title: MSCs treated with control_2 (GTC control)


title: ACLF2

status: Public on Dec 31 2025

type: SRA

city: Guangzhou

first: Jia

last: Chen

state: Guangdong

address: The Third Affiliated Hospital of Sun Yat sen University, No. 600 Tianhe Road, Tianhe District, Guangzhou

department: Department of Infectious Diseases and Guangdong Key Laboratory of Liver Disease Research

country: China

institute: Third Affiliated Hospital of Sun Yat-sen University

description: ACLF with Saline treatment

library_source: transcriptomic

data_processing:
CLC Genomics Workbench V 11.0.1
Sequence reads were trimmed for adaptor sequencelow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequnce reads were mapped to GrCM3/mm10 using CLC genomic berchwork parameters-mismat cost 2inserton cost- 3 deleton ost-3 ength faction: 0.3 similanty faction:0.3
Read count extraction and normalization were performed using CLC genomic benchwork
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 files include RPKlI values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was harvested using Rneasv miri lus kit (Ciagen). 1 3 u of total RNA was used for the construcfion of seauencina libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Sea Library Prep Kit folowino manufa cturer's protocols

tag: tissue

value: liver

tag: genotype

value: WT

tag: treatment

value: ACLF with Saline treatment


title: ACLF1

description: ACLF with Saline treatment


title: Cul4b-ChIPseq

city: Jinan

first: wenqian

last: yu

state: Shandong

address: No.105, jiefang road

department: Research Center of Translational Medicine

institute: Central Hospital Affiliated to Shandong First Medical University

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 software was used to call peaks.
Peaks were annotated by ChIPseeker package.
Assembly: mm10
Supplementary files format and content: bw

molecule: genomic DNA

source_name: MOVAS

extract_protocol:
Briefly, cells were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with anti-GATA4. The immunoprecipitated complex was washed, and DNA was extracted and purified by Universal DNA Purification Kit (TIANGEN, #DP214).
The ChIP-Seq library was prepared using original Ultra II DNA Library Kits (NEB, #E7645) according to the manufacturer's instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

tag: cell line

value: MOVAS

tag: cell type

value: mouse aortic vascular smooth muscle cells

tag: antibody

value: untreated


title: MSCs treated with  CaP@Sr-MOF_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: fpkm(.txt)

organism: Homo sapiens

source_name: mesenchymal stem cells

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

value: mesenchymal stem cells

value: incubating with 150 ug/mL CaP@Sr-MOF for 14 days


title: MSCs treated with control_1 (GTC control)

value: incubating with control for 14 days


title: MSCs treated with  CaP@Sr-MOF_2


title: MSCs treated with  CaP@Sr-MOF_1


title: Gata4-ChIPseq


title: Input


title: Sedentary, bio rep4

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

country: USA

institute: University of South Florida

data_processing:
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Assembly: mm10. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Supplementary files format and content: Excel file includes FPKM values for each Sample.

source_name: heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. 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.

value: heart

value: Sedentary


title: MSCs treated with GTC_3

value: incubating with 120 ug/mL GTC for 14 days


title: Sedentary, bio rep2


title: Sedentary, bio rep1


title: MSCs treated with control_1


title: biopsy sample CTR-19 batch 3

city: Philadelphia

first: Yusen

last: Zhou

state: PA

address: 3401 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

description:
Library name: Sample 62
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggrefation were made using the 10X Cellranger 3.1.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gastrointestinal tract

extract_protocol:
For detail information please visit our protocol for human tissue: Morral C, Ghinnagow R, Karakasheva T, et al. Isolation of Epithelial and Stromal Cells from Colon Tissues in Homeostasis and Under Inflammatory Conditions. Bio Protoc. 2023;13:e4825. doi: 10.21769/BioProtoc.4825
Single cell RNA-seq libraries were generated using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X GENOMICS INC) as per manufacturer’s instructions. Illumina NovaSeq 6000 was used to sequence libraries using parameters Read1: index5: index7:Read2:: 28:8:0:87 or 28:10:10:90

value: gastrointestinal tract

value: epithelial, immune and stromal


title: MSCs treated with control_3


title: Sedentary, bio rep3


title: Swimming, bio rep3

value: Swimming


title: biopsy sample CD-05 batch 3

description:
Library name: Sample 61
10x Genomics


title: BA2

description: ACLF with Baicalein treatment

value: ACLF with Baicalein treatment


title: Swimming, bio rep2


title: Swimming, bio rep1


title: OCI-AML2 cells, TRMT5 sgRNA KO biological rep3

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
After sequencing, reads were basecalled using Guppy basecaller v3.6.1 in high-accuracy (hac) mode. All Us were converted to Ts before mapping using BWA, with the following parameters bwa mem -W13 -k6 -xont2d -T20. Reference contained tRNAs with 5‘ and 3‘ RNA adapter sequences included. Differential tRNA modifications were analysed using various basecalling “errors” such as mismatch, insertion and deletion for each position. The basecalling “error” sum was calculated by substracting the frequency of the reference base from 1. The frequency of the reference base equals the number of reads with a basecalled equivalent to the reference base, divided by the depth of coverage for that position. In order to plot differential tRNA modifications, first, get_sum_err.py script was used to calculated the differential sum “errors”, then plot_heatmap.py was used to plot heatmaps. All the scripts were taken from NanotRNA-seq github repo (https://github.com/novoalab/Nano-tRNAseq).
Assembly: hg38
Supplementary files format and content: Each processed data file contains summed basecalling "error" that are used to analyse modification frequency at each tRNA position
Library strategy: NanotRNA-seq (Adapted Nanopore direct RNA sequencing)

extract_protocol:
Mitochondria were isolated using a MACS antibody based mitochondria extraction kit (Miltenyi Biotech) to obtain high quality and intact mitochondria for subsequent RNA isolation. Subsequently, small and large RNAs were isolated using the miRNeasy Micro Kit (Qiagen).
In order to perform NanotRNA-seq on tRNAs, small RNA fractions isolated from KO and scrambled were deacylated with the following protocol; 10 µL nuclease-free water and deacylated in 95 µL 100 mM Tris-HCl (pH 9.0) at 37°C for 30 min. Deacylated tRNAs were recovered using Zymo RNA Clean and Concentrator-5 kit (Zymo, R1016), following the manufacturer’s instructions. tRNA libraries were prepared using NanotRNA-seq library protocol with some protocol alterations described here. The 5’ and 3’ splint adapters were mix at a 1:1 molar ratio in a solution of 10 mM Tris-HCl (pH 7.5), 50 mM NaCl and 1 µL RNasin® Ribonuclease Inhibitor (Promega, N251A) to a final concentration of 1 uM. The mix was heated to 75°C for 15 s and cooled to 25°C at a rate of 0.1°C/s to anneal splint adapters. 200 ng deacylated tRNAs were ligated to the pre-annealed splint adapters at a molar ratio of 1.2:1 (with median length of 90 nucleotides. Deacylated tRNAs were ligated to the pre-annealed 5’ and 3’ splint adapters at a molar ratio of 1.2:1 (assuming an average tRNA length of 90 nt). The ligation was carried out at room temperature for 2 hours in 25 µL with 20% PEG PEG 8000 (NEB, B10048), 1X T4 RNA Ligase 2 Buffer (NEB, B0239S), 2 µL 6 mg/mL recombinant E. coli T4 RNA 2 Ligase (made in-house) and 0.5 µL RNasin® Ribonuclease Inhibitor. Ligation reaction was then cleaned up with 2X volume of RNAClean XP beads (Beckman, A63987) following manufacturer’s instructions. The RNA concentration was determined using Qubit™ RNA High Sensitivity (HS) assay kit (Thermo, Q32852). At least 50 ng of 5‘ and 3‘ ligated tRNAs were ligated to the RTA adapter (ONT, SQK-RNA002)  at a molar ratio of 1:2 in the presence of 1X Quick Ligation Reaction buffer (NEB, B6058S), 1.5 μL T4 DNA Ligase (NEB, M0202M, 2,000,000 units/mL) and 0.5 µL RNasin® Ribonuclease Inhibitor in 15 µL reaction at room temperature for 10 minutes. Consequently, the reaction mix was added to a reverse transcription mix of 11 µL nuclease-free water, 2 µL 10 mM dNTPs (NEB, N0447S), 8 µL 5X Maxima H Minus Reverse Transcriptase Buffer, and 2 µL Maxima H Minus Reverse Transcriptase (Life Technologies, EP0751). Reverse transcription mix was then mixed well and incubated at 60°C for 1 hour, 85°C for 5 minutes and then brought to 4°C. The linearized tRNAs were cleaned up using 2X RNAClean XP beads following manufacturer’s instructions. Then, 6 ul ONT RMX sequencing adapters (ONT, SQK-RNA002) were ligated at room temperature for 10 minutes in a total reaction volume of 40 µL with 1X Quick Ligation Reaction buffer, 3 μL T4 DNA Ligase. The ligation mix was cleaned up with 2X volume of RNAClean XP beads  following manufacturer’s instructions with a few adjustments. The sample was washed twice with 150 μL WSB (Wash Buffer), in which the pellet was resuspended by flicking the tube. The sample was eluted in 20 μL ELB (Elution Buffer) and incubated for 10 minutes at room temperature on a Hula mixer. The final library was prepared by adding 17.5 μL of nuclease-free water and 37.5 μL of vortexed RRB and kept on ice until loading. The MinION flow cell (FLO-MIN-106) was quality checked, primed, and loaded following the standard ONT SQK-RNA002 protocol.

value: Blood

value: Human acute myeloid leukemia cell line

tag: cell compartment

value: mitocontria


title: Muscle, C57BL/6N, male,NAC and TM-cotreated, 28 days, rep5 [D_5]

city: Changsha

first: Guolin

last: Li

state: Hunan

address: 177 Lushan Road

department: College of Life Sciences

institute: Hunan Normal University

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Cutadapt(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
HISAT2(https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package was used to align reads of all samples to the reference genome
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.
Assembly: GRCm38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: gastrocnemius muscle

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencinglibrary. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min).
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used tosynthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR.

value: gastrocnemius muscle

tag: Sex

value: male

tag: strain

value: tetrathiomolybdate (TM) and N-acetylcysteine (NAC) co-treated 28 days


title: biopsy sample CTR-18 batch 3

description:
Library name: Sample 59
10x Genomics


title: OCI-AML2 cells, TRMT5 sgRNA KO biological rep2


title: biopsy sample CTR-17 batch 3

description:
Library name: Sample 58
10x Genomics


title: MSCs treated with control_2


title: OCI-AML2 cells, scramble sgRNA control biological rep3

value: WT


title: Muscle, C57BL/6N, male,NAC and TM-cotreated, 28 days, rep4 [D_4]


title: biopsy sample CTR-16 batch 3

description:
Library name: Sample 57
10x Genomics


title: OCI-AML2 cells, scramble sgRNA control biological rep2


title: OCI-AML2 cells, scramble sgRNA control biological rep1


title: biopsy sample CTR-20 batch 3

description:
Library name: Sample 63
10x Genomics


title: sor4 LL 4

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

data_processing:
quality filtering and trimming bbduk version 38.18 (Q30)
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
Assembly: QM6a_transcript_seq.fa from Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels. 2017;10():170. doi: 10.1186/s13068-017-0825-x
Supplementary files format and content: tab-delimited .txt file include raw counts

organism: Trichoderma reesei

growth_protocol: Trichoderma reesei WT (QM6a) and deletion mutants were grown in minimal medium with cellulose as carbon source at 28°C at for 96h

extract_protocol:
RNA was extracted using Rneasy plant mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using RNA stranded kit, NEB, rRNA depletion  by the Next Generation Sequencing Facility (Vienna Biocenter Core Facilities)

treatment_protocol: cultivation under at 28°C and constant darkness

value: mycelium

tag: type

value: sor4 deletion

value: growth on cellulose in light

tag: time


title: Swimming, bio rep4

value: heart


title: Muscle, C57BL/6N, male,NAC and TM-cotreated, 28 days, rep3 [D_3]


title: Muscle, C57BL/6N, male,NAC and TM-cotreated, 28 days, rep1 [D_1]


title: Muscle, C57BL/6N, male,NAC and TM-cotreated, 28 days, rep2 [D_2]


title: biopsy sample CD-26 batch 3

description:
Library name: Sample 56
10x Genomics


title: sor4 LL 2


title: sor4 LL 3


title: biopsy sample CD-05 batch 2

description:
Library name: Sample 60
10x Genomics


title: biopsy sample CD-18 batch 3

description:
Library name: Sample 55
10x Genomics


title: biopsy sample CTR-17 batch 2

description:
Library name: Sample 54
10x Genomics


title: ku80 LL 1


title: Muscle, C57BL/6N, male,NAC-treated, 28 days, rep5 [C_5]

value: N-acetylcysteine (NAC) treated 28 days


title: biopsy sample CD-22 batch 1

description:
Library name: Sample 52
10x Genomics


title: Muscle, C57BL/6N, male,NAC-treated, 28 days, rep4 [C_4]


title: sor4 DD 3

value: growth on cellulose in darkness


title: biopsy sample CTR-17 batch 1

description:
Library name: Sample 53
10x Genomics

value: gastrointestinal tract


title: sor4 DD 2


title: OCI-AML2 cells, TRMT5 sgRNA KO biological rep1


title: Muscle, C57BL/6N, male,NAC-treated, 28 days, rep3 [C_3]


title: sor4 LL 1


title: Muscle, C57BL/6N, male,NAC-treated, 28 days, rep2 [C_2]


title: ku80 LL 2


title: ku80 DD 1


title: pph5-2_DD3_2

data_processing:
quality filtering and trimming bbduk version 38.18 (Q30)
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
Assembly: QM6a_transcript_seq.fa from Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels. 2017;10():170. doi: 10.1186/s13068-017-0825-x
Supplementary files format and content: Excel (.xlsx) file include raw counts

value: pph5-2 deletion


title: biopsy sample CD-20 batch 3

description:
Library name: Sample 51
10x Genomics

value: epithelial, immune and stromal


title: sor4 DD 1


title: ku80 DD 2


title: pph5-2_DD3_1


title: sor4 DD 4


title: pph5-2_DD3_4


title: Muscle, C57BL/6N, male,TM-treated, 28 days, rep5 [B_5]

value: tetrathiomolybdate(TM) treated 28 days


title: Muscle, C57BL/6N, male,TM-treated, 28 days, rep4 [B_4]


title: mus53_DD3_2

value: WT for pph5-2


title: pph5-2_DD3_3


title: biopsy sample CD-23 batch 2

description:
Library name: Sample 49
10x Genomics


title: biopsy sample CTR-11 batch 3

description:
Library name: Sample 48
10x Genomics


title: Muscle, C57BL/6N, male,NAC-treated, 28 days, rep1 [C_1]


title: mus53_DD3_1


title: Muscle, C57BL/6N, male,TM-treated, 28 days, rep3 [B_3]


title: pph5_DD1_3

value: pph5 deletion


title: biopsy sample CD-25 batch 3

description:
Library name: Sample 46
10x Genomics


title: biopsy sample CTR-11 batch 2

description:
Library name: Sample 47
10x Genomics


title: pp2A_DD1_4

value: pp2A deletion


title: Muscle, C57BL/6N, male,TM-treated, 28 days, rep2 [B_2]

value: gastrocnemius muscle


title: pph5_DD1_2


title: biopsy sample CD-27 batch 3

description:
Library name: Sample 45
10x Genomics


title: biopsy sample CD-19 batch 3

description:
Library name: Sample 50
10x Genomics


title: pp2A_DD1_3


title: Muscle, C57BL/6N, male,TM-treated, 28 days, rep1 [B_1]

value: male


title: pp2A_DD1_2


title: pp2A_DD1_1


title: biopsy sample CD-25 batch 2

description:
Library name: Sample 44
10x Genomics


title: mus53_DD1_2


title: biopsy sample CD-25 batch 1

description:
Library name: Sample 43
10x Genomics


title: mus53_DD1_1


title: Δ21168_LL_3

data_processing:
quality filtering and trimming bbduk version 38.18 (Q30)
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
Supplementary files format and content: excel (.xlsx) file includes raw counts

growth_protocol: Trichoderma reesei WT (QM6a) and deletion mutantswere grown in minimal medium with celluloseas carbon source at 28°C at for 96h

treatment_protocol: cultivation under at constant light or constant darkness

value: 21168 deletion


title: Muscle, C57BL/6N, male, Con, rep5 [A_5]

value: Control


title: Muscle, C57BL/6N, male, Con, rep4 [A_4]


title: Muscle, C57BL/6N, male, Con,  rep3 [A_3]


title: pph5_DD1_1

value: mycelium


title: Δ21168_LL_1


title: Δ21168_LL_2


title: biopsy sample CD-08 batch 3

description:
Library name: Sample 41
10x Genomics


title: biopsy sample CTR-03 batch 3

description:
Library name: Sample 42
10x Genomics


title: Δ80186_LL_3

value: 80186 deletion


title: Muscle, C57BL/6N, male, Con, rep2 [A_2]


title: Control QM6a_LL_3

value: WT

value: growth on cellulose in light


title: Muscle, C57BL/6N, male, Con, rep1 [A_1]


title: Δ80186_LL_1


title: biopsy sample CTR-08 batch 1

description:
Library name: Sample 39
10x Genomics


title: biopsy sample CTR-06 batch 3

description:
Library name: Sample 40
10x Genomics


title: Control QM6a_LL_2


title: 3A_LPS_RNA, rep3

first: Chun-Yan

last: Lim

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

data_processing:
High-quality clean reads from sequenced libraries were acquired after filtering by fastp (version 0.18.0) and trimming by Bowtie2 (version 2.2.8).
The paired-end clean reads were mapped to the mouse reference genome (Ensembl release 106) using HISAT 2.2.4.
The mapped reads of each sample were assembled using StringTie v1.3.1, and gene expression values were estimated with Fragments Per Kilobase of transcript per million mapped reads (FPKM) using the RSEM software.
Differential expression analysis of the RNA-seq dataset was conducted with DESeq2 (v.1.18.1). Genes were identified as differentially expressed with a false discovery rate (FDR) cut-off of 0.05 and an absolute fold change ≥ 2.
Assembly: mouse reference genome GRCm39 (Ensembl release 106)
Supplementary files format and content: tab-delimited text file (txt) includes FPKM and raw counts for each sample.

source_name: Ascites

growth_protocol: 0.5x10^6 RAW cells/well were plated in 12-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours.

extract_protocol:
RNA was isolated using the TRIzol reagent and processed as per manufacturer’s instructions.
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina, according to the manufacturer’s instructions.

treatment_protocol: RAW cells were either left unstimulated, or stimulated with the indicated PRR agonists for 14 hours.

value: Ascites

value: macrophage

value: Lamtor1 KO reconstituted with 3A

value: LPS


title: biopsy sample CD-09 batch 3

description:
Library name: Sample 38
10x Genomics

value: gastrointestinal tract

value: epithelial, immune and stromal


title: Control QM6a_LL_1


title: Δ21168_DD_3

value: growth on cellulose in darkness


title: biopsy sample CD-08 batch 2

description:
Library name: Sample 37
10x Genomics


title: 3A_LPS_RNA, rep2


title: 3A_LPS_RNA, rep1


title: Δ21168_DD_2


title: biopsy sample CD-08 batch 1

description:
Library name: Sample 36
10x Genomics


title: Δ21168_DD_1


title: Δ80186_DD_2


title: 3A_PolyIC_RNA, rep3


title: 3A_PolyIC_RNA, rep2


title: Control QM6a_DD_3


title: biopsy sample CTR-12 batch 3

description:
Library name: Sample 34
10x Genomics


title: Δ80186_DD_1


title: Δ80186_LL_2


title: Control QM6a_DD_2


title: Control QM6a_DD_1


title: 3A_PolyIC_RNA, rep1


title: Δ57513_LL_3

value: 57513 deletion


title: Δ57513_LL_1


title: Δ57513_LL_2


title: 3A_cGAMP_RNA, rep3

value: cGAMP


title: biopsy sample CTR-14 batch 2

description:
Library name: Sample 33
10x Genomics


title: mus53_LL_2

value: WT for 57513 deletion


title: biopsy sample CTR-09 batch 3

description:
Library name: Sample 32
10x Genomics


title: mus53_LL_1


title: biopsy sample CTR-06 batch 2

description:
Library name: Sample 31
10x Genomics


title: 3A_cGAMP_RNA, rep1


title: Δ80186_DD_3


title: biopsy sample CTR-06 batch 1

description:
Library name: Sample 30
10x Genomics


title: Δ57513_DD_3


title: Δ57513_DD_2


title: Δ57513_DD_1


title: biopsy sample CD-10 batch 3

description:
Library name: Sample 35
10x Genomics


title: 3A_R848_RNA, rep3


title: mus53_DD_2


title: mus53_DD_1


title: biopsy sample CD-10 batch 1

description:
Library name: Sample 27
10x Genomics


title: tmk3_LL_3

data_processing:
quality filtering and trimming bbduk version 38.18 (Q30)
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
Supplementary files format and content: tab-delimited text files include raw counts

value: tmk3 deletion


title: biopsy sample CD-10 batch 2

description:
Library name: Sample 28
10x Genomics


title: tmk3_LL_2


title: 3A_R848_RNA, rep1


title: 3A_CpG-B_RNA, rep3

value: CpG-B


title: mus53_LL_3


title: 3A_CpG-B_RNA, rep2


title: ku80_LL_2


title: ku80_LL_1


title: tmk3_LL_1


title: 3A_cGAMP_RNA, rep2


title: biopsy sample CTR-02 batch 1

description:
Library name: Sample 26
10x Genomics


title: tmk3_DD_2


title: 3A_CpG-B_RNA, rep1


title: biopsy sample CD-11 batch 3

description:
Library name: Sample 29
10x Genomics


title: tmk3_DD_1


title: biopsy sample CTR-10 batch 3

description:
Library name: Sample 24
10x Genomics


title: biopsy sample CTR-10 batch 2

description:
Library name: Sample 23
10x Genomics


title: 3A_mock_RNA, rep2

value: mock


title: 3A_mock_RNA, rep3


title: 3A_R848_RNA, rep2


title: ku80_DD_1

value: mycelium


title: ku80_DD_2


title: 3A_mock_RNA, rep1


title: biopsy sample CTR-07 batch 3

description:
Library name: Sample 21
10x Genomics


title: biopsy sample CTR-10 batch 1

description:
Library name: Sample 22
10x Genomics


title: ku80_LL_3


title: biopsy sample CTR-02 batch 3

description:
Library name: Sample 20
10x Genomics


title: biopsy sample CD-05 batch 1

description:
Library name: Sample 25
10x Genomics


title: WT_LPS_RNA, rep3

value: Lamtor1 KO reconstituted with WT


title: WT_LPS_RNA, rep2


title: tmk3_DD_3


title: WT_LPS_RNA, rep1


title: ku80_DD_3

value: WT


title: biopsy sample CTR-02 batch 2

description:
Library name: Sample 19
10x Genomics


title: biopsy sample CTR-11 batch 1

description:
Library name: Sample 18
10x Genomics


title: WT_PolyIC_RNA, rep3


title: 22L 23wpi, ApoE4, #1626

type: RNA

city: New York

first: Martin

last: Sadowski

state: NY

address: 435 E 30th St

department: Neurology

institute: NYU Langone

scan_protocol: Mouse Glial Profiling Panel was run on nCounter MAX Analysis System

data_processing: Data was normalized and analyzed using nSolver Analysis Software v4.0(NanoString Technologies)

source_name: brain cortex,

label_protocol: 100ng of Total RNA (with RIN ≥ 7 ) was used to run the nCounter Mouse Glial Profiling Panel ( NanoString Technologies). Run was performed by the Genome Technology Center at NYU Langone School of Medicine

extract_protocol: Total RNA was isolated from the brain cortex using Rneasy Mini Kit

treatment_protocol: 22L mouse adapted scrapie strain or Normal Brain Homogenate (NBH)

value: brain cortex,

value: male

tag: type of inoculum

value: 22L scrapie adapted strain

tag: endpoint

value: 23 weeks post inoculation (wpi)


title: 22L 23wpi, ApoE3, #1620

value: female


title: 22L 23wpi, ApoE4, #1627


title: 22L 23wpi, ApoE4, #1624


title: 22L 23wpi, ApoE3, #1622


title: 22L 23wpi, ApoE4, #1625


title: 22L 23wpi, ApoE3, #1623


title: biopsy sample CD-15 batch 1

description:
Library name: Sample 17
10x Genomics

value: gastrointestinal tract


title: WT_PolyIC_RNA, rep2

value: Ascites

value: macrophage


title: 22L 23wpi, ApoE3, #1618


title: 22L 23wpi, ApoE2, #1606


title: biopsy sample CTR-15 batch 1

description:
Library name: Sample 16
10x Genomics

value: epithelial, immune and stromal


title: NBH 23wpi, ApoE4, #1566

value: Normal Brain Homogenate (NBH)


title: 22L 23wpi, ApoE2, #1607


title: 22L 23wpi, ApoE2, #1610


title: biopsy sample CD-17 batch 3

description:
Library name: Sample 15
10x Genomics


title: 22L 23wpi, ApoE2, #1608


title: NBH 23wpi, ApoE4, #1564


title: WT_cGAMP_RNA, rep3

value: cGAMP


title: biopsy sample CTR-25 batch 3

description:
Library name: Sample 14
10x Genomics


title: NBH 23wpi, ApoE4, #1565


title: NBH 23wpi, ApoE4, #1563


title: NBH 23wpi, ApoE3, #1562


title: WT_cGAMP_RNA, rep2


title: WT_cGAMP_RNA, rep1


title: biopsy sample CTR-16 batch 2

description:
Library name: Sample 12
10x Genomics


title: biopsy sample CTR-16 batch 1

description:
Library name: Sample 11
10x Genomics


title: WT_R848_RNA, rep3


title: WT_R848_RNA, rep1


title: biopsy sample CD-12 batch 2

description:
Library name: Sample 10
10x Genomics


title: biopsy sample CTR-23 batch 3

description:
Library name: Sample 13
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, batch R528, replicate R_unmodified_mRNA_3

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

description:
Library name: hAECmRNA-BT-072623_S18
Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, replicate R_unmodified_mRNA_3

data_processing:
Sequencing data was demultiplexed using Illumina's BCL Convert.
De-multiplexed reads were aligned to H. sapiens version GRCh38, p7 with GENCODE annotation v. 25 using the STAR aligner v. 2.7.11a.
Read counts were extracted using featureCounts implemented in package subread v. 2.0.3.
Assembly: Read counts were extracted using featureCounts implemented in package subread v. 2.0.3.
Supplementary files format and content: tab separated file containing raw counts with ENSEMBL gene identifiers

growth_protocol: NHBEs were seeded in a 6-well plate at 300,000 cells/well overnight at 37 °C and 5% CO2

extract_protocol:
After 4 hrs, the total RNA was isolated using the Invitrogen PureLink™ RNA Mini Kit (ThermoFisher, Burnaby, BC, Canada) according to the manufacturer’s protocol.
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina).

treatment_protocol: DOPE-LNP loaded with Cas9 mRNA/sgRNA or RNP (1:1 ratio). Untreated NHBE served as control

value: unmodified mRNA

tag: batch


title: NBH 23wpi, ApoE3, #1560


title: NBH 23wpi, ApoE3, #1558


title: WT_R848_RNA, rep2


title: Primary Human Brionchial Epithelial (NHBE) cells, RNP, batch R528, replicate R_RNP_3

description:
Library name: hAECRNP-BT-072623_S19
Primary Human Brionchial Epithelial (NHBE) cells, RNP, replicate R_RNP_3

value: RNP


title: WT_PolyIC_RNA, rep1


title: biopsy sample CTR-05 batch 2

description:
Library name: Sample 9
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, untreated, batch R528, replicate R_untreated_3

description:
Library name: hAECControl-BT-072623_S17
Primary Human Brionchial Epithelial (NHBE) cells, untreated, replicate R_untreated_3

value: untreated


title: WT_CpG-B_RNA, rep3

value: CpG-B


title: biopsy sample CD-16 batch 2

description:
Library name: Sample 8
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, batch R528, replicate R_unmodified_mRNA_2

description:
Library name: HBE321mRNA-BT-072623_S21
Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, replicate R_unmodified_mRNA_2


title: Primary Human Brionchial Epithelial (NHBE) cells, RNP, batch R528, replicate R_RNP_2

description:
Library name: HBE321RNP-BT-072623_S22
Primary Human Brionchial Epithelial (NHBE) cells, RNP, replicate R_RNP_2


title: WT_CpG-B_RNA, rep2

value: Lamtor1 KO reconstituted with WT


title: NBH 23wpi, ApoE2, #1557


title: NBH 23wpi, ApoE2, #1554


title: NBH 23wpi, ApoE2, #1553


title: NBH 23wpi, ApoE2, #1556


title: biopsy sample CD-12 batch 1

description:
Library name: Sample 7
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, batch R528, replicate R_unmodified_mRNA_1

description:
Library name: HBE18mRNA-BT-080423_S24
Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, replicate R_unmodified_mRNA_1


title: NBH 23wpi, ApoE3, #1561


title: WT_CpG-B_RNA, rep1


title: Primary Human Brionchial Epithelial (NHBE) cells, RNP, batch R528, replicate R_RNP_1

description:
Library name: HBE18RNP-BT-080423_S25
Primary Human Brionchial Epithelial (NHBE) cells, RNP, replicate R_RNP_1


title: biopsy sample CD-04 batch 3

description:
Library name: Sample 6
10x Genomics


title: WT_mock_RNA, rep3

value: mock


title: Primary Human Brionchial Epithelial (NHBE) cells, untreated, batch R528, replicate R_untreated_1

description:
Library name: HBE18Control-BT-080423_S23
Primary Human Brionchial Epithelial (NHBE) cells, untreated, replicate R_untreated_1


title: Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, batch R378, replicate R_unmodified_mRNA_1

description:
Library name: NHBE_mRNA_S31
Primary Human Brionchial Epithelial (NHBE) cells, unmodified mRNA, replicate R_unmodified_mRNA_1


title: Primary Human Brionchial Epithelial (NHBE) cells, untreated, batch R378, replicate R_untreated_1

description:
Library name: NHBE_Control_S33
Primary Human Brionchial Epithelial (NHBE) cells, untreated, replicate R_untreated_1


title: biopsy sample CD-04 batch 2

description:
Library name: Sample 5
10x Genomics


title: WT_mock_RNA, rep2


title: Primary Human Brionchial Epithelial (NHBE) cells, modified mRNA, batch P3515, replicate R_modified_mRNA_3

description:
Library name: P3515_RNA_06_Donor_3_treated_S5
Primary Human Brionchial Epithelial (NHBE) cells, modified mRNA, replicate R_modified_mRNA_3

value: modified mRNA


title: Primary Human Brionchial Epithelial (NHBE) cells, untreated, batch P3515, replicate R_untreated_2

description:
Library name: P3515_RNA_05_Donor_3_untreated_S4
Primary Human Brionchial Epithelial (NHBE) cells, untreated, replicate R_untreated_2


title: biopsy sample CD-04 batch 1

description:
Library name: Sample 4
10x Genomics


title: WT_mock_RNA, rep1


title: biopsy sample CD-03 batch 1

description:
Library name: Sample 3
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, modified mRNA, batch P3515, replicate R_modified_mRNA_2

description:
Library name: P3515_RNA_04_Donor_2_treated_S3
Primary Human Brionchial Epithelial (NHBE) cells, modified mRNA, replicate R_modified_mRNA_2


title: 3A_cGAMP_ATAC, rep3

data_processing:
ATAC-seq raw reads were trimmed to remove low-quality reads and adapters using trim-galore (version 0.6.7). Next, trimmed reads were aligned to the mouse reference genome (GRCm39) using Bowtie2 (version 2.4.5) with the "--very-sensitive -X 1000" option; reads mapped to mitochondria were ignored. SAMtools (version 1.15.1) was applied to extract properly mapped reads and duplicated reads were removed by sambamba (version 0.8.2).
The Reads Per Kilobase per million mapped reads (RPKM) normalization method of deepTools bamCoverage (version 3.5.1) was used to transform alignment bam files into read coverage files in bigWig format. Peak calling was performed using MACS2 (version 2.2.7.1) with the parameter "--SPMR --nomodel -q 0.001 --cutoff analysis.
Differentially accessible peaks were identified using the DiffBind R package (version 3.8.4), peaks with FDR of < 0.05, fold change ≥ 2 were identified as significant differentially accessible regions, and stable regions were identified with a fold change < 1.5.
Motif enrichment analysis was performed using the HOMER (version 4.11) function "findMotifsGenome.pl" with default options.
The Integrative Genomics Viewer (IGV, version 2.10.0) was used for data visualization.
Assembly: mouse reference genome GRCm39 (Ensembl release 106)
Supplementary files format and content: Bigwig files were generated by deepTools
Supplementary files format and content: NarrowPeak files of called peaks were generated using MACS2

extract_protocol:
Cell pellets were resuspended in freezing medium containing 90% FBS and 10% DMSO and aliquoted into cryovials for shippping. Frozen cell samples were thawed quickly in a 37 °C water bath and centrifuged at 500 × g for 5 min at 4 °C. The cell pellets were resuspended by gentle pipetting for 3 min in cold lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630. The resuspended cell pellets were centrifuged at 500 × g for 5 min at 4 °C to generate crude nuclei. After removing the supernatant, nuclei were subjected to a transposition reaction for 30 min at 37 °C with gentle mixing. Transposed DNA was purified using the QIAGEN MinElute PCR Purification Kit (QIAGEN 28004).
Libraries were prepared using the TruePrep DNA Library Prep Kit (Vazyme TD501) according to the manufacturer’s instructions. PCR amplification was performed using N5XX and N7XX barcode oligos provided in the TruePrep Index Kit V2 for Illumina (Vazyme TD202). Amplified libraries were cleaned using AMPure XP beads (Beckman Coulter, Inc.), analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies), and sequenced using NovaSeq 6000 (Illumina).

treatment_protocol: RAW cells were either left unstimulated, or stimulated with cGAMP (5 μg/ml) for 14 hours

value: Lamtor1 KO reconstituted with 3A


title: biopsy sample CD-19 batch 2

description:
Library name: Sample 2
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, untreated, batch R528, replicate R_untreated_2

description:
Library name: HBE321Control-BT-072623_S20
Primary Human Brionchial Epithelial (NHBE) cells, untreated, replicate R_untreated_2


title: Primary Human Brionchial Epithelial (NHBE) cells, modified mRNA, batch P3515, replicate R_modified_mRNA_1

description:
Library name: P3515_RNA_02_Donor_1_treated_S1
Primary Human Brionchial Epithelial (NHBE) cells, modified mRNA, replicate R_modified_mRNA_1


title: 3A_cGAMP_ATAC, rep2


title: biopsy sample CD-19 batch 1

description:
Library name: Sample 1
10x Genomics


title: Primary Human Brionchial Epithelial (NHBE) cells, untreated, batch P3515, replicate R_untreated_1

description:
Library name: P3515_RNA_03_Donor_2_untreated_S2
Primary Human Brionchial Epithelial (NHBE) cells, untreated, replicate R_untreated_1


title: PT2_postUVB

city: Taipei

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description:
Library name: LT03
10x Genomics

data_processing:
Cell Ranger software (v.8.0.1) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq). The reference genome (refdata-gex-GRCh38-2020-A) was performed for alignment. Unique Molecular Identifiers (UMIs) were counted and gene–barcode matrices (cellranger count) were generated for further scRNA-seq analysis.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole blood

extract_protocol:
To obtain single-cell suspensions, buffy coat from peripheral blood was treated with RBC lysis buffer and washed with PBS.
10x Chromium Single Cell 5' v2 Dual Index

value: Whole blood

value: UVB


title: PT2_preUVB

description:
Library name: LT01
10x Genomics


title: 3A_cGAMP_ATAC, rep1


title: Z0684-SF-3 CIPS rep2

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

description:
Library name: Z0684-SF-3 CIPS rep2
column name in counts.csv: Z0684-SF-3 CIPS-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to hg38 whole genome using STAR v2.7.10b and annotated using gencode v47 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: csv file with raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was extracted utilizing the TGuide S32 Blood/Cell/Tissue RNA kit in conjunction with the TGuide S32 nucleic acid extractor.
For the preparation of RNA-seq libraries, the NEBNext Ultra RNA Library Prep Kit for Illumina (provided by New England BioLabs, catalog number E7775) was used. The resultant libraries, comprising fragmented and randomly primed RNA molecules, were sequenced as paired-end reads of 2 x 150 base pairs

value: EPC derived hCiPSC

value: WT


title: PT1_preUVB

description:
Library name: LJ03
10x Genomics


title: 3A_mock_ATAC, rep3

value: Ascites


title: PT1_postUVB

description:
Library name: LJ04
10x Genomics


title: Z0684-SF-3 CIPS rep1

description:
Library name: Z0684-SF-3 CIPS rep1
column name in counts.csv: Z0684-SF-3 CIPS-1


title: CLBGA_088uM_TAS1553_Rep4

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

data_processing:
Data analysis followed the workflow outlined on the Lexogen GitHub repository (https://github.com/Lexogen-Tools/quantseqpool_analysis).
RNA-Seq libraries were sequenced on the Illumina NextSeq 2000 platform using the NextSeq 2000 P3 Reagents 100 Cycles paired-end kit.
The FASTQ files were aligned to the Homo sapiens reference genome (GRCh38.96) using STAR (v2.7.2b).
Post-alignment, read counts were generated and normalized with edgeR (v3.36.0).
Differential expression analysis was performed using the Limma-Voom pipeline (v3.50.3) with three or four replicates per condition.
Assembly: GRCh38.96
Supplementary files format and content: Tab-delimited text file include STAR counts.

source_name: bone marrow

growth_protocol: The NB cell lines CLB-GA, SK-N-AS, SH-SY5Y, SH-EP, CHP-212, IMR-32, N206, NGP, SK-N-BE(2)-C and TR14 were cultured in RPMI1640 (Gibco #52400041), supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich #F0804), 2mM L-glutamine (Gibco #11548876) and 100IU/mL penicillin/streptomycin (Gibco #11548876). RPE cells were cultured in DMEM-F12 (Gibco #11594426), supplemented with 10% FBS, 2mM L-glutamine and 100IU/mL penicillin/streptomycin. The rhabdomyosarcoma (RMS) cell lines RD, Rh41, Rh30, RMS-YM and RMS-1 were cultured in RPMI1640 (Gibco #52400041), supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich #F0804 or Tico #FBSEU500), 2mM L-glutamine (Gibco #11548876) and 100IU/mL penicillin/streptomycin (Gibco #11548876). All cells were incubated at 37ºC and 5% CO2.

extract_protocol:
RNA was isolated as described in the ‘RNA isolation and RT-qPCR’ section. RNA quality was measured using the Fragment analyzer 12 capillary array prior to profiling.
During the library preparation 15 PCR cycles were used. qPCR quantification of the libraries was done using the Kapa Library Quantification Kit for the Illumina LightCycler 480 (Roche diagnostics #07960298001).
QuantSeq-Pool Sample-Barcoded 3’ mRNA-Seq Kit (Lexogen #139.96)

treatment_protocol: CLB-GA and IMR-32 were seeded in 384-well plates at a density ranging from 1500-2000 cells/well and allowed to adhere overnight. The following day, cells were treated with different compounds alone or in a combination matrix using the Tecan D300e Digital Dispenser.

value: bone marrow

value: CLB-GA

value: neuroblast


title: Primary Human Brionchial Epithelial (NHBE) cells, RNP, batch R378, replicate R_RNP_1

description:
Library name: NHBE_RNP_S32
Primary Human Brionchial Epithelial (NHBE) cells, RNP, replicate R_RNP_1


title: 3A_mock_ATAC, rep2

value: macrophage


title: 20684-SF-2 CIPS rep2

description:
Library name: 20684-SF-2 CIPS rep2
column name in counts.csv: Z0684-SF-2 CIPS-2


title: 3A_mock_ATAC, rep1


title: CLBGA_074nM_PREX_Rep4

value: 074nM prexasertib


title: 20684-SF-2 CIPS rep1

description:
Library name: 20684-SF-2 CIPS rep1
column name in counts.csv: Z0684-SF-2 CIPS-1


title: CLBGA_DMSO_PREX_Rep4

value: DMSO for prexasertib conditions


title: IMR32_074nM_PREX_Rep4

source_name: brain

value: brain


title: WT_cGAMP_ATAC, rep3

value: cGAMP


title: Z0684 EPC rep2

description:
Library name: Z0684 EPC rep2
column name in counts.csv: Z0684 EPC-2

value: EPC


title: WT_cGAMP_ATAC, rep2

value: Lamtor1 KO reconstituted with WT


title: IMR32_combi_PREX_TAS1553_Rep4

value: Combi prexasertib & TAS1553


title: Z0684 EPC rep1

description:
Library name: Z0684 EPC rep1
column name in counts.csv: Z0684 EPC-1


title: IMR32_088uM_TAS1553_Rep4


title: IMR32_DMSO_PREX_Rep4


title: CLBGA_combi_PREX_TAS1553_Rep3


title: 729B-SF-2 CIPS rep2

description:
Library name: 729B-SF-2 CIPS rep2
column name in counts.csv: 729B-SF-2 CIPS-2


title: WT_cGAMP_ATAC, rep1


title: CLBGA_DMSO_PREX_Rep3


title: WT_mock_ATAC, rep3

value: mock


title: IMR32_combi_PREX_TAS1553_Rep3


title: CLBGA_combi_PREX_TAS1553_Rep4


title: IMR32_088uM_TAS1553_Rep3


title: CLBGA_074nM_PREX_Rep3


title: IMR32_074nM_PREX_Rep3


title: 729B-SF-2 CIPS rep1

description:
Library name: 729B-SF-2 CIPS rep1
column name in counts.csv: 729B-SF-2 CIPS-1


title: 729B-SF-1 CIPS rep2

description:
Library name: 729B-SF-1 CIPS rep2
column name in counts.csv: 729B-SF-1 CIPS-2


title: WT_mock_ATAC, rep2


title: WT_mock_ATAC, rep1


title: 729B-SF-1 CIPS rep1

description:
Library name: 729B-SF-1 CIPS rep1
column name in counts.csv: 729B-SF-1 CIPS-1


title: CLBGA_088uM_TAS1553_Rep2


title: 729B EPC rep2

description:
Library name: 729B EPC rep2
column name in counts.csv: 729B EPC-2


title: CLBGA_combi_PREX_TAS1553_Rep2


title: crypt-RNA-KO3

city: HangZhou

first: xin

last: xu

state: Zhejiang

address: No. 866, Tang Road, Yuhang District, Zhejiang University, Zijingang Campus, School of Medicine.

institute: Zhejiang university

data_processing:
Sequence reads were trimmed for adaptor sequence using Cutadapt
Trimmed sequence reads were mapped to GRCm39/mm39 using STAR
For Ribo-seq RPKM  value was calculated and FPKM value was calculated for parallel paired-end mRNA-seq
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample

source_name: intestinal crypt

extract_protocol:
RNA was harvested using Trizol (Takara), and 1μg of RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq and Ribo-seq were prepared using SAMARTER mRNA-Seq Library Prep Kit and Small RNA Library Prep Kit following manufacturer's protocols

value: intestinal crypt

value: KO


title: crypt-RNA-KO2


title: 729B EPC rep1

description:
Library name: 729B EPC rep1
column name in counts.csv: 729B EPC-1


title: IMR32_combi_PREX_TAS1553_Rep2


title: T0254-SF-2 CIPS rep2

description:
Library name: T0254-SF-2 CIPS rep2
column name in counts.csv: T0254-SF-2 CIPS-2

value: EPC derived hCiPSC


title: crypt-RNA-KO1


title: IMR32_088uM_TAS1553_Rep2

value: WT


title: IMR32_074nM_PREX_Rep2


title: CLBGA_074nM_PREX_Rep2


title: CLBGA_combi_PREX_TAS1553_Rep1


title: CLBGA_088uM_TAS1553_Rep3


title: crypt-RNA-WT3


title: IMR32_DMSO_PREX_Rep2


title: T0254-SF-2 CIPS rep1

description:
Library name: T0254-SF-2 CIPS rep1
column name in counts.csv: T0254-SF-2 CIPS-1


title: CLBGA_DMSO_PREX_Rep1


title: crypt-RNA-WT2


title: CLBGA_088uM_TAS1553_Rep1


title: crypt-RNA-WT1


title: T0254-SF-1 CIPS rep2

description:
Library name: T0254-SF-1 CIPS rep2
column name in counts.csv: T0254-SF-1 CIPS-2


title: IMR32_DMSO_PREX_Rep3


title: CLBGA_074nM_PREX_Rep1


title: T0254-SF-1 CIPS rep1

description:
Library name: T0254-SF-1 CIPS rep1
column name in counts.csv: T0254-SF-1 CIPS-1


title: IMR32_combi_PREX_TAS1553_Rep1


title: IMR32_088uM_TAS1553_Rep1


title: crypt-Ribo--KO2

library_source: other

data_processing:
Sequence reads were trimmed for adaptor sequence using Cutadapt
Trimmed sequence reads were mapped to GRCm39/mm39 using STAR
For Ribo-seq RPKM  value was calculated and FPKM value was calculated for parallel paired-end mRNA-seq
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample
Library strategy: Ribo-seq

molecule: other


title: CLBGA_DMSO_PREX_Rep2


title: IMR32_074nM_PREX_Rep1


title: IMR32_DMSO_PREX_Rep1


title: T0254 EPC rep2

description:
Library name: T0254 EPC rep2
column name in counts.csv: T0254 EPC-2


title: crypt-Ribo--KO1


title: CLBGA_combi_SRA737_TAS1553_Rep4

value: Combi SRA737 & TAS1553


title: T0254 EPC rep1

description:
Library name: T0254 EPC rep1
column name in counts.csv: T0254 EPC-1


title: crypt-Ribo--WT2


title: CLBGA_051uM_TAS1553_Rep4

value: bone marrow


title: crypt-Ribo--WT1


title: IMR32_IC50_TAS1553_Rep4


title: IMR32_combi_SRA737_TAS1553_Rep4


title: CLBGA_DMSO_SRA_Rep4

value: CLB-GA

value: DMSO for SRA737 conditions


title: YB3320-SF-10 CIPS rep2

description:
Library name: YB3320-SF-10 CIPS rep2
column name in counts.csv: YB3320-SF-10#-CIPS-2


title: 14-days-DDC-28-days-post-DDC, Epithelial cells, scATAC-seq

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: OH

address: 3333 Burnet Avenue

department: Immunobiology

institute: Cincinnati children hospital

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ATAC v1.2.0  (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Samples processed through Signac following standard pipeline, low quality data were filtered based on the following criteria: peak region fragments were restricted to the range 1,000 to 40,000, >40% reads in peaks, ENCODE blacklist ratio <.03, and nucleosome signal < 2
Peaks were called using MACS2 v2.1.4  by sample, common set of reference peaks were used to combine samples through Seurat anchor based integration.
Gene activities were estimated based on number of fragments mapped to extracted gene coordinates regions, then applied for multimodal seurat anchor-based label transfer to define cell types using annotated scRNA-seq data as reference.
Final peaks were called using MACS2 v 2.1.4  by annotated cell subtypes with extension =50, shift= -25, effective genome size =2.6e9, and 5% FDR rate, peaks in blacklist regions for mm10 were removed
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, and peak bed files
Supplementary files format and content: processed seurat R object as combined across samples with defined cell types.

source_name: Liver

extract_protocol:
Nuclei isolation was conducted according to the protocol as previously described (Kudira R et al.Bio-protocol 2022;12:e4400). Briefly liver mononuclear and epithelial enriched nuclei suspensions were isolated using the double gradient based method. 100 μL of cold Lysis Buffer was added to 1 × 10^6 cells,  incubated 90 s for liver mononuclear cells, 60s for epithelial cells. Then washed with 1 mL of cold wash buffer, resuspended in 1 mL of cold diluted 1X Nuclei Buffer. The nuclei integerity was assesed with trypan blue staining, then submitted for library preparation and sequencing with around 1.6 x 10^3 nuclei.
Libray was constructed according to the manufacter’s instructions (Chromium Next GEM Single Cell ATAC Reagent Kits v1.1:CG000209). Nuclei suspensions were incubated in a transposition Mix, nuclei was fragmented by transposase in open regions of the chromatin into DNA fragments, with adapter sequences added to the ends.  The transposed nuclei was loaded together with Gel Beads,a Master Mix, and Partitioning Oil into a Chromium Next GEM Chip H to generate nanoliter-scale Gel Beads-in-emulsion (GEMs).Oligonucleotides containing Illumina® P5 sequence, 10x Barcode, and Read 1 sequence were released and mixed with DNA fragments and Master Mix. 10x barcoded single- stranded DNA were produced through thermal cycling of GEM. Silane magnetic beads were used to cleanup the chemical reagenets from mixture, Solid Phase Reversible Immobilization (SPRI) beads helped to remove unused barcodes.  P7 and a sample index were added during library construction via PCR, the final library contained P5, P7 were used in Illumina® bridge amplification.S1 or S2 Flow Cells were used with 50 cycles for read 1, 8 cycles for i7 index and 50 cycles for read 2 during sequencing.

treatment_protocol: 8-week wild type C57Bl/6 mice were fed with 5058 chow admixed with 0.1% DDC for 14 days and then allowed to recover for an additional 14-28 days (5058 chow without DDC).

value: Liver

value: Mixed liver cell types, epithelial cells enriched

value: wild type C57Bl/6

tag: age

value: 8 weeks old

value: female

value: 14 days DDC, 28 days recovery post DDC treatment


title: YB3320 S1 rep2

description:
Library name: YB3320 S1 rep2
column name in counts.csv: YB3320-S0-2

value: induced from EPC


title: IMR32_051uM_TAS1553_Rep4

value: brain

value: neuroblast


title: 14-days-DDC-14-days-post-DDC, Epithelial cells, scATAC-seq

value: 14 days DDC, 14 days recovery post DDC treatment


title: IMR32_028uM_SRA737_Rep4


title: CLBGA_combi_SRA737_TAS1553_Rep3


title: YB3320-SF-9 CIPS rep2

description:
Library name: YB3320-SF-9 CIPS rep2
column name in counts.csv: YB3320-SF-9#-CIPS-2


title: CLBGA_051uM_TAS1553_Rep3


title: CLBGA_IC50_TAS1553_Rep3


title: 14-days-DDC-14-days-post-DDC, LMNCs, scATAC-seq

value: Mixed liver cell types,mononulcear cells enriched


title: 14-days-DDC-28-days-post-DDC, LMNCs, scATAC-seq


title: CLBGA_028uM_SRA737_Rep3


title: YB3320-SF-9 CIPS rep1

description:
Library name: YB3320-SF-9 CIPS rep1
column name in counts.csv: YB3320-SF-9#-CIPS-1

value: EPC derived hCiPSC


title: YB3320 PBMC-EPC rep2

description:
Library name: YB3320 PBMC-EPC rep2
column name in counts.csv: YB3320-PBMC-EPC-2

value: EPC

value: WT


title: IMR32_IC50_TAS1553_Rep3


title: IMR32_combi_SRA737_TAS1553_Rep3

value: Combi SRA737 & TAS1553


title: CLBGA_028uM_SRA737_Rep4

value: bone marrow

value: CLB-GA


title: YB3320 S1 rep1

description:
Library name: YB3320 S1 rep1
column name in counts.csv: YB3320-S0-1


title: IMR32_051uM_TAS1553_Rep3


title: YB3320 PBMC-EPC rep1

description:
Library name: YB3320 PBMC-EPC rep1
column name in counts.csv: YB3320-PBMC-EPC-1


title: IMR32_DMSO_SRA_Rep4

value: DMSO for SRA737 conditions


title: IMR32_DMSO_SRA_Rep3


title: YB3320-SF-10 CIPS rep1

description:
Library name: YB3320-SF-10 CIPS rep1
column name in counts.csv: YB3320-SF-10#-CIPS-1


title: baseline, Epithelial cells, scATAC-seq

value: Liver

value: Mixed liver cell types, epithelial cells enriched

value: baseline


title: CLBGA_IC50_TAS1553_Rep2


title: PCPAi

city: Suzhou

first: Siying

address: Pinghai Road 899

institute: The First Affiliated Hospital of Soochow University

description: Library name: Sample2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using 10x Cell Ranger
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: breast cancer

extract_protocol:
The tumor samples used for sc-RNA sequencing were collected from 2 female patients who were diagnosed with TNBC and axillary lymph node metastasis. After the conbination treatment of pembrolizumab, carboplatin, paclitaxel and anthracycline, these two patients were divided into two groups based on treatment efficacy: sensitive and insensitive .
Library was performed according to the manufacter's instructions. Briefly, immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primel sequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction.

value: breast cancer

value: cancer cells


title: CLBGA_combi_SRA737_TAS1553_Rep2


title: baseline, LMNCs, replicate 2, scATAC-seq

value: wild type C57Bl/6

value: 8 weeks old

value: female


title: PCPAs

description: Library name: Sample1

value: pembrolizumab, carboplatin, paclitaxel and anthracycline


title: CLBGA_DMSO_SRA_Rep2

value: neuroblast


title: CLBGA_028uM_SRA737_Rep2


title: CLBGA_051uM_TAS1553_Rep2


title: A549d45

city: Malmo

first: Vaishnavi

last: Dandavate

address: Inga-Marie Nilssons gata 53

country: Sweden

institute: Lund University

description: Library name: Sample 12

data_processing:
Fastp software was used for the first steps of processing raw data to clean the reads from adapters and low quality reads.
Hisat2 v2.0.5  was used to build index of the reference genome and paired-end clean 1 reads were aligned to the reference genome (hg38) using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene  and then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
For DESeq2 with biological replicates: Differential expression analysis was performed using the DESeq2 R package (1.44.0). The resulting P-value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2(foldchange)| ≥ 1 was set as the threshold of significant differential expression.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: csv file includes FPKM values for each sample

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen)
Poly-T oligo-attached magnetic beads were utilized to purify messenger RNA from total RNA. Using random hexamer primers the first strand cDNA was synthesized post fragmentation, proceeded by second strand cDNA synthesis using dUTP, instead of dTTP. cDNA was processed by end repair, A-tailing, adapter ligation, size selection, amplification, and purification to prepare the directional library The library was analyzed by real-time PCR for quantification and Qubit and and bioanalyzer for size distribution detection.

value: epithelial cell

value: expressing only cytosolic C3 ({delta}ATG1)


title: 14-days-DDC-28-days-post-DDC, Epithelial cells, scRNA-seq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Background noises including random barcode swapping and ambient RNA were removed from count matrix using CellBender, doublets removed based on the assembly results from 5 prediction algorithms: hybrid, scDblFinder,DoubletFinde,Solo and DoubletDetection.
Downstream analysis was conducted through Seurat v4.0.4 following standard workflow, low quality data is removed as following: total UMI counts per cell < 500 or > 40,000, number of gene detected per cell < 200 or > 7,000, and >=15% of uMI are mapped to mitochondrial genes, >= 40% of uMI are mapped to ribosomes, >= 0.75% of uMI are mapped to cell cycle genes.Genes detected in < 20 cells were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: processed seurat R object as combined across samples with defined cell types.

extract_protocol:
Mice were euthanized for in situ liver digestion by retrograde perfusion using collagenase D.  Livers collected post-harvest were minced into pieces and digested with collagenase D in the digestion media, resulting in single cell suspension. Cells were washed with MACS buffer at 300xg, 4°C.  Liver mononuclear enriched and epithelial enriched cell suspensions were collected through either single(33% percoll) or double gradient(40%,70%) centrifugation based on liver cholestasis levels as previsouly described (Kudira R et al. Bio-protocol 2022;12:e4400). 1×10^6 cells were submitted to the sequencing core, 1.6x10^3 cells were used for library construction and sequencing.
For sequencing conducted in 2020, single indexed kit was used for library construction according to the manufacter’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1(Single Index): CG000204). Cells were resuspended in the master mix and loaded together with partitioning oil and barcoded Single Cell 3ʹ v3.1 Gel Beads into the Chromium Next GEM Chip G to generate nanoliter-scale Gel Beads-in-emulsion (GEMs).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina TruSeq Read 1 primer sequence, Unique Molecular Identifier (UMI), 10x Barcode and poly(dT) sequence. The pooled barcoded cDNA was purified with Silane magnetic beads, amplified by PCR for 14 cycles. Enyzymatic fragmentation and size selection were used to optimize cDNA size for subsequent library construction. During the library construction TruSeq read2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. S4, S2, or S1 Flow Cells were used with 28 cycles for read 1, 8 cycles for i7 index and 91 cycles for read 2 during sequencing.
For sequencing conducted in 2022, dual indexed kit was used for library construction according to the manufacter’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index): CG000315). Cells were resuspended in the master mix and loaded together with partitioning oil and barcoded Single Cell 3ʹ v3.1 Gel Beads into the Chromium Next GEM Chip G to generate nanoliter-scale Gel Beads-in-emulsion (GEMs).The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina TruSeq Read 1 primer sequence, Unique Molecular Identifier (UMI), 10x Barcode and poly(dT) sequence. The pooled barcoded cDNA was purified with Silane magnetic beads, amplified by PCR for 14 cycles. Enyzymatic fragmentation and size selection were used to optimize cDNA size for subsequent library construction. During the library construction TruSeq read2 primer sequence, paired-end constructs with P5 and P7 sequences and i7, i5 dual sample indexes were added. S4, S2, or S1 Flow Cells were used with 28 cycles for read 1, 10 cycles for i5 index, 10 cycles for i7 index and 90 cycles for read 2 during sequencing.

treatment_protocol: 8-week wild type C57Bl/6 mice were fed with 5058 chow admixed with 0.1% DDC for 14 days and then allowed to recover for an additional 7-28 days (5058 chow without DDC).

value: 14 days DDC, 28 days recovery post DDC treatment


title: baseline, LMNCs, replicate 1, scATAC-seq

value: Mixed liver cell types,mononulcear cells enriched


title: CLBGA_DMSO_SRA_Rep3

value: bone marrow

value: WT


title: IMR32_IC50_TAS1553_Rep2

value: brain


title: A549d4

description: Library name: Sample 10


title: IMR32_051uM_TAS1553_Rep2


title: IMR32_028uM_SRA737_Rep2


title: 14-days-DDC-14-days-post-DDC, Epithelial cells, scRNA-seq

description: 10x Genomics

value: Liver

value: 14 days DDC, 14 days recovery post DDC treatment


title: IMR32_028uM_SRA737_Rep3


title: 14-days-DDC-28-days-post-DDC, LMNCs, scRNA-seq

description: 10x Genomics


title: 14-days-DDC, LMNCs, scATAC-seq

value: 14 days DDC


title: IMR32_combi_SRA737_TAS1553_Rep2

value: Combi SRA737 & TAS1553


title: CLBGA_combi_SRA737_TAS1553_Rep1

value: CLB-GA


title: 14-days-DDC, Epithelial cells, scATAC-seq

value: Mixed liver cell types, epithelial cells enriched

value: wild type C57Bl/6


title: 14-days-DDC-14-days-post-DDC, LMNCs, replicate 3, scRNA-seq

description: 10x Genomics

value: 8 weeks old

value: female


title: A549KO2F1

description: Library name: Sample 8

value: gene-edited variants deficient of C3 (C3 KO)


title: CLBGA_028uM_SRA737_Rep1

value: neuroblast


title: A549KO2E1

description: Library name: Sample 7

value: epithelial cell


title: 14-days-DDC-14-days-post-DDC, LMNCs, replicate 2, scRNA-seq

description: 10x Genomics


title: CLBGA_051uM_TAS1553_Rep1


title: A549d42

description: Library name: Sample 11

value: expressing only cytosolic C3 ({delta}ATG1)


title: IMR32_DMSO_SRA_Rep2

value: DMSO for SRA737 conditions


title: IMR32_028uM_SRA737_Rep1


title: IMR32_051uM_TAS1553_Rep1


title: 14-days-DDC-7-days-post-DDC, Epithelial cells, scRNA-seq

description: 10x Genomics

value: 14 days DDC, 7 days recovery post DDC treatment


title: 14-days-DDC-14-days-post-DDC, LMNCs, replicate 1, scRNA-seq

description: 10x Genomics

value: Mixed liver cell types,mononulcear cells enriched


title: A549KO2A8

description: Library name: Sample 5


title: IMR32_DMSO_SRA_Rep1

value: brain

value: WT


title: A549d1B4

description: Library name: Sample 9


title: A549KO2D2

description: Library name: Sample 6


title: IMR32_IC50_TAS1553_Rep1


title: 14-days-DDC-7-days-post-DDC, LMNCs, scRNA-seq

description: 10x Genomics

value: Liver


title: A549wt29

description: Library name: Sample 4

value: wild type


title: Aorta_pericyte_spheroid_355

city: Pittsburgh

first: Julie

middle: A

last: Phillippi

address: 450 Technology Drive, Suite 300

department: Cardiothoracic Surgery

institute: University of Pittsburgh

data_processing:
Quality control reports were performed for raw, untrimmed sequences and again after sequence trimming. Sequences were trimmed per default settings in the CLC Genomics software with Molecular Bio plugin (QIAgen), with an additional requirement for a minimum length of 10 nucleotides. Trimmed sequences were then aligned to GRCh38 human genome reference and a mapping quality control report was reviewed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: Adventitial tissue was delaminated from the medial layer and digested in 0.5mg/mL collagenase and 0.25mg/mL elastase, with the resulting slurry passed through a 70 µm strainer. This single cell suspension was then cultured on type I collagen coated flasks in StemMACS MSC Expansion Medium, human (Miltenyi Biotec) until ~85-90% confluent. Cells were then enriched using magnetic bead separation to achieve a CD31-/CD146+ phenotype (Miltenyi Biotec), subcultured once and infected with lentiviral HPV for immortalization (Applied Biological Materials). Immortalized cells were serially passaged to select for cells that incorporated the HPV vector for 4-5 passages and phenotype was confirmed prior to experimentation beginning. Cells were incubated at 37°C in 5% CO2 at all time.

extract_protocol:
Monolayer cells and spheroids formed on agarose were collected in Buffer RA1 (Takara Bio) +1% beta-mercaptoethanol (Fisher Scientific). NucleoSpin RNA kit from Takara Clontech was used for RNA extraction, 50ng input RNA used for library construction.
RNA was assessed for quality using an TapeStation 4150 (Agilent) and RNA concentration was quantified on a Qubit FLEX fluorometer (Thermo Fisher). Libraries were generated from RNA samples with RIN scores >9 with the Illumina Stranded mRNA Library Prep kit (Illumina: 20040534) according to the manufacturer’s instructions. Briefly, 50ng of input RNA was used for each sample. Following adapter ligation, 14 cycles of indexing PCR were completed, using IDT for Illumina RNA UD Indexes (Illumina: 20040553-6). Library quantification and assessment was conducted using a Qubit FLEX fluorometer and an Agilent TapeStation 4150. Libraries were normalized and pooled to 2 nM by calculating the concentration determined by fragment size (base pairs) and the concentration (ng/μL) of the libraries. Sequencing was performed on an Illumina NextSeq 2000, using a P2 100 flow cell. Sequencing was carried out on the pooled library (750 pM) with read lengths of 2x58 bp and a target of 40 million reads per sample. Sequencing data was demultiplexed by Illumina using the on-board DRAGEN FASTQ Generation software (v3.10.12). Library generation and sequencing was performed by the University of Pittsburgh Health Sciences Sequencing Core (HSSC), Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.

treatment_protocol: All culturing of pericytes was performed in  StemMACS MSC Expansion Medium (Miltenyi Biotec). Monolayer culture occurred on type I collagen-coated six-well plates. Spheroids were formed on agarose-coated substrates as follows: 1.5% percent low gelling temperature agarose (Sigma-Aldrich) was dissolved in boiling DMEM (Gibco) and utilized to coat 96 well plates (100 μL/well), allowed to cool at room temperature, and cells were then seeded onto the agarose at 500 cells per spheroid.

value: Pericyte

value: Spheroid


title: Aorta_pericyte_monolayer_355

value: Monolayer


title: CLBGA_IC50_TAS1553_Rep1

value: bone marrow

value: CLB-GA


title: 14-days-DDC, Epithelial cells, replicate 2, scRNA-seq

description: 10x Genomics

value: Mixed liver cell types, epithelial cells enriched

value: wild type C57Bl/6

value: 8 weeks old

value: female

value: 14 days DDC


title: Aorta_pericyte_spheroid_336


title: A549wt25

description: Library name: Sample 3

value: epithelial cell


title: 14-days-DDC, Epithelial cells, replicate 1, scRNA-seq

description: 10x Genomics


title: CLBGA_DMSO_SRA_Rep1

value: neuroblast

value: DMSO for SRA737 conditions


title: RA_patient_7

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
The gene expression matrices were generated from raw reads using scopetools (https://anaconda.org/singleronbio/scopetools). The first step involved filtering out reads without polyT tails and extracting cell barcodes and unique molecular identifiers (UMIs). Adapters and polyA tails were trimmed before aligning the reads to the pre-mRNA reference. Then reads with the same cell barcode, UMI, and gene were grouped together to count the number of UMIs per gene per cell.
Assembly: scRNA-seq: GRCh38/hg38
Supplementary files format and content: scRNA-seq: tar file containing barcodes.tsv, genes.tsv, and matrix.mtx

source_name: cartilage

extract_protocol:
Cartilage were lysesd and pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. Tissues were resuspended in 1 mL pre-warmed (37 °C) TrypLE, and rotated at 37 °C for 15 to 30 minutes until tissues were dissociated into single cells via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C, and washed with cold PBS.
Chromium Single Cell 3' Reagents Kits version 2

tag: disease state

value: rheumatoid arthritis

value: cartilage

value: articular chondrocytes


title: Aorta_pericyte_monolayer_336


title: A549wt13

description: Library name: Sample 2

value: wild type


title: RA_patient_6


title: A549wt

description: Library name: Sample 1


title: 14-days-DDC, LMNCs, replicate 2, scRNA-seq

description: 10x Genomics

value: Liver

value: Mixed liver cell types,mononulcear cells enriched


title: RA_patient_4


title: 14-days-DDC, LMNCs, replicate 1, scRNA-seq

description: 10x Genomics


title: Patient8_LV

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

description:
Library name: Patient8_LV
PolyA RNA

data_processing:
Demultiplexing, genome alignment, and gene quantification were performed with Cell Ranger ARC 50. Specifically, data was processed using the cellranger-arc count v.2.0.2 and aligned against the human genome (GRCh38) to generate count matrices for the RNA pipeline (v.7.0.1). All subsequent analysis was done using Seurat (v5) in R.
Assembly: GRCh38
Supplementary files format and content: csv file containg gene barcode matrix for the ependymal cells and also a csv file containg metadata information of cells

source_name: Primary cells

extract_protocol:
The ventricular/subventricular dissected samples were immediately weighed, minced using scalpels, dissociated into single cell suspension using the Adult Brain Dissociation Kit (Mil-tenyi Biotec) according to the manufacturer’s protocol but without the red blood cell removal step. The isolated single cells were then counted using a hemocytometer and assessed via LIVE/DEAD viability testing (Thermo Fisher).
The single cells were processed, and single-cell libraries were generated using the 10x Ge-nomics Chromium Controller and Chromium Next GEM Single Cell 5’ Reagent Kits (10x Ge-nomics), as per the manufacturer’s protocol. The sequencing-ready libraries were quality con-trolled for size distribution and yield (LabChip GX Perkin Elmer) and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms). Libraries were loaded on NovaSeq 6000 and sequenced using the following parameters: 100 bp Read1, 10 bp Index i7, 10 bp Index i5 and 100 bp Read2.

value: Brain

value: primary CNS cells


title: RA_patient_3


title: Patient8_3V

description:
Library name: Patient8_3V
PolyA RNA


title: RA_patient_5


title: Patient7_LV

description:
Library name: Patient7_LV
PolyA RNA


title: 7-days-DDC, Epithelial cells, scRNA-seq,

description: 10x Genomics

value: 7 days DDC


title: RA_patient_1


title: RA_patient_2


title: MOC2_p62KO-2

city: Toyoake

first: Juntaro

last: Yamasaki

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

country: Japan

institute: Fujita Health University

description: Library name: Sample 5

data_processing:
Sequenced reads were processed by GLC Genomics Workbench 24.1 (Qiagen).
Assembly: GRCm39.109
Supplementary files format and content: The processed data files contain gene-level expression matrices. Columns include: gene name, Ensembl gene ID, transcript biotype, exon length, transcript count information, unique exon reads, total exon reads, and normalized expression values (TPM). Each sample is represented as a column, enabling direct comparison between parental and p62 knockout MOC2 cells.

source_name: MOC2 OSCC cells with p62 knockout (CRISPR-Cas9)

growth_protocol: MOC2 murine oral squamous cell carcinoma cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO₂. Cells were maintained under standard conditions until harvest for RNA extraction.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity were assessed with a TapeStation D5000 (Agilent Technologies), and samples with RIN values greater than 7 were used for library preparation.
Poly(A) mRNA was enriched from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions to generate stranded paired-end libraries.

treatment_protocol: No additional treatments were applied prior to RNA extraction.

value: oral squamous cell carcinoma

value: OSCC cells

value: p62 knockout


title: MOC2_p62KO-1

description: Library name: Sample 4


title: 7-days-DDC, LMNCs,  scRNA-seq

description: 10x Genomics

value: wild type C57Bl/6

value: 8 weeks old

value: female

value: 7 days  DDC


title: Patient7_3V

description:
Library name: Patient7_3V
PolyA RNA


title: MOC2_3

description: Library name: Sample 3

source_name: Parental MOC2 OSCC cells (wild-type p62)

value: wild-type


title: baseline, Epithelial cells, replicate 2, scRNA-seq

description: 10x Genomics

value: Mixed liver cell types, epithelial cells enriched

value: baseline


title: MOC2_1

description: Library name: Sample 1


title: baseline, Epithelial cells, replicate 1, scRNA-seq

description: 10x Genomics


title: Patient6_LV2

description:
Library name: Patient6_LV2
PolyA RNA


title: Diabetic, B12 treated, Biol rep 4, Kidney

city: CHAPEL HILL

first: Yukako

last: Kayashima

state: NC

address: 710 BRINKHOUS-BULLITT BUILDING CB #7525

department: Pathology Lab Med

institute: University of North Carolina at Chapel Hill

description:
Library name: Sample 16
11_26_2023_3M_TTGTGAAGGC-GTACTGACGA_S16

data_processing:
51bp, NextSeq 2000 paired end run, with 1 mismatch used in demultiplexing indexes with bcl2fastq ver 2.20.0. These reads were then aligned to the GRCm39 reference genome and Gencode vM45 for annotation via STAR, producing sorted BAM files. StringTie was subsequently used to quantify gene and transcript expression, yielding TPM, FPKM, and raw count values. The prepDE.py script from StringTie was run to assemble gene- and transcript-level count matrices, which were then imported into R.
Raw count data obtained from RNA-seq was processed using the DESeq2 package in R. Genes with low counts were filtered out, and normalization was performed to account for library size differences across samples. A negative binomial generalized linear model was fitted to the count data, and differential expression analysis was conducted using Wald tests. P-values were adjusted for multiple testing using the Benjamini-Hochberg method to control the false discovery rate (FDR).
Assembly: gencode.vM35.primary_assembly.annotation.gtf GRCm39.primary_assembly.genome.fa
Supplementary files format and content: Gene/Transcript count matrix: CSV files with one row per ENST|TranscriptID and columns of raw counts per sample.
Supplementary files format and content: Limma subgroup analysis files: tab-delimited text containing columns for gene ID (ENSG|GeneName), log2 fold change (logFC), average expression (AveExpr, log2 CPM), moderated t-statistic (t), raw p-value (P.Value), adjusted p-value (adj.P.Val), and B-statistic (B) for each condition–timepoint contrast. GSEA result files: tab-delimited text files listing pathway names, enrichment score (ES), normalized enrichment score (NES), nominal p-value (pval), FDR (padj), number of more extreme permutations (nMoreExtreme), gene set size (size), and comma-separated leading-edge gene IDs.

source_name: kidney

growth_protocol: All mice were kept under husbandry conditions conforming to the National Institutes of Health Guideline for Use and Care of Experimental Animals, and the protocols used were approved by the University of North Carolina Institutional Animal Care and Use Committee (Protocol number: 22-229)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Cat. Number 74106, Hilden,Germany) according to the manufacturer’s instructions
Watchmaker Total RNA

treatment_protocol: Mice were allocated into four groups: two groups, one comprising non-diabetic Elmo1H/HIns2+/+ mice and the other diabetic Elmo1H/HIns2Akita/+ mice, were not supplemented with B12, while the remaining two groups, consisting of non-diabetic Elmo1H/HIns2+/+ mice and diabetic Elmo1H/HIns2Akita/+ mice, were provided with B12 at a dose of 10mg/kgbw/mouse/day via drinking water, starting at 8 weeks of age for 16 weeks

value: kidney


title: Patient6_LV1

description:
Library name: Patient6_LV1
PolyA RNA


title: baseline, LMNCs, replicate 3, scRNA-seq

description: 10x Genomics


title: Diabetic, B12 treated, Biol rep 3, Kidney

description:
Library name: Sample 15
11_16_2023_1M_ACTTAGATCG-AAGAATTCCG_S15


title: Diabetic, B12 treated, Biol rep 2, Kidney

description:
Library name: Sample 14
10_24_2023_8M_AACCGGCCTT-GATCTGAACA_S14


title: Diabetic, B12 treated, Biol rep 1, Kidney

description:
Library name: Sample 13
10_09_2023_2M_CTGGAGAATA-GTTGTATGGA_S13


title: Diabetic, Control, Biol rep 4, Kidney

description:
Library name: Sample 12
10_04_2023_7M_TGATTCCACA-ACGGCTAGAG_S12

value: Control


title: Patient5_LV

description:
Library name: Patient5_LV
PolyA RNA


title: baseline, LMNCs, replicate 2, scRNA-seq

description: 10x Genomics

value: Liver


title: Patient4_LV

description:
Library name: Patient4_LV
PolyA RNA


title: MOC2_p62KO-3

description: Library name: Sample 6


title: Diabetic, Control, Biol rep 1, Kidney

description:
Library name: Sample 9
08_28_2023_4M_AACGACATCT-ATTCCAAGAC_S9


title: Patient4_3V

description:
Library name: Patient4_3V
PolyA RNA


title: ATAC-seq KO Treg 7

city: Lille

first: Artemii

last: Nikitin

address: 1,  Rue du Professeur Calmette

country: France

institute: Inserm

description: ATAC-seq RORa KO Treg 7

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie 2
Mapped reads were filtered to remove duplicates
Regions with significant changes in ATAC-seq signals induced by RORA deficiency were identified using PePr (Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014.)
Assembly: mm10
Supplementary files format and content: Bed files reporting ATAC-seq UP, DOWN in RORA KO vs WT Treg, regions identified using PePr, bigwig files showing genome wide enrichment signal

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

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:
5-15.10^4 cultured cells were washed and incubated in IGEPAL CA-630-containing lysis buffer. After lysis, nuclei were pelleted and incubated for 1 hour at 37ºC with Tn5 transposase (Illumina). DNA was isolated using Qiagen MinElute Kit. Transposed fragments were amplified with barcoding primers and NEBNext High-fidelity PCR Master Mix. Number of additional amplification cycles was determined by a side qPCR with SYBR Green
Libraries were prepared with Truseq kit (illumina) and sequenced using single-end NextSeq technology (illumina).

treatment_protocol: Mouse primary splenic Treg were prepared by FACS based on CD4 and FOXP3 expression. Cells were treated with IL-2, IL-4, IFNg antibodies and activation beads for 6 days in RPMI with 10% FCS, L-glutamine, NEAA, Sodium Pyruvate. ChIP-seq was performed using an H3K27me3 antibody (H3K27me3 Millipore ref 07449).

value: KO


title: Diabetic, Control, Biol rep 2, Kidney

description:
Library name: Sample 10
09_04_2023_1M_AACAGTGACT-ACACTGCGAT_S10


title: Non-Diabetic, B12 treated, Biol rep 3, Kidney

description:
Library name: Sample 7
08_28_2023_2M_GTGGAGGTAG-GTGACGCGAT_S7


title: Non-Diabetic, B12 treated, Biol rep 2, Kidney

description:
Library name: Sample 6
08_28_2023_1M_CTCATTCTGC-ACCGCTTCAA_S6


title: MOC2_2

description: Library name: Sample 2


title: Patient3_LV

description:
Library name: Patient3_LV
PolyA RNA

value: Brain


title: Non-Diabetic, B12 treated, Biol rep 4, Kidney

description:
Library name: Sample 8
08_28_2023_3M_GCGAGATGGA-AGTAGAGTGT_S8


title: ATAC-seq KO Treg 6

description: ATAC-seq RORa KO Treg 6


title: Non-Diabetic, Control, Biol rep 4, Kidney

description:
Library name: Sample 4
08_21_2023_3M_GTGAGAGTAT-CCTCACAGAT_S4


title: ATAC-seq KO Treg 5

description: ATAC-seq RORa KO Treg 5


title: Patient2_LV

description:
Library name: Patient2_LV
PolyA RNA

value: primary CNS cells


title: Non-Diabetic, Control, Biol rep 3, Kidney

description:
Library name: Sample 3
08_11_2023_3M_CAACAGGTAG-CACTATCGTC_S3


title: Non-Diabetic, Control, Biol rep 2, Kidney

description:
Library name: Sample 2
08_11_2023_2M_GCCAAGTAAC-TCATCACGCA_S2


title: Patient2_3V

description:
Library name: Patient2_3V
PolyA RNA


title: Diabetic, Control, Biol rep 3, Kidney

description:
Library name: Sample 11
10_04_2023_4M_AGAGGCACGA-AATTCCACGT_S11


title: Non-Diabetic, Control, Biol rep 1, Kidney

description:
Library name: Sample 1
08_07_2023_4M_TTGCAATGCG-TGAAGTCTCG_S1


title: ATAC-seq KO Treg 4

description: ATAC-seq RORa KO Treg 4


title: baseline, LMNCs, replicate 1,scRNA-seq

description: 10x Genomics

value: Mixed liver cell types,mononulcear cells enriched


title: ATAC-seq KO Treg 3

description: ATAC-seq RORa KO Treg 3


title: rIL4-13- and IFNg- treated floxed ASCs, rep6

city: Paris

first: Victoire

last: Baillet

address: 25-28 rue du Dr Roux

institute: Institut Pasteur

description: Library name: rIL4-13_IFNg_Flox_Exp4_S16

data_processing:
Reads were trimmed using Cutadapt v2.10 to remove sequencing adapters and low-quality bases (Q < 30), reads shorter than 25pb after trimming were discarded.
Reads were aligned to GRCm38 in paired-end mode using Bowtie2 with the following parameters: --very-sensitive -X 2000 --dovetail --no-mixed --no-discordant. Duplicates were removed using Picard MarkDuplicates v2.23.3, as well as reads mapping to blacklisted regions and to mitochondrial chromosome.
Peaks were called separately for each sample, converted as bed file, using MACS2 v2.2.6 with custom parameters (--nomodel --shift -100 --extsize 200 --keep-dup all --call-summits).
Peaks were then combined across replicates then across conditions to generate a consensus peaks list. Number of cutting events for each peak of the consensus peaks list were extracted using featureCounts.
TMM-normalized BigWig tracks for IGV visualization were produced using deepTools v3.4.1 using 1bp bins.
Assembly: mm10
Supplementary files format and content: TMM-normalized bigwigs

source_name: Lung

growth_protocol: Adventitial stromal cells (ASCs) were isolated from the lungs of C57BL/6 mice following experimental treatments as described in the treatment protocol. After enzymatic digestion and mechanical dissociation, PDGFRα+Sca-1+ cells were sorted by fluorescence-activated cell sorting (FACS). Sorted cells were immediately processed for bulk ATAC-seq without further in vitro manipulation.

extract_protocol:
PDGFRα+Sca-1+ lung adventitial stromal cells were isolated following tissue digestion and cell sorting. Lungs were harvested from mice and digested for 45 minutes at room temperature in a solution containing dispase (25 mg/mL) and 1% low-melting agarose. The lungs were subsequently transferred to RPMI 1640 media with DNase I (2.4 U/mL), teased apart, and incubated on a shaker at 37°C for 10 minutes. Cells were then labeled with fluorescently conjugated antibodies specific for PDGFRα and Sca-1, and PDGFRα+Sca-1+ stromal cells were sorted using FACS. The sorted cells were then resuspended in appropriate media for downstream applications.
ATACseq librairies were performed on 90,000 FACS-purified ASCs using the ATACseq kit (Active Motif, 53150) according to the manufacturer’s instructions. Briefly, cells were lysed in ATAC lysis buffer to release nuclei. The nuclei were then resuspended in the transposase reaction mix, which contains the Tn5 transposase, and incubate for 30 minutes at 37°C to cut and tag the accessible regions of the chromatin with sequencing adapters. A limited-cycle PCR was performed to amplify the transposed DNA fragments and to add indexing adapters necessary for sequencing. The PCR products were then purified to remove primers, nucleotides, and other PCR components prior to Illumina sequencing.

treatment_protocol: Recombinant cytokines (rIL-4, rIL-13, rIFNγ; 2 µg/mouse), papain (20 µg/mouse), and CpG (8 µg/mouse) were administered intranasally. Anti-IL-4, anti-IL-13, and anti-IFNγ (200 µg/mouse) were delivered intraperitoneally.

value: Lung

value: Sorted mouse lung stromal cells (ASCs)

value: rIL-4, rIL-13, and rIFNγ (Intranasal) co-administration


title: ATAC-seq KO Treg 8

description: ATAC-seq RORa KO Treg 8


title: rIL4-13- and IFNg- treated ASCs, rep5

description: Library name: rIL4-13_IFNg_Exp4_S13


title: Patient1_LV

description:
Library name: Patient1_LV
PolyA RNA


title: rIL4-13- and IFNg- treated ASCs, rep6

description: Library name: rIL4-13_IFNg_Exp4_S14


title: rIL4-13- and IFNg- treated floxed ASCs, rep5

description: Library name: rIL4-13_IFNg_Flox_Exp4_S15


title: ATAC-seq KO Treg 2

description: ATAC-seq RORa KO Treg 2


title: rIL4-13-treated ASCs, rep6

description: Library name: rIL4-13_Exp4_S12

value: rIL-4 and rIL-13 (Intranasal) co-administration


title: Patient1_3V

description:
Library name: Patient1_3V
PolyA RNA


title: Patient3_3V

description:
Library name: Patient3_3V
PolyA RNA


title: stimulated CD19⁺ B cells, DMSO control - 3

city: Lyon

first: Marlène

middle: Lucie

last: Roy

address: 21 Avenue Tony Garnier

department: Centre International de Recherche en Infectiologie (CIRI)

institute: Hormae Pharma

description:
Library name: Sample-31
Column name in raw_counts_All_Samples.txt: Sample 31

data_processing:
Reads were aligned using STAR (v2.7.10a) on the GRCh38.110 reference genome and counted at the gene level using HTSeq (v0.13.5).
Assembly: GRCh38.110
Supplementary files format and content: Individual text files with gene expression counts for each sample

source_name: CD19+ B lymphocytes

growth_protocol: Purified CD19+ B cells were seeded at a density of 106 cells per ml in complete RPMI 1640 medium, supplemented with GlutaMAX, 10% heat-inactivated FCS, 100 U/ml penicillin, 100 μg/ml streptomycin, and then stimulated with 5 μg/mL CpG-B ODN2006 and 10 μg/mL anti-Human IgG + IgM (H+L) for 24 h.

extract_protocol:
Total RNAs were extracted with Direct-zol RNA Microprep following the manufacturer’ instructions. RNA fragment analysis was performed with Agilent Bioanalyzer 2100 instrument with Agilent RNA 6000 Nano Kit.
Total RNAs were sent to a commercial sequencing service provider (Microsynth) for RNA-seq library preparation and sequencing. Briefly, libraries were generated after poly(A) enrichment and sequencing was performed on NovaSeq Illumina in 2*150 bp with 30 Mio of paired reads per sample.

treatment_protocol: Simultaneously with the stimulation, purified CD19+ B cells were either mock-treated with DMSO or treated with 10 μM A943931.

value: CD19+ B lymphocytes

value: WT

value: DMSO


title: rIL4-13-treated ASCs, rep5

description: Library name: rIL4-13_Exp4_S11

value: wild-type


title: ATAC-seq WT Treg 4

description: ATAC-seq WT Treg 4

source_name: FOXP3-CRE adult female mice


title: Non-Diabetic, B12 treated, Biol rep 1, Kidney

description:
Library name: Sample 5
08_21_2023_7M_AGAGTATGTG-GAAGCCATCT_S5


title: CpG-treated ASCs followed by Papain treatment, rep1

description: Library name: PaCPG_Exp4_S7

value: CpG (Intranasal) administration followed by Papain (intranasal) administration 30 days later


title: ATAC-seq WT Treg 5

description: ATAC-seq WT Treg 5


title: CpG-treated ASCs followed by Papain treatment, rep2

description: Library name: PaCPG_Exp4_S8


title: OM85-treated ASCs followed by Papain treatment, rep1

description: Library name: PaOM_Exp4_S5

value: OM85 (Intranasal) administration followed by Papain (intranasal) administration 30 days later


title: unstimulated CD19⁺ B cells, A943931 treatment - 3

description:
Library name: Sample-29
Column name in raw_counts_All_Samples.txt: Sample 29


title: skin_UVB_Treg2_UVB

description: Library name: skin_UVB_Treg2

data_processing:
We used trimmatomic to remove contaminants, adaptors, low-quality sequences. HISAT2, StringTie and DESeq2 software were applied for RNA-seq analysis.
Assembly: grcm38/mm10
Supplementary files format and content: FPKM, TPM

source_name: skin Tregs

extract_protocol:
Total RNA was extracted from Treg using the Direct-zolTM RNA MicroPrep (Zymo Research). The quality and integrity of RNA were evaluated by the Femto RNA assay (Agilent Technologies).
The sequencing library were prepared with the TruSeq SMARTer Ultra-Low RNA-seq Kit (Illumina). The RNA libraries were sequenced on the Illumina NextSeq P2 platform with a per-sample target of 50 million 100 bp single-end reads.

value: skin Tregs

value: Treg cells

value: UVB treatment


title: skin_UVB_Treg1_UVB

description: Library name: skin_UVB_Treg1


title: unstimulated CD19⁺ B cells, DMSO control - 3

description:
Library name: Sample-28
Column name in raw_counts_All_Samples.txt: Sample 28


title: skin_Treg2_non-UVB

description: Library name: skin_Treg2


title: ATAC-seq WT Treg 2

description: ATAC-seq WT Treg 2


title: ATAC-seq WT Treg 3

description: ATAC-seq WT Treg 3


title: skin_Treg1_non-UVB

description: Library name: skin_Treg1


title: stimulated CD19⁺ B cells, A943931 treatment - 2

description:
Library name: Sample-26
Column name in raw_counts_All_Samples.txt: Sample 26


title: rIL4-13- and IFNg- treated ASCs, rep4

description: Library name: rIL4-13_IFNg-WT_Exp3_S16


title: ATAC-seq WT Treg 1

description: ATAC-seq WT Treg 1


title: rIL4-13- and IFNg- treated ASCs, rep3

description: Library name: rIL4-13_IFNg-WT_Exp3_S15


title: stimulated CD19⁺ B cells, A943931 treatment - 3

description:
Library name: Sample-32
Column name in raw_counts_All_Samples.txt: Sample 32


title: stimulated CD19⁺ B cells, DMSO control - 2

description:
Library name: Sample-25
Column name in raw_counts_All_Samples.txt: Sample 25


title: ATAC-seq KO Treg 1

description: ATAC-seq RORa KO Treg 1

value: KO


title: 4T1 DHO BRQ-3

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 GRCm39 using  HISTA2
Read count extraction and normalization were performed using HTSeq-count
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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: Mouse breast cancer cell line

value: BRQ


title: unstimulated CD19⁺ B cells, A943931 treatment - 2

description:
Library name: Sample-23
Column name in raw_counts_All_Samples.txt: Sample 23


title: rIL4-13- and IFNg- treated ASCs, rep1

description: Library name: rIL4-13_IFNg-WT_Exp2_S11


title: rIL4-13- and IFNg- treated ASCs, rep2

description: Library name: rIL4-13_IFNg-WT_Exp2_S15


title: 4T1 DHO BRQ-2


title: OM85-treated ASCs followed by Papain treatment, rep2

description: Library name: PaOM_Exp4_S6


title: rIL4-13-treated ASCs, rep3

description: Library name: rIL4-13_Exp3_wt_S11


title: unstimulated CD19⁺ B cells, DMSO control - 2

description:
Library name: Sample-22
Column name in raw_counts_All_Samples.txt: Sample 22


title: rIL4-13-treated ASCs, rep2

description: Library name: rIL4-13_Exp2_S14


title: 4T1 DHO BRQ-1


title: Papain-treated ASCs, rep2

description: Library name: Pa_Exp2_Pa_S5

value: Papain (Intranasal) administration


title: 4T1 DHO DMSO-3


title: stimulated CD19⁺ B cells, A943931 treatment - 1

description:
Library name: Sample-20
Column name in raw_counts_All_Samples.txt: Sample 20


title: Papain-treated ASCs, rep1

description: Library name: Pa_Exp2_Pa1_S2

value: Lung


title: rIL4-13-treated ASCs, rep1

description: Library name: rIL4-13_Exp2_S10

value: Sorted mouse lung stromal cells (ASCs)


title: stimulated CD19⁺ B cells, DMSO control - 1

description:
Library name: Sample-19
Column name in raw_counts_All_Samples.txt: Sample 19


title: 4T1 DHO DMSO-2


title: Papain- and CpG- treated ASCs, rep2

description: Library name: PaCPG_Exp3_PaCPG-2_S6


title: Papain- and CpG- treated ASCs, rep1

description: Library name: PaCPG_Exp3_PaCPG-1_S5


title: Papain-, CpG- and -antiIFNg- treated ASCs, rep2

description: Library name: PaCPG_aIFNg_Exp3_S8

value: Papain, CPG (Intranasal), and aIFNγ (Intraperitoneal) co-administration


title: unstimulated CD19⁺ B cells, A943931 treatment - 1

description:
Library name: Sample-17
Column name in raw_counts_All_Samples.txt: Sample 17


title: 4T1 DHO DMSO-1


title: Papain-, CpG- and -antiIFNg- treated ASCs, rep1

description: Library name: PaCPG_aIFNg_Exp3_S7


title: unstimulated CD19⁺ B cells, DMSO control - 1

description:
Library name: Sample-16
Column name in raw_counts_All_Samples.txt: Sample 16


title: ECRG4- AD patients

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku

institute: Hokkaido University

description: Library name: ECRG4 negative

data_processing:
GeneGlobe Data Analysis Center (QIAGEN) Calibrate miRBase entries Trim adapter and low-quality bases Identify insert sequences and unique molecular index (UMI) sequences Align insert sequences Count reads and unique molecules assigned to miRNAs, piRNAs, tRNAs and otherRNAs
Supplementary files format and content: Excel® file includes read counts and clustered UMI counts for each sample

source_name: Plasma

extract_protocol:
Total RNA containing miRNA was extracted from the plasma of patients using the miRNeasy kit for plasma/serum (QIAGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were constructed using QIAseq miRNA Library Kit following the manufacturer's instructions.

value: Plasma

value: EDTA


title: 4T1 DHO KO-2