title: PD19037

city: Amsterdam

first: Vanessa

last: Donega

address: Boelelaan 1108

department: Anatomy and Neuroscience

country: Netherlands

institute: Amsterdam UMC

data_processing:
Paired end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa (version 0.7.10-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases 8 bases (except 18-105_CD271, where the length is 6 bases) representing the unique molecular identifier followed by 8 correspond to the cell specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification.
Data was normalized using the median of ratios from Deseq2 analysis pipeline
Assembly: hg19
Supplementary files format and content: *.csv: Comma separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: SVZ

extract_protocol:
RNA extraction was performed with QIAGen miRNAeasy mini kit in combination with DNAse treatment according to the manufacturers instruction.
RNA was processed using the previously described Celseq2 technique adapted for bulk sequencing. In brief, reverse transcription and second strand synthesis were performed in seperate tubes; libraries were pooled for in vitro transcription based RNA amplification. Libraries were generate using Truseq small RNA primer (rpi) library primers, Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: SVZ

tag: nbb donor number

tag: age

tag: gender

value: m

tag: disease state

value: Parkinson’s Disease


title: Hu-P-3662

status: Public on Sep 04 2025

type: SRA

city: Foster City

first: Mengshu

last: Xu

state: California

address: 300 Lakeside Drive

country: USA

institute: Gilead Sciences

description:
Library name: SAM001289
Column name in TPM_counts.txt file same as library name

library_source: transcriptomic

data_processing:
A Nextflow pipeline was developed for quality control and gene expression profiling. Multiple quality control steps were performed using FastQC (v0.11.8), RNA-SeQC2 (v2.4.2) and MultiQC (v1.10.1) to ensure high quality sequencing data for downstream analysis.
Sequencing reads were aligned to Genecode GRCh38.v38 reference genome using STAR (2.5.3a).
Gene-wise TPM and expected read counts were generated using RSEM (v1.3.1)
Assembly: GRCh38.v38
Supplementary files format and content: Tab delimited file containing TPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: tumor

growth_protocol: FFPE blocks of patient tumor tissues were procured from commercial sources

extract_protocol:
RNA were extracted from four 10µm sections from each FFPE block using the Qiagen AllPrep FFPE Kit (Cat no. 80234; Qiagen, Germantown, MD, USA) following the manufacturer’s protocol
For RNA-seq, RNA concentration and integrity were assessed using the Qubit fluorometer with the RNA High Sensitivity Assay Kit (Cat no. Q32852; ThermoFisher Scientific, Waltham, MA, USA) and using the Fragment Analyzer with Agilent High Sensitivity RNA Kit (Cat no. DNF-472; Agilent Technologies, Santa Clara, CA, USA). RNA was used as an input material for library construction using Illumina RNA Prep with Enrichment (L) Tagmentation Kit with the Illumina Exome Panel (Cat no. 20040537 and Cat no. 20020183; Illumina, San Diego, CA, USA) following the manufacturer’s protocol. The libraries were multiplexed and then sequenced on either the Illumina NextSeq2000 or NovaSeq6000 (Illumina, San Diego, CA, USA), generating 2x100bp-paired end reads with a mean aligned pair-read count of 28 Million reads per sample.

treatment_protocol: No treatment

tag: tissue

value: tumor

tag: cell type

value: HNSC


title: Hu-P-3660

description:
Library name: SAM001287
Column name in TPM_counts.txt file same as library name


title: WT_HCT116_2

city: Bethesda

first: Anjali

last: Dhall

state: MD

address: 37 Convent Drive

department: DTB

institute: NCI

description:
Library name: Sample2
Read Length 2x150 bp

data_processing:
Salmon quant (version 1.10.1) tool used for quantifying transcript expression in RNA-seq data
Assembly: hg19
Supplementary files format and content: Read count and normalized RPKM expression matrix for WT and TOP3BKO HCT116 cell line.

source_name: Colon

growth_protocol: HCT116 (Developmental Therapeutics Program, National Cancer Institute) cell lines were grown in Dulbecco’s modified Eagle’s medium (Life Technologies, Carlsbad, CA) supplemented with 10% Fetal Bovine Serum (Gemini, West Sacramento, CA, 100–106) and 1% penicillin-streptomycin (ThermoFisher Scientific, 15140122) at 37°C in humidified 5% CO2 chamber.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), followed by further purification using PureLink RNA Mini Kit (Cat No. 12183018A;Invitrogen) with DNase treatment (QIAGEN). RNA quality and quantity were analyzed with 2100 Expert (Agilent). RIN (the RNA Integrity Number) of all samples were above 8.0.
This protocol involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. 12 RNA-seq samples were pooled and sequenced on HiSeq using Illumina TruSeq Stranded Total RNA Library Preparation kit and paired-end sequencing. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a sequencing ready library. The final purified product is then quantitated by qPCR before cluster generation and paired end sequencing on HiSeq 4000.

value: Colon

tag: cell line

value: HCT116 Cell line

value: Human colon cancer cell line

tag: genotype

value: Wild Type


title: p21257-s050_RTi18_D7

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Library name: p21257-s050_RTi18_D7

data_processing:
Illumina bcl2fastq v2.20.0.422 was used for demultiplexing
Sequencing data was aligned to Mmul10 Ensembl release 100 using STAR 2.7.3a. Transcript abundance estimates were calculated using the STAR '--quantMode GeneCounts'.
Assembly: Mmul10 Ensembl release 100, Macaca_mulatta.Mmul_10.dna.toplevel.fa, Macaca_mulatta.Mmul_10.100.gtf
Supplementary files format and content: comma delimited text containing raw counts for each sample (in columns) for each transcript (in rows) by Ensembl ID.

organism: Macaca mulatta

source_name: Blood

extract_protocol:
Blood samples were collected in PAXgene Blood RNA tubes (BD Biosciences), and RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, designed for use with PAXgene Blood RNA Tubes (ThermoFisher Scientific). The quality of the RNA was evaluated with a TapeStation 4200 (Agilent), after which one microgram of total RNA underwent globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific).
For cDNA synthesis, ten nanograms of the globin-depleted RNA were used as input with the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio), following the manufacturer's protocol. The amplified cDNA was fragmented and dual-indexed bar codes were added using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated through capillary electrophoresis on a TapeStation 4200 (Agilent), pooled in equal concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, with an approximately 40 million reads per sample.

value: Blood

tag: subjectid

tag: Sex

value: Male

tag: day post_innoculation

tag: adjuvant


title: Hu-P-3657

description:
Library name: SAM001285
Column name in TPM_counts.txt file same as library name


title: PD19019

library_source: transcriptomic single cell

value: f


title: TOP3B_KO_HCT116_1

description:
Library name: Sample3
Read Length 2x150 bp

value: TOP3B Knock out


title: p21257-s048_LP78_D7

description: Library name: p21257-s048_LP78_D7


title: p21257-s046_RRv18_D7

description: Library name: p21257-s046_RRv18_D7


title: TOP3B_KO_HCT116_2

description:
Library name: Sample4
Read Length 2x150 bp


title: PD18132


title: p21257-s047_RTy18_D7

description: Library name: p21257-s047_RTy18_D7


title: PD19005


title: WT_HCT116_1

description:
Library name: Sample1
Read Length 2x150 bp


title: mouse Kras G12C PDAC cell line 7

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description: Library name: KCPC7

data_processing:
raw sequence reads were mapped to mm39 transcriptome using STAR2 v2.7.10b and salmon v1.10.2
Raw counts were collected using htseq v0.11.0 and TPM calculated using salmon reported effective gene lengths
Batch effect were removed using ComBat_seq from R package sva
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes log2 converted TPM values for each sample

organism: Mus musculus

source_name: Pancreas

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were generated from cDNA using the Illumina Nextera XT DNA Sample Preparation Kit. cDNA library quality was assessed using an Agilent 2100 Bioanalyzer

value: Pancreas

value: pancreatic cancer

value: tumor cells

value: Kras G12C

tag: batch

value: batch 3


title: Mice hippocampus tissue, Young Mice, Normal diet, Rep 3

city: Singapore

first: Valerie Chun Ling

last: Lin

address: 60, Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Library name: RMB5011

data_processing:
Trim galore was used to trim the FASTQ files for all samples. FASTQC was done on these files.
STAR was used to map the reads to the mouse genome GRCm39
featureCounts were then used to generate the gene counts.
The gene counts were then used for an DESeq2 analysis
Assembly: GRCm39
Supplementary files format and content: xlsx file for raw counts and log2tpm

source_name: Brain hippocampus

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific, USA) and treated with Dnase I using the DNA-free™ DNA Removal Kit (Invitrogen, Carlsbad, CA, USA) to remove any contaminating DNA.
The total RNA was sent to Genome Institute of Singapore, Agency for Science, Technology and Research for library preparation and pair-end sequencing

value: Brain hippocampus


title: mouse Kras G12C PDAC cell line 6

description: Library name: KCPC6


title: Hu-P-3656

description:
Library name: SAM001284
Column name in TPM_counts.txt file same as library name


title: Hu-P-3661

description:
Library name: SAM001288
Column name in TPM_counts.txt file same as library name


title: p21257-s045_RJm18_D7

description: Library name: p21257-s045_RJm18_D7

value: No adjuvant


title: ME/CFS RRBS, patient #028 at 48hr

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description: Library name: ME028_48h_PBMC_RRBS

library_source: genomic

data_processing:
The quality check and processing of the sequenced RRBS reads were performed using in-house developed bioinformatics tools.  Processed sequence reads were then aligned to the reference human genome (GRCh37) using Bismark with stringent mapping criteria by allowing only one mismatch (default = 2) in the seed. The median non-CpG DNA methylation of all samples was 0.90%, indicating effective bisulfite conversion and low levels of true non-CpG methylation.  Analyses were conducted using the updated version of the DMAP pipeline, namely the DMAP2 analysis pipeline on a macOS computer to examine methylation changes across fragments ranging from 40–220 bp. DMAP2 employed an ANOVA F-test to compare patient and control groups, ensuring that only fragments with data available for all individuals in each group were included. A raw p-value threshold of <0.05 was applied. We have used a stringent P value threshold without false discovery rate correction in order not to lose true positives from this analysis, considering our sample size is low. Genomic features overlapping with these fragments were identified using the in-built Geneloc function of DMAP2.  R packages were used for analysing the DMAP2 output.Principal Component Analysis (PCA) using default parameters (prcomp), unsupervised hierarchical clustering of CpG site methylation, using pheatmap package and cluster rows, the plots were drawn using ggplot2. Sankey Plot was drawn with network D3 and htmlwidgets, Metascape plots were drawn using Metascape website.
Assembly: GRCh37 (hg19)
Supplementary files format and content: Controls_PEM_PBMC_processed.txt format (contains Chr, Start, End, Len, CpGs, Pr, Test, X.Meth, Count_0h, Count_24h, Count_48h, Meth_0h, Meth_24h, Meth_48h, C012_0h, C036_0h, C012_24h, C036_24h, C012_48h, C036_48h, Enddist, Overlap, CpGIs_range, CpGIs_dist, CpGI_relation, Strand, GeneID, GeneRange, Biotype)
Supplementary files format and content: ME_PEM_PBMC_processed.txt format (contains Chr, Start, End, Len, CpGs, Pr, Test, X.Meth, Count_0h, Count_24h, Count_48h, Meth_0h, Meth_24h, Meth_48h, ME007_0h, ME016_0h, ME024_0h, ME026_0h, ME028_0h, ME007_24h, ME016_24h, ME024_24h, ME026_24h, ME028_24h, ME007_48h, ME016_48h, ME024_48h, ME026_48h, ME028_48h, Enddist, Overlap, CpGIs_range, CpGIs_dist, CpGI_relation, Strand, GeneID, GeneRange, Biotype)

molecule: genomic DNA

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by layering it onto Ficoll-Paque, followed by centrifuging at 400×g to separate plasma from PBMCs and the PBMCs from other cells. The removed PBMC layer was diluted with PBS and then pelleted at 100×g. The pellet was washed in PBS and stored at −80°C in a solution of FCS containing 10% DMSO. DNA was extracted from 200 μL of the PBMC fraction using the Illustra Blood Genomic Prep Mini Spin Kit, following the manufacturer’s instructions. Elution was performed using the kit’s EB buffer, and DNA concentration was measured with a Qubit 2.0 fluorometer according to the Qubit dsDNA HS Assay Kit protocol.
500 µg of genomic DNA was digested using 160 U of the MspI restriction enzyme. After end repair and adenylation of the 3′ ends, adaptors were ligated to the DNA fragments. Bisulfite conversion was carried out using the EZ DNA Methylation Kit (Zymo Research Corp, USA) according to the manufacturer’s instructions. A semi-quantitative PCR was performed on the bisulfite-converted DNA to determine the optimal number of amplifi-cation cycles required for the final large-scale PCR of the complete library. Following PCR amplification, DNA was size-selected using magnetic beads (AMPure XP beads from the TruSEq DNA nanokit -Beckman Coulter USA), isolating fragments between 40–220 bp to construct the RRBS libraries while minimizing adaptor contamination. The purified DNA was assessed for quality using a BioAnalyzer (Agilent, USA) and Qubit (Thermofisher Scientific, USA) measurements, followed by further purification with AMPure XP Beads (Beckman Coulter, USA).

value: PBMC


title: ME/CFS RRBS, patient #028 at 24hr

description: Library name: ME028_24h_PBMC_RRBS


title: mouse Kras G12C PDAC cell line 5

description: Library name: KCPC5


title: 52L, Mouse STR LEFT, male, MG-, SAL

city: Kuopio

first: Katrina

last: Albert

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Library name: 52-L

data_processing:
Reads in FASTQ format were sorted to human and mouse origin using BBsplit tool and reference genomes GRCh38 and GRCm39, respectively. Transcripts were quantified using Salmon.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Excel files containing normalized counts for each gene by sample, separate files for mouse counts and human counts

organism:
Homo sapiens
Mus musculus

source_name: microglia

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal micro kit following the manufacturer’s instructions (Qiagen)
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB)

value: microglia

value: human M-CSF knockin

tag: treatment

value: SAL


title: p21257-s049_RLv18_D7

description: Library name: p21257-s049_RLv18_D7


title: Hu-P-3658

description:
Library name: SAM001286
Column name in TPM_counts.txt file same as library name

value: tumor

value: HNSC


title: Hu-P-3655

description:
Library name: SAM001283
Column name in TPM_counts.txt file same as library name


title: ME/CFS RRBS, patient #028 at 0hr

description: Library name: ME028_0h_PBMC_RRBS

value: Blood


title: p21257-s044_LT86_D7

description: Library name: p21257-s044_LT86_D7

value: Male


title: mouse Kras G12C PDAC cell line 4

description: Library name: KCPC4


title: mouse Kras G12C PDAC cell line 3

description: Library name: KCPC3


title: ME/CFS RRBS, patient #026 at 48hr

description: Library name: ME026_48h_PBMC_RRBS


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium RIF3

city: Beijing

first: Peng

last: Wang

address: No.5 Ankang Hutong, Deshengmenwai, Xicheng District

country: China

institute: Beijing Anding Hospital affiliated to Capital Medical University

description:
Library name: RIF3
Woman with repeated implantation failure of quality embryos after multiple in vitro fertilization( IVF) attempts

data_processing:
Raw sequencing data were processed using the Space Ranger (v2.1.0) software provided by 10x Genomics.
Assembly: GRCh38
Supplementary files format and content: processed_data file includes filtered_feature_bc_matrix,spatial image alignment file and original tiff for each Sample
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: uterine endometrium

extract_protocol:
Fresh endometrial tissues were obtained and rapidly frozen in isopentane pre-chilled with liquid nitrogen. The tissues were then stored at -80°C. Fresh frozen tissues were sectioned into slices. Initially, RNA quality was assessed to ensure a minimum RNA Integrity Number (RIN) larger than 7 to minimize the degradation of RNA molecules. The optimal tissue optimization time was determined based on fluorescence imaging strength. The tissue splices were carefully placed onto designated capture areas on the 10x Visium Spatial Tissue Optimization Slide. Each slide contained four capture areas, each measuring 6.5*6.5mm and containing about 5,000 spots equipped with barcode sequences. Standard methanol fixation, hematoxylin and eosin (H&E) staining, and brightfield microscopes were utilized to visualize tissue sections. The tissue was permeabilized to release mRNA molecules, which were then captured by the adjacent spots. mRNA was subjected to reverse transcription to generate cDNA. Subsequently, libraries were constructed according to the standard protocol.
The amplified cDNA was used to construct sequencing libraries following the standard protocol of the 10x Genomics Visium Spatial Gene Expression Library Construction Kit. Libraries included sample indices for multiplexing. The libraries were quantified using a Qubit dsDNA HS Assay Kit and analyzed for fragment size distribution using an Agilent Bioanalyzer 2100.

value: uterine endometrium

value: Case set


title: ME/CFS RRBS, patient #026 at 24hr

description: Library name: ME026_24h_PBMC_RRBS


title: p21257-s042_RHj18_D7

description: Library name: p21257-s042_RHj18_D7


title: mouse Kras G12C PDAC cell line 2

description: Library name: KCPC2

value: Pancreas


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium RIF2

description:
Library name: RIF2
Woman with repeated implantation failure of quality embryos after multiple in vitro fertilization( IVF) attempts


title: mouse Kras G12C PDAC cell line 1

description: Library name: KCPC1

value: pancreatic cancer


title: ME/CFS RRBS, patient #026 at 0hr

description: Library name: ME026_0h_PBMC_RRBS


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium CTR4

description:
Library name: CTR4
Multiparous female without a history of miscarriage

value: Control set


title: mouse Kras G12D PDAC cell line 22

description: Library name: KDPC22

value: tumor cells

value: Kras G12D


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium RIF4

description:
Library name: RIF4
Woman with repeated implantation failure of quality embryos after multiple in vitro fertilization( IVF) attempts


title: p21257-s039_RLv18_D4

description: Library name: p21257-s039_RLv18_D4


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium RIF1

description:
Library name: RIF1
Woman with repeated implantation failure of quality embryos after multiple in vitro fertilization( IVF) attempts


title: p21257-s040_RTi18_D4

description: Library name: p21257-s040_RTi18_D4


title: mouse Kras G12D PDAC cell line 21

description: Library name: KDPC21

value: batch 3


title: ME/CFS RRBS, patient #024 at 24hr

description: Library name: ME024_24h_PBMC_RRBS


title: ME/CFS RRBS, patient #024 at 0hr

description: Library name: ME024_0h_PBMC_RRBS


title: ME/CFS RRBS, patient #024 at 48hr

description: Library name: ME024_48h_PBMC_RRBS


title: p21257-s038_LP78_D4

description: Library name: p21257-s038_LP78_D4


title: mouse Kras G12D PDAC cell line 20

description: Library name: KDPC20


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium CTR2

description:
Library name: CTR2
Multiparous female without a history of miscarriage


title: mouse Kras G12D PDAC cell line 19

description: Library name: KDPC19


title: ME/CFS RRBS, patient #016 at 48hr

description: Library name: ME016_48h_PBMC_RRBS


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium CTR3

description:
Library name: CTR3
Multiparous female without a history of miscarriage


title: p21257-s043_RRh18_D7

description: Library name: p21257-s043_RRh18_D7

value: No adjuvant


title: Spatial Transcriptomics sequencing of Homo sapiens: adult female endometrium CTR1

description:
Library name: CTR1
Multiparous female without a history of miscarriage


title: ME/CFS RRBS, patient #016 at 24hr

description: Library name: ME016_24h_PBMC_RRBS

value: PBMC


title: p21257-s041_RAi18_D7

description: Library name: p21257-s041_RAi18_D7


title: ME/CFS RRBS, patient #016 at 0hr

description: Library name: ME016_0h_PBMC_RRBS


title: mouse Kras G12D PDAC cell line 18 rep 1

description: Library name: KDPC18_1

value: batch 2


title: p21257-s036_RRv18_D4

description: Library name: p21257-s036_RRv18_D4


title: SSD_rep3

city: Shanghai

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
Majorbio Cloud Platform, https://cloud.majorbio
Sequence reads were trimmed for adaptor sequence/low quality sequece (Quality lomit : 0.5)
Trimmed sequence reads were mapped to GRCh38.p13 (parameters-mismatch cost: 2 insertion cost: 3 deletion cost 3 legtn faction: 0.8 semilarity fractions: 0.8)
Read count extraction and normalization were performed using Majorbio Cloud Platform
Assembly: GRCh38.p13
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 TPM for each sample

source_name: AGS

growth_protocol: C4-2B cells were mantined in RMPI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmshpore with 5% CO2 at 37℃.

extract_protocol:
The total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme RC112-01; China). The RNA quality was assessed using a Bioanalyzer 2100 (Agilent, USA), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit fellowing manufaturer's protocols.

treatment_protocol: Cells were treated with 10 uM L14-8 or vehicle and cluture for 24 h followed with RNA extraction and sequencing.

value: AGS

value: gastric adenocarcinoma

value: WT

value: SSD


title: ME/CFS RRBS, patient #007 at 24hr

description: Library name: ME007_24h_PBMC_RRBS

value: Blood


title: SSD_rep1


title: mouse Kras G12D PDAC cell line 17 rep 1

description: Library name: KDPC17_1


title: SSD_rep2


title: ME/CFS RRBS, patient #007 at 48hr

description: Library name: ME007_48h_PBMC_RRBS


title: p21257-s034_LT86_D4

description: Library name: p21257-s034_LT86_D4

value: Male


title: mouse Kras G12D PDAC cell line 17 rep 2

description: Library name: KDPC17_2


title: ME/CFS RRBS, patient #007 at 0hr

description: Library name: ME007_0h_PBMC_RRBS


title: p21257-s032_RHj18_D4

description: Library name: p21257-s032_RHj18_D4


title: p21257-s037_RTy18_D4

description: Library name: p21257-s037_RTy18_D4


title: mouse Kras G12D PDAC cell line 16 rep 2

description: Library name: KDPC16_2


title: vehicle_rep2

value: vehicle


title: p21257-s031_RAi18_D4

description: Library name: p21257-s031_RAi18_D4


title: Healthy Controls RRBS, patient #036 at 48hr

description: Library name: C036_48h_PBMC_RRBS


title: Healthy Controls RRBS, patient #036 at 24hr

description: Library name: C036_24h_PBMC_RRBS


title: mouse Kras G12D PDAC cell line 16 rep 1

description: Library name: KDPC16_1


title: mouse Kras G12D PDAC cell line 14 rep 2

description: Library name: KDPC14_2


title: vehicle_rep1


title: mouse Kras G12D PDAC cell line 18 rep 2

description: Library name: KDPC18_2


title: p21257-s030_RTi18_D2

description: Library name: p21257-s030_RTi18_D2


title: p21257-s035_RJm18_D4

description: Library name: p21257-s035_RJm18_D4


title: Healthy Controls RRBS, patient #036 at 0hr

description: Library name: C036_0h_PBMC_RRBS


title: p21257-s029_RLv18_D2

description: Library name: p21257-s029_RLv18_D2


title: Patient 21 Pre-Tx Tumor

city: Tampa

first: Roger

last: Li

state: FL

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
The raw RNA-seq reads were first assessed for quality using FastQC. Quality trimming was performed using cutadapt to remove reads with adaptor contaminants and low-quality bases. Read pairs with either end too short (<25bps) were discarded from further analysis. Next, trimmed and filtered reads were aligned to the human transcriptome GRCh37 using STAR. Gene expression was quantified as Transcript per Million (TPM) using RSEM.
Assembly: GRCh 37
Supplementary files format and content: tab-deliminited text file containing read count for each sample

source_name: Bladder tumor

extract_protocol:
Scroll (3-5, 20mm sections) from each FFPE block were used for total RNA extraction using the Qiagen RNeasy FFPE kit (cat#73504, Qiagen, Germantown, MD) in accordance with manufacturer’s instructions. RNA quality was assessed using Qubit Fluorometric Quantification (Invitrogen) and Tapestation 4200 (Agilent).
The samples were processed with the Illumina TruSeq RNA exome kit and sequence on one NovaSeq-600 SP-200 sequencing run.

value: Bladder tumor

tag: individual

value: Patient 21

tag: time

value: pre-Tx Tumor


title: p21257-s033_RRh18_D4

description: Library name: p21257-s033_RRh18_D4


title: vehicle_rep3


title: Patient 21 Post-Tx Cystectomy

value: post-Tx Cystectomy


title: mouse Kras G12D PDAC cell line 14 rep 1

description: Library name: KDPC14_1

value: Pancreas

value: pancreatic cancer

value: tumor cells


title: p21257-s028_LP78_D2

description: Library name: p21257-s028_LP78_D2


title: mouse Kras G12D PDAC cell line 13 rep 2

description: Library name: KDPC13_2

value: Kras G12D


title: Patient 20 Pre-Tx Tumor

value: Patient 20


title: Healthy Controls RRBS, patient #012 at 48hr

description: Library name: C012_48h_PBMC_RRBS

value: PBMC


title: mouse Kras G12D PDAC cell line 13 rep 1

description: Library name: KDPC13_1

value: batch 2


title: Healthy Controls RRBS, patient #012 at 0hr

description: Library name: C012_0h_PBMC_RRBS


title: Healthy Controls RRBS, patient #012 at 24hr

description: Library name: C012_24h_PBMC_RRBS


title: p21257-s027_RTy18_D2

description: Library name: p21257-s027_RTy18_D2


title: p21257-s026_RRv18_D2

description: Library name: p21257-s026_RRv18_D2


title: Patient 20 Post-Tx Cystectomy


title: mouse Kras G12D PDAC cell line 12 rep 2

description: Library name: KDPC12_2


title: mouse Kras G12D PDAC cell line 12 rep 1

description: Library name: KDPC12_1


title: HY73, DS, rep2

first: Wei

last: Ding

address: 2005 Songhu Road

institute: Fudan University

data_processing:
Raw reads were first trimmed as paired-end reads using Fastp with default parameters.
Clean reads were mapped to the the rice genome (MH63RS2, http://rice.hzau.edu.cn/rice_rs2/) by BWA-MEM with default parameters.
SAMtools was used to remove redundant reads and align low quality (map quality < 30) reads.
ChIP-seq peaks were called by MACS2 , broad peak with parameters “-f BAMPE -B --broad -g 119667750 -q 0.00001 --broad-cutoff 0.00001” and narrow peak with parameters “-f BAMPE -B -g 119667750 -q 0.00001.”
The mapped BAM files were normalized and converted to BigWig format using Deeptools to configure the tracks in IGV.
Assembly: rice genome (MH63RS2, http://rice.hzau.edu.cn/rice_rs2/)
Supplementary files format and content: narrowPeak

organism: Oryza sativa

source_name: leaves

extract_protocol:
Tissues were cross-linked with 1% formaldehyde and quenched with 0.2 M glycine at room temperature. Approximately 0.2 g of tissue were used for each ChIP-seq assay. Tissues were ground in liquid nitrogen into fine powder, lysed with Buffer S [50 mM HEPES-KOH (pH7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1% SDS] for 20 min at 4 °C and then mixed with Buffer F (Buffer S without SDS) for 10 min at 4 °C. The chromatin was fragmented to 200–600 bp through sonication.
ChIP DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs).

value: leaves

tag: developmental stage

value: grain filling stage

tag: antibody

value: histone H4K5ac

tag: cultivar

value: drought-stressed


title: Patient 19 Post-Tx Tumor

value: Patient 19

value: post-Tx Tumor


title: p21257-s025_RJm18_D2

description: Library name: p21257-s025_RJm18_D2

value: Blood

value: Male

value: No adjuvant


title: Patient 19 Pre-Tx Tumor

value: Bladder tumor

value: pre-Tx Tumor


title: HY73, DS, rep1


title: p21257-s024_LT86_D2

description: Library name: p21257-s024_LT86_D2


title: Patient 18 Pre-Tx Tumor

value: Patient 18


title: mouse Kras G12D PDAC cell line 11 rep 2

description: Library name: KDPC11_2

value: Pancreas

value: pancreatic cancer

value: tumor cells


title: HY73, WW, rep2

value: well-watered


title: mouse Kras G12D PDAC cell line 11 rep 1

description: Library name: KDPC11_1

value: Kras G12D

value: batch 2


title: Patient 18 Post-Tx Tumor


title: HY73, WW, rep1

value: leaves

value: grain filling stage


title: p21257-s022_RHj18_D2

description: Library name: p21257-s022_RHj18_D2


title: mouse Kras G12D PDAC cell line 10 rep 2

description: Library name: KDPC10_2


title: Patient 17 Pre-Tx Tumor

value: Patient 17


title: WT HPC Nicotine biol rep. 6

city: Boulder

first: Mina

last: Griffioen

state: CO

address: 1480 30th street

department: Institute for behavioral genetics

institute: University of Colorado Boulder

description:
Library name: Sample 12N
Column name in Akt2NicHPCCounts.txt: WT14_N_Aligned.out.bam

data_processing:
Bash scripting in UNIX environment
Reads were trimmed and filtered for quality using fastp (S. Chen, Zhou, & Chen, 2018), then aligned to the mm10 Mus Musculus genome using STAR (Dobin et al., 2013).
Raw read/gene counts for alignment files were obtained using featureCounts (Liao, Smyth, & Shi, 2014), and differential gene expression was analyzed using DESeq2 software (Love, Huber, & Anders, 2014) with a significance cut-off of BH-corrected adjusted p<0.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file contains DESeq2 output with basemean, log2FoldChange, lfcSE, p-value and adjusted p-value

source_name: Hippocampus

extract_protocol:
RNA was harvested using trizol extraction.
Poly(A)-selected libraries were created using the Universal Plus™ mRNA-Seq library preparation kit with NuQuant

treatment_protocol: WT male mice 2-6 months of age were treated with 5mg/kg of Lipopolysaccharide (LPS) (N=4) or 0.9% Saline solution (N=4) through intraperitoneal injection, prefrontal cortex (PFC) was dissected after 24 hours, and LPS samples were compared to saline for gene expression analysis. For nicotine studies, mice 2-6 months of age were given 0.2 mg/kg nicotine (N=6) or 0.9% saline (N=6), the hippocampus was dissected after 24 hours, and Nicotine samples were compared to saline for gene expression analysis.

value: Hippocampus

value: WT

value: Nicotine


title: p21257-s021_RAi18_D2

description: Library name: p21257-s021_RAi18_D2

value: Blood

value: Male


title: mouse Kras G12D PDAC cell line 10 rep 1

description: Library name: KDPC10_1


title: Patient 17 Post-Tx Cystectomy

value: Bladder tumor

value: post-Tx Cystectomy


title: WT HPC Nicotine biol rep. 5

description:
Library name: Sample 11N
Column name in Akt2NicHPCCounts.txt: WT10_N_Aligned.out.bam


title: p21257-s019_RLv18_D1

description: Library name: p21257-s019_RLv18_D1


title: Patient 16 Post-Tx Tumor

value: Patient 16

value: post-Tx Tumor


title: p21257-s020_RTi18_D1

description: Library name: p21257-s020_RTi18_D1


title: mouse Kras G12D PDAC cell line 9 rep 1

description: Library name: KDPC9_1

value: Pancreas

value: pancreatic cancer


title: mouse Kras G12D PDAC cell line 9 rep 2

description: Library name: KDPC9_2

value: tumor cells


title: Patient 16 Pre-Tx Tumor

value: pre-Tx Tumor


title: p21257-s018_LP78_D1

description: Library name: p21257-s018_LP78_D1


title: p21257-s017_RTy18_D1

description: Library name: p21257-s017_RTy18_D1


title: Patient 15 Pre-Tx  Tumor

value: Patient 15

value: pre-Tx  Tumor


title: mouse Kras G12D PDAC cell line 8 rep 1

description: Library name: KDPC8_1

value: Kras G12D

value: batch 2


title: WT HPC Nicotine biol rep. 2

description:
Library name: Sample 8N
Column name in Akt2NicHPCCounts.txt: WT7_N_Aligned.out.bam

value: Hippocampus


title: p21257-s016_RRv18_D1

description: Library name: p21257-s016_RRv18_D1


title: mouse Kras G12D PDAC cell line 8 rep 2

description: Library name: KDPC8_2


title: Patient 15 Post-Tx Tumor


title: p21257-s023_RRh18_D2

description: Library name: p21257-s023_RRh18_D2

value: No adjuvant


title: mouse Kras G12D PDAC cell line 7 rep 2

description: Library name: KDPC7_2

value: batch 1


title: WT HPC Nicotine biol rep. 1

description:
Library name: Sample 7N
Column name in Akt2NicHPCCounts.txt: WT6_N_Aligned.out.bam

value: WT

value: Nicotine


title: Patient 14 Pre-Tx Tumor

value: Bladder tumor

value: Patient 14


title: WT HPC Saline biol rep. 6

description:
Library name: Sample 6N
Column name in Akt2NicHPCCounts.txt: WT15_S_Aligned.out.bam

value: Saline


title: p21257-s015_RJm18_D1

description: Library name: p21257-s015_RJm18_D1

value: Blood

value: Male


title: WT HPC Nicotine biol rep. 4

description:
Library name: Sample 10N
Column name in Akt2NicHPCCounts.txt: WT9_N_Aligned.out.bam


title: Patient 14 Post-Tx Cystectomy

value: post-Tx Cystectomy


title: WT HPC Saline biol rep. 5

description:
Library name: Sample 5N
Column name in Akt2NicHPCCounts.txt: WT5_S_Aligned.out.bam


title: p21257-s014_LT86_D1

description: Library name: p21257-s014_LT86_D1


title: mouse Kras G12D PDAC cell line 6 rep 2

description: Library name: KDPC6_2

value: Pancreas

value: pancreatic cancer

value: tumor cells


title: Patient 13 Pre-Tx  Tumor

value: Patient 13

value: pre-Tx  Tumor


title: mouse Kras G12D PDAC cell line 6 rep 1

description: Library name: KDPC6_1

value: Kras G12D


title: Patient 12 Post-Tx Tumor

value: Patient 12

value: post-Tx Tumor


title: WT HPC Saline biol rep. 3

description:
Library name: Sample 3N
Column name in Akt2NicHPCCounts.txt: WT3_S_Aligned.out.bam

value: Hippocampus


title: p21257-s012_RHj18_D1

description: Library name: p21257-s012_RHj18_D1

value: No adjuvant


title: WT HPC Saline biol rep. 2

description:
Library name: Sample 2N
Column name in Akt2NicHPCCounts.txt: WT2_S_Aligned.out.bam

value: WT


title: WT HPC Nicotine biol rep. 3

description:
Library name: Sample 9N
Column name in Akt2NicHPCCounts.txt: WT8_N_Aligned.out.bam

value: Nicotine


title: p21257-s013_RRh18_D1

description: Library name: p21257-s013_RRh18_D1


title: p21257-s011_RAi18_D1

description: Library name: p21257-s011_RAi18_D1


title: WT HPC Saline biol rep. 1

description:
Library name: Sample 1N
Column name in Akt2NicHPCCounts.txt: WT1_S_Aligned.out.bam


title: mouse Kras G12D PDAC cell line 4 rep 2

description: Library name: KDPC4_2

value: batch 1


title: WT PFC LPS biol rep. 4

description:
Library name: Sample 8L
Column name in WTSalineLPS.txt: X877_WT_Sal.bam

source_name: PFC

value: PFC

value: LPS


title: Patient 11 Post-Tx Tumor

value: Bladder tumor

value: Patient 11


title: p21257-s009_RLv18_D0

description: Library name: p21257-s009_RLv18_D0

value: Blood

value: Male


title: mouse Kras G12D PDAC cell line 5 rep 1

description: Library name: KDPC5_1

value: Pancreas

value: pancreatic cancer

value: tumor cells


title: mouse Kras G12D PDAC cell line 7 rep 1

description: Library name: KDPC7_1

value: Kras G12D


title: Patient 11 Pre-Tx  Tumor

value: pre-Tx  Tumor


title: mouse Kras G12D PDAC cell line 4 rep 1

description: Library name: KDPC4_1


title: p21257-s010_RTi18_D0

description: Library name: p21257-s010_RTi18_D0


title: WT PFC LPS biol rep. 3

description:
Library name: Sample 7L
Column name in WTSalineLPS.txt: X1026_WT_LPS.bam


title: WT HPC Saline biol rep. 4

description:
Library name: Sample 4N
Column name in Akt2NicHPCCounts.txt: WT4_S_Aligned.out.bam

value: Saline


title: mouse Kras G12D PDAC cell line 3 rep 2

description: Library name: KDPC3_2


title: Patient 9 Pre-Tx  Tumor

value: Patient 9


title: Patient 10 Pre-Tx  Tumor

value: Patient 10


title: p21257-s008_LP78_D0

description: Library name: p21257-s008_LP78_D0


title: WT PFC LPS biol rep. 2

description:
Library name: Sample 6L
Column name in WTSalineLPS.txt: X1047_WT_Sal.bam

value: WT


title: p21257-s007_RTy18_D0

description: Library name: p21257-s007_RTy18_D0


title: Patient 9 Post-Tx Tumor

value: post-Tx Tumor


title: mouse Kras G12D PDAC cell line 5 rep 2

description: Library name: KDPC5_2

value: batch 1


title: p21257-s006_RRv18_D0

description: Library name: p21257-s006_RRv18_D0


title: Patient 8 Pre-Tx  Tumor

value: Patient 8


title: Patient 12 Pre-Tx  Tumor

value: Patient 12


title: mouse Kras G12D PDAC cell line 2 rep 2

description: Library name: KDPC2_2


title: p21257-s005_RJm18_D0

description: Library name: p21257-s005_RJm18_D0

value: No adjuvant


title: Patient 8 Post-Tx Tumor

value: Bladder tumor


title: mouse Kras G12D PDAC cell line 2 rep 1

description: Library name: KDPC2_1


title: WT PFC Saline biol rep. 4

description:
Library name: Sample 4L
Column name in WTSalineLPS.txt: X1023_WT_LPS.bam

value: PFC


title: mouse Kras G12D PDAC cell line 1 rep 2

description: Library name: KDPC1_2


title: Patient 7 Pre-Tx  Tumor

value: Patient 7


title: WT PFC Saline biol rep. 3

description:
Library name: Sample 3L
Column name in WTSalineLPS.txt: X946_WT_Sal.bam


title: mouse Kras G12D PDAC cell line 1 rep 1

description: Library name: KDPC1_1

value: Pancreas


title: Patient 7 Post-Tx Tumor


title: p21257-s004_LT86_D0

description: Library name: p21257-s004_LT86_D0

value: Blood

value: Male


title: WT PFC Saline biol rep. 2

description:
Library name: Sample 2L
Column name in WTSalineLPS.txt: X1046_WT_LPS.bam


title: mouse Kras G12D PDAC cell line 3 rep 1

description: Library name: KDPC3_1

value: pancreatic cancer

value: tumor cells

value: Kras G12D


title: p21257-s002_RHj18_D0

description: Library name: p21257-s002_RHj18_D0


title: scRNAseq, DKO, Aorta, ApoE, S1

city: Boston

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

description:
Library name: L-DKO_Aorta_S1
10x Genomics
combined_AortaApoE_filteredCountData.csv
combined_AortaApoE_metaData.csv

data_processing:
Cell Ranger (version 7.1.0) to map the raw reads of RNA sequencing data to the mouse genome (version mm10) and to count UMI for each gene.
Assembly: mm10
Supplementary files format and content: csv files, in metaData file some columns starts with ABC, that’s means after batch correction

source_name: Aorta

extract_protocol:
For liver cell isolation, the WT and Liver-DKO mice (n=3) were anesthetized and restrained and the skin sprayed with 70% ethanol.
single-cell RNA-seq library construction following the protocol provided by 10X Genomics.

value: Aorta


title: scRNAseq, WT, Aorta, ApoE, S1

description:
Library name: L-WT_Aorta_S1
10x Genomics
combined_AortaApoE_filteredCountData.csv
combined_AortaApoE_metaData.csv


title: Patient 6 Post-Tx Tumor

value: Patient 6


title: WT PFC Saline biol rep. 1

description:
Library name: Sample 1L
Column name in WTSalineLPS.txt: X1037_WT_Sal.bam

value: WT

value: Saline


title: WT PFC LPS biol rep. 1

description:
Library name: Sample 5L
Column name in WTSalineLPS.txt: X1034_WT_LPS.bam

value: LPS


title: p21257-s001_RAi18_D0

description: Library name: p21257-s001_RAi18_D0


title: Patient 6 Pre-Tx  Tumor

value: pre-Tx  Tumor


title: scRNAseq, WT, Liver, S1

description:
Library name: L-WT_Liver_S1
10x Genomics
combined_LiverControl_filteredCountData.csv
combined_LiverControl_metaData.csv

source_name: Liver

value: Liver


title: HPF_2

city: Chongqing

first: Ke

address: No. 30, Gaotan Yanzheng Street, Shapingba District, Chongqing

institute: Army Medical University

description: Library name: Sample 8

data_processing:
Process data using FASTP
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTP.
Trimmed sequence reads were mapped to GRCm38 using HISAT2 genomic benchwork
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: bone marrow

extract_protocol:
RNA was harvested using Total RNA Extractor (Trizol)). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using YEASEN mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: primary cell

value: bone marrow-derived dendritic cells

value: HPF


title: CG3_TTAGTCTGCT-CTTAGCGCTG_L004

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description:
Library name: Sample 9
Column name in raw_counts_All Samples.txt: CDG3

data_processing:
The libraries were sequenced from both ends of the fragments for a total of 150bp per end, to a total depth of at least 2 million reads per sample. The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA). The quality of the demultiplexed fastq files were evaluated with the FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), which generates reports with the quality scores, base composition, k-mer, GC and N contents, sequence duplication levels and overrepresented sequences.
Assembly: S. salar reference genome (Ssal_v3.1)
Supplementary files format and content: Matrix data from DEseq2 analysis
Supplementary files format and content: matrix-CGD.txt

organism: Salmo salar

source_name: Gill

extract_protocol:
Total RNA was obtained by homogenized the tissue with Trisure.1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were preapred using TruSeq Stranted Total RNA Sample Prep Kit following manufacter's protocols.

value: Gill

value: Control


title: HPF_3

description: Library name: Sample 9


title: CG2_AGTTCCGCTC-ACTCTAACGT_L004

description:
Library name: Sample 8
Column name in raw_counts_All Samples.txt: CG2


title: Patient 5 Pre-Tx Tumor

value: Bladder tumor

value: Patient 5

value: pre-Tx Tumor


title: scRNAseq, WT, Liver, ApoE, S1

description:
Library name: ApoE_S1
10x Genomics
combined_LiverApoE_filteredCountData.csv
combined_LiverApoE_metaData.csv


title: Patient 5 Post-Tx Cystectomy

value: post-Tx Cystectomy


title: PA0833_3

description: Library name: Sample 6


title: p21257-s003_RRh18_D0

description: Library name: p21257-s003_RRh18_D0

value: Blood

value: Male

value: No adjuvant


title: CG1_ACCTTCTAGA-ATCACGGTAA_L004

description:
Library name: Sample 7
Column name in raw_counts_All Samples.txt: CG1


title: scRNAseq, DKO, Liver, ApoE, S1

description:
Library name: ApoE_liverDKO_S1
10x Genomics
combined_LiverApoE_filteredCountData.csv
combined_LiverApoE_metaData.csv

value: DKO


title: Patient 4 Post-Tx TURBT

value: Patient 4

value: post-Tx TURBT


title: PA0833_2

description: Library name: Sample 5


title: Embryoid bodies, Stella pos, day 6, rep2

city: Ithaca

first: Jingyi

last: Gao

state: NY

address: 618 Tower road

department: BMS

institute: Cornell University

data_processing:
The raw fastq reads were processed with MAGeCK package to generate the raw counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains sgRNA counts for each sample
Library strategy: CRISPR interference (CRISPRi) screen

source_name: Embryoid bodies

growth_protocol: Mouse ESCs with the four transcription factors inducible system (Prdm1, Prdm14, Nanog, and Tfap2c) were cultured and maintained without feeders in N2B27 2i medium: 1μM PD0325901, 3μM CHIR99021 and 1000U/mL LIF as described in Ding et al. 2024.

extract_protocol:
Genomic DNAs from cells carrying CRISPRi sgRNA library were extracted using a Genomic DNA Purification Kit (Thermo Scientific; K0722).
To recover sgRNA sequences, both CRISPRi plasmid pools and genomic DNAs were PCR amplified with Miseq_Adaptor_F 5′-AATGATACGGCGACCACCGAGATCTACACACACTCTTTCCCTACACGACGCTCTTCCGATCTTATCTTGTGGAAAGGACGAAACACCG-3′ and Miseq_Adaptor_R 5′-CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC-3′ primers using Q5 High-Fidelity DNA Polymerase (NEB; M0491L). PCR samples were run on a 2% agarose gel and purified using a Gel Extraction Kit (Qiagen; 28704). Purified DNAs were sequenced on an Illumina Miseq (Cornell Genomics Facility) using the seqRead_Miseq 5′-GACGCTCTTCCGATCTTATCTTGTGGAAAGGACGAAACACCG-3′ primer.

treatment_protocol: ESCs were first transduced with lentiviral packaged pLX_311 and selected with Blasticidin to generate stable dCas9-KRAB expression cell lines. Approximately 1.6×107 ESCs with stable dCas9-KRAB expression were then transduced with the pXPR_050 CRISPRi sgRNA expression library at a multiplicity of infection of 0.3 to ensure at least 500× coverage of the library. The cells were selected in puromycin (1.2mg/ml) for 2 days. All cells were infected with lentivirus for 48 hours. ESCs were differentiated into PGCLCs as described in Ding et al. 2024. On the sixth day of differentiation, EBs were dispersed into individual cells and subjected to FACS to isolate both Stella-eGFP+ and Stella-eGFP- cells. DNA was extracted from each pool.

value: Embryoid bodies

value: primordial germ cell-like cells


title: IG_3_2B_TGATGTCGAA-AGGTCCTATA_L004

description:
Library name: Sample 6
Column name in raw_counts_All Samples.txt: IG_3_2B

value: CGDndt


title: Patient 3 Pre-Tx Tumor

value: Patient 3


title: PA0833_1

description: Library name: Sample 4

value: bone marrow

value: primary cell

value: bone marrow-derived dendritic cells


title: Embryoid bodies, Stella pos, day 6, rep1


title: BKD_Gi_2202_Ay_F5_2_CAGATAAGCG-TGAAGGTGAA_L004

description:
Library name: Sample 5
Column name in raw_counts_All Samples.txt: BKD_Gi_2022_Ay_F5_2

value: Gill


title: Patient 3 Post-Tx Tumor

value: Bladder tumor

value: post-Tx Tumor


title: PBS_3

description: Library name: Sample 3

value: PBS


title: Embryoid bodies, Stella neg, day 6, rep2

value: somatic cell-like cells


title: Patient 2 Pre-Tx Tumor

value: Patient 2

value: pre-Tx Tumor


title: PBS_2

description: Library name: Sample 2


title: Embryoid bodies, Stella neg, day 6, rep1


title: Patient 2 Post-Tx Tumor


title: IG_4_1_GTGTCGGATT-AAGCGGAGAA_L004

description:
Library name: Sample 2
Column name in raw_counts_All Samples.txt: IG_4_1

value: CGDdt


title: IG_5_1_CCACAACATG-TTACCAGTGG_L004

description:
Library name: Sample 3
Column name in raw_counts_All Samples.txt: IG_5_1


title: HPF_1

description: Library name: Sample 7

value: HPF


title: Patient 1 Pre-Tx Tumor

value: Patient 1


title: EM72h

first: Yang

last: Fan

address: Zhangheng Road 826

description:
Library name: SAMPLE2
BDRhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
STARsolo was utilized to calculate the raw counts and cell whitelist by default parameter
Assembly: mm10
Supplementary files format and content: Single cell matrix files

source_name: tumor

extract_protocol:
The single-cell suspension from glioma specimens was stained with Fixable Viability Dye eFluor™ 780 and antibodies of anti-mouse CD45.2 and anti-mouse CD45.1 (1:200, Biolegend) for fluorescence activated cell sorting (FACS) with sorting buffer (HBSS, 2% FCS, 5mM EDTA). Single living endogenous immune cells (eFluor™ 780-CD45.2+CD45.1-) were sorted and obtained after FACS.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: tumor

value: treated with EM


title: IG_1_1_CGCTCGATTG-AATACACAGG_L004

description:
Library name: Sample 1
Column name in raw_counts_All Samples.txt: IG_1_1


title: ESC, rep1

source_name: embryonic stem cells

value: embryonic stem cells


title: PBS

description:
Library name: SAMPLE1
BDRhapsody

value: treated with PBS


title: Iris5_6

status: Public on Sep 03 2025

city: Pamplona

first: Esther

last: Larrea

state: Navarra

address: CIMA Avda. Pio XII 55

country: Spain

institute: Institute of Tropical Health of Universidad de Navarra

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to ASM272v2.45 Leishmania major assembly using STAR v2.7.0d.
featureCounts v1.6.0 software and Ensembl Bacteria v55 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: ASM272v2.45
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

organism: Leishmania major

source_name: whole organism

extract_protocol:
Total RNA from transfected Leismania major was extracted using the automated Maxwell system (Promega)
RNA samples were shipped on dry ice to Macrogen Company (Seoul, Korea) where they were processed and sequenced. The sequencing library from mRNA was prepared using TruSeq Stranded mRNA Library Preparation Kit (Illumina) and RNA-seq was carried out using NovaSeq6000 platform following a configuration of paired readings of 100 base pairs.

value: whole organism

value: transfected with pLEXSY-LmjPES BRCT


title: Iris5_4


title: Iris5_5


title: control_6

value: transfected with empty pLEXSY


title: control_5


title: Aspergillus fumigatus AfS77, strain PxylP:hapXA/B/C/D; rep3

city: Innsbruck

first: Hubertus

last: Haas

state: Tyrol

address: Innrain 80/82

department: Institute of Molecular Biology

country: Austria

institute: Medical University of Innsbruck

description: Library name: sample 6

data_processing:
sequence reads were trimmed for adaptor sequences and mapped to the reference genome using STAR (version 2.7.11b)
obtained gene counts were normalized applying DESeq2
differentially expressed genes were filtered using log2 fold change ≤ -1 or ≥ 1 and adjusted p-value < 0.05 as cut-offs
Assembly: Aspergillus fumigatus Af293 ASM265 (NCBI RefSeq assembly: GCF_000002655.1)
Supplementary files format and content: tab-delimited tex files including the raw counts for each sample and the DESeq2 normalized gene counts

organism: Aspergillus fumigatus

source_name: fungal mycelium

extract_protocol:
total RNA was extracted using TRI Reagent (Sigma-Aldrich); RNA samples were DNaseI treated; DNaseI inactivation and removal was done by phenol/chloroform extraction of RNA samples
RNA libraries for RNA-seq were prepared by applying poly(A) enrichment

value: fungal mycelium

value: A. fumigatus wild-type


title: Aspergillus fumigatus AfS77, strain PxylP:hapXA/B/C/D; rep2

description: Library name: sample 5


title: Aspergillus fumigatus AfS77, strain PxylP:hapXA/B/C/D; rep1

description: Library name: sample 4


title: Aspergillus fumigatus AfS77, strain PxylP:hapX; rep3

description: Library name: sample 3


title: BKD_Gi_2202_Ay_F2_2_TCCGATGGAA-GTGTCGGATT_L004

description:
Library name: Sample 4
Column name in raw_counts_All Samples.txt: BKD_Gi_2022_Ay_F2_2

value: Gill

value: CGDndt


title: Aspergillus fumigatus AfS77, strain PxylP:hapX; rep2

description: Library name: sample 2


title: Aspergillus fumigatus AfS77, strain PxylP:hapX; rep1

description: Library name: sample 1


title: ESC, rep2


title: PBS_1

description: Library name: Sample 1

value: bone marrow

value: primary cell

value: bone marrow-derived dendritic cells

value: PBS


title: Tibialis Anterior, Klotho null/null 2

city: Indianapolis

first: Steven

middle: S

last: Welc

state: IN

address: 635 Barnhill Dr Apt Ms-332

department: Anatomy, Cell Biology & Physiology

institute: Indiana University School of Medicine

description:
Library name: KL-hm-3901
KL-hm-3901

data_processing:
QC of the raw sequence data with FASTQC
The sequence reads were mapped to the designated reference genome using STAR (Spliced Transcripts Alignment to a Reference)
To evaluate the quality of the RNA-seq data, the number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes was determined with bamUtils
Low quality mapped reads (including reads mapped to multiple positions) were excluded and featureCounts was used to quantify the gene level expression.
Differential gene expression analysis was performed with edgeR
Assembly: mm10
Supplementary files format and content: .txt files includes

source_name: Tibialis Anterior, male, Klotho null/null 2, 7-weeks-old

growth_protocol: Tibialis anterior muscle tissue was rapidly excised and snap frozen in liquid nitrogen.

extract_protocol:
Trizol and chloroform RNA extraction and cleanup using Qiagen RNeasy Plus kit. 100 ng of RNA was used to construct libraries
illumina total RNAseq

value: Skeletal Muscle

value: Kl knockout


title: Tibialis Anterior, Klotho null/null 4

description:
Library name: KL-hm-4156
KL-hm-4156

source_name: Tibialis Anterior, male, Klotho null/null 4, 7-weeks-old


title: Tibialis Anterior, Klotho null/null 1

description:
Library name: KL-hm-3848
KL-hm-3848

source_name: Tibialis Anterior, male, Klotho null/null 1, 7-weeks-old


title: Tibialis Anterior, Klotho wt/wt 4

description:
Library name: KL-wt-3910
KL-wt-3910

source_name: Tibialis Anterior, male, Klotho wt/wt 4, 7-weeks-old

value: wild-type


title: Tibialis Anterior, Klotho null/null 3

description:
Library name: KL-hm-4140
KL-hm-4140

source_name: Tibialis Anterior, male, Klotho null/null 3, 7-weeks-old


title: Tibialis Anterior, Klotho wt/wt 2

description:
Library name: KL-wt-3737
KL-wt-3737

source_name: Tibialis Anterior, male, Klotho wt/wt 2, 7-weeks-old


title: mESC_parental, ATRA treated, rep3

city: Dublin

first: Adrian

middle: P.

last: Bracken

address: The Smurfit Institute, The University of Dublin Trinity College, College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description:
Library name: A_flfl_r3
ATRA_flfl_r3

data_processing:
RNA-seq reads were pre-processed to remove low quality reads and Illumina sequencing adapters using cutadapt (version 3.2).
The STAR (version 2.7.3a) algorithm was used to align reads to the mouse reference genome mm10.
Read alignments were assigned to gene identifier features annotated in the Ensembl 100 mm10 genome annotation using featureCounts (version 1.6.4). Differentially abundant transcripts were identified using the DESeq2 R package (version 1.38.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: Mouse embryonic stem cells

extract_protocol:
RNA was isolated from cells using the NucleoSpin RNA Kit (Machery-Nagel) as per the manufacturer’s protocol.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first strand of cDNA was synthesised using random hexamers, followed by second strand synthesis using dTTP. cDNA was subject to end repair, A-tailing, adapter ligation before being size selected and amplified for final library generation. Library was assessed by Qubit, Bioanalyser and q-rtPCR for quality control and quantification.

value: Mouse embryonic stem cells

value: parental

value: all-trans retinoic acid (ATRA)


title: mESC_parental, ATRA treated, rep2

description:
Library name: A_flfl_r2
ATRA_flfl_r2


title: Tibialis Anterior, Klotho wt/wt 3

description:
Library name: KL-wt-3738
KL-wt-3738

source_name: Tibialis Anterior, male, Klotho wt/wt 3, 7-weeks-old


title: Tibialis Anterior, Klotho wt/wt 1

description:
Library name: KL-wt-3727
KL-wt-3727

source_name: Tibialis Anterior, male, Klotho wt/wt 1, 7-weeks-old


title: Patient 1 Post-Tx Tumor

source_name: Bladder tumor

value: Bladder tumor

value: Patient 1

value: post-Tx Tumor


title: mESC_EZH2-WT, ATRA treated, rep3

description:
Library name: A_WT_r3
ATRA_WT_r3


title: mESC_EZH2-WT, ATRA treated, rep1

description:
Library name: A_WT_r1
ATRA_WT_r1


title: mESC_EZH2-WT, ATRA treated, rep2

description:
Library name: A_WT_r2
ATRA_WT_r2


title: mESC_EZH2-Y728 mutant, ATRA treated, rep3

description:
Library name: A_Y728_r3
ATRA_Y728_r3

value: EZH2-Y728 mutant


title: control_4

value: whole organism

value: transfected with empty pLEXSY


title: mESC_parental, ATRA treated, rep1

description:
Library name: A_flfl_r1
ATRA_flfl_r1


title: mESC_EZH2-Y728 mutant, ATRA treated, rep1

description:
Library name: A_Y728_r1
ATRA_Y728_r1


title: mESC_EZH2-A677T mutant, ATRA treated, rep3

description:
Library name: A_A677T_r3
ATRA_A677T_r3

value: EZH2-A677T mutant


title: mESC_EZH2-K563E mutant, ATRA treated, rep2

description:
Library name: A_K563E_r2
ATRA_K563mESC_r2

value: EZH2-K563E mutant


title: mESC_EZH2-A677T mutant, ATRA treated, rep2

description:
Library name: A_A677T_r2
ATRA_A677T_r2


title: mESC_EZH2-A677T mutant, ATRA treated, rep1

description:
Library name: A_A677T_r1
ATRA_A677T_r1


title: mESC_EZH2-K563E mutant, ATRA treated, rep3

description:
Library name: A_K563E_r3
ATRA_K563mESC_r3


title: mESC_EZH2-Y728 mutant, ATRA treated, rep2

description:
Library name: A_Y728_r2
ATRA_Y728_r2


title: mESC_EZH2-K563E mutant, ATRA treated, rep1

description:
Library name: A_K563E_r1
ATRA_K563mESC_r1


title: mESC_EZH2-K634E mutant, ATRA treated, rep3

description:
Library name: A_K634E_r3
ATRA_K634mESC_r3

value: EZH2-K634E mutant


title: mESC_EZH2-K634E mutant, ATRA treated, rep2

description:
Library name: A_K634E_r2
ATRA_K634mESC_r2


title: mESC_EZH2-R679C mutant, ATRA treated, rep3

description:
Library name: A_R679C_r3
ATRA_R679C_r3

value: EZH2-R679C mutant


title: RNA-Seq of HEK293 cells treated with BFR at 0 min, replicate 1

city: Baltimore

first: George

middle: Henry

last: Sack

state: Maryland

address: 725 N. Wolfe Street

department: Department of Physiology, Pharmacology and Therapeutics

institute: Johns Hopkins University School of Medicine

description: Library name: BFR_Sample_22_lib1

data_processing:
Reads were initially quality checked using Fastqc (0.11.9).
Reads were aligned to the hg38 human reference genome using STAR aligner (2.7.10a).
Counts were extracted using htseq (2.0.5).
Differential RNA expression analysis was performed on R (4.4.0) using Deseq2 (1.44.0).
The adjusted p-value was calculated with Benjamini Hochberg False Discover Rate Correction (FDR).
Assembly: hg-38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Kidney

growth_protocol: Seeded at 1.7 X 10^4 cells per well and grown to confluent monolayers on poly-D-lysine coated 24-well plates using MEM-10 with penicillin and streptomycin.

extract_protocol:
RNA was isolated from cells using the PureLink® RNA MiniKit. Cells were washed with 0.5 ml of PBS, lysed in 300 µl of "Lysis Buffer," and transferred to a fresh tube. 300 µl of 70% ethanol was added, and tubes were placed at -20°C overnight. The protocol was continued, and the final sample volume was 50 µl. Samples were then frozen at -20°C.
Libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit with a 100 ng total RNA input amount. RNA quality was assessed with a Nanodrop and an Agilent Fragment Analyzer. Library concentrations were measured with a Qubit, and quality was checked with an Agilent Fragment Analyzer. Libraries were normalized to 5 nM, pooled, and a further dilution was made to 4 nM for sequencing.

treatment_protocol: N-terminal decapeptide studies: Treated with 70 µl of decapeptide 1 solution (62 pmole) or BSA alone. Full-length SAA studies: Treated with 50 µl of full-length SAA protein solution (4.3 mµmole) or HOH + 0.05% BSA (control). Incubation continued at 37°C for various times.

value: Kidney

value: BFR


title: RNA-Seq of HEK293 cells treated with BFR at 0 min, replicate 2

description: Library name: BFR_Sample_23_lib2


title: RNA-Seq of HEK293 cells treated with BFR at 0 min, replicate 3

description: Library name: BFR_Sample_24_lib3


title: mESC_parental_EZH2-heterozygote, ATRA treated, rep3

description:
Library name: A_het_r3
ATRA_het_r3


title: mESC_EZH2-R679C mutant, ATRA treated, rep2

description:
Library name: A_R679C_r2
ATRA_R679C_r2


title: RNA-Seq of HEK293 cells treated with SAA at 0 min, replicate 3

description: Library name: SAA_Sample_21_lib3

value: SAA


title: RNA-Seq of HEK293 cells treated with SAA at 0 min, replicate 2

description: Library name: SAA_Sample_20_lib2


title: mESC_EZH2-A733T mutant, ATRA treated, rep3

description:
Library name: A_A733T_r3
ATRA_A733T_r3

value: EZH2-A733T mutant


title: mESC_parental_EZH2-heterozygote, ATRA treated, rep1

description:
Library name: A_het_r1
ATRA_het_r1

value: Mouse embryonic stem cells


title: mESC_parental_EZH2-heterozygote, ATRA treated, rep2

description:
Library name: A_het_r2
ATRA_het_r2


title: RNA-Seq of HEK293 cells treated with BFR at 30 min, replicate 3

description: Library name: BFR_Sample_18_lib3


title: RNA-Seq of HEK293 cells treated with SAA at 0 min, replicate 1

description: Library name: SAA_Sample_19_lib1


title: RNA-Seq of HEK293 cells treated with BFR at 30 min, replicate 2

description: Library name: BFR_Sample_17_lib2


title: mESC_EZH2-A733T mutant, ATRA treated, rep2

description:
Library name: A_A733T_r2
ATRA_A733T_r2


title: mESC_EZH2-A733T mutant, ATRA treated, rep1

description:
Library name: A_A733T_r1
ATRA_A733T_r1


title: RNA-Seq of HEK293 cells treated with BFR at 30 min, replicate 1

description: Library name: BFR_Sample_16_lib1


title: mESC_parental,  rep2

description:
Library name: E_flfl_r2
mESC_flfl_r2

value: parental


title: mESC_EZH2-K634E mutant, ATRA treated, rep1

description:
Library name: A_K634E_r1
ATRA_K634mESC_r1

value: all-trans retinoic acid (ATRA)


title: RNA-Seq of HEK293 cells treated with SAA at 30 min, replicate 1

description: Library name: SAA_Sample_13_lib1


title: mESC_EZH2-WT,  rep3

description:
Library name: E_WT_r3
mESC_WT_r3


title: mESC_parental,  rep1

description:
Library name: E_flfl_r1
mESC_flfl_r1


title: mESC_EZH2-WT,  rep2

description:
Library name: E_WT_r2
mESC_WT_r2


title: RNA-Seq of HEK293 cells treated with BFR at 60 min, replicate 3

description: Library name: BFR_Sample_12_lib3


title: mESC_EZH2-R679C mutant, ATRA treated, rep1

description:
Library name: A_R679C_r1
ATRA_R679C_r1


title: RNA-Seq of HEK293 cells treated with SAA at 30 min, replicate 3

description: Library name: SAA_Sample_15_lib3


title: RNA-Seq of HEK293 cells treated with BFR at 60 min, replicate 2

description: Library name: BFR_Sample_11_lib2


title: RNA-Seq of HEK293 cells treated with SAA at 30 min, replicate 2

description: Library name: SAA_Sample_14_lib2


title: RNA-Seq of HEK293 cells treated with SAA at 60 min, replicate 3

description: Library name: SAA_Sample_9_lib3


title: mESC_EZH2-Y728 mutant,  rep2

description:
Library name: E_Y728_r2
mESC_Y728_r2


title: RNA-Seq of HEK293 cells treated with SAA at 60 min, replicate 2

description: Library name: SAA_Sample_8_lib2


title: RNA-Seq of HEK293 cells treated with SAA at 60 min, replicate 1

description: Library name: SAA_Sample_7_lib1


title: mESC_EZH2-Y728 mutant,  rep1

description:
Library name: E_Y728_r1
mESC_Y728_r1


title: mESC_EZH2-Y728 mutant,  rep3

description:
Library name: E_Y728_r3
mESC_Y728_r3


title: RNA-Seq of HEK293 cells treated with BFR at 120 min, replicate 3

description: Library name: BFR_Sample_6_lib3


title: Tumor_NStat3_KO_03

city: Münster

first: Carlos

last: Silvestre Roig

address: Von Esmarch Str. 56

country: Germany

institute: University of Münster

description: Library name: Sample 6

data_processing:
Raw FASTQ files were trimmed to 2×75 bp using seqtk and quantified using salmon (v1.6.0) against a GENCODE vM23 genome-decoyed transcriptome index with --validateMappings, --gcBias, and --posBias options enabled. Quantification was performed using a standardized pipeline (atpoint/rnaseq_preprocess), with sample metadata compiled into a samplesheet.csv. Transcript-level abundances were summarized to gene level using tximport with the lengthScaledTPM method, enabling compatibility with downstream count-based differential expression analysis. Command lines and software versions are available in the pipeline_info directory. The resulting count table was imported into R (version 4.2.3) for downstream analysis.
Assembly: Mus musculus GRCm38 (mm10; GENCODE release M23)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Tumor

extract_protocol:
Total RNA were extracted by using RNeasy Micro Kit (50) (Qiagen, 74004). TANs were FACS sorted into 350 µL Buffer RLT and vortexed properly to lyse cells. 350 µL of 70% ethanol added to the lysate, and mixed well by pipetting. The sample transferred to RNeasy MinElute spin columns in a 2 ml collection tubes and centrifuged for 15 s at 8000 x g. The flow-through were discarded. 350 µl Buffer RW1 added to the RNeasy MinElute spin columns and centrifuged  for 15 s at 8000 x g. The flow-through were discarded. 10 µl DNase I stock solution added to 70 µl Buffer RDD. The DNase I incubation mix (80 µl) directly added to the RNeasy MinElute spin column membrane and incubated for 15 min RT. 350 µl Buffer RW1 was added to the RNeasy MinElute spin column and centrifuged for 15 s at 8000 x g. The collection tubes were discarded. The RNeasy MinElute spin columns were placed in new 2 ml collection tubes. 500 µl Buffer RPE were added to the spin columns and centrifuged for 15 s at 8000 x g. The flow-through were discarded. 500 µl of 80% ethanol were added to the RNeasy MinElute spin columns and centrifuged for 2 min at 8000 x g. The collection tubes were discarded. The RNeasy MinElute spin columns were placed in new 2 ml collection tubes. The spin columns were centrifuged at full speed for 5 min with open lid to dry the membrane. The flow-through and collection tubes were discarded. The RNeasy MinElute spin columns were placed in new 1.5 ml collection tubes. 20 µl RNase-free water were directly added to the center of the spin column membrane and centrifuged for 1 min at full speed to elute the RNA. RNA extracts were kept at -80°C until processed further with bulkseq
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s protocol.

value: Tumor

value: Neutrophil


title: mESC_parental,  rep3

description:
Library name: E_flfl_r3
mESC_flfl_r3


title: RNA-Seq of HEK293 cells treated with BFR at 120 min, replicate 2

description: Library name: BFR_Sample_5_lib2


title: mESC_EZH2-A677T mutant,  rep3

description:
Library name: E_A677T_r3
mESC_A677T_r3


title: Tumor_NStat3_KO_02

description: Library name: Sample 5


title: RNA-Seq of HEK293 cells treated with BFR at 120 min, replicate 1

description: Library name: BFR_Sample_4_lib1


title: RNA-Seq of HEK293 cells treated with SAA at 120 min, replicate 3

description: Library name: SAA_Sample_3_lib3


title: mESC_EZH2-A677T mutant,  rep2

description:
Library name: E_A677T_r2
mESC_A677T_r2


title: Tumor_NStat3_KO_01

description: Library name: Sample 4


title: mESC_EZH2-WT,  rep1

description:
Library name: E_WT_r1
mESC_WT_r1


title: RNA-Seq of HEK293 cells treated with SAA at 120 min, replicate 1

description: Library name: SAA_Sample_1_lib1


title: mESC_EZH2-K563E mutant,  rep3

description:
Library name: E_K563E_r3
mESC_K563E_r3


title: mESC_EZH2-K563E mutant,  rep2

description:
Library name: E_K563E_r2
mESC_K563E_r2


title: mESC_EZH2-K563E mutant,  rep1

description:
Library name: E_K563E_r1
mESC_K563E_r1


title: Patient_20_miRNA

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: Small RNA-sequencing

data_processing:
The CLC Genomics Workbench version 9.5.3 program (Qiagen) was used for data analysis.
Adaptor sequences were trimmed and sequences between 15 and 35 bps were counted.
The trimmed data were mapped to the miRbase 21 database, allowing up to two mismatches.
The data was normalized with reads per million mapped reads.
Assembly: miRbase 21
Supplementary files format and content: tab-delimited text file includes RPM values for each sample

source_name: ovarian cancer

extract_protocol:
Total RNA was extracted from fresh-frozen samples using an miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries was prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA)

value: ovarian cancer

tag: age

tag: Stage

tag: neoajuvant chemotherapy

value: Yes

value: PR

tag: surgical outcome

value: complete

tag: 1st tfip


title: mESC_EZH2-K634E mutant,  rep3

description:
Library name: E_K634E_r3
mESC_K634E_r3

tag: cell type

tag: genotype


title: Patient_19_miRNA

description: Small RNA-sequencing

tag: tissue

value: No

value: Optimal


title: mESC_EZH2-K634E mutant,  rep2

description:
Library name: E_K634E_r2
mESC_K634E_r2

value: EZH2-K634E mutant


title: mESC_EZH2-K634E mutant,  rep1

description:
Library name: E_K634E_r1
mESC_K634E_r1


title: Umbilical cord blood CD34+, JARID2, WT, C&R, CB_2

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description: Library name: C_R_JARID2_CB_2

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.
Library strategy: CUT&Run

source_name: Enriched hCD34+ from umbilical cord blood

growth_protocol: Enriched human cord blood CD34+ cells were cultured in SFEM II medium (StemCell Technologies, #09605) supplemented with Penicillin-Streptomycin (50 U/mL), human SCF (100 ng/mL), human TPO (100 ng/mL), and human FLT3L (100 ng/mL). Media were refreshed every other day.

extract_protocol:
All cell sorting was performed using a BD Aria Ilu SORP cell sorter. For scRNA-seq, 10,000 sorted CD34⁺ cells were used to prepare gene expression (GEX) libraries according to the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3 User Guide. For CITE-seq, 10,000 sorted CD34⁺ cells were processed to generate GEX libraries using the 10x Chromium Single Cell 3' Reagent Kits User Guide, v3.1 Chemistry Dual Index, with Feature Barcoding Technology for Cell Surface Protein, User Guide CG000317. For RNA sequencing, approximately 5,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells were sorted, followed by RNA isolation using the NucleoSpin RNA XS kit (Macherey-Nagel #740902.250) and library preparation with the SMARTer Ultra Low RNA Kit (Clontech), according to the manufacturer's instructions. For CUT&Tag, 10,000–20,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells or enriched human cord blood CD34⁺ cells were sorted and processed following the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff's lab (DOI: dx.doi.org/10.17504/protocols.io.bcuhiwt6). For CUT&RUN, libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher #14-1001).
scRNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 (PN-1000075), following the manufacturer's user guide. CITE-seq libraries were constructed using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index Chemistry) along with Feature Barcoding Technology for Cell Surface Protein, according to the Feature Barcoding User Guide (CG000317). Bulk RNA-seq libraries were generated using the SMARTer Ultra Low RNA Kit (Clontech), following the manufacturer's instructions. CUT&Tag libraries were prepared using the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff’s laboratory (DOI: 10.17504/protocols.io.bcuhiwt6). CUT&RUN libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher, #14-1001), according to the manufacturer’s protocols.

treatment_protocol: We used an optimized microRNA lentiviral backbone to carry our shRNAs, as recommended by Fellmann et al. (2013). Lentiviral particles were produced by co-transfecting 293T cells with the packaging plasmids pMD.G, psPAX2, and pSFFV-eGFP-miR-E, in which the miR-E cassette was engineered to target Renilla, JARID2, EZH2, or STAT1. All plasmids were mixed at a 1:1:1 molar ratio. Enriched human cord blood CD34+ cells were transduced with constitutive lentiviral vectors carrying shRNAs, using LentiBOOST (1:100, SIRION Biotech, Cat No. SB-P-LV-101-12) and protamine sulfate (1:1000) to enhance transduction efficiency, as described by Schott et al. (2019).

value: Umbilical cord blood CD34+

value: WT


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K4me3, shRen, C&T, rep_4

description: Library name: C_T_H3K4me3_shRen_rep_4

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.
Library strategy: CUT&Tag

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shREN, Day8 ex vivo culture

value: Lentivirus


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, IgG, C&T, rep_4

description: Library name: C_T_IgG_shJARID2_rep_4

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shJARID2, Day8 ex vivo culture

value: shRNAs


title: Umbilical cord blood CD34+, JARID2, WT, C&R, CB_1

description: Library name: C_R_JARID2_CB_1


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K4me3, shEZH2, C&T, rep_2

description: Library name: C_T_H3K4me3_shEZH2_rep_2

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shEZH2, Day8 ex vivo culture


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, IgG, C&T, rep_3

description: Library name: C_T_IgG_rep_3

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, pooled shRNAs, Day8 ex vivo culture


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K4me3, shJARID2, C&T, rep_2

description: Library name: C_T_H3K4me3_shJARID2_rep_2


title: RNA-Seq of HEK293 cells treated with SAA at 120 min, replicate 2

description: Library name: SAA_Sample_2_lib2

value: Kidney

tag: cell line

value: SAA


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, IgG, C&T, rep_1

description: Library name: C_T_IgG_rep_1


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, IgG, C&T, rep_2

description: Library name: C_T_IgG_rep_2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K4me3, shRen, C&T, rep_2

description: Library name: C_T_H3K4me3_shRen_rep_2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K4me3, shEZH2, C&T, rep_4

description: Library name: C_T_H3K4me3_shEZH2_rep_4


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K4me3, shJARID2, C&T, rep_4

description: Library name: C_T_H3K4me3_shJARID2_rep_4


title: Patient_18_miRNA

description: Small RNA-sequencing

value: Complete


title: mESC_EZH2-A677T mutant,  rep1

description:
Library name: E_A677T_r1
mESC_A677T_r1

value: Mouse embryonic stem cells

value: EZH2-A677T mutant


title: Umbilical cord blood CD34+, H3K4me3, WT, C&T, CB_2

description: Library name: C_T_H3K4me3_CB_2


title: Patient_17_miRNA

description: Small RNA-sequencing


title: Tumor_WT_02

description: Library name: Sample 2

value: Tumor

value: Neutrophil


title: Tumor_WT_03

description: Library name: Sample 3


title: mESC_EZH2-R679C mutant,  rep3

description:
Library name: E_R679C_r3
mESC_R679C_r3

value: EZH2-R679C mutant


title: Tumor_WT_01

description: Library name: Sample 1


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shRen, C&T, rep_4

description: Library name: C_T_H3K27me3_shRen_rep_4


title: Umbilical cord blood CD34+, H3K4me3, WT, C&T, CB_1

description: Library name: C_T_H3K4me3_CB_1


title: Patient_16_miRNA

description: Small RNA-sequencing

value: ovarian cancer

value: Suboptimal


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shRen, C&T, rep_3

description: Library name: C_T_H3K27me3_shRen_rep_3


title: mESC_EZH2-R679C mutant,  rep2

description:
Library name: E_R679C_r2
mESC_R679C_r2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shRen, C&T, rep_2

description: Library name: C_T_H3K27me3_shRen_rep_2


title: Patient_15_miRNA

description: Small RNA-sequencing

value: No


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shJARID2, C&T, rep_4

description: Library name: C_T_H3K27me3_shJARID2_rep_4


title: mESC_EZH2-R679C mutant,  rep1

description:
Library name: E_R679C_r1
mESC_R679C_r1


title: mESC_parental_EZH2-heterozygote,  rep3

description:
Library name: E_het_r3
mESC_het_r3


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shJARID2, C&T, rep_2

description: Library name: C_T_H3K27me3_shJARID2_rep_2


title: Patient_11_miRNA

description: Small RNA-sequencing


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shEZH2, C&T, rep_4

description: Library name: C_T_H3K27me3_shEZH2_rep_4


title: Patient_13_miRNA

description: Small RNA-sequencing

value: Optimal


title: Umbilical cord blood CD34+, H3K27me3, WT, C&T, CB_1

description: Library name: C_T_H3K27me3_CB_1


title: mESC_parental_EZH2-heterozygote,  rep1

description:
Library name: E_het_r1
mESC_het_r1


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shEZH2, C&T, rep_2

description: Library name: C_T_H3K27me3_shEZH2_rep_2


title: mESC_parental_EZH2-heterozygote,  rep2

description:
Library name: E_het_r2
mESC_het_r2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shRen, C&T, rep_2

description: Library name: C_T_H2AK119ub1_shRen_rep_2


title: Patient_10_miRNA

description: Small RNA-sequencing

value: Yes

value: PR


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shEZH2, C&T, rep_3

description: Library name: C_T_H3K27me3_shEZH2_rep_3


title: mESC_EZH2-A733T mutant,  rep3

description:
Library name: E_A733T_r3
mESC_A733T_r3

value: EZH2-A733T mutant


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H3K27me3, shJARID2, C&T, rep_3

description: Library name: C_T_H3K27me3_shJARID2_rep_3

value: Lentivirus


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shRen, C&T, rep_3

description: Library name: C_T_H2AK119ub1_shRen_rep_3


title: Patient_12_miRNA

description: Small RNA-sequencing


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shJARID2, C&T, rep_3

description: Library name: C_T_H2AK119ub1_shJARID2_rep_3


title: Patient_9_miRNA

description: Small RNA-sequencing


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shRen, C&T, rep_1

description: Library name: C_T_H2AK119ub1_shRen_rep_1


title: mESC_EZH2-A733T mutant,  rep2

description:
Library name: E_A733T_r2
mESC_A733T_r2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shJARID2, C&T, rep_2

description: Library name: C_T_H2AK119ub1_shJARID2_rep_2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shJARID2, C&T, rep_1

description: Library name: C_T_H2AK119ub1_shJARID2_rep_1


title: Patient_14_miRNA

description: Small RNA-sequencing

value: CR


title: Umbilical cord blood CD34+, H3K27me3, WT, C&T, CB_2

description: Library name: C_T_H3K27me3_CB_2

value: Umbilical cord blood CD34+

value: WT


title: Patient_7_miRNA

description: Small RNA-sequencing


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shEZH2, C&T, rep_2

description: Library name: C_T_H2AK119ub1_shEZH2_rep_2


title: J3568_m

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description: Library name: J3568_m

data_processing:
Brain and muscle mRNA data were aligned with Rsubread (v 2.16.1), annotated with the org.Mm.eg.db package (v 3.19.1) and analyzed with edgeR (v 4.0.16). Gene ontology (GO) terms were generated in DAVID with a p-value cut-off of <0.05 followed by a fold-change cut-off of >0.5.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing normalized reads

source_name: Muscle

growth_protocol: Animal studies were approved by the University of Pittsburgh Institutional Animal Care and Use Committee governed by regulatory standards from the Guide for the Care and Use of Laboratory Animals and the United States Department of Health and Human Services. Wild-type (WT) and KLOTHO HET (KlHET) mice were internally bred for this experiment and randomly assigned to either the control group or NMES treatment group. Mice were housed in a 75°C, 12:12 h light-dark cycled room with unrestricted access to standard food and water.

extract_protocol:
Brain: 30 mg brain sections were subjected to RLT buffer from RNeasy Mini Kit (Qiagen 74106) with 10% beta-mercaptoethanol added and passed through a 25G needle. Homogenate was transferred to QIAshredder (Qiagen 79656) for further dissociation. The remaining manufacturers protocol was followed to complete the RNA isolation. Quality and concentration were analyzed via RNA Nano 600 kit for Agilent 2100 Bioanalyzer (5067-1511). Muscle: 50 mg muscle sections were powdered by the addition of N2 and manually dissociated via mortar and pestle. QIAzol (Qiagen 5,346,994) was added to the powdered muscle and passed through a 25G needle. Homogenate was added to QIAshredder and the RNeasy Mini Kit protocol was followed for the duration of RNA isolation. Quality and concentration were analyzed via RNA Nano 600 kit for Agilent 2100 Bioanalyzer (5067-1511).
Brain and Muscle: Extracted RNA was sent to Novogene Co. located in Sacramento CA, for generation of total RNA libraries and sequencing on NovaSeq X Plus Series (PE150) machine. Data was received in .fq.gz formatting.

treatment_protocol: Electrical stimulation was performed with a Neuromuscular Stimulator (Empi 300 PV, Boston, USA) at 9 mA under 2.5% isoflurane anesthesia. Mice were shaved on both right and left hind legs along the sciatic nerve and exposed skin was coated in O.C.T. compound to ensure proper probe placement and to prevent dermal burns. The double-pronged pen attachment was placed at piriformis, causing leg extension. NMES was delivered in sets of 10 consecutive stimulations per side, oscillating between each leg after each set, for a total of 2 sets on each leg. NMES mice received treatment every other day for a total of 5 treatment sessions. Perfusions and sample collection occurred 24 hours after the final treatment session. Control mice received 15 minutes of 2.5% isoflurane anesthesia exposure each day the NMES treatment group received stimulation.

value: Muscle

value: KLOTHO HET

value: NMES


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shEZH2, C&T, rep_1

description: Library name: C_T_H2AK119ub1_shEZH2_rep_1


title: Umbilical cord blood CD34+, H2AK119ub1, WT, C&T, CB_2

description: Library name: C_T_H2AK119ub1_CB_2


title: Patient_6_miRNA

description: Small RNA-sequencing

value: Complete


title: Umbilical cord blood CD34+, EZH2, WT, C&R, CB_2

description: Library name: C_R_EZH2_CB_2


title: Umbilical cord blood CD34+, H2AK119ub1, WT, C&T, CB_1

description: Library name: C_T_H2AK119ub1_CB_1


title: J3554_m

description: Library name: J3554_m


title: Patient_5_miRNA

description: Small RNA-sequencing


title: Patient_4_miRNA

description: Small RNA-sequencing


title: Umbilical cord blood CD34+, EZH2, WT, C&R, CB_1

description: Library name: C_R_EZH2_CB_1


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, CTCF, shRen, C&T, rep_2

description: Library name: C_T_CTCF_shRen_rep_2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, CTCF, shRen, C&T, rep_4

description: Library name: C_T_CTCF_shRen_rep_4


title: Patient_3_miRNA

description: Small RNA-sequencing


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, CTCF, shJARID2, C&T, rep_4

description: Library name: C_T_CTCF_shJARID2_rep_4


title: J3531_m

description: Library name: J3531_m


title: Patient_8_miRNA

description: Small RNA-sequencing


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, CTCF, shJARID2, C&T, rep_2

description: Library name: C_T_CTCF_shJARID2_rep_2


title: mESC_EZH2-A733T mutant,  rep1

description:
Library name: E_A733T_r1
mESC_A733T_r1

value: Mouse embryonic stem cells


title: J3527_m

description: Library name: J3527_m


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, CTCF, shEZH2, C&T, rep_4

description: Library name: C_T_CTCF_shEZH2_rep_4


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, CTCF, shEZH2, C&T, rep_2

description: Library name: C_T_CTCF_shEZH2_rep_2


title: GFP+CD34+CD90+EPCR+CD49f-CD71-, H2AK119ub1, shEZH2, C&T, rep_3

description: Library name: C_T_H2AK119ub1_shEZH2_rep_3


title: Patient_2_miRNA

description: Small RNA-sequencing


title: J3514_m

description: Library name: J3514_m


title: Umbilical cord blood CD34+, CTCF, WT, C&R, CB_2

description: Library name: C_R_CTCF_CB_2


title: Patient_1_miRNA

description: Small RNA-sequencing


title: J3570_m

description: Library name: J3570_m


title: J3537_m

description: Library name: J3537_m


title: Umbilical cord blood CD34+, CTCF, WT, C&R, CB_1

description: Library name: C_R_CTCF_CB_1


title: Umbilical cord blood CD34+, IgG, WT, C&T, CB_2

description: Library name: C_T_IgG_CB_2


title: J3562_m

description: Library name: J3562_m