title: SU-DHL-4-TAZ-CART19 [S23]

value: tazemetostat (500 nM) - CART19


title: SU-DHL-4-TAZ-CART19 [S22]

status: Public on Apr 24 2025

type: SRA

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blv

department: Center for Cellular Immunotherapies

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
gene counting and analysis with DESeq2 R library package
Assembly: hg38
Supplementary files format and content: excel file with raw gene counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cell lines were maintained in RPMI-10%FBS

extract_protocol:
GFP+ DLBLC cell lines (OCI-LY18 or SU-DHL-4) were pre-treated with tazemetostat (500 nM) or DMSO for 72 hs and then exposed to CART19 or UTD cells for 48 hs, in the presence of tazemetostat or DMSO. Cell lines were sorted based on viability and GFP+ and used to extract RNA for bulk RNA sequencing.
NEB NEXT Ultra II RNA seq library kit

treatment_protocol: Tazemetostat (EPZ6438; 500 nM or DMSO)

tag: cell line

tag: cell type

value: DLBCL

tag: treatment


title: Exp2, Rywal, roots, noninoculated_26h_8

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS833

data_processing:
filtering low quality reads (--quality 20) and trimming Ns (--trim-n) using Trim Galore
mapping filtered reads to reference potato genome using STAR v2.7.5c (parameters: --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.02 --quantTranscriptomeBan Singleend --outFilterType BySJout --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 10000 --alignMatesGapMax 10000)
generating raw counts table
taxonomic classification of reads using Centrifuge v1.0.4. Due to significant contamination observed in sample BS472, we have made the decision to exclude this sample from subsequent analysis.
differential expression analysis in R: filter genes with low expression, TMM normalization using edgeR v3.26.8 package, export of TMM normalized values using function cpm(log=TRUE, prior.count=0.5)
Assembly: Solanum tuberosum DM v4.04, GTF with merged PGSC and ITAG gene model annotations (https://doi.org/10.15490/fairdomhub.1.datafile.3408.1)
Supplementary files format and content: tab-delimited text files with raw count values and TMM-normalized count values for each Sample

molecule: polyA RNA

organism: Solanum tuberosum

source_name: roots

growth_protocol: Potato plants cv. Rywal were grown in stem node tissue culture for two to four weeks after in-vitro micropropagation under controlled environmental conditions (22 ± 2°C in the light and 19 ± 2°C in the dark with 70–90 μmol/m2/s2 radiation with OSRAM L 58 W/77 FLUORA lamps and a 16-h photoperiod) as previously described by Lukan et al., 2022 (https://doi.org/10.1093/hr/uhac147).

extract_protocol:
Total RNA was isolated from roots and shoots by RNeasy Plant Mini Kit (Qiagen) and treated with RNA Clean & Concentrator-5, including DNase treatment (Zymo Research).
Poly-A selection and strand-specific Illumina RNA-Seq library preparation was performed by Novogene Ltd. using their standard procedure.

treatment_protocol: For Exp1, plants were added to bacterial culture after the culture reached 107 CFU/ml and were incubated for 2 or 26 h. For Exp2, when two strains were used, bacterial cultures were mixed in the ratio of 1:1. In both experiments, plant shoots were not in contact with bacterial culture. Noninoculated plants were incubated in media for the same time.

tag: tissue

value: roots

tag: expt

tag: plant no.

tag: cultivar

value: Rywal

value: noninoculated

tag: b.subtilis strain

tag: time (after biofilm formation)


title: SU-DHL-4-TAZ-UTD [S19]

value: tazemetostat (500 nM) - UTD


title: Exp2, Rywal, roots, inoculated_PS-218_26h_YFP_14

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS839

value: inoculated


title: SU-DHL-4-DMSO-UTD [S15]

value: DMSO-UTD


title: SU-DHL-4-TAZ-CART19 [S24]


title: RCC10 cells, VHL_1

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

description: Library name: Sample 5

data_processing:
Fastq files were subjected to quality check using FastQC (Galaxy version 0.74+galaxy1) and then trimmed using Trimmomatic (Galaxy version 0.39+galaxy2). Trimmed fastq files were mapped to hg38 using HISAT2 (Galaxy version 2.2.1+galaxy1). Duplicates were removed using MarkDuplicates (Galaxy version 3.1.1.0). Read counts were generated using featureCounts (Galaxy version 2.0.8+galaxy0) and the differential expression analysis was performed using limma (Galaxy version 3.58.1+galaxy0).
Assembly: hg19
Supplementary files format and content: DifferentialExpression_normalized counts.txt

source_name: RCC10 cells

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a Kapa mRNA Hyper Prep kit (Roche).

treatment_protocol: Knockout cells were transduced with sgRNA lentivirus and selected with puromycin. VHL cells were transduced with lentivirus carrying VHL.

value: RCC10 cells

value: VHL


title: Exp2, Rywal, roots, noninoculated_26h_7

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS832


title: SU-DHL-4-DMSO-UTD [S14]


title: mouse_766_cart19 [M_766_A]

extract_protocol:
OCI-Ly18-GFP+ cells were sub-cutaneously implanted into NSG mice. 3 days later, mice were treated with tazemetostat (150 mg/kg/daily) or vehicle for 14 days. Mice were then infused with CART19 cells or UTD. 11 days post CART19 infusion, mice were sacrified, tumor were dissected and processed to prepare a single cell suspension. Cell sorting separated tumor-GFP+ cells from CART19 cells. Total RNA was extracted from tumor cells and submitted for bulk RNA sequencing.
NEB NEXT Ultra II RNA seq library kit

treatment_protocol: Tazemetostat (EPZ6438; 150 mg/kg/daily via oral gavage)


title: RCC10_1

data_processing:
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Assembly: hg19
Supplementary files format and content: TPM

treatment_protocol: Cells were treated with vehicle or SGI1027 for 2 days.

tag: agent

value: Vehicle


title: Exp2, Rywal, roots, noninoculated_26h_6

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS831


title: RCC10 cells, VHL_2

description: Library name: Sample 6


title: OCI-LY18-TAZ-CART19 [O12]


title: OCI-LY18-TAZ-CART19 [O11]


title: OCI-LY18-TAZ-CART19 [O10]


title: SU-DHL-4-TAZ-UTD [S20]


title: Exp2, Rywal, roots, inoculated_PS-216_26h_YFP_23

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS848


title: Exp2, Rywal, roots, inoculated_PS-218_26h_YFP_15

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS840


title: RCC10 cells, WT_2

description: Library name: Sample 2

value: Control


title: Exp2, Rywal, roots, noninoculated_26h_5

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS830


title: Exp1, Rywal, shoots, inoculated_PS-218-YFP_26h_237

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS486

source_name: shoots

value: shoots


title: SGI1027_1


title: OCI-LY18-DMSO-CART19 [O4]


title: RCC10 cells, WT_1

description: Library name: Sample 1


title: Exp1, Rywal, shoots, inoculated_PS-218-YFP_26h_236

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS485


title: OCI-LY18-TAZ-UTD [O9]


title: OCI-LY18-TAZ-UTD [O8]


title: OCI-LY18-DMSO-CART19 [O6]


title: OCI-LY18-TAZ-UTD [O7]


title: HIF-1alpha ChIP

library_source: genomic

data_processing:
The Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version
2.0.10), with a q-value threshold of 0.05.
Assembly: hg19
Supplementary files format and content: BED

molecule: genomic DNA

growth_protocol: DMEM+10% FBS

extract_protocol:
Chromatin was isolated using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology) and sonicated to 200-300 bp in length
ChIP DNA was used for library preparation with the KAPA Hyper Prep Kit.

treatment_protocol: 1% O2 for 24 hours

value: Breast cancer

tag: chip antibody

value: HIF-1alpha (home made)

value: 1% O2 for 24 h


title: Exp1, Rywal, shoots, inoculated_PS-218-YFP_26h_235

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS484


title: OCI-LY18-DMSO-UTD [O2]


title: Exp1, Rywal, shoots, inoculated_PS-218-YFP_26h_234

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS483


title: HepG2_Bulk_eDART-seq

city: GuangZhou

first: Zhijun

last: Ren

address: Sun Yat-sen University

country: China

institute: Sun Yat-sen University

data_processing:
The adapters of raw paired-end sequencing reads were removed by Cutadapter(v2.7). The reads were then aligned to human GRCm38/hg38 reference genome by STAR (Version 2.7.3a)
We then took advantage of rMATS-DVR, which implements Picard (v2.22.3, https://broadinstitute.github.io/picard/) to remove PCR duplicates and GATK toolkit (v3.8.0) (McKenna et al., 2010) to calibrate the bam files sequentially by splitting ‘N’ cigar reads (i.e. splice junction reads), mapping quality reassignment (program: SplitNCigarReads), and base quality score recalibration (program: BaseRecalibrator)
Mutations were identified by CTK-tools (v1.1.3) based on the calibrated bam files with default parameters. The mutation sites that match dbSNP annotated SNPs were filtered out. The samtools (v1.7) was used to calculate the number of reference and alternative nucleotides for each mutation site. Only the mutation sites with read coverages ≥ 50, mutation counts ≥ 5, and mutation rates ≥ 0.1 were used for the downstream analyses.
To avoided APOBEC1 protein induce mutation bias, the mutation sites overlap with C-to-U mutation fended in APOBEC1 over-expressed cell were removed. To define the C-to-U mutation peaks, we made 100bp sliding windows with 20bp overlapping with each other on the exon regions. The sliding windows with at least 3 C-to-U mutation sites were identified as mutation peak for each cell line, respectively.
Assembly: hg38
Supplementary files format and content: tab-delimited text include C-to-U mutation ref and alt counts for each sample

growth_protocol: ALL cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (Hyclone, SH30022.01), supplemented with 10% fetal bovine serum (FBS, Hyclone, SH30406.05) and 2 mM GlutaMAX (Gibco, 35050061) at 37 °C with 5% CO2.

extract_protocol:
The total RNA of pcDNA3.1-YTH-APOBEC-T2A-EGFP transfected HEK293T, HeLa and HepG2 was harvested using Trizol (Invitrogen) followed by treatment with RNase-Free DNase (NEB) to remove possible DNA contamination, respectively.
RNA-seq libraries were prepared with Dynabeads mRNA Purification Kit (Ambion) and TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: The pcDNA3.1-YTH-APOBEC-T2A-EGFP construct was transfected into HEK293T cells, HepG2 cells, and HeLa cells, respectively, using Lipofiter 3.0 (Hanbio) according to the manufacturer's instructions. The medium was refreshed 6 hours after transfection, and the EGFP-positive cells of the three cell lines were isolated, respectively, through cytometry 3 day after transfection.

tag: genotype

value: YTH-APOBEC-T2A-EGFP OE


title: SU-DHL-4-DMSO-UTD [S13]


title: HepG2_Bulk_CTRL


title: CUT&TAG_IP_GFP_OTX2_GFP_OE_iMeLCs_rep2

city: Jiaxing

first: Yashi

last: Gu

address: No.718, HaiZhouEastRoad

institute: zje

data_processing:
Raw reads were trimmed by Trim-Galore, and were aligned to the human genome (hg38) using Bowtie2 (version 2.4.5) with the parameter “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”. Duplicates were removed using Picard (version 2.27.5), then reads were filtered using Samtools with the parameter “-F -X04”. CUT&TAG peaks were called using SEACR (version 1.3) with the parameter “norm stringent”. The candidate peaks were assigned to the nearest genes using Homer annotatePeaks.pl. The profile plots were generated using Deeptools plotProfile (version 3.5.1).
Assembly: hg38
Supplementary files format and content: format: biwWig; content: bigWig files of each sample
Library strategy: CUT&Tag

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, 15596026). A part 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: embryonic stem cells induced incipient mesoderm-like cells

value: incipient mesoderm-like cells differentiation, CUT&TAG , antibody :GFP (Sigma-Aldrich, catalog number:G6539)


title: OCI-LY18-DMSO-UTD [O1]

value: DLBCL


title: OCI-LY18-DMSO-UTD [O3]


title: CUT&TAG_IP_GFP_OTX2_GFP_OE_iMeLCs_rep1


title: Exp1, Rywal, shoots, inoculated_PS-216-YFP_26h_232

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS481

value: Rywal


title: m6A_seq_IP_m6A_wild type_hESCs_rep2

data_processing:
Raw reads were trimmed by Trim-Galore (version 0.6.7) and the first 15 bp were cut to remove low-quality bases and adapters, then aligned to the human genome (hg38) using HISAT2 (version 2.2.1). Mapped reads were filtered using Samtools (version 1.6) using the parameter “-f 2 -F 256 -q 30”. m6A peaks were called using MACS2 (2.2.7.1) with the parameter “--nomodel --extsize 135 -q 0.05 --fe-cutoff 2”. Peaks overlapped in the two replicates were considered as candidate peaks using Bedtools (Version 2.30.0) for the subsequent analysis. The m6A candidate peaks were assigned to the nearest genes using Homer annotatePeak.pl. The genes with at least one m6A peak were considered as m6A modified genes. Then the GO terms of m6A modified genes were enriched using ClusterProfiler (version 4.2.2). The motifs of candidate peaks were calculated using Homer findMotifsGenome.pl.
Assembly: hg38
Supplementary files format and content: file1: m6A peak .bed file; file2: the annotation file of m6A peaks
Library strategy: m6A-seq

value: embryonic stem cells

value: WT

value: m6A-seq , antibody:m6A (Cell Signaling Technology, catalog number:56593S)


title: Exp1, Rywal, shoots, inoculated_PS-216-YFP_26h_231

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS480

value: inoculated


title: m6A_seq_IP_m6A_wild type_hESCs_rep1


title: CUT&TAG_IP_GFP_wild type_iMeLCs_rep2


title: RCC10 cells, DKO_1

description: Library name: Sample 3

value: RCC10 cells

value: knockout


title: Exp1, Rywal, shoots, inoculated_PS-216-YFP_26h_230

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS479


title: HeLa_Bulk_CTRL

source_name: HeLa

value: HeLa


title: HEK293T_Bulk_eDART-seq


title: m6A_seq_input_m6A_wild type_hESCs_rep1


title: m6A_seq_input_m6A_wild type_hESCs_rep2


title: Exp1, Rywal, shoots, noninoculated_26h_229

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS478

value: noninoculated


title: Hordeum vulgare cv Conrad, 5 days of germination, rep B

city: Madison

first: Sarah

middle: J

last: Whitcomb

state: WI

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

description: Library name: DoG5_B

data_processing:
Skewer (https://doi.org/10.1186/1471-2105-15-182) was used to remove adapter sequences and to trim low quality sequence from the 3'-end of reads until a Phred quality of 20 was reached.
The trimmed reads were mapped to the reference genome sequence using STAR (https://doi.org/10.1093/bioinformatics/bts635)
Reads for genes were counted in each sample using RSEM (https://doi.org/10.1186/1471-2105-12-323). RSEM was used to calculate expected read counts and TPM normalized read counts.
Assembly: Morex V3
Supplementary files format and content: tab-delimited text file includes expected read counts in each sample
Supplementary files format and content: tab-delimited text file includes Transcripts Per Million (TPM) normalized counts in each Sample

organism: Hordeum vulgare

source_name: seed

extract_protocol:
total RNA was prepared from seed samples according to Walling et al. 2018, https://doi.org/10.1371/journal.pone.0196966
Sequencing libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA kit with poly-A enrichment by the University of Wisconsin Biotechnology Center Gene Expression Center.

value: seed

value: Conrad

value: 5 days of germination, malting


title: Hordeum vulgare cv Conrad, 5 days of germination, rep C

description: Library name: DoG5_C


title: Mouse liver of Atg7flox/flox;Alb-Cre;p62T352A/p62T352A mouse -3

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

country: Japan

institute: Tokyo Women's Medical University

description: Library name: Sample 12

data_processing:
Fastq files were processed using TRIMGalore.
Resulting reads were mapped to mm10 using the Spliced Transcripts Alignment to a Reference (STAR) Aligner.
The n umber of reads was calculated using RNA-Seq by Expectation Maximization (RSEM)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for all Samples

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). The poly(A) RNA was isolated using NEBBext Poly(A) mRNA magnetic isolation module.
cDNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Liver


title: Exp1, Rywal, shoots, noninoculated_26h_228

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS477

value: shoots


title: Exp1, Rywal, shoots, inoculated_PS-216-YFP_26h_233

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS482


title: HeLa_Bulk_eDART-seq

value: YTH-APOBEC-T2A-EGFP OE


title: Hordeum vulgare cv Conrad, 5 days of germination, rep A

description: Library name: DoG5_A


title: OTX2-GFP-OE_iMeLCs_rep2

data_processing:
Quality assessment of the raw RNA-seq data was conducted using FastQC (v0.11.9), which examined the overall quality of the bulk RNA-seq fastq files. After that, cutadapt (v4.1) and trim-galore (v0.6.7) were used to remove low-quality bases and potential adapters. The processed reads were then aligned to the hg38 reference using STAR (v2.7.10a), sorted using samtools (v1.6), and the read counts per gene were quantified through featureCounts (v2.0.1) using the Gencode (v41) genomic annotation file.
Assembly: hg38
Supplementary files format and content: fomat: .xlsx; content: read count matrix

value: embryonic stem cells induced incipient mesoderm-like cells

value: incipient mesoderm-like cells differentiation


title: CUT&TAG_IP_GFP_wild type_iMeLCs_rep1

value: incipient mesoderm-like cells differentiation, CUT&TAG , antibody :GFP (Sigma-Aldrich, catalog number:G6539)


title: Mouse liver of Atg7flox/flox;Alb-Cre;p62T352A/p62T352A mouse -2

description: Library name: Sample 11


title: Exp1, Rywal, shoots, noninoculated_26h_227

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS476

value: Rywal


title: OTX2-GFP-OE_iMeLCs_rep1


title: Hordeum vulgare cv Conrad, 4 days of germination, rep B

description: Library name: DoG4_B

value: 4 days of germination, malting


title: HEK293T_Bulk_CTRL


title: Mouse liver of Atg7flox/flox;Alb-Cre;p62T352A/p62T352A mouse -1

description: Library name: Sample 10


title: OTX2-KO_iMeLCs_rep2


title: Exp1, Rywal, shoots, noninoculated_26h_226

description:
Exp1_raw_counts_allgenes.txt
Exp1_shoots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS475


title: Hordeum vulgare cv Conrad, 4 days of germination, rep A

description: Library name: DoG4_A


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_26h_237

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS474

value: roots


title: Mouse liver of Atg7flox/flox;Alb-Cre mouse -3

description: Library name: Sample 9

value: flox/flox;Alb-Cre


title: Mouse liver of Atg7flox/flox;Alb-Cre mouse -2

description: Library name: Sample 8


title: Mouse liver of Atg7flox/flox;Alb-Cre mouse -1

description: Library name: Sample 7


title: IGF2BP1-KO_hPGCLCs_rep2

value: embryonic stem cells induced human PGC-like cells

value: human PGC-like cells differentiation


title: Hordeum vulgare cv Conrad, 3 days of germination, rep C

description: Library name: DoG3_C

value: 3 days of germination, malting


title: OTX2-KO_iMeLCs_rep1


title: Hordeum vulgare cv Conrad, 3 days of germination, rep B

description: Library name: DoG3_B


title: IGF2BP1-KO_hPGCLCs_rep1


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_26h_235

description: Due to significant contamination observed in sample BS472, we have made the decision to exclude this sample from subsequent analysis.

value: inoculated


title: Mouse liver of Atg7flox/flox;p62T352A/p62T352A mouse -3

description: Library name: Sample 6


title: Hordeum vulgare cv Conrad, 4 days of germination, rep C

description: Library name: DoG4_C

value: seed


title: wild type_hPGCLCs_rep2

value: WT


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_26h_234

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS471


title: Mouse liver of Atg7flox/flox;p62T352A/p62T352A mouse -2

description: Library name: Sample 5


title: Hordeum vulgare cv Conrad, 3 days of germination, rep A

description: Library name: DoG3_A

value: Conrad


title: wild type_hPGCLCs_rep1


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_26h_233

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS470


title: Mouse liver of Atg7flox/flox;p62T352A/p62T352A mouse -1

description: Library name: Sample 4

value: Liver


title: Hordeum vulgare cv Conrad, 2 days of germination, rep B

description: Library name: DoG2_B

value: 2 days of germination, malting


title: Mouse liver of Atg7flox/flox mouse -3

description: Library name: Sample 3

value: flox/flox


title: wild type_iMeLCs_rep2

value: embryonic stem cells induced incipient mesoderm-like cells


title: Hordeum vulgare cv Conrad, 2 days of germination, rep A

description: Library name: DoG2_A


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_26h_232

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS469


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_26h_236

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS473


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_26h_231

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS468


title: Mouse liver of Atg7flox/flox mouse -2

description: Library name: Sample 2


title: Hordeum vulgare cv Conrad, 1 day of germination, rep C

description: Library name: DoG1_C

value: 1 day of germination, malting


title: IGF2BP1-KO_ectoderm_rep2

value: embryonic stem cells induced ectoderm

value: ectoderm differentiation


title: Exp1, Rywal, roots, noninoculated_26h_229

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS466

value: Rywal

value: noninoculated


title: Mouse liver of Atg7flox/flox mouse -1

description: Library name: Sample 1


title: Hordeum vulgare cv Conrad, 1 day of germination, rep B

description: Library name: DoG1_B


title: IGF2BP1-KO_ectoderm_rep1


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_26h_230

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS467

value: roots


title: Exp1, Rywal, roots, noninoculated_26h_228

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS465


title: Mouse liver of Atg7flox/flox;Alb-Cre;p62S351A/p62S351A mouse -3

description: Library name: Sample 9


title: Hordeum vulgare cv Conrad, 2 days of germination, rep C

description: Library name: DoG2_C


title: wild type_ectoderm_rep2


title: Exp1, Rywal, roots, noninoculated_26h_227

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS464


title: Hordeum vulgare cv Conrad, 0 days of germination, rep C

description: Library name: DoG0_C

value: 0 days of germination, malting out of steep


title: Mouse liver of Atg7flox/flox;Alb-Cre;p62S351A/p62S351A mouse -2

description: Library name: Sample 8


title: Mouse liver of Atg7flox/flox;Alb-Cre;p62S351A/p62S351A mouse -1

description: Library name: Sample 7


title: Hordeum vulgare cv Conrad, 0 days of germination, rep B

description: Library name: DoG0_B


title: wild type_iMeLCs_rep1

value: incipient mesoderm-like cells differentiation


title: Exp1, Rywal, roots, noninoculated_26h_226

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS463


title: IGF2BP1-KO_mesoderm_rep2

value: embryonic stem cells induced mesoderm

value: mesoderm differentiation


title: Hordeum vulgare cv Conrad, 0 days of germination, rep A

description: Library name: DoG0_A

value: seed


title: Mouse liver of Atg7flox/flox;Alb-Cre mouse -3

description: Library name: Sample 6

value: flox/flox;Alb-Cre


title: IGF2BP1-KO_mesoderm_rep1


title: Hordeum vulgare cv Conrad, dry seed, rep C

description: Library name: Dry_C

value: Conrad

value: unmalted mature seed


title: Mouse liver of Atg7flox/flox;Alb-Cre mouse -2

description: Library name: Sample 5

value: Liver


title: wild type_mesoderm_rep2

value: WT


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_2h_216

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS453

value: inoculated


title: Hordeum vulgare cv Conrad, dry seed, rep B

description: Library name: Dry_B


title: Mouse liver of Atg7flox/flox;Alb-Cre mouse -1

description: Library name: Sample 4


title: wild type_mesoderm_rep1


title: Mouse liver of Atg7flox/flox mouse -3

description: Library name: Sample 3

value: flox/flox


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_2h_215

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS452


title: Hordeum vulgare cv Conrad, dry seed, rep A

description: Library name: Dry_A


title: Hordeum vulgare cv Conrad, 1 day of germination, rep A

description: Library name: DoG1_A

value: 1 day of germination, malting


title: IGF2BP1-KO_endoderm_rep2

value: embryonic stem cells induced endoderm

value: endoderm differentiation


title: wild type_ectoderm_rep1

value: embryonic stem cells induced ectoderm

value: ectoderm differentiation


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_2h_214

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS451

value: roots

value: Rywal


title: con_4

city: HANGZHOU

first: xiaohan

last: song

address: No.1 XIANGSHAN ROAD

institute: University of the Chinese Academy of Sciences Hangzhou Institute for Advanced Study

description:
Library name: Sample 8
CTRL4

data_processing:
Raw FASTQ files were quality checked using FastQC (v0.11.9)
Reads were aligned to the hg38 reference genome using hisat2 (v2.2.1)
Gene counts were quantified using featureCounts (v2.0.3)
Differential expression genes were analyzed using edgeR (v3.40.2)
Assembly: hg38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: HEK293T cells

extract_protocol:
For RNA-seq analysis, total RNA was extracted using the TransZol Up High Performance RNA Extraction Kit (ET111-01-V2, TransGen Biotech)
For RNA-seq analysis, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

value: HEK293T cells

value: human embryonic kidney cells


title: Mouse liver of Atg7flox/flox mouse -2

description: Library name: Sample 2


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_2h_213

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS450


title: IGF2BP1-KO_endoderm_rep1


title: Mouse liver of Atg7flox/flox mouse -1

description: Library name: Sample 1


title: con_3

description:
Library name: Sample 7
CTRL3


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_2h_212

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS449


title: Exp1, Rywal, roots, inoculated_PS-218-YFP_2h_217

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS454


title: wild type_endoderm_rep2


title: wild type_endoderm_rep1


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_2h_211

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS448


title: con_2

description:
Library name: Sample 6
CTRL2


title: WT_E12_5_ChP_PRDM16_2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
Three replicates of ChIP-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The ChIP-seq coverage for these samples were generated by bedtools genomeCoverageBed and normalized to the library depths to give a read per million per base (RPM).
The CUT&TAG samples of Prdm16_E and Prdm16 mutant NSCs in four replicates, and of Prdm16 from CH and ChP area at stage 12.5 embryos in three replicates, were mapped to mm10 genome assembly using Bowtie2 (bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700). The CUT&TAG coverage for these samples were generated by bedtools genomeCoverageBed and normalized to the library depths to give a read per million per base (RPM).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: cut&tag

source_name: brain dorsal-mindline

growth_protocol: NSCs proliferation medium for primary NSCs with or without BMP4

extract_protocol:
stardard for ChIPseq or Cut&Tag
NEB ultra II DNA libary kit for ChIP-seq libararies, standard protocol for cut&tag

value: brain dorsal-mindline

tag: antibody

value: PRDM16 antibody


title: WT_E12_5_ChP_PRDM16_3


title: con_1

description:
Library name: Sample 5
CTRL1


title: Exp1, Rywal, roots, inoculated_PS-216-YFP_2h_210

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS447


title: OTX2-GFP-OE_hESCs_rep2

value: embryonic stem cells


title: WT_E12_5_ChP_IgG_3

value: IgG


title: 2-DG_4

description:
Library name: Sample 4
DG4

value: 2-DG treated


title: WT_E12_5_ChP_PRDM16_1


title: Exp1, Rywal, roots, noninoculated_2h_208

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS445

value: noninoculated


title: OTX2-KO_hESCs_rep2


title: 2-DG_2

description:
Library name: Sample 2
DG2

value: WT


title: Exp1, Rywal, roots, noninoculated_2h_207

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS444


title: OTX2-KO_hESCs_rep1


title: WT_E12_5_ChP_IgG_1


title: IGF2BP1-KO_hESCs_rep2


title: WT_E12_5_ChP_IgG_2


title: 2-DG_1

description:
Library name: Sample 1
DG1


title: Flb_500_Dox_d6

city: ANN ARBOR

first: Yuanhao

last: Huang

state: MI

address: 1418 McIntyre st

institute: University of Michigan

description:
Library name: 6239-BB-16
PE150 on a 300 cycle S4 flow cell

data_processing:
data is mapped to reference genome using STAR and processed using cuffdiff toolkit
Assembly: mm10
Supplementary files format and content: FPKM tsv file

source_name: mouse embryonic stem cell-derived neuroectoderm organoid

growth_protocol: Rx:GFP/Sox1:MCHERRY cells harboring Dox-inducible Flag-tagged PRDM13 were differentiated with GMEM supplemented with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
RNA extraction for RNA-seq was performed by combination of Trizol reagent (ThermoFisher Scientific) and RNeasy mini kit (QIAGEN)
RNAs were sent to University of Michigan DNA Sequencing Core for RNA quality analysis, PolyA+ mRNA selection and library construction, and sequencing using Illumina NovaSeq S4 Libraries platform. Duplicate samples for each group were subjected to two round of independent library preparation and sequencing to avoid sample and batch effect of mRNA-seq.

treatment_protocol: RPCs of PRDM13 were treated with or without Dox(500 ng/mL) for 5 days

value: neuroectoderm cells

value: Dox-inducible mouse FLAG-PRDM13

value: Dox treated

tag: batch


title: 48_mutantNSC_BMP4_H3K4me3_3

source_name: Primary NSCs

value: Primary NSCs

value: Prdm16 KO

value: H3K4me3 antibody


title: Exp1, Rywal, roots, noninoculated_2h_206

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS443

value: roots


title: IGF2BP1-KO_hESCs_rep1


title: Direct RNA seuqence of SMG1i treated HEK293T cell replicate 1

description: Direct RNA sequence

data_processing:
For direct RNA sequencing data, base calling was performed on each raw FAST5 file to generate FASTQ files using Guppy (v3.1.3) in high accurate mode.
The reads with mean quality score exceeded 7 were aligned to human GRCm38/hg38 reference transcriptome (GENCODE V32) using minmap2 (Li, 2018). The multi-mapped reads were removed using samtools (Li et al., 2009). The expression of transcripts was calculated based on uniquely mapped reads.
Subsequently, the reads and nanopore current were mapped to their corresponding positions of transcripts by the eventalign module of Nanopolish (version 0.13.2) (Simpson et al., 2017). Simultaneously, the mean, standard deviation, and dwelling time of ionic current from all the reads mapped to the same continuously segmented 5-mers were extracted by Nanopolish (version 0.13.2) (Simpson et al., 2017). Based on the extracted ionic current signals, m6Aiso (Supplementary related manuscript) was used to predict m6A modification at single-molecular level. Only the GLORI annotated m6A sites with read coverages ≥ 20 and modified reads ≥ 10 in gene level were used for the downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-separated counts files
Supplementary files format and content: tab-separated m6A files

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Corning, #10-013-CVRC) supplemented with 10% fetal bovine serum (FBS; QuaCell, #B21001). The cells were maintained at 37 °C in a humidified chamber with 5% CO2 and were verified to be free of mycoplasma contamination.

extract_protocol:
Total RNA was extracted from the HEK293T cell line using TRIzol reagent (Invitrogen, #15596018), according to the manufacturer’s instructions.
RNA concentrations and RNA integrity were measured using a NanoDrop 2000 Spectrophotometer and Agilent 4200 TapeStation, respectively. A 20-μg aliquot of total RNA was subjected to poly(A)+ RNA selection using the Dynabeads mRNA DIRECT purification kit (Invitrogen, #61011) following the manufacturer’s instructions. Subsequently, approximately 500 ng of poly(A)+ RNA was used for direct RNA library preparation. The libraries were generated following the standard ONT SQK-RNA002 protocol with the reverse transcription step included. The libraries were loaded onto R9.4.1 flow cells (ONT, FLO-PRO002) and sequenced on PromethION 2 Solo (ONT, PRO-SEQ002).

treatment_protocol: For NMD pathway inhibition, approximately 1 × 107 HEK293T cells were treated with either DMSO (Sigma-Aldrich, #D2650) or 300 nM of the small molecule NMD inhibitor SMG1i (compound 11j, MedChemExpress, #HY-124719) for 4 h prior to cell harvest.


title: 16_mutantNSC_BMP4_H3K4me3_1


title: Fla_500_Dox_d6

description:
Library name: 6239-BB-15
PE150 on a 300 cycle S4 flow cell

value: mouse embryonic stem cell-derived neuroectoderm organoid


title: Direct RNA seuqence of SMG1i treated HEK293T cell replicate 2

description: Direct RNA sequence


title: 46_mutantNSC_BMP4_PRDM16_3


title: FLb_0_Dox_d6

description:
Library name: 6239-BB-14
PE150 on a 300 cycle S4 flow cell

value: No


title: wild type_hESCs_rep2


title: Exp1, Rywal, roots, noninoculated_2h_209

description:
Exp1_raw_counts_allgenes.txt
Exp1_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS446

value: Rywal


title: Direct RNA seuqence of DMSO treated HEK293T cell replicate 2

description: Direct RNA sequence

value: DMSO


title: OTX2-GFP-OE_hESCs_rep1


title: 2-DG_3

description:
Library name: Sample 3
DG3

value: HEK293T cells

value: human embryonic kidney cells


title: wild type_hESCs_rep1

value: embryonic stem cells


title: FLa_0_Dox_d6

description:
Library name: 6239-BB-13
PE150 on a 300 cycle S4 flow cell


title: 45_mutantNSC_BMP4_IgG_3

value: IgG


title: Direct RNA seuqence of DMSO treated HEK293T cell replicate 1

description: Direct RNA sequence


title: CART19_tazemetostat [PP-PG-CAR19-TAZ-FeatureBarcode]

library_source: transcriptomic single cell

data_processing:
demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger Software
Assembly: hg38
Supplementary files format and content: tab separated values and matrix files

source_name: Primary T-cells

extract_protocol:
Primary Human CAR T cells were generated and injected in NSG mice engrafted with the DLBCL line OCI-LY18; 20 days post-CAR T infusion, human CAR T cells were isolated from the peripheral blood by FACS sorting
Chromium NEX GEM Single Cell 5'

value: Primary T-cells

value: tazemetostat (150 mg/kg/daily)


title: 29_mutantNSC_BMP4_IgG_2


title: ONT of m6A-isoSC-seq for HEK293T HeLa and HepG2

description: 10x genomics

data_processing:
Base calling was performed on raw FAST5 files of nanopore sequencing data to generate FASTQ files using Guppy (v3.1.3) in high accurate mode.
The NanoHunter tool (https://github.com/yangao07/NanoHunter) was utilized to identify cell barcodes and UMIs from nanopore long reads, using the matched Illumina short-read single-cell data as a reference. Briefly, NanoHunter searches for the 10X 5’ adapter (‘CTACACGACGCTCTTCCGATCT’) and polyT sequence within the nanopore long reads to locate the cell barcode and UMI sequence. To enable efficient and accurate searching of cell barcodes and UMIs, NanoHunter employs a two-level k-mer hash index. The index is constructed using the short-read cell barcodes and UMIs, with the first level corresponding to cell barcodes and the second level corresponding to UMIs. The length of the k-mer is determined as k = l/(e+1), where l represents the length of the cell barcode or UMI, and e represents the maximum allowed edit distance between the long-read and short-read cell barcodes or UMIs. By default, the maximum allowed edit distances are set to 3 for cell barcodes and 2 for UMIs. This indexing approach ensures that at least one perfectly matched k-mer can be identified even when the long-read cell barcodes/UMIs contain a maximum of e sequencing errors.
To reduce sequence depth affect in nanopore single-cell data, only cells with ≥750 expressed genes were used to cell cluster analyses. After filtering, the counts of genes were normalized using LogNormalize method implemented in Seurat with a scale factor of 10,000. The top 3000 variable isoforms defined by the FindVariableFeatures function of Seurat were used for PCA analysis. We then took the top 10 principal components of PCA for the analyses of cell clustering and UMAP projection. Clusters were identified using SNN graph and original Louvain algorithm with a resolution of 0.017. FindAllMarkers function in Seurat was used to determine the merker genes of each cell cluster by requiring p-value < 0.01 and log2 fold-change ≥ 0.25.
Instead of calling mutations solely based on ONT single-cell reads, we determined C-to-U mutation status for ONT single-cell read with previously assigned cell barcodes and UMIs at the reference C-to-U mutation sites identified from bulk RNA-seq data in HeLa HepG2 and HEK293T. “SNPMatrix” command of Sicelore tool (v2.0) was employed with default parameters to calculate the C and U counts of the reference mutation sites in each single-cell15. The obtained C-to-U mutations on the ONT reads derived from the same genes and isoforms were then aggregated to calculate the gene-wise and isoform-wise C-to-U mutation rates, respectively, for each cell.
Assembly: hg38
Supplementary files format and content: tab-sparated values files and matrix file

extract_protocol: The mixed single-cell suspension was utilized to generate a barcoded single-cell RNA-seq library using the 10x Genomics 3’ gene expression kit (v3) following the recommended protocol provided by the manufacturer. Half of the full-length cDNA generated from 10x Genomics was amplified by five cycles of PCR with TruSeq read 1 forward primer 5′-NNN CTA CAC GAC GCT CTT CCG ATC T-3′ and 3′ partial TSO reverse primer 5′-NNN AAG CAG TGG TAT CAA CGC AGA GTA CAT-3′ for Nanopore sequencing. After that, amplified full-length cDNA was treated with 0.55x SPRIselect to remove PCR primers and the cDNAs with lengths shorter than 1000bp. The purified cDNA reagent into a final elution of 51 µL in Buffer EB to allow for adequate template/volume for the necessary assessment of quality control (QC) metrics and PromethION library preparation. Single cell nanopore sequencing library was prepared with the Oxford Nanopore LSK-110 kit (PCR free) and sequenced on PromethION following the manufacturer’s instructions to generated 339 million long reads derived from about 5000 cells.

value: YTH-APOBEC-T2A-EGFP OE


title: CART19_tazemetostat [PP-PG-CAR19-TAZ-GEX]


title: 44_mutantNSC_H3K4me3_3


title: 28_mutantNSC_H3K4me3_2


title: CART19_vehicle [PP-PG-CAR19-FeatureBarcode]

value: vehicle


title: lung, OVA-chanllege, rep4

city: Shenyang

first: Lishen

last: Shan

state: Liaoning

address: No. 36, Sanhao Street, Heping District

institute: Shengjing Hospital of China Medical University

description: Library name: Sample10

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
Assembly: GRCm39
Supplementary files format and content: CSV file  indlude gene count for each sample

source_name: lung tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: lung tissue

value: OVA challenge


title: lung, OVA-chanllege, rep6

description: Library name: Sample11


title: FLC_MNX1_ATAC_4

city: Gothenburg

first: Eric

last: Malmhäll-Bah

address: Bruna stråket 16

department: Laboratory Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Reads were trimmed using Trim Galore in conjunction with Cutadapt (v. 1.14) with the options –paired”, “–nextera”, “– length_1 35”, and “–length_2 35. Trimmed reads were mapped against mm10 reference genome using Bowtie25 (v. 2.5.2). Conflicting mapped reads with a phred score lower than 20 was removed using SAMTools (v. 1.19). Finally, read ends were shifted to center of the transposition event.
BW-files were generated from BAM-files by means of the bamCoverage functionality of Deeptools v. 3.1.1 22 using the non-default parameters: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX --extendReads 200
Regions of open chromatin were retrieved from BAM-files using MACS2 with a q-value cut-off of 0.05 and the   --nomodel, --keep-dup all, --broad --gsize mm options.
Assembly: mm10
Supplementary files format and content: BAM, BW, broadPeak

source_name: Fetal liver

extract_protocol:
Bone marrow cells from MNX1-induced leukemic mice, non-transplanted mouse fetal liver cells containing MNX1-vector as well as FLCs with empty vector were lysed using a in a resuspension buffer containing 0.1% of NP40 and Tween-20 and 0.01% digitonin. Lysed cells were resuspended in transposition buffer (10 mM Tris-acetate, pH 7.6, 5 mM MgCl2, 10% dimethylformamide, 30% PBS, 0.01% digitonin and 0.1% Tween-20) together with Tn5 transposome and tagementation were allowed to proceed for 30 min at 37°C under agitation.
Sequencing libraries were generated by addition of 25 µl NEBNext High Fidelity 2× Master Mix (NEB), each 2.5 µl of 10 µM primer Tn5mCP1n and Tn5mCBar 7 and 0.5 µl of 100x SYBRGreen I using a LightCycler 480 real-time machine with 72 °C for 5 min, 98 °C for 30 sec and cycling at 98 °C, 10 sec; 63 °C, 30 sec; 72 °C, 30 sec. Amplification was stopped when an increase of about 10 fluorescence units was observed, usually between cycle 12 and 15. . Libraries were bead-purified with 70 µl HighPrep beads and eluted with 12 µl EB (Qiagen). Concentrations and fragment lengths were determined with the Qubit dsDNA High sensitivity kit (Invitrogen) and the TapeStation D1000 High sensitivity assay (Agilent), respectively. Up to ten libraries with compatible barcodes were pooled equimolarly, and pools of 5-10 nM were sequenced in the DKFZ Genomics and Proteomics Core Facility (GPCF) using an Illumina NextSeq 550 system with 75 bp paired-end, mid output mode.

value: Fetal liver

tag: strain

value: transduction with MNX1 vector


title: lung, OVA-chanllege, rep3

description: Library name: Sample9


title: CART19_vehicle [PP-PG-CAR19-GEX]


title: 42_mutantNSC_PRDM16_3

value: Primary NSCs

value: Prdm16 KO

value: PRDM16 antibody


title: OCI-LY18-DMSO-CART19 [O5]

data_processing:
gene counting and analysis with DESeq2 R library package
Assembly: hg38
Supplementary files format and content: excel file with raw gene counts

extract_protocol:
GFP+ DLBLC cell lines (OCI-LY18 or SU-DHL-4) were pre-treated with tazemetostat (500 nM) or DMSO for 72 hs and then exposed to CART19 or UTD cells for 48 hs, in the presence of tazemetostat or DMSO. Cell lines were sorted based on viability and GFP+ and used to extract RNA for bulk RNA sequencing.
NEB NEXT Ultra II RNA seq library kit

value: DLBCL


title: 41_mutantNSC_IgG_3


title: lung, OVA-chanllege, rep1

description: Library name: Sample7


title: FLC_MNX1_ATAC_3


title: CART19_TIL_tazemetostat [BC-CART19-TAZ-PP-TILs]

description: PP_CART19_TAZ_TILs_filtered_feature_bc_matrix.h5

extract_protocol:
Primary Human CAR T cells were generated and injected in NSG mice engrafted with the DLBCL line OCI-LY18; 11 days post-CAR T infusion, human CAR T cells were isolated from tumor single cells suspension by FACS sorting
Chromium NEX GEM Single Cell 5'


title: CART19_TIL_tazemetostat [GEX-CART19-TAZ-PP-TILs]


title: FLC_MNX1_ATAC_2


title: lung, OVA-chanllege, rep2

description: Library name: Sample8


title: RCC10 cells, DKO_2

description: Library name: Sample 4

data_processing:
Fastq files were subjected to quality check using FastQC (Galaxy version 0.74+galaxy1) and then trimmed using Trimmomatic (Galaxy version 0.39+galaxy2). Trimmed fastq files were mapped to hg38 using HISAT2 (Galaxy version 2.2.1+galaxy1). Duplicates were removed using MarkDuplicates (Galaxy version 3.1.1.0). Read counts were generated using featureCounts (Galaxy version 2.0.8+galaxy0) and the differential expression analysis was performed using limma (Galaxy version 3.58.1+galaxy0).
Assembly: hg19
Supplementary files format and content: DifferentialExpression_normalized counts.txt

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a Kapa mRNA Hyper Prep kit (Roche).

value: RCC10 cells

value: knockout


title: 25_mutantNSC_IgG_2


title: lung, sham, rep6

description: Library name: Sample6

value: PBS inhalation


title: FLC_MNX1_ATAC_1


title: CART19_TIL_vehicle [BC-CART19-PP-TILs]

description: PP_CART19_TILs_filtered_feature_bc_matrix.h5


title: Prdm16NSC_BMP4_PRDM16_6


title: CART19_TIL_vehicle [GEX-CART19-PP-TILs]


title: FLC_MNX1_ATAC_5


title: Prdm16NSC_BMP4_PRDM16_5


title: lung, sham, rep4

description: Library name: Sample4


title: FLC_emptyvectorcontrol_ATAC_4

value: transduction with empty vector (control)


title: short-read-m6A-isoSC-seq

description: 10x Genomics

data_processing:
Raw data were demultiplexed by mkfastq software. The reads were then aligned to human GRCm38/hg38 reference genome using Cell Ranger (v6.0.1), followed by count calculation, cell-barcode filtering with the default parameters.
The UMI counts of all genes across all single-cells were used to cluster the single-cells using Seurat. Briefly, only cells with at least 200 and at most 5000 genes and no more than 20% of mitochondrial reads were considered for the downstream analyses. After filtering, the RNA counts were normalized using LogNormalize method implemented in Seurat with a scale factor of 10,000. The top 2000 variable genes defined by the FindVariableFeatures function of Seurat were used for PCA analysis. We then took the top 10 principal components of PCA for the analyses of cell clustering and UMAP projection. Clusters were identified using SNN graph and original Louvain algorithm with a resolution of 0.1. FindAllMarkers function in Seurat was used to determine the marker genes of each cell cluster by requiring p-value < 0.01 and log2 fold-change ≥ 0.25.
The cleaned single-cell RNA sequencing reads were combined to call the raw mutations using the same pipeline as we did for the bulk RNA-seq data. The VarTrix (v1.1.22, https://github.com/10XGenomics/vartrix) was used to calculate the counts of reference and alternative nucleotides for each mutation site in each cell. The mutation sites that match dbSNP annotated SNPs were filtered out. Only the mutation sites with UMI coverage ≥ 50, mutation reads coverage ≥ 5 and mutation rate ≥ 0.05 in the combined single-cell data were used for the downstream analyses. The mutation peaks were identified based on the combined single-cell data using the same approach as we did for the bulk RNA-seq data.
Only the cells with > 200 methylated mutation peaks (at least one C-to-U mutated read) were used in the downstream analysis. To rule out the effects of gene expression on m6A-based cell clustering, we filtered out the mutation peaks on the marker genes of gene expression-based cell clusters. Then, mean C-to-U mutation rate of the filtered mutation peaks across the filtered single-cells were used to cluster the single-cells using Seurat (v3.1.0) 34. The mean C-to-U mutation rate of the filtered mutation peaks were normalized using LogNormalize method implemented in Seurat with a scale factor of 10,000. The top 3000 variable peaks defined by the FindVariableFeatures function of Seurat were used for PCA analysis. We then took the top 10 principal components of PCA for the analyses of cell clustering and UMAP projection. Clusters were identified using SNN graph and original Louvain algorithm with a resolution of 0.30. Marker mutation peaks of each cluster were identified using FindAllMarkers function in Seurat by requiring p-value < 0.01 and log2 fold-change ≥ 0.1.
Assembly: hg38
Supplementary files format and content: tab-sparated values files and matrix file

extract_protocol: The mixed single-cell suspension was utilized to generate a barcoded single-cell RNA-seq library using the 10x Genomics 3’ gene expression kit (v3) following the recommended protocol provided by the manufacturer. Half of the amplified cDNA was employed for short-read sequence library preparation following the 10x Genomics protocol and sequenced on an Illumina NovaSeq 6000 sequencing system to generate 310 million 150 bp paired-end reads.

treatment_protocol: The pcDNA3.1-YTH-APOBEC-T2A-EGFP construct was transfected into HEK293T cells, HepG2 cells, and HeLa cells, respectively, using Lipofiter 3.0 (Hanbio) according to the manufacturer's instructions. The medium was refreshed 6 hours after transfection, and the EGFP-positive cells of the three cell lines were isolated, respectively, through cytometry 3 day after transfection.The EGFP-positive HEK293T, HepG2, and HeLa cells were mixed together in a 1700:1700:1700 ratio and then isolated to create cell suspension.


title: lung, sham, rep3

description: Library name: Sample3


title: Prdm16NSC_BMP4_PRDM16_4


title: FLC_emptyvectorcontrol_ATAC_3


title: Prdm16NSC_BMP4_IgG_6

value: IgG


title: lung, sham, rep2

description: Library name: Sample2


title: Patient SG (Pure UC) Tumor2

city: San Francisco

first: Hanbing

last: Song

state: CA

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

description: Library name: SG-2_S30

data_processing:
Demultiplexed pair-end FASTQ files were aligned to hg19 whole genome using dropseq_workflow pipeline on Terra
Assembly: hg19
Supplementary files format and content: txt format matrix table with raw gene counts for every gene and every cell barcode

source_name: Bladder

extract_protocol:
Tumor and adjacent normal liver tissues were dissociated by mincing tissue in 1-2mm squares, followed by incubation in Liver Perfusion Medium (ThermoFisher Scientific) for 15 min at 37°C in a rotating oven. After being washed in PBS (ThermoFisher Scientific), tissues were incubated with Liver Digest Medium (ThermoFisher Scientific) supplemented with HEPES and collagenase type IV (Worthington Biochemical, Lakewood, NJ) (600 to 800 U/ml) for 30 min at 37°C with rotation. Further dissociation was achieved by pipetting 10 times through a 25 mL serological pipette. Single cells were then separated from clumps using a 70 µm strainer (Fisher Scientific, Hampton, NH). After lysis of red blood cells with ACK RBC Lysis Buffer (Fisher Scientific), single cells were counted using a LUNA™ Automated Cell Counter (Logos biosystems, South Korea) and processed for scRNA-seq analysis. Patient derived spheroids embedded in Matrigel were washed with PBS, then digested in TrypLE 1X (ThermoFisher Scientific) for 30 to 45 min at 37°C with rotation to obtain a single cell suspension. Cells were washed, then, filtered through a 70-µm strainer, counted using a LUNA™ Automated Cell Counter, and processed for scRNA-seq analysis.
Libraries were prepared for each pool, using 800-1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides. Library products were purified using SPRI beads, first at 0.6x and then at a 1x volumetric ratio. Libraries were then run on an HSD1000 tape (Agilent, Cat: 50675584) to determine the concentration between 100-1000 bp. For each library, 3 nM dilutions were prepared. These dilutions were pooled for sequencing on a NovaSeq S4 flow cell.

value: Bladder


title: FLC_emptyvectorcontrol_ATAC_2


title: Patient SG (Pure UC) Tumor1

description: Library name: SG-1_S29


title: Prdm16NSC_BMP4_IgG_5


title: lung, sham, rep1

description: Library name: Sample1


title: Patient 12050 (Squamous) Tumor1

description: Library name: PA_U67-12050T1_Pool_1_2_3_S72_L003


title: FLC_emptyvectorcontrol_ATAC_1


title: Patient 12049 (Pure UC) Tumor

description: Library name: PA_U67-12049_Pool_1_2_3_S20_L001


title: BM_MNX1_IgG_4

data_processing:
Reads were trimmed using Trim Galore in conjunction with Cutadapt (v. 1.14) with the options –paired”, “–nextera”, “– length_1 35”, and “–length_2 35. Trimmed reads were mapped against mm10 reference genome using Bowtie25 (v. 2.5.2). Conflicting mapped reads with a phred score lower than 20 was removed using SAMTools (v. 1.19). Finally, read ends were shifted to center of the transposition event.
BW-files were generated from BAM-files by means of the bamCoverage functionality of Deeptools v. 3.1.1 22 using the non-default parameters: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX --extendReads
H3K4me3 and H4K4me1 peaks were retrieved with from BAM-files with GoPeaks, using a q-value cut-off of 0.05 and the --broad and  --mdist 3000 options for the latter.
Assembly: mm10
Supplementary files format and content: BW, BED (except for IgG controls), JSON (except for IgG controls),
Library strategy: ACT-seq

source_name: Bone marrow

extract_protocol:
Bone marrow cells from MNX1-induced leukemic mice, non-transplanted mouse fetal liver cells containing MNX1-vector as well as FLCs with empty vector were lysed using a in a resuspension buffer containing 0.1% of NP40 and Tween-20 and 0.01% digitonin. Lysed cells were resuspended in transposition buffer (10 mM Tris-acetate, pH 7.6, 5 mM MgCl2, 10% dimethylformamide, 30% PBS, 0.01% digitonin and 0.1% Tween-20) together with Tn5 transposome and tagementation were allowed to proceed for 30 min at 37°C under agitation. For ACT-seq, targeting antibodies used for the pA-Tn5 transposome-antibody complexes were directed against H3K4me3 (Abcam_ab8580), H3K4me1 (Abcam_ab8895), HA-tag (Sigma_H6908),  IgG (Merck Millipore PP64B) and yeast histone H2B (M3930, Boster Bio. Tech., Pleasanton, CA, USA), the latter complexes being used for spike-in to enable sequence read normalization between biological replicates.
Sequencing libraries were generated by addition of 25 µl NEBNext High Fidelity 2× Master Mix (NEB), each 2.5 µl of 10 µM primer Tn5mCP1n and Tn5mCBar 7 and 0.5 µl of 100x SYBRGreen I using a LightCycler 480 real-time machine with 72 °C for 5 min, 98 °C for 30 sec and cycling at 98 °C, 10 sec; 63 °C, 30 sec; 72 °C, 30 sec. Amplification was stopped when an increase of about 10 fluorescence units was observed, usually between cycle 12 and 15. . Libraries were bead-purified with 70 µl HighPrep beads and eluted with 12 µl EB (Qiagen). Concentrations and fragment lengths were determined with the Qubit dsDNA High sensitivity kit (Invitrogen) and the TapeStation D1000 High sensitivity assay (Agilent), respectively. Up to ten libraries with compatible barcodes were pooled equimolarly, and pools of 5-10 nM were sequenced in the DKFZ Genomics and Proteomics Core Facility (GPCF) using an Illumina NextSeq 550 system with 75 bp paired-end, mid output mode.

value: Bone marrow

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl /ThomJ

value: tranplantion of fetal liver cells transduced with MNX1 vector


title: Prdm16NSC_BMP4_IgG_4


title: FLC_emptyvectorcontrol_ATAC_5


title: Patient 12041 (Nested) Tumor

description: Library name: PA_U67-12041-2_Pool_1_2_3_S22_L001


title: 24_Prdm16NSC_BMP4_H3K4me3_2

value: H3K4me3 antibody


title: BM_MNX1_IgG_3


title: 40_Prdm16NSC_BMP4_H3K4me3_3


title: Patient 11734 (Plasmacytoid) Tumor

description: Library name: PA_U67-11734-2_Pool_1_2_3_S21_L001


title: 8_Prdm16NSC_BMP4_H3K4me3_1


title: BM_MNX1_IgG_1


title: E174 primary neurons (PN) from Ai6 mice, uninfected control, rep 3

city: Tucson

first: Anita

middle: A

last: Koshy

state: AZ

address: 1657 E Helen St

institute: University of Arizona

description: Library name: PN_UI_3

data_processing:
Transcript-level count were summarized to genes using the TxImport package and mouse gene annotation package from biomaRt.
Data were filtered and normalized with the EdgeR package52 by the Trimmed Mean of M-values (TMM) method.
Genes with less than one count per million in n of the samples (3 for PN, 5 for LCM) were filtered out.
The VOOM function in Limma was used to variance stabilize the filtered, normalized data.
Assembly: GRCm39
Supplementary files format and content: PN_Normalized_Counts_nolog.txt has normalized counts for each sample with no log transformation. Samples are column names and follow the structure of Primary Neuron (PN)_Uninfected or PRU-infected (UI or PRU)_Biological Replicate Number (1-3).
Supplementary files format and content: tab delimited file of normalized counts

source_name: E174 primary cortical neurons

growth_protocol: Mouse primary cortical neurons were harvested from E174 mouse embryos obtained from pregnant ZsG mice. Dissections of E174 cortical neurons were performed and primary neuronal cell cultures were generated by methods described previously with minor modifications46. The culturing plates were prepared by coating overnight with 0.001% poly-L-lysine solution (Millipore Sigma, P4707, diluted in water 1:10) for plastic surfaces and 100 μg/ml poly-L-lysine hydrobromide (Sigma, P6282, dissolved in borate buffer, pH 8.4) for glass surfaces. They were washed three times for ten minutes each with water and transferred to plating media (MEM, 0.6% D-glucose, 10% FBS). Neurons were seeded at 500,000 in 6-well plates for RNA-seq. Four hours after plating, full media exchange to neurobasal media (Neurobasal base media, 2% B27 supplement, 1% L-glutamine and 1% penicillin-streptomycin) was performed. On day in vitro (DIV) 4, neurons received a half volume media change of neurobasal media with 5 μM cytosine arabinoside (AraC, Millipore Sigma, C6645) to stop glial proliferation. One third media exchanges with neurobasal media occurred every 3-4 days thereafter. All the experiments were performed on 10 DIV neurons.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Kit and protocol (Zymo Research, R2051)
RNA quality was measured on an Agilent 2100. Only samples with an RNA Integrity (RIN) score of >7 were used. After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long non-coding libraries, rRNA is removed using the Ribo-Zero kit. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Primary neuronal cell cultures were infected (MOI 5) for 24 hours prior to RNA isolation.

value: E174 primary cortical neurons

value: Uninfected


title: E174 primary neurons (PN) from Ai6 mice, 24 hour PRU-infected, rep 1

description: Library name: PN_PRU_1

value: 24 hour PRU-infection


title: E174 primary neurons (PN) from Ai6 mice, 24 hour PRU-infected, rep 3

description: Library name: PN_PRU_3


title: E174 primary neurons (PN) from Ai6 mice, 24 hour PRU-infected, rep 2

description: Library name: PN_PRU_2


title: Patient 12050 (Squamous) Tumor2

description: Library name: PA_U67_12050T2_Pool_1_2_3_S103_L004


title: 38_Prdm16NSC_BMP4_PRDM16_3

value: Primary NSCs


title: FLCcontrol_emptyvectorcontrol_IgG_4

value: Fetal liver


title: E174 primary neurons (PN) from Ai6 mice, uninfected control, rep 2

description: Library name: PN_UI_2


title: Patient 12050 (Squamous) Paired Normal

description: Library name: PA_U67_12050N_Pool_1_2_3_S45_L002


title: E174 primary neurons (PN) from Ai6 mice, uninfected control, rep 1

description: Library name: PN_UI_1


title: FLCcontrol_emptyvectorcontrol_IgG_3


title: 21_Prdm16NSC_BMP4_IgG_2


title: 37_Prdm16NSC_BMP4_IgG_3


title: Patient PS (Micropapillary) Tumor2 Replica2

description: Library name: HY_PS_T2-2_S23


title: Patient PS (Micropapillary) Tumor2 Replica1

description: Library name: HY_PS_T2-1_S18


title: lung, sham, rep5

description: Library name: Sample5

value: lung tissue


title: FLCcontrol_emptyvectorcontrol_IgG_2


title: Keap1 KO CD8 T cells, treated with iloprost (5 µM) for 24h- tech. rep. 3

city: Grand Rapids

first: Russell

last: Jones

address: 333 Bostwick Ave NE

department: Department of Metabolism and Nutritional Programming

institute: Van Andel Insitute

description: Library name: M24

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0; Martin, 2011). Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8; Dobin et al., 2013) with --quantMode GeneCounts.
Assembly: mm10
Supplementary files format and content: Connts per million (CPM) of each sample processed using edgeR (with low expressed genes removed)

source_name: spleen derived

growth_protocol: Keap1 KO CD8 T cells were isolated from spleens of mice using a CD8 T cell isolation kit (Stemcell, #19853) and activated (1 million cells/mL) using plate bound anti-CD3 (2 µg/mL) and anti-CD28 1 µg/mL) antibodies for 48h in T cell media. Cells were then passaged (400,000 cells/mL) for an additional 48 hours in the absence of plate bound antibodies, in T cell media.

extract_protocol:
mRNA was captured using polyA, and stranded libraries were constructed.
RNA-seq

treatment_protocol: On day 4, cells were seeded at 400,000 cells/mL and treated with either vehicle (DMSO), or iloprost (5 µM) for 24h, both in technical triplicate, then harvested for downstream RNA-seq.

value: spleen derived

value: CD8 T cell

value: Keap1 KO

value: iloprost


title: BM_MNX1_IgG_2


title: FLCcontrol_emptyvectorcontrol_IgG_1

value: transduction with empty vector (control)


title: Prdm16NSC_PRDM16_6

value: PRDM16 antibody


title: Prdm16NSC_PRDM16_5


title: Keap1 KO CD8 T cells, treated with iloprost (5 µM) for 24h- tech. rep. 1

description: Library name: M22


title: Patient PS (Micropapillary) Tumor1 Replica2

description: Library name: HY_PS_T1-2_S22

value: Bladder


title: BM_MNX1_MNX1-HA_4

value: Bone marrow


title: Patient PS (Micropapillary) Tumor1 Replica1

description: Library name: HY_PS_T1-1_S17


title: Keap1 KO CD8 T cells, treated with vehicle (DMSO) for 24h- tech. rep. 3

description: Library name: M21

value: vehicle (DMSO)


title: Patient PG_S (Paraganglioma) Tumor2

description: Library name: HY_PG_ST2_S2


title: Prdm16NSC_PRDM16_4


title: Prdm16NSC_IgG_6

value: IgG


title: Patient PG_S (Paraganglioma) Tumor1

description: Library name: HY_PG_ST1_S1


title: Keap1 KO CD8 T cells, treated with vehicle (DMSO) for 24h- tech. rep. 2

description: Library name: M20


title: BM_MNX1_MNX1-HA_2

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl /ThomJ

value: tranplantion of fetal liver cells transduced with MNX1 vector


title: BM_MNX1_MNX1-HA_3


title: Keap1 KO CD8 T cells, treated with vehicle (DMSO) for 24h- tech. rep. 1

description: Library name: M19


title: BM_MNX1_MNX1-HA_1


title: Patient PG_S (Paraganglioma) Paired Normal2

description: Library name: HY_PG_SN2_S6


title: Prdm16NSC_IgG_4


title: FLCcontrol_emptyvectorcontrol_MNX1-HA_4


title: Keap1 KO CD8 T cells, treated with iloprost (5 µM) for 24h- tech. rep. 2

description: Library name: M23


title: 36_Prdm16NSC_H3K4me3_3

value: H3K4me3 antibody


title: Patient PG_S (Paraganglioma) Paired Normal1

description: Library name: HY_PG_SN1_S5


title: Mutiplexed samples

city: Stanford

first: Claudia

middle: Katharina

last: Petritsch

state: California

address: G1115 Lorry. Lokey Stem Cell Research Bl, 265 Campus Drive, Stanford University

institute: Stanford University

description:
Library name: Multiplexed libraries
BD Rhapsody

data_processing:
Rhapsody data were processed using the Seven Bridges Genomics cloud platform (San Francisco, CA) and BD Rhapsody Sequence Analysis Pipeline (v2.0) to quantify transcript levels with default parameters against the GRCm38 genome for BD Rhapsody scRNA-seq data. The plug-in Lex BDSMK was run to separate out the Sample Tags. After analysis, output files were imported into R package Seurat (version 4) for downstream clustering analysis and visualization.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain tumor

extract_protocol:
Brains collected after intracardiac perfusion with 20ml of PBS were dissociated into single-cell suspensions using the mouse tumor dissociation kit (#130-096-730) and the gentleMACS Octo Dissociator according to the manufacturer’s protocol (Miltenyi Biotec). Single-cell libraries of dissociated single cells were prepared using the BD RhapsodyTM platform (BD Biosciences). Single-cell suspensions obtained from the brains of individual tumor-bearing mice were stained with oligonucleotide-conjugated Sample Tags using the mouse Single-Cell Multiplexing Kit (cat# 633793) following the manufacturer’s protocol (BD Biosciences). Sorted live cells from barcoded samples were counted and pooled at equal ratios and loaded onto a BD Rhapsody cartridge for capture.
Cell capture and library preparation were completed using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification Kit (cat# 633801). Briefly, cells were captured with beads in microwell plate, followed by cell lysis, bead retrieval, cDNA synthesis, template switching and Klenow extension, and library preparation following the BD Rhapsody protocol. The quality of the final libraries was assessed by using an Agilent’s Bioanalyzer high sensitivity analysis and concentrations were measured by a Qubit method. The final libraries were diluted and normalized to 4nM and then pooled for paired-end sequencing on NovaSeq 6000 sequencer (Illuminia, San Diego, CA) in Novogene (Novogene Corporation Inc., Sacramento, CA).

treatment_protocol: Dabrafenib was given at 30mg/kg daily by oral gavage. Trametinib was given at 1mg/kg daily by oral gavage. BioXCell anti-PD-L1 (clone 10F.9G2; ThermoFisher Scientific) was given at 20 mg/kg i.p. at day 1 and 8 mg/kg every 2 days thereafter, BioXCell anti-CTLA-4 (clone 9D9; ThermoFisher Scientific) was given at 8 mg/kg i.p. at day 1 and 2 mg/kg every 2 days thereafter.

value: Brain tumor

value: Sample 10, Control

value: Sample 5, BRAFi+MEKi

value: Sample 9, ICI

value: Sample 12, BRAFi+MEKi+ICI

tag: host strain


title: Patient PG_M (Paraganglioma) Tumor2

description: Library name: HY_PG_MT2_S4


title: 4_Prdm16NSC_H3K4me3_1

value: Primary NSCs


title: FLCcontrol_emptyvectorcontrol_MNX1-HA_2

value: Fetal liver


title: Patient PG_M (Paraganglioma) Tumor1

description: Library name: HY_PG_MT1_S3


title: Patient PG_M (Paraganglioma) Paired Normal2

description: Library name: HY_PG_MN2_S8


title: 34_Prdm16NSC_PRDM16_3


title: Patient PG_M (Paraganglioma) Paired Normal1

description: Library name: HY_PG_MN1_S7


title: 17_Prdm16NSC_IgG_2


title: BM_MNX1_H3K4me3_4


title: BM_MNX1_H3K4me3_3


title: Prdm16NSC_IgG_5


title: mutantNSC_BMP4_SMAD4_3

data_processing:
Three replicates of ChIP-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The ChIP-seq coverage for these samples were generated by bedtools genomeCoverageBed and normalized to the library depths to give a read per million per base (RPM).
The CUT&TAG samples of Prdm16_E and Prdm16 mutant NSCs in four replicates, and of Prdm16 from CH and ChP area at stage 12.5 embryos in three replicates, were mapped to mm10 genome assembly using Bowtie2 (bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700). The CUT&TAG coverage for these samples were generated by bedtools genomeCoverageBed and normalized to the library depths to give a read per million per base (RPM).
Assembly: mm10
Supplementary files format and content: bigwig

value: Prdm16 KO

value: SMAD4 antibody


title: mutantNSC_BMP4_SMAD4_2


title: Patient JM (Micropapillary+pleomorphic) Tumor2

description: Library name: HY_JM_T2_S14


title: Patient JM (Micropapillary+pleomorphic) Tumor1

description: Library name: HY_JM_T1_S13


title: BM_MNX1_H3K4me3_1


title: BM_MNX1_H3K4me3_2


title: mutantNSC_BMP4_SMAD4_1


title: Patient HG (Pure UC) Tumor2

description: Library name: HY_HG_T2_37


title: FLCcontrol_emptyvectorcontrol_H3K4me3_4

value: transduction with empty vector (control)


title: mutantNSC_BMP4_SMAD3_3

value: SMAD3 antibody


title: FLCcontrol_emptyvectorcontrol_H3K4me3_3


title: Patient HG (Pure UC) Tumor1 Replica1

description: Library name: HY_HG_T1_37

value: Bladder


title: mutantNSC_BMP4_pSMAD_3

value: pSMAD1/5/8 antibody


title: FLCcontrol_emptyvectorcontrol_H3K4me3_2


title: mutantNSC_BMP4_pSMAD_2


title: Patient HG (Pure UC) Tumor1 Replica2

description: Library name: HY_HG_T1_48


title: FLCcontrol_emptyvectorcontrol_MNX1-HA_1


title: FLCcontrol_emptyvectorcontrol_MNX1-HA_3


title: 33_Prdm16NSC_IgG_3

value: IgG


title: FLCcontrol_emptyvectorcontrol_H3K4me3_1


title: Patient JM (Micropapillary+pleomorphic) Paired Normal

description: Library name: HY_JMx_N1_S15


title: BM_MNX1_H3K4me1_4

value: Bone marrow

value: NOD.Cg-KitW-41J Tyr+ Prkdcscid Il2rgtm1Wjl /ThomJ


title: Murine prostate BC cells, 6W PTEN induction and p65 knock-out, replicate 2

city: Bruxelles

first: Yura

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: K5PTEN_p65_6W_BC_2

data_processing:
Quality of each raw dataset was checked with FastQC (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
The adaptor sequences and low-quality regions were trimmed by Trimmomatic.
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR aligner (v. 2.7.5a) to generate read alignments for each sample.
Duplicate reads were removed by Picard MarkDuplicates module (http://broadinstitute.github.io/picard/).
After transcript assembling, gene-level counts were obtained using HTseq (v.0.11.1) and normalized to 20 million aligned reads per count.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .csv / normalised gene expression

source_name: murine prostate

extract_protocol:
RNA extraction from FACS-isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations.
Indexed complementary DNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: murine prostate


title: Patient FG (Nested) Tumor1 Replica3

description: Library name: HY_FG_T1_48-2


title: Murine prostate BC cells, 6W PTEN induction and p65 knock-out, replicate 1

description: Library name: K5PTEN_p65_6W_BC_1


title: BM_MNX1_H3K4me1_3

value: tranplantion of fetal liver cells transduced with MNX1 vector


title: Patient FG (Nested) Tumor2 Replica1

description: Library name: HY_FG_T2_37


title: mutantNSC_BMP4_pSMAD_1

extract_protocol:
stardard for ChIPseq or Cut&Tag
NEB ultra II DNA libary kit for ChIP-seq libararies, standard protocol for cut&tag


title: Murine prostate BC cells, 6W PTEN induction, replicate 2

description: Library name: K5PTEN_6W_BC_2


title: BM_MNX1_H3K4me1_2


title: mutantNSC_BMP4_Input_3

value: Normalization control


title: Murine prostate BC cells, 6W PTEN induction, replicate 1

description: Library name: K5PTEN_6W_BC_1


title: mutantNSC_BMP4_Input_2


title: Patient FG (Nested) Tumor1 Replica2

description: Library name: HY_FG_T1_48-1


title: mutantNSC_BMP4_SMAD3_2


title: Patient FG (Nested) Tumor2 Replica2

description: Library name: HY_FG_T2_48


title: FLCcontrol_emptyvectorcontrol_H3K4me1_4


title: mutantNSC_SMAD4_3


title: FLCcontrol_emptyvectorcontrol_H3K4me1_3


title: FLC_emptyvectorcontrol_IgG_5


title: mutantNSC_SMAD4_2


title: Patient FG (CIS) Tumor2

description: Library name: HY_FG_CIS_48-1


title: Patient FG (Nested) Tumor1 Replica1

description: Library name: HY_FG_T1_37


title: BM_MNX1_H3K4me1_1


title: mutantNSC_BMP4_Input_1


title: mutantNSC_SMAD4_1


title: Cortex_4

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

description: Library name: Cortex_4

data_processing:
Sequencing outputs were demultiplexed using cellranger (6.1.2) mkfastq
Fastq files were aligned to Mus musculus mm10 reference using cellranger (6.1.2) count or multi
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped STAR output directory (Solo.out).
Supplementary files format and content: For multiple samples, cell barcode whitelists.

molecule: nuclear RNA

source_name: brain, ipsilesional cerebral cortex

extract_protocol:
The brains were dissected on ice, the cerebral cortex and hippocampus were isolated, quickly frozen using liquid nitrogen and stored at -80°C until use. Crushed tissue was added to Lysis Buffer to dissolve and extract the nuclei; Debris was removed using Debris Removal Solution (Miltenyi Biotec) and the nuclei were fixed with 80% methanol.
Libraries were prepared using a single-cell combinatorial indexing RNA sequencing technique. Reverse transcription reactions were performed using 384 different barcoded Oligo dT primers to add the 1st barcode to cDNA obtained from nuclear RNA. The DNA was then distributed into 96-well plates by Pool & Sort and subjected to double-strand synthesis and Tagmentation. PCR was performed in each well using different Index primers and a 2nd barcode was added. The resulting product was column purified and small fragments were removed with AMPure XP beads.

value: brain, ipsilesional cerebral cortex


title: Patient FG (CIS) Tumor1

description: Library name: HY_FG_CIS_37


title: mutantNSC_SMAD3_3


title: FLC_emptyvectorcontrol_IgG_4


title: Cortex_3

description: Library name: Cortex_3


title: FLC_emptyvectorcontrol_IgG_3


title: Patient 21226 (Small large cell) Tumor2

description: Library name: HY_21262_2_S40


title: Patient 21226 (Small large cell) Tumor1

description: Library name: HY_21262_1_S39


title: Cortex_2

description: Library name: Cortex_2


title: mutantNSC_SMAD3_1


title: Cortex_1

description: Library name: Cortex_1


title: mutantNSC_SMAD3_2


title: Patient FG (CIS) Tumor3

description: Library name: HY_FG_CIS_48-2


title: Patient 21226 (Squamous) Tumor2 Replica2

description: Library name: HY_21226_T2_48


title: mutantNSC_Input_3


title: FLC_MNX1_H3K4me3_4

value: transduction with MNX1 vector


title: mutantNSC_pSMAD_2


title: Hippo_1

description: Library name: Hippo_1

source_name: brain, ipsilesional hippocampus

value: brain, ipsilesional hippocampus


title: mutantNSC_pSMAD_3

value: Primary NSCs


title: Hippo_3

description: Library name: Hippo_3


title: Hippo_4

description: Library name: Hippo_4


title: Patient FG (Nested) Paired Normal

description: Library name: HY_FG_N_48


title: 119ub1-CKO_Rep2

city: Tianjin

first: Liangyu

last: Xing

address: 22nd Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Sequencing quality was checked by fastqc.
Use trim-galore to filter the adapters.
Clean reads were aligned to UCSC mm39 reference genome and λDNA (TD904, Vazyme Biotech Co.,Ltd), using bowtie2 with the following parameters: --phred33 --end-to-end --very-sensitive --no-mixed --no-discordant --no-unal -I 10 -X 700
Dupulicates were removed by sambamba.
Bam files were sorted and bulit index by samtools
Used deeptools to generate bigwig files, according to scale-factor to normalize.
Peak was calling by macs2, and annotated by ChIPseeker.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: femur

growth_protocol: Osteoblasts were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag assay of osteoblasts were performed using Hyperactive Universal CUT & Tag Assay Kit (TD904, Vazyme Biotech Co.,Ltd), the chromatin was incubated with H2AK119ub1 antibody.
The DNA Library of CUT&TAG were prepared according to the manufacturer's instructions (TD904, Vazyme).

treatment_protocol: In Aging CUT&Tag，osteoblats isolated from femur of 3-month and 18-month mice(C57BL/6J). In CKO CUT&Tag,Kdm2b-CxxC domain conditional knockout osteoblats isolated and screening from femur of Kdm2bfl/fl Ocncre Ai14 (C57BL/6J), osteoblats isolated from Ocncre Ai14 mice as control.

value: femur

value: Osteoblast

value: mice femoral osteoblast


title: Patient 21226 (Squamous) Tumor2 Replica1

description: Library name: HY_21226_T2_37


title: Patient 21226 (Squamous) Tumor3

description: Library name: HY_21226_T3_48


title: FLC_MNX1_H3K4me3_2

value: Fetal liver


title: mutantNSC_pSMAD_1

value: Prdm16 KO


title: FLC_MNX1_H3K4me3_5


title: Patient 21226 (Squamous) Paired Normal2

description: Library name: HY_21226_N_48

value: Bladder


title: mutantNSC_Input_1


title: FLC_emptyvectorcontrol_IgG_2

value: transduction with empty vector (control)


title: Patient 21222 (Micropapillary) Tumor3

description: Library name: HY_21222_T3_48


title: FLC_emptyvectorcontrol_H3K4me3_5


title: Patient 21226 (Squamous) Paired Normal1

description: Library name: HY_21226_N_37


title: 119ub1-CKO_Rep1


title: FLC_MNX1_H3K4me3_1


title: Prdm16NSC_BMP4_SMAD4_3

value: SMAD4 antibody


title: FLC_emptyvectorcontrol_IgG_1


title: Patient 21226 (Squamous) Tumor1

description: Library name: HY_21226_T1_48


title: FLC_MNX1_H3K4me3_3


title: Hippo_2

description: Library name: Hippo_2


title: 119ub1-CON_Rep2


title: mutantNSC_Input_2


title: Patient 21222 (Micropapillary) Tumor2 Replica2

description: Library name: HY_21222_T2_48


title: Prdm16NSC_BMP4_SMAD4_2


title: Prdm16NSC_BMP4_SMAD4_1


title: 119ub1-CON_Rep1


title: FLC_emptyvectorcontrol_H3K4me3_3


title: Prdm16NSC_BMP4_SMAD3_3

value: SMAD3 antibody


title: 119ub1-YOUNG_Rep1


title: 119ub1-OLD_Rep1


title: FLC_emptyvectorcontrol_H3K4me3_2


title: FLC_emptyvectorcontrol_H3K4me3_1


title: Patient 21222 (Micropapillary) Tumor1 Replica1

description: Library name: HY_21222_T1_37


title: Prdm16NSC_BMP4_SMAD3_2


title: Patient 21222 (Micropapillary) Tumor1 Replica2

description: Library name: HY_21222_T1_48


title: FLC_MNX1_H3K4me1_5


title: Patient 21222 (Micropapillary) Paired Normal2

description: Library name: HY_21222_N_48


title: CD1 prostate luminal

description: bulk ATAC-seq of FACS isolated LCs, 100k cells pooled from at least three CD1 mice

data_processing:
Adaptor sequences were removed with TrimmomaticPE using options ‘HEADCROP:10 CROP:70 ILLUMINACLIP:adaptor_file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’.
ATAC–seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (v.2.2.6) using options ‘-X 2000 –fr –very-sensitive –no-discordant –no-unal –no-mixed –non-deterministic’.
Mitochondrial reads, reads from unmapped or random counting and reads with a mapping quality <20 were removed using SAMtools.
Duplicate reads were removed by Picard MarkDuplicates module. Peak calling was performed on each individual sample by MACS2 (v.2.1.0.20151222) using options ‘-f BAMPE -g mm –nomodel– --shift 0 -q 0.01.
Peaks from the different subpopulations were merged for downstream analysis.
Reads counts of each merged peak for each individual sample were calculated by HTSeq-count using options ‘-f bam -r pos -m intersection-nonempty’.
Peaks were associated to genes with GREAT software with the following parameters: 5.0 kb in proximal upstream, 1.0 kb in proximal downstream and 100.0 kb in distal.
Assembly: mm10
Supplementary files format and content: .xlsx / normalized peak intensity with annotation

source_name: mouse prostate luminal cells

extract_protocol:
Cells were collected in 1 ml PBS supplemented with 3% FBS at 4 °C. Cells were centrifuged and cell pellets were resuspended in 100 μl lysis buffer (TrisHCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0.1%) and centrifuged at 500g for 25 min at 4 °C.
Supernatant was carefully discarded and nuclei were resuspended in 50μl reaction buffer (Tn5 transposase 2.5μl, TD buffer 22.5μl, from Nextera DNA sample preparation kit, Illumina, and 25μl H20). The reaction was performed at 37 °C for 30 min and was stopped by adding 5μl clean up buffer (NaCl 900 mM, EDTA 300 mM). DNA was purified using the MiniElute purification kit (QIAGEN) following the manufacturer’s protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800 bp (BluePippin, Sage Sciences), following the manufacturer’s recommendations.

value: mouse prostate luminal cells

value: WT


title: Prdm16NSC_BMP4_SMAD3_1


title: FLC_emptyvectorcontrol_H3K4me3_4


title: FLC_MNX1_H3K4me1_4


title: Prdm16NSC_BMP4_pSMAD_3

value: pSMAD1/5/8 antibody


title: Patient 21222 (Micropapillary) Paired Normal1

description: Library name: HY_21222_N_37


title: FLC_MNX1_H3K4me1_3


title: CD1 prostate basal

description: bulk ATAC-seq of FACS isolated BCs, 100k cells pooled from at least three CD1 mice

source_name: mouse prostate basal cells

value: mouse prostate basal cells


title: Patient 21217 (Squamous + Sarcomatoid) Tumor3

description: Library name: HY_21217_T3_48


title: CD1 prostate luminal, replicate 2

data_processing:
Quality of each raw dataset was checked with FastQC (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
The adaptor sequences and low-quality regions were trimmed by Trimmomatic.
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR aligner (v. 2.7.5a) to generate read alignments for each sample.
Duplicate reads were removed by Picard MarkDuplicates module (http://broadinstitute.github.io/picard/).
After transcript assembling, gene-level counts were obtained using HTseq (v.0.11.1) and normalized to 20 million aligned reads per count.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .xlsx / normalized gene expression

source_name: mouse prostate

value: mouse prostate


title: Prdm16NSC_BMP4_pSMAD_2


title: Patient 21222 (Micropapillary) Tumor2 Replica1

description: Library name: HY_21222_T2_37


title: FLC_MNX1_H3K4me1_2

value: transduction with MNX1 vector


title: Prdm16NSC_BMP4_pSMAD_1


title: CD1 prostate luminal, replicate 1


title: FLC_MNX1_H3K4me1_1


title: PTEN-deleted prostate basal

description: bulk ATAC-seq of FACS isolated BCs 6 weeks following Pten deletion in BC, 100k cells pooled from at least three K5CreER/Ptenfl/fl/Rosa-YFP mice

value: PTEN-deleted


title: Patient 21217 (Squamous + Sarcomatoid) Tumor2

description: Library name: HY_21217_T2_48


title: PTEN-deleted prostate luminal, replicate 2


title: Prdm16NSC_BMP4_Input_3

value: Primary NSCs

value: Normalization control


title: PTEN-deleted prostate luminal, replicate 1


title: Prdm16NSC_BMP4_Input_1


title: FLC_emptyvectorcontrol_H3K4me1_4


title: Prdm16NSC_BMP4_Input_2


title: Patient 21217 (Squamous + Sarcomatoid) Tumor1 Replica1

description: Library name: HY_21217_T1_37


title: CD1 prostate basal, replicate 1


title: Patient 21032 (CIS) Tumor

description: Library name: HY_21032_T1_S9


title: Patient 21217 (Squamous + Sarcomatoid) Paired Normal

description: Library name: HY_21217_N_48


title: FLC_emptyvectorcontrol_H3K4me1_3


title: Prdm16NSC_SMAD4_3


title: FLC_emptyvectorcontrol_H3K4me1_2


title: Patient 21032 (CIS) Paired Normal3

description: Library name: HY_21032_N3_S12


title: Prdm16NSC_SMAD4_2


title: CD1 prostate basal, replicate 2


title: PTEN-deleted prostate basal, replicate 2


title: Patient 21032 (CIS) Paired Normal2

description: Library name: HY_21032_N2_S11


title: Patient 21217 (Squamous + Sarcomatoid) Tumor1 Replica2

description: Library name: HY_21217_T1_48


title: PTEN-deleted prostate basal, replicate 1


title: Patient 21032 (CIS) Paired Normal1

description: Library name: HY_21032_N1_S10


title: Prdm16NSC_SMAD3_3


title: Prdm16NSC_SMAD4_1


title: PTEN-Pik3ca double mutant mouse prostate basal, rapamycin treated, replicate 2

data_processing:
Quality of each raw dataset was checked with FastQC (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
The adaptor sequences and low-quality regions were trimmed by Trimmomatic.
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR aligner (v. 2.7.5a) to generate read alignments for each sample.
Duplicate reads were removed by Picard MarkDuplicates module (http://broadinstitute.github.io/picard/).
After transcript assembling, gene-level counts were obtained using HTseq (v.0.11.1) and normalized to 20 million aligned reads per count.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .csv / normalized gene expression

source_name: mouse prostate basal

value: mouse prostate basal

value: Rapamycin (6mg/kg body weight)


title: FLC_emptyvectorcontrol_H3K4me1_5

value: Fetal liver


title: PTEN-Pik3ca double mutant mouse prostate basal, rapamycin treated, replicate 1


title: Patient 20847 (Lymphoepithelioma) Paired Normal1

description: Library name: HY_20847x_N1-2_S27


title: Prdm16NSC_SMAD3_2

source_name: Primary NSCs


title: Prdm16NSC_SMAD3_1


title: Patient 20847 (Lymphoepithelioma) Tumor3 Replica2

description: Library name: HY_20847_T3-2_S26


title: PTEN-Pik3ca double mutant mouse prostate basal, replicate 2

value: Etoh treated


title: PTEN-Pik3ca double mutant mouse prostate basal, replicate 1


title: Prdm16NSC_pSMAD_3


title: Patient 20847 (Lymphoepithelioma) Tumor3 Replica1

description: Library name: HY_20847_T3-1_S21

value: Bladder


title: C57BL6 mice, rAAV8-Hnf1aos1, Bio3

city: Storrs

first: Beshoy

last: Armanios

state: CT

address: 69 N Eagleville Road

institute: University of Connecticut

description:
Library name: 2T
column name: 2HT

data_processing:
00_fastq: raw data raw data in fastq format: sample_R1_001.fastq.gz sample_R2_001.fastq.gz bam: aligned data alignment file in bam format: sample.bam hit-counts: hit count for all the genes unique hit counts for each sample: sample.counts.txt DEG: differential gene expression analysis results raw gene hit counts of all samples used in the comparison: counts/raw_counts.csv normalized gene hit counts of all samples used in the comparison: counts/normalized_counts.csv rlog transformed gene hit counts of all samples used in the comparison: counts/rlog_trasnformed_counts.csv log2 fold change and (adjusted) p-value table: Differential_expression_analysis_table.csv log2 fold change and (adjusted) p-value table for significantly DE genes: Significant-DEGs.csv GO: GO enrichment analysis results GO enrichment analsysis table: comparison_GO_analysis.csv differential_splice_variant_expression: differential splicing anlysis results Results generated by DEXSeq: DEXSeqReport in zipped format
Assembly: GRCm39
Supplementary files format and content: tab-delimited tex files include raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each samples

source_name: liver

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer's protocol.
The first step involves ribosomal RNA (rRNA) depletion, where rRNA is removed to enrich for non-rRNA molecules such as mRNA, ensuring that the library focuses on the RNA of interest. Next, the RNA is subjected to fragmentation and random priming, breaking the RNA into smaller pieces to facilitate even sequencing coverage and initiating complementary DNA (cDNA) synthesis with random primers. Subsequently, the fragmented RNA is converted into double-stranded cDNA through first and second-strand cDNA synthesis. To prepare the cDNA for adapter ligation, the ends of the cDNA fragments undergo end repair, phosphorylation, and dA-tailing. This step ensures that the cDNA fragments have uniform and compatible ends for ligation with sequencing adapters. Finally, adapter ligation is performed, attaching specific adapters to the cDNA fragments for their identification and amplification. The library is then enriched through a PCR step to increase the quantity of adapter-ligated fragments. The final library is ready for high-throughput sequencing, enabling comprehensive RNA analysis.

value: liver


title: Prdm16NSC_pSMAD_1


title: C57BL6 mice, rAAV8-Hnf1aos1, Bio1

description:
Library name: 0T
column name: 0HT


title: C57BL6 mice, rAAV8-Hnf1aos1, Bio2

description:
Library name: 1T
column name: 1HT


title: Patient 20847 (Lymphoepithelioma) Tumor2 Replica2

description: Library name: HY_20847_T2-2_S25


title: CD1 mouse prostate basal, replicate 1


title: FLC_emptyvectorcontrol_H3K4me1_1

value: transduction with empty vector (control)


title: Patient 20847 (Lymphoepithelioma) Tumor2 Replica1

description: Library name: HY_20847_T2-1_S20


title: Prdm16NSC_Input_3


title: Patient 20847 (Lymphoepithelioma) Tumor1 Replica2

description: Library name: HY_20847_T1-2_S24


title: C57BL6 mice, rAAV8-Scramble, Bio3

description:
Library name: 2S
column name: 2HS


title: Prdm16NSC_Input_2