title: APF_72h

city: Waltham

first: Yerbol

last: Kurmangaliyev

state: MA

address: 415 South Street, MS 029

department: Biology

institute: Brandeis University

description: Library name: 72h

data_processing:
Raw scRNA-seq reads were processed using Cell Ranger (10X Genomics, version: 7.1.0).
Biological replicates were demultiplexed based on a unique genotypes of wild-type DGRP chromosomes using demuxlet (version 2).
The scRNA-seq analysis was performed using Seurat package (5.0.1).
Assembly: Assembly: dm6 (FlyBase 6.29)
Supplementary files format and content: Single-cell raw count matrix (Matrix Market format file, .mtx)
Supplementary files format and content: Single-cell metadata table (tab-separated values file, .tsv).  These are single-cell metadata for the whole dataset before any filtering (1), and the final dataset after filtering with cluster labels (2).

organism: Drosophila melanogaster

source_name: sorted neurons

extract_protocol:
Dissected brains were enzymatically dissociated, and GFP+ cells were isolated using FACS.
Single-cell suspensions were used to generate scRNA-seq libraries using the 10X Genomics Chromium Next GEM Single Cell 3’-kit (v3.1) following the manufacturer’s protocol.

value: sorted neurons

value: control, broad-Z3+, broad-Z4+


title: 20240809_Yosuke7_AJ-CCR5_07

status: Public on Jul 06 2026

type: RNA

city: Cleveland

first: Karen

last: Keslar

state: OH

address: 9500 Euclid Avenue NB30

country: USA

institute: Cleveland Clinic

description: transplanted kidney

hyb_protocol: RNA was hybridized to the mouse Fibrosis panel following manufacturer's instructions

data_processing: Data was processed using the online Rosalind platform

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol: RNA was isolated with Qiagen RNeasy mini kit

tag: tissue

value: kidney

tag: treatment group

value: AJ CCR5 unt d17


title: APF_48h

type: SRA

description: Library name: 48h

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq reads were processed using Cell Ranger (10X Genomics, version: 7.1.0).
Biological replicates were demultiplexed based on a unique genotypes of wild-type DGRP chromosomes using demuxlet (version 2).
The scRNA-seq analysis was performed using Seurat package (5.0.1).
Assembly: Assembly: dm6 (FlyBase 6.29)
Supplementary files format and content: Single-cell raw count matrix (Matrix Market format file, .mtx)
Supplementary files format and content: Single-cell metadata table (tab-separated values file, .tsv)    These are single-cell metadata for the whole dataset before any filtering (1), and the final dataset after filtering with cluster labels (2).

molecule: polyA RNA

tag: cell type

tag: treatment

tag: time


title: Penile tissue, case, MeRIP-seq, rep2

city: beijing

first: Jingmin

last: Zhang

address: Yabao Road

country: China

institute: CMU

description: Library name: MeRIP_case-2

library_source: transcriptomic

data_processing:
Raw sequencing reads were subjected to quality assessment and adaptor trimming.
Clean reads were aligned to the Rattus norvegicus reference genome (Rnor_6.0) using HISAT2.
m6A peaks were identified using exomePeak2.
Differential m6A methylation analysis was performed using exomePeak2 and downstream analyses were conducted using R/Bioconductor packages.
Differential gene expression and differential m6A methylation analyses were performed using standard R/Bioconductor packages.
Assembly: Rnor_6.0
Supplementary files format and content: Microsoft Excel spreadsheet containing transcriptome-wide m6A peak coordinates and peak annotation information.

organism: Rattus norvegicus

source_name: penile tissue

growth_protocol: Timed-pregnant Sprague–Dawley (SD) rats were maintained under specific pathogen-free conditions with a 12 h light/12 h dark cycle and free access to food and water. The day of vaginal plug detection was designated as gestational day 0 (GD0).

extract_protocol:
Total RNA was extracted from fetal penile tissues using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. RNA concentration and purity were determined using a NanoDrop spectrophotometer, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Total RNA was fragmented and subjected to methylated RNA immunoprecipitation using an anti-m6A antibody. Both input RNA and immunoprecipitated RNA were used for library preparation according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

treatment_protocol: Pregnant rats were randomly assigned to either the DEHP-treated group or the corn oil vehicle control group. DEHP was administered by oral gavage once daily from gestational day 12 (GD12) to GD19. Control animals received an equal volume of corn oil. Fetuses were collected by cesarean section on GD19.5.

value: penile tissue


title: TS-2

status: Public on Jul 05 2026

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

description:
Library name: Sample 5
IHNV-infected spleen tissue from rainbow trout, biological replicate 2, used for RNA-seq profiling of mRNA, lncRNA and circRNA expression.

data_processing:
Raw reads from long RNA-seq, small RNA-seq and mRNA-seq libraries were filtered to remove adapter sequences, low-quality reads and reads containing excessive unknown bases; small RNA-seq reads outside the expected length range were also removed.
Clean reads from long RNA-seq and mRNA-seq libraries were aligned to the Oncorhynchus mykiss reference genome using HISAT2, whereas clean small RNA-seq reads were mapped to the reference genome using Bowtie.
mRNA, lncRNA and hepatocyte mRNA expression levels were quantified using StringTie, and raw count and normalized FPKM expression matrices were generated for the corresponding samples.
CircRNAs were identified using find_circ and quantified based on back-splice junction reads. CircRNA raw counts and normalized expression values were generated for all spleen long RNA-seq samples.
Known and novel miRNAs were identified using miRDeep2 and annotated by comparison with public miRNA databases. miRNA expression levels were quantified as raw counts and normalized TPM values for all spleen small RNA-seq samples.
Differential expression analyses were performed between IHNV-infected and uninfected spleen samples and between circUSP47-overexpressing and empty vector control hepatocytes. Differentially expressed circRNAs, miRNAs, lncRNAs and mRNAs were integrated to construct ceRNA networks and to identify commonly regulated mRNAs and immune-related pathways associated with circUSP47-mediated antiviral regulation.
Assembly: Oncorhynchus mykiss reference genome, USDA_OmykA_1.1, GCF_013265735.2.
Supplementary files format and content: Tab-delimited text files containing raw count and normalized expression matrices for mRNAs, lncRNAs, circRNAs and miRNAs across the corresponding samples. mRNA and lncRNA files include raw count and FPKM values; circRNA files include back-splice junction read counts, normalized expression values and circRNA annotation information including circRNA identifier, genomic position, strand and host gene; miRNA files include raw count and TPM values; hepatocyte mRNA-seq files include raw count and FPKM values for mRNAs or genes.

organism: Oncorhynchus mykiss

source_name: spleen

growth_protocol: For the in vivo infection experiment, rainbow trout (Oncorhynchus mykiss) were maintained under standard aquaculture conditions before IHNV challenge. Fish were acclimated prior to the experiment, and water quality parameters, including temperature and dissolved oxygen, were monitored throughout the experiment. For the in vitro overexpression experiment, rainbow trout hepatocytes were cultured under standard conditions in DMEM supplemented with 10% fetal bovine serum at 18°C.

extract_protocol:
Total RNA was extracted from rainbow trout spleen tissues or hepatocytes using Trizol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed using NanoDrop, and RNA integrity was evaluated by agarose gel electrophoresis. RNA samples meeting quality requirements were used for long RNA-seq, small RNA-seq or mRNA-seq library construction.
For spleen long RNA-seq, ribosomal RNA was removed from total RNA, and strand-specific long RNA-seq libraries were constructed for mRNA, lncRNA and circRNA expression profiling. These libraries were sequenced on an Illumina HiSeq 4000 platform using paired-end 150 bp reads. For spleen small RNA-seq, small RNAs of approximately 18-30 nt were enriched, ligated to adapters, reverse transcribed and PCR amplified; libraries were sequenced on an Illumina HiSeq Xten platform using single-end 50 bp reads. For hepatocyte mRNA-seq, messenger RNA was enriched from total RNA using poly(A) selection, fragmented, reverse transcribed and amplified to generate libraries, which were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.

treatment_protocol: For the IHNV infection experiment, rainbow trout in the infection group were challenged with infectious hematopoietic necrosis virus (IHNV), whereas fish in the control group were maintained without IHNV infection. Spleen tissues were collected from three biological replicates per group at 48 h post infection, immediately frozen in liquid nitrogen, and stored at -80°C until RNA extraction. For the circUSP47 overexpression experiment, rainbow trout hepatocytes were transfected with a circUSP47 overexpression vector or empty vector control using INVI DNA RNA transfection reagent, and cells were collected at 48 h after transfection for RNA extraction.

value: spleen

tag: genotype

value: wild-type

value: IHNV infection

tag: batch

value: batch 1


title: TS-3

description:
Library name: Sample 6
IHNV-infected spleen tissue from rainbow trout, biological replicate 3, used for RNA-seq profiling of mRNA, lncRNA and circRNA expression.


title: CS-3

description:
Library name: Sample 3
Uninfected control spleen tissue from rainbow trout, biological replicate 3, used for RNA-seq profiling of mRNA, lncRNA and circRNA expression.

value: uninfected control


title: CS-1

description:
Library name: Sample 1
Uninfected control spleen tissue from rainbow trout, biological replicate 1, used for RNA-seq profiling of mRNA, lncRNA and circRNA expression.


title: TS-1

description:
Library name: Sample 4
IHNV-infected spleen tissue from rainbow trout, biological replicate 1, used for RNA-seq profiling of mRNA, lncRNA and circRNA expression.


title: CS-2

description:
Library name: Sample 2
Uninfected control spleen tissue from rainbow trout, biological replicate 2, used for RNA-seq profiling of mRNA, lncRNA and circRNA expression.


title: Gata3High_noDox_rep1

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

institute: University of Texas at Austin

description:
Library name: Gata3High_noDox_rep1
Gata3-High mESCs without dox induction were harvested for Gata3 RNA seq.

data_processing:
All sequencing reads were trimmed using Trim Galore v0.6.10 and aligned to the mouse reference genome (mm10) with STAR (version 2.7.3a).
Alignments were then filtered using Samtools (version 1.10) with MAPQ score >= 10.
Raw counts were quantified using featureCounts from the Subread package (version v1.5.0-p1).
Assembly: mm10
Supplementary files format and content: Raw counts quantified using featureCounts

source_name: Embryo

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen) (74136). The mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L).
The RNAs-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7770L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol. RNA-seq was conducted as paired-end sequencing on the NovaSeq 6000 (Illumina).

value: Embryo

tag: cell line

value: Mouse embryonic stem cell

value: Gata3-overexpressed mESC (Gata3-High) with no induction

value: Batch 1


title: DE+PFD+RIC3

city: Delhi

first: Aastha

last: Mishra

state: Delhi

address: Mall Road, Delhi-110 007

department: Genomics and genome biology

country: India

institute: Council Of Scientific And Industrial Research–Institute Of Genomics And Integrative Biology (CSIR–IGIB)

description: Library name: PoCDPF3

data_processing:
Raw sequenced bases in BCL format were demultiplexed to FASTQ, and read quality was assessed using FastQC v0.12.1.
Low-quality bases and adapters were trimmed using the fastp tool v0.23.4.
Trimmed reads’ quality was assessed, and high-quality reads were aligned to the latest version of the mouse reference genome, GRCm39, using the STAR aligner v 2.7.11b.
After alignment, read summarization was performed using the featureCounts tool with the mouse GENCODE VM38 GTF file
The read count matrix was imported into R v4.4.1 and DESeq2 package was used for DEG analysis.
Assembly: GRCm39
Supplementary files format and content: .csv text file containing raw counts for each sample.

source_name: Lung

extract_protocol:
Total RNA was extracted from the lung tissue stored in RNAlater using the TRIzol reagent method. 1000ng of total RNA was used for the construction of libraries.
Oligo(dT) beads were used for capturing the polyadenylated mRNA and rRNA, and other non-mRNA was washed away. The mRNA was fragmented and reverse-transcribed to synthesise first- and second-strand cDNA. The adapters were ligated to the ends of the synthesized strands, and strand-specific PCR amplification was performed. The quality (size distribution and concentration) of amplified libraries was checked before sequencing.

treatment_protocol: C57Bl/6 mice were exposed to diesel exhaust (DE) fumes for 30 minutes per day, 5 days per week, for approximately 8 weeks according to the established protocol in a specialized chamber connected to a DE-fumes-producing engine and an attached HEPA filter to induce pulmonary fibrosis (PF) pathological features. The optimized remote ischemic conditioning (RIC) protocol was provided on the left leg of mice as 3 cycles of 5 min ischemia followed by 5 min reperfusion, 3 days per week for 4 weeks in two ways: before PF induction as remote ischemic preconditioning (RIPreC) and during PF induction as remote ischemic perconditioning (RIPerC) in the respective groups. Pirfenidone (PFD) was dissolved in 0.5% carboxymethylcellulose and administered orally at 300 mg/kg/day for 6 days per week as a proven standard of care for the study.

value: Lung

tag: Sex

value: male

tag: age (weeks)

value: Exposure to diesel exhaust (DE) fumes + Pirfenidone (PFD) + Remote ischemic perconditioning (RIPerC)


title: DE+PFD+RIC2

description: Library name: PoCDPF2


title: RIC+DE+PFD3

description: Library name: PreCDPF3

value: Remote ischemic preconditioning (RIPreC) + Exposure to diesel exhaust (DE) fumes  + Pirfenidone (PFD)


title: DE+PFD+RIC1

description: Library name: PoCDPF1


title: RIC+DE+PFD1

description: Library name: PreCDPF1


title: RIC+DE+PFD2

description: Library name: PreCDPF2


title: DE+RIC3

description: Library name: PoCD3

value: Exposure to diesel exhaust (DE) fumes + Remote ischemic perconditioning (RIPerC)


title: Muscle_Baseline [20171208-0005]

type: genomic

city: Robina

first: Paul

last: Dunn

state: QLD

address: 14 University Dr

country: Australia

institute: Bond University

description: bisulfite conveted DNAextracted fromMuscle_Baseline

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human infium methylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
Channel intensities in IDAT files were analysed using MINIFI 1.28.0. Methylation distribution range was assessed using a beta density plot to check for probe type bias. Filtering was performed based on P-value detection (>0.01), beadcount (<3 in at least  5% samples), non-CpG probes, cross-reactive probes, and probes containing SNPs.
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: vastus lateralis muscle

label_protocol: Standard Illumina protocol

extract_protocol: DNA was bound to the AllPrep DNA Mini spin column (Qiagen) and oncolumn digestion performed with Proteinase K. 250ng of each DNA sample underwent bisulfite conversion using the EZ DNA  Methylation Kit (Zymo Research, Irine, CA, USA)

value: vastus lateralis muscle

value: Day 0


title: DE+RIC2

description: Library name: PoCD2


title: RIC+DE3

description: Library name: PreCD3

value: Remote ischemic preconditioning (RIPreC) + Exposure to diesel exhaust (DE) fumes


title: DE+RIC1

description: Library name: PoCD1


title: RIC+DE2

description: Library name: PreCD2


title: RIC+DE1

description: Library name: PreCD1


title: DE+PFD3

description: Library name: DPF3

value: Exposure to diesel exhaust (DE) fumes + Pirfenidone (PFD)


title: DE3

description: Library name: DE3

value: Exposure to diesel exhaust (DE) fumes


title: DE2

description: Library name: DE2


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 21

city: Guangzhou

first: Shouheng

last: Lin

address: 190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health

description: Library name: lep-21

data_processing:
The raw sequencing reads were filtered with SOAPnuke to eliminate reads containing adaptors, those with over 5% unknown bases, and low-quality reads. Subsequently, clean reads were obtained and saved in FASTQ format. Bowtie2 was utilized to align the clean reads with the reference gene set.
Assembly: hg38
Supplementary files format and content: CSV files include FPKM values for each sample

source_name: lung

extract_protocol:
RNA was extracted using TRIzol Reagent. RNA integrity was assessed using a Bioanalyzer 2100.
Genomic DNA was eliminated through two rounds of digestion using amplification-grade DNase 1. The processed RNA was fragmented and subjected to reverse transcription using random primers to generate cDNA, which was utilized for library preparation. Library quality was assessed using the Bioanalyzer 2100.

value: lung


title: DE1

description: Library name: DE1


title: DE+PFD1

description: Library name: DPF1


title: DE+PFD2

description: Library name: DPF2


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 22

description: Library name: lep-22


title: RIC3

description: Library name: R3

value: Remote ischemic conditioning (RIC)


title: RIC2

description: Library name: R2


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 20

description: Library name: lep-20


title: RIC1

description: Library name: R1


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 19

description: Library name: lep-19


title: Control2

description: Library name: C2


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 17

description: Library name: lep-17


title: Control3

description: Library name: C3


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 18

description: Library name: lep-18


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 16

description: Library name: lep-16


title: Control1

description: Library name: C1


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 15

description: Library name: lep-15


title: p4016, CSP

city: Baltimore

first: Nevil

middle: J

last: Singh

state: Maryland

address: 685 W Baltimore St., HSF1 Rm 380

department: Department of Microbiology & Immunology

institute: University of Maryland Baltimore

description: Library name: p4016_CSP

data_processing:
alignment and quantification; cellranger 7.1.0 - count (feature_reference1.csv)
demultiplexing the hashtags with Seurat HTOdemux function (feature_reference2.csv)
Assembly: mm10
Supplementary files format and content: CellRanger output files: H5 files

source_name: Spleen

extract_protocol:
Splenocytes were extracted from p40-/- mice four days post inoculation.
10x GENOMICS; Chromium Next GEM Single Cell 5'HT reagent kits v2 (dual index)

value: Spleen

value: Splenocytes

value: mixed (immune cells)

value: mixed sample (control, test plasmids)


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 14

description: Library name: lep-14


title: p4015, CSP

description: Library name: p4015_CSP


title: p4013, CSP

description: Library name: p4013_CSP


title: p4012, CSP

description: Library name: p4012_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 13

description: Library name: lep-13


title: p4014, CSP

description: Library name: p4014_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 11

description: Library name: lep-11


title: p4011, CSP

description: Library name: p4011_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 12

description: Library name: lep-12


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 10

description: Library name: lep-10


title: p4010, CSP

description: Library name: p4010_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 9

description: Library name: lep-9


title: p4009, CSP

description: Library name: p4009_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 8

description: Library name: lep-8


title: p4008, CSP

description: Library name: p4008_CSP


title: p4007, CSP

description: Library name: p4007_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 7

description: Library name: lep-7


title: p4006, CSP

description: Library name: p4006_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 6

description: Library name: lep-6


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 5

description: Library name: lep-5


title: p4004, CSP

description: Library name: p4004_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 4

description: Library name: lep-4


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 3

description: Library name: lep-3


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 2

description: Library name: lep-2


title: p4002, CSP

description: Library name: p4002_CSP


title: tumor tissues dervied from leptomeningeal-metastatic lung cancer patient 1

description: Library name: lep-1


title: p4005, CSP

description: Library name: p4005_CSP


title: p4001, CSP

description: Library name: p4001_CSP


title: p4003, CSP

description: Library name: p4003_CSP


title: p4016, GEX

description: Library name: p4016_GEX


title: PC9, PA-untreated, rep2

description: Library name: PA-untreated-2


title: p4015, GEX

description: Library name: p4015_GEX


title: PC9, PA-untreated, rep1

description: Library name: PA-untreated-1


title: p4014, GEX

description: Library name: p4014_GEX


title: PC9, PA-untreated, rep3

description: Library name: PA-untreated-3


title: PC9, PA-treated, rep3

description: Library name: PA-treated-3


title: PC9, PA-treated, rep2

description: Library name: PA-treated-2


title: PC9, PA-treated, rep1

description: Library name: PA-treated-1


title: A549-sgCtl, rep2

description: Library name: A549-sgCtl-2


title: p4007, GEX

description: Library name: p4007_GEX


title: OC + Asiatic acid-2

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: Library name: C67_2

data_processing:
Initial evaluation of the quality of raw RNA-seq fastq file was conducted utilizing FASTQC (v0.12.1).
The BBduk module within the bbmap toolkit (v39.80) was conducted with specific parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, and minlength=20 to eliminate adapter sequences and low-quality reads.
The cleaned reads were mapped to the mouse reference genome (build GRCm39, Ensembl release 115) through the STAR aligner (v2.7.10b)
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) along with the gene structure file (GRCm39.115.gtf).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: Ovary

growth_protocol: Eight- and 38-week-old BALB/c female mice were purchased from the Central Lab. Animal Inc.(Seoul, Korea). All mice were maintained on an ad libitum diet in a specific pathogen-free room under a 12-hour light-dark cycle. All animal handling and experimental procedures were approved by the Korea Institute of Oriental Medicine Institutional Animal Care and Use Committee (approval number 25-057).

extract_protocol:
After four weeks of compound administration, a post-ovulatory state was induced by intraperitoneal injection of 5 IU PMSG followed 48 h later by 5 IU hCG. Ovaries were collected 16-18h after hCG administration, weighed, and immediately preserved in liquid nitrogen until RNA extraction.  Each ovary sample was immersed in 1 mL  TRIzol reagent (Invitrogen) and homogenized using a disposable grinder (Biomasher II; 890863; LMS Co., Tokyo, Japan).
Total RNA was isolated using Trizol reagent (Invitrogen). The quality of purity and integrity of the extracted RNA samples were analyzed using a NanoDrop ND-2000 Spectrophotometer (Thermo Inc., DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. The compound administration experiment was conducted in two independent animal experimental batches. Each batch included 14 compound-treated groups and corresponding young control (YC) and old control (OC) groups. Mice in both batches followed the same treatment schedule, post-ovulatory induction procedure, and ovary collection protocol. RNA extraction, library preparation, and sequencing were performed together for all samples. Batch assignment is indicated in the sample metadata.

treatment_protocol: Mice were randomly divided into groups of n=3 each. Aged mice (38 weeks old) were orally administered either distilled water containing 0.5% Dimethyl sulfoxide (DMSO; D2650; Sigma-Aldrich, St. Louis, MO, USA) or each of the 28 single compounds at a dose of 5 mg/kg, five times a week for four weeks.

value: Ovary

value: Wildtype

value: Asiatic Acid

value: Batch 2

tag: strain

value: BALB/c


title: p4010, GEX

description: Library name: p4010_GEX


title: p4009, GEX

description: Library name: p4009_GEX


title: A549-sgFUS, rep2

description: Library name: A549-sgFUS-2


title: A549-sgCtl, rep3

description: Library name: A549-sgCtl-3


title: p4008, GEX

description: Library name: p4008_GEX


title: skeletal muscle cells MUT, at 7 days after induced damage. biological replicate 2

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

description:
Library name: 93
10x Genomics

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files with the 'mkfastq' command in Cell Ranger (v6.1.2) with default setting.
The counts were generated using 10X Genomic Cellranger analysis pipelines (CellRanger v6.1.2), with the 'count' command, using the parameter --expect-cells 10000.
Assembly: mm10 (refdata-cellranger-mm10-2020-A)
Supplementary files format and content: barcode.tsv.gz: Barcode sequences correspond to column indices, single column with barcode Ids. Content of the Cellranger output folder "filtered_feature_bc_matrix".
Supplementary files format and content: features.tsv.gz: features correspond to row indices. Tab separeted file: first column is feature ID, second clumn feature name, third column feature type. Content of the Cellranger output folder "filtered_feature_bc_matrix".
Supplementary files format and content: matrix.mtx.gz: counts matrix. Content of the Cellranger output folder "filtered_feature_bc_matrix".

source_name: skeletal muscle

extract_protocol:
Freshly isolated quadriceps were minced into small pieces and enzymatically dissociated with 1.5mg/mL Dispase (Gibco, 17105-041) and 0.12% (w/v) Collagenase type I (Sigma-Aldrich, C0130) in two cycles of 30min at 37°C under constant 240 rpm agitation. The suspension was then passed through a 16G needle, followed by a 26G needle and filtered through a 40μm sterile strainer. Then cold CMF was added to inactivate enzymes and red blood cells lysed. To remove cell debris from the suspensions, Ficoll separation was performed. Cells were resuspended in 7 mL of pre-warmed DMEM High Glucose (Gibco, 41965-039) supplemented with 10% FBS (Gibco, 10270-106), in a 15 mL falcon, and 3.5 mL of Ficoll slowly layered on top. Samples were spined at 300g for 30min with no brake nor acceleration and the cell layer formed aspirated to another falcon and washed with cell medium.
Chromium Single Cell 3′ Reagent Kit v3.1 (10xGenomics)

value: skeletal muscle

tag: timepoint

value: 7 days

tag: genetic modification

value: FOP


title: p4013, GEX

description: Library name: p4013_GEX


title: p4006, GEX

description: Library name: p4006_GEX


title: A549-sgFUS, rep3

description: Library name: A549-sgFUS-3


title: p4012, GEX

description: Library name: p4012_GEX


title: p4011, GEX

description: Library name: p4011_GEX


title: A549-sgFUS, rep1

description: Library name: A549-sgFUS-1


title: A549-sgCtl, rep1

description: Library name: A549-sgCtl-1


title: p4004, GEX

description: Library name: p4004_GEX


title: p4002, GEX

description: Library name: p4002_GEX


title: PC9-sgFUS, rep2

description: Library name: PC9-sgFUS-2


title: PC9-sgFUS, rep3

description: Library name: PC9-sgFUS-3


title: fiomut ,[U6+]/fiomut ;U6mut/U6+,larvae-1

city: hengyang

first: Juan

last: Gong

address: Hongxiang street

institute: university of south china

data_processing:
IGV
Sequence reads were trimmed for adaptor sequence/low-quality sequence using IGV
Trimmed sequence reads were mapped to drosophila flybase using IGV
Read count extractin and normalization were performed using IGV
Assembly: FBgn0033994
Supplementary files format and content: counts, FPKM

source_name: larvae

growth_protocol: Drosophila melanogaster grow at room temperature

extract_protocol: RNA extraction method

treatment_protocol: The larvae were put into trizol and quickly frozen with liquid nitrogen

value: larvae

value: fiomut ,[U6+]/fiomut ;U6mut/U6+


title: p4003, GEX

description: Library name: p4003_GEX


title: PC9-sgFUS, rep1

description: Library name: PC9-sgFUS-1


title: fiomut ,[U6+]/fiomut ;U6mut/U6+,larvae-2


title: WT Liver Pair-fed Rep 20

city: CHANGCHUN

first: Feiyu

state: Jilin

address: renmin street

institute: the first hospital of jilin university

description:
Library name: CW20
Control WT Rep 2

data_processing:
The clean reads were mapped to the reference genome (Mus musculus) using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing read counts and/or FPKM values for each gene.

source_name: Liver

growth_protocol: 8- to 10-week-old male C57BL/6 mice and Aldh2-/- mice (Stock No: NM-KO-220225, Shanghai Model Organisms Center) were utilized. Mice were maintained in a specific pathogen-free (SPF) environment with controlled temperature and light cycles.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Mice were subjected to a liver fibrosis model. Aldh2-/- and WT mice were fed either an ethanol diet (Ethanol, Macklin) or a pair-fed control diet. Concurrently, mice received intraperitoneal injections of CCl4 (Macklin) dissolved in olive oil twice weekly for 8 weeks. Mice were euthanized 24 hours after the last CCl4 injection.

value: Liver

value: male

value: Wild type

value: Pair-fed control diet + CCl4


title: PC9-sgCtl, rep3

description: Library name: PC9-sgCtl-3


title: fiomut/fiomut ;U6mut/U6+,larvae-1

value: fiomut/fiomut ;U6mut/U6+


title: WT Liver Pair-fed Rep 18

description:
Library name: CW18
Control WT Rep 1


title: p4005, GEX

description: Library name: p4005_GEX

value: Spleen

value: Splenocytes

value: mixed (immune cells)


title: fiomut/fiomut ;U6mut/U6+,larvae-2


title: p4001, GEX

description: Library name: p4001_GEX

value: mixed sample (control, test plasmids)


title: Aldh2-/- Liver Pair-fed Rep 9

description:
Library name: CK9
Control KO Rep 3


title: Aldh2-/- Liver Pair-fed Rep 2

description:
Library name: CK2
Control KO Rep 2


title: fiomut/cyo,larvae-1

value: fiomut/cyo


title: WT Liver Ethanol+CCl4 Rep 12

description:
Library name: EW12
Ethanol WT Rep 5

value: Ethanol diet + CCl4


title: PC9-sgCtl, rep2

description: Library name: PC9-sgCtl-2


title: Aldh2-/- Liver Pair-fed Rep 1

description:
Library name: CK1
Control KO Rep 1


title: WT Liver Pair-fed Rep 19

description:
Library name: CW19
Control WT Rep 3


title: WT Liver Ethanol+CCl4 Rep 11

description:
Library name: EW11
Ethanol WT Rep 4


title: MDA-MB-231 Cytokinesis failure-induced WGD TagSeq replicate 3

first: Amy

last: Brock

state: Texas

address: 107 W Dean Keaton St.

department: Biomedical Engineering

description:
Library name: MDA231_CF_TagSeq_rep3
Column name in processed files: CF_231_c

data_processing:
Raw FASTQ files from multiple sequencer lanes were combined (if applicable), and deduplication along with tag, adapter, and poly-A tail trimming was performed by the Bioinformatics Consulting Group at the University of Texas at Austin, Center for Biomedical Research Support (TagSeq deduplication; RRID:SCR_022688).
Deduplicated and trimmed FASTQ files were aligned to the human reference genome (GRCh38) and quantified using the nf-core/rnaseq Nextflow pipeline (v3.25.0) with STAR for alignment and Salmon for transcript-level quantification.
Assembly: GRCh38 (hg38)
Supplementary files format and content: salmon.merged.gene_counts.tsv: tab-delimited gene-level count matrix; rows = genes (Ensembl gene_id and gene_name), columns = samples (one per TagSeq replicate). Raw (non-normalized) counts from Salmon/nf-core rnaseq pipeline.
Supplementary files format and content: salmon.merged.gene_tpm.tsv: tab-delimited gene-level expression matrix; rows = genes (Ensembl gene_id and gene_name), columns = samples (one per TagSeq replicate). TPM (Transcripts Per Million) values from Salmon/nf-core rnaseq pipeline; provided for cross-sample comparison and browsing purposes.

growth_protocol: HCC1806 (ATCC CRL-2335) and MDA-MB-231 (ATCC HTB-26) cells were maintained in standard culture conditions. For TAGseq, cells were seeded at 200,000 cells/well in 6-well plates and grown for 48 hours prior to RNA isolation.

extract_protocol:
Total RNA was isolated using the Zymo Quick-RNA Mini Prep kit (Thermo Fisher, 50444597) according to manufacturer's instructions. RNA concentration was quantified using the Qubit RNA Broad Range (BR) Assay Kit (Thermo Fisher, Q10211). Samples were normalized prior to library preparation.
Normalized RNA was submitted to the Genome Sequencing and Analysis Facility (GSAF) at The University of Texas at Austin for high-coverage TAGseq library preparation (targeting 7-10 million reads per sample). Libraries were constructed by the core and sequenced on the Illumina NextSeq 2000 platform (NextSeq P4 flow cell, single-read 100 bp).

treatment_protocol: Cells underwent WGD by one of 3 mechanisms (cell fusion, mitotic slippage, or cytokinesis failure), were isolated via FACS, and allowed to expand, parental aneuploid populations cells were maintained as control. For TAGseq, no additional treatment was applied after passaging into 6-well plate.

value: Cytokinesis failure-induced WGD


title: A549-Lep, rep3

description: Library name: A549-Lep-3


title: PC9-sgCtl, rep1

description: Library name: PC9-sgCtl-1


title: WT Liver Ethanol+CCl4 Rep 6

description:
Library name: EW6
Ethanol WT Rep 2


title: WT Liver Ethanol+CCl4 Rep 5

description:
Library name: EW5
Ethanol WT Rep 1


title: MDA-MB-231 Cytokinesis failure-induced WGD TagSeq replicate 2

description:
Library name: MDA231_CF_TagSeq_rep2
Column name in processed files: CF_231_b


title: A549-Lep, rep2

description: Library name: A549-Lep-2


title: WT Liver Ethanol+CCl4 Rep 7

description:
Library name: EW7
Ethanol WT Rep 3


title: Aldh2-/- Liver Ethanol+CCl4 Rep 96

description:
Library name: EK96
Ethanol KO Rep 4


title: MDA-MB-231 Cytokinesis failure-induced WGD TagSeq replicate 1

description:
Library name: MDA231_CF_TagSeq_rep1
Column name in processed files: CF_231_a


title: Aldh2-/- Liver Ethanol+CCl4 Rep 90

description:
Library name: EK90
Ethanol KO Rep 3


title: fiomut/cyo,larvae-2


title: A549-Lep, rep1

description: Library name: A549-Lep-1


title: Aldh2-/- Liver Ethanol+CCl4 Rep 89

description:
Library name: EK89
Ethanol KO Rep 2


title: Aldh2-/- Liver Ethanol+CCl4 Rep 86

description:
Library name: EK86
Ethanol KO Rep 1


title: MDA-MB-231 Mitotic slippage-induced WGD TagSeq replicate 3

description:
Library name: MDA231_MS_TagSeq_rep3
Column name in processed files: MS_231_c

value: Mitotic slippage-induced WGD


title: D2_K4

city: wuhan

first: Jiayu

last: Song

address: wuhan

institute: WUHAN University

description: Library name: samples24

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated. All the downstream analyses werebasedon the clean data with high quality.
Assembly: GRCm38
Supplementary files format and content: text files include raw read count

source_name: spleen and lymph nodes

extract_protocol:
Total RNA was extracted from Th1 cells of indicated coditions cultured for 1 day, 2 days and 4 days using the Direct-zol RNA Microprep Kit (ZYMO Research,R2061).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spleen and lymph nodes

value: RASA3 KO


title: A549-Par, rep3

description: Library name: A549-Par-3


title: MDA-MB-231 Mitotic slippage-induced WGD TagSeq replicate 2

description:
Library name: MDA231_MS_TagSeq_rep2
Column name in processed files: MS_231_b


title: D2_K2

description: Library name: samples22


title: D2_K1

description: Library name: samples21


title: A549-Par, rep2

description: Library name: A549-Par-2


title: D2_K3

description: Library name: samples23


title: PC9-Lep, rep3

description: Library name: PC9-Lep-3


title: D2_W4

description: Library name: samples20

value: wild type


title: D2_W3

description: Library name: samples19


title: A549-Par, rep1

description: Library name: A549-Par-1


title: MDA-MB-231 Fusion-derived WGD TagSeq replicate 3

description:
Library name: MDA231_Fusion_TagSeq_rep3
Column name in processed files: F_231_c

value: Fusion-derived WGD


title: MDA-MB-231 Mitotic slippage-induced WGD TagSeq replicate 1

description:
Library name: MDA231_MS_TagSeq_rep1
Column name in processed files: MS_231_a


title: D2_W2

description: Library name: samples18


title: D2_W1

description: Library name: samples17


title: MDA-MB-231 Fusion-derived WGD TagSeq replicate 2

description:
Library name: MDA231_Fusion_TagSeq_rep2
Column name in processed files: F_231_b


title: PC9-Lep, rep2

description: Library name: PC9-Lep-2


title: D4_K4

description: Library name: samples16


title: MDA-MB-231 Fusion-derived WGD TagSeq replicate 1

description:
Library name: MDA231_Fusion_TagSeq_rep1
Column name in processed files: F_231_a


title: D4_K3

description: Library name: samples15


title: PC9-Lep, rep1

description: Library name: PC9-Lep-1


title: D4_K2

description: Library name: samples14


title: MDA-MB-231 Control TagSeq replicate 3

description:
Library name: MDA231_Control_TagSeq_rep3
Column name in processed files: C_231_c

value: Control (parental aneuploid)


title: PC9-Par, rep3

description: Library name: PC9-Par-3


title: D4_K1

description: Library name: samples13


title: D4_W3

description: Library name: samples11


title: PC9-Par, rep2

description: Library name: PC9-Par-2


title: MDA-MB-231 Control TagSeq replicate 2

description:
Library name: MDA231_Control_TagSeq_rep2
Column name in processed files: C_231_b


title: D4_W2

description: Library name: samples10


title: D4_W4

description: Library name: samples12


title: MDA-MB-231 Control TagSeq replicate 1

description:
Library name: MDA231_Control_TagSeq_rep1
Column name in processed files: C_231_a


title: D4_W1

description: Library name: samples9


title: HCC1806 Cytokinesis failure-induced WGD TagSeq replicate 3

description:
Library name: HCC1806_CF_TagSeq_rep3
Column name in processed files: CF_1806_c


title: PC9-Par, rep1

description: Library name: PC9-Par-1


title: D1_K4

description: Library name: samples8


title: PA4773-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4773.xlsx

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas aeruginosa (NC_002516.2)
Supplementary files format and content: xlsx files were generated from RNA-seq, containing the differential expressional genes.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: RNA-seq(LB)

extract_protocol:
The Pseudomonas aeruginosa PAO1 wild type strain and the HP mutants were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

treatment_protocol: grow until mid-log phase

value: Pseudomonas aeruginosa PAO1

value: PA4773 mutant

value: grow until mid-log phase in LB


title: D1_K3

description: Library name: samples7


title: HCC1806 Cytokinesis failure-induced WGD TagSeq replicate 2

description:
Library name: HCC1806_CF_TagSeq_rep2
Column name in processed files: CF_1806_b


title: D1_K2

description: Library name: samples6


title: Microbiota of stool from O9OG patient

city: Antalya

first: Ceren

last: Hangul

address: Dumlupınar street

country: Turkey

institute: Akdeniz University

description:
71s rRNA V2-V9 sequencing of human stool
O9OG

library_source: genomic

data_processing:
Demultiplexing: From raw to demultiplexed fastq files please contact Ceren Hangul (cerenhangul@hotmail.com)
Quality check: qiime demux summarize --i-data trim-seqs.qza --o-visualization quality --p-n 100000
Quality trimming of first raws sequences and ASV table creation: qiime dada2 denoise-single --i-demultiplexed-seqs  single_end_demux.qza --p-trunc-len 250 --o-table Featuredada.qza --o-representative-sequences data-trunc.qza --o-denoising-stats denoising-stats.qza --p-n-threads 1 --verbose
Quality trimming of second raws sequences and ASV table creation: qiime dada2 denoise-single --i-demultiplexed-seqs  single-end-demux-repeat.qza --p-trunc-len 250 --o-table Featuredada1.qza --o-representative-sequences data-trunc1.qza --o-denoising-stats denoising-stats1.qza --p-n-threads 1 --verbose
Merge of sequences in output of previous quality trimming: qiime feature-table merge-seqs --i-data data-trunc.qza --i-data data-trunc1.qza --o-merged-data rep-seqs.qza
Discard sequences from host (Homo Sapiens): bowtie2 -x GRCh38_noalt_as/GRCh38_noalt_as -U dna-sequences.fasta --un filtered.fasta -S seq_human_SAM.txt  -f -p 5
Taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads import_filtered.qza --o-classification taxonomy.qza --p-n-jobs 8 --p-reads-per-batch 1000 --verbose
Further analyses: R phyloseq package
Assembly: SILVA 138-99 nb classifier
Supplementary files format and content: feature-table1.csv: CSV text file containing the abundance table of first raw sequences
Supplementary files format and content: feature-table2.csv: CSV text file containing the abundance table of second raw sequences
Supplementary files format and content: taxonomy.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Supplementary files format and content: filtered.fasta: fasta file containing the reference sequences used for taxonomy classification

source_name: Stool

growth_protocol: Samples were sored at -80 °C before the DNA extraction. After extraction, DNA were frozen at -20 °C until sequencing.

extract_protocol:
Genomic DNA from stool was extracted using the QIAamp Fast DNA Stool Mini Kit (Qiagen, Hilden, Germany)
Amplicon libraries of the V2-V9 16S rRNA hypervariable regions were prepared. The size and concentration of the final sequencing library, formed by pooling the barcoded amplicons in equimolar concentrations, were determined using the Bioanalyzer High Sensitivity Chip (Agilent Technologies, Santa Clara, CA, USA).
Amplicons of the variable V2-V9 region of the bacterial 16S rRNA gene were sequenced in single

value: Stool

value: Subject affected by FSHD


title: D1_K1

description: Library name: samples5


title: Microbiota of stool from O8VB patient

description:
70s rRNA V2-V9 sequencing of human stool
O8VB


title: D1_W4

description: Library name: samples4


title: Microbiota of stool from O6NG patient

description:
68s rRNA V2-V9 sequencing of human stool
O6NG


title: PA4793-96-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4793-96.xlsx

value: PA4793-96 mutant


title: HCC1806 Cytokinesis failure-induced WGD TagSeq replicate 1

description:
Library name: HCC1806_CF_TagSeq_rep1
Column name in processed files: CF_1806_a


title: D1_W3

description: Library name: samples3


title: D1_W2

description: Library name: samples2


title: CS4tdpos.12w

city: Basel

first: Atul

last: Sethi

address: Grenzacherstrasse 124

country: Switzerland

institute: Hoffmann-La Roche

description: Library name: CS4tdpos.12w

data_processing:
For the bulk RNA seq data analysis, BCL files were converted to fastq files using "BCL Convert". After this, data were aligned against GRCm38/39 (mm10) mouse reference genome using STAR aligner (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/) and reads assigned to features with featureCounts (subread-2.0.2; https://bioconductor.org/packages/release/bioc/html/Rsubread.html).
Differential gene expression on the macrophage bulk RNA seq data was performed using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Pathway and transcription factor activity analysis was performed with the R package decoupleR using the list of differentially expressed genes ranked by Wald statistic from DESeq output. Pathway enrichment analysis was performed with the function enrichr from R package Enrichr using genes with log fold change > 1 (or <-1), and BH-adjusted p-value < 0.05.
Assembly: GRCm38/39 (mm10)
Supplementary files format and content: txt file

growth_protocol: Throughout the studies, mice were kept under specific-pathogen-free conditions with continuous health monitoring.

extract_protocol:
Mice were euthanized by intraperitoneal injection of pentobarbital sodium (150 mg/kg; diluted 1:2 with 0.9% NaCl physiological) and analyzed ~16 h after the last CS exposure. After perfusion of the heart with PBS, for whole lung analysis, lungs were directly collected into 1 mL PBS (2% FBS). Lungs were processed using the mouse lung dissociation kit (#130-095-927, Miltenyi Biotec) according to the manufacturer's instructions (program 37C_m_LDK_1). After termination of the program, C tubes (#130-093-237, Miltenyi Biotec) were detached from the gentleMACS dissociator and centrifuged shortly at 1500 rpm. Pellets were resuspended in the same supernatant and filtered through a 70 μm cell strainer (#CLS431751, Sigma-Aldrich) into a 50 mL tube. After centrifugation at 1500 rpm for 2 min, the supernatant was discarded and the pellets were resuspended with 1 mL ACK lysis buffer (#A1049201, Thermo Fisher Scientific) for 3-5 min. Again, the suspension was filtered through a 70 μm cell strainer (#CLS431751, Sigma-Aldrich) and spun at 1500 rpm for 2 min. The supernatant was discarded and cells were resuspended in 0.5-1 mL PBS (2% FBS) and used for subsequent flow cytometry experiments. For the bulk RNA seq experiments, per group, 8 (4 and 12 weeks experiment) or 12 (12+8 weeks experiment) mice were used. Samples from each 2 mice (4 and 12 weeks experiment) or 3 mice (12+8 weeks experiment) were pooled into 1 sample resulting in 4 biological replicates per experiment. Per sample 100.000 AM (live CD45+CD11c+SiglecF+ cells) were FACS-sorted into RLT buffer (#74106, Qiagen) on BD FACS Aria flow cytometers from whole lung digests (CS: based on the presence of the tdTom signal; RA: without tdTom signal separation) and subsequently stored in -80°C. After RNA isolation according to the manufacturer's instructions (#74106, Qiagen), samples were used for bulk RNA seq. The RNA samples were quantified using the Qubit RNA HS assay (#Q32852, Invitrogen). The RNA integrity Number (RIN) scores and the DV200 scores were determined by using the TapeStation 2200. For this, the High Sensitivity RNA screen tape (#5067-5579, Agilent) and the High Sensitivity RNA ScreenTape Sample Buffer (5067-5580, Agilent) were used, following the manufacturers instructions.
RNA library preparation was performed using the Illumina stranded total RNA Prep, Ligation with Ribo Zero Plus kit (#20040529, Illumina), according to the manufacturer's protocol. A total of 50 ng RNA was used for all libraries as input material. Prepared libraries were quantified using the Qubit 1x dsDNA HS kit (#Q33231, Invitrogen) and checked for fragment size distribution using the TapeStation 2200 using the D1000 DNA screen tape (# 5067-5582, Agilent) with D1000 Reagents (5067-5583). The quantified libraries were pooled in equimolar amounts and sequenced on the NovaSeq 6000 system with 2 x 50 bp paired-end (PE) reads, targeting 50 million PE reads per library.

treatment_protocol: In vivo room air or cigarette smoke exposure

value: Lung

value: tissue

value: Macrophage

value: Cigarette Smoke

value: Week 12


title: HCC1806 Mitotic slippage-induced WGD TagSeq replicate 2

description:
Library name: HCC1806_MS_TagSeq_rep2
Column name in processed files: MS_1806_b

value: Mitotic slippage-induced WGD


title: Microbiota of stool from O7SG  patient

description:
69s rRNA V2-V9 sequencing of human stool
O7SG


title: D1_W1

description: Library name: samples1

value: spleen and lymph nodes


title: HCC1806 Mitotic slippage-induced WGD TagSeq replicate 3

description:
Library name: HCC1806_MS_TagSeq_rep3
Column name in processed files: MS_1806_c


title: Microbiota of stool from O5CT patient

description:
67s rRNA V2-V9 sequencing of human stool
O5CT


title: CS4tdneg.12w

description: Library name: CS4tdneg.12w


title: HCC1806 Mitotic slippage-induced WGD TagSeq replicate 1

description:
Library name: HCC1806_MS_TagSeq_rep1
Column name in processed files: MS_1806_a


title: PA0276-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0276.xlsx

value: PA0276 mutant


title: CS3tdneg.12w

description: Library name: CS3tdneg.12w


title: CS2tdpos.12w

description: Library name: CS2tdpos.12w


title: Microbiota of stool from O38ENO patient

description:
65s rRNA V2-V9 sequencing of human stool
O38ENO


title: Microbiota of stool from O3MY  patient

description:
66s rRNA V2-V9 sequencing of human stool
O3MY


title: HCC1806 Fusion-derived WGD TagSeq replicate 3

description:
Library name: HCC1806_Fusion_TagSeq_rep3
Column name in processed files: F_1806_c


title: CS3tdpos.12w

description: Library name: CS3tdpos.12w


title: CS1tdpos.12w

description: Library name: CS1tdpos.12w


title: CS2tdneg.12w

description: Library name: CS2tdneg.12w


title: HCC1806 Fusion-derived WGD TagSeq replicate 2

description:
Library name: HCC1806_Fusion_TagSeq_rep2
Column name in processed files: F_1806_b


title: CS1tdneg.12w

description: Library name: CS1tdneg.12w


title: Microbiota of stool from O34MO  patient

description:
64s rRNA V2-V9 sequencing of human stool
O34MO


title: HCC1806 Fusion-derived WGD TagSeq replicate 1

description:
Library name: HCC1806_Fusion_TagSeq_rep1
Column name in processed files: F_1806_a


title: RA3.12w

description: Library name: RA3.12w

value: Room Air


title: RA2.12w

description: Library name: RA2.12w


title: RA4.12w

description: Library name: RA4.12w


title: Microbiota of stool from O33SO patient

description:
63s rRNA V2-V9 sequencing of human stool
O33SO


title: HCC1806 Control TagSeq replicate 3

description:
Library name: HCC1806_Control_TagSeq_rep3
Column name in processed files: C_1806_c


title: Microbiota of stool from O32MME patient

description:
62s rRNA V2-V9 sequencing of human stool
O32MME


title: RA1.12w

description: Library name: RA1.12w


title: RA1.4w

description: Library name: RA1.4w

value: Week 4


title: oe-circ-3

description:
Library name: Sample 18
Rainbow trout hepatocytes transfected with circUSP47 overexpression vector, biological replicate 3, used for mRNA-seq analysis of genes regulated by circUSP47.

source_name: liver

value: liver

value: hepatocyte

value: circUSP47 overexpression

value: batch 2


title: Microbiota of stool from O31EE  patient

description:
61s rRNA V2-V9 sequencing of human stool
O31EE

value: Stool


title: HCC1806 Control TagSeq replicate 2

description:
Library name: HCC1806_Control_TagSeq_rep2
Column name in processed files: C_1806_b

value: Control (parental aneuploid)


title: Microbiota of stool from O30HE  patient

description:
60s rRNA V2-V9 sequencing of human stool
O30HE

value: Subject affected by FSHD


title: PA4746-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4746.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA4746 mutant

value: grow until mid-log phase in LB


title: CS1tdneg.4w

description: Library name: CS1tdneg.4w

value: Lung

value: tissue

value: Macrophage

value: Cigarette Smoke


title: oe-circ-2

description:
Library name: Sample 17
Rainbow trout hepatocytes transfected with circUSP47 overexpression vector, biological replicate 2, used for mRNA-seq analysis of genes regulated by circUSP47.


title: CS1tdpos.4w

description: Library name: CS1tdpos.4w


title: CCS1477-pH6.5#3

city: Houston

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description: Library name: CCS_lowpH_3

data_processing:
FastQC v v0.12.1 was used to check for qualities of the FASTQ reads. Trim-galore v 0.6.10 and cutadapt v 4.5 were used to trim low-quality ends.
FASTQ reads were aligned to human genome GENCODE 29 (GRCh38) using STAR v2.7.10b. Annotation of genes was carried out using the GRCh38 annotation and aligned reads were summarized at the gene level by STAR.
Assembly: GRCh38
Supplementary files format and content: comma-separated table of read counts

extract_protocol:
Total RNA of cells was extracted using RNeasy mini Kit (Qiagen, Cat#: 74106) according to the manufacturer's instructions and digested with DNase I (Qiagen, Cat#: 79254).
RNA sequencing (RNA-seq) libraries were constructed using a NEBNext rRNA Depletion Kit (NEB, Cat#: E7405X) and a NEBNext ultra RNA Library Prep kit (NEB, Cat#: E7775L), then subjected to a 50 bp paired-end sequencing run on NextSeq 2000 system (Illumina), using Illumina's NextSeq 2000 P3 Reagents (#20040559) following the manufacturer's instructions.

value: Human Epithelial Ovarian Cancer Cell Line


title: oe-circ-1

description:
Library name: Sample 16
Rainbow trout hepatocytes transfected with circUSP47 overexpression vector, biological replicate 1, used for mRNA-seq analysis of genes regulated by circUSP47.


title: Microbiota of stool from O2GG patient

description:
59s rRNA V2-V9 sequencing of human stool
O2GG


title: PA3623-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3623.xlsx

value: PA3623 mutant


title: HCC1806 Control TagSeq replicate 1

description:
Library name: HCC1806_Control_TagSeq_rep1
Column name in processed files: C_1806_a


title: CCS1477-pH6.5#2

description: Library name: CCS_lowpH_2


title: vector-3

description:
Library name: Sample 15
Rainbow trout hepatocytes transfected with empty vector control, biological replicate 3, used for mRNA-seq analysis of transcriptomic changes associated with circUSP47 overexpression.

value: empty vector control


title: RA2.4w

description: Library name: RA2.4w

value: Room Air

value: Week 4


title: vector-2

description:
Library name: Sample 14
Rainbow trout hepatocytes transfected with empty vector control, biological replicate 2, used for mRNA-seq analysis of transcriptomic changes associated with circUSP47 overexpression.

value: liver

value: hepatocyte


title: CCS1477-pH6.5#1

description: Library name: CCS_lowpH_1


title: PA3985-86-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3985-86.xlsx

value: PA3985-86 mutant


title: Microbiota of stool from O29MB patient

description:
58s rRNA V2-V9 sequencing of human stool
O29MB

value: Stool


title: RA4.4w

description: Library name: RA4.4w


title: CCS1477-pH7.4#3

description: Library name: CCS_highpH_3


title: vector-1

description:
Library name: Sample 13
Rainbow trout hepatocytes transfected with empty vector control, biological replicate 1, used for mRNA-seq analysis of transcriptomic changes associated with circUSP47 overexpression.

value: batch 2


title: Microbiota of stool from O27NB patient

description:
56s rRNA V2-V9 sequencing of human stool
O27NB

value: Subject affected by FSHD


title: Microbiota of stool from O24FO patient

description:
55s rRNA V2-V9 sequencing of human stool
O24FO


title: CCS1477-pH7.4#2

description: Library name: CCS_highpH_2


title: Microbiota of stool from O28AB patient

description:
57s rRNA V2-V9 sequencing of human stool
O28AB


title: CS4tdneg.4w

description: Library name: CS4tdneg.4w


title: CS4tdpos.4w

description: Library name: CS4tdpos.4w


title: PC9 cells, CLIP-seq, rep2

description: Library name: CLIP-2

data_processing:
Two independent PAR-CLIP-sequencing were performed. The first sequencing of FUS CLIP RNA yielded 1,288,391 non-redundant reads (paired-end reads) mapped to human genome GRCh38, with the majority (721,605 reads (paired-end reads)) to pre mRNAs. 8,784 FUS CLIP peaks corresponding to 4,345 target genes were identified in PC9 cells using the peak-finding algorithm CTK (https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation). The second sequencing of FUS CLIP RNA yielded 516,563 non-redundant reads (paired-end reads) mapped to human genome GRCh38, with the majority (304,203 reads (paired-end reads)) to pre mRNAs. 5,119 FUS CLIP peaks corresponding to 2,719 target genes in PC9 cells were identified.
Assembly: GRCh38
Supplementary files format and content: narrowpeak files for each sample

extract_protocol:
PC9 cells were treated with 4SU and then cross-linked with 365nm UV. The collected cells were lysed and centrifuged. The resultant supernatants were digested with RNase and immunoprecipitated using FUS antibody (sc-47711)-conjugated magnetic beads. Then the beads were washed and digested again. After washing, the beads were sequentially treated with calf intestinal alkaline phosphatase and then T4 PNK, and then the samples were washed and denatured. The samples were resolved on Novex Bis-Tris 4–12% gel and transferred onto a nitrocellulose membrane. The protein-RNA bands were excised, and the membrane was cut into small slices. The RNA was extracted with Trizol extraction.
The cDNA library was constructed by a SMART-Seq® Stranded Kit according to the manufacturer’s instructions. The purified library was evaluated using Agilent 2100 TapeStation, then diluted for further cluster generation and high-throughput sequencing (2 × 150 bp) on NovaSeq 6000.


title: CS3tdpos.4w

description: Library name: CS3tdpos.4w


title: Microbiota of stool from O22SB patient

description:
54s rRNA V2-V9 sequencing of human stool
O22SB


title: PC9 cells, CLIP-seq, rep1

description: Library name: CLIP-1


title: CS2tdpos.4w

description: Library name: CS2tdpos.4w


title: CCS1477-pH7.4#1

description: Library name: CCS_highpH_1


title: IACS16559-pH6.5#3

description: Library name: IACS_lowpH_3


title: Microbiota of stool from O19FAA patient

description:
53s rRNA V2-V9 sequencing of human stool
O19FAA


title: RPE1_Exp3_SH385

city: Quebec

first: Sabine

last: Elowe

state: Quebec

address: CR-Nouveaux Centre Hospitalier, 1401 18e Rue, Site HEJ, Local L2.106

country: Canada

institute: Centre Integre en cancerologie

description: Library name: RPE1-SH385_S

data_processing:
Raw sequencing reads (FASTQ files) were processed and analyzed using the Galaxy platform
Adapter sequences and low-quality bases were trimmed before alignment using Cutadapt
Processed reads were aligned to the human reference genome using STAR and quantification of the number of reads per gene was assessed using FeatureCounts
Differential gene expression analysis was performed using DESeq2 using three biological replicates per condition
Assembly: hg38
Supplementary files format and content: Tabular files include raw counts for each samples

source_name: Retina

growth_protocol: RPE1 cells were maintened in DMEM suplemented with FBS (10%) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total mRNA was isolated from cells using the Quick-RNA Purification Kit, Miniprep, Capped Columns (Zymo Research, #R1055) then NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc.) was used to isolate poly(A)+ RNA from 1 μg of total RNA
mRNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc., Ipswich, MA, USA), following the manufacturer’s instructions.

treatment_protocol: Doxycycline at 100 ng/mL was added 72h before RNA extraction,

value: Retina

value: retinal pigment epithelial cells

value: sh induction with doxycycline


title: PA3428-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3428.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA3428 mutant

value: grow until mid-log phase in LB


title: IACS16559-pH6.5#2

description: Library name: IACS_lowpH_2

value: Human Epithelial Ovarian Cancer Cell Line


title: PA3707-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3707.xlsx

value: PA3707 mutant


title: RA3.4w

description: Library name: RA3.4w

value: Lung

value: tissue

value: Macrophage


title: CS3tdneg.4w

description: Library name: CS3tdneg.4w

value: Cigarette Smoke

value: Week 4


title: Microbiota of stool from O18MAK patient

description:
52s rRNA V2-V9 sequencing of human stool
O18MAK


title: IACS16559-pH6.5#1

description: Library name: IACS_lowpH_1


title: Microbiota of stool from O17IK patient

description:
51s rRNA V2-V9 sequencing of human stool
O17IK


title: RPE1_Exp3_SH384

description: Library name: RPE1-SH384_S


title: IACS16559-pH7.4#3

description: Library name: IACS_highpH_3


title: RPE1_Exp2_SH385

description: Library name: RPE1-SH385_R


title: RPE1_Exp3_CTL

description: Library name: RPE1-PLKO_S

value: WT


title: IACS16559-pH7.4#2

description: Library name: IACS_highpH_2


title: Microbiota of stool from O16MK patient

description:
50s rRNA V2-V9 sequencing of human stool
O16MK

value: Stool


description:
Library name: mouse_Ms4a3_12week_8rest_myeloid_tomato_positive_CS
10x Genomics

data_processing:
FASTQ and seq data was analyzed using cellranger mkfastq. Individual sample gene expression matrices were generated using the GRCm38 (mm10) mouse reference genome. Samples metadata were harmonized based on FAIR principles by transforming them into a common data model and mapping corresponding concepts to Roche Terminology System reference terminologies. Seq data were processed using Cellranger and mapped to the mouse genome (mm10).
The secondary analysis was performed with the scanpy package (version 1.9.6). Quality control measures included filtering out cells with high mitochondrial gene expression, cells with less than 200 or more than 10.000 expressed genes, and genes expressed in less than 3 cells.
The processed data were normalized per total cell counts and log1p-transformed. Highly variable genes (n=4000) were selected for downstream analyses.
Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (tSNE), and Uniform Manifold Approximation and Projection (UMAP) were employed for dimensionality reduction. Leiden clustering was performed to identify distinct cell populations within the dataset using default resolution 1. In order to overcome the batch effect between separate experiments, we used the scANVI method from the scArches package to integrate the two datasets. Downstream clustering and dimensionality reduction was performed on the latent space of the model.
Assembly: GRCm38 (mm10)
Supplementary files format and content: h5

extract_protocol:
Mice were euthanized by intraperitoneal injection of pentobarbital sodium (150 mg/kg; diluted 1:2 with 0.9% NaCl physiological) and analyzed ~16 h after the last CS exposure. After perfusion of the heart with PBS, for whole lung analysis, lungs were directly collected into 1 mL PBS (2% FBS). Lungs were processed using the mouse lung dissociation kit (#130-095-927, Miltenyi Biotec) according to the manufacturer's instructions (program 37C_m_LDK_1). After termination of the program, C tubes (#130-093-237, Miltenyi Biotec) were detached from the gentleMACS dissociator and centrifuged shortly at 1500 rpm. Pellets were resuspended in the same supernatant and filtered through a 70 μm cell strainer (#CLS431751, Sigma-Aldrich) into a 50 mL tube. After centrifugation at 1500 rpm for 2 min, the supernatant was discarded and the pellets were resuspended with 1 mL ACK lysis buffer (#A1049201, Thermo Fisher Scientific) for 3-5 min. Again, the suspension was filtered through a 70 μm cell strainer (#CLS431751, Sigma-Aldrich) and spun at 1500 rpm for 2 min. The supernatant was discarded and cells were resuspended in 0.5-1 mL PBS (2% FBS) and used for subsequent flow cytometry experiments. Per experiment, 100.000 (12+8 weeks experiment) or 250.000 cells (4 and 12 weeks experiments) were FACS-sorted (Myeloid cells: viable CD45+ single cells; excluded CD11c/CD11b double-negative cells = considered as non-myeloid cells; AM: live CD45+CD11c+SiglecF+ cells).
According to the manufacturer's instructions (Chromium Next GEM Single Cell 3' Kit v3.1 16 rxns PN-1000-268; Chromium Next GEM Chip G Single Cell Kit, 48 rxns PN- 1000120, 10x Genomics), 12.000 cells per sample (with a viability of more than 80%) were loaded onto the 10X genomics device (Chromium controller, 10x Genomics). The generated cDNA samples were submitted to Roche internal seq facilities for seq using the 10x Genomics' scRNA seq technology. ScRNA seq was performed using the Chromium Next GEM Single Cell 3' reagent kit v3.1 from 10X genomics according to the user guide Ref CG000315 Rev F. Targeted cell recovery of 8000 cells. Samples were indexed using Dual Index Kit TT Set A. Single Cell 3' gene expression libraries were sequenced using standard Illumina paired-end constructs beginning P5 and P7. Seq these libraries produces a standard Illumina BCL data output folder. Seq was performed using the NovaSeq6000 instrument from Illumina. Seq depth minimum of 20000 read pairs per cell, paired end dual indexing with a seq read cycles of 28-10-10-90. Libraries were quantified, normalized and pooled followed by denaturation and dilution according to the Illumina recommendations for the NovaSeq 6000 of 300 pM together with a 1% PhiX concentration.

value: Myeloid cell


title: RPE1_Exp2_SH384

description: Library name: RPE1-SH384_R


title: CS2tdneg.4w

description: Library name: CS2tdneg.4w


title: RPE1_Exp2_CTL

description: Library name: RPE1-PLKO_R


description:
Library name: mouse_Ms4a3_12week_8rest_myeloid_tomato_negative_RA
10x Genomics

value: Room Air


title: Microbiota of stool from O15DÖ patient

description:
49s rRNA V2-V9 sequencing of human stool
O15DÖ

value: Subject affected by FSHD


title: DMSO-pH6.5#3

description: Library name: CTR_lowpH_3

value: pH6.5 DMSO


title: IACS16559-pH7.4#1

description: Library name: IACS_highpH_1


title: DMSO-pH6.5#2

description: Library name: CTR_lowpH_2


title: RPE1_Exp1_SH385

description: Library name: RPE1-SH385_2

value: Retina

value: retinal pigment epithelial cells

value: sh induction with doxycycline


title: Microbiota of stool from O13AÖ patient

description:
48s rRNA V2-V9 sequencing of human stool
O13AÖ


title: Microbiota of stool from O37SE patient

description:
45s rRNA V2-V9 sequencing of human stool
O37SE


title: Microbiota of stool from O36ST patient

description:
44s rRNA V2-V9 sequencing of human stool
O36ST


description:
Library name: mouse_Ms4a3_12week_8rest_AMs_tomato_negative_RA
10x Genomics


title: Platelets, Healthy, Rep12

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2213 Garland Avenue South 9465

institute: Vanderbilt University

data_processing:
Raw sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7.
Trimmed reads were aligned to the hg38 reference genome and counted using STAR v2.7.9a with the `--quantMode GeneCounts` option.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Peripheral Blood Platelets

extract_protocol:
Samples were resuspended in 700 µl QIAzol Lysis Reagent (Qiagen GmbH, Hilden, Germany).
RNA was extracted from the platelet-QIAzol Lysis Reagent aliquots by application of the RNeasy Mini kit (Qiagen GmbH, Hilden, Germany; Cat: 1071023) according to the manufacturer’s recommendations.
Library preparation was completed using theNEBNext Ultra II Directional RNA Library Prep Kitand protocol (P/N: E7760L) per manufacturer recommendations.
RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by fragmentation using divalent cations under elevated temperature.
First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation were performed to generate the final cDNA library.

tag: disease state

value: healthy

value: Peripheral Blood Platelets


description:
Library name: mouse_Ms4a3_12week_8rest_AMs_tomato_negative_CS
10x Genomics


title: Platelets, Healthy, Rep10


title: RPE1_Exp1_CTL

description: Library name: RPE1-PLKO_2


title: mouse_Ms4a3_4week_myeloid_RA

description:
Library name: mouse_Ms4a3_4week_myeloid_RA
10x Genomics


title: Platelets, Healthy, Rep9


title: DMSO-pH7.4#2

description: Library name: CTR_highpH_2

value: Human Epithelial Ovarian Cancer Cell Line

value: pH7.4 DMSO


title: mouse_Ms4a3_4week_myeloid_CS

description:
Library name: mouse_Ms4a3_4week_myeloid_CS
10x Genomics

value: Lung


title: auxCAR1

city: Shenzhen

first: Chen

last: Yang

address: 1068 Xueyuan Avenue, Nanshan District, Shenzhen,China

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

description: Library name: sample3

data_processing:
QC(Fastq)
alignment to GRCh38.p14 using STAR
read quantificatio(featureCounts)
filter out zero count (50％  of the samples are greater than zero)
normalization(TMM)
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: T cell

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods, followed by strict quality control of RNA samples. The quality control methods mainly include quantitative analysis using Nanodrop and detection of RNA integrity using Agilent 4200 TapeStation.
By utilizing the structural feature that most mRNA in eukaryotes have polyA tails, Oligo (dT) magnetic beads were used to enrich mRNA with polyA tails. Subsequently, the obtained mRNA was randomly cleaved using divalent cations. The fragmented mRNA was used as a template, and random oligonucleotides were used as primers to synthesize the first strand of cDNA in the 1st Strand Enzyme reverse transcriptase system. The second strand of cDNA was then synthesized using the 2nd Strand Enzyme and dNTPs. After purification, the double stranded cDNA was subjected to terminal repair, followed by the addition of an A tail and the connection of sequencing adapters. cDNA of around 200-300 bp was screened, amplified by PCR, and the PCR product was purified again to obtain a library.

value: PBMC

value: primary CD8+ T cells

value: day5 post transduction


description:
Library name: mouse_Ms4a3_12week_myeloid_RA_tomato_positive
10x Genomics


title: Platelets, Healthy, Rep6


title: Microbiota of stool from K40SBK control

description:
39s rRNA V2-V9 sequencing of human stool
K40SBK

value: Subject not affected by FSHD


title: Platelets, Healthy, Rep5


title: PA1616-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1616.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA1616 mutant

value: grow until mid-log phase in LB


title: DMSO-pH6.5#1

description: Library name: CTR_lowpH_1


title: DMSO-pH7.4#1

description: Library name: CTR_highpH_1


description:
Library name: mouse_Ms4a3_12week_8rest_AMs_tomato_positive_CS
10x Genomics

value: Macrophage

value: Cigarette Smoke


title: Microbiota of stool from K9MTY control

description:
43s rRNA V2-V9 sequencing of human stool
K9MTY

value: Stool


title: DMSO-pH7.4#3

description: Library name: CTR_highpH_3


title: auxCAR2

description: Library name: sample4


title: Microbiota of stool from K8SS control

description:
42s rRNA V2-V9 sequencing of human stool
K8SS


title: Microbiota of stool from K7OS control

description:
41s rRNA V2-V9 sequencing of human stool
K7OS


title: Microbiota of stool from K36UGB control

description:
36s rRNA V2-V9 sequencing of human stool
K36UGB


title: Microbiota of stool from K4SD  control

description:
40s rRNA V2-V9 sequencing of human stool
K4SD


title: Platelets, FH, Rep12

value: Familial Hypercholesterolemia


title: Microbiota of stool from K34AGO  control

description:
35s rRNA V2-V9 sequencing of human stool
K34AGO


title: TSs-1

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

description:
Library name: Sample 10
IHNV-infected spleen tissue from rainbow trout, biological replicate 1, used for small RNA sequencing and miRNA expression profiling.

data_processing:
Raw reads from long RNA-seq, small RNA-seq and mRNA-seq libraries were filtered to remove adapter sequences, low-quality reads and reads containing excessive unknown bases; small RNA-seq reads outside the expected length range were also removed.
Clean reads from long RNA-seq and mRNA-seq libraries were aligned to the Oncorhynchus mykiss reference genome using HISAT2, whereas clean small RNA-seq reads were mapped to the reference genome using Bowtie.
mRNA, lncRNA and hepatocyte mRNA expression levels were quantified using StringTie, and raw count and normalized FPKM expression matrices were generated for the corresponding samples.
CircRNAs were identified using find_circ and quantified based on back-splice junction reads. CircRNA raw counts and normalized expression values were generated for all spleen long RNA-seq samples.
Known and novel miRNAs were identified using miRDeep2 and annotated by comparison with public miRNA databases. miRNA expression levels were quantified as raw counts and normalized TPM values for all spleen small RNA-seq samples.
Differential expression analyses were performed between IHNV-infected and uninfected spleen samples and between circUSP47-overexpressing and empty vector control hepatocytes. Differentially expressed circRNAs, miRNAs, lncRNAs and mRNAs were integrated to construct ceRNA networks and to identify commonly regulated mRNAs and immune-related pathways associated with circUSP47-mediated antiviral regulation.
Assembly: Oncorhynchus mykiss reference genome, USDA_OmykA_1.1, GCF_013265735.2.
Supplementary files format and content: Tab-delimited text files containing raw count and normalized expression matrices for mRNAs, lncRNAs, circRNAs and miRNAs across the corresponding samples. mRNA and lncRNA files include raw count and FPKM values; circRNA files include back-splice junction read counts, normalized expression values and circRNA annotation information including circRNA identifier, genomic position, strand and host gene; miRNA files include raw count and TPM values; hepatocyte mRNA-seq files include raw count and FPKM values for mRNAs or genes.

source_name: spleen

extract_protocol:
Total RNA was extracted from rainbow trout spleen tissues or hepatocytes using Trizol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed using NanoDrop, and RNA integrity was evaluated by agarose gel electrophoresis. RNA samples meeting quality requirements were used for long RNA-seq, small RNA-seq or mRNA-seq library construction.
For spleen long RNA-seq, ribosomal RNA was removed from total RNA, and strand-specific long RNA-seq libraries were constructed for mRNA, lncRNA and circRNA expression profiling. These libraries were sequenced on an Illumina HiSeq 4000 platform using paired-end 150 bp reads. For spleen small RNA-seq, small RNAs of approximately 18-30 nt were enriched, ligated to adapters, reverse transcribed and PCR amplified; libraries were sequenced on an Illumina HiSeq Xten platform using single-end 50 bp reads. For hepatocyte mRNA-seq, messenger RNA was enriched from total RNA using poly(A) selection, fragmented, reverse transcribed and amplified to generate libraries, which were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.

value: spleen

value: wild-type

value: IHNV infection

value: batch 1


title: CSs-3

description:
Library name: Sample 9
Uninfected control spleen tissue from rainbow trout, biological replicate 3, used for small RNA sequencing and miRNA expression profiling.

value: uninfected control


title: wtCAR1

description: Library name: sample1


title: BaP_treatment_rep3

city: Shijiazhuang

first: Hao

last: Xi

address: No. 361 Zhongshan East Road, Shijiazhuang, Hebei Province, China

institute: Hebei Medical University

description: circRNA expression profile of BaP_treatment group, biological replicate 3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10× Blocking Agent and 1 μl of 25× Fragmentation Buffer, then heated at 60°C for 30 min. 25 μl of 2× Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed onto the gasket slide and assembled with the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned.

scan_protocol: The arrays were scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Low intensity filtering was performed; circRNAs that have flags in P or M in at least 3 out of 9 samples were retained. Differentially expressed circRNAs were identified through Volcano Plot filtering (FC >= 2.0, p-value <= 0.05).

source_name: Mouse cells

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cells were cultured under standard conditions (37°C, 5% CO2 humidified incubator) in appropriate cell culture medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated from cells using standard RNA extraction methods. RNA concentration was determined by OD260 using a NanoDrop ND-1000 instrument. RNA integrity was assessed by electrophoresis on a denaturing agarose gel. Total RNAs were digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs prior to labeling.

treatment_protocol: BaP treatment group cells were treated with Benzo[a]pyrene (BaP). Control group cells received vehicle treatment only. Raw264.7 is a mouse macrophage cell line used as reference.

value: mouse MOVAS cells


title: Microbiota of stool from K3CK control

description:
38s rRNA V2-V9 sequencing of human stool
K3CK


title: Microbiota of stool from K33DA control

description:
34s rRNA V2-V9 sequencing of human stool
K33DA


title: TSs-3

description:
Library name: Sample 12
IHNV-infected spleen tissue from rainbow trout, biological replicate 3, used for small RNA sequencing and miRNA expression profiling.


title: PA1426-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1426.xlsx

value: PA1426 mutant


title: Microbiota of stool from K32BC  control

description:
33s rRNA V2-V9 sequencing of human stool
K32BC


title: BaP_treatment_rep2

description: circRNA expression profile of BaP_treatment group, biological replicate 2


title: Microbiota of stool from K38BS control

description:
37s rRNA V2-V9 sequencing of human stool
K38BS


description:
Library name: mouse_Ms4a3_12week_myeloid_CS_tomato_negative
10x Genomics

source_name: Lung

value: Lung

value: Myeloid cell


title: BaP_treatment_rep1

description: circRNA expression profile of BaP_treatment group, biological replicate 1


title: CSs-1

description:
Library name: Sample 7
Uninfected control spleen tissue from rainbow trout, biological replicate 1, used for small RNA sequencing and miRNA expression profiling.


title: Platelets, FH, Rep9

value: Peripheral Blood Platelets


title: Microbiota of stool from K31HE control

description:
32s rRNA V2-V9 sequencing of human stool
K31HE

value: Subject not affected by FSHD


title: Control_rep3

description: circRNA expression profile of Control group, biological replicate 3

value: Control


title: Platelets, FH, Rep8


title: Microbiota of stool from K30EC  control

description:
31s rRNA V2-V9 sequencing of human stool
K30EC


title: Control_rep2

description: circRNA expression profile of Control group, biological replicate 2


title: Platelets, FH, Rep7


title: NEST2-06_Baseline

type: protein

city: New York

first: MAIDER

last: ASTORKIA

state: NY

address: 1300 York Ave

institute: WEILL CORNELL MEDICINE

scan_protocol: Immunofluorescence intensity values were extracted using HALO 36.

data_processing:
Mean nuclear area intensity values were used for protein markers FOXP3, PCNA, PAX5, and MKI67, and mean cytoplasmic intensity values were used for the remaining markers. We defined three regions of interest (ROIs): (i) tumor in baseline biopsy sample, (ii) tumor, and (iii) tumor bed in post-treatment resection samples. After obtaining per-cell intensities for each ROI, we excluded 2% of cells with smallest size and 2% of lowest DAPI signal from further analysis to reduce artifact. We generated a binary expression matrix as described by Sanz-Moreno 2024 33. In brief, probe intensities within each ROI were z-score normalized and fitted onto a density function (using gaussian_filter1d from scipy.ndimage). The lowest peak value of the density was assumed to represent the background and to be normally distributed (find_peaks from scipy.signal) and cells with probe intensities above 6σ from this fitted background distribution were classified as positive for that probe.
csv file (representing Mean signal intensity)

label: Lunaphore staining

molecule: protein

source_name: non-metastatic CRC

label_protocol: Up to four slides were processed per run using the fully automated, sequential multiplex protocol based on Lunaphore’s pressurized microfluidic technology. Each staining cycle comprised six steps: (1) primary antibody incubation (mouse or rabbit anti-human antibodies); (2) secondary antibody incubation with Goat Anti-Mouse Alexa Fluor Plus 555 (Thermo Scientific, Cat. A32727, 1:100) and Goat Anti-Rabbit Alexa Fluor Plus 647 (Thermo Scientific, Cat. A32733, 1:200), followed by DAPI counterstaining (Thermo Scientific, Cat. 62248, 1:1000); (3) imaging through the DAPI, TRITC, and CY5 channels; (4) washing; (5) elution; and (6) quenching.

growth_protocol: Pretreatment biopsies and post-therapy resected specimens (residual tumor or tumor bed) were histologically assessed using formalin-fixed, paraffin-embedded (FFPE) tissue sections as part of the routine clinical workflow with H&E-stained slides. Cases were centrally reviewed by an expert gastrointestinal and molecular pathologist. Histologic response was evaluated by estimation of the percentage of residual viable tumors of the macroscopically identifiable tumor bed. Tumors with prominent Crohn’s-like lymphoid reaction 32, characterized by peritumoral lymphocytic aggregates found at the advancing edge of the tumor or in the tumor bed and resembling tertiary lymphoid structures (TLS), were identified. Prominence is defined as being present diffusely throughout the tumor (>50% of the tissue sampled) and containing at least 5 TLS /4x field. Select slides were also reviewed at a gastrointestinal pathology consensus conference with up to five expert gastrointestinal pathologists to help determine the percent of viable tumor cells in tumor beds.

extract_protocol: Prior to COMET processing, slides were manually dewaxed and subjected to antigen retrieval (pH 9, 20 min) using the Leica Bond RX system. To minimize tissue autofluorescence, a standard photobleaching protocol employing hydrogen peroxide and sodium hydroxide was applied. Slides were then washed with PBS and stored in solution until instrument initialization and reagent preparation were ready

treatment_protocol: Tonsil and corresponding colon FFPE blocks were sectioned at 5 µm thickness and mounted in close proximity on the same Leica charged slides

value: CRC tumor

tag: specimen

value: Pathologic specimen, biopsy

tag: status

value: Alive

tag: age

tag: Stage

tag: pathologic response

tag: mmr status

value: pMMR

tag: tissue preservation method

value: FFPE

tag: treatment arm

value: C


title: Platelets, FH, Rep13

value: Familial Hypercholesterolemia

tag: cell type


title: anti-P300-IACS16559

description: Library name: P300-pH74-IACS3

data_processing:
Sequence reads quality were checked by fastqc, and trimmed for adaptor /low quality sequencie using trim-galore (--paired -stringency 5 -length 27)
Trimmed reads were aligned to hg19 using bwa mem with default parameters
Aligned bam files were sorted and filtered by samtools with -q 10 option.
bam files were converted to bw files using bamCoverage reads per genomic content (1x normalization) with effective genome size of 2451960000.
Assembly: hg19
Supplementary files format and content: bigWig, processed alignment
Library strategy: CUT&Run

extract_protocol:
Cells were harvested and washed twice with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and EDTA-free protease inhibitor cocktail). The cells were then incubated overnight with the rabbit anti-P300 antibody (1:50, Cell Signaling, Cat# 54062, RRID:AB_2799450) in the buffer (Wash buffer supplemented with 0.05% digitonin and 2 mM EDTA) at 4 °C. The following day, the supernatant was removed by centrifugation and the cell pellets were washed once with Dig-wash buffer (Wash buffer containing 0.05% digitonin). The cell pellets were then incubated with Protein A-MNase (700 ng/mL in Dig-wash buffer) for 1 h by rotation at 4 °C. After three washes, the cell pellets were resuspended in 100 μl Dig-wash buffer with 2 μl of 100 mM CaCl2, incubated at 0 °C for 30 min and then the reactions were stopped by the addition of 100 μl 2×STOP buffer (340 mM NaCl, 20 mM EDTA pH 8.0, 4 mM EGTA, 0.05% digitonin, 50 μg/mL RNase A, 50 μg/mL glycogen and 2 pg/mL heterologous spike-in yeast DNA). The supernatant DNA was collected after centrifugation and further purified using phenol–chloroform–isoamyl alcohol (Sigma, Cat#: p3803), chloroform extraction and ethanol precipitation.
The CUT&RUN-seq library construction was performed using 10 ng CUT&RUN DNA and a NEBNext ultra DNA library prep kit (NEB, Cat#: E7645); the CUT&RUN-seq libraries were sequenced in a 50 bp paired-end sequencing on a NextSeq 1000 system (Illumina), using Illumina's NextSeq 1000 P2 Reagents (#20046811) following the manufacturer's instructions.

value: Human Epithelial Ovarian Cancer Cell Line

tag: treatment


title: Platelets, FH, Rep6


title: anti-P300-CCS1477

description: Library name: P300-pH74-CCS100

tag: cell line


title: NEST1-11_Baseline

tag: tissue

value: A


title: Microbiota of stool from K28ME control

description:
28s rRNA V2-V9 sequencing of human stool
K28ME

value: Stool


title: Platelets, FH, Rep5


title: anti-P300-DMSO

description: Library name: P300-pH74-DMSO

value: DMSO


title: NEST2-04_Baseline

value: B


title: Platelets, FH, Rep4


title: Microbiota of stool from K27DG  control

description:
27s rRNA V2-V9 sequencing of human stool
K27DG


title: NEST1-04_Baseline


title: Platelets, FH, Rep3


title: Microbiota of stool from K24EK control

description:
26s rRNA V2-V9 sequencing of human stool
K24EK


title: NEST1-05_Baseline

value: dMMR


title: Platelets, FH, Rep2


title: Microbiota of stool from K22SC control

description:
25s rRNA V2-V9 sequencing of human stool
K22SC


title: Platelets, FH, Rep11


title: NEST1-05_Resection

value: Pathologic specimen


title: Platelets, FH, Rep1

value: Peripheral Blood Platelets


title: Platelets, FH, Rep10


title: CSs-2

description:
Library name: Sample 8
Uninfected control spleen tissue from rainbow trout, biological replicate 2, used for small RNA sequencing and miRNA expression profiling.

value: spleen

tag: genotype

value: wild-type

value: uninfected control

tag: batch

value: batch 1


title: Microbiota of stool from K1SY control

description:
24s rRNA V2-V9 sequencing of human stool
K1SY

value: Subject not affected by FSHD


title: Control_04

city: Beijing

first: Siyuan

last: Guo

state: Beijing

address: No. 9 Fanjiacun Road, Fengtai District

department: Department of Oral and Maxillofacial Plastic and Traumatic Surgery

institute: Beijing Stomatological Hospital, Capital Medical University

description: Gene expression data of peripheral blood from normal controls

hyb_protocol: Following labeling, fragmented cDNA was hybridized for 16 hr at 45C on GeneChip Clariom D Human Assay. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: condition

value: Control

value: blood

tag: gender

value: female


title: Control_05

value: male


title: NEST1-06_Resection

value: CRC tumor

value: Alive

value: FFPE


title: Platelets, Healthy, Rep2

tag: disease state

value: healthy


title: Microbiota of stool from K19AP control

description:
23s rRNA V2-V9 sequencing of human stool
K19AP

value: Stool


title: NEST1-04_Resection

tag: specimen

value: pMMR

value: A


title: NEST2-06_Resection

value: Pathologic specimen

tag: status

value: C


title: Platelets, Healthy, Rep1

value: Peripheral Blood Platelets


title: Microbiota of stool from K18EE control

description:
22s rRNA V2-V9 sequencing of human stool
K18EE


title: Microbiota of stool from K2KS control

description:
30s rRNA V2-V9 sequencing of human stool
K2KS


title: Control_rep1

description: circRNA expression profile of Control group, biological replicate 1

value: mouse MOVAS cells


title: NEST2-08a_Baseline

value: Pathologic specimen, biopsy

tag: age

value: B


title: NEST1-08_Resection

tag: Stage


title: Control_03

value: Control


title: Microbiota of stool from K17OA control

description:
21s rRNA V2-V9 sequencing of human stool
K17OA

value: Subject not affected by FSHD


title: HN1shRNA rep3

city: JEONJU

first: SOO MI

last: KIM

state: JEONBUK

address: GUNGIRO 20

department: PHYSIOLOGY

institute: JEONBUK NATIONAL UNIVERSITY

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Human HepG2 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Hepatocellular carcinoma cell line


title: Control_02

value: blood

value: female


title: NEST1-01_Resection

value: CRC tumor

value: Alive

tag: pathologic response


title: Microbiota of stool from K16FS control

description:
20s rRNA V2-V9 sequencing of human stool
K16FS


description:
Library name: mouse_Ms4a3_12week_8rest_myeloid_tomato_positive_RA
10x Genomics

value: Lung

value: Myeloid cell

value: Room Air


title: Microbiota of stool from K29AEI control

description:
29s rRNA V2-V9 sequencing of human stool
K29AEI

value: Stool


description:
Library name: mouse_Ms4a3_12week_8rest_myeloid_tomato_negative_CS
10x Genomics

value: Cigarette Smoke


title: NEST2-03_Resection

value: Pathologic specimen

tag: mmr status

value: pMMR

value: FFPE


title: Microbiota of stool from O11NE patient

description:
47s rRNA V2-V9 sequencing of human stool
O11NE

value: Subject affected by FSHD


title: HN1shRNA rep2

description: replicate 2


title: Microbiota of stool from O10KG patient

description:
46s rRNA V2-V9 sequencing of human stool
O10KG


description:
Library name: mouse_Ms4a3_12week_8rest_AMs_tomato_positive_RA
10x Genomics

value: Macrophage


title: RPE1_Exp1_SH384

description: Library name: RPE1-SH384_2

value: Retina

value: retinal pigment epithelial cells

value: sh induction with doxycycline


title: NEST2-01_Resection

tag: tissue preservation method

value: B


title: Microbiota of stool from K13AK control

description:
19s rRNA V2-V9 sequencing of human stool
K13AK

value: Subject not affected by FSHD


title: HN1shRNA rep1

description: replicate 1

value: Hepatocellular carcinoma cell line


title: Control_01

value: Control

value: blood

value: female


title: NSCL/P_05

description: Gene expression data of peripheral blood from NSCL/P patients

value: Nonsyndromic cleft lip with or without cleft palate (NSCL/P)

value: male


title: NEST2-04_Resection

value: CRC tumor

value: Alive

tag: treatment arm


title: Microbiota of stool from K11MAK control

description:
17s rRNA V2-V9 sequencing of human stool
K11MAK

value: Stool


title: NSCL/P_04


title: NEST2-10_Resection

value: Pathologic specimen

value: pMMR

value: FFPE


title: Microbiota of stool from K10TP control

description:
16s rRNA V2-V9 sequencing of human stool
K10TP


title: NEST1-11_Resection

value: A