title: shATRX HFFs, AD169 (0.1), 3h, Rep 2

city: Madison

first: Robert

last: Kalejta

state: Wisconsin

address: 1525 Linden Dr

department: IMV

institute: University of Wisconsin-Madison

description: 2x150bp shared seq

data_processing:
Reads were aligned using the PEPATAC pipeline. Briefly, read quality was assessed with FastQC, and reads were trimmed to remove adapters with CutAdapt. Trimmed reads were aligned with Bowtie2 first to the mitochondrial genome, and unaligned reads were rerun with Bowtie2 to the combined hg38 and AD169 genomes. Deduplicated and high-quality aligned reads were then used to call peaks using MACS2. Differential peak analysis was performed using DEseq2. Coverage maps were generated using DeepTools bamCoverage.
Assembly: hg38 and a modified AD169 genome (GenBank: FJ527563.1)
Supplementary files format and content: Coverage maps were generated using DeepTools bamCoverage and are provided as bigwig files

source_name: HFF

growth_protocol: TERT-immortalized human foreskin fibroblasts were maintained in Dulbecco’s modified Eagle medium (DMEM; Gibco). Medium was supplemented with 10% fetal bovine serum (FBS; GeminiBio), 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2 mM l-glutamine (PSG; Sigma).

extract_protocol:
Cells were harvested at 3 hours post infection and extracted using the Zymo-Seq ATAC Library Kit (D5458; Zymo).
ATAC libraries were generated using Zymo-Seq ATAC Library Kit (D5458; Zymo).

treatment_protocol: Cells were grown to superconfluency and given fresh media 24hrs before infection. Cells were then incubated with HCMV-AD169 at an MOI of 0.1 in a small volume for 1 hr at 4 °C, then moved to 37°C for 15 min to allow for synchronized viral entry. Viral inoculum was removed, and medium was replaced to normal volume.

value: HFF

value: Human foreskin fibroblasts

value: shATRX


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep3

status: Public on Aug 28 2024

type: SRA

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

country: USA

institute: US EPA

description:
T2VAb2
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

library_source: transcriptomic

data_processing:
Library pools were quality-checked and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core.
Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit.
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
The zebrafish reference genome (GRCz11; RefSeq GCF_000002035.6) was indexed with STAR v2.7.10a. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 12 --sjdbOverhang 149.
After performing quality control on the raw FASTQ data using FastQC v0.11.9 and MultiQC v1.14, unique molecular indices were extracted from raw read 1 via fastp v0.23.2. Raw reads were additionally processed by fastp to perform PCR deduplication, read quality and length filtering (to retain reads >= 15 bp, with phred quality >=Q15, number of N bases =< 5, and <= 40% of unqualified bases), trimming of polyG tails, and trimming of Illumina adapters. The following command was used to perform all of the raw read processing steps: fastp -i [read1] -I [read2] -o Trimmed/[read1_trimmed] -O Trimmed/[read2_trimmed] --umi --umi_loc=read1 --umi_len=12 --dedup --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT .
Trimmed reads were then mapped and counted with STAR v2.7.10a to the indexed genome using the following sample specific parameters: --outSAMattributes NH HI AS NM MD --genomeDir [genome_index_build] --readFilesIn Trimmed/[read1_trimmed] Trimmed/[read2_trimmed] --outFileNamePrefix [sampleID]_ --readFilesCommand zcat --quantMode GeneCounts TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMheaderHD @HD VN:1.4 SO:sorted --outFilterType BySJout .
FastQC v0.11.9 and MultiQC v1.14 were used to assess the qualtiy control metrics of the processed reads.
Counts to each gene were parsed, and raw count data for each exposure condition (i.e., each chemical/control treatment by time code combination) written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Quality control screening and filter steps were applied to each raw count matrix (except for the transcription positive control and standard RNA pool matrices) using the R statistical computing software. Samples were first screened to see if any exhibited total counts < 2 million, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out. Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Principal Component Analysis (PCA) plots were generated to look for possible outliers.
Assembly: GRCz11 (RefSeq GCF_000002035.6; NCBI Annotation Release 106)

molecule: total RNA

organism: Danio rerio

source_name: whole body zebrafish embyro

growth_protocol: Adult zebrafish (AB wild type strain) were housed in an onsite culture facility at the US Environmental Protection Agency (USEPA) laboratory in Duluth, MN. The fish were raised in a flow-through system with control UV-treated, filtered Lake Superior water (LSW) at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8-hour light/dark photoperiod cycle. Fish were housed in 5.5-gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp (Artemia) nauplii twice daily. The night prior, breeding zebrafish in groups of four males x six females were separated into breeding tanks containing a plastic screened spawning basket. The next morning, approximately two hours after the lights turned on, embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hours post fertilization (hpf), zebrafish embryos were screened under a stereo microscope, and only similarly staged embryos were sorted out for chemical exposure. All dead, malformed, and unfertilized eggs were discarded.

extract_protocol:
At the end of each PFAS, DMSO control, and Chlorpyrifos exposure period, zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol, then frozen. RNA was isolated with Ambion MagMAX-96 Total RNA Isolation kit.
Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA-Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina-compatible Lexogen CORALL RNA-Seq libraries were then prepared for RNA sequencing.

treatment_protocol: Zebrafish (Danio rerio) embryos were exposed to eight concentrations of three different per- or polyfluoroalkyl substances (PFAS), perfluorooctanesulfonic acid (PFOS; DTXSID3031864); perfluorooctanoic acid (PFOA; DTXSID8031865); and perfluorohexane sulfonate (PFHxS; DTXSID90892476) in concentration-response (0-100 uM, half-log dilutions). Embryos were exposed to each of the three PFAS over seven distinct exposure periods (6 hours post fertilization [hpf]-120 hpf; 6 hpf-48 hpf; 6 hpf-24 hpf; 24 hpf – 120 hpf; 48 hpf-120 hpf; and 96 hpf-120 hpf). Zebrafish were also exposed to 0.33% DMSO (vehicle control) and 1uM chlorpyrifos (transcription positive control).

tag: tissue

value: whole body zebrafish embyro

tag: strain

value: AB wild type

tag: age

tag: developmental stage

value: embryo

tag: biological replicate

tag: time code

tag: dose (ug/l)

tag: treatment

value: VehicleControl

tag: repeat sample

value: No


title: QKO, H3K36me2, Cut&Run, R2

city: New York City

first: Kristjan

middle: H.

last: Gretarsson

state: New York

institute: Columbia University

library_source: genomic

data_processing:
Alignment was performed using Bowtie2 v.2.2.5, with multi-aligned, duplicates, and blacklist regions removed
Bigwigs were generated using Deeptools v.3.5.1
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: Cut&Run

molecule: genomic DNA

organism: Mus musculus

source_name: mESC QKO

growth_protocol:
10T cells: Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS)
QKO mESC: mESC were cultured in Serum/LIF media: DMEM-KO, 15% FBS, 1000U/ml murine recombinant LIF, 1× nonessential amino acids, 1× GlutaMax and 0.1 mM 2-mercaptoethanol

extract_protocol:
CUT&RUN reaction: 500K cells were dispensed to individual wells of a 96-well plate, immobilized onto Concanavalin-A beads, and incubated overnight (4°C) with 0.5 µg of antibody. pAG-MNase was added and activated (2 hours @ 4°C) and CUT&RUN enriched DNA purified using Serapure beads.
Recovered DNA was quantified using PicoGreen and reactions were normalized to 5ng DNA (or entirety of the reaction if <5ng DNA was recovered) before preparing sequencing libraries (CUTANA CUT&RUN Library Prep kit; EpiCypher #14-1001)

tag: cell line

value: mESC QKO

tag: cell type

value: Mouse Embryonic Stem cell

tag: genotype

value: DNMT1, DNMT3A/B/L KO + DNMT3A-WT

tag: antibody

value: H3K36me2, EpiCypher #RD130056


title: QKO, H3K27me3, Cut&Run, R2

value: H3K27me3, EpiCypher #13-0055


title: corpus callosum, Sox8 knockout, biol rep2

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used for differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files containing counts and DESeq results

source_name: corpus callosum

extract_protocol:
Animals were sacrificed 21 days after the first tamoxifen injection and corpus callosum was dissected. RNA was prepared using Trizol (Invitrogen). Following Dnase treatment samples were cleaned up using the RNeasy Mini Kit (Quiagen).
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.

treatment_protocol: Oligodendroglial knockout of Sox-genes was induced by  injection of 10mg/ml tamoxifen for five consecutive days starting at postnatal day 60.

value: corpus callosum

value: Sox8fl/fl Plp1::CreERT2/+

value: tamoxifen injection


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep2

description:
T2VAa4
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: QKO, H3K4me3, Cut&Run, R2

value: H3K4me3, EpiCypher #13-0041


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep7

description:
T2VAf6
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: corpus callosum, control, biol rep4

value: control


title: corpus callosum, Sox8 knockout, biol rep1


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep1

description:
T2VAa1
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt


title: H82 cells, treated n3 (RNA-seq)

city: New York

first: Yingqian

middle: Ada

last: Zhan

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
Raw sequencing reads were trimmed with Trim Galore (v0.4.4)
Fastq files were mapped to the human genome (hg38) and reads counts per gene were quantified using STAR with default parameters and genecode (v28) annotation file
DEGs were identified using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file include TPM values for each sample

organism: Homo sapiens

growth_protocol: H146 and H82 cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere (5%CO2, 37C)

extract_protocol:
RNA was extracted at GENEWIZ per in house protocol
RNA libraries for RNAseq were prepared at GENEWIZ by in house protocol

treatment_protocol: Cells were treated with 100 nM of FHD-286 for 14 days. Drug was renewed every 48h.

value: SCLC

value: WT

value: 100nM FHD-286 14 days


title: whole body zebrafish embyro, VehicleControl, 6-48hpf, rep5

description:
T2VAd4
Ctrl_T2_UMI_ZF_counts_matrix.txt
PFHxS_T2_ZF_counts.filtered.+1.normFinal.txt
PFOA_T2_ZF_counts.filtered.+1.normFinal.txt
PFOS_T2_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type


title: shATRX HFFs, AD169 (0.1), 3h, Rep 1

description: 2x150bp shared seq

value: HFF

value: Human foreskin fibroblasts

value: shATRX


title: shSCR HFFs, AD169 (0.1), 3h, Rep 2

description: 2x150bp shared seq

value: shScr


title: corpus callosum, control, biol rep3


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep16

description:
T1VBh8
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: embryo

value: VehicleControl

value: No


title: QKO, H2AK119Ub, Cut&Run, R1

value: mESC QKO

value: Mouse Embryonic Stem cell

value: DNMT1, DNMT3A/B/L KO + DNMT3A-WT


title: shSCR HFFs, AD169 (0.1), 3h, Rep 1

description: 2x150bp shared seq


title: QKO, IgG, Cut&Run, R2

value: IgG, EpiCypher #13-0042


title: corpus callosum, control, biol rep1

value: corpus callosum

value: control


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep14

description:
T1VBf6
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: H82 cells, treated n2 (RNA-seq)

value: SCLC

value: WT


title: QKO, H3K36me2, Cut&Run, R1

value: H3K36me2, EpiCypher #RD130056


title: H82 cells, treated n1 (RNA-seq)

value: 100nM FHD-286 14 days


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep13

description:
T1VBe5
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type


title: H82 cells, untreated n3 (RNA-seq)


title: QKO, H3K27me3, Cut&Run, R1

value: H3K27me3, EpiCypher #13-0055


title: QKO, H3K4me3, Cut&Run, R1

value: H3K4me3, EpiCypher #13-0041


title: H82 cells, untreated n2 (RNA-seq)


title: QKO, IgG, Cut&Run, R1


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep12

description:
T1VBd4
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: embryo


title: AE3

city: Hefei

first: Mengyao Wang

middle: Mengyao

last: Wang

state: None Selected

address: Hefei University of Technology

country: China

institute: hefei university of technology

data_processing:
DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted using total RNA isolation reagent according to the manufacturer's instructions. RNA purity and quantification were identified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Transcriptome libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep kit according to the manufacturer's instructions.

value: Liver

value: Lieber-Decarli ethanol liquid diet for 10 days, plus a single ethanol binge


title: AE1


title: corpus callosum, control, biol rep2


title: H146 cells, treated n3 (RNA-seq)


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep8

description:
T1VAh1
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl

value: No


title: NE1


title: H82 cells, untreated n1 (RNA-seq)


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep10

description:
T1VBb2
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: IMR32_ACBI1_24h, CTCF, ChIP

city: Bethesda

first: Zhihui

last: Liu

state: Maryland

address: 9000 rockville pike

institute: National Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30
ChIP-seq reads were aligned to the hg19 genome using bwa.
Peaks were called using MACS2 with the significance cut-off p-value ≤ 0.00001
bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.
Assembly: hg19
Supplementary files format and content: bigWig.

growth_protocol: Growth medium: RPMI-1640, 10% fetal calf serum, 100µg/mL streptomycin, 100U/mL penicillin, and L-glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to the guide of NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645).

value: Human neuroblastoma


title: IMR32_DMSO_24h, WDR5, ChIP


title: IMR32_DMSO_24h, CTCF, ChIP


title: NE3


title: H146 cells, treated n2 (RNA-seq)


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep7

description:
T1VAg2
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: RPMA replicate 3, snRNAseq

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
10x Genomics
RPMASQ233_2

library_source: transcriptomic single cell

data_processing:
For snRNA-seq data, Cell Ranger (v7.0.0) was used to demultiplex and align reads to the reference genome (mm10). Further analysis, including clustering, dimensionality reduction and differential gene expression analysis, was performed using the Seurat (V4.2.0) in R. Cells with less than 200 genes and genes expressed in less than 3 cells were removed. Cells with percentage of mitochondrial gene expression greater than 20%  were removed. Samples were integrated for clustering and cell type identification. Cell clusters were identified for the integrated data using the top 30 dimensions from the principal component analysis (PCA). Cell types were annotated manually using cell type specific marker genes. Cluster marker genes were identified using “FindAllMarkers” function in Seurat. Differential gene expression analysis between ASCL1 Mut and ASCL1 WT was done using "FindMarkers" function in Seurat with the pseudobulk method. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
For bulk RNA-seq data, adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the mouse genome (mm10) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package. Low-expressed genes (genes with the expression value of 0 in more than 30% of samples) were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were then identified using the same package. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
Assembly: mm10
Supplementary files format and content: tab delimited text files

molecule: nuclear RNA

source_name: Prostate

growth_protocol: Organoids were grown in culture in full organoid medium for 2 weeks in 3D, grown in 2D for a week and  infected with lentiviral Cre to induce Cre-recombination, and selected 48hrs after infection with puromycin/Nutlin for 2 weeks. Cells were grown in 3D for another week and grown in 2D for a week before harvesting cells for bulk RNA-sequencing and injecting subcutaneously into mice to generate tumor allografts for snRNAseq.

extract_protocol:
For bulk RNA sequencing, cells were harvested by centrifugation and resuspended in Trizol. RNA was isolated with Arcturus Picopure RNA isolation kit or Direct-zol RNA Microprep. For snRNAseq, tumors were harvested and either snapfrozen or embedded in OCT for cryosectioning. For snap-frozen tumors, nuclei were isolated with manual homogenization with Dounce homogenizer. For cryo-sectioned tumors, nuclei of cryosectioned scrolls were isolated with the Singulator.
For RNA-seq, library was constructed with NextSeq 500/550 High Output kit v2.5 (75 cycles) (Illumina #20024906)
For snRNA-seq, library was constructed according to manufacturer's instructions (10x Genomics 3' Gene Expression) with a barcode plate Dual Index Kit TT Set A

value: Prostate

value: RPMA

value: tumor

value: Lentiviral Cre infection


title: IMR32_ACBI1_24h, WDR5, ChIP


title: IMR32_ACBI1_24h, RAD21, ChIP


title: H146 cells, treated n4 (RNA-seq)

value: SCLC

value: WT


title: IMR32_DMSO_24h, RAD21, ChIP


title: H146 cells, treated n1 (RNA-seq)

value: 100nM FHD-286 14 days


title: RPMA replicate 2, snRNAseq

description:
10x Genomics
RPMASQ2


title: RPMA replicate 1, snRNAseq

description:
10x Genomics
RPMASQ1


title: H146 cells, untreated n3 (RNA-seq)


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep5

description:
T1VAe5
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro


title: SJNBL012407_X1 cells, ACBI1_250nM, 4d, rep3 [RNA-seq]

description: SJNBL012407_X1_SCM-vs-DMSO-vs-ACBI1_RawCounts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include CPM values for each Sample.

molecule: polyA RNA

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ACBI1_250nM, 4d


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep6

description:
T1VAf6
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: AB wild type


title: AE2


title: H146 cells, untreated n2 (RNA-seq)


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep15

description:
T1VBg7
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep11

description:
T1VBc3
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: NE2


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep9

description:
T1VAh8
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep4

description:
T1VAd7
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt


title: RPM replicate 3, snRNAseq

description:
10x Genomics
RPMTdGSQ228_2

value: RPM


title: SJNBL012407_X1 cells, ACBI1_250nM, 4d, rep2 [RNA-seq]


title: RPM replicate 2, snRNAseq

description:
10x Genomics
RPMTdGSQ224_1


title: SJNBL012407_X1 cells, ACBI1_250nM, 4d, rep1 [RNA-seq]


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep2

description:
T1VAc1
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: embryo


title: SJNBL012407_X1 cells, DMSO, 4d, rep2 [RNA-seq]

value: DMSO, 4d


title: pool of Lx95, Lx276, Lx761c and Lx891, Input

data_processing:
Raw sequencing reads were trimmed with Trim Galore (v0.4.4). Reads were aligned to human assembly hg38 using bowtie2 v2.3.4 with the default settings
Enriched binding regions were called against the input using MACS2 with p value less than 0.001. The bigwig format for each sample was created using the BEDTools suite (https://bedtools.readthedocs.io) with the normalization factor 10 million
ChIP density profiles were created with deeptools v3.4.0
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak (except for Input sample)

source_name: pool of PDXs

growth_protocol: Flash frozen PDXs

extract_protocol:
In house protocol (Active Motif)
In house protocol (Active Motif). ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara). Adapter sequences were not trimmed during demultiplexing

value: pool of PDXs

tag: chip antibody


title: kidney glomeruli, Col4a3 p.G799R rep5

city: Shanghai

first: shuwen

last: Yu

state: Shanghai

address: 197, Ruijin Er Road

institute: Shanghai Jiao Tong University Schoo

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low  quality bases which will affect the following assembly and analysis. Thus, to get high quality  clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the  reference genome using HISAT2. 2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a  reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression  abundance and variations, using RSEM software.
Assembly: Ensembl_release109
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: kidney glomeruli

extract_protocol:
Total RNA samples were extracted with the TRIzol reagent (Takara, #9109) according to the manufacturer’s instructions
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit (New England Biolabs, # E7530L) for Illumina.

value: kidney glomeruli

value: Col4a3 p.G799R


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep1

description:
T1VAb4
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: VehicleControl

value: No


title: Lx891, SMARCA4, ChIP

source_name: PDX

value: PDX

value: SMARCA4 #ab110641


title: RPM replicate 1, snRNAseq

description:
10x Genomics
RPMSQ2

value: Prostate

value: tumor

value: Lentiviral Cre infection


title: SJNBL012407_X1 cells, DMSO, 4d, rep3 [RNA-seq]

value: Human neuroblastoma


title: SJNBL012407_X1 cells, DMSO, 4d, rep1 [RNA-seq]


title: kidney glomeruli, Col4a3 p.G799R rep4


title: Lx761c, SMARCA4, ChIP

value: SCLC

value: WT


title: SJNBL012407_X1 cells, SCM, rep3 [RNA-seq]

value: SCM


title: kidney glomeruli, Col4a3 p.G799R rep3


title: Lx95, SMARCA4, ChIP


title: SJNBL012407_X1 cells, SCM, rep2 [RNA-seq]


title: skinagetscha_S6 _66years_scRNAseq

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

description: 10x genomics

data_processing:
Raw sequencing data were processed with the Cell Ranger v3.0.2 software (10X Genomics) for demultiplexing and alignment to a reference genome (GRCH38).
Assembly: alignment to a reference genome (GRCH38)
Supplementary files format and content: tab seperated values files and matrix files

source_name: epidermis

extract_protocol:
Epidermal samples were taken by the suction blister method.Subsequently epidermal sheets were enzymatically digested, using trypsin for 45 minutes at 37°C. The resulting single cell suspension was then passed through 100µm and 40µm nylon meshes and through a dead cell removal column before further processing.
Single-cell RNA-seq was performed using the 10X Genomics Chromium Single Cell Controller with the Chromium Single Cell 3′ V3 Kit following the manufacturer's instructions.  After quality control, RNA sequencing was performed by the Biomedical Sequencing Core Facility of the Center for Molecular Medicine (Center for Molecular Medicine, Vienna, Austria) on an Illumina HiSeq 3000/4000 (Illumina, San Diego, CA, USA).

value: epidermis

tag: Sex

value: female

value: wildtype

value: untreated


title: skinagetscha_S7_24years_scRNAseq

description: 10x genomics


title: kidney glomeruli, Col4a3 p.G799R rep2

value: kidney glomeruli


title: Lx276, SMARCA4, ChIP


title: kidney glomeruli, Col4a3 p.G799R rep1

value: Col4a3 p.G799R


title: skinagetscha_S5_67years_scRNAseq

description: 10x genomics


title: whole body zebrafish embyro, VehicleControl, 6-24hpf, rep3

description:
T1VAc3
Ctrl_T1_UMI_ZF_counts_matrix.txt
PFHxS_T1_ZF_counts.filtered.+1.normFinal.txt
PFOA_T1_ZF_counts.filtered.+1.normFinal.txt
PFOS_T1_ZF_counts.filtered.+1.normFinal.txt

value: whole body zebrafish embyro

value: AB wild type

value: embryo

value: VehicleControl


title: H146 cells, untreated n1 (RNA-seq)


title: H82 cells, treated n3 (ATAC-seq)

data_processing:
Raw sequencing reads were trimmed with Trim Galore (v0.4.4)
Reads were then aligned to human assembly hg38 using bowtie2 v2.3.4 with the default settings
Enriched open regions for each sample were called using MACS2 and filtered against genomic blacklisted regions
A union of Peak atlas was later built by merging the filtered peaks within 500 base pairs. Raw read counts were tabulated over this peak atlas using feature Counts v1.6.0. Differential peaks were called using DESeq2
The bigwig format for each sample was created using the BEDTools suite  with the normalization factor from DESeq2
Assembly: hg38
Supplementary files format and content: bed for the union of peaks
Supplementary files format and content: bigWig

extract_protocol:
gDNA was extracted at GENEWIZ per in house protocol
at GENEWIZ by in house protocol

value: 100nM FHD-286 14 days


title: SJNBL012407_X1 cells, SCM, rep1 [RNA-seq]


title: H82 cells, treated n2 (ATAC-seq)


title: SK-N-SH cells, ACBI1_600nM, 24h, rep3 [RNA-seq]

source_name: SK-N-SH

value: SK-N-SH


title: skinagetscha_S4_24years_scRNAseq

description: 10x genomics


title: kidney glomeruli, Col4a3 wild-type rep5

value: Col4a3 wild-type


title: H82 cells, treated n1 (ATAC-seq)


title: kidney glomeruli, Col4a3 wild-type rep4


title: SK-N-SH cells, ACBI1_600nM, 24h, rep2 [RNA-seq]

value: Human neuroblastoma


title: H82 cells, untreated n3 (ATAC-seq)

value: SCLC


title: skinagetscha_S2_71years_scRNAseq

description: 10x genomics


title: kidney glomeruli, Col4a3 wild-type rep2


title: SK-N-SH cells, DMSO, 24h, rep3 [RNA-seq]

value: DMSO, 24h


title: skinagetscha_S8_29years_scRNAseq

description: 10x genomics


title: kidney glomeruli, Col4a3 wild-type rep1


title: H82 cells, untreated n1 (ATAC-seq)

value: WT


title: WCM154-sgASCL1, m3

city: Boston

first: Sheng-Yu

last: Ku

state: MA

address: 44 Binney St, Dana Building, DA1422, MA 02215

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Differential gene expression between ASCL1 KO and sgGFP was calculated using DESeq2. Differentially expressed genes (DEGs) were selected based on the cut-off criterion (adjusted P value < 0.05 and |log2 (fold change)| > 0.58).
Protein-coding genes were pre-ranked based on log2 (fold change), and Gene Set Enrichment Analysis (GSEA) was performed using the pre-ranked gene list with 10,000 permutations
The Molecular Signatures Database (MSigDB) hallmark gene set (3) and a GO Biological Process was used for the analysis
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: prostate tumor

growth_protocol: 1x10^7 organoids were subcutaneously injected in the flank of male NSG mice. When tumor size reached to the humane endpoints, tumor was passaged to a cohort of male NSG mice.

extract_protocol:
Total RNA was extracted from snap frozen tumors using Qiagen RNeasy Plus Universal mini kit
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions

treatment_protocol: ASCL1 knockout was generated in organoids in vitro, and then subcutaneously inoculated in male NSG mice.

value: prostate tumor

value: WCM154 NEPC organoid line

value: ASCL1 knockout


title: skinagetscha_S3_70years_scRNAseq

description: 10x genomics

value: epidermis

value: female

value: wildtype

value: untreated


title: SK-N-SH cells, DMSO, 24h, rep2 [RNA-seq]


title: anti-BAFF antibody-treated_DI10

city: Greenville

first: Akshaya

middle: K

last: Meher

address: 600 N. Moye Blvd.

institute: East Carolina University

data_processing:
Performed by SingulOmics Corporation, Bronx, NY
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts of each samples

source_name: SVF of gonadal white adipose tissue

treatment_protocol: Mice were treated with a control antibody or anti-BAFF antibody

value: SVF of gonadal white adipose tissue

value: male

value: anti-BAFF antibody-treated


title: SK-N-SH cells, DMSO, 24h, rep1 [RNA-seq]


title: H146 cells, treated n3 (ATAC-seq)

value: 100nM FHD-286 14 days


title: WCM154-sgASCL1, m1


title: WCM154-sgASCL1, m2


title: H146 cells, treated n2 (ATAC-seq)


title: skinagetscha_S1_29years_scRNAseq

description: 10x genomics


title: IMR32 cells, ACBI1_200nM, 24h, rep3 [RNA-seq]


title: H146 cells, treated n1 (ATAC-seq)


title: control antibody-treated_DI9

extract_protocol: Performed by SingulOmics Corporation, Bronx, NY

value: control antibody-treated


title: WCM154-sgGFP, m3


title: IMR32 cells, ACBI1_200nM, 24h, rep2 [RNA-seq]


title: anti-BAFF antibody-treated_DI8


title: SK-N-SH cells, ACBI1_600nM, 24h, rep1 [RNA-seq]

value: SK-N-SH


title: H82 cells, untreated n2 (ATAC-seq)


title: H146 cells, untreated n4 (ATAC-seq)


title: IMR32 cells, ACBI1_200nM, 24h, rep1 [RNA-seq]

value: Human neuroblastoma


title: WCM154-sgGFP, m1


title: H146 cells, untreated n3 (ATAC-seq)

value: SCLC


title: WCM154-sgGFP, m2


title: control antibody-treated_DI6


title: IMR32 cells, DMSO, 24h, rep3 [RNA-seq]

value: DMSO, 24h


title: H146 cells, untreated n2 (ATAC-seq)

value: WT


title: anti-BAFF antibody-treated_DI7


title: mESC_E14_shSox2_rep2

city: Shenzhen

first: Linlin

last: Hou

state: Guangdong

address: No. 66, Gongchang Road, Guangming District

institute: School of Medicine, Sun Yat-Sen University

data_processing:
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
The paired-end reads were aligned to the Mus musculus genome (GENCODE, GRCm38/mm10 vM23) using the STAR algorithm (Ver. 2.7.9a).
The featureCounts (Ver. 2.0.1) was used for the quantification of gene expression using mapped reads.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Cells were used to extract the total RNA using the Total RNA Extraction Kit (Omega).
Oligo (dT)-attached magnetic beads were used to purified mRNA. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and paired end 150 bases reads were generated on MGISEQ-2000 platform (BGI-Shenzhen, China).

value: mouse embryonic stem cells

value: Sox2 knockdown


title: kidney glomeruli, Col4a3 wild-type rep3

value: kidney glomeruli

value: Col4a3 wild-type


title: control antibody-treated_DI2


title: H146 cells, untreated n1 (ATAC-seq)


title: IMR32 cells, DMSO, 24h, rep2 [RNA-seq]


title: mESC_E14_shSox2_rep1


title: mESC_E14_shHnrnpk_rep2

value: Hnrnpk knockdown


title: Y79,Scramble,CUT&TAG,rep3

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

data_processing:
RNA sequencing data were mapped to the GRCh38 reference genome using the STAR aligner, and quantified using featureCounts
CUT&Tag data were also mapped to the GRCh38 genome using Chromap, with peak calling performed using MACS2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596026). Take 1 µg of total RNA and perform a reverse transcription experiment using HiScript III RT SuperMix for qPCR (Vazyme, R323-01) to obtain cDNA.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-seq library prep kit following manufacturer's protocols.  The Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, TD903) was used for CUT&Tag analysis.

value: Scramble


title: control antibody-treated_DI1


title: anti-BAFF antibody-treated_DI5


title: Y79,Scramble,CUT&TAG,rep1


title: IMR32 cells, DMSO, 24h, rep1 [RNA-seq]


title: IMR5 cells, siSMARCA4-7, 48h, rep2 [RNA-seq]

value: siSMARCA4-7, 48h


title: IMR5 cells, siSMARCA4-7, 48h, rep3 [RNA-seq]


title: mESC QKO, DNMT3A1-Ubmutant, Emseq, R2

data_processing:
Raw reads were filtered with trim galore (--paired) and aligned to the mouse genome (GRCm39) using Bismark with the functions bismark and bismark_methylation_extractor(--no_overlap --ignore 3 --ignore_r2 2 --ignore_3prime 2 --ignore_3prime_r2 2) to generate bismark CpG coverage files
Assembly: GRCm39
Supplementary files format and content: bismark CpG coverage file
Library strategy: EnzymaticMethyl-seq

growth_protocol: QKO mESC were cultured in Serum/LIF media: DMEM-KO, 15% FBS, 1000U/ml murine recombinant LIF, 1× nonessential amino acids, 1× GlutaMax and 0.1 mM 2-mercaptoethanol

extract_protocol:
Genomic DNA was purified using the NEB Monarch Genomic DNA Extraction kit and 10 ng sheared to an average fragment size of ~300 bp for enzymatic conversion. Prior to sonication, fully 5mC methylated pUC19 (0.01 ng) and fully unmethylated lambda DNA (0.02 ng) were spiked into each reaction to monitor conversion efficiency.
After nine cycles of PCR, library quality and quantification were assessed on the Agilent Tapestation 4200. Libraries were sequenced on an Illumina NovaSeq 6000 to generate 100-bp paired-end reads.

value: mESC QKO

value: Mouse Embryonic Stem cell

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-Ubmutant


title: Y79,Mock,CUT&TAG,rep2

value: Mock


title: mESC QKO, DNMT3A1-Ubmutant, Emseq, R1


title: IMR5 cells, siSMARCA4-7, 48h, rep1 [RNA-seq]


title: Y79,Mock,CUT&TAG,rep1


title: mESC_E14_shHnrnpk_rep1


title: Y79,IgG,CUT&Tag,rep1

value: IgG


title: mESC QKO, DNMT3A1-R181E, Emseq, R2

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-R181E


title: mESC_E14_shCdk9_rep2

value: Cdk9 knockdown


title: mESC_E14_NG_rep2

value: negative control


title: IMR5 cells, siSMARCA4-5, 48h, rep2 [RNA-seq]

value: Human neuroblastoma

value: siSMARCA4-5, 48h


title: mESC_E14_NG_rep1

value: mouse embryonic stem cells


title: Y79,Scramble,RNA-seq,rep3

data_processing:
RNA sequencing data were mapped to the GRCh38 reference genome using the STAR aligner, and quantified using featureCounts
CUT&Tag data were also mapped to the GRCh38 genome using Chromap, with peak calling performed using MACS2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: BigWig


title: mESC QKO, DNMT3A1-R181E, Emseq, R1


title: mESC QKO, DNMT3A1-W330R, Emseq, R2

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-W330R


title: dpi7_HGPS_rep3

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

data_processing:
To analyze the transcriptome changes, raw reads were first trimmed to remove the adapter contamination, and then aligned to the mouse mm10 genome reference using STAR (2.7.10a) with default settings.
FeatureCounts (2.0.1) was used for read assignment with the following parameters, -T 5 -g gene_name -p. DEseq2 was used for data normalization, differential expression analysis, and data visualization.
Genes with P-value <0.05 and log2(fold change) >1 were considered as differentially expressed genes and used for GO analysis.
Time-series analysis was done using Mfuzz package in R (3.18)  with detectable genes (more than 10 reads were assigned from all the samples).
Assembly: mm10
Supplementary files format and content: normalized read count using Deseq2 in csv format

source_name: lung

extract_protocol:
RNA was isolated from homogenized lung tissue using TRizol with standard protocol
For polyA based mRNA-seq, 1 μg total RNAs were used for library construction. mRNA was enriched and purified using Library Preparation VAHTSTM mRNA Capture Beads (Vazyme, NR401-01). Next, purified mRNAs were fragmented, followed by cDNA synthesis, second-strand synthesis, end repair, adaptor ligation and amplification using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-01) and VAHTS DNA Clean Beads.
Libraries were sequenced for on average 20 million pair-end reads.

treatment_protocol: Male Balb/c mice with different genetic backgrounds (hACE2 and hACE2 plus Lmna c. 1827C<T) and different ages (2 months ago for young and HGPS hACE2 mice, more than 14 months ago for aged hACE2 mice) were treated with tribromoethanol (Avertin, 250mg/kg) and intranasally infected with 1 x 105 TCID50 SARS-CoV-2 in 50 μL DMEM per mouse

value: lung

value: mix cell types from lung

value: infected by SARS-CoV-2

value: male

tag: strain background

value: Balb/c


title: IMR5 cells, siSMARCA4-5, 48h, rep1 [RNA-seq]


title: mESC QKO, DNMT3A1-W330R, Emseq, R1

value: mESC QKO


title: dpi7_HGPS_rep2


title: IMR5 cells, siCtrl, 48h, rep2 [RNA-seq]

value: siCtrl, 48h


title: Y79,Scramble,RNA-seq,rep1

value: Scramble


title: IMR5 cells, siCtrl, 48h, rep3 [RNA-seq]


title: mESC QKO, DNMT3A1-WT, Emseq, R2

value: Mouse Embryonic Stem cell

value: DNMT1, DNMT3A/B/L KO +DNMT3A1-WT


title: dpi7_HGPS_rep1


title: IMR5 cells, siCtrl, 48h, rep1 [RNA-seq]


title: Y79,Mock,RNA-seq,rep2

value: Mock


title: mESC_E14_shCdk9_rep1

value: Cdk9 knockdown


title: dpi7_Aged_rep2


title: Y79,Mock,RNA-seq,rep1


title: IMR5 cells, ACBI1_200nM, 24h, rep3 [RNA-seq]


title: IMR5 cells, siSMARCA4-5, 48h, rep3 [RNA-seq]


title: mESC QKO, DNMT3A1-WT, Emseq, R1


title: dpi7_Aged_rep3


title: IMR5 cells, ACBI1_200nM, 24h, rep2 [RNA-seq]


title: mESC QKO,Emseq, R1

value: DNMT1, DNMT3A/B/L KO


title: EN Organoid, DNMT3A1-W330R-R181E, RRBS, R2

data_processing:
Raw reads were filtered with trim galore (--rrbs --paired) and aligned to the mouse genome (GRCm39) using Bismark with the functions bismark and bismark_methylation_extractor(--no_overlap --ignore 3 --ignore_r2 2 --ignore_3prime 2 --ignore_3prime_r2 2) to generate bismark CpG coverage files
Assembly: GRCm39
Supplementary files format and content: bismark CpG coverage file

source_name: EN Organoid

growth_protocol:
10T cells: Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS)
TKO mESC: mESC were cultured in Serum/LIF media: DMEM-KO, 15% FBS, 1000U/ml murine recombinant LIF, 1× nonessential amino acids, 1× GlutaMax and 0.1 mM 2-mercaptoethanol
Organoids: See Methods (Organoid Culture Isolation and propagation)

extract_protocol:
Genomic DNA (1ug) was collected using DNeasy Blood & Tissue Kit
RRBS samples were prepared by CD Genomics for library preparation and sequencing
RRBS samples for Esophogus DNMT3A expression organoids were prepared by The Epigenomics Core Facility of Weill Cornell Medicine for library preparation and sequencing

value: EN Organoid

value: Esophogus Organoid


title: dpi7_Young_rep2


title: scRNA-seq_hmSpVO_D62

first: Jinkui

last: Zhu

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

description: 10X Genomics

data_processing:
To obtain count matrices, reads were aligned to human genome GRCh38(v 3.0.0, provided by 10X genomics) using Cell Ranger (v 6.1.2) with the default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoids

extract_protocol:
For single cell RNA sequencing, hdMOs from early stage group (day 30) and late stage group (day 62) were collected and dissociated into single cells. Briefly, media was removed on a centrifuge machine at 500g for 5 min and then 1 ml dispase was added, the organoids were lightly cut with a scissor, digested in metal bath at 37℃ for 30min. The suspension was centrifuged at 500g for 5min to remove supernatant and 1ml trypsin was added to continue digesting at 37 degrees for 15-30min. After completely digested, cells were passed through a 40um sieve and washed with DPBS+10% BSA 2-3 times for further experiments.For the quality control and counting of single cell suspension, the cell survival rate is generally above 80%.
Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library V3) as described in the manufacturer’s protocol. GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. Then the GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined and was sequenced on the Illumina Novaseq 6000 instrument using 150-base-pair paired-end reads.

value: organoids

value: human embryonic stem cells

value: WT

value: Differentiation according to protocol


title: dpi7_Aged_rep1

value: lung

value: mix cell types from lung

value: infected by SARS-CoV-2


title: EN Organoid, DNMT3A1-W330R-R181E, RRBS, R1


title: scRNA-seq_hmSpVO_D30

description: 10X Genomics


title: IMR5 cells, ACBI1_200nM, 24h, rep1 [RNA-seq]

value: Human neuroblastoma


title: IMR5 cells, DMSO, 24h, rep3 [RNA-seq]

value: DMSO, 24h


title: Y79,Scramble,RNA-seq,rep2

value: Scramble


title: EN Organoid, DNMT3A1-W330R, RRBS, R2


title: Y79,Mock,RNA-seq,rep3


title: EN Organoid, DNMT3A1-W330R, RRBS, R1


title: dpi7_Young_rep1

value: male

value: Balb/c


title: hmSpVO_rep2

description: TPM matrix (column name: hdMO_rep2) in the RSEM_gene_tpm.tsv

data_processing:
Cleaned reads were aligned to the reference genome (GRCh38) using STAR v2.7.10a and RSEM v1.3.1 was used to count the reads mapped to each gene. We achieved this through the nf-core/rnaseq pipeline v3.13.2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file includes TPM for each sample.

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit according to the manufacture's protocol. Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) was used to determine the concentration and evaluate the purity of RNA samples. Agilent 2100 Bioanalyzer and 2100 RNA nano 6000 assay kit (Agilent Technologies) were used to evaluate the integrity of RNA samples.
For samples of C3,C4,C6 and hdMO_rep1,the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and were sequenced on Illumina HiSeq X Ten platform. For samples of hdMO_rep2 and hdMO_ventr,, the mRNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN) and the libraries was constructed by TIANSeq Fast RNA Library Kit (Illumina). The libraries were sequenced on Illumina NovaSeq 6000.


title: IMR5 cells, DMSO, 24h, rep1 [RNA-seq]


title: IMR5 cells, DMSO, 24h, rep2 [RNA-seq]


title: mESC QKO,Emseq, R2

value: mESC QKO

value: Mouse Embryonic Stem cell


title: IMR5 cells, ACBI1_200nM, 8h, rep3 [RNA-seq]

value: ACBI1_200nM, 8h


title: EN Organoid, DNMT3A1-WT, RRBS, R1

value: EN Organoid


title: dpi5_HGPS_rep1


title: IMR5 cells, ACBI1_200nM, 8h, rep2 [RNA-seq]


title: dpi5_HGPS_rep2


title: ZNF750i.RNAseq_2

city: La Jolla

first: Ye

state: CA

address: 9452 Medical Center Drive, Room L1W106

department: Dermatology

institute: University of California, San Diego

data_processing:
NovaSeq S4PE100 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek FLow, version 9.0.20.0202 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 93 2020-02-03). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each sample

source_name: Human epidermal keratinocyte

growth_protocol: Keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies) with calcium.

extract_protocol:
PureLinkTMRNA mini kit (Thermo Fisher Scientific; 12183025)
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: ZNF750 siRNA knockdown

value: Human epidermal keratinocyte

value: ZNF750 Knockdown

value: PolyIC treated for 4 hours


title: ZNF750i.RNAseq_1


title: ZNF750i.RNAseq_3


title: hmSpVO_ventr

description: TPM matrix (column name: hdMO_ventr) in the RSEM_gene_tpm.tsv

value: organoids

value: human embryonic stem cells

value: WT


title: TKO mESC, DNMT3A  W330R-Ubmutant, RRBS

source_name: TKO mESC

value: TKO mESC

value: mouse embryonic stem cell

value: DNMT1/3A/3B KO + DNMT3A-W330R-Ubmutant


title: IMR5 cells, ACBI1_200nM, 8h, rep1 [RNA-seq]

value: Human neuroblastoma


title: CTLi.RNAseq_3


title: IMR5 cells, DMSO, 8h, rep3 [RNA-seq]

value: DMSO, 8h


title: TKO mESC, DNMT3A W330R-R181E, RRBS

value: DNMT1/3A/3B KO + DNMT3A-W330R-R181E


title: CTLi.RNAseq_2


title: TKO mESC, DNMT3A W330R, RRBS

value: DNMT1/3A/3B KO + DNMT3A-W330R


title: EN Organoid, DNMT3A1-WT, RRBS, R2

value: Esophogus Organoid


title: dpi5_Aged_rep2

value: lung

value: mix cell types from lung

value: infected by SARS-CoV-2

value: male

value: Balb/c


title: dpi5_Aged_rep1


title: TKO mESC, DNMT3A WT, RRBS

value: DNMT1/3A/3B KO + DNMT3A-WT


title: dpi5_Young_rep3


title: CTLi.RNAseq_1

value: Human epidermal keratinocyte

value: PolyIC treated for 4 hours


title: IMR5 cells, DMSO, 8h, rep2 [RNA-seq]


title: IMR5 cells, DMSO, 8h, rep1 [RNA-seq]


title: dpi5_Aged_rep3


title: dpi5_Young_rep2


title: H25 (miRNA-seq)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 101-base single-end mode.
Before analysis of the small RNA-Seq data, reads were trimmed the 3' adapter sequence (AGATCGGAAGAGCACACGTCT).
Trimmed reads were mapped on miRBase human miRNA dataset using miRDeep2 software.
Quantification was also performed with miRDeep2 software.
Supplementary files format and content: miRBase human miRNA dataset
Supplementary files format and content: tab-delimited text files include count data for each sample

source_name: peripheral blood

extract_protocol:
Total RNA isolation was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Each library was prepared using NEBNext Multiplex Small RNA Library Prep Set for illumina (New England Biolabs).

value: peripheral blood

value: peripheral blood mononuclear cells

tag: disease state

value: healthy donor


title: ESCC Organoid, RRBS, R3

source_name: ESCC Organoid

value: ESCC Organoid

value: Esophogus SCC Organoid

value: K5CreERT2 ;R26tdTomato;Trp53 KO/KO


title: IMR32_siSMARCA4-5_72h, H3K27ac, ChIP

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30
ChIP-seq reads were aligned to the hg19 genome using bwa.
Peaks were called using MACS2 with the significance cut-off p-value ≤ 0.00001
bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.
Assembly: hg19
Supplementary files format and content: bigWig.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to the guide of NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645).

value: Human neuroblastoma


title: H24 (miRNA-seq)

tag: tissue


title: ESCC Organoid, RRBS, R2


title: H22 (miRNA-seq)


title: IMR32_siCtrl_72h, H3K27ac, ChIP


title: ESCC Organoid, RRBS, R1


title: dpi5_Young_rep1


title: dpi3_HGPS_rep2


title: IMR32_siSMARCA4-5_72h, MYCN, ChIP

value: MYCN


title: H21 (miRNA-seq)


title: dpi3_HGPS_rep1


title: H20 (miRNA-seq)


title: IMR32_siCtrl_72h, MYCN, ChIP


title: EN Organoid, RRBS, R3

value: EN Organoid

value: Esophogus Organoid


title: EN Organoid, RRBS, R2


title: H19 (miRNA-seq)


title: EN Organoid, RRBS, R1


title: IMR32_siCtrl_72h, GATA3, ChIP


title: H16 (miRNA-seq)


title: 10T, DNMT3A1 W330R-UBmutant, RRBS, R2

value: mouse mesenchymal stem cell


title: dpi3_Young_rep2

value: lung

value: mix cell types from lung

value: infected by SARS-CoV-2


title: H15 (miRNA-seq)


title: 10T, DNMT3A1 W330R-R181E, RRBS, R2


title: IMR32_siCtrl_72h, PHOX2B, ChIP


title: H14 (miRNA-seq)


title: dpi3_Young_rep1

value: male

value: Balb/c


title: IMR32_siSMARCA4-5_72h, HAND2, ChIP


title: 10T, DNMT3A1 W330R, RRBS, R2


title: H11 (miRNA-seq)


title: 10T, DNMT3A1 WT, RRBS, R2


title: dpi3_Aged_rep2


title: dpi1_HGPS_rep2


title: H9 (miRNA-seq)


title: IMR32_siCtrl_72h, HAND2, ChIP


title: dpi3_Aged_rep1


title: 10T, DNMT3A1 W330R-UBmutant, RRBS, R1


title: IMR32_siSMARCA4-5_72h, input

value: No


title: dpi1_HGPS_rep1


title: IMR32_siSMARCA4-5_72h, GATA3, ChIP


title: 10T, DNMT3A1 W330R-R181E, RRBS, R1


title: dpi3_Young_rep3


title: IMR32_siCtrl_72h, input


title: IMR32_siSMARCA4-5_72h, PHOX2B, ChIP


title: 10T, DNMT3A1 W330R, RRBS, R1


title: H7 (miRNA-seq)

value: peripheral blood


title: dpi1_Aged_rep2


title: dpi1_HGPS_rep3


title: dpi1_Aged_rep3


title: H2 (miRNA-seq)

value: peripheral blood mononuclear cells


title: IMR32_ACBI1_24h, H3K27ac, ChIP


title: dpi1_Aged_rep1


title: 10T, DNMT3A1 WT, RRBS, R1


title: H1 (miRNA-seq)

value: healthy donor


title: heart tissues, H3L overexpression, replicate 3

first: Juli

address: Zhongshan 2nd road No. 106, Yuexiu District, Guangzhou, Guangdong, China

institute: Guangdong Provincial People's Hospital

data_processing:
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.
(For DESeq2 with biological replicates) 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 . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: EXCEL file included gene count values for each Sample

source_name: heart muscle tissues

growth_protocol: Mice were maintained in SPF room.

extract_protocol:
Total RNAs were extracted and purified with miRNeasy Mini Kit (Qiagen) according to the manual.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by 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, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. 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 amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained

treatment_protocol: One month old mice were intraperitoneally injected with the lentivirus. After two months post injection, the mice were used for echocardiography and other experiments, such RNA-seq.

value: heart muscle tissues

value: tissues

value: H3L overexpression


title: P29 (miRNA-seq)

value: Sepsis


title: IMR32_ACBI1_24h, MYCN, ChIP

value: Human neuroblastoma

value: MYCN


title: H8 (miRNA-seq)


title: P28 (miRNA-seq)


title: dpi1_Young_rep3


title: dpi1_Young_rep2


title: heart tissues, H3L overexpression, replicate 2


title: IMR32_DMSO_24h, MYCN, ChIP


title: heart tissues, H3L overexpression, replicate 1


title: dpi5_HGPS_rep3


title: heart tissues, control, replicate 3

value: control


title: P26 (miRNA-seq)


title: heart tissues, control, replicate 2


title: IMR32_DMSO_24h, GATA3, ChIP


title: uninfected_HGPS_rep3


title: IMR32_DMSO_24h, H3K27ac, ChIP


title: uninfected_HGPS_rep2


title: P25 (miRNA-seq)


title: IMR32_ACBI1_24h, PHOX2B, ChIP


title: heart tissues, control, replicate 1


title: P24 (miRNA-seq)


title: uninfected_HGPS_rep1


title: P27 (miRNA-seq)


title: heart tissues, A29L overexpression, replicate 2

value: A29L overexpression


title: uninfected_Aged_rep3

value: lung


title: heart tissues, A29L overexpression, replicate 3


title: IMR32_ACBI1_24h, GATA3, ChIP


title: IMR32_ACBI1_24h, HAND2, ChIP


title: dpi1_Young_rep1

value: mix cell types from lung


title: heart tissues, A29L overexpression, replicate 1


title: P21 (miRNA-seq)


title: IMR32_DMSO_24h, HAND2, ChIP


title: uninfected_Aged_rep1


title: P23 (miRNA-seq)


title: IMR32_ACBI1_24h, input


title: uninfected_Aged_rep2


title: IMR32_DMSO_24h, input


title: LG_4

first: Yuyu

last: Chen

address: Zhongshan II road, 74th

data_processing:
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0.
Assembly: mm10
Supplementary files format and content: excel

source_name: tendon stem cells

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

value: tendon stem cells

value: primary tendon stem cells

value: LG


title: uninfected_Young_rep3

value: male

value: Balb/c


title: P19 (miRNA-seq)

value: peripheral blood

value: peripheral blood mononuclear cells


title: LG_3


title: LG_2


title: P20 (miRNA-seq)


title: P16 (miRNA-seq)


title: IMR32_DMSO_24h, PHOX2B, ChIP


title: uninfected_Young_rep1


title: IMR5_siSMA4-7_48h, rep2 [ATAC-seq]

data_processing:
The Fastq files were processed using Encode ATAC_DNase_pipelines installed on the NIH biowulf cluster.
The peak sets were further analyzed using the deepTools2 suite (v3.3.0). By using bamCoverage, peaks were normalized to reads per kilobase per million reads normalized read numbers (RPKM).
bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq was performed using the ATAC-seq kit (Active Motif, cat. 53150) follow the manual. Approximately, 100,000 NB cells were pelleted and the Tn5 transposition reaction was performed with the Nextera kit (Illumina), according to the manufacturer’s protocol.
Library was generated using the ATAC-seq kit (Active Motif, cat. 53150) follow the manual.


title: P17 (miRNA-seq)


title: LG_1


title: IMR5_siSMA4-5_48h, rep2 [ATAC-seq]


title: P15 (miRNA-seq)


title: uninfected_Young_rep2


title: IMR5_siSMA4-5_48h, rep1 [ATAC-seq]


title: HFHG_3

value: HFHG


title: BE(2)C_ACBI1_24h, rep2 [ATAC-seq]


title: IMR5_siSMA4-7_48h, rep1 [ATAC-seq]


title: HFHG_2


title: P11 (miRNA-seq)


title: P13 (miRNA-seq)


title: H22 (RNA-seq)

data_processing:
Sequencing was performed on a MGISEQ-2000RS platform in 2 x 100 bp paired-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include mapped read counts for each sample

extract_protocol:
Total RNA isolation was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions. DNA libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: healthy donor


title: H24 (RNA-seq)


title: IMR5_siCtrl_48h, rep1 [ATAC-seq]


title: mNCSC_pTGC_EV_4

city: Ames

first: Geetu

last: Tuteja

email: arnstrm@iastate.edu, geetu@iastate.edu

state: IA

address: 2437 PAMMEL DR

department: Genetics Development & Cell Biology

institute: Iowa State University

description: mNCSCs incubated with EVs from Mouse trophoblast giant cells

data_processing:
raw reads were were mapped to GRCm39 using STAR v.2.7.10b (with options --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3 )
featureCounts v.2.0.3 was used for generating raw counts using gencode.vM30 GTF file, at exon level, per gene. Reads were treated as pairs and merged counts for all sampled were created
Read count extraction and normalization were performed using DESeq2 on Rstudio.
Enrichment tests on the differentially expressed genes were performed using TissueEnrich against the mouse Encode dataset and using enrichR databases
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

source_name: Mouse Neural Cortical Stem Cells

growth_protocol: mNCSCs were maintained in an undifferentiated state in mNCSC medium with FGF4, EGF, and heparin; cells were passaged ~24 hours before receiving treatment; mNCSCs given; pTGCs were differentiated from mTSCs for 6 days in exosome-free 70% MEF-conditioned medium with retinoic acid and had EVs isolated from their culture medium at day 6 of differentiation; mTSCs were cultured for 2 days in exosome-free 70% MEF-conditioned medium with FGF4 and heparin to maintain undifferentiated state and had EVs isolated from their clulture medium at day 2 of growth

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA  Library Prep Kit following manufacturer's protocols.

treatment_protocol:
mNCSCs in the negative control group were not given any EVs from placental cells before having their RNA collected
mNCSCs in this treatment group were given EVs isolated from undifferentiated mTSCs, and incubated with the EVs for ~24 hours prior to RNA collection
mNCSCs in this treatment group were given EVs isolated from undifferentiated pTGCs, and incubated with the EVs for ~24 hours prior to RNA collection

value: Mouse Neural Cortical Stem Cells

value: Neural stem cell

value: WT

value: Incubated with EVs from pTGCs for ~24 hours


title: H25 (RNA-seq)


title: mNCSC_pTGC_EV_3


title: IMR5_siCtrl_48h, rep2 [ATAC-seq]

value: Human neuroblastoma


title: P10 (miRNA-seq)

value: Sepsis


title: H20 (RNA-seq)


title: P8 (miRNA-seq)


title: HFHG_4


title: P9 (miRNA-seq)


title: H19 (RNA-seq)


title: BE(2)C_DMSO_24h, rep2 [ATAC-seq]


title: BE(2)C_ACBI1_24h, rep1 [ATAC-seq]


title: H21 (RNA-seq)


title: BE(2)C_DMSO_24h, rep1 [ATAC-seq]


title: H16 (RNA-seq)


title: P7 (miRNA-seq)


title: H15 (RNA-seq)


title: HFHG_1


title: IMR32_ACBI1_24h, rep2 [ATAC-seq]


title: P4 (miRNA-seq)


title: H11 (RNA-seq)


title: IMR32_ACBI1_24h, rep1 [ATAC-seq]


title: mNCSC_mTSC_EV_3

description: mNCSCs incubated with EVs from Mouse trophoblast stem cells

value: Incubated with EVs from mTSCs for ~ 24 hours


title: mNCSC_mTSC_EV_4


title: H14 (RNA-seq)


title: P2 (miRNA-seq)


title: IMR32_DMSO_24h, rep2 [ATAC-seq]


title: mNCSC_mTSC_EV_2


title: COV111 (miRNA-seq)


title: COV112 (miRNA-seq)


title: IMR32_DMSO_24h, rep1 [ATAC-seq]


title: mNCSC_pTGC_EV_2


title: H9 (RNA-seq)


title: input-b-Catenin_FL_E10.5+C59+6h

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
Low quality bases and Truseq adapters were removed with cutadapt v4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 30 -m 15)
Filtered reads were mapped with bowtie2 version 2.4.5 with default parameters
Alignments with MAPQ below 30 were filtered out with samtools
Peaks were called and coverage was performed with macs2 version 2.2.7.1 (-g 1870000000 --call-summits --format BAMPE -B, input was not used)
Coverage was normalized the million fragments after filtering
Average coverage between replicates was computed with bigwigAverage from deepTools version 3.5.5
Consensus peaks were obtained with the following steps:
1. Peaks were called using all replicates with equal contribution.
In details, duplicates were removed from BAM files of each replicate with picard version 2.27.4.
Each BAM was subsampled to get the number of reads of the smallest BAM.
Peaks were called using all subsampled BAM with the same arguments as for individual replicates
2. Only peaks with summits overlapping both replicates were kept.
In details, individual narrowPeaks were overlaped with bedtools multiinter version 2.30.0, only intervals present in both replicates were kept.
The narrowPeak file of step1 was intersected with the output of multiinter and was filtered in order to keep only narrowPeaks with summits overlapping the output of multiinter.
Assembly: mm10
Supplementary files format and content: bw: normalized coverage
Supplementary files format and content: repX.narrowPeak: narrowPeak from macs2
Supplementary files format and content: consensus.narrowPeak: narrowPeak with summit overlapping both replicates

source_name: Forelimb bud

extract_protocol:
Dissected forelimb bud tissue was crosslinked in 1% formaldehyde/PBS at room temperature which was then quenched with glycine (125 mM). For β-Catenin ChIP a second crosslink step was performed using DSG (disuccinimidyl glutarate) for 40 min at RT. After lysing in hypertonic buffer chromatin fragments were generated by sonication. Immunoprecipitation was performed overnight at 4°C using the polyclonal anti beta Catenin antibody (71-2700 Invitrogen, 5 μg per sample) and anti-histone H3(acetyl K27) antibody (ChIP Grade ab4729 Abcam, 5 μg per sample). The immune-complexed chromatin complexes were extracted with magnetic beads (Fisher Scientific 11202D). After washing beads in RIPA buffer, DNA was eluted from beads followed by reverse cross-linking overnight.
Libraries were generated using the next-generation library preparation kit from Takara Bio (Japan) according to manufacturer instructions
ChIP-Seq libraries were sequenced using a NextSeq instrument (Illumina).

value: Forelimb bud

value: WT Swiss Albino

tag: timepoint of_treatment

tag: timepoint of_dissection

value: E10.5 + 6hours


title: H7 (RNA-seq)


title: mNCSC_No_EV_4

description: mNCSCs given no placental EVs

value: No treatment given


title: H8 (RNA-seq)


title: mNCSC_pTGC_EV_1


title: b-Catenin_FL_E10.5+C59+6h_rep2

value: beta Catenin antibody (Invitrogen 71-2700)


title: mNCSC_No_EV_3

description: mNCSCs given no placental EVs


title: H2 (RNA-seq)


title: mNCSC_mTSC_EV_1


title: b-Catenin_FL_E10.5+C59+6h_rep1


title: COV105 (miRNA-seq)


title: mNCSC_No_EV_2

description: mNCSCs given no placental EVs


title: H1 (RNA-seq)


title: COV109 (miRNA-seq)


title: P14 (miRNA-seq)


title: input-H3K27Ac_FL_E10.5+C59+6h


title: P29 (RNA-seq)


title: H3K27Ac_FL_E10.5+C59+6h_rep2

value: anti-histone H3(acetyl K27) antibody (Abcam ab4729)


title: COV99 (miRNA-seq)

value: peripheral blood


title: COV102 (miRNA-seq)

value: peripheral blood mononuclear cells


title: P28 (RNA-seq)


title: 2 month old D2.mdx mouse treated weekly (Q.W.) with Prednisone starting at 1 month old (Rep2) (stRNA-seq)

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
spatial transcriptomics (10x Visium)
SlideID: V10M31-105 Area: D1

data_processing:
Single cell sequencing reads were processed and aligned to the mouse reference transcriptome (mm10) with the Cell Ranger version 3.1.0 (10x Genomics, Pleasanton, CA). We used CellBender to eliminate technical artifacts. For spatial transcriptomics: reads were processed and aligned to the mouse reference transcriptome (mm10) with the Space Ranger version 1.3.1 (10x Genomics, Pleasanton, CA).
From the gene expression matrix, the downstream analysis was carried out with R version 4.0.2 (2020-06-22). Quality control, filtering, data clustering and visualization, and the differential expression analysis was carried out using Seurat (v3.2.2) R package (Butler et al., 2018) with some custom modifications to the standard pipeline. Genes expressed in less than 3 cells as well as cells < 1000 UMIs and < 200 genes were removed from the gene expression matrix. In addition, we removed any single-cell with > 5% UMIs mapped to mitochondrial genes, as well as obvious outliers in number of UMIs (cell doublets). For spatial transcriptomics: processed h5 files were analysed in R using Giotto and BayesSpace.
After log-normalizing the data, the expression of each gene was scaled regressing out the number of UMI and the percent mitochondrial gene expressed in each cell. We performed PCA on the gene expression matrix and used the first 30 principal components for clustering and visualization. Unsupervised shared nearest neighbor (SNN) clustering was performed with a resolution of 0.35 and visualization was done using t-distributed stochastic neighbor embedding (t-SNE). We performed a silhouette analysis (R cluster package) to select an optimal SNN resolution parameter, that balanced the number of expected clusters (given known marker expression) with a maximal average silhouette width. Finally, differential expression analysis was achieved using Seurat’s ‘‘FindAllMarkers’’ function using a likelihood ratio test that assumes the data follows a negative binomial distribution and only considering genes with > log2(0.25) fold-change and expressed in at least 40% of cells in the cluster. Feature plots were generated using Nebulosa package.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrix generated by cellranger (v3.1.0). Filtered feature barcode matrix generated by spaceranged (v1.3.1).
Library strategy: Spatial Transcriptomics

source_name: Gastrocnemius muscle (GAST)

extract_protocol: After tissue digestion and bead selection, CD45+ single-cell sorted suspensions were washed and resuspended in 0.04% BSA in PBS at a concentration of at least 400 cells/μL. Cells were counted manually with a hemocytometer to determine their concentration. Single-cell RNA-sequencing libraries were then prepared using the Chromium Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol. Briefly, the cells were diluted into the Chromium Single Cell A Chip as to yield a recovery of ~10,000 single-cell transcriptomes with < 5% doublet rate. Following the library preparation, the libraries were sequenced on the NovaSeq 6000 sequencer (Illumina, San Diego, CA) to produce about 450 million reads per library and on average a minimum of 40,000 reads per single cell. For spatial transcriptomics: fresh frozen skeletal muscle samples were cryosectioned (Leica CM1950). 10-µm sections were placed on the pre-chilled Optimization slides (Visium, 10X Genomics, PN-1000191), and the optimal lysis time was determined. The tissues were treated as recommended by 10X Genomics and the optimization procedure showed an optimal permeabilization time of 30 min of digestion and release of RNA from the tissue slide. Spatial gene expression slides (Visium, 10X Genomics, PN-1000185) were used for spatial transcriptomics following the Visium User Guides, and whole slide images were taken using a 20X objective of a Leica Aperio Versa scanner. Next-generation sequencing libraries were prepared according to the Visium user guide. Libraries were loaded at 300 pM and sequenced on a NovaSeq 6000 System (Illumina) as recommended by 10X Genomics.

treatment_protocol: Mice (8-12 weeks-old male) were anaesthetized with isoflurane (adjusted flow rate or concentration to 1,5%) and 50 µl of 10uM cardiotoxin (EMD Millipore, 217503-1MG) was injected in the tibialis anterior (TA) muscle. Mice were brought out of anesthesia and monitored until they were euthanized and processed at various time points. Muscles were recovered for single cell analysis at day 1 to day 8 post CTX-injury. Dystrophic gastrocnemius muscles were isolated from 2 month old D2.mdx animals that received weekly treatment of Vehicle or Prednisone (5 mg/kg) orally for a month starting at 4 weeks of age.

value: Gastrocnemius muscle (GAST)

tag: strain

value: prednisone

tag: age

value: 2 month old


title: COV108 (miRNA-seq)


title: H3K27Ac_FL_E10.5+C59+6h_rep1


title: 2 month old D2.mdx mouse treated weekly (Q.W.) with Prednisone starting at 1 month old (Rep1) (stRNA-seq)

description:
spatial transcriptomics (10x Visium)
SlideID: V10M31-105 Area: C1


title: input-b-Catenin_FL_E10.5+DMSO+6h

value: DMSO


title: COV97 (miRNA-seq)


title: 2 month old D2.mdx mouse (Rep2) (stRNA-seq)

description:
spatial transcriptomics (10x Visium)
SlideID: V19T19-105 Area: D1

value: vehicle


title: b-Catenin_FL_E10.5+DMSO+6h_rep1


title: 2 month old D2.mdx mouse (Rep1) (stRNA-seq)

description:
spatial transcriptomics (10x Visium)
SlideID: V19T19-105 Area: C1


title: b-Catenin_FL_E10.5+DMSO+6h_rep2


title: P27 (RNA-seq)


title: COV86 (miRNA-seq)


title: COV81 (miRNA-seq)


title: P23 (RNA-seq)


title: COV87 (miRNA-seq)


title: input-H3K27Ac_FL_E10.5+DMSO+6h


title: P26 (RNA-seq)


title: DBA2/J Day 8 after CTX muscle injury (stRNA-seq)

description:
spatial transcriptomics (10x Visium)
SlideID: V10M31-107 Area: D1

source_name: Tibialis Anterior (TA)

value: Tibialis Anterior (TA)

value: CTX muscle injury

tag: post-injury day

value: Day 8


title: H3K27Ac_FL_E10.5+DMSO+6h_rep2


title: P25 (RNA-seq)

value: Sepsis


title: C57 Day 8 after CTX muscle injury (stRNA-seq)

description:
spatial transcriptomics (10x Visium)
SlideID: V10M31-107 Area: C1


title: H3K27Ac_FL_E10.5+DMSO+6h_rep1

value: Forelimb bud


title: COV78 (miRNA-seq)


title: C57 Day 4 after CTX muscle injury (stRNA-seq)

description:
spatial transcriptomics (10x Visium)
SlideID: V19T19-105 Area: A1

value: Day 4


title: P24 (RNA-seq)


title: COV73 (miRNA-seq)


title: 2 month old D2.mdx mouse (scRNA-seq)

description: single-cell RNA-seq (Chromium V3)

data_processing:
Single cell sequencing reads were processed and aligned to the mouse reference transcriptome (mm10) with the Cell Ranger version 3.1.0 (10x Genomics, Pleasanton, CA). We used CellBender to eliminate technical artifacts. For spatial transcriptomics: reads were processed and aligned to the mouse reference transcriptome (mm10) with the Space Ranger version 1.3.1 (10x Genomics, Pleasanton, CA).
From the gene expression matrix, the downstream analysis was carried out with R version 4.0.2 (2020-06-22). Quality control, filtering, data clustering and visualization, and the differential expression analysis was carried out using Seurat (v3.2.2) R package (Butler et al., 2018) with some custom modifications to the standard pipeline. Genes expressed in less than 3 cells as well as cells < 1000 UMIs and < 200 genes were removed from the gene expression matrix. In addition, we removed any single-cell with > 5% UMIs mapped to mitochondrial genes, as well as obvious outliers in number of UMIs (cell doublets). For spatial transcriptomics: processed h5 files were analysed in R using Giotto and BayesSpace.
After log-normalizing the data, the expression of each gene was scaled regressing out the number of UMI and the percent mitochondrial gene expressed in each cell. We performed PCA on the gene expression matrix and used the first 30 principal components for clustering and visualization. Unsupervised shared nearest neighbor (SNN) clustering was performed with a resolution of 0.35 and visualization was done using t-distributed stochastic neighbor embedding (t-SNE). We performed a silhouette analysis (R cluster package) to select an optimal SNN resolution parameter, that balanced the number of expected clusters (given known marker expression) with a maximal average silhouette width. Finally, differential expression analysis was achieved using Seurat’s ‘‘FindAllMarkers’’ function using a likelihood ratio test that assumes the data follows a negative binomial distribution and only considering genes with > log2(0.25) fold-change and expressed in at least 40% of cells in the cluster. Feature plots were generated using Nebulosa package.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrix generated by cellranger (v3.1.0). Filtered feature barcode matrix generated by spaceranged (v1.3.1).


title: P19 (RNA-seq)


title: mNCSC_No_EV_1

description: mNCSCs given no placental EVs

value: Mouse Neural Cortical Stem Cells

value: Neural stem cell

value: WT


title: Day 2 after CTX muscle injury (scRNA-seq)

description: single-cell RNA-seq (Chromium V3)

value: Day 2


title: P20 (RNA-seq)

value: peripheral blood


title: COV72 (miRNA-seq)

value: peripheral blood mononuclear cells


title: P17 (RNA-seq)


title: Day 1 after CTX muscle injury (scRNA-seq)

description: single-cell RNA-seq (Chromium V3)

value: Day 1


title: Plekhg5-/- SOD1-G93A #3

city: Wuerzburg

first: Patrick

last: Lüningschrör

address: Versbacher Str. 5

department: Institute of Clinical Neurobiology

institute: University Hospital Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.4 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to mouse genome (GRCm38.p6) and the cDNA sequence of human SOD1 (NM_000454.4) using STAR (Dobin et al., 2013) v2.7.2b with default parameters except for including transcript annotations from RefSeq annotation version 108 combined with SOD1 annotation
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 108 for GRCm38.p6 + human SOD1) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction)
Assembly: GRCm38.p6, NM_000454.4
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

source_name: spinal cord

growth_protocol: Total RNA was isolated from spinal cord tissue of 7 months-old mice

extract_protocol:
Total RNA was exctracted using the RNeasy Lipid Tissue Mini Kit
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥8.7. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions. After 12 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~310 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

value: spinal cord

value: Plekhg5 KO SOD1-G93A


title: COV90 (miRNA-seq)


title: Plekhg5-/- SOD1-G93A #2


title: Diff_D2_4_S1

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

library_source: other

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
raw reads were were mapped to GRCm39 using STAR (with 3' adapter sequence to trim), and counts were estimated using "--quatnMode GeneCounts" option.
Read count extraction and normalization were performed using DESeq2 on Rstudio.
Enrichment tests on the differentially expressed genes were performed using TissueEnrich against the mouse Encode dataset
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample. The file row names are ENSEMBL gene ids and column names are filenames of conditions/replicates. There is an additional column with label "Group" that identify the ENSEMBL ids to its biotype.

molecule: other

source_name: pTGC cells (differentiated mTSC), Day6

growth_protocol: pTGCs were grown for a total of 6 days from an initial passage of 38,000 cells/well of a 6-well plate; mTSCs were grown for a total of 2 days from an initial passage of 600,000 cells/well of a 6-well plate; both cell groups were grown in 70% MEF conditioned TB medium and 30% regular TB medium

extract_protocol:
Cell culture medium was collected from the cells at D6 (for pTGCs) and D2 (for mTSCs) and the collected medium was used in the EveryRNA kit to isolate EVs from the medium
indexed libraries were constructed using the NEBNext Small RNA Library Prep following the manufacturer's protocol
convert small RNAs into indexed libraries from total RNA isolated from Evs using EVery EV RNA Isolation Kit following the manufacturer's protocols.

treatment_protocol:
for pTGCs, cells were grown in culture medium from passage with NO FGF4 and heparin and WITH retinoic acid to promote differentiation to giant cells for a total of 6 days
for mTSCs, cells were grown in culture medium from passages with FGF4 and heparin to maintain undifferentiated state

value: mTSC

value: Mouse trophoblast stem cells

value: cells were cultured on TB medium lacking FGF4 and heparin but in the presence of retinoic acid (RA)

tag: time

value: Day 6

tag: rna population

value: extracellular vesicle RNA


title: COV70 (miRNA-seq)


title: COV68 (miRNA-seq)


title: Plekhg5-/- SOD1-G93A #1


title: Diff_D2_3_S2

tag: treatment


title: P15 (RNA-seq)

value: Sepsis


title: P16 (RNA-seq)


title: COV65 (miRNA-seq)


title: P14 (RNA-seq)


title: P21 (RNA-seq)


title: COV62 (miRNA-seq)


title: Plekhg5+/+ SOD1-G93A #3


title: Diff_D2_2_S3

tag: cell line


title: Diff_D2_1_S4

tag: cell type


title: COV75 (miRNA-seq)


title: COV59 (miRNA-seq)


title: P13 (RNA-seq)


title: P11 (RNA-seq)


title: Plekhg5+/+ SOD1-G93A #1

tag: genotype


title: Plekhg5+/+ SOD1-G93A #2


title: Undiff_D2_4_S5

source_name: mTSC cells, Day2


title: P10 (RNA-seq)


title: Undiff_D2_3_S6


title: Plekhg5-/- #3

value: Plekhg5 KO


title: COV57 (miRNA-seq)


title: COV53 (miRNA-seq)


title: Undiff_D2_2_S7


title: P8 (RNA-seq)


title: Plekhg5-/- #2


title: Undiff_D2_1_S8


title: P9 (RNA-seq)


title: COV50 (miRNA-seq)


title: Plekhg5-/- #1


title: Plekhg5+/+ #3


title: COV43 (miRNA-seq)


title: COV45 (miRNA-seq)


title: Tumor in combined therapy group (Visium)

first: Changqing

last: Su

state: China

address: 225 Changhai Road, Yangpu District

department: Molecular Oncology

institute: National Center for Liver Cancer

data_processing:
10x genomics pipeline
The Space Ranger software pipeline (version 1.0.0) provided by 10×Genomics   was used to process Visium spatial RNA-seq output and brightfield microscope   images in order to detect tissue, align reads using the STAR aligner, generate  feature-spot matrices, perform clustering and gene expression analysis, and place   spots in spatial context on the slide image.
We processed the unique molecular  identifier (UMI) count matrix using the R package Seurat3(version 3.1.1).
We first normalized the data with sctransform in order to account for variance in sequencing  depth across data points, detecting high-variance features, and stores the data in  the SCT assay.
Briefly, the average expression and dispersion were calculated for  each gene, genes were subsequently placed into x bins based on expression. Principal   component analysis (PCA) was performed to reduce the dimensionality on the log transformed gene-barcode matrices of top variable genes. Cells were clustered based   on a graph-based clustering approach, and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in   the percentage of expressed cells was used to identify significantly differentially  expressed genes between clusters.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing gene expression and spatial contents.

source_name: xenografted tumors

extract_protocol:
Tumor were prepared according to Visium spatial protocols of tissue preparation guide (10x genomics). Firstly, freshly obtained tissue samples were snap frozen in liquid nitrogen, then embedded in chilled Optimal Cutting Temperature compound (OCT; Tissue-Tek) and frozen on dry ice, then stored at -80°C in a sealed container for later use. For Visium samples preparation, OCT-embedded tissue blocks were cut to 10 um thick using a LEICA CM1950 machine and mounted on the Visium spatial gene expression slide.
10x genomics visium spatial gene expression pipeline

value: MC38 cells

value: subcutaneous tissue


title: P4 (RNA-seq)


title: Tumor in oncolytic adenovirus-treated group (Visium)


title: P7 (RNA-seq)


title: COV41 (miRNA-seq)


title: Plekhg5+/+ #2


title: P2 (RNA-seq)


title: COV38 (miRNA-seq)


title: Plekhg5+/+ #1


title: COV112 (RNA-seq)


title: Tumor in Keytruda-treated group (Visium)


title: igg_wt_2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
CUT&TAG was aligned to genome mm10 using boCtrlie2
Assembly: mm10
Supplementary files format and content: CUT&Tag in bigwig files

source_name: Intestine

extract_protocol:
CUT&TAG is perfomed according to the manufacture's protocol(https://www.epicypher.com/technologies/cutana/cut-and-tag).
Library construction is according to the manufacture's protocol(https://www.epicypher.com/technologies/cutana/cut-and-tag).

value: mouse intestine jejunum part

value: wildtype


title: COV35 (miRNA-seq)


title: igg_fzd5ko_2

value: knockout


title: COV33 (miRNA-seq)

value: peripheral blood


title: COV111 (RNA-seq)

value: peripheral blood mononuclear cells


title: COV109 (RNA-seq)


title: Tumor in control group

data_processing:
The Cell Ranger software pipeline (version 5.0.0) 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.
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat[1] (version 3.1.1).
To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we applied a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers.
Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >20% of the counts belonged to mitochondrial genes.
ibrary size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing the raw gene expression count and cell

extract_protocol:
Tissue was processed to prepare scRNA-seq libraries by using Chromium Single Cell 3’ Reagent v3 Kits (10x Genomics, Pleasanton, CA, USA). Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/ volume BSA. Then, single-cell suspensions were loaded onto a Chromium Single Cell Controller Instrument (10XGenomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsions (GEMs).
After generation of GEMs, reverse transcription, cDNA PCR amplification and library preparation were performed accroding to the 10x Genomics 3’ gene expression protocol.

tag: sample type


title: COV108 (RNA-seq)


title: OK6>mCherry-NLS,unc-13 RNAi(attP2) type I MNs, bio rep 3

city: Berkeley

first: Caroline

last: Cypranowska

address: 271 Weill Hall #3200

department: Molecular & Cell Biology

institute: University of California, Berkeley

data_processing:
Fastq files for each library were analyzed with FastQC (version 0.11.7) to check for quality and trimmed with Trimmomatic (version 0.38) with parameters SLIDINGWINDOW:4:20 MINLEN:20 ILLUMINACLIP:nextera.fa:2:40:15 to remove low quality reads and to remove adapter sequences.
Trimmed reads were aligned to a custom reference genome built from Berkeley Drosophila Genome Project (dm6, release 95), including the pUAST-mCherry-NLS vector sequence for the detection of mCherry mRNA reads. Samples with the dsRNA construct were mapped to the custom genome build described along with the sequence of dsRNA construct. Mapping was performed with HISAT2 (version 2.1.0).  The counts matrix was generated with featureCounts from Subread (v1.6.4). Genes with fewer than 5 read counts across two libraries were considered undetectable and removed from downstream analysis.
Differential expression between knockdown conditions was calculated with DESeq2 (version 1.26.0) using the built-in median of ratios method to normalize the read counts for each gene prior to comparison with wild type controls.
Assembly: dm6
Supplementary files format and content: Comma-separated output of featureCounts for each Sample

organism: Drosophila melanogaster

source_name: ventral nerve cord

growth_protocol: Drosophila larvae were raised to the 3rd instar stage on cornmeal and molasses media in an incubator at 25°C. Female parents bearing the OK6-Gal4 driver, UAS-mCherry-NLS and UAS-Dcr2 transgenes were crossed with male parents bearing either the attP2 empty vector or RNAi construct to obtain control and knockdown progeny. Larvae were screened for mCherry fluorescence in the ventral nerve cord immediately prior to dissection of ventral nerve cord.

extract_protocol:
Larvae were washed twice with PBS, followed by a wash in 70% ethanol and a final wash in PBS before being placed in a droplet of Schneider's complete media with 10% FBS for ventral nerve cord dissection. Ventral nerve cord tissue was sequentially recovered for each larva dissected in ice cold Schneider's media with 10% FBS, pooled by the appropriate genotype. Dissected tissue was rinsed three times in Schneider's media containing 1.5 mM EDTA and 1.5 mM L-Cysteine. Cells were dissociated in Schneider's media with 1.5 mM EDTA, 1.5 mM L-Cysteine, papain, and 1.25 mg/mL collagenase type-I at 25C on a nutator for 5 minutes and then triturated 30 times with a P200 pipette. The incubation and trituration step was repeated once before the tissue was sheared 7 times with a 27G1/2 needle. The dissociation reaction was quenched with the addition of Schneider's media with 10% FBS. Dissociated cells were passed through a 40 uM cell strainer, spun down at 0.7xg for 7 minutes before being resuspended in 1 mL of Schneider's media with 5% FBS. Cells were stained with 0.3 uM of Sytox Green to assess viability before being sorted on a BD Influx Cell Sorter or BD FACS Aria. Cells were sorted for high mCherry fluorescence and low Sytox Green fluorescence. Sorted cells were recovered in RLT buffer with 3.5 mM BME from the QIAGEN RNEasy Micro kit and processed according to manufacturer's instruction omitting the DNase digestion step.
Libraries were prepared using a modified SMART-Seq2 protocol (Picelli et al., Nature Protocols, 2014). RNA was annealed with an oligo-dT primer and first-strand synthesis was performed with SuperScriptII kit using a custom template-switching oligo. cDNA preamplification, lambda exonuclease digestion and size-selection were performed as described in Li et al., Cell, 2017. Libraries were constructed with the Nextera XT kit and sequenced on the Illumina Hi-Seq 4000 instrument (PE100).

value: ventral nerve cord

value: motor neuron

value: unc-13 knockdown


title: COV30 (miRNA-seq)


title: COV105 (RNA-seq)


title: COV13 (miRNA-seq)