title: WT U2OS cells exposed to 0 nM trabectedin, biological replicateR1

data_processing:
*library strategy: genome-wide ligation of 3'-OH ends followed by sequencing (GLOE-Seq)
After demultiplexing of sequencing data, each sample was represented by two fastq.gz files, with the first file containing 101-nucleotide-long genomic reads (R1) and the second storing the respective 10-nucleotide long UMIs (R2). The quality of the R1 and R2 data was checked using FastQC/0.11.9 (Andrews, 2010). Low-quality and adaptor-containing reads were removed via trimmomatic/0.38 (Bolger et al., 2014), using the following parameters: for R1, SE ILLUMINACLIP:Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:101; for R2, SLIDINGWINDOW:4:15 MINLEN:10. Using a custom Python/3.7.4 script employing the module Biopython/1.79, we merged the R1 and R2 records that passed trimming, incorporating the 10-nucleotide-long R2 sequences in the name of respective R1 reads. These reads were mapped to human reference genome GRCh38 via bowtie2/2.3.5.1, using the pre-built bowtie2 (Langmead & Salzberg, 2012) index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip and default settings. Read duplicates were removed by the tool dedup of umi_tools/1.1.2 toolkit (Smith et al., 2017), grouping reads with the same R2 sequence stored in the read name (method=unique). samtools/1.12 (Li et al., 2009) were employed to remove unmapped reads, sort, index and generate statistics of bam files. bedtools2/2.29.2 (Quinlan & Hall, 2010) was used to covert bam files to bed files. Each read represented one unit of DNA-break signal, which we positioned at the nucleotide located immediately upstream of the 5’ end of the read. Since a GLOE-Seq read is the reverse complement of the DNA fragment captured in the protocol (Sriramachandran et al., 2020), the strand of the nucleotide bearing the signal was changed to the opposite to the one on which the respective read was mapped. In this way signal positioning, the original DNA break is on the 5’ side of the nucleotide bearing the signal. Using AWK and a custom Python/3.7.4 script with the modules numpy/1.21.5 and pandas/0.25.1, we implemented the described DNA-break-signal positioning, which resulted in the deposited sample-specific tsv-files. In these tsv-files, each line reflects one DNA break revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate and 3) the strand of the nucleotide bearing the signal (this nucleotide is immediately downstream of the break), 4) MAPQ score of the read. All code: https://gitlab.ethz.ch/eth_toxlab/trabi-seq
Assembly: GRCh38
Supplementary files format and content: In the provided sample-specific tsv-files, each line reflects one DNA break revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate and 3) the strand of the nucleotide bearing the signal (this nucleotide is immediately downstream of the break), 4) MAPQ score of the read.


title: CSB knockout U2OS cells exposed to 50 nM trabectedin, biological replicateR1

status: Public on Dec 22 2023

type: SRA

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HAP1 cells were maintained in IMDM containing 4.5 g/L glucose with 10% fetal bovine serum, 1% penicillin-streptomycin, and GlutaMAXTM (Gibco) at 37°C with 5% CO2. U2OS WT, XPC-KO, CSB-KO and XPA-KO cells were maintained in McCoy’s 5a modified cell culture medium (Gibco) with 10% fetal bovine serum, 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
For the Nb.BsrDI treatment experiment, genomic DNA was extracted using the Monarch genomic DNA purification kit (T3010) from untreated U2OS wildtype cells after harvesting (5 min incubation with 0.25 % trypsin). For the experiments with cells, nuclei isolation followed the GLOE-seq protocol for mammalian cells (PMID: 32320643) with the following modification. Isolation of genomic DNA from mammalian cell culture: Agarose plugs were incubated with 6 mL of proteinase K solution and shaken at 170 rpm.
For the Nb.BsrDI treatment experiment, DNA library for Illumina sequencing was prepared according to GLOE-Seq protocol ‘Steps y23 – 28: Denaturation and ligation of 3’-OH termini (yeast)’ onwards (PMID: 32320643). For the experiments with cells, nuclei isolation and DNA library preparation for sequencing followed the GLOE-seq protocol for mammalian cells (PMID: 32320643) with the following modifications. Isolation of genomic DNA from mammalian cell culture: Agarose plugs were incubated with 6 mL of proteinase K solution and shaken at 170 rpm. Fragmentation and capture of biotinylated single-stranded DNA: DNA was sonicated with an average fragment length of 300 nucleotides with Qsonica for 5 min at 4 °C in cycles of 15 s ON and 5 s OFF with 20 % amplitude. DNA was purified twice with AMPure beads with elution in 50 μL dH2O. Streptavidin MyOne C1 dynabeads were resuspended after washing in 50 μL bind and wash buffer (2x) for a 1:1 beads to sample ratio. Second strand synthesis, end polishing and ligation of the distal adaptor: Reagents for second strand synthesis, end polishing and distal adaptor ligation were combined on ice and mixed by pipetting. For the distal adaptor either 3792-UMI or 3792-UMI.v2 (different indexes) were annealed with 3791. DNA was purified with AMPure beads and eluted in 30 μL of dH2O. qPCR: Before the final library amplification described in (Sriramachandran et al., 2020), qPCR with reaction conditions identical to the final PCR used for library amplification was done for quality control. Samples (1 μL) were diluted in deionized water (9.4 μL) and combined with 1x Q5 buffer, 0.2mM dNTPs, 0.1 μM i5 illumina indexing primer, 0.1 μM P7-short primer, 1x EvaGreen and 0.1 units of Q5 high-fidelity DNA polymerase. qPCR protocol included 120 s initial denaturation at 95 °C, 40 cycles of 15 s denaturation at 95 °C, 30 s annealing at 60 °C and 20 s extending at 72 °C, as well as 95 s final extension at 72 °C. Library amplification: The library was scaled up from 20 μL to 50 μL using entire samples. A customized P7-short primer compatible with the UMI-containing distal adaptors was used. Samples were purified with AMPure beads with a 1:1 bead to sample ratio. The DNA libraries were sequenced on an Illumina NovaSeq 6000 with a single-read protocol and the read length of 101 nucleotides (R1); additionally, 15 cycles were run on R2 to read UMI and custom indexes introduced by the oligos 3792-UMI or 3792-UMI.v2. For each sample, we deposited these R1 and R2 sequencies. Supplementary Table 1 of the manuscript (titled the same way) summarizes the reagents, enzymes, kits, oligonucleotides, and other materials used for GLOE-seq experiments.

treatment_protocol: For the Nb.BsrDI treatment experiment, genomic DNA was extracted using the Monarch genomic DNA purification kit (T3010) from untreated U2OS wildtype cells after harvesting (5 min incubation with 0.25 % trypsin). Existing breaks were blocked by incubating 5 μg DNA first with 10 units of T4 PNK per 4 ng DNA and 1x NEBuffer 2 for 30 min at 37 °C, and then with 250 μM ddNTP mix, 2 units of Therminator IX DNA polymerase and 1x ThermoPol buffer for 10 min at 60 °C. DNA was purified with ProNex size-purification system (NG2001, Promega) with 8:5 beads to sample ratio. DNA was incubated with 2.5 units of Nb.BsrDI and 1x CutSmart buffer for 90 min at 65 °C and then with 5 units antarctic phosphatase and 1x antarctic phosphatase buffer for 30 min at 37 °C, and purified as described above. In the experiments with cells, cells were grown up to 60-80 % confluency and incubated for 24 h with 1 mM palbociclib isethionate for G1 enrichment. Cells were then treated with 0.1 % DMSO, 20 nM or 50 nM trabectedin in combination with 1mM palbociclib isethionate for 2 h. Cells were washed with PBS and underwent a 2-h recovery in cell culture media without trabectedin in the presence of 1 mM palbociclib isethionate.

tag: cell line

tag: genotype

value: CSB knockout

tag: treatment

value: 50 nM trabectedin


title: E15_5_KO scRNA-seq

city: Shanghai

first: Ping

last: Lu

address: No 1630 Dongfang Road, Pudong New Area

country: China

institute: Shanghai Cancer Institute

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using an internal pipeline
Cell type identification and clustering analysis were performed by Seurat program
the Seurat program (http://satijalab.org/seurat/, R package, v.3.0.1) was applied for analysis of RNA-Sequencing data. UMI count tables were loaded into R using read.table function
parameter resolution to 0.6 was set for FindClusters function to clustering analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files

molecule: total RNA

organism: Mus musculus

source_name: E15.5 fetal pancreas

extract_protocol:
Pancreatic tissues of E13.5 and E15.5 embryos were collected, disassociated by TrypLE™ Express (ThermoFisher 12605010), labelled with EpCAM and then purified by flow cytometry.
Individual libraries were diluted to 4 nM and pooled for sequencing. At last, pools were sequenced on Illumina novaseq6000 with 150 bp paired end reads. Individual libraries were diluted to 4 nM and pooled for sequencing. At last, pools were sequenced on Illumina novaseq6000 with 150 bp paired end reads

tag: tissue

value: E15.5 fetal pancreas

tag: strain background

value: PdxcreSetd2 f/f; KO


title: CSB knockout U2OS cells exposed to 20 nM trabectedin, biological replicateR2

value: 20 nM trabectedin


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_9]

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

description:
CelSeq-2
barcodes.tsv

data_processing:
Failed reactions were identified by low levels of ERCC external RNA controls and excluded. Furthermore, a liveness threshold was calculated for each plate based on the wells with no cell added, in order to distinguish live cells from dead and/or apoptotic cells. This threshold was set to a minimum of 500 transcripts.
The percentage of transcripts mapping to the mitochondrial genome was calculated and cells with more mitochondrial‐encoded transcripts over nuclear ones were removed. Mitochondrial and ERCC transcripts were removed from the dataset, as well as cells with <1000 nuclear‐encoded transcripts or <500 genes. In addition, cells with >150.000 nuclear‐encoded transcripts were removed. Genes with low expression, that is either having less than 5 cells expressing the gene or less than two cells with less than two transcripts, were removed. A total of 105 cells, forming a distinct cluster of erythroid lineages, was identified based on high 515 levels of hemoglobin complex genes, and was removed. To improve cross‐sample comparisons, ambient mRNA contamination in individual cells was estimated and removed using DecontX. DecontX was run for all samples (batches) individually. Removal of cells with less than 1000 nuclear‐encoded transcripts was repeated on the decontaminated counts matrix outputted by DecontX.
All subsequent analyses were performed using R (version 4.0.2) and the package Seurat (version 3.2.2,RRID:SCR_007322) with default parameters unless stated otherwise. The SCTransform() function was used to normalize and scale the data, and to identify variable genes. To avoid clustering of cells based on specific cell processes, genes associated with sex (XIST, TSIX, and Y chromosome‐specific genes), cell cycle phase, dissociation stress (heat shock proteins; GO:0006986), and activity (ribosomal protein genes; GO:0022626), were removed as described before.
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NBL tumor left adrenal gland

extract_protocol:
Tumor material was collected in the operating room by Truecut biopsy (samples at diagnosis) or surgical resection (debulking procedure after induction chemotherapy). The Dutch samples were gently dissociated into single‐cells and sorted by flow cytometry for single‐cell RNA sequencing using the CEL‐Seq2 platform. In brief, preparation of the tumor pieces for single‐cell RNA sequencing was started within 4 hours after the surgery. The material was minced into pieces <1mm3 and dissolved by enzymatic digestion with collagenase I, II and IV (2.5 mg/mL) at 37°C with agitation for max. 1 hour. The samples were filtered through a 70 μm cell strainer and washed in DMEM. Cells were further separated into a single cell suspension with the NeuroCult dissociation kit according to the manufacturer's protocol (StemcellTM Technologies, cat#05707), washed and stained with DAPI and DRAQ5. Next to this unbiased strategy, some samples were additionally stained with antibodies to enrich for T cell populations (NB124, NB125 with CD3‐PE (Biolegend, cat#300308); NB124 with TCRγδ‐BV421 (Biolegend, cat#331217) or with GD2‐FITC (BD Biosciences, cat#563439) to enrich for tumor cells (000GGU, 000GXF, NB106, NB107, NB098, NB125, NB125, NB130, NB152). Single live cells were sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a FACSJazz, FACSAria II or Sony SH800S machine and subsequently spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing. Peripheral blood mononuclear cells (PBMC) from 5 healthy young adult donors (mean age 28) were isolated by Ficoll-Paque (VWR) density centrifugation and stained with fixable viability dye efluor506 (eBioscience, cat#65‐0866‐14), CD3‐PE (Biolegend, cat#300308) and CD56‐APC (Biolegend, cat#318310) antibodies. Subsequently, live CD3+ T cells and CD56+ NK cells were FACS sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a Sony SH800S machine. The plates were spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing.
All samples were processed for total transcriptome amplification, library preparation and sequencing into Illumina sequencing libraries as previously described70. Paired‐end 2x75 bp sequencing read length was used to sequence the prepared libraries using the Illumina NextSeq sequencer. Sharq preprocessing and QC pipeline were applied to process the single‐cell RNA‐seq data as described71. Read mapping was done using STAR version 2.6.1 (RRID:SCR_004463) on the hg38 Patch 10 human genome. Function featureCounts (RRID:SCR_012919) of the subread package (version 1.5.2) was used to assign reads based on GENCODE version 26 (RRID:SCR_014966).

value: NBL tumor left adrenal gland

tag: tumor type

value: High-risk NBL

tag: tumor stage

value: post-treatment

tag: Sex

value: male

value: MYCN non-amplified


title: WT U2OS cells exposed to 20 nM trabectedin, biological replicateR2

value: wild type


title: CSB knockout U2OS cells exposed to 20 nM trabectedin, biological replicateR1


title: E13_5_WT scRNA-seq

source_name: E13.5 fetal pancreas

value: E13.5 fetal pancreas

value: Setd2 f/f; WT


title: WT U2OS cells exposed to 20 nM trabectedin, biological replicateR1


title: Neuron Veh-2-1

city: Tucson

first: Tian

last: Wang

state: AZ

address: 1230 N Cherry Avenue

department: Center for innovation in brain science

country: USA

institute: Univeristy of Arizona

library_source: transcriptomic

data_processing:
Transcripts were mapped to rat genome (ensemble release 95) using Salmon 0.14
Tximport V1.6.0 was used to generate a counts table
DESeq2 V1.18.1 was used to calculate normalized read counts for each gene and/or transcript and to perform expression analysis
Assembly: rat genome (ensemble release 95)
Supplementary files format and content: csv files of normalized count
Supplementary files format and content: csv files of VST-nomalized expression

organism: Rattus norvegicus

source_name: E18 Primary Neuron

extract_protocol:
RNA was purified using PureLink™ RNA Mini Kit (Invitrogen, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries for RNA-seq were prepared using the Stranded mRNA-Seq library prep kit following manufacturer's protocols.

tag: cell type

value: E18 Primary Neuron

value: Veh treated


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_8]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_7]

description:
CelSeq-2
barcodes.tsv


title: Fetal pancreas of E18.5 RNA-seq

data_processing:
The library was qualified and sequenced in Illumina NovaSeq 6000
The end reading of 150bp pairing is generated.
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)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Fetal pancreas

extract_protocol:
RNA was harvested using TRI REAGENT. At least 20 thousand cells were collected for each samples.
cDNA fragments of preferentially 370~420 bp in length were selected by AMPure XP system (Beckman Coulter, Beverly, USA), amplified by PCR and then purified by AMPure XP beads to establish the libraries.

value: Fetal pancreas

tag: developmental stage

tag: strain

value: WT


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_6]

description:
CelSeq-2
barcodes.tsv


title: Neuron Veh-1-1


title: Fetal pancreas of E13.5 RNA-seq


title: Neuron Veh-1-2


title: Fetal pancreas of E15.5 RNA-seq


title: WT U2OS cells exposed to 50 nM trabectedin, biological replicateR1


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_10]

description:
CelSeq-2
barcodes.tsv


title: Neuron Veh-2-2


title: U2OS WT gDNA treated with Nb.BsrDI endonuclease

description: Nb.BsrDI

value: Nb.BsrDI endonuclease


title: Fetal pancreas of E11.5 RNA-seq


title: B cells donor 3119 TP1, VDJ

city: San Antonio

first: Evelien

middle: M

last: Bunnik

state: TX

address: 7703 Floyd Curl Drive

department: MIMG

institute: UT Health San Antonio

description:
V(D)J
V(D)J: read1 file contains cell barcode and UMI; read2 contains variable region reads
3119_TP1_filtered_contig_annotations.csv
3119_TP1_VDJ_heavy_productive_germ-pass.tsv

data_processing:
V(D)J sequencing data was processed using CellRanger vdj. Single-cell heavy chain variable region sequences were then analyzed using the Immcantation pipeline. The Immcantation package Change-O v0.4.4 was used to align lymphocyte receptor sequences to germline sequences for downstream analysis.
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: _barcodes.tsv, _genes.tsv, _matrix.mtx
Supplementary files format and content: Germline annotations for V-gene, D-gene, and J-gene segments, constant region assignments, CDR3 sequences, and clonotype assigments for heavy and light chains: _filtered_contig_annotations.csv
Supplementary files format and content: Change-O output files for productively rearranged antibody heavy chains: _VDJ_heavy_productive_germ-pass.tsv
Supplementary files format and content: Seurat object of gene expression and antibody-derived tag data: SeuratObj_Res_0.6.rds
Library strategy: VDJ-seq

source_name: PBMCs

extract_protocol:
Cryopreserved PBMCs were thawed, followed by isolation of B cells by negative magnetic selection. Naïve B cells (CD21+CD27-) and antigen-experienced B cells (all other B cells) were then isolated by fluorescence-activated cell sorting by first gating on live CD19+CD20+ cells, and subsequently on CD21 and CD27 expression. Antigen-experienced cells were mixed with a small proportion of naive B cells and then loaded onto the 10x Genomics controller.
Standard 10x Genomics instructions were followed for the construction of 5' gene expression, antibody-derived tag (ADT), and V(D)J sequencing libraries.

value: PBMCs

value: CD19+ CD20+ B cells


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv


title: B cells donor 3119 TP2, VDJ

description:
V(D)J
V(D)J: read1 file contains cell barcode and UMI; read2 contains variable region reads
3119_TP2_filtered_contig_annotations.csv
3119_TP2_VDJ_heavy_productive_germ-pass.tsv


title: B cells donor 3119 TP2, ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
3119_TP2_barcodes.tsv
3119_TP2_genes.tsv
3119_TP2_matrix.mtx
SeuratObj_Res_0.6.rds

library_source: other

data_processing:
From the single-cell RNA sequencing Seurat object, the antibody capture component (assay = ADT) was extracted. This antibody matrix was normalized using CLR normalization (Seurat method NormalizeData) and scaled using Seurat routine ScaleData.
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: _barcodes.tsv, _genes.tsv, _matrix.mtx
Supplementary files format and content: Germline annotations for V-gene, D-gene, and J-gene segments, constant region assignments, CDR3 sequences, and clonotype assigments for heavy and light chains: _filtered_contig_annotations.csv
Supplementary files format and content: Change-O output files for productively rearranged antibody heavy chains: _VDJ_heavy_productive_germ-pass.tsv
Supplementary files format and content: Seurat object of gene expression and antibody-derived tag data: SeuratObj_Res_0.6.rds
Library strategy: CITE-seq

molecule: protein

tag: adt

value: TotalSeq-C0005 anti-human CD80, TotalSeq-C0053 anti-human CD11c, TotalSeq-C0136 anti-human IgM, TotalSeq-C0140 anti-human CD183 (CXCR3), TotalSeq-C0154 anti-human CD27, TotalSeq-C0181 anti-human CD21, TotalSeq-C0375 anti-human IgG Fc, TotalSeq-C0577 anti-human CD73 (Ecto-5'-nucleotidase)


title: 13_5-3_CUT&Tag

data_processing:
library strategy: CUT&Tag
All raw sequence data were quality trimmed for adaptor sequences, and reads shorter than 50bp were discarded using Fastp v0.20.1.
All reads were aligned to the mm10 mouse genome using Bowtie2 version 2.4.2 with the following parameters: --very-sensitive-local--no-una--no-mixed--no-discordant--phred33 -I 10 -X700.
Reads were then normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM).
Accessible regions across all samples were combined and the read counts in each region were tabulated
Assembly: mm10
Supplementary files format and content: FPKM

source_name: E13.5 fetal pancreatic epithelial cells

extract_protocol:
Fetal pancreas were harvest at E11.5, E13.5 and E15.5, digested in  TrypLE™ Express (ThermoFisher 12605010) and then purified by flow cytometry.
H3K36me3 CUT&Tag seq; DNA libraries were prepared based on the manufacturer’s instructions of the Trueprep index kit v2 (Vazyme, TD202). The DNA library was sequenced to an average of 20 million reads per sample.

value: E13.5 fetal pancreatic epithelial cells

tag: antibody


title: WT U2OS cells exposed to 50 nM trabectedin, biological replicateR2

value: 50 nM trabectedin


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland

value: High-risk NBL


title: 15_5-3_CUT&Tag

source_name: E15.5 fetal pancreatic epithelial cells

value: E15.5 fetal pancreatic epithelial cells


title: 11_5-3_CUT&Tag

source_name: E11.5 fetal pancreatic epithelial cells

value: E11.5 fetal pancreatic epithelial cells


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: post-treatment

value: male

value: MYCN non-amplified


title: B cells donor 3119 TP1, ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
3119_TP1_barcodes.tsv
3119_TP1_genes.tsv
3119_TP1_matrix.mtx
SeuratObj_Res_0.6.rds


title: E13_5_KO scRNA-seq

value: E13.5 fetal pancreas

value: PdxcreSetd2 f/f; KO


title: B cells donor 3342 TP1, ADT

description:
Antibody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
3342_TP1_barcodes.tsv
3342_TP1_genes.tsv
3342_TP1_matrix.mtx
SeuratObj_Res_0.6.rds


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M732AAA_T, not paired, scRNAseq [M732AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: E15_5_ATAC_1

data_processing:
Raw FASTQ reads were trimmed adapters generated by Trim Galore (v. 0.6.6) and then aligned to the mm10 reference genome through Bowtie2 (v.2.4.2) with the parameters --very-sensitive -X 2000
Multiple mapped and duplicated reads were removed
ATAC-seq accessible regions were called using MACS2 v 2.2.7.1 with the following parameters: --nomodel --shift -100 --extsize 200 --format BAMPE -p 0.01
Assembly: mm10
Supplementary files format and content: narrow peak

extract_protocol:
Fetal pancreas were harvest at E11.5, E13.5 and E15.5, digested in  TrypLE™ Express (ThermoFisher 12605010) and then purified by flow cytometry.
DNA libraries were constructed following the manufacturer’s instructions of the Trueprep index kit v2 (Vazyme, TD202) and thereafter sequenced to an average of 20 million reads per sample

value: E15.5 fetal pancreas


title: B cells donor 3119 TP2, GEX

description:
RNA
GEX (5' RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
3119_TP2_barcodes.tsv
3119_TP2_genes.tsv
3119_TP2_matrix.mtx
SeuratObj_Res_0.6.rds

data_processing:
Sequencing reads were mapped to the human reference genome and assigned to individual cells of origin using cell-specific barcodes in CellRanger v3.1.0. Sequence data were then processed using Seurat v3.2.3, following their default pipeline. Low-quality cells with high (>2500) or low (<200) UMI counts were filtered from the samples. Prior to clustering and UMAP visualization, all IGH, IGK, and IGL transcripts were removed from the single cell gene expression data. Gene expression levels for each cell were normalized by total expression, multiplied by a scale factor (10,000), and log-transformed. Cells with >5% mitochondrial reads were excluded. The 2000 most variable genes based on their average expression and dispersion were used for principal component analysis to reduce the dimensionality of the data. Clustering was performed using the Louvain algorithm implemented in the FindClusters function of Seurat (algorithm = 1, resolution = 0.6, dims. use = 1:20).
CellRanger
Assembly: hg38
Supplementary files format and content: CellRanger output files: _barcodes.tsv, _genes.tsv, _matrix.mtx
Supplementary files format and content: Germline annotations for V-gene, D-gene, and J-gene segments, constant region assignments, CDR3 sequences, and clonotype assigments for heavy and light chains: _filtered_contig_annotations.csv
Supplementary files format and content: Change-O output files for productively rearranged antibody heavy chains: _VDJ_heavy_productive_germ-pass.tsv
Supplementary files format and content: Seurat object of gene expression and antibody-derived tag data: SeuratObj_Res_0.6.rds
Library strategy: CITE-seq


title: E15_5_ATAC_2

value: WT


title: SM adjacent normal 7

type: RNA

city: Bunkyo-ku

first: Sayaka

last: Nagao

state: Tokyo

department: Gastroenterology

country: Japan

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Human gastric normal mucosa

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA was extracted (miRNeasy Mini kit, Qiagen) from tissue samples

tag: gender

value: M

value: normal mucosa


title: SM tumor 8

source_name: Human gastric adenocarcinoma

value: adenocarcinoma


title: SM adjacent normal 8


title: B cells donor 3119 TP1, GEX

description:
RNA
GEX (5' RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
3119_TP1_barcodes.tsv
3119_TP1_genes.tsv
3119_TP1_matrix.mtx
SeuratObj_Res_0.6.rds

value: PBMCs

value: CD19+ CD20+ B cells


title: SM tumor 7


title: Posttreatment NBL M694AAA_T, not paired, scRNAseq [M694AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: E13_5_ATAC_2


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2_6]

description:
CelSeq-2
barcodes.tsv

value: MYCN amplified


title: B cells donor 3342 TP2, GEX

description:
RNA
GEX (5' RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
3342_TP2_barcodes.tsv
3342_TP2_genes.tsv
3342_TP2_matrix.mtx
SeuratObj_Res_0.6.rds


title: E13_5_ATAC_1


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: B cells donor 3342 TP1, GEX

description:
RNA
GEX (5' RNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
3342_TP1_barcodes.tsv
3342_TP1_genes.tsv
3342_TP1_matrix.mtx
SeuratObj_Res_0.6.rds


title: H85-t8

city: Bethesda

first: Xin

middle: Wei

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: *** Due to patient privacy concerns, patient data will be submitted to dbGaP. ***

data_processing:
After demultiplexing with bcl2fastq, reads were aligned, tagged, and counted with Cell Ranger (version 6.0.1). All samples yielded a high number of reads ranging from 100-500 million and with >95% Q30 bases in barcodes.
Raw gene counts were normalized to the same sequencing depth using Cell Ranger. The raw counts were used to construct a Seurat object, which kept all genes expressed in at least 0.1% of cells.
All cells with fewer than 500 detected genes or with at least 50% of their detected genes being mitochondrial were filtered out.
Log-normalization was run with a scale factor of 10,000 using Seurat (version 4.1.0).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver tumor

extract_protocol:
Single cells were then captured either directly or from cryopreserved cell stocks, following the protocol of the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000127).
The libraries were prepared with the Chromium Next GEM Single Cell 3’ Kit (10x Genomics, PN-1000269) following the kit instruction manuals. Libraries were then pooled and sequenced with Illumina HiSeq 4000/NovaSeq 6000 platforms, targeting sequencing depth of 50,000 raw reads per cell.

treatment_protocol: Tumor tissues were stored in a tissue storage buffer (Miltenyi Biotec, Catalog #130-100-008) immediately after surgical removal and were digested with a Tumor Dissociation Kit (Miltenyi Biotec, Catalog #130-095-929) in Tumor Dissociation C Tubes (Miltenyi Biotec, Catalog #130-093-237).

value: Liver tumor

tag: cancer type

value: Hepatocellular carcinoma

tag: age


title: E11_5_ATAC_1

source_name: E11.5 fetal pancreas

value: E11.5 fetal pancreas


title: SM adjacent normal 5


title: SM tumor 5


title: SM tumor 6


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: post-treatment

value: male


title: H85-t0


title: Posttreatment NBL M315AAA_T, not paired, scRNAseq [M315AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: MYCN non-amplified


title: SM tumor 4


title: H77-t30


title: Posttreatment NBL M315AAA_T, not paired, scRNAseq [M315AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: Pretreatment NBL M124AAA_T, not paired, scRNAseq [M124AAA_T_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv

value: Intermediate-risk NBL

value: pre-treatment


title: E11_5_ATAC_2

value: WT


title: SM adjacent normal 4

value: M


title: H08-t76


title: sample study ID#_serum_liver disease diagnosis_gender [89_MASLD w/o MASH_Male]

type: protein

city: Boston

first: Simon

middle: T

last: Dillon

state: Massachusetts

address: 99 Brookline Ave, Research North Bldg, Room 107

department: IMBIO

institute: BIDMC RESEARCH

hyb_protocol: Hybridized overnight (19 hours) at 55 C as recommended by SomaLogic.

scan_protocol: SOMAmer matching probes printed onto Agilent slides.  After overnight hybridization slides were scanned on an Agilent Microarray SureScan Scanner model D.

data_processing: Standard data processing method as per SomaLogic recommended methods.  Normalized and calibrated using kit control samples.

label: Cy3 labelled SOMAmer

source_name: serum, after diagnostic liver biopsy, MASLD w/o MASH

label_protocol: Samples run in the manual version of the 1.3k SomaScan assay protocol.

extract_protocol: Serum samples and clinical data were collected within 3 months of liver biopsy.  Serum samples were all stored in -800C freezers in aliquots until use. Other forms of chronic liver diseases (CLDs) or daily consumption of greater than 20g of alcohol were excluded.  69 subjects with significant fibrosis (NAS<4, F2-4) were excluded, since they did not show MASH on biopsy.

treatment_protocol: Adult subjects (age 18+) with suspected MASLD who agreed to a liver biopsy for diagnosis and staging were prospectively enrolled between December 2009 and September 2014.  Biopsy was done on all subjects enrolled in this study.  Histological diagnosis was performed by the centers’ liver pathologists using liver biopsies of appropriate size (at least 8 portal tracts) that were scored for fibrosis (stages F0-F4) and features of MASH (steatosis, inflammation, ballooning) and given a NAS score (0-8) according to the NASH CRN criteria. Active MASH was defined as NAS > 4. Extended standard clinical laboratory parameters were determined by standardized test systems in the participating centers’ clinical laboratories.

value: Male

tag: biopsy

value: serum taken within 3 months of liver biopsy, MASLD = metabolic dysfunction-associated steatotic fatty liver disease, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: sample study ID#_serum_liver disease diagnosis_gender [75_MASLD w/o MASH_Female]

value: Female


title: sample study ID#_serum_liver disease diagnosis_gender [42_MASLD w/o MASH_Female]


title: H08-t54


title: sample study ID#_serum_liver disease diagnosis_gender [121_MASLD w/o MASH_Female]


title: sample study ID#_serum_liver disease diagnosis_gender [195_MASLD w/o MASH_Male]


title: SM tumor 3

value: adenocarcinoma


title: Pretreatment NBL M124AAA_T, not paired, scRNAseq [M124AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: SM adjacent normal 3

value: normal mucosa


title: SM adjacent normal 2


title: SM tumor 2


title: Control, replicate 2, post-treatment

city: Helsinki

first: Shuyu

last: Zheng

state: Uusimaa

address: Biomedicum 1U, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Cell quality control was performed using Seurat v4.0.4 (https://satijalab.org/seurat/)
Supplementary files format and content: GDCh38.d1.vd1
Supplementary files format and content: Tab-separated values files for cell annotation and matrix files for UMI counts

source_name: natural killer (NK) cells

extract_protocol:
All samples were detatched and resuspended in PBS + 0.04% BSA buffer.
Libraries were performed according to the manufacter’s instructions [Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index), 10x Genomics].

value: natural killer (NK) cells


title: Pretreatment NBL M124AAA_T, not paired, scRNAseq [M124AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland


title: SM adjacent normal 1


title: H49-t75

value: Liver tumor


title: sample study ID#_serum_liver disease diagnosis_gender [84_MASLD w/o MASH_Female]


title: Control, replicate 2, pre-treatment

description: 10x Genomics


title: SM adjacent normal 6


title: sample study ID#_serum_liver disease diagnosis_gender [199_MASLD w/o MASH_Male]


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL

value: MYCN amplified


title: Posttreatment NBL M313AAB_T, not paired, scRNAseq [M313AAB_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: post-treatment


title: Control, replicate 1, post-treatment

description: 10x Genomics


title: M tumor 8


title: SM tumor 1


title: sample study ID#_serum_liver disease diagnosis_gender [216_MASLD w/o MASH_Male]


title: M adjacent normal 8


title: Control, replicate 1, pre-treatment

description: 10x Genomics


title: sample study ID#_serum_liver disease diagnosis_gender [3_MASLD w/o MASH_Female]


title: Posttreatment NBL M481AAA_T, not paired, scRNAseq [M481AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor right adrenal gland

value: NBL tumor right adrenal gland

value: male


title: Pretreatment NBL M124AAA_T, not paired, scRNAseq [M124AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: Intermediate-risk NBL

value: MYCN non-amplified


title: NK, replicate 2, post-treatment

description: 10x Genomics


title: sample study ID#_serum_liver disease diagnosis_gender [113_MASLD w/o MASH_Male]


title: M adjacent normal 7


title: sample study ID#_serum_liver disease diagnosis_gender [26_MASLD w/o MASH_Male]


title: sample study ID#_serum_liver disease diagnosis_gender [96_MASLD w/o MASH_Male]


title: M adjacent normal 6

value: F


title: NK, replicate 1, pre-treatment

description: 10x Genomics

value: pre-treatment


title: Olaparib, replicate 2, post-treatment

description: 10x Genomics

source_name: KURAMOCHI

value: High grade ovarian serous adenocarcinoma cells

tag: cell line

value: KURAMOCHI

value: Olaparib


title: NK, replicate 2, pre-treatment

description: 10x Genomics


title: M tumor 7

value: M

value: adenocarcinoma


title: Posttreatment NBL M481AAA_T, not paired, scRNAseq [M481AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

tag: genotype


title: NK, replicate 1, post-treatment

description: 10x Genomics

value: natural killer (NK) cells

tag: treatment


title: M tumor 5

tag: tissue


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2_6]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland


title: sample study ID#_serum_liver disease diagnosis_gender [58_MASLD w/o MASH_Male]

value: Male

value: serum taken within 3 months of liver biopsy, MASLD = metabolic dysfunction-associated steatotic fatty liver disease, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: Olaparib, replicate 2, pre-treatment

description: 10x Genomics


title: Pretreatment NBL M124AAA_T, not paired, scRNAseq [M124AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: M adjacent normal 5

value: normal mucosa


title: M tumor 6


title: sample study ID#_serum_liver disease diagnosis_gender [16_MASLD w/o MASH_Female]

value: Female


title: Posttreatment NBL M481AAA_T, not paired, scRNAseq [M481AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor right adrenal gland

value: High-risk NBL

value: post-treatment

value: MYCN amplified


title: Posttreatment NBL M481AAA_T, not paired, scRNAseq [M481AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: male


title: Olaparib, replicate 1, pre-treatment

description: 10x Genomics

value: pre-treatment


title: Olaparib, replicate 1, post-treatment

description: 10x Genomics

value: High grade ovarian serous adenocarcinoma cells


title: M adjacent normal 4


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: Carboplatin, replicate 2, pre-treatment

description: 10x Genomics

value: KURAMOCHI


title: sample study ID#_serum_liver disease diagnosis_gender [115_MASLD w/o MASH_Male]


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [118_MASLD w/o MASH_Female]


title: Carboplatin, replicate 1, post-treatment

description: 10x Genomics

value: Carboplatin


title: Carboplatin, replicate 2, post-treatment

description: 10x Genomics


title: sample study ID#_serum_liver disease diagnosis_gender [179_MASLD w/o MASH_Female]


title: sample study ID#_serum_liver disease diagnosis_gender [219_MASLD w/o MASH_Male]


title: M tumor 4

value: M


title: sample study ID#_serum_liver disease diagnosis_gender [175_MASLD w/o MASH_Female]


title: Carboplatin, replicate 1, pre-treatment

description: 10x Genomics


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [160_MASH_Male]

source_name: serum, after diagnostic liver biopsy, MASH

value: serum taken within 3 months of liver biopsy, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: Posttreatment NBL M761AAA_T, not paired, scRNAseq [M761AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor left adrenal gland

value: MYCN non-amplified


title: GM12878_RNA-seq_Rep2

city: Nashville

first: Tyler

middle: J

last: Hansen

state: TN

address: 2215 Garland Ave

department: Biochemistry

institute: Vanderbilt University

description:
GM12878+LCL8664_DESeq2-normalized_counts.tsv
GM12878+LCL8664_TPM-normalized_counts.tsv

data_processing:
active regions for each condition were called using a custom process described in the manuscript
activity signal was created using a custom process described in the manuscript
cis/trans regions were called using a custom process described in the manuscript
normalized RNA-seq counts were generated using a custom process described in the manuscript
Assembly: hg38 or rheMac10
Supplementary files format and content: region files (BED/narrowPeak)
Supplementary files format and content: ATAC-STARR-seq signal files (bigWig)
Supplementary files format and content: normalized RNA-seq count data (tsv)

growth_protocol: We cultured both cell lines with RPMI 1640 Media containing 15% fetal bovine serum, 2mM GlutaMAX, 100 units/mL penicillin and 100 μg/mL streptomycin. Cells were cultured at 37°C, 80% relative humidity, and 5% CO2. Cell density was maintained between 0.2×106 and 1.5×106 cells/mL with a 50% media change every 2-4 days. All cell lines were regularly screened for mycoplasma contamination.

extract_protocol:
ATAC-STARR-seq samples were extracted 24hrs after transfection with the reporter plasmid library. For RNA-seq, total RNA was harvested using TRIzol™ Reagent and Phasemaker™ Tubes Complete System 24 hours after transfection with hSTARR_ORI plasmid.
ATAC-STARR-seq libraries were generated following the protocols described in Hansen & Hodges 2022. RNA-seq libraries were generated from total RNA using the SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian from Takara bio.

value: Lymphoblasotid cell line (immortalized B cells)

value: mock plasmid DNA transcfection

tag: biomaterial provider

tag: molecule type

value: total RNA, ribo (-)


title: sample study ID#_serum_liver disease diagnosis_gender [111_MASLD w/o MASH_Male]

value: Male

value: serum taken within 3 months of liver biopsy, MASLD = metabolic dysfunction-associated steatotic fatty liver disease, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: Sperm_HFD_rep3

city: Hefei

first: Yong-Wei

last: Xiong

state: Anhui

address: Hefei 230032, China

institute: Anhui Medical University

description: IP (immunoprecipitated, Cy5-labelled), Sup (supernatant, Cy3-labelled)

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar). After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

scan_protocol: Scanned on an Agilent G2505C scanner. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).
matrix values: normalized log 2 ratio (Cy5/Cy3) representing test/reference

source_name: Sperm, HFD3, immunoprecipitated

label_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, the total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Sperm

value: week 10

source_name: Sperm, HFD3, supernatant


title: M adjacent normal 3

value: F

value: normal mucosa


title: M tumor 2

value: adenocarcinoma


title: M adjacent normal 2


title: M adjacent normal 1


title: M tumor 3


title: Posttreatment NBL M671AAA_T, not paired, scRNAseq [M671AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland

tag: tumor type

value: High-risk NBL

tag: tumor stage

value: post-treatment

value: male

value: MYCN amplified


title: GM12878_RNA-seq_Rep1

tag: cell type


title: Sperm_HFD_rep2

source_name: Sperm, HFD2, immunoprecipitated

source_name: Sperm, HFD2, supernatant


title: sample study ID#_serum_liver disease diagnosis_gender [187_MASH_Female]

tag: Sex

value: Female

value: serum taken within 3 months of liver biopsy, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: Posttreatment NBL M761AAA_T, not paired, scRNAseq [M761AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: MYCN non-amplified


title: sample study ID#_serum_liver disease diagnosis_gender [87_MASH_Female]


title: Sperm_HFD_rep1

source_name: Sperm, HFD1, immunoprecipitated

source_name: Sperm, HFD1, supernatant


title: hESC, nucleus, Day0, rep2 [D0_nucleus-2]

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatics (version 0.36).
Trimmed sequence reads were mapped to hg38 (GENCODE v28) human genome using Hisat2 (v2.0.5) with parameter “--rna-strandness RF”.
The gatk was used to remove PCR duplicates from aligned BAM files.
Raw counts at the gene level were calculated with featureCounts (version 1.6.2). Isoform-level expression was quantified as transcripts per million reads (TPM) with Salmon (version 1.3.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

source_name: H1 hESC

growth_protocol: Human ESC line H1 were maintained in mTeSR1 (StemCell Technologies, 85850) on matrigel (Corning, 354277)-coated plates. hESCs were fed with fresh hESC medium daily.

extract_protocol:
definitive mesoderm cells differentiation protocol:
To initiate mesoderm differentiation, hESCs were plated onto matrigel-coated 6-well plates with 70% of cell confluence, and then these cells were cultured in IMDM medium (Gibco, 12440053) plus 10% FBS (Gibco, 10099141), 2 mM Glutamine (Gibco, 25030164), 50 μg/mL Ascorbic Acid (StemCell Technologies, 72132), 0.1 μM Monothioglycerol (Sigma, M6145), 10 ng/mL BMP4 (StemCell Technologies, 02524) for 1 day. And then cells were cultured 4 days in the above medium supplemented with bFGF (2.5 ng/mL, StemCell Technologies, 78003.1). Cells were fed with fresh medium daily.
subcellular isolation protocol:
Operations refer to Subcellular Protein Fractionation Kit’s (Thermo Fisher, 78840) instruction. We collected cells and added cytoplasmic extraction buffer in the tube. After incubating the tube at 4°C for 10 min and centrifuging at 500 × g for 5 min, we immediately transferred the supernatant (cytoplasmic extract). Then we added the membrane extraction buffer, incubated at 4℃ for 10 min and centrifuged at 3000 × g for 5 min, and transferred the supernatant (membrane extract). We further added the nuclear extraction buffer. After incubating at 4℃ for 30 min and centrifuging at 5000 × g for 5 min, we transferred the supernatant (soluble nuclear extract) fraction. Similarly, we added nuclear extraction buffer containing CaCl2 (5 mM) and micrococcal nuclease (300 units), incubated at room temperature for 15 min, centrifuged at 20,000 × g for 5 min, and transferred the supernatant (chromatin-bound nuclear extract) fraction. Finally, pellet extraction buffer was added in tube. After incubating at room temperature for 10 min and centrifuging at 20,000 × g for 5 min, we obtained the supernatant (i.e., the cytoskeletal extract). All of the buffers were supplemented with protease inhibitor and RNase inhibitor.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: H1 hESC

value: embryonic stem cells

value: WT

tag: time

value: Day 0


title: Sperm_C_rep3

source_name: Sperm, C2, immunoprecipitated

value: Sperm

source_name: Sperm, C2, supernatant


title: Posttreatment NBL M017AAB_T2, paired with 000BNB, scRNAseq [M017AAB_T2_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

value: female


title: Posttreatment NBL M017AAB_T2, paired with 000BNB, scRNAseq [M017AAB_T2_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: Sperm_C_rep2

value: week 10


title: hESC, cytoplasm, Day0, rep2 [D0_cytoplasm-2]


title: hESC, nucleus, Day0, rep1 [D0_nucleus-1]


title: Posttreatment NBL M017AAB_T2, paired with 000BNB, scRNAseq [M017AAB_T2_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [170_MASH_Male]

value: Male


title: Posttreatment NBL M017AAB_T2, paired with 000BNB, scRNAseq [M017AAB_T2_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [214_MASH_Female]


title: Sperm_C_rep1

source_name: Sperm, C1, immunoprecipitated

source_name: Sperm, C1, supernatant


title: sample study ID#_serum_liver disease diagnosis_gender [67_MASH_Female]


title: M tumor 1

source_name: Human gastric adenocarcinoma

value: M

value: adenocarcinoma


title: sample study ID#_serum_liver disease diagnosis_gender [191_MASH_Male]


title: Posttreatment NBL M017AAB_T2, paired with 000BNB, scRNAseq [M017AAB_T2_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland

value: High-risk NBL


title: Posttreatment NBL M017AAB_T2, paired with 000BNB, scRNAseq [M017AAB_T2_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: post-treatment


title: RNA-seq_ HuLM_TP-472 rep3

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

description: TP-472-HuLM RNA

data_processing:
Quasi-mapping and quantification: salmon 1.4.0
Genome_build: GRCh38
Supplementary_files_format_and_content: gene level raw abdunance in TSV format

source_name: uterine fibroid cell line

growth_protocol: The immortalized human leiomyoma cell line (HuLM) were cultured and maintained in phenol red-free, 10% fetal bovine serum Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12

extract_protocol:
Cell pellets were  flash-frozen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The immortalized human leiomyoma cell line (HuLM) were treated with I-BRD9 (5 uM) or TP-472 (5 uM) for 48 hours

value: HuLM

value: uterine fibroid

value: BRD9 inhibitor


title: ARCAPM_9B_si_1

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
The Illumina TruSeq RNA kit was used for 100nt/single end reads, 4 samples were run per lane using the standard Truseq indices.  Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx format; the read count for each gene

source_name: ARCAPM

growth_protocol: Prostate cancer DU145, 22Rv1, and ARCaPM were obtained from ATCC and Novicure grown in RPMI media with 10% FBS in a humidified 37°C atmosphere with 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini kit (QIAGEN) in accordance with manufacturer’s instructions.
High-quality total RNA samples (RNA Integrity score > 8 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol. The libraries were sequenced by HiSeq 2500 genome sequencer (Illumina) to generate 100 bp single-end reads.
Hi-Seq, 100nt, Single-End Read, 4 samples per lane

treatment_protocol: DU145, 22Rv1 and ARCaPM, were collected after 48 hours of being transfected with siRNA control or two siRNAs targeting MITF.

tag: diagnosis

value: Prostate cancer

value: male

tag: repository source fibroblast id

value: ARCAPM (ATCC)


title: Posttreatment NBL M348AAB_T2, paired with M348AAB_T1, scRNAseq [M348AAB_T2_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

data_processing:
Failed reactions were identified by low levels of ERCC external RNA controls and excluded. Furthermore, a liveness threshold was calculated for each plate based on the wells with no cell added, in order to distinguish live cells from dead and/or apoptotic cells. This threshold was set to a minimum of 500 transcripts.
The percentage of transcripts mapping to the mitochondrial genome was calculated and cells with more mitochondrial‐encoded transcripts over nuclear ones were removed. Mitochondrial and ERCC transcripts were removed from the dataset, as well as cells with <1000 nuclear‐encoded transcripts or <500 genes. In addition, cells with >150.000 nuclear‐encoded transcripts were removed. Genes with low expression, that is either having less than 5 cells expressing the gene or less than two cells with less than two transcripts, were removed. A total of 105 cells, forming a distinct cluster of erythroid lineages, was identified based on high 515 levels of hemoglobin complex genes, and was removed. To improve cross‐sample comparisons, ambient mRNA contamination in individual cells was estimated and removed using DecontX. DecontX was run for all samples (batches) individually. Removal of cells with less than 1000 nuclear‐encoded transcripts was repeated on the decontaminated counts matrix outputted by DecontX.
All subsequent analyses were performed using R (version 4.0.2) and the package Seurat (version 3.2.2,RRID:SCR_007322) with default parameters unless stated otherwise. The SCTransform() function was used to normalize and scale the data, and to identify variable genes. To avoid clustering of cells based on specific cell processes, genes associated with sex (XIST, TSIX, and Y chromosome‐specific genes), cell cycle phase, dissociation stress (heat shock proteins; GO:0006986), and activity (ribosomal protein genes; GO:0022626), were removed as described before.
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NBL tumor right adrenal gland

value: NBL tumor right adrenal gland

value: MYCN non-amplified


title: RNA-seq_ HuLM_I-BRD9 rep4

description: I-BRD9-HuLM RNA


title: Posttreatment NBL M348AAB_T2, paired with M348AAB_T1, scRNAseq [M348AAB_T2_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv


title: RNA-seq_ HuLM_I-BRD9 rep3

description: I-BRD9-HuLM RNA


title: RNA-seq_ HuLM_TP-472 rep1

description: TP-472-HuLM RNA


title: sample study ID#_serum_liver disease diagnosis_gender [130_MASH_Female]

source_name: serum, after diagnostic liver biopsy, MASH

value: Female

value: serum taken within 3 months of liver biopsy, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: sample study ID#_serum_liver disease diagnosis_gender [72_MASH_Male]


title: ARCAPM_9C_si_2

tag: gender


title: hESC, cytoplasm, Day0, rep1 [D0_cytoplasm-1]

value: H1 hESC

value: embryonic stem cells

value: WT

value: Day 0


title: ARCAPM_8A_Control_2


title: RNA-seq_ HuLM_I-BRD9 rep2

description: I-BRD9-HuLM RNA


title: Posttreatment NBL M348AAB_T2, paired with M348AAB_T1, scRNAseq [M348AAB_T2_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

value: female


title: sample study ID#_serum_liver disease diagnosis_gender [28_MASH_Male]

value: Male


title: Posttreatment NBL M348AAB_T2, paired with M348AAB_T1, scRNAseq [M348AAB_T2_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL

value: post-treatment


title: ARCAPM_7C_si_2


title: ARCAPM_9A_Control_3


title: sample study ID#_serum_liver disease diagnosis_gender [64_MASH_Female]


title: RNA-seq_ HuLM_TP-472 rep2

description: TP-472-HuLM RNA

value: HuLM

value: uterine fibroid


title: Posttreatment NBL M348AAB_T2, paired with M348AAB_T1, scRNAseq [M348AAB_T2_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: RNA-seq_ HuLM_VEH rep4

description: VEH-HuLM RNA

value: DMSO (VEH)


title: ARCAPM_7B_si_1

value: Prostate cancer

value: male


title: ARCAPM_8C_si_2

value: ARCAPM (ATCC)


title: sample study ID#_serum_liver disease diagnosis_gender [97_MASH_Male]


title: Posttreatment NBL M348AAB_T2, paired with M348AAB_T1, scRNAseq [M348AAB_T2_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor right adrenal gland

value: MYCN non-amplified


title: ARCAPM_7A_Control_1


title: ARCAPM_8B_si_1


title: sample study ID#_serum_liver disease diagnosis_gender [152_MASH_Female]

value: Female

value: serum taken within 3 months of liver biopsy, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: Pretreatment NBL M017AAB_T1, paired with 000GXF, scRNAseq [M017AAB_T1_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor left adrenal gland

value: NBL tumor left adrenal gland

value: pre-treatment


title: sample study ID#_serum_liver disease diagnosis_gender [181_MASH_Male]


title: RNA-seq_ HuLM_VEH rep3

description: VEH-HuLM RNA


title: sample study ID#_serum_liver disease diagnosis_gender [168_MASH_Female]


title: 22Rv1_6C_si_2

value: 22Rv1 (ATCC)


title: sample study ID#_serum_liver disease diagnosis_gender [211_MASH_Male]


title: Pretreatment NBL M017AAB_T1, paired with 000GXF, scRNAseq [M017AAB_T1_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: female


title: 22Rv1_6B_si_1


title: RNA-seq_ HuLM_VEH rep2

description: VEH-HuLM RNA


title: RNA-seq_ HuLM_VEH rep1

description: VEH-HuLM RNA


title: RNA-seq_ HuLM_I-BRD9 rep1

description: I-BRD9-HuLM RNA

value: BRD9 inhibitor


title: Pretreatment NBL M017AAB_T1, paired with 000GXF, scRNAseq [M017AAB_T1_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL


title: sample study ID#_serum_liver disease diagnosis_gender [205_MASH_Male]

value: Male


title: 22Rv1_6A_Control_3


title: sample study ID#_serum_liver disease diagnosis_gender [129_MASH_Female]


title: Nef_3

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

description: SupT1/Nef rep3

data_processing:
Raw image files were transformed to sequence reads by CASAVA base calling.
Sequenced reads were trimmed for adapater sequences, then mapped to hg19 using STAR.
Differential expression was performed by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: count data and differential expression data

source_name: T-lymphoblast cell line

growth_protocol: SupT1 cells were routinely passaged 2-3 times per week. Twenty-four hours prior to transductions, SupT1 cells were split 1:4.

extract_protocol:
Total RNA was extracted using phenol/chlorform prior to ethanol precipitation.
stranded RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SupT1 cells ( 10^6 cells) were transduced with each virus stock using an moi of 2.

value: T-lymphoblast

value: HIV Nef


title: Posttreatment NBL M993AAA_T2, paired with M993AAA_T1, scRNAseq [M993AAA_T2_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv

value: post-treatment

value: MYCN amplified


title: sample study ID#_serum_liver disease diagnosis_gender [194_MASH_Male]


title: Nef_2

description: SupT1/Nef rep2


title: Nef_1

description: SupT1/Nef rep1


title: 22Rv1_5B_si_1

value: Prostate cancer

value: male


title: sample study ID#_serum_liver disease diagnosis_gender [45_MASH_Female]


title: Posttreatment NBL M993AAA_T2, paired with M993AAA_T1, scRNAseq [M993AAA_T2_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [198_MASH_Male]


title: Posttreatment NBL M993AAA_T2, paired with M993AAA_T1, scRNAseq [M993AAA_T2_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M993AAA_T2, paired with M993AAA_T1, scRNAseq [M993AAA_T2_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv


title: Rev_1

description: SupT1/Rev rep1

value: HIV Rev


title: 22Rv1_4C_si_2


title: Rev_3

description: SupT1/Rev rep3


title: sample study ID#_serum_liver disease diagnosis_gender [33_MASH_Male]


title: 22Rv1_4B_si_1


title: 22Rv1_4A_Control_1


title: sample study ID#_serum_liver disease diagnosis_gender [135_MASH_Male]


title: EV_3

description: SupT1/EV rep3

value: empty vector


title: Pretreatment NBL M260AAB_T, not paired, scRNAseq [M260AAB_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor right cervical primary tumor

value: NBL tumor right cervical primary tumor


title: Posttreatment NBL M993AAA_T2, paired with M993AAA_T1, scRNAseq [M993AAA_T2_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: Posttreatment NBL M993AAA_T2, paired with M993AAA_T1, scRNAseq [M993AAA_T2_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [120_MASH_Female]

value: Female

value: serum taken within 3 months of liver biopsy, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: 22Rv1_5C_si_2


title: sample study ID#_serum_liver disease diagnosis_gender [162_MASH_Male]


title: DU145_3C_si_2

value: DU145 (ATCC)


title: Pretreatment NBL M260AAB_T, not paired, scRNAseq [M260AAB_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: pre-treatment


title: EV_2

description: SupT1/EV rep2


title: sample study ID#_serum_liver disease diagnosis_gender [209_MASH_Female]


title: DU145_3B_si_1


title: EV_1

description: SupT1/EV rep1


title: 22Rv1_5A_Control_2

value: 22Rv1 (ATCC)


title: Pretreatment NBL M260AAB_T, not paired, scRNAseq [M260AAB_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: female


title: Rev_2

description: SupT1/Rev rep2


title: SupT1_3

description: SupT1 rep3

value: untreated


title: Pretreatment NBL M260AAB_T, not paired, scRNAseq [M260AAB_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL


title: DU145_3A_Control_3


title: sample study ID#_serum_liver disease diagnosis_gender [90_MASH_Male]

value: Male


title: Posttreatment NBL M228AAA_T2, paired with M228AAA_T1, scRNAseq [M228AAA_T2_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland

value: MYCN non-amplified


title: SupT1_2

description: SupT1 rep2

value: T-lymphoblast


title: sample study ID#_serum_liver disease diagnosis_gender [22_MASH_Male]


title: DU145_2C_si_2

value: Prostate cancer


title: DU145_2B_si_1

value: male


title: SupT1_1

description: SupT1 rep1


title: Posttreatment NBL M228AAA_T2, paired with M228AAA_T1, scRNAseq [M228AAA_T2_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv

value: post-treatment


title: Posttreatment NBL M228AAA_T2, paired with M228AAA_T1, scRNAseq [M228AAA_T2_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: sample study ID#_serum_liver disease diagnosis_gender [105_MASH_Female]


title: sample study ID#_serum_liver disease diagnosis_gender [69_MASH_Male]


title: DU145_2A_Control_2


title: DU145_1C_si_2


title: Posttreatment NBL M228AAA_T2, paired with M228AAA_T1, scRNAseq [M228AAA_T2_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: RNA-seq_SupT1/Nef rep2

value: HIV Nef


title: sample study ID#_serum_liver disease diagnosis_gender [95_MASH_Female]


title: DU145_1B_si_1


title: RNA-seq_SupT1/Nef rep1


title: sample study ID#_serum_liver disease diagnosis_gender [88_MASH_Male]


title: sample study ID#_serum_liver disease diagnosis_gender [137_MASH_Male]


title: RNA-seq_SupT1/Rev rep3

value: HIV Rev


title: Posttreatment NBL M228AAA_T2, paired with M228AAA_T1, scRNAseq [M228AAA_T2_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: DU145_1A_Control_1


title: sample study ID#_serum_liver disease diagnosis_gender [165_MASH_Male]


title: Pretreatment NBL M264AAB_T, not paired, scRNAseq [M264AAB_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: RNA-seq_SupT1/Rev rep2


title: RNA-seq_SupT1/Rev rep1


title: sample study ID#_serum_liver disease diagnosis_gender [197_MASH_Male]


title: sample study ID#_serum_liver disease diagnosis_gender [171_MASH_Female]

value: Female


title: RNA-seq_SupT1/Nef rep3


title: Pretreatment NBL M264AAB_T, not paired, scRNAseq [M264AAB_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: LCL8664_RNA-seq_Rep2

organism: Macaca mulatta

value: Lymphoblasotid cell line (immortalized B cells)

value: mock plasmid DNA transcfection

value: total RNA, ribo (-)


title: RNA-seq_SupT1/EV rep3

value: empty vector


title: LCL8664_RNA-seq_Rep1


title: Pretreatment NBL M264AAB_T, not paired, scRNAseq [M264AAB_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: pre-treatment

value: female


title: Pretreatment NBL M264AAB_T, not paired, scRNAseq [M264AAB_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL


title: sample study ID#_serum_liver disease diagnosis_gender [213_MASH_Male]

value: Male

value: serum taken within 3 months of liver biopsy, MASH = metabolic dysfunction-associated steatohepatitis metabolic dysfunction-associated steatohepatitis


title: RNA-seq_SupT1/EV rep1


title: RNA-seq_SupT1/EV rep2


title: Pretreatment NBL M787AAA_T, not paired, scRNAseq [M787AAA_T_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland

value: CDK4 amplified


title: LCL8664-DNA_in_LCL8664-cells_RNA_Rep3

description:
MM_active.regions.bed
MM_merged-reps_RNA-to-DNA_log2.crossmap.bw
HH_active.regions.bed
HH_merged-reps_RNA-to-DNA_log2.bw
conserved_active.regions.bed
human-specific.regions.bed
macaque-specific.regions.bed
human-specific_cis.bed
human-specific_trans.bed
macaque-specific_cis.bed
macaque-specific_trans.bed
human-specific_cis-only.bed
human-specific_trans-only.bed
human-specific_cis+trans.bed
macaque-specific_cis-only.bed
macaque-specific_trans-only.bed
macaque-specific_cis+trans.bed

data_processing:
library strategy: ATAC-STARR-seq
active regions for each condition were called using a custom process described in the manuscript
activity signal was created using a custom process described in the manuscript
cis/trans regions were called using a custom process described in the manuscript
normalized RNA-seq counts were generated using a custom process described in the manuscript
Assembly: hg38 or rheMac10
Supplementary files format and content: region files (BED/narrowPeak)
Supplementary files format and content: ATAC-STARR-seq signal files (bigWig)
Supplementary files format and content: normalized RNA-seq count data (tsv)

molecule: other

value: reporter RNA


title: RNA-seq_SupT1 rep2

value: T-lymphoblast

value: untreated


title: RNA-seq_SupT1 rep3


title: Posttreatment NBL M228AAA_T2, paired with M228AAA_T1, scRNAseq [M228AAA_T2_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: post-treatment

value: MYCN non-amplified


title: Pretreatment NBL M787AAA_T, not paired, scRNAseq [M787AAA_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: RNA-seq_SupT1 rep1


title: LCL8664-DNA_in_LCL8664-cells_RNA_Rep1


title: LCL8664-DNA_in_LCL8664-cells_RNA_Rep2


title: LCL8664-DNA_in_LCL8664-cells_DNA_Rep3

value: plasmid DNA


title: Pretreatment NBL M277AAB_T, not paired, scRNAseq [M277AAB_T_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor right adrenal gland

value: male

value: MYCN amplified


title: Pretreatment NBL M787AAA_T, not paired, scRNAseq [M787AAA_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: s1_KO_fin_4dpa.rep3

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7, with cutadapt v 3.5) and mapped with STAR (v 2.7.10, with parameters --twopassMode Basic and supplying the Ensembl danRer11 annotation) to zebrafish genome (danRer11).
The mapped reads were counted using R/Bioconductor GenomicAlignments package(v 1.30.0).
Assembly: danRer11
Supplementary files format and content: tab-delimited text files include normalized counts  for each Sample by library size

organism: Danio rerio

source_name: caudal fin

growth_protocol: Zebrafish of the outbred Ekkwill (EK) strain at about 4-8 months of age and regeneration-associated silencer (s1) knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily, and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.

extract_protocol:
Fins were amputated at 50% of their original length using scalpel (Sterile Scalpel Blades #22, Feather). Biological triplicate pools of caudal fin clips from regeneration-associated silencer (s1) knockout fish and their WT siblings were collected at 0 dpa (freshly amputated), 1 dpa, or 4 dpa time points via scalpel (Sterile Scalpel Blades #22, Feather) from 10 fish per pool. Fin tissues were homogenized in Tri-reagent (Sigma) and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit-5 (Zymo).
cDNA was synthesized from 20 ng of total RNA with a Maxima H-minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel-cutting and extraction, and 300 - 800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ-MGI2000, 100 bp PE, by BGI Americas.

treatment_protocol: Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water.

value: caudal fin

value: s1 silencer homozygous knockout


title: LCL8664-DNA_in_LCL8664-cells_DNA_Rep2

value: Lymphoblasotid cell line (immortalized B cells)


title: Pretreatment NBL M277AAB_T, not paired, scRNAseq [M277AAB_T_scR-CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

extract_protocol:
Tumor material was collected in the operating room by Truecut biopsy (samples at diagnosis) or surgical resection (debulking procedure after induction chemotherapy). The Dutch samples were gently dissociated into single‐cells and sorted by flow cytometry for single‐cell RNA sequencing using the CEL‐Seq2 platform. In brief, preparation of the tumor pieces for single‐cell RNA sequencing was started within 4 hours after the surgery. The material was minced into pieces <1mm3 and dissolved by enzymatic digestion with collagenase I, II and IV (2.5 mg/mL) at 37°C with agitation for max. 1 hour. The samples were filtered through a 70 μm cell strainer and washed in DMEM. Cells were further separated into a single cell suspension with the NeuroCult dissociation kit according to the manufacturer's protocol (StemcellTM Technologies, cat#05707), washed and stained with DAPI and DRAQ5. Next to this unbiased strategy, some samples were additionally stained with antibodies to enrich for T cell populations (NB124, NB125 with CD3‐PE (Biolegend, cat#300308); NB124 with TCRγδ‐BV421 (Biolegend, cat#331217) or with GD2‐FITC (BD Biosciences, cat#563439) to enrich for tumor cells (000GGU, 000GXF, NB106, NB107, NB098, NB125, NB125, NB130, NB152). Single live cells were sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a FACSJazz, FACSAria II or Sony SH800S machine and subsequently spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing. Peripheral blood mononuclear cells (PBMC) from 5 healthy young adult donors (mean age 28) were isolated by Ficoll-Paque (VWR) density centrifugation and stained with fixable viability dye efluor506 (eBioscience, cat#65‐0866‐14), CD3‐PE (Biolegend, cat#300308) and CD56‐APC (Biolegend, cat#318310) antibodies. Subsequently, live CD3+ T cells and CD56+ NK cells were FACS sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a Sony SH800S machine. The plates were spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing.
All samples were processed for total transcriptome amplification, library preparation and sequencing into Illumina sequencing libraries as previously described70. Paired‐end 2x75 bp sequencing read length was used to sequence the prepared libraries using the Illumina NextSeq sequencer. Sharq preprocessing and QC pipeline were applied to process the single‐cell RNA‐seq data as described71. Read mapping was done using STAR version 2.6.1 (RRID:SCR_004463) on the hg38 Patch 10 human genome. Function featureCounts (RRID:SCR_012919) of the subread package (version 1.5.2) was used to assign reads based on GENCODE version 26 (RRID:SCR_014966).

value: High-risk NBL

value: pre-treatment


title: LCL8664-DNA_in_LCL8664-cells_DNA_Rep1


title: Pretreatment NBL M277AAB_T, not paired, scRNAseq [M277AAB_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv


title: Pretreatment NBL M277AAB_T, not paired, scRNAseq [M277AAB_T_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: s1_KO_fin_1dpa.rep3


title: s1_KO_fin_4dpa.rep1


title: M. bovis AF2122/97 with B12 replicate 2

city: Zaragoza

first: Jesus

last: Gonzalo-Asensio

state: Zaragoza

address: C/ Domingo Miral sn

department: Microbiology

country: Spain

institute: University of Zaragoza

description: AF2122/97 B12 R2

data_processing:
analysis of the generated raw sequence data was carried out using CLC Genomics Workbench 12.0.3.
The bioinformatics analysis started with trimming of raw sequences to generate high quality data only.  000962.3) or M. bovis AF2122/97 (NC_002945.3)
The high-quality sequencing reads were mapped against the reference genomes, M. tuberculosis H37Rv (NC_000962.3), M. tuberculosis GC1237 (NC_000962.3) or M. bovis AF2122/97 (NC_002945.3)
Assembly: NC_000962.3 (H37 and GC1237 strains) and NC_002945.3 (AF2122/97 strain)
Supplementary files format and content: wig format

organism: Mycobacterium tuberculosis variant bovis

growth_protocol: Mycobacteria were cultured at 37ºC in Middlebrook 7H9 liquid medium (Difco) containing 0.05% (vol/vol) Tween-80 (Sigma) and supplemented with 10% (vol/vol) of ADC (Middlebrook)

extract_protocol:
RNA extraction was performed with a Fast-prep instrument following the protocol described in PMID: 32361249
Library construction of cDNA molecules was carried out using a Ribosomal Depletion Library Preparation Kit (TruSeq with Ribo-Zero Kit) following the manufacturer's recomendatiopns.

treatment_protocol: When required adenosylcobalamin (Sigma) was added at concentrations of 10 mg/mL

tag: strain

value: Estándar media + B12


title: s1_KO_fin_4dpa.rep2


title: s1_KO_fin_1dpa.rep2


title: Pretreatment NBL M348AAB_T1, paired with M348AAB_T2, scRNAseq [M348AAB_T1_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

value: female


title: M. bovis AF2122/97 with B12 replicate 1

description: AF2122/97 B12 R1


title: Pretreatment NBL M348AAB_T1, paired with M348AAB_T2, scRNAseq [M348AAB_T1_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: s1_KO_fin_1dpa.rep1


title: Pretreatment NBL M787AAA_T, not paired, scRNAseq [M787AAA_T_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland

value: CDK4 amplified


title: Y479A, SMI, Rep4

first: Brian

last: Carrick

address: 433 Babcock Drive

institute: University of Wisconsin-Madison

data_processing:
Full pipeline eCLIP-seq Processing Pipeline v1.P 20160215 (https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.3810/MediaObjects/41592_2016_BFnmeth3810_MOESM199_ESM.pdf)
Reads from Lane 1 and Lane 2 were concatenated before processing.
Adapters trimmed using cutadapt v 1.18
Reads were mapped to the C. elegans genome (ce10) with STAR v 2.7.2a
PCR duplicates were removed and peaks using Yeo lab scripts (https://github.com/gpratt/gatk/releases/tag/2.3.2)
Peaks were called by Clipper (https://github.com/YeoLab/clipper/releases/tag/1.1)
Assembly: UCSC ce10
Supplementary files format and content: bigWig eCLIP peaks

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were grown on standard NGM plates seeded with OP50 at 20C until 24 hours after the L4 stage.

extract_protocol:
Animals were lysed by bead milling.
Libraries were prepared as described in VanNostrand et al 2016. doi: 10.1038/nmeth.3810

treatment_protocol: Animals were UV irradiated 3 times sequentially at 254 nm with 400 mJ/cm2

value: whole animal

tag: developmental stage

value: L4 + 24 hours

value: hermaphrodite

tag: eclip ip antibody


title: Y479A, SMI, Rep1


title: Y479A, IP, Rep3

value: αFLAG(M2) (Sigma F1804)


title: s1_KO_fin_0dpa.rep2


title: Pretreatment NBL M348AAB_T1, paired with M348AAB_T2, scRNAseq [M348AAB_T1_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: MYCN non-amplified


title: M. bovis AF2122/97 without B12 replicate 1

description: AF2122/97 wo B12 R1

value: Estándar media


title: s1_KO_fin_0dpa.rep1


title: Y479A, IP, Rep2


title: Pretreatment NBL M348AAB_T1, paired with M348AAB_T2, scRNAseq [M348AAB_T1_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor right adrenal gland


title: pmm,bamapig,snRNA_seq

city: chengdu

first: chen

last: long

state: sichuan

address: 211 Huimin Road, Wenjiang District

department: animal science and technology

institute: Sichuan Agricultural University

description: 10x Genomics

data_processing:
The 10x Genomics Chromium Single Cell 3’ Gene Expression solution was harnessed for this purpose. All experimental protocols were meticulously executed in adherence to the manufacturer's guidelines, accessible at （www.10xgenomics.com/support/single-cell-gene-expression）.
Assembly: hg8
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: subcutaneous adipose tissue of the back

extract_protocol:
The quality control standards for preparing single-cell suspension samples encompassed specific criteria: a cell viability threshold surpassing 80%, a cell concentration range of 700 to 1200 cells/μL, and cell diameters within 5 to 30 μm. For the PMM, SAT, and GOM samples, cell nuclei extraction took place during sample preparation using the 10x Chromium Nuclei Isolation Kit due to their notably enlarged cell diameters.
Ensuring the viability of cell/cell nucleus suspensions, which met the set standards, these were subsequently loaded onto 10x Genomics Single Cell 3.0 Chips.During this loading step, cells were partitioned into Gel Beads-in-Emulsion (GEMs) along with gel beads coated with 10x barcode oligonucleotides, encompassing a 14-bp index and a 10-bp UMI. Following GEMs generation, the samples were transferred to PCR tubes for reverse transcription, a step executed employing a T100 Thermal Cycler (Bio-Rad).

value: subcutaneous adipose tissue of the back

tag: age

value: 2 years old

value: Skeletal muscle cells


title: sat,bamapig,snRNA_seq

description: 10x Genomics

source_name: greater omentum

value: greater omentum

value: Adipocytes


title: Y479A, SMI, Rep3

tag: genotype


title: Pretreatment NBL M348AAB_T1, paired with M348AAB_T2, scRNAseq [M348AAB_T1_scR_CEL-Seq2_4]

first: Sander

institute: AUMC

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL

tag: treatment

value: pre-treatment


title: WT_fin_4dpa.rep3

tag: tissue

value: caudal fin

value: Ekkwill


title: WT_fin_4dpa.rep2


title: Posttreatment NBL M609AAA_T2, paired with M609AAA_T1, scRNAseq [M609AAA_T2_scR_CEL-Seq2_5]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor left cervical primary tumor

value: NBL tumor left cervical primary tumor

value: post-treatment

value: female


title: Y479A, SMI, Rep2

value: whole animal

value: L4 + 24 hours

value: hermaphrodite


title: Y479A, IP, Rep1

value: αFLAG(M2) (Sigma F1804)


title: Posttreatment NBL M609AAA_T2, paired with M609AAA_T1, scRNAseq [M609AAA_T2_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv

value: MYCN non-amplified


title: gom,bamapig,snRNA_seq

description: 10x Genomics

source_name: psoas major muscle

value: psoas major muscle


title: M. bovis AF2122/97 without B12 replicate 2

description: AF2122/97 wo B12 R2

value: Estándar media


title: WT, SMI, Rep4


title: s1_KO_fin_0dpa.rep3

value: s1 silencer homozygous knockout


title: Posttreatment NBL M609AAA_T2, paired with M609AAA_T1, scRNAseq [M609AAA_T2_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv


title: WT_fin_4dpa.rep1


title: spleen,bamapig,scRNA_seq

description: 10x Genomics

source_name: spleen

value: spleen

value: 2 years old

value: Spleen cells


title: WT, SMI, Rep3


title: Posttreatment NBL M609AAA_T2, paired with M609AAA_T1, scRNAseq [M609AAA_T2_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv

value: High-risk NBL


title: Y479A, IP, Rep4


title: WT_fin_1dpa.rep3

value: caudal fin


title: lung,bamapig,scRNA_seq

description: 10x Genomics

source_name: lung

value: lung

value: Lung cells


title: WT, SMI, Rep2


title: WT_fin_1dpa.rep2

value: Ekkwill


title: Posttreatment NBL M609AAA_T2, paired with M609AAA_T1, scRNAseq [M609AAA_T2_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left cervical primary tumor

value: post-treatment

value: female


title: WT, SMI, Rep1

value: whole animal

value: L4 + 24 hours

value: hermaphrodite


title: liver,bamapig,scRNA_seq

description: 10x Genomics

source_name: liver

value: liver

value: Liver cells


title: kidney,bamapig,scRNA_seq

description: 10x Genomics

source_name: kidney

value: kidney

value: Kidney cells


title: Posttreatment NBL M609AAA_T2, paired with M609AAA_T1, scRNAseq [M609AAA_T2_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv

value: MYCN non-amplified


title: WT_fin_0dpa.rep3


title: WT_fin_1dpa.rep1


title: LCL8664-DNA_in_GM12878-cells_RNA_Rep3

description:
MH_active.regions.bed
MH_merged-reps_RNA-to-DNA_log2.crossmap.bw
HH_active.regions.bed
HH_merged-reps_RNA-to-DNA_log2.bw
conserved_active.regions.bed
human-specific.regions.bed
macaque-specific.regions.bed
human-specific_cis.bed
human-specific_trans.bed
macaque-specific_cis.bed
macaque-specific_trans.bed
human-specific_cis-only.bed
human-specific_trans-only.bed
human-specific_cis+trans.bed
macaque-specific_cis-only.bed
macaque-specific_trans-only.bed
macaque-specific_cis+trans.bed

organism:
Macaca mulatta
Homo sapiens

tag: cell line

value: Lymphoblasotid cell line (immortalized B cells)

tag: biomaterial provider

value: reporter RNA


title: WT, IP, Rep4

value: αFLAG(M2) (Sigma F1804)


title: Pretreatment NBL M993AAA_T1, paired with M993AAA_T2, scRNAseq [M993AAA_T1_scR_CEL-Seq2_4]

description:
CelSeq-2
barcodes.tsv

source_name: NBL tumor lymph node left inguinal

value: NBL tumor lymph node left inguinal

tag: tumor type

value: High-risk NBL

value: pre-treatment

value: MYCN amplified


title: WT_fin_0dpa.rep2

value: caudal fin

value: Ekkwill


title: WT, IP, Rep3

value: whole animal


title: WT, IP, Rep2

value: L4 + 24 hours


title: LCL8664-DNA_in_GM12878-cells_RNA_Rep1

tag: molecule type


title: LCL8664-DNA_in_GM12878-cells_RNA_Rep2

tag: cell type


title: Pretreatment NBL M993AAA_T1, paired with M993AAA_T2, scRNAseq [M993AAA_T1_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

tag: tumor stage

tag: Sex

value: female


title: Pretreatment NBL M993AAA_T1, paired with M993AAA_T2, scRNAseq [M993AAA_T1_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: LCL8664-DNA_in_GM12878-cells_DNA_Rep2

value: plasmid DNA


title: M. tuberculosis GC1237 with B12 replicate 2

description: GC1237 B12 R2

organism: Mycobacterium tuberculosis

value: Estándar media + B12


title: WT, IP, Rep1

value: hermaphrodite


title: 4_dpa_rep3

data_processing:
library strategy: HiCAR (Hi-C on accessible regulatory DNA)
The data were analyzed by https://github.com/jianhong/nf-core-hicar pipeline. Reads were aligned to danRer11 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MAPS is used to call the significant chromatin interaction fro HiCAR library.
Assembly: danRer11
Supplementary files format and content: Chromatin interactions  identified by MAPS, provided in BEDPE formate.

source_name: fish fin

growth_protocol: Zebrafish of the outbred Ekkwill (EK) strain at about 6-8 months of age were used for collecting fin nuclei. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily, and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.

extract_protocol:
Fins were amputated at 50% of their original length using scalpel (Sterile Scalpel Blades #22, Feather). Biological triplicate pools of WT caudal fin clips were collected at 0 dpa (freshly amputated), 1 dpa, or 4 dpa time points via scalpel (Sterile Scalpel Blades #22, Feather) from 10 fish per pool. Fin tissues were frozen in liquid nitrogen and grinded using a motar and a pestle on dry ice for 5 min.
Nuclei collected by pulverizing frozen zebrafish fin tissues (0, 1 and 4 dpa) were cross-linked and treated with Tn5 transposase that were assembled with an engineered DNA adaptor. The Tn5 adaptor contains a Mosaic End (ME) sequence for Tn5 recognition and a single-stranded flanking sequence that can be ligated to the CviQI-digested DNA fragment with a splint oligo. The nuclei were treated with the 4-base cutter CviQI and then T4-ligase for connecting the Tn5 adaptor to the spatially proximal genomic DNA. The cross-links were reversed, and the purified DNA was digested by another 4-base cutter NlaIII, followed by circularization and PCR amplification to generate HiCAR DNA libraries for Next-Generation-Sequencing (NGS).

value: fish fin

tag: time point

value: 4 dpa


title: 1_dpa_rep3

value: 1 dpa


title: Pretreatment NBL M993AAA_T1, paired with M993AAA_T2, scRNAseq [M993AAA_T1_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: LCL8664-DNA_in_GM12878-cells_DNA_Rep3

value: Lymphoblasotid cell line (immortalized B cells)


title: LCL8664-DNA_in_GM12878-cells_DNA_Rep1


title: 0_dpa_rep3

value: 0 dpa (freshly amputated)


title: M. tuberculosis GC1237 with B12 replicate 1

description: GC1237 B12 R1


title: M. tuberculosis GC1237 without B12 replicate 1

description: GC1237 wo B12 R1

value: Estándar media


title: Pretreatment NBL M609AAA_T1, paired with M609AAA_T2, scRNAseq [M609AAA_T1_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left cervical primary tumor

value: High-risk NBL

value: MYCN non-amplified


title: 1_dpa_rep2


title: M. tuberculosis H37Rv with B12 replicate 2

description: H37Rv B12 R2


title: 0_dpa_rep2


title: Pretreatment NBL M609AAA_T1, paired with M609AAA_T2, scRNAseq [M609AAA_T1_scR_CEL-Seq2_3]

description:
CelSeq-2
barcodes.tsv

value: pre-treatment


title: GM12878-DNA_in_LCL8664-cells_RNA_Rep3

description:
HM_active.regions.bed
HM_merged-reps_RNA-to-DNA_log2.bw
HH_active.regions.bed
HH_merged-reps_RNA-to-DNA_log2.bw
conserved_active.regions.bed
human-specific.regions.bed
macaque-specific.regions.bed
human-specific_cis.bed
human-specific_trans.bed
macaque-specific_cis.bed
macaque-specific_trans.bed
human-specific_cis-only.bed
human-specific_trans-only.bed
human-specific_cis+trans.bed
macaque-specific_cis-only.bed
macaque-specific_trans-only.bed
macaque-specific_cis+trans.bed

value: reporter RNA


title: M. tuberculosis GC1237 without B12 replicate 2

description: GC1237 wo B12 R2


title: Pretreatment NBL M609AAA_T1, paired with M609AAA_T2, scRNAseq [M609AAA_T1_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: GM12878-DNA_in_LCL8664-cells_RNA_Rep1


title: M. tuberculosis H37Rv with B12 replicate 1

description: H37Rv B12 R1


title: GM12878-DNA_in_LCL8664-cells_RNA_Rep2


title: 1_dpa_rep1

value: Ekkwill


title: WT_fin_0dpa.rep1

value: caudal fin

tag: time


title: Pretreatment NBL M993AAA_T1, paired with M993AAA_T2, scRNAseq [M993AAA_T1_scR_CEL-Seq2_1]

description:
CelSeq-2
barcodes.tsv

value: NBL tumor lymph node left inguinal

value: female

value: MYCN amplified


title: 4_dpa_rep2


title: 0_dpa_rep1


title: M. tuberculosis H37Rv without B12 replicate 1

description: H37Rv wo B12 R1


title: GM12878-DNA_in_LCL8664-cells_DNA_Rep2

value: plasmid DNA


title: GM12878-DNA_in_LCL8664-cells_DNA_Rep3


title: Pretreatment NBL M609AAA_T1, paired with M609AAA_T2, scRNAseq [M609AAA_T1_scR_CEL-Seq2_2]

description:
CelSeq-2
barcodes.tsv


title: 4_dpa_rep1

value: fish fin


title: T47D_Estrogen, rep2

status: Public on Dec 21 2023

first: Thomas

middle: G

last: Scott

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://github.com/guertinlab/Nascent_RNA_Methods
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts files
Library strategy: PRO-seq

growth_protocol: T47D cells from ATCC were were grown in Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate

treatment_protocol: For each sample, 2x10^6 cells were grown for 3 days in complete medium. After 3 days, a final concentration of 100nM fulvestrant, raloxifene, or tamoxifen or 0.1% volume/volume DMSO was added, and the cells were incubated for 1 hour.

value: 1nM beta estradiol

tag: molecule subtype

value: nascent RNA


title: Pretreatment NBL M228AAA_T, paired with M228AAA_T2, scRNAseq [M228AAA_T1_scR_CEL-Seq2_1]

last: van Hooff

address: Meibergdreef 9

description:
CelSeq-2
barcodes.tsv

value: NBL tumor left adrenal gland


title: T47D_DMSO, rep2

value: 0.1% volume/volume DMSO


title: T47D_DMSO, rep1


title: Pretreatment NBL M228AAA_T, paired with M228AAA_T2, scRNAseq [M228AAA_T1_scR_CEL-Seq2]

description:
CelSeq-2
barcodes.tsv


title: M. tuberculosis H37Rv without B12 replicate 2

description: H37Rv wo B12 R2

tag: strain

value: Estándar media


title: Q402X

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

institute: NIH Clinical center

data_processing:
Alignment and mapping, QC, and peak calling with MACS2 were performed by the Basepair's ATAC-Seq piplines (https://www.basepairtech.com/)
Differential testing, annotation, and visualization were performed using R (v.4.3.1) and the following Bioconductor R packages (https://bioconductor.org/): DESeq2 (v.1.40.2), DiffBind (v.3.10.1), ChIPQC (v.1.36.1), ChIPseeker (v.1.36.0), clusterProfiler (v.4.8.2), and goseq (v.1.52.0) .
Assembly: hg38
Supplementary files format and content: tab-delimited gene matrix of raw (non-normalized) peak counts for each sample, with chromatin regions in the rows and samples in the columns

source_name: Peripheral blood

extract_protocol: ATAC-Seq was performed using the Active Motif ATAC-Seq Kit following the manufacturer’s protocol and sequenced using the Illumina NextSeq 2000

value: Peripheral blood

value: T-cell blasts

value: AIOLOS Q402X heterozygous


title: GM12878-DNA_in_LCL8664-cells_DNA_Rep1

value: Lymphoblasotid cell line (immortalized B cells)


title: HC_5

value: WT


title: HC_4


title: HC_3


title: HC_1


title: E82K_3

value: AIOLOS E82K heterozygous


title: E82K_1


title: HC_2


title: E82K_6


title: E82K_5


title: E82K_4


title: E82K_2


title: T47D_Estrogen, rep1


title: Young, Obese-20

city: West Lafayette

first: Dianne

last: Little

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

data_processing:
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location. Read counts for each gene feature for each animal were compiled using the HTSeq tool (Version 0.7.0). The parameters used for HTSeq-Count were set for unstranded RNA-Seq. Counts from all biological replicates were merged into one file using custom Perl scripts to generate a merged read count matrix for all samples. The merged count matrix was used for downstream differential gene expression analysis, and the quality of the count matrix was verified by determining basic statistics including data range and matrix size prior to downstream evaluation. Genes that had at least 5 or more counts in at least 50% of the animals from each group were retained for subsequent analysis. Normalization, gene-wise dispersion, and differential gene expression (DGE) analysis between different groups was carried out using the DESeq2 (version 1.12.4) Bioconductor package with the R statistical programming environment (version 3.4.0). To identify the genes that affected differently by age across different diet groups, interaction analysis was conducted in DESeq2.
Assembly: GRCm38v73
Supplementary files format and content: tab-delimited text; gene_count_matrix

source_name: Inguinal Fat

extract_protocol:
Qiagen's All Prep kit (Qiagen catalog # 80284) standard methods
Illumina protocol

value: Inguinal Fat

tag: cell markers

value: adipose-derived stem cells

value: Young, Obese


title: Young, Obese-21


title: Young, Obese-23


title: Young, Obese-1


title: Young, Obese-2


title: Young, Obese-22


title: Young, Lean-24

value: Young, Lean


title: Young, Lean-1


title: Young, Obese-19


title: Young, Lean-7


title: Young, Obese-18


title: Young, Lean-512


title: Young, Lean-26


title: Aged, Obese-16

value: Aged, Obese


title: Young, Lean-25


title: Young, Lean-23


title: Young, Lean-27


title: HC_6


title: Aged, Lean-20

value: Aged, Lean


title: Aged, Obese-17


title: Aged, Obese-12


title: Aged, Obese-10


title: Aged, Lean-17