title: Primary human skin fibroblast replicate 2

description: Library name: LJ6

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
CUT-RUNTools-2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) was used to trim, align, and call peaks. Used default settings, EXCEPT set "frag_120" to "FALSE".
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters -of bigwig --effectiveGenomeSize 2913022398 --normalizeUsing RPGC --ignoreForNormalization chrX chrM --binSize 10
Assembly: Gencode GRCh38 p14 Release 47
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Run

source_name: Primary skin fibroblast

growth_protocol: Primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Medium was refreshed as needed, and cells were subcultured before reaching full confluence to maintain normal morphology and proliferative capacity.

extract_protocol:
Detach fibroblasts (passages 2–5) using 0.05–0.25% trypsin-EDTA until cells are in suspension.Neutralize trypsin with complete growth medium and collect cells by centrifugation (300 × g, 5 min). Wash cells with PBS.
Cells were permeabilized and incubated with an anti-RUNX2 antibody, followed by protein A–MNase to cleave DNA at RUNX2-bound sites. Released DNA fragments were purified and used to prepare sequencing libraries via end repair, A-tailing, adapter ligation, and limited-cycle PCR amplification, followed by size selection for ~150–400 bp fragments. Libraries were quality-checked and quantified prior to sequencing.

treatment_protocol: Cells were treated with or without TGF‑β, for 48 hours.

value: Primary skin fibroblast


title: Biological replicate 1, technical replicate 1, Eater macrophages

status: Public on Jun 10 2026

type: SRA

city: San Francisco

first: Balyn

last: Zaro

state: CA

address: 555 Mission Bay Blvd S, Rm 484

country: USA

institute: UCSF

description:
Library name: Sample 3
B1T1_Eat_S3_L001.counts

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed to remove sequencing adapters using Trimmomatic (v0.39) with the TruSeq3-PE-2 adapter sequences. Low-quality bases and short reads were filtered using the parameters LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b). Gene expression levels were quantified using HTSeq-count, where aligned reads were counted against gene features defined in the Gencode v45 GTF annotation.
Assembly: human reference genome (hg38) using STAR (v2.7.11b)
Supplementary files format and content: Processed data file for all samples is: RNA_seq_raw_reads_count_all and contains columns with raw counts for each individua sample outlined above. Rows represent ensembl gene ids.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Cells were sorted via FACS following co-incubation as indicated. Following PBS washing steps to remove excess FBS, samples were lysed into TRI Reagent (Zymo Research, R2071) and then snap frozen and stored at -80°C until RNA extraction was performed. RNA extraction was performed using Direct-zol RNA MiniPrep Plus (Zymo Research, R2071) following manufacturer’s instructions.
Two biological replicates of each cell type (Eaters, Non-eaters, Uneaten, SW620, and Naive macrophages) were used for RNA sequencing, with each biological replicate consisting of two technical replicates. RNA-seq libraries were prepared using the Single Cell/Low Input RNA Library Prep Kit (NEB, E6420), following the manufacturer's protocol. In brief, 200 ng of total RNA was used as input. First, reverse transcription was performed, followed by 7 cycles of cDNA amplification and clean-up. The cDNA was then fragmented, repaired, ligated with NEBNext adaptors, and enriched using 4-5 cycles of PCR. Libraries were sequenced on a NovaSeq X 10B platform using paired-end 150 bp (PE150) reads.

tag: cell line

tag: cell type

value: Human colorectal cancer cells

value: Human monocyte derived macrophages

tag: treatment

value: Isolated following co-incubation and phagocytosis of live SW620 colorectal cancer cells


title: hTERT-HM cells day 3 rep1

city: St. Louis

first: Ritu

last: Dave

address: 425 S Euclid Ave

institute: Washington University School of Medicine

description:
Library name: sample4
column name in all.gene_counts.xlsx: sample.Day_3_B

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s DRAGEN BCLconvert version 4.3.13.
RNA-seq reads were then aligned to the Ensembl GRCh38.113 primary assembly with STAR version 2.7.11b.
Gene counts were derived from the number of uniquely aligned unambiguous fragments by Subread:featureCount version 2.0.8. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.10.0.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 5.04.
Assembly: GRCh38.113
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: myometrium

extract_protocol:
RNA was extracted using the Zymo Research RNA Miniprep kit. Library preperation was done with 1ug of total RNA.
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (NEBNext Poly(A) mRNA Magnetic Isolation module, New England Biolabs). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

tag: tissue

value: myometrium

value: hTERT-HM

value: myometrial cell

tag: genotype

value: WT


title: Mmac_vas lat_CTR_20

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Library name: Sample_M_9

data_processing:
FastQC was used to check quality quality of reads.
Next, reads were trimmed using bbduk.
Cleaned FASTQ files were aligned to Mmul_10 using STAR.
Transcript data was generated using RSEM.
Finally, count data was generated by using featureCounts.
Assembly: Mmul_10
Supplementary files format and content: Count data

organism: Macaca mulatta

source_name: vastus lateralis skeletal muscle

extract_protocol:
RNeasy Fibrous Tissue Mini Kit  protocol (Qiagen, Cat. No. 74704) in QIAcube Connect (Qiagen, Cat. No. 9002864)
Library was prepared using Illumina Stranded Total RNA Prep. Ligation was performed with Rib-Zero Plus kit.

treatment_protocol: Caloric Restriction

value: vastus lateralis skeletal muscle

tag: age

value: CTR


title: hTERT-HM cells, day 1 rep3

description:
Library name: sample3
column name in all.gene_counts.xlsx: sample.Day_1_E


title: Biological replicate 1, technical replicate 1, Non-Eater macrophages

description:
Library name: Sample 4
B1T1_Noneat_S4_L001.counts

source_name: Human monocyte derived macrophages

value: Isolated following co-incubation with live SW620 colorectal cancer cells


title: Biological replicate 1, technical replicate 1, naive human macrophages

description:
Library name: Sample 2
B1T1_Mac_S2_L001.counts


title: hTERT-HM cells, day 1 rep2

description:
Library name: sample2
column name in all.gene_counts.xlsx: sample.Day_1_D


title: cortical brain tissue, B6F1

city: Copenhagen

first: Shohreh

last: Issazadeh-Navikas

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Raw data were demultiplexed, aligned, and quantified using Cell Ranger version (v)3.1.0. To allow for counting of unspliced pre-mRNA, a custom version of the mm10-3.0.0 mouse reference genome provided by 10x Genomics was used, where the feature ‘type of transcripts’ was changed from ‘transcript’ to ‘exon’.
Data analysis was performed in R using Seurat v3.1.5 and Conos v1.2.1. The -barcode matrices were filtered to include cells meeting the following criteria: 200<nFeature_RNA<6000, nCount_RNA>1000, and percent_MT<10. Doublets were filtered out using the Scrublet package
Data were log-normalized, and individual samples were integrated using the fast mutual nearest neighbors (fastMNN) method based on the top 3,000 variable features. Clustering and UMAP visualization were performed using the first 40 dimensions of the MNN reduction.
The integrated dataset was annotated using canonical correlation analysis (CCA) based label transfer in Seurat with the Allen Brain Map Mouse Whole Cortex and Hippocampus SMART-seq dataset [https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq] as the reference
Assembly: mm10-3.0.0
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: nuclear RNA

organism: Mus musculus

source_name: Cortex (brain)

extract_protocol:
16,000 nuclei per sample were loaded on the 10x Chromium chip for library preparation using the Single Cell 3’ v3 chemistry according to manufacturer instructions. For cDNA amplification, 12 PCR cycles were applied. For each sample, 230 ng of purified cDNA was used for library construction.
The libraries were diluted to a concentration of 10 nM and pooled for sequencing. After denaturation, the library pool was diluted to a loading concentration of 300 pM and sequenced on a Novaseq6000 in paired-end mode (2x100) (read 1:28 cycles, read 2:91 cycles, and i7 index: 8 cycles) at an average depth of 50,000 reads per nucleus.
single nuclei (sn)RNA-seq

value: Cortex (brain)

value: Cortical cells

value: 6 week old

tag: gender

value: Female

tag: strain

value: naive


title: Mmac_vas lat_CTR_19

description: Library name: Sample_M_8


title: hTERT-HM cells, day 1 rep1

description:
Library name: sample1
column name in all.gene_counts.xlsx: sample.Day_1_C


title: vh75sample

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

description: Library name: vh75sample

library_source: transcriptomic single cell

data_processing:
fastq files were run through 10X cellranger pipeline
downstream analysis was done by R package Seurat,details were described in 'Methods'
Assembly: hg38
Supplementary files format and content: h5 format with cell by gene matrix

source_name: bladder

extract_protocol:
NMIBC clinical samples were selected from the Hospital del Mar-Parc de Salut Mar-Biobank, Barcelona, Spain. Nuclei isolation was performed using a modified protocol optimized for FFPE material (Cejas and Long, 2022). Paraffin was removed through sequential xylene washes, followed by tissue rehydration in a graded ethanol series ending in distilled water. The tissue pellet was resuspended in dissociation buffer containing PBS, Liberase TM, Collagenase D, and RNase inhibitor, and incubated at 37°C for 1 hour in a thermomixer. Following enzymatic dissociation, samples were washed with PBS and centrifuged. The pellet was resuspended in 300 µL of lysis buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, and incubated overnight at 37°C. After adding 700 µL of 0.1% Tween-20 RSB buffer, nuclei were filtered through a 40 µm cell strainer and counted before pelleting by centrifugation at 1,250 × g for 10 minutes at 4°C. Approximately 10,000 nuclei per sample were used for downstream library preparation.
Nuclei were processed following the 10x Genomics GEM-X Flex Single-Nucleus Gene Expression protocol. Libraries were prepared, multiplexed, and sequenced as 150 bp paired-end reads on an Illumina NovaSeq XP platform.

value: bladder

tag: histological variants

value: URO

tag: uro subtype

value: mix

tag: batch


title: Mmac_vas lat_CTR_18

description: Library name: Sample_M_7


title: Biological replicate 1, technical replicate 1, Uneaten SW620s

description:
Library name: Sample 1
B1T1_UE_S1_L001.counts

value: Human colorectal cancer cells

value: Isolated following co-incubation with human monocyte derived macrophages


title: vh61sample

description: Library name: vh61sample

value: LLI


title: Cortical neurons, shControl, Day 11, normal IgG ChIP

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

library_source: genomic

data_processing:
fastq files were verified with multiQC.
Sequencing adaptors were trimmed and duplicates were removed.
ChIP peaks were called using MACS2.
Bigwig files were generated using bamCoverage for data visualization.
Assembly: mm10

molecule: genomic DNA

source_name: brain

growth_protocol: Primary cortical neurons were prepared from embryonic cortices at day E14.5-15 of CD1 mice and cultured in vitro for 11 days.

extract_protocol:
Chromatin were cross-linked with formaldehyde for 30 minutes. Chromatin was lysed and sonicated (Covaris) into average 150bp fragments.
ChIP-seq library was prepared using Illumina ChIP-seq library preparation kit.

treatment_protocol:
Cells were seeded at a density of 1 million cells/ml. Neurons were cultured in neurobasal media containing 1X B27; 1X N2; 100 Units/mL Penicillin/Streptomycin, and 0.6 mM L-glutamine. Cells were treated with the mitotic inhibitor cytosine arabinoside at 2uM.
A 50 % Media change is performed every 3-4 days and a full media change 3 days following Ara-C treatment. Lentiviral transduction was performed at day 6 and cells were harvested for RNA extraction on day 11.

value: brain

value: primary cell

value: cortical neurons

value: neuron differentiation


title: KOLF_KO_rpf_rep3

first: Elena

last: Turkalj

description:
Library name: KOLF_KO_rpf_rep3
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv

data_processing:
Read processing: Raw single-end Ribo-seq reads were adapter-trimmed using cutadapt v4.9 with options “--trimmed-only -m 15 -e 0.2 -a TAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.” Trimmed reads were then aligned in two steps using bowtie2 v2.5.4. First, reads mapping to a custom rRNA/tRNA index were discarded. The remaining reads were then aligned end-to-end to a GRCh38-based mRNA transcriptome (Ensembl release v96), in which each gene is represented by the isoform containing the longest annotated coding sequences (CDS). The associated total RNA-Seq sample reads were aligned to the same longest CDS reference transcriptome using bowtie2.
TE analysis with Ribolog: Ribo-seq and matched RNA-seq reads (BAM files) were imported into Ribolog v0.0.0.9 for differential translation efficiency (TE) analysis. Ribo-seq reads were filtered to retain only in-frame ribosome-protected fragments (RPFs) 40-44 nucleotides long. Codon-level counts derived from these RPFs were corrected for ribosome stalling using the CELP (Consistent Excess of Loess Preds) method implemented in Ribolog. CELP-corrected Ribo-seq and total RNA-seq reads were median-normalized, and lowly expressed transcripts were excluded: specifically, transcripts with fewer than 5 RNA-seq reads in each RNA-seq sample or fewer than 2 RPFs on average across all Ribo-seq samples were removed. TE for each transcript was calculated as the ratio of Ribo-seq to total RNA-seq transcript counts. Differential TE between wild-type and METTL5-knockout samples was modeled using logistic regression and Benjamini–Hochberg correction for multiple testing, as implemented in Ribolog’s logit_seq function.
TE analysis with DESeq2: Transcript-level Ribo-seq and RNA-seq counts generated from the Ribolog pipeline were reanalyzed using DESeq2 to assess differential translation efficiency (TE). Ribo-seq counts were obtained from reads filtered for reads with a P-site mapping to the coding sequence (CDS) and a footprint length of 40–44 nucleotides long. RNA-seq counts were extracted using the bam2count function in Ribolog. A two-factor design was used to model differential TE in DESeq2, incorporating sample condition (wild-type or METTL5-knockout) and sequencing assay type (RNA-seq or Ribo-seq), with the following design formula: ∼ assay_type + condition + assay_type:condition.
RNA-seq differential analysis: RNA-seq transcript counts were extracted using the bam2count function in Ribolog. Differential expression analysis was performed using DESeq2 (v.1.42.1) to compare the wild-type and METTL5-knockout samples.
Assembly: hg38
Supplementary files format and content: csv file of the raw RPF and RNA-seq transcript counts for each sample
Supplementary files format and content: csv file of differential translational efficiency (TE) results from Ribolog
Supplementary files format and content: csv file of the RNA-seq differential analysis results from DESeq2
Library strategy: Ribo-Seq

source_name: cortical forebrain neural progenitor cells

growth_protocol: hiPSCs at 80-90% confluency were cultured in N I(GMEM 76.8%, KSR 20%, NEAA, sodium pyruvate, antibiotic-antimycotic, 0.18 mM β-mercaptoethanol) supplemented with 10 µM SB431542, 100 nM LDN-193189, and 5 µM XAV939. Medium was changed daily for 7 days. On day 7, NPCs were dissociated with Accutase and seeded on Matrigel-coated 6-well plates in MM1(DMEM/F12 47.4%, Neurobasal 47.4%, B27 minus vitamin A, N2, GlutaMAX, NEAA, antibiotic-antimycotic, 0.1 mM β-mercaptoethanol supplemented fresh with EGF 10 ng/mL and FGF10 ng/mL) with 10 µM Ri; Ri was removed the following day.

extract_protocol:
Control or METTL5-KO NPCs were grown on 15cm plates (3 plates were combined to make 1 replicate, and control and KO had three biological replicates each) and harvested at 80% confluency and immediately treated with cycloheximide (100 µg/mL) for 3 minutes at 37°C to halt ribosomes on mRNAs. Cells were washed once with ice-cold PBS containing cycloheximide (100 µg/mL) and lysed in polysome lysis buffer [20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl₂, 1% Triton X-100, 1 mM DTT, 100 µg/mL cycloheximide, DNAse I 25U/ml), H20], followed by a 30 minute incubation on ice. Lysates were clarified by centrifugation at 10,000 X g for 10 minutes at 4°C. 1-2ug of RNA was saved for RNA-seq. 30ug of RNA was incubated with 30U/ml RNAse P1 for 1hr at 37°C. The Illustra MicroSpin Columns S-400HR were used for monosome isolation and downstream steps were the same as reported in McGlincy & Ingolia, 2017.
RNA-seq:1-2 ug of RNA was purified using the Direct-zol RNA miniprep kit (Zymo) then used in RNA seq library prep kits: NEBNext rRNA Depletion Kit V2 (human/mouse/rat) (NEB), NEBNext Ultra II Directional RNA Library Prep Kit of Illumina (E7760), with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (E6440S) Ribo-seq: library was constructed in the same manner as McGlincy & Ingolia, 2017.

value: Neural progentor cells

value: METTL5 KO


title: vh24sample

description: Library name: vh24sample


title: Mmac_vas lat_CTR_17

description: Library name: Sample_M_6

value: vastus lateralis skeletal muscle

value: CTR


title: vh1sample

description: Library name: vh1sample

value: BL


title: F8_tsc_XRN2_g1_nd_RNA

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

institute: UNC Chapel Hill

description: Library name: F8_tsc_XRN2_g1_nd_RNA

data_processing:
RNA-Seq reads were aligned using STAR v2.5.4b with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools.
Assembly: mm10
Supplementary files format and content: Wiggle tracks were normalized to q30 aligned reads to mm10

source_name: mouse TSCs 6-2

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate. For RNA-seq, cells were then split off of feeders for a second time, but without pre-plating and then cultured for three to four days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
RNA was harvested with trizol and purified with the Zymo Clean and Concentrator kit.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of 100ng/ul RNA + 1uL ERCC RNA spike-in

treatment_protocol: To induce RBP knockdown, TSCs were treated with 1000ng/mL of doxycycline for four days.

value: mouse TSCs 6-2

value: XRN2 sgRNA 1 knockdown


title: F8_tsc_XRN2_g1_dox_RNA

description: Library name: F8_tsc_XRN2_g1_dox_RNA

value: 4-day 1000ng/mL dox-treated


title: KOLF_KO_rpf_rep2

description:
Library name: KOLF_KO_rpf_rep2
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv

value: cortical forebrain neural progenitor cells


title: vh176sample

description: Library name: vh176sample

value: bladder

value: URO

value: mix


title: Mmac_vas lat_CTR_16

description: Library name: Sample_M_5


title: vh15sample

description: Library name: vh15sample


title: Mmrn1-low LT-HSCs, rep3

city: Chongqing

first: Naicheng

last: Chen

state: Chongqing

address: Gaotanyan Street 30

department: College of Preventive Medicine

country: China

institute: Third Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCm38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

source_name: Mmrn1-low long term hematopoietic stem cells from murine bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Bone marrow

value: stem cells

value: Mmrn1-GFP type

tag: mmrn1 status


title: Mmrn1-low LT-HSCs, rep2


title: shRUNX2-3

city: Birmingham

first: Lin

last: Jin

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description: Library name: Jin_E6

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw paired-end FASTQ files were quality- and adapter-trimmed using Trimmomatic v0.36 in paired-end mode with parameters: PE -threads 8 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Paired trimmed reads were retained for downstream analysis.
Trimmed paired-end reads were aligned to the human hg38 reference genome using STAR v2.7.3a with parameters: --readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts --limitBAMsortRAM 64000000000.
Gene-level read counts were generated from STAR coordinate-sorted BAM files using htseq-count with the hg38 refGene GTF annotation file and parameters: -f bam -r pos -s reverse -t exon -i gene_id -m union -a 10.
Count tables were used for downstream differential gene expression analysis.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file consisting of raw counts (transcript abundances) for each sample for each Ensembl Gene ID

source_name: immortalized skin fibroblast

growth_protocol: Immortalized human skin fibroblasts or primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Cells were maintained by replacing the medium every 2–3 days and subcultured before reaching full confluence to preserve normal morphology and proliferative capacity.

extract_protocol:
Total RNA was extracted from cultured fibroblasts using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and samples were stored at –80°C until further use
Using the NEBNext Ultra II RNA Library Prep Kit for Illumina with poly(A) selection, we begin with high-quality total RNA and enrich mRNA using oligo-dT magnetic beads to capture polyadenylated transcripts, followed by washing and elution; we then fragment the purified mRNA under heat and prime it for reverse transcription to generate first-strand cDNA, after which we perform second-strand synthesis to produce double-stranded cDNA (optionally incorporating strand specificity), and subsequently carry out end repair and dA-tailing to create adapter-compatible ends; we ligate sequencing adapters, purify the library using magnetic beads (with optional size selection), and amplify it by PCR with indexed primers to enrich adapter-ligated fragments, and finally we assess library size distribution and concentration before pooling and sequencing on an Illumina platform.

treatment_protocol: Cells were treated either with or without TGF‑β or with compoound F05650303 for 48 hours.

value: immortalized skin fibroblast

value: fibroblast

value: wt


title: KOLF_KO_rpf_rep1

description:
Library name: KOLF_KO_rpf_rep1
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv

value: Neural progentor cells

value: METTL5 KO


title: vh12sample

description: Library name: vh12sample


title: Mmac_vas lat_CALRES_20

description: Library name: Sample_M_4

value: vastus lateralis skeletal muscle

value: CALRES


title: F18_tsc_HU_g5_Dox__r2_RNA

description: Library name: F18_tsc_HU_g5_Dox__r2_RNA

value: mouse TSCs 6-2

value: HNRNPU sgRNA 5 knockdown


title: vh125sample

description: Library name: vh125sample


title: KOLF_rpf_rep3

description:
Library name: KOLF_rpf_rep3
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv

value: WT


title: vh122sample

description: Library name: vh122sample

value: LLI


title: F18_tsc_HK_g3_4_nodox_r1_RNA

description: Library name: F18_tsc_HK_g3_4_nodox_r1_RNA

value: HNRNPK sgRNAs 3+4 knockdown


title: F18_tsc_HU_g5_Dox_r1_RNA

description: Library name: F18_tsc_HU_g5_Dox_r1_RNA

value: 4-day 1000ng/mL dox-treated


title: Biological replicate 1, technical replicate 2, naive SW620s

description:
Library name: Sample 10
B1T2_SW620_S10_L001.counts

value: Human colorectal cancer cells


title: MPBC2_sample

description: Library name: MPBC2_sample

value: bladder

value: MP


title: Mmac_vas lat_CALRES_19

description: Library name: Sample_M_3


title: KOLF_rpf_rep2

description:
Library name: KOLF_rpf_rep2
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv

value: cortical forebrain neural progenitor cells


title: MPBC1_sample

description: Library name: MPBC1_sample


title: KOLF_rpf_rep1

description:
Library name: KOLF_rpf_rep1
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv


title: MPBC2

description: Library name: MPBC2

data_processing:
raw files go through spaceranger pipelines
Assembly: hg38
Supplementary files format and content: 2um bin by gene expression matrix in h5 format
Library strategy: Spatial Transcriptomics

extract_protocol:
FFPE tissue blocks were sectioned at 5 μm thickness and mounted onto standard glass slides. Sections were fixed, stained with hematoxylin and eosin (H&E), and imaged using a high-resolution slide scanner to capture tissue morphology. Following imaging, tissue sections underwent permeabilization to facilitate probe access, and probe hybridization was performed overnight to target mRNA sequences.
Spatially barcoded probes were transferred to the Visium HD capture areas using the Visium CytAssist instrument. Libraries were then constructed using the 10x Genomics Visium HD library construction kit according to the manufacturer’s protocol (with minor modifications) and sequenced on an Illumina NovaSeq system to a depth sufficient for high-resolution spatial gene expression analysis.


title: cortical brain tissue, IfnarM1

value: Cortex (brain)

value: Cortical cells

value: 6 week old

value: Male

value: naive


title: Mmac_vas lat_CALRES_18

description: Library name: Sample_M_20

value: vastus lateralis skeletal muscle


title: MPBC1

description: Library name: MPBC1


title: F14_tsc_HU_g1_3_nodox_RNA

description: Library name: F14_tsc_HU_g1_3_nodox_RNA

value: HNRNPU sgRNAs 1+3 knockdown


title: Stage 5 HNF1A-MODY CRISPER line 3

city: Bergen

first: Ulrik

last: Larsen

address: Haukelandsbakken 15

department: Clinical Science

country: Norway

institute: University of Bergen

description: Library name: R12_1

data_processing:
CLC Genomic Workbench version 24.0
Assembly: hg38 (Refseq)
Supplementary files format and content: Geneexpression Track for each sample als xlsx file

source_name: Differentiating cells

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini
Performed by QIAGEN

value: Differentiating cells

value: induced pluripotent stem cells

value: Differentiation towards pancreatic endocrine progenitors


title: Mmac_vas lat_CALRES_17

description: Library name: Sample_M_2

value: CALRES


title: KOLF_KO_rna_rep3

description:
Library name: KOLF_KO_rna_rep3
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv
METTL5_KO_WT_RNAseq_DESeq2_results.csv

data_processing:
Read processing: Raw single-end Ribo-seq reads were adapter-trimmed using cutadapt v4.9 with options “--trimmed-only -m 15 -e 0.2 -a TAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.” Trimmed reads were then aligned in two steps using bowtie2 v2.5.4. First, reads mapping to a custom rRNA/tRNA index were discarded. The remaining reads were then aligned end-to-end to a GRCh38-based mRNA transcriptome (Ensembl release v96), in which each gene is represented by the isoform containing the longest annotated coding sequences (CDS). The associated total RNA-Seq sample reads were aligned to the same longest CDS reference transcriptome using bowtie2.
TE analysis with Ribolog: Ribo-seq and matched RNA-seq reads (BAM files) were imported into Ribolog v0.0.0.9 for differential translation efficiency (TE) analysis. Ribo-seq reads were filtered to retain only in-frame ribosome-protected fragments (RPFs) 40-44 nucleotides long. Codon-level counts derived from these RPFs were corrected for ribosome stalling using the CELP (Consistent Excess of Loess Preds) method implemented in Ribolog. CELP-corrected Ribo-seq and total RNA-seq reads were median-normalized, and lowly expressed transcripts were excluded: specifically, transcripts with fewer than 5 RNA-seq reads in each RNA-seq sample or fewer than 2 RPFs on average across all Ribo-seq samples were removed. TE for each transcript was calculated as the ratio of Ribo-seq to total RNA-seq transcript counts. Differential TE between wild-type and METTL5-knockout samples was modeled using logistic regression and Benjamini–Hochberg correction for multiple testing, as implemented in Ribolog’s logit_seq function.
TE analysis with DESeq2: Transcript-level Ribo-seq and RNA-seq counts generated from the Ribolog pipeline were reanalyzed using DESeq2 to assess differential translation efficiency (TE). Ribo-seq counts were obtained from reads filtered for reads with a P-site mapping to the coding sequence (CDS) and a footprint length of 40–44 nucleotides long. RNA-seq counts were extracted using the bam2count function in Ribolog. A two-factor design was used to model differential TE in DESeq2, incorporating sample condition (wild-type or METTL5-knockout) and sequencing assay type (RNA-seq or Ribo-seq), with the following design formula: ∼ assay_type + condition + assay_type:condition.
RNA-seq differential analysis: RNA-seq transcript counts were extracted using the bam2count function in Ribolog. Differential expression analysis was performed using DESeq2 (v.1.42.1) to compare the wild-type and METTL5-knockout samples.
Assembly: hg38
Supplementary files format and content: csv file of the raw RPF and RNA-seq transcript counts for each sample
Supplementary files format and content: csv file of differential translational efficiency (TE) results from Ribolog
Supplementary files format and content: csv file of the RNA-seq differential analysis results from DESeq2

value: Neural progentor cells

value: METTL5 KO


title: Stage 5 HNF1A-MODY CRISPER line 2

description: Library name: R11_1


title: Mmac_vas lat_CALRES_16

description: Library name: Sample_M_19


title: KOLF_KO_rna_rep2

description:
Library name: KOLF_KO_rna_rep2
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv
METTL5_KO_WT_RNAseq_DESeq2_results.csv


title: Stage 5 Non-Carrier 3

description: Library name: R15_1

value: non carrier


title: Stage 5 HNF1A-MODY CRISPER line 1

description: Library name: R10_1


title: Mmac_vas lat_CTR_15

description: Library name: Sample_M_18

value: CTR


title: Stage 5 Non-Carrier 2

description: Library name: R14_1


title: KOLF_KO_rna_rep1

description:
Library name: KOLF_KO_rna_rep1
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv
METTL5_KO_WT_RNAseq_DESeq2_results.csv


title: cortical brain tissue, IfnarF1

value: Female


title: Stage 5 Non-Carrier 1

description: Library name: R13_1


title: Mmac_vas lat_CTR_14

description: Library name: Sample_M_17


title: Stage 3 day 1 HNF1A-MODY Patient 3

description: Library name: R9_1

value: Patient-derived


title: KOLF_rna_rep3

description:
Library name: KOLF_rna_rep3
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv
METTL5_KO_WT_RNAseq_DESeq2_results.csv

value: cortical forebrain neural progenitor cells

value: WT


title: Stage 3 day 1 HNF1A-MODY Patient 2

description: Library name: R8_1


title: Mmac_vas lat_CTR_13

description: Library name: Sample_M_16


title: Stage 3 day 1 HNF1A-MODY Patient 1

description: Library name: R7_1


title: Stage 3 day 1 Non-Carrier 3

description: Library name: R3_1


title: Mmac_vas lat_CTR_12

description: Library name: Sample_M_15


title: KOLF_rna_rep1

description:
Library name: KOLF_rna_rep1
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv
METTL5_KO_WT_RNAseq_DESeq2_results.csv


title: Stage 3 day 1 Non-Carrier 2

description: Library name: R2_1


title: Stage 3 day 1 Non-Carrier 1

description: Library name: R1_1


title: Mmac_vas lat_CTR_11

description: Library name: Sample_M_14


title: skin cells, Pacritinib treated

city: Ann Arbor

first: Chenguang

last: Wang

state: Michigan

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

institute: University of Michigan

description:
Library name: Patient-Pacritinib
10× Genomics

data_processing:
Gene expression was imported to generate anndata object using scanpy (v1.9.6).Data from each patient and normal controls was integrated using the concatenate function in anndata. Scrublet (v0.2.3) was applied to obtain per-cell scrublet scores and used for doublet removal (7). Cells with greater than 20% mitochondrial gene expression or expression of fewer than 200 detected genes were excluded. Genes that were expressed in fewer than 3 cells were also removed. Data normalization and highly variable genes were processed by scanpy with following parameters: flavor="seurat_v3", n_top_genes=4000, layer="raw_counts", batch_key="sample_id",span=1, subset=True. Batch correction and integration were performed using scVI (1.2.2) (6). If one patient has multiple batches of sequencing data, each batch were considered as a sample and were marked correspondingly in ‘sample_id’ metadata. The following parameters were used for scVI integration: layer="raw_counts", batch_key='sample_id', categorical_covariate_keys=['platform'], n_layers=1, n_latent=6, gene_likelihood="zinb". Neighborhood was calculated and embedded using the umap function. The neighborhood graph was clustered using leiden function in Scanpy. Annotation was performed based on well-established and lineage-specific cell markers or Celltypist (v1.6.3).
Assembly: GRCh38(2020-A)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
Biopsies were bisected and incubated in 0.4% dispase and vehicle control/10 μM pacritinib in HBSS at 4°C overnight. Then, epidermis were enzymatically digested in 0.25% Trypsin-EDTA (Gibco, Thermo Fisher Scientific) with 10 U/mL DNase I (Thermo Fisher Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals). Dermis was incubated in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (MilliporeSigma), with 10U/mL DNase I in plain medium for 1.5 hours at 37°C with rotation. Shred both epidermis and dermis through 40 μm cell strainers twice and centrifuged at 800 g for 5 minutes at 4°C. Dermal and epidermal cells were combined in a 2:1 ratio before submitting for scRNA-seq.
Libraries were constructed by the University of Michigan Advanced Genomics Core using the single-cell gene expression flex kit from 10x Genomics and sequenced on the Illumina NovaSeq X plus sequencer to generate 150 bp paired-end reads.

value: Skin

value: Pacritinib


title: skin cells, DMSO treated

description:
Library name: Patient-DMSO
10× Genomics

value: DMSO


title: MB135_iDUX4ca_3xFLAG_KLF18_NoVNTR_3 PlusDox

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description: Library name: KLF18-NoVNTR_PlusDOX_3

data_processing:
Reads trimmed using trim galore 0.6.7
Reads aligned using Rsubread 2.18.0 to GRCh38 p14
Gene features were called using featureCounts 2.18.0 against the Gencode R45 annotation release
Differential expression was analyzed using DESeq2 1.44.0
Assembly: GRCh38 p14
Supplementary files format and content: xlsx, DESeq2 differential expression output

molecule: polyA RNA

growth_protocol: Grown in F10 media supplemented with 10% FBS, 1% P/S,

extract_protocol:
total RNA was extracted using Takara Nucleospin RNA extraction kit following mfr protocol
150bp paired end libraries were prepared using Illumina's TruSeq stranded mRNA kit following mfr protocol.

treatment_protocol: Cells were treated ± 0.25µg/mL doxycycline (DOX) for 18 hours.

value: Human Myoblasts

value: 3xFLAG KLF18 NoVNTR

value: 0.25ug/mL doxycyclien for 18hr


title: hVEC ALI alone repC

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
Library name: 1C
Column name in hVEC_counts.tsv: hVEC_C

data_processing:
BCL convert v4.2.4 for demultiplexing, quality control, and adapter trimming
STAR v2.7.10b for read alignment
featureCounts v2.0.6 to assign counts
Assembly: GRCh38 (NCBI; human)
Assembly: Assembly 22 (CGD; C. albicans)
Assembly: NZ_HG939456.1 with sRNAs (S. agalactiae)
Supplementary files format and content: hVEC_counts.tsv is a tab-delimited text file of counts for human genes for each sample containing hVECs
Supplementary files format and content: Ca_counts.tsv is a tab-delimited text file of counts for C. albicans genes for each sample containing C. albicans
Supplementary files format and content: GBS_counts.tsv is a tab-delimited text file of counts for S. agalactiae genes for each sample containing S. agalactiae

growth_protocol: S. agalactiae (strain COH1) was grown statically in Todd Hewitt Broth at 37°C. C. albicans (strain 529L) was grown shaking in Yeast Peptone Dextrose Broth at 30°C. Human vaginal epithelial cells (hVEC; cell line VK2-E6/E7) were grown in Keratinocyte Serum-Free Medium supplemented with 0.05 mg/mL bovine pituitary extract and 0.5 ng/mL epidermal growth factor (KSFM). hVECs were grown in 6-well transwell inserts at an air-liquid interface for 16 days.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini Kit, then treated with Invitrogen Dnase.
Libraries were prepared with the Illumina Stranded Total RNA Prep ligation with Ribo-Zero Plus rRNA depletion kit.

treatment_protocol: 2x10^7 C. albicans yeast cells and/or 2x10^8 S. agalactiae CFU at mid-log were washed and resuspended in KSFM and added to hVEC air-liquid interface cultures in the apical compartment, then incubated at 37°C with 5% CO2 for six hours. Microbial mono- and co-cultures were grown in 6-well plates in KSFM at 37°C with 5% CO2 for six hours.

value: Vaginal epithelial cells

value: Epithelial cells grown at air-liquid interface


title: MB135_iDUX4ca_3xFLAG_KLF18_NoVNTR_2 PlusDox

description: Library name: KLF18-NoVNTR_PlusDOX_2


title: Mmac_vas lat_CALRES_15

description: Library name: Sample_M_13

value: vastus lateralis skeletal muscle

value: CALRES


title: hVEC ALI alone repA

description:
Library name: 1A
Column name in hVEC_counts.tsv: hVEC_A


title: MB135_iDUX4ca_3xFLAG_KLF18_NoVNTR_1 PlusDox

description: Library name: KLF18-NoVNTR_PlusDOX_1


title: MB135 GFP Rep3

description:
Library name: MB135 GFP Rep3
Column name in processed file: 12_MB135_GFP_readcount

data_processing:
Raw reads were quality checked using FastQC 0.12.1
Trimmed reads were aligned to hg38 genome using Rsubread
Feature counts were called against Gencode R45 annotation using FeatureCounts()
Differential expression was called using DESeq2
Assembly: hg38
Supplementary files format and content: DESeq2 differential expression output plus normalized counts per sample.

growth_protocol: F-10 media, 10% Fetal Bofine Serum, 10ng/mL rhFGF, 1uM dexamethasone

extract_protocol:
RNA was extracted using Takara Nucleospin RNA per mfr protocol
Libraries prepared using Illumina TruSeq Stranded mRNA kit following mfr protocol

treatment_protocol: Cells were transiently transteced using a Neon NXT with either a KLF17, KLF18, or GFP expression vector 48 hours prior to harvest

value: Neon NXT transient transfection of GFP expression vector


title: MB135_iDUX4ca_3xFLAG_KLF18_NoVNTR_3 NoDox

description: Library name: KLF18-NoVNTR_NoDOX_3

value: No Dox


title: MB135 GFP Rep2

description:
Library name: MB135 GFP Rep2
Column name in processed file: 11_MB135_GFP_readcount


title: Mmac_vas lat_CALRES_13

description: Library name: Sample_M_11


title: MB135_iDUX4ca_3xFLAG_KLF18_NoVNTR_2 NoDox

description: Library name: KLF18-NoVNTR_NoDOX_2


title: MB135 KLF18 Rep2

description:
Library name: MB135 KLF18 Rep2
Column name in processed file: 05_MB135_KLF18gencode_readcount

value: Neon NXT transient transfection of KLF18 expression vector


title: MB135 KLF18 Rep1

description:
Library name: MB135 KLF18 Rep1
Column name in processed file: 04_MB135_KLF18gencode_readcount


title: Mmac_vas lat_CALRES_11

description: Library name: Sample_M_1


title: MB135_iDUX4ca_3xFLAG_KLF18_NoVNTR_1 NoDox

description: Library name: KLF18-NoVNTR_NoDOX_1


title: MB135 KLF17 Rep3

description:
Library name: MB135 KLF17 Rep3
Column name in processed file: 03_MB135_KLF17_readcount

value: Neon NXT transient transfection of KLF17 expression vector


title: Mmac_vas lat_CALRES_10

description: Library name: Sample_9_602


title: Mmac_vas lat_CALRES_9

description: Library name: Sample_8_9GV


title: MB135_iDUX4ca_3xFLAG_KLF18_Cl2_3 PlusDox

description: Library name: KLF18-Long2_PlusDOX_3

source_name: MB135 iDUX4ca_3xFLAG_KLF18_Cl2

value: MB135 iDUX4ca_3xFLAG_KLF18_Cl2

value: 3xFLAG KLF18 cl2


title: MB135 KLF17 Rep2

description:
Library name: MB135 KLF17 Rep2
Column name in processed file: 02_MB135_KLF17_readcount


title: MB135 KLF17 Rep1

description:
Library name: MB135 KLF17 Rep1
Column name in processed file: 01_MB135_KLF17_readcount


title: MB135_iDUX4ca_3xFLAG_KLF18_Cl2_2 PlusDox

description: Library name: KLF18-Long2_PlusDOX_2


description: Library name: MB135-iDUX4ca 3xFLAG-KLF18 FLAG ChIP Rep3

data_processing:
Raw data trimmed and quality checked with Trim Galore 0.6.7
Trimmed reads were processed using ENCODE Transcription Factor and Histone ChIP-seq pipeline
MEME-ChIP 5.57 was used to identfy motifs enriched in identified peaks.
Assembly: hg38
Supplementary files format and content: IDR output from ENCODE pipeline

extract_protocol:
12m cells were crosslinked for 10m @ RT in 1% formaldehyde before quenching with glycine @ 125mM final concentration, incubated for 5m @ RT before two washes with PBS and finally resuspended in ChIP buffer. Samples were then treated with 600 units of Mnase following NEB protocol to yield a chromatin size range of 200-700bp. MNase digestion was terminated by addition of EDTA, chromatin centrifuged then resuspended in ChIP buffer and sonicated for 20m using a Bioruptor sonicator
Takara's ThruPLEX DNA-seq kit was used for library prep following the kit protocol with a final size selection using SPRI beads at a 1:1 ratio.

treatment_protocol: Cells were treated with 1ug/mL for 18hr prior to harvest

value: Human myoblast

tag: chip antibody

value: 3xFLAG, (Cell Signalling Technologies, #14793S)


title: Mmac_vas lat_CTR_10

description: Library name: Sample_7_1505

value: CTR


title: tsc_nxf1_rip

description: Library name: tsc_nxf1_rip

data_processing:
RIP-Seq reads were aligned using STAR v2.5.4b with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools.
Assembly: mm10
Supplementary files format and content: Wiggle tracks were normalized to q30 aligned reads to mm10

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three to four days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
Both input and immunoprecipitated RNA were purified with the Zymo Clean and Concentrator.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP/input RNA + 1uL ERCC RNA spike-in

treatment_protocol: To induce RBP knockdown, TSCs were treated with 1000ng/mL of doxycycline for four days. For all RIP experiments, trypsinized cells were crosslinked with 0.3% formaldehyde (Thermo Fisher, cat #: 28908) in PBS for 30 minutes at 4C with rotation, then quenched with 200mM glycine for 5 minutes at room temperature with rotation. Crosslinked cells were then washed thrice with ice-cold PBS, followed by resuspension in ice-cold PBS and divided into 10-million cell aliquots.

tag: antibody

value: NFX1(Bethyl Laboratories, A303-915A)

value: mouse TSCs 6-2

value: WT


title: hVEC ALI + Ca repA

description:
Library name: 2A
Column name in hVEC_counts.tsv: hVEC_Ca_A; Column name in Ca_counts.tsv: Ca_hVEC_A

organism:
Candida albicans
Homo sapiens

value: Fungus

value: Epithelial cells grown at air-liquid interface, inoculated with C. albicans


title: MB135_iDUX4ca_3xFLAG_KLF18_Cl2_1 PlusDox

description: Library name: KLF18-Long2_PlusDOX_1

value: Human Myoblasts

value: 0.25ug/mL doxycyclien for 18hr


description: Library name: MB135-iDUX4ca 3xFLAG-KLF18 FLAG ChIP Rep2


title: Fus infected, 7 dpi; rep 3

city: Scarborough

first: Mehran

last: Dastmalchi

address: 1265 Military Trail

department: Cell & Systems Biology

institute: University of Toronto

description: Library name: FusL-3

data_processing:
Raw reads were quality checked using FASTQC and trimmed using Trimmomatic (Adaptor read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; adaptor read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
Reads were aligned to a reference genome (RefSeq: GCF_020283565.1) and gene counts were extracted using STAR 2.7.11 (parameters set to defaults unless otherwise noted -> quantMode: GeneCounts, sjdbGTFfile: GTF_FILE, outSAMtype: BAM SortedByCoordinate)
Assembly: ARS_RC_1.1 (RefSeq: GCF_020283565.1)
Supplementary files format and content: Raw gene counts for each sample are in tab-delimited text files

organism: Trifolium pratense

source_name: Roots

growth_protocol: Bleach-sterilized red clover seeds were germinated for 10 days in the dark on damp filter paper, then transplanted into sterile, semi-solid 1/2x Murashige-Skoog media in magenta boxes. Seedlings were grown in culture chambers with 16:8 h light:dark cycle at 22ºC and 50% humidity for 3 weeks.

extract_protocol:
Flash frozen roots were homogenized under liq N2 using mortar and pestle. Total RNA was extracted using the Plant RNeasy plant mini kit (QIAgen) following the manufacturer's protocol.
Library preparation was carried out by Genome Québec, using a stranded poly(A)-enrichment workflow and NEBNext dual-indexed (i5/i7) multiplex adaptors

treatment_protocol: Agar plugs of hyphal edges of fungi grown on potato dextrose agar (PDA) were placed faced down at the root of each stem. Plants were grown under the same conditions, and harvested at 3 or 7 dpi. Sterile PDA plugs were used for mock inoculations.

value: Roots

value: fungal inoculation (F. oxysporum)

tag: time

value: 7 dpi


description: Library name: MB135-iDUX4ca 3xFLAG-KLF18 FLAG ChIP Rep1


title: MB135_iDUX4ca_3xFLAG_KLF18_Cl2_3 NoDox

description: Library name: KLF18-Long2_NoDOX_3

value: No Dox


title: Fus infected, 7 dpi; rep 2

description: Library name: FusL-2


title: MB135_iDUX4ca_3xFLAG_KLF18_Cl2_2 NoDox

description: Library name: KLF18-Long2_NoDOX_2


title: MB135-iDUX4ca WT FLAG ChIP Rep3

description: Library name: MB135-iDUX4ca WT FLAG ChIP Rep3


title: MB135_iDUX4ca_3xFLAG_KLF18_Cl2_1 NoDox

description: Library name: KLF18-Long2_NoDOX_1


title: Fus infected, 7 dpi; rep 1

description: Library name: FusL-1


title: MB135-iDUX4ca WT FLAG ChIP Rep2

description: Library name: MB135-iDUX4ca WT FLAG ChIP Rep2


title: Fus infected, 3 dpi; rep 3

description: Library name: FusS-3

value: 3 dpi


title: Mmac_vas lat_CTR_8

description: Library name: Sample_3_9GK

data_processing:
FastQC was used to check quality quality of reads.
Next, reads were trimmed using bbduk.
Cleaned FASTQ files were aligned to Mmul_10 using STAR.
Transcript data was generated using RSEM.
Finally, count data was generated by using featureCounts.
Assembly: Mmul_10
Supplementary files format and content: Count data

extract_protocol:
RNeasy Fibrous Tissue Mini Kit  protocol (Qiagen, Cat. No. 74704) in QIAcube Connect (Qiagen, Cat. No. 9002864)
Library was prepared using Illumina Stranded Total RNA Prep. Ligation was performed with Rib-Zero Plus kit.

value: vastus lateralis skeletal muscle


title: MB135_iDUX4ca_3xFLAG_KLF18_Long_Cl2_3

description: Library name: KLF18_Long2_3

source_name: MB135-iDUX4ca 3xFLAG-KLF18_Long_2

value: MB135-iDUX4ca 3xFLAG-KLF18_Long_2

value: Human Myoblast

value: 3xFLAG-KLF18 Long 2

value: 0.25ug/mL Dox for 18hr


title: MB135-iDUX4ca WT FLAG ChIP Rep1

description: Library name: MB135-iDUX4ca WT FLAG ChIP Rep1

value: Human myoblast

value: 3xFLAG, (Cell Signalling Technologies, #14793S)


title: Mmac_vas lat_CALRES_6

description: Library name: Sample_20_77Z

value: CALRES


title: Fus infected, 3 dpi; rep 2

description: Library name: FusS-2

value: WT


title: Stage 3 Day HNF1A-MODY + Purmorphamine 3

first: Lucas

last: Unger

address: Haukelansbakken 15

institute: University of bergen

description: Library name: Sample 12

treatment_protocol: Some of the conditions were treated with 10 µM purmorphamine instead of SANT1 on the first day of stage 3, for a duration of 24 hours.

value: Differentiating cells

value: induced pluripotent stem cells

value: Differentiation towards pancreatic endocrine progenitors treated with Purmorphamine


title: Fus infected, 3 dpi; rep 1

description: Library name: FusS-1

value: Roots


title: Stage 3 Day HNF1A-MODY + Purmorphamine 2

description: Library name: Sample 11


title: Phoma infected, 7 dpi; rep 3

description: Library name: PhomaL-3

value: fungal inoculation (P. medicaginis)


title: MB135_iDUX4ca_3xFLAG_KLF18_Long_Cl1_3

description: Library name: KLF18_Long1_3

source_name: MB135-iDUX4ca 3xFLAG-KLF18_Long_1

value: MB135-iDUX4ca 3xFLAG-KLF18_Long_1

value: 3xFLAG-KLF18 Long 1


title: Mmac_vas lat_CTR_7

description: Library name: Sample_18_609

value: CTR


title: Phoma infected, 7 dpi; rep 2

description: Library name: PhomaL-2

value: 7 dpi


title: MB135_iDUX4ca_3xFLAG_KLF18_Long_Cl1_2

description: Library name: KLF18_Long1_2


title: Stage 3 Day HNF1A-MODY 3

description: Library name: Sample 9

value: Differentiation towards pancreatic endocrine progenitors


title: Mmac_vas lat_CALRES_3

description: Library name: Sample_17_CH170

value: vastus lateralis skeletal muscle


title: MB135_iDUX4ca_3xFLAG_KLF18_Long_Cl1_1

description: Library name: KLF18_Long1_1

value: Human Myoblast


title: Stage 3 Day HNF1A-MODY 2

description: Library name: Sample 8


title: Mmac_vas lat_CTR_6

description: Library name: Sample_16_371


title: Phoma infected, 3 dpi; rep 3

description: Library name: PhomaS-3

value: 3 dpi


city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC Laboratory of Medical Sciences (LMS)

description:
Library name: PECHiC_naive-to-primed_transition_Day5_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day5

data_processing:
Read processing, alignment, and filtering were performed using the Hi-C User Pipeline (HiCUP, (Wingett et al. 2015), modified to consider both across- and within-read ligation junctions (https://github.com/StevenWingett/HiCUP/tree/combinations, v0.7.4,  (Freire-Pritchett et al. 2021)). CHiCAGO input files were generated using chicagoTools v1.30.0 (Cairns et al. 2016) for bins of DpnII fragments spanning ~5 kb, leaving the captured (‘baited’) PE-harbouring fragments unbinned to increase resolution. CHiCAGO (v1.30.0) was run as previously described (Cairns et al. 2016; Freire-Pritchett et al. 2021) on combined replicates from each time point/condition. The ‘other ends’ of detected contacts were annotated with transcription start sites downloaded from GENCODE (v.36 Frankish et al.). CHiCAGO results were summarised across samples using makePeakMatrix.R from ChicagoTools with default parameters.
Assembly: GRCh38
Supplementary files format and content: A table of CHiCAGO interaction scores for pooled duplicates in each time point/condition (naive, day1, day3, day5, day7, day10, day14, primed, DE, NE).  Only interactions that exceed the CHiCAGO score threshold of 5 in at least one condition are reported in the table.
Library strategy: Capture-C

source_name: HNES1 cells

growth_protocol: All cells were grown at 37 °C, 5 % CO2. HNES1 hPSCs were maintained in the naive state as described in (Rostovskaya 2022). In brief, cells were cultured on irradiated mouse embryonic fibroblast (MEF) feeder cells in N2B27 supplemented with 1 µM PD0325901, 10 ng/ml human LIF (made in-house), 2 µM Gö6983 (Tocris Bio-Techne), and 2 µM XAV939 (Tocris Bio-Techne). N2B27 basal medium was prepared as follows: Neurobasal and DMEM-F12 in the ratio 1:1; 0.5% N2 supplement; 1 % B27 supplement (with vitamin A); 2 mM L-glutamine; 100 mM 2-mercaptoethanol (all from ThermoFisher Scientific). Cells were passaged through single-cell dissociation using TrypLE Express (ThermoFisher Scientific). 0.5 µL/mL Geltrex (ThermoFisher Scientific) was added to the medium during passaging. 10 µM ROCK inhibitor (Y-27632, Millipore) was added for 24 hours after replating. Naive-to-primed transition was performed as described in (Rostovskaya et al. 2019; Rostovskaya 2022). For this, naive hPSCs were passaged once in feeder-free conditions, adding 1 µL/mL Geltrex to the medium during passaging, otherwise as described above. Upon reaching confluency, cells were plated at a density of 1.6 x 104/cm2 in the medium for naive hPSC maintenance supplemented with 10 µM ROCK inhibitor, on plates pre-coated with 1% Geltrex. After 48 h, the medium was exchanged to N2B27 supplemented with 2 µM XAV939. The medium was refreshed daily. At confluency, cells were passaged using TrypLE Express at a 1:2 ratio in the transition medium supplemented with 10 µM ROCK inhibitor for 24 h, on Geltrex pre-coated plates. The H9 cells were grown in mTeSR-E8 basal media (StemCell Technologies), in feeder-free conditions using Geltrex (1:100 dilution in DMEM-F12, ThermoFisher Scientific) as a coating matrix.

extract_protocol:
Cells were dissociated into single-cell suspensions using TrypLE. 1 million cells per condition were fixed in 1X D-PBS (Sigma-Aldrich) containing 2 % paraformaldehyde (Electron Microscopy Sciences) for 10 min at room temperature.
Crosslinking was quenched with incubation in 0.125 M glycine for 5 min at room temperature followed by 5 min on ice. Cells were pelleted by centrifugation, washed with PBS, and lysed for 30 min on ice in Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, protease inhibitors). All centrifuging steps during the lysis, prior to DpnII digestion, were carried out in a swinging-bucket centrifuge at 4°C, 300 x g for 5 min.The released nuclei were permeabilised and digested overnight with DpnII (NEB). Restriction overhangs were filled in with biotin-dATP (Jena Bioscience), and proximity ligation was performed for 4 h at 16 °C using T4 DNA ligase (Invitrogen). Crosslinks were reversed overnight at 65 °C with proteinase K, and DNA was purified with AMPure XP beads (Beckman Coulter). DNA was fragmented by tagmentation to generate fragments ≤1,000 bp fragments, and biotinylated junctions were enriched using MyOne C1 streptavidin beads (Life Technologies). Libraries were amplified directly on beads with 5 PCR cycles, purified with AMPure XP beads, and subjected to poised enhancer capture using a custom-designed Agilent SureSelect system, following the manufacturer’s protocol. Libraries were sequenced as 150 bp paired-end reads.

treatment_protocol: The primed state was reached by day 14 of the transition. Cells were harvested for PECHi-C experiments in duplicate on day 0 (in the naive conditions), 1, 3, 5, 7, 10, and 14 of the transition. Differentiation was performed with HNES1 hPSC after 14 days of the naive-to-primed transition. Neuroectoderm was induced according to (Chambers et al. 2009). N2B27 basal medium was prepared as follows: Neurobasal and DMEM-F12 in the ratio 1:1; 0.5 % N2 supplement; 1 % B27 supplement (with vitamin A); 2 mM L-glutamine; 100 mM 2-mercaptoethanol (all from ThermoFisher Scientific). hPSCs were dissociated to single cells and plated at 2.5x105/cm2 to Geltrex-coated plates (ThermoFisher Scientific) in N2B27 supplemented with 1 mM A8301 (Tocris Bio-Techne) and 500 nM LDN193189 (Axon Medchem). 10 mM ROCK inhibitor (Y-27632, Millipore) was added for 24 h after plating. Cells were cultured in the differentiation conditions for 10 days. To obtain a pure neuroectoderm cell population, the cells were stained for the expression of CD56 (BD, Cat. 345812) and absence of EpCAM (Biolegend, Cat. 324212), and sorted using flow cytometry. Definitive endoderm was induced according to (Loh et al. 2014). CDM2 basal medium was prepared as follows: IMDM and F12 in the ratio 1:1, 2 mM L-Glutamine, 1 % chemically defined lipid concentrate (all from ThermoFisher Scientific), 0.1 % BSA or polyvinyl alcohol, 15 mg/mL transferrin, 450 mM monothioglycerol, 0.7 mg/mL insulin (all from Sigma). hPSCs were plated at 4x104/cm2 to Geltrex-coated plates in their culture medium with 10 mM ROCK inhibitor. After 24 h, the medium was exchanged to CDM2 basal medium supplemented with 100 ng/mL Activin A, 3 µM CHIR99021, 10 ng/mL FGF2 (all produced in house), 100 nM PI-103 (Tocris, Bio-Techne), 3 ng/mL BMP4 (Peprotech), 10 µg/mL heparin (Sigma-Aldrich) for one day; then for the next two days the following supplements were applied: 100 ng/mL Activin A, 100 nM PI-103, 20 ng/mL FGF2, 250 nM LDN193189, 10 µg/mL heparin. To obtain a pure definitive endoderm cell population, the cells were stained with antibodies against CXCR4 (BD) and CD117 (RnD Bio-Techne) and sorted using flow cytometry.

value: HNES1 cells

tag: time point

value: day 5 of the transition

value: naive-to-primed transition


title: MB135_iDUX4ca_3xFLAG_KLF18_Short_Cl2_3

description: Library name: KLF18_Short2_3

source_name: MB135-iDUX4ca 3xFLAG-KLF18_Short_2

value: MB135-iDUX4ca 3xFLAG-KLF18_Short_2

value: 3xFLAG-KLF18 Short 2

value: 0.25ug/mL Dox for 18hr


title: Stage 3 Day HNF1A-MODY 1

description: Library name: Sample 7

value: Differentiating cells

value: induced pluripotent stem cells


title: Mmac_vas lat_CALRES_2

description: Library name: Sample_15_113Z

source_name: vastus lateralis skeletal muscle

value: CALRES


title: MB135_iDUX4ca_3xFLAG_KLF18_Short_Cl2_2

description: Library name: KLF18_Short2_2


description:
Library name: PECHiC_naive-to-primed_transition_Day1_rep2
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: day1

value: day 1 of the transition


title: Stage 3 Day Non-carrier + Purmorphamine 3

description: Library name: Sample 6

value: non carrier

value: Differentiation towards pancreatic endocrine progenitors treated with Purmorphamine


title: Mmac_vas lat_CALRES_1

description: Library name: Sample_14_CH178


title: Phoma infected, 3 dpi; rep 1

description: Library name: PhomaS-1

value: Roots

value: WT

value: fungal inoculation (P. medicaginis)


title: Phoma infected, 7 dpi; rep 1

description: Library name: PhomaL-1

value: 7 dpi


title: MB135_iDUX4ca_3xFLAG_KLF18_Short_Cl2_1

description: Library name: KLF18_Short2_1

value: Human Myoblast


title: Stage 3 Day Non-carrier + Purmorphamine 2

description: Library name: Sample 5


title: Mmac_vas lat_CTR_5

description: Library name: Sample_13_52Z

value: vastus lateralis skeletal muscle

value: CTR


title: Mock control, 7 dpi; rep 3

description: Library name: Mock-3

value: mock inoculation


title: MB135_iDUX4ca_3xFLAG_KLF18_Short_Cl1_3

description: Library name: KLF18_Short1_3

source_name: MB135-iDUX4ca 3xFLAG-KLF18_Short_1

value: MB135-iDUX4ca 3xFLAG-KLF18_Short_1

value: 3xFLAG-KLF18 Short 1


title: Stage 3 Day Non-carrier + Purmorphamine 1

description: Library name: Sample 4


title: Mmac_vas lat_CTR_4

description: Library name: Sample_12_366


title: KOLF_rna_rep2

description:
Library name: KOLF_rna_rep2
METTL5_KO_WT_rna_rpf_raw_transcript_counts.csv
METTL5_KO_WT_TE_Ribolog_results.csv
METTL5_KO_WT_RNAseq_DESeq2_results.csv

value: cortical forebrain neural progenitor cells

value: Neural progentor cells


title: Mock control, 7 dpi; rep 2

description: Library name: Mock-2


title: hVEC ALI alone repB

description:
Library name: 1B
Column name in hVEC_counts.tsv: hVEC_B

value: Vaginal epithelial cells

value: Epithelial cells grown at air-liquid interface


title: MB135_iDUX4ca_3xFLAG_KLF18_Short_Cl1_2

description: Library name: KLF18_Short1_2

value: 0.25ug/mL Dox for 18hr


title: Stage 3 Day Non-carrier 3

description: Library name: Sample 3

value: Differentiating cells

value: induced pluripotent stem cells

value: non carrier

value: Differentiation towards pancreatic endocrine progenitors


title: MB135 GFP Rep1

description:
Library name: MB135 GFP Rep1
Column name in processed file: 10_MB135_GFP_readcount

value: Human Myoblasts

value: Neon NXT transient transfection of GFP expression vector


title: Mmac_vas lat_CALRES_14

description: Library name: Sample_M_12

value: CALRES


title: Mmac_vas lat_CTR_3

description: Library name: Sample_11_83Z

value: vastus lateralis skeletal muscle


title: Mock control, 7 dpi; rep 1

description: Library name: Mock-1

value: Roots

value: WT

value: 7 dpi


title: MB135_iDUX4ca_3xFLAG_KLF18_Short_Cl1_1

description: Library name: KLF18_Short1_1

value: MB135-iDUX4ca 3xFLAG-KLF18_Short_1

value: Human Myoblast

value: 3xFLAG-KLF18 Short 1


title: MB135 KLF18 Rep3

description:
Library name: MB135 KLF18 Rep3
Column name in processed file: 06_MB135_KLF18gencode_readcount

value: Neon NXT transient transfection of KLF18 expression vector


title: Mmac_vas lat_CALRES_12

description: Library name: Sample_M_10


description:
Library name: PECHiC_naive-to-primed_transition_Naive_rep1
Column name in the processed data file Peakmatrix_chicago_score_naive-to-primed_transittion_differentiation_allSamples.txt: naive

value: HNES1 cells

value: day 0 of the transition (naive cells)

value: naive-to-primed transition


title: Stage 3 Day Non-carrier 2

description: Library name: Sample 2

value: Differentiating cells

value: induced pluripotent stem cells


title: Mmac_vas lat_CTR_2

description: Library name: Sample_10_9CA

value: CTR


title: RdV-UB4-3

city: Villenave d'Ornon

first: Amèlia

last: GASTON

address: av. E. Bourlaux

department: UMR1332 - BFP

country: France

institute: INRAE

description: Library name: RdV-UB4-3

data_processing:
Reads were mapped using STAR with default parameters.
Gene level draw counts and Transcripts per Million (TPM) values were obtained with RSEM.
Assembly: F. vesca v4.0.a1 reference genome (Edger et al., 2017) and annotation v4.a2 (Li et al., 2019).
Supplementary files format and content: Resultats_expected_count.csv contains the gene-level counts obtained with RSEM
Supplementary files format and content: Resultats_TPM.csv contains the TPMs (transcript per million) obtained with RSEM

organism: Fragaria vesca

source_name: axillary bud

growth_protocol: Seeds were sown in a mixture of two-thirds loam and one-third grit and grown in long day conditions (16-h/8-h day/night at 22°C/18°C; 250 μmol m−2 sec−1).

extract_protocol:
AXB were immediately frozen in liquid nitrogen and stored at -80°C until analysis. Total RNA was extracted as described in Gaston et al., (2021).
Stranded mRNA-seq libraries were prepared and sequenced by GenoToul (Toulouse, France) as 150 bp paired-end reads on an Illumina NovaSeq instrument.

treatment_protocol: No treatment

value: axillary bud

value: 4-leaf stage plants

tag: ecotype

value: RdV

value: no treatment


title: Phoma infected, 3 dpi; rep 2

description: Library name: PhomaS-2

value: Roots

value: fungal inoculation (P. medicaginis)

value: 3 dpi


title: MB135_iDUX4ca_KLF18_KO1_3

description: Library name: KLF18_KO1_3

source_name: MB135-iDUX4ca KLF18 KO1

tag: cell line

value: MB135-iDUX4ca KLF18 KO1

value: KLF18 KO 1

value: 0.25ug/mL Dox for 18hr


title: Stage 3 Day Non-carrier 1

description: Library name: Sample 1

tag: cell type

value: non carrier

value: Differentiation towards pancreatic endocrine progenitors


title: RdV-UB4-2

description: Library name: RdV-UB4-2

tag: treatment


title: Mmac_vas lat_CTR_1

description: Library name: Sample_1_1895

tag: tissue

value: vastus lateralis skeletal muscle


title: MB135_iDUX4ca_KLF18_KO1_2

description: Library name: KLF18_KO1_2

value: Human Myoblast

tag: genotype


title: 20251210-iNeuron-WT-20uM-cispt-DRB-SAR-seq-rep2

city: Bethesda

first: Chuanyuan

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

description: Library name: Sample14

data_processing:
Reads were mapped to reference genome using bowtie with -n 2 -l 50 -m 1.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization
Assembly: hg19
Supplementary files format and content: bw files include normliazed value

source_name: WTC11 i3Neuron

growth_protocol: To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium. N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase and replated onto new plates freshly coated with poly-L-ornithine in BrainPhys medium to complete differentiation. For SAR-seq experiments, 10-15 million day3 neurons were plated onto 10-cm plates. Cells were treated on day 6 or 7 (3-4 days after plating on PLO-coated plates).

extract_protocol:
Cells were harvested as single cells by incubating with accutase for 15-20 minutes and resuspending by repeated pipetting. Cells were washed with PBS, resuspended in 1 mL PBS, and then fixed by dropwise addition of 4 mL ice cold methanol under mild vortexing. Fixed cells were washed with PBS, permeabilized with 0.2% Triton X-100/PBS for 10 minutes on ice, washed with PBS, and then resuspended in the Click-iT reaction mix for 2 hours shaking at room temperature to label EdU with biotin. Cells were then lysed with Proteinase K overnight at 37C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions.
DNA was sonicated to 150-200 bp fragments using a Covaris S220 sonicator. Biotin-conjugated DNA fragments were isolated using MyOne Streptavidin C1 Beads added to the fragmented sample DNA and incubated at 24°C while in a ThermoMixer while shaking for 30 minutes. Dynabeads (now bound to DNA) were washed three times in 1 mL of 1x W&B, twice in 1 mL EB, and once in 1 mL 1x T4 DNA ligase buffer (NEB). Dynabeads were resuspended in 50 µL end-repair reaction mix (1x T4 DNA ligase buffer, 2.7 U T4 DNA polymerase (NEB), 9 U T4 Polynucleotide Kinase (NEB), 1 U Klenow fragment (NEB), and 0.4 mM dNTPs) and incubated with shaking at 24°C for 30 minutes. Beads were washed once in 1 mL 1x W&B, twice in 1 mL EB, once in 1 mL NEBuffer 2 (NEB), and resuspended in 50 µL A-tailing reaction mix (1x NEB dA-Tailing Buffer with 20 U Klenow fragment exo- (NEB)). Samples were incubated at 37°C with shaking for 30 minutes. Dynabeads were then washed in 1 mL NEBuffer 2 and resuspended in 115 µL ligation reaction mix (1x Quick Ligase Buffer (NEB), 6,000 U Quick Ligase (NEB), 5 nM annealed TruSeq truncated adapter) and incubated with shaking at 25°C for 20 minutes. 50 mM EDTA was added to terminate the reaction and Dynabeads were then washed three times with 1 mL 1x W&B and three times with 1 mL EB. Beads were resuspended in 8 µL EB + 10 µL 2x Kapa HiFI HotStart Ready Mix (Kapa Biosciences). Primers (10 mM) 5′-CAAGCAGAAGACGGCATACGAGATxrefGTGACTGG AGTTCAGACGTGTGCTCTTCCGATC*T-3′ and 5′-AATGATACGGCGA CCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (asterisk indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added to 37 µL PCR reaction mix (20 µL 2x Kapa HiFI HotStart Ready Mix added to 17 µL H2O) for a final volume of 60 µL. DNA was amplified using the following PCR parameters: 98°C (45 seconds); 16 cycles of 98°C (15 seconds), 63°C (30 seconds), 72°C (30 seconds); 72°C (5 minutes). The finished PCR reaction was cleaned using 1.8x volume AMPure Beads XP (Beckman Coulter), following the manufacturer’s instructions. Samples were then separated on a 2% agarose gel, with 150-200 bp DNA being excised and purified using a QIA-quick Gel Extraction Kit (Qiagen). Library concentrations were measured using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) and then sequenced using Illumina NextSeq 550 or NextSeq 2000 instruments.

treatment_protocol: Day 6 or 7 iNs were incubated with 20 μM EdU, 5-50 µM cisplatin, 1 µM THZ1, and/or 100 µM DRB for 24 hr

value: WTC11 i3Neuron

value: iPSC-derived neurons

value: WT

value: EdU (20 µM), 20 µM cisplatin, 100 µM DRB; 24 hours


title: XZ71702-XZ71703 background reads

city: Houston

first: Tobie

middle: D

last: Lee

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: XZ71702-XZ71703_background
XZ71702-XZ71703 background reads

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed with 10x Genomics Cell Ranger v8.0.0.
Assembly: mRatBN7.2
Supplementary files format and content: tab-separated value files for counts matrices, barcodes, and genes

organism: Rattus norvegicus

source_name: Rat mammary tumor

extract_protocol:
Mammary tumors were harvested from female Cas9-expressing rats, minced, and enzymatically digested with 1.5 mM collagenase I and 1 μg/mL DNase I at 37°C for 1 hour with rotation. Digested tissue was passed through a 70 μm strainer, washed with PBS containing 2% FBS, and live cells were sorted for downstream analysis.
Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 3′ Gene Expression platform (v3.1 chemistry) according to the manufacturer’s instructions. Libraries were prepared from sorted live cells, amplified, and sequenced on Illumina X platform at BCM RNA Profiling Core.

value: Rat mammary tumor


title: RdV-UB4-1

description: Library name: RdV-UB4-1

value: axillary bud

tag: age

value: 4-leaf stage plants

value: RdV


title: hVEC ALI + Ca repB

description:
Library name: 2B
Column name in hVEC_counts.tsv: hVEC_Ca_B; Column name in Ca_counts.tsv: Ca_hVEC_B

value: Vaginal epithelial cells

value: Fungus

value: Epithelial cells grown at air-liquid interface, inoculated with C. albicans


title: 20251210-iNeuron-WT-20uM-cispt-DRB-SAR-seq-rep1

description: Library name: Sample13


title: MB135_iDUX4ca_KLF18_KO1_1

description: Library name: KLF18_KO1_1

value: MB135-iDUX4ca KLF18 KO1

value: KLF18 KO 1


title: XZ71233-XZ71234 background reads

description:
Library name: XZ71233-XZ71234_background
XZ71233-XZ71234 background reads


title: FT3-UB4-3

description: Library name: FT3-UB4-3

value: no treatment


title: MB135_iDUX4ca_WT_KLF18_3

description: Library name: WT_iDUX4_3

source_name: MB135-iDUX4ca WT

value: MB135-iDUX4ca WT

value: WT KLF18

value: 0.25ug/mL Dox for 18hr


title: 20251210-iNeuron-WT-20uM-cispt-SAR-seq-rep2

description: Library name: Sample12

value: WTC11 i3Neuron

value: EdU (20 µM), 20 µM cisplatin; 24 hours


title: Mmac_vas lat_CTR_9

first: Supriyo

last: De

institute: NIA-IRP, NIH

description: Library name: Sample_6_G765

value: vastus lateralis skeletal muscle

value: CTR


title: XZ71045-XZ71046 background reads

description:
Library name: XZ71045-XZ71046_background
XZ71045-XZ71046 background reads

value: Rat mammary tumor


title: MB135_iDUX4ca_WT_KLF18_2

description: Library name: WT_iDUX4_2

value: Human Myoblast


title: FT3-UB4-2

description: Library name: FT3-UB4-2

value: axillary bud

value: 4-leaf stage plants


title: XZ69803-XZ69804 background reads

description:
Library name: XZ69803-XZ69804_background
XZ69803-XZ69804 background reads


title: 20251210-iNeuron-WT-20uM-cispt-SAR-seq-rep1

description: Library name: Sample11

value: iPSC-derived neurons

value: WT


title: FT3-UB4-1

description: Library name: FT3-UB4-1


title: Mmac_vas lat_CALRES_8

description: Library name: Sample_5_1577

value: CALRES


title: Mmac_vas lat_CALRES_7

description: Library name: Sample_4_7N8


title: MB135_iDUX4ca_WT_KLF18_1

description: Library name: WT_iDUX4_1


title: 230306-iNeuron-20uM-Cisplatin-CDK7i-SAR-seq

description: Library name: Sample10

value: EdU (20 µM), 20 µM cisplatin, 1 µM THZ1 (CDK7i); 24 hours


title: XZ69320-XZ69321 background reads

description:
Library name: XZ69320-XZ69321_background
XZ69320-XZ69321 background reads


title: H4-US4-3

description: Library name: H4-US4-3


title: MB135iDUX4ca_KLF18KO2_PlusDox_3

description: Library name: MB135iDUX4ca_KLF18KO2_PlusDox_3

treatment_protocol: MB135-iDUX4ca WT,  KLF18 Knockout clone 1, or clone 2 cells were treated with 1ug/mL Dox for 18 hours prior to harvest

value: iDUX4ca, WT KLF18 KO Clone 2

value: 18hr Plus Dox


title: 230306-iNeuron-20uM-Cisplatin-SAR-seq

description: Library name: Sample9


title: 241218-iNeuron-WT-50uM-cisplatin-SAR-seq-rep2

description: Library name: Sample8

value: EdU (20 µM), 50 µM cisplatin; 24 hours


title: H4-US4-2

description: Library name: H4-US4-2

value: no treatment


title: MB135iDUX4ca_KLF18KO2_PlusDox_2

description: Library name: MB135iDUX4ca_KLF18KO2_PlusDox_2


title: XZ64126-XZ64127 background reads

description:
Library name: XZ64126-XZ64127_background
XZ64126-XZ64127 background reads


title: H4-US4-1

description: Library name: H4-US4-1


title: MB135iDUX4ca_KLF18KO2_PlusDox_1

description: Library name: MB135iDUX4ca_KLF18KO2_PlusDox_1


title: 241218-iNeuron-WT-50uM-cisplatin-SAR-seq-rep1

description: Library name: Sample7


title: XZ63068-XZ63069 background reads

description:
Library name: XZ63068-XZ63069_background
XZ63068-XZ63069 background reads


title: E6d_rep3

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description:
Library name: Sample 19
g219

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: TAIR10
Supplementary files format and content: rawCounts
Supplementary files format and content: DEseq2

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Arabidopsis seedlings were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle.

extract_protocol:
Total RNAs were extracted using purelink Plant RNA Reagent (Thermo Fisher Scientifc Inc., Waltham, MA, USA).
The sequencing library was prepared using the Lasy-Seq method (Kamitani et al. 2019). Specifically, 200 ng of total RNA was used per sample.

treatment_protocol: Fourteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 6 days. After ethanol pretreatment, the pots were subjected to freezing temperature treatment at -4.0 °C onvernight by a low-temperature incubator. During the freezing temperature stress treatment, the pots were electrically rotated in the incubator to avoid the local effect. After the treatment, the pots were returned to the growth room and maintained for the indicated time periods.

value: shoot


title: MB135iDUX4ca_KLF18KO1_PlusDox_3

description: Library name: MB135iDUX4ca_KLF18KO1_PlusDox_3

value: iDUX4ca, WT KLF18 KO Clone 1


title: 241218-iNeuron-WT-20uM-cisplatin-SAR-seq-rep2

description: Library name: Sample6

value: WTC11 i3Neuron

value: EdU (20 µM), 20 µM cisplatin; 24 hours


title: XZ71233-XZ71234 Rat mammary tumor AAV-rPT 3

description:
Library name: XZ71233-XZ71234_29607
XZ71233-XZ71234, AAV-rPT, rat Pik3caH1047R and Tp53-Indel edited tumor

value: Pik3caH1047R; Tp53-Indel


title: MB135iDUX4ca_KLF18KO1_PlusDox_2

description: Library name: MB135iDUX4ca_KLF18KO1_PlusDox_2


title: E6d_rep2

description:
Library name: Sample 18
g218


title: 241218-iNeuron-WT-20uM-cisplatin-SAR-seq-rep1

description: Library name: Sample5


title: MB135iDUX4ca_KLF18KO1_PlusDox_1

description: Library name: MB135iDUX4ca_KLF18KO1_PlusDox_1


title: E6d_rep1

description:
Library name: Sample 17
g217


title: XZ71045-XZ71046 Rat mammary tumor AAV-rPT 1

description:
Library name: XZ71045-XZ71046_29548
XZ71045-XZ71046, AAV-rPT, rat Pik3caH1047R and Tp53-Indel edited tumor

value: Rat mammary tumor


title: MB135iDUX4ca_WT_PlusDox_3

description: Library name: MB135iDUX4ca_WT_PlusDox_3

value: Human Myoblast

value: iDUX4ca, WT KLF18


title: 241218-iNeuron-WT-5uM-cisplatin-SAR-seq-rep1

description: Library name: Sample3

value: EdU (20 µM), 5 µM cisplatin; 24 hours


title: XZ69320-XZ69321 Rat mammary tumor AAV-NT Veh 3

description:
Library name: XZ69320-XZ69321_29236
XZ69320-XZ69321, AAV-NT, rat Nf1-Indel and Tp53-Indel edited tumor, vehicle-treated

value: Nf1-Indel; Tp53-Indel

value: Vehicle


title: W6d_rep6

description:
Library name: Sample 14
g214


title: XZ69320-XZ69321 Rat mammary tumor AAV-NT Veh 2

description:
Library name: XZ69320-XZ69321_29253
XZ69320-XZ69321, AAV-NT, rat Nf1-Indel and Tp53-Indel edited tumor, vehicle-treated


title: 241218-iNeuron-WT-NT-SAR-seq-rep2

description: Library name: Sample2

value: iPSC-derived neurons

value: WT

value: EdU (20 µM); 24 hours


title: XZ69320-XZ69321 Rat mammary tumor AAV-NT Veh 1

description:
Library name: XZ69320-XZ69321_29250
XZ69320-XZ69321, AAV-NT, rat Nf1-Indel and Tp53-Indel edited tumor, vehicle-treated


title: W6d_rep5

description:
Library name: Sample 13
g213


title: MB135iDUX4ca_WT_NoDox_3

description: Library name: MB135iDUX4ca_WT_NoDox_3

value: No Dox


title: iNeuron-WT-20uM-cispt-dN-day14-RNA-seq-rep3

description: Library name: Sample6

data_processing:
Raw reads were trimmed by Trim Galore!.
Trimmed reads were mapped to reference genome using STAR.
Bigwig files were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM.
The gene expression raw counts were calculated using featureCounts function in Bioconductor Rsubread package.
Assembly: hg19
Supplementary files format and content: bw files include normliazed value
Supplementary files format and content: csv files include raw count expression matrix

growth_protocol: To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium. N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase and replated onto new plates freshly coated with poly-L-ornithine in BrainPhys medium to complete differentiation. For RNA-seq experiments, 3 million day3 neurons were plated onto each well of 6-well plates. Cells were treated on day 6 (4 days after plating on PLO-coated plates).

extract_protocol:
Total RNA was harvested using TRIzol reagent (Thermo Fisher, 15596018) following the manufacturer’s instructions. DNA was removed using DNAse and rRNA was removed using NEBNext rRNA Depletion kit v.2 (Human/Mouse/Rat) (NEB, E7400).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, E7760), using 1 µg of starting RNA material and following the manufacturer’s instructions. cDNA was amplified for 11 cycles. Libraries were sequenced on an Illumina NextSeq2000 with 100-bp single-end reads.

treatment_protocol: Day 6 iNs were either not treated or incubated with 20 µM cisplatin and 150 µM dN for 7 days

value: 20 µM cisplatin, 150 µM dN; 7 days


title: XZ69317-XZ69318 Rat mammary tumor AAV-rPNT 3

description:
Library name: XZ69317-XZ69318_29247
XZ69317-XZ69318, AAV-rPNT, rat Pik3caH1047R, Tp53-Indel, and Nf1-Indel edited tumor

value: Pik3caH1047R; Nf1-Indel; Tp53-Indel


title: W6d_rep4

description:
Library name: Sample 12
g212

value: shoot


title: MB135iDUX4ca_WT_NoDox_2

description: Library name: MB135iDUX4ca_WT_NoDox_2


title: XZ69317-XZ69318 Rat mammary tumor AAV-rPNT 2

description:
Library name: XZ69317-XZ69318_29244
XZ69317-XZ69318, AAV-rPNT, rat Pik3caH1047R, Tp53-Indel, and Nf1-Indel edited tumor


title: W6d_rep3

description:
Library name: Sample 11
g211


title: MB135iDUX4ca_WT_NoDox_1

description: Library name: MB135iDUX4ca_WT_NoDox_1


title: XZ69317-XZ69318 Rat mammary tumor AAV-rPNT 1

description:
Library name: XZ69317-XZ69318_29241
XZ69317-XZ69318, AAV-rPNT, rat Pik3caH1047R, Tp53-Indel, and Nf1-Indel edited tumor


title: MB135_iDUX4ca_siKLF18_20hDOX_3

description: Library name: siKLF18_20hDOX_3

treatment_protocol: MB135iDUX4 cells were treated with siRNAs targeting KLF17 (siKLF17), KLF18 (siKLF18), or non-targeting controls (siCTRL), ± 1 µg/mL doxycycline (DOX) for 20 hours

value: human myoblast with inducible DUX4 transgene

value: siKLF18, 20hr Dox treatment


title: W6d_rep2

description:
Library name: Sample 10
g210


title: iNeuron-WT-NT-day14-RNA-seq-rep3

description: Library name: Sample3

value: WTC11 i3Neuron

value: NT


title: W6d_rep1

description:
Library name: Sample 9
g209


title: XZ64126-XZ64127 Rat mammary tumor AAV-Tp53 tumor 3

description:
Library name: XZ64126-XZ64127_27754_nonimm
XZ64126-XZ64127, AAV-Tp53, rat Tp53-Indel edited tumor (CD45-negative) cells

value: Rat mammary tumor


title: MB135_iDUX4ca_siKLF18_20hDOX_2

description: Library name: siKLF18_20hDOX_2


title: iNeuron-WT-NT-day14-RNA-seq-rep2

description: Library name: Sample2


title: BeforePretreatment_rep8

description:
Library name: Sample 8
g208


title: iNeuron-WT-NT-day14-RNA-seq-rep1

description: Library name: Sample1


title: BeforePretreatment_rep7

description:
Library name: Sample 7
g207


title: MB135_iDUX4ca_siKLF18_noDOX_3

description: Library name: siKLF18_noDOX_3

value: siKLF18, No Dox


title: Exosome Purification_Urine_Cancer_3

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

country: Belgium

institute: University Ghent

description: Library name: RNA022654

data_processing:
BCL files were processed using the Illumina Bcl2fastq (v. 2.20) software to generate and demultiplex fastq files. Raw reads were assessed for quality using FastQC (v. 0.11.9). The unique molecular identifier (UMI) sequences in the Pico v3 SMART UMI adapters were first extracted and added to the read name with UMI-tools (v. 1.0.0). Next, the sequencing data were processed with an in-house developed and validated pipeline using cutadapt (v. 1.16), SAMtools (v. 1.9), and STAR (v. 2.7.3a) to obtain deduplicated, high-quality and aligned RNA counts against the human genome (hg38). Ribosomal contamination was assessed using the BBMap tool (v. 38.87). Additional QC statistics were generated by using multiQC (v. 1.9) software package. Gene counts were determined with HTSeq (v. 0.11.0) in reverse stranded mode, only considering uniquely mapping reads. Ensembl release 91 was used to annotate reads within human genes.
Assembly: hg38
Supplementary files format and content: Tab seperated format, rows are genese, columns are samples, first 3 columns are ensembl ID, hgnc symbol and external gene name extacted from biomart

source_name: Urine

extract_protocol:
Total and small RNA were isolated from samples using the miRNeasy Micro kit (urine and cell culture medium) and miRNeasy Serum/Plasma Advanced kit (blood plasma) according to manufacturer’s instructions (cat. no. 217084 and 217204, Qiagen, Valencia, CA, USA), and eluted in 12 µL DNase/RNase-free water. To allow for a proper method comparison during RNA sequencing, synthetic spike-in controls were added as previously described 43,44. In short, per initial amount of biofluid input volume, 2 µL Sequin spike-in control [JV1] (Garvan Institute of Medical Research) and 2 µL RNA extraction Control (RC) spike-ins (Integrated DNA Technologies) were added to the lysate. Following RNA isolation, 2 µL of External RNA Control Control Consortium (ERCC) and 2 µL Library Prep (LP) spike-ins were added. RNA samples were stored at -80 °C until further use.
treated to remove residual genomic DNA by adding 1 µL of HL-dsDNase (#70800-202, ArcticZymes, 2 U/µL) and 1 µL reaction buffer (#66001, ArcticZymes) to 12 µL RNA, followed by 10 min incubation at 37 °C, and 10 min incubation at 55 °C to inactivate the DNase. Total RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (#634487, Takara), including a ribosomal RNA depletion step at the cDNA level, as originally published in 53, with some modifications as reported 54. 8 µL of DNase treated RNA was fragmented for 4 min at 94 °C, followed by the ‘highly degraded RNA’ workflow. Library quality control was performed with the Fragment Analyzer high sense small fragment kit (Agilent Technologies, sizing range 50-1000 bp). Libraries were quantified using the KAPA Library Quantification Kit (#KK4854, Roche), followed by equimolar pooling and Qubit quantification. The loading concentration of the pool was 0.58 nM with 2% phiX on an S2 100 cycles flow cell (paired-end 2 x 50 nucleotides) on a NovaSeq 6000 instrument (Illumina)

value: Urine

tag: preparation protocol

value: Exosome Purification


title: MB135_iDUX4ca_siKLF18_noDOX_2

description: Library name: siKLF18_noDOX_2


title: iNeuron-WT-cisplatin-20uM-S1-END-seq

description: Library name: Sample8

data_processing:
Raw reads were trimmed by Trimmomatic or Trim Galore!.
Trimmed reads were mapped to reference genome using bowtie.
Bigwig were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM. The resulting BigWig files were then adjusted using spike-in normalization.
For spike-in normalization, a scaling factor was calculated by dividing the reads mapped to the mouse spike-in locus (TCRβ) by the total reads mapped to the human genome. The signal was then divided by this factor.
Assembly: hg19
Supplementary files format and content: bw files include spike-in normliazed value for each sample

growth_protocol: To differentiate iPSCs into neurons, iPSCs were grown on matrigel pre-coated plates in N2 medium. N2 medium was removed and changed daily for two additional days. 3 days post-plating, cells (“day3 neurons”) were dissociated in accutase and replated onto new plates freshly coated with poly-L-ornithine in BrainPhys medium to complete differentiation. For END-seq experiments, 10 million day3 neurons were plated onto 10-cm plates. Cells were treated on day 6 or 7 (3-4 days after plating on PLO-coated plates).

extract_protocol:
Cells were harvested by treatment with accutase for 20 minutes and gentle pipetting to reach approximate single-cell suspension. Neurons were counted and spike-in cells (G1-arrested Lig4-/- mouse pre-B cells expressing a site-specific zinc-finger endonuclease) were added at 10% of cell count. Cells were embedded in 1% agarose plugs and processed.
Agarose-embedded cells were lysed and digested using Proteinase K (50°C for 1 hour, then 37°C for 7 hours). Plugs were washed in TE buffer and treated with RNase A at 37°C for 1 hour. For S1-END-seq, plugs were then washed in EB and equilibrated in S1 nuclease buffer (40 mM sodium acetate pH 4.5, 300 mM NaCl, 2 mM ZnSO4) for 30 minutes. Plugs were added to 100 µL S1 nuclease buffer containing 1.8 U S1 nuclease and incubated for 15 minutes on ice to allow the enzyme to diffuse into the plug. Plugs were then incubated with the reaction mix at 37°C for 20 minutes before addition of EDTA (10 mM final concentration) to terminate the reaction. After this, the standard END-seq protocol was followed. Plugs were then washed first in TE buffer, then in ExoVII Buffer (NEB), before incubating with ExoVII (NEB, M0379S) in ExoVII buffer for 1 hour at 37°C. Plugs were washed twice in NEBuffer 4 and then incubated with ExoT (NEB, M0265S) in NEBuffer 4 for 1 hour at 24°C. After blunting, plugs were washed twice in NEBNext dA-Tailing Reaction Buffer (NEB, B6059S) and then incubated with Klenow exo- (NEB, M0212S) in dA-Tailing Reaction Buffer at 37°C for 30 minutes. Plugs were washed once in NEBuffer 2 and incubated with END-seq hairpin adapter 1 and NEB Quick Ligase in NEB Quick Ligation buffer for 20 minutes at 25°C. Agarose plugs were then melted and digested with β-Agarase I (NEB) and DNA was sonicated to approximately 200 bp using a Covaris S220 sonicator for 4 min at 10% duty cycle, peak incident power 175, 200 cycles per burst, 4°C. DNA was ethanol-precipitated and dissolved in 70 μL TE buffer. Biotin-containing DNA fragments were isolated using MyOne Streptavidin C1 Beads (Thermo Fisher, 650–01). 35 μL of beads were washed twice with 1 mL 1x wash and binding buffer (1x W&B; 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1 M NaCl, 0.1% Tween 20) on a DynaMag-2 magnetic separator (Invitrogen, 12321D) and resuspended in 70 µL of 2x W&B (10 mM Tris-HCl pH 7.5, 2 mM EDTA, 2 M NaCl, 0.2% Tween 20). This was added to the fragmented sample DNA and incubated at 24°C while in a ThermoMixer while shaking for 30 minutes. Dynabeads (now bound to DNA) were washed three times in 1 mL of 1x W&B, twice in 1 mL EB, and once in 1 mL 1x T4 DNA ligase buffer (NEB). Dynabeads were resuspended in 50 µL end-repair reaction mix (1x T4 DNA ligase buffer, 2.7 U T4 DNA polymerase (NEB), 9 U T4 Polynucleotide Kinase (NEB), 1 U Klenow fragment (NEB), and 0.4 mM dNTPs) and incubated with shaking at 24°C for 30 minutes. Beads were washed once in 1 mL 1x W&B, twice in 1 mL EB, once in 1 mL NEBuffer 2 (NEB), and resuspended in 50 µL A-tailing reaction mix (1x NEB dA-Tailing Buffer with 20 U Klenow fragment exo- (NEB)). Samples were incubated at 37°C with shaking for 30 minutes. Dynabeads were then washed in 1 mL NEBuffer 2 and resuspended in 115 µL ligation reaction mix (1x Quick Ligase Buffer (NEB), 6,000 U Quick Ligase (NEB), END-seq hairpin adaptor 2) and incubated with shaking at 25°C for 30 minutes. 50 mM EDTA was added to terminate the reaction. Hairpin adaptors were digested using USER enzyme (NEB, M5505S) for 30 minutes at 37°C. Dynabeads were then washed three times with 1 mL 1x W&B and three times with 1 mL EB. Beads were resuspended in 8 µL EB + 10 µL 2x Kapa HiFI HotStart Ready Mix (Kapa Biosciences). Primers (10 mM) 5′-CAAGCAGAAGACGGCATACGAGATxrefGTGACTGG AGTTCAGACGTGTGCTCTTCCGATC*T-3′ and 5′-AATGATACGGCGA CCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (asterisk indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added to 37 µL PCR reaction mix (20 µL 2x Kapa HiFI HotStart Ready Mix added to 17 µL H2O) for a final volume of 60 µL. DNA was amplified using the following PCR parameters: 98°C (45 seconds); 15 cycles of 98°C (15 seconds), 63°C (30 seconds), 72°C (30 seconds); 72°C (5 minutes). The finished PCR reaction was cleaned using 1.8x volume AMPure Beads XP (Beckman Coulter), following the manufacturer’s instructions. Samples were then separated on a 2% agarose gel, with ≈200 bp DNA being excised and purified using a QIA-quick Gel Extraction Kit (Qiagen). Library concentrations were measured using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems) and then sequenced using Illumina NextSeq 550 or NextSeq 2000 instruments.

treatment_protocol: Day 6 or 7 iNs were incubated with 20 µM cisplatin for 24 hr

value: 20 µM cisplatin; 24 hours. S1-in-situ-treatment


title: XZ64126-XZ64127 Rat mammary tumor AAV-Tp53 immune 2

description:
Library name: XZ64126-XZ64127_27751_imm
XZ64126-XZ64127, AAV-Tp53, rat Tp53-Indel edited immune (CD45-positive) cells


title: BeforePretreatment_rep6

description:
Library name: Sample 6
g206


title: iNeuron-WT-cisplatin-20uM-END-seq

description: Library name: Sample7

value: 20 µM cisplatin; 24 hours


title: Exosome Purification_Urine_Healthy_2

description: Library name: RNA022650


title: XZ64126-XZ64127 Rat mammary tumor AAV-Tp53 tumor 1

description:
Library name: XZ64126-XZ64127_27748_nonimm
XZ64126-XZ64127, AAV-Tp53, rat Tp53-Indel edited tumor (CD45-negative) cells


title: BeforePretreatment_rep5

description:
Library name: Sample 5
g205


title: exoEasy_Urine_Healthy_1

description: Library name: RNA022655

value: exoEasy


title: MB135_iDUX4ca_siKLF18_noDOX_1

description: Library name: siKLF18_noDOX_1


title: 25717-iNeuron-CSB-KO-A6-20uM-Cisplatin-END-seq

description: Library name: Sample6

value: iPSC-derived neurons

value: CSB KO


title: XZ64126-XZ64127 Rat mammary tumor AAV-Tp53 immune 1

description:
Library name: XZ64126-XZ64127_27748_imm
XZ64126-XZ64127, AAV-Tp53, rat Tp53-Indel edited immune (CD45-positive) cells


title: BeforePretreatment_rep4

description:
Library name: Sample 4
g204


title: MB135_iDUX4ca_siKLF17_20hDOX_3

description: Library name: siKLF17_20hDOX_3

value: siKLF17, 20hr Dox treatment


title: 25717-iNeuron-XPC-KD-20uM-Cisplatin-END-seq

description: Library name: Sample5

value: XPC KD


title: XZ63068-XZ63069 Rat mammary tumor AAV-Nf1 tumor 3

description:
Library name: XZ63068-XZ63069_27702_tumor
XZ63068-XZ63069, AAV-Nf1, rat Nf1-Indel edited tumor (CD45-negative) cells


title: BeforePretreatment_rep3

description:
Library name: Sample 3
g203