title: neonatal_at2_pbs_rep3

description: Library name: McGrath_04152021_PBSat2_P3_S11


title: WT TVM 7

status: Public on Nov 10 2025

type: SRA

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Ave, Biomedical Research Tower

department: Microbial Infection and Immunity

country: USA

institute: The Ohio State University College of Medicine

description:
Library name: Sample 3
TVM-WT7

library_source: transcriptomic

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Total RNA was isolated from cell pellets using the Macherey-Nagel Nucleospin RNA isolation kit according to the manufacturer's instructions.
Libraries were generated and sequenced according to standard protocols from Azenta Life Sciences, to which the samples were sent for library preparation and analysis.

treatment_protocol: Untreated CD8+ TVM cells were sorted from the spleen of WT and Aiolos KO mice following total CD8+ T cell isolation. Anti- CD8a, anti-Cd44, anti-CD62L, and anti-CD49d antibodies were used to sort the TVM cells. Naïve CD8+ T cells were isolated from the spleen of WT mice using naïve CD8+ T cell isolation kit.

tag: tissue

value: Spleen

tag: cell type

value: CD8+ TVM cells

tag: genotype

value: WT

tag: treatment

value: untreated cells


title: REVERB WT Treg, REVERBaD5

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

library_source: genomic

data_processing:
Raw read quality was checked using FASTQC v0.11.8 and the adaptors were trimmed with Trim Galore v0.4.4.
Reads were mapped to mm10 mouse genome using STAR v2.5.3a. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Peaks were identified using HOMER ‘findpeaks’, using input IgG condition as background reference and default parameters (four-fold enrichment over input control, four-fold enrichment over local tag count, FDR < 0.001, and style factor).
Assembly: mm10
Supplementary files format and content: bigWig file for every sample
Library strategy: cut&run

molecule: genomic DNA

source_name: Treg cells

growth_protocol: RPMI, FBS(10%), hIL-2(50U/ml), TFGβ(5ng/ml), anti-CD3(2μg/ml), anti-CD28(2μg/ml)

extract_protocol:
Cells were fixed with 1X Permeabilization buffer from ebioscience Foxp3 fixation kit . After antibody incubation, chromatin was cut using pA-MNase and DNA was extracted using QIAGEN MinElute kit.
cut&run libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645)  from NEB. 6 ng of DNA was used as starting material for input and samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 150-350bp in length using Agencourt AMPure XP beads.

treatment_protocol: IL-6(5ng/ml), VitC(100μg/ml)

value: Treg cells

value: REVERB WT

tag: antibody

value: REVERBa


title: 30C_100mMNAIN3_bioreplicate2_techreplicate3

city: singapore

first: YUE

last: WAN

address: 1, #20-10 Fusionopolis Way, Connexis, North Tower, 138632

country: Singapore

institute: Genome Institute of Singapore,A*STAR

description: Library name: 221025_30C_100mMNAIN3_Rep2_3

data_processing:
Preprocessing of raw signals.
Reads were base-called with Guppy version 4.2.2+effbaf8. Both passed- and failed-quality reads from nanopore direct RNA sequencing were mapped to the reference using the software Minimap2 with the following parameters:  -ax map-ont -F2064.
For reads that were not successfully mapped by Minimap2, their original fast5 files were used for mapping with subseqDTW.  For the C. albicans transcriptome, a GPU-accelerated cuDTW was used to do the mapping for unmapped reads from minimap2.
Alignment  using subseqDTW to align event signal levels with expected signal levels.
After aligning of read signals to reference signals, events corresponding to the same reference  5-mer were collapsed.
Assembly: riboswitch/ribosnitch used synthetic 14 riboswitch/ribosnitch reference, candida used candida bruno_et_al_2010_tx_loci.fasta
Supplementary files format and content: *_final_alignment.txt.gz files. They contain the alignment results from DTW.

molecule: polyA RNA

organism: Candida albicans

source_name: Candida albicans

growth_protocol: C. albicans (SC5314) was inoculated in 10ml YPD medium for 16-18 hours at 30ºC, with constant shaking at 250rpm. We then transferred 2ml of the overnight culture to a fresh tube (1:50) of 100ml YPD medium with shaking for 3-5hours at 250rpm until the culture reaches an OD600 of 0.5-0.6. For hyphae induction, we added 10% FBS to the 30°C C. albicans culture, transferred it to 37°C with shaking at 250rpm for 1hour. For in vivo structure probing, we added NAI-N3 to a final concentration of 100mM with shaking of the culture for 10min. We then collected the cell pellet after centrifugation at 4000 RPM for 5min. The cell pellet was stored at -80°C until needed.

extract_protocol:
To extract RNA from C. albicans, we first thawed the frozen pellet at room temperature and then placed it on ice. The pellets were re-suspended in 2.8ml yeast lysis buffer (100ml lysis buffer: 0.7ml 1M Tris-HCl, pH 7.0, 0.3ml 1M Tris-HCl, pH 8.0, 2ml of 0.5M EDTA, 5ml of 10%SDS). We transferred 700μl of this mixture into a 1.5ml Eppendorf tube, added 700μl of acid phenol, and vortexed rigorously. We then incubated the tubes at 65°C in a thermomixer for one hour, with constant shaking at 1000 rpm. After the incubation, we centrifuged the sample at maximum speed for 10 minutes at 4°C. We then transferred the aqueous phase into a new tube, added the same volume of fresh acid phenol, vortexed it, and spun it at maximum speed for 10 minutes at 4°C. We performed acid phenol extraction at least 2-3 times until the aqueous phase looked clear. To precipitate the RNA from the aqueous phase, we transferred the aqueous phase into a 2 ml tube and added 1/10 volume of 3M sodium acetate and 3x ice-cold 100% ethanol. We precipitated the RNA at -20°C for 1 hour before spinning it at maximum speed for 20-30 mins at 4°C. The pelleted RNA was then washed in 800μl of ice-cold 70% ethanol, centrifuged to remove the ethanol, and then air dried for 2 min before being dissolved in 50μl of nuclease-free water.
We used 600ng of in vitro transcribed (IVT) RNA for library preparation following the manufacturer’s protocol for the direct RNA library preparation kit SQK-RNA004 from Oxford Nanopore Technologies. The libraries were loaded onto FLO-PRO004RA PromethION RNA flow cells and sequenced on a PromethION 2 Solo device.The library preparation steps were the same as those for SQK-RNA002 except the following: 1) 1μl of SUPERase·In™ RNase Inhibitor (Invitrogen, AM2694) is added during the RT Adapter ligation reaction, 2) 6μl of RNA Ligation (RLA) instead of 6μl of RNA Adapter (RMX) is added in the second adapter ligation reaction, 3) the adapter-ligated RNA is eluted in 33μl of RNA Elution Buffer (REB), and 4) we prepared the sample for loading by adding 100μl of Sequencing Buffer (SB) and 68μl of Library Solution (LIS) to 32μl of the library sample.

treatment_protocol: The cells and IVT RNAs  are treated with structure probine compound to table RNA structure

value: Candida albicans

tag: cell line


title: REVERB KO Treg, retroviral vector,  IgG control

value: retroviral vector

value: IgG control


title: neonatal_at2_pbs_rep2

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

description: Library name: McGrath_04152021_PBSat2_P2_S10

data_processing:
Reads demultiplexed to fastq using BCL2FASTQ v2.17.1.14 with default parameters
Reads in fastq format were aligned to the NCBI RefSeq mouse reference genome (mm10) and quantified at the gene level using the nf-core/rnaseq v3.8.1 Nextflow pipeline.
Differential gene expression analysis was performed using PyDESeq2
Assembly: mm10
Supplementary files format and content: Raw counts tables for fibroblasts or AT2 cells in tab-separated value (TSV) format.

source_name: lung

extract_protocol:
Cells were digested from whole mouse lungs and subjected to FACS to isolate either alveolar epithelial type II cells (AT2) or PDGFRa+ fibroblasts. Total RNA was immediately extracted from sorted cells.
Bulk RNA-seq libraries prepared using QIAGEN AllPrep DNA/RNA micro kit and the TAKARA SMARTer Stranded Total RNA-seq Kit v2.

value: lung

tag: strain

value: pbs

tag: batch


title: REVERB WT Treg, normal IgGD1 control


title: WT TVM 6

description:
Library name: Sample 2
TVM-WT6


title: WT TVM 5

description:
Library name: Sample 1
TVM-WT5


title: 30C_100mMNAIN3_bioreplicate2_techreplicate2

description: Library name: 221007_30C_100mMNAIN3_Rep2_2


title: neonatal_at2_pbs_rep1

description: Library name: McGrath_04152021_PBSat2_P1_S9


title: REVERB WT Treg, H3K27ac2D1


title: 30C_100mMNAIN3_bioreplicate2_techreplicate1

description: Library name: 221005_30C_100mMNAIN3_Rep2


title: SAA1_4

city: Shanghai

first: Yikai

last: Lin

state: Shanghai

address: Dongchuan Road, No.800

country: China

institute: SJTU

data_processing:
Reads were aligned to human genome [National Center for Biotechnology Information (NCBI); GRCh38] using Hisat v.2.1.0 with default options.
High‐throughput sequencing (HTseq) was used to get gene counts, and reads per kilo base per million mapped reads (RPKM) were used to determine gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: Primary human amnion fibroblasts

extract_protocol:
Total RNA from SAA1-treated amnion fibroblasts was extracted.
RNA sequence libraries were prepared using a TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocol.

value: Primary human amnion fibroblasts

value: SAA1 (50 ng/mL)

tag: time

value: 24 hours


title: REVERB WT Treg, REVERBa


title: neonatal_at2_ecoli_rep4

description: Library name: McGrath_04152021_ecoliAT2_E4_S16

value: ecoli


title: SAA1_3


title: 30C_100mMNAIN3_bioreplicate1_techreplicate2

description: Library name: 221031_30C_100mMNAIN3_Rep1_2


title: SAA1_2


title: Aiolos KO TVM 5

description:
Library name: Sample 5
TVM-AKO5


title: neonatal_at2_ecoli_rep3

description: Library name: McGrath_04152021_ecoliAT2_E3_S15


title: 30C_100mMNAIN3_bioreplicate1_techreplicate1

description: Library name: 220908_30C_100mMNAIN3


title: REVERB WT Treg, normal IgG control


title: 30C_100mMNAIN3_bioreplicate2_techreplicate4

description: Library name: 221025_30C_100mMNAIN3_Rep2_4


title: neonatal_at2_ecoli_rep1

description: Library name: McGrath_04152021_ecoliAT2_E1_S13


title: SAA1_1


title: REVERB WT Treg, H3K27AC


title: 30C_DMSO

description: Library name: 220908_30C_DMSO

value: DMSO


title: Control_4

value: Control


title: ITA_4 (biol rep 4)

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
RNAseq reads were quality checked using FastQC. Low-quality reads and adapters sequences were removed using Trimmomatic v.0.32 software
QC-filtered reads were aligned to S. scitamineum SscI8 genome (GCA_900002365.1) available at GenBank database using the Hisat2 software
Reads counts of each gene were calculated using the featureCounts function from the Rsubread package
Differential expression analysis was performed using the DESeq2 package using adjusted p-value <0.01 and log2 fold-change >1 or log2 fold-change <-1, as thresholds. Gene Ontology (GO) terms were assigned to S. scitamineum protein coding genes using the online annotation tool PANNZER2 and to improve GO terms assignment the annotation of S. scitamineum SSC39B was also used.
Assembly: Sporisorium scitamineum SscI8 genome (GCA_900002365.1)
Supplementary files format and content: Text file (.txt) including raw counts
Supplementary files format and content: Text file (.tsv) including differentiall expression results

organism: Sporisorium scitamineum

source_name: mycelium

growth_protocol: S. scitamineum were co-cultivated in a bipartite petri dish, with one compartment containing solid LB medium for posterior bacterial inoculum, and in the other, 5 microtubes of 1.5 mL without the lid with 200 µL of liquid YM medium containing 4 x 104 teliospores of S. scitamineum. The plates were sealed with Parafilm M® and incubated at 28°C for 5 days for fungal pre-growth, to ensure that we would have S. scitamineum mass for subsequent experiments.

extract_protocol:
RNA extraction was performed with RNeasy Plant Mini Kit (Qiagen), with the protocol modified only for the lysis step. This step involved the addition of 500 µL of glass beads and 450 µL of RLC buffer with β-mercaptoethanol, followed by three lysis cycles of vortex and ice (30 seconds each). RNA integrity was verified with the Agilent RNA 6000 Nano kit on the 2100 Bioanalyzer (Agilent Technologies). RNA quality and quantification was performed using the Qubit™ RNA High Sensitivity – HS kit (Thermo Fischer Scientific) and Qubit 2.0 equipment (Thermo Fischer Scientific)
Twelve libraries were prepared using the TruSeq Stranded mRNA Sample Prep LS Kit (Illumina) following the manufacturer’s protocol, and the quality of the libraries was evaluated using the 2100 Bioanalyzer with the Agilent DNA 1000 Kit, following the manufacturer’s protocol. Libraries were quantified using the KAPA qPCR Master Mix kit (Roche) on the Viia7 Real-Time PCR System equipment (Applied Biosystems) and were sequenced on the Illumina HiSeq 2500.

treatment_protocol: After 5 days, in the compartment with LB medium, a 20 μL drop of fresh bacterial suspension at 108 CFU of the bacteria ITA P2F2 and E. coli DH5α was inoculated; plates contaning only the fungus (without any bacterial inoculum) were used as control. The plates were sealed with Parafilm M® and incubated at 28°C for 2 days.

value: mycelium

value: ITA P2F2 VOC-treatment


title: REVERB WT Treg, Foxp3


title: ITA_3 (biol rep 3)


title: Control_3


title: REVERB KO Treg, REVERBa

value: REVERB KO


title: Control_2


title: ITA_2 (biol rep 2)


title: REVERB KO Treg, RORgt

value: Treg cells

value: RORgt


title: neonatal_fibroblasts_pbs_rep2

description: Library name: McGrath_04072021_PBSfibro_P2_S6

value: fibroblasts


title: Control_1


title: REVERB KO Treg, normal IgG control


title: REVERB WT Treg, RORgt

value: REVERB WT


title: Liver-Wtchow-1mo-rep1

type: RNA

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

description: 5 µm section from FFPE tissue panel block

hyb_protocol: Tissue panel slides underwent 15 rounds of fluorescent probe hybridization, imaging, and probe removal using the Xenium In Situ Analyzer (chemistry version v1). Xenium captured Z-stacks in all channels across imaging cycles, stitched, and processed into a spatial transcriptomic map. Decoding of transcripts was performed using the Xenium codebook associated with the mMulti_440g probe set. Cell segmentation was performed using multimodal methods combining boundary stains, nuclear expansion, and RNA-based segmentation

scan_protocol: Xenium In Situ Analyzer

data_processing: Data were processed using Xenium Ranger software (analysis version xenium-3.3.0.1; instrument software version 3.3.0.1; instrument serial number XETG00177).Raw Xenium data were processed and filtered using the spatialdata-io module.

label: Xenium Custom Probe Set (mMulti_440g, Design ID: YNEBQY)

source_name: Liver, WT, age-matched

label_protocol: mMulti_440g probe set designed with Designer v3.5.0

extract_protocol: Liver tissues were collected, fixed in formalin, transferred to 70% ethanol, and underwent paraffin-embedding with our instiutional histology core facility. To enable multiplex profiling within the Xenium capture area, a custom 3-D printed mold was used to assemble FFPE blocks into two tissue panel blocks. This approach maximized use of the imaging area and allowed all samples within a panel to be sectioned in a single pass. Each tissue panel block was sectioned once at 5 μm thickness, and the resulting panel sections were mounted directly on Xenium slides for in situ analysis.

value: Liver

value: WT


title: DH_4 (biol rep 4)

value: E. coli DH5a VOC-treatment


title: neonatal_at2_ecoli_rep2

description: Library name: McGrath_04152021_ecoliAT2_E2_S14

value: lung


title: REVERB KO Treg, H3K27AC


title: DH_3 (biol rep 3)


title: Liver-Cyp-1mo-rep1

source_name: Liver, zone 3 Cre, 1 month post-tamoxifen

value: C57BL/6J and Swiss Webster mix

value: Cyp1a2-CreERT2; Ctnnb1(ex3)fl/+; Arid2fl/+; Rosa26LSL-tdTomato/+


title: neonatal_fibroblasts_ecoli_rep4

description: Library name: McGrath_04072021_ecolifibro_Ec4_S4


title: DH_2 (biol rep 2)


title: REVERB KO Treg, Foxp3


title: neonatal_fibroblasts_ecoli_rep3

description: Library name: McGrath_04072021_ecolifibro_Ec3_S3


title: neonatal_fibroblasts_pbs_rep4

description: Library name: McGrath_04072021_PBSfibro_P4_S8

value: pbs


title: Liver-Gls-1mo-rep1

source_name: Liver, zone 1 Cre, 1 month post-tamoxifen

value: Gls2-CreERT2; Ctnnb1(ex3)fl/+; Arid2fl/+; Rosa26LSL-tdTomato/+


title: neonatal_fibroblasts_ecoli_rep2

description: Library name: McGrath_04072021_ecolifibro_Ec2_S2

value: ecoli


title: Aiolos KO 3

description: Library name: Sample 6

data_processing:
Resultant sequences were trimmed and aligned to mm10 using Bowtie2 (v2.5.1).
They were processed with SAMtools (v1.21) and converted to bigwigs with deepTools v(3.5.6).
Assembly: mm10
Supplementary files format and content: bigwig (.bw) format

extract_protocol:
50,000 TVM cells were sorted from the spleen of WT or KO mice. Nuclei was isolated following cell lysis with ATAC buffer containing 0.1% NP40, 0.1%Tween-20, and  0.01% Digitonin. Transposed fragments were purified and amplified DNA was sent for sequencing.
Libraries were generated using Tn5 Transposase, and sequenced according to standard protocols from CD Genomics.

treatment_protocol: Untreated CD8+ TVM cells were sorted from the spleen of WT and Aiolos KO mice following total CD8+ T cell isolation. Anti- CD8a, anti-Cd44, anti-CD62L, and anti-CD49d antibody were used to sort the TVM cells

value: Spleen

value: CD8+ TVM cells

value: KO

value: untreated cells


title: Colon Tregs in TNBS induced colitis, REV-ERB WT, Rep3

data_processing:
Sequenced reads were quality-tested using FASTQC v0.11.8 and were trimmed by Trim Galore v0.4.4.
The trimmed reads were aligned to the mm10 mouse genome using STAR v2.5.3a with default parameters. Raw or TPM (Transcript Per Million) gene expression levels were quantified using HOMER v4.9.1 by calculating the uniquely aligned reads to the exons of RefSeq genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Colon

extract_protocol:
RNA was extracted using Trizol protocol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA kit (Illumina) following manufacturer's protocols.

treatment_protocol: presensitized with 150ul 1% (w/v) TNBS on skin, intra-rectal injected with 100ul 2.5% (w/v) TNBS 7 days later.

value: Colon

value: Tregs

value: REV-ERB WT

value: TNBS induced colitis


title: neonatal_fibroblasts_pbs_rep3

description: Library name: McGrath_04072021_PBSfibro_P3_S7

value: fibroblasts


title: Colon Tregs in TNBS induced colitis, REV-ERB WT, Rep2


title: CT_4 (biol rep 4)

value: mycelium

value: control:No VOC-treatment


title: Aiolos KO 2

description: Library name: Sample 5


title: DH_1 (biol rep 1)

value: E. coli DH5a VOC-treatment


title: E14 cells, high-LD clone 2 (H2), scRNAseq

city: London

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing data were processed and mapped against the 10X Genomics pre-built mouse reference transcriptome (mm10-2020-A) using 10X Genomics Cell Ranger (v6.1.2). The resulting raw count matrices were further analyzed in R.
The DropletUtils package (v1.16.0) was used to perform barcode ranking (barcodeRanks::DropletUtils with lower = 2500 and fit.bounds = 8000 - ∞) and filter out barcodes of empty droplets (emptyDrops::DropletUtils function with lower = 7000). The retained barcodes were filtered using the Seurat package (v4.3.0.1) (2100-3000 < nFeature_RNA < 9000 and nCount_RNA > 7500). Barcodes with more than 15-15.5% mitochondrial counts were removed. Additional filtering was performed with the DropletQC package (v0.0.0.9000) that identifies damaged cells based on the total RNA content and the fraction of unspliced nuclear RNA (identify_damaged_cells::DropletQC with nf_sep = 0.10 and umi_sep_perc = 50).
The count matrices were normalized and scaled individually using SCTransform::Seurat while regressing for the percentage of nuclear RNA and percentage of ribosomal protein counts. The count matrices were then concatenated with merge::Seurat.
Assembly: mm10-2020-A
Supplementary files format and content: Tab separated values files and matrix files

growth_protocol: E14 WT and derived clones were maintained in GMEM-BHK21 (GIBCO 21710-025) supplemented with 10% FBS (GIBCO 10270-106), 2mM L-glutamine, 0.1mM NEAA, 0.25% Na-bicarbonate, 1mM Na-pyruvate, 0.1mM 2-mercaptoethanol, 1x home-made mLIF and 0.5x PenStrep. Cells were cultured on gelatin-coated culture plates in a humidified atmosphere with 5% CO2 at 37C. Medium was refreshed every day, and cells were passaged every 3-4 days using 0.05% Trypsin-EDTA.

extract_protocol:
Cells were washed with DPBS and dissociated with 0.05% Trypsin-EDTA for 5min at 37C. Dissociated cells were collected in 8ml medium and pelleted at 300g for 5min. Cell pellets were resuspended in fresh medium and filtered through a 70um cell strainer and then pelleted again at 300g for 5min. Pelleted cells were washed twice in DPBS supplemented with 0.04% BSA and then filtered through a 40um cell strainer to obtain single cell suspensions. Cells were kept on ice during further steps. The cell concentrations were determined using a hemocytometer and adjusted to 1*10^6 cells/ml in DPBS with 0.04% BSA.
Single cell RNA-seq libraries were prepared from the single cell suspensions using a Chromium Next GEM Single Cell 3’ Reagent Kit and 10X Chromium single-cell platform (10X Genomics) according to the manufacturer’s instructions (Doc. No. CG000204, revision B to C). DNA concentrations were assessed after cDNA amplification using a Qubit 1x dsDNA HS assay kit (Thermo Fisher, Q33231) and spectrophotometer (DeNovix ds-11). The DNA concentrations of the final libraries were determined in similar fashion. The peak size distributions of the final libraries were measured before pooling using a 2100 Bioanalyzer (Agilent) in combination with high sensitivity DNA Chips and Reagents (Agilent, 5067-4626). The final library pools were sequenced on a NextSeq 500 (Illumina) sequencing instrument using a NextSeq 500/550 High Output 75-cycli kit (Illumina) with the following run type: 26bp read-1, 56bp read-2 and a 8bp index. Library preparation and sequencing were performed at the Department of Molecular Biology of the Radboud Institute for Molecular Life Sciences (RIMLS).

value: Embryonic stem cells

value: WT

tag: clone

value: H-clone 2 (H2)


title: neonatal_fibroblasts_ecoli_rep1

description: Library name: McGrath_04072021_ecolifibro_Ec1_S1

value: lung


title: Colon Tregs in TNBS induced colitis, REV-ERB WT, Rep1


title: ITA_1 (biol rep 1)

value: ITA P2F2 VOC-treatment


title: Colon Tregs in TNBS induced colitis, REV-ERB KO, Rep3

value: REV-ERB KO


title: E14 cells, high-LD clone 1 (H1), scRNAseq

description: 10X Genomics

value: H-clone 1 (H1)


title: CT_2 (biol rep 2)


title: neonatal_fibroblasts_pbs_rep1

description: Library name: McGrath_04072021_PBSfibro_P1_S5

value: pbs


title: E14 cells, low-LD clone (L), scRNAseq

description: 10X Genomics

value: L-clone (L)


title: WT 2

description: Library name: Sample 2

value: Spleen

value: CD8+ TVM cells

value: untreated cells


title: CT_1 (biol rep 1)


title: Colon Tregs in TNBS induced colitis, REV-ERB KO, Rep1

value: Colon

value: Tregs

value: TNBS induced colitis


title: E14 cells, Wild-type (E14), scRNAseq

description: 10X Genomics

value: control


title: PBMC, T1D, Donor_106

status: Public on Nov 09 2025

city: Moscow

first: Vadim

last: Chechekhin

address: Leninskie gory 1

country: Russia

institute: Lomonosov Moscow State University

description: Library name: Donor_106

data_processing:
Raw sequencing scRNA-seq data were processed using bcl2fastq2 12.20 to generate FASTQ files. Reads were aligned to the GRCh38-2020-A human reference genome using Cell Ranger 7.1.0. Ambient RNA contamination was removed using SoupX 1.6.2, and doublets were identified using scDblFinder 1.12.0 in R 4.2.1. High-quality cells were retained based on the following criteria: mitochondrial gene content <6%, heat shock protein gene content <2%, and at least 200 expressed genes per cell.
Further analyses were conducted using scanpy 1.10.2 in Python 3.9.16. Data were normalized by a shifted logarithm algorithm, and 2000 highly variable genes were identified using the seurat_v3 method. Integration was performed using scANVI. Cell type annotation was performed using scParadise and Azimuth, supplemented by gene expression analysis based on marker databases, including CellMarker 2.0, PanglaoDB, and GeneCards.
Assembly: 10x Genomics GRCh38-2020-A
Supplementary files format and content: LADA.h5ad - file in H5AD format with expression of genes in scRNA-seq samples of patients with LADA
Supplementary files format and content: T1D.h5ad - file in H5AD format with expression of genes in scRNA-seq samples of patients with T1D
Supplementary files format and content: Healthy.h5ad - file in H5AD format with expression of genes in scRNA-seq samples of healthy donors

source_name: PBMC

extract_protocol:
Venous blood samples for fasting plasma glucose and glycated hemoglobin (HbA1c) measurements were collected into BD Vacutainer® tubes (Becton, Dickinson and Company, USA) containing either a gel separator or ethylenediaminetetraacetic acid (EDTA), respectively (4 mL per tube). Peripheral-blood mononuclear cells (PBMCs) were isolated from whole blood collected into BD Vacutainer® Cell Preparation Tubes (CPT) containing sodium heparin, Ficoll, and a separation gel (8 mL per participant). Tubes were gently inverted 3–4 times to ensure uniform distribution of the anticoagulant and processed within 2 hours of collection at room temperature. PBMCs were isolated by centrifugation at 20°C for 20 minutes at 1,800 × g using minimal acceleration and deceleration. The upper 5 mL of plasma was discarded, and the remaining fraction—including the PBMC layer—was transferred to 50-mL conical tubes for washing. Cells were washed twice with 1× phosphate-buffered saline (PBS) supplemented with 1% heat-inactivated fetal bovine serum (FBS; HyClone, USA) and 1 mM EDTA, followed by centrifugation at 300 × g for 10 minutes. Residual red blood cells were lysed using ACK Lysing Buffer (Thermo Fisher Scientific, USA), followed by additional wash and centrifugation steps. The final PBMC pellet was resuspended in CryoStor® CS10 (StemCell Technologies, Canada) and stored at −80°C for short-term preservation or at −150°C for long-term storage.
Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index)

value: PBMC

value: 10x Genomics GRCh38-2020-A


title: PBMC, T1D, Donor_38

description: Library name: Donor_38


title: WT 3

description: Library name: Sample 3

value: WT


title: PBMC, T1D, Donor_33

description: Library name: Donor_33


title: PBMC, T1D, Donor_6

description: Library name: Donor_6


title: Aiolos KO 1

description: Library name: Sample 4

value: KO


title: PBMC, T1D, Donor_26

description: Library name: Donor_26


title: PBMC, T1D, Donor_7

description: Library name: Donor_7


title: PBMC, T1D, Donor_34

description: Library name: Donor_34


title: PBMC, T1D, Donor_101

description: Library name: Donor_101


title: CT_3 (biol rep 3)

value: mycelium

value: control:No VOC-treatment


title: Colon Tregs in TNBS induced colitis, REV-ERB KO, Rep2

value: REV-ERB KO


title: PBMC, T1D, Donor_4

description: Library name: Donor_4


title: PBMC, T1D, Donor_72

description: Library name: Donor_72


title: PBMC, T1D, Donor_109

description: Library name: Donor_109


title: PBMC, T1D, Donor_125

description: Library name: Donor_125


title: PBMC, T1D, Donor_17

description: Library name: Donor_17


title: PBMC, T1D, Donor_24

description: Library name: Donor_24


title: PBMC, T1D, Donor_14

description: Library name: Donor_14


title: PBMC, LADA, Donor_124

description: Library name: Donor_124


title: WT 1

description: Library name: Sample 1


title: PBMC, LADA, Donor_37

description: Library name: Donor_37


title: PBMC, LADA, Donor_39

description: Library name: Donor_39


title: PBMC, LADA, Donor_105

description: Library name: Donor_105


title: PBMC, LADA, Donor_35

description: Library name: Donor_35


title: PBMC, LADA, Donor_50

description: Library name: Donor_50


title: PBMC, LADA, Donor_10

description: Library name: Donor_10


title: PBMC, LADA, Donor_60

description: Library name: Donor_60


title: PBMC, LADA, Donor_21

description: Library name: Donor_21


title: PBMC, T1D, Donor_88

description: Library name: Donor_88


title: PBMC, LADA, Donor_27

description: Library name: Donor_27


title: PBMC, LADA, Donor_63

description: Library name: Donor_63


title: PBMC, LADA, Donor_30

description: Library name: Donor_30


title: PBMC, LADA, Donor_22

description: Library name: Donor_22


title: PBMC, T1D, Donor_66

description: Library name: Donor_66


title: PBMC, T1D, Donor_87

description: Library name: Donor_87


title: H9_shVGLL1_EO3_D4_C_S54

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description: Library name: H9_shVGLL1_EO3_D4_C_S54

data_processing:
Reads were mapped to GRCh38.p14 (GENCODE release 45) using STAR (v.2.7.9a) and annotated using featureCounts (subread v.2.0.6).
Ensembl genes without at least three samples with 10 or more reads were removed from analysis.
Normalization and differential expression analysis was performed using the R (v.4.4.0) package DESeq2 (v.1.46.0).
Assembly: GRCh38.p14
Supplementary files format and content: csv file contains raw counts of all samples
Supplementary files format and content: csv file contains normalized counts of samples

source_name: cells

growth_protocol: WA09/H9 cell lines containing doxycyline-inducible dCas9-VPR and gRNA for VGLL1 were cultured with mTeSR Plus (StemCell Technologies cat. no. 100-1130) on Geltrex (Gibco cat. no. A14133-02)-coated tissue culture plates with 2 μg/mL puromycin and 8 μg/mL blasticidin S (Gibco cat. no. A1113903) until treatment. shRNA WA09/H9 cell lines were maintained in mTeSR Plus on Geltrex coated tissue culture plates with 10 μg/mL puromycin. Cells were cultured at 37ºC at 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the mirVana miRNA isolation kit (Ambion). RNA was quantified with Qubit RNA BR assay kit (Invitrogen) and quality control was done with Bioanalyzer (Agilent).
Libraries were prepared using Illumina Ribo-Zero Plus rRNA Depletion Kit with IDT for Illumina RNA UD Indexes

treatment_protocol: WA09/H9 cell lines containing doxycyline-inducible dCas9-VPR and gRNA for VGLL1 treated with 2 μg/mL doxycycline (Millipore Sigma cat. no. D3447-500MG), 2 μM doxycycline and 2μM IWP2 (Selleck Chemicals cat. no. S7085), or DMSO for 4 days in mTeSR Plus on Geltrex(Gibco cat. no. A14133-02)-coated tissue culture plates. shRNA WA09/H9 cell lines were differentiated into TE-like cells over 4 days with DMEM/F12 (Corning, cat. no. 10-092-CV), 1x ITS (MilliporeSigma, cat. no. I1884), L-ascorbic acid 64 μg/mL (MilliporeSigma, cat. no. A8960), sodium bicarbonate 543 μg/mL (ThermoFisher, cat. no. 25080094), 2% BSA (Gemini Bio-Products, cat. no. 700-110), 10 ng/mL recombinant human BMP4 (R&D Systems cat. no. 314-BP-010), and 2 μM IWP2 (Selleck Chemicals cat. no. S7085) on Geltrex(Gibco cat. no. A14133-02)-coated tissue culture plates. Cells were cultured at 37ºC at 5% CO2.

value: cells

value: TE-like cell

value: BMP4 (10ng/mL) and IWP2 (2µM)

value: Day 4


title: PBMC, T1D, Donor_114

description: Library name: Donor_114


title: PBMC, T1D, Donor_23

description: Library name: Donor_23


title: PBMC, T1D, Donor_31

description: Library name: Donor_31


title: H9_shVGLL1_EO3_D4_B_S53

description: Library name: H9_shVGLL1_EO3_D4_B_S53


title: H9_shVGLL1_EO3_D0_C_S51

description: Library name: H9_shVGLL1_EO3_D0_C_S51

value: ESC

value: Day 0


title: H9_shVGLL1_EO3_D0_B_S50

description: Library name: H9_shVGLL1_EO3_D0_B_S50


title: H9_shVGLL1_EO3_D0_A_S49

description: Library name: H9_shVGLL1_EO3_D0_A_S49


title: H9_shVGLL1_EO3_D4_A_S52

description: Library name: H9_shVGLL1_EO3_D4_A_S52


title: H9_shVGLL1_6_D4_B_S47

description: Library name: H9_shVGLL1_6_D4_B_S47


title: H9_shVGLL1_6_D0_C_S45

description: Library name: H9_shVGLL1_6_D0_C_S45


title: H9_shVGLL1_6_D0_A_S43

description: Library name: H9_shVGLL1_6_D0_A_S43


title: H9_shVGLL1_6_D4_C_S48

description: Library name: H9_shVGLL1_6_D4_C_S48


title: H9_shVGLL1_6_D0_B_S44

description: Library name: H9_shVGLL1_6_D0_B_S44


title: H9_shScramble_CT_D4_C_S42

description: Library name: H9_shScramble_CT_D4_C_S42


title: H9_shVGLL1_6_D4_A_S46

description: Library name: H9_shVGLL1_6_D4_A_S46


title: PBMC, LADA, Donor_5

description: Library name: Donor_5


title: H9_shScramble_CT_D4_B_S41

description: Library name: H9_shScramble_CT_D4_B_S41


title: H9_shScramble_CT_D4_A_S40

description: Library name: H9_shScramble_CT_D4_A_S40


title: H9_shScramble_CT_D0_C_S39

description: Library name: H9_shScramble_CT_D0_C_S39


title: H9_shScramble_CT_D0_B_S38

description: Library name: H9_shScramble_CT_D0_B_S38


title: PBMC, LADA, Donor_16

description: Library name: Donor_16


title: H9_VPR5_DOX_D4_C_63_S21

description: Library name: H9_VPR5_DOX_D4_C_63_S21

value: Doxycycline (2 μg/mL)


title: H9_VPR5_DOXIWP2_D4_C_66_S24

description: Library name: H9_VPR5_DOXIWP2_D4_C_66_S24

value: Doxycycline (2 μg/mL) and IWP2 (2µM)


title: H9_shScramble_CT_D0_A_S37

description: Library name: H9_shScramble_CT_D0_A_S37


title: H9_VPR5_DOXIWP2_D4_A_64_S22

description: Library name: H9_VPR5_DOXIWP2_D4_A_64_S22


title: H9_VPR5_DOXIWP2_D4_B_65_S23

description: Library name: H9_VPR5_DOXIWP2_D4_B_65_S23


title: H9_VPR5_DMSO_D4_C_69_S27

description: Library name: H9_VPR5_DMSO_D4_C_69_S27

value: DMSO


title: H9_VPR5_DMSO_D4_B_68_S26

description: Library name: H9_VPR5_DMSO_D4_B_68_S26


title: H9_VPR5_DMSO_D4_A_67_S25

description: Library name: H9_VPR5_DMSO_D4_A_67_S25


title: H9_VPR2_DOX_D4_C_99_S12

description: Library name: H9_VPR2_DOX_D4_C_99_S12


title: H9_VPR2_DOX_D4_A_97_S10

description: Library name: H9_VPR2_DOX_D4_A_97_S10


title: H9_VPR2_DOX_D4_B_98_S11

description: Library name: H9_VPR2_DOX_D4_B_98_S11


title: H9_VPR2_DOXIWP2_D4_C_102_S15

description: Library name: H9_VPR2_DOXIWP2_D4_C_102_S15


title: H9_VPR1_DOX_D4_C_87_S3

description: Library name: H9_VPR1_DOX_D4_C_87_S3


title: H9_VPR2_DMSO_D4_C_105_S18

description: Library name: H9_VPR2_DMSO_D4_C_105_S18


title: H9_VPR2_DOXIWP2_D4_B_101_S14

description: Library name: H9_VPR2_DOXIWP2_D4_B_101_S14


title: H9_VPR1_DOX_D4_A_85_S1

description: Library name: H9_VPR1_DOX_D4_A_85_S1


title: H9_VPR1_DOX_D4_B_86_S2

description: Library name: H9_VPR1_DOX_D4_B_86_S2


title: H9_VPR5_DOX_D4_A_61_S19

description: Library name: H9_VPR5_DOX_D4_A_61_S19


title: H9_VPR1_DOXIWP2_D4_C_90_S6

description: Library name: H9_VPR1_DOXIWP2_D4_C_90_S6


title: H9_VPR5_DOX_D4_B_62_S20

description: Library name: H9_VPR5_DOX_D4_B_62_S20


title: H9_VPR1_DOXIWP2_D4_A_88_S4

description: Library name: H9_VPR1_DOXIWP2_D4_A_88_S4


title: H9_VPR1_DMSO_D4_93_C_S9

description: Library name: H9_VPR1_DMSO_D4_93_C_S9


title: H9_VPR1_DMSO_D4_92_B_S8

description: Library name: H9_VPR1_DMSO_D4_92_B_S8


title: H9_VPR1_DMSO_D4_91_A_S7

description: Library name: H9_VPR1_DMSO_D4_91_A_S7


title: d0_A_6

description: Library name: d0_A_6

data_processing:
Reads were mapped to GRCh38.p14 (GENCODE release 45) using STAR (v.2.7.9a) and annotated using featureCounts (subread v.2.0.6).
Ensembl genes without at least three samples with 10 or more reads were removed from analysis.
Normalization and differential expression analysis was performed using the R (v.4.4.0) package DESeq2 (v.1.46.0).
Genes with an adjusted p-value < 0.05 and log2 fold change > 1 were considered differentially expressed.
Assembly: GRCh38.p14
Supplementary files format and content: csv file contains raw counts of all samples
Supplementary files format and content: csv file contains normalized counts of samples

growth_protocol: WA09/H9 were cultured with mTeSR Plus (StemCell Technologies cat. no. 100-1130) on Geltrex(Gibco cat. no. A14133-02)-coated tissue culture plates until treatment. Cells were cultured at 37ºC at 5% CO2.

treatment_protocol: WA09/H9 differentiated into TE-like cells over 4 days with DMEM/F12 (Corning, cat. no. 10-092-CV), 1x ITS (MilliporeSigma, cat. no. I1884), L-ascorbic acid 64 μg/mL (MilliporeSigma, cat. no. A8960), sodium bicarbonate 543 μg/mL (ThermoFisher, cat. no. 25080094), 2% BSA (Gemini Bio-Products, cat. no. 700-110), 10 ng/mL recombinant human BMP4 (R&D Systems cat. no. 314-BP-010), and 2 μM IWP2 (Selleck Chemicals cat. no. S7085) on Geltrex(Gibco cat. no. A14133-02)-coated tissue culture plates. Cells were cultured at 37ºC at 5% CO2.

value: vehicle control, DMSO


title: d0_A_2

description: Library name: d0_A_2


title: d0_A_1

description: Library name: d0_A_1


title: d0_A_3

description: Library name: d0_A_3


title: BMP4IWP2_A_d4_3

description: Library name: BMP4IWP2_A_d4_3


title: d0_A_5

description: Library name: d0_A_5


title: d0_A_4

description: Library name: d0_A_4


title: BMP4IWP2_A_d4_1

description: Library name: BMP4IWP2_A_d4_1


title: BMP4IWP2_A_d2_2

description: Library name: BMP4IWP2_A_d2_2

value: Day 2


title: BMP4IWP2_A_d4_2

description: Library name: BMP4IWP2_A_d4_2


title: BMP4_A_d4_3

description: Library name: BMP4_A_d4_3

value: BMP4 (10ng/mL)


title: BMP4IWP2_A_d2_3

description: Library name: BMP4IWP2_A_d2_3


title: BMP4IWP2_A_d2_1

description: Library name: BMP4IWP2_A_d2_1


title: H9_VPR2_DMSO_D4_A_103_S16

description: Library name: H9_VPR2_DMSO_D4_A_103_S16


title: BMP4_A_d2

description: Library name: BMP4_A_d2


title: BMP4_A_d2_1

description: Library name: BMP4_A_d2_1


title: H9_VPR1_DOXIWP2_D4_B_89_S5

description: Library name: H9_VPR1_DOXIWP2_D4_B_89_S5


title: BMP4_A_d4_2

description: Library name: BMP4_A_d4_2


title: LE-532-3

city: Shenzhen

first: haoqiang

last: Wan

address: 1066 Xueyuan Avenue, Nanshan District

institute: shenzhen university

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: Genome: http://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
Supplementary files format and content: raw counts, FPKM for each sample

growth_protocol: A549 cells were cultured in DMEM/F12 media supplemented with penicillin, streptomycin and 10% fetal bovine serum (FBS) at 37°C in a 5% CO2 incubator.

extract_protocol:
The RNA was extracted using FastPure Total RNA Isolation Kit (Vazyme, Nanjing, China). 1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: The cells were seeded 6-well plate for 24 hours, then treated with DMSO or 40 JFB for 24 hours.

value: WT

value: Japoflavone B


title: BMP4_A_d4_1

description: Library name: BMP4_A_d4_1


title: DMSO-1


title: DMSO-2


title: Subject 5, vehicle, challenge 3

city: Copenhagen

first: Kelvin

last: Yeung

address: Blegdamsvej 3B

country: Denmark

institute: LEO SIC

description:
S5P3
10x Genomics

data_processing:
Demultiplexing and data preprocessing including quality control, read alignment (hg38), and gene quantification was conducted using the 10x Cell Ranger software (v6.0.2).
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Epidermis

extract_protocol:
Skin samples were incubated overnight in 2.4 mg/ml Dispase (Roche) in phosphate buffered saline (PBS) solution at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.5 mg/ml Collagenase D (Roche) with deoxyribonuclease (0.1%, Sigma-Aldrich) in PBS for a total of 1 hour at 37°C, quenched with 2% bovine serum albumin (BSA) (Sigma Aldrich) in PBS, and strained through a 70-μm mesh strainer. The strainer was washed through with 2% BSA in PBS to collect any remaining cells. The single cell suspension was always kept on ice.
We used 10X Genomics Chromium Next GEM Single Cell 5’ kit, v2 with 5’ Feature Barcode kit alongside Chromium Single Cell Human TCR Amplification kit for TCRαβ and Dual Index Kit TT and TN Set A. The kit was used to the manufacturer’s instructions. The samples were multiplexed, using TotalSeq-C hashtag antibodies (Biolegend). The sequencing was carried out on an Illumina NovaSeq 6000 using a S4 flow cell, 200 cycles, to the manufacturer’s instructions.

value: Epidermis

tag: subject id

value: Subject 5

value: Petrolatum


title: BMP4_A_d2_2

description: Library name: BMP4_A_d2_2

value: cells


title: Subject 5, vehicle, challenge 2

description:
S5P2
10x Genomics


title: LE-532-1


title: Subject 5, vehicle, challenge 1

description:
S5P1
10x Genomics


title: Subject 5, nickel, challenge 3

description:
S5N3
10x Genomics

value: Nickel


title: Subject 5, nickel, challenge 2

description:
S5N2
10x Genomics


title: DMSO-3


title: Subject 4, vehicle, challenge 2

description:
S4P2
10x Genomics

value: Subject 4


title: Subject 4, nickel, challenge 2

description:
S4N2
10x Genomics


title: Subject 4, vehicle, challenge 3

description:
S4P3
10x Genomics


title: Subject 4, nickel, challenge 1

description:
S4N1
10x Genomics


title: Subject 4, vehicle, challenge 1

description:
S4P1
10x Genomics


title: Subject 4, nickel, challenge 3

description:
S4N3
10x Genomics


title: Subject 3, vehicle, challenge 3

description:
S3P3
10x Genomics

value: Subject 3


title: Subject 3, vehicle, challenge 2

description:
S3P2
10x Genomics


title: Subject 3, nickel, challenge 1

description:
S3N1
10x Genomics


title: Subject 3, vehicle, challenge 1

description:
S3P1
10x Genomics


title: LE-532-2


title: Subject 3, nickel, challenge 2

description:
S3N2
10x Genomics


title: Subject 2, vehicle, challenge 3

description:
S2P3
10x Genomics

value: Subject 2


title: Subject 3, nickel, challenge 3

description:
S3N3
10x Genomics


title: Subject 2, vehicle, challenge 2

description:
S2P2
10x Genomics


title: Subject 2, nickel, challenge 2

description:
S2N2
10x Genomics


title: Subject 5, nickel, challenge 1

description:
S5N1
10x Genomics


title: Subject 2, vehicle, challenge 1

description:
S2P1
10x Genomics


title: Subject 2, nickel, challenge 3

description:
S2N3
10x Genomics


title: Subject 2, nickel, challenge 1

description:
S2N1
10x Genomics


title: GFAPsh-SA6-iCre, 7 days post injection n2

city: Toronto

first: Hussein

last: Ghazale

state: Ontario

address: 2075 Bayview Ave, North York

department: Biological Sciences

country: Canada

institute: Sunnybrook Research Institute

description: Library name: CS29

data_processing:
Downstream analysis of scRNA-seq data was performed using R (v.4.4.1). Quality control, data clustering and visualization were performed using the Seurat (v.5.1.0) packags. Datasets were processed following Seurat recommended tutorial instructions, using a CCA method for dataset integration. PCA was performed for dimensionality reduction and the first 30 components were used for UMAP embedding and clustering. Differential expression analysis was performed using the DElegate (v.1.2.1) package and for pathway analysis and gene ontology we relied on the package clusterProfiler (v.4.12.6). The monocle3 (v 1.3.7) package was used for calculating pseudotrajectories.
Assembly: Mouse
Supplementary files format and content: barcodes,matrix and raw files

source_name: Brain Cortex

extract_protocol:
Brains were harvested into cold 1X PBS 7 and 50 days post AAV injection. Using a brain slicer, brains were cut into coronal sections and the injected region in the cortex was microdissected. Dissected tissue was dissociated into single cell suspension according to the manufacturer’s instructions using Worthington Papain System kit (Worthington, LK003150). Using Dead cell removal kit (130-090-101, Miltenyi Biotec), dead cells were removed following the manufacturer’s instructions. Trypan blue staining was used to determine cell viability, and samples with 90% viable cells were processed for analysis.
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10X genomics, Cat # 1000263), following the manufacturer’s protocol. Briefly, cell suspensions were prepared at a concentration of 1 × 10⁶ cells/mL, and 16500 cells were loaded into each lane of a Chromium GEM Chip K for an expected recovery of 10,000 cells. Gel Bead-in-Emulsions (GEMs) were generated using the Chromium Controller (Wang Lab, Biological Sciences Platform of Sunnybrook Research Institute) followed by cDNA generation and amplification. For each sample, a total of 50 ng of cDNA was used to generate libraries according to the manufacturer’s instructions. Equal molar quantities of each library were sequenced on the Illumina NovaSeq 6000 platform using the S4 flow cell system (The Centre for Applied Genomics, The Hospital for Sick Children, Toronto).

treatment_protocol: AAV injection in the brain cortex

value: Brain Cortex

value: Astrocytes/neurons

value: Brain cells

value: AAV

value: GFAPsh-SA6-iCre, 7 days post injection


title: GFAPsh-SA6-iCre, 7 days post injection n3

description: Library name: CS30


title: GFAPsh-SA6-iCre-miR124T, 50 days post injection n2

description: Library name: CS26


title: GFAPsh-SA6-iCre, 7 days post injection n1

description: Library name: CS28


title: Subject 1, vehicle, challenge 1

description:
S1P1
10x Genomics

value: Subject 1


title: Subject 1, vehicle, challenge 2

description:
S1P2
10x Genomics


title: GFAPsh-SA6-iCre-miR124T, 50 days post injection n3

description: Library name: CS27


title: GFAPsh-iCre-miR124T, 50 days post injection n2

description: Library name: CS23


title: GFAPsh-iCre-miR124T, 50 days post injection n3

description: Library name: CS24


title: GFAPsh-iCre-miR124T, 50 days post injection n1

description: Library name: CS22


title: Subject 1, nickel, challenge 1

description:
S1N1
10x Genomics


title: lib_frac5_utp_b

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
Library name: Library 79
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 5 of polysome profiling (heavy polysome) using primers containing Illumina-compatible overhangs

library_source: other

data_processing:
The analysis pipeline for the mRNA-seq and Ribo-seq libraries included the following steps: 1. Linker trimming with Cutadapt v4.9. 2. Alignment to rRNA and tRNA reference sequences, with exclusion of matching reads. 3. Alignment of the remaining reads to the hg19 genome and the relevant in vitro transcript (IVT). 4. Alignment to the hg19 transcriptome.
All alignments were performed with Bowtie v1.3.1. To obtain frame-accurate information on the IVT, PRICE v1.0.4 was used. Additional processing was carried out with in-house scripts.
For the library screen, reads were aligned to a reference that included the specific barcodes of each sequence together with ~40 bp of flanking sequence on each side. These alignments were performed with STAR v2.7.11b using the parameter --alignEndsType EndToEnd.
Assembly: hg19 plus IVT and library sequences which are provided in the supplementary materials of the paper.
Supplementary files format and content: Wiggle (WIG) files from the chase experiment.
Supplementary files format and content: TSV files reporting: read counts per gene for both RNA-seq and Ribo-seq; read counts per nucleotide for the IVT in the Ribo-seq libraries

molecule: other

source_name: HEK 293T PKR KO

growth_protocol: HEK293T cells or HEK293T PKR KO were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 2mM l-glutamine, 100 U/ml penicillin, 0.1 mg/ml streptomycin.

extract_protocol:
Cells were scraped from 10-cm plates on ice and in the presence of 500ul lysis buffer (1% Triton X-100 in 20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol supplemented with 10 U ml−1 Turbo DNase and 100 μg ml−1 CHX). After lysis, samples stood on ice for 20 min and then were centrifuged at 14,000 x g for 15 min to remove cell debris. Supernatants were split into two tubes - one for RNAseq and one for Ribo-Seq library preparation. For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted. poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen).
RNA-seq: mRNA samples were subjected to DNAseI treatment and 3’ dephosphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. or RNA-seq  libraries were prepared using NEbNext Ultra II directional RNA library prep kit. Ribo-seq: samples were treated with RNaseI for 45 min at room temperature followed by SUPERase-In (Invitrogen) quenching. Subsequent Ribo-seq library generation was performed/ In brief, digested samples were loaded onto a sucrose solution (34% sucrose, 20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol and 100 μg ml−1 CHX) and spun for 1 h at 100,000 rpm in a TLA-110 rotor (Beckman) at 4 °C. Pellet was collected using TRI reagent (Sigma-Aldrich) and the RNA was extracted using chloroform phase separation. For size selection, 15 μg total RNA was separated on a 15% TBE-urea gel for 65 min, and 28–34 bp footprints were excised using 28 and 34 flanking RNA oligos, followed by RNA extraction and rRNA depletion (NebNext rRNA Depletion Kit v2) and the subsequent Ribo-seq protocol.

treatment_protocol: Cells were transfected with UTP or m1Y incorporated IVT mRNA. For Riboseq and Chase samples cells were washed with ice cold PBS and then immediately frozen in liquid nitrogen or pretreated with harringtonine (2 mg/ml) and cycloheximide (100 mg/ml).

value: HEK 293T PKR KO


title: Subject 1, nickel, challenge 3

description:
S1N3
10x Genomics


title: lib_frac5_utp_a

description:
Library name: Library 78
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 5 of polysome profiling (heavy polysome)  using primers containing Illumina-compatible overhangs


title: GFAPsh-iCre-miR124T, 7 days post injection n3

description: Library name: CS18


title: lib_frac5_n1m_b

description:
Library name: Library 76
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 5 of polysome profiling (heavy polysome)  using primers containing Illumina-compatible overhangs


title: GFAPsh-SA6-iCre, 50 days post injection n3

description: Library name: CS21

value: GFAPsh-SA6-iCre, 50 days post injection


title: lib_frac5_n1m_a

description:
Library name: Library 75
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 5 of polysome profiling (heavy polysome) using primers containing Illumina-compatible overhangs


title: lib_frac4_utp_c

description:
Library name: Library 74
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 4 of polysome profiling (light polysome) using primers containing Illumina-compatible overhangs


title: lib_frac5_n1m_c

description:
Library name: Library 77
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 5 of polysome profiling (heavy polysome)  using primers containing Illumina-compatible overhangs


title: GFAPsh-SA6-iCre, 50 days post injection n1

description: Library name: CS19


title: lib_frac4_utp_b

description:
Library name: Library 73
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 4 of polysome profiling (light polysome) using primers containing Illumina-compatible overhangs


title: GFAPsh-SA6-iCre-miR124T, 7 days post injection n2

description: Library name: CS14


title: GFAPsh-SA6-iCre-miR124T, 50 days post injection n1

description: Library name: CS25


title: GFAPsh-iCre-miR124T, 7 days post injection n1

description: Library name: CS16


title: GFAPsh-SA6-iCre-miR124T, 7 days post injection n3

description: Library name: CS15


title: Colonic tissue, M-3

city: hefei

first: duo

last: ma

address: No.81 Meishan Road, Shushan District

institute: Anhui Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Assembly: mm10
Supplementary files format and content: excel format

source_name: Colonic tissue

growth_protocol: Male C57BL/6J mice (6–8 weeks old, 20–22 g)

extract_protocol:
RNA was harvested using GenSeq® Low Input RNA Library Prep Kit, Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: C57 mice in the model group were injected with 5% w/v TNBS by anal insertion into the colon

value: Colonic tissue

value: WT

value: TNBS-induced IBD


title: Colonic tissue, M-2


title: lib_frac4_n1m_c

description:
Library name: Library 71
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 4 of polysome profiling (light polysome)  using primers containing Illumina-compatible overhangs


title: lib_frac4_utp_a

description:
Library name: Library 72
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 4 of polysome profiling (light polysome)  using primers containing Illumina-compatible overhangs


title: GFAPsh-SA6-iCre-miR124T, 7 days post injection n1

description: Library name: CS13


title: Subject 1, nickel, challenge 2

description:
S1N2
10x Genomics

value: Epidermis


title: lib_frac5_utp_c

description:
Library name: Library 80
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 5 of polysome profiling (heavy polysome) using primers containing Illumina-compatible overhangs


title: GFAPsh-SA6-iCre, 50 days post injection n2

description: Library name: CS20


title: lib_frac4_n1m_a

description:
Library name: Library 69
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 4 of polysome profiling (light polysome) using primers containing Illumina-compatible overhangs


title: Colonic tissue, M-1


title: Subject 1, vehicle, challenge 3

description:
S1P3
10x Genomics

value: Petrolatum


title: lib_frac3_utp_c

description:
Library name: Library 68
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 3 of polysome profiling (80S) using primers containing Illumina-compatible overhangs


title: Colonic tissue, N-3

value: Normal feeding


title: lib_frac3_utp_b

description:
Library name: Library 67
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 3 of polysome profiling (80S) using primers containing Illumina-compatible overhangs


title: Colonic tissue, N-2


title: Myoepithelial PBX3 25-084202

type: other

city: New York

first: Cristina

last: Antonescu

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPICv2 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system and standard recommended Illumina scanner setting

data_processing: minfi package v1.52.1 in R environment (v4.1)

label: Cy3 and Cy5

source_name: formalin-fixed paraffin-embedded

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue after manual macrodissection to ensure at least 10% tumor content, followed by bisulfite converstion.

value: formalin-fixed paraffin-embedded

tag: age group [years]

tag: site

value: knee

tag: histology

value: syncytial myoepithelioma


title: lib_frac3_utp_a

description:
Library name: Library 66
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 3 of polysome profiling (80S)  using primers containing Illumina-compatible overhangs


title: lib_frac3_n1m_b

description:
Library name: Library 64
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 3 of polysome profiling (80S)  using primers containing Illumina-compatible overhangs


title: NFATC2 24-214935

data_processing:
minfi package v1.52.1 in R environment (v4.1)
processed value definition: Average Beta (bVals_myoepithelial.csv)

source_name: formalin-fixed paraffin-embedded tumor

value: arm

value: NFATC2-rearranged sarcoma


title: lib_frac3_n1m_a

description:
Library name: Library 63
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 3 of polysome profiling (80S) using primers containing Illumina-compatible overhangs


title: lib_frac3_n1m_c

description:
Library name: Library 65
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 3 of polysome profiling (80S)  using primers containing Illumina-compatible overhangs


title: PLAG1 24-168448

value: foot

value: cutaneous PLAG1-rearranged mixed tumor


title: Myoepithelial PBX3 24-236112

value: mediastinum

value: myoepithelial tumor


title: GFAPsh-iCre-miR124T, 7 days post injection n2

description: Library name: CS17

value: Brain Cortex

value: Astrocytes/neurons

value: Brain cells

value: AAV


title: lib_frac4_n1m_b

description:
Library name: Library 70
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 4 of polysome profiling (light polysome)  using primers containing Illumina-compatible overhangs

value: HEK 293T PKR KO


title: PLAG1 756-25

value: PLAG1 IHC


title: lib_frac2_utp_c

description:
Library name: Library 62
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 2 of polysome profiling (40S,60S) using primers containing Illumina-compatible overhangs


title: lib_frac2_n1m_c

description:
Library name: Library 59
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 2 of polysome profiling (40S,60S)  using primers containing Illumina-compatible overhangs


title: PLAG1 755-25


title: lib_frac2_utp_b

description:
Library name: Library 61
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 2 of polysome profiling (40S,60S) using primers containing Illumina-compatible overhangs


title: lib_frac2_n1m_a

description:
Library name: Library 57
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 2 of polysome profiling (40S,60S) using primers containing Illumina-compatible overhangs


title: lib_frac2_n1m_b

description:
Library name: Library 58
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 2 of polysome profiling (40S,60S)  using primers containing Illumina-compatible overhangs


title: lib_frac1_utp_c

description:
Library name: Library 56
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 1 of polysome profiling (non-ribosomal fraction) using primers containing Illumina-compatible overhangs


title: lib_frac2_utp_a

description:
Library name: Library 60
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from  fraction 2 of polysome profiling (40S,60S)  using primers containing Illumina-compatible overhangs


title: PLAG1 752-25

value: calf


title: PLAG1 748-25


title: lib_frac1_utp_b

description:
Library name: Library 55
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 1 of polysome profiling (non-ribosomal fraction) using primers containing Illumina-compatible overhangs


title: Colonic tissue, N-1

value: Colonic tissue

value: WT

value: Normal feeding


title: lib_frac1_utp_a

description:
Library name: Library 54
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 1 of polysome profiling (non-ribosomal fraction) using primers containing Illumina-compatible overhangs


title: NFATC2 746-25

value: formalin-fixed paraffin-embedded


title: NFATC2 25-010119

value: thigh


title: lib_frac1_n1m_c

description:
Library name: Library 53
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 1 of polysome profiling (non-ribosomal fraction) using primers containing Illumina-compatible overhangs


title: Myoepithelial PBX1 24-146083

value: knee

value: syncytial myoepithelioma


title: Myoepithelial POU5F1 25-032845

value: back


title: lib_frac1_n1m_b

description:
Library name: Library 52
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 1 of polysome profiling (non-ribosomal fraction) using primers containing Illumina-compatible overhangs


title: Myoepithelial PBX1 24-063000

value: elbow


title: PLAG1 13741-24

value: eye

value: cutaneous PLAG1-rearranged mixed tumor


title: lib_frac1_n1m_a

description:
Library name: Library 51
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from fraction 1 of polysome profiling (non-ribosomal fraction) using primers containing Illumina-compatible overhangs


title: Myoepithelial KLF17 1-43670

value: leg

value: myoepithelial tumor


title: PLAG1 13740-24

value: foot


title: PLAG1 13743-24


title: lib_all_utp_c

description:
Library name: Library 50
In cells transfected with the pooled IVT luciferase library which incorporated UTP at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from whole cell lysates using primers containing Illumina-compatible overhangs

value: HEK 293T PKR KO


title: lib_all_n1m_c

description:
Library name: Library 47
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from whole cell lysates using primers containing Illumina-compatible overhangs


title: lib_all_utp_b

description:
Library name: Library 49
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from whole cell lysates using primers containing Illumina-compatible overhangs


title: lib_all_n1m_b

description:
Library name: Library 46
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from whole cell lysates using primers containing Illumina-compatible overhangs


title: PLAG1 13742-24

value: lip


title: Myoepithelial SS18-POU5F1 13668-24

value: parotid


title: Myoepithelial POU5F1 10597-24


title: lib_all_n1m_a

description:
Library name: Library 45
In cells transfected with the pooled IVT luciferase library which incorporated m1Y at each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from whole cell lysates using primers containing Illumina-compatible overhangs


title: chase_utp_150

description:
Library name: Library 44
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position and treated with Harringtonine for 150 seconds

data_processing:
The analysis pipeline for the mRNA-seq and Ribo-seq libraries included the following steps: 1. Linker trimming with Cutadapt v4.9. 2. Alignment to rRNA and tRNA reference sequences, with exclusion of matching reads. 3. Alignment of the remaining reads to the hg19 genome and the relevant in vitro transcript (IVT). 4. Alignment to the hg19 transcriptome.
All alignments were performed with Bowtie v1.3.1. To obtain frame-accurate information on the IVT, PRICE v1.0.4 was used. Additional processing was carried out with in-house scripts.
For the library screen, reads were aligned to a reference that included the specific barcodes of each sequence together with ~40 bp of flanking sequence on each side. These alignments were performed with STAR v2.7.11b using the parameter --alignEndsType EndToEnd.
Assembly: hg19 plus IVT and library sequences which are provided in the supplementary materials of the paper.
Supplementary files format and content: Wiggle (WIG) files from the chase experiment.
Supplementary files format and content: TSV files reporting: read counts per gene for both RNA-seq and Ribo-seq; read counts per nucleotide for the IVT in the Ribo-seq libraries
Library strategy: Ribo-Seq


title: Myoepithelial POU5F1 10595-24


title: PLAG1 747-25

value: occipital


title: PLAG1 10894-24


title: chase_utp_120

description:
Library name: Library 43
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position and treated with Harringtonine for 120 seconds


title: chase_utp_90

description:
Library name: Library 42
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position and treated with Harringtonine for 90 seconds


title: Myoepithelial POU5F1 10593-24

value: kidney


title: Myoepithelial KLF17 10368-24


title: chase_utp_60

description:
Library name: Library 41
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position and treated with Harringtonine for 60 seconds


title: chase_n1m_150

description:
Library name: Library 40
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position and treated with Harringtonine for 150 seconds


title: Myoepithelial KLF15 10367-24

value: spine


title: Myoepithelial PBX3 10366-24

value: formalin-fixed paraffin-embedded

value: radius


title: chase_n1m_120

description:
Library name: Library 39
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position and treated with Harringtonine for 120 seconds


title: Myoepithelial POU5F1 10365-24

value: thumb


title: chase_n1m_90

description:
Library name: Library 38
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position and treated with Harringtonine for 90 seconds


title: lib_all_utp_a

description:
Library name: Library 48
In cells transfected with the pooled IVT luciferase library which incorporated UTPat each uridine position, barcode regions of the luciferase library transcripts were specifically amplified from whole cell lysates using primers containing Illumina-compatible overhangs


title: Myoepithelial PBX3 10364-24

value: scapula


title: Myoepithelial KLF17 10369-24

value: shoulder


title: mrna_spike_utp_b

description:
Library name: Library 36
RNA-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates UTP at each uridine position

source_name: HEK 293T

value: HEK 293T


title: chase_n1m_60

description:
Library name: Library 37
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position and treated with Harringtonine for 60 seconds


title: Myoepithelial PBX1 10363-24

value: pleura


title: mrna_spike_utp_a

description:
Library name: Library 35
RNA-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporatesUTP at each uridine position


title: mrna_spike_pseudo_a

description:
Library name: Library 33
RNA-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates Y at each uridine position


title: mrna_spike_n1m_b

description:
Library name: Library 32
RNA-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates m1Y at each uridine position


title: mrna_spike_pseudo_b

description:
Library name: Library 34
RNA-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates Y at each uridine position


title: mrna_spike_n1m_a

description:
Library name: Library 31
RNA-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates m1Y at each uridine position


title: Myoepithelial POU5F1 10358-24

value: back


title: Myoepithelial POU5F1 10359-24

value: thigh


title: Myoepithelial POU5F1 10354-24

value: myoepithelial tumor


title: mrna_fluc_WT_utp_b

description:
Library name: Library 30
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: mrna_fluc_WT_utp_a

description:
Library name: Library 29
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: mrna_fluc_WT_n1m_b

description:
Library name: Library 28
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: mrna_fluc_WT_n1m_a

description:
Library name: Library 27
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: Myoepithelial ZNF444 10341-24


title: Myoepithelial POU5F1 10340-24

value: arm


title: mrna_fluc_minU_utp_b

description:
Library name: Library 26
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates UTP at each uridine position

value: HEK 293T PKR KO


title: mrna_fluc_minU_utp_a

description:
Library name: Library 25
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates UTP at each uridine position


title: Myoepithelial PBX1 10352-24

value: foot


title: mrna_fluc_minU_n1m_b

description:
Library name: Library 24
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates m1Y at each uridine position


title: Myoepithelial POU5F1 10350-24


title: Myoepithelial POU5F1 10351-24

value: popliteal


title: Myoepithelial PBX1 10362-24


title: mrna_fluc_utp_b

description:
Library name: Library 22
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: Myoepithelial POU5F1 10349-24


title: mrna_fluc_minU_n1m_a

description:
Library name: Library 23
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates m1Y at each uridine position


title: Myoepithelial POU5F1 10361-24


title: Myoepithelial PBX3 10346-24

value: skin

value: syncytial myoepithelioma


title: mrna_fluc_utp_a

description:
Library name: Library 21
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: mrna_fluc_n1m_b

description:
Library name: Library 20
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: Myoepithelial PBX3 10347-24

value: navicular


title: Myoepithelial POU5F1 10345-24

value: formalin-fixed paraffin-embedded


title: Input_rep3_H9TELC

description: Library name: Input_rep3_H9TELC

data_processing:
Adapters were trimmed from reads using Trim Galore (v0.6.10).
Trimmed reads were aligned to GRCh38 using bowtie2 (v2.4.1).
Peaks were called using MACS2 (v2.2.6) with significance cut-off value q-value <= 0.05.
DiffBind (v3.16.0) was used to find consensus peaks among replicates using minOverlapmembers = 2.
BigWig files were generated with deeptools (v3.5.5) bamCoverage using CPM for normalization for individual replicates, then an average bigWig was generated from replicates using bigWigAverage for visualization with deeptools plotHeatmap.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were crosslinked with 1% formaldehyde (Pierce cat. no. 28906) for 10 minutes at room temperature on a horizontal rocker and quenched with 2.5 M glycine. After nuclear lysis, chromatin was sheared in microtube-500 AFA (Covaris cat. no. 520185) using Covaris E220 Focused-Ultrasonicator with settings 5% duty, PiP 140, 15 minutes in 30 second bursts, cycles 200.
Sequencing libraries were generated using 50% of the volume (8 uL)  from each ChIP using the KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA, USA) following manufacturer’s instructions using 13 cycles of amplification. The quality of the library was assessed using High Sensitivity D1000 kit on a 4200 TapeStation instrument (Agilent Technologies, Santa Clara, CA, USA).

value: cells

value: TE-like cell

value: BMP4 (10ng/mL) and IWP2 (2µM)

tag: chip antibody


title: Myoepithelial KLF17 10344-24


title: mrna_fluc_n1m_a

description:
Library name: Library 19
RNA-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: fp_spike_utp_b

description:
Library name: Library 18
Ribo-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates UTP at each uridine position


title: Input_rep1_H9TELC

description: Library name: Input_rep1_H9TELC


title: Input_rep2_H9TELC

description: Library name: Input_rep2_H9TELC


title: Myoepithelial ZNF444 10353-24

value: flank


title: Myoepithelial POU5F1 10343-24

value: vulva


title: VGLL1_ChIPseq_rep2_H9TELC

description: Library name: VGLL1_ChIPseq_rep2_H9TELC

value: VGLL1 antibody (Sigma Aldrich cat. no. HPA042403-100UL)


title: fp_spike_utp_a

description:
Library name: Library 17
Ribo-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporatesUTP at each uridine position

value: HEK 293T


title: VGLL1_ChIPseq_rep1_H9TELC

description: Library name: VGLL1_ChIPseq_rep1_H9TELC


title: fp_spike_pseudo_b

description:
Library name: Library 16
Ribo-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates Y at each uridine position


title: NFATC2 5907-24

value: NFATC2-rearranged sarcoma


title: H9_d0_C

description: Library name: H9_d0_C

data_processing:
The bcbio-nextgen (v1.2.8) ATAC-seq pipeline was used to process the reads.
The nucleosome free fraction was normalized using deeptools (v3.5.1) bamCoverage by CPM.
BigWig for biological replicates were combined using wiggletools (v1.2.11) mean.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were lysed in ATAC-seq Lysis Buffer and nuclear pellet was resuspended in Transposition Mix and incubated at 37ºC as described in Grandi et al. 2022. Transposition reaction was terminated by adding 5x (vol/vol) DNA Binding Buffer. DNA clean up was perfomed with DNA Clean & Concentrator-5 kit (Zymo Research).
Transposed fragments were barcoded with unique combination of adapter sequences. NEBNext Ultra II Q5 (NEB) was used for library amplification for 9 cycles of PCR. Libraries were cleaned using DNA Clean & Concentrator-5 kit (Zymo Research), and size selection was performed with AMPure XP beads (0.55x sample volume followed by 1.8x sample volume).

value: embryonic stem cell


title: TEAD4_ChIPseq_rep1_H9TELC

description: Library name: TEAD4_ChIPseq_rep1_H9TELC

value: TEAD4 (Abcam cat. no. ab58310)


title: fp_spike_n1m_b

description:
Library name: Library 14
Ribo-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates m1Y at each uridine position


title: NFATC2 6797-24


title: H9_d0_B

description: Library name: H9_d0_B


title: BMP4-IWP2_d4_E

description: Library name: BMP4-IWP2_d4_E


title: H9_d0_A

description: Library name: H9_d0_A


title: BMP4-IWP2_d4_D

description: Library name: BMP4-IWP2_d4_D


title: BMP4-IWP2_d4_C

description: Library name: BMP4-IWP2_d4_C


title: BMP4-IWP2_d4_B

description: Library name: BMP4-IWP2_d4_B


title: H9_d0_D

description: Library name: H9_d0_D


title: fp_fluc_WT_utp_a

description:
Library name: Library 11
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position

value: HEK 293T PKR KO


title: Pancreatic Sox2 KO tumor 3

city: East Lansing

first: Bin

last: Gu

state: MI

address: 755 Woodlot Drive

department: OBGYN

institute: Michigan State University

description: Library name: Pancreatic Sox2 KO tumor 3

data_processing:
Raw reads were trimmed with TrimGalore (v0.6.10) with the default parameters. FastQC (v0.12.1) was used to ensure the quality of data.
Trimmed reads were quantified with Kallisto (v0.50.0) using the GENCODE mouse transcriptome (GRCm38, release M23) with settings --rf-stranded -b 100.
Differential gene expression analysis was conducted using DESeq2.
Gene set enrichment analysis (GSEA) [28] was performed using clusterProfiler.
Assembly: GENCODE mouse transcriptome (GRCm38, release M23)
Supplementary files format and content: csv file containing raw count for each sample

source_name: mNC tumor

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
One microgram of RNA per sample was subjected to ribosomal RNA (rRNA) depletion and library preparation using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, following the manufacturer’s instructions

value: mNC tumor

value: Pdx1-Cre; NCT+/-; Sox2fl; fl


title: fp_fluc_WT_utp_b

description:
Library name: Library 12
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: Pancreatic Sox2 KO tumor 1

description: Library name: Pancreatic Sox2 KO tumor 1


title: BMP4-IWP2_d2_E

description: Library name: BMP4-IWP2_d2_E


title: fp_fluc_WT_n1m_b

description:
Library name: Library 10
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: TEAD4_ChIPseq_rep2_H9TELC

description: Library name: TEAD4_ChIPseq_rep2_H9TELC


title: BMP4-IWP2_d2_D

description: Library name: BMP4-IWP2_d2_D


title: BMP4-IWP2_d4_A

description: Library name: BMP4-IWP2_d4_A


title: Pancreatic wild-type tumor 4

description: Library name: Pancreatic wild-type tumor 4

value: Pdx1-Cre; NCT+/-


title: BMP4-IWP2_d2_C

description: Library name: BMP4-IWP2_d2_C


title: fp_spike_pseudo_a

description:
Library name: Library 15
Ribo-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates Y at each uridine position


title: H9_d0_E

description: Library name: H9_d0_E


title: BMP4_d4_E

description: Library name: BMP4_d4_E

value: BMP4 (10ng/mL)


title: Pancreatic wild-type tumor 3

description: Library name: Pancreatic wild-type tumor 3


title: fp_fluc_minU_utp_b

description:
Library name: Library 8
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates UTP at each uridine position


title: Pancreatic wild-type tumor 2

description: Library name: Pancreatic wild-type tumor 2


title: fp_spike_n1m_a

description:
Library name: Library 13
Ribo-seq of cells transfected with in vitro transcribed (IVT) Spike mRNA which incorporates m1Y at each uridine position


title: BMP4_d4_C

description: Library name: BMP4_d4_C


title: BMP4_d4_D

description: Library name: BMP4_d4_D


title: BMP4_d4_B

description: Library name: BMP4_d4_B


title: Pancreatic Sox2 KO tumor 2

description: Library name: Pancreatic Sox2 KO tumor 2


title: fp_fluc_minU_utp_a

description:
Library name: Library 7
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates UTP at each uridine position


title: BMP4_d4_A

description: Library name: BMP4_d4_A


title: Pancreatic wild-type tumor 1

description: Library name: Pancreatic wild-type tumor 1


title: BMP4_d2_D

description: Library name: BMP4_d2_D


title: fp_fluc_minU_n1m_b

description:
Library name: Library 6
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates m1Y at each uridine position


title: Oral Sox2 KO tumor 2

description: Library name: Oral Sox2 KO tumor 2

value: KRT4Cre; NCT+/-; Sox2fl/fl


title: BMP4_d2_E

description: Library name: BMP4_d2_E


title: fp_fluc_WT_n1m_a

description:
Library name: Library 9
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: BMP4_d2_C

description: Library name: BMP4_d2_C


title: Oral Sox2 KO tumor 1

description: Library name: Oral Sox2 KO tumor 1


title: GRZ_BELL_F3

city: Cologne

first: David

last: Willemsen

address: Joseph-Stelzmann-Str 9b

department: Valenzano

country: Germany

institute: Max Planck Institute for Biology of Ageing

data_processing:
Reads were trimmed with trimmomatic  (Bolger et al., 2014)
Reads were mapped with STAR (Dobin et al., 2013, v.2.7.8a) and the following parameters: --outSAMmapqUnique 200, --outFilterIntronMotifs RemoveNoncanonicalUnannotated, --outFilterType BySJout , --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --alignIntronMax 1000000, --alignMatesGapMax 1000000.
Raw reads were counted with featureCounts (Liao et al., 2014, v.1.6.2) using a minimum mapping quality of 30.
Differential gene expression analyses were performed using DESeq2 (Love et al., 2014)
Genome_build: NFZv2.0 genome assembly (Willemsen et al., 2020)

organism: Nothobranchius furzeri

source_name: tail fin

extract_protocol:
For each sample, the pigmented region (or the corresponding region in females) of the tailfin was excised and stored at -20°C in RNAlater. We then extracted total RNA using QIAzol (Qiagen) according to the manufacturer’s protocol with modifications. Briefly, tissue taken out of the RNA later was rinsed with 1xPBS buffer and then dipped on a clean paper towel. After transferring the tissue into a 1.5ml Eppendorf tube containing 200µl Qiazol solution, we homogenized the tissue with a micro pestle. After 5 min incubation on ice, 80 µl chloroform was added and the tube was vigorously shaken for 20 s. The tube was incubated at RT for 3 min and then centrifuged at 12,000 x g for 15 min at 4°C. The aqueous phase was transferred into a fresh tube and 100 µl isopropanol was added. The tube was inverted 4-5 times for mixing and then incubated at RT for 10 min. To precipitate RNA, we centrifuged the tube at 21,130 x g for 30 min at 4°C. The supernatant was removed and the pellet was washed with 200µl of 75% EtOH. The aspirated pellet was resuspended in 26 µl nuclease-free water and treated with DNase using DNA-free Kit (Ambion). After measurements of concentration with Qubit-BR RNA Assay Kit (Invitrogen), samples were stored at -80°C.
For first-strand cDNA synthesis, 125ng of total RNA purified with 1.2X SeraSure beads (2.5M NaCl (Roth), 20 mM PEG8000 (Sigma), 10mM Tris-HCl pH 8.0  (Sigma), 1mM EDTA (Sigma), 1 ml SeraMag GE Healthcare, 65152105050250 beads in 100mL solution) was added to 1 µl of 3’ SfiI Oligo T primer (10µM) and 1µl of dNTP mix (10mM, Invitrogen) and incubated at 72°C for 3 min. Then, a first-strand mix containing 0.5 µl superscript II (200U/µl, Invitrogen), 0.25 µl RNAse inhibitor (40U/µl, Thermo Scientific), 2 µl Superscript II buffer (5X, Invitrogen), 0.25 µl DTT (100mM), 2 µl Betaine (5M, Sigma), 0.9 µl MgCl2 (100mM, Sigma), 1 µl 5’ sfiI plug oligo (10mM), and 0.1 µl water was mixed into a tube and then incubated in a thermocycler with the following program: 90 min at 42°C, 10 cycles of 2 min at 50°C and 2 min at 42°C, and 15 min at 72°C. For preamplification, 12.5 µl 2X KAPA HiFi HotStart ReadyMix, 1 µl of cDNA universal primer (10uM), 2 µl of 1st strand cDNA, and 9.5 µl of water were mixed and incubated in a thermocycler with the following program: 3 min at 98°C, 16 cycles of 15 s at 98°C, 20 s at 67°C, and 6 min at 72°C, and 5 min at 72°C. 2 µl NEB CutSmart buffer (10X) and 1 µl SfiI (10U/µl, NEB) were added into the PCR mix and incubated overnight at 50°C. The resulting PCR product was purified with 1X SeraSure beads. For library preparation, a maximum of 250ng of cDNA was added for a 10 µl reaction mix containing 1µl of dsDNA fragmentase (NEB), 1µl fragmentase buffer (10X, NEB), and water and then incubated for 22.5 min at 37°C. The reaction was stopped with 5 µl of EDTA (0.5 M, Sigma). 5 µl of nuclease-free water (Qiagen) was added to the reaction mixture, which was followed by a purification with 1.2X SeraSure beads and resuspension in 5µl of Tris buffer. 1 µl of end repair reaction buffer (10X, NEB), 0.5 µl of Klenow (NEB), 0.5 µl of Taq polymerase (Invitrogen), 0.2 µl of T4 polynucleotide kinase (10U/µl, NEB) was added to 5 µl of fragmented DNA and incubated in a thermocycler for end-repair reaction with the following program: 30 min at 25°C and 30 min at 75°C. Then, cDNA was ligated with adaptors containing 8-bp barcodes using Quick Ligase (NEB). The resulting cDNA was enriched with 7-9 cycles of PCR.  After amplification, we performed size selection using 0.55X SeraSure beads. The quality of libraries was assessed with an Agilent 4200 TapeStation. Libraries were pooled and sequenced across one lane of Illumina HiSeq X at NGX bio (US).

value: GRZ-BELL


title: GRZ_BELL_F1


title: fp_fluc_minU_n1m_a

description:
Library name: Library 5
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase minU mRNA which incorporates m1Y at each uridine position


title: fp_fluc_utp_a

description:
Library name: Library 3
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: Oral wild-type tumor 4

description: Library name: Oral wild-type tumor 4

value: KRT14-Cre; NCT+/-


title: GRZ_BELL_Y1


title: fp_fluc_n1m_b

description:
Library name: Library 2
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: GRZ_BELL_F2


title: fp_fluc_utp_b

description:
Library name: Library 4
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates UTP at each uridine position


title: Oral wild-type tumor 3

description: Library name: Oral wild-type tumor 3


title: GRZ_BELL_Y3


title: MZCS002_F1


title: Oral wild-type tumor 2

description: Library name: Oral wild-type tumor 2


title: fp_fluc_n1m_a

description:
Library name: Library 1
Ribo-seq of cells transfected with in vitro transcribed (IVT) luciferase mRNA which incorporates m1Y at each uridine position


title: MZCS002_R3