title: ESC, Input

city: Bron

first: Clémence

last: Kress

address: 18 avenue du Doyen Lépine

institute: INRAE, Inserm

data_processing:
Basecalls were performed using bcl2fastq 2.0. Quality control was performed on fastq files using the FastQC v0.11.3 software.
Reads were aligned using Bowtie2 and multi-mapping reads were filtered out.
Reads were aligned using Bowtie2 and multi-mapping reads were filtered out.
SICER was used to identify the enriched regions in the immuno-precipitated samples compared to the input samples taken as control condition; MACS2 was used to confirm the outputs.
Assembly: Gallus_gallus-5.0
Supplementary files format and content: List of the genome coordinates of the validated H3K9me3 domains for each cell type (csv format)

organism: Gallus gallus

source_name: embryonic stem cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 5 min at 37°C. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
Libraries were prepared from immunoprecipitated DNA using the NEBNext® UltraTM Library Prep Kit by Helixo (https://www.helixio.fr/)

value: embryonic stem cells


title: Graft TP53 wild-type replicate 2

status: Public on Apr 26 2024

type: SRA

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment and gene quantification using CellRanger
Assembly: hg38
Supplementary files format and content: Sparse matrix of gene quantifications

molecule: total RNA

organism: Homo sapiens

extract_protocol:
No extraction
Library construction protocol was followed per MSKCC's IGO core facility.
10x Single cell RNA-seq

tag: cell line

tag: cell type

value: Human PSC derived neurons

tag: genotype

value: WT


title: U2OS csRNAinput-seq EGFP mRNA rep1

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
short RNAs (20-65nt)
tss.U2OS.dnNRF1vsEGFP.bed.gz

library_source: transcriptomic

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and csRNAinput-seq reads were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”).  Reads for all genome-based assays (i.e. everything except TSS-MPRA) were aligned to the appropriate genome (GRCh38/hg38, GRCm38/mm10, ChlSab1.1) using STAR version 2.7.9a with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis.  In the case of mouse SPRET BMDM csRNA-seq, these data were analyzed in the context of C57Bl6 BMDM csRNA-seq previously published as part of GSE135498 [PMID:31649059]. To compare how TSS change between the two strains of mice, only TSS positions that were homologous between C57Bl6 and SPRET genomes and were uniquely alignable in both genomes were considered for downstream analysis (additional details available in the manuscript)
To analyze TSS positions, csRNA/csRNAinput-seq reads with spliced or soft clipped alignments were first discarded to ensure accurate TSS assignments. The alignment position of the 5’ nucleotide of each csRNA-seq read was used to create a map of putative TSS locations in the genome for each sample set. To ensure we use high quality TSS that could be reliably quantified across different conditions, only TSS locations with at least 7 reads per 10^7 total aligned reads across all compared replicates and conditions (e.g. Ctrl siRNA, NRF1 siRNA, etc.) were kept for further analysis. Furthermore, any TSS position that had higher normalized read density in the small csRNAinput-seq data was discarded as a likely false positive TSS location. These sites often include miRNAs and other high abundance RNA species which are not entirely depleted in the csRNA-seq cap enrichment protocol. To quantify the change in TSS levels between conditions, a unified map of confident TSS positions is first determined across the set of compared experiment as described above. Then, the TSS activity levels are assessed for each replicate and each experimental condition by first counting the raw read coverage and normalizing the dataset using DESeq2’s rlog variance stabilizing transform [PMID: 25516281]. Changes in transcriptional activity were then reported as the log2 fold change representing the difference between averaged rlog transformed activity levels across conditions (similar to a shrunken fold change).
ChIP-seq peaks were found using HOMER's findPeaks program using "-style factor".
TSS-MPRA anlysis: Raw sequencing reads were trimmed for the 5’ adapter sequence GGTAACCGGTCCAGCTCA on the R1 read using cutadapt version 3.4. The trimmed reads were aligned to the reporter library using STAR version 2.7.9a, specifying an option to preclude soft-clipping at the 5’ end of R1 (STAR --outSAMattributes All --genomeDir library/tfsweep.STARIndex --runThreadN 12 --readFilesIn file.fastq --outFileNamePrefix star/Sweep_1. --alignEndsType Extend5pOfRead1 --outSAMtype BAM SortedByCoordinate). For DNA plasmid control samples, the uniquely aligned read pairs were counted to later scale transcriptional output. For RNA samples, uniquely aligned read pairs were further processed to identify exact transcription start sites, yielding a matrix of start sites per sequence position. Any alignments showing mismatches at their 5’ ends were not counted and reporter sequences with fewer than 50 total DNA alignments were also ignored. A scaling factor for each sequence was determined by calculating min(10000/plasmid, 100). After multiplying the start site counts by the scaling factor, a pseudocount of 1 was added and values were log2 transformed.
Assembly: hg38, mm10, ChlSab1.1
Supplementary files format and content: bed files: Locations indicate TSS or ChIP-seq peak positions. Numerical values associated with the files represent normalized read densities or log2 ratios between two conditions as indicated by the file names.  fa files: FASTA files containing the designed insert sequences used for TSS-MPRA experiments  tsv files: tab-delimited text files containing the TSS activity levels for each TSS-MPRA insert. Each column represents the TSS position starting within the insert starting from the beginning of the variable sequence region.  fpkm.txt file: tab-delimited text file containing RNA-seq FPKM expression values for GENCODE annotated genes.

source_name: small RNA mapping in U2OS cells expressing EGFP

growth_protocol: U2OS cells were grown at 37°C in DMEM (Cellgro) supplemented with 10% FBS (Gibco), 50 U Penicillin and 50 μg Streptomycin per mL (Gibco). For siRNA transfection, cells were washed once with PBS (Gibco), trypsinized for about 5 minutes and then washed twice with PBS (Gibco) by centrifugation at 400 g for 5 minutes. Subsequently, about 3 million cells were resuspended in 150 µl Gene Pulser® Electroporation Buffer (Biorad) and siRNAs in 1x siRNA buffer (60 mM KCl, 6 mM Hepes 7.5, 0.2 mM MgCl2). The following siRNAs were used: M-011796-02- 0005 siGENOME Human YY1 (7528) siRNA, M-017924-01- 0005 siGENOME Human NRF1 (4899) siRNA, and siGFP (CCACUACCUGAGCACCCAGU, (Meade et al. 2014)) as control. For transfection of the dominant-negative NRF1 mutant (AA1-304 (Gugneja, Virbasius, and Scarpulla 1996)), sequence was cloned into pGEM-T and mRNA synthesized using the mMESSAGE mMACHINE™ T7 Transcription Kit (Thermo Fisher Scientific). siRNAs and dnNRF1 were used at a final concentration of 10 μM. Mixture was transferred to a 0.2 cm cuvette and pulsed once at 250 V for a constant 20 msec. Following electroporation, 1 ml complete growth media was added and cells grown for 24h in a 6 cm dish.   Bone marrow derived macrophages (BMDMs) from SPRET mice were generated and treated with KLA as described in Link et. al (2018) [PMID:29779944].  TSS-MPRA experiments in HEK293T cells: MPRA inserts sequences were ordered as 200 bp oligos from Twist Bioscience and cloned Gibson-assembled into a BsaI-linearized pTSS-MPRA-Empty plasmid based on the background-reduced pGL4.10 reporter backbone (Promega), with a cloning site harboring the 18-bp pMPRA1-LH sequence followed by tandem BsaI sites for linearization and the TruSeq Read 2-compatible pMPRA1-RH sequence and a downstream landing site for reverse transcription primer RS2, and an EGFP ORF replacing the Luciferase 2 gene. About 800k HEK293T cells were used and 25 µg plasmid DNA was transfected using Lipofectamine® 3000 (Thermo Fisher Scientific) as described by the manufacturer. After 8 h, cells were washed 3x with PBS (Gibco) and RNA extracted using 1 ml Trizol (Thermo Fisher Scientific).

extract_protocol:
For all csRNA, RNA-seq, and TSS-MPRA experiments, to harvest RNA, plates were washed three times using ice cold PBS and 1 ml TRIzol™ Reagent added. Cells were scraped and RNA extracted as described by the manufacturer with addition of 1 μl 15 mg/ml GlycoBlue™ Coprecipitant (Thermo Fisher Scientific).  For ChIP-seq, cells were fixed for 10 minutes with 1% formaldehyde/PBS, and the extracted chromatin was sheared to an average DNA size of 300–500 bp.
csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. small RNA input (csRNAinput-seq) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.  Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina NovaSeq 6000.  For ChIP-seq, one percent of the lysate was kept as ChIP input, and dnNFR1-HA was immunoprecipiated with 2 μg anti-HA antibody (Abcam ab9110) and 20 μl of Dynabeads Protein A. Libraries were prepared directly on the antibody/chromatin-bound beads using NEBNext Ultra II reagents according to the manufacturer’s protocol. Libraries were sequenced single-end for 75 cycles (SE75) to a depth of 20-25 million reads on an Illumina NextSeq 500 instrument.  For TSS-MPRA, starting with 10-15 µg RNA (⅓ of the total), non-capped RNAs were dephosphorylated with Quick CIP (NEB) and DNA digested. Samples were mixed well and incubated at 37°C for 90 minutes. For more complete dephosphorylation of uncapped transcripts, RNA was denatured a second time at 75°C for 30 seconds in a pre-warmed water bath and then quickly chilled on ice for 2 minutes before incubating the sample at 37°C for another 30 minutes. As Quick CIP is thermolabile, the brief heat treatment leaves the enzyme active. Following Cap-enrichment, RNA was purified and then vortexed hard and subsequently spun for 10 minutes at 12k g at RT. Following phase separation, the upper layer was taken, and RNA precipitated. RNA pellets were then resuspended and 5' caps removed. Following decapping, 5’ adapters were ligated by T4RNA Ligase 1 and RNA extracted. RNA pellets were then resuspended and reverse transcribed. Samples were amplified and sequenced paired-end on a NextSeq 500 (additional details available in the manuscript)

value: U2OS cell line

tag: assay

value: small RNA-seq (control for csRNA-seq)

tag: genetic perturbation

value: EGFP mRNA

tag: treatment

tag: mouse strain


title: U2OS csRNA-seq EGFP mRNA rep1

source_name: TSS mapping in U2OS cells expressing EGFP

value: csRNA-seq (transcription initiation)


title: U2OS csRNAinput-seq YY1 siRNA rep2

description:
short RNAs (20-65nt)
tss.U2OS.siYY1vsGFP.bed.gz

source_name: small RNA mapping in U2OS cells with YY1 siRNA (rep2)

value: YY1 siRNA


title: Pituitary gland nicotine 2

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were mapped onto rn7 assembly of rat genome using Hisat2 (v2.1.0).
For each biological replicate, a transcriptome was generated using featureCounts and Gene annotation file ncbiRefSeq.gtf.gz from UCSC
Differentially expressed genes were determined by DESeq2 (Version 2.11.40.7). All analyses were performed using Galaxy platform, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351
Assembly: rn7
Supplementary files format and content: featureCount.txt

organism: Rattus norvegicus

source_name: Pituitary gland

growth_protocol: Specific pathogen-free male and female Sprague Dawley rats were purchased from Envigo (USA). Females were purchased at 8 weeks of age and were allowed 1 week to acclimate. At 9 weeks of age, females were randomly assigned to one of 4 treatment groups. Two groups of females were mated, and two groups of females remained virgins. Mating included placing a single female overnight with a male and examination on the following morning for the presence of sperm via vaginal swabs. If sperm was present, the dam was weighed and placed in a separate cage, and this period was marked as gestational day (GD) 0

extract_protocol:
Testes were stored at –80 ºC before the RNA extraction. The extraction was performed using RNeasy Plus Mini Kit 250 (QIAGEN™). Approximately 30 mg of each testis was used . Testis samples were lysed and homogenized using TissueLyser (QIAGEN™). Once homogenized, the RNA extraction protocol was followed. We added additional DNA extraction step using RNase-Free DNase Set (Qiagen, 79254).
The libraries were prepared using the NEBNEXT® Ultra II Directional RNA Library kit for Illumina® (NEB E7760S) using 1µg of total RNA according to the manufacturer’s instructions.

treatment_protocol: Using a sterile technique, a 28-day osmotic mini-pump (2ML4-ALZET, Durect Corp., Cupertino, CA, USA) filled with either sterile saline (control; CON) or a nicotine tartrate (6 mg/kg; NIC), dissolved in sterile saline was placed subcutaneously between the scapulae, as described before (Boychuk and Hayward 2011)(Chang, Karatayev, and Leibowitz 2013). On GD19, or 13 days following pump surgery, dams were allowed to give birth.  Male progeny from both control and nicotine dams was sacrificed at 11 weeks of age.

tag: tissue

value: Pituitary gland

tag: developmental stage

value: adult 11-week-old

tag: Sex

value: male

tag: strain

value: Sprague-Dawley

value: nicotine 6mg/kg/day


title: Graft TP53 wild-type replicate 1

description: 10x Genomics


title: ESC, H3K9me3, ChIP

library_source: genomic

molecule: genomic DNA

tag: antibody

value: H3K9me3 (Abcam, #ab8898)


title: Pituitary gland nicotine 1


title: PGC, Input

source_name: primordial germ cells

value: primordial germ cells


title: U2OS csRNA-seq YY1 siRNA rep2

source_name: TSS mapping in U2OS cells with YY1 siRNA (rep2)


title: RNA-seq LD-3

city: Ann Arbor

first: Xiaoxue

last: Qiu

state: MI

address: 210 Washtenaw

department: Life Sciences Institute

institute: University of Michigan

description:
LK_6
DESeq2_Ms4a7_RNA_seq_FDR0.05.csv

data_processing:
FastQC was used to asses the sequencing qualtiy on fastq files; STAR was used for alignment to generate bam files; The reads aligned to each gene feature were counted by Rsubread package (version 2.0.1); DESeq2 pacakge was used for differential gene expression analysis
snRNA-seq fastq files were processed by CellRanger to generate aligned matrix data that were further analyzed using Seurat package (version 4.0.1).
Assembly: mm10
Supplementary files format and content: DEseq2 normalized reads counts for bulk RNA-seq data
Supplementary files format and content: average UMI counts for snRNA-seq data

organism: Mus musculus

source_name: Liver, Chow diet, LD injection, consecutively 6 days, rep3

extract_protocol:
Nuclei were isolated from frozen liver tissues using salt-Tris based protocol. Isolated nuclei were stained with propidium iodide before FACS sorting. Sorted nuclei were processed for snRNA sequencing. Total liver RNA was extracted from frozen tissues using RNA extract kit (Invitrogen, Cat: 12183025)
Bulk RNA libraries were prepared using high-throughput sequenicng set following the user manual; snRNA libraries were prepared using standard Illumina and 10X genomics Chromium single cell guide

value: liver tissue

value: wild type

value: LD tail-vein injection, consecutively 6 days


title: Day 1 graft replicate 2

data_processing:
Two-pass alignment using STAR 2.5.0a
Gene quantification using GENCODE v38 on hg19
Assembly: hg19
Supplementary files format and content: Tab-delimited text

molecule: polyA RNA

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) according to the manufacturer’s instructions.
Library construction protocol was followed per MSKCC's IGO core facility.

value: Human PSC derived neurons

tag: condition

value: Day 1 graft


title: PGC, H3K9me3, ChIP


title: Graft TP53 KO replicate 2

description: 10x Genomics

value: TP53 KO


title: Day 1 graft replicate 1

value: WT


title: U2OS csRNAinput-seq YY1 siRNA rep1

source_name: small RNA mapping in U2OS cells with YY1 siRNA (rep1)

value: U2OS cell line

value: small RNA-seq (control for csRNA-seq)


title: RNA-seq LD-1

description:
LK_4
DESeq2_Ms4a7_RNA_seq_FDR0.05.csv


title: Day 1 culture replicate 2

value: Day 1 culture


title: U2OS csRNA-seq YY1 siRNA rep1

source_name: TSS mapping in U2OS cells with YY1 siRNA (rep1)

value: csRNA-seq (transcription initiation)

value: YY1 siRNA


title: RNA-seq LD-2

description:
LK_5
DESeq2_Ms4a7_RNA_seq_FDR0.05.csv


title: RNA-seq PBS-2

description:
LK_2
DESeq2_Ms4a7_RNA_seq_FDR0.05.csv

source_name: Liver, Chow diet, PBS injection, consecutively 6 days, rep3

value: PBS tail-vein injection, consecutively 6 days


title: Day 0 replicate 2

value: Day 0


title: U2OS csRNAinput-seq NRF1 siRNA rep2

description:
short RNAs (20-65nt)
tss.U2OS.siNRF1vsGFP.bed.gz

source_name: small RNA mapping in U2OS cells with NRF1 siRNA (rep2)

value: NRF1 siRNA


title: CDM-3008_PHH#2

type: RNA

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

hyb_protocol: SurePrint G3 Human_miRNA_version 21.0_Microarray (8×60K) and miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned with an Agilent Technologies G2505C Microarray Scanner.

data_processing: Raw data were processed using Agilent Feature Extraction software with default parameters to calculate the intensities of the measured spots.

source_name: Primary human hepatocytes (PHH#2), treated cells #2, CDM-3008 (10 µM) 8 hours

label_protocol: miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies) according to the manufacturer's instructions. Cyanine-3 (Cy3).

growth_protocol: Human hepatocytes isolated from chimeric mice with humanized livers were purchase from PhoenixBio (Higashi-Hiroshima, Japan) and cultured on collagen type I-coated 96-well cell culture plates in hepatocyte clonal growth medium, as recommended by PhoenixBio.

extract_protocol: Total RNA was purified using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations, followed by DNase I treatment (2 units, 37°C for 30 minutes) using a TURBO DNA-free Kit (Invitrogen). RNA concentrations was determined using a DeNovix spectrophotometer. The integrity of the samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Primary human hepatocytes were treated with 10 µM CDM-3008 for 8 hours. CDM-3008 (RO8191; PubChem CID: 2768133) was from SIGMA and dissolved in DMSO as a 1,000 µM working solution.

value: Human hepatocytes

tag: type

value: Primary culture


title: Day 0 replicate 1


title: U2OS csRNAinput-seq NRF1 siRNA rep1

source_name: small RNA mapping in U2OS cells with NRF1 siRNA (rep1)


title: RNA-seq PBS-1

description:
LK_1
DESeq2_Ms4a7_RNA_seq_FDR0.05.csv

value: liver tissue


title: U2OS csRNA-seq NRF1 siRNA rep2

source_name: TSS mapping in U2OS cells with NRF1 siRNA (rep2)


title: RNA-seq KO-3

description:
LK06
DEseq2.mliver.LD.LK.csv

source_name: Liver, NASH diet, 22 weeks, rep3

value: Ms4a7 KO

value: NASH diet for 22 weeks


title: E0771_Malt1_WT3

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

country: China

institute: Tsinghua university

data_processing:
The adaptors of paired-end reads were trimmed and quality control checks were carried out using trim-galore (v.0.6.0). Reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using STAR (v.2.7.3a). featureCounts (v.1.6.3) counted reads stored in BAM format to exon sites of genes included in GTF files from GENCODE.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was isolated from cells using RNAiso Plus Regent (Takara, Cat# 9108) following the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat# E7765) was used to generate sequencing libraires from 1 μg of total RNA. All library preparations were conducted according to the manufacturer’s instructions. Paired-end 150bp sequencing was performed using an Illumina NovaSeq platform.

value: cancer cell


title: CDM-3008_PHH#1

source_name: Primary human hepatocytes (PHH#1), treated cells #1, CDM-3008 (10 µM) 8 hours


title: Control_DMSO_PHH#2

source_name: Primary human hepatocytes (PHH#2), negative control #2, DMSO 8 hours

value: control


title: U2OS RNA-seq YY1 siRNA rep2

description:
RNA
fpkm.txt.gz

source_name: total RNA-seq in U2OS cells with YY1 siRNA (rep2)

value: total RNA-seq (stable transcripts)


title: U2OS RNA-seq YY1 siRNA rep1

description:
RNA
fpkm.txt.gz

source_name: total RNA-seq in U2OS cells with YY1 siRNA (rep1)


title: E0771_Malt1_WT1


title: U2OS csRNA-seq NRF1 siRNA rep1

source_name: TSS mapping in U2OS cells with NRF1 siRNA (rep1)


title: RNA-seq KO-2

description:
LK05
DEseq2.mliver.LD.LK.csv


title: RNA-seq KO-1

description:
LK04
DEseq2.mliver.LD.LK.csv


title: Control_DMSO_PHH#1

source_name: Primary human hepatocytes (PHH#1), negative control #1, DMSO 8 hours


title: U2OS RNA-seq NRF1 siRNA rep2

description:
RNA
fpkm.txt.gz

source_name: total RNA-seq in U2OS cells with NRF1 siRNA (rep2)


title: U2OS csRNAinput-seq GFP(Ctrl) siRNA rep2

description:
short RNAs (20-65nt)
tss.U2OS.siGFP.bed.gz

source_name: small RNA mapping in U2OS cells with GFP(Ctrl) siRNA (rep2)

value: GFP (Control) siRNA


title: RNA-seq WT-3

description:
LK03
DEseq2.mliver.LD.LK.csv

value: wild type


title: E0771_Vector control3


title: RNA-seq PBS-3

description:
LK_3
DESeq2_Ms4a7_RNA_seq_FDR0.05.csv


title: U2OS csRNA-seq GFP(Ctrl) siRNA rep2

source_name: TSS mapping in U2OS cells with GFP(Ctrl) siRNA (rep2)

value: U2OS cell line


title: U2OS RNA-seq NRF1 siRNA rep1

description:
RNA
fpkm.txt.gz

source_name: total RNA-seq in U2OS cells with NRF1 siRNA (rep1)


title: U2OS csRNAinput-seq GFP(Ctrl) siRNA rep1

source_name: small RNA mapping in U2OS cells with GFP(Ctrl) siRNA (rep1)

value: small RNA-seq (control for csRNA-seq)


title: Day 1 culture replicate 1

value: Human PSC derived neurons

value: WT

value: Day 1 culture


title: RNA-seq WT-2

description:
LK02
DEseq2.mliver.LD.LK.csv


title: E0771_Vector control1


title: U2OS csRNA-seq GFP(Ctrl) siRNA rep1

source_name: TSS mapping in U2OS cells with GFP(Ctrl) siRNA (rep1)

value: csRNA-seq (transcription initiation)


title: RNA-seq WT-1

description:
LK01
DEseq2.mliver.LD.LK.csv


title: E0771_Malt1_WT2


title: U2OS RNA-seq GFP(Ctrl) siRNA rep1

description:
RNA
fpkm.txt.gz

source_name: total RNA-seq in U2OS cells with GFP(Ctrl) siRNA (rep1)


title: hiPSC-CM, circZFPM2 siRNA, differentiation 2

status: Public on Apr 25 2024

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

data_processing:
Alignment using HISAT2
Quantification using featureCounts
Assembly: Human reference (GRCh38) datasets
Supplementary files format and content: csv file containing raw counts

source_name: cardiomyocyte

extract_protocol:
RNA was issolated using the miRNease Mini Kit (Qiagen). 500 ng of total RNA were used for sequencing librabry construction.
Library was prepared utilizing the 'Novogene NGS RNA Library Prep Set (PT042)* (Novogene). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Life Technologies)-encapsulated siRNAs at a concentration of 100 nM.

value: cardiomyocyte

value: circZFPM2 siRNA


title: hiPSC-CM, scrambled siRNA, differentiation 3

value: scrambled siRNA


title: hiPSC-CM, circZFPM2 siRNA, differentiation 1


title: hiPSC-CM, circZFPM2 siRNA, differentiation 3


title: hiPSC-CM, scrambled siRNA, differentiation 1


title: hiPSC-CM, scrambled siRNA, differentiation 2


title: PB001_1_cDC1_b2_S6

city: Parkville

first: Stemformatics

state: VIC

address: 30 Royal Parade

country: Australia

institute: The University of Melbourne

description: induced pluripotent stem cell (iPSC)  HDF51 line, replicate 1, batch 1, differentiated to cDC1 in a three dimentional (embryoid body) culture.

data_processing:
Reads were aligned to GRCh38.91 Rsubread (2.10.5)
Raw counts were analysed using Limma package. Low-count genes were filtered using the default settings of filterByExpr() from EdgeR while counting for the variance between biological groups. Filtered counts were normalised to logCPM and were used for further analysis.
Assembly: Homo_sapiens.GRCh38.91
Supplementary files format and content: tab-delimited text file including raw counts for each sample

growth_protocol: Progenitors were expanded in RPMI supplemented with heat-inactivated FCS (10%), L-glutamine, sodium pyrovate, FLT3L (100 ng/ml), SCF (100 ng/ml), TPO (50ng/ml), IL3 (20ng/ml) and SR1 (1µM).

extract_protocol:
RNA was harvested using Qiagen RNeasy® Plus micro Kit (Qiagen, cat#74034)
Multiplex RNA-Seq libraries were processed starting with 10ng of total RNA. The libraries were made by individual first strand synthesis to add the i7 index sequences. Samples were then pooled for subsequent processing.

treatment_protocol: Expanded progenitors from both sources were differentiated in RPMI 1640 supplemented with heat-inactivated FCS (10%), L-glutamine, sodium pyrovate, FLT3L (100 ng/ml), SCF (20 ng/ml), TPO (20ng/ml), GM-CSF (5 ng/mL) and IL-4 (5 ng/mL).

tag: sample source

value: induced pluripotent stem cell

value: dendritic cell type one (CD141-positive) differentiated from induced pluripotent stem cell

tag: phenotype

value: HLA-DR+ CD11c+ CD141+ CLEC9A+

tag: batch

value: in vitro differentiation


title: PB001_1_CD14_neg_DC2_b2_S8

description: induced pluripotent stem cell (iPSC)  HDF51 line, replicate 1, batch 1, differentiated to CD14-negative cDC2 in a three dimentional (embryoid body) culture.

tag: cell line

value: dendritic cell type two (CD1c-positive CD14-negative) differentiated from induced pluripotent stem cell

value: HLA-DR+ CD11c+ CD1c+ CD14-


title: PB001_1_CD14_pos_DC2_b1_S10

description: induced pluripotent stem cell (iPSC)  HDF51 line, replicate 1, batch 1, differentiated to CD14-positive cDC2 in a three dimentional (embryoid body) culture.

tag: cell type

value: dendritic cell type two (CD1c-positive CD14-positive) differentiated from induced pluripotent stem cell

value: HLA-DR+ CD11c+ CD1c+ CD14+


title: PB001_1_CD14_pos_DC2_b2_S7


title: PB001_1_CD14_neg_DC2_b1_S11


title: PB001_1_cDC1_b1_S9


title: HDF51_cDC1_b3_S1


title: HDF51_CD14_pos_DC2_b3_S2


title: E0771_Vector control2

value: cancer cell


title: HDF51_CD14_neg_DC2_b3_S3


title: CB-D6_cDC1_b3_S12

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 6, differentiated to cDC1

source_name: dendritic cell type one (CD141-positive) differentiated from cord blood CD34-positive hematopoietic stem cell

value: CD34-positive hematopoietic precursor cell isolated from cord blood

tag: donor


title: HDF51_CD14_pos_DC2_b1_S4


title: CB-D6_CD14_neg_DC2_b3_S14

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 6, differentiated to CD14-negative cDC2

source_name: dendritic cell type two (CD1c-positive CD14-negative) differentiated from cord blood CD34-positive hematopoietic stem cell


title: U2OS RNA-seq GFP(Ctrl) siRNA rep2

description:
RNA
fpkm.txt.gz

source_name: total RNA-seq in U2OS cells with GFP(Ctrl) siRNA (rep2)

value: U2OS cell line

tag: assay

value: total RNA-seq (stable transcripts)

value: GFP (Control) siRNA


title: HDF51_CD14_neg_DC2_b1_S5


title: CB-D4_CD14_pos_DC2_b2_S15

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 4, differentiated to CD14-positive cDC2

source_name: dendritic cell type two (CD1c-positive CD14-positive) differentiated from cord blood CD34-positive hematopoietic stem cell


title: CB-D4_cDC1_pool_S19

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, pooled from donor 3 and donor 4, differentiated to cDC1

value: dendritic cell type one (CD141-positive) differentiated from cord blood CD34-positive hematopoietic stem cell

value: pooled b1 and b2


title: CB-D6_CD14_pos_DC2_b3_S13

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 6, differentiated to CD14-positive cDC2

value: dendritic cell type two (CD1c-positive CD14-positive) differentiated from cord blood CD34-positive hematopoietic stem cell


title: CB-D4_CD14_neg_DC2_b2_S16

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 4, differentiated to CD14-negative cDC2

value: dendritic cell type two (CD1c-positive CD14-negative) differentiated from cord blood CD34-positive hematopoietic stem cell


title: CB-D3_CD14_pos_DC2_b1_S17

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 3, differentiated to CD14-positive cDC2


title: CB-D3_CD14_neg_DC2_b1_S18

description: CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 3, differentiated to CD14-negative cDC2


title: AF47A_hBim_DMSO

first: Sarah

middle: T

last: Diepstraten

address: 1G Royal Pde

institute: The Walter and Eliza Hall Institute

description: C01_47A hBim DMSO

data_processing:
Data was analysed on the Galaxy Australia server
Sequencing reads were aligned to mm10 using hisat2 v2.2.1.
Read counts were obtained using featureCounts from subread v2.0.3.
Read filtering, normalisation and differential expression analysis was performed using limma-voom v3.50.1. Genes that did not meet a minimum expression level of CPM > 0.5 in at least 2 samples were filtered out. Normalisation performed using the TMM method.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes limma-voom filtered and normalised read counts for each sample

source_name: Eu-Myc mouse lymphoma

growth_protocol: Cels were maintained in FMA media (DME Kelso, 10% heat-inactivated FBS, 100 uM L-asparagine,  50 uM beta-mercaptoethanol) at 37C with 5% CO2.

extract_protocol:
Cell pellets were resuspended in TRIzol reagent (Invitrogen) and RNA extracted according to the manufacturer's instructions.
RNA libraries were constructed from 200 ng of RNA per sample using the TruSeq RNA Library Prep Kit v2 (Illumina), according to the manufacturer's instructions.

treatment_protocol: Cells were pretreated for 15 min with caspase inhibitor QVD-O-Ph, followed by DMSO, S63845 (300 nM), diABZI (100 nM) or both S63845 and diABZI for 24 h.

value: Eu-Myc mouse lymphoma

value: lymphoma

tag: genotype

value: WT

value: DMSO


title: 560_StingKO_diABZI

description: B11_560 StingKO diABZI

value: Sting KO

tag: treatment

value: diABZI


title: 560_StingKO_diABZI_S6

description: B12_560 StingKO diABZI S6


title: AF47A_p53KO_DMSO

description: C03_47A p53KO DMSO

value: p53 KO


title: AF47A_hBim_S6

description: C02_47A hBim S6


title: 560_StingKO_S6

description: B10_560 StingKO S6


title: 560_StingKO_DMSO

description: B09_560 StingKO DMSO


title: 560_p53KO_diABZI_S6

description: B08_560 p53KO diABZI S6


title: 560_p53KO_DMSO

description: B5_560 p53KO DMSO


title: 560_hBim_diABZI_S6

description: B04_560 hBim diABZI S6


title: 560_p53KO_S6

description: B06_560 p53KO S6


title: 560_p53KO_diABZI

description: B07_560 p53KO diABZI


title: 560_hBim_DMSO

description: B01_560 hBim DMSO


title: 560_hBim_S6

description: B02_560 hBim S6


title: AH15A_StingKO_diABZI_S6

description: A12_15A StingKO diABZI S6


title: AH15A_StingKO_diABZI

description: A11_15A StingKO diABZI


title: AH15A_StingKO_DMSO

description: A09_15A StingKO DMSO


title: AH15A_p53KO_diABZI

description: A07_15A p53KO diABZI


title: AH15A_StingKO_S6

description: A10_15A StingKO S6 24h


title: AH15A_p53KO_S6

description: A06_15A p53KO S6 24h


title: AH15A_hBim_diABZI_S6

description: A04_15A hBim diABZI S6


title: AH15A_hBim_diABZI

description: A03_15A hBim diABZI


title: AH15A_p53KO_DMSO

description: A05_15A p53KO DMSO


title: AH15A_hBim_S6

description: A02_15A hBim S6


title: AF47A_p53KO_S6

description: C04_47A p53KO S6


title: AH15A_hBim_DMSO

description: A01_15A hBim DMSO


title: 560_hBim_diABZI

description: B03_560 hBim diABZI


title: PerSC, glass+hypoxia, rep2

city: Glasgow

first: Hannah

last: Donnelly

address: Glasgow University

department: Centre for the Cellular Microenvironment

country: United Kingdom

institute: University of Glasgow

data_processing:
Libraries were sequenced in 75 base, paired end mode on the Illumina NextSeq 500 platform.
Raw sequence reads were trimmed for contaminating sequence adapters and poor quality bases using the program Cutadapt
Bases with an average Phred score lower than 15 were trimmed. Reads that were trimmed to less than 54 bases were discarded.
The quality of the reads were checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) before and after trimming. The reads were “pseudo aligned” to the transcriptome using the program Kallisto
The differential expression for the analysis groups were assessed using the Bioconductor package DESeq2. This was provided as a service by Glasgow Polyomics Facility
Assembly: GRCH38 from the Ensembl database
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: adipose-derived

growth_protocol: PerSCs, after passage 1, were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich) with 20% FBS (Thermo Fisher), 1% nonessential amino acids (Sigma-Aldrich), 1% 100 mM sodium pyruvate (Sigma-Aldrich) and an antibiotic mix consisting of 10 mg/ml penicillin/streptavidin (Sigma-Aldrich), 200 nM L-glutamate (Sigma-Aldrich), and 0.5% Fungizone (Thermo Fisher). Cells were incubated in a 5% humidified CO2 atmosphere at 37°C. For cell culture on polymer substrates, cells were seeded at 1.5 x103/cm2 on 13 mm coverslips in 24 well-plates and cultured in DMEM containing 2% with human AB serum (HS; Sigma Aldrich, H4522) in a 5% humidified CO2 atmosphere at 37°C. Hypoxic culture carried out in hypoxic workstation (Ruskinn) at an oxygen tension of 1%, CO2 5% and 37oC. Medium was exchanged every 3 days.

extract_protocol:
RNA was harvested using Rneasy mini kit.
Sequencing libraries then prepared from total RNA using the Illumina TruSeq Stranded mRNA Sample Preparation Kit.

value: adipose-derived

value: Perivascular stem cells

value: glass+hypoxia


title: PerSC, PMA/FN+gel, rep3

value: PMA/FN+gel


title: PerSC, PEA/FN/BMP+hypoxia, rep2

value: PEA/FN/BMP+hypoxia


title: PerSC, PMA/FN/BMP+gel, rep3

value: PMA/FN/BMP+gel


title: PerSC, glass+hypoxia, rep1


title: PerSC, PEA/FN/BMP+hypoxia, rep3


title: PerSC, glass+hypoxia, rep3


title: PerSC, PEA/FN/BMP+hypoxia, rep1


title: PerSC, PMA/FN+gel, rep2


title: PerSC, PEA/FN/BMP2+gel, rep2


title: PerSC, PMA/FN+gel, rep1


title: AH15A_p53KO_diABZI_S6

description: A08_15A p53KO diABZI S6


title: PerSC, PEA/FN/BMP2+gel, rep1


title: PerSC, PEA/FN+gel, rep3

value: PEA/FN+gel


title: PerSC, PEA/FN/BMP2+gel, rep3


title: 3T3L1 cells, HFD-WT-vWAT

city: Shanghai

first: Yunkai

last: Lin

address: Qianju Road 366

department: National Center for Liver Cancer

institute: Second Military Medical University

data_processing:
Fastp software was used to remove reads that contained adapter contamination and low-quality bases with default parameters and to verify sequence quality.
HISAT2 was used to map the reads to the reference genome of Homo sapiens GRCh381. The mapped reads of each sample were assembled using StringTie.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare.
StringTie was used to determine the expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs were selected with fold change >2 or fold change <0.5 and with the parametric F test comparing nested linear models (p value <0.05) by the R package edgeR.
Assembly: gffcompare.
Supplementary files format and content: excel includes raw counts for each Sample
Supplementary files format and content: excel file includes FPKM values for each Sample

growth_protocol: 3T3-L1 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with penicillin-streptomycin and 10% NCS (Gibco). For differentiation into adipocytes, the medium was replaced with DMEM containing 1% penicillin-streptomycin, 10% FBS, 10 μg/ml insulin (Sigma-Aldrich), 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Selleck) and 1 μM dexamethasone (Selleck) starting 2 days after the cells reached confluence (day 0). On day 3, the medium was replaced every other day with complete DMEM containing insulin (10 μg/ml). Fully differentiated 3T3-L1 adipocytes (days 8-10) were used for assays

extract_protocol:
Total RNA of 3T3-L1 cells was isolated after the intervention using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

treatment_protocol: For the AT-Exo stimulation assay, approximately 2x1012 AT-Exos from vWAT, iWAT and BAT were added to fully differentiated 3T3-L1 adipocytes or BMDMs in 6-well cell culture plates. After incubation for 48 h at 37°C, cells were washed and lysed with RLT lysis buffer (Qiagen) for RNA extraction and further analysis.

value: Mouse embryonic fibroblasts

value: HFD-vWAT-Exosmes


title: PerSC, PEA/FN+gel, rep2


title: PerSC, PEA/FN+gel, rep1


title: 3T3L1 cells, HFD-WT-iWAT

value: HFD-iWAT-Exosmes


title: 3T3L1 cells, LFD-WT-vWAT

value: LFD-vWAT-Exosmes


title: PerSC, PEA/FN/BMP2-gel, rep1


title: 3T3L1 cells, LFD-WT-iWAT

value: LFD-iWAT-Exosmes


title: 3T3L1 cells, BLK

value: WT

value: No treatment


title: PerSC, PEA/FN/BMP2-gel, rep3


title: PerSC, PMA/FN/BMP+gel, rep1


title: 3T3L1 cells, LFD-WT-BAT

value: LFD-BAT-Exosmes


title: PerSC, PMA/FN/BMP+gel, rep2


title: PerSC, glass+sol.BMP2, rep3


title: Liver, KO-6, HFD, 12wks

city: 南京市

first: 映蓉

last: 冷

state: 江苏省

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

institute: 中国药科大学

data_processing:
Majorbio Cloud Platform
For read mapping, the raw reads were trimmed and quality controlled by SeqPrep  (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle).
The clean reads were aligned to a reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtmL)51 software, and the mapped reads were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example)
The RNA-seq analysis was performed at the online platform Majorbio Cloud Platform (www.majorbio.com).
Assembly: RNA-seq transcriptome library was prepared using a TruSeqTM RNA sample preparation Kit
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: global Lix1l knockout

growth_protocol: 6-week-old WT littermates and Lix1l-KO mice were fed a low-fat diet (LFD) or high-fat diet (HFD) for 12 weeks.

extract_protocol:
Total RNA was purified to poly (A) RNA after the RNA amount and purity were quantified, 1.3μg total RNA was used for the construction of suquencing libraries.
RNA-seq transcriptome library was prepared using a TruSeqTM RNA sample preparation Kit

treatment_protocol: Mouse liver tissues, rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction

value: liver

value: Lix1l knockout

value: HFD-diet


title: PerSC, glass, rep2

value: adipose-derived

value: Perivascular stem cells

value: glass


title: PerSC, glass+sol.BMP2, rep2


title: 3T3L1 cells, HFD-WT-BAT

value: HFD-BAT-Exosmes


title: Liver, KO-4, LFD, 12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

value: LFD-diet


title: PerSC, glass, rep3


title: Liver, KO-5, LFD, 12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学


title: PerSC, glass, rep1


title: short telomere (passage 5 doxycyline treated)

description:
N1823
10x Genomics

data_processing:
The proprietary 10x Genomics CellRanger pipeline (v3.0.2) was used with default parameters except for the setting of expected cells (7000-cells)
After default CellRanger quality filtering, transcriptomes from 6109, 9045 and 7716 cells were kept from day 12 of the hiPSC-cardiomyocyte differentiation pool with long, intermediate and short telomeres, respectively
mkfastq command was used to demultiplex the data from the raw BCL sequencer images, given the supplied sample sheet with the 10X barcodes. This step resulted in standard FASTQ files and 10X specific metadata
CellRanger was used to align read data to the reference genome provided using the aligner STAR, counting aligned reads per gene
Assembly: reference genome provided by 10X Genomics (Human reference dataset 3.0.0; November 19, 2018; GRCh38
Supplementary files format and content: gene expression matrix

source_name: CRISPRi TERT hiPSCs

extract_protocol:
For each sample, cell suspension was prepared using mild digestion to maintain viability of the sample followed by filtration to obtain single cell suspension. More than 6000 cells were utilized from each condition for the single cell sequencing
Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium Single Cell 3ʹ Reagent Kit v3 User Guide (Manual Part Number CG000183 Rev A; 10x Genomics). According to the protocol a given 1.6-fold excess of cells was loaded to the 10x controller in order to reach a target number of 7000 cells per sample. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific)

value: CRISPRi TERT hiPSCs

value: day 12 of cardiomyogenic differentiation pool from CRISPRi TERT hiPSCs intermediate telomere (passage 5 doxycyline treated)


title: Liver, WT-6, HFD,12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

source_name: Litter control


description:
N1822
10x Genomics

value: day 12 of cardiomyogenic differentiation pool from CRISPRi TERT hiPSCs intermediate telomere (passage 2 doxycyline treated)


title: long telomere

description:
N1821
10x Genomics

value: day 12 of cardiomyogenic differentiation pool from CRISPRi TERT hiPSCs long telomere


title: Liver, KO-2, LFD, 12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学


title: Liver, WT-2, HFD,12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学


title: Liver, WT-1, HFD,12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学


title: PerSC, PEA/FN/BMP2-gel, rep2


title: Liver, WT-7, LFD,12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学


title: HFD_WT_WAT

library_source: other

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCh38
Supplementary files format and content: excel includes normalized_counts for each Sample

molecule: other

source_name: Adipose tissue exosome

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: WAT-Exos and BAT-Exos were isolated from 6 weeks wild-type C57BL/6 (B6) mice fed a high-fat diet (HFD) or low-fat diet (LFD) over 4 months.

value: Adipose tissue exosome

value: Wild type

value: high-fat diet


title: HFD_WT_BAT


title: Liver, WT-4, LFD,12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

value: WT


title: Young SPF, biol rep 3 [SPFY3]

city: Minneapolis

first: Christina

middle: D

last: Camell

state: MN

address: 312 Church St; NHH 4-108

department: Biochemisty, Biophysics and Molecular Biology

institute: University of Minnesota

data_processing:
The University of Minnesota Research Informatics groups at MSI analyzed the RNA Seq output. 2 x 150bp FastQ paired-end reads for 14 samples (n=199 million average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (GRCm38.94) as reference
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: GRCm38.94
Supplementary files format and content: txt files with each column as a different sample containing gene symbols and ensembl symbols

source_name: Liver

extract_protocol:
Tissues were snap frozen after harvest. RNA was extracted using 1mL TRIzol Reagent (ThermoFisher Cat#15596018). After homogenization in bullet blender storm 24SMPL (ThermoFisher Cat#NC0956230). After homogenization, 200mL of chloroform was added to each sample followed by centrifugation to separate the aqueous layer. One volume of EtOH was added to aqueous layer or cell lysate, RNA was purified using columns (PureLink RNA Mini Kit; Cat#12183018A) according to the manufacturer’s instructions. Standard RNA extraction protocol was used with the addition of a wash step using 80L PureLink DNase (ThermoFisher Cat#12185-010). Samples were eluted using 30L nuclease-free H2O.
Total RNA samples are converted to Takara sequencing libraries using Takara Bio’s SMARTer Stranded Total RNA-Seq – Pico Mammalian Kit v2 (Cat. # 634414). ).  Please see www.takarabio.com for a detailed list of kit contents and methods. In summary, between 250 pg – 10 ng of total RNA is fragmented (fragmentation is skipped if samples are sufficiently degraded) and then reverse transcribed into cDNA using random primers. The Template Switching Oligo (TSO) is incorporated during cDNA synthesis and allows for full length cDNA synthesis and strand specificity to be retained. Illumina sequencing adapters and barcodes are then added to the cDNA via limited PCR amplification. Next, mammalian ribosomal cDNA is enzymatically cleaved. Uncleaved fragments are PCR enriched 12-16 cycles. Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Indexed libraries are then normalized and pooled for sequencing.

treatment_protocol: Mice were exposed to petstore mice fomite for 7 days

value: Liver

value: SPF


title: Liver, KO-5, HFD, 12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

value: liver

value: Lix1l knockout


title: Liver, KO-1, HFD, 12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

value: HFD-diet


title: PerSC, glass+sol.BMP2, rep1

value: adipose-derived

value: Perivascular stem cells


title: Young SPF, biol rep 2 [SPFY2]


title: LFD_WT_BAT

value: low-fat diet


title: LFD_WT_WAT


title: KI763_mRNA_heart_59619

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

data_processing:
High-throughput sequencing reads were aligned to the mouse mm39 reference genome with the Gencode vM27 basic annotation using STAR version 2.7.9 73 with the default alignment parameters except “clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA”. From raw read counts per transcript, TPM (transcripts per million) was calculated in R as follows: TPM=106 x RPK/sum(RPK), where RPK=read count/transcript length in kp and sum(RPK) is the sum of RPKs of all transcripts.
Assembly: Mouse mm39/Gencode basic vM27
Supplementary files format and content: Counts or TPMs in a text file

source_name: Adult heart

extract_protocol:
Hearts were perfused with 100 mM KCl and removed for RNA extraction. Total RNAs were extracted with Trizol LS (Invitrogen, 10296010), treated with DNaseI, and purified.
For tamoxifen time course experiments, mRNA sequencing libraries were generated using the poly-A selection module in the NEBNext UltraII Directional RNA Library Prep Kit (NEB E7760) and sequenced on the Illumina HiSeq 2500 sequencer with single-end 50 cycles. For cGas/Lmna double knockout experiments, libraries were generated using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, K01596) and sequenced on the Illumina NovaSeq 6000 sequencer with single-end 100 cycles.

treatment_protocol: All mice used in experiments were administered with tamoxifen (Sigma, T5648) at 6-8 weeks of age via intraperitoneal injections (100 μL of 4 mg/mL solution per day for 4 consecutive days) dissolved in corn oil (Sigma, C8267).

value: Adult heart

tag: treatment 1

value: 11 days post tamoxifen

value: Lmna +/+; Myh6MCM Tg/0

value: M

tag: library type

tag: pool id


title: Old SPF, biol rep 2 [SPFO2]

tag: tissue


title: Young SPF, biol rep 1 [SPFY1]


title: Young NME, biol rep 4 [1469-2]

value: 7 day NME


title: KI759_mRNA_heart_59615

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/F; My6MCM Tg/0

tag: Sex

value: F

value: NEBNext UltraII Directional RNA Library Prep


title: KI762_mRNA_heart_59618

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: KI757_mRNA_heart_59613

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: KI756_mRNA_heart_59612

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Young NME, biol rep 3 [1468-5]

value: WT


title: KI733_mRNA_heart_57551

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: 2 weeks post tamoxifen


title: Young NME, biol rep 2 [1467-3]

value: Liver


title: Young NME, biol rep 1 [1467-1]


title: Liver, WT-8, LFD,12wks

address: 江苏省南京市江宁区龙眠大道639号中国药科大学

value: liver

value: LFD-diet


title: KI731_mRNA_heart_56746

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: KI732_mRNA_heart_56749

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: scRNA-seq_Mettl14_ff

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: single cell

data_processing:
Raw data of fastq files were aligned to the mm10 mouse reference genome by using the CellRanger software v3.0.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files

source_name: whole uterus

extract_protocol:
Uterine tissues were minced with a blade and then incubated in dissociation buffer containing 2 mg/ml Collagenase II (#C6885, Sigma-Aldrich), 10 mg/ml Dispase II (#354235, Corning) and 50000 U/ml DNase I (#DN25, Sigma-Aldrich) for up to 30 min at 37 °C in a shaking incubator.To remove undigested tissues, the single-cell suspension was then passed through a 40-μm cell strainer and cells were spun down at 250 g at 4°C for 4 min. Red blood cells (RBC) were removed by using RBC Lysis Buffer (#00-4333, Invitrogen). In order Cell viability was measured by AO/PI solution (#CS2-0106, Nexcelom Bioscience). The quality control criteria for single-cell suspension were cell viability > 80% and the percentage of cell clumps < 10%.
The final concentration of single-cell suspension was adjusted to 1000 cells/μl. In order to recover 8000-10000 cells, a volume of 15 µl was loaded into one channel of the ChromiumTM Single Cell B Chip (#1000073, 10x Genomics). Single-cell bar-coding, cDNA synthesis and library preparation were performed by using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (#1000075, 10x Genomics). DNA libraries were then sequenced on an Illumina novaseq 6000 system configured with the paired-end 150-bp protocol for a sequencing depth of approximately 400 million reads per library.

value: whole uterus

tag: time

value: gestational day 4

value: f/f


title: scRNA-seq_Mettl14_dd

description: single cell

value: d/d


title: Old NME, biol rep 4 [1466-2]


title: KI730_mRNA_heart_56745

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Adult heart


title: KI716_mRNA_heart_57259

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Old NME, biol rep 1 [1464-3]


title: WT-3

first: Luis

middle: O

last: Correa-Medero

address: 109 Zina Pitcher Place

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et
al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment
options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: CSV file containing "ENSEMBL geneID, entrezgene_id, external gene name, description,  counts
Supplementary files format and content: CSV file containing "ENSEMBL geneID, entrezgene_id, external gene name, description,  counts .

source_name: P14 CD8 T cell

extract_protocol:
RNA ws isolated using the Qiagen RNAeasy micro kit (74004) according to manufacturer's protocol.
SMART-Seq v4 PLUS Kit (Takara, R400753)

value: P14 CD8 T cell

value: d8 LCMV-A


title: KI718_mRNA_heart_57123

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Old SPF, biol rep 3 [SPFO3]

value: SPF


title: KO-5


title: KI717_mRNA_heart_57122

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna +/+; Myh6MCM Tg/0


title: KI729_mRNA_heart_56743

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna F/F; My6MCM Tg/0

value: M


title: KI715_mRNA_heart_57257

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: NEBNext UltraII Directional RNA Library Prep


title: WT-5

value: WT


title: KI714_mRNA_heart_57255

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: 2 weeks post tamoxifen


title: KI713_mRNA_heart_57250

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: KI712_mRNA_heart_57249

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Old SPF, biol rep 1 [SPFO1]

value: Liver


title: Old NME, biol rep 2 [1465-3]

value: 7 day NME


title: KO-3


title: Artery, Ubr4KO, tdTPos, rep2

city: Aurora

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

description: 10x Genomics

data_processing:
Fastq files were aligned to GRCm39 reference (Ensembl, r104) using Cell Ranger 6.1.2.
Scanpy 1.9.3 was used for the downstream analysis including quality control, normalization, clustering, based on Single-cell best practices
Cells with less than 200 genes and genes expressed by less than 10 cells were filtered out. Cells with a percentage of mitochondrial counts exceeding 8 % or with more than 7500 genes were filtered.
Pseudobulk samples were created from the single-cell dataset for differential gene expression analysis using edgeR 3.42.4. GOBP enrichment analysis was performed using GSEApy 1.0.5 with GO_Biological_Process_2021.gmt obtained from Enrichr gene-set library.
Assembly: GRCm39 (Ensembl, r104)
Supplementary files format and content: raw_count.csv.gz contains the count matrix file
Supplementary files format and content: obs_meta.csv.gz contains metadata describing the cells
Supplementary files format and content: umap.csv.gz contains umap embedding for the cells

source_name: Carotid and aortic artery

extract_protocol:
Single cell suspension was prepared and fluorescence activated cell sorting (FACS) was performed to separate tdT+ and tdT- cell. Sorted cells from two animals were pool together into one sample.
Duplicated tdT+ and tdT- samples of each genotype were subjected to scRNA-seq using the Chromium Single Cell 3’ Library and Gel Bead Kit (v3.1 10x Genomics, Pleasanton, CA) and the Chromium X.

value: Carotid and aortic artery

tag: age

value: 9-10 months

value: female

value: 8-9 months post Tamoxifen


title: KI675_mRNA_heart_54904

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: 1 week post tamoxifen


title: KI677_mRNA_heart_54823

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Adult heart


title: Artery, Ubr4KO, tdTNeg, rep1

description: 10x Genomics


title: WT-2

value: P14 CD8 T cell


title: Artery, Ubr4KO, tdTPos, rep1

description: 10x Genomics


title: KI673_mRNA_heart_54818

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: KI674_mRNA_heart_54815

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Artery, Ubr4WT, tdTPos, rep2

description: 10x Genomics


title: KI676_mRNA_heart_54901

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Artery, Ubr4KO, tdTNeg, rep2

description: 10x Genomics


title: KI672_mRNA_heart_54817

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: Old NME, biol rep 3 [1465-4]


title: KI669_mRNA_heart_54813

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: F


title: Artery, Ubr4WT, tdTNeg, rep1

description: 10x Genomics


title: KI670_mRNA_heart_54907

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv


title: KI989_SLAMIT_heart_0500

data_processing:
Raw reads were processed by the slamdunk all function in the the slamdunk package with the following alignment parameters: --trim-5p 12 --topn 100 --multimap --max-read-length 101 with default --var-fraction (0.8) and default -c (1). This function aligned reads to 3’ UTRs of Gencode vM27 genes (total 208,307 UTRs from 37,065 unique genes) in the mm39 mouse reference genome. Aligned reads were processed by the alleyoop utrrates function in the slamdunk package with default parameters to quantify C-to-T conversion events. UTRs with at least one read coverage for all 21 samples were retained for further analyses (47,717 UTRs from 14,250 unique genes).
Assembly: Mouse mm39/Gencode basic vM27 UTR
Supplementary files format and content: A csv file containing C-to-T conversion rate, CPM, T content, Read coverages for each UTR
Library strategy: SLAM-IT-seq

extract_protocol:
Mice were sacrificed, and hearts were perfused with 100 mM KCl and removed. RNAs from the left ventricular free wall were extracted by Trizol LS and purified and DNaseI treated using Directzol RNA miniprep kit (Zymo, R2052). Purified RNAs (1.5 µg) were subjected to alkylation in the presence of 12 mM Iodoacetamide (IAA, Sigma I1149).
High-throughput sequencing libraries were generated from the alkylated RNAs using Quant-seq 3’ mRNA-seq FWD kit (Lexogen K01596) and sequenced 100 bases on the single-end mode on an Illumina NovaSeq6000 sequencer.

treatment_protocol: All mice used in experiments were administered with tamoxifen (Sigma, T5648) at 6-8 weeks of age via intraperitoneal injections (100 μL of 4 mg/mL solution per day for 4 consecutive days) dissolved in corn oil (Sigma, C8267). At 2 weeks post tamoxifen, mice were intraperitoneally injected with 4-thiouracil (4sU) dissolved in a DMSO/corn oil (1:3) solution at a dose of 10 mg per gram of body weight. Hearts were harvested after six hours of 4sU administration.

tag: treatment 2

value: 4-thiouracil administration and RNA alkylation

value: QuantSeq 3’ mRNA-Seq Library Prep Kit FWD


title: Artery, Ubr4WT, tdTPos, rep1

description: 10x Genomics


title: KI671_mRNA_heart_54824

description:
rnaseq_count_geo.csv
rnaseq_tpm_geo.csv

value: Lmna +/+; Myh6MCM Tg/0


title: Artery, Ubr4WT, tdTNeg, rep2

description: 10x Genomics


title: PPARγ-/- Tumor, scRNAseq

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description: 10x Genomics

data_processing:
The Cell Ranger 6.0.1 pipeline (10x Genomics) was used to align reads from scRNA-seq collected from immune cells to the 10x mm10 mouse reference genome v1.2.0 and produce the associated cell-by-gene count matrix. Default parameters were used.
Unique molecular identifier (UMI) counts were analyzed using the Seurat R package v.4.0.1(Hao et al., 2021).
The top 3000 variable genes for each line were then used to integrate sample datasets with the SCT method (SCTransform, SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors and IntegrateData PCA was performed on the scaled integrated data for the variable genes and the top 30 principal components were used for the unsupervised clustering.
Cells were clustered in PCA space using the FindNeighbors function (top 30 principal components) and FindClusters function. UMAP plots were used to visualize variation in the data.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Mice were fed a doxycycline containing chow (625 ppm) obtained from Harlan-Tekland. Both male and female mice were used at approximately equivalent levels and were randomly assigned to treatment groups. Cells were pooled between three separate mice per treatment group.

extract_protocol:
Lungs were excised from the chest, washed with PBS, dried on paper towels and then minced into small pieces and suspended in digestion media consisting of RPMI 1640 with 10% FBS, 0.5 ug/mL of DNase I and 1 unit/mL collagenase Type I (Sigma-Aldrich Cat# 0000137295) and placed in an incubator at 37°C for 45 minutes, shaking once during digestion. Lungs were then mashed against 70 μM cell strainers (VWR Cat# 10199-657) to filter and then red blood cells were lysed using ACK lysis buffer, mixed with RPMI 1640 containing 10% FBS and 1% pen-strep, centrifuged at 400g for 5 minutes at 4°C to obtain a single-cell suspension. Cells were then stained and sorted by FACS for alveolar macrophages (CD45+CD11c+SigF+), macrophages (CD45+CD11b+Ly6G-), T cells (CD45+ CD3+) and epithelial cells (CD45-EPCAM+), washed, counted, and then an equal proportion of each population was used for sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Alveolar Macrophages, Macrophage, T cells, Epithelial Cells

value: Lung

value: 16-20 weeks old


title: KO-2

value: d8 LCMV-A


title: KI986_SLAMIT_heart_0422

value: 2 weeks post tamoxifen

value: Lmna F/F; Myh6MCM Tg/0

value: M


title: WT Healthy, scRNAseq

description: 10x Genomics


title: KI988_SLAMIT_heart_0498


title: WT Tumor, scRNAseq

description: 10x Genomics

source_name: Ccsp-rtTA;TetO-EGFRL858R; Pparγfl/fl


title: KI987_SLAMIT_heart_0484

value: Lmna F/F; Myh6MCM Tg/0; Uprt Tg/0


title: adult pancreas; PB2410-PAAD-T_S2_L002

city: Ulsan

first: Semin

last: Lee

address: 50, UNIST-gil

department: Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
The Cell Ranger pipeline was applied for pre-processing, including demultiplexing of sequencing results, barcode processing, read alignment, filtering of estimated droplets, and the generation of gene/barcode matrices. Reads were aligned to the GRCh38 human reference genome, and the UMI matrix of cell barcodes according to genes was generated for each sample.
Assembly: GRCh38
Supplementary files format and content: Raw_counts.txt.gz is a tab-delimited text file which includes UMI counts for all cells.

source_name: pancreas

extract_protocol:
All remaining tissues are collected in MACS® Tissue Storage Solution (Miltenyi Biotec., Auburn, CA, USA) on ice, and processed to the single cell dissociation immediately.
The sequenced libraries were processed using the HiSeqX platform from Illumina to obtain the requisite data for our study.

value: pancreas


title: adult liver; PB2410-Livermeta-T_S1_L001

source_name: liver

value: liver


title: adult pancreas; PB2409-PAAD-T_S2_L002


title: adult liver; PB2409-Livermeta-T_S1_L002


title: KI985_SLAMIT_heart_0418


title: DSP-1012340055901-B-B11

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

institute: Klinikum rechts der Isar

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.
Murine DRG T8 to T12 were extracted bilaterally from TPAC (Ela-TGFα; Ptf1a-Cre; Trp53fl/fl;RelAfl/fl , n=6, 47-54 weeks old), KPC (Ptf1a-Cre; LSL-Kras+/G12D; Trp53+/fl , n=3, 20-21 weeks old) and age-similar tumor-free control mice (Ela-TGFα; Trp53fl/fl;RelAfl/fl , n=3, 48-50 weeks old for TPAC and LSL-Kras+/G12D; Trp53+/fl , n=1, 20 weeks old; Trp53+/fl , n=1, 21 weeks old and LSL-Kras+/G12D; n=1, 22 weeks old for KPC). Following the extraction, DRGs were briefly washed in ice-cold, fresh PBS (D5262, Sigma-Aldrich) and fixated in freshly prepared 4% PFA (15710, Electron Microscopy Sciences; diluted with PBS) for 24 hours at room temperature. The samples were consecutively dehydrated, paraffine embedded and sectioned. For the human spatial transcriptome studies, two patient derived biopcies with pancreatic ductal adenocarcinoma analysed with HE staining for the neural invasion were fixed in freshly prepared 4% PFA (15710, Electron Microscopy Sciences; diluted with PBS) for 24 hours at room temperature. Three FFPE tissue sections of 5-μm from DRG biopsy tissue microarray (TMA) with VILI (n=6) and AIH (n=8) (TMA construction described below in the Immunoprofiling with CO-Detection by indEXing (CODEX)) were mounted on positively charged histology slides. Sections were incubated at 65 °C for 1 hour. Then, sections were deparaffinized in 3 xylol baths of 5 minutes and rehydrated in ethanol gradient from 100% EtOH 2 baths of 5 minutes, followed by 95% EtOH 5 minutes. Slides were then washed in 1X PBS. Antigen retrieval was carried out with Tris-EDTA pH 9.0 buffer at 100°C for 20 minutes at low pressure. Slides were first immersed into hot water for 10 seconds and then immersed into Tris-EDTA buffer. The cooker vent kept open during the procedure to ensure low pressure and it was allowed to reach 100°C. Slides were then washed with 1X PBS, and incubated in proteinase K containing PBS (1ug/ml) for 15 minutes at 37°C and washed again in 1X PBS. Tissue were post-fixed in 10% neutral-buffered formalin (NBF) for 5 minutes, washed two times 5 minutes in NBF stop buffer (0.1M Tris Base, 0.1M Glycine) and finally one time in 1X PBS. The mix of Whole Transcriptome Atlas probes (WTA, Nanostring) was dropped on each section and covered with HybriSlip Hybridization Covers. Slides were then incubated for hybridization overnight at 37°C in a Hyb EZ II hybridization oven (Advanced cell Diagnostics). The day after, HybriSlip covers were gently removed and 25 minutes stringent washes were performed twice in 50% formamide and 2X saline sodium citrate (SSC) at 37 °C. Tissues were washed for 5 min in 2× SSC, then blocked in Buffer W (Nanostring Technologies) for 30 min at room temperature in a humidity chamber. Next, 500 nM Syto83 and antibodies targeting NeuN (Channel-647, host-mouse, company -abCam, clone # EPR12763, dilution 1:100); GFAP (Channel-488, host-mouse, company -Novus, clone # GA-5, dilution 1:200); CD68 (Channel-594, host-mouse, company -Santa Cruz, clone # KP1, dilution 1:200) in Buffer W were applied to each section for 1 h at room temperature. Slides were washed twice in fresh 2× SSC then loaded on the GeoMx DSP. DSP Instrument (NanoString Technologies, Inc.), nCounter (NanoString Technologies, Inc.), Immunohistochemistry Pressure Cooker (BioSB), PCR instrument (Biorad) was used.

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4

source_name: Tumor

extract_protocol:
DNA oligonucleotide probes were designed to bind mRNA targets. From 5′ to 3′, each probe is comprised of a 35- to 50-nucleotide target complementary sequence, an ultraviolet (UV) photo cleavable linker and a 66-nucleotide indexing oligonucleotide sequence containing a unique molecular identifier (UMI), RNA ID sequence and primer binding sites. Oligomers from ROIs were disintegrated by UV irradiation, passed through capillaries, pooled into collection plates, and resealed with DAPI fluoromount G mounting medium.
Entire slides were imaged at ×20 magnification and morphologic markers were used to select Region Of Interest (ROI) either using circle or organic shapes. Automatic segmentation of ROI based on NeuN marker was used to defined Area of Illumination (AOIs). This allowed to separate Neurons (NeuN+) and cells around. A total of AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited in a 96-well plate for subsequent processing. The indexing oligonucleotides were dried down overnight and resuspended in 10 μl of DEPC-treated water. Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled and purified twice using AMPure XP beads (Beckman Coulter, A63881), according to the manufacturer’s protocol. Pooled libraries were single-sequenced at 27 base pairs and with the single-index workflow on an Illumina NovaSeq S4 instrument. FastQ files were converted into DCC files according to manufacturer’s pipeline. Digital Count Conversion files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.4.2.2 (Nanostring).

treatment_protocol: no treatment

value: Tumor

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: characteristic


title: DSP-1012340055901-B-B12


title: adult pancreas; PB2366-PAAD-T_S1_L003


title: DSP-1012340055901-B-C01

value: Nerve


title: KI983_SLAMIT_heart_0392

value: Adult heart

tag: genotype

value: Lmna +/+; Myh6MCM Tg/0; Uprt Tg/0


title: DSP-1012340055901-B-B10


title: KI984_SLAMIT_heart_0399

value: 4-thiouracil administration and RNA alkylation

value: F


title: adult pancreas; PB2349-PAAD-T_S56_L008


title: adult pancreas; PB2349-PAAD-T_S55_L008


title: adult pancreas; PB2349-PAAD-T_S56_L004


title: DSP-1012340055901-B-B09


title: DSP-1012340055901-B-B08


title: adult pancreas; PB2349-PAAD-T_S54_L004


title: KI982_SLAMIT_heart_0362

value: Lmna +/+; Myh6MCM Tg/0

value: QuantSeq 3’ mRNA-Seq Library Prep Kit FWD


title: KI981_SLAMIT_heart_0349


title: adult pancreas; PB2349-PAAD-T_S54_L008


title: adult pancreas; PB2349-PAAD-T_S55_L004


title: adult pancreas; PB2349-PAAD-T_S53_L008


title: DSP-1012340055901-B-B07

value: Geometric Segment


title: KI980_SLAMIT_heart_0344


title: adult pancreas; PB2349-PAAD-T_S23_L007


title: adult pancreas; PB2349-PAAD-T_S53_L004


title: adult pancreas; PB2349-PAAD-T_S22_L007


title: DSP-1012340055901-B-B06


title: DSP-1012340055901-B-B05


title: adult pancreas; PB2349-PAAD-T_S21_L007


title: KI978_SLAMIT_heart_0293


title: adult liver; PB2349-Livermeta-T_S60_L008


title: adult liver; PB2349-Livermeta-T_S60_L005


title: KI977_SLAMIT_heart_0292


title: KI976_SLAMIT_heart_0290


title: adult liver; PB2349-Livermeta-T_S59_L005


title: DSP-1012340055901-B-B02


title: KI975_SLAMIT_heart_0224


title: DSP-1012340055901-B-B03


title: adult liver; PB2349-Livermeta-T_S58_L008


title: adult liver; PB2349-Livermeta-T_S58_L005


title: DSP-1012340055901-B-B04


title: adult liver; PB2349-Livermeta-T_S57_L005


title: adult liver; PB2349-Livermeta-T_S55_L008


title: adult liver; PB2349-Livermeta-T_S57_L008


title: DSP-1012340055901-B-A12


title: adult pancreas; PB2349-PAAD-T_S24_L007


title: KI974_SLAMIT_heart_0222


title: adult liver; PB2349-Livermeta-T_S56_L008


title: KI973_SLAMIT_heart_0221


title: DSP-1012340055901-B-B01


title: KI979_SLAMIT_heart_0296


title: adult liver; PB2349-Livermeta-T_S54_L008


title: adult liver; PB2349-Livermeta-T_S53_L008


title: DSP-1012340055901-B-A11


title: KI972_SLAMIT_heart_0218


title: adult liver; PB2349-Livermeta-T_S59_L008


title: adult pancreas; PB2341-PAAD-T_S1_L002


title: KI971_SLAMIT_heart_0156


title: adult pancreas; PB2311-PAAD-T_S48_L008


title: DSP-1012340055901-B-A09


title: adult pancreas; PB2311-PAAD-T_S47_L008


title: adult pancreas; PB2311-PAAD-T_S48_L003


title: KI970_SLAMIT_heart_0154


title: adult pancreas; PB2311-PAAD-T_S47_L003


title: DSP-1012340055901-B-A08


title: adult pancreas; PB2311-PAAD-T_S46_L008


title: KI969_SLAMIT_heart_0151


title: adult pancreas; PB2311-PAAD-T_S45_L003


title: adult pancreas; PB2311-PAAD-T_S45_L008


title: KI990s96_heart_nuclei

description:
sce14111_2w_07-07-2023.rds
RT_barcode_sample_lookup.csv
Ligation_barcode_plate.csv
P7_barcode_PCR_plate.csv

data_processing:
Pre-processing of the single-nucleus RNA-seq data was performed using the published sci-RNA-seq3 pipeline  76, available in Github (https://github.com/JunyueC/sci-RNA-seq3_pipeline). The sci-RNA-seq3 pipeline takes fastq files separated by the P7 index as input, aligns reads to the genome, and returns a gene-by-cell read count matrix. First, raw reads were trimmed to remove poly A tails, aligned to the mm39 mouse reference genome using STAR, and filtered for MAPQ greater than or equal to 30. Duplicate reads were removed based on UMI. Read counts per gene were computed for each cell defined by the unique combination of the RT index, ligation index, and P7 index. The gene-by-cell count matrix produced by the sci-RNA-seq3 pipeline was further processed in the SingleCellExperiment package framework in R (Amezquita et al. 2020). We used the scDblFinder package for doublet detection and the scuttle package for mitochondrial RNA quantification in R. We obtained 14,111 cells after filtering for cells with the scDblFinder doublet score less than 0.25 and mitochondrial RNA contamination percentage less than 2% of total RNAs per cell. Read counts for a gene were normalized by per-cell read depth and then log-transformed to obtain normalized expression values (“logcounts”). Logcounts were used to plot expression values in graphs. Principal component analysis (PCA) was performed on logcounts for 2,000 highly variable genes across cells using the fixedPCA function in the scran package. The top 50 principal components were used in the runUMAP function in the scater package with n_neighbors=20 and min_dist=1 parameters to obtain UMAP dimensions. To cluster cells, logcounts were processed in the clusterCells function in the scran package using the top 50 principal components, with the number of nearest neighbors k=12. Cell clusters were annotated manually with cell type names based on marker gene expression.
Assembly: Mouse mm39/Gencode basic vM27
Supplementary files format and content: gene_by_cell normalized read coverage in SingleCellExperiment object
Supplementary files format and content: 96-well RT primer index sequences in text file
Supplementary files format and content: 96-well Ligation primer index sequences in text file

growth_protocol: We used wild-type (n=3) and LmnaCKO mice (n=3) at 2 weeks post tamoxifen.

extract_protocol:
Mice were anesthetized with isoflurane, euthanized by cervical dislocation, and then hearts were perfused with 100 mM KCl. Removed hearts were diced into small pieces in cold PBS containing Diethyl pyrocarbonate (DEPC, Sigma D5758). Fresh heart pieces were dounce-homogenized to liberate nuclei in Hypotonic lysis buffer B (7.7 mM Na2HPO4, 4.5 mM NaH2PO4, 1.8 mM KH2PO4, 2.7 mM KCl, 10.3 mM NaCl, 3 mM MgCl2, 0.08% BSA, 0.025% Igepal CA-630, 1% DEPC) and passed through cell strainers. Nuclei were fixed in 1 mg/mL dithiobis(succinimidyl propionate) (DSP, Thermo Fisher 22585) for 15 min on ice, washed, and stored at –80°C until use.
For each mouse, 50,000 nuclei were placed in each of 8 wells of a 96-well plate (total 48 wells for 6 mice). The remaining 48 wells were filled with similarly processed mouse heart nuclei with comparable sample quality from an unrelated project. Nuclei were subjected to reverse-transcription with 96-indexed poly-T RT primers that contained a unique molecular identifier (UMI) sequence. Nuclei from all wells were combined and redistributed evenly to 96 wells. Redistributed cells were subjected to ligation with 96-indexed ligation primers in 96 wells (Table SX). Nuclei from all wells were combined again and redistributed evenly to 96 wells at 1,000 nuclei per well. Redistributed cells underwent second strand synthesis, protease digestion, tagmentation using N7-loaded Tn5 transposase, and PCR-amplified using 96-indexed PCR P7 primers and the unindexed P5 primer, for 16 cycles. PCR amplicons were combined and size-selected for DNA fragments between 250 bp and 600 bp.
Combinatorial indexing-based single-nucleus RNA-seq (sci-RNA-seq3)


title: KI990s94_heart_nuclei


title: adult pancreas; PB2311-PAAD-T_S35_L006


title: adult pancreas; PB2311-PAAD-T_S36_L006


title: DSP-1012340055901-B-A06


title: DSP-1012340055901-B-A04


title: KI990s95_heart_nuclei


title: adult pancreas; PB2311-PAAD-T_S33_L006


title: DSP-1012340055901-B-A05


title: adult liver; PB2311-Livermeta-T_S52_L008


title: adult liver; PB2311-Livermeta-T_S51_L008


title: DSP-1012340055901-B-A10


title: KI990s93_heart_nuclei


title: DSP-1012340055901-B-A03


title: adult liver; PB2311-Livermeta-T_S52_L004


title: adult liver; PB2311-Livermeta-T_S51_L004


title: KI990s92_heart_nuclei


title: adult liver; PB2311-Livermeta-T_S50_L008


title: DSP-1012340055901-B-A02


title: adult liver; PB2311-Livermeta-T_S50_L004


title: adult pancreas; PB2311-PAAD-T_S46_L003


title: No Template Control

value: No Template Control


title: adult liver; PB2311-Livermeta-T_S49_L008


title: DSP-1012340055901-B-A07


title: KI990s90_heart_nuclei


title: adult pancreas; PB2311-PAAD-T_S34_L006


title: adult liver; PB2311-Livermeta-T_S49_L004


title: adult liver; PB2311-Livermeta-T_S40_L006


title: KI990s89_heart_nuclei


title: adult liver; PB2311-Livermeta-T_S38_L006


title: KI990s88_heart_nuclei


title: adult liver; PB2311-Livermeta-T_S39_L006


title: adult liver; PB2311-Livermeta-T_S37_L006


title: adult pancreas; PB2287-PAAD-T_S1_L001


title: A549, Input

city: jinan

first: Deyu

last: Guo

state: Shandong Province

address: Science and Education Park

department: Shandong Provincial Hospital

institute: Shandong University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19  genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg19
Supplementary files format and content: bigWig

growth_protocol: A549 cells were cultured in F12K (MAC GENE), and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) and were incubated at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

tag: cell type

value: Human lung adenocarcinoma

tag: chip antibody


title: A549, ZBTB16, ChIP

value: ZBTB16 (Active Motif, #39988)


title: KI990s87_heart_nuclei

tag: pool id


title: adult pancreas; PB2286-PAAD-T_S40_L008

tag: tissue


title: adult pancreas; PB2287-PAAD-N_S1_L001


title: Parental,GNB1-KO_Replicate 1

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Sequence reads were trimmed for adapter sequnece/low quality Trimmoatic-0.39, Fastqc was then used for quality control
Trimmed sequence were aligned to reference genome hg38 using hisat2
Read counts extraction was peformed on the aligned reads using featurecounts
Data analysis was then performed using Deseq2
Assembly: hg38
Supplementary files format and content: Featurecounts ---produced counts includes raw counts for eahc sample

source_name: HEK 293

growth_protocol: HEK293 cells were in DMEM  supplemented with 10% fetal bpvine serum and antibiotics in humidified atmosphere  with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
mRNA stranded library preparation performed by Genome Quebec

treatment_protocol: CRISPR-KO of KCTD5, 2 and 17 as well as the CRISPR-KO of GNB1 protein

value: HEK 293

value: Human embryonic kidney

value: WT

tag: treatment


title: Parental,GNB1-KO_Replicate 2


title: adult pancreas; PB2286-PAAD-T_S40_L002

value: pancreas


title: KI990s86_heart_nuclei


title: KI990s85_heart_nuclei


title: adult pancreas; PB2286-PAAD-T_S39_L008


title: KI990s91_heart_nuclei


title: GNB1-KO_Replicate2


title: adult pancreas; PB2286-PAAD-T_S39_L002


title: KI990s84_heart_nuclei


title: adult pancreas; PB2286-PAAD-T_S38_L002


title: KI990s83_heart_nuclei


title: GNB1-KO_Replicate1


title: adult pancreas; PB2286-PAAD-T_S37_L008


title: adult pancreas; PB2286-PAAD-T_S37_L002


title: adult pancreas; PB2286-PAAD-T_S38_L008


title: adult pancreas; PB2286-PAAD-T_S20_L007


title: KI990s82_heart_nuclei


title: adult pancreas; PB2286-PAAD-T_S19_L007


title: KI990s81_heart_nuclei


title: KCTD2-5-KO_Replicate2


title: adult pancreas; PB2286-PAAD-T_S18_L007


title: KI990s80_heart_nuclei


title: KCTD2-5-KO_Replicate1


title: ZFL, Ctrl-input

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

data_processing:
Base-calling was performed by bcl2fastaq for the Novaseq output.
Datas were filtered with trimmomatic software to remove adapter and low quality reads.
The clean reads were then aligned to reference genome (ensembl_GRCz11_109 ) sequences using the bwa program
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Reads distributions (from bigwig) across gene are presented as an average plot (average of reads signals across all genes). The deeptools tool is used for this analysis.
Peaks were annotated by the bedtools.
Assembly: GRCz11_109
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak(except for input sample)

organism: Danio rerio

source_name: ZFL cells

extract_protocol:
Cells were fixed with 1% formaldehyde for the cross-linking of chromatin before lysing with SDS buffer. The chromatin was sonicated using ultrasonic cell disruptor (SCIENTZ)
ChIP-Seq library was prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) as the protocal mentioned.

value: ZFL cells

value: zebrafish liver cell

value: Opti-MEM


title: adult pancreas; PB2286-PAAD-T_S17_L007


title: ZFL, Ctrl-H3K4me3 ChIP

value: H3K4me3 (GeneTex,Cat#GTX128954;)


title: KI990s79_heart_nuclei

value: Adult heart


title: KCTD-5-KO_Replicate1


title: adult pancreas; PB2281-PAAD-T_S36_L008


title: ZFL, BG-input

value: β-Glucan


title: KI990s78_heart_nuclei


title: ZFL, BG-H3K4me3 ChIP


title: adult pancreas; PB2281-PAAD-T_S36_L002


title: KCTD2-5-17-KO_Replicate2


title: Parental_KCTD_Replicate2


title: KI990s77_heart_nuclei


title: KCTD-5-KO_Replicate2


title: KCTD2-5-17-KO_Replicate1


title: KI990s76_heart_nuclei


title: Parental_KCTD_Replicate1


title: prefrontal cortex, IUO 4

city: Omaha

first: Adrian

last: Flores

state: NE

address: 4355 Davenport Street, 14

institute: UNMC

data_processing:
Raw data cleaned using fastq format remove low quality reads using perscrips in house, cutapt
mapping to genome bam format. HISAT2
Transcript assembly. StringTie
Merged all assemblies to creat String Tie merged gtf. StringTie and gftcompare
mRNA expression profiling using StringTie
ballgown
Supplementary files format and content: text file raw counts for each sample
Supplementary files format and content: text file FPKM expression one for whole analysis

source_name: prefrontal cortex

extract_protocol:
RNA Isolation was completed using the Direct-Zol RNA kits (Zymo Research Corp., Irvine, CA, USA) following the manufacturer’s protocol
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature

treatment_protocol: 15 mg/kg of oxycodone via oral gavage prior to pregnancy or after pregnancy until P21.

value: prefrontal cortex

value: in utero oxycodone


title: prefrontal cortex, IUO 3


title: Resilient 11

city: Amsterdam

first: Luuk

middle: Elard

last: de Vries

address: Meibergdreef 47

department: Neuroregeneration

country: Netherlands

institute: Netherlands Institute for Neuroscience

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using cutadapt v 2.10. Reads were aligned to the human genome (GRCh38.p13) using STAR (2.7.10a) with default settings. Feature counting was performed with HTSeq v0.11.0. Samples were sequenced in two batches, with a minimal batch effect between runs. Sequence reads were trimmed to remove possible adapter sequences using cutadapt v 2.10. Reads were aligned to the human genome (GRCh38.p13) using STAR (2.7.10a) with default settings. Feature counting was performed with HTSeq v0.11.0. Samples were sequenced in two batches, with a minimal batch effect between runs.
Assembly: GRCh38.p13
Supplementary files format and content: Raw counts for each sample

source_name: Grey matter SFG

extract_protocol:
RNA was isolated with RNeasy Mini Kit RNA (Qiagen, Valencia, CA, USA) in combination with Trizol (3 ml Trizol per 100 mg tissue; Life Technologies, Grand Island, NY, USA).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process 35 samples (GenomeScan, Leiden, The Netherlands). Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB #E6310). After fragmentation of the depleted rRNA, a cDNA synthesis was performed for ligation with the sequencing adapters and PCR amplification. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. At least 15 Gb, yielding ~30-40 million read pairs, was generated per sample with a quality score of ≥30.

value: Grey matter SFG

tag: condition

value: Resilient

tag: Sex

value: M

tag: batch

value: B


title: adult pancreas; PB2281-PAAD-T_S35_L002


title: KI990s75_heart_nuclei


title: prefrontal cortex, IUO 2


title: KI990s74_heart_nuclei


title: adult pancreas; PB2281-PAAD-T_S34_L008


title: Resilient 10

value: F


title: adult pancreas; PB2281-PAAD-T_S9_L005


title: adult pancreas; PB2281-PAAD-T_S34_L002


title: prefrontal cortex, IUO 1


title: KI990s73_heart_nuclei


title: Resilient 6

value: A


title: adult pancreas; PB2281-PAAD-T_S35_L008


title: Resilient 8


title: adult pancreas; PB2281-PAAD-T_S33_L002


title: Resilient 7


title: prefrontal cortex, PNO 3

value: postnatal oxycodone


title: prefrontal cortex, PNO 4

value: WT


title: adult pancreas; PB2281-PAAD-T_S12_L005

value: pancreas


title: Resilient 5


title: adult pancreas; PB2281-PAAD-T_S11_L005


title: prefrontal cortex, PNO 2


title: Resilient 4


title: KI990s72_heart_nuclei


title: prefrontal cortex, Saline 2

value: Control


title: KI990s70_heart_nuclei


title: prefrontal cortex, Saline 3


title: adult pancreas; PB2281-PAAD-T_S33_L008


title: Resilient 2


title: KI990s71_heart_nuclei


title: KI990s67_heart_nuclei


title: prefrontal cortex, Saline 4


title: prefrontal cortex, PNO 1


title: adult pancreas; PB2281-PAAD-T_S10_L005


title: KI990s68_heart_nuclei


title: adult pancreas; PB2268-PAAD-T_S32_L007


title: adult pancreas; PB2268-PAAD-T_S31_L007


title: Resilient 9


title: Resilient 3


title: KI990s69_heart_nuclei


title: prefrontal cortex, Saline 1


title: adult pancreas; PB2268-PAAD-T_S30_L007


title: Resilient 1


title: Control 12


title: KI990s65_heart_nuclei


title: KI990s64_heart_nuclei


title: adult pancreas; PB2268-PAAD-T_S29_L007


title: KI990s66_heart_nuclei


title: Control 11


title: KI990s63_heart_nuclei


title: adult pancreas; PB2268-PAAD-T_S22_L008


title: Control 9


title: Rat-mouse chimera_muscle

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: 10X Genomics

data_processing:
Demultiplexing, alignment, barcode processing, and gene counting were carried out using 10X CellRanger 7.1.0
For the rat-mouse chimera, rat and mouse feature names were manually disambiguated in R to avoid overlaps
Assembly: mRatBN7.2, GRCm39
Supplementary files format and content: Tab-separated values and matrix files

source_name: Mus musculus, Rattus norvegicus chimera

growth_protocol: Animals were housed in Allentown cages, under standard conditions at room temperature 23°C and a relative humidity of 50-60%, with a 12h light-dark cycle. All animals had ad libitum access to food and water.

extract_protocol:
Animals were euthanized and skeletal muscle tissue was collected from the whole body. 2-3g of tissue was minced and transferred to the falcon tube. PBS was added to the tube and the tissue was centrifuged at 350g for 5min. The pellet was re-suspended in HBSS (14025050, Thermo Fisher Scientific) supplemented with 1.5% BSA (A1391, AppliChem) and 0.2% Collagenase II (17101015, Thermo Fisher Scientific) and incubated at 37°C for 90min. One volume of Low glucose DMEM (31885049, Thermo Fisher Scientific) supplemented with 10% FBS (10270106, Thermo Fisher Scientific) was added to the sample. After vortexing, the sample was passed through a 100mm cell strainer and centrifuged at 350g for 5min. The pellet was re-suspended in 2ml of ACK lysis buffer (A1049201, Thermo Fisher Scientific), kept on ice for 1min, topped up with approximately 10 volumes of cold PBS, vortexed and passed through a 40mm cell strainer. Following 8min centrifugation at 650g, the pellet was re-suspended in cold PBS supplemented with 0.5% BSA (A1391, AppliChem), transferred to the FACS tube and centrifuged at 450g for 5min. The pellet was re-suspended in PBS supplemented with 0.5% BSA (A1391, AppliChem) and Calcein Violet 450 AM Viability Dye (65-0854-39, Thermo Fisher Scientific) was added to the sample at the 1:10 000 dilution. After 3 min incubation, live cells were sorted based on the fluorescence intensity of Calcein Violet 450 AM Viability Dye (65-0854-39, Thermo Fisher Scientific) using FACS. The sorted cells were centrifuged at 650g for 5min and pellet was re-suspended in PBS supplemented with 0.5% BSA (A1391, AppliChem). 20 000 live cells were counted using Neubauer’s chamber and used for library preparation.
Libraries were prepared according to the manufacturer’s Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) protocol using the 10X Genomics platform.

value: skeletal muscle


title: Control 8


title: adult pancreas; PB2268-PAAD-T_S24_L008


title: adult pancreas; PB2268-PAAD-T_S21_L008


title: Control 10


title: KI990s60_heart_nuclei


title: adult pancreas; PB2268-PAAD-T_S23_L008


title: SD rat_muscle

description: 10X Genomics

source_name: Rattus norvegicus


title: Control 7


title: adult pancreas; PB2266-PAAD-T_S28_L007