title: RGNEF06

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

description: Replicate treated with siRNA against RGNEF

data_processing:
1 Raw Data  Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.FASTQ format described by four lines:  @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT    ANTTGTTAACAGGTCAAAATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCACCCTAGAGGTGGAGCCCAGTGACACCATCGAGAACGTGAAG + F#,FFFFFFFFFFFFF:FFFF::FFFFF:FFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF:FF:FFFFFF:FFFFFFF  Line 1 begins with a '@' character and is followed by the Illumina Sequence Identifiers and an optional description. Line 2 is the raw sequence read. Line 3 begins with a '+' character and is optionally followed by the same sequence identifier and description. Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of characters as there are bases in the sequence.
2 Data Filtering  Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.  The filtering process is as follows: (1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%). (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
3 Mapping To Reference Genome  Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR (v. 2.5) to accomplish the mapping. For the Human species, if only need the differential expression significant genes, can map reads to the transcriptome directly. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely, as shown below.
4 Quantification  Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used.  HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode.  The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.  Comparison between Gene Expression Levels: To compare gene expression levels under different conditions, an FPKM distribution diagram and violin Plot are used. For biological replicates, the final FPKM would be the mean value.
5 Differential expression analysis  The input data for differential gene expression analysis are read counts from gene expression level analysis. The differential gene expression analysis contains three steps: 1) Read counts Normalization; 2) Model dependent p-value estimation; 3) FDR value estimation based on multiple hypothesis testing.  The differential gene expression analysis was performed by DESeq2 R package (v.1.22.2) using the following threshold: up-regulated genes Fold Change (FC) >1.3 and Padjust < 0.05; down-regulated genes FC < 0.7 and Padjust < 0.05. Representation of RNA sequencing data was done by volcano plots using ggplot2 R package (v3.3.5). Over-represented KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis was also performed on the RNA sequencing data using GOseq R package (version 3.14.3).
Assembly: Homo Sapiens (GRCh37/hg19)
Supplementary files format and content: gene.FPKM.annot.xls: FPMK + Gene annotations (Excel format)
Supplementary files format and content: gene.readcount.annot.xls: Readcounts + Gene annotations (Excel format)

source_name: Neuroblastoma (SH-SY5Y) cell line

growth_protocol: Human neuroblastoma SH-SY5Y cell line (ECACC) was cultured up to 20 passages in Dulbecco’s modified Eagle’s medium (DMEM)/Nutrient Mixture F-12 Ham (Sigma-Aldrich), supplemented with 15% fetal bovine serum (FBS) (Sigma-Aldrich), 1% MEM Non-essential Amino Acid Solution (100X) (Sigma-Aldrich), and 1% Antibiotic-Antimycotic-stabilized suspension (Sigma-Aldrich) at 37°C with humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) with on column DNA digestion (Qiagen) following the manufacturer’s instructions.
RNA sequencing  (150PE, 60M read pair per sample) was performed by Novogene (https://en.novogene.com/). RNA libraries were prepared for sequencing using standard Illumina protocols. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies). Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: Genes knock-down has been achieved through one round of silencing through Lipofectamine RNAiMAX (Invitrogen, ThermoFisher) according to the manufacturer’s instructions. The silencing of RGNEF was performed by plating 8 x 105 cells in p35 plates and using a reverse transfection with a mixture composed of: 150µL of Opti-MEM (LifeTechnologies), 3µL of  10µM siRGNEF and control and 9µL of Lipofectamine RNAiMAX reagent (Invitrogen). RGNEF silencing was performed in two rounds: one at day 0 using 20nM final concentration of siRNA using reverse transfection, while a second round of forward transfection was performed in day 1 following the same protocol. Cells were collected on day 2 and prepared for protein and/or gene expression analysis.

value: Neuroblastoma (SH-SY5Y) cell line

value: siRNA human RGNEF (siRGNEF)


title: Mouse-3T3_L1-3

status: Public on Dec 31 2025

type: SRA

city: Shanghai

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

description: 24 commonly used cell lines samples

library_source: transcriptomic

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: tab-delimited text files include absolute quantification of miRNA expression for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

tag: cell line

tag: tissue

tag: libtype

value: qMap-seq


title: chronic hepatitis B 2

city: kunming

first: You

last: Jing

address: 295 Xichang Road

institute: The First Affiliated Hospital of Kunming Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood mononuclear cells

tag: cell type

value: CD4+T cells

tag: disease state

value: chronic hepatitis B


title: RGNEF05

tag: treatment


title: RGNEF04


title: Healthy Control 3

value: healthy


title: CTR03

description: Replicate treated with Control siRNA

value: siRNA Negative Control (siNEG)


title: Sample 5 (B02)

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
PE150 high throughout data
B.gene.count.matrix.annot
Sample 5 (B02)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BLEO 02

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or cocoa extract (CCE).

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, the medicinal agent cocao extract (CCE) was applied to the media at 200 µM, individually.

value: Normal human prostate derived primary stromal cells

tag: passage


title: f-Hep-2 ATAC-seq

city: Beijing

first: Jie

last: Hao

state: 北京

address: Beijing

institute: Tsinghua University

library_source: genomic

data_processing:
ATAC-seq adapter sequence were identified and trimmed with cutadapt tool.
ATAC-seq reads were aligned to human hg19 reference genome using BWA-MEM with default parameters. Fragments were identified as read pairs with mapping quality >10 and non-mitochondrial reads.
PCR duplicates were removed with sambamba (v0.8.0). The start and end of the fragments were adjusted (+4 for +strand and −5 for −strand) to account for the Tn5 transposase enzyme occupied region.
ATAC peak calling was performed using MACS with a p-value threshold of 0.01, and with other settings as --nomodel --shift -75 --extsize 150 --SPMR.
ATAC bigWig files were generated using the bamCoverage tools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg19
Supplementary files format and content: bigWig, bed

molecule: genomic DNA

source_name: hESC (H9)

extract_protocol:
f-Heps, mid-Heps, and a-Heps were dissociated with Accutase, and collected in HCM medium. Frozen PHHs purchased from Celsis IVT (Lot: ONO) were recovered according to the manufacturer’s instructions.
ATAC libraries were prepared using Omni-ATAC protocol as previously described, and TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, China) was employed. Briefly, 50,000 cells were washed with cold PBS once and lysed with 50 μl cold ATAC-Resuspension Buffer (RSB) (10 mM pH 7.4 Tris-HCl, 10 mM NaCl, and 3 mM MgCl) containing 0.1% NP40 and 0.1% Tween-20. After incubation on ice for 3 minutes, 1 ml of cold ATAC-RSB containing 0.1% Tween-20 (without NP40) was added to the cell lysate and mixed by inverting 3 times. The nuclei were collected by centrifuging at 500 g for 10 minutes at 4 °C. For the transposition reaction, nuclei were incubated with Tn5 Transposition mix (10 μl 5 × TTBL buffer, 3 μl TTE Mix V50 transposase, 16.5 μl PBS, 0.5 μl 10% Tween-20 and 20 μl H2O) at 37 °C for 30  minutes. Next, the stop buffer was directly added to end the reaction, and  PCR was performed to amplify the library for 12 cycles. Then the libraries were purified with 1.2 × AMPure beads (Beckman), and sequenced using an Illumina Novaseq 6000.

treatment_protocol: human pluripotent stem cells (hPSCs) were maintained in matrigel-coated plates with mTeSR (Stem Cells). For mesendoderm differentiation, hPSCs were cultured in RPMI1640 (Gibco) supplemented with 100ng/ml Activin A (R&D), 3μM CHIR-99021 (Selleck), 1% GlutamaxTM (Gibco) and 1% penicillin/streptomycin (Gibco) for one day. For endoderm differentiation, mesendoderm cells were cultured in RPMI 1640 supplemented with 0.2% FBS (Gibco), 100ng/ml Activin A, 1% GlutamaxTM and 1% penicillin/ streptomycin for 1 days, and then cultured in RPMI1640 supplemented with 2% FBS (Gibco), 100ng/ml Activin A, 1% GlutamaxTM and 1% penicillin/ streptomycin for another day. For hepatoblast differentiation, endoderm cells were induced in DMEM (Gibco) supplemented with 20ng/ml bFGF (Invitrogen), 20ng/ml human BMP4 (R&D), 0.5μM A83-01 (Tocris Bioscience), 0.1μM Dex (Invitrogen), 0.05% BSA (Invitrogen), 2% B27 (Gibco) and 1%P/S for 4 days, and the medium was changed every other day. For f-Hep differentiation, hepatoblasts were further cultured in hepatocyte differentiated medium (HDM) for 10 days. HDM medium was prepared with HCM (without EGF, Lonza) with 20ng/ml human HGF (R&D), 20ng/ml human OSM (R&D), 0.1μM Dex (Sigma-Aldrich), 0.5μM A83-01(Tocris Bioscience) and 0.1μM Compound E (Tocris Bioscience), and the medium was changed every other day.

value: hESC (H9)

value: Pluripotent stem cells derived hepatocytes


title: Healthy Control 2


title: S1_Ext_CeA_1

city: New York

first: Kwanghoon

last: Park

address: 1230 York Ave

country: USA

institute: The Rockefeller University

data_processing:
StringTie
Assembly: StringTie
Supplementary files format and content: Excel files include raw counts for each sample

growth_protocol: BLA and CeA samples were collected from B6 and S1 mice

extract_protocol:
RNA was extracted by using RNeasy Mini Kit (Qiagen)
RNA librarie for RNA-seq were prepared by using TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Samples were collected before and after fear conditioning and extinction

tag: strain

tag: Sex

value: Male

tag: brain area

value: CeA

tag: genotype

value: WT

value: Fear extionction


title: CTR02

description: Replicate treated with Control siRNA


title: Healthy Control 1


title: Sample 3 (A03)

description:
PE150 high throughout data
A.gene.count.matrix.annot
Sample 3 (A03)

source_name: CTRL 03


title: Sample 4 (B01)

description:
PE150 high throughout data
B.gene.count.matrix.annot
Sample 4 (B01)

source_name: BLEO 01


title: CTR01

description: Replicate treated with Control siRNA


title: S1_Ext_BLA_1

value: BLA


title: B6_Ext_CeA_1


title: HTR8/SVneo cells，Nagative Control_3

city: 上海

first: 卢

last: 文静

state: 上海市

address: 高科西路2699号

department: 附属第一妇婴保健院

institute: 同济大学

data_processing:
Raw data (raw reads) were processed using Trimmomatic 1 The reads containing ploy N and the low quality reads were removed to obtain the clean reads Then the clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks ,and the read counts of each gene were obtained by htseq count . DEGs were identified using the DESeq ( 2012 )R package functions estimateSizeFactors and nbinomTest. Pvalue ＜0.05 and foldChange ＞2 or foldChange＜ 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG 7 pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM  and read counts value of each transcript (protein_coding) was calculated using bowtie 2  and eXpress . DEGs were identified using the DESeq ( 2012) functions estimateSizeFactors and nbinomTest. P value ＜0.05 and foldChange ＞2 or foldChange ＜0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG  pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using StringTie. Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using Asprofile. SNP and INDEL were called using samtools and bcftools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM value for all Sample

source_name: trophoblast cell line

growth_protocol: The HTR-8/SVneo cells were cultured in DMEM/F12 medium  that contained 10% fetal bovine serum ,100 μg/ml streptomycin and 100 U/ml penicillin at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using smarter mRNA-seq library prep kit following protocols.

treatment_protocol: Overexpression Siglec-6 was achieved by transfection of the pHBLV-CMV-MCS-EF1-ZsGreen1-T2A-puro (HANBIO Shanghai, China), and an empty vector was designed as a negative control . 48 h post-transfection cells were selected using 1 µg/mL puromycin.

value: trophoblast cell line

value: HTR8/SVneo cells

value: Human choriotrophoblast cells

value: NC


title: B6_Ext_BLA_1


title: Sample 2 (A02)

description:
PE150 high throughout data
A.gene.count.matrix.annot
Sample 2 (A02)

source_name: CTRL 02


title: Sample 1 (A01)

description:
PE150 high throughout data
A.gene.count.matrix.annot
Sample 1 (A01)

source_name: CTRL 01


title: Panc1 BRQ-2

first: Yujia

last: Wang

address: Dongdan

institute: Peking Union Medical College

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to hg38 using  HISTA2
Read count extraction and normalization were performed using HTSeq-count
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Panc1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Human Pancreatic Carcinoma Cell

value: BRQ


title: Mouse-3T3_L1-2

description: 24 commonly used cell lines samples

value: qMap-seq


title: HTR8/SVneo cells，Nagative Control_2


title: Mouse-3T3_L1-1

description: 24 commonly used cell lines samples


title: S1_FC_CeA_1

value: Fear conditioning


title: S1_FC_BLA_1


title: Panc1 BRQ-1


title: Sample 6 (B03)

description:
PE150 high throughout data
B.gene.count.matrix.annot
Sample 6 (B03)

source_name: BLEO 03


title: BLEO/RTE-02

description: Sample 8 (I02)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Prostate stromal cell line

growth_protocol: Normal human prostate-derived stromal cells (PSC27) were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO) and/or ginkgo boliba extract (GBE) or rattan tea extract (RTE).

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change. To suppress the senescence-associated secretory phenotype (SASP) by a specific mechanism, medicinal agents ginkgo boliba extract (GBE) and rattan tea extract (RTE) were applied to the media at 900 µM, individually.

value: bleomycin/rattan tea extract


title: HTR8/SVneo cells，Nagative Control_1


title: Panc1 DMSO-3

value: DMSO


title: S1_Naive_CeA_1

value: Naive


title: HTR8/SVneo cells，overexpressing Siglec-6_3

value: Siglec-6 overexpressing


title: Panc1 DMSO-2


title: BLEO/RTE-01

description: Sample 7 (I01)

value: Normal human prostate derived primary stromal cells


title: Panc1 BRQ-3


title: chronic hepatitis B 3

value: peripheral blood mononuclear cells

value: CD4+T cells

value: chronic hepatitis B


title: S1_Naive_BLA_1

value: Male

value: BLA

value: WT


title: HTR8/SVneo cells，overexpressing Siglec-6_2

value: trophoblast cell line

value: HTR8/SVneo cells

value: Human choriotrophoblast cells


title: BLEO/GBE-03

description: Sample 9 (H03)

value: bleomycin/ginkgo boliba extract


title: Panc1 DMSO-1

value: Human Pancreatic Carcinoma Cell


title: HTR8/SVneo cells，overexpressing Siglec-6_1


title: B6_FC_BLA_1

value: Fear conditioning


title: BLEO/GBE-01

description: Sample 7 (H01)


title: BLEO/RTE-03

description: Sample 9 (I03)

value: bleomycin/rattan tea extract


title: A549 BRQ-2

growth_protocol: A549 cells were maintained in F12K supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: Human hypotriploid alveolar basal epithelial cell

value: BRQ


title: A549 BRQ-1


title: B6_Naive_CeA_1

value: CeA

value: Naive


title: IRECT22

city: Ulm

first: Simon

last: Laban

address: Frauensteige 14a, Haus 18

department: Department of Otorhinolaryngology and Head & Neck Surgery

country: Germany

institute: Ulm University Medical Center

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq (2.20.0.422).
High-quality SE reads were mapped to the human genome (hg38) using STAR (2.0.9) and, following the removal of multimapping reads, converted to gene specific read counts for annotated genes using featureCounts (2.0.0).
Genome_build: hg38
Supplementary_files_format_and_content: Two matrix tables with raw gene counts and TPM values for every gene and every sample

source_name: Oropharynx cancer

extract_protocol:
Primary tumors were snap-frozen immediately after obtaining the tissue. AllPrep DNA/RNA Kit (Qiagen, Germany) was used for RNA extraction following the manufacturer's instructions.
Libraries were prepared from 500ng of input material using TruSeq Stranded mRNA (manufacturer's instructions) and subsequently quantified and quality checked using Agilent 2100 Bioanalyzer Instrument (DNA 7500 kit).
Libraries were pooled and sequenced in one lane of HiSeq 2500 System running in 51 cycle/single-end/high output mode.

tag: age

value: male

value: Positive

value: Oropharynx squamous cell carcinoma

tag: pt

tag: pn

tag: cm

tag: Stage

value: II

value: Hot


title: IRECT7


title: BLEO-03

description: Sample 6 (B03)

value: bleomycin

value: Normal human prostate derived primary stromal cells


title: IRECT20


title: B6_Naive_BLA_1

value: Male

value: BLA

value: WT


title: BLEO-02

description: Sample 5 (B02)


title: HNU1581

value: III


title: chronic hepatitis B 1

value: peripheral blood mononuclear cells

value: CD4+T cells

value: chronic hepatitis B


title: BLEO/GBE-02

description: Sample 8 (H02)

value: bleomycin/ginkgo boliba extract


title: scRNA-seq_WT_BM to WT_Mice

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis. After sample demultiplexing, raw PF reads were processed through the CellRanger software (10X Genomics Inc., CA) to obtain the gene expression levels in single cells and quality control matrices for each sample.
Downstream analysis was performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: CD45 positive live cells from tumors in recipient of Mtdh wild type mice with Mtdh wild type bone marrow

growth_protocol: Py8119 tumors were harvested from mouse, and processed into single cell suspspension using tissu disscociator with tumor dissociatio kit from Milltenyi biotec. Red blood cells were removed with RBC lysis buffer.The cell suspension was filtered through a 70-μm strainer and stained with live dye and CD45 antibody.

extract_protocol:
Single cell suspension samples were examined for cell density and viability. For each sample, 15,000 sorted cells were resuspended in 15 ul of PBS containing 0.5% BSA for library preparation. Viability of cells are more than 90%.
Around 15,000 cells from each sample were loaded into each channel of the 10X Genomics Chromium X system using the Chromium Single Cell 3’ v3.1 Reagent Kits (10X Genomics Inc., CA) to generate and amplify cDNA from individual cells. The amplified cDNA samples were purified with Ampure XP magnetic beads (Beckman Coulter, CA), quantified by Qubit fluorometer (Invitrogen, CA), and examined on Bioanalyzer with High Sensitivity DNA chips (Agilent, CA) for size distribution. Illumina sequencing libraries were generated from the amplified cDNA samples using the Illumina Tagment DNA Enzyme and Buffer kit (Illumina, CA). These libraries were examined by Qubit and Bioanalyzer, then pooled at equal molar amount and sequenced on Illumina NovaSeq 6000 S Prime flowcells as 28+94 nt pair-end reads following the standard Illumina protocol.

treatment_protocol: Live CD45+ cells were sorted for scRNAseq.

value: Tumors

value: immune cells

value: CD45 postive live

tag: site

value: Mammary tumor


title: HNU1580

value: male

value: Negative

value: Oropharynx squamous cell carcinoma

value: IVB

value: Cold


title: A549 DMSO-2

tag: cell line

value: Human hypotriploid alveolar basal epithelial cell

value: DMSO


title: A549 DMSO-3


title: A549 DMSO-1


title: scRNA-seq_KO_BM to WT_Mice

description: 10x Genomics

source_name: CD45 positive live cells from tumors in recipient of Mtdh wild type mice with Mtdh KO bone marrow

tag: tissue


title: BLEO-01

description: Sample 4 (B01)

value: bleomycin

value: Normal human prostate derived primary stromal cells


title: A549 BRQ-3

value: BRQ


title: B6_FC_CeA_1

value: Male

value: CeA

value: WT

value: Fear conditioning


title: CTRL-03

description: Sample 3 (A03)

value: control


title: BM1 KMT5C overexpression tumor #823

city: Chicago

first: Marsha

middle: Rich

last: Rosner

state: IL

address: 929 E 57th St

institute: University of Chicago

data_processing:
For the single-cell RNA-seq experiment, the RNA sequencing data were demultiplexed using the manufacturer-supplied API script to generate individual FASTQ files for single cells based on the barcodes used (Fluidigm, mRNASeqHT_demultiplex.pl). The reads were mapped to the human genome (UCSC hg38 with GENCODE annotations) using RNA STAR. The resulting mapped reads from every single cell were counted by featureCounts to generate per-gene read counts. Gene expression data from three biological replicates were combined, and the batch effect was corrected via the “BatchCorrectedCounts” function in the CountClust package by specifying the replicate number as the variable to regress out.
For the bulk RNA-seq experiment, all ten samples were sequenced in four runs by a NovaSeq 6000 sequencer (Illumina) to generate paired-end 100bp reads. The raw FASTQ files from four flow cells were combined for each sample before downstream processing. RNA-seq data were analyzed using a local Galaxy instance. Quality and adapter trimming were applied to the raw sequencing reads using the Trim Galore! Package (Felix Krueger, github.com/FelixKrueger/TrimGalore). The reads were mapped to the human genome (UCSC hg19 with GENCODE annotation) using RNA STAR. Per gene read counts from each sample were generated by featureCounts.
Assembly: Single-cell study: Human (hg38). Bulk tumor study: Human (hg19).
Supplementary files format and content: Comma delimited text file containing a matrix table with raw gene counts for every gene and every sample.

source_name: BM1 with KMT5C overexpression xenograft primary mammary tumor

growth_protocol:
BM1 cells were cultured in DMEM media (Gibco, 11965-118) with 10% fetal bovine serum (FBS, Avantor, 97068-085) and 1% penicillin-streptomycin (Gibco, 15140-122).
1 × 10^6 BM1-VC or BM1-KMT5C cells were injected orthotopically into the mammary fat pad of athymic nude mice (Charles River). The mice were euthanized four weeks post tumor cell implantation. Primary tumors were collected.

extract_protocol:
Fresh tumors were placed inside M Tubes (Miltenyi Biotec, 130-093-236), then homogenized with TRI Reagent (Zymo Research, R2050-1) by the gentleMACS Dissociator (Miltenyi Biotec 130-093-235). Total RNA extraction with genomic DNA removal was performed using the Direct-zol RNA MiniPrep Plus kit (Zymo Research, R2072).
RNA libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.
none provided by the submitter

value: Stable BM1 cells were generated with human KMT5C (NM_032701.4) overexpression or vector control (pLV-EF1a-IRES-Hygro) through lentiviral transduction followed by selection.

tag: sequencing type

value: Bulk RNA-seq


title: HNU1565

value: female

value: III


title: scRNA-seq_WT_BM to KO_Mice

description: 10x Genomics

source_name: CD45 positive live cells from tumors in recipient of Mtdh KO mice with Mtdh wild type bone marrow

value: Tumors

tag: cell type

value: immune cells

value: CD45 postive live

value: Mammary tumor


title: CTRL-02

description: Sample 2 (A02)


title: HNU1556

value: male

value: Negative

value: Oropharynx squamous cell carcinoma

value: IVB

value: Cold


title: CTRL-01

description: Sample 1 (A01)

value: Normal human prostate derived primary stromal cells


title: BM1 KMT5C overexpression tumor #820


title: HNU1504

value: II


title: scRNA-seq_KO_BM to KO_Mice

description: 10x Genomics

source_name: CD45 positive live cells from tumors in recipient of Mtdh KO mice with Mtdh KO bone marrow


title: scRNA-seq_WT mice

description: 10x Genomics

source_name: CD45 positive live cells from tumors in Mtdh wild type mice


title: HNU1497

value: Positive

value: I

value: Hot


title: A549_exosomes_miRNA

city: Tianjin

first: Jian

last: Zhang

address: Huanhu West Road, Hexi District

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Sequenced reads were removed the 3’ end adaptor, converted to the fasta format, and masked for low-complexity or low-quality sequence.
The reads was mapped against human microRNA reference (miRBase, v23) using basic local alignment search tool (BLAST) with default parameters. The mapped reads retained are no mismatch or 1 base deletion at 3’ end.
Reads counts were calculated and were processed with DEGseq v1.14.0 (Bioconductor), which is a package based on the R language (v2.15.3) for differential gene expression analysis.
Genome_build: miRBase (v23)
Supplementary_files_format_and_content: Processed data files contain the raw counts from the raw data.

source_name: A549 cell line

growth_protocol: A549 cells were cultured in RPMI-1640 culture medium supplemented with 10%  Fetal Bovine Serum (FBS).

extract_protocol:
miRNA derived from A549 cells and A549 cells-derived exosomes was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were cultured in serum-free medium for 48 h. The medium was collected and centrifuged for 15 min at 3000 g, followed by 16,000 g for 1 h to remove cellular debris, and then concentrated to 20% of its original volume using a centrifugal concentrator (Millipore, Germany). After filtrated through 0.22 μm filters (Millipore), the concentrate was subjected to high-speed centrifugation at 120,000 g for 2 h. The exosome-enriched pellet was resuspended in PBS or MEM medium.

value: Lung adenocarcinoma cell-derived exosomes


title: BM1 KMT5C overexpression tumor #816

value: Stable BM1 cells were generated with human KMT5C (NM_032701.4) overexpression or vector control (pLV-EF1a-IRES-Hygro) through lentiviral transduction followed by selection.

value: Bulk RNA-seq


title: scRNA-seq_KO mice

description: 10x Genomics

source_name: CD45 positive live cells from tumors in Mtdh KO mice

value: Tumors


title: A549_cell_miRNA

value: Lung adenocarcinoma cell


title: BM1 KMT5C overexpression tumor #809


title: MRC5_shRNA_Scramble_mRNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.9. Tophat analysis was performed using Bowtie v2.1.0 with default parameters.
Reads counts were calculated using HTseq v0.5.4 with parameters -s no -a 10. All of the programs used hg19 (GRCh37) and RefGene as reference genome and gene model.
Reads counts data were processed with DEGseq v1.14.0 (Bioconductor), which is a package based on the R language (v2.15.3) for differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain the raw counts from the raw data.

source_name: MRC5 cell line

growth_protocol: MRC5 cells were cultured in MEM culture medium supplemented with 10%  Fetal Bovine Serum (FBS) and Glutamine (1X).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In one group, MRC5 cells were trasnfected with shRNAs targeting FOXN3 or scramble shRNAs for 72 h. In another group, MRC5 cells were incubated with A549 cells-derived exosomes or culture medium  (blank control) for 72 h.

value: Human embryonic lung fibroblast


title: HNU1475


title: BM1 KMT5C overexpression tumor #807


title: HNU1468

value: IVa


title: BM1 CTRL tumor #815

source_name: BM1 CTRL xenograft primary mammary tumor


title: MRC5_shRNA_FOXN3_mRNA


title: HNU1444

value: male

value: III


title: CD3e+CD8+ T cells in Py8119 tumors from WT mice, rep1

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a.Gene counts were obtained by quantifying against the mm39-Ensembl Transcripts release 104 annotation model. After noise filtering, counts were normalized using the DESeq2 package.
Assembly: mm39-Ensembl Transcripts release 104
Supplementary files format and content: tab-delimited text files with counts normalized as median ratio by DESeq2 in Partek software package

source_name: tumors

extract_protocol:
Total RNA were extracted using RNAeasy micro-prep kit from Qiagen
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

treatment_protocol:
Cell preparation protocol: Py8119 tumors were harvested from mouse, and processed into single cell suspspension using tissu disscociator with tumor dissociatio kit from Milltenyi biotec. Red blood cells were removed with RBC lysis buffer.The cell suspension was filtered through a 70-μm strainer and stained with live dye and related antibodies.
FACS sorting protocol: Target cells were sorted from live cells with CD45+CD3e+CD8+.

value: tumors

value: CD8+ T cells

tag: host genotype

value: WT


title: MRC5_Con_mRNA


title: CD3e+CD8+ T cells in Py8119 tumors from WT mice, rep3


title: CD3e+CD8+ T cells in Py8119 tumors from MTDH KO mice, rep4

value: Mtdh KO


title: MRC5_CAF_mRNA


title: N3_KC_UVB

city: Bangkoknoi

first: Uraiwan

last: Panich

state: Bangkok

address: 2 Siriraj Hospital, Wang Lang, Siriraj

department: Department of Pharmacology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital

data_processing:
Sequencing was performed on the Illumina HiSeq platform, in a 2x150bp paired-end (PE) configuration, with 2.0 Gigabyte raw data per sample.
Base calling is performed by Illumina RTA software in sequencer, further demultiplexing is performed by Illumina bcl2fastq 2.17 software based on index information, the number of reads and quality score (Q30) are counted as well.
The STAR (v2.5.3a) was used to align reads to human reference genome (hg19 release).
Other pipelines were used including sambamba (v0.6.6) for sorting the BAM files, samtools (v1.6): for indexing the BAM files, fastp (v0.19.4) for the read trimming and QC and subread (v1.6.2) for the gene/isoform quantification.
The expression levels for each gene were normalized to transcripts per million (TPM) to facilitate the comparison of transcript levels among samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include count and TPM values for each sample.

source_name: skin

growth_protocol: We cultured KC in Medium 154 (#M-154CF-500) supplemented with human keratinocyte growth supplement (HKGS). HaCaT were grown in high glucose (4.5 g/L) Dulbecco’s modified Eagle’s medium (DMEM) and Ham’s F-12 (DMEM/F-12) supplemented with 10% fetal bovine serum and 1% penicillin (100 U/ml)/streptomycin (100 mg/ml). HDF were cultured in high glucose (4.5 g/L) Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1% 200 mM glutamax and 1% Antibiotic-Antimycotic Solution. All cell lines were tested mycoplasma before perform an experiment.

extract_protocol:
Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agarose gel. 1 μg total RNA with RIN value above 7 was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KC, HaCaT, HDF cells were irradiated with UVB under a thin layer of Dulbecco`s phosphate buffered saline (DPBS). The UV intensity determined at a distance of 21 cm from the UVR lamp was 1 W/cm2 using a UV-meter (Dr Honle, Martinsried, Germany). The culture plates were exposed for 45 s to achieve a single dose of 125 mJ/cm2. Immediately after UVB exposure, DPBS were replaced with DMEM without FBS. All cells were harvested at 6 h post-irradiation for RNA extraction.

value: Primary human keratinocytes

tag: treatment

value: UVB


title: CD3e+CD8+ T cells in Py8119 tumors from MTDH KO mice, rep3


title: BM1 CTRL tumor #803


title: N3_KC_NOUV

value: no irradiation


title: BM1 CTRL tumor #813


title: HNU1420

value: Positive

value: Oropharynx squamous cell carcinoma

value: I

value: Cold


title: CD3e+CD8+ T cells in Py8119 tumors from MTDH KO mice, rep2


title: N3_HDF_UVB

value: Primary human dermal fibroblasts


title: BM1 CTRL tumor #801

value: Stable BM1 cells were generated with human KMT5C (NM_032701.4) overexpression or vector control (pLV-EF1a-IRES-Hygro) through lentiviral transduction followed by selection.

value: Bulk RNA-seq


title: CD3e+CD8+ T cells in Py8119 tumors from WT mice, rep4


title: HNU1416

value: Hot


title: F1

city: Changsha

first: Lin

last: Qi

address: 139 Renmin Road

institute: The Second Xiangya Hospital, Central South University

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2
Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package between groups.
DETs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database.
Assembly: Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
Supplementary files format and content: The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.

source_name: Osteosarcoma

growth_protocol: Patients with osteosarcoma undergoing NACT were included in this study.

extract_protocol:
Total RNA was isolated from each thymic sample using the RNAmini kit ( Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA).
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

treatment_protocol: Pre-NACT specimens were collected by biopsy from patients without receiving any anti-tumor therapy prior to the biopsy. Osteosarcoma patients were treated with standard chemotherapy. Post-NACT osteosarcoam samples were obtained during surgery.

tag: individual

value: F

tag: disease state

value: osteosarcoma

value: Osteosarcoma

value: after NACT

value: Male

value: Upper-extremity


title: CD3e+CD8+ T cells in Py8119 tumors from MTDH KO mice, rep1

value: tumors

value: CD8+ T cells

value: Mtdh KO


title: HNU1445

tag: Sex

value: male

value: Positive

value: III


title: HNU1427

value: Negative

value: Oropharynx squamous cell carcinoma

value: IVa


title: F0

value: before NACT


title: N3_HDF_NOUV

value: Primary human dermal fibroblasts

value: no irradiation


title: CD3e+CD8+ T cells in Py8119 tumors from WT mice, rep2

value: WT


title: BM1 CTRL tumor #804

value: Stable BM1 cells were generated with human KMT5C (NM_032701.4) overexpression or vector control (pLV-EF1a-IRES-Hygro) through lentiviral transduction followed by selection.

value: Bulk RNA-seq


title: HNU1404

value: female

value: Hot


title: E1

value: E

value: osteosarcoma

value: Osteosarcoma

value: after NACT

value: Female

value: Lower-extremity


title: HNU1435

value: Negative

value: I

value: Cold


title: N2_HA_NOUV

value: Human keratinocytes


title: HNU1407

value: male

value: Positive

value: Oropharynx squamous cell carcinoma


title: livers from tumor-bearing WT mice, rep3

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a.Gene counts were obtained by quantifying against the mm39-Ensembl Transcripts release 108 annotation model. After noise filtering, counts were normalized using the DESeq2 package.
Assembly: mm39-Ensembl Transcripts release 108
Supplementary files format and content: tab-delimited text files with counts normalized as median ratio by DESeq2 in Partek software package

source_name: liver

extract_protocol:
Cell preparation protocol: Livers were harvested from the indicated mice and snap frozen in liquid nitrogen. The frozen livers were ground into a powder. Equal amounts of the powdered liver tissue were lysed in RNA extraction buffer and then processed for RNA extraction.
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

value: liver

value: all cells in the liver

value: WT

value: Py8119 allograft mammary tumor


title: livers from tumor-bearing WT mice, rep2


title: HNU1403

value: IVa

value: Hot


title: livers from tumor-bearing WT mice, rep1


title: E0

value: E

value: osteosarcoma

value: Osteosarcoma

value: before NACT


title: D1

value: D

value: after NACT

value: Female

value: Lower-extremity


title: HNU1401

value: male

value: Negative

value: II

value: Cold


title: livers from tumor-bearing MTDH KO mice, rep3

value: liver

value: all cells in the liver

value: Mtdh KO


title: N1_KC_NOUV

value: Primary human keratinocytes

value: no irradiation


title: HNU1393

value: Positive

value: Oropharynx squamous cell carcinoma

value: IVB

value: Hot


title: livers from tumor-bearing MTDH KO mice, rep2

value: Py8119 allograft mammary tumor


title: HNU1385


title: N1_HDF_UVB

value: Primary human dermal fibroblasts

value: UVB


title: livers from tumor-bearing MTDH KO mice, rep1


title: B1

value: B

value: osteosarcoma

value: Osteosarcoma

value: after NACT

value: Male

value: Lower-extremity


title: B0

value: before NACT


title: HNU1382

value: male

value: Negative

value: III

value: Cold


title: N1_HDF_NOUV

value: no irradiation


title: N2_HA_UVB

value: Human keratinocytes


title: livers from normal, non-tumor WT mice, rep2

value: liver

value: all cells in the liver

value: WT

value: normal, no tumor


title: HNU1376

value: female

value: Oropharynx squamous cell carcinoma

value: IVa


title: N1_HA_UVB

value: UVB


title: livers from normal, non-tumor WT mice, rep3


title: HNU1372

value: Positive

value: II

value: Hot


title: A0

value: A

value: osteosarcoma

value: Osteosarcoma

value: before NACT

value: Male

value: Lower-extremity


title: A1

value: after NACT


title: 143B_PXDDOX3

growth_protocol: 143B osteosarcoma cells were plated in 10-cm dishes at 2,000,000 cells per dish  in DMEM + 10% FBS + 1% penicillin/streptomycin the day prior to compound treatment.

treatment_protocol: 143B osteosarcoma cells were treated with 0.1μM DOX, 1.5μM PXD101, 1.5μM PCI-24781, the combination of 0.1μM DOX and 1.5μM PXD101, the combination of 0.1μM DOX and 1.5μM PCI-24781 and DMSO  for 24 hours.  Three biological replicates of each sample were processed for next-generation sequencing (NGS).

value: the combination of 0.1μM DOX and 1.5μM PXD101 for 24 hours


title: N1_HA_NOUV

value: Human keratinocytes

value: no irradiation


title: livers from normal, non-tumor WT mice, rep1

value: liver

value: all cells in the liver

value: WT

value: normal, no tumor


title: HNU1365

value: male

value: Positive

value: Oropharynx squamous cell carcinoma


title: N1_KC_UVB

value: Primary human keratinocytes

value: UVB


title: livers from normal, non-tumor MTDH KO mice, rep3

value: Mtdh KO


title: 143B_PXDDOX2

value: osteosarcoma


title: D0

value: D

value: Osteosarcoma

value: before NACT

value: Female


title: HNU1361

value: II

value: Cold


title: livers from normal, non-tumor MTDH KO mice, rep2

value: liver


title: 143B_PXDDOX1

value: the combination of 0.1μM DOX and 1.5μM PXD101 for 24 hours


title: livers from normal, non-tumor MTDH KO mice, rep1

value: all cells in the liver


title: 143B_PXD3

value: 1.5μM PXD101 for 24 hours


title: HNU1359

value: male

value: I

value: Hot


title: HNU1349

value: Positive

value: Oropharynx squamous cell carcinoma


title: WT_T_Cells_TCR

city: Novato

first: Fei

last: Wu

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: 10x Genomics

data_processing:
Post sequencing, to align read and generate feature barcode matrices raw data was subjected to the Cell Ranger pipeline 6.1.2.
Assembly: mm10-2020-A
Supplementary files format and content: Market Exchange Format (MEX) matrix; Comma Separated Value (CSV) of contigs annotations and clone types

source_name: Spleen

extract_protocol:
Mice were euthanized using CO2 fixation prior to collecting organs, blood, and lymphoid organs. Spleens were processed into single cell suspensions and filtered through 40 µm cell strainer followed by hemolysis. Cells were blocked with Fc-block CD16/32 (93) and stained with viability dye zombie aqua, CD45 (30-F11), CD3 (17A2), CD19 (6D5) (BioLegend), using methods described above for surface staining. Live CD45+ CD3+ CD19- were sorted using a MoFlo Astrios Sorting Machine, at the Princess Margaret Hospital Flow Cytometry Facility, University Health Network (Toronto, Canada), and collected into Eppendorf tubes containing a 500 uL cushion of RPMI-1640 (Wisent) with 10% heat-inactivated FBS (Wisent).
Samples were processed according to protocols for 5’ v2 chemistry with VDJ (T) library enrichment from 10X Genomics.

treatment_protocol: Aged WT and Aged µMT were assessed at 22 months of age.

value: Spleen

value: T Cells

value: WT C57BL6J Mice

value: Aged


title: HNU1345


title: 143B_PXD2

value: osteosarcoma


title: 143B_PXD1


title: WT_T_Cells

description: 10x Genomics


title: mediastinal-LN-HDM-Tregs-KO-4

type: RNA

city: Lille

first: Artemii

last: Nikitin

address: 1,  Rue du Professeur Calmette

country: France

institute: Inserm

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: RMA and Quantile Normalization with median polish using Partek. The data obtained are log2-transformed.

label: biotin

source_name: RORA-FLOX-FOXP3-CRE adult female mice

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: RNAs extracted with RNeasy Micro Kit - QIAGEN according to the manufacturer’s instructions

treatment_protocol: TCRb+CD4+Foxp3+ Treg cells were isolated from varions murine tissues using FACS

value: KO

value: Mice treated with HDM


title: KO_T_Cells_TCR

description: 10x Genomics


title: HNU1209

source_name: Oropharynx cancer

value: III


title: TCRseq treatment

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

institute: Charité University Medicine

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x genomics Cell Ranger expression profiling and VDJ pipelines at default settings (v5.0.0)
Further processing was done with Seurat v5.0.3 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10 (refdata-gex-mm10-2020-A, pre-built 10x genomics mouse reference)
Supplementary files format and content: Cellranger gene expression pipeline output files: barcodes.tsv.gz, features.tsv.gz, matrix.mts.gz
Supplementary files format and content: Cellranger VDJ pipeline output files: filtered_contig_annotations.csv
Library strategy: TCR-seq

molecule: polyA RNA

source_name: Tumor-draining lymph node

extract_protocol:
Tumor-draining lymph nodes were resected on day 8 post tumor cell injection, finely minced using scalpels and enzymatically digested with collagenase I/IV and DNAse I. Cells were then strained and APCs and T cells were isolated by flow cytometric sorting.
Libraries were generated according to manufacturer's instructions (10x 5' scRNAseq, 10x VDJ kit)

treatment_protocol: Mice were administered with RGX-104 containing chow starting on day 3 post tumor cell injection. Control mice received control chow.

value: Tumor-draining lymph node

value: T cells

value: wildtype


title: HNU1118

value: II


title: 143B_PCIDOX3

value: the combination of 0.1μM DOX and 1.5μM PCI-24781 for 24 hours


title: KO_T_Cells

description: 10x Genomics


title: HNU1024

value: male

value: Negative

value: IVB

value: Cold


title: TCRseq control

value: Control chow


title: 143B_PCIDOX1


title: 143B_PCI3

value: 1.5μM PCI-24781 for 24 hours


title: HNU1014

value: Oropharynx squamous cell carcinoma


title: mediastinal-LN-HDM-Tregs-KO-3


title: scRNAseq treatment

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x genomics Cell Ranger expression profiling and VDJ pipelines at default settings (v5.0.0)
Further processing was done with Seurat v5.0.3 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10 (refdata-gex-mm10-2020-A, pre-built 10x genomics mouse reference)
Supplementary files format and content: Cellranger gene expression pipeline output files: barcodes.tsv.gz, features.tsv.gz, matrix.mts.gz
Supplementary files format and content: Cellranger VDJ pipeline output files: filtered_contig_annotations.csv

value: T cells and APCs


title: mediastinal-LN-HDM-WT-Tregs-4

source_name: FOXP3-CRE adult female mice

value: WT


title: mediastinal-LN-HDM-WT-Tregs-2


title: mediastinal-LN-HDM-WT-Tregs-1


title: Lung-HDM-Tregs-KO-4

value: KO


title: mediastinal-LN-HDM-Tregs-KO-2

value: Mice treated with HDM


title: mediastinal-LN-HDM-WT-Tregs-3


title: 143B_PCI2

value: osteosarcoma


title: mediastinal-LN-HDM-Tregs-KO-1


title: 143B_PCI1


title: carbo_td_2_ccr2.pos

city: St Louis

first: Ruijun

last: He

state: Missouri

address: 660 S Euclid Ave

department: Cardiology

institute: Washington University School of Medicine

data_processing:
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. All gene counts were then imported into the R studio and processed and analyzed with R/Bioconductor packages including cpm (Counts per million), EdgeR, DESeq2. Packages including ggplot2, ggrepel, pheatmap, dplyr were utilized for visualization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: heart

extract_protocol:
enzyme-based mouse heart digestion, FACS, Qiagen micro RNAeasy extraction kit
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq version 2.20 software.  RNA-seq reads were then aligned to the Ensembl release 76 Mus musculus primary assembly with STAR version 2.5.1a1.

treatment_protocol: Carboplatin (Carbo, 45mg/kg) or equal volume of PBS was intraperitoneally injected twice a week for two weeks. The mice were harvested at day3, or 4 weeks after the 2-week treatement of Carbo/PBS.

value: heart

value: CCR2 positive macrophage

value: CBP+Recovery

tag: time


title: carbo_td_1_ccr2.pos


title: HNU1021

value: III


title: Lung-HDM-Tregs-KO-3

tag: genotype


title: HNU1008

tag: age

value: IVa


title: HNU1012

value: female

tag: pt


title: Lung-HDM-Tregs-KO-2


title: 143B_NC2

value: DMSO for 24 hours


title: HNU1003

value: Negative

tag: pn

value: II


title: carbo_3_ccr2.pos


title: Human Normozoospermic Sample 3

city: Barcelona

first: Meritxell

last: Jodar

state: Barcelona

address: C/ Casanova, 143 Planta 1 Ala nord

department: Biomedical Sciences

country: Spain

institute: Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona - Universitat de Barcelona

data_processing:
To apply the KNIFE algorithm created by Szabo et al., 2015 (doi: 10.1186/s13059-015-0690-5), fastq files were mapped using the Bowtie2 to indexed reference genome (h38), ribosomal RNA, and databases of linear exon-exon junctions and scrambled exon-exon junctions.
the KNIFE algorithm calculates a statistical confidence score for each read based on the alignment properties, including mismatches and mapping quality to reduce the number of false-positives. Furthermore, it applies a two-step logistic generalized linear model (GLM) to determine whether a junction matching to a circRNA is a true positive or an artefactual alignment, giving a high-confident p value score. Described in Szabo et al., 2015 (doi: 10.1186/s13059-015-0690-5)
KNIFE output files named combined reports were employed. Only ≥ 2 reads containing a circularized junction with a p value score ≥ 0.9 were considered true positives.
Genome_build: Hg38
Supplementary_files_format_and_content: circular RNA reads and p-value score text file

source_name: Spermatozoa

extract_protocol:
Purified spermatozoa from ejaculates was prepared and stored at -80 ºC in RLT buffer (Qiagen) and 1.5 % β-mercaptoethanol until further processing. Long RNA fraction was individually extracted following the RNeasy Mini Kit protocol (Qiagen) with some modifications previously established in Goodrich et al. 2013 (doi: 10.1007/978-1-62703-038-0_33)
Five ng of each quality sperm RNA sample (n=3) were reverse transcribed and cDNA was amplified with SeqPlex RNA Amplification (Sigma-Aldrich). Residual nucleotides and primer dimers were removed with the MiniElute PCR Purification kit (Qiagen) following the manufacturer’s instructions. Library construction was performed with 50 ng of amplified cDNA, previously quantified using Quant-iT™ dsDNA Assay Kit (Thermo Fisher Scientific), and the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs). NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (New England Biolabs) were included for sample barcoding. The surplus of primer dimers was cleaned-up with AmpureXP (Beckman Coulter). The correct elimination of primer dimers was assessed with the DNA High Sensitivity Assay in the Bioanalyzer 2100 (Agilent Technologies). Libraries were quantified through KAPA Library Quantification Kit (Roche) and pooled. Paired-end sequencing was performed for 2x75 base pairs (bp) using the Illumina HiSeq-2500 sequencer.

value: Spermatozoa


title: 143B_DOX3

value: 0.1μM DOX for 24 hours


title: carbo_4_ccr2.pos


title: 143B_NC1


title: Lung-HDM-Tregs-WT-4


title: HNU1010

value: Positive

value: Oropharynx squamous cell carcinoma

tag: cm

value: I

value: Cold


title: Lung-HDM-Tregs-KO-1

value: KO

value: Mice treated with HDM


title: scRNASeq control

value: Tumor-draining lymph node

value: T cells and APCs

value: wildtype

value: Control chow


title: Human Normozoospermic Sample 2


title: Human Normozoospermic Sample 1


title: 143B_NC3

value: osteosarcoma


title: carbo_td_2_ccr2.neg

value: heart

value: CCR2 negative macrophage

value: CBP+Recovery


title: 143B_DOX2


title: 143B_PCIDOX2

value: the combination of 0.1μM DOX and 1.5μM PCI-24781 for 24 hours


title: 143B_DOX1


title: carbo_td_1_ccr2.neg


title: IMR_B03

description: PE150 high throughout data

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome (UCSC GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: Lung stroma

growth_protocol: Normal human stromal cells were routinely cultured in stromal complete media supplemented with 10% FBS, until a total number of approximately 1,000,000 was reached in each flask and subject to treatment by the chemotherapeutic agent bleomycin (BLEO).

extract_protocol:
Cells were lysed for RNA preparation using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To induce senescence, bleomycin (BLEO) was added to the media at 50 μg/ml, and cells were treated for 12 h before media change.

value: Lung stroma

value: Normal human primary stromal cell line

value: Stromal

value: wild type

value: Bleomycin


title: sinc3A

city: Yangling

first: ya

middle: long

last: an

address: Xinong No.22

institute: Northwest Agriculture & Forestry University

description: Ctrol of small interference

data_processing:
Sequence reads were trim-glore for adaptor / low-quality sequence
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited txt files includes raw counts values for each Sample
Supplementary files format and content: tab-delimited txt files includes FPKM counts values for each Sample

organism: Sus scrofa

source_name: Porcine primary muscle satellite cells

extract_protocol:
RNA was harvested using
Library type: DNBSEQ Eukaryotic Strand-specific mRNA library; Sequencing Platform: DNBseq; Sequencing read Length: PE150; Clean fastq phred quality score encoding:Phred+33.

value: Porcine primary muscle satellite cells


title: pbs_td_1_ccr2.pos

value: CCR2 positive macrophage

value: PBS+Recovery


title: Lung-HDM-Tregs-WT-1

value: WT

value: Mice treated with HDM


title: sinc2A

description: Ctrol of small interference


title: IMR_B02

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

institute: Chinese Academy of Sciences

description: PE150 high throughout data


title: Tregs-Spleen-CD-KO-4

source_name: RORA-FLOX-FOXP3-CRE adult male mice

value: KO

value: Mice on Chow Diet


title: Lung-HDM-Tregs-WT-3


title: Tregs-Spleen-CD-KO-3


title: Tregs-Spleen-CD-WT-3

source_name: FOXP3-CRE adult male mice


title: sinc1A

description: Ctrol of small interference


title: Tregs-Spleen-CD-WT-4


title: Lung-HDM-Tregs-WT-2


title: IMR_B01

description: PE150 high throughout data


title: pbs_11_ccr2.pos


title: carbo_4_ccr2.neg


title: si3A

description: Small interference of NUDT3

value: Small interference


title: pbs_10_ccr2.pos

value: heart


title: IMR_C02

description: PE150 high throughout data

value: CTRL


title: si2A

description: Small interference of NUDT3


title: pbs_td_1_ccr2.neg

value: CCR2 negative macrophage


title: pbs_3_ccr2.neg


title: pbs_10_ccr2.neg


title: IMR_C01

description: PE150 high throughout data


title: IMR_C03

description: PE150 high throughout data


title: si1A

description: Small interference of NUDT3


title: PC4A

description: Overexpression of NUDT3

value: Overexpression


title: PC6A

description: Overexpression of NUDT3


title: HUVE_B03

description: PE150 high throughout data

source_name: Umbilical vein stroma

value: Umbilical vein stroma


title: pbs_pos_m12_d3

value: PBS


title: PC3A

description: Overexpression of NUDT3


title: HUVE_B02

description: PE150 high throughout data

value: Normal human primary stromal cell line

value: Stromal


title: Tregs-Spleen-CD-KO-2


title: pbs_11_ccr2.neg


title: HUVE_B01

description: PE150 high throughout data

value: wild type

value: Bleomycin


title: NC3A

description: Ctrol of Overexpression

value: Porcine primary muscle satellite cells


title: Tregs-Spleen-CD-WT-2


title: pbs_pos_f41_d3

value: CCR2 positive macrophage


title: HUVE_C03

description: PE150 high throughout data


title: pbs_pos_22y3_d3


title: NC2A

description: Ctrol of Overexpression

value: Ctrol _Overexpression


title: Tregs-Spleen-CD-KO-1


title: Tregs-eWAT-HFD-KO-3

value: Mice on HFD


title: HUVE_C02

description: PE150 high throughout data


title: pbs_neg_m3_d3


title: HUVE_C01

description: PE150 high throughout data


title: NC1A

description: Ctrol of Overexpression


title: pbs_neg_147_d3


title: TM rep10

first: zhang

middle: ying

last: ying

state: Shanghai

address: Beidi Road No.2901

department: Institute of Animal Husbandry & Veterinary Science

institute: Shanghai Academy of Agricultural Sciences

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis .
Remove the reads of 3 'end band connectors and reads with Q20(%)
The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
HTSeq(0.9.1) statistics were used to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Sus_scrofa.Sscrofa11.1.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include counts values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: trapezius muscle

growth_protocol: Male Chalu black pigs with similar genetic backgrounds, produced by one sire, were born and raised under the same environmental and nutritional conditions and housed at Ningbo RUINOGN Animal Husbandry Co., LTD in Ningbo, Zhejiang Province, China.

extract_protocol:
Total RNA from samples in each group (n=10) was extracted using the Trizol method (Invitrogen Life Technologies, Gaithersburg, MD), according to the manufacturer’s instructions. The RNA concentration, quality and integrity were determined with NanoDrop spectrophotometer (Thermo Scientific).
The transcriptome libraries of each group (n=10) were constructed for sequencing using the KAPA-Stranded RNA-Seq Library Prep Kit (Illumina).

treatment_protocol: All pigs were transported to Ninghai HUATONG Food Co., LTD (Ningbo, Zhejiang Province, China) and slaughtered following routine abattoir procedures after fasting 24h. Pigs were electrocuted at slaughter house, followed by exsanguination, using standard industry protocols. Within 45 minutes after death, the LDM, HM, TM and PB was collected for meat quality index detection. All samples were taken from the left side of the carcass. Simultaneously, the muscle samples were separated to avoid fascia and stored in liquid nitrogen for subsequent experiments.

value: trapezius muscle


title: TM rep9


title: huc_B03

description: PE150 high throughout data


title: pbs_neg_3_d3


title: huc_B02

description: PE150 high throughout data


title: Tregs-eWAT-HFD-KO-2

value: KO


title: TM rep8


title: pbs_neg_2y_d3


title: huc_B01

description: PE150 high throughout data


title: Tregs-eWAT-HFD-WT-3

value: WT


title: Tregs-Spleen-CD-WT-1

value: Mice on Chow Diet


title: Tregs-eWAT-HFD-KO-1


title: pbs_neg_2.1_d3

value: heart


title: Treg-5d-in-vitro-IL-2-and-IL-4-KO-5


title: huc_C03

description: PE150 high throughout data

value: CTRL


title: Tregs-eWAT-HFD-WT-1


title: TM rep6


title: huc_C02

description: PE150 high throughout data


title: Tregs-eWAT-HFD-WT-2


title: TM rep5


title: pbs_neg_1_d3

value: CCR2 negative macrophage


title: Treg-5d-in-vitro-IL-2-and-IL-4-KO-4


title: pbs_neg_2_d3


title: Treg-5d-in-vitro-IL-2-KO-5


title: huc_C01

description: PE150 high throughout data

value: Umbilical vein stroma


title: cbp_pos_456_d3

value: Carbo


title: TM rep3


title: HBF_B03

description: PE150 high throughout data

source_name: Breast stroma

value: Breast stroma

value: Normal human primary stromal cell line


title: Treg-5d-in-vitro-IL-2-and-IL-4-WT-5


title: TM rep7


title: Treg-5d-in-vitro-IL-2-KO-4


title: Treg-5d-in-vitro-IL-2-WT-5


title: TM rep2


title: cbp_pos_256_d3


title: Treg-5d-in-vitro-IL-2-and-IL-4-WT-4


title: HBF_B01

description: PE150 high throughout data

value: Stromal

value: wild type


title: TM rep1


title: TM rep4


title: HBF_B02

description: PE150 high throughout data

value: Bleomycin


title: cbp_pos_145_d3

value: CCR2 positive macrophage


title: HBF_C03

description: PE150 high throughout data


title: Treg-5d-in-vitro-IL-2-WT-4


title: cbp_neg_68_d3


title: PB rep10

source_name: pork belly muscle

value: pork belly muscle


title: cbp_neg_f26_d3


title: PB rep9


title: Treg-5d-in-vitro-IL-2-and-IL-4-KO-3


title: HBF_C02

description: PE150 high throughout data


title: HBF_C01

description: PE150 high throughout data


title: cbp_neg_38y_d3


title: PB rep7


title: Treg-5d-in-vitro-IL-2-KO-3


title: Treg-5d-in-vitro-IL-2-KO-2


title: Combined Proximal, Distal, and Whole Lung Organoid, SARS-CoV-2 Infected, Replicate 1

city: La Jolla

first: Sandra

middle: L.

last: Leibel

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

description:
Combined_LO_Infected_Rep1
H9 embryonic stem cells

data_processing:
Demultiplexing, barcoded processing, and gene counting were performed using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: 10x Genomics Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

source_name: combined proximal, distal, and whole lung organoid

extract_protocol: 10X Genomics scRNA-seq 3’ v3.1 kit was used to generate the GEM, cDNA and sequencing library according to the manufacturer’s instructions (10X Genomics) and sequenced on Illumina NovaSeq 6000.

value: SARS-CoV-2 Infected


title: Combined Proximal, Distal, and Whole Lung Organoid, SARS-CoV-2 Infected, Replicate 2

description:
Combined_LO_Infected_Rep2
H9 embryonic stem cells

value: combined proximal, distal, and whole lung organoid


title: Treg-5d-in-vitro-IL-2-and-IL-4-KO-2

value: KO


title: cbp_neg_14_d3


title: cbp_neg_f5_d3


title: Combined Proximal, Distal, and Whole Lung Organoid, Control, Replicate 2

description:
Combined_LO_Control_Rep2
H9 embryonic stem cells

value: Control


title: PB rep8


title: cbp_neg_5.1_d3


title: carbo_pump_d7

data_processing:
All the codes used in the manuscript is deposited in GitHub. The obtained single-cell RNA sequencing data contain 21681 feature genes across 38066 cells. Downstream data processing was performed in the R package Seurat (v4) (Hao et al., 2021). After being filtered as mitochondrial gene proportion(prompt) < 10.0%, nCounts of RNA<30000, and nFeature RNA counts< 7000 & >500, 20290 features across 17438 samples remained. SCTransform was used to scale and normalize the data for RNA counts. PCA was used for dimensionality reduction, data was clustered at multiple resolutions, and UMAP projections were generated for data visualization. We utilized graph-based clustering and UMAP (Uniform Manifold Approximation and Projection) visualization of the combined four groups (Dim=1:80, resolution=0.6) (FigureS10.C-D). Differentially expressed genes were identified using the FindAllMarkers function with a minimum fraction (min.pct) of 0.1 and a logFC threshold of 0.1. According to the feature genes of each cluster, the contamination from cardiomyocytes, endothelial cells, fibroblasts, lymphocytes were identified and removed. Cells showing co-expression of multiple cell-type-specific genes were identified as doublets and removed from any downstream analysis (FigureS10.D). Due to the substantial difference between the injured and uninjured groups, we used aggregated method to avoid over-representation. The proliferating cells, monocytes, and mono-phagocytes including Dendritic cells and macrophages are kept for further analysis (Dim= 1:80, resolution = 0.4). Seurat different expression analysis was performed using Findmarker function to compare the expression data across experimental groups. Differential gene expression between CBP+Sham and PBS+Sham; and between CBP+AngII/PE and PBS+AngII/PE was performed through Seurat
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
enzyme-based mouse heart digestion, FACS, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 from 10X Genomics.
The Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 from 10X Genomics was used following manufacturer’s instruction. For each experimental group, 10,000 cells were loaded into one well of a Chip G kit for GEM generation. The reverse transcription, barcoding, post-RT cleanup with Dynbeads, cDNA amplification, and purification with SPRIselect were performed according to the Chromium 10x 3’v1 protocol as the library preparation step. Each sample was sequenced on a NovaSeq 6000 S4 platform with a sequencing depth of approximately 20,000–30,000 reads per cell. Sequencing reads were aligned to the whole genome mRNA reference generated from the mm10 transcriptome using the Cell Ranger V3 software (10X Genomics) according to the 10X Genomics instructions. The count matrices were pre-processed and analyzed using R package Seurat (v3.2.3).

treatment_protocol: Carboplatin (Carbo, 45mg/kg) or equal volume of PBS was intraperitoneally injected twice a week for two weeks. These mice then underwent a 4-week recvoery period before being subcutaneously implanted with an osmotic minipump. They will either be infused with AngII (1.5mg/kg/d) and PE (50mg/kg/d), or saline for 7 days. Mice were euthanized at day 7 of the minipump infusion.

value: mononuclear phagocytes


title: cbp_neg_5_d3

value: heart


title: Treg-5d-in-vitro-IL-2-WT-3

value: WT


title: PB rep4


title: Combined Proximal, Distal, and Whole Lung Organoid, Control, Replicate 1

description:
Combined_LO_Control_Rep1
H9 embryonic stem cells


title: Treg-5d-in-vitro-IL-2-and-IL-4-WT-3


title: PB rep5


title: HN391

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq (2.20.0.422).
High-quality SE reads were mapped to the human genome (hg38) using STAR (2.0.9) and, following the removal of multimapping reads, converted to gene specific read counts for annotated genes using featureCounts (2.0.0).
Genome_build: hg38
Supplementary_files_format_and_content: Two matrix tables with raw gene counts and TPM values for every gene and every sample

extract_protocol:
Primary tumors were snap-frozen immediately after obtaining the tissue. AllPrep DNA/RNA Kit (Qiagen, Germany) was used for RNA extraction following the manufacturer's instructions.
Libraries were prepared from 500ng of input material using TruSeq Stranded mRNA (manufacturer's instructions) and subsequently quantified and quality checked using Agilent 2100 Bioanalyzer Instrument (DNA 7500 kit).
Libraries were pooled and sequenced in one lane of HiSeq 2500 System running in 51 cycle/single-end/high output mode.

value: male

value: Positive

value: Oropharynx squamous cell carcinoma

tag: Stage

value: Hot


title: L4443


title: HN348


title: LDM rep10

source_name: longissimus dorsi muscle

value: longissimus dorsi muscle


title: Treg-5d-in-vitro-IL-2-and-IL-4-WT-2


title: pbs_sham_d7


title: PB rep3


title: PB rep6


title: HN341


title: Treg-5d-in-vitro-IL-2-WT-2


title: Treg-5d-in-vitro-IL-2-and-IL-4-KO-1


title: L4442

value: female

value: Negative

value: Cold


title: PB rep2


title: pbs_pump_d7


title: Treg-5d-in-vitro-IL-2-KO-1


title: LDM rep9


title: HN340


title: RP

city: Chongqing

first: He

address: No. 426 Songshi North Road, Yubei District, Chongqing, China

institute: Chongqing Medical University Affiliated Stomatological Hospital

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: murine maxillary periodontium

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: murine maxillary periodontium


title: PB rep1


title: carbo_sham_d7


title: cbp_neg_4_d3

value: CCR2 negative macrophage

value: Carbo


title: LDM rep8


title: HN328


title: LDM rep7


title: aKO, snRNAseq

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were using Cellranger-arc-2.0.0.
SnATAC sequence data were deleted due to low quality.
Ambient RNA was removed using Cellbender
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
Tissue samples were subjected to lysis in 1 ml of lysis buffer (10 mM Tris-HCl, 5% Nonidet P40, 3 mM MgCl2, and 10 mM NaCl) along with 1 U/μl RNasin Plus RNase Inhibitor (Promega) for 15 minutes in a douncing tube placed on ice. The tissue was then homogenized using a loose pestle with ten dounces. The resulting suspension was filtered through a 70 μm mesh and centrifuged at 500 g for 5 minutes at 4°C. Post-lysis, the sample was treated with 2 ml of ice-cold nucleus wash buffer (5% wt/vol BSA, 0.25% wt/vol glycerol, 40 U/mL Protector RNAse inhibitor, 0.5X PBS), passed through a 20 μm mesh twice, and re-centrifuged under the same conditions. The supernatant was discarded, and the nuclear pellet was resuspended in 500 μl of wash buffer. An additional 500 μl of 50% (wt/vol) iodixanol (Optiprep) working solution was added to aid in further cleaning. This suspension was then layered over 1 mL of 29% (wt/vol) iodixanol solution in a 2 mL centrifuge tube and centrifuged at 10,000g for 30 minutes at 4°C. Finally, the nuclei were resuspended in a suitable volume of nuclei buffer to achieve a concentration of 500-1,000 nuclei/μl for subsequent capture.
Library was constructed according to manufacter's instructions (https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevF.pdf).

value: Hippocampus

value: Brain cells

value: Astrocyte specific MAGL-KO


title: 377P

last: Wang

description: 10x Genomics


title: Treg-5d-in-vitro-IL-2-and-IL-4-WT-1


title: HN322

first: Simon

last: Laban

address: Frauensteige 14a, Haus 18

institute: Ulm University Medical Center

source_name: Oropharynx cancer


title: 2-KO HFDfast_ins

description: eWAT from WT  fasted HFD-fed mice with Treg-specific RORa KO injected with insulin

extract_protocol: total RNA extracted with the trizol protocol, clean up with the Nucleospin RNA XS column Macherey Nagel according to the manufacture's instuctions

treatment_protocol: Mice were fed chow diet or HFD

value: KO


title: Treg-5d-in-vitro-IL-2-WT-1


title: 1-KO HFDfast_ins


title: HN315


title: LDM rep4


title: 2-WT HFDfast_ins

description: eWAT from WT fasted HFD-fed mice injected with insulin


title: LDM rep5


title: HN314


title: 3-KO HFDfast

description: eWAT from fasted HFD-fed mice with Treg-specific RORa KO

value: HFDfast


title: 1-WT HFDfast_ins

value: WT


title: tKO, snRNAseq

description: 10x Genomics

value: Total/global MAGL-KO


title: WT, snRNAseq

description: 10x Genomics

value: Wild type


title: TS, scRNA seq

city: Shenzhen

first: Jiajie

last: Lin

address: 3025# Shennan Road

institute: The Eighth Affiliated Hospital, Sun Yat-sen University

description: 10x genomics

data_processing:
CellRanger (v5.0.1) was used to process the raw data to generate gene expression matrix
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: the enthesis tissue of the Achilles tendon

extract_protocol:
Achilles's tendon enthesis of the SKG mice were dissected and transferred to sterile centrifuge tubes, the tissues were cut into 2 mm tissue blocks and digested with 0.5 % collagenase type II for 2 hours in a 37℃constant temperature shaker. The cell suspension was filtered through a 40 µm cell strainer, then centrifuged at 400×g for 6 min at room temperature and discard the supernatant to collect dissociated cells. Red blood cell lysis buffer was added to resuspend cells and incubated for 5min at room temperature. The cell suspension was centrifuged again at 400×g for 6 min at room temperature and the Dead Cell Removal Kit was used to remove dead cell. Cell viability was assessed by trypan blue, sample with greater than 80% cell viability were qualified to perform 10× Genomics single-cell RNA sequencing.
Single-cell suspension was loaded to a Chromium Controller and partitioned into Gel Bead-In-Emulsions (GEMs) by the microfluidic cross-system according to the manufacturer’s protocol. Reverse transcription reaction was performed to synthesize cDNA, followed by fragmentation, adapter ligation, PCR amplification and products purification. The libraries were sequenced on Illumina NovaSeq 6000

value: tail suspension


title: HN295

city: Ulm

value: male

value: Positive

value: Oropharynx squamous cell carcinoma

value: Hot


title: LDM rep3

value: longissimus dorsi muscle


title: nKO, snRNAseq

description: 10x Genomics

value: Neuron specific MAGL-KO


title: 9318 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

type: genomic

city: Maywood

first: Alexandra

middle: L

last: Nowak

institute: Loyola University Chicago

hyb_protocol: Bisufate converted DNA was amplifiled, fragented, and hybridized to human Infinium EPIC Methylation BeadChip per Illumina protocol

scan_protocol: EPIC Methylation BeadChip scanning performed using the Illumina iScan System.

data_processing: “mediation” R package, v.4.5,1

label: Cy3 and Cy5

source_name: Peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Extraction was performed from DNA Paxgene tubes using a chemical precipitatin method.

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

value: Peripheral blood leukocytes

tag: data collectin


title: LDM rep2

tag: tissue


title: LDM rep6


title: Y-TBI_3

city: Nantong

first: Zhichao

last: Lu

address: 20 Xisi Rd,

institute: Affiliated Hospital of Nantong University

data_processing:
R version 4.3.3.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using R version 4.3.3.
Trimmed sequence reads were mapped to GrCM38/mm10 using R version 4.3.3.
Read count extraction and normalization were performed using R version 4.3.3.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: bone marrow

extract_protocol:
Bone marrow from aged and young C57BL/6 mice using TRIzol for RNA.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manunufacturer's protocols.

value: bone marrow

tag: strain

tag: sample group

value: young-Traumatic Brain Injury (Young-TBI)


title: NTS, scRNA seq

description: 10x genomics

value: the enthesis tissue of the Achilles tendon

tag: treatment

value: non-tail suspension


title: 9302 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Term


title: 2-KO HFDfast

value: KO

value: HFDfast


title: 9285 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: Y-TBI_2


title: 9294 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: LDM rep1


title: 1-KO HFDfast


title: Y-TBI_1


title: 9278 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: HM rep8

source_name: hamstring muscle

value: hamstring muscle


title: Y-con_3

value: Young-control (Young-CON)


title: 9273 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 2-WT HFDfast

description: eWAT from WT fasted HFD-fed mice

value: WT


title: 3-WT HFDfast

description: eWAT from WT fasted HFD-fed mice


title: 1-WT HFDfast

description: eWAT from WT fasted HFD-fed mice


title: Y-con_2


title: HM rep7


title: HM rep10


title: 9267 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 5-KO Cdfast

description: eWAT from fasted CD-fed mice with Treg-specific RORa KO

value: Cdfast


title: HM rep6


title: Y-con_1


title: 9257 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 4-KO Cdfast


title: 9255 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: A-TBI_3

value: aged-Traumatic Brain Injury (Aged-TBI)


title: HM rep9


title: HM rep5


title: 3-KO Cdfast


title: 9254 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: A-TBI_2


title: 2-KO Cdfast


title: HM rep3


title: A-TBI_1


title: A-con_3

value: aged-control (Aged-CON)


title: 9229 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 9232 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: HM rep2


title: 4-WT Cdfast

description: eWAT from WT fasted CD-fed mice


title: 1-KO Cdfast


title: HM rep1


title: A-con_2


title: 9223 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: Ncs2elp6hel2_2_mRNA

city: Bern

first: Jie

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

data_processing:
Reads from RNA-seq data were mapped to CDS without adapter trimming using bowtie with the parameters "-n 1 -l 28 -m 1 --no-unal --best --strata". Gene expression for each CDS were quantified with a custom script.
Assembly: sacCer3
Supplementary files format and content: mRNA raw count matrix

organism: Saccharomyces cerevisiae

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 ncs2Δ::HIS3MX elp6Δ::URA3 hel2Δ::LEU2

growth_protocol: Cells were grown in YPD at 30C and 200 RPM

extract_protocol:
Total RNA was extracted with acidic phenol and enriched for mRNAs using the Poly(A) tail
Libraries were prepared using TruSeq stranded mRNA kit

tag: cell line

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3 hel2{delta}::LEU2


title: A-con_1


title: Forager,rep 3, scRNAseq

city: Beijing

first: Xiasang

address: 2 Yuanmingyuan West Road. Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

institute: State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger mkfastq pipeline within the Cell Ranger software v6.1.1.
Assembly: Amel_HAv3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Apis mellifera

source_name: honeybee brain

extract_protocol:
Fresh brain tissues were first dissected from the heads of pupae, nurses, and foragers, respectively, and then stored in MACS Tissue Storage Solution on ice to maintain tissue viability. The cell suspension was obtained through enzymatic digestion of the dissected honeybee brain tissue from each biological replicate using a mixture of activated papain solution (50 mg/mL), Liberase TM solution (2.5 mg/L), and DNase I solution (10 mg/mL). The brain tissue underwent two rounds of enzymatic digestion. Prior to digestion, the brain tissue was washed three times with PBS buffer containing 0.4% BSA, each wash lasting 10 minutes.
Library was performed according to the manufacter's instructions(Chromium Single Cell 3’ Reagent Kits v3.1 protocol, 10x Genomics).

value: honeybee brain

value: neural cell

tag: cell type

tag: developmental stage

value: Adult


title: 2-WT Cdfast

description: eWAT from WT fasted CD-fed mice

data_processing: RMA and Quantile Normalization with median polish using Partek. The data obtained are log2-transformed.


title: HM rep4


title: 9222 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Black/Female

value: Peripheral blood leukocytes


title: Ncs2elp6hel2_1_mRNA


title: 3-WT Cdfast

description: eWAT from WT fasted CD-fed mice


title: 9186 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Preterm


title: 9206 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: Forager, rep 2, scRNAseq

description: 10x Genomics


title: Mouse heart, F_DM 4

city: Galveston

first: Qingjie

last: Li

address: 301 University Boulevard

department: Internal Medicine

institute: UTMB

data_processing:
A cDNA library constructed by the pooled RNA 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.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
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.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Heart

growth_protocol: Nineteen two-month-old male and female C57BL/6NTac germ-free mice were housed in the UTMB Germ-Free Mouse Facility with a 12-hour light/dark cycle, temperature range of 24-26°C, and a relative humidity of 40-70%.

extract_protocol:
Mice were euthanized under anesthesia and a piece of cardiac tissue was snap-frozen in liquid nitrogen. Total RNAs were isolated from pulverized frozen heart tissue using the PureLink RNA Mini Kit (Thermo Fisher). RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: There were four groups of 4 or 5 mice receiving the following treatments: (1) males with normal microbiome (M_NM), (2) males with dysbiotic microbiome (M_DM), (3) females with normal microbiome (F_NM), and (4) females with dysbiotic microbiome (F_DM).

value: Heart

value: Cardiocytes

value: DM FMT


title: Mouse heart, F_DM 3


title: Ncs2elp6_2_mRNA

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 ncs2Δ::HIS3MX elp6Δ::URA3

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 ncs2{delta}::HIS3MX elp6{delta}::URA3


title: Ncs2elp6_1_mRNA