title: FIL-FAPs 2+SAFit2

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome  using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Assembly: hg19
Supplementary files format and content: file includes raw counts for each Sample

source_name: Adipose tissue

growth_protocol: FIL-FAPs were maintained in basal medium (Cyagen, USA, HUXMD-90011) with antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany) , after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA).
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: FIL-FAPs was cultured in basal medium with 500nM SAFit2 for 24h

value: Adipose tissue

value: fibro-adipose progenitor cells

value: PIK3CA E418K

value: 500nM SAFit2 treated for 24h


title: Enterobacter cloacae, ST2260, blaNDM eliminated, asmA knocked out 3

status: Public on Aug 08 2025

type: SRA

city: Guangzhou

first: Xu

last: Yang

address: Postal address, 151 Yanjiang Rd, Yuexiu District,

country: China

institute: the First Affiliated Hospital of Guangzhou Medical University

description: Library name: CY-8-A-3

library_source: transcriptomic

data_processing:
The data generated from Illumina platform were used for bioinformatics analysis. All of the analyses were performed using the free online platform of Majorbio Cloud Platform (www.majorbio.com) from Shanghai Majorbio Bio-pharm Technology Co.,Ltd. The major software and parameters are as follows.
Assembly: High quality reads in each sample were mapped to the reference genome provided by the customer.
Supplementary files format and content: fastq file includes raw data for each Sample

molecule: total RNA

organism: Enterobacter cloacae

source_name: bacteria

extract_protocol:
RNA was harvested using CTAB about 25 ug of total RNA was used for theconstruction of sequencing libraries.
Ribosomal RNA (rRNA) depletion instead of poly(A) purification is performed by RiboCop rRNA Depletion Kit for Mixed Bacterial Samples（lexogen，USA）and then all mRNAs were broken into short (200nt) fragments by adding fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers (Illumina). When the second strand cDNA was synthesized, dUTP was incorporated in place of dTTP. Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using of total RNA. paired-end RNA-seq library was sequenced with the Illumina Novaseq 6000 (or other new sequenator) (Illumina Inc., San Diego, CA, USA) .

tag: tissue

value: bacteria


title: Jurkat, 0h, rep2

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

country: USA

institute: UC Berkeley

description: Library name: mRNA_J0h2

data_processing:
Adapters were trimmed with cutadapt, followed by trimming the first 5'-> 7 nucleotides in each read. Then, reads were also filtered with a quality score (-q 10) and by length (> 25 nt).
Reads were mapped in a sequential fashion against rRNA references, tRNA reference by tRAX, mtDNA, and ncRNAs before mapped against the Gencode v.37 GRCh38.p13 protein coding reference, resulting in only high quality mappings against mRNA sequences.
Gene counts were filtered out if any sampled had a zero count, and,then normalized with DESEq2.
Assembly: GRCh38.p13
Supplementary files format and content: CSV containing raw gene counts from RSEM
Supplementary files format and content: log2 normalized (DESeq2's median ratio method) gene expression

organism: Homo sapiens

source_name: Human Jurkat Clone E6-1 (ATCC TIB-152)

growth_protocol: Cells were maintained in RPMI 1640 Medium (ATCC modification) with 10% FBS (VWR Seradigm Life Science), 0.01% Penicillin-Streptomycin (10,000 U/mL) (ThermoFisher),  density 1 x 10^5 cells ml^–1 to 1 × 10^6 cells ml^–1

extract_protocol:
RNA samples were extracted using the Direct-zol RNA Miniprep kit (Zymo Research)
mRNA-seq libraries were prepared from total RNA using the RealSeq RNA sequencing kits (Somagenics)

treatment_protocol: Jurkat cells were activated using anti-CD3/anti-CD28 antibodies (Tonbo). Flat bottom plates were coated with anti-CD3 antibody at a 10 μg/mL concentration at 4C for at least 12h. Then, anti-CD28 antibody was added to the cell culture media at a concentration of 5 µg/mL and, cells were incubated for the required timepoints.

tag: cell line

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

tag: cell type

value: T lymphoblast

tag: treatment

value: control


title: Enterobacter cloacae, ST78, eliminates blaNDM 1

description: Library name: CY-9-1


title: A-PJI01

city: Fuzhou

first: Xinyu

last: Fang

address: Chazhong road

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
Pass filter data of fastq format were processed by Cutadapt[1](version 1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Bowtie2 (v2.2.6) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2(v2.2.6).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Assembly: Staphylococcus aureus (ID 154) - genome - NCBI (NIH. Gov)

organism: Staphylococcus aureus

source_name: MSSA

extract_protocol:
RNA was harvested using TRIzol.
RNA libraries for RNA-seq were prepared using VAHTS Total RNA-seq (Bacteria) Library Prep Kit for Illumina following manufacturer's protocols.

tag: strain

value: MSSA

tag: condition

value: acute periprosthetic joint infection


title: D12.P2.3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: day12CD25nFoxp3p.3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
For population-level RNA-seq, samples were double-sorted, and 1,000 MmSCs were collected into 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich) in DNA LoBind tubes (Eppendorf). For whole-tissue RNA-seq, muscles were dissected and immediately frozen in liquid nitrogen until all samples were collected. Fresh-frozen muscles were homogenized in TRIzol followed by RNA isolation according to the manufacturer's protocol. 2 ng RNA were resuspended in 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich).
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: Thymus

value: Treg Progenitor

value: CD25- Foxp3+ Treg Progenitor

tag: Sex

value: male

tag: genotype

value: WT

tag: age

value: day 12


title: D49.P1.2

description: Library name: 7weeksCD25pFoxp3n.2

value: CD25+ Foxp3- Treg Progenitor

value: day 49


title: FIL-FAPs 3

city: Shanghai

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

value: Adipose tissue

value: fibro-adipose progenitor cells

value: PIK3CA H1047Y


title: Enterobacter cloacae, ST2260, blaNDM eliminated, asmA knocked out 1

description: Library name: CY-8-A-1

value: bacteria


title: FIL-FAPs 1+SAFit2

value: PIK3CA H1047R

value: 500nM SAFit2 treated for 24h


title: D12.P2.2

description: Library name: day12CD25nFoxp3p.2


title: Jurkat, 12h, rep1

description: Library name: mRNA_J12h1

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast

value: 12h post-activation


title: D49.P1.1

description: Library name: 7weeksCD25pFoxp3n.1

value: Thymus


title: Enterobacter cloacae, ST2260, eliminates blaNDM 3

description: Library name: CY-8-3


title: Patient4, PRE4, TCR

city: Zhongshan

first: Ming

last: Hong

state: Guangdong

address: NO. 2 Sunwen East Road

institute: Zhongshan City People's Hospital

description:
Library name: Patient4, PRE4, TCR
10x Genomics

data_processing:
Reads converted to FASTQ with mkfastq (Cell Ranger 7.0.0). Alignment, V(D)J assembly, and quantification performed via Cell Ranger Multi Pipeline (default parameters) using human references: refdata-gex-GRCh38-2020-A (expression) and refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 (repertoire).
Assembly: Human refdata-gex-GRCh38-2020-A (gene expression); Human refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 (V(D)J repertoire).
Supplementary files format and content: Tab-separated values files, matrix files (gene expression), and V(D)J repertoire files (FASTQ, clonotype tables) from Cell Ranger output.
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
PBMCs subjected to 10x Genomics Chromium 5’ Single Cell V(D)J immuno-profiling workflow (B/T cell enrichment), followed mRNA gene expression analysis per manufacturer’s instructions.
Library constructed via 10x Genomics 5’ V(D)J + gene expression workflow. Sequenced on Illumina HiSeq 2500 (mean depth: 339.4 million reads for expression).

treatment_protocol: Dual-target (BCMA/CD19) CAR-T therapy for SLE

value: Blood

value: T cell

value: No


title: Patient4, POST4, TCR

description:
Library name: Patient4, POST4, TCR
10x Genomics

value: Yes


title: D12.P1.3

description: Library name: day12CD25pFoxp3n.3

value: Treg Progenitor

value: male

value: WT

value: day 12


title: Enterobacter cloacae, ST2260, eliminates blaNDM 2

description: Library name: CY-8-2


title: D12.P2.1

description: Library name: day12CD25nFoxp3p.1

value: CD25- Foxp3+ Treg Progenitor


title: FIL-FAPs 2

value: Adipose tissue

value: fibro-adipose progenitor cells

value: PIK3CA E418K


title: FIL-FAPs 1

value: PIK3CA H1047R


title: FIL-FAPs 3+SAFit2

value: PIK3CA H1047Y

value: 500nM SAFit2 treated for 24h


title: Patient3, PRE3, TCR

description:
Library name: Patient3, PRE3, TCR
10x Genomics


title: Enterobacter cloacae, ST2260, eliminates blaNDM 1

description: Library name: CY-8-1

value: bacteria


title: Enterobacter cloacae, ST2260, blaNDM eliminated, asmA knocked out 2

description: Library name: CY-8-A-2


title: Patient5, PRE5, TCR

description:
Library name: Patient5, PRE5, TCR
10x Genomics


title: D12.P1.2

description: Library name: day12CD25pFoxp3n.2

value: Thymus

value: CD25+ Foxp3- Treg Progenitor


title: Slc25a13 -/- Gpd2 -/-, Male, M195, 2 days 5% glycerol

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: DKO_glycerol_3

data_processing:
Processed reads were mapped back to the mouse genome (mm10) using STAR software (v. 2.6.0.a)102. HTSeq software (v.0.11.1) was employed to generate the count matrix with default parameters103. Differential expression analysis was performed by normalizing read counts to expression values using the TMM normalization method in edgeR104,105. Generalized linear models were applied to identify differentially expressed genes between glycerol and water- exposed liver samples of the same genotype or between liver samples of different genotypes. Normalized expression levels from TMM were used as the dependent variable, while sequencing batches were included as an independent variable to account for batch effects. Genes with an FDR-adjusted p-value below 0.05 and a fold change greater than 2 or less than 0.5 were classified as significantly upregulated or downregulated, respectively.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

growth_protocol: Mice were maintained at 21 °C under a standard 12:12-hour light-dark cycle and provided with ad libitim access to food and water.

extract_protocol:
20 mg liver aliquots were used for RNA isolation (Qiagen, RNeasy Mini Kit, 74104) and DNase I treatment (Qiagen, RNase-Free DNase Set, 79254). From the isolated RNA, 20uL with at least 200ng total RNA was sent to 7 Traits of Watertown, MA.
Libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs, Ipswich, MA), following the manufacturer’s protocol using 150 ng RNA per sample. mRNA was enriched using poly(A) selection. Enriched mRNA was fragmented, reverse transcribed, and converted to cDNA. cDNA underwent end repair, adapter ligation, and size selection. PCR amplification was performed using 11 cycles to ensure sufficient library yield while minimizing amplification bias. Library quality and size distribution were assessed using a Tapestation (Agilent) and quantified by Qubit (Thermo Fisher Scientific). Libraries were pooled on an equimolar basis and sequenced on an Illumina NovaSeq X Plus platform using a 25B lane configuration with paired-end 150 bp reads with a minimum of 20 million paired reads per sample. Base calling and demultiplexing were performed using Illumina’s DRAGEN Bio-IT platform. Raw sequencing reads were processed for quality control using FastQC and trimmed to remove adapters and low-quality bases using Trimmomatic100and polyA tails using FASTP101.

treatment_protocol: Mice had two days of ad libitum access to a bottle of water or a bottle of 5% glycerol as their water source.

value: Liver

value: 2 days glycerol

tag: batch

value: A

value: Male


title: D12.P1.1

description: Library name: day12CD25pFoxp3n.1

value: Treg Progenitor

value: male


title: Patient3, POST3, TCR

description:
Library name: Patient3, POST3, TCR
10x Genomics

value: Blood

value: T cell

value: Yes


title: Jurkat, 5h, rep2 (RIBOseq)

data_processing:
Reads were trimmed using cutadapt v.3.2 to remove adapters (GATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Reads shorter than 25 nt or with quality scores less than 10 were also filtered out.
Unspecific reads were eliminated by a sequential mapping analysis using bowtie. First, trimmed reads were mapped to the rRNA and mtDNA references. The remaining reads were then mapped to the mRNA references (Gencode v37 GRCh38.p13 protein coding transcripts).
To quantify gene-level CDS occupancy, we used Bedtools intersect (v.2.25.0) to exclude reads which aligned outside of the +15th to −10th codon of the CDS.
Reads were counted using RSEM's routine rsem-calculate-expression
Counts were normalized with DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: CSV containing raw gene counts (from RSEM)
Supplementary files format and content: CSV with log2 normalized (DESeq2's median of ratios) gene expression.
Library strategy: RIBOseq (Ribosome profiling)

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast

value: 5h post-activation


title: Patient5, POST5, TCR

description:
Library name: Patient5, POST5, TCR
10x Genomics


title: Jurkat, 5h, rep3 (RIBOseq)


title: Patient2, PRE2, TCR

description:
Library name: Patient2, PRE2, TCR
10x Genomics

value: No


title: Slc25a13 -/- Gpd2 -/-, Male, M191, 2 days 5% glycerol

description: Library name: DKO_glycerol_2


title: Patient2, POST2, TCR

description:
Library name: Patient2, POST2, TCR
10x Genomics


title: Jurkat, 5h, rep1 (RIBOseq)


title: Slc25a13 -/- Gpd2 -/-, Male, M186, 2 days 5% glycerol

description: Library name: DKO_glycerol_1


title: D5.P2.3

description: Library name: day5CD25nFoxp3p.3

value: CD25- Foxp3+ Treg Progenitor

value: WT

value: day 5


title: D5.P2.2

description: Library name: day5CD25nFoxp3p.2

value: Thymus


title: Slc25a13 -/- Gpd2 -/-, Male, M119, 2 days 5% glycerol

description: Library name: DKO_glycerol_4

value: Liver

value: MGB


title: Patient1, PRE1, TCR

description:
Library name: Patient1, PRE1, TCR
10x Genomics


title: D5.P1.3

description: Library name: day5CD25pFoxp3n.3

value: CD25+ Foxp3- Treg Progenitor


title: Slc25a13 -/- Gpd2 -/-, Male, M255, 2 days water

description: Library name: DKO_water_2

value: 2 days water

value: A

value: Male


title: Patient1, POST1, TCR

description:
Library name: Patient1, POST1, TCR
10x Genomics

value: Blood


title: Jurkat, 12h, rep1 (RIBOseq)

value: 12h post-activation


title: Patient5, PRE5, BCR

description:
Library name: Patient5, PRE5, BCR
10x Genomics

data_processing:
Reads converted to FASTQ with mkfastq (Cell Ranger 7.0.0). Alignment, V(D)J assembly, and quantification performed via Cell Ranger Multi Pipeline (default parameters) using human references: refdata-gex-GRCh38-2020-A (expression) and refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 (repertoire).
Assembly: Human refdata-gex-GRCh38-2020-A (gene expression); Human refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 (V(D)J repertoire).
Supplementary files format and content: Tab-separated values files, matrix files (gene expression), and V(D)J repertoire files (FASTQ, clonotype tables) from Cell Ranger output.
Library strategy: BCR-Seq

value: B cell


title: Jurkat, 12h, rep3 (RIBOseq)

value: Human Jurkat Clone E6-1 (ATCC TIB-152)


title: Slc25a13 -/- Gpd2 -/-, Male, M253, 2 days water

description: Library name: DKO_water_1


title: Jurkat, 12h, rep2 (RIBOseq)

value: T lymphoblast


title: Slc25a13 -/- Gpd2 -/-, Male, M124, 2 days water

description: Library name: DKO_water_4


title: Jurkat, 0h, rep3 (RIBOseq)

value: control


title: Patient5, POST5, BCR

description:
Library name: Patient5, POST5, BCR
10x Genomics

value: Yes


title: H4K12ac, 8mM, Rings, rep2

city: Cambridge

first: Sida

last: Ye

state: Massachusetts

address: 48 CREIGHTON ST

department: Department of Mathematics

institute: UMass Boston

description: Library name: 8mM_H4K12ac_Rings_BR2_S20

library_source: genomic

data_processing:
The reference genome and gene annotations for P. falciparum (3D7, release 63) were downloaded from https://plasmodb.org/plasmo/. Raw reads were processed by MultiQC v1.20 (PMID: 27312411) to assess quality metrics and trimmed by Cutadapt v.2.10 (DOI: https://doi.org/10.14806/ej.17.1.200) to remove residual adapter sequences and low quality reads(phred score < 20). Trimmed reads were aligned to the reference genome by using BWA-mem v.0.7.17 (PMID: 19451168). Then, SAMtools v.1.10 was used to sort and index the bam files. Narrow peaks and broad peaks were called separately by MACS2(PMID: 18798982) against corresponding IgG controls at different stages with settings: “-p 0.01 --nomodel --extsize 200” and “-q 0.2 --nomodel --broad --keep-dup auto --max-gap 500”, respectively. The consensus peaks between two replicates were defined as those peaks have at least 50% overlaps by using  the BEDtools (PMID: 20110278) with settings: “bedtools intersect  -a -b -f 0.5 -F 0.5  -e -wo”. Consensus peaks were assigned and annotated by the custom R script using the following criteria: for narrow peak assignment, the occupancy of the peaks have been classified into genic peaks and non-genic peaks, the proportion of spanning range of genic peaks occupied on promoter(<=1000bp upstream of TSS), 5’UTR, exon, intron, 3’UTR were calculated, unique location was assigned to the location with highest proportion of occupancy for each peak, non-genic peaks with <= 2000bp distance to the nearest annotated gene was assigned to the nearest gene while those non-genic peaks has > 2000bp distance to the closest gene have no assignment; for broad peak assignment, those genic peaks covered only 1 gene will be piped into narrow peak assignment pipeline described above, while those broad genic peaks covered more than 1 gene have no assignment, broad non-genic peaks with <= 2000bp distance to the nearest annotated gene or overlapped with the nearest genes promoter regions were assigned to the nearest gene while those non-genic peaks has > 2000bp distance to the closest gene have no assignment. Normalized fold enrichment tracks and BigWig files were generated and visualized following the steps as previously published(PMID: 36379668)
Assembly: P. falciparum (3D7, release 63) were downloaded from https://plasmodb.org/plasmo/
Supplementary files format and content: BigWig files fpr 4 epigenetic antibodies with ring, troph and schizont stage after substracting the signal of IgG, which can be visualized in IGV
Library strategy: CUT&Run

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: H4K12ac antibody

extract_protocol:
Parasites were treated for 12 hours and then harvested at ring stage (12-16 hpi), trophozoite stage (28-32hpi) and schizont (40-44 hpi). Both panKla antibody and a site-specific H4K12la antibody were employed, alongside H3K4me3 and H4K12ac as positive controls and IgG as a negative control.
Library was constructed by follow the protocol of NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, NEB)

value: H4K12ac antibody

value: Human red blood cell

tag: cell subtype

value: O type

value: Lactylation treatment


title: D5.P1.1

description: Library name: day5CD25pFoxp3n.1

value: Thymus

value: Treg Progenitor

value: male

value: WT

value: day 5


title: Jurkat, 0h, rep2 (RIBOseq)


title: Jurkat, 0h, rep1 (RIBOseq)


title: Patient4, PRE4, BCR

description:
Library name: Patient4, PRE4, BCR
10x Genomics

value: No


title: Patient4, POST4, BCR

description:
Library name: Patient4, POST4, BCR
10x Genomics

value: Blood


title: Slc25a13 -/- Gpd2 -/-, Male, M105, 2 days water

description: Library name: DKO_water_3

value: Liver

value: 2 days water

value: MGB

value: Male


title: Embryonic neural stem cells (eNSC), PML knockout, rep 3

city: Heraklion-Voutes

first: Syrago

last: Spanou

address: N.Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: KO4
PML KO - KO4

data_processing:
Differential Expression Analysis (DEA) and of bulk quant RNA-seq data: The quality of the raw sequences in output FASTQ files was assessed with the FastQC software. Reads were aligned to the mouse (mm10) genome with the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). Htseq-counts  was utilized to summarize reads at the gene level (htseq-count -f bam -s yes-I gene_id bam/$FILE_ID.bam data/refs/ Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf>$COUNTS_DIR/NGS$FILE_ID). Differential expression analysis (DEA) was conducted by running EdgeR via SARTools 1.5.0 ( https://github.com/PF2-pasteur-fr/SARTools).
For each comparison (Pml-/- vs WT), DEGs in either group of the comparison) were defined by applying the following thresholds |Log2FC| >0.58 and p-adj <0.05, which was considered statistically significant.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing the results from Differential gene expression testing by EdgeR

source_name: Primary cells

growth_protocol: NSCs were cultured in proliferation medium (complete NSC medium supplemented with 20ng/ml epidermal growth factor and 20ng/ml fibroblast growth factor 2) at a density of 2 × 105 cells/ml, as neurospheres. Fresh medium was added every other day. Cells were incubated at 37°C in 5% CO2 and 20% oxygen at 95% humidity.

extract_protocol:
Neurospheres were directly lysed using Nucleozol (Macherey-Nagel) as per the manufacturer’s protocol and total RNA was extracted. The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent.
RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions.  DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent).  Amplification was controlled for obtaining optimal unbiased libraries across samples by assessing the number of cycles (ranging from 20-24) required by qPCR. Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH according to the manufacturer’s instructions.

treatment_protocol: Neurospheres from culture were collected on the 4th day after dissociation, for RNA sample preparation

value: Brain tissue

value: primary embryonic neural stem cells, E13.5

value: PML knockout


title: Embryonic neural stem cells (eNSC), PML knockout, rep 2

description:
Library name: KO3
PML KO - KO3


title: D5.P2.1

description: Library name: day5CD25nFoxp3p.1

value: CD25- Foxp3+ Treg Progenitor


title: Patient3, PRE3, BCR

description:
Library name: Patient3, PRE3, BCR
10x Genomics

value: B cell


title: Jurkat, 5h, rep3 (miRNA-Seq)

data_processing:
Reads were trimmed to remove the first base at the 5'-end, the adapter, and filtered for length (> 15).
Trimmed reads were mapped against mtDNA. Then, unmapped reads were used as input in miRDeep2's routine quantifier.pl using the miRGeneDB references.
Unmapped reads were rescued and mapped sequentially against tRNA, rRNA (tRAX), and gDNA references for identification.
miRNA counts were used for differential expression in DESEq2.
DESeq2 median of ratios method was used for data normalization.
Assembly: GRCh38.p13
Supplementary files format and content: CSV containing raw miRNA counts (from miRDeep2's quantifier.pl)
Supplementary files format and content: log2 normalized (DESeq2's median of ratios) miRNA expression.

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast

value: 5h post-activation


title: Gpd2 -/-, M093, Male, 2 days 5% glycerol

description: Library name: GPD2_glycerol_4

value: 2 days glycerol


title: Embryonic neural stem cells (eNSC), PML knockout, rep 1

description:
Library name: KO2
PML KO - KO2


title: Patient3, POST3, BCR

description:
Library name: Patient3, POST3, BCR
10x Genomics

value: Yes


title: Jurkat, 5h, rep2 (miRNA-Seq)


title: Gpd2 -/-, M092, Male, 2 days 5% glycerol

description: Library name: GPD2_glycerol_2

value: B


title: D5.P1.2

description: Library name: day5CD25pFoxp3n.2

value: Thymus

value: Treg Progenitor

value: CD25+ Foxp3- Treg Progenitor

value: male

value: WT

value: day 5


title: Embryonic neural stem cells (eNSC), control, rep 3

description:
Library name: C3
CONTROL - C3

value: Brain tissue


title: Jurkat, 5h, rep1 (miRNA-Seq)


title: Patient2, PRE2, BCR

description:
Library name: Patient2, PRE2, BCR
10x Genomics

value: Blood

value: No


title: Jurkat, 12h, rep3 (miRNA-Seq)

value: 12h post-activation


title: Gpd2 -/-, M040, Male, 2 days 5% glycerol

description: Library name: GPD2_glycerol_3

value: Liver

value: A

value: Male


title: Patient2, POST2, BCR

description:
Library name: Patient2, POST2, BCR
10x Genomics

value: B cell


title: Jurkat, 12h, rep2 (miRNA-Seq)

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast


title: Embryonic neural stem cells (eNSC), control, rep 2

description:
Library name: C2
CONTROL - C2

value: primary embryonic neural stem cells, E13.5


title: Patient1, PRE1, BCR

description:
Library name: Patient1, PRE1, BCR
10x Genomics


title: Gpd2 -/-, M095, Male, 2 days 5% glycerol

description: Library name: GPD2_glycerol_5

value: 2 days glycerol

value: MGB


title: Embryonic neural stem cells (eNSC), control, rep 1

description:
Library name: C1
CONTROL - C1


title: Gpd2 -/-, M039, Male, 2 days 5% glycerol

description: Library name: GPD2_glycerol_1

value: B


title: mouse uterus, Pre-dysplastic-32DPI, sample 7, scRNAseq

city: Ithaca

first: Matalin

last: Pirtz

state: New York

address: 147 Grandview Ct., #147LA

institute: Cornell University

description: 10X Genomics (Single Cell 3' v3)

library_source: transcriptomic single cell

data_processing:
The raw sequencing reads were aligned to the custom mm39 + tdTomato sequence reference genome and quantified using the cellranger (v7.1.0, 10x Genomics) or spaceranger (v2.1.1, 10x Genomics) count function. The outputs are barcode, feature, and matrix files for further analysis involving gene counts
Assembly: mm39 + tdTomato sequence
Supplementary files format and content: Tab-separated values files and matrix files

source_name: uterus

extract_protocol:
scRNA - Mice were sacrificed at various time points in the diestrus phase of the estrous cycle. Each mouse was collected and processed independently to generate single-cell suspensions. Both uterine horns of individual mice were collected and placed in sterile 1X PBS containing 100 IU ml-1 of penicillin and 100 μl ml-1 streptomycin (Corning, 30-002-Cl). A portion of one uterine horn per mouse was set aside in 4% paraformaldehyde at 4˚C for paraffin embedding. The remaining uterine horns were placed in a 200 μL drop of the same PBS solution, cut open lengthwise, and minced into 1.5-2.5 mm pieces with scalpels. Minced tissues were transferred with the help of a sterile, wide bore 200 μl pipette tip into a 15 ml centrifuge tube containing 2 ml of the same PBS solution and then centrifuged for 6 minutes at 400 rcf at 4˚C. Then, the minced tissues for individual mice were digested using a Papain Dissociation System (Worthington Biochemical Corporation, New Jersey). Tissue was digested in papain mixture from the kit at 37˚C for 1.5 hours with periodic mechanical perturbation. After papain digestion, the papain was inhibited with 3 ml of our stop solution, a DMEM/FBS solution (DMEM Ham’s F12, Corning 10-092-CV; 20% fetal bovine serum [FBS], Sigma-Aldrich F4135; and 0.1 mg ml-1 DNase I, Stem Cell Technologies 07900). Cell suspension was placed in a new tube. Cells were centrifuged as before, and the supernatant was removed. Next, 1.35 ml of the albumin-ovomucoid inhibitor provided by the kit was added to the suspended cells, and the cells were resuspended gently. The reaction was stopped using 3 ml of our stop solution, mixed, and then cells were spun down at the same rate as before. The supernatant was removed, and the pellet was resuspended in 2 ml of 0.25% TrypLE Express Enzyme solution (Invitrogen, 12604013) prewarmed to 37˚C. The tube was then incubated at 37˚C with a loose cap for 10 minutes in a 5% CO2 incubator. Cells were resuspended with a 1-ml pipette tip 40 times, and then digestion was inhibited with our stop solution. Cells were spun down and supernatant was removed before the addition of 1 ml Dispase-mUE (Dispase II [7 mg ml-1 DMEM Ham’s F12], Neutral Protease, Worthington NPRO2; and 10 μg μL-1 DNase). Cells were aspirated in the solution gently 40 times using a 1 ml pipette tip. Then suspensions were filtered through a 35 μm filter (Falcon 08-771-23) to remove debris, and remaining cells were spun down. Cells were resuspended in 100 μl A-scR-Medium (5% FBS in DMEM Ham’s F12 with 1 mM Y-27632 [Toris 1257], placed on ice and transferred to Cornell’s Genomics Core for single-cell RNA sequencing for library preparation.
Visium - Mouse uteri from Doxycyline induced Pax8-rtTA Tre-Cre Trp53loxP/loxPRb1loxP/loxP Ai9 experimental mice and control littermates were dissected and frozen in O.C.T. (Tissue Tek O.C.T. Compound, VWR, 25608-930) filled molds (Disposable Based Molds, 15 x 15 mm, VWR, 60872-488) on a metal block chilled in dry ice for 10 minutes. Molds were wrapped in aluminum foil, placed and sealed in zip lock plastic bags and stored at -80°C (10xGenomics, protocol CG000240RevD). Embedded samples, and all materials for cryosectioning were equilibrated in a cryostat (Leica CM1950) chamber temperature -21°C (object head, -16°C) for 30 minutes. Transverse uterus sections of 10µm thickness were placed on chilled Visium Tissue Optimization Slides (10xGenomics, 1000191 Slide Kit), and Visium Spatial Gene Expression Slides (10xGenomics, 1000187 Slide Kit). Tissues processed on the Visium Tissue Optimization Slides (10xGenomics, protocol CG000238RevD) indicated the optimal uterine tissue permeabilization time was 12 minutes. For tissue optimization experiments Tiff fluorescent images (Microscope Olympus EX51, Camera Olympus XM10) were captured with a TRITC filter cube, 2x objective, and 700-ms exposure time. Uterine tissues on Visium Spatial Gene Expression Slides were processed for Hematoxylin & Eosin (H&E) staining (10xGenomics, protocol CG000160RevC). Immediately after staining, digital brightfield histology images were taken at 40x (Leica BioSystems, Aperio ScanScope CS2). Without delay cDNA Synthesis, Second Strand Synthesis & Denaturation, and cDNA Amplification was performed (10xGenomics, protocol CG000239RevE). Samples were frozen at -20°C and transferred to Cornell Genomics Facility for Quality Control (QC), Gene Expression Library Construction and sequencing.
scRNA - To begin single-cell RNA sequencing library preparation, cell aliquots were stained with trypan blue for live and dead cell calculation. Live cell preparations with a target cell recovery of 5,000 cells were loaded on a Chromium Controller (10X Genomics, Single Cell 3’ v3 chemistry) to perform single-cell partitioning and barcoding using the microfluidic platform device. The NextSeq500 System was used to sequence the cDNA library samples after barcode preparation.
Visium - The Illumina Sequencing parameters for all Visium samples were as follows, visium library preparations were run 2 times, they were re-balanced and re-pooled in between the 2 runs. The estimated dPCR was 2.5 nMol. Samples were run on a NextSeq2K P2 100bp flowell instrument, sequencing Kit NextSeq 2K P2 100 bp, read length 28+10+10+90, sequencing primer type TruSeq Compatible DNA/RNA, barcode type Dual barcode i7 and i5.

value: uterus

tag: estrous stage

value: diestrus

tag: sec stage

value: Pre-dysplastic

value: Doxycycline, 32 DPI


title: Gpd2 -/-, M091, Male, 2 days water

description: Library name: GPD2_water_4

value: 2 days water


title: Jurkat, 12h, rep1 (miRNA-Seq)


title: Patient1, POST1, BCR

description:
Library name: Patient1, POST1, BCR
10x Genomics

value: Blood

value: Yes


title: mouse uterus, Pre-dysplastic-31DPI, sample 6, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Doxycycline, 31 DPI


title: Jurkat, 0h, rep3 (miRNA-Seq)

value: control


title: Patient5, PRE5, scRNA

description:
Library name: Patient5, PRE5, scRNA
10x Genomics

data_processing:
Reads converted to FASTQ with mkfastq (Cell Ranger 7.0.0). Alignment, V(D)J assembly, and quantification performed via Cell Ranger Multi Pipeline (default parameters) using human references: refdata-gex-GRCh38-2020-A (expression) and refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 (repertoire).
Assembly: Human refdata-gex-GRCh38-2020-A (gene expression); Human refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 (V(D)J repertoire).
Supplementary files format and content: Tab-separated values files, matrix files (gene expression), and V(D)J repertoire files (FASTQ, clonotype tables) from Cell Ranger output.

value: PBMC

value: No


title: Gpd2 -/-, M090, Male, 2 days water

description: Library name: GPD2_water_3

value: Liver

value: A

value: Male


title: mouse uterus, Pre-dysplastic-33DPI, sample 5, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Doxycycline, 33 DPI


title: Gpd2 -/-, M036, Male, 2 days water

description: Library name: GPD2_water_2


title: Gpd2 -/-, M035, Male, 2 days water

description: Library name: GPD2_water_1


title: Patient4, PRE4, scRNA

description:
Library name: Patient4, PRE4, scRNA
10x Genomics


title: Jurkat, 0h, rep2 (miRNA-Seq)

value: Human Jurkat Clone E6-1 (ATCC TIB-152)

value: T lymphoblast


title: Patient5, POST5, scRNA

description:
Library name: Patient5, POST5, scRNA
10x Genomics


title: mouse uterus, Pre-dysplastic-31DPI, sample 4, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: uterus


title: Slc25a13 -/-, Male, M011, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_7

value: 2 days glycerol


title: Jurkat, 0h, rep1 (miRNA-Seq)


title: mouse uterus, Normal-38DPI, sample 5, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: diestrus

value: Normal

value: Doxycycline, 38 DPI


title: Slc25a13 -/-, Male, M010, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_6

value: B


title: Model

city: Nanjing

first: Yuanhao

last: Xu

state: --- Select One ---

address: Longmian Avenue 639

institute: China Pharmaceutical University

description:
Library name: Model
Model(raw)

data_processing:
Reads were trimmed (TruSeq adapters, Q ≥ 20) via ACGT101-miR v4.2 and mapped to GRCm38/mm10.
MiRNAs were identified against miRBase v22.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain and intestinal

growth_protocol: Male C57BL/6J mice (18–22 g) were housed under SPF conditions (25 ± 1 °C, 50–60 % humidity, 12 h light/dark) with free access to food and water.

extract_protocol:
Total RNA from brain and colon tissues was extracted using TRIzol reagent (Vazyme) according to the manufacturer’s instructions.
Small-RNA libraries were prepared using TruSeq Small RNA Sample Prep Kit (Illumina) with 1 µg total RNA.

treatment_protocol: Ischemic stroke with gut dysbiosis (IS-GD) was induced by fecal-slurry gavage (150 mg/mL, 1.5 g/kg, 3 days) followed by permanent middle cerebral artery occlusion (pMCAO). Xinqingning Tablet (0.61 g/kg) or vehicle was given intragastrically once daily for 7 days starting 2 h post-pMCAO.

value: Brain and intestinal


title: Patient4, POST4, scRNA

description:
Library name: Patient4, POST4, scRNA
10x Genomics

value: Blood

value: Yes


title: mouse uterus, Pre-dysplastic-35DPI, sample 3, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Pre-dysplastic

value: Doxycycline, 35 DPI


title: Slc25a13 -/-, Male, M026, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_3

value: Liver

value: MGB


title: Control

description:
Library name: Control
Control(raw)


title: Patient3, PRE3, scRNA

description:
Library name: Patient3, PRE3, scRNA
10x Genomics

value: PBMC

value: No


title: mouse uterus, Pre-dysplastic-35DPI, sample 1, scRNAseq

description: 10X Genomics (Single Cell 3' v3)


title: Patient2, PRE2, scRNA

description:
Library name: Patient2, PRE2, scRNA
10x Genomics


title: WT islets sample 2

city: Chicago

first: Brian

middle: T

last: Layden

state: Illinois

address: 835 S Wolcott

department: Division of Endocrinology, Diabetes & Metabolism, Department of Medicine,

institute: University of Illinois at Chicago

description: Library name: BL8

data_processing:
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome. Raw reads values were extracted from the cuffdiff results.
Assembly: mm10
Supplementary files format and content: Differential Expression Layden FFAR2 original.xlsx
Supplementary files format and content: raw reads.xlsx

source_name: pancreatic islets

extract_protocol:
total cellular RNA was extracted from isolated islets (pooled from 2 mice) using an RNeasy Mini kit (QIAGEN, Venlo, Linburg). Experiments were run in triplicate for each genotype.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets

value: WT

value: normal chow fed 10-12 weeks old


title: WT islets sample 3

description: Library name: BL9


title: WT islets sample 1

description: Library name: BL7


title: Patient3, POST3, scRNA

description:
Library name: Patient3, POST3, scRNA
10x Genomics


title: Patient2, POST2, scRNA

description:
Library name: Patient2, POST2, scRNA
10x Genomics


title: mouse uterus, Normal-51DPI, sample 4, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: uterus

value: Doxycycline, 51 DPI


title: mouse uterus, Normal-50DPI, sample 3, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: diestrus

value: Normal

value: Doxycycline, 50 DPI


title: FFA2 global KO islets sample 3

description: Library name: BL12

value: FFA2 global KO


title: Slc25a13 -/-, Male, M191/20, 2 days water

description: Library name: SLC25A13_water_2

value: 2 days water

value: B

value: Male


title: FFA2 global KO islets sample 2

description: Library name: BL11


title: mouse uterus, Dysplastic-147DPI, sample 5, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Dysplastic

value: Doxycycline, 147 DPI


title: FFA2 global KO islets sample 1

description: Library name: BL10


title: mouse uterus, Pre-dysplastic-36DPI, sample 2, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Pre-dysplastic

value: Doxycycline, 36 DPI


title: vascular tissue Iso_5

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: SHR  with 10-week Iso (5mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it if the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window, remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed, if the truncated read length is less than 50 bp, the entire read is removedRemove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

organism: Rattus norvegicus

source_name: vascular tissue

extract_protocol:
The abdominal aorta were dissected and  stored in RNA later.Total RNA was extracted with trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

value: SHR

value: vascular tissue

value: Isoliensinine

tag: group

value: SHR+Iso


title: Slc25a13 -/-, Male, M009, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_4

value: Liver

value: 2 days glycerol


title: Slc25a13 -/-, Male, M190/20, 2 days water

description: Library name: SLC25A13_water_1


title: mouse uterus, Dysplastic-95DPI, sample 4, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: uterus

value: diestrus

value: Doxycycline, 95 DPI


title: Slc25a13 -/-, Male, M025, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_5

value: MGB


title: ST2 OSTEO 48h GRO-seq biol rep4

city: Kuopio

first: Ana

last: Hernández de Sande

email: anah@uef.fi, ahdesande@gmail.com

state: North-Savo

address: Yliopistonranta 1E

country: Finland

institute: University of Eastern Finland

description: GROseq in control cell line

data_processing:
library strategy: GRO-seq
Single-end sequencing (51-55bp) was performed with HiSeq 2000, according to the manufacturer instructions. Fastq files were demultiplexed using custom code.
GRO-seq reads were quality controlled (FastQC). Reads were adapter trimmed using HOMER (version 4.9(Heinz, Benner et al. 2010)) and filtered (min 95% of positions have a minphredquality score of 10) using theFastXtoolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads mapping to rRNA regions (AbundantSequencesas annotated byiGenomes) were discarded.
The Bowtie software (version 1.1.2 Langmead et al., 2009) was then used for alignment of remaining reads to the mm9 genome version, allowing up to two mismatches and no more than three matching locations. The best alignment was reported. Reads corresponding with so-called blacklisted regions that include unusual low or highmappabilityas defined by ENCODE, ribosomal and small nucleolar RNA (snoRNA) loci from ENCODE and a custom collection of unusually high signal depth regions from GRO-seq was used to filter the data.
bigWig files were generated using the HOMER software http://biowhat.ucsd.edu/homer/. GRO-seq tagDirectorieswere generated from aligned reads with fragment length set to 75 and data visualized using makeMultiWigHub.pl with strand-specificity HOMER (version 4.9)
Assembly: mm9
Supplementary files format and content: bigWig GRO-seq signal files, separately for plus and minus strand

growth_protocol: Cells were cultured in RPMI1640 (Lonza) supplemented with 10% FBS (Gibco, Thermo Fisher) and 1% L-glutamine (Gibco, Thermo Fisher).

extract_protocol:
Five million nuclei were collected from ST2 cells after DMSO (vehicle) treatment. The nuclear run-on reaction buffer (496 mMKCl, 16.5 mM Tris-HCl, 8.25 mM MgCl2 and 1.65%Sarkosyl(Sigma-Aldrich, Steinheim, Germany) was supplemented with 1.5 mM DTT, 750 uMATP, 750 uMGTP, 4.5 uMCTP, 750 uMBr-UTP (B7166,Sigma-Aldrich) andRNAse inhibitors (RNase Inhibitor (Thermo Fisher, Carlsbad, CA, USA, andRNasin Plus RNase Inhibitor Promega). To each 100 ulof nuclei samples 50 μlof the run-on reaction buffer was added and incubated for 5 min at 30C.
RNA was collected using Trizol LS, fragmented and run-on reaction products were immuno-purified two times using anti-Br-UTP antibody (ab-6326, Abcam) bound to 30 μl of magnetic beads (Protein GDynabeadsThermo Fisher Scientific) and washed with 300μlof PBST wash buffer four times (refer to detailed protocol in Roberts et al. 2015). The cDNA template was PCR amplified (Illumina barcoding) for 12 cycles and size selected to 225–350 bp length. The ready libraries were sequenced with Illumina Hi-Seq2000 (GeneCore, EMBL Heidelberg, Germany).

treatment_protocol: For adipo- and osteogenic differentiation, once cells have become confluent, they are referred to be in Day -2 pre-differentiation, and are maintained for 48h in normal growth medium to allow contact inhibition and cell cycle arrest. On Day 0 either adipo- or osteogenic differentiation can then be induced.  Cell differentiation into adipo- and osteoblast lineages is detailed in  Gérard et al., 2018 publication. Briefly, we follow the adipogenic differentiation protocol established for the 3T3-L1 cell line, and achieved best osteogenic differentiation using BMP-4 with a concentration of 100 ng/ml (Peprotech, U.K.). Controls were treated with DMSO.

value: stromal bone marrow derived cell line

value: fibroblast

tag: contruct/treatment

value: OSTEO

tag: time

tag: replicate


title: Slc25a13 -/-, Male, M189, 2 days water

description: Library name: SLC25A13_water_7

tag: tissue

value: 2 days water

value: Male


title: Slc25a13 -/-, Male, M188, 2 days water

description: Library name: SLC25A13_water_6


title: ST2 OSTEO 48h GRO-seq biol rep3

description: GROseq in control cell line

tag: cell line


title: Slc25a13 -/-, Male, M187, 2 days water

description: Library name: SLC25A13_water_5

value: A


title: ST2 OSTEO 48h GRO-seq biol rep2

description: GROseq in control cell line

tag: cell type


title: vascular tissue Iso_3

tag: treatment


title: mouse uterus, Normal-95DPI, sample 2, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Normal


title: Slc25a13 -/-, Male, M024, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_2


title: mouse uterus, Dysplastic-91DPI, sample 3, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Dysplastic

value: Doxycycline, 91 DPI


title: Slc25a13 -/-, Male, M012, 2 days water

description: Library name: SLC25A13_water_4


title: mouse uterus, Dysplastic-148DPI, sample 6, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Doxycycline, 148 DPI


title: ST2 OSTEO 24h GRO-seq biol rep1

description: GROseq in control cell line


title: Patient1, PRE1, scRNA

description:
Library name: Patient1, PRE1, scRNA
10x Genomics

value: Blood

value: PBMC

value: No


title: vascular tissue Iso_1

tag: strain

value: SHR

value: vascular tissue

value: Isoliensinine

value: SHR+Iso


title: mouse uterus, Normal-91DPI, sample 1, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: uterus

value: diestrus


title: Patient1, POST1, scRNA

description:
Library name: Patient1, POST1, scRNA
10x Genomics

value: Yes


title: Slc25a13 -/-, Male, M022, 2 days 5% glycerol

description: Library name: SLC25A13_glycerol_1

value: Liver

value: 2 days glycerol


title: vascular tissue SHR_5

description: SHR  with 10-week  double distilled water  treatment

value: double distilled water


title: Slc25a13 -/-, Male, M004, 2 days water

description: Library name: SLC25A13_water_3

value: 2 days water

value: A

value: Male


title: ST2 OSTEO 10h GRO-seq biol rep1

description: GROseq in control cell line

value: stromal bone marrow derived cell line

value: fibroblast

value: OSTEO


title: vascular tissue Iso_4


title: mouse uterus, Dysplastic-132DPI, sample 1, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: Dysplastic

value: Doxycycline, 132 DPI


title: vascular tissue SHR_4

value: SHR

value: vascular tissue


title: ST2 OSTEO 6h GRO-seq biol rep1

description: GROseq in control cell line


title: INTS11DEG_PRO_6h_rep2

city: MIAMI

first: Raghu

middle: Ram

last: Edupuganti

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

data_processing:
FASTQ data were trimmed by Cutadapt 1.14 and Trimmomatic v0.32.
Bowtie 1.1.2 was used to align the data on the Mouse (mm10) or Drosophila (dm3) genome. The single nucleotide ends of aligned reads were made with BEDTools v2.28 with genomecov as bedgraph format. The number of reads mapped to the spike-in dm3 genome was used to normalize the bedgraph data before it was changed to bigwig data for further analysis. To determine the accurate TSS for each gene, we separated the mapped reads from PRO-seq by strand and individually called peaks using MACS2.1.2  with the following parameters: --nomodel, --extsize 200 and –narrow to identify narrow peaks. We merged the common peaks from each sample (time 0, 1h, 3h, and 6h) for each stranded peak and used the BedTools command to annotate the peaks against mouse Ensembl (v96).
Assembly: mm10
Supplementary files format and content: The processed data files are in bigWig format.
Library strategy: PRO-seq

source_name: Embryonic origin

growth_protocol: E14 ESCs were routinely grown on 0.1% gelatin  coated plates in DMEM (high glucose, GlutaMAX Supplement) medium  supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin/100 U/mL streptomycin, 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% Embryonic stem-cell FBS, and 1000 U/mL recombinant leukemia inhibitory factor (LIF). Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Nuclear run-on experiments were performed on ten million ESC nuclei for three minutes at 30 °C using 25 µM Biotin-11-ATP/UTP/CTP/GTP.
After extracting the total RNA, it was fragmented using 0.2 M NaOH for 10 min on ice. Streptavidin beads M-280 were used to purify biotinylated nascent RNAs. 5’ end repair was performed using RppH and PNK. SuperScript III was used for reverse transcription after adapter ligation. Following PCR amplification, 140–350 bp libraries were size-selected by AMpure XP and sequenced with single-read runs on an Illumina NextSeq 500.

treatment_protocol: INTS11DEG cells were routinely maintained in ESC medium containing 10 µM Trimethoprim. To deplete INTS11DEG, cells were washed twice with PBS to remove Trimethoprim. After two washes, fresh ESC medium and DMSO (1µl/ ml) were added to the cells. The cells were incubated with out drug for the predetermined time (0h, 1h, 3h, 6h) and harvested.

value: Embryonic origin

value: Mouse Embryonic Stem cells

value: INTS11 depletion 6h


title: vascular tissue SHR_3


title: vascular tissue Iso_2

value: Isoliensinine

value: SHR+Iso


title: WT, Male, M004, 2 days 5% glycerol

description: Library name: WT_glycerol_4

value: Liver

value: WT

value: 2 days glycerol

value: MGB


title: INTS11DEG_PRO_6h_rep1


title: ST2 OSTEO 2h GRO-seq biol rep1

description: GROseq in control cell line


title: vascular tissue SHR_2

value: double distilled water


title: ST2 OSTEO 1h GRO-seq biol rep1

description: GROseq in control cell line

value: stromal bone marrow derived cell line


title: INTS11DEG_PRO_3h_rep2

value: INTS11 depletion 3h


title: INTS11DEG_PRO_3h_rep1


title: mouse uterus, Dysplastic-91DPI, sample 2, scRNAseq

description: 10X Genomics (Single Cell 3' v3)

value: uterus

value: diestrus

value: Doxycycline, 91 DPI


title: WT, Male, M003, 2 days 5% glycerol

description: Library name: WT_glycerol_2

value: B

value: Male


title: ST2 INSULIN 48h GRO-seq biol rep3

description: GROseq in control cell line

value: fibroblast

value: INSULIN


title: vascular tissue WKY_5

description: WKY with 10-week double distilled water treatment

value: WKY

value: vascular tissue


title: WT, Male, M4, 2 days water

description: Library name: WT_water_2

value: 2 days water


title: vascular tissue WKY_6


title: WT, Male, M001, 2 days 5%glycerol

description: Library name: WT_glycerol_3

value: Liver

value: A


title: WT, Male, M002, 2 days 5% glycerol

description: Library name: WT_glycerol_1

value: WT

value: 2 days glycerol


title: WT, Male, M005, 2 days 5% glycerol

description: Library name: WT_glycerol_5

value: MGB


title: ST2 IBMX 48h GRO-seq biol rep4

description: GROseq in control cell line

value: stromal bone marrow derived cell line

value: IBMX


title: INTS11DEG_PRO_1h_rep1

value: Embryonic origin

value: Mouse Embryonic Stem cells

value: INTS11 depletion 1h


title: WT, Male, M3, 2 days water

description: Library name: WT_water_4

value: MBG


title: vascular tissue WKY_2

value: double distilled water


title: ST2 IBMX 48h GRO-seq biol rep3

description: GROseq in control cell line

value: fibroblast


title: INTS11DEG_PRO_0h_rep2

value: INTS11 control 0h


title: WT, Male, M2, 2 days water

description: Library name: WT_water_3

value: Male


title: ST2 IBMX 48h GRO-seq biol rep2

description: GROseq in control cell line


title: WT, Male, M1, 2 days water

description: Library name: WT_water_1

value: B


title: vascular tissue WKY_1

value: WKY

value: vascular tissue


title: ST2 INSULIN 48h GRO-seq biol rep4

description: GROseq in control cell line

value: INSULIN


title: wt_1

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

data_processing:
We used MISO105 for alternative splicing analysis, as this tool is known for its consistent performance and wide use 106. Specifically, RNA-seq data was processed as follows: (1) to fulfill MISO requirements (see below), the reads obtained with different sequencing lengths were truncated to 75bps with cutadapt (v.2.10) -l option, (2) the truncated reads were mapped to the human hg38 genome assembly with GENCODE v38 comprehensive gene annotation using STAR (v.2.7.9) with options --outFilterScoreMinOverLread and --outFilterMatchNminOverLread both set to 0.25 107, (3) non-unique alignments were filtered and the replicates were merged, (4) the insert size distribution was estimated for each merged bam file separately using pe_utils –compute-insert-len from MISO (v.0.5.4), constitutive exons were retrieved using exon_utils with --get-const-exons and --min-exon-size 1000 105, (5) alternative splicing events were identified using miso --run with --read-len set to 75 and --paired-end set to the previously estimated insert size parameters. Finally, only cases with non-zero numbers of exclusion and inclusion reads and sum of these reads >=10 in at least one sample are left and shown in Figure 4.
Assembly: hg38, gencode v38
Supplementary files format and content: The processed data contains the MISO outputs for all events for the comparison of WT vs Control

growth_protocol: All cells were cultured in a 37°C 5% CO2 humidified incubator. The K562 cell line was cultured in RPMI-1640 medium supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). All cell lines were routinely screened for mycoplasma with a PCR-based assay.

extract_protocol:
Total RNA for RNA-seq and RT-qPCR was isolated using the Zymo QuickRNA isolation kit with in-column DNase treatment per the manufacturer’s protocol.
RNA-seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara), and sequenced on Illumina NovaSeq 6000 instrument, in a PE150 (paired end 150 cycles) setting, at Novogene Corporation.

treatment_protocol: K562 and K562 TAF15 knockdown cell lines were seeded at 1M/1mL density in 2 replicates. Cells were infected with 10 μg/mL α-amanitin(Sigma-Aldrich A2263) for 8-9 h prior to total RNA extractions. Total RNA for downstream RNA-seq was isolated using Zymo QuickRNA Microprep isolation kit with in-column DNase treatment per the manufacturer’s protocol.

value: Lymphocyte

value: Control


title: ST2 DMSO 48h GRO-seq biol rep4

description: GROseq in control cell line

value: DMSO


title: vascular tissue SHR_1

value: SHR


title: ChIP_Input

data_processing:
Raw FASTQ data were processed with Trimmomatic (v0.32) to remove low-quality reads and then aligned to the mouse genome (mm10) using STAR aligner v2.7.9a. We used deepTool2 to generate normalized bigwig (bamCoverage), and heatmaps (computeMatrix and plotHeatmap). Peaks were called using MACS2.1.2 with default parameters –shiftsize 75 –nomodel --extsize 200 –p 0.01 for all datasets. Whole cell extract input from the corresponding cell lines was used as a control. Peaks with fold change > 3 and a q-value < 0.01 were used for downstream analysis. Homer annotatePeaks v4.9.1-5 was used for peak annotation. BEDTools v2.28 function intersect was used to overlap common peaks.
Assembly: mm10
Supplementary files format and content: The processed data files are in bigWig format.

growth_protocol: E14 ESCs were routinely grown on 0.1% gelatin coated plates in DMEM (high glucose, GlutaMAX Supplement) medium supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin/100 U/mL streptomycin, 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% Embryonic stem-cell FBS, and 1000 U/mL recombinant leukemia inhibitory factor (LIF). Cells were cultured at 37°C with 5% CO2.

extract_protocol:
ESCs were washed with PBS and fixed with ChIP cross-link GOLD reagent in PBS containing 1 mM MgCl2 for 30 minutes at room temperature. The cells were washed twice with PBS and fixed with 1% Formaldehyde for 10 minutes. Formaldehyde was quenched by the addition of Glycine to 125 mM. Fixed cells were scrapped and washed twice with chilled PBS, pelleted, and resuspended in NP Rinse 1 buffer (50 mM HEPES, pH 8.0, 140 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and incubated for 10 min on ice to isolate nuclei. The cells were pelleted at 1200g for 10 min and resuspended in NP1 Rince buffer 1 again and incubated for a further 10 min on ice and pelleted at 1200g.  The resulting nuclei were suspended in NP Rinse 2 buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0, 200 mM NaCl) and incubated on ice for 10 min. The pellet was washed twice with shearing buffer (10 mM Tris-HCl, pH 8.0, 0.1% SDS, 1 mM EDTA, pH 8.0) without disturbing the pellet. Pellets were resuspended in shearing buffer with protease and phosphatase inhibitor cocktail and sonicated in a Covaris E220 sonicator for 20 min using settings 5% duty cycle, PIP 140 and 200 cycles burst, to generate DNA fragments between approximately 200 and 1,000 bp in length. Insoluble material was pelleted by centrifugation for 15 min at 16,000g. Chromatin was immunoprecipitated overnight at 4 °C with antibodies bound to ChIP-grade Protein A/G Magnetic beads in ChIP buffer (50 mM HEPES, pH 7.5, 300 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% DOC, 0.1% SDS). After incubation, bead slurry was washed 5 times with ChIP buffer, once with DOC buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% DOC, 1 mM EDTA pH 8.0) and once with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0). Chromatin was eluted with elution solution (0.1% NaHCO3, 1% SDS, and 1 mM EDTA) by incubating at 55 degrees for 15 min. After RNase A and Proteinase K digestion and de-crosslinking at 65 °C overnight, DNA was extracted with ChIP DNA Clean & Concentrator.
A minimum of 2 ng of DNA was used for library preparation according to the NEBNextUltra II DNA Library Prep Kit for Illumina. Purity and size distribution were analyzed on Tapestation 2200. The constructed libraries were pooled and subjected to single-end sequencing with 75 base pairs read length on a NextSeq 500 platform.

tag: chip antibody


title: STK25 wKO

city: Beijing

first: Xiaowen

last: Qiao

address: No.52 Fucheng Road, Haidian District

institute: Peking University

data_processing:
cellranger reanalyze takes feature-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings.The Seurat package was used to normalise data, dimensionality reduction, clustering,differential expression. we used Seurat alignment method canonical correlation analysis (CCA) [Nat. Biotechnol. 36, 411–420 (2018).] for integrated analysis of datasets. For clustering, highly variable genes were selected and the principal components based on those genes used to build a graph, which was segmented with a resolution of 0.6
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colorectal cancer

extract_protocol:
Fresh tumor samples obtained from groups of WT and STK25 wKO mice were pooled, rinsed with PBS, minced, and dissociated with 1× Trypsin-EDTA solution for 20 minutes at 37°C. A Countstar Fluorescence Cell Analyzer was used to assess the cell viability of dissociated single cells.
The cell suspension was loaded into Chromium microfluidic chips with 3’ (v2 or v3,depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq ,depends on project) according to the manufacturer’s instructions (Illumina).

value: colorectal cancer


title: INTS11DEG_PRO_1h_rep2

value: Embryonic origin


title: ZC3H11A_2

value: ZC3H11A KO


title: ChIP_RNA_PolII_rep1

value: Mouse Embryonic Stem cells

value: RNA PolII (CST, #14958S)


title: ChIP_RNA_PolII_rep2


title: ST2 INSULIN 48h GRO-seq biol rep2

description: GROseq in control cell line

value: stromal bone marrow derived cell line


title: WT


title: ST2 DMSO 48h GRO-seq biol rep3

description: GROseq in control cell line

value: fibroblast


title: ChIP_RING1B_rep2


title: ST2 DMSO 24h GRO-seq biol rep1

description: GROseq in control cell line


title: vascular tissue WKY_4

value: double distilled water


title: wt_2


title: apj1d ydj1-4xcga, riboseq, steadystate, bio rep3

city: Heidelberg

first: Lucia

last: Svoboda

address: Im Neuenheimer Feld 345

country: Germany

institute: ZMBH

description: Library name: apj1dydj14x_3_25

data_processing:
sequences were trimmed for adaptors and sequence/ low-quality sequence using cutadapt version 3.5
UMIs were extracted from trimmed sequence reads using a custom Julia script
reads were aligned to S. cerevisiae rRNA sequences with bowtie version 1.3.1 using  -n 2 alignment mode and --best reporting mode. Only reads that did not align were kept.
reads were mapped to S. cerevisiae S288C Genome (Assembly: GCA_000146045.2) using STAR version 2.7.10a. Following mapping parameters were used: --outSAMmultNmax 1; --outFilterType BySJout; --alignIntronMin 5; --quantMode GeneCounts; --twopassMode Basic; --outSAMattributes All XS
With a custom Julia script reads were processed as described here: Reads from PCR dupicates were detected using UMI and were collapsed to a single read. Ribosomal positions were assigned.
Assembly: GCA_000146045.2
Supplementary files format and content: cds_umi_psite.h5
Supplementary files format and content: Reads mapped to the CDS, filtered for UMIs, aligned to the p-site
Library strategy: Ribo-Seq

organism: Saccharomyces cerevisiae

source_name: Whole cell

growth_protocol: Yeast were inocculated from overnight culture at OD600 0.05 in homemade YPD, and grown shaking with 140 rpm at 25°C (steady state) or 30°C (heat-shock timecourse) until OD600 0.5-0.6, before harvest.

treatment_protocol: Cells were heat-shocked in a shaking waterbath at 140 rpm and 38°C for the indicated times (10 mins or 60 mins) after reaching OD600 0.3 (60 mins) or OD600 0.4 (10 mins), before harvest

value: Whole cell

value: BY4741 apj1d ydj1-4xcga


title: ZC3H11A_1


title: INTS11DEG_PRO_0h_rep1

value: INTS11 control 0h


title: ST2 DMSO 10h GRO-seq biol rep1

description: GROseq in control cell line


title: apj1d ydj1-4xcga, riboseq, steadystate, bio rep1, tech rep 2

description: Library name: apj1dydj14x_1_25_2


title: ChIP_INTS12_rep2

value: INTS12 (Sigma prestige, #HPA035772)


title: ChIP_RING1B_rep1


title: apj1d ydj1-4xcga, riboseq, steadystate, bio rep2

description: Library name: apj1dydj14x_2_25


title: ST2 DMSO 48h GRO-seq biol rep2

description: GROseq in control cell line


title: ST2 DMSO 6h GRO-seq biol rep1

description: GROseq in control cell line


title: apj1d ydj1-4xcga, riboseq, steadystate, bio rep1, tech rep 1

description: Library name: apj1dydj14x_1_25_1


title: ST2 IBMX 48h GRO-seq biol rep1

description: GROseq in control cell line


title: 1000922_D6-WT-LT-control

city: Tarrytown

first: Wei Keat

last: Lim

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron

description:
Library name: 1000922_1_1_1-H3T5KBGX5
10x Chromium

data_processing:
CellRanger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core.
Replicates from time points were aligned to mm10 genome, while downstream analysis was performed with Seurat 3.0
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files

source_name: gluteus medius

extract_protocol:
Induction of the FOP mouse model in Acvr1[R206H]FlEx/+; Gt(ROSA26)SorCreERT2/+ mice and Acvr1+/+; Gt(ROSA26)SorCreERT2/+ control mice were performed as described [S.J. Hatsell et al, "ACVR1R206H receptor mutation causes fibrodysplasia ossificans progressiva by imparting responsiveness to activin A", Sci. Transl. Med. 7 (303) (2015) 303ra137.].
Library was performed according to the manufacter's insturction - 10× Genomics Chromium Controller (v2 reagent kit)

value: gluteus medius


title: 1000921_D6-WT-RT-Injured

description:
Library name: 1000921_1_1_1-H3T5KBGX5
10x Chromium


title: apj1d sis1-4xcga, riboseq, steadystate, bio rep3

description: Library name: apj1dsis14x_3_25

value: BY4741 apj1d sis1-4xcga


title: 1000919_D6-WT-RT-Injured

description:
Library name: 1000919_1_1_1-HCNJJBGX5
10x Chromium


title: ChIP_HA_INTS11_rep1


title: 1000920_D6-WT-LT-control

description:
Library name: 1000920_1_1_1-H3VLLBGX5
10x Chromium


title: apj1d sis1-4xcga, riboseq, steadystate, bio rep2

description: Library name: apj1dsis14x_2_25


title: ChIP_INTS12_rep1


title: ST2 DEXA 48h GRO-seq biol rep4

description: GROseq in control cell line

value: DEXA


title: INTS11DEG_RNA_24h_rep2

data_processing:
Raw FASTQ data were processed with Trimmomatic (v0.32), removing adapters, and low-quality reads.
Reads were aligned to the mouse genome (mm10) using STAR aligner (v.2.7.9a)  with default parameters. RSEM (v1.2.31) was used to obtain the expected gene counts against the mouse Ensembl reference (release 96). Gene expression is normalized as Transcript Per Million (TPM). We determined the differential gene expression (DEG) between conditions using DESeq2 using the time series parameters.
Assembly: mm10
Supplementary files format and content: The processed data files are in bigWig format.

growth_protocol: E14 ESCs were routinely grown on 0.1% gelatin  coated plates in DMEM (high glucose, GlutaMAX Supplement) medium  supplemented with 1 mM sodium pyruvate, 100 U/mL penicillin/100 U/mL streptomycin , 1X MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 15% Embryonic stem-cell FBS, and 1000 U/mL recombinant leukemia inhibitory factor (LIF). Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from freshly collected time-course samples using TRIzol reagent and ethanol precipitation as per the guidelines provided by the manufacturer. The obtained total RNA underwent Turbo DNase treatment to eliminate any genomic DNA contamination.
Subsequently, RNA-seq libraries for sequencing were generated using the TruSeq Stranded Total RNA library preparation kit (Illumina). One μg of DNase-treated input RNA was utilized for library construction, and the ERCC RNA Spike-In Mix (Invitrogen) was incorporated following the manufacturer's instructions. The constructed libraries were pooled and subjected to single-end sequencing with 75 base pairs read length on a NextSeq 500 platform.

treatment_protocol: INTS11DEG cells were routinely maintained in ESC medium containing 10 µM trimethoprim. To deplete INTS11DEG, cells were washed twice with PBS to remove Trimethoprim. After two washes, fresh ESC medium and DMSO (1µl/ ml) were added to the cells. The cells were incubated for the predetermined time (0h, 3h, 6h, 24h) and harvested.

value: INTS11 depletion 24h


title: 1000918_D6-FOP-LT-control

description:
Library name: 1000918_1_1_1-H3T5KBGX5
10x Chromium


title: 1000917_D6-FOP-RT-Injured

description:
Library name: 1000917_1_1_1-H3T5KBGX5
10x Chromium


title: ChIP_INTS11_rep1

value: INTS11 (Sigma prestige, #HPA029025)


title: apj1d sis1-4xcga, riboseq, steadystate, bio rep1

description: Library name: apj1dsis14x_1_25


title: INTS11DEG_RNA_6h_rep2

value: INTS11 depletion 6h


title: ST2 DEXA 48h GRO-seq biol rep3

description: GROseq in control cell line


title: ST2 DMSO 0h GRO-seq biol rep1

description: GROseq in control cell line

value: DMSO


title: ST2 DEXA 48h GRO-seq biol rep2

description: GROseq in control cell line


title: 1000916_D6-FOP-LT-control

description:
Library name: 1000916_1_1_1-HCNJJBGX5
10x Chromium


title: ydj1-4xcga, riboseq, steadystate, bio rep2

description: Library name: ydj14xcga_2_25

value: BY4741 ydj1-4xcga


title: 1000914_D4-WT-LT-control

description:
Library name: 1000914_1_1_1-H3VLLBGX5
10x Chromium


title: INTS11DEG_RNA_6h_rep1

value: Embryonic origin

value: Mouse Embryonic Stem cells


title: ydj1-4xcga, riboseq, steadystate, bio rep1, tech rep 1

description: Library name: ydj14xcga_1_25_1


title: ST2 ADIPO 48h GRO-seq biol rep4

description: GROseq in control cell line

value: stromal bone marrow derived cell line

value: ADIPO


title: ST2 DMSO 1h GRO-seq biol rep1

description: GROseq in control cell line

value: fibroblast


title: ydj1-4xcga, riboseq, steadystate, bio rep3

description: Library name: ydj14xcga_3_25

value: Whole cell


title: ydj1-4xcga, riboseq, steadystate, bio rep1, tech rep 2

description: Library name: ydj14xcga_1_25_2


title: INTS11DEG_RNA_3h_rep2

value: INTS11 depletion 3h


title: ST2 ADIPO 48h GRO-seq biol rep3

description: GROseq in control cell line


title: sis1-4xcga, riboseq, steadystate, bio rep3

description: Library name: sis14xcga_3_25

value: BY4741 sis1-4xcga


title: INTS11DEG_RNA_3h_rep1


title: 1000912_D4-WT-LT-control

description:
Library name: 1000912_1_1_1-H3T5KBGX5
10x Chromium


title: ST2 ADIPO 48h GRO-seq biol rep2

description: GROseq in control cell line


title: sis1-4xcga, riboseq, steadystate, bio rep1

description: Library name: sis14xcga_1_25


title: INTS11DEG_RNA_24h_rep1


title: INTS11DEG_RNA_0h_rep1

value: INTS11 control 0h


title: 1000911_D4-WT-RT-Injured

description:
Library name: 1000911_1_1_1-H3T5KBGX5
10x Chromium

value: gluteus medius


title: ST2 ADIPO 24h GRO-seq biol rep1

description: GROseq in control cell line


title: INTS11DEG_RNA_0h_rep2


title: ST2 ADIPO 10h GRO-seq biol rep1

description: GROseq in control cell line


title: 1000915_D6-FOP-RT-Injured

description:
Library name: 1000915_1_1_1-HCNJJBGX5
10x Chromium


title: 1000910_D4-FOP-LT-control

description:
Library name: 1000910_1_1_1-H3T5KBGX5
10x Chromium


title: apj1d, riboseq, steadystate, bio rep1, tech rep 2

description: Library name: apj1d_1_25_2

value: BY4741 apj1d


title: 1000909_D4-FOP-RT-Injured

description:
Library name: 1000909_1_1_1-H3VLLBGX5
10x Chromium


title: CRE_IKZF-KO_CTNNB1_rep2

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

data_processing:
Reads were aligned with BWA v0.7.17 against the mouse genome (mm10/GRCm38, gencode vM24).
Peak calling was performed with MACS2 v2.2.7.1
BigWig were generated using DeepTools, in the case of histone modifications signal was normalized to total library size (RPM) whereas for TFs, signal was normalized to total signal within peak regions.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig tracks of normalised signal within 50bp windows with 100bp smoothing

source_name: mouse pre-B cells transformed with BCR-ABL1

growth_protocol: Bone marrow cells were harvested from 6-12 weeks old mice by flushing cavities of femur and tibia with ice-cold PBS supplemented with 2% FBS and cells were filtered through 70 μm mesh to generate single cell suspensions. Cells from spleen and thymus were extracted by forcing tissues through a 40 μm strainer into ice-cold PBS with 2% FBS. Erythrocyte lysis was performed for bone marrow and spleen cells (RBC Lysis Buffer, BioLegend). After making single cell suspensions, bone marrow cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM; Gibco) with GlutaMAX containing 20% FBS, 50 μmol ml-1 2-mercaptoethanol, 100 IU ml-1 P/S. Bone marrow cells were cultured in 10 ng ml-1 recombinant mouse IL-7 (Peprotech) to generate IL-7 dependent pre-B cells. Pre-B cells were retrovirally transduced by BCR-ABL1 and IL-7 was removed to promote the outgrowth of the transformed cells.

extract_protocol:
B-ALL cells were counted and fixed with 1% formaldehyde for 10 min at room temperature and quenched by 125 mmol l-1 glycine. B-ALL cells were spiked with fixed Drosophila S2 cells, and subjected to nuclear extraction. Nuclei were lysed with SDS lysis buffer and sonicated by Bioruptor (Diagenode). After sonication, cell debris was removed by centrifugation (13,000 rpm, 10 min), while supernatant was diluted and pre-cleared by incubation with a blend of isotype control IgG, Dynabeads Protein A and Dynabeads Protein G (Invitrogen). ChIP was performed using antibodies specifically recognizing either H3K27ac (Active motif, #39133) or H3K4me3 (Millipore, MC315). ChIPed DNA was reverse-crosslinked overnight at 65℃, and purified by QIAquick PCR purification kit (Qiagen). For ChIP-seq of IKZF1 and IKZF3, B-ALL cells were crosslinked by 2 mmol l-1 disuccinimidyl glutarate for 45 min and 1% formaldehyde for 10 min at room temperature before chromatin enrichment and library construction. These antibodies were used for ChIP-seq of  IKZF1 (GeneTex, GTX129438) and IKZF3 (CST, D1C1E). β-catenin ChIP was performed by Active Motif, Inc. (Carlsbad, CA, USA) using the monoclonal antibody CAT-15 (Thermo).
ChIP-seq libraries were constructed by a SMARTer ThruPLEX DNA-seq Kit (Takara).

treatment_protocol: CRISPR/Cas9-RNP electroporation was performed by using NeonTM Transfection system (Invitrogen) with either non-targeting or IKZF1/IKZF3-targeting guides. Single cell derived colonies were generated to obtain fully knock-out cell lines. These cells were transduced with ERT2 and Cre-ERT2 vectors expressing GFP and sorted for GFP+ cells. Chip-seq analysis was performed 1 day after 4-OHT mediated b-catenin activation.

tag: chip target

value: preB-ALL

value: BCR-ABL1 Ctnnb1Ex3fl/+ Cre-ERT2 sgIkzf1 Ikzf3 clone 3E


title: apj1d, riboseq, steadystate, bio rep3

description: Library name: apj1d_3_25

tag: genotype


title: pooled_input_rep2

value: input


title: apj1d, riboseq, steadystate, bio rep2

description: Library name: apj1d_2_25


title: 1000908_D4-FOP-LT-control

description:
Library name: 1000908_1_1_1-HCNJJBGX5
10x Chromium


title: apj1d, riboseq, steadystate, bio rep1, tech rep 1

description: Library name: apj1d_1_25_1


title: 1000907_D4-FOP-RT-Injured

description:
Library name: 1000907_1_1_1-H3T5KBGX5
10x Chromium


title: CRE_IKZF-KO_CTNNB1_rep1


title: WT, riboseq, steadystate, bio rep3

description: Library name: WT_3_25

value: BY4741 WT


title: ST2 ADIPO 6h GRO-seq biol rep1

description: GROseq in control cell line


title: ST2 ADIPO 1h GRO-seq biol rep1

description: GROseq in control cell line


title: 1000913_D4-WT-RT-Injured

description:
Library name: 1000913_1_1_1-H3VLLBGX5
10x Chromium


title: 999874_D1-WT-LT-control

description:
Library name: 999874_1_1_1-H3VLLBGX5
10x Chromium


title: CRE_IKZF-WT_CTNNB1_rep2

value: BCR-ABL1 Ctnnb1Ex3fl/+ Cre-ERT2 sgNTC clone 6H


title: Legionella pneumophila subsp. pneumophila strain Philadelphia 1, control, rep_3

city: Yamaguchi City

first: Istiana

middle: Nur

last: Vidayanti

state: Yamaguchi Prefecture

address: 1677-1 Yoshida

country: Japan

institute: Yamaguchi University

description:
Library name: Phi_1_rep_3 (GE)
Normalized read_All samples (GE).csv

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000.
The raw reads were mapped onto the Genomic Contig Format (GCF)_001753085.1 L. pneumophila sequence.
Comparative expression analysis was performed using the RNA-Seq analysis tool of CLC Genomics Workbench.
Assembly: GCF_001753085.1
Supplementary files format and content: csv file include RPKM value for each sample
Supplementary files format and content: csv file include normalized gene expression value, fold change, and p value

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: bacteria

extract_protocol:
total RNA was prepared using the Maxwell RSC Simply RNA Tissue Kit (Promega). Following rRNA removal with the NEBNext rRNA Depletion Kit (New England BioLabs)
the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used with 20 ng of total RNA for library construction.

treatment_protocol: Phil-1 and Ofk308 strains were cultured at 37°C to the exponential phase in AYE, then diluted and cultured again at 30°C for 24 h

value: bacteria

value: GTC_00296 control

value: Culture at 37 and trasfer into 30 ℃

value: 48 hours


title: WT, riboseq, steadystate, bio rep2

description: Library name: WT_2_25


title: ST2 ADIPO 2h GRO-seq biol rep1

description: GROseq in control cell line

value: stromal bone marrow derived cell line

value: ADIPO


title: CRE_IKZF-WT_CTNNB1_rep1


title: WT, riboseq, steadystate, bio rep1, tech rep 2

description: Library name: WT_1_25_2

value: Whole cell


title: Legionella pneumophila subsp. pneumophila strain Philadelphia 1, control, rep_2

description:
Library name: Phi_1_rep_2 (GE)
Normalized read_All samples (GE).csv


title: 999873_D1-WT-RT-Injured

description:
Library name: 999873_1_1_1-HCNJJBGX5
10x Chromium


title: Vegetative growing cells, replicate 2, nanopore

city: Bryan

first: GEOFFREY

last: KAPLER

state: TX

address: 4209B Medical Research Education Building II

institute: Texas A&M University

data_processing:
MinKNOW software version 21.05.25 was used. Raw reads were basecalled using Guppy (version 5.0.16). Reads were aligned to reference genome (T_Thermophila_MAC_2021) using minimap2 and sorted with samtools. BrdU signal and origins were detected using DNAscent2.
Assembly: Tetrahymena genome (SB210, 2021 version, TGD)
Supplementary files format and content: bed
Library strategy: DNA-seq

organism: Tetrahymena thermophila

growth_protocol: Tetrahymena cells grown in 2% PPYS up to 2.5 x10e5/ml.

extract_protocol:
DNA was purified by a previously described NDS extraction method.
MinION sequencing libraries were prepared according to the manufacturer protocols using SQK-LSK109 kit.

treatment_protocol: Pulse labeling with 100 µM (or 500 µM) of BrdU for 5 min and chase with 50 µM (or 250 µM) of thymidine for 5 min, then add final 1 mM (or 2 mM) of thymidine for 20 min (Hennion et al. 2020).

value: vegetative growing cells

value: WT


title: WT, riboseq, steadystate, bio rep1, tech rep 1

description: Library name: WT_1_25_1


title: Legionella pneumophila subsp. pneumophila strain Philadelphia 1, control, rep_1

description:
Library name: Phi_1_rep_1 (GE)
Normalized read_All samples (GE).csv


title: 999871_D1-WT-RT-Injured

description:
Library name: 999871_1_1_1-H3VLLBGX5
10x Chromium


title: TPP-4SK_S38_3

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

description: Library name: TPP-4SK_S38

data_processing:
Bioinformatics processing and data interpretation were carried out in consultation with the Bioinformatics Core at the NCSU Center for Human Health and the Environment. The quality of sequenced data was assessed using FastQC and poor-quality bases were trimmed from the 5’-end. The remaining good quality reads were aligned to the medaka reference genome (ASM223467V1) using STAR aligner (Dobin et al., 2013). For each replicate, per-gene counts of uniquely mapped reads were calculated using htseq-count script from the HTSeq python package. We imported the count matrix to the R statistical computing environment (V 4.5.1) for further analysis. Gene count data was normalized for sequencing depth and distortion, and dispersion was estimated using DESeq2 Bioconductor package (V 1.40.2) in the R statistical computing environment (Love et al., 2014). We fitted a linear model using the treatment levels, and differentially expressed genes were identified after applying multiple testing corrections using the Benjamini-Hjockberg procedure (padj<0.05) (Benjamini Y, Hochberg, 1995). Ingenuity Pathway Analysis (IPA, Qiagen, Valencia, CA) version 01-10(01-10) provided predictive models of pathway modulation based on transcript abundance (control vs. TPhP treatment) (Krämer et al., 2014). Gene set enrichment analysis (GSEA (version 4.0.3)) software (Subramanian et al., 2005) was used to show statistically significant differences between control and TPhP treatments (Subramanian et al., 2005.) Briefly, we pre-ranked all genes that were measured using RNA-Seq using fold change * -log10(p value) and sorted in descending order. Enrichment analyses were conducted against curated C2 all version 7.1 symbols. In the GSEA application we modified the following parameters (Enrichment statistics: classic, exclude large sets: 5000, exclude smaller sets: 15). We then assessed the top 20 differentially enriched gene sets and chose to present the most relevant gene set based on our described phenotypes.
Assembly: HdrR version 93
Supplementary files format and content: resultDATA_COUNT_countcombined_formated.csv

organism: Oryzias latipes

source_name: axial skeleton/tissue

growth_protocol: All medaka (Oryzias latipes) in this study were cared for in accordance with standard protocols approved by the North Carolina State University Institutional Animal Care and Use Committee (#22-378). Adult medaka were housed at appropriate densities in 10L and 30L tanks in an enclosed, recirculating aquaculture system under a 14:10 hr light:dark cycle. Conditions were monitored daily, maintaining temperature at 26 ± 2˚C and pH at 7.2 ± 0.2. The inbred Orange-red Hd-dR (OR) and previously described transgenic strains (Watson et al., 2017) were used for the following experiments. All fish were monitored daily to ensure there was no change in health and prevent pain and suffering. TPhP exposure did not result in any physical harm to the animals and no fish had to be sacrificed due to a decline in health and or increased stress from exposures. Additionally, none of the assessed endpoints induced any harm to any fish. Upon completion of each experiment, fish were euthanized using ice water at indicated time points for morphological assessment or RNA collection.

extract_protocol:
At 14 dpf, larval medaka were euthanized in ice-cold embryo rearing medium (ERM), and pooled in microcentrifuge tubes to obtain 15–20 individuals per RNA sample. Re-sidual water was removed, and Leibovitz’s L-15 medium (Corning, Mediatech, Inc., Manassas, VA, USA) supplemented with 10% fetal bovine serum (FBS; Atlanta Biolog-icals) was added. To isolate axial skeletal tissue, hatched larvae were passed multiple times through a 20–22-gauge hypodermic needle attached to a 3-mL syringe (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). The resulting tissue suspension was filtered through 105-μm nylon mesh (Component Supply Co., Fort Meade, FL, USA) and transferred to fresh L-15/10% FBS medium. Under a dissecting microscope (Nikon SMZ1500, Nikon Instruments, Inc., Melville, NY, USA), axial tissue was carefully ex-amined and trimmed to remove any remaining craniofacial or abdominal tissue. Cleaned samples were immediately flash-frozen in liquid nitrogen. Tissues were homogenized in TRI Reagent® (Ambion®, Life Technologies, Carlsbad, CA, USA) using a handheld BioVortexer (Thomas Scientific, Swedesboro, NJ, USA), and total RNA was extracted following the manufacturer's protocol. RNA concentration was determined using the Qubit® RNA HS Assay Kit (Invitrogen) with the Qubit® 3.0 Fluorometer
Illumina RNA library preparation and sequencing were performed at the NC State Genomic Sciences Laboratory (Raleigh, NC). Total RNA was extracted from DMSO- and TPhP-treated embryos/larvae (n= 3-4 technical replicates of 3-4 biological replicates of 15-20 pooled larvae), and assessed for quality, concentration, and integrity using RIN > 9) an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, Cary, NC). From 1 µg of total RNA, messenger RNA (mRNA) was purified using oligo-dT magnetic beads from the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA). Complementary DNA (cDNA) libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina, following the manufacturer’s instructions. In brief, purified mRNA was chemically fragmented and reverse-transcribed into first-strand cDNA using random primers. Second-strand synthesis incorporated dUTPs to retain strand specificity. The resulting double-stranded cDNA was purified, end-repaired, and adenylated prior to adapter ligation. Size selection was performed using AMPure XP beads (Beckman Coulter, USA) to isolate library fragments between 400–550 bp (including adapters). Libraries were then PCR-amplified to enrich fragments and incorporate unique index barcodes. Final libraries were purified and assessed for size distribution and concentration using an Agilent 2200 TapeStation with a High Sensitivity DNA chip and a Qubit fluorometer (Thermo Fisher, Raleigh, NC). Indexed libraries were pooled in equimolar amounts and sequenced on an Illumina HiSeq 2500 platform using a 125 bp single-end sequencing kit. Base calling was conducted with Real Time Analysis (RTA) software to produce raw BCL files, which were subsequently demultiplexed into FASTQ files for downstream analysis.

treatment_protocol: OR embryos were collected from breeding tanks, cleaned, and staged by previously described methods (Iwamatsu, 2004). Fertilized embryos were transferred to glass crystallizing dishes containing 10 mL of 1X embryo rearing medium (ERM) as previously described (Watson et al., 2017) at a density of 20-30 embryos per dish using four replicates dishes per treatment. Exposure to 0.1% Dimethyl Sulfoxide (DMSO) or 1.0 µM of TPhP (Sigma Aldrich) in DMSO began during early development at 4-6 hours post fertilization (hpf) (blastula stage). The use of 1.0 µM TPhP was based upon previous studies in aquatic models demonstrating non-lethal, sub-chronic developmental effects on embryonic development following aqueous exposures to TPhP (Hong et al., 2021; Tran et al., 2021). Embryos were cultured at 26 – 28˚C with static media with compound renewal (~80%) every 2 – 3 days until termination of the experiment at 14-20 days post fertilization (dpf). Free swimming hatched larvae were fed 1 – 2 mg of ground Otohime B1 larval diet (Pentair) daily until termination

value: axial skeleton/tissue

value: TPhP


title: Vegetative growing cells, replicate 1, nanopore


title: apj1d sis1-4xcga, riboseq, 60min, bio rep2, tech rep 2

description: Library name: apj1dsis14x_2_t60_2

value: BY4741 apj1d sis1-4xcga

value: 60 min HS 38°C


title: TPP-3SK_S37_3

description: Library name: TPP-3SK_S37


title: 999869_D1-FOP-RT-Injured

description:
Library name: 999869_1_1_1-HCNJJBGX5
10x Chromium

value: gluteus medius


title: 999870_D1-FOP-LT-control

description:
Library name: 999870_1_1_1-HCNJJBGX5
10x Chromium


title: apj1d sis1-4xcga, riboseq, 60min, bio rep2, tech rep 1

description: Library name: apj1dsis14x_2_t60_1


title: TPP-2SK_S36_2

description: Library name: TPP-2SK_S36


title: apj1d sis1-4xcga, riboseq, 10min, bio rep2, tech rep 2

description: Library name: apj1dsis14x_2_t10_2

value: 10 min HS 38°C


title: DMSO-4SK_S34_4

description: Library name: DMSO-4SK_S34

value: DMSO


title: apj1d sis1-4xcga, riboseq, 10min, bio rep2, tech rep 1

description: Library name: apj1dsis14x_2_t10_1


title: 999867_D1-FOP-RT-Injured

description:
Library name: 999867_1_1_1-H3T5KBGX5
10x Chromium


title: 999868_D1-FOP-LT-control

description:
Library name: 999868_1_1_1-H3VLLBGX5
10x Chromium


title: TPP-1SK_S35_1

description: Library name: TPP-1SK_S35


title: 967898_D2-WT-LT-Control

description:
Library name: 967898_1_1_1-HGFW7BGX3
10x Chromium


title: apj1d sis1-4xcga, riboseq, 0min, bio rep2

description: Library name: apj1dsis14x_2_t0


title: DMSO-3SK_S33_3

description: Library name: DMSO-3SK_S33


title: apj1d sis1-4xcga, riboseq, 60min, bio rep1, tech rep 2

description: Library name: apj1dsis14x_1_t60_2


title: DMSO-2SK_S32_2

description: Library name: DMSO-2SK_S32


title: 967897_D2-FOP-LT-control

description:
Library name: 967897_1_1_1-HGFW7BGX3
10x Chromium


title: 967896_D2-FOP-LT-control

description:
Library name: 967896_1_1_1-HGFW7BGX3
10x Chromium


title: 999872_D1-WT-LT-control

description:
Library name: 999872_1_1_1-HCNJJBGX5
10x Chromium


title: DMSO-1SK_S31_1

description: Library name: DMSO-1SK_S31