title: 315.SNP.12h

description:
SNP.12h.315
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 407_MDAMB231_doc_DPT10

status: Public on Sep 13 2024

type: SRA

city: LOS ANGELES

first: Michaek

middle: James

last: Schmidt

state: CA

address: 1002 Childs Way

department: Cancer Biology and Genomics

country: USA

institute: University of Southern California

library_source: transcriptomic single cell

data_processing:
raw fastq files
Assembly: hg19
Supplementary files format and content: RDS file contains gene counts processed with htseq-count and aligned with hisat2
Supplementary files format and content: for RDS file: hisat2 & htseq-count

molecule: polyA RNA

organism: Homo sapiens

source_name: breast

extract_protocol:
smart-seq2
Nextera-XT

treatment_protocol: treat with chemotherapy for 72 hours and then allowed to recover for 1 or 10 days in regular medium.

tag: tissue

value: breast

tag: cell line

tag: cell type

value: epithelial cell line

tag: treatment


title: 391_MDAMB231_doc_DPT10


title: 399_MDAMB231_doc_DPT10


title: 419_MDAMB231_cis_DPT1


title: 232.WT.12h

city: Toulouse

first: Jean-Charles

last: Guery

address: CHU Purpan – BP 3028

country: France

institute: INSERM

description:
WT.12h.232
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS

library_source: transcriptomic

data_processing:
Raw sequencing FASTQ files were processed using nf-core/rnaseq pipeline (v3.8.1) on genotoul SLURM cluster using -profile genotoul, --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa, --gtf Homo_sapiens.GRCh38.104.gtf ,-- aligner star_salmon options.
Raw sequencing FASTQ files were quality controlled using FASTQC (v0.11.9)
Adapter and quality trimming was performed using Trim Galore! (v3.4)
Trimmed reads were aligned to reference genome using STAR (v2.7.10a), BAM files were sorted and indexed using samtools (v1.15.1), duplicates were marked using picard MarkDuplicates (v 2.26.10)
Pseudo-alignment and quantification were performed using salmon (v 1.5.2)
Salmon transcripts quantification files (quant.sf) were imported into R/Rstudio using R ‘tximport’ package and a file linking Transcript ID to Gene ID (‘tx2gene’ file) generated by the nf-core/rnaseq pipeline to produce the raw counts matrix. TPMs values were retrieved from the abundance slot of tximport generated list.
For differential gene expression analyses, the raw count matrix was converted to a DESeq2 object using ‘DESeq2::DESeqDataSetFromTximport’  function with design : ~ group, where the group represent the combination of Genotype (i.e. WT for rs736631C/CD226-307Gly protective allele or SNP for rs736631T/CD226-307Ser risk allele) and treatment time (i.e. WT.0h, SNP.0h, WT.4h, SNP.4H, WT.12h, SNP.12h, WT.24h, SNP.24h).
Raw count matrix was further processed to remove genes that have low / inconsistent gene expression level in samples from the same ‘Group’ (i.e. WT.0h, WT.4h, WT.12h, WT.24h,  SNP.0h, SNP.4h, SNP.12h, SNP.24h). Raw counts were normalized using DESeq2::counts function and genes having less than 10 normalized counts in all groups in 2 of the 10 samples from the same group were filtered out yielding a normalized count matrix with 14965 genes.
Pairwise differential gene expression analyses were performed to compare SNP.0h vs WT.0h; SNP.4h vs WT.4h; SNP.12h vs WT.12h; SNP.24h vs WT.24h; SNP.4h vs SNP.0h; SNP.12h vs SNP.0h; SNP.24h vs SNP.0h; WT.4h vs WT.0h; WT.12h vs WT.0h and WT.24h vs WT.0h groups using DESeq2::results function with options lfcThreshold set to 0 and alpha set to 0.05.
For each pairwise comparison, DESeq2 results were exported as a tab-delimited file with raw counts, normalized counts and TPMs for all samples being compared.
Assembly: ENSEMBL GRCh38 (hg38) v104
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes DESeq2 normalized counts for each sample
Supplementary files format and content: Tab-delimited text file includes Transcript-per-Million (TPMs) counts for each sample
Supplementary files format and content: RDS file holding sample information
Supplementary files format and content: RDS file holding Transcript ID to GeneID mapping info (i.e. tx2gene file used to import salmon quantification file in R using Tximport)
Supplementary files format and content: RDS file for raw count matrix
Supplementary files format and content: RDS file for DESeq2 filtered normalized counts matrix
Supplementary files format and content: RDS file holding Ensembl gene mapping information for annotation of genes in count matrices

molecule: total RNA

source_name: CD3+CD8+ CD8 T cells

growth_protocol: Peripheral blood mononuclear leukocytes (PBMCs) were purified from buffy coat preparations obtained from consenting healthy blood donors. PBMCs were prepared by gradient centrifugation of buffy coats and kept in frozen in liquid nitrogen. Genotyping of the CD226 SNP rs763361 was performed using TaqMan SNP Genotyping assay. rs763361T expressing CD226-307Ser represented the risk allele, whereas rs763361C expressing CD226-307Gly represented the protective allele. Experiments were performed on cells form male donors homozygous for either allele.Frozen PBMCs were thawed, monocytes removed by plastic adherence and CD8 T cells were purified by negative selection. The percentage of residual CD4 T cells after depletion was always  less than 0.5% and the remaining populations consisted of 95-98% CD8 T cells.

extract_protocol:
RNA was extracted using RNAeasy Micro Kit (Qiagen) following manufacturer’s instructions.
Libraries were prepared using the Illumina Stranded Total RNA Prep kit starting from 7.5 ng of total RNA and using 14 PCR cycles for library amplification. The kit for the index sequences used was IDT Illumina RNA UDI A Lig 96 Indexes 96 Spl. RNA sequencing was  performed on one S4 lane on an Illumina NovaSeq 6000 sequencer, using NovaSeq 6000 S4 v1.5 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy. Between 20 and 44 million paired-end raw reads were produced per library.

treatment_protocol: FACS-sorted CD3+CD8+ T cells from healthy donors homozygous for either the protective (CD226-307Gly, N = 10) or risk allele (CD226-307Ser, N = 10) cultured in complete medium RPMI and stimulated with anti-CD3 and anti-CD28 monoclonal antibodies for 0h, 4h and 24h were subjected to RNA extraction using RNeasy Micro Kit. Paired-end (2x150pb) sequencing libraries were prepared using  Illumina’s Stranded Total RNA prep kit starting from 7,5ng of total RNA using 14 PCR cycles for library amplification. Sequencing libraries were indexed using IDT Illumina UDI A Lig 96 indexes 96 Sp1. RNA sequencing was performed on one S4 lane on an Illumina Novaseq 6000 sequencer using Novaseq 6000 S4 1v5 Reagent Kit (300 cycles) yielding between 20 and 40 millions raw paired-end reads per library.

value: CD3+CD8+ CD8 T cells

tag: genotype

tag: cd226 allele

value: anti-CD3/anti-CD28 mAbs

tag: time


title: 101.SNP.12h

description:
SNP.12h.101
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 181.SNP.12h

description:
SNP.12h.181
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 144,WT.24h

description:
WT.24h.144
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 378_MDAMB231_doc_DPT10


title: 320.WT.12h

description:
WT.12h.320
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 230.WT.12h

description:
WT.12h.230
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 316.WT.12h

description:
WT.12h.316
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 389_MDAMB231_doc_DPT10


title: 371_MDAMB231_doc_DPT10


title: 411_MDAMB231_doc_DPT10


title: 365_MDAMB231_doc_DPT10


title: 368_MDAMB231_doc_DPT10


title: 374_MDAMB231_doc_DPT10


title: 223.WT.12h

description:
WT.12h.223
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 403_MDAMB231_doc_DPT10


title: 380_MDAMB231_cis_DPT1


title: 322.WT.12h

description:
WT.12h.322
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 144,WT.12h

description:
WT.12h.144
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 362_MDAMB231_ctrl

value: DMSO


title: 161.WT.12h

description:
WT.12h.161
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 356_MDAMB231_ctrl


title: 91.WT.12h

description:
WT.12h.91
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 353_MDAMB231_ctrl


title: 360.SNP.4h

description:
SNP.4h.360
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 347_MDAMB231_cis_DPT1


title: 359.SNP.4h

description:
SNP.4h.359
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 350_MDAMB231_ctrl


title: 350.SNP.4h

description:
SNP.4h.350
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 337_MDAMB231_doc_DPT1


title: 334_MDAMB231_doc_DPT1


title: 315.SNP.4h

description:
SNP.4h.315
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 167.WT.12h

description:
WT.12h.167
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
WT.12h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 295.SNP.4h

description:
SNP.4h.295
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 181.SNP.4h

description:
SNP.4h.181
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 110.SNP.4h

description:
SNP.4h.110
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 246.SNP.4h

description:
SNP.4h.246
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 322_MDAMB231_doc_DPT1


title: 359_MDAMB231_ctrl


title: 319_MDAMB231_doc_DPT1


title: 322.WT.4h

description:
WT.4h.322
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 328_MDAMB231_doc_DPT1


title: 316_MDAMB231_cis_DPT1


title: 314_MDAMB231_doc_DPT1


title: 316.WT.4h

description:
WT.4h.316
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 320.WT.4h

description:
WT.4h.320
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 311_MDAMB231_doc_DPT1


title: 232.WT.4h

description:
WT.4h.232
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 342_MDAMB231_ctrl


title: 308_MDAMB231_doc_DPT1


title: 230.WT.4h

description:
WT.4h.230
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 223.WT.4h

description:
WT.4h.223
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 325_MDAMB231_doc_DPT1


title: 306_MDAMB231_doc_DPT1


title: 303_MDAMB231_doc_DPT1


title: 331_MDAMB231_doc_DPT1


title: 167.WT.4h

description:
WT.4h.167
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 332.SNP.4h

description:
SNP.4h.332
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 101.SNP.4h

description:
SNP.4h.101
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
SNP.4h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 300_MDAMB231_doc_DPT1


title: 144,WT.4h

description:
WT.4h.144
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 294_MDAMB231_doc_DPT1


title: 297_MDAMB231_doc_DPT1


title: 360.SNP.0h

description:
SNP.0h.360
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 359.SNP.0h

description:
SNP.0h.359
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 290_MDAMB231_doc_DPT1


title: 286_MDAMB231_cis_DPT1


title: 91.WT.4h

description:
WT.4h.91
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 161.WT.4h

description:
WT.4h.161
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.4h.vs.WT.4h.tsv
WT.4h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 284_MDAMB231_doc_DPT1


title: 350.SNP.0h

description:
SNP.0h.350
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 332.SNP.0h

description:
SNP.0h.332
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 278_MDAMB231_doc_DPT1


title: 281_MDAMB231_doc_DPT1


title: 315.SNP.0h

description:
SNP.0h.315
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 246.SNP.0h

description:
SNP.0h.246
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 181.SNP.0h

description:
SNP.0h.181
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 269_MDAMB231_doc_DPT1


title: 110.SNP.0h

description:
SNP.0h.110
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 263_MDAMB231_ctrl


title: 260_MDAMB231_ctrl


title: 292_MDAMB231_doc_DPT1


title: 257_MDAMB231_ctrl


title: 101.SNP.0h

description:
SNP.0h.101
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 322.WT.0h

description:
WT.0h.322
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 316.WT.0h

description:
WT.0h.316
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 320.WT.0h

description:
WT.0h.320
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 253_MDAMB231_cis_DPT1


title: 246_MDAMB231_ctrl


title: 251_MDAMB231_ctrl


title: 232.WT.0h

description:
WT.0h.232
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 230.WT.0h

description:
WT.0h.230
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 295.SNP.0h

description:
SNP.0h.295
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
SNP.4h.vs.SNP.0h.tsv
SNP.12h.vs.SNP.0h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 243_MDAMB231_ctrl


title: 167.WT.0h

description:
WT.0h.167
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 275_MDAMB231_doc_DPT1


title: 223.WT.0h

description:
WT.0h.223
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 210_MDAMB231_cis_DPT1


title: 161.WT.0h

description:
WT.0h.161
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 144,WT.0h

description:
WT.0h.144
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 184_MDAMB231_cis_DPT1


title: 223_MDAMB231_cis_DPT1


title: 91.WT.0h

description:
WT.0h.91
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.0h.vs.WT.0h.tsv
WT.4h.vs.WT.0h.tsv
WT.12h.vs.WT.0h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 171_MDAMB231_cis_DPT1


title: 197_MDAMB231_cis_DPT1


title: 272_MDAMB231_doc_DPT1


title: 167_MDAMB231_cis_DPT1


title: 144_MDAMB231_cis_DPT1


title: 119_MDAMB231_cis_DPT1


title: 156_MDAMB231_cis_DPT1


title: 106_MDAMB231_cis_DPT1


title: HDF-siALKBH5_IP

city: Shanghai, China

first: Ruoqing

last: Xu

address: Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, P.R. China

country: China

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine.

description:
For Merip-Seq
Si2_1-IP

data_processing:
library strategy: meRIP-seq
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
MeRIPseq reads were aligned to the hg38 genome using STAR.
m6A Peaks were called uing MetPeak  with the significance cut-off p-value <=0.05
Assembly: hg38
Supplementary files format and content: BED (except for Input sample)

source_name: primary human dermal fibroblasts

extract_protocol:
Total RNA was extracted using TRIzol reagent (Solarbio, USA).
further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol.

treatment_protocol: Transfection of scramble siRNA or ALKBH5 knockdown siRNA

value: primary human dermal fibroblasts

value: fibroblasts

tag: merip antibody


title: HDF-siALKBH5_Input

department: Department of Plastic and Reconstructive Surgery

description:
For Merip-Seq
Si2_1-input


title: 65_MDAMB231_ctrl


title: HDF-siALKBH5-replicate

data_processing:
Quality control: the image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<0.05 and |log2(foldchange)| > 1 were set as the threshold for significantly differential expression.
Assembly: GRCh37
Supplementary files format and content: FPKM

source_name: Primary human dermal fibroblasts

growth_protocol: Primary human dermal fibroblasts (HDFs) were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% P/S (Gibco) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from cultured HDFs using TRIzol reagent (Solarbio, USA).
The  library was constructed using SMARTer Stranded Total RNA-Seq Kit-version 2 (Pico Input Mammalian，Takara/Clontech，634413).

treatment_protocol: Knockdown of ALKBH5 in HDFs was realized by transfection with siRNAs. Cells grown in six-well plates were transfected with 200 pmol siRNAs using lipofectamine 3000 transfection reagent (Invitrogen, L3000008) according to the manufactuer’s instructions.

value: Primary human dermal fibroblasts

value: ALKBH6 knockdown

value: Transfection of ALKBH5 knockdown siRNA


title: HDF-siControl_IP

description:
For Merip-Seq
SiNC_1-IP

value: siControl


title: HDF-siALKBH5-replicate_Input

description:
For Merip-Seq
Si2_2-input


title: 93_MDAMB231_cis_DPT1


title: HDF-siControl-replicate_IP

description:
For Merip-Seq
SiNC_2-IP


title: 63_MDAMB231_ctrl


title: HDF-siALKBH5-replicate_IP

description:
For Merip-Seq
Si2_2-IP


title: HDF-siALKBH5

value: ALKBH5 knockdown


title: 67_MDAMB231_ctrl


title: HDF-siControl-replicate

value: WT

value: Transfection of scramble siRNA


title: HDF-siControl-replicate_Input

description:
For Merip-Seq
SiNC_2-input


title: HDF-siControl


title: HDF-siControl_Input

description:
For Merip-Seq
SiNC_1-input


title: patient11_ACTP

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

library_source: genomic

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina) and primary data analysis performed with the Cell Ranger ARC pipeline (version 2.0.1, 10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Cellranger (version 2.0.1, 10X Genomics) processed atac_fragments.tsv.gz file (scATAC-seq) and filtered_feature_bc_matrix.h5 file (scRNA-seq)
Library strategy: Multiome

molecule: genomic DNA

source_name: melanoma

extract_protocol:
Nuclei were isolated following the 10x Genomics Demonstrated Protocol for Single Cell Multiome ATAC Sequencing + Gene expression sequencing (CG000365-Rev C). After lysis and washing steps, extracted nuclei were resuspended in 10X Genomics diluted nuclei buffer. Viability, counting and visual inspection were assessed automatically using the LunaFX cell counter (Logos Biosystems) and manually with a Trypan blue staining. Nuclei were resuspended in a final volume of 15-20 μL according to the estimated count number and following the nuclei concentration guideline of the protocol. After a transposition step, 16’000 transposed nuclei per sample were separately loaded into the Chromium controller machine for encapsulation. Following 10X Genomics protocol (CG000338-Chromium NextGEM Multiome ATAC GEX User Guide RevF), barcoded mRNA and barcoded transposed DNA were then processed to construct ATAC and 3’ Gene Expression libraries. Quality controls and quantification of final libraries were respectively performed with Fragment Analyzer (Agilent) and Qubit HS dsDNA assay kit (Invitrogen).
Sequencing was performed on Illumina NovaSeq 6000 v1.5 flow cells with 28-10-10-90 cycles and 50-8-24-50 cycles (read1 - index i7 - index i5 - read2) for Gene Expression and ATAC-seq, respectively. 1% PhiX was spiked in the sequencing run.

treatment_protocol: The sample preparation was performed as follows: for the ACT product samples, one day before the assay, ACT product vials were thaw in 10mL of R20 (RPMI + 20% FBS), washed one time with R10 (RPMI + 10% FBS) and plated for resting overnight at 1.5x106 cells/mL with R8-3000 (RPMI + 8% Human serum AB Male (biowest / S419H-100 / S16545S419H) + 3000U IL2 (Proleukin S / Novartis)) in a 24 well plate at 37°C. The day after, cells were collected, washed with PBS + 0.04% BSA (Sigma #A2153) + 0.01% RNAsin (Promega #N2611), and manually counted with hemocytometer by Trypan blue (Gibco #15250) exclusion staining. Cells were resuspended in 1mL PBS + 0.04% BSA + 0.01% RNAsin and stain for viability with DAPI (Invitrogen, 1/1000) before sorting. For the pathofrozen tumor sample, the vial was thawed in R20 on the day of the assay and tissue was chopped in small pieces using a scalpel. Pieces were dissociated in RPMI + 2% Gelatin (#G7041, Sigma-Aldrich) + 200 IU/mL Collagenase I (#17100-017, ThermoFisher Scientific) + 400 IU/mL Collagenase IV (#17104-019, ThermoFisher Scientific) + 5 IU/mL Deoxyribonuclease I (#D4527, Sigma-Aldrich) + 0.1% RNasin Plus RNase Inhibitor (#N2618, Promega) for 20min at 37°C and shaken at 140 rpm. Digested cells were filtered using a 70 μm strainer and resuspended in PBS + 1% Gelatin + 0.1% RNasin. Cells were manually counted with a hemocytometer by Trypan blue exclusion and FcR blocked (#130-059-901, Miltenyi Biotec) for 15min at RT. After incubation, cells were stained with CD8-FITC (#344703, SK1 clone BioLegend) for 20min at 4°C, then washed and resuspended in PBS + 0.04% BSA + 0.1% RNasin. DAPI staining was performed before sorting. Approximately 800’000 cells (CD8+ from pathofrozen tumor and viable cells from ACT products) were sorted on a MoFlo Astrios (Beckman Coulter) and collected for each sample in separated 1.5mL Eppendorf tube. After sorting, cells were manually counted with a hemocytometer and viability was assessed using Trypan blue exclusion.

value: melanoma

tag: patient

value: ACTP


title: 57_MDAMB231_ctrl


title: 55_MDAMB231_ctrl


title: patient8_Tumor

value: Baseline Tumor


title: 51_MDAMB231_cis_DPT10

value: breast


title: 47_MDAMB231_cis_DPT1

value: epithelial cell line


title: 53_MDAMB231_ctrl


title: 70_MDAMB231_cis_DPT1


title: 43_MDAMB231_cis_DPT10


title: 41_MDAMB231_cis_DPT10


title: 39_MDAMB231_cis_DPT10


title: 61_MDAMB231_ctrl


title: 30_MDAMB231_cis_DPT10


title: 28_MDAMB231_cis_DPT10


title: patient 12 tumor

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Cells that had either lower than 200 or higher than 10,000 expressed genes were eliminated from our analysis. Furthermore, we discarded cells with more than 30,000 unique molecular identifiers (UMIs) and mitochondria content higher than 15%.  We performed dimensionality reduction and unsupervised nuclei clustering using methods from the Seurat software suite, followed by normalization for batch effects among multiple samples and sequencing runs.  The results were presented using Uniform Manifold Approximation and Projection (UMAP) and 17 distinct clusters were originally identified (Supplementary Figure 1).  After gene expression analysis, Seurat-determined clusters were collapsed into biologically relevant clusters that align with cell type.  Batch effect was accounted for by regressing out variance due to different runs and patient by using ScaleData() function in Seurat.  Harmony was used to remove patient-to-patient variance and separate sequencing runs and to strengthen associations of cells into clusters.
Assembly: GRCh37
Supplementary files format and content: Matrix, features, and barcode data

molecule: nuclear RNA

source_name: uterine serous carcinoma

extract_protocol:
Pieces of resected tumor were flash frozen in liquid nitrogen and stored at -80oC.  Frozen tumors were processed with the 10X Nuclei Isolation Kit as instructed by the manufacturer (PN-1000493). The nuclei were counted using the “dead” concentration on a Countess 3 instrument.  The concentration of the single nuclei suspension was adjusted to 1 × 105 nuclei/mL in the resuspension buffer. Single-nuclei suspension was then loaded onto a microfluidic chip (Chromium Next GEM Chip G, 10X Genomics) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (10X Genomics)
Any libraries with a concentration of under 2000 pg/µL were concentrated using the Eppendorf 5301 Vacufuge Concentrator System. The resulting snRNA-seq libraries were pooled and sequenced on an Illumina NovaSeq instrument with 150 bp paired end reads.
The demultiplexing, alignment, and gene quantification were all performed using Cell Ranger from 10X Genomics with default parameters.  The run data was demultiplexed using cellranger mkfastq and the resulting FASTQ files were aligned and counted using the 10X Genomics pre-built human reference genome refdata-gex-GRCh38-2020-A with cellranger count.

tag: racial group

value: Black, Non-Hispanic

value: uterine serous carcinoma

value: multiple

value: TP53 MUT


title: patient 4 tumor

value: White, Non-Hispanic


title: patient 1 tumor


title: patient 9 tumor


title: patient 13 tumor


title: patient 11 tumor


title: patient 3 tumor


title: patient8_ACTP


title: patient 10 tumor


title: 59_MDAMB231_ctrl

value: DMSO


title: patient 8 tumor


title: 37_MDAMB231_cis_DPT10


title: patient 6 tumor


title: 34_MDAMB231_cis_DPT10


title: patient 5 tumor


title: patient 7 tumor


title: ARK2 cells, PAX8KD5, 24 hr

data_processing:
Raw reads were trimmed with Trimmomatic, reads were mapped using STAR, and FPKM tables were generated using StringTie.  DESeq2 was used to conduct differential gene expression analysis and generate plots.  GOATools and Cluster Profiler was used to conduct gene ontology enrichment analysis
Assembly: GRCh37
Supplementary files format and content: counts

growth_protocol: ARK2 cells were obtained from the lab of Dr. Alessandro D. Santin (Yale University, New Haven, Connecticut, USA) and grown in DMEM media supplemented with 10% FBS, penicillin, streptomycin, and 1X NEAA.  All cell lines used were tested for mycoplasma and found to be negative

extract_protocol:
ARK2 cells were extracted with the Direct-zol RNA Microprep Kit according to the manufacturer's instructions
PAX8 expression was knocked down with siRNA for 48 hours.  RNA was harvested and sent to Admera Health (South Plainfield, New Jersey) for library preparation and sequencing.

treatment_protocol: ARK2 cells were cultured to 70% confluency and then washed 3X with PBS.  Cells were put into antibiotic free media directly before transfection with siRNA.  Lipofectamine RNAiMAX Transfection Reagent was used to transfect a pool of siRNAs (Horizon L-003778-00-0010) against PAX8 into ARK2 cells.  Cells were transfected for 6 hours, until full media was added.  Twenty-four hours after the initial knock down, cells were washed 3X with PBS and then cultured in full media for 48 hours

value: serous endometrial cancer - patient derived

value: PAX8 KD

value: PAX8 siRNA


title: 20_MDAMB231_cis_DPT10


title: ARK2 cells, PAX8KD3, 24 hr


title: 32_MDAMB231_cis_DPT10


title: 45_MDAMB231_cis_DPT10


title: 12_MDAMB231_cis_DPT10


title: 14_MDAMB231_cis_DPT10


title: ARK2 cells, PAX8KD1, 24 hr


title: ARK2 cells, Control6, 24 hr

value: scrambeled siRNA


title: 24_MDAMB231_cis_DPT1


title: patient 2 tumor


title: 23_MDAMB231_cis_DPT10


title: ARK2 cells, PAX8KD6, 24 hr


title: 21_MDAMB231_cis_DPT10


title: 18_MDAMB231_cis_DPT10


title: ARK2 cells, PAX8KD4, 24 hr


title: M4_sh2_rep2

city: Urbana

first: Prasanth

last: Kannanganattu

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RNA-seq reads were aligned to human reference genome GRCh38 assembly using HISAT2
raw gene counts were first analyzed by HTSEQ-Count
Assembly: GRCh38
Supplementary files format and content: Individual files include gene count information in tsv format

source_name: Breast

growth_protocol: Cells were cultured at 37 degrees Celsius with 5% carbon dioxide.

extract_protocol:
RNA was extracted using Trizol and cleaned up using Qiagen RNeasy column.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads.

treatment_protocol: Stable knockdown of MANCR was done using shRNA (shRNA1 and shRNA2) and CRISPRi. A Dox-inducible MANCR construct was stably expressed in M1 cells and overexpressed using Doxycycline.

value: Breast

value: MCF10A derivative

value: Breast epithelial cell

value: MANCR shRNA2


title: 97_PC3_docDPT10

data_processing:
copy number profiling for segmented means
Assembly: hg19
Supplementary files format and content: csv file containing segmented means
Library strategy: scDNA-seq

source_name: Prostate

extract_protocol:
WGA4
NEB NEXT ultra FS II

value: Prostate


title: M4_rep2

value: WT


title: 96_PC3_docDPT10

value: epithelial cell line


title: 9_MDAMB231_cis_DPT10

value: breast


title: ARK2 cells, Control5, 24 hr


title: ARK2 cells, PAX8KD2, 24 hr


title: 11_MDAMB231_cis_DPT10


title: ARK2 cells, Control3, 24 hr


title: 16_MDAMB231_cis_DPT10


title: 7_MDAMB231_cis_DPT10


title: ARK2 cells, Control2, 24 hr


title: ARK2 cells, Control4, 24 hr


title: 9_MDAMB231_cisDPT10


title: M4_rep1


title: ARK2 cells, Control1, 24 hr


title: 3_MDAMB231_cis_DPT1


title: M3_rep2


title: 93_PC3_docDPT10


title: 92_PC3_docDPT10


title: 99_PC3_docDPT10


title: 94_PC3_docDPT10


title: M1_MANCR_OE_rep2

value: MANCR overexpression


title: 95_PC3_docDPT10


title: M1_rep2


title: 98_PC3_docDPT10


title: M3_rep1


title: 90_PC3_docDPT1


title: 91_PC3_docDPT10


title: M1_rep1


title: M1_WT_rep2


title: 88_PC3_docDPT1


title: 8_MDAMB231_cisDPT10


title: M4_MANCR_CRISPRi_KD_rep2

value: MANCR CRISPRi


title: M1_MANCR_OE_rep1


title: M4_sh2_rep1


title: M4_MANCR_CRISPRi_KD_rep1


title: M1_WT_rep1


title: 85_PC3_docDPT1


title: 89_PC3_docDPT1


title: M4_MANCR_sh1_KD_rep1

value: MANCR shRNA1


title: M4_dcas9_Krab_ZIM3_rep2


title: 87_PC3_docDPT1


title: M4_dcas9_Krab_ZIM3_rep1


title: 86_PC3_docDPT1


title: 84_PC3_docDPT1


title: M4_MANCR_sh1_KD_rep2


title: 81_PC3_docDPT1


title: 83_MDAMB231_cisDPT1


title: 82_PC3_docDPT10


title: M4_WT_rep1


title: M4_WT_rep2


title: 80_PC3_docDPT1


title: 78_PC3_docDPT1


title: FKRO202185563-1A

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
20 mRNA-seq samples were sequenced on Novaseq 6000 using paired-end sequencing.
Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
The manuscript reports results after counts were filtered, transformed into CPM and quantile normalized using Limma voom, and analyzed using differential expression of genes analysis.
Assembly: Release 30 (GRCh38.p12)
Supplementary files format and content: A CSV (comma-separated values) file consisting of the RSEM Raw Counts for these samples used in our downstream analysis reported in the manuscript.

source_name: cell line

growth_protocol: Thyroid 8505 cell ( WT, IFT57KO, CD47KO and control ) lines were cultured using complete RPMI media  for 24hrs. The  cell  pellets were harvested and freezed at -140C until RNA extracted.

extract_protocol:
Total RNA, QC and mRNA sequencing was performed by NOVAGENE platform
mRNA library preparation (poly A enrichment)

treatment_protocol: CD47 and IFT57 crispr knockout cell lines generated

value: cell line

tag: thyroid cancer_cells

value: Thyroid Cancer cells

value: Cancer cell line

value: KO-C


title: endplate cells, patient 2, scRNAseq

city: Zhengzhou

first: Chenhao

last: Shi

state: He'nan

address: No.1 Jianshe Dong Road, Erqi District, 450052, Zhengzhou, Henan, China

institute: The first affiliated hospital of Zhengzhou university

description: 10X Genomics

data_processing:
The gene-level unique molecular identifier (UMI) count matrices were obtained by using Cell Ranger 3.1.0 (10X Genomics).
Generated read counts matrices were analyzed in R (v3.5.2, https://www.R-project.org) via Seurat (v3.1.1) following its filtering, variable gene selection, normalization, scaling, dimensionality reduction, clustering and visualization.
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms were applied by clusterProfiler (v3.10.1) with the database org.Hs.eg.db (v3.7.0).
The cells of several chondrocyte cell types were performed an unsupervised sub-clustering by Seurat with the first 30 principal components.
Monocle 2 (version 2.10.1) was used to estimate a pseudotemporal path of neuron cell differentiation.
To assess cellular crosstalk between different cell types, we used UMI count data and the Python package CellPhoneDB v2.1.2 with the human database v2.0.0 to infer cell–cell communication networks from single cell transcriptome data.
The gene regulatory network of stem cells was built by SCENIC (version 1.1.2).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cartilage endplate tissue

extract_protocol:
The cartilage endplate tissue of the intervertebral discs resected during the surgery was transported immediately to the laboratory under 4°C cold storage for single-cell suspension preparation. The vertebral endplate tissues were washed twice with sterile PBS buffer to remove any blood and prevent contamination, left to stand, and the supernatants were aspirated. The tissues were cut quickly into small 1-2 mm pieces with pre-cooled ophthalmic scissors and placed on ice. And added pre-warmed digestive enzymes (collagenase, neutral protease and DNAase I), mixed gently with a pasteurizing pipette and digested in a 37°C water bath for 20-25 min, mixed gently with a pasteurizing pipette every 5 min. At the end of digestion, added an equal volume of complete medium containing FBS to terminate the digestion. The isolated cells were filtered using 70-μm disposable filter and washed twice with PBS, centrifuged for 5 min at 500 g at 4°C to collect the cell precipitate. To perform erythrocyte lysis, added 1X erythrocyte lysis solution and incubated at room temperature for 5-10min, centrifuged for 5min at 500g, collected cell precipitate. Added PBS (0.04% BSA) and washed 1-2 times, centrifuged for 5 min, discarded the supernatant and resuspend in PBS. For scRNA-seq, the cell density was subsequently changed to 106/ml.
Single cell suspensions of vertebral endplate tissue were prepared and tested (cell viability >80%). They were subjected to single cell library construction according to the 10x Single Cell 3' Reagent Kits manual. Using a microfluidic chip, cells and gel beads with cell labeling sequences were wrapped in a droplet, and the cell-wrapped droplet was collected. In the droplet, the cells were lysed so that the mRNA in the cells was connected to the cell Barcode of the bead, forming Single Cell GEMs. These were subjected to RT reactions in the droplet, followed by the disruption of emulsions and cDNA library construction. Cells and reaction reagents were placed in one lane on the microfluidic chip and gel beads in the other lane to form a GEM. Reverse transcription was performed independently in each GEM. Afterward, the labeled cDNA was mixed, then amplified, and the library was constructed. Agilent bioanalyzer and qPCR were used for library quality inspection and library quantification, respectively. The qualified library was sequenced using Novaseq 6000 PE150 mode, and each library measured 60G data.

value: Cartilage endplate tissue

value: Chondrocytes, T cells/natural killer cells, and macrophages


title: 7_PC3_docDPT1


title: 79_PC3_docDPT1


title: FKRO202185562-1A


title: endplate cells, patient 1, scRNAseq

description: 10X Genomics


title: FKRO202185561-1A


title: FKRO202185560-1A


title: 75_PC3_docDPT1


title: 77_PC3_docDPT1


title: 74_PC3_docDPT1


title: FKRO202185557-1A

value: KO-B


title: FKRO202185559-1A


title: 73_PC3_docDPT1


title: 76_PC3_docDPT1


title: FKRO202185558-1A


title: FKRO202185556-1A


title: FKRO202185555-1A

value: Control B


title: 72_MDAMB231_cisDPT1

value: Breast


title: 70_PC3_cisDPT10


title: 69_PC3_cisDPT10


title: FKRO202185553-1A


title: 71_PC3_cisDPT10


title: 6_MDAMB231_cisDPT10


title: FKRO202185554-1A


title: FKRO202185552-1A


title: 68_PC3_cisDPT10


title: FKRO202185551-1A

value: KO-A


title: 67_MDAMB231_cisDPT1


title: FKRO202185550-1A


title: 66_PC3_docDPT10

value: Prostate


title: 65_PC3_cisDPT1


title: FKRO202185548-1A


title: 64_PC3_cisDPT10


title: FKRO202185547-1A

value: Control A


title: FKRO202185546-1A


title: FKRO202185549-1A


title: 62_PC3_cisDPT10

value: epithelial cell line


title: 63_PC3_cisDPT1


title: FKRO202185545-1A


title: FKRO202185544-1A


title: 61_PC3_cisDPT1


title: 60_PC3_cisDPT10


title: CSC_DMSO F2

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

data_processing:
Reads were trimmed by Trimmomatic
trimmed reads were mapped to hg38 with STAR
gene quantification processed with featureCounts
gencode.v34.primary_assembly were used as the annotation
the full ananlysis processed by OneStopRNASeq
Assembly: hg38
Supplementary files format and content: raw count table
Supplementary files format and content: normalized expression values in TPM

growth_protocol: GBM0308 cells were cultured in neurobasal medium containing N-2 and B-27 supplements, EGF, bFGF, L-glutamine, and Penicillin-Streptomycin in humified atmosphere with 5% CO2 at 37 C

extract_protocol:
Total RNA was extracted from DMSO treated or the compound treated samples using Rneasy Mini kit (Qiagen)
PE

treatment_protocol: Cell were trysinised and seeded in 6 well plates to form neurospheres. After three days  the neurospheres were treated  with either DMSO or Roc ASF derivative (-)- 20, at concentration 0.1 mM, or 1 mM for 12 hours and 24 hours respectively.

value: glioblastoma stem cell

value: DMSO


title: 5_PC3_docDPT1


title: CSC_DMSO F3


title: 59_PC3_cisDPT1


title: CSC_0.1um_24h D3

value: 0.1 uM Roc ASF derivative (-)-20


title: CSC_DMSO F1


title: 57_PC3_cisDPT1


title: CSC_0.1um_24h D2


title: 56_PC3_cisDPT10


title: CSC_1um_24h C3

value: 1 uM Roc ASF derivated (-)-20


title: 54_PC3_docDPT10


title: 55_MDAMB231_cisDPT1


title: CSC_1um_24h C2

value: 1 uM Roc ASF derivative (-)-20


title: CSC_1um_24h C1


title: CSC_0.1um_12h B2


title: 52_PC3_cisDPT10


title: CSC_0.1um_12h B3


title: 51_PC3_cisDPT1


title: 4_PC3_docDPT1


title: 49_PC3_cisDPT1


title: 50_PC3_cisDPT10


title: CSC_1um_12h A3


title: CSC_0.1um_24h D1


title: 45_PC3_cisDPT10


title: 53_PC3_cisDPT1


title: 46_PC3_cisDPT10


title: E8.25,RNAseq,allantoises,MUT2

city: 上海市

first: 泽悦

last: 朱

address: 四平路1239号

institute: 同济大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and nepalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: allantoises

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ¦Ìg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer¡¯s protocols.

value: allantoises

value: Isl1 knockout


title: CSC_1um_12h A2


title: 44_PC3_cisDPT10


title: RD PD circHIPK3 ODD

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

data_processing:
RNA-Seq fastq processing and microRNAs quantification from were performed according to Potla et al. 2021(Potla, Ali and Kapoor, 2021) using miRbase (v22) reference sequences(Kozomara, Birgaoanu and Griffiths-Jones, 2019).
Assembly: GRCh38
Supplementary files format and content: miRNA_counts.tsv
Supplementary files format and content: miRNA_CPM.tsv

source_name: RD

growth_protocol: Cells were grown at 37°C and 5% CO2 and were cultured in DMEM high-glucose supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
10-15x106 cells were pelleted and resuspended in 1 ml of cold Lysis Buffer (Tris-HCl pH 7.5 50mM, NaCl 150mM, MgCl2 3mM, NP40 0,5%, EDTA 2mM) supplemented with PIC 1X, RNAse Inhibitor 1:400 and DTT 1mM. Cells were lysed, lysates were subjected to RNA pulldown with biotynilated probes and streptadivine beads and RNA was precipitated through phenol/chloroform extraction.
QIAseq miRNA library kit (QIAGEN, Hilden, Germany) has been used for library preparation following the manufacturer’s instructions. Libraries were then prepared for sequencing and sequenced on single-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA)

treatment_protocol: No treatment was performed before extraction

value: RD

value: Embryonal rhabdomyosarcoma


title: 58_PC3_cisDPT10


title: CSC_1um_12h A1


title: E8.25,RNAseq,allantoises,MUT3


title: RD PD LacZ


title: E8.25,RNAseq,allantoises,MUT1


title: 47_PC3_cisDPT10


title: CSC_0.1um_12h B1

value: 0.1 uMRoc ASF derivated (-)-20


title: 42_PC3_cisDPT10


title: 48_PC3_cisDPT10


title: 43_PC3_cisDPT10


title: RD PD circHIPK3 EVEN


title: RD input


title: E8.25,RNAseq,allantoises,WT2

value: WT


title: 39_PC3_docDPT10


title: RH4 PD LacZ #2

data_processing:
Cutadapt (v3.2) (Martin, 2011) with parameters: -u 1 -U 1 –nextseq-trim=20 –trim-n and Trimmomatic (v0.39) (Bolger, Lohse and Usadel, 2014) with parameters: -PE ILLUMINACLIP:adapter_path:2:30:10:8:3:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 were used to remove adapter sequences and poor quality bases; for both software the minimum read length after trimming was set to 35
Reads aligning to rRNAs were filtered out; this first alignment was performed using Bowtie2 software (v2.4.2) (Langmead and Salzberg, 2012)
Then, STAR software (v2.7.7a)(Dobin et al.,2013) was used to align reads to GRCh38 genome using the following parameters: --outSAMstrandField intronMotif --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --peOverlapNbasesMin 50.
PCR duplicates were removed from all samples using MarkDuplicates command from Picard suite (v2.24.1) (https://broadinstitute.github.io/picard/) and multi-mapped and un-properly paired reads were filtered out using bamtools (v2.5.1) (Barnett et al., 2011) and samtools (v1.7) (Li et al., 2009)  respectively.
Gene quantification of RNA fragments was performed using htseq-count software (v0.13.5) (Anders, Pyl and Huber, 2015) with the following parameters -s reverse -m union and using Ensembl  gene annotation (release 99) (Yates et al., 2020).
Assembly: GRCh38
Supplementary files format and content: counts_table.tsv contains the  RNA fragments quantifications for each annotated gene
Supplementary files format and content: gene_abundance_table.FPKM_withoutTMM.tsv cpntains gene level FPKMs quantification in each sample

extract_protocol:
40 million of cells for each biological replicate were pelleted, resuspended in 1 ml of cold PBS supplemented with 0.5 mg/ml of 4’- aminomethyl-4,5’,8-trimethylpsoralen (AMT, Cayman Chemical) per 10.000.000 cells and crosslinked at 365 nm for five 2-minute cycles. 1 volume of Guanidinium Hydrochloride 6M per each volume of AMT was added. Lysates were subjected to RNA pulldown with biotynilated probes and streptadivine beads and  RNA was precipitated through phenol/chloroform extraction.
RNA library was produced using Stranded Total RNA Prep with Ribo-Zero Plus (Illumina). All samples were sequenced on an Illumina Novaseq 6000 Sequencing system.

value: Alveolar rhabdomyosarcoma


title: 3_PC3_docDPT1


title: 37_PC3_cisDPT10


title: RH4 PD LacZ #1


title: 36_PC3_cisDPT10


title: E8.25,RNAseq,allantoises,WT1


title: E8.75,RNAseq,allantoises,MUT3


title: E8.25,RNAseq,allantoises,WT3


title: 41_PC3_cisDPT10


title: 33_PC3_docDPT1


title: E8.75,RNAseq,allantoises,MUT2


title: 34_PC3_docDPT1


title: RH4 PD circHIPK3 ODD #1


title: E8.75,RNAseq,allantoises,WT3


title: 40_MDAMB231_cisDPT1

value: Breast


title: 38_PC3_cisDPT10


title: 31_PC3_docDPT1


title: E8.75,RNAseq,allantoises,MUT1


title: E8.75,RNAseq,allantoises,WT2


title: 30_PC3_docDPT1


title: RH4 PD circHIPK3 EVEN #1


title: RH4 PD circHIPK3 EVEN #2


title: RH4 input #2


title: 27_PC3_docDPT1


title: 26_PC3_docDPT1


title: E8.75,RNAseq,allantoises,WT1


title: RH4 input #1


title: RH4 PD circHIPK3 ODD #2


title: 25_PC3_docDPT1


title: 35_PC3_cisDPT10


title: 29_MDAMB231_cisDPT1


title: 24_PC3_docDPT1


title: iNK1-4, PBMC-NK93-97, CBU-NK38-41

city: Woolloongabba

first: Gustavo

last: Rodrigues Rossi

state: QLD

address: 37 Kent Street

country: Australia

institute: University of Queensland

description: Parse WT mini kit

data_processing:
Data were processed using the ParseBiosciences pipeline, version 1.2.1.
Assembly: hg38
Supplementary files format and content: Tab-separeted values files and matrix files

source_name: iPSC-dervied NK cells and NK cells

extract_protocol:
Freshly differentiated iPSC-derived NK cells, and PBMC or cord blood-derived NK cells cultured for 7 days, were fixed using the Parse Biosciences Cell Fixation (v2) kit , according to the manufacturer's instructions
Library was perfomed using Evercode Whole Transcriptome Mini (v2) kit (Parse Biosciences), as per the manufacturer’s instructions.

value: iPSC-dervied NK cells and NK cells


title: 32_PC3_docDPT1

value: Prostate


title: MV411 ENLsg2 rep2

city: Grand Rapids

first: Xiaobing

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Read counts were generated by HTSeq (v0.11.3).
Assembly: hg38
Supplementary files format and content: txt file, read counts from HTseq.

growth_protocol: Human leukaemia cell lines MV4;11 and SEMK2 were maintained in RPMI (Corning, 10-040-CV) 10% Fetal Bovine Serum (Sigma, F4135) supplemented with 2 mM l-glutamine and 100 U ml−1 penicillin/streptomycin (Corning, 30-009-CI).

extract_protocol:
Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN, Cat. 74136).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: Human leukaemia cell lines are treated with DMSO, 100 nM MS41, 100 nM MS47N and 100 nM PFI-6  for 6h or 24h. Then cells are collected for RNA extraction.

value: cell line

value: human leukeima cell

value: ENL KO


title: 2_PC3_docDPT1

value: epithelial cell line


title: 23_PC3_docDPT1


title: 22_PC3_docDPT1


title: 21_PC3_docDPT1


title: SUP-B15, Input

city: Guiyang

first: Qian

last: Kang

address: No. 28 Guimedi Street

department: Hematology Department

institute: Affiliated Hospital of Guizhou Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Homo sapiens from GEO using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by a python script，using fisher test. The Homer（version 4.10）was used for motifs analysis.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Bone marrow

growth_protocol: 1640,10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The grinded powder/cells was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA. The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-BRG1 antibody（HUABIO, ET1611-85）and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively.
The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: Bone marrow

value: B-cell acute lymphoblastic leukemia


title: 28_PC3_docDPT10


title: MV411 ENLsg2 rep1


title: MV411 ENLsg1 rep2


title: SUP-B15, BRG1, ChIP


title: 212_PC3_progeny_2

value: DMSO


title: Nalm-6, Input


title: MV411 ENLsg1 rep1


title: 20_MDAMB231_cisDPT10


title: 209_PC3_progeny_2


title: Nalm-6, BRG1, ChIP


title: 211_PC3_progeny_2


title: MV411 Negsg rep2


title: 207_PC3_progeny_2


title: MV411 Negsg rep1


title: 206_PC3_progeny_2


title: UA-2

city: Guangzhou

first: Hongwei

last: Yang

address: Nanshitou Street

institute: Southern Medical University

data_processing:
SOAPnuke (V1.5.6)
Assembly: Homo_sapiens ensembl release-105
Supplementary files format and content: tab-delimited text file includes fpkm, tpm, read counts for each sample

source_name: Human vasculr smooth muscle cells

extract_protocol:
Total RNA of human smooth muscle cells was extracted using TRIzol regennts and RNA quality was determmined using Agilent 2100 Bioanalyser.
RNA libraries for RNAseq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for MGI.

value: Human vasculr smooth muscle cells

value: UA


title: 204_PC3_progeny_2


title: 203_PC3_progeny_2


title: UA-1


title: 205_PC3_progeny_2


title: 202_PC3_progeny_2


title: Model-3


title: 200_PC3_progeny_2


title: 210_PC3_progeny_2


title: 201_PC3_progeny_2


title: Model-2


title: SEMK2 MS41 rep1


title: 199_PC3_progeny_2


title: 198_PC3_progeny_2


title: Model-1


title: 197_PC3_progeny_2


title: 208_PC3_progeny_2


title: High DIPs, sc-RNAseq

city: Changchun

first: Weiheng

last: Su

state: Jilin

address: No. 2699, Qianjin Street

department: School of Life Sciences

institute: Jilin University

description: 10x Genomics

data_processing:
Data files were processed using the count pipeline of the Cellranger toolkit v6.0 against the mm10 mouse reference
Assembly: mm10
Supplementary files format and content: Tab seperated value files and matrix files

source_name: Turbinate

extract_protocol:
The turbinate and adjacent mucosal tissues were isolated at 48 hpi. The tissues of three mice in each group were mixed together and digested with LiberaseTM (Roche) and DNase I (Roche) for 1 h at 37 ℃. After filtering through a 70-mm strainer, red blood cells were lysed using ACK buffer (Thermo Fisher). Cells were counted and prepared as single-cell suspensions for scRNA-seq.
scRNA-seq library preparation was conducted using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 according to the manufacturer’s instructions for 10x Genomics. Briefly, mRNA from approximately 1.2×104 cells was reverse-transcribed into cDNA, and a unique barcode was added using poly(T) RT primers. After cDNA amplification, the scRNA-seq library was sequenced using the Illumina NovaSeq6000 sequencing platform.

treatment_protocol: Female 6–8-week-old BALB/c mice were intranasally immunized with 30 μL of low DIPs LAIV (5.25×106 EID50, 1.46×107 total particles), high DIPs LAIV (same STV, 5.25×106 EID50, 1.05×109 total particles) or placebo (PBS) 48 h before the tissue collection.

value: Turbinate

value: 48 hpi

value: immunized with High DIPs LAIV


title: SEMK2 DMSO rep1

value: WT


title: SEMK2 MS41 rep3


title: UA-3


title: SEMK2 MS41 rep2


title: 194_PC3_progeny_2


title: Low DIPs, sc-RNAseq

description: 10x Genomics

value: immunized with low DIPs LAIV


title: 193_PC3_progeny_2


title: MV411 PFI6 6h rep3


title: 192_PC3_progeny_2


title: Placebo, sc-RNAseq

description: 10x Genomics

value: Placebo treatment


title: 19_PC3_docDPT1


title: 191_PC3_progeny_2


title: 190_PC3_progeny_1


title: SEMK2 DMSO rep3


title: Liver, C1

city: Taiyuan

first: Tingjuan

last: Huang

address: NO.56 Road Jiefang

institute: Shanxi Medical University

data_processing:
Transcriptome sequencing done with the Illumina sequencing platform converts the sequencing image signal into a text signal through CASAVA Base Calling and stores it in FASTQ format as raw data.
Sample-to-sample correlation and sample-to-sample PCA were analyzed
The software was used to quantify the overall expression levels of genes/transcripts individually, so that the differential expression of genes/transcripts between samples could be subsequently analyzed
Based on the quantitative results of expression level, the differential gene analysis between the two groups was carried out, and the differentially expressed genes between the two groups were obtained, the difference analysis software was DESeq2, and the screening threshold was: |log2FC| >=1 & padjust <0.05
Assembly: mm9
Supplementary files format and content: processed data files.txt contains gene count and gene id of each group of samples

source_name: Liver

growth_protocol: A standard diet and water audibility were fed to the animals under care (25± 2°C, 12 hours of light/dark cycle)in the animal room

extract_protocol:
Total RNA was extracted from tissue samples and the concentration and purity of the RNA were measured using Nanodrop2000,mRNA can be isolated from total RNA by A-T base pairing with ployA using magnetic beads with Oligo(dT)
RNA Library construction was performed using the Illomena Trusektena Samppur Prepkit method

treatment_protocol: One million BMSCs were injected into the tail vein for the treatment of a BDL liver fibrosis model for two weeks

value: Liver

value: Control


title: MV411 PFI6 6h rep1

value: cell line


title: 189_PC3_progeny_1

city: LOS ANGELES

first: Michaek

address: 1002 Childs Way

institute: University of Southern California

value: Prostate


title: Liver, C2


title: 196_PC3_progeny_2


title: 18_MDAMB231_cisDPT10

value: Breast


title: 188_PC3_progeny_1

value: epithelial cell line


title: SEMK2 DMSO rep2

value: human leukeima cell


title: 187_PC3_progeny_1


title: MV411 PFI6 24h rep3


title: Lesion, Spontaneous, S07

first: Gregory

last: Burns

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: PA6762 (S07)

library_source: other

data_processing:
Quality and adapter-trimmed reads (Trim Galore v0.3.3) were mapped to the human miRNAs from miRbase (release 22) using the miRDeep2 (v0.0.7) pipeline.
Differential expression analysis was conducted with edgeR (v3.22.5) using the edgeR-robust method.
Assembly: Panu_3.0
Supplementary files format and content: Excel file with read counts per sample for each microRNA

molecule: other

organism: Papio anubis

source_name: Endometriotic Lesion

extract_protocol:
Total RNA was extracted from the endometrium and endometriotic lesions from baboons with induced endometriosis for 15 months  or spontaneous disease. Total RNA was isolated using the Trizol reagent (Life Technologies, Carlsbad, CA, USA), and RNA concentration was checked using the NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA).
Illumina TruSeq small RNA library preparation

treatment_protocol: Induction of Endometriosis

value: Endometriotic Lesion

tag: sample group

value: baboons with spontaneous disease


title: MV411 PFI6 24h rep2


title: Liver, C3


title: Liver, B1

value: BDL


title: Eutopic Endometrium, Spontaneous, S08

description: PA6762 (S08)

source_name: Eutopic Endometrium

value: Eutopic Endometrium


title: 186_PC3_progeny_1

last: Schmidt

value: DMSO


title: MV411 PFI6 6h rep2


title: 185_PC3_progeny_1


title: Liver, B2


title: MV411 PFI6 24h rep1


title: MV411 MS41 6h rep3


title: Eutopic Endometrium, Spontaneous, S06

description: PA6627 (S06)


title: MV411 MS41 6h rep2


title: Liver, B3


title: Lesion, Spontaneous, S04

description: PA6303 (S04)


title: 184_PC3_progeny_1


title: MV411 MS41 6h rep1


title: Liver, M1

value: BDL+BMSC


title: 183_PC3_progeny_1


title: Liver, M2


title: MV411 MS41 24h rep3


title: 195_PC3_progeny_2


title: Liver, M3


title: MV411 MS41 24h rep2


title: 182_PC3_progeny_1


title: Lesion, Spontaneous, S01

description: PA5655 (S01)


title: Eutopic Endometrium, Spontaneous, S02

description: PA5655 (S02)


title: smgGDS knockdown, cisplatin-treated, replicate 4

city: Houston

first: Yuxue

state: Texas

address: 1100 Bate Ave

institute: Baylor college of medicine

data_processing:
Raw sequencing reads were first processed to obtain high-quality clean reads by using fastp (version 0.18.0). This included the removal of adapter sequences, reads containing more than 10% unknown nucleotides (N), and low-quality reads with more than 50% bases having a Q-value ≤ 20. The clean reads were then aligned to a ribosomal RNA (rRNA) database using Bowtie2 (version 2.2.8), and any rRNA-mapped reads were excluded from further analysis.
Subsequently, the remaining clean reads were aligned to the reference genome using HISAT2 (version 2.4) with default parameters and the -rna-strandness RF setting. For quantification of gene expression, the aligned reads were assembled using StringTie (version 1.3.1), and gene abundance was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) using RSEM. This method allows for normalization across different gene lengths and sequencing depths.
For sample relationship analysis, correlation analysis of replicates was performed using R to evaluate the repeatability of experimental results. Additionally, principal component analysis (PCA) was conducted using the gmodels package in R to explore the overall structure and relationships among samples based on gene expression data.
Finally, differential expression analysis was conducted using DESeq2 for comparisons between different groups, and edgeR for pairwise comparisons between samples. Genes were considered differentially expressed if they had a false discovery rate (FDR) of less than 0.05 and an absolute fold change of 2 or more.
Assembly: ncbi_GRCm38.p6
Supplementary files format and content: csv: FPKM, raw count of the gene expression

source_name: Kidney

growth_protocol: Cells cultured in MEM containing 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin (AA) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from the samples using the Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol. The quality of the extracted RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified through RNase-free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads [After total RNA was extracted, prokaryotic mRNA was enriched by removing rRNA by Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA)]. The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcribed into cDNA using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

treatment_protocol: Then, TCMK-1 were treated with cisplatin (20 μM) dissolved in saline, and the control group was treated with saline.

value: Kidney

value: Kidney epithelial cell

value: smgGDS shRNA

value: TCMK-1 cell line - smgGDS knockdown (20μM Cisplatin)


title: smgGDS knockdown, cisplatin-treated, replicate 3


title: 180_PC3_progeny_1


title: 181_PC3_progeny_1


title: Lesion, Spontaneous, S05

description: PA6627 (S05)


title: Lesion, 15 month, E27

description: PA7696 (E27)

value: baboons with induced endometriosis for 15 months


title: MV411 MS41 24h rep1

value: WT


title: MV411 MS41N 6h rep3

value: cell line


title: smgGDS knockdown, cisplatin-treated, replicate 2


title: Eutopic Endometrium, Spontaneous, S03

description: PA6303 (S03)


title: Eutopic Endometrium, 15 month, E28

description: PA7696 (E28)


title: 17_PC3_docDPT1

value: Prostate


title: smgGDS knockdown, cisplatin-treated, replicate 1


title: MV411 MS41N 6h rep2


title: Control, cisplatin-treated, replicate 4

value: smgGDS control

value: TCMK-1 cell line - Control (20μM Cisplatin)


title: MV411 MS41N 6h rep1

value: human leukeima cell


title: 178_PC3_progeny_1

value: epithelial cell line


title: Eutopic Endometrium, 15 month, E25

description: PA7539 (E25)


title: MV411 MS41N 24h rep3


title: 177_PC3_progeny_1


title: Control, cisplatin-treated, replicate 3


title: Lesion, 15 month, E21

description: PA7524 (E21)

value: Endometriotic Lesion


title: Eutopic Endometrium, 15 month, E22

description: PA7524 (E22)


title: MV411 MS41N 24h rep2


title: Control, cisplatin-treated, replicate 2


title: 176_PC3_progeny_1


title: 179_PC3_progeny_1


title: MV411 MS41N 24h rep1


title: 175_PC3_ctrl

value: ctrl


title: Lesion, 15 month, E24

description: PA7539 (E24)


title: 174_PC3_ctrl


title: Eutopic Endometrium, 15 month, E19

description: PA7223 (E19)

value: Eutopic Endometrium


title: sh2Cldn7-R4

city: Baltimore

first: Junior

last: West

address: 855 N Wolfe St.

department: Cell Biology

institute: Johns Hopkins

data_processing:
The quality of the RNA libraries was assessed using FastQC_0.74 with default parameters.
llumina adapter sequences were removed using Trimmomatic_0.39 by performing initial ILLUMINACLIP step and an average read quality of 20.
The sequences were then mapped to the mm10 genome using RNAStar_2.7.11 in paired-end mode and default parameters with over 90% uniquely mapped reads for all conditions
Mapped reads were then converted to gene counts using featureCounts2.0.3 with the following parameters: unstranded, paired-end and a minimum mapping quality per read of 10.
Differential expression analysis was performed using DeSeq2_1.34.0 with multi-factor design accounting for all experimental groups and experimental batches.
Log2 fold change values were then shrunk using lfcShrink with default parameters.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts from each sample

source_name: mammary gland

growth_protocol: Organoids were freshly isolated from MMTV-Neu primary tumors and seeded in collagen for invasion assay supplemented with DMEM-F12, 1% PenStrep, 1% isulin-transferrin-selenium-ethanolamin and 2.5 nM FGF2.

extract_protocol:
1 µg of total RNA was subjected to library synthesis using
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Virus at a multiplicity of infection (MOI) of 20 was mixed with with 3 μl of ViroMag R/L (RL41000, OZ Biosciences) in a final volume of 50 μl and was incubated for 30 min at ambient temperature. This solution was then mixed with 1,000 organoids and allocated into one well of a non-adherent 96 well plate (655970, Greiner BioOne). The plate was placed on a magnetic plate (MF10096, OZ Biosciences) for 90 min at 37 °C and 5% CO2. After 24 h, 50 μl was removed and 200 μl of organoid media was added. The next day, 200 μl of media was replaced by organoid media containing 3 μg/ml of puromycin (A1113803, Gibco). After 3 days of puromycin selection, the organoids were either plated in 3D fibrillar collagen I gels

value: mammary gland

value: primary epithelial cells

value: sh2Cldn7 knockdown

value: sh2 treatment


title: 173_PC3_ctrl


title: Eutopic Endometrium, 15 month, E16

description: PA7457 (E16)


title: MV411 DMSO 6h rep1

value: DMSO


title: 171_PC3_ctrl


title: Lesion, 15 month, E15

description: PA7457 (E15)


title: 172_PC3_ctrl


title: sh2Cldn7-R2


title: sh1Cldn7-R4

value: sh1Cldn7 knockdown

value: sh1 treatment


title: MV411 DMSO 24h rep3

value: WT


title: Lesion, 15 month, E11

description: PA7258 (E11)

value: baboons with induced endometriosis for 15 months


title: MV411 DMSO 24h rep2

value: cell line


title: sh2Cldn7-R1


title: MV411 DMSO 6h rep2


title: MV411 DMSO 6h rep3


title: Control, cisplatin-treated, replicate 1

value: Kidney

value: Kidney epithelial cell

value: smgGDS control


title: 170_PC3_ctrl

value: Prostate

value: epithelial cell line


title: MV411 MS41 6h Pol2 MNase rep3

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

growth_protocol: Human leukaemia cell lines MV4;11, was  maintained in RPMI (Corning, 10-040-CV) 10% Fetal Bovine Serum (Sigma, F4135) supplemented with 2 mM l-glutamine and 100 U ml−1 penicillin/streptomycin (Corning, 30-009-CI).

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: Human leukaemia cell lines are treated with DMSO, 100 nM MS41for 6h or 24h. Then cells are collected for Chip assay.

value: human leukemia cell


title: MV411 DMSO 24h rep1

value: human leukeima cell


title: Eutopic Endometrium, 15 month, E08

description: PA7255 (E08)

value: Eutopic Endometrium


title: Lesion, 15 month, E18

description: PA7223 (E18)

value: Endometriotic Lesion


title: sh1Cldn7-R2

value: mammary gland

value: primary epithelial cells


title: Lesion, 15 month, E07

description: PA7255 (E07)


title: 169_PC3_ctrl

data_processing:
copy number profiling for segmented means
Assembly: hg19
Supplementary files format and content: csv file containing segmented means
Library strategy: scDNA-seq

extract_protocol:
WGA4
NEB NEXT ultra FS II

treatment_protocol: treat with chemotherapy for 72 hours and then allowed to recover for 1 or 10 days in regular medium.

value: ctrl


title: sh1Cldn7-R3

value: sh1Cldn7 knockdown


title: sh2Cldn7-R3

value: sh2Cldn7 knockdown

value: sh2 treatment


title: sh1Cldn7-R1

value: sh1 treatment


title: Lesion, 15 month, E03

description: PA7254 (E03)

value: baboons with induced endometriosis for 15 months


title: MV411 MS41 6h Pol2 MNase rep2

value: cell line

value: WT


title: 167_PC3_ctrl


title: MV411 MS41 6h Pol2 MNase rep1


title: shControl-R4

value: Non-targetting sh


title: shControl-R3


title: Sample C, Day 14

city: Columbus

first: Birkan

last: Gokbag

state: Ohio

address: 281 W Lane Ave

department: Department of Biomedical Informatics

institute: The Ohio State University

description: Harvested at day 14, thirteen days after fresh media with puromycin was added.

data_processing:
Mali Dual CRISPR Pipeline v0.4.1 (https://github.com/ucsd-ccbb/mali-dual-crispr-pipeline)
In the parameters file, minimum and maximum sgRNA lengths were set at 18 and 21 respectively, and up to 3 mismatches were allowed.
The pipeline was ran with the prepared library (targeted_sgRNA_pair_library.txt).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (targeted_counts_combined.txt).
Supplementary files format and content: tab-delimited text file includes targeted sgRNA pair library (targeted_sgRNA_pair_library).
Library strategy: PCR Amplicon sequencing

growth_protocol: The 22Rv1 cell line transfected with SpCas9 was a gift from the Xiaoqi Liu lab at the University of Kentucky. The cells were grown in RPMI 1640 media supplemented with 10% FBS, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific).

extract_protocol:
The genomic DNA was extracted from each sample using GeneJET Genomic DNA Purification Kit (Thermo Fisher Scientific) and quantified by QUBIT.
The genonic DNA was amplified by two-round PCR as described in Tang et al., 2022 (PMID: 36060092). Six PCR products with different i5 and i7 indices were pooled in equal molar ratios and sequenced by the Illumina NextSeq 2000 platform with PE 100bp kit.

treatment_protocol: The plasmid library was transfected to HEK 293T cells with psPAX2 and pMD2.G plasmids to generate the lentivurus supernatant. The virus was transfected to 22RV1/Cas9 cells and the MOI was determined following the protocol of Tang et al., 2022 (PMID: 36060092). In the CRISPR screening experiment, ten million 22Rv1/Cas9 cells were seeded in each 150mm cell culture plate, and MOI at transfection was controlled within the range of 0.1-0.3. After transfection, the cells were selected by 2ug/mL puromycin (Sigma) for three days. At the end of puromycin selection, the samples were pooled and split into two aliquots. One aliquot was referred to as T0, and the other aliquot was harvested after 10 days as Tend samples.  Each sample consisted of about 20 million cells. The experiment was repeated in replicate.

value: Day 14

value: CRISPR-Cas9 Double Knockout (CDKO)


title: Eutopic Endometrium, 15 month, E04

description: PA7254 (E04)


title: Eutopic Endometrium, 15 month, E12

description: PA7258 (E12)


title: 166_PC3_ctrl

value: Prostate

value: epithelial cell line


title: Sample B, Day 14


title: shControl-R1


title: MV411 MS41 6h Pol2S2P MNase rep3

value: human leukemia cell


title: TET2 KO UUO, snRNAseq

city: Philadelphia

first: Xiujie

last: Liang

state: Pennsylvania

address: 12-188 Smilow Translational Research Center, 3400 Civic Center Blvd

department: Department of Medicine

institute: University of Pennsylvania

data_processing:
For RNAseq: RNA-seq reads were aligned to the human genome (hg19) using STAR based on GENCODE annotations. RSEM was used to quantify gene-level read counts and transcripts per million.
For snRNAseq: The quality control (QC) included removing ambient mRNA contamination, eliminating low-quality cells and genes, and excluding doublet-like cells. We used “SoupX” to remove ambient mRNA. We defined low-quality cells as those with the following criteria: unique molecular identifiers (UMI) ≤ 500 or ≥ 10,000, the number of detected genes ≤300 or ≥ 3000, the percentage of mitochondrially encoded genes reads > 1%, complex ≥ 0.25.  We further removed genes that were expressed in ＜ 10 cells. “DoubletFinder” was used to exclude doublet-like cells. To process the data, we used Seurat 4.0.4.
Assembly: hg19 for RNAseq, mm10 for snRNAseq
Supplementary files format and content: RNAseq: txt file includes TPM values for each sample, snRNAseq: matrix

source_name: kidney

extract_protocol:
For RNA seq: RNA was extracted using Rneasy mini kit (Qiagen); for snRNAseq, Nuclei were extracted from flash-frozen kidney tissue. Briefly, 10-30 mg frozen kidney tissue were minced on ice into pieces in lysis buffer (Tris-HC, NaCl, MgCl2, NP40, and RNAse inhibitor), transferred into a gentleMACS C tube and homogenized using gentleMACS homogenizer. Next, the homogenized tissue was filtered through a 40 μm strainer (Fisher Scientific, #08-771-1) and then centrifuged at 500 × g for 5 mins at 4°C. The pellet was resuspended in wash buffer (BSA, RNAse inhibitor, 1× PBS) and then filtered through a 40 μm Flowmi cell strainer (Sigma Aldrich, #BAH136800040-50EA).
RNA-Seq libraries were generated using the NEB's non-directional RNA seq kit; For snRNAseq libraries, the cDNA libraries were constructed using the 10X Chromium library construction kit (PN-1000190).

value: kidney

value: kidney cells

value: TET2 KO

value: UUO


title: Sample A, Day 14


title: 168_PC3_ctrl

value: ctrl


title: MV411 MS41 6h Pol2S2P MNase rep2


title: 165_PC3_ctrl


title: shControl-R2

value: mammary gland

value: primary epithelial cells


title: MV411 MS41 6h Pol2S2P MNase rep1


title: 162_PC3_ctrl


title: Sample B, Day 4

description: Harvested at day 4, three days after fresh media with puromycin was added.

value: Day 4


title: MV411 MS41 6h ENL soni rep2


title: MV411 MS41 6h ENL soni rep1


title: 163_PC3_ctrl


title: 164_PC3_ctrl


title: 161_PC3_ctrl


title: Sample C, Day 4


title: MV411 MS41 6h ENL soni rep3


title: Sample A, Day 4


title: WT Sham2, snRNAseq

value: sham


title: 160_PC3_ctrl


title: MV411 MS41 6h DOT1L MNase rep3

value: cell line


title: WT UUO, snRNAseq

value: WT


title: 15_PC3_docDPT1


title: MV411 MS41 6h DOT1L MNase rep2


title: Cell INS4

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: small RNAseq (75bp single-end reads)

data_processing:
UMI counts were generated by using Qiagen RNA-seq Analysis Portal
Assembly: mm10

extract_protocol:
RNA was extracted by Trizol chloroform method and purified using Qiagen Rneasy kit
Libraries were prepared using Qiagen smRNA/miRNA Library Kit

value: Adipocyte (differentiated)

value: INS


title: WT Sham1, snRNAseq


title: MV411 MS41 6h DOT1L MNase rep1


title: GW_5

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Quality score trimming and filtering were performed with cutadapt.
reads were aligned to the annotated hg38 using Hisat2 (v2.1.0)
Per gene read counts were calculated from the Hisat2 output using htseq-count (v0.11.2)
Differential gene expression was analyzed using the R package DESeq2 (v1.22.2)
Assembly: hg38

source_name: Prostate cancer

growth_protocol: RPMI-1640, FBS10%, L-Glu 2mM

extract_protocol:
P2884
DirectZol RNA miniprep mRNA (Ozyme)
P2884 : Total RNA-Seq libraries were generated from 200 or 500 ng of total RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes, Ligation (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, abundant ribosomal RNAs were depleted by hybridization to specific DNA probes and enzymatic digestion. The depleted RNAs were purified and fragmented using divalent cations at 94oC for 8 minutes. After random hexamers annealing, fragmented RNAs were then reverse transcribed into first strand complementary DNA (cDNA). Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: DMSO as vehicle, GW3965 1µM

value: Prostate cancer

value: Epithelial


title: 159_PC3_ctrl

value: Prostate

value: epithelial cell line


title: 158_PC3_ctrl


title: MV411 MS41 6h CDK9 DSG rep2

value: human leukemia cell


title: Cell INS2

description: small RNAseq (75bp single-end reads)


title: GW_3


title: Cell INS3

description: small RNAseq (75bp single-end reads)


title: MV411 MS41 6h CDK9 DSG rep3


title: GW_2


title: Cell PBS4

description: small RNAseq (75bp single-end reads)

value: PBS


title: 156_PC3_ctrl


title: 157_PC3_ctrl


title: MV411 MS41 6h CDK9 DSG rep1


title: Cell INS1

description: small RNAseq (75bp single-end reads)


title: GW_1


title: MV411 MS41 6h AFF1 MNase rep3


title: DMSO_5

value: DMSO


title: 155_PC3_ctrl


title: Cell PBS3

description: small RNAseq (75bp single-end reads)


title: DMSO_4


title: MV411 MS41 6h AFF1 MNase rep2


title: 154_PC3_ctrl


title: GW_4


title: 153_PC3_ctrl


title: Cell PBS2

description: small RNAseq (75bp single-end reads)


title: DMSO_3


title: Cell PBS1

description: small RNAseq (75bp single-end reads)


title: DMSO_2


title: MV411 MS41 6h AFF1 MNase rep1


title: DMSO_1


title: MV411 MS41 24h H3K79me2 soni rep3


title: sEV INS4

description: small RNAseq (75bp single-end reads)


title: MV411 MS41 24h H3K79me2 soni rep1


title: MV411 MS41 24h DOT1L MNase rep3


title: 150_PC3_ctrl


title: sEV INS2

description: small RNAseq (75bp single-end reads)


title: 151_PC3_ctrl


title: MV411 MS41 24h H3K79me2 soni rep2


title: 14_MDAMB231_cisDPT1

source_name: Breast

value: Breast


title: sEV PBS3

description: small RNAseq (75bp single-end reads)


title: 152_PC3_ctrl

source_name: Prostate

value: ctrl


title: sEV INS1

description: small RNAseq (75bp single-end reads)


title: sEV INS3

description: small RNAseq (75bp single-end reads)


title: 147_MDAMB231_docDPT10


title: 149_MDAMB231_cisDPT1


title: sEV PBS4

description: small RNAseq (75bp single-end reads)


title: sEV PBS1

description: small RNAseq (75bp single-end reads)


title: MV411 MS41 24h DOT1L MNase rep1

source_name: cell line


title: B12WT

type: RNA

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

description: Nfat5 fl/fl Vav-Cre mice have been described in Huerga Encabo et al., 2020, J Exp Med, 2020. doi: 10.1084/jem.20190449

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Human array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: Biotin

source_name: Total RNA from bone marrow hematopoietic stem cells (HSC), wild-type

label_protocol: 300pg of total RNA from each sample was processed and labelled according to manual NuGEN Ovation® One-Direct System (M01312 v2), Encore™ Biotin Module (M01111 v8) (NuGEN, San Carlos, CA, USA)

growth_protocol: FACS-sorted HSC (CD48-CD150+ within LSK) and MPP (CD48+CD150- within LSK) populations from Nfat5 +/+ Vav-Cre and Nfat5 fl/fl Vav-Cre mice in steady-state conditions

extract_protocol: Total RNA was extracted following Qiagen protocol

treatment_protocol: No treatment was done. Cells were directly isolated from the bone marrow and FACS-sorted

tag: mouse

tag: population

value: B (hematopoietic stem cell, HSC)


title: 144_MDAMB231_docDPT10


title: 148_MDAMB231_docDPT10


title: B11KO

source_name: Total RNA from bone marrow hematopoietic stem cells (HSC), NFAT5-deficient

value: KO


title: B3WT


title: MV411 DMSO 6h input soni

last: Shi


title: B70KO


title: sEV PBS2

description: small RNAseq (75bp single-end reads)


title: A70KO

source_name: Total RNA from bone marrow hematopoietic multipotent progenitors (MPP), NFAT5-deficient

value: A (hematopoietic multipotent progenitor, MPP)


title: A64WT

source_name: Total RNA from bone marrow hematopoietic multipotent progenitors (MPP), wild-type


title: MV411 DMSO 6h input MNase


title: B64WT


title: 146_MDAMB231_docDPT10


title: FUS RIP-replicate 1

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to mouse genome mm10, Ensembl v89 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to generate gene counts
Differential expression analysis of gene counts was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: text files containing counts

extract_protocol:
After immunoprecipitation, RNA was extracted using Acid-Phenol:Chloroform (Ambion).
Libraries were constructed using the TruSeq Stranded Total RNA protocol (Illumina) according to manufacturer's instructions.

value: mouse myoblasts

tag: molecule subtype

value: RNA bound to FUS


title: A12WT

value: WT


title: MV411 DMSO 6h input DSG

value: cell line


title: 145_MDAMB231_docDPT10

department: Cancer Biology and Genomics


title: IgG RIP-replicate 3

value: RNA bound to IgG


title: FUS RIP-replicate 2


title: MV411 DMSO 6h Pol2 MNase rep3


title: FUS RIP-replicate 3


title: 141_MDAMB231_docDPT10


title: A11KO


title: IgG RIP- replicate 2


title: MV411 DMSO 6h Pol2 MNase rep2


title: MV411 DMSO 6h Pol2S2P MNase rep2


title: 16_MDAMB231_cisDPT10


title: MV411 DMSO 6h Pol2 MNase rep1


title: 140_MDAMB231_ctrl


title: 143_MDAMB231_docDPT10


title: B2KO


title: A3WT


title: Input- replicte 3

value: total RNA


title: 13_PC3_docDPT10


title: 142_MDAMB231_docDPT10


title: MV411 DMSO 6h ENL soni rep3


title: IgG RIP-replicate 1


title: MV411 DMSO 6h Pol2S2P MNase rep1


title: MV411 DMSO 6h Pol2S2P MNase rep3


title: 139_MDAMB231_ctrl


title: Input-replicate 2


title: 138_MDAMB231_ctrl


title: MV411 DMSO 6h ENL soni rep2


title: Input-replicate 1


title: A2KO


title: FUS siRNA 3U D3 replicate 2

description: Cells were transfected with Fus siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 72 h - replicate 2

extract_protocol:
RNA was extracted with TriPure™ Isolation Reagent (Sigma-Aldrich) using Direct-zol RNA MiniPrep kit (ZYMO RESEARCH) following the manufacturer’s instructions.
Libraries were constructing using the TruSeq Stranded Total RNA protocol (Illumina) according to manufacturer's instructions.

value: FUS siRNA transfection for 96 h in differentiation medium for 72 h


title: MV411 DMSO 6h ENL soni rep1


title: MV411 DMSO 6h DOT1L MNase rep3


title: 135_MDAMB231_ctrl


title: MV411 DMSO 6h DOT1L MNase rep2


title: FUS siRNA 3U D3 replicate 1

description: Cells were transfected with Fus siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 72 h - replicate 1


title: Control siRNA D3 replicate 2

description: Cells were transfected with Control siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 72 h - replicate 2

value: Control siRNA transfection for 96 h in differentiation medium for 72 h


title: WT67A

growth_protocol: FACS-sorted CD45.2+ HSC (CD48-CD150+ within LSK) and CD45.2+ MPP (LSK CD48+CD150- within LSK) populations of Nfat5 +/+ Vav-Cre (wild-type) and Nfat5 fl/fl Vav-Cre (NFAT5-deficient) from bone marrow-transplated CD45.1+ wild-type mice 13 weeks after transplantation

treatment_protocol: Bone marrow was isolated from the respective mouse genotypes (CD45.2 background) and transplanted into irradiated wild-type CD45.1 recipient mice

value: A


title: WT75B

value: B


title: MV411 DMSO 6h DOT1L MNase rep1

value: human leukemia cell


title: 134_MDAMB231_ctrl

value: epithelial cell line


title: MV411 DMSO 6h CDK9 DSG rep3

value: DMSO


title: Control siRNA D3 replicate 1

description: Cells were transfected with Control siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 72 h - replicate 1


title: WT66B


title: WT75A


title: 137_MDAMB231_ctrl

value: Breast

value: ctrl


title: FUS siRNA 3U D1 replicate 2

description: Cells were transfected with Fus siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 24 h - replicate 2

value: FUS siRNA transfection for 48 h in differentiation medium for 24 h


title: 136_MDAMB231_ctrl


title: FUS siRNA 3U D1 replicate 1

description: Cells were transfected with Fus siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 24 h - replicate 1


title: MV411 DMSO 6h CDK9 DSG rep2


title: 132_MDAMB231_docDPT1


title: WT66A

value: A (hematopoietic multipotent progenitor, MPP)


title: WT67B

value: B (hematopoietic stem cell, HSC)


title: MV411 DMSO 6h CDK9 DSG rep1


title: 130_MDAMB231_docDPT1


title: Control siRNA D1 replicate 2

description: Cells were transfected with Control siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 24 h - replicate 2

value: mouse myoblasts

value: Control siRNA transfection for 48 h in differentiation medium for 24 h


title: KO76A

value: KO


title: MV411 DMSO 6h AFF1 MNase rep3

value: cell line

value: WT


title: KO70A


title: MV411 MS41 24h DOT1L MNase rep2


title: KO70B


title: Control siRNA D1 replicate 1

description: Cells were transfected with Control siRNA, cultured in growth medium for 24 h, and then cultured in differentiation medium for 24 h - replicate 1


title: 131_MDAMB231_docDPT1


title: KO76B


title: KO64B


title: 133_MDAMB231_ctrl


title: MV411 DMSO 6h AFF1 MNase rep2


title: FUS siRNA 3U D0 replicate 2

description: Cells were transfected with Fus siRNA, and cultured in growth medium for 24 h - replicate 2

value: FUS siRNA transfection for 24 h in growth medium


title: 12_MDAMB231_cisDPT10


title: MV411 DMSO 6h AFF1 MNase rep1


title: 129_MDAMB231_docDPT1


title: FUS siRNA 3U D0 replicate 1

description: Cells were transfected with Fus siRNA, and cultured in growth medium for 24 h - replicate 1


title: 128_MDAMB231_docDPT1