title: dTAG-SPT5-HCT116, WT_NVP2, Inde4

extract_protocol:
About 20 million HCT116 cells grown on the 150 mm dish were cross-linked with 1% formaldehyde for 10 min at room temperature. Cross-linking was quenched with 125 mM glycine for 5 min. Cells were collected with a cell lifter (Costar) in 2 ml ChIP nuclei fractionation buffer [50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% Glycerol, 1% NP-40, 0.25% Triton X-100] with proteinase and phosphatase inhibitors and incubated on ice for 10 min. Cell nuclei were collected by centrifugation at 4 °C at 600 × g for 10 min and washed with wash buffer [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0)]. The pellets were lysed in 1.8 mL RIPA buffer with proteinase and phosphatase inhibitors and sheared by sonication in a Bioruptor (Diagenode) at high power, for 2× 20 min with cycles of 30 s ON and 30 s OFF. Lysates were clarified by centrifugation at 16,000 × g for 10 min at 4 °C. 600 μL pre-cleared lysates were incubated with 4 μg antibodies overnight at 4 °C with end-to-end rotation. 22 μL Protein G magnetic beads (New England Biolabs) were added to the tube on the second day and the samples were incubated for another 4 hours at 4 °C with end-to-end rotation. The beads were washed with RIPA buffer three times, IP wash buffer [100 mM Tris-HCl (pH 8.0), 500 mM lithium chloride, 1% NP-40, 1% sodium deoxycholate] three times and TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0)] twice. Reversal of cross-linking was done by incubating beads in the elution buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 1% SDS, 200mM NaCl, 0.8 U Proteinase K] at 55 °C with heated lid for 16 h. On the third day, 1 μg of RNase A was added and the samples were incubated at 37 °C for 30 min. DNA was purified by using DNA Cleanup Kit (5 μg) (New England Biolabs).
The purified DNA was used for qPCR and library preparation. Spike-In DNA (S. cerevisiae) (Cell Signaling Technology) were added to each sample and DNA libraries were prepared with NEBnext Ultra II DNA library kit (New England Biolabs).

value: Human colon cancer cell line


title: PNOC005-05_D04, RNAexome

status: Public on Apr 17 2025

type: SRA

city: San Francisco

first: Aaron

last: Diaz

state: CA

country: USA

institute: UCSF

description: Library name: PNOC005-05_D04_RNAexome

library_source: transcriptomic

data_processing:
Quality control of bulk and RNA exome sequencing data was performed using FASTQC (v0.11.0). Adapter sequences (Illumina TruSeq: AGATCGGAAGAGC) and polyA/G tails were trimmed using fastp (v0.23.4). Reads with Phred scores <20 or lengths <16 bp were excluded. Processed reads were aligned to either the human (GRCh38) or mouse (mm10) reference genome using STAR (v2.7.10b) with two-pass mode, based on sample origin. Gene-level counts were generated using featureCounts (v2.0.1).
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separated files include raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Peripheral whole blood samples were collected in EDTA tubes and either processed directly or used for PBMC isolation via density gradient centrifugation with Ficoll-Paque. Total RNA was extracted from whole blood or PBMCs using a silica column-based method, including on-column DNase treatment to remove residual genomic DNA. All samples were processed promptly to preserve RNA integrity and ensure suitability for downstream library construction.
Approximately 100 ng of total RNA was used for library preparation following the 3′ Tag-Seq protocol. Polyadenylated transcripts were captured using anchored oligo(dT) primers during reverse transcription, incorporating unique molecular identifiers (UMIs) and sample-specific barcodes. Second-strand synthesis and PCR amplification were performed to generate sequencing-ready libraries with Illumina adapters. Libraries were sequenced on an Illumina NextSeq using single-end reads, following the standard 3′ Tag-Seq workflow.

tag: tissue

value: Whole blood

tag: cell type

value: Medulloblastoma

tag: treatment

value: MV-NIS


title: BMMCs of M5 AML (primary) remission from Patient 1 [AML03M5_P]

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

country: China

institute: Shanghai OE Biotech Co., Ltd

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline (version 2.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: primary isolated cells

growth_protocol: These samples were directly isolated from AML patients without cell culture.

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v2 Kits according to the manufacturer’s protocol.

treatment_protocol: All of dead cells were removed using dead cell removal kit (Miltenyi Biotec). Furthermore, all of patients at relapse and partial remission stages were already treated with HSCs transplantation.

tag: cell line

value: primary isolated cells

value: human bone marrow cells

tag: genotype

value: before HSCs transplantation


title: PNOC005-05_D01, RNAexome

description: Library name: PNOC005-05_D01_RNAexome


title: PNOC005-01_D28, RNAexome

description: Library name: PNOC005-01_D28_RNAexome


title: PNOC005-05_D00, RNAexome

description: Library name: PNOC005-05_D00_RNAexome

value: Pre-MV-NIS


title: dTAG-SPT5-HCT116, muR1_∆CTR2, Rep2

city: NYC

first: Rui

last: Sun

state: New York

address: 1425 Madison

institute: Icahn school of medicine at Mount Sinai

library_source: genomic

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). PCR duplicates were removed using Picard Tools (version 3.1.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals

molecule: genomic DNA

growth_protocol: dTAG-SPT5 HCT116 cells were cultured in McCoy’s 5A medium (Corning) supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) and 1× Penicillin-Streptomycin (Corning) at 37°C and 5% CO2.

treatment_protocol: 125 nM dTAGv-1 for 4 hours; 250 nM NVP2 for 1 hour in specified experiments

tag: genetic modification

tag: chip antibody

value: Bethyl Laboratories;Cat. # A304-405A


title: Liver, PE-MP containing food, 71weeks, rep1

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

country: South Korea

institute: Chung-Ang

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to GRCm39 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: liver

growth_protocol: C57BL/6 male mice were reared over a period of 71 weeks in a controlled environment, with temperatures consistently maintained between 18 to 22 degrees Celsius.

extract_protocol:
Total RNA was isolated from liver using Direct-Zol™ RNA microprep kit (Zymo research, CA, USA) according to the manufacturer’s protocol.
RNA Libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA magnetic Isolation Module and NEBNext Ultra II Derectional RNA Library Prep Kit for Illumina

treatment_protocol: Chow containing PE-MP

value: liver

tag: strain

tag: Sex

value: male

value: Chow containing PE-MP


title: BMMCs of M5 AML (relapse) from Patient 1 [AML02M5_RE]

value: post HSCs transplantation


title: Liver, normal food, 71weeks, rep3

value: Normal Chow


title: dTAG-SPT5-HCT116, WT_∆CTR2, Rep2


title: PNOC005-01_D14, RNAexome

description: Library name: PNOC005-01_D14_RNAexome


title: PNOC005-05_D07, RNAexome

description: Library name: PNOC005-05_D07_RNAexome


title: Liver, normal food, 71weeks, rep2


title: dTAG-SPT5-HCT116, muLR1_∆CTR2, Rep1


title: BMMCs of M4 AML (primary remission) from Patient 1 [AML01M4_P]


title: PNOC005-01_D07, RNAexome

description: Library name: PNOC005-01_D07_RNAexome


title: Liver, PE-MP containing food, 71weeks, rep3


title: Liver, normal food, 71weeks, rep1


title: PNOC005-01_D04, RNAexome

description: Library name: PNOC005-01_D04_RNAexome


title: C57BL/6 male mice, PS-MP containing food, 71weeks, rep3

treatment_protocol: Chow containing PS-MP

value: Chow containing PS-MP


title: dTAG-SPT5-HCT116, muR1_∆CTR2, Rep1


title: BMMCs of M4 AML (partial remission) from Patient 1 [AML01M4_CR]


title: dTAG-SPT5-HCT116, WT_∆CTR2, Rep1


title: PNOC005-01_D01, RNAexome

description: Library name: PNOC005-01_D01_RNAexome


title: dTAG-SPT5-HCT116, muALL, Rep2


title: Liver, PE-MP containing food, 71weeks, rep2


title: U04

source_name: mesenchymal stem cells

growth_protocol: The culture medium for MSCs was added 1% antibiotics and 10%FBS with 1ug/100 bFGF. All of the cells were cultured in  the humidified incubator with standard cultivation conitions(37C,5%CO2)

treatment_protocol: At the zero (dissociated directly from  Umbilical Cords tissues) or fourth passage, the MSCs for individual donors were trypsinized  and washed twice with 1xPBS at the same day. All of the cells were sorted by flow cytometry for specific surface markers(Positive for CD90,CD73,CD105, and negative for CD11b,CD19,CD34,CD45, and HLA-DR)

value: Umbilical-cord-derived MSCs

tag: in vivo &in vitro

value: In vitro expansion


title: PNOC005-01_D00, RNAexome

description: Library name: PNOC005-01_D00_RNAexome


title: C57BL/6 male mice, PS-MP containing food, 71weeks, rep2


title: BMMCs of M5 AML (primary) remission from Patient 1 [AML02M5_P]


title: C57BL/6 male mice, PS-MP containing food, 71weeks, rep1


title: U03


title: dTAG-SPT5-HCT116, muLR1_∆CTR2, Rep2

value: Human colon cancer cell line


title: C57BL/6 male mice, normal food, 71weeks, rep3


title: BMMCs of M4 AML (relapse) from Patient 1 [AML01M4_RE]


title: HK-374 cells RT + MXC-017 treated

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

description:
Library name: HK_374-MXC017_RT_MXC017
10x Genomics

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) and processed using the PIPseeker software, version 3.3.3 (Fluent Biosciences). Raw matrices were in processed in Seurat version 5 20. Cells with less than 500 genes were filtered out and cells with high mitochondrial gene count (>5%) were removed.
Assembly: human genome (hg38)
Supplementary files format and content: FASTQ and matrix files

source_name: Glioblastoma

growth_protocol: Patient-derived HK-374 gliomaspheres were cultured in serum-free conditions in ultra-low adhesion plates in DMEM/F12, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
At day 5, the gliomaspheres in the suspension culture were collected and dissociated with TrypLE (no phenol red), and the adherent differentiated cells were washed with HBSS and de-attached with Trypsin/EDTA. The cells were then pooled and filtered through a 40-µm strainer and counted with a hemacytometer. The samples were pelleted by centrifugation at 300 g for 5 minutes at 4°C, resuspended in the provided Cell Resuspension Buffer (Fluent Bioscience, Watertown, MA), and 50,000 cells were targeted for capture and processed for single-cell transcriptomics using the PIPseqTM T2 3’ Single Cell RNA Kit v4.0 Plus (Fluent Biosciences).
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp, with 3.25 billion reads in total for 8 samples.

treatment_protocol: HK-374 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.

value: Glioblastoma

value: patient-derived cell line


title: U02


title: U01


title: dTAG-SPT5-HCT116, muALL, Rep1


title: C57BL/6 male mice, normal food, 71weeks, rep2


title: dTAG-SPT5-HCT116, muR1R2, Rep2


title: 4C-seq_chicken_FNP_enhancer

city: Cambridge

first: Michaela

last: Bartusel

state: Massachusetts

address: 31 Ames St

institute: Massachusetts Institute of Technology

data_processing:
4C-seq reads were assigned to samples based on the first 10 bases of the read. Then, the primer sequences were removed from the reads and the remaining sequence was trimmed to 36 bp. These 36 bases were then aligned to the human (hg19) or the chicken (galGal4) reference genome using Bowtie (Langmead et al., 2009).
The resulting reads were analyzed with R3C-seq  to generate RPM-normalized bedgraph files for downstream visualization and analysis (Thongjuea et al., 2013).
Assembly: hg19 for human samples, galGal4 for chicken samples
Supplementary files format and content: bedgraph
Library strategy: 4C-seq

organism: Gallus gallus

source_name: embryonic facial tissue

growth_protocol: The differentiation of hiPSCs into cranial neural crest cells (cNCCs) was performed based on an established protocol using 3D neuroectodermal spheres (NESs), as reported in prior studies (Bajpai et al., 2010; Laugsch et al., 2019; Prescott et al., 2015). In summary, hiPSCs were cultured until they reached 80-90% confluency and the formation of NESs was initiated by detaching the hiPSC colonies from the surface of the plate through treatment with collagenase. Cell aggregates were then carefully washed with PBS and transferred to Petri dishes in a specialized cNCC differentiation medium (Neurobasal and DMEM F12 media in 1:1 ratio, 0.5x B27 with Vitamin A and 0.5x N2 supplements, 20ng/mL epidermal fibroblast growth factor, 20ng/mL basic fibroblast growth factor and 5μg/mL Insulin). NESs formed over the next two days, spontaneously adhered to the surface of the Petri dish by day 9 of the differentiation, and then gave rise to cNCC outgrowths. Throughout this process, the differentiation medium was changed every two to three days. On day 11 of the differentiation, cNCCs were harvested for downstream experiments.

extract_protocol:
Isolation of chicken facial mesenchyme: Fertilized chicken eggs were incubated at 37°C for 4 days until they reached stage HH24 (Hamburger and Hamilton, 1992). Embryos were isolated from the eggs and transferred to 1x PBS to remove extraembryonic membranes. Frontonasal prominences were isolated using surgical scissors and pooled in a 1.5 mL tube for immediate use or flash-frozen in liquid nitrogen for storage at -80°C.
Circular Chromatin Conformation Capture (4C) was performed as previously described (Laugsch et al., 2019), based on a published protocol (Stadhouders et al., 2013) with minor modifications. 2-3x107 neural crest cells or 25 frontonasal prominences of stage HH24 chicken embryos were crosslinked with 1% formaldehyde. NlaIII (NEB, R0125) was used as the first restriction enzyme, DpnII (NEB, R0543) as the second restriction enzyme. The resulting 4C DNA was amplified by inverse PCR with the expand long template PCR system (11681842001, Roche) using 32 amplification cycles and primers designed as previously described (Stadhouders et al., 2013) (see Supplemental Table 1) Illumina adaptors P5 and P7 were added to the primers close to the NlaIII and the DpnII restriction site, respectively, with barcodes for multiplex sequencing.
multiplexed 4C-seq libraries were sequenced on the HiSeq2500 platform, chicken samples run on a single lane, human samples spread across two lanes (therefore generating two raw data files), generating reads of either 74 or 100 bp in length, respectively.

value: embryonic facial tissue

value: WT

value: no treatment


title: C57BL/6 male mice, normal food, 71weeks, rep1


title: HK-374 cells irradiated

description:
Library name: HK_374-MXC017_RT
10x Genomics


title: dTAG-SPT5-HCT116, muR2, Rep2


title: HK-374 cells MXC-017 treated

description:
Library name: HK_374-MXC017_MXC017
10x Genomics


title: DDX1 ON NCC rep3

data_processing:
*library strategy: Ribosome profiling
Reads were processed for downstream analysis as follows: Illumina libraries were demultiplexed into replicates, adapter sequences were trimmed using fastp (Chen, 2023). Libraries were further demultiplexed into samples by using UMI-tools to assign correctable barcodes to reads then using SeqKit2 to split the files (Shen et al., n.d.; Smith et al., 2017). Reads aligning to rRNA were identified with BowTie and removed (Langmead et al., 2009). The remaining reads were aligned to the genome using human reference assembly (GRCh38.p13) with STAR (Dobin et al., 2013). STAR was run using the following relevant parameters: --outFilterType BySJout --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd. Aligned reads were then deduplicated using the 6 nt unique molecular identifier with UMI-tools (Smith et al., 2017).
Read lengths and their phasing were quantified on maximal spanning windows generated using plastid (Dunn and Weissman, 2016).
Differential analysis was performed by counting the ribosome profiling reads aligned to each gene with featureCounts (Liao et al., 2014).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: cytoplasmic RNA

growth_protocol: The differentiation of hiPSCs into cranial neural crest cells (cNCCs) was performed based on an established protocol using 3D neuroectodermal spheres (NESs), as reported in prior studies (Bajpai et al., 2010; Laugsch et al., 2019; Prescott et al., 2015). In summary, hiPSCs were cultured until they reached 80-90% confluency and the formation of NESs was initiated by detaching the hiPSC colonies from the surface of the plate through treatment with collagenase. Cell aggregates were then carefully washed with PBS and transferred to Petri dishes in a specialized cNCC differentiation medium (Neurobasal and DMEM F12 media in 1:1 ratio, 0.5x B27 with Vitamin A and 0.5x N2 supplements, 20ng/mL epidermal fibroblast growth factor, 20ng/mL basic fibroblast growth factor and 5μg/mL Insulin). NESs formed over the next two days, spontaneously adhered to the surface of the Petri dish by day 9 of the differentiation, and then gave rise to cNCC outgrowths. Throughout this process, the differentiation medium was changed every two to three days. On day 11 of the differentiation, cNCCs were either harvested for downstream experiments or passaged for short-term maintenance by removing the NESs and dissociating the monolayer of cNCC with Accutase. cNCCs were then seeded on a fibronectin (5 mg/mL) coated cell culture dish (500,000 cells per well of a 6-well plate) in NCC maintenance medium (Neurobasal and DMEM F12 media in 1:1 ratio, 0.5x B27 with Vitamin A and 0.5x N2 supplements, 20ng/mL epidermal fibroblast growth factor, 20ng/mL basic fibroblast growth factor and 1 mg/mL BSA) (Prescott et al., 2015). After another passage with Accutase into fibronectin-coated 10 cm dishes, cNCCs were harvested at 80% confluency for downstream analysis.

extract_protocol:
cNCCs derived from three separate differentiations were rapidly washed twice with ice-cold PBS supplemented with 100 μg/mL cycloheximide and lysed on-plate in 500 μL ice-cold Polysome Lysis Buffer (20mM HEPEs pH 7.3, 100mM KCl, 5mM MgCl, 1% Tritonx-100, 2 μM DTT, 100 μg/mL cycloheximide). Lysate was passed through a 26 gauge needle 10 times and clarified by centrifugation for 5 minutes at 1,300 x g, 4°C, and the supernatant was further clarified by centrifugation for 5 minutes at 20,000 x g, 4°C.
Samples were normalized to the same concentration, as measured by NanoDrop Spectrophotometer, and treated with 350 U Ambion RNAseI (Invitrogen) per O.D. of absorbance at 260 nM per mL for 16 hours at 4°C. Samples were loaded on cold 10-50% sucrose gradients generated by layering 6 mL of 10% sucrose gradient buffer (20 mM HEPES pH 7.3, 100 mM KCl, 5 mM MgCl, 1 mM DTT, 100 μg/mL cycloheximide, 10% sucrose w/v) on 6 mL of 50% sucrose gradient buffer (20 mM HEPES pH 7.3, 100 mM KCl, 5 mM MgCl, 1 mM DTT, 100 μ/mL cycloheximide, 50% sucrose w/v) and mixed using a BioComp Gradient Station (BioComp, New Brunswick, Canada). Sample-loaded gradients were spun at 210,000 x g for 2.5 hours at 4°C using a SW-41 swinging-bucket rotor (Beckman Coulter) and Optima XPN Ultracentrifuge (Beckman Coulter). These gradients were fractionated on a BioComp Gradient Station and the monosome peaks were collected. RNA was extracted from the collected monosome peaks using Trizol LS (Invitrogen) and purified using a Direct-zol RNA Miniprep kit (Zymo Research).
Fragments between 17-34 nt long were isolated and libraries were prepared from them as described in McGlincy and Ingolia (2017), except with a depletion of rRNA immediately before reverse transcription using a mixture of rRNA-complementary biotinylated oligos (http://bartellab.wi.mit.edu/protocols.html)
Libraries were sequenced with a 75 nt single-end protocol on a 150 nt high output flowcell of an Aviti sequencer (Element Biosciences) after Adept library conversion (Element Biosciences).

treatment_protocol: DDX1-/-::TetON-DDX1 cNCCs were cultured with 0.4 ng/mL DOX (DDX1 ON) or without DOX for 5 days (DDX1 OFF).

value: cranial neural crest cells

value: 0.4 μM DOX


title: HK-374 cells 0 Gy Control

description:
Library name: HK_374-MXC017_0Gy
10x Genomics

value: control


title: dTAG-SPT5-HCT116, muR2, Rep1

value: Bethyl Laboratories;Cat. # A304-405A


title: Mrps5 fl/+;Myh6-Cre mouse heart tissue, cHET, postnatal day 4, rep 4

city: Hang Zhou

first: Feng

last: Gao

state: Zhejiang

address: Kaixuan road 268

department: Department of Cardiology

institute: Second Afliated Hospital, Zhejiang University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

growth_protocol: Mrps5 fl/fl mouse cross with Myh6-Cre mouse to obtain the Mrps5 fl/+;Myh6-Cre mouse and its control littermates Mrps5 fl/+ mouse. So that one allele of Mrps5 gene was depleted upon Myh6 gene promoter drivened Cre expression at the later stage of embyronic stage.

extract_protocol:
RNA was harvested using Trizol (Life). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mrps5 fl/+;Myh6-Cre mouse and its control littermates Mrps5 fl/+ mouse hearts were harvested at postnatal day 4.

value: Heart

value: Mrps5 fl/+; Myh6-Cre

value: One allele of Mrps5 gene depletion

tag: time

value: Postnatal day 4


title: Mrps5 fl/+;Myh6-Cre mouse heart tissue, cHET, postnatal day 4, rep 3


title: HK-244 cells RT + MXC-017 treated

description:
Library name: HK_244-MXC017_RT_MXC017
10x Genomics

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) and processed using the PIPseeker software, version 3.3.3 (Fluent Biosciences). Raw matrices were in processed in Seurat version 5 20. Cells with less than 500 genes were filtered out and cells with high mitochondrial gene count (>5%) were removed.
Assembly: human genome (hg38)
Supplementary files format and content: matrix files

growth_protocol: Patient-derived HK-244 gliomaspheres were cultured in serum-free conditions in ultra-low adhesion plates in DMEM/F12, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
At day 5, the gliomaspheres in the suspension culture were collected and dissociated with TrypLE (no phenol red), and the adherent differentiated cells were washed with HBSS and de-attached with Trypsin/EDTA. The cells were then pooled and filtered through a 40-µm strainer and counted with a hemacytometer. The samples were pelleted by centrifugation at 300 g for 5 minutes at 4°C, resuspended in the provided Cell Resuspension Buffer (Fluent Bioscience, Watertown, MA), and 50,000 cells were targeted for capture and processed for single-cell transcriptomics using the PIPseqTM T2 3’ Single Cell RNA Kit V5 (Fluent Biosciences).
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp, with 3.25 billion reads in total for 8 samples.

treatment_protocol: HK-244 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.


title: dTAG-SPT5-HCT116, muR1, Rep2


title: DDX1 ON NCC rep2


title: dTAG-SPT5-HCT116, muR1, Rep1


title: HK-244 cells MXC-017 treated

description:
Library name: HK_244-MXC017_MXC017
10x Genomics


title: DDX1 OFF NCC rep2


title: HK-244 cells irradiated

description:
Library name: HK_244-MXC017_RT
10x Genomics


title: dTAG-SPT5-HCT116, WT, Rep2


title: DDX1 ON NCC rep1


title: Mrps5 fl/+;Myh6-Cre mouse heart tissue, cHET, postnatal day 4, rep 1


title: HK-244 cells 0 Gy Control

description:
Library name: HK_244-MXC017_0Gy
10x Genomics


title: Mrps5 fl/+ mouse heart tissue, control, postnatal day 4, rep 4

value: Mrps5 fl/+


title: dTAG-SPT5-HCT116, WT, Rep1


title: dTAG-SPT5-HCT116, muR1R2, Rep1


title: dTAG-SPT5-HCT116, dTAGv-1(+), Rep2


title: FS, scRNAseq

city: NY

first: zhixiong

last: sun

state: NY

address: 3908 pardes building, NYSPI

department: Psychiatry

institute: Columbia University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (5.0.1) pipeline (10x Genomics)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Forebrain organoids

extract_protocol:
DIV70 forebrain organoids were incubated for 30 min at 37 °C in Earle’s Balanced Salt Solution (EBSS)/Albumin-ovomucoid inhibitor/papain with gentle shaking and mechanical dissociation. The pellet was resuspended and incubated with (EBSS)/Albumin-ovomucoid inhibitor/DNAse for 2 min followed by incubation with ovomucoid for 2 min. The cells were washed and resuspended with DMEM/F12. After determination of high cell viability (>90%), the single cell suspension was sequenced on the 10x Genomics platform at the Columbia Genome Center to recover ~5000 sequenced cells per sample
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, The Cell Ranger (5.0.1) pipeline (10x Genomics) was used to align and aggregate all reads from scRNA-seq to the GRCh38 human reference genome with default settings and produce a balanced combined “filtered feature bc matrix” for all samples. The data was imported into the SCANPY software (Version 1.7.1), where genotype information was added. Quality control was conducted to ensure all samples analyzed contained highly consistent quality. Cells expressing a minimum of 200 genes were kept, and counts were normalized for each cell by the total expression, multiplied by 106 and log-transformed. LIGER (Version 2.0.1) software was used to integrate the different samples and variation in the cells’ transcriptional profile was visualized by uniform manifold approximation and projection for dimension reduction (UMAP) function in SCANPY. To annotate the cell types in brain organoids, we downloaded the gene-cell count matrix and cell type annotation files of the single-cell RNAseq analysis of human embryonic prefrontal cortex tissue from the cell browser(https://cells.ucsc.edu/). We then utilized this dataset to train the SingleR software (Version 1.0.6 to infer the cell types in our dataset. Differentially expressed genes (DEGs) were determined using model-based analysis of single-cell transcriptomics (MAST, Version 1.12.0) algorithm implemented in Seurat (Version 4.2).

value: dissociated cells

value: Forebrain organoids

value: FS

tag: age


title: Mrps5 fl/+ mouse heart tissue, control, postnatal day 4, rep 3


title: DDX1 OFF NCC rep1


title: DDX1 OFF NCC rep3


title: WT, scRNAseq

description: 10x Genomics


title: Cox cells Sampled at TP4 biological replicate3

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

data_processing:
FASTQ files were imported into CLC Genomics Workbench v22, with poor-quality reads (<Q30) discarded. For each library, reads were trimmed and filtered based on the following criteria: sequence quality <0.01, up to 2 ambiguous nucleotides allowed, minimum read length >35 nucleotides, trimming against Illumina adaptor sequences, and a hard trim of 10 nucleotides at the 5’ end. The filtered reads were then mapped to the Malus x domestica GDDH13 V1.1 transcriptome (Daccord et al., 2017) using stringent mapping criteria: mismatch, gap, and insertion costs set at 2, 3, and 3, respectively. Reads with more than 10 hits were removed, and only reads with 80% identity and 80% coverage to the reference transcriptome were retained. Expression values were calculated using the RPKM (Reads Per Kilobase of transcript per Million reads) method (Mortazavi et al., 2008).
Differentially expressed genes among apple cells collected at T1, T2, T3, and T4 (n=3) were identified using an ANOVA test (Baggerly et al., 2003). A false discovery rate (FDR) corrected p-value (Benjamini-Hochberg correction) was set at 0.05, with a fold-change cut-off value of 2-fold increase or decrease in expression, and a minimum mean RPKM difference of 5 between groups. Gene ontology (GO) enrichment analysis was performed on the significantly regulated genes using Cytoscape v3.1.0 with the ClueGO v2.1.1 and CluePedia v1.1.1 plugins (Bindea et al., 2009; Bindea et al., 2013), focusing on GO terms from levels 3 to 8 and a kappa score set at 0.2. Principle component analysis (PCA) and pathways analysis conducted using iDEP
Assembly: Malus x domestica transcriptome assembly (Daccord et al 2017)
Supplementary files format and content: tab delimited text with RPKM, read count for each samples

organism: Malus domestica

source_name: Dedifferentiated cells

growth_protocol:
Calli of apple (Malus × domestica) cultivar “Cox Orange Pippin” were initiated from fruit flesh parenchymatic explants at 23 °C in the dark. The medium was supplemented with 30 g/L sucrose, 1 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D), 0.5 mg/L kinetin and 8 g/L agar
Cell suspension cultures were established by resuspending calli in the same calli-maintaining medium without agar.
Three 6 L Infors Minifors 2 bioreactors (Infors AG, Switzerland) were used for the experiment, each with a working volume of 4 L
Once the temperature stabilized at 22°C, with an airflow of 0.5 v.v.m and an agitation speed of 150 rpm, the bioreactor was inoculated with 15% (v/v) of a 1-week-old cell suspension culture in the exponential phase, resulting in a final culture volume of 4 L. Growth parameters were monitored and recorded using EVE software (Infors AG, Switzerland).

extract_protocol:
Fresh cell samples were ground to a fine powder using a mortar and pestle in liquid nitrogen. Due to the high-water content of the cells (approximately 95%), we increased the starting material mass to obtain a sufficient amount of total RNA. Total RNA was extracted from 1 g of cells using the RNeasy Plant Mini Kit (QIAGEN, Leusden, The Netherlands) with an adjusted protocol. The volume of RLT buffer was modified according to the starting material quantity as per the manufacturer's guidelines. The lysis buffer was applied to the RNeasy column using a 3-pass method. The remaining steps, including an on-column DNase I treatment (QIAGEN, Leusden, The Netherlands), were performed following the manufacturer's instructions.
Total RNA integrity was evaluated using the RNA Nano 6000 assay (Agilent Technologies, Diegem, Belgium) and a 2100 Bioanalyzer, with quality parameters tailored for plant RNA profiles (Agilent Technologies, Santa Clara, CA, USA). Samples with RNA Integrity Numbers (RINs) below 8 were excluded from the study. RNA purity was assessed by measuring absorbance at 230 nm, 260 nm, and 280 nm with a Nanodrop ND1000 spectrophotometer (Thermo Scientific, Villebon-sur-Yvette, France). Subsequently, mRNA was purified using the Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific, France) and quantified with a Qubit RNA assay kit (Life Technologies, Carlsbad, CA, USA).
cDNA libraries were prepared from 10 ng of mRNA using the SMARTer Stranded RNA-Seq Kit according to the manufacturer's guidelines (Takara Bio USA, Mountain View, CA, USA). The libraries were analyzed and quantified as described in Legay et al. (2015). Pooled libraries were sequenced on an Illumina NextSeq500 using the Illumina Mid Output Kit V2.5 (150 cycles) to generate 75 base-pair paired-end reads.

treatment_protocol:
MeJA (Merck, Darmstadt, Germany) was added to the bioreactors 25 days after inoculation following culture sampling (see below), to achieve a final concentration of 100 µM
During the batch duration,  50 mL culture was collected from each bioreactor using a sterile sampler at four time points: T1 = day 13, T2 = day 20, T3 = day 25, and T4 = day 28. The cells were vacuum filtrated , and immediately flash frozen in liquid nitrogen for subsequent analysis.

value: Dedifferentiated cells

value: Cox Orange Pippin

tag: time point


title: dTAG-SPT5-HCT116, dTAGv-1(-), Rep2

value: Human colon cancer cell line

value: Mock


title: B16F10 KD_4

type: RNA

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

description:
B16F10 cells transfected with FOXD1 plasmid replicate 4
SAMPLE 7

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using quantile normalisation with Chipster software (Chipster VM1)

label: biotin

source_name: Murine melanoma cell line, were tranduced with shFOXD1 plasmid

label_protocol: Affymetrix protocol

growth_protocol: Melanoma cell lines were cultivated in DMEM medium supplemented with heat-inactivated FCS, non-essential amino acids solution (NEAA), β-mercaptoethanol and antibotics. All cell lines were cultured in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit purchased from QIAGEN followed by clean-up and DNase I treatment according to the manufacturer’s instructions

value: B16F10 cell line


title: Mrps5 fl/+ mouse heart tissue, control, postnatal day 4, rep 2


title: Cox cells Sampled at TP4 biological replicate2


title: dTAG-SPT5-HCT116, dTAGv-1(+), Rep1


title: dTAG-SPT5-HCT116, dTAGv-1(-), Rep1


title: Mrps5 fl/+;Myh6-Cre mouse heart tissue, cHET, postnatal day 4, rep 2


title: Mrps5 fl/+ mouse heart tissue, control, postnatal day 4, rep 1


title: B16F10 KD_3

description:
B16F10 cells transfected with FOXD1 plasmid replicate 3
SAMPLE 6


title: Cox cells Sampled at TP3 biological replicate3


title: 4C-seq_cNCC_CYRIA prom

value: cranial neural crest cells

value: WT

value: no treatment


title: B16F10 KD_2

description:
B16F10 cells transfected with FOXD1 plasmid replicate 2
SAMPLE 5


title: B16F10 KD_1

description:
B16F10 cells transfected with FOXD1 plasmid replicate 1
SAMPLE 4


title: 4C-seq_cNCC_MYCNprom


title: Cox cells Sampled at TP3 biological replicate1


title: P310s,HSV-1, replicate 3

first: Erlin

last: Wang

state: Shanghai

address: 748 Zhongshan Middle Road, Songjiang District, Shanghai

department: Songjiang Hospital

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads.
HISAT2 (version 2.1.0)
Samtools (version 1.9)
featureCounts (version 2.0.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated files include raw-count values for each Sample
Supplementary files format and content: Tab-separated files include normalized values for each Sample

source_name: hippocampus

growth_protocol: Animals were maintained in facilities with a 12-h light/dark cycle, an average ambient temperature of 21°C, an average humidity of 48%, and had free access to food and water.

extract_protocol:
Hippocampous were removed, flash frozen on dry ice, and total RNA was extracted using TRIzol reagent (Cat#15596018, ThermoFisher Scientific) according to the manufacturer’s instructions.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hippocampus

value: Infection


title: B16F10 EM_3

description:
B16F10 cells transfected with empty vector backbone of FOXD1 plasmid replicate 3
SAMPLE 3

source_name: Murine melanoma cell line, were tranduced with empty vector backbone of shFOXD1 plasmid


title: Cox cells Sampled at TP3 biological replicate2


title: P310s,HSV-1, replicate 5


title: 4C-seq_cNCC_DDX1prom


title: P310s,HSV-1, replicate 1


title: Cox cells Sampled at TP2 biological replicate3


title: B16F10 EM_2

description:
B16F10 cells transfected with empty vector backbone of FOXD1 plasmid replicate 2
SAMPLE 2


title: 4C-seq_cNCC_enhancer


title: Cox cells Sampled at TP4 biological replicate1


title: Cox cells Sampled at TP2 biological replicate2


title: P310s,Mock, replicate 5

value: MOCK


title: MV_Post_310, bulkRNA

description:
Library name: MV_Post_310_bulkRNA
Medulloblastoma PDX model

source_name: Brain

value: Brain

value: CSCG

value: Medulloblastoma

value: MV-NIS


title: 107378 DDX1 ON rep3

data_processing:
Basic read quality control was performed using FastQC (Babraham Bioinformatics)
Read statistics were obtained with SAMtools.
Reads (61-73 million per sample) were mapped to the human reference assembly (GRCh38.p13) using STAR Aligner (Dobin et al., 2013).
Aligned reads were sorted with featureCounts (Liao et al., 2014), specifying for paired end reads.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: The differentiation of hiPSCs into cranial neural crest cells (cNCCs) was performed based on an established protocol using 3D neuroectodermal spheres (NESs), as reported in prior studies (Bajpai et al., 2010; Laugsch et al., 2019; Prescott et al., 2015). In summary, hiPSCs were cultured until they reached 80-90% confluency and the formation of NESs was initiated by detaching the hiPSC colonies from the surface of the plate through treatment with collagenase. Cell aggregates were then carefully washed with PBS and transferred to Petri dishes in a specialized cNCC differentiation medium (Neurobasal and DMEM F12 media in 1:1 ratio, 0.5x B27 with Vitamin A and 0.5x N2 supplements, 20ng/mL epidermal fibroblast growth factor, 20ng/mL basic fibroblast growth factor and 5μg/mL Insulin). NESs formed over the next two days, spontaneously adhered to the surface of the Petri dish by day 9 of the differentiation, and then gave rise to cNCC outgrowths. Throughout this process, the differentiation medium was changed every two to three days. On day 11 of the differentiation, cNCCs were either harvested for downstream experiments or passaged for short-term maintenance by removing the NESs and dissociating the monolayer of cNCC with Accutase. cNCCs were then seeded on a fibronectin (5 mg/mL) coated cell culture dish (500.000 cells per well of a 6-well plate) in NCC maintenance medium (Neurobasal and DMEM F12 media in 1:1 ratio, 0.5x B27 with Vitamin A and 0.5x N2 supplements, 20ng/mL epidermal fibroblast growth factor, 20ng/mL basic fibroblast growth factor and 1 mg/mL BSA) (Prescott et al., 2015). After another passage with Accutase, cNCCs were harvested for downstream analysis.

extract_protocol:
Total RNA was isolated from cultured cells, using TRIzol reagent (Invitrogen) followed by isopropanol precipitation with GlycoBlue (Invitrogen) according to the manufacturer’s instructions.
cDNA libraries were prepared using the TruSeq v2 RNA sample preparation kit (Ilumina) as previously described (Respuela et al. 2016)

treatment_protocol: DDX1-/-::TetON-DDX1 cNCCs were cultured with 0.4 ng/mL DOX (DDX1 ON) or without DOX for 4 days (DDX1 OFF).

value: 0.4 microM DOX


title: P310s,Mock, replicate 4


title: P310s,HSV-1, replicate 4


title: MV_Post_307, bulkRNA

description:
Library name: MV_Post_307_bulkRNA
Medulloblastoma PDX model


title: 107376 DDX1 ON rep2


title: 107374 DDX1 ON rep1


title: Cox cells Sampled at TP1 biological replicate2


title: MV_Post_306, bulkRNA

description:
Library name: MV_Post_306_bulkRNA
Medulloblastoma PDX model


title: P310s,Mock, replicate 3


title: P310s,HSV-1, replicate 2


title: P310s,Mock, replicate 2


title: Cox cells Sampled at TP1 biological replicate1


title: P310s,Mock, replicate 1


title: MV_Mid_808, bulkRNA

description:
Library name: MV_Mid_808_bulkRNA
Medulloblastoma PDX model


title: 107372 DDX1 OFF rep3


title: MV_Mid_809, bulkRNA

description:
Library name: MV_Mid_809_bulkRNA
Medulloblastoma PDX model


title: hACE2 cortex, BA5, 5dpi, replicate 5

description:
cortex_BA.5_5
cortex_raw_count.tsv
cortex_raw_norm.tsv

source_name: cortex

growth_protocol: Animals were maintained in a Biosafety Level 3 (BSL-3) animal facility with a 12-h light/dark cycle, an average ambient temperature of 21°C, an average humidity of 48%, and had free access to food and water.

extract_protocol:
Specific tissues were removed, flash frozen on dry ice, and total RNA was extracted using TRIzol reagent (Cat#15596018, ThermoFisher Scientific) according to the manufacturer’s instructions.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: hACE2 mice were intranasally inoculated with 10^4 plaque-forming units (PFU) of SARS-CoV-2 variants (Delta, BA.2.75, or BA.5) or Vero E6 cell supernatant for a duration of 5 days.

value: cortex

value: hACE2 knock-in

value: male


title: NCI-H23 cells, TRA2A/B dual KD, replicate 3

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

description: Library name: NCIH23_TRA2-DKD_rep3

data_processing:
Reads were aligned to the GRCh38 genome and Gencode v34 annotation using STAR v2.7.3.
Alternative splicing events were quantified using MAJIQ v2.5.
Transcript levels were quantified with kallisto v0.48.0.
Assembly: GRCh38
Supplementary files format and content: excel files for each cell line containing MAJIQ dPSI values
Supplementary files format and content: csv files for each cell line containing gene TPM values

extract_protocol:
Total RNA was extracted from cells using the Maxwell RSC simplyRNA Cells Kit (Promega, AS1390) and the Maxwell RSC48 Instrument (Promega).
RNA-seq library preparation was performed by Novogene. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, PCR amplification, and purification.

value: TRA2A/B dual knockdown by CRISPRi


title: 107370 DDX1 OFF rep2


title: MV_Mid_805, bulkRNA

description:
Library name: MV_Mid_805_bulkRNA
Medulloblastoma PDX model


title: hACE2 cortex, BA5, 5dpi, replicate 4

description:
cortex_BA.5_4
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: 107368 DDX1 OFF rep1


title: B16F10 EM_1

description:
B16F10 cells transfected with empty vector backbone of FOXD1 plasmid replicate 1
SAMPLE 1


title: NCI-H23 cells, TRA2A/B dual KD, replicate 2

description: Library name: NCIH23_TRA2-DKD_rep2


title: WT2-3

city: Hangzhou

first: Fengli

last: Zhao

address: No. 28 of Shuidaosuo Road

department: State Key Laboratory of Rice Biology and Breeding

institute: China National Rice Research Institute

description: Library name: WT2-3

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: Rice, Os7 of msu annotation (Nip)
Supplementary files format and content: bw file; TPM result (output of TPMCalculator)

organism: Oryza sativa

source_name: seed of 25 days after flowering

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: seed of 25 days after flowering

value: ZH11, WT2

value: Sowed on June 20, 2024


title: Cox cells Sampled at TP2 biological replicate1

value: Dedifferentiated cells

value: Cox Orange Pippin


title: NCI-H23 cells, TRA2A/B dual KD, replicate 1

description: Library name: NCIH23_TRA2-DKD_rep1


title: HI_341, bulkRNA

description:
Library name: HI_341_bulkRNA
Medulloblastoma PDX model

value: Heat inactivated control


title: Cox cells Sampled at TP1 biological replicate3


title: NCI-H23 cells, TRA2B KD, replicate 3

description: Library name: NCIH23_TRA2B-KD_rep3

value: TRA2B knockdown by CRISPRi


title: hACE2 cortex, BA5, 5dpi, replicate 2

description:
cortex_BA.5_2
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: hACE2 cortex, BA5, 5dpi, replicate 3

description:
cortex_BA.5_3
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: WT2-1

description: Library name: WT2-1


title: NCI-H23 cells, TRA2B KD, replicate 2

description: Library name: NCIH23_TRA2B-KD_rep2


title: HI_340, bulkRNA

description:
Library name: HI_340_bulkRNA
Medulloblastoma PDX model


title: PBS_820, bulkRNA

description:
Library name: PBS_820_bulkRNA
Medulloblastoma PDX model

value: PBS control


title: hACE2 cortex, BA5, 5dpi, replicate 1

description:
cortex_BA.5_1
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: NCI-H23 cells, TRA2B KD, replicate 1

description: Library name: NCIH23_TRA2B-KD_rep1


title: WT1-3

description: Library name: WT1-3

value: ZH11, WT1

value: Sowed on June 15, 2024


title: WT1-2

description: Library name: WT1-2


title: PBS_331, bulkRNA

description:
Library name: PBS_331_bulkRNA
Medulloblastoma PDX model

value: Brain

value: CSCG

value: Medulloblastoma


title: NCI-H23 cells, TRA2A KD, replicate 3

description: Library name: NCIH23_TRA2A-KD_rep3

value: TRA2A knockdown by CRISPRi


title: hACE2 cortex, BA.2.75, 5dpi, replicate 4

description:
cortex_BA.2.75_4
cortex_raw_count.tsv
cortex_raw_norm.tsv

value: cortex

value: hACE2 knock-in


title: hACE2 cortex, BA.2.75, 5dpi, replicate 5

description:
cortex_BA.2.75_5
cortex_raw_count.tsv
cortex_raw_norm.tsv

value: male


title: HI_886, bulkRNA

description:
Library name: HI_886_bulkRNA
Medulloblastoma PDX model


title: EE-G-3-3

description: Library name: EE-G-3-3

value: seed of 25 days after flowering

value: ZH11, OsGTPCH1 overexpression


title: WT1-1

description: Library name: WT1-1


title: PBS_329, bulkRNA

description:
Library name: PBS_329_bulkRNA
Medulloblastoma PDX model


title: NCI-H23 cells, TRA2A KD, replicate 1

description: Library name: NCIH23_TRA2A-KD_rep1


title: NCI-H23 cells, TRA2A KD, replicate 2

description: Library name: NCIH23_TRA2A-KD_rep2


title: hACE2 cortex, BA.2.75, 5dpi, replicate 3

description:
cortex_BA.2.75_3
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: WT2-2

description: Library name: WT2-2

value: ZH11, WT2

value: Sowed on June 20, 2024


title: NCI-H23 cells, Control KD, replicate 3

description: Library name: NCIH23_CTRL-KD_rep3

value: Control knockdown by CRISPRi


title: EE-G-3-2

description: Library name: EE-G-3-2


title: Cortex_3D_SALINE_CS_42D3_BiolRep3

city: New York

first: Anthony

middle: G

last: Pacholko

address: 465 Main Street

department: BMRI

institute: Weill Cornell Medicine

description:
Library name: SMS_200227CS
Papain digestion. Drop-seq

data_processing:
Demultiplexed fastq files were cleaned of reads not passing the Illumina Passing Filter with fastq_illumina_filter (version 0.1) and processed with the Drop-seq Tools (version 2.3.0) pipeline. Briefly, each transcriptome Read2 was tagged with the cell barcode (bases 1 to 12) and unique molecular identifier (UMI) barcode (bases 13 to 20) obtained from Read1, trimmed for sequencing adapters and poly-A sequences, and aligned using STAR v2.7.3a to the mouse reference genome assembly (Ensembl GRCm38.94 release). Reads aligning to exons were tagged with the respective gene symbol and counts of UMI-deduplicated reads per gene within each singular cell barcode were used to build a digital gene expression (DGE) matrix. The DGE matrix contained 40,000 cell barcodes associated with the highest numbers of UMIs. Cells with fewer than 200 UMIs, more than 10,000 UMIs, or more than 20% mitochondrial genes were excluded. Doubletfinder (RRID:SCR_018771) was used to computationally detect cell doublets with an expected doublet rate of 5% as the input parameter. Cells tagged with a “Doublet” call were removed. The corrected DGE matrices were merged into a single matrix.
Assembly: Mouse GRCm38.94
Supplementary files format and content: Tab separate csv files containing count matrices or metadata information

extract_protocol:
A total of 12 cell suspensions were generated, with 3 biologic replicates per treatment group. Within each replicate, 2 cortical hemispheres were pooled from 2 identically treated mice. Mice were anesthetized by isoflurane inhalation (5% induction, 2% maintenance) and perfused transcardially with ice-cold sucrose-HEPES “Cutting Buffer” containing (in mM) 110 NaCl, 2.5 KCl, 10 HEPES, 7.5 MgCl2, 25 glucose, and 75 sucrose (~350 mOsm kg−1). The brain was removed, placed in ice-cold Cutting Buffer, then transferred to a slicing chamber filled with ice-cold Cutting Buffer. 400 μm thick brain slabs were cut with a vibrating microtome. Slabs containing the regions of interest were gently transferred to a dissection dish with ice-cold dissociation buffer (DB) containing (in mM): 82 Na2SO4, 30 K2SO4, 10 HEPES, 10 glucose and 5 MgCl2. Regions of interest were isolated, then transferred into a 15 ml falcon tube filled with 5 ml of DB + enzyme buffer (DEB) consisting of DB with 3 mg/ml of Protease XXIII (Sigma-Aldrich, P5380), 10 units/ml of Papain (Sigma-Aldrich, P4762), 0.5 mM L-Cysteine (Sigma-Aldrich, 168149), and 0.25 mM EDTA (Worthington, LK003153). Digestion was performed at 34 °C for 2 hours. Tubes containing digested tissue were transferred onto ice and the DEB was replaced with 10 ml of a DB + stop solution (DBS) containing DB and 1 mg/ml Trypsin Inhibitor (Sigma-Aldrich, T6522), 2 mg/ml BSA (Sigma-Aldrich, A2153), and 1 mg/ml Ovomucoid Protease Inhibitor (Worthington, LK003153). Digested tissues were then dissociated using a series of 4 fire-polished Pasteur pipets with successively smaller bores. Bubbles were avoided. Falcon tubes containing 10 ml of dissociated cells were then centrifuged at 300 g for 10 minutes. The supernatant was removed and discarded, taking care not to disturb the cell pellet. The pellet was resuspended in 5 ml of DBS and centrifuged again under the same conditions. The supernatant was once again removed, and the cleaned cell pellet was resuspended to a volume of 3 ml in DB containing 0.01% BSA (w/v). Suspensions were passed into a new tube through a pre-wet 40 μm filter and held on ice. 2 samples of 10 μl were drawn from the suspension and mixed 1:1 with 10 μl of 2× dye mix containing DB and 20 μM EthD-1 (Thermo Fisher Scientific, L-3224), 20 μM Calcein-AM (Thermo Fisher Scientific, L-3224), and 40 μM Hoechst 33342 (Thermo Fisher Scientific, 62249). After 5 minutes of incubation at room temperature, 10 μl from each sample were loaded onto a haemocytometer and imaged using a fluorescent Olympus IX83 microscope. For each of the 2 samples, three random locations were imaged using DIC and three fluorescent channels to capture the dyes. These images were used to calculate cell concentrations and metrics of cell intactness. Afterward, cells were resuspended in 0.01% BSA-PBS at a concentration of 100,000 cells/ml for Drop-seq processing.
Single-cell transcriptomes of cortical brain cells were prepared by Drop-seq. Cells were resuspended in 0.01% BSA-PBS to a final concentration of 100 cells/μl. Barcoded capture beads (ChemGenes Corporation, Wilmington, MA) were resuspended in 1.8 ml lysis buffer consisting of 4M Guanidine HCL (Thermofisher Scientific, 24110), 6% Ficoll PM-400 (Sigma-Aldrich, F4375), 0.2% Sarkosyl (Sigma-Aldrich, 61747), 20mM EDTA (Thermofisher Scientific, 17892), 200mM Tris pH 7.5 (Sigma-Aldrich, DB0339), and 50mM DTT (Sigma-Aldrich, D0632) at a concentration of 120 beads/μl. A 5 mm diameter, 1.7 mm thick PVDF encapsulated magnetic stir disc and rotary magnetic tumble stirrer (V&P Scientific, VP772DP-N42-5-2) was used along with a 3 ml syringe that contained the beads in lysis buffer to maintain the beads in suspension. Next, single cells and beads were encapsulated in nanoliter-scale droplets using a Drop-seq microfluidic device coated with Aquapel (FlowJEM); flow rates were 15 ml/hour for the Droplet generation oil (BioRad, 1863005) and 4 ml/hour for the cells and beads. Each run lasted approximately 18 minutes. After removing the oil, droplets were resuspended in 30 ml of room temperature 6X SSC (Promega, V4261) and 1 ml perfluorooctanol (Sigma-Aldrich, 370533) and shaken vigorously 6 times vertically to break the droplets. Beads were then captured by loading them into a 20 ml syringe with an attached 0.22 μm Millex-Gv syringe filter (Millipore Sigma, SLGV033R). Beads were washed with 2 x 20 ml of ice cold 6X SCC. After washing, the syringe filter was inverted and flushed 3x with 10 ml of ice cold 6x SSC using a 10 ml syringe. Beads were collected from the resultant solution via centrifugation at 1,250 x g for 2 min at 4°C with low brake setting. cDNA was amplified by PCR using the following parameters: 95 °C (3 min); 4 cycles of 98 °C (20 s), 65 °C (45 s), and 72 °C (3 min); 11 cycles of 98 °C (20 s), 67 °C (20 s), and 72 °C (3 min). Libraries were quantified by quantitative PCR and checked for quality and size distribution on a Bioanalyzer (Agilent) before sequencing on an Illumina NextSeq500 instrument using the 75 cycle High Output v2 kit (Genomics Core Facility, Cornell University, Ithaca, NY). Three to four libraries were multiplexed into a single run. We loaded a 1.8 pM library and provided Drop-seq Custom Read1 Primer at 0.3 μM in position 7 of the reagent cartridge without PhiX spike-in using a read configuration of 20 bases (Read1), 8 bases (Index1), and 64 bases (Read2).

treatment_protocol: Angiotensin II induced hypertension - 3 or 42 days - osmotic minipump (s.c.)

value: Male

tag: timepoint

value: SALINE

tag: batch

tag: biological replicate

value: Biol rep 3 - 42D timepoint


title: EE-G-3-1

description: Library name: EE-G-3-1


title: hACE2 cortex, BA.2.75, 5dpi, replicate 1

description:
cortex_BA.2.75_1
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: Cortex_3D_ANGII_CA_42D3_BiolRep3

description:
Library name: SMS_200225CA
Papain digestion. Drop-seq

value: ANGII


title: hACE2 cortex, BA.2.75, 5dpi, replicate 2

description:
cortex_BA.2.75_2
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: NCI-H23 cells, Control KD, replicate 2

description: Library name: NCIH23_CTRL-KD_rep2


title: hACE2 cortex, Delta, 5dpi, replicate 5

description:
cortex_Delta_5
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: Cortex_3D_ANGII_CA_42D2_BiolRep2

description:
Library name: SMS_191107CA
Papain digestion. Drop-seq

value: Biol rep 2 - 42D timepoint


title: EE-A-G-4-3

description: Library name: EE-A-G-4-3

value: ZH11, OsADCS and OsGTPCH1 overexpression

value: Sowed on June 15, 2024


title: Cortex_3D_SALINE_CS_42D2_BiolRep2

description:
Library name: SMS_191105CS
Papain digestion. Drop-seq


title: A549 cells, TRA2A/B dual KD, replicate 3

description: Library name: A549_TRA2-DKD_rep3

value: TRA2A/B dual knockdown by CRISPRi


title: Cortex_3D_ANGII_CA_42D1_BiolRep1

description:
Library name: SMS_190808CA
Papain digestion. Drop-seq

value: Biol rep 1 - 42D timepoint


title: hACE2 cortex, Delta, 5dpi, replicate 3

description:
cortex_Delta_3
cortex_raw_count.tsv
cortex_raw_norm.tsv

value: cortex


title: A549 cells, TRA2A/B dual KD, replicate 2

description: Library name: A549_TRA2-DKD_rep2


title: Cortex_3D_SALINE_CS_42D1_BiolRep1

description:
Library name: SMS_190806CS
Papain digestion. Drop-seq


title: EE-A-G-4-2

description: Library name: EE-A-G-4-2


title: EE-A-G-4-1

description: Library name: EE-A-G-4-1


title: A549 cells, TRA2A/B dual KD, replicate 1

description: Library name: A549_TRA2-DKD_rep1


title: hACE2 cortex, Delta, 5dpi, replicate 4

description:
cortex_Delta_4
cortex_raw_count.tsv
cortex_raw_norm.tsv

value: hACE2 knock-in


title: hACE2 cortex, Delta, 5dpi, replicate 1

description:
cortex_Delta_1
cortex_raw_count.tsv
cortex_raw_norm.tsv

value: male


title: EE-A-1-3

description: Library name: EE-A-1-3

value: seed of 25 days after flowering

value: ZH11, OsADCS overexpression


title: EE-A-1-2

description: Library name: EE-A-1-2


title: Cortex_3D_SALINE_CS_3D3_BiolRep3

description:
Library name: SMS_200109CS
Papain digestion. Drop-seq

value: Biol rep 3 - 3D timepoint


title: hACE2 cortex, mock, 5dpi, replicate 5

description:
cortex_mock_5
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: EE-A-1-1

description: Library name: EE-A-1-1


title: Cortex_3D_ANGII_CA_3D3_BiolRep3

description:
Library name: SMS_200109CA
Papain digestion. Drop-seq


title: Cortex_3D_SALINE_CS_3D2_BiolRep2

description:
Library name: SMS_191206CS
Papain digestion. Drop-seq

value: Biol rep 2 - 3D timepoint


title: CR-G-1-3

description: Library name: CR-G-1-3

value: ZH11, OsGTPCH1 knockout


title: A549 cells, TRA2B KD, replicate 2

description: Library name: A549_TRA2B-KD_rep2

value: TRA2B knockdown by CRISPRi


title: A549 cells, TRA2B KD, replicate 1

description: Library name: A549_TRA2B-KD_rep1


title: hACE2 cortex, mock, 5dpi, replicate 4

description:
cortex_mock_4
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: hACE2 cortex, Delta, 5dpi, replicate 2

description:
cortex_Delta_2
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: CR-G-1-2

description: Library name: CR-G-1-2


title: Cortex_3D_ANGII_CA_3D2_BiolRep2

description:
Library name: SMS_200114CA
Papain digestion. Drop-seq

value: Male


title: NCI-H23 cells, Control KD, replicate 1

description: Library name: NCIH23_CTRL-KD_rep1

value: Control knockdown by CRISPRi


title: A549 cells, TRA2A KD, replicate 3

description: Library name: A549_TRA2A-KD_rep3

value: TRA2A knockdown by CRISPRi


title: hACE2 cortex, mock, 5dpi, replicate 2

description:
cortex_mock_2
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: CR-G-1-1

description: Library name: CR-G-1-1


title: Cortex_3D_ANGII_CA_3D1_BiolRep1

description:
Library name: SMS_191012CA
Papain digestion. Drop-seq

value: ANGII

value: Biol rep 1 - 3D timepoint


title: A549 cells, TRA2A KD, replicate 2

description: Library name: A549_TRA2A-KD_rep2


title: Cortex_3D_SALINE_CS_3D1_BiolRep1

description:
Library name: SMS_191009CS
Papain digestion. Drop-seq

value: SALINE


title: CR-A-G-1-3

description: Library name: CR-A-G-1-3

value: ZH11, OsADCS and OsGTPCH1 knockout

value: Sowed on June 20, 2024


title: A549 cells, TRA2B KD, replicate 3

description: Library name: A549_TRA2B-KD_rep3


title: A549 cells, TRA2A KD, replicate 1

description: Library name: A549_TRA2A-KD_rep1


title: hACE2 lung, BA5, 5dpi, replicate 5

description:
lung_BA.5_5
lung_raw_count.tsv
lung_raw_norm.tsv

source_name: lung

value: lung


title: Double_Repli2

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

data_processing:
Stranded RNA-seq data were mapped to the Drosophila melanogaster dm6 genome using STAR (version 2.7.0) with default parameters.
Aligned sequencing reads mapped to gene transcripts were counted using htseq-count with default parameters. Annotation file used: dmel-all-r6.34.gtf.gz
Differentially expressed genes (DEGs) were identified using the DESeq2 R package.
Assembly: dm6
Supplementary files format and content: Tab-delimited text files containing htseq raw counts for each library

organism: Drosophila melanogaster

source_name: larval imaginal leg discs

growth_protocol: Drosophila Melanogaster flies grown at 25°C on standard medium

extract_protocol:
20 third-instar larval leg discs per replicate were rapidly dissected in Schneider medium on ice. Total RNA was extracted with TRIzol reagent and purified using the RNA Clean & Concentrator™-5 kit (Zymo Research, cat. R1015).
>1μg of total RNA was sent to Novogene for strand-specific poly-A enrichment mRNA-seq library preparation. Paired-end sequencing of the libraries was performed on Novogene's NovaSeq 6000 PE150 platform.  (https://www.novogene.com/eu-en/services/research-services/transcriptome-sequencing/mrna-sequencing/)

value: larval imaginal leg discs


title: A549 cells, Control KD, replicate 3

description: Library name: A549_CTRL-KD_rep3


title: Double_Repli3


title: A549 cells, Control KD, replicate 2

description: Library name: A549_CTRL-KD_rep2


title: CR-A-G-1-2

description: Library name: CR-A-G-1-2


title: hACE2 cortex, mock, 5dpi, replicate 3

description:
cortex_mock_3
cortex_raw_count.tsv
cortex_raw_norm.tsv

value: cortex

value: hACE2 knock-in

value: male


title: hACE2 lung, BA5, 5dpi, replicate 4

description:
lung_BA.5_4
lung_raw_count.tsv
lung_raw_norm.tsv


title: A549 cells, Control KD, replicate 1

description: Library name: A549_CTRL-KD_rep1


title: Double_Repli1


title: hACE2 lung, BA5, 5dpi, replicate 2

description:
lung_BA.5_2
lung_raw_count.tsv
lung_raw_norm.tsv


title: WT_Repli3


title: CR-A-1-2

description: Library name: CR-A-1-2

value: seed of 25 days after flowering

value: ZH11, OsADCS knockout

value: Sowed on June 15, 2024


title: WT_Repli2


title: hACE2 lung, BA5, 5dpi, replicate 3

description:
lung_BA.5_3
lung_raw_count.tsv
lung_raw_norm.tsv


title: CR-A-1-3

description: Library name: CR-A-1-3


title: CR-A-1-1

description: Library name: CR-A-1-1


title: hACE2 cortex, mock, 5dpi, replicate 1

description:
cortex_mock_1
cortex_raw_count.tsv
cortex_raw_norm.tsv


title: hACE2 lung, BA5, 5dpi, replicate 1

description:
lung_BA.5_1
lung_raw_count.tsv
lung_raw_norm.tsv


title: hACE2 lung, BA.2.75, 5dpi, replicate 5

description:
lung_BA.2.75_5
lung_raw_count.tsv
lung_raw_norm.tsv


title: WT_Repli1


title: K562_treated_with_EPZ719_RNAPIIS2P_CUTnTAG_(20240401_WW1074_240325)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: K562_treated_with_EPZ719_RNAPIIS2P_CUTnTAG
CUT&Tag targeting RNAPIIS2P in K562 in EPZ719

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We made tracks in one of three ways with bedtools 2.30.0 "genomecov": (i) Fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw) or (ii) Calibrated number of counts using a scaling factor of 10000/(number of fragments mapped to E.coli GCF_000005845.2_ASM584v2) (Supplementary file .hg19.spike.bw) or (iii) Raw number of counts using scaling factor of 1 which is the number of fragments aligned at each position (Supplementary file .hg19.raw_counts.bw).
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

tag: antibody

value: Cell Signaling Technology, 13499S


title: K562_DMSOcontrol_for_EPZ719_treatment_RNAPIIS2P_CUTnTAG_(20240401_WW1086_240325)

description:
Library name: K562_DMSOcontrol_for_EPZ719_treatment_RNAPIIS2P_CUTnTAG
CUT&Tag targeting RNAPIIS2P in K562 in DMSO


title: Synoviocyte_5

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

description: Library name: Syn BB 159

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 (Andrews 2010) and multiQC v1.10 (Ewels et al. 2016). Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v3.3 (Martin 2011) and filtered for a minimum length of 17nt. Mapping steps were performed with bowtie v1.3.0 (Langmead et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012), whereas reads were mapped first against the genomic reference EquCab.3.0 provided by Ensembl (Zerbino et al. 2018) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004), filtered for miRNAs of eca only, allowing for one mismatch. For a general RNA composition overview, non-miRNA mapped reads were mapped against RNAcentral (Sweeney et al. 2019) and then assigned to various RNA species of interest. Statistical analysis of preprocessed NGS data was done with R v4.0 and the packages pheatmap vNA, pcaMethods v1.82 and genefilter v1.72. Differential expression analysis with edgeR v3.32 (Robinson, McCarthy, and Smyth 2009) used the quasi-likelihood negative binomial generalized log-linear model functions provided by the package. The independent filtering method of DESeq2 (Love, Huber, and Anders 2014) was adapted for use with edgeR to remove low abundante miRNAs and thus optimize the false discovery rate (FDR) correction.
Assembly: EquCab.3.0
Supplementary files format and content: Raw and RPM normlized miRNA reads as reported by miRDeep2

organism: Equus caballus

source_name: Synoviocyte

growth_protocol: Cells were initially cultured in monolayer at a density of 20 000 cells/cm2 with complete media (Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum, 1% Penicillin-Streptomycin and 0.2% Amphotericin B), and incubated at 37°C. Chondrocytes were incubated in hypoxic conditions (5% O2 and 5% CO2) and synoviocytes were incubated in normoxic conditions (25% O2 and 5% CO2). Complete media changes were carried out every two days until cells reached 80% confluence.

extract_protocol:
Total RNA was extracted from EV-recipient cells using the miRNeasy® Serum/Plasma Advanced kit (Qiagen, Manchester, UK) following the manufacturer’s protocol, with the recommended adaptations according to an input volume of 500 μl. RNA was eluted in 18 μl of RNAse free water.
RealSeq single-adapter ligation protocol for small RNA-sequening of biofluids

treatment_protocol: EV-donor cells were thawed, cultured in T175 flasks with complete media at a density of 20 000 cells/cm2 and used at passage 1. Complete media changes were performed every two days until cells reached 50–60% confluency. The flasks were then washed thrice with sterile PBS and incubated with 20 ml of EV media (phenol-red free Dulbecco's Modified Eagle Medium supplemented with 1% Penicillin-Streptomycin, 0.2% Amphotericin B and 1% L-Glutamate), with the addition of 5-ethynyl uridine (5-EU) at 1 μl/ml. Four controls (chondrocyte, n=2; synoviocyte, n=2) were cultured in parallel in EV media with no added label. Cells were incubated for 48h, after which the cell culture media was collected from each flask and stored in the fridge until further processing. The 5-EU treatment was repeated, and a second batch of media was collected after 48 h. EV-recipient cells were thawed, cultured in T75 flasks with complete media at a density of 20 000 cells/cm2 and used at P2. Complete media changes were performed every two days until cells reached 40–50% confluency. Once confluent, the flasks were washed thrice with sterile PBS. Chondrocyte-derived EVs were pooled together and distributed among the EV recipient synoviocyte flasks in equal volumes. Similarly, synoviocyte derived EVs were pooled together and evenly split among EV-recipient chondrocyte flasks. Finally, control recipient chondrocytes (n=1) were incubated with EVs derived from control donor synoviocytes, and control recipient synoviocytes (n=1) were incubated with EVs from control donor chondrocytes. All cells were incubated with EVs for 24 h. After this period, cells were trypsinized and kept in TRIzol until further processing.

value: Synoviocyte


title: K562_treated_with_ActinomycinD_U2AF1_CUTnRUN_2_(20240401_WW1050_240315)

description:
Library name: K562_treated_with_ActinomycinD_U2AF1_CUTnRUN_2
CUT&RUN targeting U2AF1 in K562 in ActinomycinD

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We made tracks in one of three ways with bedtools 2.30.0 "genomecov": (i) Fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw) or (ii) Calibrated number of counts using a scaling factor of 10000/(number of fragments mapped to E.coli GCF_000005845.2_ASM584v2) (Supplementary file .hg19.spike.bw) or (iii) Raw number of counts using scaling factor of 1 which is the number of fragments aligned at each position (Supplementary file .hg19.raw_counts.bw).
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

value: Bethyl Laboratories, A302-079A


title: PH WT_Repli2

data_processing:
Libraries sequencing quality were analyzed using fastQC software.
Assembly: dm6
Supplementary files format and content: bigwigs
Library strategy: Cut&Run

extract_protocol:
Cut&Run experiments were performed as described by Kami Ahmad in protocilas.io (https://dx.doi.org/10.17504/protocols.io.umfeu3n)
Libraries were preapred according the protocol of the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

tag: tissue

value: Wild type


title: Synoviocyte_4

description: Library name: Syn BB 169

tag: cell type


title: hACE2 lung, BA.2.75, 5dpi, replicate 4

description:
lung_BA.2.75_4
lung_raw_count.tsv
lung_raw_norm.tsv


title: CR-A-G-1-1

description: Library name: CR-A-G-1-1

tag: treatment


title: K562_treated_with_ActinomycinD_U2AF1_CUTnRUN_1_(20240401_WW1049_240315)

description:
Library name: K562_treated_with_ActinomycinD_U2AF1_CUTnRUN_1
CUT&RUN targeting U2AF1 in K562 in ActinomycinD


title: PH WT_Repli1


title: Synoviocyte_3

description: Library name: Syn BB 164


title: K562_treated_with_Flavopiridol_U2AF1_CUTnRUN_2_(20240401_WW1044_240315)

description:
Library name: K562_treated_with_Flavopiridol_U2AF1_CUTnRUN_2
CUT&RUN targeting U2AF1 in K562 in Flavopiridol


title: H3K27me3 WT_Repli2


title: Synoviocyte_2

description: Library name: Syn BB 163


title: hACE2 lung, BA.2.75, 5dpi, replicate 3

description:
lung_BA.2.75_3
lung_raw_count.tsv
lung_raw_norm.tsv


title: K562_treated_with_Flavopiridol_U2AF1_CUTnRUN_1_(20240401_WW1043_240315)

description:
Library name: K562_treated_with_Flavopiridol_U2AF1_CUTnRUN_1
CUT&RUN targeting U2AF1 in K562 in Flavopiridol


title: H3K27me3 WT_Repli1


title: K562_treated_with_Triptolide_U2AF1_CUTnRUN_2_(20240401_WW1038_240315)

description:
Library name: K562_treated_with_Triptolide_U2AF1_CUTnRUN_2
CUT&RUN targeting U2AF1 in K562 in Triptolide


title: Synoviocyte_1

description: Library name: Syn BB 162


title: hACE2 lung, BA.2.75, 5dpi, replicate 1

description:
lung_BA.2.75_1
lung_raw_count.tsv
lung_raw_norm.tsv


title: Chondrocyte_5

description: Library name: Chond BB 218

source_name: Chondrocyte

value: Chondrocyte


title: PH TSSUP_Repli1


title: PH TSSUP_Repli2


title: hACE2 lung, Delta, 5dpi, replicate 4

description:
lung_Delta_4
lung_raw_count.tsv
lung_raw_norm.tsv


title: Chondrocyte_4

description: Library name: Chond BB 216


title: K562_treated_with_DMSO_U2AF1_CUTnRUN_2_(20240401_WW1032_240315)

description:
Library name: K562_treated_with_DMSO_U2AF1_CUTnRUN_2
CUT&RUN targeting U2AF1 in K562 in DMSO


title: H3K27me3 TSSUP_Repli2


title: hACE2 lung, Delta, 5dpi, replicate 3

description:
lung_Delta_3
lung_raw_count.tsv
lung_raw_norm.tsv


title: K562_treated_with_DMSO_U2AF1_CUTnRUN_1_(20240401_WW1031_240315)

description:
Library name: K562_treated_with_DMSO_U2AF1_CUTnRUN_1
CUT&RUN targeting U2AF1 in K562 in DMSO


title: Chondrocyte_3

description: Library name: Chond BB 214


title: H3K27me3 TSSUP_Repli1


title: Chondrocyte_2

description: Library name: Chond BB 193


title: K562_treated_with_ActinomycinD_SF3B1_CUTnRUN_2_(20240401_WW1048_240315)

description:
Library name: K562_treated_with_ActinomycinD_SF3B1_CUTnRUN_2
CUT&RUN targeting SF3B1 in K562 in ActinomycinD

value: Cell Signaling Technology, 14434S


title: hACE2 lung, BA.2.75, 5dpi, replicate 2

description:
lung_BA.2.75_2
lung_raw_count.tsv
lung_raw_norm.tsv


title: hACE2 lung, Delta, 5dpi, replicate 1

description:
lung_Delta_1
lung_raw_count.tsv
lung_raw_norm.tsv


title: PH end3_Repli2


title: Chondrocyte_1

description: Library name: Chond BB 140


title: PH end3_Repli1


title: HT144 miR-581_3

description:
HT144 cells treated with miR-581 mimics replicate 3
SAMPLE 13

source_name: Human melanoma cell line, treated with miR-581 mimics

tag: cell line

value: HT144 cell line


title: hACE2 lung, mock, 5dpi, replicate 5

description:
lung_mock_5
lung_raw_count.tsv
lung_raw_norm.tsv

tag: genotype


title: hACE2 lung, Delta, 5dpi, replicate 5

description:
lung_Delta_5
lung_raw_count.tsv
lung_raw_norm.tsv


title: HT144 miR-581_2

description:
HT144 cells treated with miR-581 mimics replicate 2
SAMPLE 12


title: K562_treated_with_Triptolide_U2AF1_CUTnRUN_1_(20240401_WW1037_240315)

description:
Library name: K562_treated_with_Triptolide_U2AF1_CUTnRUN_1
CUT&RUN targeting U2AF1 in K562 in Triptolide


title: H3K27me3 end3_Repli2


title: hACE2 lung, mock, 5dpi, replicate 4

description:
lung_mock_4
lung_raw_count.tsv
lung_raw_norm.tsv


title: H3K27me3 end3_Repli1


title: K562_treated_with_Flavopiridol_SF3B1_CUTnRUN_2_(20240401_WW1042_240315)

description:
Library name: K562_treated_with_Flavopiridol_SF3B1_CUTnRUN_2
CUT&RUN targeting SF3B1 in K562 in Flavopiridol


title: hACE2 lung, mock, 5dpi, replicate 3

description:
lung_mock_3
lung_raw_count.tsv
lung_raw_norm.tsv


title: K562_treated_with_Flavopiridol_SF3B1_CUTnRUN_1_(20240401_WW1041_240315)

description:
Library name: K562_treated_with_Flavopiridol_SF3B1_CUTnRUN_1
CUT&RUN targeting SF3B1 in K562 in Flavopiridol


title: HT144 miR-581_1

description:
HT144 cells treated with miR-581 mimics replicate 1
SAMPLE 11


title: K562_treated_with_Triptolide_SF3B1_CUTnRUN_2_(20240401_WW1036_240315)

description:
Library name: K562_treated_with_Triptolide_SF3B1_CUTnRUN_2
CUT&RUN targeting SF3B1 in K562 in Triptolide


title: PH end3UP_Repli2


title: hACE2 lung, mock, 5dpi, replicate 2

description:
lung_mock_2
lung_raw_count.tsv
lung_raw_norm.tsv


title: HT144 miR-NC_3

description:
HT144 cells treated with miR-NC mimics replicate 3
SAMPLE 10

source_name: Human melanoma cell line, treated with miR-NC mimics


title: K562_treated_with_Triptolide_SF3B1_CUTnRUN_1_(20240401_WW1035_240315)

description:
Library name: K562_treated_with_Triptolide_SF3B1_CUTnRUN_1
CUT&RUN targeting SF3B1 in K562 in Triptolide


title: hACE2 lung, Delta, 5dpi, replicate 2

description:
lung_Delta_2
lung_raw_count.tsv
lung_raw_norm.tsv


title: HT144 miR-NC_2

description:
HT144 cells treated with miR-NC mimics replicate 2
SAMPLE 9


title: hACE2 lung, mock, 5dpi, replicate 1

description:
lung_mock_1
lung_raw_count.tsv
lung_raw_norm.tsv


title: H3K27me3 end3UP_Repli2


title: K562_treated_with_ActinomycinD_SF3B1_CUTnRUN_1_(20240401_WW1047_240315)

description:
Library name: K562_treated_with_ActinomycinD_SF3B1_CUTnRUN_1
CUT&RUN targeting SF3B1 in K562 in ActinomycinD


title: K562_treated_with_DMSO_SF3B1_CUTnRUN_2_(20240401_WW1030_240315)

description:
Library name: K562_treated_with_DMSO_SF3B1_CUTnRUN_2
CUT&RUN targeting SF3B1 in K562 in DMSO


title: HT144 miR-NC_1

description:
HT144 cells treated with miR-NC mimics replicate 1
SAMPLE 8


title: H3K27me3 end3UP_Repli1


title: K562_treated_with_DMSO_SF3B1_CUTnRUN_1_(20240401_WW1029_240315)

description:
Library name: K562_treated_with_DMSO_SF3B1_CUTnRUN_1
CUT&RUN targeting SF3B1 in K562 in DMSO


title: K562_RNAPIIS2P_plus_RNAseA_CUTnTag_3_(20240319_WW1019_240312)

description:
Library name: K562_RNAPIIS2P_plus_RNAseA_CUTnTag_3
CUT&Tag targeting RNAPIIS2P in K562 ( RNAseA plus)


title: Single nucleus 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 2

city: St. Louis

first: Julie

state: MO

address: 4370 Duncan Avenue

department: Genetics

institute: Washington University in St. Louis

description:
Library name: Nmnat2 V98M/R232Q Single Nuc Sciatic 2
10X Genomics GemX
TH_WT_2-3mo_sc_sn_sciatic_processed.rds

data_processing:
The reads were aligned to mouse genome version GRCm38/mm10 using CellRanger 8.0.1-7.1.0 from 10X Genomics which includes intronic reads in alignment by default. For nuclei, CellBender was used for ambient RNA removal (v0.3.0), followed by QC filtering to remove nuclei with numbers of genes outside the threshold (nFeatures <500 and >7500) and high mitochondrial percentage (>1%). Doublets were removed using Scrublet (v0.2.3). For single cell, the low-quality cells were removed from down-stream analysis by filtering for number of genes over the threshold (nFeatures <500 and >7500) and high mitochondrial percentage (>10%). The single cell and single nuclei libraries were normalized by SCTransform (v2) and integrated using Harmony in Seurat (v5.1.0) in R (v2023.03.0). The CD45+ libraries were normalized using SCTransform (v2) and integrated using the IntegrateData function in Seurat (v5.1.0) in R (v2023.03.0). The dimensions were reduced using principal component analysis (PCA) and visualized using UMAP. Standard Seurat pipeline was applied throughout the analysis process.
Assembly: Mouse mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: RDS file of integrated single cell and single nucleus from WT and Nmnat2 V98M/R232Q
Supplementary files format and content: RDS file of integrated single cell immune subclusters and CD45+ FACS cells from WT and Nmnat2 V98M/R232Q

molecule: nuclear RNA

source_name: Sciatic nerve

extract_protocol:
Single Cells For single cell RNA-sequencing, sciatic nerves from 2 mice were pooled. Mice were euthanized and perfused with ice cold PBS. Nerves were collected and immediately kept on ice in DMEM with 1% FBS, RNase-In RNase inhibitor (Promega N2518), and SUPERase-In RNase Inhibitor (Invitrogen AM2696) at 1:1000 ratio. The nerves were mechanically dissociated with shears and incubated in DMEM with 1% FBS containing collagenase II (4 mg/mL; Worthington Biochemical LS004176) and Dispase II (2 mg/mL; Sigma-Aldrich D4693-1G) at 37˚C for 30 minutes with gentle shaking. The samples were pipetted up and down at 15 minutes. The cells were filtered through pre-wet 70-µm cell strainers and washed twice with buffer containing DMEM, 1% FBS, RNase-In, and SUPERase-In. Myelin was removed using Myelin Removal Beads II (Miltenyi Biotec 130-096-731) and LS columns (Miltenyi Biotec 130-042-401) per manufacturer’s manuals (Miltenyi Biotec IM0001691). Additional debris and dead cells from the single cell suspensions were excluded by immediate FACS using propidium iodide (PI). Cells were collected into PBS with 10% FBS prior to library preparation.  Single Nuclei For single nucleus RNA-sequencing, sciatic nerves from 2 mice were pooled. Mice were euthanized and perfused with ice cold PBS. The nerves were collected and immediately fresh frozen in dry ice. The nerves were mechanically dissociated with shears in cold lysis buffer containing 10mM Tris buffer, 5mM CaCl2, 3mM Mg(Ac)2, 0.05% CHAPS, 320mM sucrose, 1mM DTT, 5X EDTA-free protease inhibitor (Millipore Sigma 11873580001), RNase-In RNase inhibitor (Promega N2518), and SUPERase-In RNase Inhibitor (Invitrogen AM2696) at 1:1000 ratio in nuclease-free water. The samples were transferred into a glass Dounce homogenizer on ice and mechanically dounced with 10 loose strokes and 20 tight strokes. The samples were filtered through a pre-wet 40-µm cell strainer (Fisher Scientific MT4040) and washed twice with cold wash buffer containing PBS, 0.1% BSA, RNase-In, and SUPERase-In. After removing the supernatant, the nuclear pellet was washed with 3mL of cold wash buffer. The samples were further purified using Anti-Nucleus MicroBeads (Miltenyi Biotec 130-132-997) per manufacturer’s manuals.  CD45+ Single Cells For CD45+ scRNA-seq, sciatic nerves from 5-9 mice were pooled per genotype for one replicate. The samples were processed using the same procedure described above until the myelin removal step. After myelin removal, cells were incubated in CD45+ antibody (Invitrogen MCD4528; 1:250) for 20 minutes and FAC sorted using highly modified Beckman Coulter MoFlo at the Siteman Flow Cytometry core at Siteman Cancer Center. Additional debris and dead cells from the single cell suspensions were excluded during FAC sorting using propidium iodide (PI) as well. Cells were collected into PBS with 10% FBS prior to library preparation.
Single Cells (All and CD45+) The purified single cells were used to prepare scRNA-seq libraries following the 10X Genomics manufacturer’s manuals at the Genome Technology Access Center (GTAC) @ McDonnell Genome Institute (MGI) using 10X Genomics v3.1 chemistry.  Single Nuclei The purified single nuclei were used to prepare scRNA-seq libraries following the 10X Genomics manufacturer’s manuals at the Genome Technology Access Center (GTAC) @ McDonnell Genome Institute (MGI) using 10x Genomics GEM-X v3.4 chemistry.  All libraries were sequenced using Illumina NovaSeq 6000/X accordingly to the manufacturer’s manuals at the GTAC @ MGI at Washington University in St. Louis.

value: Sciatic nerve

value: Nerve cells


title: Double_H3K27me3_Disc2


title: Single nucleus 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 1

description:
Library name: Nmnat2 V98M/R232Q Single Nuc Sciatic 1
10X Genomics GemX
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: K562_RNAPIIS2P_plus_RNAseA_CUTnTag_2_(20240319_WW1018_240312)

description:
Library name: K562_RNAPIIS2P_plus_RNAseA_CUTnTag_2
CUT&Tag targeting RNAPIIS2P in K562 ( RNAseA plus)


title: K562_RNAPIIS2P_plus_RNAseA_CUTnTag_1_(20240319_WW1017_240312)

description:
Library name: K562_RNAPIIS2P_plus_RNAseA_CUTnTag_1
CUT&Tag targeting RNAPIIS2P in K562 ( RNAseA plus)


title: Double_H3K27me3_Disc1


title: Single cell 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 4

description:
Library name: Nmnat2 V98M/R232Q Single Cell Sciatic 4
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: ADMSCsAd-Exo-C

city: Tongliao

first: Cong

last: Ma

address: 1742 East Section of Huolinhe Street

department: Dermatology

institute: The Affiliated Hospital of Inner Mongolia University for the Nationalities

description: miRNA

hyb_protocol: Cover the slides with the SureHyb chamber cover, secure with the clamp assembly, and tighten by hand. Wet the gasket and check for bubble mobility. Place the chamber in a rotisserie in a hybridization oven set to 55°C with a rotation speed of 20 rpm for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Gene Expression Wash Buffer Kit (Agilent p/n 5188-5327), and using one color scan setting for Agilent Microarray Scanner (Agilent p/n G2505C) (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ADMSCsAd-Exo-C

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 0.5 ug RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions. Resuspend dried miRNA samples in 18 μL nuclease-free water, then add 4.5 μL 10× Gene Expression Blocking Agent and 2×Hi-RPM Hybridization Buffer. Incubate at 100°C for 5 minutes, then place on ice for 5 minutes to prevent further reaction.

growth_protocol: Liposuction-derived adipose tissue was digested with 0.2% collagenase I. The resulting ADMSCs were suspended in DMEM/F-12 with 10% FBS and 1% penicillin-streptomycin and seeded in T25 flasks. Cultured at 37°C in 5% CO2, media were changed every 2-3 days, and morphology was checked on day 3.

extract_protocol: Exosomes were isolated from serum-free culture medium at 4°C through multiple centrifugations. RNA was prepared using the TRIzol® Reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: ADMSCs were cultured in adipogenic differentiation medium with periodic medium replacement. The adipogenic differentiation medium comprised high-glucose Dulbecco’s Modified Eagle Medium, supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 0.5 mM IBMX, 200 μM indomethacin, 10 μg/ml insulin, and 1 μM dexamethasone.

value: Adipose


title: WT_H3K27me3_Disc2

value: larval imaginal leg discs


title: Single cell 2-3-month Nmnat2 V98M/R232Q sciatic nerves rep 3

description:
Library name: Nmnat2 V98M/R232Q Single Cell Sciatic 3
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: K562_RNAPIIS2P_Minus_RNAseA_CUTnTag_3_(20240319_WW1013_240312)

description:
Library name: K562_RNAPIIS2P_Minus_RNAseA_CUTnTag_3
CUT&Tag targeting RNAPIIS2P in K562 ( RNAseA minus)


title: K562_RNAPIIS2P_Minus_RNAseA_CUTnTag_2_(20240319_WW1012_240312)

description:
Library name: K562_RNAPIIS2P_Minus_RNAseA_CUTnTag_2
CUT&Tag targeting RNAPIIS2P in K562 ( RNAseA minus)


title: Double_H3K27me3_Embryo2


title: PH end3UP_Repli1


title: WT_H3K27me3_Disc1


title: Single nucleus 2-3-month WT sciatic nerves rep 2

description:
Library name: WT Single Nuc Sciatic 2
10X Genomics GemX
TH_WT_2-3mo_sc_sn_sciatic_processed.rds

value: WT


title: mng_bap1_35

type: genomic

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

source_name: MNG BAP1

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

value: Female

tag: disease state

tag: outcome


title: Single nucleus 2-3-month WT sciatic nerves rep 1

description:
Library name: WT Single Nuc Sciatic 1
10X Genomics GemX
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: ADMSCs-Exo-2

description: miRNA


title: K562_SRSF3_CUTnRUN_2_(20241016_WW1250_241007)

description:
Library name: K562_SRSF3_CUTnRUN_2
CUT&RUN targeting SRSF3  in K562

value: MBL International, RN080PW


title: Single cell 2-3-month WT sciatic nerves rep 3

description:
Library name: WT Single Cell Sciatic 3
10X Genomics
TH_WT_2-3mo_sc_sn_sciatic_processed.rds


title: WT_H3K27me3_Embryo2


title: K562_RNAPIIS2P_Minus_RNAseA_CUTnTag_1_(20240319_WW1011_240312)

description:
Library name: K562_RNAPIIS2P_Minus_RNAseA_CUTnTag_1
CUT&Tag targeting RNAPIIS2P in K562 ( RNAseA minus)


title: Double_H3K27me3_Embryo1


title: mng_bap1_29

tag: Sex


title: K562_SRSF3_CUTnRUN_1_(20240319_WW990_240308)

description:
Library name: K562_SRSF3_CUTnRUN_1
CUT&RUN targeting SRSF3  in K562


title: ADMSCsAd-Exo-A

description: miRNA

source_name: ADMSCsAd-Exo-A


title: WT_H3K27me3_Embryo1


title: ADMSCsAd-Exo-B

description: miRNA

source_name: ADMSCsAd-Exo-B


title: ADMSCs-Exo-1

description: miRNA


title: ADMSCs-Exo-3

description: miRNA


title: mng_bap1_14

value: progressive

value: dead


title: TAK1_KO2

city: Hong Kong

first: Jing

last: Zhang

address: 11 Yuk Choi Rd, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.

country: Hong Kong

institute: The Hong Kong Polytechnic University

description: Library name: TAK1_KO2

data_processing:
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
Assembly: mm10
Supplementary files format and content: FPKM values for each sample

source_name: retina

extract_protocol:
200 cells per sample were sorted in 3ul cell lysis buffer (final concentration: 2.5mM dNTP, 1U/ul RNase Inhibitor, 0.1% Triton X-100) and frozen immediately on dry ice after isolation. The reaction system is configured for reverse transcription. First-strand cDNA is synthesized with SMART-SeqII. The reaction system is configured for PCR amplification to process preamplification of cDNAs.
Qualified amplified cDNAs use transposon-based method for further library construction. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.

treatment_protocol: Adult Cx3cr1CreER/+;Tak1fl/fl mice were treated with tamoxifen (TAK1_KO) or vehicle (CON). The microglia were collected by FACS using EYFP labeling.

value: retina

value: microglia

value: 5-day consecutive intraperitoneal tamoxifen injection (75mg/kg)


title: TAK1_KO1

description: Library name: TAK1_KO1


title: mng_bap1_08

value: Male


title: IgG_Embryo_Repli2

value: Wild type


title: CON2

description: Library name: CON2

value: 5-day consecutive intraperitoneal corn-oil injection


title: IgG_Embryo_Repli1


title: K562_SRSF1_CUTnRUN_1_(20240319_WW989_240308)

description:
Library name: K562_SRSF1_CUTnRUN_1
CUT&RUN targeting SRSF1  in K562

value: Fortis Life Sciences,  #A302-052A


title: CON1

description: Library name: CON1


title: mng_bap1_34

value: alive