title: Human liver tissue

city: Amsterdam

first: Joana

last: Silva

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: The Netherlands Cancer Institute

description: Library name: Human_Liver_invivo

data_processing:
Reads from all samples were adapter-trimmed using the cutadapt tool (--action=trim -m 18 --adapter=TGGAATTCTCGGGTGCCAAGG --overlap=15 --error-rate=0.1). Then, trimmed reads were mapped to the hg38 and mm10 genomes using the STAR aligner.
Mouse data was analyzed solely using Gencode vM21 annotation. For human data, gencode v34 mitochondrial annotation was supplemented with the MDP annotation, 46 MS-supported ORFs identified in Kienzle et al. and 9 MDPs (MOTS-c, Humanin, SHMOOSE, and SHLPs 1-6) from the literature. For up- & down-stream analyses, the human annotation was extended further by defining all 30-nucleotide regions immediately upstream and downstream from any ORF as independent pseudo-ORFs.
Read quantification was done with the Rsubread package in R using these annotations. Multimapped reads were counted at a fractional count. Processed data includes the quantification results, including the RPKM values which represents the number of reads per kb million mitochodrial protein-coding region mapped reads.
Assembly: For human: hg38, gencode v34, Kienzle23&literature MDP annotation ; for mouse: mm10, gencode vM21
Supplementary files format and content: htseq.tsv files are tab-seperated files that reports the ORF ribosome occupancy levels based on respective annotations in file names. Ribosome occupancy is calculated by number of reads that are mapped to given ORF regions. Multimapping reads are fractioned into multimapped regions.
Library strategy: Ribo-Seq

growth_protocol: 143B and cybrid lines were cultured and maintained in Dulbecco’s modified Eagle’s media (DMEM) High Glucose, Glutamax-supplemented media (Thermo Fisher Scientific) supplemented with 10% fetal calf serum (FCS), 100 U/ml penicillin and 100 µg/ml streptomycin (Thermo Fisher Scientific). LN751 lines were cultured and maintained in Minimal Essential Medium, MEM, supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine, 1% MEM-Vitamins, 1% Non-Essential Amino Acids, 1% Penicillin-Streptomycin and 1% Sodium Pyruvate (MEM complete) (all purchased from Invitrogen, Grand Island, NY, USA). All lines were grown in standard conditions (37ºC and 5% CO2) and were routinely tested for mycoplasma contamination.

extract_protocol:
Briefly, for cell lines we used use 4x 15cm plates at approximately 80% confluent. For tissues, use approximately 0,027cm3 of snap-frozen material, bith from mouse and human, and grind them with the mortar and pestle, using liquid nitrogen to preserve the cold. Cells/ttissues were resuspended in ice-cold lysis buffer (20mM Tris-HCl pH 7.8, 10mM KCl, 10mM MgCl2, 1% Triton X-100, 0,1% NP-40, 1mM DTT, 100µg/ml chloramphenicol and 1x EDTA-free proteinase inhibitor), homogeneized with a 25G serynge and incubated for 10 min on ice. Lysates were then centrifuged at max speed for 10 min at 4°C and the supernatants were digested with 10ul of RNase I (ThermoFisher Scientific) for 40min at 25’C and the reaction was stopped by adding 13ul of SUPERASE (ThermoFisher Scientific). Mitoribosomal protected fragments were loaded onto 10-60% sucrose gradients and centrifuged for 2h at 38000rpm and at 4ºC, using a SW41 rotor. By splitting into fractions of 750ul, fractions 4, 5 and 6 were collected and mixed with 0.2mg/ml proteinase K, 0.01M of EDTA and 0.01% SDS. Samples were incubated at 42ºC for 30min. RNA was extracted using phenol:chloroform and precipitated with EtOH, sodium acetate and glycoblue.
MitoRiboSeq library preparation was performed as previously described (Loayza-Puch et al., 2013) with some modifications. To discard undigested RNA fragments, RPFs were run in a 10% TBE-Urea polyacrylamide gel and size selected between 26 nt and 48 nt using marker RNAs. 3’ ends were dephosphorylated using T4 polynucleotide kinase (PNK) (NEB) and 1.5xMES buffer (150mM MES-NaOH, 15mM MgCl2, 15mM ß-mercaptoethanol and 450mM NaCl, pH 5.5) and incubated at 37’C for 4h. After purifying RNAs with Trizol, 3’adpaters were ligated with T4 RNA ligase I (NEB) and incubated overnight at 24’C. After size-selecting the ligated products, 5’ ends were phosporylated with T4 PNK and incubated at 37’C during 30min. 5’ adapters were then ligated with T4 RNA ligase I and incubated 37’C for 2,5 hours. The RPFs containing both adapters were then size-selected one more time. cDNA was synthesized with SuperScript III (ThermoFisher Scientific) according to manufacturer’s instructions and using the RTP primer (seq). After purification with G50 columns (Merck), cDNA was amplified using Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific) for 18 cycles, with primers containing different indexes to allow for sequencing (see table). PCR products were purified using the QIAquick PCR purification kit (Qiagen) followed by a final size selection with a E-Gel SizeSelect II 2%, (ThermoFisher Scientific). All samples were accessed with the Agilent 2100 Bioanalyzer to assure high quality and quantify the molarity and the libraries were sequenced on the Illumina HiSeq2500.

treatment_protocol: LN751 cells were subjected to the PMCi triple combination therapy for 7 days. This treatment included Buparlisib (P) as the PI3K inhibitor, Mirdametinib (M) as the MEK inhibitor, and Palbociclib (C) as the CDK4/6 inhibitor.


title: shell ventricle rep3

status: Public on Jan 01 2026

type: SRA

city: Qingdao

first: Long

last: Zhao

address: 5 Yushan Rd

country: China

institute: Ocean University of China

description:
shell_v3
shell_DESeq2_diffgene.csv

library_source: transcriptomic

data_processing:
Alignment of paired-end clean reads to the reference were built using Hisat2 (2.0.5).
The featureCounts (1.5.0) (Liao et al. 2014) was used to count the read numbers mapped to each gene
TPM of each gene was calculated by StringTie (1.3.3b)
Differential expression analysis of the atrium and ventricle in snails and scallops was performed using the DESeq2 (1.20.0)
Constructing the gene co-expression network using the WGCNA package
Assembly: Taxonomy ID: 2315439 & Taxonomy ID: 6573
Supplementary files format and content: tab-delimited text file include raw counts and log2FoldChange for each sample

molecule: total RNA

organism: Mizuhopecten yessoensis

source_name: heart

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100  system (Agilent Technologies, CA, USA). (Refer to RNA quality inspection report for specific instruments)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using  poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

tag: tissue

value: heart

tag: tissue region

value: ventricle

tag: genotype

value: WT


title: Single-cell RNA-seq day3 cell23

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

library_source: transcriptomic single cell

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample

organism: Mus musculus

source_name: Mouse embryonic fibroblasts reprgramming cells

growth_protocol: Reprogramming cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were collected by trypsin digestion. Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

treatment_protocol: MEF cells were infected with OvSvK for reprogramming.

tag: cell type

tag: treatment

value: OvSvK single-cell RNA-seq reprogramming day3


title: PLC_KPT330

city: Shanghai

last: Wang

address: Building 5, No.1630 Dongfang Road

institute: Shanghai Cancer Institute

data_processing:
Illumina Casava 1.8.2 software used for basecalling. The quality score encoding is in +Phred 33.
Raw sequencing reads were mapped to the human genome (GRCh38) using STAR (version 2.4.2g1).
Gene-level read counts were generated using featureCounts from the subRead package with default settings.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Homo sapiens

source_name: Liver

extract_protocol:
Total RNA was extracted and purified using the Trizol reagent (Invitrogen)
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).

treatment_protocol: We treated liver cancer cells with vehicle, CDK4/6 inhibitor, XPO1 inhibitor and the combination. Then, RNA sequencing was conducted to quantify the mRNA expression level of vehicle-treated or CDK4/6 inhibitor, XPO1 inhibitor and the combination treated liver cancer cells. CDK4/6 inhibitor, XPO1 inhibitor and the combination induced expression changes were obtained based on the resultant data.

tag: cell line

value: PLC

value: liver cancer cell line

value: XPO1 inhibitor

value: Liver


title: Single-cell RNA-seq day3 cell27

value: Mouse embryonic fibroblasts reprgramming cells


title: snail atrium rep3

description:
snail_a3
snail_DESeq2_diffgene.csv

organism: Lissachatina fulica

value: atrium


title: snail ventricle rep3

description:
snail_v3
snail_DESeq2_diffgene.csv


title: LN751 cell line, PMC treated for 7d #2

description: Library name: PMC_2

value: Glioblastoma

value: PMCi


title: 97H_Control

value: Control


title: Single-cell RNA-seq day3 cell22


title: PLC_CDK46

value: CDK4/6 inhibitor


title: shell ventricle rep1

description:
shell_v1
shell_DESeq2_diffgene.csv


title: Single-cell RNA-seq day3 cell24


title: LN751 cell line, PMC treated for 7d #3

description: Library name: PMC_3


title: Huh7_CDK46


title: LN751 cell line, control #3

description: Library name: Ctrl_3

value: untreated


title: shell ventricle rep2

description:
shell_v2
shell_DESeq2_diffgene.csv


title: Huh7_Control


title: Single-cell RNA-seq day3 cell25


title: Single-cell RNA-seq day3 cell18


title: PLC_Combination

value: CDK4/6 inhibitor + XPO1 inhibitor


title: FG4592_3

city: Nanjing

first: Wenwen

last: yang

address: 163 Xianlin Avenue, Qixia Districtc

institute: nanjing university

data_processing:
Sequence and filtering of Clean Reads. A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
Alignment with Reference Genome. We aligned reads of all samples to the human reference genome using HISAT2 package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
Quantification of Gene Abundance. The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Differentially expressed genes (DEGs) Analysis. Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Human hg38
Supplementary files format and content: tab-delimited excle file includes gene abundance for each sample

source_name: HK2 cell

growth_protocol: HK2 cells were cultured with Dulbecco's modified Eagle's smedium-F12 medium supplemented with 10% fetal bovine serum in a 37°C incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: HK2 cells were induced with H2O2 for 4 hours or cultured in 45℃ for 1 hours or treated with FG4592 for 12 hours and then isolated stress granules from HK2 cells.

value: HK2 cell

value: renal tubular epithelial cells

value: FG4592 induced 12 hours


title: snail atrium rep1

description:
snail_a1
snail_DESeq2_diffgene.csv

value: heart

value: WT


title: LN751 cell line, control #1

description: Library name: Ctrl_1


title: Chap_PTEN_KO_D80

city: Cleveland

first: Ya

last: Chen

state: OH

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

country: USA

institute: Case Western Reserve University

description:
Library name: sample9
drop-seq

data_processing:
Seurat pipeline
Assembly: merge and List
Supplementary files format and content: rds

source_name: Chap human iPSC

growth_protocol: All iPSC cells were cultured on a feeder layer of iMEF cells in hES medium consisting of DMEM/F12, 20% knockout serum replacement, 1% GlutaMAX, and 1% Non-essential AA . Prior to the experiment, ReleSR media was used to remove iMEF cells. Subsequently, iPSC cells were plated onto vitronectin-coated culture dishes and cultured in E8 medium until they reached approximately 60% confluence. The iPSC cells were then collected and dissociated into single cells using TrypLE.

extract_protocol:
10x used: Chromium Nest GEM single Cell 3' Reagent Kits V3.1 (Dual Index). Drop-seq used: McCarroll laboratory publised protocol (34. Macosko,E.Z., Basu,A., Satija,R., Nemesh,J., Shekhar,K., Goldman,M., Tirosh,I., Bialas,A.R., Kamitaki,N., Martersteck,E.M., et al. (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell, 161, 1202-1214)
Seurat scRNA-seq

treatment_protocol: Cells were plated at a density of 6000 cells per well of V-shaped 96-well plates in CDM medium containing DMEM/F12, 250mg/ml BSA, 15µg/ml apo-transferrin , 39nl/ml 1-thioglycerol, and 7µg/ml insulin. On the first day, half of the CDM medium was replaced with fresh medium containing 50ng/ml βFgf2 and 10µM SB431542. On day 7 of the differentiation protocol, fresh CDM medium containing 25ng/ml βFgf2 and 5µM SB431542 was added to the cells. On day 14, the organoids were transferred from the V-shaped 96-well plate to a U-shaped 96-well plate containing a new CDM medium supplemented with 100ng/ml Fgf19. On day 21, the culture medium was switched to CMM1 medium, which contained neurobasal medium, N2 supplement, and 1% Penicillin-streptomycin. On day 28, fresh CMM1 medium containing 300ng/ml recombinant human SDF-1α (CXCL12) was added. From day 35 onwards, all organoids were maintained in CMM1 medium.

value: Chap human iPSC

value: stem cells

value: neuronal differentiation

tag: batch


title: Single-cell RNA-seq day3 cell21

value: OvSvK single-cell RNA-seq reprogramming day3


title: Chap_PTEN_I135L_D80

description:
Library name: sample8
drop-seq


title: transmitochondrial cybrid result from fusing 143p0 cells with A549 mtDNA from donor 1.14 #3

description: Library name: 143B_RL14_3


title: LN751 cell line, PMC treated for 7d #1

description: Library name: PMC_1


title: Chap_WT_D80

description:
Library name: sample7
drop-seq


title: Single-cell RNA-seq day3 cell19

value: Mouse embryonic fibroblasts reprgramming cells


title: Single-cell RNA-seq day3 cell20


title: shell atrium rep3

description:
shell_a3
shell_DESeq2_diffgene.csv

value: atrium


title: shell atrium rep2

description:
shell_a2
shell_DESeq2_diffgene.csv


title: shell atrium rep1

description:
shell_a1
shell_DESeq2_diffgene.csv


title: DMSO3

value: dmso induced 12 hours


title: Single-cell RNA-seq day3 cell15


title: FG4592_2


title: PLC_Control

value: PLC

value: liver cancer cell line

value: Liver


title: Single-cell RNA-seq day3 cell17


title: transmitochondrial cybrid result from fusing 143p0 cells with A549 mtDNA from donor 1.14 #2

description: Library name: 143B_RL14_2.htseq,tsv


title: transmitochondrial cybrid result from fusing 143p0 cells with A549 mtDNA from donor 1.14 #1

description: Library name: 143B_RL14_1


title: FA_3

city: Zunyi

first: yan

last: Zhang

state: Guizhou

address: Honghuagang

department: College of Basic Medicine

institute: Zunyi Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations
Data were fltered using the following specifications
peaks were called using PeaksFind version 2.2 with the following setting: RNA threshold (0 .2), Enrichment Fold (2 .5), Rescue Fold (3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
Total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

value: whole worms

value: 10 uM Forsythia


title: Single-cell RNA-seq day3 cell14


title: transmitochondrial cybrid result from fusing 143p0 cells with A549 mtDNA from donor 1.12 #2

description: Library name: 143B_RL12_2


title: FA_2


title: LN751 cell line, control #2

description: Library name: Ctrl_2

value: Glioblastoma

value: untreated


title: Single-cell RNA-seq day3 cell16


title: Single-cell RNA-seq day3 cell13


title: DMSO1

value: HK2 cell

value: renal tubular epithelial cells


title: DMSO2

value: WT


title: transmitochondrial cybrid result from fusing 143p0 cells with A549 mtDNA from donor 1.12 #3

description: Library name: 143B_RL12_3


title: media3


title: media2


title: FA_1


title: heatshock3

value: 45degreeC for 1 hours


title: Single-cell RNA-seq day3 cell10


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 3, tech rep 2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

library_source: genomic

data_processing:
adapter filtering with cutadapt (version  4.8) --quality-cutoff 10 -m 20 --pair-filter=both -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA
alignment with bowtie2 (version 2.5.4) -X 1000 --sensitive --no-unal
R/bioconductor GAlignedReads to GRanges to coverage and rtracklayer::export.bw
Assembly: XENLA 10.1
Supplementary files format and content: bigWig files with per-base coverage genome-wide

molecule: genomic DNA

organism: Xenopus laevis

source_name: animal cap

growth_protocol: Xenopus laevis embryos were cultured in MMR until NF9 at which point animal caps were cut in Steinberg Solution and cultured until NF16.

extract_protocol:
2 animal caps were harvested and prepared for ATAC seq according to Esmaeli et al. 2020 (PMID: 32119833)
ATAC-seq libraries were prepared using the Illumina®Tagment DNA Enzyme and with indexing primers from Buenrostro et al., 2013 (PMID: 24097267)

treatment_protocol: Xenopus laevis embryos were injected in both cells of the 2-cell stage with either control morpholino or suv4-20h1 morpholino.

value: animal cap

value: Suv4-20h1 morpholino injected


title: transmitochondrial cybrid result from fusing 143p0 cells with A549 mtDNA from donor 1.12 #1

description: Library name: 143B_RL12_1


title: osteosarcoma cell line, control #3

description: Library name: 143B_Parental_3

value: osteosarcoma


title: Single-cell RNA-seq day3 cell9

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day3


title: media1


title: heatshock2


title: osteosarcoma cell line, control #1

description: Library name: 143B_Parental_1


title: Single-cell RNA-seq day3 cell11


title: DMSO, Input, rep2

city: Yiwu

first: Yixuan

last: Yu

address: 1575 Chouzhou North Road, Futian Street

institute: The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine

description: Library name: DMSO-2.Input

data_processing:
Following sequencing, process the raw reads by first using FastQC for quality assessment and Trimmomatic to remove adapters and low-quality bases. Align the cleaned reads to the human reference genome (e.g., GRCh38) using a splice-aware aligner like STAR. Then, using the aligned BAM files, generate a count matrix for each gene with a tool like featureCounts, assigning reads to genomic features based on the chosen annotation. Finally, import the count matrix into a statistical environment (e.g., R with DESeq2) for downstream differential expression analysis between the DMSO and FB23-2 treatment groups.
Assembly: hg38
Supplementary files format and content: excel file include methylated sites value for each samples
Library strategy: MeRIP-Seq

molecule: polyA RNA

extract_protocol:
Treat H69 cells with either DMSO or FB23-2 and lyse them to extract total RNA. Isolate polyA RNA from the total RNA using magnetic Oligo(dT) beads. Elute the purified mRNA from the beads in RNase-free water. Check the concentration and quality of the mRNA using a fluorometer and bioanalyzer. Store the final polyA RNA at -80°C for library preparation and sequencing.
Following polyA RNA extraction from DMSO or FB23-2 treated H69 cells, proceed with library construction by first fragmenting the mRNA and synthesizing double-stranded cDNA. Then, perform end repair, dA-tailing, and ligation of indexed sequencing adapters to the cDNA fragments. Amplify the adapter-ligated library via a limited-cycle PCR to enrich for properly constructed fragments. Clean up the final product using a bead-based purification system to select for the correct insert size. Finally, validate the library's concentration and size distribution by fluorometry and bioanalyzer before pooling and sequencing.

value: Human small cell lung cancer cells

value: DMSO


title: Single-cell RNA-seq day3 cell7


title: Single-cell RNA-seq day3 cell8


title: Single-cell RNA-seq day3 cell6


title: CTR_3

value: Control


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 3, tech rep 1


title: Single-cell RNA-seq day3 cell12


title: CTR_1


title: heatshock1


title: CTR_2


title: osteosarcoma cell line, control #2

description: Library name: 143B_Parental_2


title: DMSO, Input, rep1

description: Library name: DMSO-1.Input


title: DMSO, IP, rep1

description: Library name: DMSO-1.IP


title: FG4592_1

value: FG4592 induced 12 hours


title: Control Morpholino injected animal caps, NF16, biol rep 3, tech rep 2

value: Control morpholino injected


title: Control Morpholino injected animal caps, NF16, biol rep 3, tech rep 1


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 2, tech rep 2


title: H2O2_3

value: H2O2 induced for 4 hours


title: H2O2_2


title: Control Morpholino injected animal caps, NF16, biol rep 2, tech rep 2


title: Single-cell RNA-seq day3 cell5


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 2, tech rep 1


title: Single-cell RNA-seq day3 cell1


title: Single-cell RNA-seq day3 cell4


title: FB23-2, IP, rep1

description: Library name: FB23-2-1.IP


title: DMSO, Input, rep3

description: Library name: DMSO-3.Input


title: Single-cell RNA-seq day2 cell94

value: OvSvK single-cell RNA-seq reprogramming day2


title: Control Morpholino injected animal caps, NF16, biol rep 2, tech rep 1


title: OE3 IP

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/).
Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome Homo sapiens (Version: v101). Peak calling and diff peak analysis were performed by R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
Assembly: Human hg38
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited excel file includes gene abundance for each sample
Library strategy: MeRIP-Seq

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.

treatment_protocol: HK2 cells were also transfected with YTHDF1-expressing plasmids using FuGENE® HD Transfection Reagent.

tag: fraction

value: IP

value: YTHDF1 overexpression


title: DMSO, IP, rep3

description: Library name: DMSO-3.IP


title: RIP_Input

data_processing:
Sequence and filtering of Clean Reads. A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
Alignment with Reference Genome. We aligned reads of all samples to the human reference genome using HISAT2 package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
Quantification of Gene Abundance. The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Differentially expressed genes (DEGs) Analysis. Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Human hg38
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited excel file includes gene abundance for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The enriched RNA was divided into fragments by Fragmentation Buffer. Using the fragment mRNA as template, a cDNA strand was synthesized by six-base random primers, and then a two-strand cDNA was synthesized by adding buffer, dNTPs and DNA polymerase I. The eluted and purified double-stranded cDNA was then treated with terminal repair, base A and sequencing joint. Magnetic beads were used to recover the target size fragments and PCR amplification was performed. The constructed library was inspected by agarose electrophoresis. Qubit 2.0 was used to quantify the library and determine whether the concentration of the library was suitable for the computer. After qualified library quality, different libraries were sequenced on Illumina sequencer according to the requirements of effective concentration and target data volume.

value: HK2 cell

value: renal tubular epithelial cells

value: Flag-tag YTHDF1 overexpression


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 2, tech rep 3

value: animal cap


title: Single-cell RNA-seq day3 cell2


title: RIP_IP

value: RIP antibody:Flag antibody


title: FB23-2, Input, rep1

description: Library name: FB23-2-1.Input


title: DMSO, IP, rep2

description: Library name: DMSO-2.IP


title: OE2 IP


title: Single-cell RNA-seq day3 cell3


title: H2O2_1

value: WT


title: FB23-2, Input, rep3

description: Library name: FB23-2-3.Input


title: FB23-2, IP, rep2

description: Library name: FB23-2-2.IP


title: OE1 IP


title: FB23-2, Input, rep2

description: Library name: FB23-2-2.Input


title: Single-cell RNA-seq day2 cell93

value: Mouse embryonic fibroblasts reprgramming cells


title: Single-cell RNA-seq day2 cell92


title: NC3 IP


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 1, tech rep 1

value: Suv4-20h1 morpholino injected


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 1, tech rep 2


title: Control Morpholino injected animal caps, NF16, biol rep 1, tech rep 2


title: NC1 IP


title: Single-cell RNA-seq day2 cell90


title: healthy donor 3 bulk RNA-seq

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave. N.

department: Immunotherapy Integrated Research Center

institute: Fred Hutchinson Cancer Center

description:
Library name: HC-3
SmartSeq2

data_processing:
To match the processing of the whole-genome sequencing datasets, droplet-based sequencing data from patient samples were realigned and quantified against the GRCh37 human reference genome using the Cell Ranger Single-Cell Software Suite (version 2.0). The patient origin of each barcoded cell was then determined using the tool demuxlet. In brief, demuxlet can be used to deconvolute droplet-based scRNA-seq experiments in which cells are pooled from multiple genetically distinct individuals. Given a set of genotypes corresponding to these individuals, demuxlet infers the most likely genetic identity of each droplet by estimating the likelihood of observing scRNA-seq reads from the droplet overlapping known single nucleotide polymorphisms. Demuxlet inferred the identities of cells in this study by analyzing each Cell Ranger-aligned BAM file from patient samples in conjunction with a VCF file, containing the high-quality RNA-sequence variant calls from the corresponding patient. Each droplet was assigned by patient identification or unknown in origin (ambiguous or a potential doublet), and these identities were then linked with the transcriptome-based cell clustering data to confirm the patient identity of each annotated cell type.
Assembly: GRCh37/hg38
Supplementary files format and content: tab-delimited files containing cell barcode whitelist calls from demuxlet output

source_name: PBMC

extract_protocol:
For bulk RNA-sequencing, PBMCs from renal cell carcinoma and healthy patients were isolated and prepared as described above. Once resuspended, 150,000 cells were aliquoted. From these cells, RNA was extracted using the Invitrogen RNAqueous-Micro Total RNA Isolation Kit (#AM1931), and reverse transcription and tagmentation were conducted according to Picelli et al. using the SmartSeq2 protocol.
For bulk RNA-sequencing, after cDNA synthesis and tagmentation, the library was amplified with the Nextera XT DNA Sample Preparation Kit (#FC-131-1096) according to protocol. Samples were then sequenced on one lane of the Illumina Hiseq4000 with paired end 100-bp read length.

value: PBMC

value: healthy donor


title: FB23-2, IP, rep3

description: Library name: FB23-2-3.IP

value: Human small cell lung cancer cells


title: OE2 input

value: input


title: OE3 input


title: healthy donor 1 bulk RNA-seq

description:
Library name: HC-1
SmartSeq2


title: Control Morpholino injected animal caps, NF16, biol rep 1, tech rep 1

value: Control morpholino injected


title: healthy donor 4 bulk RNA-seq

description:
Library name: HC-4
SmartSeq2


title: healthy donor 2 bulk RNA-seq

description:
Library name: HC-2
SmartSeq2


title: Control Morpholino + MCI-hGR injected animal cap, with dexamethasone, NF16, biol rep 3

data_processing:
Expression quantitation with kallisto (version 0.48)  -b 30
Assembly: XENLA 10.1
Supplementary files format and content: kallisto abundances with est_counts and TPM values

extract_protocol:
RNA was harvested using the Rneasy Mini Kit with On column DNAse digestion. PolyA(+) mRNA was selected using NEBNext®Poly(A) Magnetic Isolation Module
RNA libraries for RNA-seq were prepared using the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs). NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) were used for sample indexing.

treatment_protocol: Xenopus laevis embryos were injected in both cells of the 2-cell stage with morpholino alone or in conjunction with mRNA. MCI-hGR injected animal caps were induced at NF11 with 10µm dexamethasone.

tag: treatment 2

value: MCI-hGR injected

tag: treatment 3

value: Dexamethasone induced


title: Suv4-20h1 Morpholino + MCI-hGR injected animal cap, with dexamethasone, NF16, biol rep 3

value: Suv4-20h2 morpholino injected


title: Single-cell RNA-seq day2 cell88

value: OvSvK single-cell RNA-seq reprogramming day2


title: Single-cell RNA-seq day2 cell89


title: OE1 input

value: HK2 cell

value: YTHDF1 overexpression


title: Suv4-20h1 Morpholino injected animal caps, NF16, biol rep 1, tech rep 3


title: Single-cell RNA-seq day2 cell86


title: RCC patient 3 bulk RNA-seq

description:
Library name: RCC-3
SmartSeq2

value: renal cell carcinoma


title: NC2 IP

value: IP

value: renal tubular epithelial cells


title: Control Morpholino injected animal cap, with dexamethasone, NF16, biol rep 3

value: animal cap


title: RCC patient 1 bulk RNA-seq

description:
Library name: RCC-1
SmartSeq2


title: Single-cell RNA-seq day2 cell87

value: Mouse embryonic fibroblasts reprgramming cells


title: Single-cell RNA-seq day2 cell91


title: Suv4-20h1 Morpholino + MCI-hGR injected animal cap, with dexamethasone, NF16, biol rep 2


title: Single-cell RNA-seq day2 cell84


title: NC3 input

value: WT


title: NC2 input


title: Control Morpholino injected animal cap, No dexamethasone, NF16, biol rep 3


title: Control Morpholino + MCI-hGR injected animal cap, with dexamethasone, NF16, biol rep 2


title: Single-cell RNA-seq day2 cell83


title: DE_sh_SETD7_I

first: shoupei

last: liu

address: 9th Floor, Building b, Huanyu 2nd Road, Haizhu District

department: Institute of Clinical Medicine

institute: Guangzhou First People's Hospital

description: Library name: Sample 16

data_processing:
Raw reads were trimmed with Trimmomatic (v0.39) to remove adapters and low-quality bases. Cleaned reads were aligned to the GRCh38 genome using STAR (v2.7.10a), and gene counts were quantified with featureCounts (v2.0.3) against GENCODE v44 annotation. Normalization was performed using DESeq2’s median-of-ratios method.
Assembly: All analyses were based on the GRCh38.p14 genome assembly with GENCODE v44 gene annotations.
Supplementary files format and content: gene_counts.csv (raw counts matrix, gene × sample)

source_name: embryonic stem cells

extract_protocol:
Total RNAs were extracted using Trizol reagent (Takara), and RNA-Seq was performed by Novogene (Beijing).
Sequencing libraries were constructed using Illumina mRNA-Seq Prep Kit. Fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 4000.

value: embryonic stem cells

value: SETD7 knockdown

value: Hepatic differentiation, Lentivirus infection


title: RCC patient 2 bulk RNA-seq

description:
Library name: RCC-2
SmartSeq2

value: PBMC


title: Control Morpholino injected animal cap, with dexamethasone, NF16, biol rep 2

value: Control morpholino injected


title: ductal_H3K27ac_1

city: San Antonio

first: Pei

state: TX

address: 7703 Floyd Curl Dr

department: Cell Systems & Anatomy

institute: University of Texas Health San Antonio

data_processing:
Genomic alignment to hg38 was performed with Bowtie 2.4.4. Fastq files were concatenated by lineage and antibody prior to subsequent analysis.
bigWigs were generated with deepTools 3.5.1 with bin size of 1.
peaks were called with MACS2 2.2.7.1 with default parameters
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak of concatenated sequences by lineage and by antibody
Library strategy: CUT&Tag

source_name: exocrine pancreas

extract_protocol:
Nuclear DNA was tagmented and extracted with Active Motif ATAC-seq kit.
Tagmented DNA was amplified by PCR and PCR products were subjected to size-selection with SPRI bead solution.

value: exocrine pancreas

value: ductal

tag: c&t antibody


title: DE_sh_SETD7_III

description: Library name: Sample 18


title: acinar_H3K27ac_2

value: acinar


title: Single-cell RNA-seq day2 cell85

value: OvSvK single-cell RNA-seq reprogramming day2


title: NC1 input

value: input

value: HK2 cell


title: Single-cell RNA-seq day2 cell81


title: DE_sh_SETD7_II

description: Library name: Sample 17


title: Control Morpholino injected animal cap, No dexamethasone, NF16, biol rep 2


title: Control Morpholino + MCI-hGR injected animal cap, with dexamethasone, NF16, biol rep 1

value: MCI-hGR injected

value: Dexamethasone induced


title: Single-cell RNA-seq day2 cell82


title: DE_sh_CON_II

description: Library name: Sample 14

value: VECTOR control


title: acinar_H3K27ac_1


title: Single-cell RNA-seq day2 cell80


title: Single-cell RNA-seq day2 cell79


title: DE_sh_CON_I

description: Library name: Sample 13


title: ductal_H3K4me1_3


title: ductal_H3K27ac_2


title: ductal_H3K4me1_2


title: DE_PFI2_2μM_II

description: Library name: Sample 11

value: Definitive endoderm differentiation


title: Control Morpholino injected animal cap, with dexamethasone, NF16, biol rep 1

value: animal cap


title: Suv4-20h1 Morpholino + MCI-hGR injected animal cap, with dexamethasone, NF16, biol rep 1

value: Suv4-20h1 morpholino injected


title: DE_PFI2_2μM_III

description: Library name: Sample 12

value: embryonic stem cells

value: WT


title: DE_sh_CON_III

description: Library name: Sample 15

value: Hepatic differentiation, Lentivirus infection


title: Suv4-20h2 Morpholino injected animal cap, NF16, biol rep 3

value: Suv4-20h2 morpholino injected


title: Single-cell RNA-seq day2 cell75

value: Mouse embryonic fibroblasts reprgramming cells


title: Control Morpholino injected animal cap, No dexamethasone, NF16, biol rep 1

value: Control morpholino injected


title: Control Morpholino injected animal cap, NF16, biol rep 3


title: DE_PFI2_2μM_I

description: Library name: Sample 10


title: Single-cell RNA-seq day2 cell74


title: Suv4-20h1 Morpholino injected animal cap, NF16, biol rep 3


title: Single-cell RNA-seq day2 cell76


title: ductal_H3K4me1_1

value: exocrine pancreas

value: ductal


title: DE_PFI2_CON_III

description: Library name: Sample 9


title: acinar_H3K4me1_1

value: acinar


title: DE_PFI2_CON_II

description: Library name: Sample 8


title: Single-cell RNA-seq day2 cell77

value: OvSvK single-cell RNA-seq reprogramming day2


title: Single-cell RNA-seq day2 cell78


title: acinar_H3K4me1_2


title: Suv4-20h1 Morpholino injected animal cap, NF16, biol rep 2


title: Single-cell RNA-seq day2 cell73


title: ductal_ATAC_3

data_processing:
Cutadapt 1.15 was used to trim tagmentation adapter from fastq reads. Trimmed fastq was aligned to hg38 with Bowtie 2.4.4.
bigWigs were generated with deepTools 3.5.1 with bin size of 1.
peaks were called with MACS2 2.2.7.1 with default parameters
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak


title: 3D_hDE_III

description: Library name: Sample 6


title: Control Morpholino injected animal cap, NF16, biol rep 2


title: ductal_ATAC_4


title: ductal_ATAC_2


title: Single-cell RNA-seq day2 cell71


title: acinar_H3K4me1_3


title: Single-cell RNA-seq day2 cell70


title: Single-cell RNA-seq day2 cell72


title: DE_PFI2_CON_I

description: Library name: Sample 7


title: Suv4-20h2 Morpholino injected animal cap, NF16, biol rep 2


title: ductal_ATAC_1


title: Suv4-20h1 Morpholino injected animal cap, NF16, biol rep 1


title: 3D_hDE_I

description: Library name: Sample 4


title: Single-cell RNA-seq day2 cell69


title: 3D_hDE_II

description: Library name: Sample 5


title: 3D_hESCs_I

description: Library name: Sample 1


title: Single-cell RNA-seq day2 cell68


title: acinar_ATAC_3


title: acinar_ATAC_4


title: Single-cell RNA-seq day2 cell67


title: acinar_ATAC_1


title: Suv4-20h2 Morpholino injected animal cap, NF16, biol rep 1


title: 3D_hESCs_II

description: Library name: Sample 2


title: Single-cell RNA-seq day2 cell65


title: HL60 small EV enriched glycoRNA, rep2

city: Thuwal

first: Jing

last: Kai

address: King Abdullah University of Science and Techonology

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

description:
Library name: HL60_sEV_rPAL_2
Column name in raw_count.tsv: HL_sEV_rPAL2

library_source: other

data_processing:
SOAPnuke was used to generate clean sequencing reads
Genome coordinate files for human (homo_sapiens.GRCh38.gff3) were downloaded from RNAcentral, and reference noncoding RNA sequences were extracted from the corresponding genome assembly, where RNAs belonging to the categories of long noncoding RNAs, piRNAs, and misc_RNAs sequences were removed from the reference database.
The final reference database was then used for mapping clean reads ≥15 nt using Bowtie2. Unmapped reads were subsequently aligned to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: tsv file includes raw counts of all sample

molecule: other

source_name: small extracellular vehicles

growth_protocol: For cell RNA and glycoRNA purification, the KG1a and HL60 cells were cultured in RPMI-1640 media with glutamine supplemented with 10% FBS and 1× penicillin-streptomycin. For EV collection, cells were cultured with the full media without FBS for two days before EV isolation.

extract_protocol:
Total RNA and enriched glycoRNAs were both extracted using RNAzol combined with Zymo column purification
Library preparation is performed using the MGIEasy Small RNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA is ligated 3’ and 5’ adaptors sequentially in two reaction systems for adaptor ligation. After adaptor ligation, RNA is reverse transcribed into cDNA and PCR amplified. The library is fragment size selected by polyacrylamide gel electrophoresis and subjected to quality control.

value: small extracellular vehicles

value: human acute myeloid leukemia cell line


title: acinar_ATAC_2


title: Control Morpholino injected animal cap, NF16, biol rep 1


title: CEBPB_OE_hEH_10d cells, II

description: Library name: Sample 18

value: CEBPB overexpression


title: Control diet, Ich infection 7

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: Z7

data_processing:
Adaptor sequences and low quality reads removed
Mapped to D. rerio genome (GRCz11_release100)
DEG determined using DESeq2
Assembly: GRCz11_release100
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Danio rerio

source_name: Gill

extract_protocol:
RNA was extracted from 37 fish gills using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich). This was done according to the manufacturer’s protocol for fibrous tissue preparation, except that the tissue was lysed by Bead Beating in a TissueLyser at 25Hz for 4 minutes.
standard Illumina

value: Gill


title: Control diet, Ich infection 8

description: Library name: Z9


title: HL60 small EV enriched glycoRNA, rep1

institute: King Abdullah University of Science and Techonology

description:
Library name: HL60_sEV_rPAL_1
Column name in raw_count.tsv: HL_sEV_rPAL1


title: Inulin diet, no infection 8

description: Library name: Z19


title: HL60 small EV total RNA, rep3

description:
Library name: HL60_sEV_total_3
Column name in raw_count.tsv: HL_sEV_to3


title: Control diet, Ich infection 9

description: Library name: Z13


title: HL60 small EV enriched glycoRNA, rep3

description:
Library name: HL60_sEV_rPAL_3
Column name in raw_count.tsv: HL_sEV_rPAL3


title: Inulin diet, no infection 9

description: Library name: Z21


title: 3D_hESCs_III

description: Library name: Sample 3

value: Definitive endoderm differentiation


title: PHH_24h cells, II

description: Library name: Sample 14

value: Hepatic differentiation

value: PHH_24h cells, II


title: VECTOR_hEH_10d cells, II

description: Library name: Sample 16

value: embryonic stem cells

value: VECTOR control


title: CEBPB_OE_hEH_10d cells, I

description: Library name: Sample 17

value: Hepatic differentiation, Lentivirus infection


title: Single-cell RNA-seq day2 cell66


title: Inulin diet, no infection 10

description: Library name: Z23


title: VECTOR_hEH_10d cells, I

description: Library name: Sample 15


title: Single-cell RNA-seq day2 cell64


title: Single-cell RNA-seq day2 cell62


title: Single-cell RNA-seq day2 cell63


title: PHH_24h cells, I

description: Library name: Sample 13

value: WT

value: PHH_24h cells, I


title: hEH_10d cells, II

description: Library name: Sample 12

value: hEH_10d cells, II


title: HL60 large EV enriched glycoRNA, rep3

description:
Library name: HL60_lEV_rPAL_3
Column name in raw_count.tsv: HL_lEV_rPAL3

source_name: large extracellular vehicles

value: large extracellular vehicles


title: Inulin diet, Ich infection 9

description: Library name: Z40


title: Control diet, Ich infection 6

description: Library name: Z37


title: HL60 small EV total RNA, rep1

description:
Library name: HL60_sEV_total_1
Column name in raw_count.tsv: HL_sEV_to1


title: Single-cell RNA-seq day2 cell59

value: Mouse embryonic fibroblasts reprgramming cells


title: Control diet, Ich infection 5

description: Library name: Z36


title: Single-cell RNA-seq day2 cell58


title: Single-cell RNA-seq day2 cell57


title: Inulin diet, no infection 7

description: Library name: Z38


title: Control diet, no infection 7

description: Library name: Z32


title: HL60 large EV total RNA, rep3

description:
Library name: HL60_lEV_total_3
Column name in raw_count.tsv: HL_lEV_to3


title: HL60 small EV total RNA, rep2

description:
Library name: HL60_sEV_total_2
Column name in raw_count.tsv: HL_sEV_to2


title: Single-cell RNA-seq day2 cell61


title: HL60 large EV total RNA, rep1

description:
Library name: HL60_lEV_total_1
Column name in raw_count.tsv: HL_lEV_to1


title: HL60 large EV enriched glycoRNA, rep2

description:
Library name: HL60_lEV_rPAL_2
Column name in raw_count.tsv: HL_lEV_rPAL2


title: Single-cell RNA-seq day2 cell54


title: Single-cell RNA-seq day2 cell60


title: Control diet, no infection 8

description: Library name: Z33


title: HL60 cell rPAL enriched glycoRNA, rep3

description:
Library name: HL60_cell_rPAL_3
Column name in raw_count.tsv: HL_ce_rPAL3

source_name: cell

value: cell


title: hEH_10d cells, I

description: Library name: Sample 11

value: hEH_10d cells, I


title: hEH_2d cells, I

description: Library name: Sample 7

value: hEH_2d cells, I


title: Inulin diet, Ich infection 7

description: Library name: Z30


title: hEH_6d cells, II

description: Library name: Sample 10

value: hEH_6d cells, II


title: Single-cell RNA-seq day2 cell56

value: OvSvK single-cell RNA-seq reprogramming day2


title: HPC_14d cells, I

description: Library name: Sample 5

value: HPC_14d cells, I


title: Single-cell RNA-seq day2 cell53


title: hEH_6d cells, I

description: Library name: Sample 9

value: hEH_6d cells, I


title: Control diet, no infection 9

description: Library name: Z35

value: Gill


title: Inulin diet, Ich infection 8

description: Library name: Z31


title: Inulin diet, Ich infection 5

description: Library name: Z28


title: HPC_12d cells, II

description: Library name: Sample 4

value: Hepatic differentiation

value: HPC_12d cells, II


title: Single-cell RNA-seq day2 cell50


title: Inulin diet, Ich infection 3

description: Library name: Z26


title: HL60 cell total RNA, rep2

description:
Library name: HL60_cell_total_2
Column name in raw_count.tsv: HL60_to_2A

value: human acute myeloid leukemia cell line


title: Inulin diet, Ich infection 4

description: Library name: Z27


title: Single-cell RNA-seq day2 cell55


title: HPC_8d cells, I

description: Library name: Sample 1

value: embryonic stem cells

value: HPC_8d cells, I


title: HPC_8d cells, II

description: Library name: Sample 2

value: WT

value: HPC_8d cells, II


title: HL60 cell total RNA, rep1

description:
Library name: HL60_cell_total_1
Column name in raw_count.tsv: HL60_to_1A


title: Single-cell RNA-seq day2 cell49


title: HL60 large EV enriched glycoRNA, rep1

description:
Library name: HL60_lEV_rPAL_1
Column name in raw_count.tsv: HL_lEV_rPAL1

value: large extracellular vehicles


title: Inulin diet, Ich infection 1

description: Library name: Z24


title: hEH_2d cells, II

description: Library name: Sample 8

value: hEH_2d cells, II


title: Single-cell RNA-seq day2 cell47

value: Mouse embryonic fibroblasts reprgramming cells


title: HL60 large EV total RNA, rep2

description:
Library name: HL60_lEV_total_2
Column name in raw_count.tsv: HL_lEV_to2


title: Inulin diet, no infection 6

description: Library name: Z22


title: HPC_14d cells, II

description: Library name: Sample 6

value: HPC_14d cells, II


title: Single-cell RNA-seq day2 cell52


title: KG1a small EV enriched glycoRNA, rep1

description:
Library name: KG1a_sEV_rPAL_1
Column name in raw_count.tsv: KG_sEV_rPAL1

value: small extracellular vehicles


title: KG1a small EV total RNA, rep3

description:
Library name: KG1a_sEV_total_3
Column name in raw_count.tsv: KG_sEV_to3


title: HL60 cell rPAL enriched glycoRNA, rep1

description:
Library name: HL60_cell_rPAL_1
Column name in raw_count.tsv: HL_ce_rPAL1

value: cell


title: HL60 cell rPAL enriched glycoRNA, rep2

description:
Library name: HL60_cell_rPAL_2
Column name in raw_count.tsv: HL_ce_rPAL2


title: Single-cell RNA-seq day2 cell51

value: OvSvK single-cell RNA-seq reprogramming day2


title: Inulin diet, Ich infection 6

description: Library name: Z29


title: HPC_12d cells, I

description: Library name: Sample 3

value: HPC_12d cells, I


title: Single-cell RNA-seq day2 cell43


title: Inulin diet, Ich infection 2

description: Library name: Z25


title: Single-cell RNA-seq day2 cell42


title: KG1a small EV enriched glycoRNA, rep3

description:
Library name: KG1a_sEV_rPAL_3
Column name in raw_count.tsv: KG_sEV_rPAL3


title: HL60 cell total RNA, rep3

description:
Library name: HL60_cell_total_3
Column name in raw_count.tsv: HL60_to_3A


title: KG1a small EV total RNA, rep1

description:
Library name: KG1a_sEV_total_1
Column name in raw_count.tsv: KG_sEV_to1


title: Inulin diet, no infection 1

description: Library name: Z15


title: Single-cell RNA-seq day2 cell41


title: KG1a small EV enriched glycoRNA, rep2

description:
Library name: KG1a_sEV_rPAL_2
Column name in raw_count.tsv: KG_sEV_rPAL2


title: Single-cell RNA-seq day2 cell48


title: Control diet, Ich infection 4

description: Library name: Z14


title: KG1a large EV enriched glycoRNA, rep3

description:
Library name: KG1a_lEV_rPAL_3
Column name in raw_count.tsv: KG_lEV_rPAL3


title: Inulin diet, no infection 5

description: Library name: Z20


title: Single-cell RNA-seq day2 cell44


title: Single-cell RNA-seq day2 cell46


title: SK470, EtOH-ATAC

city: Chicago

first: Sonia

middle: S

last: Kupfer

state: IL

department: Human Genetics

institute: University of Chicago

description: Library name: B3SK47

data_processing:
RNA-seq sequence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2 (v1.30.1) after first filtering for protein coding biotype and using DESeq's independent filtering.
ATAC-seq sequence alignment was performed with bwa (v0.7.17). Read filtering was performed with samtools (v1.10) with retained reads having mapping quality >=10. PCR duplicates were also removed using samtools.
Peak calling on mapped ATAC-seq sequences was performed with MACS2 (v.2.1.0).
Assembly: transcriptome reference was generated from the 1000genomes Phase2 Reference Genome Sequence (hs37d5) and transcript annotations from the Gencode comprehensive gene annotation GTF  (Release 29). ATAC-seq sequences were also mapped to hs37d5.
Supplementary files format and content: RSEM output files of transcript level abundances in tab-delimited plain text format
Supplementary files format and content: ATAC-seq alignment files are in compressed BAM format. MACS2 output peak files are in the narrowPeak plain text format.

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. ATAC-seq: cells were treated using the Omni-ATAC protocol with some modifications. Briefly, cells were treated with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then suspended in the transposition reaction mix (50% TD Tagment DNA buffer, 5% TDE1 Tagment DNA Enzyme, 33% PBS) for 30 minutes.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina and sequenced using an Illumina NovaSeq6000 (paired end 100 bp). ATAC-seq libraries were prepared using the Nextera Index kit (Illumina #15055289) and were sequenced on the Hi-Seq 4000 platform (50 bp single end reads).

treatment_protocol: Organoids were treated with either 100nm/L 1α,25-dihydroxyvitamin D or vehicle control (0.1% ethanol) for 4 hours for ATAC-seq and 6 hours for RNA-seq.

value: colonic organoid

tag: Sex

value: M

tag: ancestry

value: EA

value: EtOH


title: SK470, VD-ATAC

description: Library name: B3SK48

value: VD


title: KG1a small EV total RNA, rep2

description:
Library name: KG1a_sEV_total_2
Column name in raw_count.tsv: KG_sEV_to2

value: human acute myeloid leukemia cell line


title: Control diet, Ich infection 3

description: Library name: Z12

value: Gill


title: SK302, VD-ATAC

description: Library name: B3SK08

value: F

value: AA


title: SK418, VD-ATAC

description: Library name: B3SK32


title: SK418, EtOH-ATAC

description: Library name: B3SK31


title: KG1a large EV enriched glycoRNA, rep2

description:
Library name: KG1a_lEV_rPAL_2
Column name in raw_count.tsv: KG_lEV_rPAL2

value: large extracellular vehicles

value: WT


title: Control diet, Ich infection 2

description: Library name: Z11


title: SK426, EtOH-ATAC

description: Library name: B3SK35


title: SK420, VD-ATAC

description: Library name: B1SK24


title: Inulin diet, no infection 2

description: Library name: Z16


title: Control diet, Ich infection 1

description: Library name: Z8


title: KG1a large EV total RNA, rep2

description:
Library name: KG1a_lEV_total_2
Column name in raw_count.tsv: KG_lEV_to2


title: Single-cell RNA-seq day2 cell37

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample

value: Mouse embryonic fibroblasts reprgramming cells


title: SK406, VD-ATAC

description: Library name: B3SK30


title: Control diet, no infection 6

description: Library name: Z6


title: Inulin diet, no infection 4

description: Library name: Z18


title: SK300, VD-ATAC

description: Library name: B1SK22


title: KG1a large EV total RNA, rep1

description:
Library name: KG1a_lEV_total_1
Column name in raw_count.tsv: KG_lEV_to1


title: Single-cell RNA-seq day2 cell38


title: Single-cell RNA-seq day2 cell40


title: SK406, EtOH-ATAC

description: Library name: B3SK29


title: KG1a large EV enriched glycoRNA, rep1

description:
Library name: KG1a_lEV_rPAL_1
Column name in raw_count.tsv: KG_lEV_rPAL1


title: Inulin diet, no infection 3

description: Library name: Z17


title: Single-cell RNA-seq day2 cell34


title: Single-cell RNA-seq day2 cell39


title: KG1a cell rPAL enriched glycoRNA, rep3

description:
Library name: KG1a_cell_rPAL_3
Column name in raw_count.tsv: KG_ce_rPAL3


title: Single-cell RNA-seq day2 cell33


title: Control diet, no infection 3

description: Library name: Z3


title: Control diet, no infection 2

description: Library name: Z2


title: SK426, VD-ATAC

description: Library name: B3SK36


title: SK300, EtOH-ATAC

description: Library name: B1SK21


title: KG1a cell rPAL enriched glycoRNA, rep2

description:
Library name: KG1a_cell_rPAL_2
Column name in raw_count.tsv: KG_ce_rPAL2


title: KG1a large EV total RNA, rep3

description:
Library name: KG1a_lEV_total_3
Column name in raw_count.tsv: KG_lEV_to3


title: Single-cell RNA-seq day2 cell45


title: SK302, EtOH-ATAC

description: Library name: B3SK07


title: SK420, EtOH-ATAC

description: Library name: B1SK23


title: Single-cell RNA-seq day2 cell32


title: SK250, VD-ATAC

description: Library name: B1SK18


title: Control diet, no infection 1

description: Library name: Z1


title: Control diet, no infection 5

description: Library name: Z5


title: Single-cell RNA-seq day2 cell36


title: SK244, VD-ATAC

description: Library name: B1SK16


title: KG1a cell rPAL enriched glycoRNA, rep4

description:
Library name: KG1a_cell_rPAL_4
Column name in raw_count.tsv: KG_ce_rPAL4


title: Single-cell RNA-seq day2 cell31


title: SR006552_sham_7248_Male_26

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

description:
Library name: 7248
10xV3.1 snRNA-seq

data_processing:
Count matrices were created with cellranger-9.0.0 and mm10-2020-A version of transcriptome
Assembly: mm10-2020-A
Supplementary files format and content: Processed files include barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz

extract_protocol:
Single nuclear suspensions were produced from murine sham and SBR liver samples using modifications of a previously published protocol by Nadelmann et al. as detailed below, with modifications made to utilize our available tissue lysis equipment and best homogenize our tissue samples while preserving nuclear integrity. Liver samples frozen in RNAlater (Thermo Fisher Scientific, cat. no. AM7021) were removed from the -80°C freezer and thawed on ice. Tissue homogenizer block (ServiceBio; Hubei, China) was placed in -20°C freezer to be cooled for tissue processing. Four working solutions were made to use in our protocol, according to the recipes published by Nadelmann et al; nuclei isolation buffer 1 (NIM1), nuclei isolation buffer 2 (NIM2), homogenization buffer (HB), and storage buffer (SB). Thawed liver samples were kept on ice throughout the nuclei preparation. RNAlater was removed from tubes by pipette, and 1mL of HB was added to each sample tube. The cooled tissue homogenizer block was loaded with sample tubes and into the tissue lysis machine (ServiceBio; Hubei, China), which was run for one minute at 40 Hz. Each sample was assessed for adequate lysis and homogenization. Samples were placed on ice to allow for further lysis in HB for 5 minutes. Homogenized tissue was each filtered through 40-m cell strainer into 50mL tubes, then filtrates were transferred to 1.5mL Eppendorf tubes and centrifuged at 4°C for 2min at 2000g. Supernatant fluid was removed via pipette and the nuclei pellet was resuspended with 500 L of SB. Suspension was transferred and filtered into a fluorescence activated cell sorting (FACS) tube (35 um filter). An unstained, negative control was prepared by pipetting 100 L of filtered sample into a separate FACS sorting tube. 4',6-diamidino-2-phenylindole (DAPI) was added to the remaining solution, mixed by pipette, and placed on ice for 15min to allow for sufficient staining. 150 L of SB was pipetted individually into new 1.5mL nonstick RNase-free microcentrifuge tubes and placed on ice, to collect nuclei samples after FACS sorting. Samples were sorted on an Aria-3 cell sorter (BD biosciences; Franklin Lakes, NJ) into new 1.5mL nonstick RNase-free microcentrifuge tubes containing 150 L of SB and centrifuged at 4°C for 5min at 500g. Supernatant was removed slowly without disturbing nuclei. Nuclei pellet was resuspended with a volume of SB according to sort count from FACS to achieve a concentration of approximately 1.0 x 10^6 nuclei for each sample. Samples were centrifuged afterwards at 4C at 500g for 5 minutes, then resuspended in SB. For each sample, 2L of the nuclei suspension was mixed with 18uL Trypan blue (1:1) dilution in a new 1.5mL non-stick RNase-free microcentrifuge tube. 10uL of each sample was loaded into a Countess cell counting chamber slide alongside 10uL of unstained samples into adjacent wells on the slide. Nuclei were counted to confirm concentration between 8 x 10^5 and 1.2 x 10^6. Wells loaded without Trypan blue staining were visualized under microscopy to confirm nuclei presence without debris and intact nuclear morphology.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeqX instrument.  Normalized libraries were sequenced on a NovaSeqX Flow Cell using the 151x10x10x151 sequencing recipe according to manufacturer's protocol.  Read 1 was trimmed to the 10x Genomics recommendation of 28bp. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

treatment_protocol: All animal studies were approved by Washington University in St. Louis Institutional Animal Care and Use Committee protocol  #(23-0421). All experiments were performed in accordance with relevant guidelines and regulations, including the ARRIVE guidelines (https://arriveguidelines.org/). 8-week-old male C57BL/6J mice (purchased from The Jackson Laboratory; Bar Harbor, ME) received sham or 75% proximal small bowel resection (SBR). Mice were randomized into 2-, 5-, 10-, 26-, and 52-week cohorts. The sham operation involves a transection of the small bowel 6 cm proximal to the cecum with primary end-to-end anastomosis with 9-0 nylon sutures placed in an interrupted fashion. For the 75% SBR operations, the small bowel is transected at two points: 1-2cm distal to the ligament of Treitz and 6cm proximal to the cecum. The intervening mesentery is tied off and the small bowel is resected. An end-to-end primary anastomosis is completed with 9-0 nylon sutures placed in an interrupted fashion. Postoperative care included no food for 24 hours and 1 week of incubator housing. All mice were fed a liquid enteral diet (LD101 #0007551, Test Diet; Richmond, IN) ad lib.

value: Liver

tag: strain

value: sham


title: SK242, VD-ATAC

description: Library name: B1SK14


title: SK242, EtOH-ATAC

description: Library name: B1SK13


title: SR006552_sbr_7260_Male_26

description:
Library name: 7260
10xV3.1 snRNA-seq

value: sbr


title: SK238, VD-ATAC

description: Library name: B1SK12


title: SK250, EtOH-ATAC

description: Library name: B1SK17


title: Single-cell RNA-seq day2 cell35

extract_protocol:
Cells were collected by trypsin digestion. Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

value: OvSvK single-cell RNA-seq reprogramming day2


title: KG1a cell rPAL enriched glycoRNA, rep1

description:
Library name: KG1a_cell_rPAL_1
Column name in raw_count.tsv: KG_ce_rPAL1

value: cell


title: shDDX24-2

city: Taoyuan

first: Ming-Chih

last: Lai

address: No. 259, Wenhua 1st Road, Guishan District, Taoyuan City 333, Taiwan (R.O.C.)

department: Department of Biomedical Sciences

country: Taiwan

institute: Chang Gung University

description: Library name: Sample 3

data_processing:
Paried-end 100 bp reads were sequenced utilizing the DNBSEQ-G400 sequencing instrument carried out by Helix Technology Co., Ltd. Raw FASTQ reads were aligned to the human reference genome (GRCh38, Ensembl) using STAR (v2.7.3a) with the two-pass mapping strategy. Gene-level read counts were quantified using GENCODE v32 annotation and normalized using DESeq2 (v1.26).
Assembly: hg38
Supplementary files format and content: genes.raw.read.counts.xlsx

source_name: embryonic kidneys

growth_protocol: Cells were cultured in high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin, and 2 mM L-glutamine. The cultures were maintained at 37˚C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cells using TRIzol Reagent (Thermo Fisher Scientific) according to the manufacturer's instructions. The TURBO DNA-free Kit (Thermo Fisher Scientific) was utilized to remove genomic DNA. The RNA was then dissolved in 20-30 μL of DEPC-treated water, and its concentration was measured using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Total RNA was subjected to mRNA enrichment using poly(A) selection. RNA sequencing libraries were prepared using the MGIEasy RNA Library Prep Kit following the manufacturer’s protocol. Double-stranded cDNA was synthesized, followed by end repair, A-tailing, adapter ligation, and PCR amplification. Subsequently, the amplified libraries were circularized to generate DNA nanoballs, which were then loaded onto the DNBSEQ-G400 sequencing platform. Sequencing was performed using 100 bp paired-end reads.

treatment_protocol: The pLKO.1 vectors expressing short hairpin RNAs (shRNAs) included shDDX24-1 (TRCN0000312585, Taiwan) and shDDX24-2 (TRCN0000312527, Taiwan). Lentiviral particles were generated by transfecting HEK293T cells with a packaging plasmid (psPAX2), an envelope plasmid (pMD2.G), and a pLKO.1-based shRNA vector. To knockdown endogenous DDX24, cells were transduced with the shRNA-expressing lentivirus at a multiplicity of infection (MOI) of 5 particles/cell in DMEM medium supplemented with 8 μg/mL polybrene at 37˚C and 5% CO2.

value: embryonic kidneys

value: embryonic kidney cells

value: DDX24 knockdown

value: lentiviral infection

tag: time

value: 72 hr


title: Single-cell RNA-seq day2 cell27


title: Control diet, no infection 4

description: Library name: Z4


title: Single-cell RNA-seq day2 cell30


title: SR006552_sham_7249_Male_26

description:
Library name: 7249
10xV3.1 snRNA-seq


title: KG1a cell total RNA, rep4

description:
Library name: KG1a_cell_total_4
Column name in raw_count.tsv: KG1A_to_4A

value: human acute myeloid leukemia cell line


title: SR006552_sbr_7254_Male_26

description:
Library name: 7254
10xV3.1 snRNA-seq


title: SK238, EtOH-ATAC

description: Library name: B1SK11

value: colonic organoid

value: M

value: EtOH


title: KG1a cell total RNA, rep2

description:
Library name: KG1a_cell_total_2
Column name in raw_count.tsv: KG1A_to_2A


title: SK236, VD-ATAC

description: Library name: B1SK10

value: F

value: AA

value: VD


title: Single-cell RNA-seq day2 cell28

value: Mouse embryonic fibroblasts reprgramming cells


title: SR006552_sbr_7259_Male_26

description:
Library name: 7259
10xV3.1 snRNA-seq

value: Liver


title: SR006342_sham_7435_Male_10

description:
Library name: 7435
10xV3.1 snRNA-seq

value: sham


title: KG1a cell total RNA, rep3

description:
Library name: KG1a_cell_total_3
Column name in raw_count.tsv: KG1A_to_3A

value: WT


title: SK244, EtOH-ATAC

description: Library name: B1SK15


title: SR006342_sbr_7548_Male_10

description:
Library name: 7548
10xV3.1 snRNA-seq

value: sbr


title: Single-cell RNA-seq day2 cell23

value: OvSvK single-cell RNA-seq reprogramming day2


title: KG1a cell total RNA, rep1

description:
Library name: KG1a_cell_total_1
Column name in raw_count.tsv: KG1A_to_1A

value: cell


title: SK230, EtOH-ATAC

description: Library name: B1SK05

value: EA


title: SR006342_sham_7434_Male_10

description:
Library name: 7434
10xV3.1 snRNA-seq


title: SR006342_sbr_7452_Male_10

description:
Library name: 7452
10xV3.1 snRNA-seq


title: SK228, VD-ATAC

description: Library name: B1SK04


title: SK230, VD-ATAC

description: Library name: B1SK06


title: Single-cell RNA-seq day2 cell29


title: Single-cell RNA-seq day2 cell26


title: SK222, VD-ATAC

description: Library name: B1SK02


title: pLKO.1

description: Library name: Sample 1

value: embryonic kidneys

value: embryonic kidney cells

value: lentiviral infection


title: shDDX24-1

description: Library name: Sample 2

value: DDX24 knockdown

value: 72 hr


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, quercetin treated, rep1

city: Gebze

first: Tunahan

last: Cakir

state: Kocaeli

address: Gebze, Kocaeli, Turkey

department: Department of Bioengineering

country: Turkey

institute: Gebze Technical University

description:
Library name: Sample 17
17-V300071532_L02_101

data_processing:
Raw reads in the sequenced RNA-Seq data were trimmed to remove low-quality bases using the trimmomatic (v0.38) tool with options trailing: 20 and  slidingwindow: 5:20. Additionally, reads shorter than 20 bases were removed from the data using the same tool.
Transcript abundances were calculated using the pseudo-alignment tool Kallisto (v0.46.2). The index file for Kallisto was built from the transcript sequences of GrCh38, available from the Ensembl database through GRCh38.cdna.all.fa (release-94).
The transcript-level estimated counts were converted into gene-level counts using the tximport R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts of the genes in each sample

source_name: LUHMES

extract_protocol:
InnuPREP RNA Mini Kit 2.0 was used for RNA isolation as per manufacturer’s instructions.
RNA libraries were prepeared using MGIEasy RNA Library Prep set as per manufacturer's instructions

value: LUHMES

value: human mesencephalic cells

value: alpha-synuclein overexpressed

value: 6-OHDA, quercetin


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rutin treated, rep1

description:
Library name: Sample 20
22-V300071532_L02_122

value: 6-OHDA, rutin


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rutin treated, rep3

description:
Library name: Sample 22
24-V300071532_L02_124


title: Single-cell RNA-seq day2 cell19

value: Mouse embryonic fibroblasts reprgramming cells


title: Single-cell RNA-seq day2 cell21


title: SK236, EtOH-ATAC

description: Library name: B1SK09

value: colonic organoid

value: F

value: AA

value: EtOH


title: Single-cell RNA-seq day2 cell20

value: OvSvK single-cell RNA-seq reprogramming day2


title: Single-cell RNA-seq day2 cell24


title: Single-cell RNA-seq day2 cell25


title: d25A99, mESC, Mouse

city: Beijing

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

description:
Library name: d25A99
d25

data_processing:
Samples with more than 50,000 remaining contacts were retained for downstream analysis. For diploid samples, the haplotype of contacts was phased according to SNP sites. Each chromosome in each sample was treated as a polymer chain, evenly divided into 20kb sections, with each section treated as a particle of the polymer chain. The contacts of the sample were used as restraints to search for the optimal x, y, z spatial coordinates of particles using the Force-Directed Graph (FDG) algorithm implemented by “hickit”. To assess the quality of the chromatin 3D structure reconstruction, we generated five replicates using different random seeds and calculated the median RMSD for each combination of three replicates. If the median RMSD of the combination with the lowest value was less than 1.5, the first replicate in that combination was used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: 3dg file: each line sequentially listing the chromosome name, start position, x, y, and z coordinates, delimited by tab characters
Supplementary files format and content: dip pairs file: A tab-separated file recording allele-specific contacts that conforms to 4DN Consortium standards with chromosomes
Supplementary files format and content: pairs file: A tab-separated file recording contacts that conforms to 4DN Consortium standards with chromosomes

source_name: mESC

extract_protocol:
We utilized a female mouse embryonic stem cell (mESC) line derived from blastocysts at embryonic day 3.5 (E3.5) from crossbred embryos (female C57BL/6J × male CAST/EiJ). The procedures for derivation and culturing followed the methods provided by Arenas et al. (2006). Cells were cultured on flasks coated with 0.1% gelatin in an ES cell medium containing serum. The medium composition included DMEM (Gibco, 10829018), 15% ESC-grade fetal bovine serum (FBS) (VivaCell, C04002-100), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% P/S (ThermoFisher, 10378016), NEAA (Sigma, M7145), L-Glutamine (Gibco, 25030-081), nucleotides (Millipore, ES-008-D), and 1000 U/ml leukemia inhibitory factor (LIF) (PeproTech, AF-250-02-25UG). Additionally, the medium was supplemented with 2i: 3 μM Gsk3 inhibitor CT99021 (Selleck, S1263) and 1 μM MEK inhibitor PD0325901 (Selleck, S1036). Differentiation was initiated by withdrawing 2i/LIF in DMEM supplemented with 10% FBS, 1% P/S, NEAA, L-Glutamine, nucleotides, and 0.1 mM β-mercaptoethanol. The cells were plated at a density of 1.5 × 10⁴ cells/cm² on 6 well cell culture plates coated with 10 μg/ml fibronectin (GLPBIO, GP23499).
The single-cell preamplification product was diluted to 5ng/ul and 2 μL of each diluted sample was transposed by the addition of 3 μL Transposition Mixture (1 μL 5 X TTBL, 0.25 μL TTE Mix V50 (Vayme TD501), 1.75 μL water) and incubated at 55 °C for 10 min. Transposition was stopped by adding 1.25 μL 0.2% SDS and then the plate 40 was incubated at room temperature for 10 min. For a slight enrichment of cDNA reads, 2 μL 5 μM i5 unique dual (UD) index and 11.75 ul PCR mixture (4 μL 5X KAPA HiFi GC Buffer, 0.6 μL 10 mM dNTP, 0.2 μL 50 μM RNA-P7 primer, 0.4 μL KAPA HiFi DNA Polymerase (KAPA KK2102) and 6.55 μL water) were added to each well and incubated with the following program: Step 1: 72 °C × 3 min; Step 2: 98 °C × 30 s; Step 3: 98 °C × 15 s, 60 °C × 30 s, 72 °C.

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: Single-cell RNA-seq day2 cell17

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

source_name: Mouse embryonic fibroblasts reprgramming cells


title: SR006552_sbr_7251_Male_26

description:
Library name: 7251
10xV3.1 snRNA-seq

source_name: Liver

value: Liver

value: sbr


title: d25A97, d25A98, mESC, Mouse

description:
Library name: d25A97_d25A98
d25


title: SR006342_sbr_7450_Male_10

description:
Library name: 7450
10xV3.1 snRNA-seq


title: d25A191, d25A192, mESC, Mouse

description:
Library name: d25A191_d25A192
d25


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rep2

description:
Library name: Sample 14
14-V300071532_L02_98


title: SK336, VD-ATAC

description: Library name: B2SK21

value: M

value: EA

value: VD


title: Single-cell RNA-seq day2 cell22


title: SK344, VD-ATAC

description: Library name: B2SK22


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, quercetin treated, rep3

description:
Library name: Sample 19
19-V300071532_L02_103

value: LUHMES

value: human mesencephalic cells


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rutin treated, rep2

description:
Library name: Sample 21
23-V300071532_L02_123

value: alpha-synuclein overexpressed


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rep1

description:
Library name: Sample 13
13-V300071532_L02_97


title: Single-cell RNA-seq day2 cell14


title: d25A187, d25A188, mESC, Mouse

description:
Library name: d25A187_d25A188
d25


title: SK228, EtOH-ATAC

description: Library name: B1SK03


title: LUHMES cells, control, 6-OHDA treated, rep3

description:
Library name: Sample 11
7-V300071532_L01_37

value: wild type


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, quercetin treated, rep2

description:
Library name: Sample 18
18-V300071532_L02_102

value: 6-OHDA, quercetin


title: d25A185, d25A186, mESC, Mouse

description:
Library name: d25A185_d25A186
d25


title: SK358, EtOH-ATAC

description: Library name: B2SK17

value: colonic organoid


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rep3

description:
Library name: Sample 15
15-V300071532_L02_99


title: d25A183, d25A184, mESC, Mouse

description:
Library name: d25A183_d25A184
d25


title: LUHMES cells, alpha-synuclein overexpressed, 6-OHDA treated, rep4

description:
Library name: Sample 16
16-V300071532_L02_100


title: SK222, EtOH-ATAC

description: Library name: B1SK01


title: Single-cell RNA-seq day2 cell12

value: Mouse embryonic fibroblasts reprgramming cells


title: LUHMES cells, control, 6-OHDA treated, rep4

description:
Library name: Sample 12
8-V300071532_L01_38


title: Single-cell RNA-seq day2 cell18


title: SR006342_sbr_7448_Male_10

description:
Library name: 7448
10xV3.1 snRNA-seq


title: SK358, VD-ATAC

description: Library name: B2SK23

value: F

value: AA


title: SK336, EtOH-ATAC

description: Library name: B2SK15

value: EtOH


title: Single-cell RNA-seq day2 cell15

value: OvSvK single-cell RNA-seq reprogramming day2


title: LUHMES cells, control, 6-OHDA treated, rep1

description:
Library name: Sample 9
5-V300071532_L01_35


title: LUHMES cells, alpha-synuclein  overexpressed, untreated, rep4

description:
Library name: Sample 8
12-V300071532_L01_53_116_55_56

value: untreated


title: SK316, VD-ATAC

description: Library name: B2SK19


title: Single-cell RNA-seq day2 cell16


title: d25A189, d25A190, mESC, Mouse

description:
Library name: d25A189_d25A190
d25

value: mESC

value: C57BI6/J(female)x CAST/EiJ(male)


title: SK326, VD-ATAC

description: Library name: B2SK20

value: M


title: d25A181, d25A182, mESC, Mouse

description:
Library name: d25A181_d25A182
d25


title: SK344, EtOH-ATAC

description: Library name: B2SK16

value: EA


title: Single-cell RNA-seq day2 cell8


title: LUHMES cells, alpha-synuclein  overexpressed, untreated, rep2

description:
Library name: Sample 6
10-V300071532_L01_115


title: SK316, EtOH-ATAC

description: Library name: B2SK13


title: Single-cell RNA-seq day2 cell9


title: Single-cell RNA-seq day2 cell13


title: LUHMES cells, alpha-synuclein  overexpressed, untreated, rep1

description:
Library name: Sample 5
9-V300071532_L01_39


title: Single-cell RNA-seq day2 cell10


title: SK326, EtOH-ATAC

description: Library name: B2SK14


title: d25A171, d25A172, mESC, Mouse

description:
Library name: d25A171_d25A172
d25


title: d25A179, d25A180, mESC, Mouse

description:
Library name: d25A179_d25A180
d25


title: LUHMES cells, control, 6-OHDA treated, rep2

description:
Library name: Sample 10
6-V300071532_L01_36


title: Single-cell RNA-seq day2 cell11


title: d25A177, d25A178, mESC, Mouse

description:
Library name: d25A177_d25A178
d25


title: SK304, EtOH-ATAC

description: Library name: B2SK12


title: d25A175, d25A176, mESC, Mouse

description:
Library name: d25A175_d25A176
d25


title: SK288, EtOH-ATAC

description: Library name: B2SK10


title: Single-cell RNA-seq day2 cell7


title: SK304, VD-ATAC

description: Library name: B2SK11

value: VD


title: Single-cell RNA-seq day2 cell6


title: LUHMES cells, control, untreated, rep4

description:
Library name: Sample 4
4-V300071532_L01_34

value: LUHMES


title: SK276, EtOH-ATAC

description: Library name: B2SK08


title: LUHMES cells, alpha-synuclein  overexpressed, untreated, rep3

description:
Library name: Sample 7
11-V300071532_L01_49_50_51_52

value: human mesencephalic cells


title: LUHMES cells, control, untreated, rep2

description:
Library name: Sample 2
2-V300071532_L01_32


title: LUHMES cells, control, untreated, rep3

description:
Library name: Sample 3
3-V300071532_L01_33


title: Single-cell RNA-seq day2 cell4


title: d25A163, d25A164, mESC, Mouse

description:
Library name: d25A163_d25A164
d25


title: d25A167, d25A168, mESC, Mouse

description:
Library name: d25A167_d25A168
d25


title: LUHMES cells, control, untreated, rep1

description:
Library name: Sample 1
1-V300071532_L01_114


title: SK288, VD-ATAC

description: Library name: B2SK09


title: Single-cell RNA-seq day2 cell3


title: SK276, VD-ATAC

description: Library name: B2SK07


title: Single-cell RNA-seq day2 cell5


title: d25A165, d25A166, mESC, Mouse

description:
Library name: d25A165_d25A166
d25


title: d25A173, d25A174, mESC, Mouse

description:
Library name: d25A173_d25A174
d25


title: w3_180

city: Chongqing

first: Hongxiang

last: Xu

address: Tiansheng Road

institute: Southwest University

description:
Library name: w3_180
WT infected with SWU1

data_processing:
All analyses were performed in the R statistical environment (v4.2.2) using RStudio as the integrated development environment. For differential expression analysis of RNA-seq data, the limma package (v3.54.0) was employed, with the voom method applied for variance stabilization.
Assembly: CP000480
Supplementary files format and content: gene expression count in csv format

organism: Mycolicibacterium smegmatis

extract_protocol:
M. smegmatis and its ΔkuΔligD were cultured in 7H9 medium to an OD600 of 2.0. Bacterial cells were collected by centrifugation and resuspended in fresh 7H9 medium to an OD600 of 1.0. The cultures were then infected with SWU1 phage at an MOI of 10, followed by a 30 minutes adsorption period at 37℃. Subsequent incubation was carried out at 37°C with shaking at 200 rpm for 30 and 180 minutes. At each time point, bacteria were harvested by centrifugation, and total RNA was extracted for RNA-seq analysis.
RNA was fragmented and then used as template for first-strand cDNA synthesis with reverse transcriptase and random hexamer primers, followed by second-strand cDNA synthesis using RNase H and DNA polymerase I. The resulting double-stranded cDNA fragments underwent end repair, addition of a single “A” base, and adapter ligation. Adaptor-ligated fragments were selected using AMPure XP beads and amplified by PCR to generate the final cDNA library. Transcriptome sequencing was performed by Wuhan Feisha Gene Company using an Illumina platform.

value: cell

value: WT

value: Mycobacterium phage SWU1


title: Single-cell RNA-seq day2 cell2

city: Guangzhou

first: Hui

last: Zheng

address: No.190 Kaiyuan Avenue, Science Park


title: d25A169, d25A170, mESC, Mouse

description:
Library name: d25A169_d25A170
d25


title: SK266, EtOH-ATAC

description: Library name: B2SK06

value: colonic organoid


title: w3

description:
Library name: w3
WT infected with SWU1


title: w2

description:
Library name: w2
WT infected with SWU1


title: d25A159, d25A160, mESC, Mouse

description:
Library name: d25A159_d25A160
d25


title: d25A161, d25A162, mESC, Mouse

description:
Library name: d25A161_d25A162
d25


title: w2_180

description:
Library name: w2_180
WT infected with SWU1


title: Single-cell RNA-seq day1 cell74

value: Mouse embryonic fibroblasts reprgramming cells

value: OvSvK single-cell RNA-seq reprogramming day1


title: Single-cell RNA-seq day1 cell73


title: SK254, EtOH-ATAC

description: Library name: B2SK04

value: F


title: w1_180

description:
Library name: w1_180
WT infected with SWU1


title: SK254, VD-ATAC

description: Library name: B2SK02


title: Single-cell RNA-seq day2 cell1


title: d25A155, d25A156, mESC, Mouse

description:
Library name: d25A155_d25A156
d25


title: Single-cell RNA-seq day1 cell70


title: ICAM1+ DPSCs-3

city: Hangzhou

first: Yi

state: Zhejiang

address: 166 North Qiutao Rd

department: Department of Endodontics

institute: Zhejiang University

description:
Library name: ICAM1-3
ICAM1-3

data_processing:
After passing the library check, the different libraries were sequenced in Illumina after pooling them according to the effective concentration and the target sequencing output data volume, yielding 150bp paired-end reads. The basic principle of sequencing is to synthesize and sequence at the same time. Four types of fluorescently labeled dNTPs, DNA polymerase, and junction primers were added to the sequencing flow cell for amplification. When extending the complementary strand of each sequencing cluster, each fluorescently labeled dNTP added emits corresponding fluorescence, and the sequencer captures the fluorescence signals, and converts the light signals into sequencing peaks through computer software, so as to obtain the sequence information of the fragment to be tested.
1. Data Quality Control  Data quality control was performed using fastp to remove reads with adapters. Paired reads were removed under the following conditions: when the the number of N in any sequencing read exceeded 10% of the length of that read, and when any sequencing read contained low-quality bases (Q<=20) exceeding 50% of the length of that read. Subsequent analyses were based on clean reads. 2. Sequence Alignment to the Reference Genome  The reference genome and its annotation files were downloaded from a specified website. HISAT was used to build an index, and clean reads were aligned to the reference genome. 3. Quantification of Gene Expression Levels  Gene expression levels were quantified using featureCounts to calculate gene alignment statistics. Subsequently, FPKM (Fragments Per Kilobase Million) values for each gene were computed based on gene length. FPKM is currently the most used method for estimating gene expression levels. 4. Differential Analysis  DESeq2 was used for differential gene expression analysis between two groups, and Benjamini & Hochberg correction was applied to P-values. Corrected P-values and log2 fold change were used as thresholds for significant differential expression. 5. Differential Gene Enrichment Analysis  Enrichment analysis was performed based on the hypergeometric test, with pathway-based hypergeometric distribution testing for KEGG and GO term-based analysis for GO. 6. Differential Splicing Analysis  rMATS was used to analyze alternative splicing events, including SE (skipped exon), RI (retained intron), MXE (mutually exclusive exons), A5SS (alternative 5' splice site), and A3SS (alternative 3' splice site). 7. SNP Analysis  GATK was used for variant site analysis, and annovar was used for variant annotation. 8. Fusion Gene Analysis STAR-Fusion was used for Gene Fusion Analysis 9. Differential Gene-Protein Interaction Analysis  Analysis of protein interactions for differentially expressed genes was based on the STRING database, which contains known and predicted protein-protein interactions. For species present in the database, a network was constructed by extracting the target gene list from the database. Otherwise, blastx was used to align target gene sequences with selected reference protein sequences, and a network was established based on known interactions in the selected reference species. 10. Gene Set Enrichment Analysis (GSEA)  Gene set enrichment analysis ( GSEA ) was conducted using the clusterProfiler R packages. 11. Weighted Gene Co-expression Network Analysis (WGCNA)  WGCNA was performed for weighted gene co-expression network analysis
reference genome: uses Ensembl database as a reference genome: Homo_sapiens.GRCh38.109.
Supplementary files format and content: All_DEG.Summary, count, fpkm

source_name: Dental Pulp Stem Cells

extract_protocol:
Plant samples were extracted by ethanol precipitation and CTAB-PBIOZOL. Animal samples were extracted by Trizol method. After successful extraction, RNA was dissolved by adding 50 µL of DEPC-treated water. Subsequently, total RNA was identified and quantified using a Qubit fluorescence quantifier and a Qsep400 high_x0002_throughput biofragment analyzer.
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection.

value: Dental Pulp Stem Cells


title: ICAM1+ DPSCs-1

description:
Library name: ICAM1-1
ICAM1-1


title: d25A153, d25A154, mESC, Mouse

description:
Library name: d25A153_d25A154
d25


title: k3_180

description:
Library name: k3_180
kuligD-KO infected with SWU1

value: kuligD-KO


title: k3

description:
Library name: k3
kuligD-KO infected with SWU1


title: d25A151, d25A152, mESC, Mouse

description:
Library name: d25A151_d25A152
d25


title: Single-cell RNA-seq day1 cell71


title: Single-cell RNA-seq day1 cell69


title: ICAM1+ DPSCs-2

description:
Library name: ICAM1-2
ICAM1-2


title: SK266, VD-ATAC

description: Library name: B2SK05


title: Single-cell RNA-seq day1 cell68


title: d25A149, d25A150, mESC, Mouse

description:
Library name: d25A149_d25A150
d25


title: d25A147, d25A148, mESC, Mouse

description:
Library name: d25A147_d25A148
d25


title: Single-cell RNA-seq day1 cell72


title: ICAM1- DPSCs-3

description:
Library name: CON-3
CON-3


title: w1

description:
Library name: w1
WT infected with SWU1


title: k1

description:
Library name: k1
kuligD-KO infected with SWU1


title: ICAM1- DPSCs-1

description:
Library name: CON-1
CON-1


title: d25A157, d25A158, mESC, Mouse

description:
Library name: d25A157_d25A158
d25


title: Single-cell RNA-seq day1 cell67