title: H139-0068-T6-4_S3_L001

description:
Library name: H139-0068-T6-4_S3_L001
data_processed2.xlsx


title: CTL-AcPbKO-04

status: Public on Dec 18 2024

type: SRA

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

country: USA

institute: Washington State University

library_source: transcriptomic

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.20 was used to convert base-calling files to fastq files and to trim adaptors.
HISAT2 v2.2.1 was used for alignment
featureCounts (from Subrea v2.0.1) was used to quantify genes and transcripts.
DESeq2 v1.31.16 was used for differential gene expression analysis.
Assembly: UCSC mm10
Supplementary files format and content: comma-delimited text files including read counts in genes and differential gene expression

molecule: total RNA

organism: Mus musculus

source_name: somatosensory cortex

growth_protocol: Male C57BL/6 and male IL1 receptor AcPb-/- mice were obtained from Jackson Laboratories, Bar Harbor, ME, as authorized by Amgen, Thousand Oaks, CA, and were bred for 5-7 generations at Washington State University. Subsequent homozygotic offspring, aged 2-3 months, were utilized in the experiments. All mice were genotyped from tail snips by Transnetyx (Cordova, TN).  Mice were maintained in plastic filter-top cages at 23-24° C under a 12:12 light-dark cycle (light onset = ZT0) and during recordings in sound-attenuated environmental chambers.  Food and water were available ad libitum.  All animal procedures were approved by the Washington State University Animal Care and Use Committee and conformed to National Institutes of Health guidelines.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: We exposed both wild-type (WT) and AcPb-/- mice to sleep disruption (SD) from ZT20-4 using a gentle handling technique, with four mice in each group (SD-WT [n=4], SD-AcPb [n=4]). Control mice from both strains, consisting of three WT mice (CTL-WT [n=3]) and five AcPb-/- mice (CTL-AcPb-/- [n=5]), were left undisturbed before being euthanized at ZT4. Total RNA was extracted from somatosensory cortex tissues collected post-euthanasia from both WT and AcPb-/- mice for RNA sequencing.

tag: tissue

value: somatosensory cortex

tag: genotype

value: AcPb-/-

tag: treatment

value: Control


title: PCP, wild type, IP, 3 days, Rep2.

city: Wuhan

first: weidong

last: liu

address: donghu street

country: China

institute: Wuhan University

description: Library name: IP-WT-PCP-Rep2

data_processing:
All input and IP samples’ raw sequencing data were preprocessed using fastp (v. 0.20.1), aligned with HISAT2 (v. 2.2.1) to GRCm38 reference genome, and generated read counts by featureCounts (v.2.0.1). For calculating the relative m6A level for each gene, we used the DESeq2 to compare the read counts of genes between IP samples and input samples on a transcriptome-wide scale. Based on the adjusted fold change (Wald statistic, fourth column of output of DESeq2) of each gene from the output of DESeq2, we further calculated the Z-score of adjusted fold change in each cell type, and this Z-score represents the relative m6A level. We identified high-confidence m6A-tagged mRNAs by setting up the cutoff line based on log2(fold change) > 1 and P value < 0.05
Assembly: mm10
Supplementary files format and content: txt

source_name: long bone

extract_protocol: SCs and other targets cells were sorted into TRIzol reagent (Takara) to extract RNA.

value: long bone

tag: strain

tag: cell type

value: skeletal stem and progenitor cells

value: wild type

value: no treatment

tag: batch


title: H139-0057-T1_S7_L001

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

description:
Library name: H139-0057-T1_S7_L001
data_processed2.xlsx

library_source: genomic

data_processing:
NGS output was uploaded to the ARResT/Interrogate immunoprofiler. Samples with <20.000 junctioned reads, excluding spiked sequences, were regarded as QC-failed and discarded. Reads were converted to cell equivalents using the EuroClonality central in-tube quality control. Clonotypes were defined as sequences with identical TRBV and TRBJ gene usage, and 100% complementarity determining region 3 (CDR3) amino acid sequence identity. Unproductive TRB rearrangements were discarded. Clonotypes associated with <0.5 cell equivalents were regarded as likely spillover reads and discarded. Shared clonotypes were cross-referenced against the VDJdb T cell compendium.
Assembly: hg19
Supplementary files format and content: xslx file contained the QC-output of the Arrest/Interrogate immunoprofiler

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
DNA was extracted using a QIA-cube
TRB libraries were amplified from genomic DNA, using the EuroClonality two-step TRB assay, developed by the Euroclonality-NGS Working Group (manuscript in preparation), aiming for 1μg of PBMC DNA input per sample. After each PCR step, amplification success was checked using the D1000 DNA ScreenTape assay on a 4200 Agilent TapeStation (Agilent, Santa Clara, CA, USA) and libraries were purified using the AMPure XP kit (Beckman Coulter, Brae, CA, USA.

treatment_protocol: See methods section of HOVON-139 main publication

value: PBMC

value: Venetoclax/Obinutuzumab


title: CTL-AcPbKO-03


title: Control_NFkB2_Rep2

city: Chapel Hill

first: Albert

middle: S.

last: Baldwin

state: North Carolina

address: 450 West Drive, Room 21-211

department: Lineberger Comprehensive Cancer Center

institute: UNC at Chapel Hill

data_processing:
The original raw data from Illumina platform are transformed to Raw Reads, by base calling of CASAVA v1.8 and recorded in a FASTQ file - as described by Novogene Report
ChIP-seq reads were trimmed using Skewer v0.1.126 discarding reads whose length are less than 18nt after trimming  - as described by Novogene Report
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA v0.7.12. Duplicates are labeled using SAMBLASTER (Faust et al., 2014) and mapping quality value is calculated by MAPQ (Li et al., 2008). Reads with MAPQ no lower than 13 , can be interpreted as the chance of non-accurate mapping (same score for the random mapping) is 0.05. Only one read pair is kept for the duplicates in the followed peak calling  - as described by Novogene Report
Peaks were called uing MACS v2.1.0 (threshold p value = 0.05) - as described by Novogene Report
Peak annotation was performed by PeakAnnotator_Cpp v1.4 (TSS peaks.bed / NDG peaks.bed) - as described by Novogene Report
FoldEnrich is used for differential analysis of peaks in different experimental groups by diffbind (ip/input>2) - as described by Novogene Report
Assembly: hg38
Supplementary files format and content: Bigwig, narrowPeak (except for Input sample)

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37oC at 5% CO2.

extract_protocol:
Cells were fixed with 2 nM disuccinimidyl glutarate for 45 minutes at room temperature, 1% formaldehyde for 8 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated for 45 minutes (30 secs on and 30 secs off).
ChIP-seq libraries were prepared by Novogene Corporation Inc., California.

treatment_protocol: T47D cells were transduced with lentiviruses containing DAB2IP targeting shRNAs or empty vector control shRNA. Post 24 hours of infection, cells were maintained in normal medium for another 24 hours. Next, puromycin selection (2 μg/ml) was done for 72 hours.

tag: cell line

value: Luminal A Breast Cancer Cell

tag: chip antibody


title: SD-AcPbKO-02

value: Sleep disruption (SD)


title: PCP, wild type, IP, 3 days, rep1

description: Library name: IP-WT-PCP-Rep1


title: H139-0055-T1_S6_L001

description:
Library name: H139-0055-T1_S6_L001
data_processed2.xlsx


title: BCSP, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-BCSP-Rep2


title: CTL-AcPbKO-02


title: H139-0032-T6-4_S5_L001

description:
Library name: H139-0032-T6-4_S5_L001
data_processed2.xlsx


title: Control_RelB_Rep2


title: CTL-AcPbKO-01


title: Control_P65_Rep2


title: BCSP, wild type, IP, 3 days, rep1

description: Library name: IP-WT-BCSP-Rep1


title: H139-0053-T1_S9_L001

description:
Library name: H139-0053-T1_S9_L001
data_processed2.xlsx


title: Control_Input_Rep2


title: SD-WT-04

value: wild-type


title: SD-WT-03


title: pre-BCSP, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-pre-BCSP-Rep2


title: H139-0052-T1_S8_L001

description:
Library name: H139-0052-T1_S8_L001
data_processed2.xlsx


title: pre-BCSP, wild type, IP, 3 days, rep1

description: Library name: IP-WT-pre-BCSP-Rep1


title: SD-WT-02


title: H139-0051-T1_S7_L001

description:
Library name: H139-0051-T1_S7_L001
data_processed2.xlsx


title: Control_NFkB2_Rep1


title: Control_RelB_Rep1


title: Control_P65_Rep1


title: H139-0050-T1_S6_L001

description:
Library name: H139-0050-T1_S6_L001
data_processed2.xlsx


title: H139-0068-T5_S10_L001

description:
Library name: H139-0068-T5_S10_L001
data_processed2.xlsx


title: SD-WT-01


title: SSC, wild type, IP, 3 days, rep1

description: Library name: IP-WT-SSC-Rep1


title: CTL-WT-03


title: Control_Input_Rep1


title: H139-0049-T1_S5_L001

description:
Library name: H139-0049-T1_S5_L001
data_processed2.xlsx


title: HEC, wild type, 3 days, Rep2.

description: Library name: WT-HEC-Rep2


title: CTL-WT-02


title: DAB2IP KD_NFkB2_Rep2


title: CTL-WT-01


title: H139-0041-T5_S4_L001

description:
Library name: H139-0041-T5_S4_L001
data_processed2.xlsx


title: HEC, wild type, 3 days, rep1

description: Library name: WT-HEC-Rep1


title: DAB2IP KD_RelB_Rep2


title: H139-0032-T5_S3_L001

description:
Library name: H139-0032-T5_S3_L001
data_processed2.xlsx


title: 6C3, wild type, 3 days, Rep2.

description: Library name: WT-6C3-Rep2


title: kidney, PND28, WT, rep4

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

data_processing:
Reads were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p" for the paired-end samples (PND14) or "-s0" for the single-end samples (PND7,PND28).
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Unstranded --outWigNorm RPM", followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Note that each age should be treated as an independent dataset; since age and batch are conflated, results from direct comparisons across ages should be interpreted with caution.
Assembly: mm10
Supplementary files format and content: counts-per-gene matrix per dataset (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)

source_name: kidney

extract_protocol:
Purelink RNA mini kit was used for RNA extraction
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.

value: kidney

tag: age

value: WT


title: H139-0024-T6-4_S2_L001

description:
Library name: H139-0024-T6-4_S2_L001
data_processed2.xlsx


title: 6C3, wild type, 3 days, rep1

description: Library name: WT-6C3-Rep1


title: BLSP, wild type, 3 days, Rep2.

description: Library name: WT-BLSP-Rep2


title: kidney, PND28, WT, rep3


title: DAB2IP KD_Input_Rep2


title: DAB2IP KD_P65_Rep2


title: DAB2IP KD_NFkB2_Rep1


title: LSEC CTL-2

city: Xi'an

first: Luo

last: Yuru

state: Shannxi

address: 28 Xianning West Road

department: Health Science Center

institute: Xi'an Jiaotong University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: txt files of readcount value for each sample

organism: Mus

source_name: Liver

extract_protocol:
Total RNA was extracted from heart ventricles using TRIzol reagent (Sigma)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L)

value: Liver

value: liver sinusoidal endothelial cells

value: treat with CCl4


title: kidney, PND28, WT, rep2


title: THY, wild type, 3 days, Rep2.

description: Library name: WT-THY-Rep2


title: kidney, PND28, Glis3 KO, rep4

value: Glis3 KO


title: kidney, PND28, WT, rep1


title: THY, wild type, 3 days, rep1

description: Library name: WT-THY-Rep1


title: LSEC CTL-1


title: DAB2IP KD_RelB_Rep1


title: DAB2IP KD_P65_Rep1


title: kidney, PND28, Glis3 KO, rep3


title: DAB2IP KD_Input_Rep1


title: COPD_06

city: Pittsburgh

first: Melanie

last: Königshoff

state: Pennsylvania

address: 200 Lothrop St

institute: University of Pittsburgh

library_source: transcriptomic single cell

data_processing:
Following sequencing, the generation of count matrices was performed by using the Cellranger computational pipeline (v3.1.0, STAR v2.5.3a). The reads were aligned to the hg38 human reference genome (GRCh38.97)
Batch affection of samples were regressed out via BBKNN (v1.4.0). Cells with high counts were filtered out using sample specific thresholds (>12,000 counts, > 18,000 counts, or > 25000 counts). Then, cells with less than 350 genes and cells with more than 20% mitochondria reads were filtered out.  Genes were only considered if they were expressed in at least 3 cells in the data set.
Doublets were detected with Scrublet (v0.2.3) and the ambient genes were removed via SoupX (v1.6.1).
The filtered gene expression matrix was normalized based on size factors using Scran (v1.24.1) before being log-transformed.
The top 2,000 highly variable genes were selected via the Scanpy function scanpy.pp.highly_variable_genes() before dimensionality reduction and data visualization.
Assembly: GRCh38.97
Supplementary files format and content: h5ad file with annotated data; h5ad file with raw counts

source_name: lung

extract_protocol:
Two to three pieces (2cm x2cm) of parenchymal lung tissues were sampled from regions with visible air trapping under pleura in each COPD lungs or comparable regions in donor lungs. Tissues without pleura were minced with sterile scissors and digested by collagenase and dispase for 1 hour at 37°C (collagenase: 0.1 Wünsch U·mL−1; dispase: 0.8Wünsch U·mL−1; Roche 11097113001). The homogenized tissues after digestion were filtered through 100µm and 20µm pore size sterile nylon mesh (Sefar) sequentially in vacuum system and washed with DMEM/F12 media (Gibco, 11330-032) with PenStrep (100U/ml, Gibco 15140122) and DNAseI (0.1mg/ml, Roche 11284932001). The single cell suspension was centrifuged at 300g for 10min at 15°C, followed by immune cell depletion with MACS beads conjugated with anti-human CD45 antibody (Miltenyi 130-045-801) and MACS LS column (Miltenyi 130-042-401). Then cells were stained for PerCP/Cyanine5.5 anti-human EpCAM antibody (BioLegend 369804) and DAPI (4',6-Diamidino-2-Phenylindole, Dihydrochloride) (Invitrogen D1306) for FACS sort.
Epcam+/DAPI- live single epithelial cell Single-cell suspensions were loaded onto a Chromium single cell chip (Chromium™ Single Cell 3' Reagent Kit, v2 Chemistry) to obtain single cell 3’ libraries for sequencing. cDNA obtained after droplet reverse transcription was amplified for 14 cycles and qualitied using Agilent Bioanalyzer. The barcoded libraries were sequenced using Illumina NovaSeq 6000HiSeq 4000 (Illumina, San Diego, CA, USA) aiming for 100,000 reads per cell and capturing 10,000 per library.

tag: disease state

value: COPD

tag: Sex

value: male


title: 48h_Mock_R3

city: Badalona

first: Cristina

last: Gálvez

state: Barcelona

address: Ctra. de Canyet s/n

department: Data Management

country: Spain

institute: IrsiCaixa

data_processing:
All samples passed quality control checks and were aligned using bowtie2 version 2.5.1 . RSEM v1.3.1 was used to create the indexes of these genomes and calculate the gene expression.
Used RSEM with bowtie2 aligner changing the strand and the reference as needed from the following command: “rsem-calculate-expression --bowtie2 --paired-end --time -p ${threads} --append-names --no-bam-output --strandedness ${strand}     ${forward} ${reverse} ${reference}”
Assembly: The viral genome used was the SARS-CoV-2 variant EPI_ISL_510689 and the reference ASM985889v3. For host alignment, the reference genome GCA_023783515.1 and the human genome (GRCh38, ENSEMBL version 109) were used.
Supplementary files format and content: A csv file with the counts of the mapping into several indexes. Colum names indicate the content: “h” for host, “v”  for viral; “genome” for mapping to the genome, “transcriptome” for mapping to the transcriptome,  “+” for positive strand, “-” for negative strand and “all” if it is irrespectively of the strand.

organism: Chlorocebus aethiops

source_name: Kidney

extract_protocol:
RNA was extracted with a Nucleospin RNA Magenerey-Nagel extraction kit
Illumina TruSeq RNA w/ Ribo-Zero library
Novaseq 6000 150bp PE (150x2bp) 60M reads/spl (9Gb/spl) by Macrogen. Paired-end sequencing was performed according to standard TruSeq Stranded Total RNA Reference Guide (1000000040499 v00) protocol using TruSeq Stranded Total RNA Library Prep Gold Kit.

value: Kidney

value: Vero E6

value: kidney epithelial cells

tag: time

value: 48 hours

tag: replicate


title: PCP, wild type, 3 days, rep1

description: Library name: WT-PCP-Rep1

value: long bone

value: skeletal stem and progenitor cells

value: wild type

value: no treatment


title: PCP, wild type, 3 days, Rep2.

description: Library name: WT-PCP-Rep2


title: kidney, PND28, Glis3 KO, rep2


title: LSEC P1KO-2


title: BCSP, wild type, 3 days, Rep2.

description: Library name: WT-BCSP-Rep2


title: 48h_Mock_R1


title: COPD_04


title: BCSP, wild type, 3 days, rep1

description: Library name: WT-BCSP-Rep1


title: COPD_03

value: female


title: 24h_Mock_R2

value: 24 hours


title: pre-BCSP, wild type, 3 days, Rep2.

description: Library name: WT-pre-BCSP-Rep2


title: COPD_02


title: kidney, PND7, WT, rep1

value: kidney

value: WT


title: COPD_01


title: 24h_Mock_R1


title: kidney, PND7, Glis3 KO, rep3

description:
outlier removed from analysis
KO-PND7.rep3


title: 48h_Mock_R2


title: 4h_Mock_R3

value: 4 hours


title: SSC, wild type, 3 days, Rep2.

description: Library name: WT-SSC-Rep2


title: Control_04

value: Healthy


title: kidney, PND28, Glis3 KO, rep1

value: Glis3 KO


title: COPD_05

value: COPD


title: 4h_Mock_R2


title: SSC, wild type, 3 days, rep1

description: Library name: WT-SSC-Rep1


title: kidney, PND7, Glis3 KO, rep2


title: kidney, PND7, Glis3 KO, rep1


title: WT rep3

city: Guangzhou

first: YAO

last: LUO

address: Dong Feng East Road

institute: SYSUCC

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. W
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: xenograft

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: xenograft

value: NSCLC

value: untreated


title: kidney, PND7, WT, rep3


title: kidney, PND7, WT, rep2


title: 4h_Mock_R1

value: Kidney

value: Vero E6

value: kidney epithelial cells


title: La_Lin28a_rep2

city: Beijing

first: Dan

last: Song

state: Beijing

address: 3 Datun Road, Chaoyang District, Beijing 100101, P.R.china

institute: CHINESE ACADEMY OF SCIENCES STEM CELL AND REGENERATIVE MEDICINE INNOVATION INSTITUTE

data_processing:
The raw data from RNA-seq and RIP-seq were preprocessed by removing adapter sequences, filtering low-quality reads, and trimming low-quality bases using FastQC.
The data were aligned to the GRCh38 reference genome using Hisat2 (version 2.0.4).
Differential gene expression analysis of the transcriptome was performed using DESeq2 (version 1.42.0) (p < 0.05).
The differentially methylated m6A peaks were identified using MACS2 (version 1.4.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes count values for each Sample

source_name: MuSCs-Lin28a positive

growth_protocol: The culture plates were first coated with 1% Matrigel. MuSCs  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃。

extract_protocol:
MuSCs were collected in 1 mL of Trizol and left on ice for 5 minutes. 200 μL of chloroform was added and mixed thoroughly. The cell samples were centrifuged at 12000 rpm for 10 minutes at 4°C. The supernatant was collected, and an equal volume of isopropanol was added, followed by incubation at -20°C for 2 hours. Finally, the RNA was collected by centrifugation at 12000 rpm for 10 minutes at 4°C, and the precipitate was washed with 80% ethanol, followed by dissolution in nuclease-free water.
RNA was used to construct a sequence library using an RNA-seq Library Prep Kit (Vazyme, NR605), followed by sequencing analysis using Illumina HiSeq X10.

treatment_protocol: RNA immunoprecipitation sequencing

value: Skeletal muscle

value: muscle stem cells

value: Lin28a  positive


title: 24h_Mock_R3


title: WT rep2


title: pre-BCSP, wild type, 3 days, rep1

description: Library name: WT-pre-BCSP-Rep1

value: long bone

value: skeletal stem and progenitor cells

value: wild type

value: no treatment


title: 0h_Mock_R3

value: 0 hours


title: WT rep1

value: WT


title: Zebrafish embryos, dose 100, replicate C

city: Metz

first: Sophie

last: Prud'homme

address: Bâtiment IBISE, Rue Claude Bernard, Metz

department: Toxicologie de l'Environnement

country: France

institute: Université de Lorraine

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.csv : 100C

data_processing:
Raw mRNAseq data processing was performed on the Galaxy french server provided by the ‘Institut Français de Bioinformatique’  (IFB). Raw reads were filtered according to size (>55 bp) and quality parameters (mean Phred score >20 on 5’ and 3’ bases and on a 4 pb sliding window) using Trimmomatic, leading to keep 87 to 92% of total reads according to the sample.
Cleaned reads were mapped to the zebrafish reference transcriptome GCRz11 and quantified using Salmon quant (v. 1.5.1)
Assembly: GCRz11
Supplementary files format and content: raw_counts_All_Samples.csv includes raw counts for each Sample
Supplementary files format and content: xx_TPM.csv files include TPM values for each Sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (Danio rerio) embryos (AB strain) were obtained from the Luxembourg Centre for Systems Biomedicine (LCSB) aquatic plateform (Luxembourg University, Belval, Luxembourg). They were collected within 1 hour after spawn, placed in standardized fish water at 26°C (NF EN ISO 7346-2 (1998), pre-oxygenated by bubbling for 12h) and transferred to the LIEC facilities (Metz, France).

extract_protocol:
RNA was extracted using the Rneasy mini extraction kit (Qiagen).
Quality and integrity assessment: After quality and integrity assessment of extracted RNA by NanoDrop (Thermo Fisher Scientific, Waltham, MA) and by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), the 3 higher quality RNA samples per condition (A260/A280 > 1.7, A260/A230 > 2, RIN >8.8) were selected for high throughput mRNA sequencing.
RNA libraries were prepared from 250 ng total RNA using UltraTMII Directional RNA library Prep kit (New England Biolabs) and library size was checked by the DNA 1000 Assay Kit of the Bioanalyzer 2100 system. Libraries were sequenced on a NextSeq500 Illumina sequencer with 1x 75 bp single reads, providing 40 to 57 million reads for each sample. Library preparation, quality check and sequencing were performed by Helixio, France.

treatment_protocol: Commercial DBP (99% purity, CAS no. 84-74-2; Sigma-Aldrich, USA) was prepared as a solvent-free stock solution in fish water at 5.4 mg/L. Stock and fish water DBP concentrations were quantified one day before exposure using UPLC-UV with a detection limit of 3 µg/L. The analysis, performed on a 10 µL injection volume, used an Acquity UPLC HSS T3 column (2.5 µm, 2.1x100 mm; Waters, Germany) with a mobile phase of 60% acetonitrile and 40% H₂O at a flow rate of 8 mL/min and 25 °C. DBP concentrations in fish water were below the limit of detection. Stock solutions were stored in the dark at 26 °C and remained stable throughout the experiment. Test solutions were freshly prepared daily in oxygenated fish water by serial dilution of the stock solution to achieve a dose gradient [0, 5, 10, 30, 100 µg/L]. Glassware was exclusively used to prevent contamination by phthalates or plasticizers. Zebrafish embryos (256-cell stage) were randomly assigned to glass beakers containing 60 mL of test solution, with 30 embryos per beaker and five replicates per dose. Embryos were maintained in a climate-controlled chamber at 26 (±0.5) °C under a 14:10 light/dark cycle. Exposure was semi-dynamic, with daily renewal of one-third of the solution volume using freshly prepared test solutions. After 120 hours of exposure, pools of 10 embryos (‘protruding mouth’ stage) were flash-frozen in liquid nitrogen and stored at −80 °C for RNA extraction.

value: whole embryo

tag: developmental stage

value: protuding mouth

value: AB wild type

value: 120h post-fertilization

value: 100 µg/L DBP exposure

tag: biological replicate

value: C


title: 0h_Mock_R2

value: Kidney

value: Vero E6


title: Zebrafish embryos, dose 100, replicate A

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.csv : 100A

value: A


title: La_Lin28a_rep1

value: Skeletal muscle

value: muscle stem cells


title: sgHKDC1-1 rep3

value: xenograft

value: NSCLC

value: HKDC1 knockout

value: untreated


title: 0h_Mock_R1

value: kidney epithelial cells

value: 0 hours


title: La_m6A_rep1

molecule: polyA RNA

value: Lin28a  positive


title: Zebrafish embryos, dose 50, replicate D

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.csv : 50D

value: whole embryo

value: protuding mouth

value: 50 µg/L DBP exposure

value: D


title: Zebrafish embryos, dose 100, replicate E

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.csv : 100E

value: AB wild type

value: 120h post-fertilization

value: 100 µg/L DBP exposure

value: E


title: sgHKDC1-1 rep2


title: 48h_Apli_R3

value: Kidney

value: Vero E6

value: 48 hours

value: Plitidepsin 50nM


title: Con_m6A_rep2

source_name: MuSCs-control

value: Skeletal muscle

value: muscle stem cells

value: Control


title: 48h_Apli_R2

value: kidney epithelial cells


title: Zebrafish embryos, dose 50, replicate A

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.csv : 50A

value: A


title: Zebrafish embryos, dose 50, replicate B

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.csv : 50B

value: whole embryo

value: B


title: sgHKDC1-1 rep1

value: xenograft

value: NSCLC

value: HKDC1 knockout

value: untreated


title: KYSE-70, IVM-2 [KYSE70-64-2]

city: Kaifeng

first: Mengmeng

last: Lu

state: Henan

address: Henan Kaifeng

department: School of life Sciences

institute: Henan Univesity

data_processing:
To remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by  Cutadapt (V1.9.1) to be high quality clean data.
Reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL. Hisat2 (v2.0.1) was used to index  reference genome sequence. Clean data were aligned to reference genome via software Hisat2  (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data.
Read count extraction and normalization were performed using Htseq(V 0.6.1)
Supplementary files format and content: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: KYSE 30 or KYSE-70  cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit  (Qiagen)/other kits. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq  were constructed according to the manufacturer’s protocol

treatment_protocol: The cells were treated with various concentrations of ivermectin for 24 h at 37℃ under 5% CO2 conditions.

value: Esophageal squamous cell carcinoma cells

value: WT

value: ivermectin treatment


title: 48h_Apli_R1

value: Kidney

value: Vero E6


title: La_Igf2bp3_rep2

value: Lin28a  positive


title: KYSE-70, IVM-1 [KYSE70-64-1]


title: Con_m6A_rep1

value: Skeletal muscle


title: La_m6A_rep2

value: muscle stem cells


title: La_Igf2bp3_rep1


title: Zebrafish embryos, dose 10, replicate C

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.csv : 10C

value: protuding mouth

value: AB wild type

value: 120h post-fertilization

value: 10 µg/L DBP exposure

value: C


title: Zebrafish embryos, dose 10, replicate B

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.csv : 10B

value: whole embryo

value: B


title: 24h_Apli_R2

value: kidney epithelial cells

value: 24 hours

value: Plitidepsin 50nM


title: KYSE-70, control-3 [KYSE70-C-3]

value: Esophageal squamous cell carcinoma cells

value: WT

value: DMSO treatment


title: Zebrafish embryos, dose 10, replicate A

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.csv : 10A

value: A


title: 24h_Apli_R1

value: Kidney

value: Vero E6


title: Con_Igf2bp3_rep1

value: Skeletal muscle

value: muscle stem cells

value: Control


title: Con_Igf2bp3_rep2


title: KYSE-70, control-1 [KYSE70-C-1]


title: Zebrafish embryos, dose 5, replicate E

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.csv : 5E

value: protuding mouth

value: AB wild type

value: 120h post-fertilization

value: 5 µg/L DBP exposure

value: E


title: KYSE-30, IVM-2 [KYSE30-28-2]

value: ivermectin treatment


title: Zebrafish embryos, dose 5, replicate B

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.csv : 5B

value: whole embryo

value: B


title: 4h_Apli_R3

value: kidney epithelial cells

value: 4 hours

value: Plitidepsin 50nM


title: Zebrafish embryos, dose 5, replicate A

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.csv : 5A

value: A


title: La_In_rep1

value: Lin28a  positive

value: no treatment


title: 24h_Apli_R3

value: Kidney

value: Vero E6

value: 24 hours


title: KYSE-30, IVM-1 [KYSE30-28-1]

value: Esophageal squamous cell carcinoma cells

value: WT


title: Con_In_rep2

value: Skeletal muscle

value: muscle stem cells

value: Control


title: Zebrafish embryos, dose 0, replicate E

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.csv : 0E

value: protuding mouth

value: AB wild type

value: 120h post-fertilization

value: 0 µg/L DBP exposure

value: E


title: 4h_Apli_R1

value: kidney epithelial cells

value: 4 hours

value: Plitidepsin 50nM


title: KYSE-30,control-3 [KYSE30-C-3]

value: DMSO treatment


title: 0h_Apli_R3

value: Kidney

value: 0 hours


title: 0h_Apli_R2

value: Vero E6


title: KYSE-30,control-1 [KYSE30-C-1]

value: Esophageal squamous cell carcinoma cells


title: Zebrafish embryos, dose 0, replicate B

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.csv : 0B

value: whole embryo

value: B


title: Islet beta cells derived from MSCs

city: Yangling

first: Pengxiu

last: Dai

address: No.3 Taicheng Road,

institute: Northwest A&F University (Northwest Agriculture and Forestry University)

description: In this project [LC-X20231110017], a total of [1] [domestic dog] [islet cell] samples were loaded on the computer. Through data analysis, a total of [7530] cells were obtained, the number of cells in each sample was [7530], and the median gene was [2424]. After filtration, [6482] high-quality cells were obtained in each sample. After cluster analysis, a total of [12] clusters are obtained.

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0) The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in UMAP.These steps include:1. calculating gene expression values using the LogNormalize method of Seurat's "NormalizeData" function; 2. performing principal component analysis (PCA) using the normalized expression values, using the top 20 PCs for clustering, and Findcluster analysis. 3. analyze the marker genes of each cluster based on Findallmarker, and the marker genes were selected based on the following criteria: expressed in more than 10% of cells in each cluster, P value ≤ 0.01, gene expression ploidy logFC ≥0.26; Hypergeometric testing was used to perform GO and KEGG enrichment analysis on the differential genes of each cluster obtained from Findallmarker analysis relative to other clusters. In human and mouse species, singleR database, scCATCH database and our self-developed LC-Marker were used to identify each cluster cell type, and some cells were re-clustered based on the identification results of SingleR database to find marker genes, cell communication analysis and Pseudotime analysis to provide ideas for further analysis
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0) The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in UMAP.These steps include:1. calculating gene expression values using the LogNormalize method of Seurat's "NormalizeData" function; 2. performing principal component analysis (PCA) using the normalized expression values, using the top 20 PCs for clustering, and Findcluster analysis. 3. analyze the marker genes of each cluster based on Findallmarker, and the marker genes were selected based on the following criteria: expressed in more than 10% of cells in each cluster, P value ≤ 0.01, gene expression ploidy logFC ≥0.26; Hypergeometric testing was used to perform GO and KEGG enrichment analysis on the differential genes of each cluster obtained from Findallmarker analysis relative to other clusters. In human and mouse species, singleR database, scCATCH database and our self-developed LC-Marker were used to identify each cluster cell type, and some cells were re-clustered based on the identification results of SingleR database to find marker genes, cell communication analysis and Pseudotime analysis to provide ideas for further analysis
Supplementary files format and content: tsv
Supplementary files format and content: mtx

organism: Canis lupus familiaris

source_name: Adipose tissue

growth_protocol: Further optimization of the laboratory's previous program of differentiation of canine ADSCs into neonatal islet β-cells induced by a highly effective regulatory gene combination of 6 genes (Dai et al., 2022).

extract_protocol:
The obtained tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS (0.04% BSA) solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μl
Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell

value: Adipose tissue

value: Mesenchymal stem cells

value: Islet beta cells

value: WT

value: Induction differentiation


title: KYSE-30,control-2 [KYSE30-C-2]


title: KYSE-70, control-2 [KYSE70-C-2]


title: Con_In_rep1

value: Skeletal muscle

value: muscle stem cells

value: Control

value: no treatment


title: Zebrafish embryos, dose 0, replicate D

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.csv : 0D (identified as an outlier during data analysis)

value: protuding mouth

value: AB wild type

value: 120h post-fertilization

value: 0 µg/L DBP exposure

value: D


title: 4h_Apli_R2

value: Kidney

value: Vero E6

value: kidney epithelial cells

value: 4 hours

value: Plitidepsin 50nM


title: HippoCortex_Young_EGFP_3

status: Public on Dec 17 2024

city: Stanford

first: Sophia

middle: Michelle

last: Shi

state: California

address: 63 Abrams Court

institute: Stanford University

data_processing:
Cellranger (v4.0.0) was used to de-multiplex and align reads to the mm10 genome
Assembly: mm10
Supplementary files format and content: matrix files from Cellranger

molecule: nuclear RNA

source_name: Hippocampus and cortex

extract_protocol:
Nuclei were extracted from pooled cortical and hippocampal tissues using dounce homogenization and EZ lysis buffer (Sigma). Singlet nuclei stained with Hoechst were collected via FACS.
Libraries were prepared using the Chromium Single Cell 3’ Kit v3.1 (10X Genomics) according to the manufacturer’s protocol, targeting 10,000 nuclei per sample.

treatment_protocol: AAVs were injected retro-orbitally at 8x10^11 vg per mouse 8 weeks before takedown.

value: Hippocampus and cortex

value: AAV-EGFP


title: La_In_rep2

value: Lin28a  positive


title: HippoCortex_Young_EGFP_2

value: WT


title: Exp4_Control1_rep4

city: St. Louis

first: Andrew

middle: Lee

last: Young

state: MO

address: 660 South Euclid Ave

institute: Washington University in St. Louis

description: Library name: Exp4_Control1_rep4

data_processing:
For WGBS, reads were sequenced using NovaSeq platform. Reads were aligned to mm10,  deduplicated and CpG methylation extracted using Bismark.
Assembly: mm10
Supplementary files format and content: reads are aligned to mm10
Supplementary files format and content: bw

source_name: KSL

growth_protocol: 200 CD45.2 HSCs of the indicated genotypes were competitively transplanted with competetive 250,000 CD45.1 whole bone marrow cells in lethally irradiated primary recipient mice.  Serial transplant was performed by repeating this process.

extract_protocol:
For WGBS, genomic DNA (gDNA) was prepared from the cells using PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific #K1820-02).
For WGBS, using 200 ng of gDNA and 0.2% lambda DNA was bisulfite treated using EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research #D5042) and processed with xGen™ Methyl-Seq Library Prep (IDT, 10009824) to generate Illumina-compatible WGBS libraries.

treatment_protocol: No treatment

tag: Stage

value: Primary

value: KSL

value: Vav-Cre


title: WGBS_exp5_1TX-3a-R878H

description: Library name: WGBS_exp5_1TX-3a-R878H


title: HippoCortex_Young_EGFP_1


title: Exp4_Control1_rep1

description: Library name: Exp4_Control1_rep1


title: HippoCortex_Aged_B3GNT3_2


title: HippoCortex_Aged_B3GNT3_3


title: HippoCortex_Aged_EGFP_2


title: HippoCortex_Aged_B3GNT3_1


title: HippoCortex_Aged_EGFP_1


title: BLM_2

city: Shenyang

first: Yingying

last: Chen

address: 39 Huaxiang Road

institute: Shengjing Hospital of China Medical University

description:
Library name: Sample 8
BLM_2:FPKM

data_processing:
After paired-end sequencing, the raw data in FASTQ format was obtained from Illumina platform. The information of raw data of each sample were collected, including sample name, read(s) number, total number of bases, GC%, and Q20(%) and Q30(%) scores (A Q-score was used to evaluate sequencing quality of the Raw data). FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for Quality Control (QC) statistics, which mainly included single base quality, base content distribution. Subsequently, the clean data were obtained by filtering out the adapter sequences and  low-quality reads. Ensembl database was used for gene annotation. Hisat2 v2.2.1 was used to map clean reads. Mapped reads were counted via HTseq v2.0.2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes counts and FPKM for each sample.

source_name: Lung

extract_protocol:
Total RNA was extracted using the TRK1002U Kit (LC Sciences) according to the manufacturer's protocol. The total RNA quantity and purity were analyzed by NanoDrop ND-1000 (NanoDrop).
The polyA-tailed RNA was captured by the specific capture using Dynabeads Oligo (dT) (Thermo Fisher), and fragmented by a Magnesium RNA Fragmentation Module(NEBNext®). cDNA was synthesized by Reverse Transcriptase (Invitrogen), followed by two-stranded synthesis of double-stranded DNA with adding dUTP（Thermo Fisher). The end repair and adenlation of the double-stranded DNA were performed. The polymerase chain reaction (PCR) was carried out and the library was constructed. Finally, the paired-end sequencing was performed using illumina Novaseq™ 6000 (LC Bio Technology CO., Ltd).

value: Lung

value: Bleomycin (BLM)


title: BLM_5

description:
Library name: Sample 11
BLM_5:FPKM


title: BLM_4

description:
Library name: Sample 10
BLM_4:FPKM


title: BLM_3

description:
Library name: Sample 9
BLM_3:FPKM


title: 0h_Apli_R1

value: 0 hours


title: Control_6

description:
Library name: Sample 6
Control_6:FPKM

value: saline solution


title: BLM_1

description:
Library name: Sample 7
BLM_1:FPKM


title: Control_4

description:
Library name: Sample 4
Control_4:FPKM


title: HippoCortex_Aged_EGFP_3


title: Control_3

description:
Library name: Sample 3
Control_3:FPKM


title: Control_2

description:
Library name: Sample 2
Control_2:FPKM


title: IEC, B6N, GF, Pup, Biol rep2

city: Aachen

first: Mathias

last: Hornef

address: Pauwelstr. 30

department: Institute for Medical Microbiology

country: Germany

institute: University Hospital RWTH Aachen

data_processing:
Sequence reads were trimmed for adapter/low quality reads using cutadapt v4.9 (-j 16 -a "poly A=A{20}" --quality-cutoff 20 -m 20 -u 12)
Trimmed sequences were mapped to the murine reference genome GRCm39_112 using STAR v2.7.11b (genomeGenerate with --sjdbOverhang 63 on GRCm39.112; then alignment with --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts)
Read count matrix was created using featureCounts function from Rsubread v2.14.2
Assembly: GRCm39_112
Supplementary files format and content: comma-delimited Excel file including raw counts for each sample

source_name: small intestine

extract_protocol:
Total RNA was isolated from small intestinal epithelial cells using TRIzol reagent, following manufacturer's instructions.
3'mRNA libraries were prepared using QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina, following manufacturer's instructions.
3'mRNA-Seq

treatment_protocol: Newborn mice were orally infected at birth with 100-200 CFU Salmonella Typhimurium (in 1µl PBS). Adult mice were gavaged with 20mg streptomycin (in 50µl H2O) 24 hours prior to being gavaged with 108 CFU Salmonella Typhimurium (in 100µl PBS). Small intestinal epithelial cells were isolated 4 days after infection in both cases.

value: small intestine

value: epithelial cells

tag: housing condition

value: gf

value: wt

tag: infection

value: control


title: IEC, B6N, GF, Pup, Biol rep4

tag: tissue

tag: genotype


title: IEC, B6N, GF, Pup, Biol rep1


title: IEC, B6N, SPF, Pup, Biol rep4

value: spf


title: IEC, B6N, SPF, Pup, Biol rep3


title: Control_1

description:
Library name: Sample 1
Control_1:FPKM

tag: treatment


title: IEC, B6N, SPF, Pup, Biol rep1

tag: cell type


title: IEC, B6N, GF, Pup, Biol rep3


title: IEC, Myd88ko, Salmonella, Pup, Biol rep3

value: Salmonella


title: IEC, Myd88ko, Salmonella, Pup, Biol rep2


title: IEC, Myd88ko, Salmonella, Pup, Biol rep1


title: IEC, Myd88ko, Uninfected, Pup, Biol rep2


title: IEC, Myd88ko, Uninfected, Pup, Biol rep4


title: IEC, Myd88ko, Uninfected, Pup, Biol rep1


title: IEC, B6J, Salmonella, Adult, Biol rep4


title: IEC, B6J, Salmonella, Adult, Biol rep3


title: H841 cells, treated with 200 mM trehalose, rep2

city: Tianjin

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

description: Library name: H841_Tre_2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

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

value: SCLC cells

value: treated with 200 mM trehalose for 12 hours


title: H841 cells, control, rep2

description: Library name: H841_2

value: WT


title: H841 cells, control, rep3

description: Library name: H841_3


title: H841 cells, treated with 200 mM trehalose, rep3

description: Library name: H841_Tre_3


title: H841 cells, control, rep1

description: Library name: H841_1


title: H841 cells, treated with 200 mM trehalose, rep1

description: Library name: H841_Tre_1


title: IEC, B6J, Salmonella, Adult, Biol rep2


title: IEC, B6N, SPF, Pup, Biol rep2


title: IEC, Myd88ko, Salmonella, Pup, Biol rep4


title: IEC, B6J, Uninfected, Adult, Biol rep4


title: shCON_2

city: Dalian

first: Jianxin

last: Wang

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

description:
Library name: Sample 2
Negative Control

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: counts.xlsx

growth_protocol: Human ovarian cancer cell linesTOV-112D were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
After the total RNA extraction,RNA degradation and contamination was detected by 1% agarose gels; RNA purity and concentration was checked by Nanodrop2000（Thermo Fisher Scientific，MA，USA）；RNA concentration was checked using the Qubit® 3.0 Flurometer（Thermo Fisher Scientific，MA，USA）；RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviral vectors encoding short hairpin RNAs (GIPZ shRNAs) targeting ZDHHC15 and scrambled shRNA were purchased from Dharmacon (America). The plasmids were transiently transfected into cells with Lipofectamine 3000 (Invitrogen, CA) according to the manufacturer’s protocol. Cells were harvested and analyzed 36 h after transfection.

value: Ovarian cancer


title: shZDHHC15_1

description:
Library name: Sample 3
Knowdown ZDHHC15 gene


title: IEC, B6J, Salmonella, Adult, Biol rep1


title: IEC, B6J, Uninfected, Adult, Biol rep3


title: IPF IPFrc 3, RNA-seq

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

description:
ipf_ipfrc3_gex
1247_0012_IPF_IPFrc
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

data_processing:
The nf-core ataq-seq pipeline (v2.1.2) was used to perform alignment and downstream analysis. Briefly, pre-alignment quality control and adapter trimming of the FASTQ files was performed with the default parameters. The reads were then aligned to the human reference genome (GRCh38.86) and alignments from multiple libraries per sample were merged.
Assembly: GRCh38.86
Supplementary files format and content: bigWig files (ATAC-seq), raw and normlized count matrices (RNA-seq)

extract_protocol:
Matched bulk-ATAC and RNA-seq was performed on IPF- and control-derived airway organoids originating from three donors. For RNA-seq, cells were pelleted and lysed in RLT Plus buffer. Total RNA was extracted and purified on the MagMAX instrument (Thermo Fisher) using the MagMAX™ 96 Total RNA Isolation Kit following manufacturer’s instructions. Total RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). For ATAC-seq library prep was performed as previously described with minor adaptions. 70,000 cells of singularized AOs were lysed in lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40) for 5 min and centrifuged. Pelleted cells were transposed using Tagment DNA TDE1 Enzyme and Buffer Kit for 60 min at 37 °C with shaking. Afterwards, samples were purified using clean-up buffer (0.5 M NaCl, 400 mM EDTA, 1 % SDS, 2 mg/ml Proteinase K) and normal phase 2x AMPureXP (Beckman Coulter, #A63881) bead clean-up, followed by PCR amplification. Finally, amplified samples were purified using DNA Clean & Concentrator Kit (Zymo, #ZYM-D4029) and double-sided clean-up with AMPure beads.
For RNA-seq, a total RNA input of 250ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7760), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490) and NEBNext Multiplex Oligos for Illumina (#E7600). RNA-seq libraries were processed on a Biomek i7 Hybrid instrument (Beckman Coulter) using 13 PCR cycles, following the manufacturer’s protocol, except for the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification and PCR clean-up. Final sequencing libraries were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled, and sequenced on an Illumina NovaSeq 6000 using an S2 Reagent Kit v1.5. ATAC-seq libraries were normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). Libraries were sequenced on an Illumina NovaSeq 6000 using an S2 Reagent Kit v1.5 (#20028315; Read parameters: Rd1:101bp, Rd2: 8bp, Rd3: 8bp, Rd4:101bp) with an average sequencing depth of ~100 million reads passed filter per sample.

value: Airway epithelium

value: IPF

value: IPF-relevant cocktail


title: IEC, Myd88ko, Uninfected, Pup, Biol rep3


title: NETB

city: DALIAN

first: Zhao

middle: Dong

last: Yi

address: No. 467, Zhongshan Road, Shahekou District

institute: The Second Hospital of Dalian Medical University

description: Library name: S041

data_processing:
Quality control
scRNA-seq reads were aligned to the homo_sapiens_ensembl_92 genome assembly using STAR version 2.7.5a
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Assembly: homo sapiens ensembl_92
Supplementary files format and content: expression matrix file using RNA raw count

source_name: Breast cancer organoids

growth_protocol: Breast cancer organoids culture

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

value: Breast cancer organoids


title: IPF IPFrc 2, RNA-seq

description:
ipf_ipfrc2_gex
1247_0011_IPF_IPFrc
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

value: Lung


title: shZDHHC15_2

description:
Library name: Sample 4
Knowdown ZDHHC15 gene


title: IPF IPFrc 1, RNA-seq

description:
ipf_ipfrc1_gex
1247_0010_IPF_IPFrc
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt


title: IEC, B6J, Salmonella, Pup, Biol rep3


title: IEC, B6J, Salmonella, Pup, Biol rep4


title: IEC, B6J, Salmonella, Pup, Biol rep2


title: IPF untreated 2, RNA-seq

description:
ipf_ctrl2_gex
1247_0005_IPF_Control
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt


title: BLSP, wild type, 3 days, rep1

city: Wuhan

first: weidong

last: liu

address: donghu street

institute: Wuhan University

description: Library name: WT-BLSP-Rep1

data_processing:
All input and IP samples’ raw sequencing data were preprocessed using fastp (v. 0.20.1), aligned with HISAT2 (v. 2.2.1) to GRCm38 reference genome, and generated read counts by featureCounts (v.2.0.1). For calculating the relative m6A level for each gene, we used the DESeq2 to compare the read counts of genes between IP samples and input samples on a transcriptome-wide scale. Based on the adjusted fold change (Wald statistic, fourth column of output of DESeq2) of each gene from the output of DESeq2, we further calculated the Z-score of adjusted fold change in each cell type, and this Z-score represents the relative m6A level. We identified high-confidence m6A-tagged mRNAs by setting up the cutoff line based on log2(fold change) > 1 and P value < 0.05
Assembly: mm10
Supplementary files format and content: txt

extract_protocol: SCs and other targets cells were sorted into TRIzol reagent (Takara) to extract RNA.

value: long bone

tag: strain

value: skeletal stem and progenitor cells

value: wild type

value: no treatment

tag: batch


title: IPF untreated 1, RNA-seq

description:
ipf_ctrl1_gex
1247_0004_IPF_Control
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt


title: shCON_1

description:
Library name: Sample 1
Negative Control

tag: cell line


title: IEC, B6J, Salmonella, Pup, Biol rep1

value: small intestine

value: epithelial cells

value: wt

tag: age


title: Control IPFrc 3, RNA-seq

description:
healthy_ipfrc3_gex
1247_0009_Healthy_IPFrc
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

tag: disease state

value: control resection from tumor


title: LSEC P1KO-1

city: Xi'an

first: Luo

last: Yuru

address: 28 Xianning West Road

institute: Xi'an Jiaotong University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: txt files of readcount value for each sample

extract_protocol:
Total RNA was extracted from heart ventricles using TRIzol reagent (Sigma)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L)

value: Liver

value: liver sinusoidal endothelial cells

value: treat with CCl4


title: Control IPFrc 2, RNA-seq

description:
healthy_ipfrc2_gex
1247_0008_Healthy_IPFrc
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt


title: IEC, B6J, Uninfected, Pup, Biol rep3

value: spf

value: control


title: Control untreated 3, RNA-seq

description:
healthy_ctrl3_gex
1247_0003_Healthy_Control
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

value: Airway epithelium


title: IEC, B6J, Uninfected, Pup, Biol rep1


title: Control IPFrc 1, RNA-seq

description:
healthy_ipfrc1_gex
1247_0007_Healthy_IPFrc
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

value: IPF-relevant cocktail


title: IEC, B6J, Uninfected, Pup, Biol rep2


title: DKO-Fx_3_5hmC

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

data_processing:
FASTQ files were aligned utilizing BSseeker2 (https://github.com/BSSeeker/BSseeker2) against the GRCm38 (mm10) genome using bowtie2.
Adapters sequences and the CCGG motif were removed during alignment
Post-alignment, methylation calling was conducted to determine methylation levels and coverage for each cytosine position within the library.
Differential methylation and hydroxymethylation studies were made using Bioconductor R package DSS (Park 2016).
Assembly: GRCm38
Supplementary files format and content: bedgraph
Library strategy: EhM-seq

source_name: Spermatozoa

extract_protocol:
The collected spermatozoa were centrifuged for 3 min at 1100g and resuspended in 200 μl of solution A (75 mM NaCl and 25 mM EDTA) and 200 μl of solution B (10 mM Tris-HCl pH 8, 10 mM EDTA, 2% SDS, 80 mM DTT) complemented with 1 μg of RNAse A (Qiagen) and incubated for 1 h at 37°C. One hundred μg of Proteinase K (Sigma-Aldrich) per 0.5 ml of solution A+B was subsequently added and incubated overnight at 55°C. Sperm genomic DNA was further purified using phe-nol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. DNA pellet was resuspended in RNAse/DNAse free distilled water (Invitrogen).
For EM-seq: A total of 200 ng of genomic DNA was combined with 1.0 ng of unmethylated Lambda DNA (New England Biolabs) and 0.1 ng of CpG methylated pUC19 (New England Bi-olabs). This mixture was then subjected to digestion using 400 units of MspI (New England Biolabs) in NEB Ultra II buffer (New England Biolabs) in a final volume of 57 μL. The digestion was carried out for 2 hours at 37°C. Following enzymatic digestion, the resulting DNA fragments underwent end-repair and A-tailing using 15 units of Klenow 3’-5’ exo- (New England Biolabs). Once end-repair and A-tailing were com-pleted, Illumina universal methylated adapters were ligated to the DNA fragments using the NEB Ultra II ligation module, following the manufacturer’s recommenda-tions. After ligation, the DNA fragments were purified and size-selected using a two-step SPRI beads purification method to retain fragments ranging from 40 bp to 400 bp. The cleaned ligated DNA was eluted in 10 mM Tris pH 8. The purified product was then converted using the Enzymatic methyl-seq module (New England Biolabs), according to the manufacturer’s instructions. In brief, 5mC were converted to 5hmC using TET2, and subsequently, 5hmC were protected from APOBEC deamination through T4-BGT glycosylation. After glycosylation, libraries were denatured at 85°C for 10 minutes in the presence of 20% formamide. Unmodified cytosines were then subjected to APOBEC deamination. The converted product underwent PCR amplifica-tion using indexing primers and KAPA HiFi Hotstart U+ Ready Mix 2X polymerase in a final volume of 50 μL for 9 cycles. The resulting PCR product was purified using a 1.2X SPRI ratio and subsequently size-assessed using capillary electrophoresis on a Fragment Analyzer.                                                                                For EhM-seq: A starting input of 200 ng DNA was used, along with 1.0 ng of unmethylated Lambda DNA and 0.1 ng of CpG methylated pUC19. After MspI digestion and Klenow 3’-5’ exo- mediated repair, pyrrolo-dC Illumina adapters were utilized in the ligation step instead of 5mC adapters. During the conversion step involving TET2, H2O replaces TET2 enzyme and Fe2+ to prevent 5mC protection. The ensuing product was deami-nated, amplified, assessed, and sequenced under conditions identical to those of RREMseq libraries.

value: Spermatozoa


title: Control untreated 2, RNA-seq

description:
healthy_ctrl2_gex
1247_0002_Healthy_Control
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

value: Lung


title: IEC, B6J, Uninfected, Adult, Biol rep2


title: IEC, B6J, Uninfected, Adult, Biol rep1


title: IPF untreated 3, RNA-seq

description:
ipf_ctrl3_gex
1247_0006_IPF_Control
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt

value: IPF


title: DKO-Fx_2_5hmC


title: IPF IPFrc 3, ATAC-seq


title: IEC, B6J, Uninfected, Pup, Biol rep4


title: DKO_3_5hmC


title: Control untreated 1, RNA-seq

description:
healthy_ctrl1_gex
1247_0001_Healthy_Control
saec_bulkRNA_processed_counts.txt
saec_bulkRNA_raw_counts.txt


title: IPF IPFrc 1, ATAC-seq


title: DKO_2_5hmC


title: IPF untreated 3, ATAC-seq


title: IPF untreated 2, ATAC-seq


title: IPF untreated 1, ATAC-seq


title: WT-Fx_2_5hmC

value: Wild-type


title: Control IPFrc 2, ATAC-seq


title: WT-Fx_3_5hmC


title: Control_5

description:
Library name: Sample 5
Control_5:FPKM

value: saline solution


title: DKO_1_5hmC


title: DKO-Fx_1_5hmC


title: Control untreated 3, ATAC-seq


title: WT_3_5hmC


title: WT_2_5hmC


title: Control IPFrc 3, ATAC-seq


title: WT_1_5hmC


title: DKO-Fx_3_5mC

data_processing:
FASTQ files were aligned utilizing BSseeker2 (https://github.com/BSSeeker/BSseeker2) against the GRCm38 (mm10) genome using bowtie2.
Adapters sequences and the CCGG motif were removed during alignment
Post-alignment, methylation calling was conducted to determine methylation levels and coverage for each cytosine position within the library.
Differential methylation and hydroxymethylation studies were made using Bioconductor R package DSS (Park 2016).
Assembly: GRCm38
Supplementary files format and content: bedgraph
Library strategy: EM-seq


title: SSC, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-SSC-Rep2

source_name: long bone

value: long bone

value: skeletal stem and progenitor cells

value: wild type

value: no treatment


title: Control untreated 1, ATAC-seq

value: control resection from tumor


title: Control untreated 2, ATAC-seq


title: Control IPFrc 1, ATAC-seq


title: DKO-Fx_2_5mC


title: DKO_3_5mC


title: IPF II scATAC

description: ATAC-seq

data_processing:
De-multiplexed scRNA-seq and scATAC-seq FASTQ files were run in the Cell Ranger ARC pipeline (10X Genomics, v2.0.2) to produce barcoded count matrices and fragment files.
Assembly: GRCh38.86
Supplementary files format and content: Tab-separated meta data files, ATAC-seq fragment files and processed h5ad files
Library strategy: single cell multiome

extract_protocol:
For simultaneous scATAC and snRNA-seq, AOs were singularized as previously described. Cells were resuspended in ice-cold buffer (1x PBS + 0.04 % BSA) and filtered through a 40 µm cell filter (Flowmi® BelArt). Cell concentration, viability, and aggregate were determined with the NucleoCounter NC-3000 (Chemometec) using Via-1 cassette and on NucleoView NC-3000 software (Chemometec, v.2.1). A total of 850,000 cells per sample, with an average cell viability of 92.2 ± 1.7% and cell aggregate <5%, were used for nuclei isolation using 10x Genomics Demonstrated Protocol for Nuclei Isolation for Single Cell Multiome ATAC + GEX Sequencing (CG000365-RevC).
4 single-nuclei suspensions were employed to generate scATAC and snRNA-seq libraries which were prepared with the Chromium Next GEM Single Cell Multiome kit ATAC + Gene Expression according to the manufacturer’s instructions (CG000338 Rev E, 10x Genomics). For scATAC-seq, 35µL from the purified Pre-Amplification eluate was used for cDNA amplification with 12 cycles and purified with SPRI beads. For snRNA-seq, a total of 250 ng of cDNA per sample was employed for library preparation with an additional 1x SPRISelect bead clean-up. snRNA-seq and scATAC-seq libraries were amplified with 12 and 7 PCR cycles, respectively, and quantified with the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) using a Synergy HTX microplate reader (BioTek) and qualitatively assessed with the High Sensitivity NGS Fragment 1-6000bp Kit on a 96-channel Fragment Analyzer (Agilent). Final libraries were normalized, pooled, spiked in with 5% PhiX Control v3 (Illumina) and sequenced on an Illumina Novaseq 6000 at a depth of ~50,000 reads/cell with dual index, paired end read

value: lung


title: DKO-Fx_1_5mC


title: IPF I scATAC

description: ATAC-seq


title: DKO_2_5mC


title: Control II scATAC

description: ATAC-seq

value: healthy


title: WT-Fx_1_5hmC


title: WT-Fx_3_5mC


title: Control I scATAC

description: ATAC-seq


title: IPF I scRNA

description: RNA-seq


title: WT-Fx_2_5mC


title: DKO_1_5mC


title: Control II scRNA

description: RNA-seq


title: WT-Fx_1_5mC


title: CD45+CD3+CD8+ immune cells from post-treatment tumor of patient P58 (R)

city: Hangzhou

first: Chen

last: Dong

state: Zhejiang

address: Shilongshan Street No.18, Xihu District

institute: Westlake University

description:
10X
GSE235863_five_patients_scRNAseq_cd8t_raw_counts.h5ad.gz
GSE235863_five_patients_TCR.csv.gz
GSE235863_five_patients_dCODE_dextramer_counts.csv.gz

data_processing:
For scRNA-seq samples, reads were aligned and quantified using the Cell Ranger Single-Cell toolkit (v.6.1.2) against the GRCh38 human reference genome (refdata-gex-GRCh38-2020-A). Preliminary filtered raw count data generated from Cell Ranger were used for downstream analysis. Further quality control was applied to filter out low-quality cells with either (1) <500 expressed genes, (2) >6,000 expressed genes, (3) >20% mitochondrial UMI counts, or <1% hemoglobin UMI counts (sum of UMI counts of HBA1, HBA2 and HBB genes) and filter out genes detected in less than 3 cells. Scrublet (v.0.2.3) was applied to each sequencing library to remove potential doublets with default setting.
For 10X dCODE dextramer experiments, data
For scTCR-seq samples, reads were aligned and quantified using Cell Ranger Single-Cell toolkit (v.6.1.2) with the manufacturer-supplied human VDJ reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0). For each sample, the output file all_contig_annotations.csv, containing TCR α- and β-chain complementarity determining region 3 (CDR3) amino acid sequence, was used for downstream analysis. These files were combined using scirpy (v.0.11.0) and quality control was performed with the following criterions: 1) low-confidence, non-productive chains or those with UMIs < 2 were discarded; 2) cells with more than four productive chains: two VJ and two VDJ chains were discarded; 3) cells with only one VD or only one VDJ chain were discarded; 4) for T cells with two α- or β- chains assembled, the α-β pair showing the highest expression level (UMIs) was defined as the domain α- β pair in the corresponding T cells. For each patient, T cells comprising the same VJ and VDJ CDR3 amino acid sequences for each patient were considered as having originated from the same clone and were therefore identified as clonal cells.
For bulk RNA-seq samples, we applied FastQC (v.0.11.9) to determine the quality of the raw sequencing data. Adapters, low quality bases and reads were removed using 'Trim Galore' (v.0.6.5). Then, the expression levels of transcripts were quantified by Salmon (v.1.9.1). The gene expression levels of genes, including raw count and transcript per million (TPM), were generated by tximport (v.1.18.0) with the inputs from Salmon.
Assembly: hg38
Supplementary files format and content: csv and txt files for TCR summary, and deCODE dextramer summary.
Supplementary files format and content: h5ad files for expression matrices

source_name: HBV+ HCC

extract_protocol:
To perform single-cell sequencing, single-cell suspensions from tumor and blood samples were stained with antibodies against CD45 and sorted using a BD FACSAriaTM III instrument. Based on FACS analysis, single cells were sorted into 15 ml tubes (Nest) and manually counted under a microscope. To perform bulk RNA analysis, small fragments of tumor tissues were first preserved in RNAlater RNA stabilization reagent (QIAGEN) immediately after surgical resection, and stored on ice to prevent RNA degradation. The RNA was then extracted from the tumor tissue samples using the RNeasy Mini Kit (QIAGEN), following the manufacturer's specifications. The concentration of RNA was quantified using the NanoDrop instrument (Thermo), and the quality of RNA was evaluated using the fragment analyzer (AATI).
To construct scRNA-seq libraries, the concentration of single cell suspensions was adjusted to 1,000 cells/ul, and cells were loaded between 5,000 and 20,000 cells/reaction using 10X Chromium Single Cell 5' and human variable, diversity, and joining (VDJ) (10X Genomics). All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina NovaSeq 6000 sequencer with 150-bp paired-end reads. The bulk RNA-seq libraries were constructed using the NEBNext Poly (A) mRNA Magnetic Isolation Module kit (NEB) and the NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB). Finally, the samples were sequenced on the Illumina Hiseq 4000 sequencer with 150 bp paired-end reads.
10x Chromium Single cell 5’ + VDJ library; 10x Chromium Single cell 5’ + VDJ library + deCODE dextramer library; bulk RNA-seq

treatment_protocol: All patients included in this study were pathologically diagnosed with HBV-infected hepatocellular carcinoma and received lenvatinib (12 mg/day for bodyweight ≥ 60 kg or 8 mg/day for bodyweight < 60 kg) orally once daily and a PD-1 inhibitor intravenously on day 1 of a 21-day treatment cycle. The anti-PD-1 antibodies and their single-dose infusion were sintilimab 200 mg, pembrolizumab 200 mg, tislelizumab 200 mg, or toripalimab 240 mg.

tag: patient

tag: response

value: R

value: CD45+CD3+CD8+ immune cells

tag: library type

value: scRNA-seq & scTCR-seq & deCODE-Dextramer-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: CD45+CD3+CD8+ immune cells from post-treatment blood of patient P58 (R)


title: CD45+CD3+CD8+Dextramer+ immune cells from post-treatment tumor of patient P58 (R)

value: CD45+CD3+CD8+Dextramer+ immune cells


title: CD45+CD3+CD8+ immune cells from post-treatment tumor of patient P53 (NR)

value: NR


title: WT_2_5mC

value: Spermatozoa


title: mouse cortex, ad, traditional sncRNA-seq, rep7

city: Salt Lake City

first: Qi

state: Utah

department: Department of Human Genetics

institute: university of utah

data_processing:
The raw reads were trimmed by performing SPORTS1.1.1 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse),
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: cortex

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: cortex

value: 6 months

value: The 15-50nt RNAs were sequenced with standard protocols.


title: Control I scRNA

description: RNA-seq

value: Airway epithelium


title: mouse cortex, ad, traditional sncRNA-seq, rep6


title: mouse cortex, ad, traditional sncRNA-seq, rep4


title: CD45+CD3+CD8+ immune cells from post-treatment tumor of patient P57 (R)


title: CD45+CD3+CD8+ immune cells from post-treatment blood of patient P57 (R)


title: mouse cortex, ad, traditional sncRNA-seq, rep5


title: WT_1_5mC

value: Wild-type


title: mouse cortex, ad, traditional sncRNA-seq, rep1


title: Post-treatment liver tumor of patient P51 (NR/SD)

description:
10X
GSE235863_nine_patients_scRNAseq_cd45_raw_counts.h5ad.gz
GSE235863_nine_patients_TCR.csv.gz

value: liver tumor

value: NR/SD

value: scRNA-seq & scTCR-seq


title: Post-treatment liver tumor of patient P52 (NR/SD)


title: IPF II scRNA

description: RNA-seq

value: lung

value: IPF


title: WT_3_5mC


title: mouse cortex, wt, traditional sncRNA-seq, rep5

value: WT


title: CD45+CD3+CD8+ immune cells from post-treatment blood of patient P53 (NR)

value: CD45+CD3+CD8+ immune cells


title: mouse cortex, ad, traditional sncRNA-seq, rep3


title: PA_2

description: Knowdown SPTLC2 gene

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: gene.expression.annot.xlsx

growth_protocol: Human ovarian cancer cell lines TOV-112D were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
1. Freeze 2ml Eppendorf microcentrifuge tube with tissue sample and glass ball at -80°C and then grind the sample in the MM300 Mixer Mill at 30Hz for two minutes.2. Add 1 ml fresh TRIzol Reagent to the mechanically disrupted tissue sample, vortex well, and incubate the sample at room temperature for 5 minutes.3. Add 0.2 ml of chloroform to the microcentrifuge tube for homogenization. Vortex well, and incubate the sample at room temperature for 3 minutes.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Ovarian Cancer TOV-112D cells treatment with Palmitic acid of 200 μM for 24h and BSA as a negative control.  shCON and shZDHHC15 cells were extracted for RNA

value: Ovarian cancer

value: Palmitic acid （200 μM,24h）


title: mouse cortex, wt, traditional sncRNA-seq, rep7


title: Post-treatment blood of patient P51 (NR/SD)

value: blood

value: anti-PD-1 plus lenvatinib combination therapy


title: PA_1

description: Knowdown SPTLC2 gene


title: mouse cortex, ad, traditional sncRNA-seq, rep2


title: mouse cortex, wt, traditional sncRNA-seq, rep6


title: Post-treatment blood of patient P52 (NR/SD)


title: BSA_2

description: Negative Control

value: BSA（200 μM,24h）


title: mouse cortex, wt, traditional sncRNA-seq, rep3

value: cortex


title: mouse cortex, wt, traditional sncRNA-seq, rep4

value: 6 months


title: H226R_7883_KDFOSL1_IgG_2

city: San Fransisco

first: Xiaosai

last: Yao

state: CA

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Roche/Genentech

data_processing:
For each sequence library, raw reads were aligned on the hg38 human genome reference using Bowtie2  (v2.4.1) followed by alignments sorting (samtools v1.9) of resulting bam files with filtering out of unmapped  reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s  (v2.23.9) MarkDuplicates function followed by indexation of resulting bam files with samtools. For each bam  file, genome coverage was computed with bedtools (v2.29.2) followed by generation of bigwig  (wigToBigWig v357) files. Peaks were called with macs2 (v2.7.1) for each treatment sample using their  corresponding IgG control. Downstream analyses were performed with DiffBind v3.11.1 with default  parameters, except for summits=250 in dba.count(). dba.contrast() and dba.analyzed() were used to  compute significant differential peaks with DESeq2.
Assembly: hg38.p10
Supplementary files format and content: bigWig, Macs2 peaks
Library strategy: CUT&RUN

source_name: Lung, Epithelial

growth_protocol: Cell lines were maintained in RPMI 1640 supplemented with 10% FBS and 2 mM L-glutamine in a humidified incubator maintained at 37 °C with 5% CO2. TEAD SMI resistant NF2 null NCI-H226 (i.e. NCI-H226_CL3) cells were generated by incubation with increasing concentrations of TEAD SMI over time (0.25 μM to 3 μM at bi-weekly with 0.1-0.5 μM increments), ensuring at least a 25% confluence at all times. For the knockdown cell lines generation, CRISPR transfection was conducted in H226 and H226-7883R cells. Cells were seeded at 2 × 10 6 cells per 10 cm plate and incubated for 24 hours. The cells were then electroporated with an RNP complex containing pre-designed Alt-R CRISPR-Cas9 gRNA (final concentration 44 µM) and Cas9 protein (final concentration 36 µM) purchased from IDT (Alt-R™ S.p. Cas9 Nuclease V3, Cat. #1081058). Two guide RNAs were used for FOSL1: sgFOSL1_1 (CAAGGCCTTCGACGTACCCC) and sgFOSL1_2 (GATTTTGCAGATGGGTCGGT) at a concentration of 22 µM each. Guide RNA for CD81 (TGATGACGCCAACAACGCCA) was used as a control. Three days post-electroporation, H226 cells were treated with DMSO in the background of CD81 and FOSL1 KD, and H226-7883R resistant cells were maintained in 1 µM GNE-7883 in the background of CD81 and FOSL1 KD. After 48 hours of treatment, 500k cells from each condition were processed for CUT&RUN.

extract_protocol:
H226/ H226-7883R cells were trypsinized into single-cell suspension with 0.05% Trypsin, EDTA 0.5 mM.  500k cells were used for each reaction.
We used the CUTANA ChIC/CUT&RUN Kit from Epicypher (#14- 1048) following manufacturer’s instructions. ConA Beads were briefly resuspended and 11 μl of beads per  reaction was transferred to a 1.5 ml tube. Beads were resuspended in 100 μl bead activation buffer per  reaction and washed 2✕. Then resuspended in 11 μl buffer per reaction and aliquoted 10 μl into 8-strip PCR  tubes, and kept on ice. Harvested cells were spun down at 600 × g for 3 min at room temperature. Cells  were then resuspended in 100 μl/reaction of wash buffer and aliquoted into 8 strip tubes with the 10 μl of  activated ConA beads. After 10 mins incubation, 50 μl of cold antibody buffer was added. YAP antibody  (CST Cat. #14074) was used at 1:50 dilution, TEAD1 antibody (BD Cat. #610923) or FOSL1 antibody  (ThermoFisher Cat. #PA5-66880) was added at 0.5 μg per reaction. Tubes were incubated on nutator  overnight at 4 °C. The next day, tubes were collected and washed 2✕ with 200 μl cell permeabilization  buffer. Beads were resuspended in 50 μl cell permeabilization buffer and 2.5 μl pAG-MNase was added.  After 10 min incubation at room temperature, beads were washed with another 200 μl cell permeabilization  buffer 2✕. Finally beads were resuspended in 50μl cell permeabilization buffer. 1 μl of 100 mM CaCl2 was  added to activate the enzyme. Tubes were then incubated for 2 h on nutator at 4 °C. Finally, the reaction  was stopped with 33 μl of stop master mix. DNA was then purified and quantified using a Qubit fluorometer.  For library preparation, we used the CUTANA CUT&RUN Library Prep Kit from Epicypher (#14-1001). End  Repair step, Adapter ligation and U-excision were performed following manufacturer’s instructions. We  used 1✕ SPRIselect beads for DNA cleanup. After indexing PCR, we then used 1✕ SPRIselect beads for  DNA cleanup prior to sequencing. Analysis of the library fragment size was done using Tapestation.  10 million Paired End Reads (PE) per sample.

value: Lung, Epithelial

value: Mesothelioma

value: Resistant to TEAD inhibitor GNE-7883

tag: cutnrun antibody


title: ABT-263 476

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (Dobin et al., 2013) (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.23.10) (Love et al., 2014).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 7 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 7 matrix of variance-stabilizing-transformed (VST) expression values

source_name: skin

growth_protocol: All procedures were carried out under the National Institutes of Health's Guide for the Care and Use of Laboratory Animals and approved by the Boston University Subcommittee on Research and Animal Care (202000006). Wild type aged (24 months) and young (2 month) C57BL/6 male mice were obtained from the National Institute of Health – National Institute of Aging.

extract_protocol: The gentleMACS dissociator (Miltenyl Biotec) was used to homogenize the tissue and the TRIzolTM Plus RNA Purification Kit (Catalog number: 12183555) was used to extract RNA from skin tissue isolated after 5 days from aged male mice treated with ABT-263 and DMSO.

treatment_protocol: Recipient aged (24 months) mice were anesthetized with isoflurane anesthesia before topical senolytic treatment. Dorsal hair will be removed with clippers and then treatment with NairTM (Church & Dwight Co., Inc, Ewing, NJ) hair removal lotion. 70% ethanol was used to cleanse the skin. Topical senolytic 5µM ABT-263 or control vehicle-alone (DMSO) was applied topically on skin and covered with a semi-occlusive dressing (3M™ Tegaderm™) for 5 days before wounding.  5 days after topical senolytic treatment, a 1 cm2 full-thickness excisional wound was created on the dorsal skin of mice that received irradiated or non-irradiated fibroblast cells under isoflurane anesthesia. 3MTM TegadermTM Transparent Film Dressing was used to cover the wounds. For analgesia, mice were given 0.03 mg/kg buprenorphine subcutaneously and were housed with food and water ad libitum. Postoperatively, mice were imaged digitally every three days. ImageJ software was used to calculate the wound area (Version 1.53k).

value: skin

tag: Sex

value: male


title: H226R_7883_KDcd81_IgG_2


title: mouse cortex, wt, traditional sncRNA-seq, rep2

value: The 15-50nt RNAs were sequenced with standard protocols.


title: mouse cortex, ad, PANDORA-seq, rep7

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: ABT-263 478


title: BSA_1

description: Negative Control

value: BSA （200 μM,24h）


title: mouse cortex, ad, PANDORA-seq, rep8


title: mouse cortex, ad, PANDORA-seq, rep6


title: H226P_DMSO_KDFOSL1_IgG_2

value: Sensitive to TEAD inhibitor GNE-7883


title: ABT-263 477


title: DMSO 481

value: DMSO


title: DMSO 483


title: DMSO 480


title: mouse cortex, ad, PANDORA-seq, rep5


title: H226R_7883_KDcd81_IgG_1


title: H226P_DMSO_KDFOSL1_IgG_1


title: mouse cortex, ad, PANDORA-seq, rep4


title: mouse cortex, ad, PANDORA-seq, rep3


title: H226-P_DMSO_KD_cd81_IgG_1


title: mouse cortex, ad, PANDORA-seq, rep2


title: H226_R_7883_KD_FOSL1_FOSL1_2

value: ThermoFisher Cat. #PA5-66880)


title: H226_R_7883_KD_FOSL1_YAP_2


title: mouse cortex, ad, PANDORA-seq, rep1


title: H226-P_DMSO_KD_cd81_IgG_2


title: mouse cortex, wt, PANDORA-seq, rep8

value: WT


title: trrKD, rep5

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

institute: Radboudumc

data_processing:
Raw sequence reads were trimmed using Trimmomatic (version 0.39), removing low quality leading and tailing bases (below quality 3) and reads below 30 bases.
Trimmed reads were aligned to D. melanogaster genome (dm6) using STAR (version 2.7.5a). Reads were also aligned to C. elegans unc-84 gene (NC_003284.9).
Reads that aligned to multiple loci, or to one loci with >4 mismatches, and genes that mapped to Drosophila rRNA were removed.
Gene counts were obtained using using FeatureCounts from the Rsubread R package (version 2.4.2).
Assembly: dm6
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Drosophila melanogaster

source_name: Mushroom body

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from MB-fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Tecan Universal Plus Total RNA-Seq library preparation kit (Tecan: 3061-A01) according to manufacturer instructions.

value: Mushroom body


title: trrKD, rep4


title: H226_R_7883_KD_FOSL1TEAD1_2


title: mouse cortex, wt, PANDORA-seq, rep7


title: trrKD, rep2


title: RS3

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

scan_protocol: Arrays were scanned in two-color channels by an Agilent Scanner G2505C.  Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing: Raw intensities of IP RNA (immunoprecipitate, Cy5-labelled) and Sup RNA (supernate, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.  After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 9 samples were retained as “All Targets Value” (normalized data reported here) in the Excel sheet for further “m6A methylation level” and “m6A quantity” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. RNAs differentially methylated at m6A between two comparison groups were identified by filtering with fold change |FC| >= 1.5 and and statistical significance p <= 0.05.

growth_protocol: Human WI-38 diploid fibroblasts (Coriell Institute) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS, 1% antibiotics, and 1% non-essential amino acids (Gibco). Cells were maintained in an incubator at 37 °C and 5% CO2 and tested negative for mycoplasma. Replicative senescence (RS) of WI-38 fibroblasts was achieved by passaging proliferating cells [typically at population doubling level (PDL) 20 to 22] until they stopped proliferating (typically >PDL50); pre-senescent cells (~PDL40) displayed strongly reduced proliferation rates.  Ionizing radiation-induced senescence (IR-IS) was induced by exposure to 10 Gy IR and incubation for 10 days.

extract_protocol: Total RNA was extracted using a single-step liquid phase separation procedure and the TriPure isolation reagent (Sigma-Aldrich). Total RNA was then immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.

treatment_protocol: Replicative senescence (RS) of WI-38 fibroblasts was achieved by passaging proliferating cells [typically at population doubling level (PDL) 20 to 22] until they stopped proliferating (typically >PDL50); pre-senescent cells (~PDL40) displayed strongly reduced proliferation rates.  Ionizing radiation-induced senescence (IR-IS) was induced by exposure to 10 Gy IR and incubation for 10 days. Detection of m6A modification in proliferating (PDL22) and senescent (RS PDL50, IR-IS) WI-38 cells was performed using the mRNA&LncRNA Epitranscriptomic Array Service (Arraystar).  Briefly, total RNA was immunoprecipitated with anti-N6-methyadenosine (m6A) antibody.  The modified RNA was then eluted from the immunoprecipitated magnetic beads (IP RNA), and the unmodified RNAs was recovered from the supernatant (Sup RNA).  The IP and Sup RNAs were labeled with Cy5 and Cy3, respectively, using the Arraystar Super RNA Labeling Kit.  The fractions were combined and used to hybridize the Arraystar Human mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).  After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.  Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.  Raw intensities of IP RNA (immunoprecipitated, Cy5-labelled) and Sup RNA (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.  RNAs differentially methylated at m6A between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds reported in figure legends.

value: fibroblast

tag: cell state

value: Senescent

tag: pdl


title: IR3

hyb_protocol: The fractions were combined and used to hybridize the Arraystar Human mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).

label_protocol: The IP and Sup RNAs were labeled with Cy5 and Cy3, respectively, using the Arraystar Super RNA Labeling Kit.

value: 10 Gy irradiation


title: IR2


title: H226_R_7883_KD_cd81_FOSL1_2


title: RS1


title: trrKD, rep3


title: mouse cortex, wt, PANDORA-seq, rep6

value: cortex

value: 6 months


title: DMSO 482


title: P3

value: Proliferating


title: P1


title: trrKD, rep1


title: IR1


title: RS2


title: Set1KD, rep4


title: H226R_7883_KDFOSL1_IgG_1_

value: Lung, Epithelial

value: Mesothelioma

value: Resistant to TEAD inhibitor GNE-7883


title: H226_R_7883_KD_cd81_YAP_2


title: H226_R_7883_KD_cd81_TEAD1_2


title: Set1KD, rep2


title: mouse cortex, wt, PANDORA-seq, rep4


title: control, rep5


title: P2


title: Set1KD, rep1


title: control, rep3


title: control, rep2