-AKO mouse


title: MG_6_v_sort

city: Boston

first: George

last: Murphy

state: MA

address: 670 Albany Street

institute: Center for Regenerative Medicine of Boston University and Boston Medical Center

description: 6 Days in culture, adherent

data_processing:
10X Cellranger bcl2fastq, converting bcl files to fastq files
Alignment of fastq files to mm10 using STARSolo, generating counts matrices
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene for each individual sample

source_name: Fetal Lung

growth_protocol: The fetal lungs are isolated and digested with liberase into a single cell suspension. These cells are frozen down in 10% DMSO and replated on a thin later of diluted matrigel with HSPC media (containing mTPO, IL6, SCF, FGF, VEGF, Flt3). On D3, wells are washed with PBS and replaced with fresh media.

extract_protocol:
On D4, D5 and D6, suspension cells are collected prepped for 10x. Adherent layers are digested with accutase, and sorted to enrich for live-VECAD+ cells, which are then prepped for 10x.
10X 3'v3 (3' Biased Single Cell RNA Seq)

tag: develomental stage

value: Fetal Lung

tag: culture condition

value: HSPC media

tag: cell type

value: adherent cells

tag: days in culture

value: 6 days


title: WT_Si_25C_3

value: Si-incubated at 25 degrees C for 7 days


title: WT_CK_28C_3

value: 28 degrees C for 7 days


title: Inguinal fat, WT biological rep2

description: Inguinal fat from wild-type mouse

source_name: Inguinal fat from 8-week-old wild-type mouse

tag: strain


title: 32255_cornea  [Sample_46]

tag: breed

value: New Zealand white rabbit

value: 6 months

value: unoperated


title: 32255_iris  [Sample_45]

value: iris & ciliary body


title: H3.3-rep2-HS-H3ChIP

city: Szeged

first: Andrea

last: Ábrahám

state: Csongrád

address: Közép fasor 52.

country: Hungary

institute: University of Szeged

data_processing:
trimming via Trim Galore (0.6.6.)
alignment to the Drosophila melanogaster (dm6) genome with Bowtie2 (2.4.2)
filter to blacklisted reads via BAM Filter Galaxy Version 0.5.9 software
determining reads on genes via BedCov Galaxy Version 2.0.2
converting to BigWig via MACS (2.2.7.1)
Genome_build: dm6
Supplementary_files_format_and_content: bigwig

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Flies were held on standard Drosophila media until treatment

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext Ultra II DNA Library Prep Kit for Ilumina according the recommendations of the manufacturer, without size selection

treatment_protocol: heat-shocked flies were exposed to heat shock at 37°C for 20 minutes, heat-shocked and regenerated flies were exposed to heat shock at 37°C for 20 minutes and regenerated at room temperature for 3 hours prior to freeze in liquid nitrogen

value: Brain

value: heat-shocked

value: elav-Gal4; UAS-H3.3-3xFlag


title: H3.3-rep2-HS3-H3ChIP

value: heat-shocked and regenerated


title: MG_4_v_sort

description: 4 Days in culture, adherent

value: 4 days


title: MG_5_sus

description: 5 Days in culture, suspension cells

value: suspension cells

value: 5 days


title: H3.3-rep1-HS3-H3ChIP


title: 32254_iris  [Sample_43]

value: operated


title: Inguinal fat, WT biological rep1

description: Inguinal fat from wild-type mouse

value: Inguinal fat

value: 8 weeks

value: wild type


title: 32253_cornea  [Sample_42]

value: cornea


title: MG_4_sus

description: 4 Days in culture, suspension cells

value: Fetal Lung

value: HSPC media


title: H3.3-rep1-HS-H3ChIP


title: H3.3-rep2-NC-H3ChIP

value: non-treated


title: intron19 of ARFGEF1 sequencing

city: Taipei

first: Trees-Juen

last: Chuang

address: 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academic Sinica

description: The PCR product amplified by exon19F and exon 20R primers

data_processing:
A total of 3,040,649 nanopore long reads were generated and then aligned against the reference genome (GRCh38) using minimap2.  (chr8:67,240,164-67,251,450) using MUMmer (version 3.0)
We found that 92 % (2,808,975/3,040,649) of the nanopore reads uniquely mapped (mapping quality=60) to intron19.
The uniquely mapped reads were assembled by minimap2 (minimap2 -x ava-ont) and then formed a consensus sequence by Racon.
We aligned the consensus sequence against the genomic sequence including exon19, intron19, and exon20
Genome_build: hg38
Supplementary_files_format_and_content: After specific amplification of intron 19 region of ARFGEF1, the sequences were sequenced by nanopore sequecing. The result indicated the number of reads containing exon19-intron19-exon20 region or exon26 insertion.

source_name: human breast cancer cell line

growth_protocol: MCF-7 cells were culture in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin at 37oC and placed in a humidified atmosphere containing 5% CO2

extract_protocol:
To examine the full-length sequence of intron19 of ARFGEF1, we conducted the long-range PCR experiment by PrimeSTAR GXL DNA polymerase (TaKaRa, Cat. R050B).
A total of 100 fmol of gel-purified PCR products was sequenced by the protocol of ONT Amplicons by Ligation (Oxford Nanopore Technologies, SQK-LSK109).
Briefly, DNA was repaired by FFPE (New England Biolabs, Cat. M6630) and end-prepped/dA-tailed by using the NEBNext End Repair/dA-tailing module (New England Biolabs, Cat. E7546). Next, the kit-supplied sequencing adapters are ligated onto the prepared ends. After purification by AMPure XP beads, a total of 50 fmole DNA was sequenced by an R9.4 Flow cell.

treatment_protocol: No treatment

tag: cell line

value: MCF-7 cell line

value: human breast cancer cell line

tag: molecule subtype

value: amplified amplicons of intron 19


title: MG_6_sus

description: 6 Days in culture, suspension cells

value: 6 days


title: MG_5_v_sort

description: 5 Days in culture, adherent

value: adherent cells


title: 32253_iris  [Sample_41]

value: New Zealand white rabbit

value: iris & ciliary body

value: 6 months


title: H3.3-rep1-NC-H3ChIP

value: Brain

value: elav-Gal4; UAS-H3.3-3xFlag


title: RNAcapture for ts-ARFGEF1

data_processing:
Sequencing was generated using MinKNOW Core 3.6.5 software, Bream 4.3.16 and Guppy 3.2.10.
On the basis of the identified  non-colinear (NCL) events,  the pass fastq reads were used to detect trans-splicing events and their supported read counts  using NCLscan-hybird
Genome_build: hg38
Supplementary_files_format_and_content: The result demonstrated the numbers of out-of-circle supported reads containing NCL junction after ts-ARFGEF1 pull-down.

extract_protocol:
To capture the transcript of ts-ARFGEF1, we performed a TERRA-capture RNA experiment as previously described. (PMID: 28692038) 20 g of Trizol-purified total RNA was treated with 4 U of TURBO DNase (Thermo Fisher Scientific, Cat. AM2238) at 37 oC 10 min in 100l with 1 l RNaseOUT (Thermo Fisher Scientific, Cat. 10777019). The RNA was purified by Trizol. 20 g RNA was mixed with 10 pmol of biotin-labeled oligo probes against NCL region of ts-ARFGEF1 (TCCAAGCCAACTGTTCCGTT/3’BioTEG) or scramble negative control probe (GAATTCGTCCTCCGATTCAC/3’BioTEG), denatured at 70 oC in 100 l6×SSC hybridization buffer for 10 min and then lowered the incubation temperature to 44 oC (0.5 oC/s). RNA was then captured by 100 l Dynabeads MyOne Streptavidin C1 (ThermoFisher, Cat. 65001) and washed with 2×SSC/0.1% NP40 at 37 oC 5 min for 4 times, washed twice with 1×SSC/0.1% NP40 at 37 oC, and rinsed once with 1×SSC at room temperature. After serial wash steps, the captured RNA was eluted by 30 l DEPC treated water at 70 oC for 5 min. 3 l elution was used for the analysis of capture efficiency.
After capturing the transcript of ts-ARFGEF1 by biotin-labeled probe against NCL junction, captured RNA was used for generating cDNA for nanopore sequencing according to the ONT cDNA-PCR Sequencing protocol by the manufacturers (Oxford Nanopore Technologies, SQK-PCS109).
Complementary strand synthesis from RNA and strand switching was conducted by using kit-supplied oligonucleotides. Double strand cDNA is then generated by PCR amplification using primers that contain 5’ tags which facilitate the ligase-free attachment of Rapid Sequencing Adapters. Finally, three libraries with ~11 ng PCR products were sequenced by an R9.4 Flow cell with three times priming.

value: RNA products after ts-ARFGEF1 pull-down


title: RNA_human_donor3

city: St. Louis

first: Lite

last: Yang

state: MO

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw fastq files are prepared by demultiplexing Illumina Nextseq runs using v3 indrops python scripts (github/indrops). Barcoded nuclei in a biological sample are divided into 2-3 tubes and their libararies are prepared and sequenced separately, which are then added together for each sample informatically after mapping.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
10X Genomics gene expression assay data were demultiplexed and mapped using cellranger
10X Genomics ATAC assay data were demultiplexed and mapped using cellranger-atac
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts tables from each sample were then combined by their respective experiment into the raw counts files available in GEO

source_name: Trigeminal ganglia

extract_protocol:
For snRNA-seq data, mouse trigeminal ganglia were dissociated into a single nuclei suspension as described in Renthal et al. 2020 and Yang et al. 2021. Briefly, tissue was dissociated by dounce homogenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al. 2020. For snATAC-seq samples, TG were collected using a non-gradient protocol described previously (Slyper et al., 2020), and GFP+ nuclei were sorted and collected using FACS.
inDrops libraries were constructued as described in Zilionis et al., Nat. Protoc. 2017. 10X Genomics gene expression assay and ATAC assay were prepared according to the user manuals.

tag: subject id

value: donor 3

tag: assay

value: 10X Genomics gene expression assay


title: H3.3-rep2-HS3-FLAGChIP

value: heat-shocked and regenerated


title: 32252_cornea  [Sample_40]

value: cornea

value: operated


title: 32251_iris  [Sample_37]


title: 32252_iris  [Sample_39]


title: H3.3-rep1-HS3-FLAGChIP


title: H3.3-rep2-HS-FLAGChIP

value: heat-shocked


title: ATAC_human_donor4

value: donor 4

value: 10X Genomics ATAC assay


title: RNA_human_donor1

value: donor 1


title: H3.3-rep1-HS-FLAGChIP


title: 32250_iris  [Sample_35]

value: unoperated


title: H3.3-rep2-NC-FLAGChIP

value: non-treated


title: ATAC_human_donor2

value: donor 2


title: H3.3-rep1-NC-FLAGChIP


title: ATAC_human_donor1


title: RNA_human_donor2


title: PBMC_CZY-10XBCR

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

data_processing:
Raw sequencing data was processed using the 10x CellRanger pipeline, cellranger count to and cellranger vdj generate a UMI count matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: the UMI count matrixes which were generated by cellranger count and cellranger vdj are provided.

source_name: male trauma patients

extract_protocol:
Ficoll centrifugation to isolate PBMC
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

tag: group

value: polytrauma

tag: Sex

value: male


title: PBMC_SZS-10XTCR

tag: tissue


title: PBMC_CZY-10XTCR


title: PBMC_SZS-10XBCR


title: 32248_cornea  [Sample_32]

value: New Zealand white rabbit

value: 6 months


title: PBMC_CZY-10X5


title: PBMC_SZS-10X5


title: iPSC-derived off-target tissue, biological rep1

city: Kobe

first: Kenji

last: Watari

address: 5th floor, 1-5-2 Minatojima Minamimachi, Chuo-ku

institute: Sumitomo Pharma Co., Ltd.

description: Sample-D

hyb_protocol: Biotinylated cRNA were hybridized for 16 hr at 45°C on U133 Plus2.0 Array in the hybridization oven 640 (Affymetrix 800138). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix 00-0079).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix 00-0074).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software ver1.4 (Affymetrix 690036).

label: biotin

source_name: off-target tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Feeder-free human iPSCs were self-organized into 3D-retinas by previously described methods (Kuwahara et al., Nat Commun, 2015; Kuwahara et al., Sci Rep, 2019) with slight modifications. See a preprint on bioRxiv for more details (doi:10.1101/2022.02.18.480968).

extract_protocol: Tissues were lysed with Buffer RLT (Qiagen) containing 1% 2-mercaptoethanol, and total RNA was extracted and purified using an RNeasy Micro Kit (Qiagen).

value: hiPSC-derived off-target tissue