title: 8808R2_001_IndexUDI0001_CCGCGGTT+AGCGCTAG_L003_001


title: 8808R2_006_IndexUDI0006_GCTTGTCA+GAACATAC_L003_001

status: Public on Dec 31 2022

type: SRA

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

library_source: transcriptomic

data_processing:
Bioinformatics analyses of RNA-seq raw data were performed using the OmicSoft studio software package version 10.1.2.9 (Qiagen)
Mapping of RNA-seq reads (fastq files) to the human genome was done using OmicSoftGenCode V19 as gene model with B.38 as reference genome and OSA4 as aligner
Genes with FPKM <1 were filtered out according to a 50% fraction rule for each sample group to exclude minimally expressed genes. Differentially expressed genes were detected by applying the DESeq2 statistical test and P-values were adjusted by the Benjamini-Hochberg procedure to control FDR
Supplementary files format and content: Tab-delimited text file include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: RA-FLS and T-cells

extract_protocol:
RNA was isolated with the Qiagen RNeasy Micro Kit for cell cultures according to the manufacturer´s instructions.
For RNA-seq library preparation the Ovation RNA-Seq System V2 combined with Illumina Nextera XT Library Preparation Kit was used for cell cultures. RNA libraries were subjected to paired-end sequencing on a Novaseq 6000 system with a reading depth of 80 million raw reads per sample.

treatment_protocol: Firstly, a coculture of fibroblast-like synoviocytes from RA donors with CD4 T cells from healthy donors was stimulated with 1ng/ml recombinant human TNF, 10ng/ml IL-6 with 100ng/ml sIL-6R or a combination of TNF and IL-6/sIL-6R for 24h. Secondly, a coculture of fibroblast-like synoviocytes from RA donors with CD4 T cells from healthy donors was stimulated with IL-17, sIL-6R and anti-CD3 (100ng/ml each) for 24h. Monospecific antibodies against TNF, IL-6 or a combination of them as well as anti-TNF/IL-6 NANOBODY® VHH  and corresponding isotype controls were added to the coculture in 200nM concentration (combination 200nM each; n=9, 3 RA-FLS donors combined with 3 different CD4 donors).

tag: fls donor

tag: blood t-cell donor

tag: cell type

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

tag: treatment

value: anti-IL-6 mAb


title: MA1

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mmul_1 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: mmul_1
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

organism: Macaca mulatta

source_name: monkey blood-derived peripheral blood mononuclear cell

extract_protocol:
Total RNA was extracted using the TRIZOL following the manufacturer's instructions.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina

tag: tissue

value: PBMC

tag: age

value: Aged


title: MA7


title: F2_D2 individual, grown at 16C [T16_P2.F10_F2_D2]

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: genotype


title: TTslamSeq_t2_pulldiwn untreated TTslamSeq_t2_untreated

first: Stefan

middle: Ludwig

last: Ameres

address: Dr.-Bohr-Gasse 3

institute: Institute of Molecular Biotechnology

description:
TTslamSeq_t2_pulldiwn untreated
total RNA

data_processing:
3' end sequencing data were used to creat custom annotations using 3' GAmES
SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome
Additional SNP filtering was performed using samtools pileup
TTSLAMseq data were sequentially mapped to rRNA sequences, mitochondrial sequences and then the genome.
other RNAseq data were mapped to dr11 using STAR and counted using featureCounts
Genome_build: dr11
Supplementary_files_format_and_content: count files of SLAMseq data were created using custom scripts after SNP filtering
Supplementary_files_format_and_content: bedgraph files were genererated using deeptools
Supplementary_files_format_and_content: Count files of TTSLAmseq data were obtained from SLAMdunk

organism: Danio rerio

source_name: Zebrafish embryos

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14 hour light/10 hour dark cycle). TLAB fish were generated by crossing zebrafish AB and the natural variant TL (Tupfel Longfin) stocks, and used for all experiments.

extract_protocol: QuantSeq 3' end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. (NEB). Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and indexed with NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set I) (New England Biolabs).

treatment_protocol: Zebrafish embryos were injected with 4sU or incubated in 4sU

value: Whole embryos

tag: strain

value: TLAB (TL X AB)

tag: chip antibody

value: RNA sequencing

value: Untreated SLAMseq at 2hpf


title: F2_D2 individual, grown at 16C [T16_P2.E9_F2_D2]


title: 26914

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

country: France

institute: APHP Hôpital Robert Debré

data_processing:
We used BS-Seeker2 (55) to map RRBS data to the Human hg38 genome and retrieve the number of methylated and unmethylated cytosines at each covered CpG site. Methylation rates were then integrated across CpG island (CGI)-based and gene-based features. CGI-based features were defined as follows: CpG islands (from UCSC database), shores (2 kb on each side of the island) and shelves (2 kb on each side of the shores). DNA methylation outside CpG islands was analyzed by grouping CpG sites not located in CGI-based features every 100kb window. Gene-based features were defined based on Gencode v26 assembly.
Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 24 -r 150 -g 2 --library-type fr-firststrand). Gene expression was quantified using the full Gencode v26lift37. We used HTSeq (Anders et al., 2015) to obtain the number of reads associated to each gene in the Gencode v26lift37 database (restricted to protein-coding genes, antisense and lincRNAs). Bioconductor DESeq package (Anders and Huber, 2010) was used to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
We used BS-Seeker2 (55) to map RRBS data to the Human hg38 genome and retrieve the number of methylated and unmethylated cytosines at each covered CpG site. Methylation rates were then integrated across CpG island (CGI)-based and gene-based features. CGI-based features were defined as follows: CpG islands (from UCSC database), shores (2 kb on each side of the island) and shelves (2 kb on each side of the shores). DNA methylation outside CpG islands was analyzed by grouping CpG sites not located in CGI-based features every 100kb window. Gene-based features were defined based on Gencode v26 assembly.

source_name: Bone Marrow

extract_protocol:
Genomic DNA was extracted from mononuclear cells using a Qiagen Mini or Midi Kit (Qiagen Gmbh).
Quantitative and qualitative control of DNA was carried out by specific double-stranded fluorescence assay and gel migration. Preparation of RRBS libraries for 'paird-end' sequencing on Illumina® sequencer, with the Premium RRBS kit (Diagenode®), including an MspI enzymatic digestion step (targeting CCGG sites), size selection and bisulfite conversion. Paired-end sequencing of 2x100 bases on NovaSeq™6000 (Illumina®) was performed

treatment_protocol: Mononuclear cells were isolated on a Ficoll gradient (Eurobio)

value: Bone Marrow

value: Mononucleated cells

tag: disease state

value: Healthy postnatal sample

tag: jmml patients unique identifier


title: 28502


title: TTslamSeq_t2_pulldiwn treated TTslamSeq_t2_pulldiwn

description:
TTslamSeq_t2_pulldiwn treated
total RNA

value: Injected with 4sU, SLAMseq at 2hpf


title: 23334

value: JMML_NRAS mutated


title: 21243

source_name: Peripheral blood

value: Peripheral blood

value: JMML_Other mutated


title: Fertilized oocyte replicate 3 Fertilized oocyte_3

description:
Fertilized oocyte replicate 3
Polyadenylated RNA

source_name: Zebrafish oocytes

value: oocyte

value: 3' end sequencing

value: Untreated


title: 8808R2_003_IndexUDI0003_GGACTTGG+CGCAGACG_L003_001

value: Fibroblast-like synoviocytes from rheumatoid arthritis (RA) donors cocultured with CD4 T cells from healthy donors

value: IgG1 isotype control


title: F2_D1 individual, grown at 16C [T16_P2.E7_F2_D1]

value: leaf

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P2.E6_F2_D1]


title: Fertilized oocyte replicate 2 Fertilized oocyte_2

description:
Fertilized oocyte replicate 2
Polyadenylated RNA

value: TLAB (TL X AB)


title: Fertilized oocyte replicate 1 Fertilized oocyte_1

description:
Fertilized oocyte replicate 1
Polyadenylated RNA


title: 19845

value: JMML_PTPN11 mutated


title: F2_D1 individual, grown at 16C [T16_P2.E5_F2_D1]


title: Oblong/Sphere (~4.5hpf) replicate 3 Oblong/Sphere (~4.5hpf)_3_polyAselected

description:
Oblong/Sphere (~4.5hpf) replicate 3
Polyadenylated RNA

value: Whole embryos

value: RNAseq poly(A) selected, wildtype


title: HeLa-S3 cells, MCM Input, Control DNA

first: Chunlong

last: Chen

address: 26 rue d’Ulm

institute: Institut Curie

data_processing:
Trim Galore (adapter trimming)
Bowtie version 1.2.0 (alignment)
Picard version 2.23.4 (Mark duplicate)
bedtools version 2.30.0 (transform to bed)
own R script (IZ calling)
own bash script (early IZ calling, S50 < 0.25)
Assembly: human genome hg19 (GRCh37)
Supplementary files format and content: bigwig file for the normalized read density (RPKM)

source_name: Cervical carcinoma cells

growth_protocol: Human cell line HeLa S3 was cultured in DMEM (gibco, 10569044) containing 10% heat-inactivated FBS (gibco, 10270106) and maintained at 37℃ with 5% CO2.

extract_protocol:
The solubilized chromatin fraction was collected for isolating the input DNA. The protein-DNA samples were then treated with 0.5 mg/ml of proteinase K (Thermo, 25530049) and 0.25 mg/ml of RNase A (Sigma, R5503) at 65℃ for 30 min. Cold isopropanol was added to precipitate DNA overnight at 4℃. Pellet DNA by centrifuge at 21,500 g for 30 min. The pellet was washed twice with 70% ethanol and dissolved in elution buffer (5 mM Tris/HCl, pH 8.5). DNA concentration was measured by Qubit 4 Fluorometer (Invitrogen) with Qubit dsDNA HS Assay Kit (Invitorgen, Q32854) and fragment size was analyzed by Fragment Analyzer System (Agilent).
5 ng DNA was ligated to adapters at a ratio of 1:200 using KAPA HyperPrep Kit (Roche, 07962347001). Sequencing Libraries were generated with KAPA HyperPrep Kit according to the manufacturer’s protocol.
Quantification of adaptor-ligated DNA was performed using quantitative real-time PCR (KAPA Library Quantification Kit) before library amplification to determine the optimal PCR cycle number. The fragment size of amplified libraries was analyzed on a fragment analyzer (Agilent) before library pooling and sequencing. The libraries were sequenced on an Illumina Nextseq 500 system.

treatment_protocol: MCM7-Stag-3×FLAG HeLa S3 cells were first treated with nocodazole (Sigma, M1404) at 50 ng/ml for 16 hours. After being released into fresh medium for 8 hours, cell samples were harvested by centrifuge at 1200 rpm for 2 minutes and lysed by extraction buffer (EBX, 100 mM L-Glutamic acid potassium salt, 50mM HEPES/KOH pH 7.5, 10 mM Magnesium acetate, 1 mM EDTA, 0.5% Triton X-100, 3 mM ATP, 2 mM NaF, 1 mM Na3VO4, 1 mM phenylmethanesulfonylfluoride (PMSF), 1× protease inhibitor cocktail (Roche)) on ice for 30 minutes.

tag: cell line

value: Cervical carcinoma cells

value: untreated


title: F2_D1 individual, grown at 16C [T16_P2.F11_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P2.E4_F2_D2]


title: HeLa-S3 cells, MCM-DH ChIP-seq, Rep2

description: MCM-DH ChIP-seq Rep2


title: 19748

value: Bone Marrow

value: Mononucleated cells


title: Oblong/Sphere (~4.5hpf) relpicate 2 Oblong/Sphere (~4.5hpf)_2_polyAselected

description:
Oblong/Sphere (~4.5hpf) relpicate 2
Polyadenylated RNA


title: F2_D1 individual, grown at 16C [T16_P2.E3_F2_D1]


title: 19408

value: Peripheral blood

value: JMML_KRAS mutated


title: Oblong/Sphere (~4.5hpf) relpicate 1 Oblong/Sphere (~4.5hpf)_1_polyAselected

description:
Oblong/Sphere (~4.5hpf) relpicate 1
Polyadenylated RNA


title: 19644


title: F2_D2 individual, grown at 16C [T16_P2.E2_F2_D2]


title: HeLa-S3 cells, MCM-DH ChIP-seq, Rep1

description: MCM-DH ChIP-seq Rep1


title: HeLa S3

description: HeLa S3 OK-seq

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
BWA 0.6.2-r126 (mapping) then merge the original BAM with re-amplificated BAM together by samtools
OKseqHMM toolkit for replication fork direction (RFD) and initiation zone (IZ) termination zone (TZ) calling
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file for RFD profile and bed file for the initiation and termination zones

growth_protocol: HeLa S3 cells were rountinely cultured with DMEM supplemented with 10% FBS.

extract_protocol:
Okazaki fragments were isolated from gDNA with sucrose gradient centrifuge plus streptavidin capture of EdU-biotinylated DNA.
Okazaki fragments were hydrolyzed to remove 5' RNA, 5' phosphorylated and ligated to adapters on both ends before index amplification.

treatment_protocol: The cells were treated with 20 µM EdU for 2 min when 70-80% confluent.


title: F2_D2 individual, grown at 16C [T16_P2.E8_F2_D2]


title: 23884

value: JMML_NRAS mutated


title: 22265


title: F2_D2 individual, grown at 16C [T16_P2.E1_F2_D2]


title: 256-512 (~3.5hpf) replicate 2 256-512 (~3.5hpf)_2_polyAselected

description:
256-512 (~3.5hpf) replicate 2
Polyadenylated RNA


title: F2_D2 individual, grown at 16C [T16_P2.E12_F2_D2]


title: 20842


title: 23344


title: 256-512 (~3.5hpf) replicate 1 256-512 (~3.5hpf)_1_polyAselected

description:
256-512 (~3.5hpf) replicate 1
Polyadenylated RNA


title: F2_D1 individual, grown at 16C [T16_P2.E10_F2_D1]


title: HLMVEC-O2

city: Seoul

first: Hye-ram

last: Jo

address: Nowon-ro 75, Nowon-gu

country: South Korea

institute: Korea Institute of Radiological & Medical Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: hsa
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Human lung microvascular endothelial cells

growth_protocol: HLMVECs were grown in EGM-2MV medium (Lonza, Basel, Switzerland). Cells were plated in 100-mm culture dish and cultured for 3 days. Two days after seeding, add 5 mL medium and subculture the next day for serial passages.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: To analyze miRNA expression in old endothelial cells, HLMVECs were cultured with serial passages. We harvested total RNA from young ECs (PDL23) and old ECs (PDL49).

value: old

value: lung

value: endothelial cells

tag: pdl


title: HLMVEC-Y2

value: young


title: 64-128 cell (~2.5hpf) replicate 3 64-128 cell (~2.5hpf)_3_polyAselected

description:
64-128 cell (~2.5hpf) replicate 3
Polyadenylated RNA

value: Untreated


title: 64-128 cell (~2.5hpf) replicate 2 64-128 cell (~2.5hpf)_2_polyAselected

description:
64-128 cell (~2.5hpf) replicate 2
Polyadenylated RNA


title: F2_D1 individual, grown at 16C [T16_P2.D9_F2_D1]

value: leaf

value: 7-10 leave rosette


title: 21683

value: JMML_PTPN11 mutated


title: 64-128 cell (~2.5hpf) replicate 1 64-128 cell (~2.5hpf)_1_polyAselected

description:
64-128 cell (~2.5hpf) replicate 1
Polyadenylated RNA

value: Whole embryos

value: TLAB (TL X AB)


title: HLMVEC-Y1


title: 23306


title: 256-512 (~3.5hpf) replicate 3 256-512 (~3.5hpf)_3_polyAselected

description:
256-512 (~3.5hpf) replicate 3
Polyadenylated RNA

value: RNAseq poly(A) selected, wildtype


title: F2_D2 individual, grown at 16C [T16_P2.D8_F2_D2]


title: 17971


title: F2_D1 individual, grown at 16C [T16_P2.D7_F2_D1]


title: 4 cell (1hpf) replicate 3 4 cell (1hpf)_3_polyAselected

description:
4 cell (1hpf) replicate 3
Polyadenylated RNA


title: 19477


title: 1 uM RG7112 treated A549 cells rep 2

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing reads were pseudoaligned to the human reference transcriptome GRCh38.95
Transcript abundance was estimated using kallisto (v0.45.0)
Genome_build: GRCh38.95
Supplementary_files_format_and_content: A549_H1792_counts.txt

source_name: lung adenocaricnoma

growth_protocol: H1792 and A549 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.

treatment_protocol: A549 and H1792 cells were treated with DMSO or 1μM RG7112 for 48hr.

tag: treatment condition


title: 4 cell (1hpf) replicate 2 4 cell (1hpf)_2_polyAselected

description:
4 cell (1hpf) replicate 2
Polyadenylated RNA


title: 16896


title: F2_D2 individual, grown at 16C [T16_P2.D6_F2_D2]


title: 1 uM RG7112 treated A549 cells rep 1


title: HLMVEC-O1


title: 28758

value: Healthy prenatal sample


title: DMSO treated A549 cells rep 3

value: DMSO


title: 21886

value: Bone Marrow

value: Mononucleated cells

value: JMML_Other mutated


title: 28510


title: F2_D1 individual, grown at 16C [T16_P2.D5_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P2.D4_F2_D1]


title: Oblong/Sphere (~4.5hpf) relpicate 2 Oblong/Sphere (~4.5hpf)_2_rRNAdepleted

description:
Oblong/Sphere (~4.5hpf) relpicate 2
rRNA depleted

value: RNAseq rRNA depleted, wildtype


title: F1_D2 individual, grown at 16C [T16_P2.D2_F1_D2]


title: THP-x432-2

city: Atlanta

first: Michael

middle: E.

last: Davis

address: 2015 Uppergate Dr NE

institute: Emory University

description:
Sample 35
THPcounts.csv

data_processing:
Base calling was conducted with RTA v3.4.4 and demultiplexing was performed with bcl2fastq v2.20.0.422
Total RNA was aligned and gene counts were determined with STAR aligner in the Illumina BaseSpace app, RNA-Seq Alignment.
Genome_build: Sample 1-~18 reads aligned with rn5 reference genome; sample 19-36 reads aligned with hg19 reference genome.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: RCFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM-ThermoFisher) supplemented with 10% FBS and 1% penstrep. THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (ThermoFisher) supplemented with 10% FBS, 1% penstrep, and 1% L-glutamine.

extract_protocol:
Total RNA were isolated by using Qiagen RNeasy mini kit following manufacturer's protocol.
1 ng of RNA was used as input for library preparation with the Takaro Bio SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian

treatment_protocol: To stimulate fibroblasts, RCFs were quiesced for 12 h, treated with 20 µg/mL sEVs for 12 h, and then treated with 10 ng/mL transforming growth factor beta (TGF-β; ThermoFisher) for another 12 h. THP-1 cells were then differentiated into macrophages by 24 h incubation with 150 nM phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich) followed by 24 h incubation in RPMI medium. Macrophages were then treated with 20 µg/mL sEVs for 12 h and activated with 20 ng/mL tissue necrosis factor alpha (TNF-⍺; R&D Systems, Minneapolis, MN, USA) for 12 h.

value: Peripheral blood

value: Monocyte

value: Acute monocytic leukemia

value: ATCC, #TIB-202

value: miR-432-5p inhibitor for 24 hours


title: 4 cell (1hpf) replicate 1 4 cell (1hpf)_1_polyAselected

description:
4 cell (1hpf) replicate 1
Polyadenylated RNA

value: Untreated


title: Oblong/Sphere (~4.5hpf) replicate 3 Oblong/Sphere (~4.5hpf)_3_rRNAdepleted

description:
Oblong/Sphere (~4.5hpf) replicate 3
rRNA depleted


title: DMSO treated A549 cells rep 1


title: 1 uM RG7112 treated A549 cells rep 3


title: Oblong/Sphere (~4.5hpf) relpicate 1 Oblong/Sphere (~4.5hpf)_1_rRNAdepleted

description:
Oblong/Sphere (~4.5hpf) relpicate 1
rRNA depleted


title: 256-512 (~3.5hpf) replicate 3 256-512 (~3.5hpf)_3_rRNAdepleted

description:
256-512 (~3.5hpf) replicate 3
rRNA depleted


title: F2_D2 individual, grown at 16C [T16_P2.D1_F2_D2]

value: leaf

value: 7-10 leave rosette


title: THP-x432-3

description:
Sample 36
THPcounts.csv


title: THP-x192-3

description:
Sample 33
THPcounts.csv

value: miR-192-5p inhibitor for 24 hours


title: 256-512 (~3.5hpf) replicate 1 256-512 (~3.5hpf)_1_rRNAdepleted

description:
256-512 (~3.5hpf) replicate 1
rRNA depleted

value: Whole embryos

value: TLAB (TL X AB)


title: THP-x432-1

description:
Sample 34
THPcounts.csv


title: 1 uM RG7112 treated H1792 cells rep 2


title: 256-512 (~3.5hpf) replicate 2 256-512 (~3.5hpf)_2_rRNAdepleted

description:
256-512 (~3.5hpf) replicate 2
rRNA depleted


title: 1 uM RG7112 treated H1792 cells rep 1


title: 1 uM RG7112 treated H1792 cells rep 3


title: F2_D1 individual, grown at 16C [T16_P2.D11_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P2.D12_F2_D1]


title: DMSO treated A549 cells rep 2


title: THP-x192-2

description:
Sample 32
THPcounts.csv


title: THP-x192-1

description:
Sample 31
THPcounts.csv


title: 64-128 cell (~2.5hpf) replicate 3 64-128 cell (~2.5hpf)_3_rRNAdepleted

description:
64-128 cell (~2.5hpf) replicate 3
rRNA depleted


title: P_6191 individual, grown at 16C [T16_P2.D10_P_6191]


title: DMSO treated H1792 cells rep 2


title: F2_D2 individual, grown at 16C [T16_P2.D3_F2_D2]


title: 64-128 cell (~2.5hpf) replicate 2 64-128 cell (~2.5hpf)_2_rRNAdepleted

description:
64-128 cell (~2.5hpf) replicate 2
rRNA depleted


title: THP-x432exo-3

description:
Sample 30
THPcounts.csv

value: miR-432-5p depleted CPC sEVs for 24 hours


title: DMSO treated H1792 cells rep 1

value: DMSO


title: F2_D2 individual, grown at 16C [T16_P2.C9_F2_D2]


title: 64-128 cell (~2.5hpf) replicate 1 64-128 cell (~2.5hpf)_1_rRNAdepleted

description:
64-128 cell (~2.5hpf) replicate 1
rRNA depleted


title: NBC RNA-seq, replicate 3

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

institute: INSERM

data_processing:
Quality of sequencing data was monitored by FastQC. If needed, residual adapters from sequencing were trimmed using cutadapt
Reads were then aligned on the hg19 human genome using tophat2, accepting only reads with a single alignment. Reads with MAPQ < 20 were removed by SAMtools.
Raw counts by samples were obtained with HTSeq-counts. Differential expression on filtered genes (HTSfilter 1.7.1), were performed using DESeq2 in R v.3.3.1. Genes were declared differentially expressed with a false discovery rate < 5%.
Genome_build: hg19
Supplementary_files_format_and_content: Raw and normalized counts matrices after DESeq2 analysis, in txt.

molecule: polyA RNA

source_name: FACS sorted human peripheral blood B cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) from healthy volunteers were obtained from the Etablissement Français du Sang (Rennes, France) after Ficoll density centrifugation (Sigma-Aldrich, St Louis, MO). Subjects were recruited under institutional review board approval and informed consent according to the Declaration of Helsinki. Cells were stained with surface markers and sorted as MBC IgG+ (CD27+/IgG+/IgM-), MBC IgG+ (CD27+/IgG-/IgM+), NBC (CD27--/IgG+/Ig+-) using a FACsARIA cell sorter (BD Biosciences).  PB data were extracted from our previous GEO dataset GSE136988 as raw counts and used together with the present data for the DESeq2 differential expression analysis (see below).
QC, library preparation and sequencing were performed by Helixio Company (Clermont-Ferrand, France). After QC by BioAnalyzer, Nanodrop and Qubit, libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina).  Librairies were sequenced on an Illumina NextSeq 500 using 75-bp single-end reads (NextSeq 500 High Output v2, Illumina).

tag: days in culture

value: Day 0

tag: cell population

value: Naive B cells


title: THP-x432exo-2

description:
Sample 29
THPcounts.csv


title: F2_D2 individual, grown at 16C [T16_P2.C8_F2_D2]


title: 4 cell (1hpf) replicate 3 4 cell (1hpf)_3_rRNAdepleted

description:
4 cell (1hpf) replicate 3
rRNA depleted


title: F2_D2 individual, grown at 16C [T16_P2.C7_F2_D2]


title: THP-x192exo-3

description:
Sample 27
THPcounts.csv

value: miR-192-5p depleted CPC sEVs for 24 hours


title: F2_D1 individual, grown at 16C [T16_P2.C6_F2_D1]


title: DMSO treated H1792 cells rep 3


title: 4 cell (1hpf) replicate 2 4 cell (1hpf)_2_rRNAdepleted

description:
4 cell (1hpf) replicate 2
rRNA depleted

value: RNAseq rRNA depleted, wildtype


title: 4 cell (1hpf) replicate 1 4 cell (1hpf)_1_rRNAdepleted

description:
4 cell (1hpf) replicate 1
rRNA depleted


title: F2_D1 individual, grown at 16C [T16_P2.C5_F2_D1]


title: NBC RNA-seq, replicate 1


title: THP-x192exo-2

description:
Sample 26
THPcounts.csv

value: Peripheral blood


title: THP-x192exo-1

description:
Sample 25
THPcounts.csv

value: Monocyte


title: F2_D2 individual, grown at 16C [T16_P2.C4_F2_D2]


title: THP-CTRexo-3

description:
Sample 24
THPcounts.csv

value: Acute monocytic leukemia

value: CPC sEVs for 24 hours


title: MBC IgM+ RNA-seq, replicate 3

value: IgM+ memory B cells


title: 5.5hpf (-4sU) Untreated_TP9

description:
5.5hpf (-4sU)
Polyadenylated RNA

value: SLAMseq combined with 3' end RNAseq

value: Untreated sample, SLAMseq at 5.5hpf


title: 4.0hpf (-4sU) Untreated_TP6

description:
4.0hpf (-4sU)
Polyadenylated RNA

value: Untreated sample, SLAMseq at 4hpf


title: MBC IgM+ RNA-seq, replicate 2


title: MBC IgM+ RNA-seq, replicate 1


title: MBC IgG+ RNA-seq, replicate 3

value: IgG+ memory B cells


title: F2_D1 individual, grown at 16C [T16_P2.C2_F2_D1]

value: leaf

value: 7-10 leave rosette


title: 0.75hpf (-4sU) Untreated_TP1

description:
0.75hpf (-4sU)
Polyadenylated RNA

value: Whole embryos

value: TLAB (TL X AB)

value: Untreated sample, SLAMseq at 0.75hpf


title: THP-x432exo-1

description:
Sample 28
THPcounts.csv

value: ATCC, #TIB-202

value: miR-432-5p depleted CPC sEVs for 24 hours


title: THP-CTRexo-1

description:
Sample 22
THPcounts.csv


title: MBC IgG+ RNA-seq, replicate 2

value: Day 0


title: NBC RNA-seq, replicate 2

value: Naive B cells


title: F2_D1 individual, grown at 16C [T16_P2.C1_F2_D1]


title: 5.5hpf (+4sU) incubation replicate 2 Inc_R2_TP9

description:
5.5hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 5.5hpf


title: 5.5hpf (+4sU) incubation replicate 1 Inc_R1_TP9

description:
5.5hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: P_6191 individual, grown at 16C [T16_P2.C12_P_6191]


title: THP-NT-3

description:
Sample 21
THPcounts.csv

value: Peripheral blood

value: Monocyte

value: Acute monocytic leukemia

value: untreated


title: MBC IgG+ RNA-seq, replicate 1


title: THP-NT-2

description:
Sample 20
THPcounts.csv


title: F2_D2 individual, grown at 16C [T16_P2.C3_F2_D2]


title: HU+ATRi S6/G2/M

description: Enrichment of BrdU labelled DNA

data_processing:
Library strategy: Repli-seq
Demultiplexing: bcl2fastq2
Adapter trimming: Cutadapt
Mapping: bwa
PCR duplicates were removed by Picard tools (http://broadinstitute.github.io/picard)
The sequence reads located within the regions likely resulted from the sequencing hotspots (defined as the 0,5% windows with the highest amount of reads within 200bp windows) were also removed.
The read density was them computed for each 50 kb nonoverlapping windows (w) for each sample Si corresponding to different S phase fractions (i = 1–6).
The background levels were them estimated and the density profiles were normalized as described in previous studies (Chen Genome Res 2010, Brison Nat Commun 2019).
The six S-Phase fractions were resized based on a symulation of the number of active forks in each fraction.
A Under-Replication Index (URI) for the average profile of each treated sample was calculated as in Brison Nat Commun 2019
Genome_build: hg19
Supplementary_files_format_and_content: All processed provided data are bigwig: files marked with the prefix URI_ contain the average URI for each condition; files marked as S50_ contain the average replication timing for each condition; files marked as Average_profile_ are the average profiles for each S-phase fraction in each condition.

source_name: human lymphoblastoid cells

growth_protocol: Epstein–Barr-virus-immortalized human B lymphocytes (JEFF cells) were grown in RPMI-1640 plus GlutaMAX-I medium (GIBCO) with 10% fetal calf serum (PAN-Biotech GmbH), 100 µg/ml of penicillin and streptomycin (GIBCO).

extract_protocol:
Cells were incubated overnight in lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, 0.1% SDS, 50 ug/mL RNAse A, 100 ug/mL Proteinase K). DNA was purified from the lysates by phenol extraction.
Four µg of genomic DNA was fragmented to a mean size of 500 bp on a Covaris S220 intrument (peak power: 140, duty factor: 10%, cycle/burst: 200, time: 80 seconds). Fragmented DNA was treated with the End-Repair module (New England BioLabs, E6050) and the A-Tailing module (New England BioLabs, E6053), according to the manufacturer recommendations. Illumina Truseq indexed adapters were ligated on the resulting fragments, using the Quick Ligation module (New England BioLabs, E6056), according to the manufacturer recommendations. Following heat denaturation, BrdU-DNA was isolated by immunoprecipitation using an anti-BrdU monoclonal antibody (BD Biosciences, 347580). Immunoprecipitated fragments were amplified for 10 cycles using the KAPA Hifi DNA polymerase (KAPABiosystems, KK2502) and the resulting libraries were purified with AMPure XP beads (Beckman Coulter, A63881). Illumina libraries were pooled and sequenced on a NextSeq500 instrument on Paired-end 2x43 bp runs, using a NextSeq 500/550 High Output Kit v2 (75 cycles) kit.

treatment_protocol: Exponentially growing lymphoblastoid cells (~200x106), were pulse-labelled with 50 µM BrdU (Merck, B-5002) prior to recovery. Untreated cells were pulse labeled for 1 h, while all the other conditions were labeled for the last 3 h. Cells were then fixed in 70% ethanol and incubated overnight at 4°C in the presence of 15 µg/ml Hoescht 33342 (ThermoFisher Scientific, H3570). Cells were re-suspended in 1X PBS and sorted in six fractions at a time by flow cytometry based on their DNA content using a BD Biosciences INFLUX cell sorter. The first fraction contains cells in the second half of the G1 phase plus very early S (called G1/S1); the rest of the S phase was divided into four fractions (S2 to S5); and the last fraction contains cells in very late S, G2 and M phases (S6/G2/M).Aphidicolin (A0781), RO (CDK1 Inhibitor IV - Calbiochem; 217699), VE-821 (Sigma-Aldrich SML1415) and hydroxyurea (Sigma-Aldrich H8627) were obtained from Merck.

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes

tag: s phase


title: F2_D1 individual, grown at 16C [T16_P2.C11_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P2.C10_F2_D1]


title: THP-NT-1

description:
Sample 19
THPcounts.csv

value: THP-1 (ATCC, #TIB-202)


title: F2_D2 individual, grown at 16C [T16_P2.B9_F2_D2]

value: leaf


title: THP-CTRexo-2

description:
Sample 23
THPcounts.csv

value: CPC sEVs for 24 hours


title: HU+ATRi S5

description: Enrichment of BrdU labelled DNA


title: HU+ATRi S4

description: Enrichment of BrdU labelled DNA


title: siTET2+EndMT3.WGBS

first: Kou

last: wenxin

address: 301 middle yanchang road

institute: tongji university

data_processing:
NOT PROVIDED
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: NOT PROVIDED

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol:
RNA-seq: HUVECs were cultured in ECM (Cat# 1001, Sciencell) with 5% FBS, 1% ECGS, 1% P/S
WGBS: HUVECs were cultured in ECM (Cat# 1001, Sciencell) with 5% FBS, 1% ECGS, 1% P/S

extract_protocol:
RNA-seq: Total RNA was isolated using Trizol reagent
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
WGBS: Genomic DNA was isolated by Shanghai OE Biotech Co., Ltd
WGBS: DNA libraries were prepared for sequencing by Shanghai OE Biotech Co., Ltd

treatment_protocol:
RNA-seq: HUVECs were transfected with siNC or siTET2 for 48 h and then treated with TGF-β (10 ng/ml) and IL-1β (1 ng/ml) for 5 days.
WGBS: HUVECs were transfected with siNC or siTET2 for 48 h and then treated with TGF-β (10 ng/ml) and IL-1β (1 ng/ml) for 5 days.

value: Human Umbilical Vein Endothelial Cells

tag: genotype/treatment


title: F2_D2 individual, grown at 16C [T16_P2.B8_F2_D2]

value: 7-10 leave rosette

tag: cell type


title: siTET2+EndMT2.WGBS


title: HU+ATRi S3

description: Enrichment of BrdU labelled DNA

tag: treatment


title: F2_D2 individual, grown at 16C [T16_P2.B7_F2_D2]

tag: tissue


title: HLMVEC-O3

value: old

value: lung

value: endothelial cells


title: siTET2+EndMT1.WGBS


title: 4.5hpf (+4sU) incubation replicate 2 Inc_R2_TP7

description:
4.5hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Whole embryos

value: TLAB (TL X AB)

value: SLAMseq combined with 3' end RNAseq

value: Incubated in 4sU, SLAMseq at 4.5hpf


title: 4.0hpf (+4sU) incubation replicate 2 Inc_R2_TP6

description:
4.0hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 4hpf


title: 4.5hpf (+4sU) incubation replicate 1 Inc_R1_TP7

description:
4.5hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: 5.0hpf (+4sU) incubation replicate 1 Inc_R1_TP8

description:
5.0hpf (+4sU) incubation replicate 1
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 5hpf


title: HU+ATRi S2

description: Enrichment of BrdU labelled DNA


title: 4.0hpf (+4sU) incubation replicate 1 Inc_R1_TP6

description:
4.0hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: siNC+EndMT3.WGBS


title: HU+ATRi G1/S1

description: Enrichment of BrdU labelled DNA


title: F2_D1 individual, grown at 16C [T16_P2.B6_F2_D1]


title: 5.0hpf (+4sU) incubation replicate 2 Inc_R2_TP8

description:
5.0hpf (+4sU) incubation replicate 2
Polyadenylated RNA


title: F2_D1 individual, grown at 16C [T16_P2.B5_F2_D1]


title: siNC+EndMT2.WGBS


title: F2_D2 individual, grown at 16C [T16_P2.B4_F2_D2]


title: siNC+EndMT1.WGBS


title: 3.5hpf (+4sU) incubation replicate 2 Inc_R2_TP5

description:
3.5hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 3.5hpf


title: 3.5hpf (+4sU) incubation replicate 1 Inc_R1_TP5

description:
3.5hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: HU S5

description: Enrichment of BrdU labelled DNA

value: JEFF cells


title: HU S6/G2/M

description: Enrichment of BrdU labelled DNA

value: Epstein-Barr-virus-immortalized human B lymphocytes


title: siTET2+EndMT3.RNA-seq


title: HU S4

description: Enrichment of BrdU labelled DNA


title: F2_D1 individual, grown at 16C [T16_P2.B3_F2_D1]


title: 3.0hpf (+4sU) incubation replicate 2 Inc_R2_TP4

description:
3.0hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 3hpf


title: 3.0hpf (+4sU) incubation replicate 1 Inc_R1_TP4

description:
3.0hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: P_6046 individual, grown at 16C [T16_P2.B2_P_6046]

value: leaf


title: 2.5hpf (+4sU) incubation replicate 2 Inc_R2_TP3

description:
2.5hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 2.5hpf


title: HU S2

description: Enrichment of BrdU labelled DNA


title: F2_D1 individual, grown at 16C [T16_P2.B1_F2_D1]


title: siTET2+EndMT1.RNA-seq

value: Human Umbilical Vein Endothelial Cells


title: HU S3

description: Enrichment of BrdU labelled DNA


title: siNC+EndMT2.RNA-seq


title: F1_D2 individual, grown at 16C [T16_P2.B11_F1_D2]

value: 7-10 leave rosette


title: siNC+EndMT3.RNA-seq


title: HU G1/S1

description: Enrichment of BrdU labelled DNA


title: ARO-2 S6/G2/M

description: Enrichment of BrdU labelled DNA (Replicate 2)


title: 2hpf (+4sU) incubation replicate 2 Inc_R2_TP2

description:
2hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Incubated in 4sU, SLAMseq at 2hpf


title: F2_D1 individual, grown at 16C [T16_P2.B10_F2_D1]


title: 2.5hpf (+4sU) incubation replicate 1 Inc_R1_TP3

description:
2.5hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: 2hpf (+4sU) incubation replicate 1 Inc_R1_TP2

description:
2hpf (+4sU) incubation replicate 1
Polyadenylated RNA


title: siNC+EndMT1.RNA-seq


title: ARO-2 S4


title: ARO-2 S5


title: Kasumi-1 treated with I1_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM value

source_name: Kasumi-1 cell line treated with I1 3

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: protocol

value: incubating with I1 for 48 h

tag: agent


title: F2_D1 individual, grown at 16C [T16_P2.A8_F2_D1]

tag: developmental stage

tag: genotype


title: siTET2+EndMT2.RNA-seq


title: ARO-2 S3


title: Kasumi-1 treated with I1_2

source_name: Kasumi-1 cell line treated with I1 2


title: 5.5hpf (+4sU) injection replicate 2 Inj_R2_TP9

description:
5.5hpf (+4sU) injection replicate 2
Polyadenylated RNA

tag: strain

tag: chip antibody

value: Injected with 4sU, SLAMseq at 5.5hpf


title: 0.75hpf (+4sU) incubation replicate 2 Inc_R2_TP1

description:
0.75hpf (+4sU) incubation replicate 2
Polyadenylated RNA

value: Whole embryos

value: Incubated in 4sU, SLAMseq at 0.75hpf


title: 0.75hpf (+4sU) incubation replicate 1 Inc_R1_TP1

description:
0.75hpf (+4sU) incubation replicate 1
Polyadenylated RNA

value: TLAB (TL X AB)

value: SLAMseq combined with 3' end RNAseq


title: Kasumi-1 treated with I1_1

source_name: Kasumi-1 cell line treated with I1 1


title: F2_D2 individual, grown at 16C [T16_P2.A7_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P2.B12_F2_D2]


title: 5.5hpf (+4sU) injection replicate 1 Inj_R1_TP9

description:
5.5hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: Kasumi-1 treated with control_#3

source_name: Kasumi-1 cell line treated with control 3

value: incubating with control for 48 h

value: Control


title: 5.0hpf (+4sU) injection replicate 2 Inj_R2_TP8

description:
5.0hpf (+4sU) injection replicate 2
Polyadenylated RNA

value: Injected with 4sU, SLAMseq at 5hpf


title: Kasumi-1 treated with control_#2

source_name: Kasumi-1 cell line treated with control 2


title: ARO-1 S6/G2/M

description: Enrichment of BrdU labelled DNA (Replicate 1)

value: JEFF cells


title: 5.0hpf (+4sU) injection replicate 1 Inj_R1_TP8

description:
5.0hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: Kasumi-1 treated with control_#1

source_name: Kasumi-1 cell line treated with control 1


title: F2_D2 individual, grown at 16C [T16_P2.A4_F2_D2]

source_name: leaf


title: F2_D1 individual, grown at 16C [T16_P2.E11_F2_D1]


title: ARO-1 S5

value: Epstein-Barr-virus-immortalized human B lymphocytes


title: F2_D2 individual, grown at 16C [T16_P2.A9_F2_D2]


title: 4.5hpf (+4sU) injection replicate 2 Inj_R2_TP7

description:
4.5hpf (+4sU) injection replicate 2
Polyadenylated RNA

source_name: Zebrafish embryos

value: Injected with 4sU, SLAMseq at 4.5hpf


title: P_6191 individual, grown at 16C [T16_P2.A3_P_6191]

value: leaf


title: ARO-1 S4


title: ARO-1 S3


title: F2_D2 individual, grown at 16C [T16_P2.A2_F2_D2]


title: 4.5hpf (+4sU) injection replicate 1 Inj_R1_TP7

description:
4.5hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: F2_D2 individual, grown at 16C [T16_P2.A1_F2_D2]


title: ARO-2 S2


title: F2_D1 individual, grown at 16C [T16_P2.A6_F2_D1]


title: 4.0hpf (+4sU) injection replicate 2 Inj_R2_TP6

description:
4.0hpf (+4sU) injection replicate 2
Polyadenylated RNA

value: Injected with 4sU, SLAMseq at 4hpf


title: ARO-2 G1/S1


title: ARO-1 S2


title: 4.0hpf (+4sU) injection replicate 1 Inj_R1_TP6

description:
4.0hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: F2_D1 individual, grown at 16C [T16_P2.A5_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P2.A12_F2_D2]


title: Hs578T CTRL sh-1

first: Incheol

last: Shin

address: Wangsimni-ro 222

department: Life science

institute: Hanyang university

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36)
To estimate expression levels, the RNA-Seq reads were mapped to Homo sapiens genome (GRCh38) using HISAT2 version 2.1.0, , which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 2.1.3d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure.  DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hs578T CTRL sh

growth_protocol: Cells were maintained in DMEM containing 10% fetal bovine serum (FBS) and 1% antibiotics.

extract_protocol:
Total RNA of each cell line was extracted by Tri-RNA Reagent (Favorgen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s instructions.

value: Breast; Mammary gland

value: breast cancer cell

tag: disease state

value: Carcinoma


title: Hs578T CTRL sh-2

tag: cell line


title: Hs578T CCN3 sh-3

source_name: Hs578T CCN3 sh

value: CCN3 KD


title: ARO-1 G1/S1


title: F2_D2 individual, grown at 16C [T16_P2.A11_F2_D2]

value: 7-10 leave rosette


title: Hs578T CCN3 sh-2


title: NT S6/G2/M

description: Enrichment of BrdU labelled DNA

value: Untreated


title: F2_D1 individual, grown at 16C [T16_P2.A10_F2_D1]


title: NT S5

description: Enrichment of BrdU labelled DNA


title: 3.0hpf (+4sU) injection replicate 2 Inj_R2_TP4

description:
3.0hpf (+4sU) injection replicate 2
Polyadenylated RNA

value: Whole embryos

value: Injected with 4sU, SLAMseq at 3hpf


title: Hs578T CTRL sh-3


title: F2_D1 individual, grown at 16C [T16_P1.H9_F2_D1]


title: NT S4

description: Enrichment of BrdU labelled DNA


title: 3.5hpf (+4sU) injection replicate 1 Inj_R1_TP5

description:
3.5hpf (+4sU) injection replicate 1
Polyadenylated RNA

value: TLAB (TL X AB)

value: SLAMseq combined with 3' end RNAseq

value: Injected with 4sU, SLAMseq at 3.5hpf


title: Hs578T CCN3 sh-1


title: 3.0hpf (+4sU) injection replicate 1 Inj_R1_TP4

description:
3.0hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: NSC2

city: Hefei

first: Chao

state: Anhui

address: 81 Meishan Road

department: Histology and Embryology

institute: Anhui Medical University

data_processing:
Library strategy: CUT&Tag
Clustering of index-coded samples was performed on the cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer's instructions. Library preparation was performed on the Illumina NovaSeq platform for sequencing. NovaSeq Technology (Beijing, China) sequenced the libraries and generated 150 bp paired-end reads. We used FastQC to perform basic statistics on the quality of the raw reads. Then, the read sequences produced by the Illumina pipeline in FASTQ format were preprocessed using Trimmomatic software. The remaining reads that passed all the filtering steps were counted as clean reads, and all subsequent analyses were based on this. Finally, we used FastQC to perform basic statistics on the quality of the clean reads.
Reference genome and gene model annotation files were downloaded from the genome website directly. The index of the reference genome was built using BWA v0.7.12 (Burrows Wheeler Aligner), and clean reads were aligned to the reference genome using BWA mem v0.7.12. All peak calling was performed with MACS2. For simulations of peaks called per input read, aligned and deduplicated BAM files were used without any additional filtering. A peak annotator was used to identify the nearest TSS of every peak, and the distance distribution between peaks and TSS is shown. In addition, the distribution of peak summits on different functional regions, such as the 5’ UTR, CDS, and 3’UTR, was determined.
Peak-related genes were confirmed by PeakAnnotator, and then Gene Ontology (GO) enrichment analysis was performed to identify the functional enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P values less than 0.05 were considered significantly enriched by peak-related genes. We used KOBAS software to test the statistical enrichment of peak-related genes in KEGG pathways.
Different peak analyses were based on the fold enrichment of peaks of different experiments. A peak was determined as a different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified, and GO and KEGG enrichment analyses were performed.
Genome_build: hg38
Supplementary_files_format_and_content: peak, bigWig files

source_name: Spinal cord neural stem cells

growth_protocol: A human ESC line, H9 cells, were maintained on Matrigel (Corning, REF356234) in mTeSRTM1 medium (Stem Cell Technologies, #85850). Human ESCs were passaged using Dispase (Stem Cell Technologies) and replated in mTeSRTM1 medium at a dilution of 1:4.

extract_protocol:
Cells (1x10^5) were counted and centrifuged at 500 x g for 5 min at room temperature. The CUT&Tag assay was performed as described previously (Kaya-Okur, Wu et al., 2019). Briefly, cells were bound to concanavalin A-coated magnetic beads and permeabilized through the cell membrane by digitonin. The enzyme pA-Tn5 transductase binds precisely to DNA sequences near the target protein under the guidance of antibodies. The enzyme pA-Tn5 transglutaminase binds precisely to DNA sequences near the target protein under the guidance of BAF45D antibodies, thus enabling the targeted labeling of factors.
DNA sequences are labeled, and connectors are added simultaneously at both ends, which can be enriched by PCR to form a sequencing-ready library. The library was enriched by PCR to form a sequencable library. After PCR, the library was purified with AMPure beads, and the library quality was assessed on an Agilent Bioanalyzer 2100 system.

treatment_protocol: H9 cells were cultured in mTeSRTM 1 supplemented with 10 mM Y-27632 (ROCK inhibitor, Stemgent) at 37 °C for 1 h. Then, the cells were passaged 1:3 using Accutase enzymatic digestion to single cells and replated on Matrigel-coated 6-well plates in mTeSRTM 1 supplemented with 10 mM Y-27632. When cells were at approximately 70% confluence, mTeSRTM1 medium was replaced with neural induction media (N2B27 medium supplemented with 100 nM LDN-193189, 10 μM SB431542, 4 μM CHIR-99021, 100 ng/ml FGF2, 100 ng/ml FGF8, and 10 μM DAPT). The medium was replaced with fresh neural induction media every day, and the cells were split 1:3 with Accutase (Innovative Cell Technologies Inc.). Y-27632 (10 μM, ROCK inhibitor, Stemgent) was used to enhance cell survival at each passage. Ten days after neural induction, neural induction media was replaced with neural maintenance media (N2B27 medium supplemented with 2 μM SB-431542, 3 μM CHIR-99021, and 200 nM Hh-Ag 1.5). Neural induction medium was used to culture the cells for five subpassages, and then the medium was replaced with neural stem cell medium N2B27 supplemented with 20 ng/ml FGF2 and 20 ng/ml epidermal growth factor (EGF).

value: Neural stem cells

tag: cut&tag antibody

value: CUT&Tag (rabbit anti-BAF45D antibodies, Catalog number:12111-1-AP, Proteintech )


title: F2_D2 individual, grown at 16C [T16_P1.H8_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P1.H5_F2_D2]


title: NT S3

description: Enrichment of BrdU labelled DNA

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes


title: 2.5hpf (+4sU) injection replicate 2 Inj_R2_TP3

description:
2.5hpf (+4sU) injection replicate 2
Polyadenylated RNA

value: Injected with 4sU, SLAMseq at 2.5hpf


title: NSC1


title: ESC2

source_name: Embryonic stem cells

value: Embryonic stem cells


title: 3.5hpf (+4sU) injection replicate 2 Inj_R2_TP5

description:
3.5hpf (+4sU) injection replicate 2
Polyadenylated RNA


title: 2.5hpf (+4sU) injection replicate 1 Inj_R1_TP3

description:
2.5hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: 2hpf (+4sU) injection replicate 2 Inj_R2_TP2

description:
2hpf (+4sU) injection replicate 2
Polyadenylated RNA

value: Injected with 4sU, SLAMseq at 2hpf


title: F2_D2 individual, grown at 16C [T16_P1.H3_F2_D2]

value: leaf


title: NT S2

description: Enrichment of BrdU labelled DNA


title: 2hpf (+4sU) injection replicate 1 Inj_R1_TP2

description:
2hpf (+4sU) injection replicate 1
Polyadenylated RNA


title: ESC1


title: Participant10_4

city: Tianjin

first: Huiyuan

last: Li

address: 288 Nanjing Road

institute: Institute of Hematology & Blood Diseases Hospital

data_processing:
Processed paired-end reads obtained from RNA-seq were aligned to the human genome GRCh38 reference by using cellranger (v3.1.0; 10× Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

source_name: peripheral blood mononuclear cell

growth_protocol: Peripheral blood was collected into vaccutainer tubes containing  EDTA-anticoagulant. Then peripheral blood mononuclear cells were isolated  from blood samples using Ficoll–Hypaque (1.077 g/mL) density  gradient centrifugation.

extract_protocol:
(1)The single cell suspension was washed twice with 1x PBS + 0.04% BSA; (2)The cell number and concentration was confirmed with TC20™ Automated Cell Counter; (3)Approximately Number (5000, etc.) cells were subjected immediately onto the 10XGenomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation.
RNA libraries were prepared with Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 according to the manufacturer's protocol.

tag: response

tag: time point

value: stop GCs


title: F2_D1 individual, grown at 16C [T16_P1.H4_F2_D1]


title: 0.75hpf (+4sU) injection replicate 2 Inj_R2_TP1

description:
0.75hpf (+4sU) injection replicate 2
Polyadenylated RNA

value: Injected with 4sU, SLAMseq at 0.75hpf


title: F2_D1 individual, grown at 16C [T16_P1.H1_F2_D1]

value: 7-10 leave rosette


title: Participant10_3

value: Day 7


title: F2_D2 individual, grown at 16C [T16_P1.H2_F2_D2]


title: 0.75hpf (+4sU) injection replicate 1 Inj_R1_TP1

description:
0.75hpf (+4sU) injection replicate 1
Polyadenylated RNA

value: Whole embryos


title: F2_D2 individual, grown at 16C [T16_P1.H12_F2_D2]


title: Participant10_2

value: Day 0


title: Participant10_1

value: Day -7


title: NPC43 scONEseq 167

city: Hong Kong

first: Angela

middle: Ruohao

last: WU

address: Clear water bay street

department: LIFS

institute: HKUST

description:
RNA+DNA
NPC single cell 167

data_processing:
Library strategy: scONE-Seq
fastq files were filtered with fastp.
For scONE-seq dataset, RNA and DNA from the same singel cell / nucleus can be separated with DNA barcode "TCATG" and RNA barcode "ATCGT" by using seqkit and bbduk.
RNA data were quantified with Kallisto.
RNA data from nuclei were quantified with Salmon to consider the pre-mature RNA.
RNA data from 10x were quantified with kb-python to consider the pre-mature RNA.
DNA data were mapped with BWA mem; filter reads with MAPQ higher than 59; transfered to bed files with bedtools; then used Ginkgo to get the normalized counts in 500kb genome bin size.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each genome bins (500kb) for each sample or cell.
Supplementary_files_format_and_content: coma-delimited text files include gene expression raw counts for each cell.

source_name: NPC43 cell line

growth_protocol: HCT116 cells are cultured in DMEM; NPC43 cells are cultured in RPMI1640 with additional Rho-associated coiled-coil containing kinases inhibitor (Y-27632) at 4 μM; HUVEC are cultured in EGM BulletKit Medium (CC-3124) plus CC-4133 SingleQuots Kit (CC-4133);H9 cell line is purchased from WiCell. Cells are cultured in mTeSR™ Plus medium (Catalog #05825). Matrigel (Catalog #354230) coated 6-well plate (Catalog #140675) was used to culture stem cells.

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics

value: nasopharyngeal carcinoma

tag: method

value: scONE-seq


title: F2_D2 individual, grown at 16C [T16_P1.H11_F2_D2]


title: NPC43 scONEseq 170

description:
RNA+DNA
NPC single cell 170


title: NPC43 scONEseq 169

description:
RNA+DNA
NPC single cell 169


title: NPC43 scONEseq 168

description:
RNA+DNA
NPC single cell 168


title: CD_HL_POS

first: Tiffany

last: Au

address: Sassoon Road 21, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: Unitversity of Hong Kong

data_processing:
Reads was preprocessed and aligned to the mouse GRCm38 (mm10) reference  genome and expression levels were quantified using the nfcore/rnaseq workflow. The  count matrix from featureCounts was used in the downstream analyses. The Nextflow pipeline for downstream analysis is available at  https://github.com/fuxialexander/sox9.
With R (4) library edgeR 3.36.0 (13, 14), read counts were normalized using the  ‘TMM’ method. We identified differentially expressed genes between the WT and CD  groups in GFP+ or GFP- samples with the ‘glmQLFTest’ function and a Benjamini &  Hochberg(15) adjusted P-value cutoff of 0.05.
Assembly: mm10 (GRCm38)
Supplementary files format and content: the EdgeR DEG table with RPKM value

organism: Mus musculus

source_name: Hindlimb

extract_protocol:
Limb buds were removed from E13.5 mouse fetuses and then kept on ice. Limb tissues were dissociated with  and RNA was harvested using Collagenase Type II (Worthington Biochemical, Cat. CLS-2) and Neutral protease (Worthington Biochemical, Cat. LSO2100) in DMEM for <1 h at 37oC.  Single cell suspension was subjected for FACS (BD FACSAriaTM SORP Cell Sorter) to separate GFP+ and GFP- cells. Total RNA for each sample was extracted using Ambion RNA isolation kit (Cat. AM1560).
100 ng of total RNA was usd for cDNA library construction using TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to manufacturer instructions.

value: Hindlimb

tag: age

tag: egfp status

value: positive


title: NPC43 scONEseq 166

description:
RNA+DNA
NPC single cell 166


title: CD_HL_NEG

value: negative


title: F2_D1 individual, grown at 16C [T16_P1.H10_F2_D1]

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

tag: cell type


title: Participant9_4


title: Participant9_3


title: CD_FL_POS

source_name: Forelimb

value: Forelimb


title: F2_D2 individual, grown at 16C [T16_P1.G9_F2_D2]

tag: treatment


title: CD_FL_NEG

tag: tissue


title: NPC43 scONEseq 164

description:
RNA+DNA
NPC single cell 164


title: NPC43 scONEseq 165

description:
RNA+DNA
NPC single cell 165


title: F1_D2 individual, grown at 16C [T16_P1.G7_F1_D2]


title: Participant9_1


title: F2_D2 individual, grown at 16C [T16_P1.G6_F2_D2]


title: Participant9_2


title: 135_HL_POS

value: wild type


title: F2_D2 individual, grown at 16C [T16_P1.G5_F2_D2]


title: Participant8_3


title: NPC43 scONEseq 161

description:
RNA+DNA
NPC single cell 161


title: Participant8_4


title: 135_FL_POS


title: NPC43 scONEseq 162

description:
RNA+DNA
NPC single cell 162


title: NPC43 scONEseq 160

description:
RNA+DNA
NPC single cell 160


title: 135_FL_NEG


title: Participant8_1


title: NPC43 scONEseq 159

description:
RNA+DNA
NPC single cell 159


title: F2_D1 individual, grown at 16C [T16_P1.G3_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P1.G2_F2_D1]


title: Participant7_4


title: EFPC-DOXn-IL3p

city: Kyoto

first: Azusa

last: Mayumi

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Pediatrics

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Gene expression data from non-induced Ba/F3 cells not expressing ETV6-FRK (control)

data_processing:
TruSeq Stranded mRNA Reference Guide #1000000040498 v00
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  an Illumina TruSeq Stranded mRNA library prep work flow.  workflow
Trimmed sequence reads were mapped to reference genome mm10 with HISAT2, splice-aware aligner.
Read count extraction and normalization were performed using Relative Log Expression (RLE) method in DESeq2 R library.
Assembly: mm10

source_name: Ba/F3, ETV6::FRK(-), rep3

growth_protocol: Ba/F3 cells transduced with ETV6::FRK fusion protein by the Retro-X Tet-on Advanced Inducible System (Takara Bio) were washed twice with phosphate-buffered saline and seeded in triplicate with or without 500 ng/ml doxycycline.

extract_protocol:
Total RNA was extracted 48 hours later from Ba/F3 cells with or without expression of ETV6::FRK using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and the quality was checked on a NanoDrop 2000 (Thermo Fisher Scientific) and a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Ba/F3 cells expressing ETV6::FRK under doxycycline dependent manner were established, and ETV6::FRK protein expression was induced using 500 ng/ml doxycycline.

value: interleukin-3-dependent murine pro-B cell line

value: non-induced Ba/F3 cells not expressing ETV6::FRK (control)


title: EF2-DOXn-IL3p

source_name: Ba/F3, ETV6::FRK(-), rep2


title: F1_D1 individual, grown at 16C [T16_P1.G1_F1_D1]

value: leaf


title: NPC43 scONEseq 158

description:
RNA+DNA
NPC single cell 158


title: NPC43 scONEseq 163

description:
RNA+DNA
NPC single cell 163


title: Participant7_3


title: EF1-DOXn-IL3p

source_name: Ba/F3, ETV6::FRK(-), rep1


title: F2_D1 individual, grown at 16C [T16_P1.G12_F2_D1]


title: 135_HL_NEG


title: EFPC-DOXp-IL3n

description: Gene expression data from ETV6::FRK-expressing Ba/F3 cells induced by doxycycline (Ba/F3-ETV6::FRK)

source_name: Ba/F3, ETV6::FRK(+), rep3


title: NPC43 scONEseq 156

description:
RNA+DNA
NPC single cell 156


title: Participant7_2


title: NPC43 scONEseq 155

description:
RNA+DNA
NPC single cell 155


title: Participant8_2


title: F2_D1 individual, grown at 16C [T16_P1.G11_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P1.G4_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P1.G10_F2_D2]


title: NPC43 scONEseq 154

description:
RNA+DNA
NPC single cell 154


title: EF2-DOXp-IL3n

source_name: Ba/F3, ETV6::FRK(+), rep2

value: ETV6::FRK-expressing Ba/F3 cells induced by doxycycline (Ba/F3-ETV6::FRK)


title: Participant6_3


title: EF1-DOXp-IL3n

source_name: Ba/F3, ETV6::FRK(+), rep1


title: NPC43 scONEseq 153

description:
RNA+DNA
NPC single cell 153


title: P_6191 individual, grown at 16C [T16_P1.F8_P_6191]


title: Participant6_4

value: stop GCs


title: NPC43 scONEseq 157

description:
RNA+DNA
NPC single cell 157


title: Participant6_2


title: NPC43 scONEseq 151

description:
RNA+DNA
NPC single cell 151


title: F2_D1 individual, grown at 16C [T16_P1.F6_F2_D1]

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P1.F7_F2_D1]


title: NK cells_Input_rep1

city: duarte

first: Shoubao

last: Ma

state: California

address: 1500 East Duarte Road

institute: City of Hope

data_processing:
All reads were trimmed with Trim Galore v0.6.7, and subject to quality control with FastQC v0.11.9 before and after adaptor trimming
After trimming, the reads were then mapped to the mouse genome (GRCm38/mm10) using Bowtie2 v2.4.5
Peak calling for each ChIP replicate to the input DNA was performed using MACS2 v2.2.7.1
The peaks were annotated to mm10 genomic features using the annotatePeaks.pl function from the HOMER v4.11.1, and the motifs enriched in ChIP peaks were analyzed by findMotifsGenome.pl function from the HOMER v4.11 (http://homer.ucsd.edu/homer/motif/)
ChIP peaks were visualized using Integrative Genomics Viewer software (http://www.igv.org).
Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis of peaks was performed using DAVID (https://david.ncifcrf.gov/).
Assembly: mm10
Supplementary files format and content: Peak text files

source_name: mouse immune cells

growth_protocol: Mouse NK cells were isolated from the spleen of mice using the EasySep Mouse NK Cell Isolation Kit (STEMCELL Technologies)

extract_protocol:
The cells were then crosslinked with fresh 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were washed three times in cold PBS containing protease inhibitors. Nuclei were isolated using the SimpleChIP Enzymatic Chromatin IP Kit (#91820, CST), and chromatin was sheared on ice using a Fisher sonic dismembrator with the setting of 10 cycles of 4 sec “on” and 8 sec “off”. 2% input fraction was saved, and the remaining sheared chromatin was used for ChIP with a rabbit anti-Xbp1s antibody (Cat No. 40435, CST) or rabbit anti-T-bet antibody (97135, CST) or an IgG isotype control (Millipore) in 1 × ChIP buffer with rotating overnight at 4°C. Protein G magnetic beads were added to each immunoprecipitation and incubated for 2 h at 4°C with rotation. The chromatin bead antibody complexes were then washed three times with low salt wash buffer and one-time with high salt wash buffer. Chromatin was then eluted using 1% SDS in tris-EDTA. Cross-linking was reversed by incubation with 5M NaCl and Proteinase K at 65°C overnight. DNA was purified with ChIP DNA Clean & Concentrator kit (Zymo Research).
ChIP-Seq libraries were prepared using kapa Hyper DNA kit (Roche) and sequenced on an Illumina NovaSeq 6000 platform with 100-bp paired-end reads at the Translational Genomics Research Institute (TGen).

treatment_protocol: 5 × 106 purified mouse primary NK cells  were pretreated with IL-15 (50 ng/ml) for 1 h

value: mouse NK cells

tag: antibody


title: NK cells_IP_rep2

value: XBP1s (Cat No. 40435, CST)


title: Participant6_1


title: Participant5_4


title: NK cells_Input_rep2


title: Participant7_1


title: NPC43 scONEseq 149

description:
RNA+DNA
NPC single cell 149


title: Participant5_3

value: Day 7


title: F2_D2 individual, grown at 16C [T16_P1.F9_F2_D2]

first: Rahul

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute

source_name: leaf


title: F2_D1 individual, grown at 16C [T16_P1.F3_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P1.F4_F2_D1]


title: NPC43 scONEseq 150

description:
RNA+DNA
NPC single cell 150


title: NK cells_IP_rep1


title: F2_D1 individual, grown at 16C [T16_P1.F2_F2_D1]


title: KO tumor 2

city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

country: Taiwan

institute: China Medical University

description: tumor ≦1000 mm³

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1).
Assembly: GRCm38
Supplementary files format and content: Original_read_count.txt

source_name: tumor ≦1000 mm³

extract_protocol:
RNA was harvested using TRIzol™ Reagent method (Invitrogen MAN0001271).
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

value: tumor

value: colon adenocarcinoma cells

value: KLF K74R


title: NPC43 scONEseq 148

description:
RNA+DNA
NPC single cell 148

value: nasopharyngeal carcinoma

value: scONE-seq


title: Participant5_1

value: Day -7


title: NPC43 scONEseq 152

description:
RNA+DNA
NPC single cell 152


title: Participant5_2

value: Day 0


title: F2_D2 individual, grown at 16C [T16_P1.F1_F2_D2]

last: Pisupati


title: NPC43 scONEseq 147

description:
RNA+DNA
NPC single cell 147


title: KO tumor 1

description: tumor ≦1000 mm³


title: NPC43 scONEseq 146

description:
RNA+DNA
NPC single cell 146


title: Participant4_4


title: WT tumor 3

description: tumor ≦1000 mm³

value: KLF WT


title: F2_D2 individual, grown at 16C [T16_P1.F12_F2_D2]


title: Participant4_3


title: NPC43 scONEseq 145

description:
RNA+DNA
NPC single cell 145


title: WT tumor 2

description: tumor ≦1000 mm³


title: F2_D1 individual, grown at 16C [T16_P1.F11_F2_D1]


title: KO tumor 3

description: tumor ≦1000 mm³


title: WT tumor 1

description: tumor ≦1000 mm³


title: F2_D1 individual, grown at 16C [T16_P1.F10_F2_D1]


title: Participant4_2


title: Participant4_1


title: NPC43 scONEseq 144

description:
RNA+DNA
NPC single cell 144


title: KO MSC 2

source_name: MSC

value: MSC


title: KO MSC 1


title: NHD1, rep2

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Cell Ranger Software Suite (v5.0.0) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCh38-2020-A, quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: brain

extract_protocol: Post-mortem frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.

value: NHD

tag: dap12 genotype

value: DAP12 c.2T>C

tag: sample identifier

tag: Sex

value: female

value: occipital cortex

tag: batch


title: NPC43 scONEseq 142

description:
RNA+DNA
NPC single cell 142


title: NPC43 scONEseq 141

description:
RNA+DNA
NPC single cell 141


title: F2_D2 individual, grown at 16C [T16_P1.E8_F2_D2]

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: genotype


title: F2_D1 individual, grown at 16C [T16_P1.E7_F2_D1]


title: F1_D1 individual, grown at 16C [T16_P1.E9_F1_D1]


title: NPC43 scONEseq 140

description:
RNA+DNA
NPC single cell 140


title: Control1, rep2

extract_protocol:
Post-mortem frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
single nucleus RNA sequencing

tag: disease state

value: control

value: WT

value: male


title: WT MSC 1


title: F2_D1 individual, grown at 16C [T16_P1.E6_F2_D1]


title: NHD2

value: DAP12 c.141Gdel


title: F2_D1 individual, grown at 16C [T16_P1.E5_F2_D1]


title: WT MSC 2


title: NHD1, rep1


title: NPC43 scONEseq 139

description:
RNA+DNA
NPC single cell 139


title: NPC43 scONEseq 138

description:
RNA+DNA
NPC single cell 138


title: Control1, rep1


title: NPC43 scONEseq 143

description:
RNA+DNA
NPC single cell 143


title: NPC43 scONEseq 137

description:
RNA+DNA
NPC single cell 137


title: KO BM 2

source_name: bone marrow

value: bone marrow

value: KLF K74R


title: A549_CSP5

city: Chongqing

first: Hong

last: Zheng

address: 30 Gaotanyan Street

institute: Army Medical University (Third Military Medical University)

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG[7] pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: non-small cell lung cancer cells

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (Hyclone Laboratories, Logan, UT, USA) with 10% fetal bovine serum (Gibco Laboratories, Gaithersburg, MD, USA), 1% penicillin-streptomycin, and 2 mM L-glutamine (Sangon Biotech, Shanghai, China) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA from control and CSP stable expression A549 cells was extracted by Trizol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: A549 cells were infected with control or CSP-overexpressing lentiviruses at a multiplicity of infection of 15 for 48 h. Cells were limited-diluted and monoclonal-cultured during puromycin challenge (3 µg/mL, Gibco) to select infection-positive cells. The control and OE-CSP cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1 µg/mL puromycin. A549 cells (1×106) were seeded in 6-well plates and treated with HBSS for 24 h.

tag: cell line

value: non-small cell lung cancer cells

value: CSP overexpression


title: F2_D2 individual, grown at 16C [T16_P1.E2_F2_D2]


title: KO BM 1


title: NPC43 scONEseq 136

description:
RNA+DNA
NPC single cell 136

value: nasopharyngeal carcinoma

value: scONE-seq


title: Control2


title: NPC43 scONEseq 135

description:
RNA+DNA
NPC single cell 135


title: WT BM 2

value: KLF WT


title: WT BM 3


title: A549_CSP3


title: WT BM 1


title: F2_D2 individual, grown at 16C [T16_P1.E1_F2_D2]


title: NPC43 scONEseq 134

description:
RNA+DNA
NPC single cell 134


title: F2_D1 individual, grown at 16C [T16_P1.E12_F2_D1]


title: KO BM 3


title: A549_CSP2


title: NPC43 scONEseq 133

description:
RNA+DNA
NPC single cell 133


title: EMT6, PFKFB4-KO, biol rep 3

city: Buffalo

first: Subhamoy

last: Dasgupta

address: Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using Tophat (v2.1.1)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE v25 (MDA-MB-231)
Assembly: mm10 (EMT6)
Supplementary files format and content: csv file; raw counts

growth_protocol: Both EMT6 and MDA-MB-231 cells were maintained in high-glucose DMEM supplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The purification of total RNAs is prepared using the miRNeasy mini kit (Qiagen).
The sequencing libraries are prepared with the mRNA HyperPrep kit (Roche), from 500ng total RNA.

value: breast cancer cells


title: NPC43 scONEseq 132

description:
RNA+DNA
NPC single cell 132


title: EMT6, PFKFB4-KO, biol rep 2


title: A549_Con5

value: wildtype


title: F2_D1 individual, grown at 16C [T16_P1.E4_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P1.E10_F2_D1]


title: F2_D1 individual, grown at 16C [T16_P1.E3_F2_D1]


title: EMT6, PFKFB4-KO, biol rep 1


title: A549_Con4


title: F2_D2 individual, grown at 16C [T16_P1.D9_F2_D2]


title: NPC43 scONEseq 131

description:
RNA+DNA
NPC single cell 131


title: A549_CSP4


title: F2_D2 individual, grown at 16C [T16_P1.D8_F2_D2]


title: NPC43 scONEseq 129

description:
RNA+DNA
NPC single cell 129


title: EMT6, WT, biol rep 2


title: EMT6, WT, biol rep 3


title: A549_Con3


title: A549_Con2


title: A549_Con1


title: EMT6, WT, biol rep 1


title: F2_D2 individual, grown at 16C [T16_P1.D6_F2_D2]


title: NPC43 scONEseq 128

description:
RNA+DNA
NPC single cell 128


title: F2_D1 individual, grown at 16C [T16_P1.E11_F2_D1]


title: A549_CSP1


title: F2_D1 individual, grown at 16C [T16_P1.D5_F2_D1]


title: NPC43 scONEseq 127

description:
RNA+DNA
NPC single cell 127


title: NPC43 scONEseq 126

description:
RNA+DNA
NPC single cell 126


title: NPC43 scONEseq 130

description:
RNA+DNA
NPC single cell 130


title: Digested tumor, Reprogrammed, Day 5

city: San Francisco

first: Amy

last: Fan

state: CA

address: 769 25th Ave

department: Pathology

institute: UCSF

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
aligned to the transcriptome assembly mm10-2020-A and counts were obtained using Cellranger Single Cell Software Suite version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Assembly: mm10-2020-A

source_name: Digested tumor

extract_protocol:
Subcutaneous tumors were dissected, cut into small chunks, and digested with Collagenase IV (Millipore Sigma) for 30 min at 37C, followed by physical disruption through a 100uM cell strainer. Tumor cells were stained with CD45.2, endogenous immune cells were stained with CD45.1, and dead cells were stained with Fixable Live/Dead stain for FACS based purification. Live CD45.1+ immune cells and live CD45.2+ tumor cells were FACS isolated, counted, and pooled at a 1:1 ratio.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics)

value: Digested tumor

value: B Cell Leukemia

tag: time

value: Day 5

value: Doxycycline


title: Digested tumor, Untreated, Day 5

description: 10x Genomics

value: Untreated


title: NPC43 scONEseq 125

description:
RNA+DNA
NPC single cell 125

source_name: NPC43 cell line


title: F2_D1 individual, grown at 16C [T16_P1.D3_F2_D1]

city: Vienna

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P1.D4_F2_D2]


title: a17_CCA14_H38

city: Rotterdam

first: Monique

last: Verstegen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: ErasmusMC

data_processing:
Bulk RNA-sequencing was performed by Novogene (Beijing, China) resulting in 20-30 million, 150 nucleotides long, paired-end reads.
Sequencing data were uploaded to the Galaxy Web platform public server usegalaxy.org
Sequences were trimmed for adapters using Trim Galore! (version 0.4.3.1), and mapped using RNA STAR (version 2.6.8a) against the human reference genome GRCh38. Mapped reads were translated to counts using FeatureCounts (version 2.0.1) applying the built-in hg38 genome annotation file.
All raw counts were batch corrected using ComBat-seq (available via sva package version 3.36.0) using a negative binomial regression model. After filtering for genes with low expression, we could compare the expression profiles of 16.637 genes. Analysis of differential expression was performed using edgeR (version 3.32.1) and Limma (version 3.46.0) R packages.
Genes were considered differentially expressed when the adjusted p-value was <0.05 (Benjamini Hochberg FDR corrected).
Genome_build: Hg38
Supplementary_files_format_and_content: Dataframe counts and genens and gene length; Metadata information samples for subsequent analysis

source_name: Cholangiocarcinoma tumor organoids

growth_protocol: Broutier et al. Nat Med 2017. Organoids were cultured according previous protocol. For culturing on decellularized matrix, organoids were dissociated to single cells and seeded on top of the matrix.

extract_protocol:
RNA from CCAOs cultured in expansion medium was collected in lysis buffer (QIAzol lysing reagent, Qiagen) and the RNA was isolated using the miRNeasy mini kit (Qiagen) according to the manufacturer’s protocol
Sequencing data were uploaded to the Galaxy Web platform public server usegalaxy.org (Afgan E., Baker D., van den Beek M., Blankenberg D., Bouvier D., et al., 2016 The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44: W3–W10). Sequences were trimmed for adapters using Trim Galore! (version 0.4.3.1), and mapped using RNA STAR (version 2.6.8a) against the human reference genome GRCh38).

treatment_protocol: no treatment

value: human CCA organoids cultured in expansion medium

tag: sample group

value: Culture substrate decellularized liver matrix

tag: scaffold

value: H

tag: cellid


title: NPC43 scONEseq 124

description:
RNA+DNA
NPC single cell 124

tag: method


title: a16_CCA1_H38

tag: cell type


title: Digested tumor, Untreated, Day 10

description: 10x Genomics

value: Day 10

tag: treatment


title: NPC43 scONEseq 123

description:
RNA+DNA
NPC single cell 123

tag: tissue


title: a15_CCA27_H37


title: P_6191 individual, grown at 16C [T16_P1.D1_P_6191]


title: N3

city: Cincinnati

first: Koichi

last: Araki

state: Ohio

address: 240 Albert Sabin Way, Room S8.544

department: Division of Infectious Diseases

institute: Cincinnati Children's Hospital Medical Center

data_processing:
HISAT2 (Galaxy Version 2.2.1+galaxy0) to align the reads with the mm10 genome
Read counts were generated with featureCounts (Galaxy Version 2.0.1+galaxy1)
The differential gene expression analysis was performed using the DESeq2
Assembly: mm10

source_name: spleen

extract_protocol:
RNA extracted by Trizol reagent and zymo RNA Clean and Concentrator-5
RNA library provided by by Novogene Co.

value: spleen

value: CD44lo Naive CD8 T cells

value: WT

value: uninfected


title: NPC43 scONEseq 122

description:
RNA+DNA
NPC single cell 122

value: nasopharyngeal carcinoma

value: scONE-seq


title: N2


title: a14_CCA14_H37


title: NPC43 scONEseq 121

description:
RNA+DNA
NPC single cell 121


title: F2_D2 individual, grown at 16C [T16_P1.D12_F2_D2]


title: a18_CCA27_H38


title: a13_CCA1_H37


title: F2_D1 individual, grown at 16C [T16_P1.D11_F2_D1]


title: N1


title: a12_CCA27_H35


title: F2_D2 individual, grown at 16C [T16_P1.D7_F2_D2]


title: V3_T3

value: CXCR5-Tim3+ more terminally differentiated CD8 T cells

value: vehicle control tretment


title: NPC43 scONEseq 120

description:
RNA+DNA
NPC single cell 120


title: F2_D2 individual, grown at 16C [T16_P1.D10_F2_D2]


title: a11_CCA14_H35


title: NPC43 scONEseq 119

description:
RNA+DNA
NPC single cell 119


title: Digested tumor, Reprogrammed, Day 10

description: 10x Genomics

value: Digested tumor

value: B Cell Leukemia


title: V2_T3


title: a10_CCA1_H35


title: a9_CCA27_T2017

value: Culture substrate decellularized tumor matrix

value: T


title: NPC43 scONEseq 118

description:
RNA+DNA
NPC single cell 118


title: F2_D2 individual, grown at 16C [T16_P1.C8_F2_D2]

value: leaf

value: 7-10 leave rosette


title: F2_D1 individual, grown at 16C [T16_P1.C9_F2_D1]


title: NPC43 scONEseq 117

description:
RNA+DNA
NPC single cell 117


title: a8_CCA27_T12J

value: human CCA organoids cultured in expansion medium


title: F2_D2 individual, grown at 16C [T16_P1.C7_F2_D2]


title: R3_T3

value: rapamycin treatment


title: R2_T3


title: NPC43 scONEseq 115

description:
RNA+DNA
NPC single cell 115


title: NPC43 scONEseq 116

description:
RNA+DNA
NPC single cell 116


title: a6_CCA14_T2017


title: F2_D1 individual, grown at 16C [T16_P1.D2_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P1.C5_F2_D2]


title: a7_CCA27_T6D


title: R1_T3


title: F2_D2 individual, grown at 16C [T16_P1.C4_F2_D2]


title: NPC43 scONEseq 113

description:
RNA+DNA
NPC single cell 113


title: V2_X5

value: CXCR5+Tim3- stem-like CD8 T cells


title: V3_X5

value: spleen


title: F2_D2 individual, grown at 16C [T16_P1.C6_F2_D2]


title: V1_T3


title: NPC43 scONEseq 112

description:
RNA+DNA
NPC single cell 112


title: NPC43 scONEseq 114

description:
RNA+DNA
NPC single cell 114


title: F2_D2 individual, grown at 16C [T16_P1.C1_F2_D2]


title: a3_CCA1_T2017


title: NPC43 scONEseq 111

description:
RNA+DNA
NPC single cell 111


title: F2_D2 individual, grown at 16C [T16_P1.C2_F2_D2]


title: a4_CCA14_T6D


title: a2_CCA1_T12J


title: R3_X5


title: NPC43 scONEseq 110

description:
RNA+DNA
NPC single cell 110


title: a1_CCA1_T6D


title: F2_D2 individual, grown at 16C [T16_P1.C12_F2_D2]


title: R2_X5


title: F2_D1 individual, grown at 16C [T16_P1.C11_F2_D1]


title: NPC43 scONEseq 109

description:
RNA+DNA
NPC single cell 109


title: V1_X5


title: a5_CCA14_T12J


title: F2_D1 individual, grown at 16C [T16_P1.C10_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P1.B9_F2_D2]


title: F2_D2 individual, grown at 16C [T16_P1.B8_F2_D2]


title: NPC43 scONEseq 108

description:
RNA+DNA
NPC single cell 108


title: NPC43 scONEseq 106

description:
RNA+DNA
NPC single cell 106


title: NPC43 scONEseq 105

description:
RNA+DNA
NPC single cell 105


title: Lipe-AKO Mier1 KO 36h 2

city: Shanghai

first: Yanhao

last: Chen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description:
Lgene.count.matrix.annot.txt
MKO_36_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM v1.2.31 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.10.1
Assembly: GRCm39
Supplementary files format and content: Gene counts for each samples

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol reagent in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: Lipe-AKO; Cas9

tag: aav treatment

value: AAV-Mier1 sgRNA

value: PHx 36 h


title: Lipe-AKO 36h 2

description:
Lgene.count.matrix.annot.txt
LKO_36_2

value: AAV-Cre


title: F2_D2 individual, grown at 16C [T16_P1.B7_F2_D2]


title: Lipe-AKO Mier1 KO 36h 1

description:
Lgene.count.matrix.annot.txt
MKO_36_1


title: Lipe-AKO 36h 1

description:
Lgene.count.matrix.annot.txt
LKO_36_1


title: F2_D1 individual, grown at 16C [T16_P1.B6_F2_D1]


title: Lipe Control 36h 2

description:
Lgene.count.matrix.annot.txt
WT_36_2

value: Lipe Control; Cas9


title: NPC43 scONEseq 104

description:
RNA+DNA
NPC single cell 104

value: nasopharyngeal carcinoma

value: scONE-seq


title: F2_D1 individual, grown at 16C [T16_P1.B5_F2_D1]


title: F2_D2 individual, grown at 16C [T16_P1.B2_F2_D2]


title: NPC43 scONEseq 103

description:
RNA+DNA
NPC single cell 103


title: NPC43 scONEseq 102

description:
RNA+DNA
NPC single cell 102


title: R1_X5

value: WT


title: F2_D2 individual, grown at 16C [T16_P1.B1_F2_D2]


title: NPC43 scONEseq 107

description:
RNA+DNA
NPC single cell 107


title: NPC43 scONEseq 100

description:
RNA+DNA
NPC single cell 100


title: Lipe-AKO Mier1 KO 0h 1

description:
Lgene.count.matrix.annot.txt
MKO_0_1

value: PHx 0 h


title: Lipe-AKO 0h 2

description:
Lgene.count.matrix.annot.txt
LKO_0_2


title: NPC43 scONEseq 099

description:
RNA+DNA
NPC single cell 099


title: F2_D1 individual, grown at 16C [T16_P1.B11_F2_D1]


title: Lipe-AKO 0h 1

description:
Lgene.count.matrix.annot.txt
LKO_0_1


title: F2_D1 individual, grown at 16C [T16_P1.B10_F2_D1]


title: Lipe Control 0h 2

description:
Lgene.count.matrix.annot.txt
WT_0_2


title: Lipe Control 0h 1

description:
Lgene.count.matrix.annot.txt
WT_0_1


title: F2_D1 individual, grown at 16C [T16_P1.A8_F2_D1]


title: Aging Mier1 KO 48h 2

description:
HAgene.count.matrix.annot.xls
AK_48h_2

value: PHx 48 h

tag: age

value: aged


title: Lung

city: Changchun

first: Cong

last: Fu

state: Jilin

address: NO.17  Xinmin Street

institute: The First Hospital of Jilin University

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to the reference human genome (version hg38) using STAR (version 2.7.3a)
expression levels were calculated as Fragments per Kilobase of transcript per Million reads(FPKM) using Cufflinks (version 2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: Human lung samples from uninfected NSG-L mice

extract_protocol:
Human lung samples were removed from uninfected or SARS-CoV-2 infected NSG-L mice. Flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human lung samples

value: from uninfected NSG-L mice


title: Lipe Control 36h 1

description:
Lgene.count.matrix.annot.txt
WT_36_1


title: Aging Mier1 KO 48h 1

description:
HAgene.count.matrix.annot.xls
AK_48h_1


title: Lipe-AKO Mier1 KO 0h 2

description:
Lgene.count.matrix.annot.txt
MKO_0_2


title: NPC43 scONEseq 095

description:
RNA+DNA
NPC single cell 095


title: L_E21

source_name: Human lung samples from infected NSG-L mice 21 days after SARS-CoV-2 inoculation


title: L_E5

source_name: Human lung samples from infected NSG-L mice 5 days after SARS-CoV-2 inoculation


title: NPC43 scONEseq 101

description:
RNA+DNA
NPC single cell 101


title: Aging Mier1 KO 0h 2

description:
HAgene.count.matrix.annot.xls
AK_0h_2


title: F2_D1 individual, grown at 16C [T16_P1.A5_F2_D1]

value: leaf

value: 7-10 leave rosette


title: ARP1_IP

city: Nanjing

first: Yuanjiao

last: Zhang

state: China

address: Xianlin Road

institute: nanjing university of chinese medicine

data_processing:
Fastp 0.19.11 software performs basic quality statistics for raw reads
QC analysis was used by  fastqc v0.11.5
burrows Wheeler aligner(0.7.12-r1039) can  compare reads to reference genome
Peak calling was performed by MACS22.1.0
The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: annotated peaks
Supplementary_files_format_and_content: SE.MATS.JunctionCountOnly.xlsx: IJC_SAMPLE_1 and SJC_SAMPLE_1 represented by the ARP1-IP samples; IJC_SAMPLE_2 and SJC_SAMPLE_2 represented by the ARP1-input samples

source_name: Multiple Myeloma cells

growth_protocol: Human multiple myeloma cell lines ARP1 were cultured in RPMI 1640 Medium  with 10% fetal bovine serum 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured in a humidified atmosphere of 5 % CO2 at 37℃.

extract_protocol:
~5-20 × 10e6 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of SFRS8 and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using a phenol-chloroform lysate to obtain a purified product.
RNA samples were fragmented by RNA fragmentation buffer (10 mM Tris-HCl [pH 7.0], 10 mM ZnCl2). Fragmented RNA was  incubated for 2 hr at 4C with 0.5 mg/mL antim6A polyclonal antibody in IP buffer (150  mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl [pH 7.4]) supplemented with RNasin  Plus RNase inhibitor (Promega). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase（RNase H - ）. Second strand cDNA  synthesis was subsequently performed using DNA Polymerase I and RNase H.  Remaining overhangs were converted into blunt ends via exonuclease/polymerase  activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with  hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA  fragments of preferentially 150~200 bp in length, the library fragments were purified  with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µL USER Enzyme  (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min  followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion  High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last,  PCR products were purified (AMPure XP system) and library quality was assessed on  the Illumina HiSeqTM 2500 system.

value: Multiple Myeloma

tag: sample type

value: IP

tag: rip antibody

value: anti-SFRS8 (abcam)


title: NPC43 scONEseq 093

description:
RNA+DNA
NPC single cell 093


title: F2_D2 individual, grown at 16C [T16_P1.A4_F2_D2]


title: NPC43 scONEseq 094

description:
RNA+DNA
NPC single cell 094


title: NPC43 scONEseq 097

description:
RNA+DNA
NPC single cell 097


title: F2_D2 individual, grown at 16C [T16_P1.A9_F2_D2]


title: Aging Control 48h 2

description:
HAgene.count.matrix.annot.xls
AC_48h_2

value: Liver


title: NPC43 scONEseq 096

description:
RNA+DNA
NPC single cell 096


title: F2_D2 individual, grown at 16C [T16_P1.A3_F2_D2]


title: ARP1_Input

value: input


title: RE-CL [A5]

city: Cheonan

first: Ngu

middle: Van

last: Trinh

state: Chungcheongnam

address: 25Bongjeong-ro, Cheonan-si, Korea

institute: SoonChunHyang Institute of Medi-Bio Science

data_processing:
Sequencing Protocol: NovaSeq 6000 System User Guide Document # 1000000019358 v02
FASTQ files were did quality control using FastQC v0.11.5. Sequenced reads were trimmed using Trimmomatic 0.32 , and masked for low-complexity or low-quality sequence, then mapped to UCSC hg19 using HISAT2 through Bowtie2 aligner
Assembles transcripts were count using Stringtie. Raw counts were normalized using FPKM: Fragments per kilobase of transcript per million read pairs
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample

source_name: Breast Epithelial Cell Line

growth_protocol: Cells were grown in DMEM + 10% FBS + 1% PEN/STREP

extract_protocol:
RNA was extracted by RNeasy mini kit
TruSeq Stranded mRNA Sample Preparation Guide. Part # 15031047 Rev. E

treatment_protocol: Cells were grown on suspension and then re-attachment

value: Breast Epithelial Cell Line

tag: collection

value: cluster cells reattached


title: NPC43 scONEseq 091

description:
RNA+DNA
NPC single cell 091

extract_protocol:
Nuclei isolation was adapt from Omni-ATAC protocol. Single cells / nuclei were sorted with Aria III with propidium iodide or DAPI to remove dead cells or select nuclei.
scONE-seq; Smart-seq2; 10x Genomics

value: nasopharyngeal carcinoma


title: F2_D1 individual, grown at 16C [T16_P1.B12_F2_D1]

tag: developmental stage


title: Aging Control 48h 1

description:
HAgene.count.matrix.annot.xls
AC_48h_1

tag: genotype

value: AAV-Cre


title: RE-SC [A3]

value: single cells reattached


title: F2_D1 individual, grown at 16C [T16_P1.A2_F2_D1]


title: DE-CL [A4]

value: cluster cells suspension


title: NPC43 scONEseq 090

description:
RNA+DNA
NPC single cell 090

value: scONE-seq


title: F2_D1 individual, grown at 16C [T16_P1.A1_F2_D1]


title: NPC43 scONEseq 089

description:
RNA+DNA
NPC single cell 089


title: Aging Control 0h 1

description:
HAgene.count.matrix.annot.xls
AC_0h_1

value: PHx 0 h

value: aged


title: HFD Mier1 KO 48h 2

description:
HAgene.count.matrix.annot.xls
HK_48h_2

value: AAV-Mier1 sgRNA

value: PHx 48 h

tag: diet

value: HFD


title: Aging Mier1 KO 0h 1

description:
HAgene.count.matrix.annot.xls
AK_0h_1


title: DE-SC [A2]

tag: cell line

value: single cells suspension


title: F2_D1 individual, grown at 16C [T16_P1.A12_F2_D1]

value: leaf

value: 7-10 leave rosette


title: Aging Control 0h 2

description:
HAgene.count.matrix.annot.xls
AC_0h_2

value: Liver


title: NPC43 scONEseq 087

description:
RNA+DNA
NPC single cell 087


title: F2_D2 individual, grown at 16C [T16_P1.A10_F2_D2]


title: NPC43 scONEseq 088

description:
RNA+DNA
NPC single cell 088


title: HFD Mier1 KO 48h 1

description:
HAgene.count.matrix.annot.xls
HK_48h_1


title: ATT-SC [C3]

value: single cells