title: NT2.5-LM_WES

first: Aaron

last: Baugh

address: 1441 Eastlake Ave

institute: University of Southern California

data_processing:
bcl2fastq v2.15.0 (Illumina) was used to convert BCL files to FASTQ files using default parameters. Running alignments against the mm10 genome was done by bwa v0.7.7 (mem) along with Piccard-tools1.119 to add read groups and remove duplicate reads. GATK v3.6.0 base call recalibration steps were used to create a final alignment file. MuTect2 v3.6.0 was used to call somatic variants against a panel of normal using default parameters. snpEFF (v4.1) was used to annotate the variant calls and to create a clean tab separated table of variants. IGV v2.13.2 was used to identify breast cancer specific mutations from MuTect2 files. SnapGene Viewer v.6.2 was used to visually align and determine the mutations between the two cell lines against the mRNA sequences of selected genes. Annotations were created to visualize mutational differences.
Assembly: mm10
Supplementary files format and content: annotated passed somatic SNPs and indels in .vcf format
Library strategy: Whole exome-seq

extract_protocol:
Genomic DNA from NT2.5 and NT2.5-LM cell lines were collected using Qiagen kits.
One microgram or more of mouse genomic DNA from each sample was analyzed by whole exome sequencing using the SureSelectXT Mouse All Exon kit (Agilent)

value: breast cancer cell line


title: A375 cells - OTX015 - N1

status: Public on Jun 30 2024

type: SRA

city: MONTREAL

first: Antoine

last: MEANT

state: QC

address: 3755 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

library_source: transcriptomic

data_processing:
The overall quality of sequencing was assessed before and after trimming with the FastQC package (Babraham Bioinformatics).
Before mapping, reads were trimmed with Trimmomatic (Bolger et al., 2014), with the following parameters: ILLUMINACLIP:$Adapters:2:30:10:8:true, HEADCROP:4, SLIDINGWINDOW:4:30, LEADING:3, TRAILING:3, MINLEN:30.
Sequence alignment was performed with STAR 2.5.4b and compared with hg19 human reference genome using default parameters (Dobin et al., 2013) and converted into bam format using Samtools 1.9 (Li et al., 2009).
Differential expression analysis was generated using the featureCounts matrix (Liao et al., 2014).
Comparison across samples was performed with DESeq2 analysis using default parameters (Love et al., 2014).
Assembly: hg19 human reference genome
Supplementary files format and content: tab-delimited text file containing raw counts for each samples

molecule: polyA RNA

organism: Homo sapiens

source_name: melanoma cell line

growth_protocol: A375 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Wisent Inc.) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted using GenElute™ Total RNA Purification Kit (Sigma) as described by the manufacturer.
Extracted RNA was sent to The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) for stranded poly(A) mRNA library preparation (NEBNext) and sequencing using the Illumina NovaSeq S4 flow cell (150 bp paired ends reads; 2/2.5 billion reads total).

treatment_protocol: A375 cells treated for 72 hrs - [SEL201] = 2.5 μM; [OTX015] =  50nM.

tag: tissue

value: melanoma cell line

tag: cell line

tag: cell type

value: BRAF-V600E melanoma

tag: treatment


title: Week 1 control 5

city: Singapore

first: Zun Siong

last: Low

address: 11 Mandalay Rd

country: Singapore

institute: Lee Kong Chian School of Medicine

data_processing:
Alignment done by HISAT2
Raw counts using featurecounts
DEGs determined using DESeq2 with cutoff of log2fc > ±1
Genome_build: grcm38
Supplementary_files_format_and_content: FPM

molecule: total RNA

organism: Mus musculus

source_name: Mice from age of 8 weeks

extract_protocol:
TRIzol RNA extraction followed by E.Z.N.A.® HP Total RNA for purification, according to manufacturer’s protocol
Illumina library preparation done by NovogeneAIT

treatment_protocol: Mice from age of 8 weeks were fed either control or LIDPAD

tag: strain

value: Liver

tag: diet

value: Control

tag: diet duration (weeks)


title: MSCs from MCB, passage 3, donor 205, sequenced by MACE

city: Bogota

first: Cristian

middle: Camilo

last: Galindo

state: Bogota DC

address: Cra. 32 #12 - 81 Puente Aranda

country: Colombia

institute: Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud IDCBIS

description:
I5
all_counts_merged_MACE.txt

data_processing:
Sequencing data from both RNA-seq and MACE-Seq were uploaded and analyzed on the GenXPro bioinformatics tools platform (https://tools.genxpro.net/).
Sequencing reads were adapter-trimmed, quality-trimmed, and cleaned from library-preparation artifacts using cutadapt (version 3.2).
Expression quantification was done using HTSeq (version 1.99.2) for MACE-Seq data and STAR for RNA-Seq data. QC was done using FASTQC (version 0.11.9), Samtools (version 1.12) and MultiQC (version 1.12).
Normalization and test for differential expression was performed in the statistical programming language R (www.rproject.org) with the DEseq2 package (version 1.34.0).
Assembly: Processed reads were mapped and annotated to the reference human genome GRCh38.p12 from ENSEMBL (version 102) using bowtie2 (version 2.4.3) for MACE-Seq data and using STAR (version 2.7.9a) for RNA-Seq data
Supplementary files format and content: Expression levels are given in transcripts per million (TPM)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Library strategy: MACE-seq

source_name: Wharton's jelly from umbilical cord

growth_protocol: Wharton's jelly mesenchymal stromal cells were cultured in DMEM with low glucose an 10% human platelet lysate in a humidified atmosphere with CO2 at 37 °C

extract_protocol:
Cells were used and treated with the PureLink RNA Mini Kit (Thermo Fisher). The RNA concentration was measured with nanodrop (Thermo Fisher). Each sample was split into two tubes (25 ul each) and concentration varied between 50 and 2,760 ng/ml.
Conventional RNA-Seq libraries were prepared by Genwiz from Azenta Life Sciences an MACE-seq libraries were prepared by GenXPro GmbH MACE-Kit V2
RNA-seq
Massive Analysis of cDNA Ends (MACE-Seq)-RNA sequencing

treatment_protocol: Upon passage 1, cells were seeded at low (3000 - 4600 cells/cm2) or high denisity (4600 cm2) and expanded until reaching adequate number for cryopreservation

tag: passage

tag: donor

value: donor 205

value: Wharton's jelly from umbilical cord

value: Primary cells

value: Mesenchymal stromal cells

tag: genotype

value: WT

value: High seeding density


title: HIV+PSU_4

city: Omaha

first: Pendyala

last: Gurudutt

state: NE

address: University of Nebraska Medical Center

country: USA

institute: University of Nebraska Medical Center

data_processing:
The original fastq format reads were trimmed by fqtirm tool  to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30). The trimmed fastq files were processed by FastQC
Rat mRatBN7.2 (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_015227675.2/) and HIV-1 GCF_000864765.1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000864765.1) reference genome and annotation files were downloaded from NCBI RefSeq
The downloaded rat and HIV-1 ref genome and annotation files were combined, respectively, as one rat_HIV-1 ref genome file and one rat_HIV-1 annotation file
The trimmed fastq files were mapped to rat_HIV-1 by CLC Genomics Workbench 22
Assembly: Rattus norvegicus (mRatBN7.2) and and HIV-1 (GCF_000864765.1)
Supplementary files format and content: tab-delimited text files include Expression value, TPM, RPKM values for each Sample

organism: Rattus norvegicus

source_name: brain

extract_protocol: RNA was extracted from rat striatum using Direct-Zol RNA kit (Zymo Research, Irvine, CA). An approximate of 2mg was used for library reconstruction

value: brain

value: HIV-Tg (HIV-transgenic)

value: METH+oxy

tag: condition


title: HIV+PSU_3


title: NT_2cell, WDR5-0103, replicate 3

city: Shanghai

first: Xiaolei

last: Zhang

address: N0.1239 of Siping Road, Shanghai, China

country: China

institute: Tongji University

data_processing:
Sequence reads were trimmed from 3' end until the final base had a quality score > 20, using Trim_galore, discarding reads left with < 20 bp.
Sequence reads were aligned to the UCSC mm10 genome using HISAT2. Only reads uniquely mapped to genome were retained.
Read count extraction and normalization were performed using SringTie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: Mouse embryo

extract_protocol:
Mouse SCNT embryos were lysed using lysis buffer, followed by reverse transcripted to cDNA.
RNA libraries were prepared using the KAPA HyperPrep Kit. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: Mouse embryo

tag: developmental stage

value: 2 cell embryo


title: NT2.5-LM_V4

city: Los Angeles

description: Illumina HiSeqX Ten or NovaSeq

library_source: transcriptomic single cell

data_processing:
For gene filtering, all genes expressed in less than 3 cells within a tumor (NT2.5 and NT2.5-LM) were removed. Cells expressing less than 200 genes or more than 8,000 genes or having more than 15% mitochondrial gene expression were also removed. Gene expression was total-count normalized to 10,000 reads per cell and log transformed. Highly variable genes were identified using default ScanPy parameters, and the total counts per cell and the percent mitochondrial genes expressed were regressed out. Finally, gene expression was scaled to unit variance and values exceeding 10 standard deviations were removed. Neighborhood graphs were constructed using 10 nearest neighbors and 30 principal components. Tumors were clustered together within cell lines using Louvain clustering (with resolution parameter 0.09) and cancer cells were identified as Lcn+, Wfd2c+, Cd24a+, Cd276+, Col9a1+, Erbb2+.[18], [19], [20], [21], [22], [23] All other cell clusters were removed. There were ~15,000 NT2.5 cancer cells and ~13,000 NT2.5-LM cancer cells. The 250 top differentially expressed genes in the cancer clusters from each cell line were identified using the Wilcoxon rank-sum test and compared for overlap with pathways from the ‘KEGG_2019_Mouse’ database using GSEAPY (Gene Set Enrichment Analysis in Python).
Assembly: mm10
Supplementary files format and content: filtered features, barcodes, and matrix files for each sample

source_name: breast tumor

extract_protocol:
RNA was extracted from single-cell suspensions of tumor tissues using tumor dissociation kits (Miltenyi) and RNA extraction kits (Qiagen), following manufacturer's instructions
For library preparation, 10x Genomics Chromium Single Cell 3′ RNA-seq kits v3 were used. Gene expression libraries were prepared per the manufacturer’s instructions.

value: breast tumor


title: A375 cells - UNTREATED - N3

value: DMSO


title: HIV_3

value: Saline

value: HIV-transgenic/saline treatment


title: MSCs from MCB, passage 3, donor 199, sequenced by MACE

description:
I1
all_counts_merged_MACE.txt

value: donor 199


title: A375 cells - SEL201 - N3

value: melanoma cell line

value: BRAF-V600E melanoma


title: HIV+PSU_2


title: Week 1 control 2

value: Liver

value: Control


title: NT_4cell, WDR5-0103, replicate 2

value: 4 cell embryo


title: A375 cells - SEL201 - N2


title: MSCs from MCB, passage 3, donor 197, sequenced by MACE

description:
G9
all_counts_merged_MACE.txt

value: donor 197

value: Wharton's jelly from umbilical cord

value: Primary cells

value: Mesenchymal stromal cells

value: WT


title: HIV+PSU_1

value: brain

value: HIV-Tg (HIV-transgenic)

value: METH+oxy


title: Second_kidney_xeno_recipient_PBMC_scRNA-seq_53h

city: New York

first: Weimin

state: NY

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

description: subject 2, 53h

data_processing:
Raw single-cell sequencing data were processed with the CellRanger pipeline of 10X Genomics to generate single-cell raw gene expression matrices. Kidney single-cell sequencing data were separately mapped to both human genome (GRCh38) and porcine genome (Sscrofa11) to distinguish the species origin of cells, while recipient’s PBMC single cell data were mapped to human genome (GRCh38) only. Single-cell raw expression matrices were then processed and analyzed using Seurat v4.3.049. Cells with less than 500 expressed genes, 1000 UMI, or more than 8% of transcripts from mitochondrial genes were removed from the kidney single cells, resulting in a total of 23,868 cells. A library of homologous genes between human and pig, obtained from the HGD Database50, was used as a reference to subset the filtered gene expression data for downstream analyses. Within the scope of gene expression of human-porcine one-to-one homologous genes, single cells with greater proportion of transcripts mapped to the porcine genome than the human genome are identified to be porcine cells, and vice versa to be human cells.
Each filtered dataset obtained from the kidneys and PBMC samples were normalized using SCTransform v2 from Seurat followed by integration using most commonly deemed variable features within each dataset. Dimensionality reduction analyses were performed on integrated kidney and PBMC datasets separately using Principal Component Analysis (PCA: npcs = 30) and Uniform Manifold Approximation and Projection (UMAP: dims = 1:30). Cell clusters were generated using the original Louvain algorithm with a resolution of 0.7 for integrated kidney dataset and 0.5 for the integrated PBMC dataset. Individual clusters were annotated based on the expression of cell type-specific markers.
Assembly: sscrofa11, hg38
Supplementary files format and content: h5

source_name: blood

extract_protocol:
Fresh kidney tissues were minced rapidly in a cell culture dish followed by washing with DPBS buffer. Minced tissue was resuspended in 5mL of 37°C pre-warmed 0.25% Trypsin for 20 min with mechanical dissociation using serological pipette every 5 min. Following digestion, dissociation mix was filtered through a 100µm strainer. The remaining large tissues on the strainer were further ground and washed to collect additional cells. Cell debris and dead cells were removed using Miltenyi Biotech Dead Cell Removal Kit before loading for 10X Genomics single-cell RNA-seq (v3.1 Chemistry). Longitudinal single-cell RNA-seq of the recipient’s PBMCs were prepared at the same time after collecting all samples across timepoints. Fresh PBMCs of each timepoint were first collected through gradient centrifugation, followed by cryopreservation of the prepared PBMCs according to the 10X Genomics protocol (protocol number: CG00039). Upon collecting all PBMC samples, the frozen cells were thawed at the same time, then loaded for 10X Genomics single-cell RNA-seq (v3.1 Chemistry).
prepared signle cells were sequenced using 10X Genomics single-cell RNA-seq (v3.1 Chemistry) following manufacturer's protocol.

value: blood

value: PBMC

tag: time point


title: A375 cells - SEL201 - N1


title: A375 cells - UNTREATED - N2

value: DMSO


title: NT2.5-LM_V2

description: Illumina HiSeqX Ten or NovaSeq

value: breast tumor


title: NT2.5_WES

library_source: genomic

molecule: genomic DNA

value: breast cancer cell line


title: HIV_4

value: Saline

value: HIV-transgenic/saline treatment


title: NT_14hpa, replicate 2, Input

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trim_galore, discarding reads left with < 20 bp.
ChIP-seq reads were aligned to the UCSC mm10 genome using BWA. Only reads with MapQ > 30 and uniquely mapped to genome were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells or embryos were lysed, and chromatin was treated with MNase.
ChIP-seq libraries were prepared using the KAPA HyperPrep Kit. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: Mouse embryo

tag: chip antibody


title: Second_kidney_xeno_recipient_PBMC_scRNA-seq_48h

description: subject 2, 48h


title: WT+PSU_3

value: wild-type/Methamphetamine+Oxy treatment


title: MSCs from MCB, passage 3, donor 203, sequenced by MACE

description:
I3
all_counts_merged_MACE.txt

value: donor 203

value: High seeding density


title: Second_kidney_xeno_recipient_PBMC_scRNA-seq_24h

description: subject 2, 24h


title: NT2.5_V4

description: Illumina HiSeqX Ten or NovaSeq


title: NT2.5-LM_V3

description: Illumina HiSeqX Ten or NovaSeq


title: WT+PSU_2


title: NT2.5_V3

description: Illumina HiSeqX Ten or NovaSeq


title: MSCs from MCB, passage 2, donor 206, sequenced by MACE

description:
G3
all_counts_merged_MACE.txt

value: donor 206

value: Wharton's jelly from umbilical cord

value: Primary cells

value: Low seeding density


title: Second_kidney_xeno_recipient_PBMC_scRNA-seq_12h

description: subject 2, 12h


title: A375 cells - UNTREATED - N1

value: melanoma cell line

value: BRAF-V600E melanoma


title: NT2.5_V2

description: Illumina HiSeqX Ten or NovaSeq


title: MSCs from MCB, passage 2, donor 202, sequenced by MACE

description:
G1
all_counts_merged_MACE.txt

value: donor 202

value: Mesenchymal stromal cells

value: WT


title: HIV_1

value: brain

value: HIV-Tg (HIV-transgenic)


title: Control Mouse Testis Replicate 2

type: RNA

city: NANJING

first: YU

last: ZHOU

address: NO. 169, HUSHAN ROAD

institute: THE AFFILIATED JIANGNING HOSPITAL OF NANJING MEDICAL UNIVERSITY

description: Biological replicate 2 of 5. Control mouse testis, prenatally solvent treated, 3-months-aged.

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10 Blocking Agent and 1 μL of 25 Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2 Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 5 out of 10 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.

source_name: Control Mouse Testis

label_protocol: The “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: Female C57BL/6 mice, 6-8 weeks old, were purchased from Charles River Laboratories and housed in temperature-controlled (21–22°C) pathogen-free conditions with 12-hour light 12-hour dark cycle in Nanjing Medical University.

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

treatment_protocol: The F0 pregnant C57BL/6 mice were daily subcutaneously injected with testosterone (T) in a dose of 2.5 mg/kg body weight or equivalent solvent (sesame oil and benzyl benzoate) as control starting from day 14 to 19 post coitum (dpc). After parturition, male offspring of maternal T treated mice were defined as PTF1. Meanwhile, male offspring of maternal solvent treated mice were defined as PCF1. At the age of 12-14 weeks, PTF1 and PCF1 male mice were mated with unrelated healthy female C57BL/6 mice to generate the second generation of maternal T treated mice, which were defined as PTF2 and PCF2, respectively.

value: Supernatant

tag: gender

value: Male

value: testis

value: immunoprecipitated


title: MSCs from MCB, passage 3, donor 195, sequenced by MACE

description:
G7
all_counts_merged_MACE.txt

value: donor 195


title: WT+PSU_4

value: METH+oxy

value: wild-type/Methamphetamine+Oxy treatment


title: NT2.5-LM_V1

description: Illumina HiSeqX Ten or NovaSeq

value: breast tumor


title: WT_4

value: Saline

value: wild-type/saline treatment


title: MSCs from MCB, passage 2, donor 200, sequenced by MACE

description:
E9
all_counts_merged_MACE.txt

value: donor 200

value: Wharton's jelly from umbilical cord

value: Primary cells

value: Low seeding density


title: MSCs from MCB, passage 3, donor 190, sequenced by MACE

description:
G5
all_counts_merged_MACE.txt

value: donor 190

value: Mesenchymal stromal cells

value: WT

value: High seeding density


title: HIV_2

value: brain

value: HIV-Tg (HIV-transgenic)

value: HIV-transgenic/saline treatment


title: WT_3


title: MSCs from MCB, passage 2, donor 196, sequenced by MACE

description:
E3
all_counts_merged_MACE.txt

value: donor 196


title: Fibroblast Normoxic Co-Culture 1

first: Megan

middle: L

last: McCain

state: CA

address: 1024 Downey Way

institute: USC

data_processing:
Samples were trimmed using Phred score and min read lengths of 20 and 25, respectively
Samples were mapped to hg38 genome using STAR (2.7.8a)
Samples were quantified, normalized, and analyzed for differential gene expression using Partek Flow Genomics Software
Assembly: hg38
Supplementary files format and content: text file ("counts.txt") includes normalized counts for each sample

source_name: Primary Adult

growth_protocol: Primary human adult cardiac fibroblasts were grown in 10% fetal bovine serum (FBS) low glucose (1g/L) DMEM and 1% penicillin-streptomycin in T-75 flasks and passaged at 70-80% confluence.

extract_protocol:
Immediately following treatment, the co-culture region was cut to separate hypoxic and normoxic cells with a sterile razor blade and then 0.5 mL TriZOL was added to each of four regions (0% control, 0% co-culture, 10% control, 10% co-culture). TRIzol-chloroform separation followed by RNA purification using a Qiagen miRNA Mini Kit were used to isolate mRNA transcripts.
xGen Broad-Range RNA Library Prep Kit

treatment_protocol: Cells were seeded onto PDMS devices coated with fibronectin at a density of 22,500 cells. lls per square centimeter and then serum arrested for 48 hours with 0.1% FBS low glucose DMEM. After serum arresting, devices were hooked up to gas cylinders that provided 0% oxygen, 5% carbon dioxide, bal nitrogen, and 10% oxygen, 5% carbon dioxide, bal nitrogen to cells for 24h.

value: Primary Adult

value: Human Cardiac Fibroblast

value: 10% O2 Co-Cultured with 0% O2, 24h


title: MSCs from MCB, passage 0, donor 205, sequenced by MACE

description:
C9
all_counts_merged_MACE.txt

value: donor 205


title: Fibroblast Normoxic Control 4


title: WT+PSU_1

value: METH+oxy

value: wild-type/Methamphetamine+Oxy treatment


title: MSCs from MCB, passage 0, donor 203, sequenced by MACE

description:
C7
all_counts_merged_MACE.txt

value: donor 203

value: Wharton's jelly from umbilical cord


title: Compound FBSA, 1 mg/L Replicate 3

city: Saskatoon

first: Hannah

last: Mahoney

state: Saskatchewan

address: 120 Veterinary Rd

department: Vaccine and Infectious Disease Organization

institute: University of Saskatchewan

data_processing:
Raw sequence fastq files were assessed for quality with fastqc and multiqc. Only files with a minimum 10 million reads and a minimum average quality score of 30 were kept for further analysis. Rep 3 of the FBSA 0.1 mg/L treatment group did not pass and was therefore removed from further analyses
Files were trimmed in trimmomatic, reads were trimmed to a minimum phred score of 20 using a window of 4 with a minimum length of 35 base pairs, and adapters were removed using the TruSe3-PE adapter sequences
Transcript alignment and paired end merging was done in salmon with a reference D.rerio cDNA genome (GenBank Accession #: GCA_000002035.4)
Metadate and expression count files were merged in Rstudio
Assembly: GenBank Accession #: GCA_000002035.4
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

organism: Danio rerio

source_name: whole organism

growth_protocol: Zebrafish (D. rerio) fertilized eggs were collected at ~2 hours post fertilization (hpf) and allowed to develop until 24 hpf in 75 mL petridishes at 100 embryos/dish. The embryos were kept at 26 ± 0.5˚C with a light:dark period of 16:8 hours.

extract_protocol:
Embryos were exposed for 72 hours until 96 hpf. Exposure solutions followed semi-static renewal, where ~80% of the exposure solution was replaced per day.
At the end of the exposure period, embryos were euthanized on ice before being pooled according to treatment group and replicate. 20 embyros were pooled per replicate resulting in three replicates of each treatment group for each compound (n = 15/PFAS)
Total RNA was extracted using the Rneasy universal mini kit (Qiagen), with quality and quantity being assured using a tape station (Bioanalyzer). All sampels containing minimum 20ng/uL with a RIN > 8 were sent to GenomeQuebec for RNA-seq.

treatment_protocol: At 24 hpf, embryos displaying proper development were randomly assigned to one of 5 treatment groups of three compounds: a solvent control (0.1% DMSO), 0.001, 0.1, 1, and 5 mg/L of either the replacement PFAS perfluoroethlycyclohexane sulphonate (PFECHS) and perfluorobutanesulphamide (FBSA), or the legacy PFAS perfluorooctane sulphonate (PFOS).

value: whole organism

value: 1 mg FBSA/L


title: Compound FBSA, 5 mg/L Replicate 1

value: 5 mg FBSA/L


title: MSCs from MCB, passage 0, donor 202, sequenced by MACE

description:
C5
all_counts_merged_MACE.txt

value: donor 202

value: Primary cells

value: Mesenchymal stromal cells

value: WT


title: Fibroblast Normoxic Control 2


title: Second_kidney_xeno_recipient_PBMC_scRNA-seq_6h

description: subject 2, 6h

value: blood

value: PBMC


title: NT2.5_V1

description: Illumina HiSeqX Ten or NovaSeq

value: breast tumor


title: Fibroblast Hypoxic Co-Culture 4

value: Primary Adult

value: Human Cardiac Fibroblast

value: 0% O2 Co-Cultured with 10% O2, 24h


title: MSCs from MCB, passage 2, donor 199, sequenced by MACE

description:
E7
all_counts_merged_MACE.txt

value: donor 199

value: Low seeding density


title: Fibroblast Normoxic Co-Culture 2

value: 10% O2 Co-Cultured with 0% O2, 24h


title: Second_kidney_xeno_recipient_PBMC_scRNA-seq_0h

description: subject 2, 0h


title: Fibroblast Normoxic Co-Culture 4


title: MSCs from MCB, passage 2, donor 198, sequenced by MACE

description:
E5
all_counts_merged_MACE.txt

value: donor 198

value: Wharton's jelly from umbilical cord


title: Compound FBSA, 0.1 mg/L Replicate 2

value: whole organism

value: 0.1 mg FBSA/L


title: WT_2

value: brain

value: Saline

value: wild-type/saline treatment


title: WT_1

value: WT


title: Fibroblast Normoxic Co-Culture 3


title: Fibroblast Hypoxic Co-Culture 2


title: Compound FBSA, 0.1 mg/L Replicate 1


title: Compound FBSA, 5 mg/L Replicate 3

value: 5 mg FBSA/L


title: MSCs from MCB, passage 0, donor 206, sequenced by MACE

description:
E1
all_counts_merged_MACE.txt

value: donor 206

value: Primary cells

value: Mesenchymal stromal cells


title: Fibroblast Hypoxic Co-Culture 1

value: Primary Adult

value: Human Cardiac Fibroblast


title: MSCs from MCB, passage 0, donor 200, sequenced by MACE

description:
C3
all_counts_merged_MACE.txt

value: donor 200


title: Compound FBSA, 5 mg/L Replicate 2


title: Fibroblast Normoxic Control 3


title: MSCs from MCB, passage 0, donor 196, sequenced by MACE

description:
A5
all_counts_merged_MACE.txt

value: donor 196


title: Compound FBSA, 0.001 mg/L Replicate 2

value: 0.001 mg FBSA/L


title: Compound FBSA, 1 mg/L Replicate 2

value: 1 mg FBSA/L


title: Fibroblast Hypoxic Control 3


title: Compound FBSA, 1 mg/L Replicate 1


title: Compound FBSA, 0.001 mg/L Replicate 1


title: Compound FBSA, Solvent Control Replicate 3

value: SC


title: Fibroblast Hypoxic Control 2


title: MSCs from MCB, passage 0, donor 199, sequenced by MACE

description:
C1
all_counts_merged_MACE.txt

value: donor 199

value: Wharton's jelly from umbilical cord


title: 10A_JUNoe_dox, IgG, rep3

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute on Aging

data_processing:
Adapter removal and quality trimming was performed by Cutadapt. Since the carry-over DNA of pAG-MNase purification from E. coli was used as spike-in control, mapping was performed to hg19 and a human repeat-masked E. coli genome by Bowtie2. Paired-end reads mapped to hg19 with inserts <120 bp were extracted using alignment Sieve (deepTools). A scaling factor was inferred by: scaling factor= (mapped reads < 120 bp to hg19)⁄(mapped reads to E.coli).
The scaling factor was used to generate spike-in normalized bigWig files by bamCoverage (deepTools).
Assembly: hg19
Library strategy: CUT&RUN

extract_protocol:
CUT and RUN experiments were performed as described previously (Kim et al., Nat. Commun., 2022). Briefly, for each CUT and RUN reaction 200,000 cells were trypsinized, washed, resuspended in 100 µl wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine) and bound to 10 µl activated BioMag®Plus Concanavalin A magnetic beads (Polysciences) for 10 min at room temperature. The cells were then incubated with antibodies diluted in 100 µl antibody buffer (wash buffer + 0.01% digitonine and 2 mM EDTA) overnight at 4°C. IgG rabbit antibody was used as negative control. After incubation with antibodies, the beads were washed in digitonin wash buffer (wash buffer + 0.01% digitonin) and incubated 1h at 4°C with 1 µg/ml protein A/G Micrococcal Nuclease fusion protein (pA/G MNase). After washing with digitonin wash buffer, beads were rinsed with low salt buffer (20 mM HEPES, pH7.5, 0.5 mM Spermidine, 0.01% digitonine), resuspended in 200 µl incubation buffer (20 mM HEPES, pH7.5, 10 mM CaCl2, 0.01% digitonin) and placed at 0°C to initiate cleavage. After 30 min, reactions were stopped by adding 200 µl STOP buffer (170 mM NaCl, 20 mM EGTA, 0.01% digitonin, 50 µg/ml RNAse A) and the samples were incubated 30 min at 37°C to digest the RNA and release the DNA fragments. The samples were then treated with proteinase K for 1 h at 50°C and the DNA was purified using Phenol/Chloroform/Isoamyl alcohol. After precipitation with glycogen and Ethanol, the DNA pellet was resuspended in 0.1 X TE and used for library preparation.
For DNA library generation, the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) was used. Adaptor ligation was performed with 1:25 diluted adaptor and 15 cycles were used for library amplification using dual indices (NEB dual index kit). Paired-end 2x25 bp sequencing was performed.

treatment_protocol: MCF10A cells expressing a doxycycline-inducible YAP5SA allele were infected with JUN overexpression vectors (WT or M14) or an empty vector control. YAP induction was induced by doxycycline addition (100 ng/ml) and control cells were treated with solvent control (EtOH).

tag: cut&run antibody

value: breast epithelial

value: JUN Wtoe

value: doxycycline


title: Fibroblast Hypoxic Co-Culture 3

value: 0% O2 Co-Cultured with 10% O2, 24h


title: MSCs from MCB, passage 0, donor 198, sequenced by MACE

description:
A9
all_counts_merged_MACE.txt

value: donor 198

value: WT


title: Rep4_SKPCE40CAF_B500NID2KRAB_D

city: Darlinghurst

first: Leonard

last: Goldstein

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Sequence reads were aligned using STAR (version 2.7.3a; Dobin et al. 2013) to the Mus musculus (mm10) assembly with the gene, transcript, and exon features of Genecode release M10 gene model.
Expression counts were estimated using RSEM (version 1.2.26; Li and Dewey 2011).
Assembly: Mus musculus (mm10)
Supplementary files format and content: Expression count matrix

source_name: Pancreas

growth_protocol: KPC CAFs (Vennin et al. 2019) were cultured in Dulbecco’s modified Eagle media (DMEM; high glucose, high pyruvate; Gibco) supplemented with 10% fetal bovine serum (FBS; Hyclone) and 1% penicillin/streptomycin (Thermo Fisher Scientific) at 37℃ with 20% O2 and 5% CO2.

extract_protocol:
The Qiagen RNeasy Mini Kit (Catalog No. 74104) was used according to manufacturer's instructions for animal cells.
Illumina Stranded Total RNA library kit

treatment_protocol: For CRISPR-Cas9 interference (CRISPRi) (Qi et al. 2013), S.Py. Cas9 was rendered catalytically inactive by introducing D10A and H840A mutations and cloned in frame with a KRAB domain at its N-terminus into the third-generation lentiviral vector as previously described (Vennin et al. 2019). Lentiviral particles were harvested from transfected HEK293T culture media, filtered (0.45 µm) and used to transduce KPC CAFs. After 48 hours, CAFs were selected for puromycin resistance (40 µg per ml) in the presence of Polybrene (8 μg/ml; Millipore).

value: Pancreas

value: mt-CAF (Vennin et al. 2019)

value: KPC cancer-associated fibroblast (CAF)

value: Derived from KPC mouse model (Pdx1-Cre, LSL-Kras G12D/+, LSL-Trp53 R172H/+)

value: B500 NID2 KRAB 5'-AGCAGCGATAGCGGTGATGG(CGG)-3'


title: MSCs from MCB, passage 0, donor 197, sequenced by MACE

description:
A7
all_counts_merged_MACE.txt

value: donor 197

value: Primary cells

value: Mesenchymal stromal cells


title: 10A_JUNoe_dox, YAP1, rep3


title: 10A_JUNoe_etoh, IgG, rep3

value: etoh


title: Compound FBSA, 0.001 mg/L Replicate 3

value: whole organism

value: 0.001 mg FBSA/L


title: 10A_JUNoe_dox,TEAD1, rep3

value: breast epithelial


title: MSCs from MCB, passage 0, donor 195, sequenced by MACE

description:
A3
all_counts_merged_MACE.txt

value: donor 195

value: Wharton's jelly from umbilical cord


title: MSCs from MCB, passage 0, donor 190, sequenced by MACE

description:
A1
all_counts_merged_MACE.txt

value: donor 190


title: Compound PFECHS, 5 mg/L Replicate 1

value: 5 mg PFECHS/L


title: Rep3_SKPCE40CAF_C500NID2KRAB_A

value: C500 NID2 KRAB 5'-TGCGGACCAGAGGTCCAAGT(TGG)-3'


title: Fibroblast Hypoxic Control 4

value: Primary Adult

value: Human Cardiac Fibroblast


title: UQAM-ST6_Treg

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Assembly: GRCh38.96
Supplementary files format and content: comma-separated text file includes raw counts for each sample
Supplementary files format and content: comma-separated text file includes log-CPM values for each sample

source_name: Treg

growth_protocol: N/Ap

extract_protocol:
All Prep DNA/RNA/miRNA Universal Kit, Qiagen)
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-NovaSeq(depth was above 150 million reads).

treatment_protocol: Total CD4+T cells were first enriched from freshly isolated PBMCs obtained from fresh leukapheresis samples by negative magnetic selection using the EasySep Human CD4+ T-cell Enrichment Kit (STEMCELL, Vancouver, Canada) with a purity higher than 95%. Cells were then stained extracellularly with anti-human CD3-Alexa Fluor 700/CD4-FITC/CD25-PE/CD127-PE-Cy7/CD45RA-BV-650/CCR6-BV-786 antibodies all from BD Biosciences (New Jersey, USA), and LIVE/DEAD™ FixablBlue Dead Cell Stain Kit (Invitrogen, Oregon, USA) to exclude dead cells for 1h at 4 °C. To exclude the Tregs, the sorting gates for non-Tregs Memory CCR6+ cells (MemCCR6+ cells) were set on CD4+CD25negCD45RA-CCR6+, which were sorted using a BD FACSAria.

tag: disease state

value: ST

value: Treg


title: Rep3_SKPCE40CAF_B500NID2KRAB_B

tag: tissue

value: Pancreas

value: mt-CAF (Vennin et al. 2019)

value: KPC cancer-associated fibroblast (CAF)

value: Derived from KPC mouse model (Pdx1-Cre, LSL-Kras G12D/+, LSL-Trp53 R172H/+)

value: B500 NID2 KRAB 5'-AGCAGCGATAGCGGTGATGG(CGG)-3'


title: 10A_JUNoe_etoh,TEAD1, rep3

tag: cell line

value: JUN Wtoe

value: etoh


title: 10A_JUNoe_etoh, JUN, rep3

tag: cell type

value: breast epithelial


title: Rep4_SKPCE40CAF_GFP1KRAB_D

tag: treatment


title: Fibroblast Hypoxic Control 1


title: 10A_JUNoe_etoh, YAP1, rep3


title: Compound FBSA, Solvent Control Replicate 2

value: whole organism

value: WT

value: SC


title: 10A_JUNoe_dox, JUN, rep3

value: doxycycline


title: Compound FBSA, Solvent Control Replicate 1


title: Rep4_SKPCE40CAF_C500NID2KRAB_D

value: C500 NID2 KRAB 5'-TGCGGACCAGAGGTCCAAGT(TGG)-3'


title: UQAM-ST3_Treg


title: Rep2_SKPCE40CAF_C500NID2KRAB_B


title: Compound PFECHS, 1 mg/L Replicate 1

value: 1 mg PFECHS/L


title: Compound PFECHS, 5 mg/L Replicate 3

value: 5 mg PFECHS/L


title: UQAM-ST2_Treg

value: ST


title: Compound PFECHS, 0.1 mg/L Replicate 2

value: 0.1 mg PFECHS/L


title: Compound PFECHS, 5 mg/L Replicate 2


title: Control 3

city: Beijing

first: Ling

last: Zhong

address: Wangfujing Street

department: Department of Endocrinology

institute: Peking Union Medical College Hospital

data_processing:
illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include PRKM values for each sample.

source_name: inguinal white adipose tissue

extract_protocol:
Inguinal white adipose tissue (iWAT) of individual mice from each experimental group were collected after 10 hours of fasting. These samples were snap frozen in liquid nitrogen and stored at -80°C until further use.Total RNA was isolated from iWAT (3mice each group) using the Total RNA Isolation Reagent (TRIzol) method (Invitrogen, Bio-Tek, Inc., USA).
RNA libraries were prepared for sequencing using standard illumina protocols.

value: inguinal white adipose tissue

tag: strain

value: C57 BL/6N

value: control


title: UQAM-ST5_Treg

value: Treg


title: UQAM-ST6_Th17


title: Control 2


title: Compound PFECHS, 1 mg/L Replicate 3


title: UQAM-ST5_Th17


title: Rep3_SKPCE40CAF_GFP1KRAB_B

value: Pancreas

value: mt-CAF (Vennin et al. 2019)

value: KPC cancer-associated fibroblast (CAF)

value: Derived from KPC mouse model (Pdx1-Cre, LSL-Kras G12D/+, LSL-Trp53 R172H/+)


title: UQAM-HD4_Treg

value: HD


title: Compound PFECHS, 1 mg/L Replicate 2

value: whole organism

value: WT


title: UQAM-ST3_Th17


title: 10A_ev_dox, IgG, rep3

value: breast epithelial

value: empty vector

value: doxycycline


title: SF 8w-SR 2w 3

value: sleep fragmentation and recovery


title: Rep2_SKPCE40CAF_B500NID2KRAB_A

value: B500 NID2 KRAB 5'-AGCAGCGATAGCGGTGATGG(CGG)-3'


title: 10A_ev_dox, JUN, rep3


title: Rep2_SKPCE40CAF_GFP1KRAB_D


title: 10A_ev_dox,TEAD1, rep3


title: UQAM-ST2_Th17

value: ST


title: Compound PFECHS, 0.1 mg/L Replicate 1

value: 0.1 mg PFECHS/L


title: 10A_ev_dox, YAP1, rep3


title: UQAM-ST1_Treg


title: SF 8w-SR 2w 2

value: inguinal white adipose tissue

value: C57 BL/6N


title: 10A_ev_etoh, YAP1, rep3

value: etoh


title: UQAM-EC3_Treg

value: EC

value: Treg


title: Compound PFECHS, 0.001 mg/L Replicate 3

value: 0.001 mg PFECHS/L


title: Compound PFECHS, Solvent Control Replicate 2

value: SC


title: Compound PFECHS, Solvent Control Replicate 1


title: UQAM-EC3_Th17


title: UQAM-ST1_Th17


title: Compound PFECHS, 0.001 mg/L Replicate 2


title: 10A_ev_etoh, H3K4me1, rep3


title: Compound PFECHS, 0.1 mg/L Replicate 3


title: Control 1

value: control


title: 10A_ev_etoh, JUN, rep3


title: Compound PFECHS, 0.001 mg/L Replicate 1

value: whole organism


title: 10A_ev_etoh,TEAD1, rep3


title: 10A_ev_etoh, H3K27ac, rep2

value: (abcam, ab4729)


title: 10A_ev_etoh, IgG, rep3

value: breast epithelial


title: Compound PFECHS, Solvent Control Replicate 3

value: WT


title: SF 8w-SR 2w 1


title: Compound PFOS, 5 mg/L Replicate 1

value: 5 mg PFOS/L


title: control, rep3, scRNAseq

city: Albuquerque

first: Tou Yia

last: Vue

state: New Mexico

address: 915 Camino De Salud NE, Fitz Hall 145

department: Neurosciences

institute: University of New Mexico Health Sciences Center

description: 10X Genomics

data_processing:
Data were demultiplexed and fastq files were generated using bcl2fastq (v2.20.0.422, Illumina) with parameter “--barcode-mismatches” set to 1. Fastq files were aligned and genes/cells were counted against the mouse reference genome (mm10) using CellRanger (v6.0.0, 10xGenomics) (1).
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Brains of control (tdTOM+, N=3) or experimental (Ascl1-Overexpression; GFP+, N=3) tumor-bearing mice with neurological symptoms were freshly harvested and tumors were dissected out in a bath of Hank’s Balanced Salt Solution (without calcium or magnesium). Working on ice, tumor tissue was weighed and then transferred to a gentleMACS C tube and dissociated using the Miltenyi Neural Tissue Dissociation Kit (P) and an Octo-Dissociator with Heaters. Following this, cells underwent FACS
The 10x Chromium Next GEM 3’ protocol was used to create 3’ libraries for sequencing at the University of Colorado Anschutz Medical Campus’s Genomics Shared Resource Cancer Center using Illumina NovaSEQ 6000 instruments on S4 flow cells. Briefly, cells were lysed and barcoded within each GEM before first strand cDNA synthesis, and also within each GEM. Cells were pooled prior to library completion as described in the manufacturer’s protocol.

value: Brain

value: Tumor cells


title: UQAM-EC1_Treg


title: experimental, rep3, scRNAseq

description: 10X Genomics

value: R26R-tTA/+ TetO-AIG/+


title: experimental, rep2, scRNAseq

description: 10X Genomics


title: UQAM-EC1_Th17


title: Compound PFOS, 5 mg/L Replicate 2


title: experimental, rep1, scRNAseq

description: 10X Genomics


title: 10A_ev_etoh, H3K4me1, rep2

value: empty vector


title: Compound PFOS, 5 mg/L Replicate 3


title: Compound PFOS, 1 mg/L Replicate 2

value: 1 mg PFOS/L


title: HGG_70, Ampliseq

city: Temuco

first: Mauricio

middle: A.

last: Saez

address: Manuel Montt 56

country: Chile

institute: Universidad Catolica de Temuco

data_processing:
Reads of low quality and adapter contamination were removed using the trim_galore tool. Processed reads were aligned to the GRCh38 reference genome using the Bowtie2 tool. The aligned *.sam results were then converted to *.bam files using the samtools application for subsequent analysis.
Somatic mutations were called according to GATK recommendations, including additional considerations for amplicon panels, as described below. Bam files were analyzed with MarkDuplicatesSpark and BaseRecalibrator, using gnomadV2 database, to finally recalibrate with ApplyBQSR to meet GATK standards. Somatic variants were detected using Mutect2 , only on target regions. To identify and discard artifactual variants, GetPileupSummaries with CalculateContamination, LearnReadsOrientation and a panel of normal were used, Additionally, the Integrative Genomics Viewer (IGV 2.10) was used to identify and correct potential errors. Finally, we used FilterMutectCalls to recover clustered events and to discard variants with an allelic frequency <0.05 or <10 reads supporting the variant.
Variants in vcf files were annotated with Funcotator and reports were generated in vcf and maf files. All genomic coordinates are mapped to the GRCh 38 assembly. Posterior analysis was performed with Variant Effect Predictor (McLaren et al., 2016) to predict pathogenicity. Novel variants and variants not previously reported in gliomas that are predicted to result in singleamino acid substitutionswere subsequently evaluated using Sorting Intolerant From tolerant (SIFT) and polymorphism phenotyping-2 (PolyPhen-2) to predict the effect of the change on protein function while variants that resulted in frameshifts were evaluated using SIFT indel . Maftools R package was used to prepare oncoplots.
Assembly: GRCh38
Supplementary files format and content: vcf files for each sample, containig snp and short indel, after pass filters for quality, and  allelic frequency <0.05 and/or <10 reads supporting the variant.
Supplementary files format and content: maf file used for oncoplots after removing known polymorphisms

source_name: Tumor

extract_protocol:
Formalin-fixed paraffin-embedded tissue samples were obtained from the Pathology Service at the Asenjo Neurosurgery Institute. After neuropathologist confirmation of a tumor percentage greater than 70% in each area to be extracted, 3-6 sections of 10 microns were prepared from each paraffin block using the GeneJET FFPE DNA Purification Kit. No matched blood samples were available. The extracted DNA was quantified using fluorescence-based methods (Quant-iT™ PicoGreen™ dsDNA and/or Qubit™ dsDNA HS), resulting in an average concentration of 40 ng/µL. We
For both AmpliSeq™ and TruSeq™ libraries, library generation efficiency was evaluated with different initial amounts of DNA to adjust the various stages of the process based on the specific sample and panel characteristics. Automated electrophoresis of the first libraries were performed for quality control and size estimation using the DNA 1000 kit on the Agilent 2100 Bioanalyzer system. All libraries were quantified by qPCR using the Illumina KAPA library quantification kit and were pooled at a concentration of 10 nM before sequencing. A Mid Output Kit v2.5 (150 cycles) was used on a NextSeq sequencer with 25% phi-X for all Ampliseq™ libraries, and a Micro Kit v2 (300 cycles) with 25% phi-X on a MiSeq sequencer was used for all TruSeq™ libraries.
Amplicon sequencing

value: Tumor

tag: Sex

value: Male

tag: histological diagnosis

value: Glioblastoma

tag: age at_diagnosis

tag: overall survival_(months)


title: control, rep1, scRNAseq

description: 10X Genomics

tag: genotype


title: 10A_ev_etoh, H3K27ac, rep3

value: etoh


title: control, rep2, scRNAseq

description: 10X Genomics


title: HD3_Treg

value: HD

value: Treg


title: HD2_Treg


title: HD3_Th17


title: 10A_ev_etoh, H3K27ac, rep1


title: Compound PFOS, 1 mg/L Replicate 1


title: HD4_Th17


title: Compound PFOS, 0.1 mg/L Replicate 3

value: 0.1 mg PFOS/L


title: Compound PFOS, 1 mg/L Replicate 3

value: whole organism


title: UQAM-HD4_Th17


title: Calvarial bone, Blank_D7_2

first: Zhuqing

last: Wan

address: 22 Zhongguancun Avenue South, Haidian District, Beijing

department: Department of Prosthodontics

institute: Peking University School and Hospital of Stomatology

description: 10 x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Calvarial bone

extract_protocol:
Freshly collected from calvarial bone tissues, the cell viability was assessed with Trypan blue exclusion on a TC20TM automated cell counter (BIO-RAD, Hercules, CA, USA)
single-cell RNA-seq sample libraries were prepared with the 10x Genomics Chromium Single Cell 3′v3.1 according to the manufacturer’s instructions and sequenced using the Illumina HiSeq 6000 platform

value: Calvarial bone

value: all cells

tag: time

value: bone defect repaired without Col+nHA materials


title: Calvarial bone, Col_nHA_D7_2

description: 10 x Genomics

value: bone defect repaired with Col+nHA materials


title: HGG_69, Ampliseq


title: HD4_Treg


title: HD2_Th17


title: HGG_68, Ampliseq


title: Compound PFOS, 0.1 mg/L Replicate 2

value: WT


title: Calvarial bone, Col_nHA_D7_1

description: 10 x Genomics


title: 10A_ev_etoh, H3K4me1, rep1

value: breast epithelial


title: HGG_67, Ampliseq

value: Female


title: HD1_Treg


title: Calvarial bone, Blank_D7_1

description: 10 x Genomics


title: Compound PFOS, 0.001 mg/L Replicate 3

value: 0.001 mg PFOS/L


title: Compound PFOS, 0.1 mg/L Replicate 1


title: HD1_Th17


title: HGG_65, Ampliseq


title: HGG_66, Ampliseq


title: Calvarial bone, Col_nHA_D2_2

description: 10 x Genomics


title: CHUM-ST1_Treg

value: ST


title: Compound PFOS, 0.001 mg/L Replicate 2


title: Calvarial bone, Blank_D2_2

description: 10 x Genomics


title: HGG_64, Ampliseq

value: Tumor


title: Calvarial bone, Col_nHA_D2_1

description: 10 x Genomics


title: Compound PFOS, 0.001 mg/L Replicate 1


title: HGG_63, Ampliseq

value: Male


title: Compound PFOS, Solvent Control Replicate 2

value: SC


title: CHUM-EC3_Treg

value: EC


title: Compound PFOS, Solvent Control Replicate 3


title: Compound PFOS, Solvent Control Replicate 1


title: HGG_61, Ampliseq

value: Glioblastoma


title: Calvarial bone, Blank

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

growth_protocol: The calvarial bone-defects were implanted with or without collagen/nHA materials, the bone samples were harvested after 7 days' observation

treatment_protocol: Frozen in OCT, cut the OCT-embedded samples for HE staining ans spatial transcripmics analysis

value: bone defect repaired without collagen/nHA materials


title: HGG_60, Ampliseq


title: HCTRAD21D_ChIPseq_TBP_DMSO_r2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
mRNA-seq half-life estimation: htseq count file generation from mRNA-seq aligned both for ERCC spike-in control and genomic sequence
mRNA-seq half-lfe estimation:estimate the decay rate constant (kdecay) by fitting the exponential curve on concentration changes upon timepoints using SSasymp R function. From the decay constant, we calculated the mRNA half-lives using the following equation: ln(2)/kdecay
Assembly: mm9, mm10 (only for scRNAseq), hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file

growth_protocol: HCT-116 degron cell lines: RAD21- mAID-mClover1 and HCT116-OsTIR1-MED26-AID2 were cultured in McCoy's 5A medium supplemented with L-Glutamine (Gibco), 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), at 37 °C; 5% CO2.  ES (E14) RAD213 and CTCF degron4 cell lines were cultured in knock-out DMEM (Gibco), ES cell qualified FBS (ATCC), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 1:10,000LIF (10,000x) on 0.1% gelatin coated dishes at 37 °C; 5% CO2.  Primary WT and Myc knockout B cells were derived from Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (Sigma) (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice).  The deletion of floxed allele was checked as previously5 with PCR or intracellular staining of Myc protein. B cells were isolated from spleen of WT and KO mice, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies) and activated for 4 hours with 50 mg/ml LPS and 2.5 ng/ml IL4 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco), at 37 °C; 5% CO2 B220 positive primary bone marrow B cells were derived from C57BL/6J wild-type mice, enriched with CD45R (B220) MicroBeads Kit (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec). Splenic B cells were derived from C57BL/6J wild-type mice immunized with a keyhole limpet haemocyanin (KLH; 25 µg/footpad, Sigma-Aldrich) in the presence of 10% CFA adjuvant (Sigma-Aldrich). After 5 days B cells were isolated from spleen, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies), and activated for 72 hours with 50 mg/ml LPS, 2.5 ng/ml IL4 and anti-CD180 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco),  at 37 °C; 5% CO2.  CH12 B lymphoma cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco), at 37 °C; 5% CO2. LNK (NK cell line) cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 10 mM HEPES, 1:100 NEAA (Gibco), 1:100 sodium pyruvate (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 200 IU/ml IL-2 (Sigma-Aldrich). Skin cells for scRNA-Seq: whole epidermis from mouse neonates. Keratinocytes were isolated from Fvb neonate (P0-P2) skin (n = 2) as described in Lichti et al., 20086. Cells were subjected to MACS Dead Cell removal kit (Miltenyi Biotech) using the manufacturer’s protocol. Skin cells for mRNA half-lives estimation: primary keratinocyte. Skins from a pool of Fvb neonatal mice were collected at P0-P2 and incubated overnight in 2.0 U/mL Dispase II (Sigma) in KBM-Gold (Lonza) on an end-over-end rotator. The following day, skins were washed twice in 1x PBS (Sigma), and epidermises were separated from dermises. Epidermises were placed basal side down and floated in pre-warmed 0.25% Trypsin-EDTA (Thermo Scientific) for 20min on an orbital shaker at room temperature. An equal volume of pre-warmed 2.5mg/mL Soybean Trypsin Inhibitor (Thermo Scientific) was added to finish trypsinization, and epidermises were rubbed vigorously against bottom of plate using curved forceps to dislodge keratinocytes. Dislodged cells were pooled into a tube on ice in KBM-Gold. Pooled cells were pipetted ~40 times with a 10ml serological pipette and strained with a 100um filter before pelleting cells at 300xg for 10min at 4°C. Cells were resuspended in 4.5mL KBM-Gold per epidermis and cell count was obtained using Cellometer ViaStain AOPI Solution (Sigma). The cells were subjected to Percoll (GE LifeSciences; ratio of 10X PBS:Percoll:KBM-Gold media was 1:4:5, where the cells were at a concentration of 1 million per mL of final volume) gradient ultracentrifugation using a swinging bucket rotor (11,000 rpm for 42 minutes at 4°C) to separate the basal and suprabasal fractions. The cells at the top band were suprabasal cells and separated from the pellet at the bottom of the tube which were basal cells. The basal cell sample was carefully pipetted out, washed twice with 4°C 1x PBS, seeded onto collagen-coated (Collage Type I; Corning) 6-well plates at 1x106 cells per well, and incubated at 37°C overnight to allow cells to attach to the plate before proceeding with experiments.  Mast cells: Mouse bone marrow-derived mast cells (BMMC) were differentiated from the marrow of tibias and femurs of C57/BL6 mice and cultured for 8 weeks in RPMI 1640 containing 10% FBS, 1M HEPES, 100 U/mL penicillin, 100 μg/mL streptomycin, 4 mM l-glutamine, 1 mM sodium pyruvate, non-essential amino acids, 50 μM 2-mercaptoethanol, IL-3 (20 ng/mL) and stem cell factor (SCF) (20 ng/mL). The purity of mast cells was monitored by assessing the expression of the receptors for SCF (CD117;Kit) and for IgE (FcεRI) by flow cytometry. By the end of 6-8 weeks in culture more than 98% of the cultured population was FcεRI+/CD117+ double-positive mast cells.

extract_protocol:
RNA-Seq Cells (0.5M) were harvested and lysed in 100 µl of the lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen). RNA was isolated and DNase treated according to manufacturer’s protocol. High RNA quality was confirmed using the Agilent TapeStation system before library preparation. mRNA polyA- purification, reverse transcription and library preparation were performed using NEBNext Poly(A) mRNA Magnetic Isolation Module. For spike-in control ERCC RNA Spike-In Mix (Invitrogen) was added before RNA isolation.   ChIP-Seq Cells were fixed with 1% formaldehyde (Sigma) for 10 min at 37°C, treated with 1/20 volume of 2.5 M Glycine, washed with PBS, snap-frozen on dry ice and stored at -80°C until further processing. After thawing cells were resuspended in RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) supplemented with Complete Mini EDTA free proteinase inhibitor (Roche) and sonicated using ultrasonicator (Covaris) in 1 ml AFA tubes (Covaris): duration (s): 1200, peak power: 75, duty % factor: 15, cycles/burst:1000. Sonicated chromatin was pre-cleared with Dynabeads and incubated overnight at 4˚C with rotation with following antibodies: RAD21: ab992 (Abcam); MED26: 13641S (Cell Signaling Technology); TATA binding protein TBP: ab28175 (Abcam); BRD4: ab128874 (Abcam); RNA Pol II: ab26721 (Abcam). Next day samples were washed (10 min at 4˚C with rotation): 2x with RIPA buffer, 2x with RIPA buffer + 0.3 M NaCl, 2x with 1 ml of LiCl buffer (0.25M LiCl, 0.5% Igepal CA-630, 0.5% NaDOC, store at 4˚C), 1x with 1 ml of TE + 0.2 % Triton X-100, 1x with 1 ml of TE. After washes beads were resuspended with 100 ul of TE, followed by addition of 3 µl of 10% SDS and 5 µl of 20 mg/ml Proteinase K and incubated at 65˚C for 4h. After decrosslinking DNA was purified on columns using ChIP DNA Clean & Concentrator kit (Zymo Research). In the next step DNA was quantified using Qubit system (Invitrogen).  mRNA half-lives estimation  Cells were treated with 5 µg/mL actinomycin D (Sigma) and harvested (0.5M cells) at timepoint 0 hours and up to 24 hours: at 1, 2, 4, 8, 12 and 24 hours timepoints7. After each timepoint the viability of cells was checked with FACS, or Nexcelom cell counter after staining with Acridine Orange/Propidium Iodide (AO/PI) (Nexcelom Bioscience). Some cell types did not survive longer actinomycin D treatment than 8 hours, so the last collected timepoint was determined based on cell type viability (details in Extended Data Fig.1a). Pellets were lysed in 100 µl of the lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen), ERCC RNA Spike-In Mix (Invitrogen) was added, RNA isolated (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen), and RNA-Seq was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module.   scRNA-Seq Cells were washed twice with 1x PBS containing 0.04% weight/volume BSA, resuspended in the same buffer and encapsulated into droplets using 10X Genomics system.
RNA-Seq NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).  ChIP-Seq Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).  scRNA-Seq Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).

treatment_protocol: HCT-116 degron cell lines: Starvation: cells were FBS depleted for 14 hours, followed by an additional incubation with FBS free medium for another 6 hours in the presence of DMSO (control), 500 µM auxin (indole-3-acetic acid, IAA) (Sigma-Aldrich) for degradation of the AID-tagged RAD21 and MED26 or 500nM JQ-1 (Sigma-Aldrich) for BRD4 displacement. Cells were analyzed after addition of FBS in the presence of DMSO or drugs at timepoints: 0h (RAD21 degron), 0.5h (RAD21 degron) and 2h (RAD21 and MED26 degron, JQ-1 treatment). ES (E14) For the AID-tagged proteins 500 µM auxin (indole-3-acetic acid, IAA) (Sigma-Aldrich) was added for 6 hours (RAD21) or 24 hours (CTCF). Splenic B cells To measure mRNA half-lives in activated B cells Actinomycin D was added after 2 days of stimulation with LPS, IL4 and anti-CD180 (more details: mRNA half-lives estimation). Skin cells To estimate mRNA half-lives in skin cells we used basal cells.

value: colorectal carcinoma cell

value: DMSO 6h


title: CHUM-ST1_Th17


title: HGG_62, Ampliseq


title: mskin_mRNA_r2_8h

source_name: skin

value: skin

value: basal cell

value: actinomycin D 8h


title: hDOMTs

city: Changchun

first: zhuoran

last: wang

address: Tsinghua Road

institute: Jilin university

data_processing:
Fastp software was used to process raw reads in fastq format, and clean reads were obtained after removing low-quality reads for subsequent data analysis.
The clean reads were mapped to the reference genome using HISAT2.
Fragments Per Kilobase of exon model per Million fragments mapped (FPKM) of each gene was calculated.
The read counts of each gene were obtained through HTSeq-count.
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 files include FPKM values for each Sample

source_name: human dental pulp tissues

growth_protocol: Mesenchymal stem cells were maintained in MEM α supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using RNAiso reagent (TAKARA, USA). RNA purity and quantification were evaluated using the NanoDrop2000 Spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The transcriptome libraries were constructed using VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol:
Osteogenic differentiation was induced by treatment of hDPSCs with Osteogenic Differentiation Kits (Oricell).
The control group was cultured in two-dimensional plates. The cells were cultured in normal complete culture medium overnight and the medium was replaced by differentiation induction medium on the next day. The renewing time of the medium was 3 days.

value: human dental pulp tissues

value: mesenchymal stem cells

value: three-dimensional culture


title: HGG_58, Ampliseq


title: Cont

value: two-dimensional culture


title: Calvarial bone, Col_nHA

value: Calvarial bone

value: bone defect repaired with collagen/nHA materials


title: HCTRAD21D_ChIPseq_TBP_DMSO_r1


title: mskin_mRNA_r2_2h

value: WT

value: actinomycin D 2h


title: CHUM-EC3_Th17


title: HGG_57, Ampliseq

value: Tumor

value: Female


title: HGG_59, Ampliseq

value: Glioblastoma


title: HCTRAD21D_ChIPseq_TBP_AUXIN_r2

value: IAA 6h


title: mskin_mRNA_r2_4h

value: actinomycin D 4h


title: Breast tumor 03_031 from Fulvestrant Arm sample type W

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Raw gene read counts were generated by BioSpyder.  Genes with multiple probes were summed to unique genes. Samples with <40% mapping rate were discarded.  Lowly expressed genes were discarded by removing those expressed in less than 10 samples or with less than 1 count per million across all samples.
Assembly: Human transcriptome
Supplementary files format and content: Text file containing filtered sample and gene counts

source_name: Breast tumor

extract_protocol:
The TempO-Seq Human Whole Transcriptome kit from BioSpyder was used to lyse and prepare the samples.
TempO-Seq Human Whole Transcriptome kit from BioSpyder (Carlsbad, CA)

value: Breast tumor

value: Fulvestrant Arm

tag: study id

tag: sample type

value: W

tag: paired

value: TRUE


title: Breast tumor 03_031 from Fulvestrant Arm sample type B

value: B


title: mskin_mRNA_r2_24h

value: skin

value: basal cell

value: actinomycin D 24h


title: HGG_56, Ampliseq

value: Male


title: Breast tumor 03_032 from Combination Arm sample type W

value: Combination Arm


title: HCTRAD21D_ChIPseq_TBP_AUXIN_r1

value: colorectal carcinoma cell


title: mskin_mRNA_r2_1h

value: WT

value: actinomycin D 1h


title: HGG_55, Ampliseq

value: Tumor

value: Female


title: Breast tumor 03_032 from Combination Arm sample type B


title: Breast tumor 03_030 from Fulvestrant Arm sample type B


title: HCTRAD21D_ChIPseq_PolII_DMSO

value: DMSO 6h


title: Breast tumor 03_030 from Fulvestrant Arm sample type W


title: HGG_54, Ampliseq

value: Glioblastoma


title: mskin_mRNA_r2_12h

value: actinomycin D 12h


title: Breast tumor 03_029 from Combination Arm sample type W

value: Breast tumor

value: FALSE


title: HGG_53, Ampliseq


title: HCTMED26D_ChIPseq_TBP_DMSO_r2


title: HCTRAD21D_ChIPseq_PolII_AUXIN

value: IAA 6h


title: mskin_mRNA_r1_8h

value: actinomycin D 8h


title: mskin_mRNA_r2_0h

value: skin


title: Breast tumor 03_028 from Combination Arm sample type W

value: W

value: TRUE


title: HGG_52, Ampliseq


title: HCTMED26D_ChIPseq_Rad21_DMSO_r2

value: DMSO 2h


title: HGG_51, Ampliseq


title: HCTMED26D_ChIPseq_TBP_AUXIN_r2

value: IAA 2h


title: mskin_mRNA_r1_4h

value: basal cell

value: actinomycin D 4h


title: HGG_50, Ampliseq

value: Male


title: Breast tumor 03_023 from Fulvestrant Arm sample type B

value: Fulvestrant Arm

value: B


title: HGG_49, Ampliseq

value: Tumor


title: Breast tumor 03_022 from Combination Arm sample type W

value: Combination Arm


title: mskin_mRNA_r1_2h

value: WT

value: actinomycin D 2h


title: Calvarial bone, Blank_D2_1

description: 10 x Genomics

value: Calvarial bone

value: all cells

value: bone defect repaired without Col+nHA materials


title: HGG_48, Ampliseq

value: Female

value: Glioblastoma


title: Breast tumor 03_022 from Combination Arm sample type B

value: Breast tumor

value: TRUE


title: HCTMED26D_ChIPseq_PolII_DMSO_r2

value: colorectal carcinoma cell

value: DMSO 2h


title: mskin_mRNA_r1_1h

value: skin

value: basal cell

value: actinomycin D 1h


title: HCTMED26D_ChIPseq_PolII_AUXIN_r2

value: IAA 2h


title: HCTMED26D_ChIPseq_Brd4_DMSO_r2


title: mskin_mRNA_r1_0h


title: Breast tumor 03_020 from Fulvestrant Arm sample type W

value: Fulvestrant Arm

value: W

value: FALSE


title: HCTMED26D_ChIPseq_Brd4_AUXIN_r2


title: Breast tumor 03_028 from Combination Arm sample type B

value: Combination Arm

value: B


title: Breast tumor 03_019 from Fulvestrant Arm sample type B


title: HCTMED26D_ChIPseq_Rad21_AUXIN_r2


title: mNK_mRNA_r2_4h

source_name: LNK

value: LNK

value: NK cell

value: WT

value: actinomycin D 4h


title: HCTJQ1_ChIPseq_TBP_JQ1_r2

value: JQ1 2h


title: HGG_46, Ampliseq

value: Tumor

value: Male

value: Glioblastoma


title: HGG_44, Ampliseq


title: Breast tumor 03_023 from Fulvestrant Arm sample type W

value: Breast tumor

value: TRUE


title: Breast tumor 03_019 from Fulvestrant Arm sample type W


title: mNK_mRNA_r2_8h

value: actinomycin D 8h


title: mskin_mRNA_r1_12h

value: skin

value: basal cell

value: actinomycin D 12h


title: HGG_45, Ampliseq


title: HGG_43, Ampliseq

value: Female


title: HCTJQ1_ChIPseq_TBP_DMSO_r2

value: colorectal carcinoma cell

value: DMSO 2h


title: mskin_mRNA_r1_24h

value: actinomycin D 24h


title: mNK_mRNA_r2_1h

value: LNK

value: NK cell

value: actinomycin D 1h


title: Breast tumor 03_018 from Combination Arm sample type W

value: Combination Arm

value: W


title: HCTJQ1_ChIPseq_TBP_JQ1_r1

value: WT

value: JQ1 2h


title: mNK_mRNA_r2_2h

value: actinomycin D 2h


title: HGG_47, Ampliseq

value: Tumor

value: Glioblastoma


title: HCTJQ1_ChIPseq_TBP_DMSO_r1


title: HGG_42, Ampliseq

value: Male


title: mNK_mRNA_r2_12h


title: HGG_41, Ampliseq


title: mNK_mRNA_r2_0h


title: Breast tumor 03_016 from Fulvestrant Arm sample type W

value: Breast tumor

value: Fulvestrant Arm

value: TRUE


title: HGG_39, Ampliseq


title: mNK_mRNA_r1_8h

value: actinomycin D 8h


title: Breast tumor 03_017 from Combination Arm sample type B

value: B


title: HGG_40, Ampliseq


title: HCTJQ1_ChIPseq_PolII_DMSO

value: colorectal carcinoma cell

value: DMSO 2h


title: HCTJQ1_ChIPseq_Brd4_JQ1_r2


title: mNK_mRNA_r1_4h

value: LNK

value: NK cell

value: actinomycin D 4h


title: HGG_38, Ampliseq

value: Female


title: HGG_37, Ampliseq


title: mNK_mRNA_r1_2h

value: WT


title: Breast tumor 03_018 from Combination Arm sample type B

value: Combination Arm


title: Breast tumor 03_014 from Combination Arm sample type B


title: HCTJQ1_ChIPseq_Brd4_JQ1_r1

value: JQ1 2h


title: Breast tumor 03_014 from Combination Arm sample type W

value: W


title: Breast tumor 03_017 from Combination Arm sample type W


title: HCTJQ1_ChIPseq_Brd4_DMSO_r2


title: HGG_36, Ampliseq

value: Tumor

value: Glioblastoma


title: mNK_mRNA_r1_1h

value: actinomycin D 1h


title: Breast tumor 03_013 from Fulvestrant Arm sample type W

value: Breast tumor

value: Fulvestrant Arm


title: mNK_mRNA_r1_12h

value: actinomycin D 12h


title: HCTJQ1_ChIPseq_PolII_JQ1


title: HGG_35, Ampliseq

value: Male


title: HCTMED26D_mRNA_DMSO_r3

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+IAA 6h, FBS + IAA 2h


title: Breast tumor 03_013 from Fulvestrant Arm sample type B

value: B

value: TRUE


title: HCTMED26D_mRNA_DMSO_r2


title: Breast tumor 03_016 from Fulvestrant Arm sample type B


title: mNK_mRNA_r1_0h

value: LNK

value: NK cell


title: HGG_34, Ampliseq

value: Female


title: HGG_33, Ampliseq


title: Breast tumor 03_011 from Combination Arm sample type B

value: Combination Arm


title: mmast_mRNA_r2_4h

source_name: Bone marrow

value: Bone marrow

value: mast cell

value: WT

value: actinomycin D 4h


title: mmast_mRNA_r2_8h

value: actinomycin D 8h


title: HGG_32, Ampliseq

value: Tumor

value: Glioblastoma


title: HCTMED26D_mRNA_AUXIN_r3

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HCTJQ1_ChIPseq_Brd4_DMSO_r1

value: DMSO 2h


title: HCTMED26D_mRNA_DMSO_r1

value: colorectal carcinoma cell


title: Breast tumor 03_010 from Fulvestrant Arm sample type W

value: Breast tumor

value: Fulvestrant Arm

value: W


title: HGG_31, Ampliseq

value: Male


title: mmast_mRNA_r2_2h

value: actinomycin D 2h


title: mmast_mRNA_r2_24h

value: actinomycin D 24h


title: HCTMED26D_mRNA_AUXIN_r2


title: HGG_30, Ampliseq

value: Female


title: Breast tumor 03_010 from Fulvestrant Arm sample type B

value: B

value: TRUE


title: HGG_29, Ampliseq


title: HCTMED26D_mRNA_AUXIN_r1


title: Breast tumor 03_008 from Combination Arm sample type W

value: Combination Arm


title: mmast_mRNA_r2_1h

value: Bone marrow

value: mast cell

value: WT

value: actinomycin D 1h


title: HCTJQ_mRNA_JQ1_r3

value: JQ1 2h


title: HCTJQ_mRNA_JQ1_r2


title: mmast_mRNA_r2_12h

value: actinomycin D 12h


title: HCTJQ_mRNA_JQ1_r1

value: colorectal carcinoma cell


title: HGG_27, Ampliseq

value: Tumor

value: Glioblastoma


title: Breast tumor 03_007 from Fulvestrant Arm sample type W

value: Breast tumor

value: Fulvestrant Arm

value: W


title: HGG_28, Ampliseq


title: Breast tumor 03_011 from Combination Arm sample type W


title: mmast_mRNA_r2_0h


title: Breast tumor 03_008 from Combination Arm sample type B


title: HGG_26, Ampliseq


title: HCTJQ_mRNA_DMSO_r3

value: DMSO 2h


title: mmast_mRNA_r1_8h

value: actinomycin D 8h


title: Breast tumor 03_001 from Fulvestrant Arm sample type B

value: B

value: FALSE


title: HCTJQ_mRNA_DMSO_r2


title: Breast tumor 02_014 from Combination Arm sample type W

value: Combination Arm

value: TRUE


title: HGG_24, Ampliseq

value: Male


title: HCTJQ_mRNA_DMSO_r1

value: WT


title: mmast_mRNA_r1_2h

value: Bone marrow

value: mast cell

value: actinomycin D 2h


title: Breast tumor 03_007 from Fulvestrant Arm sample type B


title: mmast_mRNA_r1_24h

value: actinomycin D 24h


title: HGG_23, Ampliseq

value: Tumor

value: Female


title: Breast tumor 02_013 from Fulvestrant Arm sample type W

value: Breast tumor


title: Breast tumor 02_014 from Combination Arm sample type B


title: HCT_nonstarved_mRNA_r2_8h

value: colorectal carcinoma cell


title: mmast_mRNA_r1_1h

value: actinomycin D 1h


title: Breast tumor 02_013 from Fulvestrant Arm sample type B

value: Fulvestrant Arm


title: HGG_22, Ampliseq

value: Glioblastoma


title: HCT_nonstarved_mRNA_r2_4h

value: actinomycin D 4h


title: HGG_21, Ampliseq


title: HCT_nonstarved_mRNA_r2_2h


title: Breast tumor 02_012 from Combination Arm sample type W

value: W


title: mmast_mRNA_r1_4h


title: HGG_20, Ampliseq


title: mmast_mRNA_r1_0h


title: Breast tumor 02_012 from Combination Arm sample type B

value: Combination Arm

value: B


title: HCT_nonstarved_mRNA_r2_24h


title: HGG_25, Ampliseq


title: maB_mRNA_r3_8h

source_name: spleen

value: spleen

value: activating B cell

value: LPS+IL4+antiCD180 48h, nactinomycin D 8h


title: HCT_nonstarved_mRNA_r2_1h

value: WT


title: HGG_19, Ampliseq

value: Anaplastic Astrocytoma


title: Breast tumor 02_011 from Fulvestrant Arm sample type W

value: TRUE


title: maB_mRNA_r3_4h

value: LPS+IL4+antiCD180 48h, nactinomycin D 4h


title: maB_mRNA_r3_2h

value: LPS+IL4+antiCD180 48h, nactinomycin D 2h


title: Breast tumor 02_011 from Fulvestrant Arm sample type B

value: Breast tumor


title: HGG_18, Ampliseq

value: Tumor

value: Female


title: HCT_nonstarved_mRNA_r2_12h

value: colorectal carcinoma cell

value: actinomycin D 12h


title: maB_mRNA_r3_1h

value: LPS+IL4+antiCD180 48h, nactinomycin D 1h


title: Breast tumor 02_010 from Combination Arm sample type W

value: W


title: HGG_17, Ampliseq

value: Male

value: Glioblastoma


title: HCT_nonstarved_mRNA_r2_0h


title: HGG_16, Ampliseq


title: HCT_nonstarved_mRNA_r1_4h

value: actinomycin D 4h


title: HCT_nonstarved_mRNA_r1_8h

value: actinomycin D 8h


title: Breast tumor 02_010 from Combination Arm sample type B

value: Combination Arm

value: B


title: maB_mRNA_r3_12h

value: spleen

value: activating B cell

value: WT

value: LPS+IL4+antiCD180 48h, nactinomycin D 12h


title: HGG_15, Ampliseq


title: Breast tumor 02_008 from Fulvestrant Arm sample type W

value: Breast tumor

value: Fulvestrant Arm

value: TRUE


title: mmast_mRNA_r1_12h

value: Bone marrow

value: mast cell


title: Breast tumor 02_008 from Fulvestrant Arm sample type B


title: maB_mRNA_r2_8h

value: LPS+IL4+antiCD180 48h, nactinomycin D 8h


title: Breast tumor 02_007 from Fulvestrant Arm sample type W

value: W


title: maB_mRNA_r2_4h

value: LPS+IL4+antiCD180 48h, nactinomycin D 4h


title: HCT_nonstarved_mRNA_r1_24h

value: colorectal carcinoma cell

value: actinomycin D 24h


title: maB_mRNA_r3_0h

value: LPS+IL4+antiCD180 48h, none


title: HGG_14, Ampliseq

value: Tumor

value: Female

value: Glioblastoma


title: HCT_nonstarved_mRNA_r1_2h

value: actinomycin D 2h


title: HGG_12, Ampliseq

value: Male


title: Breast tumor 02_007 from Fulvestrant Arm sample type B

value: B


title: HGG_13, Ampliseq


title: HCT_nonstarved_mRNA_r1_1h

value: WT

value: actinomycin D 1h


title: HGG_11, Ampliseq


title: Breast tumor 02_005 from Fulvestrant Arm sample type W

value: Breast tumor

value: Fulvestrant Arm

value: TRUE


title: maB_mRNA_r2_2h

value: spleen

value: activating B cell

value: LPS+IL4+antiCD180 48h, nactinomycin D 2h


title: maB_mRNA_r2_1h

value: LPS+IL4+antiCD180 48h, nactinomycin D 1h


title: HCT_nonstarved_mRNA_r1_0h

value: colorectal carcinoma cell


title: Breast tumor 02_005 from Fulvestrant Arm sample type B


title: HCT_nonstarved_mRNA_r1_12h

value: actinomycin D 12h


title: HGG_9, Ampliseq

value: Tumor


title: maB_mRNA_r2_12h

value: LPS+IL4+antiCD180 48h, nactinomycin D 12h


title: HCT_mRNA_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 8h


title: Breast tumor 02_004 from Combination Arm sample type W

value: Combination Arm

value: W


title: HGG_8, Ampliseq

value: Male

value: Glioblastoma


title: maB_mRNA_r1_8h

value: WT

value: LPS+IL4+antiCD180 48h, nactinomycin D 8h


title: Breast tumor 02_004 from Combination Arm sample type B

value: Breast tumor

value: B


title: maB_mRNA_r2_0h

value: spleen

value: LPS+IL4+antiCD180 48h, none


title: HCT_mRNA_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 4h


title: HGG_7, Ampliseq


title: HCT_mRNA_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 2h


title: maB_mRNA_r1_4h

value: activating B cell

value: LPS+IL4+antiCD180 48h, nactinomycin D 4h


title: HGG_6, Ampliseq

value: Tumor

value: Female


title: Breast tumor 02_003 from Combination Arm sample type W

value: TRUE


title: HGG_5, Ampliseq

value: Anaplastic Astrocytoma


title: HCT_mRNA_24h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 24h


title: HCT_mRNA_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 1h


title: HGG_4, Ampliseq

value: Male

value: Glioblastoma


title: HGG_10, Ampliseq


title: maB_mRNA_r1_2h

value: WT

value: LPS+IL4+antiCD180 48h, nactinomycin D 2h


title: maB_mRNA_r1_12h

value: spleen

value: LPS+IL4+antiCD180 48h, nactinomycin D 12h


title: Breast tumor 02_002 from Combination Arm sample type B

value: Breast tumor

value: Combination Arm

value: B


title: maB_mRNA_r1_1h

value: activating B cell

value: LPS+IL4+antiCD180 48h, nactinomycin D 1h


title: Breast tumor 02_003 from Combination Arm sample type B


title: Breast tumor 02_001 from Fulvestrant Arm sample type W

value: Fulvestrant Arm

value: W


title: scRNA_HCTMED26D_IAAr2

value: 10% FBS 14h, noFBS+IAA 6h, FBS + IAA 2h


title: Breast tumor 02_002 from Combination Arm sample type W

value: TRUE


title: HGG_3, Ampliseq

value: Tumor

value: Female

value: Anaplastic Astrocytoma


title: Breast tumor 02_001 from Fulvestrant Arm sample type B


title: HGG_2, Ampliseq

value: Glioblastoma


title: scRNA_mmast

value: Bone marrow

value: mast cell

value: WT


title: HCT_mRNA_12h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 12h


title: scRNA_HCTMED26D_IAAr1


title: scRNA_mrB

value: spleen

value: resting B cell


title: scRNA_HCTMED26D_DMSOr2

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HGG_1, Ampliseq

value: Male


title: endoSTARR_5bp_gDNA_rep3

city: Lausanne

first: Bart

last: Deplancke

address: SV Station 19

country: Switzerland

institute: EPFL

data_processing: Insert seqeunes were mapped to the 12bp barcodes located at the 3 prime end with respect to the TSS using a custom script. STARR activity for each insert sequence was computed by taking the log2 ratio of mRNA over input DNA counts. For endogenous experiments 'endogenous' STARR-seq activity for each insert seqeunce was computed by first normalizing each replicate barcode count by the total library size (reads per million seqeunces; RPM), before computing an average mRNA over genomic DNA ratio across all three replicates. Only barcodes that had at least 2 RPM counts in all three replicates were retained in the filtered count table.

growth_protocol: MEC1 cells were cultured in IMDM media (Gibco) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin. For Endogenous STARR-seq experiments MEC1 cells containing a CRE-recombinase under the control of Blasticidin and an RMCE landing pad (loxP-CMV-GFP-lox2272) were cultured with the addition of 5ug/ml Blasticidin for 5 days prior to library transfection.

extract_protocol:
Cells were harvested 24h post transfection and lysed in Trizol. RNA was extracted by Chloroform extraction, followed by Isopropanol precipitation with a 1:1 ratio. RNA pellets were resuspended in RNAse-free water and digested with DNAseI for 20 min at room-temperature. DNAseI-treated RNA was purified with a RNA-clean&concentrator-25 kit (Zymo). A total of 10-12 μg RNA was reverse transcribed using the STARR-seq specific RT primer. For each μl of Maxima H minus RT 3 μg input was used. RT reactions were diluted 1:4 with RNAse & DNAse-free water before further amplification. The splice-junction PCR was run using the STARR-seq thio-splice-junction primer and a custom reverse primer spanning the SalI restriction site used for linearizing the STARR-seq vector and the read1 Nextera adapter sequence inserted with the library. About one third of the RT reaction was amplified for 19-22 cycles. Illumina barcodes were added by a final PCR with 8 cycles using the Illumina Nextera guidelines. After each amplification step, PCR products were cleaned up using AMPure XP magenetic beads (Beckman Coulter). Plasmid libraries were directly amplified with a 8-cycle PCR using NEXTERA-specific index primers. For endogenous libraries, cells were grown for ~10-12 days in standard media before FACS sorting for GFP-negative cells. After sorting, library-containing cells were grown for another 6-7 days before RNA and genomicDNA extraction. Extractions were done in triplicates using a Mini Allprep mRNA/gDNA extraction kit (QIagen). A total of 24 μg RNA was reverse transcribed per replicate using the STARR-seq specific RT primer. RT reactions were cleaned up using a Clean&Concentrator kit (Zymo) with 7x Binding Buffer. gDNA and mRNA samples were amplified (20 cycles) using either an intron-specific primer (gDNA) or the standard STARR-seq splice-junction primer (mRNA) together with a custom reverse primer (see above). Illumina barcodes were added by a final PCR with 9 cycles using the Illumina Nextera guidelines. After each amplification step, PCR products were cleaned up using AMPure XP magenetic beads (Beckman Coulter). Plasmid libraries were directly amplified with a 8-cycle PCR using NEXTERA-specific index primers.
NEXTERA

treatment_protocol: Transfections of 5-bp and 10-bp libraries were done in duplicates using ~ 6 Mio cells and 30 μg plasmid per replicate. Transfections were carried out with the Neon Transfection System (Thermo Fisher) as follows: 3 pulses of 20 ms at 1200 V in R buffer using 100 ul tips. Transfections of 5-bp libraries for the endogneous STARR-seq were done in 8 sets, using ~ 6 Mio cells and 30 μg plasmid per transfection. Transfections were carried out with the Neon Transfection System (Thermo Fisher) as follows: 3 pulses of 20 ms at 1200 V in R buffer using 100 ul tips.

value: CLL cell line


title: Breast tumor 01_023 from Combination Arm sample type W

value: Breast tumor

value: Combination Arm

value: W


title: Breast tumor 01_023 from Combination Arm sample type B

value: B

value: TRUE


title: scRNA_mLNK

value: LNK

value: NK cell


title: Breast tumor 01_021 from Combination Arm sample type W


title: scRNA_mCH12_r2

value: B lymphoma cell


title: HCT_mRNA_0h


title: endoSTARR_5bp_gDNA_rep2


title: maB_mRNA_r1_0h

value: activating B cell

value: LPS+IL4+antiCD180 48h, none


title: scRNA_HCTMED26D_DMSOr1

value: colorectal carcinoma cell


title: endoSTARR_5bp_gDNA_rep1

value: WT


title: Breast tumor 01_021 from Combination Arm sample type B


title: scRNA_HCTJQ1_JQ1r2

value: 10% FBS 14h, noFBS+JQ1 6h, FBS + JQ1 2h


title: endoSTARR_5bp_mRNA_rep2


title: scRNA_HCTJQ1_JQ1r1


title: Breast tumor 01_020 from Combination Arm sample type W


title: endoSTARR_5bp_mRNA_rep3


title: scRNA_mBMB220

value: Bone marrow

value: B220 positive cell


title: scRNA_HCTJQ1_DMSOr1

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: endoSTARR_5bp_mRNA_rep1

value: CLL cell line


title: endoSTARR_5bp_plDNA


title: scRNA_maBMYCKO_WTr2

value: spleen

value: LPS+IL4 4h


title: scRNA_HCT_DMSOr2

value: DMSO 2h


title: Breast tumor 01_016 from Fulvestrant Arm sample type B

value: Breast tumor

value: Fulvestrant Arm

value: B

value: FALSE


title: scRNA_HCTJQ1_DMSOr2


title: Breast tumor 01_018 from Combination Arm sample type B

value: Combination Arm


title: RNA989 Endometrium, advanced maternal age

city: Maastricht

first: Darina

last: Obukhova

state: Limburg

address: P. Debyelaan 25

department: Department of Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center +

description:
RNA989
raw_counts.csv
batch_corrected_filtered_counts.csv

data_processing:
Reads were mapped to the Homo sapiens reference genome (UCSC release GRCh37/hg19),  using STAR (v.2.7.9) in “Basic” two-pass mode and in “GeneCounts” quantification mode..
The mapped reads were estimated at gene level using the Ensembl database for annotation. The raw expression count matrix was produced using FeatureCounts (v.2.0.1).
Batch effect of the sequencing run was corrected for  using the ‘Combat-Seq2’ method from the sva R package (v.3.42.0)
Genes in which the number of mapped reads was <5 in more than 75% of samples were filtered out.
Assembly: GRCh37/hg19
Supplementary files format and content: comma-separated values text file includes raw counts for each sample
Supplementary files format and content: comma-separated values text file includes batch-corrected counts for each sample

source_name: endometrium

extract_protocol:
Total RNA was extracted from all samples using miRNeasy kit (Qiagen, cat.no. 217084), followed by DNase treatment (DNase Free, Life Technologies, cat.no. EN0521), RNA integrity was assessed with Qubit RNA IQ Assay kit (Thermo Fisher, cat.no. Q33221)
cDNA libraries were randomly assigned into two sequencing batches  and prepared using the TruSeq Stranded mRNA Sample Preparation Guide (Illumina, cat.no. 20020595).

value: endometrium

tag: age

value: advanced


title: scRNA_HCT_DMSOr1

value: colorectal carcinoma cell


title: Breast tumor 01_015 from Combination Arm sample type W

value: W


title: scRNA_maBMYCKO_Mycmr1

value: activating B cell

value: Myc-/-


title: RNA893 Endometrium, young maternal age

description:
RNA893
raw_counts.csv
batch_corrected_filtered_counts.csv

value: young


title: scRNA_mCH12_r1

value: B lymphoma cell

value: WT


title: scRNA_maB_72h

value: spleen

value: LPS+IL4 72h


title: Breast tumor 01_014 from Fulvestrant Arm sample type B


title: RNA886 Endometrium, advanced maternal age

description:
RNA886
raw_counts.csv
batch_corrected_filtered_counts.csv


title: iPMSCs,osteogenic induction group,rep3

city: Chang chun

first: huixin

last: Lv

address: 1500 Tsinghua Road

institute: School and Hospital of Stomatology, Jilin University

source_name: human maxillary sinus membrane

treatment_protocol:
Osteogenic differentiation was induced by treatment of hLMSCs and hPMSCs with Osteogenic Differentiation Kits (Oricell).
The control group was cultured in normal complete medium (NCM). For osteogenic induction group, the cells were cultured in NCM overnight and the medium was replaced by differentiation induction medium on the next day. The renewing time of the medium was 3 days.

value: human maxillary sinus membrane

value: mesenchymal stem cells

value: osteogenic differentiation


title: Breast tumor 01_020 from Combination Arm sample type B

value: Breast tumor

value: B

value: TRUE


title: Breast tumor 01_013 from Combination Arm sample type B

value: Combination Arm


title: Brain slice, eae, 6

city: Baltimore

first: Matthew

middle: D

last: Smith

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Alignment and preprocessing: SpaceRanger software (v.1.3.1)
Filtering / QC: Exclude spots with less than 250 measured genes and less than 500 unique molecular identifiers (UMIs)
Normalization: Sctransform (Seurat v.4.3.0)
Dimensionality reduction, nearest neighbor calculation (Seurat v.4.3.0)
Merge (Seurat v.4.3.0)
Export Seurat object as RDS file
Assembly: mm10-2020A
Supplementary files format and content: 20X TIF images of tissue sections with fiducials for Spatial Alignment
Supplementary files format and content: Hdf5 feature-barcode matrix of filtered features generated per sample by Spaceranger
Supplementary files format and content: RDS file containing merged Seurat object

extract_protocol:
At 12 weeks post-immunization, animals were euthanized in CO2 chamber and perfused with cold PBS. Brains were dissected and one hemisphere drop fixed in isopentane cooled on dry ice. Fresh frozen brain samples were then cut coronally at a thickness of 10μm and placed on the capture area of Visium Gene Expression slides (v1; 10x Genomics). Each slide contained four 6.5 mm x 6.5 mm capture areas. Sample preparation was carried out according to manufacturer’s instructions. After fixation with methanol at -20C, Hematoxylin and Eosin (H&E) staining was performed for morphological analysis and spatial alignment of the sequencing data. After the enzymatic permeabilization, mRNA was captured by probes and cDNA generated.
Barcoded cDNA was isolated using SPRIselect-cleanup (Beckman Coulter) and amplified. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10x-specific sample indexing as per the manufacturer’s instructions. Following assessment of RNA quality, sequencing was performed using a Novaseq S2 100.

treatment_protocol: Female SJL/J mice were immunized subcutaneously at two sites over the lateral abdomen with 100 μg PLP139-151 peptide with complete Freund’s adjuvant containing 4 μg/ml Mycobacterium tuberculosis H37RA (Difco Laboratories). Mice were weighed and scored serially to document disease course. Scoring was performed using the following scale: 0, normal; 1, limp tail; 2, hind limb weakness; 3, hind limb paralysis; 4, hind limb and forelimb weakness; and 5, death.

value: Brain

value: SJL/J

value: eae

value: Wild Type

value: Kleptose (vehicle)


title: RNA859 Endometrium, advanced maternal age

description:
RNA859
raw_counts.csv
batch_corrected_filtered_counts.csv

value: endometrium

value: advanced


title: iPMSCs,osteogenic induction group,rep1


title: Brain slice, eae, 5


title: RNA868 Endometrium, advanced maternal age

description:
RNA868
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Brain slice, eae, 4


title: iPMSCs,osteogenic induction group,rep2


title: PMSCs,control group,rep3

value: normal culture medium


title: PMSCs,control group,rep2


title: scRNA_maBMYCKO_Mycmr2

value: spleen

value: activating B cell

value: Myc-/-

value: LPS+IL4 4h


title: scRNA_maBMYCKO_WTr1

value: WT


title: Brain slice, eae, 3


title: Breast tumor 01_012 from Combination Arm sample type B

value: Breast tumor


title: RNA709 Endometrium, advanced maternal age

description:
RNA709
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Breast tumor 01_011 from Combination Arm sample type W

value: W


title: Brain slice, eae, 2


title: RNA705 Endometrium, advanced maternal age

description:
RNA705
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Breast tumor 01_013 from Combination Arm sample type W

value: TRUE


title: RNA638 Endometrium, young maternal age

description:
RNA638
raw_counts.csv
batch_corrected_filtered_counts.csv

value: young


title: iLMSCs,osteogenic induction group,rep3

value: human maxillary sinus membrane

value: mesenchymal stem cells

value: osteogenic differentiation


title: Brain slice, eae, 1

value: Brain

value: SJL/J

value: eae

value: Wild Type


title: Breast tumor 01_011 from Combination Arm sample type B

value: Combination Arm

value: B


title: Breast tumor 01_012 from Combination Arm sample type W


title: RNA516 Endometrium, advanced maternal age

description:
RNA516
raw_counts.csv
batch_corrected_filtered_counts.csv

value: endometrium

value: advanced


title: RNA562 Endometrium, young maternal age

description:
RNA562
raw_counts.csv
batch_corrected_filtered_counts.csv


title: iLMSCs,osteogenic induction group,rep1


title: iLMSCs,osteogenic induction group,rep2


title: Breast tumor 01_009 from Combination Arm sample type W


title: Brain slice, naïve, 3


title: Breast tumor 01_007 from Fulvestrant Arm sample type W

value: Fulvestrant Arm


title: Breast tumor 01_009 from Combination Arm sample type B


title: Brain slice, naïve, 2


title: RNA473 Endometrium, young maternal age

description:
RNA473
raw_counts.csv
batch_corrected_filtered_counts.csv


title: LMSCs,control group,rep1

value: normal culture medium


title: Brain slice, naïve, 4


title: LMSCs,control group,rep3


title: PMSCs,control group,rep1


title: RNA208 Endometrium, advanced maternal age

description:
RNA208
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Breast tumor 01_008 from Fulvestrant Arm sample type W

value: Breast tumor

value: FALSE


title: PMSCs,rep2

value: non


title: Breast tumor 01_006 from Combination Arm sample type B

value: TRUE


title: LMSCs,control group,rep2

value: human maxillary sinus membrane


title: RNA358 Endometrium, advanced maternal age

description:
RNA358
raw_counts.csv
batch_corrected_filtered_counts.csv


title: PMSCs,rep1

value: mesenchymal stem cells


title: Brain slice, naïve, 5


title: RNA164 Endometrium, young maternal age

description:
RNA164
raw_counts.csv
batch_corrected_filtered_counts.csv

value: young


title: LMSCs,rep3


title: RNA268 Endometrium, advanced maternal age

description:
RNA268
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Breast tumor 01_006 from Combination Arm sample type W

value: W


title: RNA148 Endometrium, young maternal age

description:
RNA148
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Brain slice, naïve, 1

value: Brain

value: SJL/J


title: RNA191 Endometrium, young maternal age

description:
RNA191
raw_counts.csv
batch_corrected_filtered_counts.csv


title: RNA145 Endometrium, young maternal age

description:
RNA145
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Breast tumor 01_004 from Combination Arm sample type W


title: RNA166 Endometrium, advanced maternal age

description:
RNA166
raw_counts.csv
batch_corrected_filtered_counts.csv


title: Breast tumor 01_007 from Fulvestrant Arm sample type B


title: Breast tumor 01_004 from Combination Arm sample type B


title: LMSCs,rep1